diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index f176b596d76..252a6a166b0 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -21,6 +21,8 @@ jobs: fail-fast: false steps: - uses: actions/checkout@v2 + with: + fetch-depth: 0 # Required for git merge-base to work - name: Cache source files in /tmp/sources id: cache-sources diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 3faa98793bf..7dfcc97840b 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,95 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 12,266 easyconfig files, for 2,349 different software packages, +The latest version of easybuild-easyconfig provides 12,607 easyconfig files, for 2,388 different software packages, incl. 36 different (compiler) toolchains. +v4.4.1 (July 6th 2021) +---------------------- + +update/bugfix release + +- added example easyconfig files for 39 new software packages: + - AMPHORA2 (#13003), AOMP (#12909), CAMPARI (#13152), CSB (#12877), dijitso (#10719), DosageConvertor (#13278), + dSFMT (#12971), exiv2 (#13204), FEniCS (#10719), FreeFEM (#9902), futhark (#12921), futile (#12864), + gappa (#13186), GenomeWorks (#13083, #13092), gexiv2 (#13204), HAL (#13267), hipify-clang (#12961), inline (#12029), + libcint (#13214), LTR_retriever (#13125), mapDamage (#13172), MbedTLS (#13061), microctools (#13010), + Nektar++ (#12664), NINJA (#13125), OBITools3 (#12969), ont-fast5-api (#13033), OpenMM-PLUMED (#13268), + phototonic (#13241), PyFoam (#12675), RagTag (#13247), RcppGSL (#13172), RECON (#13123), RepeatScout (#13124), + retworkx (#13228), UCX-CUDA (#13260), unimap (#13247), Vala (#13204), WhatsHap (#12989) +- added additional easyconfigs for various supported software packages, including: + - Amber 20.11, BBMap 38.90, Beast 2.6.4, BLIS 3.0 (AMDo fork), Bonito 0.4.0, CellRanger-ARC 2.0.0, + CellRanger-ATAC 2.0.0, Check 0.15.2, CubeGUI 4.6, CubeLib 4.6, CubeWriter 4.6, cuDNN 8.2.1.32, CVXOPT 1.2.6, + DOLFIN 2019.1.0.post0, eggnog-mapper 2.1.4, ELPA 2021.05.001, FDS 6.7.6, FFC 2019.1.0.post0, FFmpeg 4.3.2, + FIAT 2019.1.0, flatbuffers 2.0.0, flatbuffers-python 2.0, FLTK 1.3.6, gc 8.0.4, GCC 8.4.0 + 9.4.0, GDAL 3.3.0, + Gdk-Pixbuf 2.42.6, geopy 2.1.0, Ghostscript 9.54.0, git 2.32.0, GitPython 3.1.18, GLFW 3.3.4, gmsh 4.8.4, + gnuplot 5.4.2, GnuTLS 3.7.2, Go 1.16.5, GObject-Introspection 1.68.0, gperftools 2.9.1, GraphicsMagick 1.3.36, + Graphviz 2.47.2, GSL 2.7, GTK+ 2.24.33, Guile 2.2.7, h5py 3.2.1, HarfBuzz 2.8.1, Horovod 0.22.0, Hypre 2.21.0, + ICU 69.1, ImageMagick 7.0.11-14, IOR 3.3.0, IPython 7.25.0, IRkernel 1.2, ispc 1.16.0, JupyterLab 3.0.16, + LDC 1.26.0, libcerf 1.17, libepoxy 1.5.8, libgd 2.3.1, libStatGen 1.0.15, libxc 5.1.5, LittleCMS 2.12, + LMfit 1.0.2, Lua 5.4.3, M4 1.4.19, MCR R2021a.3, medaka 1.4.3, Mercurial 5.8, minimap2 2.20, MMseqs2 13, + MrBayes 3.2.7, MUMPS 5.4.0, NCCL 2.9.9, netCDF 4.8.0, Nim 1.4.8, nodejs 14.17.0, Nsight-Compute 2021.2.0, + numba 0.53.1, NVHPC 21.5.eb, nvtop 1.2.1, Octave 6.2.0, OPARI2 2.0.6, openkim-models 20210128, OpenMPI 4.0.6, + OTF2 2.3, p11-kit 0.24.0, Pango 1.48.5, parallel 20210622, petsc4py 3.12.0, picard 2.25.5, Pillow 8.2.0, + PROJ 8.0.1, protobuf 3.17.3, protobuf-python 3.17.3, PSolver 1.8.3, PySCF 1.7.6, pyspoa 0.0.8, pytest-xdist 2.3.0, + PyTorch 1.9.0, PyYAML 5.4.1, Qhull 2020.2, Quandl 3.6.1, R 4.0.5 + R 4.1.0, Ragout 2.3, RE2 2021-06-01, + ReFrame 3.6.2, RepeatMasker 4.1.2, rgdal 1.5-23, RMBlast 2.11.0, Ruby 3.0.1, scikit-learn 0.24.2, + Score-P 7.0, Seurat 4.0.3, slepc4py 3.12.0, spoa 4.0.7, Subread 2.0.2, Subversion 1.14.1, SuiteSparse 5.10.1, + sympy 1.8, tensorboardX 2.2, TensorFlow 2.5.0, Tk 8.6.11, tmux 3.2a, torchtext 0.8.1, torchvision 0.9.1, + UDUNITS 2.2.28, UFL 2019.1.0, utf8proc 2.6.1, VEP 103.1, VMD 1.9.4a51, vsc-mympirun 5.2.6, XCFun 2.1.1, + Xvfb 1.20.11, Z3 4.8.11, ZeroMQ 4.3.4 +- minor enhancements, including: + - update cuDNN 8.0.x easyconfigs with a download location (#12368) + - add extensions to recent R easyconfigs: GxEScanR (#13039), cSEM (#13208), cubelyr + broom.mixed (#13252), + grf (#13261), twang + xgboost (#13284), neuralnet (#13330) + - add check to easyconfigs test suite to ensure OpenSSL wrapper is used in easyconfigs using a recent toolchain (#13079) + - add gipaw to QuantumESPRESSO/6.7 (#13087) + - add checksum for aarch64 installation file for CUDAcore easyconfigs (#13014, #13097) + - add Perl dependency to makeinfo easyconfigs (#13166) + - set minimal OpenSSL version to 1.1.1 for OpenSSL v1.1 wrapper (#13188) + - add JIT support for CUDA 11 to PyTorch 1.7.1 (#13207) + - add 'ninja --version' as sanity check command in Ninja easyconfigs (#13222) + - code cleanup + improvements for easyconfigs test suite (#13257) +- various bug fixes, including: + - download sources via git for XGBoost 20171120 easyconfig due to use of submodules (#6880) + - add elfutils as build dependency for Clang 8.0.x and 9.0.1 (#13015) and Clang 11.0.1 (#13008) easyconfigs that have a CUDA dependency + - add missing CMake option to Geant4 v10.7.1 in order to actually use external CLHEP (#13019) + - add new checksum for mvabund extension to R v4.0.4 eaysconfigs (#13020, #13021) + - add patch to fix numpy test_ccompiler_opt in SciPy-bundle v2021.05 (#13042) + - add patch to fix installation of HDF 4.2.15 on aarch64 (#13059) + - make sure that MbedTLS' Makefile uses 'python' rather than 'python2' (#13061) + - fix checksum for snpEff 5.0 (#13062) + - fix source URL for LIBSVM 3.24 by downloading from GitHub (#13076) + - add preinstallopts for minimap2 to fix installation on aarch64 (#13080) + - add patch for GCC 10.2.0 to fix internal compiler error on aarch64 (#13086) + - switch to NCCL 2.8.3 built from source for CuPy, Horovod, libgpuarray, PyTorch and TensorFlow using fosscuda/2020b (#13103) + - add astor to dependencies of TensorFlow with 2019b (#13111) and 2020b (#13103, #13112) toolchains + - break cyclic dependency between groff, makeinfo and Perl by adding Perl-minimal and makeinfo-minimal easyconfigs (#13163-#13165) + - add missing rgdal dep to R-INLA (#13179) + - add patch to fix uniq operation in TensorFlow 2.4.1 (#13181) + - add Perl build dependency for PnetCDF 1.12.1 (#13183) + - disable own avx detection of libfabric v1.12.1 (#13215) + - add GCCcore-[1-9][0-9].x to test_dep_versions_per_toolchain_generation (#13243, #13249, #13251) + - add patch to fix installation of TensorFlow 2.0.x (#13248) + - add patch for recent GCCcore versions to fix compability with CUDA 11 (#13290) + - fix install step for glew (#13297) + - update Boost 1.74.0 easyconfigs to use tagged_layout rather than boost_multi_thread (#13300) + - avoid using PMIx from system instead of PMIx dependency specified via --with-pmix for OpenMPI 4.x (#13307) + - add patch for GCCcore 10.3.0 to prevent issues when compiling with nvcc (#13310) + - add patch for OpenMPI 4.0.x to fix building against (system) UCX version > 1.7 (#13329) + - fix build of manta 1.6.0 on top of Boost 1.74.0 (#13338) + - fix recent taxator-tk easyconfigs by adding (back) -DBoost_NO_BOOST_CMAKE=ON configure option (#13342) +- other changes: + - disable debuginfod for elfutils to minimize required dependencies (#13034) + - add bare Python 3.9.5 easyconfig and use that as builddep for LLVM 11.1.0 (#13035) + - remove misleading comment from Python >= 3.7 easyconfigs, libffi is now also required for Python itself (no longer bundled) (#13041) + - use new custom easyblock in torchvision easyconfigs (#13102) + - remove superflous TensorFlow patch (#13223) + - cleanup of easyconfigs for (bundles) of Python packages: remove default PYPI_SOURCE source URLs + use PythonBundle rather than Bundle easyblock (#13253, #13295, #13336) + - update README with instructions for MATLAB easyconfigs (#12597) + + v4.4.0 (June 2nd 2021) ---------------------- diff --git a/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb index 5236c8830ea..b6b0a50377f 100644 --- a/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ description = """lib3to2 is a set of fixers that are intended to backport code w toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] dependencies = [('Python', '2.7.12')] diff --git a/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2016b-Python-2.7.12.eb index 264a6e4ac82..8011ee907e8 100644 --- a/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ description = """lib3to2 is a set of fixers that are intended to backport code w toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] dependencies = [('Python', '2.7.12')] diff --git a/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2017a-Python-2.7.13.eb index 2ad009a7ab9..8f1f43dc116 100644 --- a/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2017a-Python-2.7.13.eb @@ -10,7 +10,6 @@ description = """lib3to2 is a set of fixers that are intended to backport code w toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['fef50b2b881ef743f269946e1090b77567b71bb9a9ce64b7f8e699b562ff685c'] diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-foss-2020b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-foss-2020b.eb new file mode 100644 index 00000000000..57583831e08 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-foss-2020b.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.4.1' + +homepage = 'https://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ec74133ef9d247cb6ad44c205675694919cf36d7f1682a9b85cae8bdecdc22a8'] + +builddependencies = [ + ('Python', '3.8.6'), +] +dependencies = [ + ('libxc', '4.3.4'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('HDF5', '1.10.7'), + ('Wannier90', '3.1.0'), +] + +# Needed due to changes in GCC10. +configopts = 'FCFLAGS="-fallow-argument-mismatch -ffree-line-length-none $FCFLAGS" ' +configopts += 'FFLAGS="-fallow-argument-mismatch $FFLAGS" ' + +# Ensure MPI +configopts += '--with-mpi="yes" --enable-openmp="no" ' +# configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# BLAS/Lapack from OpenBLAS +configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="${LIBLAPACK_MT}" ' + +# FFTW +configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/AGFusion/AGFusion-1.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/AGFusion/AGFusion-1.2-foss-2019a-Python-3.7.2.eb index 92801d24512..8f892ce944e 100644 --- a/easybuild/easyconfigs/a/AGFusion/AGFusion-1.2-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/AGFusion/AGFusion-1.2-foss-2019a-Python-3.7.2.eb @@ -20,39 +20,30 @@ use_pip = True exts_list = [ ('memoized-property', '1.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/memoized-property/'], 'checksums': ['4be4d0209944b9b9b678dae9d7e312249fe2e6fb8bdc9bdaa1da4de324f0fcf5'], }), ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), ('serializable', '0.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/serializable/'], 'checksums': ['87f9fadbd0fba5c7951858d16ae9109afa4c96fd486e663419f3051f352a22d9'], }), ('gtfparse', '1.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gtfparse/'], 'checksums': ['2f27aa2b87eb43d613edabf27f9c11147dc595c8683b440ac1d88e9acdb85873'], }), ('typechecks', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typechecks/'], 'checksums': ['7d801a6018f60d2a10aa3debc3af65f590c96c455de67159f39b9b183107c83b'], }), ('appdirs', '1.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs/'], 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), ('datacache', '1.1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/d/datacache/'], 'checksums': ['b2ca31b2b9d3803a49645ab4f5b30fdd0820e833a81a6952b4ec3a68c8ee24a7'], }), ('pyensembl', '1.7.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyensembl/'], 'checksums': ['378fb2ef7d2d5438b90514e7b616276d2a5e749d8cf150182401e12f35b999e4'], }), ('agfusion', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/agfusion/'], 'checksums': ['62733254ceaba970a018f16d36bfb1907e0505cc98eaf2dc49ee4938aaf4fd4d'], }), ] diff --git a/easybuild/easyconfigs/a/ALFA/ALFA-1.1.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ALFA/ALFA-1.1.1-foss-2019a-Python-3.7.2.eb index f885cb879cf..4ad25b6ddeb 100644 --- a/easybuild/easyconfigs/a/ALFA/ALFA-1.1.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ALFA/ALFA-1.1.1-foss-2019a-Python-3.7.2.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('python-utils', '2.3.0', { 'modulename': 'python_utils', diff --git a/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb b/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb new file mode 100644 index 00000000000..c9a3002ee86 --- /dev/null +++ b/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb @@ -0,0 +1,51 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'Tarball' + +name = 'AMPHORA2' +version = '20190730' +local_commit = '9fb9ce8' +local_raxmlsuffix = '-pthreads-avx2' +local_javasuffix = '-Java-%(javaver)s' +versionsuffix = local_javasuffix + local_raxmlsuffix + +homepage = 'https://github.com/wu-lab-uva/AMPHORA2' +description = "An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences." + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'wu-lab-uva' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +checksums = ['2d361fcc2b800c3daaf25692988af6105669cba2ff513aba82f36089beb2839f'] + +dependencies = [ + ('Perl', '5.32.0'), + ('Java', '13', '', True), + ('BioPerl', '1.7.8'), + ('HMMER', '3.3.2'), + ('EMBOSS', '6.6.0', local_javasuffix), + ('RAxML', '8.2.12', local_raxmlsuffix), +] + +local_scripts = ['%s.pl' % x for x in ['MarkerAlignTrim', 'MarkerScanner', 'Phylotyping']] +fix_perl_shebang_for = ['Scripts/*.pl'] + +# Exit with code 0 when running -Help +preinstall_cmd = "sed -i 's|die $usage if $help|if ($help) {print $usage; exit 0}|g' Scripts/*.pl && " +# Fix RAxML binary name +preinstall_cmd += "sed -i 's|raxmlHPC-PTHREADS|raxmlHPC%s|g' Scripts/Phylotyping.pl" % local_raxmlsuffix.upper() + +sanity_check_paths = { + 'files': ['Scripts/%s' % x for x in local_scripts], + 'dirs': [], +} + +sanity_check_commands = ["%s -Help" % x for x in local_scripts] + +modextrapaths = { + 'AMPHORA2_home': '', + 'PATH': 'Scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..008bcc0a9d3 --- /dev/null +++ b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Jorgen Nordmoen +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'AOMP' +version = '13.0-2' + +homepage = 'https://github.com/ROCm-Developer-Tools/aomp' +description = "AMD fork of LLVM, setup for OpenMP offloading to Accelerators" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/ROCm-Developer-Tools/aomp/releases/download/rel_%(version)s/'] +sources = ['aomp-%(version)s.tar.gz'] +patches = ['AOMP-%(version)s_remove_hardcoded_paths.patch'] +checksums = [ + # aomp-13.0-2.tar.gz: + '0256a84aefcbf7c49112f068321b84e0620f4c43a9d490c64d820e40658e0d67', + # AOMP-13.0-2_remove_hardcoded_paths.patch: + 'ec41ffcec63d079b6a73c93bea29e0b8d77ca7b059725aa1d47c334f7e476ff0', +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), + ('elfutils', '0.183'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('binutils', '2.35'), + ('libffi', '3.3'), + ('ncurses', '6.2'), + ('numactl', '2.0.13'), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-gcccuda-2020a.eb b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-gcccuda-2020a.eb new file mode 100644 index 00000000000..0e43cda4894 --- /dev/null +++ b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-gcccuda-2020a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Jorgen Nordmoen +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'AOMP' +version = '13.0-2' + +homepage = 'https://github.com/ROCm-Developer-Tools/aomp' +description = "AMD fork of LLVM, setup for OpenMP offloading to Accelerators" + +toolchain = {'name': 'gcccuda', 'version': '2020a'} + +source_urls = ['https://github.com/ROCm-Developer-Tools/aomp/releases/download/rel_%(version)s/'] +sources = ['aomp-%(version)s.tar.gz'] +patches = ['AOMP-%(version)s_remove_hardcoded_paths.patch'] +checksums = [ + # aomp-13.0-2.tar.gz: + '0256a84aefcbf7c49112f068321b84e0620f4c43a9d490c64d820e40658e0d67', + # AOMP-13.0-2_remove_hardcoded_paths.patch: + 'ec41ffcec63d079b6a73c93bea29e0b8d77ca7b059725aa1d47c334f7e476ff0', +] + +builddependencies = [ + ('CMake', '3.16.4'), + ('Perl', '5.30.2'), + ('Python', '3.8.2'), + ('elfutils', '0.182'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('binutils', '2.34'), + ('libffi', '3.3'), + ('ncurses', '6.2'), + ('numactl', '2.0.13'), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2_remove_hardcoded_paths.patch b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2_remove_hardcoded_paths.patch new file mode 100644 index 00000000000..2e6905e6c79 --- /dev/null +++ b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2_remove_hardcoded_paths.patch @@ -0,0 +1,225 @@ +# This patch removes many of the hardcoded assumptions that the AOMP build +# expects around system GCC. In addition it fixes a few hardcoded variables +# that EasyBuild would like to have control over, such as the number of +# threads. Most of the changes are down to linking the LLVM build with the +# EasyBuild supplied GCC. +# +# This patch was manually created +--- a/aomp/bin/aomp_common_vars ++++ b/aomp/bin/aomp_common_vars +@@ -80,8 +80,6 @@ AOMP_STANDALONE_BUILD=${AOMP_STANDALONE_BUILD:-1} + if [ "$AOMP_PROC" == "ppc64le" ] ; then + AOMP_BUILD_CUDA=1 + AOMP_STANDALONE_BUILD=1 +-else +- AOMP_BUILD_CUDA=0 + fi + if [ $AOMP_STANDALONE_BUILD == 1 ] ; then + # Default is to build nvptx for STANDALONE build +@@ -139,16 +137,17 @@ GFXLIST=${GFXLIST:-"gfx700 gfx701 gfx801 gfx803 gfx900 gfx902 gfx906 gfx908"} + export GFXLIST + + # Calculate the number of threads to use for make +-NUM_THREADS= ++_THREADS= + if [ ! -z `which "getconf"` ]; then +- NUM_THREADS=$(`which "getconf"` _NPROCESSORS_ONLN) ++ _THREADS=$(`which "getconf"` _NPROCESSORS_ONLN) + if [ "$AOMP_PROC" == "ppc64le" ] ; then +- NUM_THREADS=$(( NUM_THREADS / 6)) ++ _THREADS=$(( _THREADS / 6)) + fi + if [ "$AOMP_PROC" == "aarch64" ] ; then +- NUM_THREADS=$(( NUM_THREADS / 4)) ++ _THREADS=$(( _THREADS / 4)) + fi + fi ++NUM_THREADS=${NUM_THREADS:-$_THREADS} + + # These are the web sites where the AOMP git repos are pulled from + GITROC="https://github.com/radeonopencompute" +--- a/aomp/bin/build_aomp.sh ++++ b/aomp/bin/build_aomp.sh +@@ -28,19 +28,6 @@ thisdir=$(getdname $0) + # --- end standard header ---- + + function build_aomp_component() { +- osversion=$(cat /etc/os-release | grep -e ^VERSION_ID) +- +- if [[ $osversion =~ '"7.' ]]; then +- echo "OS version 7 found `cat /etc/os-release`" +- [ -f /opt/rh/devtoolset-7/enable ] && . /opt/rh/devtoolset-7/enable +- elif [[ $osversion =~ '"8' ]]; then +- echo "OS version 8 found `cat /etc/os-release`" +- echo +- echo "Get updated gcc 8: export PATH=/usr/bin:\$PATH" +- export PATH=/usr/bin:$PATH +- gcc --version +- fi +- + $AOMP_REPOS/$AOMP_REPO_NAME/bin/build_$COMPONENT.sh "$@" + rc=$? + if [ $rc != 0 ] ; then +--- a/aomp/bin/build_comgr.sh ++++ b/aomp/bin/build_comgr.sh +@@ -96,6 +96,7 @@ if [ "$1" != "nocmake" ] && [ "$1" != "install" ] ; then + -DROCM_DIR=$AOMP_INSTALL_DIR \ + -DLLVM_DIR=$AOMP_INSTALL_DIR \ + -DClang_DIR=$AOMP_INSTALL_DIR \ ++ -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE \ + $AOMP_REPOS/$AOMP_COMGR_REPO_NAME/lib/comgr + + if [ $? != 0 ] ; then +--- a/aomp/bin/build_extras.sh ++++ b/aomp/bin/build_extras.sh +@@ -113,7 +113,7 @@ if [ "$1" != "nocmake" ] && [ "$1" != "install" ] ; then + fi + + if [ $AOMP_STANDALONE_BUILD == 1 ] ; then +- MYCMAKEOPTS="-DLLVM_DIR=$LLVM_DIR $AOMP_ORIGIN_RPATH -DCMAKE_BUILD_TYPE=$BUILDTYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_EXTRAS -DROCM_DIR=$ROCM_DIR -DAOMP_STANDALONE_BUILD=$AOMP_STANDALONE_BUILD -DAOMP_VERSION_STRING=$AOMP_VERSION_STRING -DCMAKE_PREFIX_PATH=$BUILD_DIR/build/libdevice" ++ MYCMAKEOPTS="-DLLVM_DIR=$LLVM_DIR $AOMP_ORIGIN_RPATH -DCMAKE_BUILD_TYPE=$BUILDTYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_EXTRAS -DROCM_DIR=$ROCM_DIR -DAOMP_STANDALONE_BUILD=$AOMP_STANDALONE_BUILD -DAOMP_VERSION_STRING=$AOMP_VERSION_STRING -DCMAKE_PREFIX_PATH=$BUILD_DIR/build/libdevice -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE" + else + MYCMAKEOPTS="-DLLVM_DIR=$LLVM_DIR $AOMP_ORIGIN_RPATH -DCMAKE_BUILD_TYPE=$BUILDTYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_EXTRAS -DROCM_DIR=$ROCM_DIR -DAOMP_STANDALONE_BUILD=$AOMP_STANDALONE_BUILD -DDEVICELIBS_ROOT=$DEVICELIBS_ROOT -DAOMP_VERSION_STRING=$AOMP_VERSION_STRING" + fi +--- a/aomp/bin/build_flang.sh ++++ b/aomp/bin/build_flang.sh +@@ -45,7 +45,7 @@ REPO_BRANCH=$AOMP_FLANG_REPO_BRANCH + REPO_DIR=$AOMP_REPOS/$AOMP_FLANG_REPO_NAME + COMP_INC_DIR=$REPO_DIR/runtime/libpgmath/lib/common + +-MYCMAKEOPTS="-DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_FLANG -DLLVM_ENABLE_ASSERTIONS=ON $AOMP_ORIGIN_RPATH -DLLVM_CONFIG=$INSTALL_FLANG/bin/llvm-config -DCMAKE_CXX_COMPILER=$AOMP_INSTALL_DIR/bin/clang++ -DCMAKE_C_COMPILER=$AOMP_INSTALL_DIR/bin/clang -DCMAKE_Fortran_COMPILER=gfortran -DLLVM_TARGETS_TO_BUILD=$TARGETS_TO_BUILD -DFLANG_OPENMP_GPU_AMD=ON -DFLANG_OPENMP_GPU_NVIDIA=ON -DLLVM_INSTALL_TOOLCHAIN_ONLY=ON -DFLANG_INCLUDE_TESTS=OFF -DCMAKE_C_FLAGS=-I$COMP_INC_DIR -DCMAKE_CXX_FLAGS=-I$COMP_INC_DIR" ++MYCMAKEOPTS="-DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_FLANG -DLLVM_ENABLE_ASSERTIONS=ON $AOMP_ORIGIN_RPATH -DLLVM_CONFIG=$INSTALL_FLANG/bin/llvm-config -DCMAKE_CXX_COMPILER=$AOMP_INSTALL_DIR/bin/clang++ -DCMAKE_C_COMPILER=$AOMP_INSTALL_DIR/bin/clang -DCMAKE_Fortran_COMPILER=gfortran -DLLVM_TARGETS_TO_BUILD=$TARGETS_TO_BUILD -DFLANG_OPENMP_GPU_AMD=ON -DFLANG_OPENMP_GPU_NVIDIA=ON -DLLVM_INSTALL_TOOLCHAIN_ONLY=ON -DFLANG_INCLUDE_TESTS=OFF -DCMAKE_C_FLAGS=-I$COMP_INC_DIR -DCMAKE_CXX_FLAGS=-I$COMP_INC_DIR -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE" + + + +--- a/aomp/bin/build_flang_runtime.sh ++++ b/aomp/bin/build_flang_runtime.sh +@@ -48,7 +48,7 @@ REPO_BRANCH=$AOMP_FLANG_REPO_BRANCH + REPO_DIR=$AOMP_REPOS/$AOMP_FLANG_REPO_NAME + COMP_INC_DIR=$REPO_DIR/runtime/libpgmath/lib/common + +-MYCMAKEOPTS="-DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_FLANG -DLLVM_ENABLE_ASSERTIONS=ON $AOMP_ORIGIN_RPATH -DLLVM_CONFIG=$INSTALL_FLANG/bin/llvm-config -DCMAKE_CXX_COMPILER=$AOMP_INSTALL_DIR/bin/clang++ -DCMAKE_C_COMPILER=$AOMP_INSTALL_DIR/bin/clang -DCMAKE_Fortran_COMPILER=$AOMP_INSTALL_DIR/bin/flang -DLLVM_TARGETS_TO_BUILD=$TARGETS_TO_BUILD -DLLVM_INSTALL_RUNTIME=ON -DFLANG_BUILD_RUNTIME=ON -DOPENMP_BUILD_DIR=$BUILD_DIR/build/openmp/runtime/src -DFLANG_INCLUDE_TESTS=OFF -DCMAKE_C_FLAGS=-I$COMP_INC_DIR -DCMAKE_CXX_FLAGS=-I$COMP_INC_DIR" ++MYCMAKEOPTS="-DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_FLANG -DLLVM_ENABLE_ASSERTIONS=ON $AOMP_ORIGIN_RPATH -DLLVM_CONFIG=$INSTALL_FLANG/bin/llvm-config -DCMAKE_CXX_COMPILER=$AOMP_INSTALL_DIR/bin/clang++ -DCMAKE_C_COMPILER=$AOMP_INSTALL_DIR/bin/clang -DCMAKE_Fortran_COMPILER=$AOMP_INSTALL_DIR/bin/flang -DLLVM_TARGETS_TO_BUILD=$TARGETS_TO_BUILD -DLLVM_INSTALL_RUNTIME=ON -DFLANG_BUILD_RUNTIME=ON -DOPENMP_BUILD_DIR=$BUILD_DIR/build/openmp/runtime/src -DFLANG_INCLUDE_TESTS=OFF -DCMAKE_C_FLAGS=-I$COMP_INC_DIR -DCMAKE_CXX_FLAGS=-I$COMP_INC_DIR -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE" + + if [ "$1" == "-h" ] || [ "$1" == "help" ] || [ "$1" == "-help" ] ; then + help_build_aomp +--- a/aomp/bin/build_hipvdi.sh ++++ b/aomp/bin/build_hipvdi.sh +@@ -112,7 +112,8 @@ if [ "$1" != "nocmake" ] && [ "$1" != "install" ] ; then + -D__HIP_ENABLE_PCH=OFF \ + -DLIBROCclr_STATIC_DIR=$ROCclr_BUILD_DIR \ + -DCMAKE_PREFIX_PATH=$ROCclr_BUILD_DIR;$ROCM_DIR/include;$ROCM_DIR;$ROCM_DIR/lib \ +- -DCMAKE_CXX_FLAGS=-Wno-ignored-attributes " ++ -DCMAKE_CXX_FLAGS=-Wno-ignored-attributes \ ++ -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE" + # -DLLVM_INCLUDES=$ROCM_DIR/include " + + echo mkdir -p $BUILD_DIR/build/hipvdi +--- a/aomp/bin/build_libdevice.sh ++++ b/aomp/bin/build_libdevice.sh +@@ -44,7 +44,7 @@ REPO_BRANCH=$AOMP_LIBDEVICE_REPO_BRANCH + REPO_DIR=$AOMP_REPOS/$AOMP_LIBDEVICE_REPO_NAME + checkrepo + +-MYCMAKEOPTS="-DLLVM_DIR=$LLVM_DIR -DBUILD_HC_LIB=ON" ++MYCMAKEOPTS="-DLLVM_DIR=$LLVM_DIR -DBUILD_HC_LIB=ON -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE" + + if [ ! -d $AOMP_INSTALL_DIR/lib ] ; then + echo "ERROR: Directory $AOMP/lib is missing" +--- a/aomp/bin/build_openmp.sh ++++ b/aomp/bin/build_openmp.sh +@@ -88,14 +88,14 @@ function getgcc9orless(){ + _loc=`which gcc` + [ "$_loc" == "" ] && return + gccver=`$_loc --version | grep gcc | cut -d")" -f2 | cut -d"." -f1` +- [ $gccver -gt $GCCMIN ] && _loc=`which gcc-$GCCMIN` ++ [ $gccver -gt $GCCMIN ] + echo $_loc + } + function getgxx9orless(){ + _loc=`which g++` + [ "$_loc" == "" ] && return + gxxver=`$_loc --version | grep g++ | cut -d")" -f2 | cut -d"." -f1` +- [ $gxxver -gt $GCCMIN ] && _loc=`which g++-$GCCMIN` ++ [ $gxxver -gt $GCCMIN ] + echo $_loc + } + +@@ -126,7 +126,8 @@ COMMON_CMAKE_OPTS="-DOPENMP_ENABLE_LIBOMPTARGET=1 + -DROCDL=$AOMP_REPOS/$AOMP_LIBDEVICE_REPO_NAME + -DLIBOMP_COPY_EXPORTS=OFF + -DAOMP_STANDALONE_BUILD=$AOMP_STANDALONE_BUILD +--DLLVM_DIR=$LLVM_DIR" ++-DLLVM_DIR=$LLVM_DIR ++-DGCC_INSTALL_PREFIX=$EBROOTGCCCORE" + + if [ "$AOMP_STANDALONE_BUILD" == 0 ]; then + COMMON_CMAKE_OPTS="$COMMON_CMAKE_OPTS +--- a/aomp/bin/build_pgmath.sh ++++ b/aomp/bin/build_pgmath.sh +@@ -45,9 +45,9 @@ fi + COMP_INC_DIR=$(ls -d $AOMP_INSTALL_DIR/lib/clang/*/include ) + + if [ "$AOMP_PROC" == "ppc64le" ] ; then +- MYCMAKEOPTS="-DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_FLANG -DLLVM_ENABLE_ASSERTIONS=ON $AOMP_ORIGIN_RPATH -DCMAKE_Fortran_COMPILER=$AOMP_INSTALL_DIR/bin/flang -DLLVM_TARGETS_TO_BUILD=$TARGETS_TO_BUILD -DCMAKE_C_FLAGS=-I$COMP_INC_DIR -DCMAKE_CXX_FLAGS=-I$COMP_INC_DIR" ++ MYCMAKEOPTS="-DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_FLANG -DLLVM_ENABLE_ASSERTIONS=ON $AOMP_ORIGIN_RPATH -DCMAKE_Fortran_COMPILER=$AOMP_INSTALL_DIR/bin/flang -DLLVM_TARGETS_TO_BUILD=$TARGETS_TO_BUILD -DCMAKE_C_FLAGS=-I$COMP_INC_DIR -DCMAKE_CXX_FLAGS=-I$COMP_INC_DIR -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE" + else +- MYCMAKEOPTS="-DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_FLANG -DLLVM_ENABLE_ASSERTIONS=ON $AOMP_ORIGIN_RPATH -DLLVM_CONFIG=$INSTALL_FLANG/bin/llvm-config -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DLLVM_TARGETS_TO_BUILD=$TARGETS_TO_BUILD -DCMAKE_C_FLAGS=-I$COMP_INC_DIR -DCMAKE_CXX_FLAGS=-I$COMP_INC_DIR" ++ MYCMAKEOPTS="-DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_FLANG -DLLVM_ENABLE_ASSERTIONS=ON $AOMP_ORIGIN_RPATH -DLLVM_CONFIG=$INSTALL_FLANG/bin/llvm-config -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DLLVM_TARGETS_TO_BUILD=$TARGETS_TO_BUILD -DCMAKE_C_FLAGS=-I$COMP_INC_DIR -DCMAKE_CXX_FLAGS=-I$COMP_INC_DIR -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE" + fi + + if [ "$1" == "-h" ] || [ "$1" == "help" ] || [ "$1" == "-help" ] ; then +--- a/aomp/bin/build_project.sh ++++ b/aomp/bin/build_project.sh +@@ -42,7 +42,7 @@ if [ "$AOMP_PROC" == "ppc64le" ] ; then + COMPILERS="-DCMAKE_C_COMPILER=/usr/bin/gcc-7 -DCMAKE_CXX_COMPILER=/usr/bin/g++-7" + TARGETS_TO_BUILD="AMDGPU;${AOMP_NVPTX_TARGET}PowerPC" + else +- COMPILERS="-DCMAKE_C_COMPILER=$AOMP_CC_COMPILER -DCMAKE_CXX_COMPILER=$AOMP_CXX_COMPILER" ++ COMPILERS="-DCMAKE_C_COMPILER=$AOMP_CC_COMPILER -DCMAKE_CXX_COMPILER=$AOMP_CXX_COMPILER -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE" + if [ "$AOMP_PROC" == "aarch64" ] ; then + TARGETS_TO_BUILD="AMDGPU;${AOMP_NVPTX_TARGET}AArch64" + else +--- a/aomp/bin/build_qmcpack.sh ++++ b/aomp/bin/build_qmcpack.sh +@@ -118,6 +118,7 @@ $AOMP_CMAKE -DCMAKE_C_COMPILER=$OPENMPI_INSTALL/bin/mpicc \ + -DCMAKE_CXX_FLAGS="-march=native -Xopenmp-target=amdgcn-amd-amdhsa -march=$AOMP_GPU" \ + -DQMC_MIXED_PRECISION=1 -DENABLE_OFFLOAD=ON -DOFFLOAD_TARGET="amdgcn-amd-amdhsa" \ + -DENABLE_TIMERS=1 \ ++-DGCC_INSTALL_PREFIX=$EBROOTGCCCORE \ + .. + fi + +--- a/aomp/bin/build_rocminfo.sh ++++ b/aomp/bin/build_rocminfo.sh +@@ -110,7 +110,7 @@ if [ "$1" != "nocmake" ] && [ "$1" != "install" ] ; then + rm -rf $BUILD_DIR/build/rocminfo + fi + +- MYCMAKEOPTS="$AOMP_ORIGIN_RPATH -DCMAKE_BUILD_TYPE=$BUILDTYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_RINFO -DROCM_DIR=$ROCM_DIR -DROCRTST_BLD_TYPE=$BUILDTYPE -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON -DCMAKE_INSTALL_RPATH='\$ORIGIN/../lib' -DCMAKE_EXE_LINKER_FLAGS='-Wl,--disable-new-dtags'" ++ MYCMAKEOPTS="$AOMP_ORIGIN_RPATH -DCMAKE_BUILD_TYPE=$BUILDTYPE -DCMAKE_INSTALL_PREFIX=$INSTALL_RINFO -DROCM_DIR=$ROCM_DIR -DROCRTST_BLD_TYPE=$BUILDTYPE -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON -DCMAKE_INSTALL_RPATH='\$ORIGIN/../lib' -DCMAKE_EXE_LINKER_FLAGS='-Wl,--disable-new-dtags' -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE" + + mkdir -p $BUILD_DIR/build/rocminfo + cd $BUILD_DIR/build/rocminfo +--- a/aomp/bin/build_rocr.sh ++++ b/aomp/bin/build_rocr.sh +@@ -80,7 +80,7 @@ if [ "$1" != "nocmake" ] && [ "$1" != "install" ] ; then + BUILDTYPE="Release" + echo rm -rf $BUILD_AOMP/build/rocr + rm -rf $BUILD_AOMP/build/rocr +- MYCMAKEOPTS="-DCMAKE_INSTALL_PREFIX=$INSTALL_ROCM -DCMAKE_BUILD_TYPE=$BUILDTYPE -DCMAKE_PREFIX_PATH=$ROCM_DIR -DIMAGE_SUPPORT=OFF $AOMP_ORIGIN_RPATH" ++ MYCMAKEOPTS="-DCMAKE_INSTALL_PREFIX=$INSTALL_ROCM -DCMAKE_BUILD_TYPE=$BUILDTYPE -DCMAKE_PREFIX_PATH=$ROCM_DIR -DIMAGE_SUPPORT=OFF $AOMP_ORIGIN_RPATH -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE -DCMAKE_C_FLAGS=-fuse-ld=bfd -DCMAKE_CXX_FLAGS=-fuse-ld=bfd" + mkdir -p $BUILD_AOMP/build/rocr + cd $BUILD_AOMP/build/rocr + echo " -----Running rocr cmake ---- " +--- a/aomp/bin/build_roct.sh ++++ b/aomp/bin/build_roct.sh +@@ -76,7 +76,7 @@ if [ "$1" != "nocmake" ] && [ "$1" != "install" ] ; then + BUILDTYPE="Release" + echo $SUDO rm -rf $BUILD_AOMP/build/roct + $SUDO rm -rf $BUILD_AOMP/build/roct +- MYCMAKEOPTS="-DCMAKE_INSTALL_PREFIX=$INSTALL_ROCT -DCMAKE_BUILD_TYPE=$BUILDTYPE $AOMP_ORIGIN_RPATH -DCMAKE_INSTALL_LIBDIR=$AOMP_INSTALL_DIR/lib" ++ MYCMAKEOPTS="-DCMAKE_INSTALL_PREFIX=$INSTALL_ROCT -DCMAKE_BUILD_TYPE=$BUILDTYPE $AOMP_ORIGIN_RPATH -DCMAKE_INSTALL_LIBDIR=$AOMP_INSTALL_DIR/lib -DGCC_INSTALL_PREFIX=$EBROOTGCCCORE -DCMAKE_C_FLAGS=-fuse-ld=bfd -DCMAKE_CXX_FLAGS=-fuse-ld=bfd" + mkdir -p $BUILD_AOMP/build/roct + cd $BUILD_AOMP/build/roct + echo " -----Running roct cmake ---- " diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..0b61fd76828 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.1' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('APR', '1.7.0'), + ('SQLite', '3.35.4'), + ('expat', '2.2.9'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..11da24736d8 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-10.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.0' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2'] + +builddependencies = [('binutils', '2.36.1')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/ARCH/ARCH-4.5.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/a/ARCH/ARCH-4.5.0-intel-2018a-Python-3.6.4.eb index e2f2bd79a37..8c9bcdfba11 100644 --- a/easybuild/easyconfigs/a/ARCH/ARCH-4.5.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/a/ARCH/ARCH-4.5.0-intel-2018a-Python-3.6.4.eb @@ -19,15 +19,12 @@ use_pip = True exts_list = [ ('patsy', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), ('statsmodels', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/arch'], 'source_tmpl': 'arch-%(version)s.tar.gz', 'checksums': ['022a01cea492ffde934e23ed6d2bc7f9723df57c406f5739f41c672a91c8dea1'], 'installopts': "--install-option '--no-binary'", diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-foss-2018b-Python-3.6.6.eb index c8d89fbc754..40ea8207954 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-foss-2018b-Python-3.6.6.eb @@ -20,31 +20,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['5e63e7dc18fd13dcc3cb46ab3de019375b9d62c6c3a845a99f34b6928251f4c2'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-intel-2018b-Python-3.6.6.eb index 39267334f2c..0d3ea7a06fa 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-intel-2018b-Python-3.6.6.eb @@ -20,31 +20,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['5e63e7dc18fd13dcc3cb46ab3de019375b9d62c6c3a845a99f34b6928251f4c2'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018.02-Python-3.6.4.eb b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018.02-Python-3.6.4.eb index baed396abd3..6c0c8a76eda 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018.02-Python-3.6.4.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018.02-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'ASE' version = '3.16.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://wiki.fysik.dtu.dk/ase' +homepage = 'https://wiki.fysik.dtu.dk/ase' description = """ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.""" @@ -20,31 +20,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['5e63e7dc18fd13dcc3cb46ab3de019375b9d62c6c3a845a99f34b6928251f4c2'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018a-Python-3.6.4.eb index db67909de37..81bc6191940 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'ASE' version = '3.16.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://wiki.fysik.dtu.dk/ase' +homepage = 'https://wiki.fysik.dtu.dk/ase' description = """ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.""" @@ -20,31 +20,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['5e63e7dc18fd13dcc3cb46ab3de019375b9d62c6c3a845a99f34b6928251f4c2'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018b-Python-3.6.6.eb index bd0388b1568..9c259705e8f 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018b-Python-3.6.6.eb @@ -20,31 +20,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['5e63e7dc18fd13dcc3cb46ab3de019375b9d62c6c3a845a99f34b6928251f4c2'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2018b-Python-3.6.6.eb index ce0d8d1b5dd..6942e20ad76 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2018b-Python-3.6.6.eb @@ -20,31 +20,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['8fe49ddc5a554b69b6468dd1f45a29f67c61997319d0cb7e217e41a5aeef8fb4'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb index 40ff474e221..70ed68686f5 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb @@ -21,31 +21,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['8fe49ddc5a554b69b6468dd1f45a29f67c61997319d0cb7e217e41a5aeef8fb4'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2018b-Python-3.6.6.eb index 102e7c81306..749fbc1daa0 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2018b-Python-3.6.6.eb @@ -20,31 +20,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['8fe49ddc5a554b69b6468dd1f45a29f67c61997319d0cb7e217e41a5aeef8fb4'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb index 7d9d0f47dc1..d3ad77479dc 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb @@ -24,31 +24,24 @@ check_ldshared = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['8fe49ddc5a554b69b6468dd1f45a29f67c61997319d0cb7e217e41a5aeef8fb4'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-iomkl-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-iomkl-2018b-Python-3.6.6.eb index e5713f644a7..8ed5b229625 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-iomkl-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-iomkl-2018b-Python-3.6.6.eb @@ -20,31 +20,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['8fe49ddc5a554b69b6468dd1f45a29f67c61997319d0cb7e217e41a5aeef8fb4'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.18.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ASE/ASE-3.18.0-foss-2018b-Python-3.6.6.eb index 433192368b4..7b35514c878 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.18.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.18.0-foss-2018b-Python-3.6.6.eb @@ -20,31 +20,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('Jinja2', '2.10.1', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['065c4f02ebe7f7cf559e49ee5a95fb800a9e4528727aec6f24402a5374c65013'], }), ('Werkzeug', '0.15.5', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['a13b74dd3c45f758d4ebdb224be8f1ab8ef58b3c0ffc1783a8c7d9f4f50227e6'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['39d45f12def2669605bffc82926acfb13a0d0610e6d82740fa316aafa70f97f9'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.18.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.18.0-foss-2019a-Python-3.7.2.eb index 9caf3be595c..73b0982c46a 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.18.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.18.0-foss-2019a-Python-3.7.2.eb @@ -21,31 +21,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('Jinja2', '2.10.1', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['065c4f02ebe7f7cf559e49ee5a95fb800a9e4528727aec6f24402a5374c65013'], }), ('Werkzeug', '0.15.5', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['a13b74dd3c45f758d4ebdb224be8f1ab8ef58b3c0ffc1783a8c7d9f4f50227e6'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['39d45f12def2669605bffc82926acfb13a0d0610e6d82740fa316aafa70f97f9'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.18.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ASE/ASE-3.18.0-intel-2018b-Python-3.6.6.eb index 071d197e254..14eb7bdf641 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.18.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.18.0-intel-2018b-Python-3.6.6.eb @@ -20,31 +20,24 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('Jinja2', '2.10.1', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['065c4f02ebe7f7cf559e49ee5a95fb800a9e4528727aec6f24402a5374c65013'], }), ('Werkzeug', '0.15.5', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['a13b74dd3c45f758d4ebdb224be8f1ab8ef58b3c0ffc1783a8c7d9f4f50227e6'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['39d45f12def2669605bffc82926acfb13a0d0610e6d82740fa316aafa70f97f9'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.18.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.18.0-intel-2019a-Python-3.7.2.eb index 708ca9ca6e0..9c31b908a24 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.18.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.18.0-intel-2019a-Python-3.7.2.eb @@ -24,31 +24,24 @@ check_ldshared = True exts_list = [ ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('Jinja2', '2.10.1', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['065c4f02ebe7f7cf559e49ee5a95fb800a9e4528727aec6f24402a5374c65013'], }), ('Werkzeug', '0.15.5', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['a13b74dd3c45f758d4ebdb224be8f1ab8ef58b3c0ffc1783a8c7d9f4f50227e6'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52'], }), ('ase', version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], 'checksums': ['39d45f12def2669605bffc82926acfb13a0d0610e6d82740fa316aafa70f97f9'], }), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2018b-Python-3.6.6.eb index f6d5b5eaa84..89dc43a8a85 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2018b-Python-3.6.6.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2019b-Python-3.7.4.eb index 9f20e270435..62f464b03ab 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-fosscuda-2019b-Python-3.7.4.eb index a53791d30a0..b2f5b91f088 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-fosscuda-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2018b-Python-3.6.6.eb index b425c8214a1..9f600428731 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2018b-Python-3.6.6.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2019b-Python-3.7.4.eb index b98da7b60d7..410d946be28 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2019b-Python-3.7.4.eb @@ -22,8 +22,6 @@ sanity_pip_check = True # required because we're building Python packages (MarkupSafe) using Intel compilers on top of Python built with GCC. check_ldshared = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2019b-Python-3.7.4.eb index 98d9a051f09..cb8d68cce49 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2019b-Python-3.7.4.eb @@ -22,8 +22,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2019b-Python-3.7.4.eb index 1876fe3ad4d..37579a714f0 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2019b-Python-3.7.4.eb @@ -25,8 +25,6 @@ sanity_pip_check = True # required because we're building Python packages (MarkupSafe) using Intel compilers on top of Python built with GCC. check_ldshared = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..ac14d358c3f --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.21.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Flask', '1.1.2', versionsuffix), + ('matplotlib', '3.2.1', versionsuffix), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0', versionsuffix), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ase', version, { + 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..cf41c4d87a5 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.36.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['fb76247e369402be23f1f5c65d38a9639c1164d934e40f6a9cf3c9e96b652788'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.68.0'), +] + +dependencies = [ + ('GLib', '2.68.2'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb index af4d962fae4..a503cfc0ecc 100644 --- a/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Albacore' version = '2.0.2' @@ -10,9 +10,6 @@ description = """Albacore is a software project that provides an entry point to toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - local_pyver = '3.6.1' local_pymajmin = ''.join(local_pyver.split('.')[:2]) @@ -24,12 +21,10 @@ dependencies = [ exts_list = [ ('ont-fast5-api', '0.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/o/ont-fast5-api'], 'checksums': ['9c738b592613f5013c4cd3001c4448b5378454ce92e63ff795d134a4eca30fd0'], 'modulename': 'ont_fast5_api', }), ('progressbar33', '2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/progressbar33'], 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], 'modulename': 'progressbar', }), @@ -48,6 +43,4 @@ sanity_check_paths = { } sanity_check_commands = ["read_fast5_basecaller.py --help"] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/Alpha/Alpha-20200430-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/a/Alpha/Alpha-20200430-foss-2019b-Python-2.7.16.eb index 05bee948667..73a5ce2031c 100644 --- a/easybuild/easyconfigs/a/Alpha/Alpha-20200430-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/a/Alpha/Alpha-20200430-foss-2019b-Python-2.7.16.eb @@ -31,7 +31,7 @@ components = [ ('progressbar', '2.5', { 'easyblock': 'PythonPackage', 'source_urls': [PYPI_SOURCE], - 'sources': ['%(name)s-%(version)s.tar.gz'], + 'sources': [SOURCE_TAR_GZ], 'checksums': ['5d81cb529da2e223b53962afd6c8ca0f05c6670e40309a7219eacc36af9b6c63'], 'start_dir': '%(name)s-%(version)s', }), diff --git a/easybuild/easyconfigs/a/Amara/Amara-1.2.0.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/a/Amara/Amara-1.2.0.2-foss-2019a-Python-2.7.15.eb index 7ed2d771b8a..99eda3da63d 100644 --- a/easybuild/easyconfigs/a/Amara/Amara-1.2.0.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/Amara/Amara-1.2.0.2-foss-2019a-Python-2.7.15.eb @@ -15,8 +15,6 @@ dependencies = [('Python', '2.7.15')] # ancient software, doesn't support installing with pip use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('4Suite-XML', '1.0.2', { 'patches': ['4Suite-XML-1.0.2_fixes.patch'], diff --git a/easybuild/easyconfigs/a/Amara/Amara-1.2.0.2-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/a/Amara/Amara-1.2.0.2-intel-2019a-Python-2.7.15.eb index 3f11bc21a99..9ef6332f61a 100644 --- a/easybuild/easyconfigs/a/Amara/Amara-1.2.0.2-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/Amara/Amara-1.2.0.2-intel-2019a-Python-2.7.15.eb @@ -15,8 +15,6 @@ dependencies = [('Python', '2.7.15')] # ancient software, doesn't support installing with pip use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('4Suite-XML', '1.0.2', { 'patches': ['4Suite-XML-1.0.2_fixes.patch'], diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb new file mode 100644 index 00000000000..2cc15a50cb3 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -0,0 +1,60 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 20 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (15, 11) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s-Python-%%(pyver)s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + 'AmberTools-%s_cmake-locate-netcdf.patch' % local_ambertools_ver, + 'AmberTools-%s_fix_missing_MPI_LIBRARY_error.patch' % local_ambertools_ver, +] +checksums = [ + 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 + 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools20.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', +] + +builddependencies = [ + ('Bison', '3.5.3'), + ('CMake', '3.16.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('Boost', '1.72.0'), + ('bzip2', '1.0.8'), + ('libreadline', '8.0'), + ('matplotlib', '3.2.1', '-Python-%(pyver)s'), + ('netCDF-Fortran', '4.5.2'), + ('netCDF', '4.7.4'), + ('Perl', '5.30.2'), + ('PnetCDF', '1.12.1'), + ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA + ('Tkinter', '3.8.2'), + ('X11', '20200222'), + ('zlib', '1.2.11'), +] + +# Tests are flaky +runtest = False + +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb new file mode 100644 index 00000000000..ee8d80b6270 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb @@ -0,0 +1,63 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 21 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (3, 11) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', +] +checksums = [ + 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 + 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools21.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # mpi4py required for MMPBSA + ('Perl', '5.32.0'), + ('Boost', '1.74.0'), + ('libreadline', '8.0'), + ('matplotlib', '3.3.3'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.2'), + ('Tkinter', '3.8.6'), + ('X11', '20201008'), +] + +# All tests are expected to pass or be skipped +runtest = True + +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb new file mode 100644 index 00000000000..5a8159af3bb --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -0,0 +1,61 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 20 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (15, 11) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s-Python-%%(pyver)s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'fosscuda', 'version': '2020a'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + 'AmberTools-%s_cmake-locate-netcdf.patch' % local_ambertools_ver, + 'AmberTools-%s_fix_missing_MPI_LIBRARY_error.patch' % local_ambertools_ver, +] +checksums = [ + 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 + 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools20.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', +] + +builddependencies = [ + ('Bison', '3.5.3'), + ('CMake', '3.16.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('Boost', '1.72.0'), + ('bzip2', '1.0.8'), + ('libreadline', '8.0'), + ('matplotlib', '3.2.1', '-Python-%(pyver)s'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('netCDF-Fortran', '4.5.2'), + ('netCDF', '4.7.4'), + ('Perl', '5.30.2'), + ('PnetCDF', '1.12.1'), + ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA + ('Tkinter', '3.8.2'), + ('X11', '20200222'), + ('zlib', '1.2.11'), +] + +# Tests are flaky +runtest = False + +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb new file mode 100644 index 00000000000..fc45e8660c5 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb @@ -0,0 +1,64 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 21 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (3, 11) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', +] +checksums = [ + 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 + 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools21.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # mpi4py required for MMPBSA + ('Perl', '5.32.0'), + ('Boost', '1.74.0'), + ('libreadline', '8.0'), + ('matplotlib', '3.3.3'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.2'), + ('Tkinter', '3.8.6'), + ('X11', '20201008'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), +] + +# Some CUDA tests differs from expected results +runtest = False + +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-20_cmake-locate-netcdf.patch b/easybuild/easyconfigs/a/Amber/AmberTools-20_cmake-locate-netcdf.patch new file mode 100644 index 00000000000..3ece09e84c1 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/AmberTools-20_cmake-locate-netcdf.patch @@ -0,0 +1,13 @@ +Ensure that CMake recurses available paths if the Fortran libs aren't available in the netCDF module + +James Carpenter 2021-01-23 +--- amber20_src/cmake/jedbrown/FindNetCDF.cmake.orig 2020-04-28 02:19:51.000000000 +0100 ++++ amber20_src/cmake/jedbrown/FindNetCDF.cmake 2021-01-25 11:41:47.005657000 +0000 +@@ -52,6 +52,7 @@ + + macro (NetCDF_check_interface lang header libs) + find_path (NetCDF_INCLUDES_${lang} NAMES ${header} HINTS "${NetCDF_INCLUDES}" NO_DEFAULT_PATH) ++ find_path (NetCDF_INCLUDES_${lang} NAMES ${header} HINTS "${NetCDF_INCLUDES}") + + find_library (NetCDF_LIBRARIES_${lang} NAMES ${libs} HINTS "${NetCDF_lib_dirs}") + diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch new file mode 100644 index 00000000000..8d96ce176c0 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch @@ -0,0 +1,21 @@ +When using "usempi" there will be no MPI_xxx_LIBRARIES set and that causes +import_libraries to error out. We know it is correct so comment out that +FATAL_ERROR. + +Åke Sandgren, 2021-06-16 +diff -ru amber20_src.orig/cmake/LibraryTracking.cmake amber20_src/cmake/LibraryTracking.cmake +--- amber20_src.orig/cmake/LibraryTracking.cmake 2021-04-25 02:51:44.000000000 +0200 ++++ amber20_src/cmake/LibraryTracking.cmake 2021-06-16 13:30:26.568317368 +0200 +@@ -170,9 +170,9 @@ + + cmake_parse_arguments(IMP_LIBS "" "" "LIBRARIES;INCLUDES" ${ARGN}) + +- if("${IMP_LIBS_LIBRARIES}" STREQUAL "") +- message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") +- endif() ++ #if("${IMP_LIBS_LIBRARIES}" STREQUAL "") ++ # message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") ++ #endif() + + if(NOT "${IMP_LIBS_UNPARSED_ARGUMENTS}" STREQUAL "") + message(FATAL_ERROR "Incorrect usage. Extra arguments provided.") diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_xblas_missing_make_dependency.patch b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_xblas_missing_make_dependency.patch new file mode 100644 index 00000000000..5a8a55682c3 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_xblas_missing_make_dependency.patch @@ -0,0 +1,19 @@ +Fix a missing dependency in xblas causing problems when building with large -j + +Åke Sandgren, 2021-07-01 +diff -ru amber20_src.orig/AmberTools/src/xblas/Makefile amber20_src/AmberTools/src/xblas/Makefile +--- amber20_src.orig/AmberTools/src/xblas/Makefile 2020-01-02 18:26:09.000000000 +0100 ++++ amber20_src/AmberTools/src/xblas/Makefile 2021-07-01 11:34:05.281580939 +0200 +@@ -97,10 +97,10 @@ + grep 'FAIL/TOTAL' testall.result >testall.summary + cat testall.summary + +-common-lib: ++common-lib: header + cd $(SRC_DIR)/common && $(MAKE) + +-common-test-lib: ++common-test-lib: header + cd $(TEST_DIR)/common && $(MAKE) + + diff --git a/easybuild/easyconfigs/a/Annif/Annif-0.40.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/Annif/Annif-0.40.0-foss-2019a-Python-3.7.2.eb index 0addec65705..3e12804b5d8 100644 --- a/easybuild/easyconfigs/a/Annif/Annif-0.40.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/Annif/Annif-0.40.0-foss-2019a-Python-3.7.2.eb @@ -18,14 +18,8 @@ dependencies = [ use_pip = True -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'source_tmpl': SOURCE_TAR_GZ, -} - exts_list = [ ('sklearn', '0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sklearn'], 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], }), ('swagger-ui-bundle', '0.0.5', { diff --git a/easybuild/easyconfigs/a/Annif/Annif-0.40.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/Annif/Annif-0.40.0-intel-2019a-Python-3.7.2.eb index ed8c0e7d1c6..5e8beb80efc 100644 --- a/easybuild/easyconfigs/a/Annif/Annif-0.40.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/Annif/Annif-0.40.0-intel-2019a-Python-3.7.2.eb @@ -18,14 +18,8 @@ dependencies = [ use_pip = True -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'source_tmpl': SOURCE_TAR_GZ, -} - exts_list = [ ('sklearn', '0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sklearn'], 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], }), ('swagger-ui-bundle', '0.0.5', { diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-foss-2018b-Python-2.7.15.eb index 862cc51a596..11d2da152e0 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-foss-2018b-Python-2.7.15.eb @@ -36,6 +36,7 @@ configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DCMAKE_INSTALL_LIBDI exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } @@ -43,7 +44,6 @@ exts_default_options = { # Python bindings require futures for Python < 3.2 exts_list = [ ('futures', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], 'modulename': 'concurrent.futures', }), diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb index d993e2df07f..81cb0dcd22c 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb @@ -36,6 +36,7 @@ configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DCMAKE_INSTALL_LIBDI exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } @@ -43,7 +44,6 @@ exts_default_options = { # Python bindings require futures for Python < 3.2 exts_list = [ ('futures', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], 'modulename': 'concurrent.futures', }), diff --git a/easybuild/easyconfigs/a/Assimulo/Assimulo-2.9-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/Assimulo/Assimulo-2.9-intel-2018b-Python-2.7.15.eb index 4d32f1082b4..a5cf7d77c80 100644 --- a/easybuild/easyconfigs/a/Assimulo/Assimulo-2.9-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/Assimulo/Assimulo-2.9-intel-2018b-Python-2.7.15.eb @@ -10,7 +10,6 @@ description = """Assimulo is a simulation package for solving ordinary different toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'pic': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] patches = ['Assimulo-2.9_fix-python-buildopts.patch', 'Assimulo-2.9_fix-intel_i8_r8.patch'] checksums = [ @@ -28,9 +27,4 @@ dependencies = [ download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2021.02.19-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2021.02.19-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d5997d95813 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2021.02.19-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU Free Documentation License +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Autoconf-archive' +version = '2021.02.19' + +homepage = "https://www.gnu.org/software/autoconf-archive" + +description = """ +The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf +that have been contributed as free software by friendly supporters of the cause from +all over the Internet. Every single one of those macros can be re-used without +imposing any restrictions whatsoever on the licensing of the generated configure script. +In particular, it is possible to use all those macros in configure scripts that +are meant for non-free software. This policy is unusual for a Free Software Foundation +project. The FSF firmly believes that software ought to be free, and software licenses +like the GPL are specifically designed to ensure that derivative work based on free +software must be free as well. In case of Autoconf, however, an exception has been made, +because Autoconf is at such a pivotal position in the software development tool chain +that the benefits from having this tool available as widely as possible outweigh the +disadvantage that some authors may choose to use it, too, for proprietary software. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e8a6eb9d28ddcba8ffef3fa211653239e9bf239aba6a01a6b7cfc7ceaec69cbd'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('makeinfo', '6.7'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/%s' % x for x in + ['aclocal', 'doc', 'info']], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2018b-Python-3.6.6.eb index 278d0ec7c61..fc3efb86cc1 100644 --- a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = "A small library for automatically adjustment of text position in toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'] diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-intel-2019a-Python-3.7.2.eb index fd53dd79b47..81ec7bfddd6 100644 --- a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-intel-2019a-Python-3.7.2.eb @@ -10,7 +10,6 @@ description = "A small library for automatically adjustment of text position in toolchain = {'name': 'intel', 'version': '2019a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'] diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.5.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.5.4-foss-2018b-Python-3.6.6.eb index 21287eb13dd..3e7d29257a5 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.5.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.5.4-foss-2018b-Python-3.6.6.eb @@ -18,54 +18,38 @@ use_pip = True exts_list = [ ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('multidict', '4.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/m/multidict/'], 'checksums': ['024b8129695a952ebd93373e45b5d341dbb87c17ce49637b34000093f243dd4f'], }), ('yarl', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/y/yarl/'], 'checksums': ['024ecdc12bc02b321bc66b41327f930d1c2c543fa9a561b39861da9388ba7aa9'], }), ('async-timeout', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/async-timeout/'], 'checksums': ['0c3c816a028d47f659d6ff5c745cb2acf1f966da1fe5c19c77a70282b25f4c5f'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('idna-ssl', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna-ssl/'], 'checksums': ['a933e3bb13da54383f9e8f35dc4f9cb9eb9b3b78c6b36f311254d6d0d92c6c7c'], }), ('typing_extensions', '3.7.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing_extensions/'], 'checksums': ['fb2cd053238d33a8ec939190f30cfd736c00653a85a2919415cecf7dc3d9da71'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/aiohttp/'], 'checksums': ['9c4c83f4fa1938377da32bc2d59379025ceeee8e24b89f72fcbccd8ca22dc9bf'], }), ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('aiohttp-jinja2', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/aiohttp-jinja2/'], 'checksums': ['aef9b6595f962182ad00c990095fb51d731c280e1d183e2b28cf0bdb5a942d0c'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/amplimap/amplimap-0.4.16-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/amplimap/amplimap-0.4.16-foss-2018b-Python-3.6.6.eb index 73d9d4da888..c1e6439c35e 100644 --- a/easybuild/easyconfigs/a/amplimap/amplimap-0.4.16-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/amplimap/amplimap-0.4.16-foss-2018b-Python-3.6.6.eb @@ -27,8 +27,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pysam', '0.13', { # older version required 'checksums': ['1829035f58bddf26b0cb6867968178701c2a243518ea697dcedeebff487979af'], diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb index c882904ce07..54876beb23c 100644 --- a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb @@ -46,8 +46,6 @@ components = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('helperlibs', '0.1.11', { 'checksums': ['261ddfff1d8f8860198128d51571470dee3a628cc36a2a141c19ce67263b94d3'], diff --git a/easybuild/easyconfigs/a/anvio/anvio-6.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/anvio/anvio-6.1-intel-2019b-Python-3.7.4.eb index 990eaac384d..9063e0b06b5 100644 --- a/easybuild/easyconfigs/a/anvio/anvio-6.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/anvio/anvio-6.1-intel-2019b-Python-3.7.4.eb @@ -14,8 +14,6 @@ toolchain = {'name': 'intel', 'version': '2019b'} github_account = 'merenlab' -exts_default_options = {'source_urls': [PYPI_SOURCE]} - dependencies = [ ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), @@ -138,7 +136,6 @@ exts_list = [ 'checksums': ['409cd48d4db7052af495b09dec721011634af3753ae1ef92d2b32f73a745f832'], }), (name, version, { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/%(github_account)s/%(name)s/releases/download/v%(version)s/'], 'checksums': [ 'a766514d47ba012b45fef51c0ad3a810f930687c6f59531f0d2e0bd96cb05db9', # anvio-6.1.tar.gz diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb index de8a9ab2b28..574183e62e3 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb @@ -45,8 +45,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('zipp', '1.0.0', { 'checksums': ['d38fbe01bbf7a3593a32bc35a9c4453c32bc42b98c377f9bff7e9f8da157786c'], @@ -89,7 +87,8 @@ exts_list = [ 'modulename': False, 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/artic-network/fieldbioinformatics/archive'], - 'checksums': ['7083f67b1188e8f9b55f8bd4f7a46853e9c74ae7dde324b1fc8e792a85e58073'], + 'checksums': [('7083f67b1188e8f9b55f8bd4f7a46853e9c74ae7dde324b1fc8e792a85e58073', + '778ed3cf2f1b0457c696acbed8b99951b2ec042a2035f08bddd95da3884b146b')], }), # This is not upstream version, but artic tweaked one, which is exactly required. ('Porechop', '0.3.2pre', { diff --git a/easybuild/easyconfigs/a/astropy/astropy-2.0.12-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/astropy/astropy-2.0.12-foss-2018b-Python-2.7.15.eb index dd72f1b5271..ac8714e8e31 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-2.0.12-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-2.0.12-foss-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'astropy' version = '2.0.12' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.astropy.org/' +homepage = 'https://www.astropy.org/' description = """The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.""" @@ -20,37 +20,29 @@ use_pip = True exts_list = [ ('py', '1.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/py/'], 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('atomicwrites', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/A/atomicwrites/'], 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/more-itertools/'], 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('pluggy', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/pluggy/'], 'checksums': ['95eb8364a4708392bae89035f45341871286a333f749c3141c20573d2b3876e1'], }), ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/A/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('pytest', '3.6.4', { - 'source_urls': ['https://pypi.python.org/packages/source/P/pytest/'], 'checksums': ['341ec10361b64a24accaec3c7ba5f7d5ee1ca4cebea30f76fad3dd12db9f0541'], }), ('astropy-helpers', '2.0.9', { - 'source_urls': ['https://pypi.python.org/packages/source/A/astropy-helpers/'], 'checksums': ['3bb4c3b85f5778a3f727e72b5d2243f567d57b28761ebaab71ee8c7ee9c9d0e8'], }), (name, version, { 'patches': ['astropy-ah_no_auto_use.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/A/astropy/'], 'checksums': [ '81bae35320d7c72ae8569eeabc596e3a5ed416249b3fb2de9b40f30673085d0b', # astropy-2.0.12.tar.gz 'fb339ff90fff8ed760b5ea9b8b65be3babb355f956a5588fd7e2e2656b4a7ca8', # astropy_ah_no_auto_use.patch diff --git a/easybuild/easyconfigs/a/astropy/astropy-2.0.12-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/astropy/astropy-2.0.12-intel-2018b-Python-2.7.15.eb index 11b78a048e5..26fe0101191 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-2.0.12-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-2.0.12-intel-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'astropy' version = '2.0.12' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.astropy.org/' +homepage = 'https://www.astropy.org/' description = """The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.""" @@ -20,37 +20,29 @@ use_pip = True exts_list = [ ('py', '1.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/py/'], 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('atomicwrites', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/A/atomicwrites/'], 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/more-itertools/'], 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('pluggy', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/pluggy/'], 'checksums': ['95eb8364a4708392bae89035f45341871286a333f749c3141c20573d2b3876e1'], }), ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/A/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('pytest', '3.6.4', { - 'source_urls': ['https://pypi.python.org/packages/source/P/pytest/'], 'checksums': ['341ec10361b64a24accaec3c7ba5f7d5ee1ca4cebea30f76fad3dd12db9f0541'], }), ('astropy-helpers', '2.0.9', { - 'source_urls': ['https://pypi.python.org/packages/source/A/astropy-helpers/'], 'checksums': ['3bb4c3b85f5778a3f727e72b5d2243f567d57b28761ebaab71ee8c7ee9c9d0e8'], }), (name, version, { 'patches': ['astropy-ah_no_auto_use.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/A/astropy/'], 'checksums': [ '81bae35320d7c72ae8569eeabc596e3a5ed416249b3fb2de9b40f30673085d0b', # astropy-2.0.12.tar.gz 'fb339ff90fff8ed760b5ea9b8b65be3babb355f956a5588fd7e2e2656b4a7ca8', # astropy_ah_no_auto_use.patch diff --git a/easybuild/easyconfigs/a/astropy/astropy-2.0.14-foss-2019a.eb b/easybuild/easyconfigs/a/astropy/astropy-2.0.14-foss-2019a.eb index c39f31e25d8..de4ea74d4ed 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-2.0.14-foss-2019a.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-2.0.14-foss-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'astropy' version = '2.0.14' -homepage = 'http://www.astropy.org/' +homepage = 'https://www.astropy.org/' description = """The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.""" @@ -20,12 +20,10 @@ use_pip = True exts_list = [ ('astropy-helpers', '2.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/A/astropy-helpers/'], 'checksums': ['c5ca146e2b8607087f907b5cd1c5aabb0854cca0df43043a38aea1757e5eb65c'], }), (name, version, { 'patches': ['astropy-ah_no_auto_use.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/A/astropy/'], 'checksums': [ '618807068609a4d8aeb403a07624e9984f566adc0dc0f5d6b477c3658f31aeb6', # astropy-2.0.14.tar.gz 'fb339ff90fff8ed760b5ea9b8b65be3babb355f956a5588fd7e2e2656b4a7ca8', # astropy-ah_no_auto_use.patch diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/astropy/astropy-4.0.1-foss-2019b-Python-3.7.4.eb index 9aef82263fa..395f2b09714 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-4.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-4.0.1-foss-2019b-Python-3.7.4.eb @@ -27,8 +27,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('html5lib', '1.0.1', { 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.0.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/astropy/astropy-4.0.1-foss-2020a-Python-3.8.2.eb index 473a469f6c2..0d2bd5d3fb1 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-4.0.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-4.0.1-foss-2020a-Python-3.8.2.eb @@ -22,12 +22,10 @@ sanity_pip_check = True exts_list = [ ('astropy-helpers', version, { - 'source_urls': ['https://pypi.python.org/packages/source/A/astropy-helpers/'], 'checksums': ['f1096414d108778218d6bea06d4d9c7b2ff7c83856a451331ac194e74de9f413'], }), (name, version, { 'patches': ['astropy-ah_no_auto_use.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/A/astropy/'], 'checksums': [ 'f1135f2637867bf4eb44b754d905462be738165ae5535540670938bbc2dcc62c', # astropy-4.0.1.tar.gz 'fb339ff90fff8ed760b5ea9b8b65be3babb355f956a5588fd7e2e2656b4a7ca8', # astropy-ah_no_auto_use.patch diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.0.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/astropy/astropy-4.0.1-intel-2020a-Python-3.8.2.eb index 6e3e1bb3d24..1dfede9e143 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-4.0.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-4.0.1-intel-2020a-Python-3.8.2.eb @@ -22,12 +22,10 @@ sanity_pip_check = True exts_list = [ ('astropy-helpers', version, { - 'source_urls': ['https://pypi.python.org/packages/source/A/astropy-helpers/'], 'checksums': ['f1096414d108778218d6bea06d4d9c7b2ff7c83856a451331ac194e74de9f413'], }), (name, version, { 'patches': ['astropy-ah_no_auto_use.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/A/astropy/'], 'checksums': [ 'f1135f2637867bf4eb44b754d905462be738165ae5535540670938bbc2dcc62c', # astropy-4.0.1.tar.gz 'fb339ff90fff8ed760b5ea9b8b65be3babb355f956a5588fd7e2e2656b4a7ca8', # astropy-ah_no_auto_use.patch diff --git a/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb index 6a33cf7fb22..3ad38618dc2 100644 --- a/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb @@ -9,7 +9,6 @@ description = """atomate has implementations of FireWorks workflows for Material toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c92bbdd8197 --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-10.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.5.1' + +homepage = 'https://savannah.nongnu.org/projects/attr' + +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['bae1c6949b258a0d68001367ce0c741cebdacdd3b62965d17e5eb23cd78adaf8'] + +builddependencies = [('binutils', '2.36.1')] + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', + 'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h', + 'include/%(name)s/libattr.h', 'lib/libattr.a', + 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/attrdict/attrdict-2.0.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/a/attrdict/attrdict-2.0.1-GCCcore-8.3.0-Python-3.7.4.eb index 3f6e57f2a8a..892719f8a7d 100644 --- a/easybuild/easyconfigs/a/attrdict/attrdict-2.0.1-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/attrdict/attrdict-2.0.1-GCCcore-8.3.0-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """AttrDict is a Python library that provides mapping objects that toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['35c90698b55c683946091177177a9e9c0713a0860f0e049febd72649ccd77b70'] diff --git a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb index 30d6c3f6037..d186e6251cc 100644 --- a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb @@ -31,8 +31,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - local_augur_preinstallopts = """sed -i'' 's/"matplotlib >=2.0,.*/"matplotlib >=2.0",/' setup.py && """ local_augur_preinstallopts += """sed -i'' 's/"cvxopt >=1.1.9,.*/"cvxopt >=1.1.9",/' setup.py && """ local_augur_preinstallopts += """sed -i'' 's/"seaborn >=0.9.0,.*/"seaborn >=0.9.0",/' setup.py && """ diff --git a/easybuild/easyconfigs/a/autopep8/autopep8-1.4.4-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/a/autopep8/autopep8-1.4.4-intel-2018a-Python-3.6.4.eb index c6173ef2ef6..296b4a99ad8 100644 --- a/easybuild/easyconfigs/a/autopep8/autopep8-1.4.4-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/a/autopep8/autopep8-1.4.4-intel-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = """A tool that automatically formats Python code to conform to the toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4d8eec30cc81bc5617dbf1218201d770dc35629363547f17577c61683ccfb3ee'] @@ -22,9 +21,4 @@ download_dep_fail = True use_pip = True sanity_pip_check = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/awscli/awscli-1.11.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/awscli/awscli-1.11.1-intel-2016b-Python-2.7.12.eb index ce1d7a97a91..0132ae473a2 100644 --- a/easybuild/easyconfigs/a/awscli/awscli-1.11.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/awscli/awscli-1.11.1-intel-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = 'Universal Command Line Environment for AWS' toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb index 729a10008ff..0ee6b647bef 100644 --- a/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = 'Universal Command Line Environment for AWS' toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/a/awscli/awscli-1.16.290-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/awscli/awscli-1.16.290-foss-2018b-Python-3.6.6.eb index 5d3e2977aa2..c902be9791e 100644 --- a/easybuild/easyconfigs/a/awscli/awscli-1.16.290-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/awscli/awscli-1.16.290-foss-2018b-Python-3.6.6.eb @@ -16,8 +16,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('colorama', '0.4.1', { 'checksums': ['05eed71e2e327246ad6b38c540c4a3117230b19679b875190486ddd2d721422d'], diff --git a/easybuild/easyconfigs/a/awscli/awscli-1.17.7-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/a/awscli/awscli-1.17.7-GCCcore-8.3.0-Python-3.7.4.eb index 0fdad54cbcb..b78670a8fc6 100644 --- a/easybuild/easyconfigs/a/awscli/awscli-1.17.7-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/awscli/awscli-1.17.7-GCCcore-8.3.0-Python-3.7.4.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('colorama', '0.4.1', { 'checksums': ['05eed71e2e327246ad6b38c540c4a3117230b19679b875190486ddd2d721422d'], diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb new file mode 100644 index 00000000000..94e6c8540fe --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '38.90' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1'] + +dependencies = [('Java', '11', '', True)] + +prebuildopts = 'cd jni && ' + +local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % local_suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-9.3.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-9.3.0.eb new file mode 100644 index 00000000000..6d1053ec36a --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-9.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '38.90' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1'] + +dependencies = [('Java', '11', '', True)] + +prebuildopts = 'cd jni && ' + +local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % local_suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-2.7.14.eb index 4c1f9477296..1cf2d1231df 100644 --- a/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'BDBag' version = '1.4.1' @@ -10,22 +10,16 @@ working with BagIt packages that conform to the Bagit and Bagit/RO profiles.""" toolchain = {'name': 'intel', 'version': '2018a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_download_dep_fail = True - dependencies = [ ('Python', '2.7.14'), ] exts_list = [ ('tzlocal', '2.0.0b1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tzlocal'], 'source_tmpl': 'tzlocal-2.0.0b1.tar.gz', 'checksums': ['27d58a0958dc884d208cdaf45ef5892bf2a57d21d9611f2ac45e51f1973e8cab'], }), ('bagit', '1.6.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bagit'], 'source_tmpl': 'bagit-1.6.4.tar.gz', 'checksums': ['91c5e253ad4ae0c5a5e795c689cda348c01286c671e9f6ca5cab0018980f9be9'], }), @@ -36,11 +30,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb index 84c8901bac4..f947ccbe942 100644 --- a/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb @@ -18,12 +18,10 @@ use_pip = True exts_list = [ ('tzlocal', '2.0.0b1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tzlocal'], 'source_tmpl': 'tzlocal-2.0.0b1.tar.gz', 'checksums': ['27d58a0958dc884d208cdaf45ef5892bf2a57d21d9611f2ac45e51f1973e8cab'], }), ('bagit', '1.6.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bagit'], 'source_tmpl': 'bagit-1.6.4.tar.gz', 'checksums': ['91c5e253ad4ae0c5a5e795c689cda348c01286c671e9f6ca5cab0018980f9be9'], }), diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020a.eb new file mode 100644 index 00000000000..1df31a40131 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020a.eb @@ -0,0 +1,57 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.11.0' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('PCRE', '8.44'), + ('Boost', '1.72.0'), + ('GMP', '6.2.0'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.4'), + ('LMDB', '0.9.24'), +] + + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb new file mode 100644 index 00000000000..0143981fdeb --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb @@ -0,0 +1,43 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '3.0' +versionsuffix = '-amd' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' +description = """AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/amd/blis/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = [ + 'ac848c040cd6c3550fe49148dbdf109216cad72d3235763ee7ee8134e1528517', # 3.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), + ('Perl', '5.32.1'), +] + +# Build Serial and multithreaded library +configopts = ['--enable-cblas --enable-shared CC="$CC" auto', + '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto'] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT, + 'lib/libblis-mt.a', 'lib/libblis-mt.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-10.2.0.eb new file mode 100644 index 00000000000..799b63b5ea2 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +# Author: Pablo Escobar Lopez (1/1) +# Biozentrum - University of Basel +easyblock = 'Tarball' + +name = 'Beast' +version = '1.10.4' + +homepage = 'https://beast.community' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/%(namelower)s-dev/%(namelower)s-mcmc/releases/download/v%(version)s/'] +sources = ['BEASTv%(version)s.tgz'] +checksums = ['be652c4d55953f7c6c7a9d3eb3de203c77dc380e81ad81cfe0492408990c36a8'] + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '3.1.2'), +] + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.6.3-gcccuda-2019b.eb b/easybuild/easyconfigs/b/Beast/Beast-2.6.3-gcccuda-2019b.eb new file mode 100644 index 00000000000..7f013a04e85 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.6.3-gcccuda-2019b.eb @@ -0,0 +1,40 @@ +easyblock = 'Tarball' + +name = 'Beast' +version = '2.6.3' + +homepage = 'http://beast2.org/' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'gcccuda', 'version': '2019b'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%(version)s.Linux.tgz'] +checksums = ['8899277b0d7124ab04dc512444d45f0f1a13505f3ce641e1f117098be3e2e20d'] + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '3.1.2'), +] + +builddependencies = [ + ('Autotools', '20180311'), + ('libtool', '2.4.6'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': ['bin/beast'], + 'dirs': [] +} + +sanity_check_commands = ["beast -help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb new file mode 100644 index 00000000000..6a056e1d190 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'Tarball' + +name = 'Beast' +version = '2.6.4' + +homepage = 'http://beast2.org' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%(version)s.Linux.tgz'] +checksums = ['4f80e2920eb9d87f3e9f64433119774dc67aca390fbd13dd480f852e3f8701a4'] + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '3.1.2'), +] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': ['bin/beast'], + 'dirs': [] +} + +sanity_check_commands = ["beast -help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.7.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.7.1-intel-2018b-Python-3.6.6.eb index c39f815fe57..dc6707dd155 100644 --- a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.7.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.7.1-intel-2018b-Python-3.6.6.eb @@ -15,7 +15,6 @@ use_pip = True exts_list = [ ('soupsieve', '1.8', { - 'source_urls': ['https://pypi.python.org/packages/source/s/soupsieve'], 'checksums': ['eaed742b48b1f3e2d45ba6f79401b2ed5dc33b2123dfe216adb90d4bfa0ade26'], }), (name, version, { diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.8.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.8.0-GCCcore-8.2.0.eb index 150146a3b63..6395d0abc42 100644 --- a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.8.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.8.0-GCCcore-8.2.0.eb @@ -14,8 +14,6 @@ multi_deps = {'Python': ['3.7.2', '2.7.15']} use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('backports.functools_lru_cache', '1.5', { 'checksums': ['9d98697f088eb1b0fa451391f91afb5e3ebde16bbdb272819fd091151fda4f1a'], diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.1-GCCcore-8.3.0.eb index 32fa838525c..d57f88b03b2 100644 --- a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.1-GCCcore-8.3.0.eb @@ -15,8 +15,6 @@ multi_deps = {'Python': ['3.7.4', '2.7.16']} use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('backports.functools_lru_cache', '1.6.1', { 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.7-GCCcore-9.3.0.eb index abaa102f37b..65ea07ea386 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.7-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.7-GCCcore-9.3.0.eb @@ -37,7 +37,6 @@ exts_list = [ 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], }), ('BioPerl', version, { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], 'checksums': ['730e2bd38b7550bf6bbd5bca50d019a70cca514559702c1389d770ff69cff1bb'], }), diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb index e16f7e4642d..8e7eb5871f9 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb @@ -37,7 +37,6 @@ exts_list = [ 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], }), ('BioPerl', version, { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], }), diff --git a/easybuild/easyconfigs/b/BioServices/BioServices-1.7.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/BioServices/BioServices-1.7.9-foss-2020a-Python-3.8.2.eb index 27c150885fe..43828591da8 100644 --- a/easybuild/easyconfigs/b/BioServices/BioServices-1.7.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/b/BioServices/BioServices-1.7.9-foss-2020a-Python-3.8.2.eb @@ -5,7 +5,7 @@ name = 'BioServices' version = '1.7.9' versionsuffix = '-Python-%(pyver)s' -homepage = "http://bioservices.readthedocs.io/" +homepage = "https://bioservices.readthedocs.io/" description = """Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols).""" @@ -20,8 +20,8 @@ dependencies = [ ('scikit-learn', '0.23.1', versionsuffix), ] -sanity_pip_check = True use_pip = True +sanity_pip_check = True exts_list = [ ('colorlog', '4.4.0', { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb new file mode 100644 index 00000000000..2530ede83d4 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.3.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '8.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.32', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb new file mode 100644 index 00000000000..7b61d615084 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.7.6' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '9.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['69dc0bb46ea8fc307d4ca1e0b61c8c355eb207d0b0c69f4f8462328e74d7b9ea'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.36.1', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.1.0-foss-2019b-Python-3.7.4.eb index 90d2c1ef6e5..559e3d5be40 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.1.0-foss-2019b-Python-3.7.4.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('toml', '0.10.0', { 'checksums': ['229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c'], diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.1.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.1.0-fosscuda-2019b-Python-3.7.4.eb index 7eb58c27adb..17240e9f9b2 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.1.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.1.0-fosscuda-2019b-Python-3.7.4.eb @@ -22,8 +22,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('toml', '0.10.0', { 'checksums': ['229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c'], diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.1.4-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.1.4-fosscuda-2019b-Python-3.7.4.eb index 7b979b2f820..d7a267a65cf 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.1.4-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.1.4-fosscuda-2019b-Python-3.7.4.eb @@ -22,8 +22,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('toml', '0.10.0', { 'checksums': ['229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c'], diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.2.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.2.0-fosscuda-2019b-Python-3.7.4.eb index d8ceb468453..b869b529966 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.2.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.2.0-fosscuda-2019b-Python-3.7.4.eb @@ -22,8 +22,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('toml', '0.10.1', { 'checksums': ['926b612be1e5ce0634a2ca03470f95169cf16f939018233a670519cb4ac58b0f'], diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.2.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.2.2-fosscuda-2019b-Python-3.7.4.eb index 750d6379dda..e0dd7ee3b08 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.2.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.2.2-fosscuda-2019b-Python-3.7.4.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('toml', '0.10.1', { 'checksums': ['926b612be1e5ce0634a2ca03470f95169cf16f939018233a670519cb4ac58b0f'], diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.3.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.3.2-fosscuda-2019b-Python-3.7.4.eb index d7a6856c176..f1a115eec74 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.3.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.3.2-fosscuda-2019b-Python-3.7.4.eb @@ -24,8 +24,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('toml', '0.10.2', { 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.3.5-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.3.5-fosscuda-2019b-Python-3.7.4.eb index 58f4dad70a6..719edc53b76 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.3.5-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.3.5-fosscuda-2019b-Python-3.7.4.eb @@ -24,8 +24,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('toml', '0.10.2', { 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..59554e81a1b --- /dev/null +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb @@ -0,0 +1,126 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'Bonito' +version = '0.4.0' + +homepage = 'https://github.com/nanoporetech/bonito' +description = "Convolution Basecaller for Oxford Nanopore Reads" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyTorch', '1.7.1'), + ('h5py', '3.1.0'), + ('Mako', '1.1.3'), + ('PyYAML', '5.3.1'), + ('python-parasail', '1.2.4'), + ('tqdm', '4.56.2'), + ('apex', '20210420'), + ('minimap2', '2.18'), + ('CuPy', '8.5.0'), + ('GenomeWorks', '2021.02.2'), + ('pyspoa', '0.0.8'), + ('ont-fast5-api', '3.3.0'), +] + +use_pip = True + +# strip out too strict version requirements for dependencies +local_bonito_preinstallopts = "sed -i 's/[><=]=.*//g' requirements.txt && " +# fix requirements for stuff we include as a proper dependency +local_bonito_preinstallopts += "sed -i 's/genomeworks-cuda-10-2/genomeworks/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/cupy-cuda102/cupy/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && " +local_bonito_preinstallopts += "export PATH=%(installdir)s/bin/:$PATH && " + +exts_list = [ + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('alembic', '1.6.4', { + 'checksums': ['becb572c6701c90ca249f97fc1ae231468cc9516df367a350901eeb9310a8d43'], + }), + ('cmd2', '1.5.0', { + 'checksums': ['701a8c9975c4abc45e5d13906ab149f959f812869106347323a3f89ac0e82a62'], + }), + ('prettytable', '2.1.0', { + 'checksums': ['5882ed9092b391bb8f6e91f59bcdbd748924ff556bb7c634089d5519be87baa0'], + }), + ('cliff', '3.7.0', { + 'preinstallopts': "sed -i'' 's/cmd2.*/cmd2/g' requirements.txt && ", + 'checksums': ['389c81960de13f05daf1cbd546f33199e86c518ba4266c79ec7a153a280980ea'], + }), + ('colorlog', '5.0.1', { + 'checksums': ['f17c013a06962b02f4449ee07cfdbe6b287df29efc2c9a1515b4a376f4e588ea'], + }), + ('greenlet', '1.1.0', { + 'checksums': ['c87df8ae3f01ffb4483c796fe1b15232ce2b219f0b18126948616224d3f658ee'], + }), + ('SQLAlchemy', '1.4.15', { + 'checksums': ['0ff100c75cd175f35f4d24375a0b3d82461f5b1af5fc8d112ef0e5ceea8049e6'], + }), + ('cmaes', '0.8.2', { + 'checksums': ['1c04ba23ded925ef13b96f42cfbd667a905ea5b80754c750e6448b9fcda96a5d'], + }), + ('optuna', '2.7.0', { + 'checksums': ['eb1595108ec444e840deb0037351074144fecb7a4eff6870fc11569ab782cfc6'], + }), + ('colorama', '0.4.4', { + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('importlib_metadata', '4.0.1', { + 'checksums': ['8c501196e49fb9df5df43833bdb1e4328f64847763ec8a50703148b73784d581'], + }), + ('stevedore', '3.3.0', { + 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], + }), + ('fast-ctc-decode', '0.3.0', { + 'source_tmpl': 'fast_ctc_decode-%(version)s-cp38-cp38-manylinux2010_x86_64.whl', + 'unpack_sources': False, + 'checksums': ['623d83f8de5e02199a09bfe0160a1e477f0db8d4ab612b26a7e42c2a335b378c'], + }), + ('mappy', '2.18', { + 'checksums': ['18fffdb4b831cc3f5399b919b0942c640bf9a943ca22102ac446f53af3b905a8'], + }), + ('seqdist', '0.0.3', { + 'preinstallopts': "sed -i 's/cupy-cuda102//g' settings.ini && sed -i 's/[<>=]=[0-9].*//g' settings.ini && ", + 'checksums': ['bdbbea6ebba1c6dd6698d46e23ba7858f93a7cdf0c7cbc2ea66660291acb044f'], + }), + ('crf-beam', '0.0.1a0', { + 'modulename': 'kbeam', + 'sources': ['crf_beam-%(version)s-cp38-cp38-manylinux1_x86_64.whl'], + 'unpack_sources': False, + 'checksums': ['0cba80ff4d7f90595f498921cf904736e3bce558dba80de5611874d89e72312e'], + }), + ('networkx', '2.5.1', { + 'checksums': ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'], + }), + ('ont-bonito', version, { + 'modulename': 'bonito', + 'preinstallopts': local_bonito_preinstallopts, + 'checksums': ['429310d56e2d7dabd91a9a9c972504a0aa2b6d6469563b14d4aae30adfe9a87e'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bonito'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "bonito --help", + "bonito convert --help", + "bonito download --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index 6d96a0ef07e..faa5a1229d3 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -27,8 +27,8 @@ dependencies = [ configopts = '--without-libraries=python,mpi' -# disable MPI, enable threading support +# disable MPI, build Boost libraries with tagged layout boost_mpi = False -boost_multi_thread = True +tagged_layout = True moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb index 49052e54795..ab084d66fba 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb @@ -25,8 +25,8 @@ dependencies = [ configopts = '--without-libraries=python,mpi' -# disable MPI, enable threading support +# disable MPI, build Boost libraries with tagged layout boost_mpi = False -boost_multi_thread = True +tagged_layout = True moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.2.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.2.1-intel-2018a-Python-3.6.4.eb index 0956110f550..02075bd209c 100644 --- a/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.2.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.2.1-intel-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = "Fast NumPy array functions written in C" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6efcde5f830aed64feafca0359b51db0e184c72af8ba6675b4a99f263922eb36'] @@ -17,9 +16,4 @@ dependencies = [('Python', '3.6.4')] download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/basemap/basemap-1.2.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/basemap/basemap-1.2.0-intel-2018b-Python-3.6.6.eb index 93282d13a55..c34a4b61654 100644 --- a/easybuild/easyconfigs/b/basemap/basemap-1.2.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/basemap/basemap-1.2.0-intel-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'basemap' version = '1.2.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org/basemap/' +homepage = 'https://matplotlib.org/basemap/' description = """The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python""" toolchain = {'name': 'intel', 'version': '2018b'} @@ -20,12 +20,10 @@ use_pip = True exts_list = [ ('pyshp', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyshp'], 'checksums': ['e65c7f24d372b97d0920b864bbeb78322bb37b83f2606e2a2212631d5d51e5c0'], 'modulename': 'shapefile', }), ('pyproj', '1.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyproj'], 'checksums': ['e0c02b1554b20c710d16d673817b2a89ff94738b0b537aead8ecb2edc4c4487b'], }), (name, version, { diff --git a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb index c687edfaa09..d8369eacf8c 100644 --- a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb @@ -22,36 +22,28 @@ use_pip = True exts_list = [ ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.1.18', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['edbc3f203427eef571f79a7692bb160a2b0f7ccaa31953e99bd17e307cf63f7d'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('pathtools', '0.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathtools'], 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], }), ('argh', '0.26.2', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argh'], 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], }), ('watchdog', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/w/watchdog'], 'checksums': ['7e65882adb7746039b6f3876ee174952f8eaaa34491ba34333ddf1fe35de4162'], }), (name, version, { 'patches': ['bat-0.3.3-fix-pyspark.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/b/bat'], 'checksums': [ 'ebc012826c23b25a890d88eb355467940c77ac50ef85fbd891a6e8ddb2620d44', # bat-0.3.3.tar.gz '5ed4fdea82733ad8a47707867803b9522100307d1bcd0c1fd8f624c778020256', # bat-0.3.3-fix-pyspark.patch diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..8e067a6bd05 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'bcl2fastq2' +version = '2.20.0' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html' +description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by + Illumina sequencing systems to standard FASTQ file formats for downstream analysis.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] +sources = [{ + 'filename': '%s-v%s-tar.zip' % (name, version.replace('.', '-')), + 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz +}] +patches = [ + 'bcl2fastq2-%(version)s-fix-cmake-target-libs.patch', + # bcl2fastq2 v2.20.0 is not compatible with recent Boost versions, use bundled Boost + 'bcl2fastq2-%(version)s-find-boost.patch', +] +checksums = [ + '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3', # bcl2fastq2-v2-20-0-tar.zip + '7908c268c213a6cfeafe05afcd5d3b34098241b6ab0a62c11ea47664cd0a63c5', # bcl2fastq2-2.20.0-fix-cmake-target-libs.patch + '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1', # bcl2fastq2-2.20.0-find-boost.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), +] + +start_dir = 'src' + +# check versions of libxml2 and libxslt from EB +local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' +local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} +preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} + +# remove hardcoded compilation flags +local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' +preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx + +configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' +configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' +configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' + +sanity_check_paths = { + 'files': ['bin/bcl2fastq'], + 'dirs': ['lib'], +} + +sanity_check_commands = ["bcl2fastq --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-find-boost.patch b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-find-boost.patch new file mode 100644 index 00000000000..3e5eb650ec3 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-find-boost.patch @@ -0,0 +1,13 @@ +disable finding Boost libraries in the system to force use of bundled Boost +author: justbennet +--- bcl2fastq/src/cmake/boost.cmake.orig 2021-05-29 13:08:27.575571488 -0400 ++++ bcl2fastq/src/cmake/boost.cmake 2021-05-29 12:17:10.140267869 -0400 +@@ -101,7 +101,7 @@ + set(Boost_USE_STATIC_LIBS ON) + endif (BCL2FASTQ_FORCE_STATIC_LINK) + +-find_package(Boost ${BCL2FASTQ_BOOST_VERSION} COMPONENTS ${BCL2FASTQ_BOOST_COMPONENTS}) ++# find_package(Boost ${BCL2FASTQ_BOOST_VERSION} COMPONENTS ${BCL2FASTQ_BOOST_COMPONENTS}) + # + # If the right version of boost is not found, it will be built from the distribution + # diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch new file mode 100644 index 00000000000..0e1cfe2e2a3 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch @@ -0,0 +1,44 @@ +find and set appropriate targets for libxml2 and libxslt libraries found in the system +author: Alex Domingo (Vrije Universiteit Brussel) +--- src/cmake/cxxConfigure.cmake.orig 2017-06-22 19:14:50.000000000 +0200 ++++ src/cmake/cxxConfigure.cmake 2021-06-03 00:46:03.509256295 +0200 +@@ -101,6 +101,9 @@ + if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) + find_package_version(LibXml2 ${BCL2FASTQ_LIBXML2_VERSION}) + find_package_version(LibXslt ${BCL2FASTQ_LIBXSLT_VERSION}) ++ find_library_env(LIBXML2 libxml/xpath.h xml2) ++ find_library_env(LIBEXSLT libexslt/exslt.h exslt) ++ find_library_env(LIBXSLT libxslt/xsltconfig.h xslt) + endif((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) + + if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) +--- src/cmake/bcl2fastq_redist_macros.cmake.orig 2017-06-22 19:14:50.000000000 +0200 ++++ src/cmake/bcl2fastq_redist_macros.cmake 2021-06-03 00:45:41.825960000 +0200 +@@ -103,4 +103,27 @@ + + endmacro(find_library_redist name pathhint header) + ++# ++# Find a library in environment, assume version will be correct ++# ++macro(find_library_env name header library) ++ unset(${name}_LIBRARIES CACHE) ++ # Search for library ++ unset(${name}_LIBRARIES CACHE) ++ find_library(${name}_LIBRARIES NAMES ${CMAKE_STATIC_LIBRARY_PREFIX}${library}${CMAKE_STATIC_LIBRARY_SUFFIX} HINTS ENV LIBRARY_PATH) ++ ++ message(STATUS "Find library ${namenolib}: ${${name}_LIBRARIES}") ++ # Search for include path ++ unset(${name}_INCLUDE_DIR CACHE) ++ string(TOLOWER ${name} namel) ++ find_path(${name}_INCLUDE_DIR ${header} HINTS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH) ++ set(${name}_INCLUDE_DIR ${${name}_INCLUDE_DIR} CACHE STRING "lib BOOL" FORCE) ++ ++ if(${name}_INCLUDE_DIR AND ${name}_LIBRARIES) ++ set (HAVE_${name} true CACHE BOOL "lib bool" FORCE) ++ message (STATUS "Found ${name} header: ${${name}_INCLUDE_DIR}/${header}") ++ message (STATUS "Found ${name} library: ${${name}_LIBRARY}") ++ endif(${name}_INCLUDE_DIR AND ${name}_LIBRARIES) ++ ++endmacro(find_library_env name pathhint header) + diff --git a/easybuild/easyconfigs/b/bcolz/bcolz-1.1.1-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/bcolz/bcolz-1.1.1-foss-2017a-Python-2.7.13.eb index 40d8f88375b..7fe0902d490 100644 --- a/easybuild/easyconfigs/b/bcolz/bcolz-1.1.1-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/b/bcolz/bcolz-1.1.1-foss-2017a-Python-2.7.13.eb @@ -4,7 +4,7 @@ name = 'bcolz' version = '1.1.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://bcolz.blosc.org/en/latest/' +homepage = 'https://bcolz.blosc.org/en/latest/' description = """bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, @@ -12,7 +12,6 @@ description = """bcolz provides columnar, chunked data containers that can be co toolchain = {'name': 'foss', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6c55769bbcfc64d13649c8bc03db4293204c49bea8163539f2deedb895fa14bc'] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb new file mode 100644 index 00000000000..f40b3b1712f --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '3.1.2' + +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('Java', '11', '', True), + ('pkg-config', '0.29.2'), + ('pocl', '1.6'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--with-opencl=$EBROOTPOCL --with-cuda=$EBROOTCUDA " + +sanity_check_paths = { + 'files': ['include/libhmsbeagle-1/libhmsbeagle/%s' % x for x in ['beagle.h', 'platform.h']] + + ['lib/libhmsbeagle%s.%s' % (x, SHLIB_EXT) for x in ['-cpu', '-cpu-sse', '-jni', '']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb new file mode 100644 index 00000000000..ecacb7868ce --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '3.1.2' + +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'gcccuda', 'version': '2019b'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] + +dependencies = [ + ('Java', '11', '', True), + ('pkg-config', '0.29.2'), + ('pocl', '1.4'), +] + +builddependencies = [ + ('Autotools', '20180311'), + ('libtool', '2.4.6'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--with-opencl=$EBROOTPOCL --with-cuda=$EBROOTCUDA " + +sanity_check_paths = { + 'files': ['include/libhmsbeagle-1/libhmsbeagle/%s' % x for x in ['beagle.h', 'platform.h']] + + ['lib/libhmsbeagle%s.%s' % (x, SHLIB_EXT) for x in ['-cpu', '-cpu-sse', '-jni', '']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb index 515ba575892..010af5730d2 100644 --- a/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb @@ -12,7 +12,6 @@ software project.""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/b/behave/behave-1.2.6-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/b/behave/behave-1.2.6-intel-2018a-Python-3.6.4.eb index 3a42621268a..c7bf6bcf835 100644 --- a/easybuild/easyconfigs/b/behave/behave-1.2.6-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/b/behave/behave-1.2.6-intel-2018a-Python-3.6.4.eb @@ -12,7 +12,6 @@ software project.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['b9662327aa53294c1351b0a9c369093ccec1d21026f050c3bd9b3e5cccf81a86'] diff --git a/easybuild/easyconfigs/b/bgen-reader/bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bgen-reader/bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb index d6e2f626226..24b89573e3a 100644 --- a/easybuild/easyconfigs/b/bgen-reader/bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/bgen-reader/bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pytest-runner', '4.5.1', { 'modulename': False, diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-1.1.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-1.1.0-GCCcore-8.2.0.eb index 1e3de0334e5..c902164f7dd 100644 --- a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-1.1.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-1.1.0-GCCcore-8.2.0.eb @@ -8,7 +8,6 @@ description = """Bibtex parser in Python 2.7 and 3.x""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['df8966ea752db6d74657a69b9d684a61aa33457ad6d9d50e41c50ef7f374907f'] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb new file mode 100644 index 00000000000..5fe10da2880 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.36.1' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '8.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e68edeaaeb6ca9687b6dcbaedd1b376506baad2d48de26a885fc5ab6acb839da'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.3.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.11'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb new file mode 100644 index 00000000000..9440aa2ae70 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.36.1' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '9.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e68edeaaeb6ca9687b6dcbaedd1b376506baad2d48de26a885fc5ab6acb839da'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.11'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-2.7.15.eb index 7748a353739..c06331e8cc0 100644 --- a/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-2.7.15.eb @@ -9,7 +9,6 @@ description = "bitarray provides an object type which efficiently represents an toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['050cd30b810ddb3aa941e7ddfbe0d8065e793012d0a88cb5739ec23624b9895e'] @@ -18,9 +17,4 @@ dependencies = [('Python', '2.7.15')] download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-3.6.6.eb index 73e048151c3..214ef422a83 100644 --- a/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = "bitarray provides an object type which efficiently represents an toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['050cd30b810ddb3aa941e7ddfbe0d8065e793012d0a88cb5739ec23624b9895e'] @@ -18,9 +17,4 @@ dependencies = [('Python', '3.6.6')] download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/bitarray/bitarray-1.2.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/bitarray/bitarray-1.2.1-foss-2019b-Python-3.7.4.eb index d8c59fc93fe..fdde86ae408 100644 --- a/easybuild/easyconfigs/b/bitarray/bitarray-1.2.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/bitarray/bitarray-1.2.1-foss-2019b-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "bitarray provides an object type which efficiently represents an toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2ed675f460bb0d3d66fd8042a6f1f0d36cf213e52e72a745283ddb245da7b9cf'] @@ -18,11 +17,6 @@ dependencies = [('Python', '3.7.4')] download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_pip_check = True moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb index 7b2a191b72c..138a0a59d7f 100644 --- a/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb @@ -34,7 +34,6 @@ use_pip = False exts_list = [ ('memory-profiler', '0.55.0', { 'source_tmpl': 'memory_profiler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/m/memory-profiler'], 'checksums': ['5fa47b274c929dd2cbcd9190afb62fec110701251d2ac2d301caaf545c81afc1'], }), ('munkres', '1.0.12', { @@ -43,13 +42,11 @@ exts_list = [ 'checksums': ['70b3b32b4fed3b354e5c42e4d1273880a33a13ab8c108a4247140eb661767a0b'], }), ('sphinx-gallery', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx-gallery'], 'checksums': ['b49356b5516cc7dab67b1b378f6bf8146fe2372ee73d5e1ea2c483a2e3f4f182'], }), (name, version, { 'prebuildopts': "export EIGENPATH=$EBROOTEIGEN/include BOOSTMATHPATH=$EBROOTBOOST/include/boost && ", 'preinstallopts': "export EIGENPATH=$EBROOTEIGEN/include BOOSTMATHPATH=$EBROOTBOOST/include/boost && ", - 'source_urls': ['https://pypi.python.org/packages/source/b/bnpy'], 'checksums': ['6d6e4c2ca46c6b0cb331f1365933895728cf7333cef95d58249c7c01667b54d0'], }), ] diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-0.12.15-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.15-intel-2018a-Python-3.6.4.eb index a11f54168eb..470d1deb70f 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-0.12.15-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.15-intel-2018a-Python-3.6.4.eb @@ -1,17 +1,14 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'bokeh' version = '0.12.15' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/bokeh/bokeh' +homepage = 'https://github.com/bokeh/bokeh' description = "Statistical and novel interactive HTML plots for Python" toolchain = {'name': 'intel', 'version': '2018a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.6.4'), ('PyYAML', '3.12', versionsuffix), @@ -19,15 +16,12 @@ dependencies = [ exts_list = [ ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], 'checksums': ['2891b883b30107dc610a7e963a21222f1fd096844d157c09db115179cfab6513'], }), ] @@ -37,6 +31,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-2.7.12.eb index 471a4020a2c..a3fe3e1e02a 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-2.7.12.eb @@ -1,35 +1,23 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'bokeh' version = '0.12.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/bokeh/bokeh' +homepage = 'https://github.com/bokeh/bokeh' description = "Statistical and novel interactive HTML plots for Python" toolchain = {'name': 'intel', 'version': '2016b'} - -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ('PyYAML', '3.12', versionsuffix), ] exts_list = [ - ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], - }), - ('requests', '2.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests'], - }), - ('tornado', '4.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], - }), + ('Jinja2', '2.8'), + ('requests', '2.11.1'), + ('tornado', '4.4.2'), + (name, version), ] sanity_check_paths = { @@ -37,6 +25,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-3.5.2.eb index 3b459208d1a..382bd75a27e 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-3.5.2.eb @@ -1,35 +1,24 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'bokeh' version = '0.12.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/bokeh/bokeh' +homepage = 'https://github.com/bokeh/bokeh' description = "Statistical and novel interactive HTML plots for Python" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.5.2'), ('PyYAML', '3.12', versionsuffix), ] exts_list = [ - ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], - }), - ('requests', '2.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests'], - }), - ('tornado', '4.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], - }), + ('Jinja2', '2.8'), + ('requests', '2.11.1'), + ('tornado', '4.4.2'), + (name, version), ] sanity_check_paths = { @@ -37,6 +26,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb index 26e6fe6c5b0..fdff9cfe4d4 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'bokeh' version = '1.0.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/bokeh/bokeh' +homepage = 'https://github.com/bokeh/bokeh' description = "Statistical and novel interactive HTML plots for Python" toolchain = {'name': 'foss', 'version': '2018b'} @@ -19,23 +19,18 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('packaging', '19.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0c98a5d0be38ed775798ece1b9727178c4469d9c3b4ada66e8e6b7849f8732af'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], 'checksums': ['ceeb6a75afc1b2de00c2b8b6da121dec3fb77031326897b80d4375a70e96aebf'], }), ] diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-intel-2018b-Python-3.6.6.eb index dad8cde51de..24554523fd9 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-intel-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'bokeh' version = '1.0.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/bokeh/bokeh' +homepage = 'https://github.com/bokeh/bokeh' description = "Statistical and novel interactive HTML plots for Python" toolchain = {'name': 'intel', 'version': '2018b'} @@ -19,23 +19,18 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('packaging', '19.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0c98a5d0be38ed775798ece1b9727178c4469d9c3b4ada66e8e6b7849f8732af'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], 'checksums': ['ceeb6a75afc1b2de00c2b8b6da121dec3fb77031326897b80d4375a70e96aebf'], }), ] diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-1.3.4-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/b/bokeh/bokeh-1.3.4-foss-2019a-Python-3.7.2.eb index a70800fd6ad..27e0a019e94 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-1.3.4-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-1.3.4-foss-2019a-Python-3.7.2.eb @@ -4,7 +4,7 @@ name = 'bokeh' version = '1.3.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/bokeh/bokeh' +homepage = 'https://github.com/bokeh/bokeh' description = "Statistical and novel interactive HTML plots for Python" toolchain = {'name': 'foss', 'version': '2019a'} @@ -20,11 +20,9 @@ use_pip = True exts_list = [ ('tornado', '6.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['c845db36ba616912074c5b1ee897f8e0124df269468f25e4fe21fe72f6edd7a9'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], 'checksums': ['e2d97bed5b199a10686486001fed5c854e4c04ebe28859923f27c52b93904754'], }), ] diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-foss-2019b-Python-3.7.4.eb index 10577b13526..3d404c1b8dd 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-foss-2019b-Python-3.7.4.eb @@ -20,11 +20,9 @@ use_pip = True exts_list = [ ('tornado', '6.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['c845db36ba616912074c5b1ee897f8e0124df269468f25e4fe21fe72f6edd7a9'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], 'checksums': ['c60d38a41a777b8147ee4134e6142cea8026b5eebf48149e370c44689869dce7'], }), ] diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-fosscuda-2019b-Python-3.7.4.eb index 4c8ede756e5..cf89183a975 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-fosscuda-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('tornado', '6.0.3', { 'checksums': ['c845db36ba616912074c5b1ee897f8e0124df269468f25e4fe21fe72f6edd7a9'], diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-intel-2019b-Python-3.7.4.eb index af24aac1792..61c70e2d49b 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-1.4.0-intel-2019b-Python-3.7.4.eb @@ -20,11 +20,9 @@ use_pip = True exts_list = [ ('tornado', '6.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['c845db36ba616912074c5b1ee897f8e0124df269468f25e4fe21fe72f6edd7a9'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], 'checksums': ['c60d38a41a777b8147ee4134e6142cea8026b5eebf48149e370c44689869dce7'], }), ] diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-GCCcore-8.2.0.eb index 7603df4d2c4..64036097aab 100644 --- a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-GCCcore-8.2.0.eb @@ -10,7 +10,6 @@ Log Cursor, Sequence and Transaction objects.""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['42d621f4037425afcb16b67d5600c4556271a071a9a7f7f2c2b1ba65bc582d05'] @@ -26,9 +25,4 @@ download_dep_fail = True # Need to unset LIBS or pip install crashes. preinstallopts = 'unset LIBS && ' -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb index 6e90acf6729..244cd34a3a5 100644 --- a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb @@ -11,7 +11,6 @@ Log Cursor, Sequence and Transaction objects.""" toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['42d621f4037425afcb16b67d5600c4556271a071a9a7f7f2c2b1ba65bc582d05'] @@ -25,9 +24,4 @@ download_dep_fail = True # Need to unset LIBS or pip install crashes. preinstallopts = 'unset LIBS && ' -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a2429cf4d08 --- /dev/null +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'bsddb3' +version = '6.2.9' + +homepage = 'https://pypi.org/project/bsddb3/' +description = """bsddb3 is a nearly complete Python binding of the +Oracle/Sleepycat C API for the Database Environment, Database, Cursor, +Log Cursor, Sequence and Transaction objects.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['70d05ec8dc568f42e70fc919a442e0daadc2a905a1cfb7ca77f549d49d6e7801'] + +osdependencies = [('libdb-dev', 'libdb-devel')] + +builddependencies = [('binutils', '2.35')] +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# Need to unset LIBS or pip install crashes. +preinstallopts = 'unset LIBS && ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 45fd3fb9827..f0aa3e61a94 100644 --- a/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -22,7 +22,6 @@ use_pip = True exts_list = [ ('toolshed', '0.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolshed'], 'checksums': ['9541d45f14f9c9ee665289fddc2a40135a8b7abdb600acd85d6c074475ce8238'], }), (name, version, { diff --git a/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.2-iccifort-2019.5.281.eb b/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.2-iccifort-2019.5.281.eb index 872a3c94363..61fd2d4fbed 100644 --- a/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.2-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.2-iccifort-2019.5.281.eb @@ -22,7 +22,6 @@ use_pip = True exts_list = [ ('toolshed', '0.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolshed'], 'checksums': ['9541d45f14f9c9ee665289fddc2a40135a8b7abdb600acd85d6c074475ce8238'], }), (name, version, { diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-foss-2016b-Python-2.7.12.eb index 258642baa07..5e2d9abf4ca 100644 --- a/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'bx-python' version = '0.7.4' @@ -15,16 +15,12 @@ dependencies = [ ('LZO', '2.10'), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " exts_list = [ ('python-lzo', '1.11', { 'modulename': 'lzo', 'source_tmpl': 'python-lzo-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-lzo/'], 'checksums': ['38a0ea4ceb27cdd8e3526509fe1b7a936e5dfa57c64608fd32085c129e8be386'], }), (name, version, { @@ -40,6 +36,4 @@ sanity_check_paths = { 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb index 6b1955f417f..66c0cd0120f 100644 --- a/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'bx-python' version = '0.7.4' @@ -16,15 +16,11 @@ dependencies = [ ('LZO', '2.10'), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " exts_list = [ ('python-lzo', '1.11', { 'modulename': 'lzo', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-lzo/'], 'source_tmpl': 'python-lzo-%(version)s.tar.gz', }), (name, version, { @@ -39,6 +35,4 @@ sanity_check_paths = { 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.1-intel-2018a-Python-2.7.14.eb index a2313e6f31f..afee6730f8e 100644 --- a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.1-intel-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'bx-python' version = '0.8.1' @@ -15,22 +15,15 @@ dependencies = [ ('LZO', '2.10'), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " -exts_download_dep_fail = True - exts_list = [ ('python-lzo', '1.12', { 'modulename': 'lzo', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-lzo/'], 'checksums': ['97a8e46825e8f1abd84c2a3372bc09adae9745a5be5d3af2692cd850dac35345'], }), (name, version, { 'modulename': 'bx', - 'source_urls': ['https://pypi.python.org/packages/source/b/bx-python/'], 'checksums': ['057b560c669527a784197a2f8005689d331f62f4765ae4d14bc2217e82dcd8af'], }), ] @@ -40,6 +33,4 @@ sanity_check_paths = { 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb index b484b92185d..209b66ec90b 100644 --- a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb @@ -19,17 +19,13 @@ prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " use_pip = True -exts_download_dep_fail = True - exts_list = [ ('python-lzo', '1.12', { 'modulename': 'lzo', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-lzo/'], 'checksums': ['97a8e46825e8f1abd84c2a3372bc09adae9745a5be5d3af2692cd850dac35345'], }), (name, version, { 'modulename': 'bx', - 'source_urls': ['https://pypi.python.org/packages/source/b/%(name)s/'], 'checksums': ['faeb0c7c9fcb2f95c4fc1995af4f45287641deee43a01659bd30fe95c5d37386'], }), ] diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb index 383a112a1eb..2f4fab34531 100644 --- a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb @@ -20,8 +20,6 @@ prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('python-lzo', '1.12', { 'modulename': 'lzo', diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb index 50116881235..250d603d1f2 100644 --- a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('python-lzo', '1.12', { 'modulename': 'lzo', diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb new file mode 100644 index 00000000000..8ce474d08a4 --- /dev/null +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'CAMPARI' +version = '4.0' +_date = '12202020' + +homepage = 'http://campari.sourceforge.net/V4/index.html' +description = """ +CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological +relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte +Carlo and molecular dynamics in seamless fashion.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['campari_v%s_%s.zip' % (version.split('.')[0], _date)] +checksums = ['bc627fb286b5461a5c68aa3e1a551ecd81016495163685800163c734f7c4f1bd'] + +dependencies = [ + ('netCDF-Fortran', '4.5.3'), + ('libtirpc', '1.3.1'), +] + +start_dir = 'source' + +configopts = '--enable-mpi=auto LIBS="$LIBS $LIBFFT -ltirpc"' + +buildopts = 'all LIBS="$LIBS $LIBFFT -ltirpc"' + +maxparallel = 10 + +postinstallcmds = ['cp -a %(builddir)s/campari/{data,doc,examples,params,tools,LICENSE} %(installdir)s/'] + +_binaries = ['campari', 'campari_mpi', 'campari_mpi_threads', 'campari_threads', 'camp_ncminer', 'camp_ncminer_threads'] +_libraries = ['lcampari.a', 'lcampari_mpi.a', 'lcampari_mpi_threads.a', 'lcampari_threads.a', 'libxdrf.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/%s' % x for x in _libraries], + 'dirs': [], +} + +sanity_check_commands = ['campari -h | grep "USAGE: CAMPARI"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CDAT/CDAT-8.2.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CDAT/CDAT-8.2.1-foss-2020a-Python-3.8.2.eb index 49e1f5ce948..dfde0b95606 100644 --- a/easybuild/easyconfigs/c/CDAT/CDAT-8.2.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/CDAT/CDAT-8.2.1-foss-2020a-Python-3.8.2.eb @@ -30,14 +30,14 @@ exts_default_options = { 'source_urls': [GITHUB_SOURCE], 'sources': [{ 'download_filename': 'v%(version)s.tar.gz', - 'filename': '%(name)s-%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, }] } exts_list = [ ('pycf', '1.6.9', { 'patches': ['pycf-1.6.9-openblas-extern.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], - 'sources': ['%(name)s-%(version)s.tar.gz'], + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], 'checksums': [ '622fc99f7d258d2931edc080dbdb81d2bf1be1ebac922f2fca0b71173ada7520', # pycf-1.6.9.tar.gz 'df04e4f48dfa69ecbae31b743047478bf2a3649642bfd6cf36b9d0ebc5d01896', # pycf-1.6.9-openblas-extern.patch @@ -45,13 +45,13 @@ exts_list = [ }), ('lazy-object-proxy', '1.5.2', { 'modulename': 'lazy_object_proxy', - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], - 'sources': ['%(name)s-%(version)s.tar.gz'], + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], 'checksums': ['5944a9b95e97de1980c65f03b79b356f30a43de48682b8bdd90aa5089f0ec1f4'], }), ('eofs', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], - 'sources': ['%(name)s-%(version)s.tar.gz'], + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], 'checksums': ['5ae9afc159b8cfb2be476d257fc469b2cdd473c76f5411c508010007a5ae6bd2'], }), ('cdat_info', version, { diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.2.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.2.0-intel-2018b-Python-3.6.6.eb index 04647dea163..2f8c7f2d775 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.2.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.2.0-intel-2018b-Python-3.6.6.eb @@ -11,7 +11,6 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['92510a886dc68f9a13bc05dc46aa9881ff61fbd02ecbb40d3a2d6a9f2611358e'] diff --git a/easybuild/easyconfigs/c/CIRCexplorer/CIRCexplorer-1.1.10-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CIRCexplorer/CIRCexplorer-1.1.10-intel-2017b-Python-2.7.14.eb index 8ed6942d357..74c81729200 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer/CIRCexplorer-1.1.10-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer/CIRCexplorer-1.1.10-intel-2017b-Python-2.7.14.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'CIRCexplorer' version = '1.1.10' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://circexplorer2.readthedocs.io/' +homepage = 'https://circexplorer2.readthedocs.io/' description = "CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset." toolchain = {'name': 'intel', 'version': '2017b'} @@ -19,16 +19,12 @@ dependencies = [ ] # requests, certifi, urllib3, chardet, docopt -exts_defaultclass = 'PythonPackage' - exts_list = [ ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), (name, version, { 'modulename': 'circ', - 'source_urls': ['https://pypi.python.org/packages/source/C/CIRCexplorer/'], 'checksums': ['19d1345db3a88211e6a3c66e67d16c7fe4d7c82c2a71c366ffed21ac696fefd6'], }), ] diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb index 0ae1172d1a1..18103c12dc1 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'CIRCexplorer2' version = '2.3.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://circexplorer2.readthedocs.io/' +homepage = 'https://circexplorer2.readthedocs.io/' description = "CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset." toolchain = {'name': 'intel', 'version': '2017b'} @@ -22,31 +22,23 @@ dependencies = [ ('pybedtools', '0.7.10', versionsuffix), ] -exts_defaultclass = 'PythonPackage' - exts_list = [ ('certifi', '2017.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['5ec74291ca1136b40f0379e1128ff80e866597e4e2c1e755739a913bbc3613c0'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/C/CIRCexplorer2/'], 'checksums': ['eb3a3ba97384e904c0a9841a3b2b225a17dd33999abc4d316aca72a6dcce427c'], 'modulename': 'circ2', }), diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb index 39fac0ba31f..edff9ff989f 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'CIRCexplorer2' version = '2.3.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://circexplorer2.readthedocs.io/' +homepage = 'https://circexplorer2.readthedocs.io/' description = "CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset." toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['30f9273e4a9ab1575a001d1165ba19972995f68d2acbfbc1b113fca49054d8ae'] diff --git a/easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2018b-Python-3.6.6.eb index 0f816af8ac0..19c36976545 100644 --- a/easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2018b-Python-3.6.6.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pybktree', '1.1', { 'checksums': ['eec0037cdd3d7553e6d72435a4379bede64be17c6712f149e485169638154d2b'], @@ -36,9 +34,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2019b-Python-3.7.4.eb index 9305c8fb5eb..ca822550f68 100644 --- a/easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2019b-Python-3.7.4.eb @@ -17,8 +17,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pytest-dependency', '0.5.1', { 'checksums': ['c2a892906192663f85030a6ab91304e508e546cddfe557d692d61ec57a1d946b'], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb b/easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb new file mode 100644 index 00000000000..4ccea17fa08 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb @@ -0,0 +1,27 @@ +name = 'CMake' +version = '3.18.4' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = SYSTEM + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['597c61358e6a92ecbfad42a9b5321ddd801fc7e7eca08441307c9138382d4f77'] + +builddependencies = [('ncurses', '6.2')] + +# Use OS dependencies in order to ensure that CMake can build software that depends on them +osdependencies = [OS_PKG_OPENSSL_DEV] + +configopts = "-- " +configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " +configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " +configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a " + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.2-intel-2017b-Python-2.7.14.eb index 6c99f53f4b9..0c54ad51c4c 100644 --- a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.2-intel-2017b-Python-2.7.14.eb @@ -1,18 +1,15 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'CNVkit' version = '0.9.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/etal/cnvkit' +homepage = 'https://github.com/etal/cnvkit' description = """A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.""" toolchain = {'name': 'intel', 'version': '2017b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.14'), ('Biopython', '1.70', versionsuffix), @@ -25,19 +22,15 @@ dependencies = [ exts_list = [ ('reportlab', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/reportlab'], 'checksums': ['5beaf35e59dfd5ebd814fdefd76908292e818c982bd7332b5d347dfd2f01c343'], }), ('pyfaidx', '0.5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyfaidx'], 'checksums': ['d94d4254f79869bbf61c6d8673cfa3c042a8240b2565e9816302c224979e4b56'], }), ('future', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'], }), ('futures', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], 'modulename': 'concurrent.futures', }), @@ -55,6 +48,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.3-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.3-intel-2018a-Python-3.6.4.eb index 2efe1a09686..b42c4abf430 100644 --- a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.3-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.3-intel-2018a-Python-3.6.4.eb @@ -24,15 +24,12 @@ use_pip = True exts_list = [ ('reportlab', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/reportlab'], 'checksums': ['5beaf35e59dfd5ebd814fdefd76908292e818c982bd7332b5d347dfd2f01c343'], }), ('pyfaidx', '0.5.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyfaidx'], 'checksums': ['2a15b8820bc1f27c4b6fe7c82a98d2520972cb6c167055d158562778af8aa53e'], }), ('future', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'], }), (name, version, { diff --git a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.6-foss-2019a-Python-3.7.2-R-3.6.0.eb b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.6-foss-2019a-Python-3.7.2-R-3.6.0.eb index 6689a125bc5..326b8a95bd4 100644 --- a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.6-foss-2019a-Python-3.7.2-R-3.6.0.eb +++ b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.6-foss-2019a-Python-3.7.2-R-3.6.0.eb @@ -4,7 +4,7 @@ name = 'CNVkit' version = '0.9.6' versionsuffix = '-Python-%(pyver)s-R-%(rver)s' -homepage = 'http://github.com/etal/cnvkit' +homepage = 'https://github.com/etal/cnvkit' description = """A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.""" @@ -26,11 +26,9 @@ use_pip = False exts_list = [ ('reportlab', '3.5.23', { - 'source_urls': ['https://pypi.python.org/packages/source/r/reportlab'], 'checksums': ['6c81ee26753fa09062d8404f6340eefb02849608b619e3843e0d17a7cda8798f'], }), ('pyfaidx', '0.5.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyfaidx'], 'checksums': ['9ac22bdc7b9c5d995d32eb9dc278af9ba970481636ec75c0d687d38c26446caa'], }), ('pomegranate', '0.11.1', { diff --git a/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb new file mode 100644 index 00000000000..c3feca2d8ad --- /dev/null +++ b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb @@ -0,0 +1,47 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/05 +easyblock = 'PythonPackage' + +name = 'CSB' +version = '1.2.5' + +homepage = 'https://github.com/csb-toolbox' +description = """Computational Structural Biology Toolbox +CSB is a python library and application framework, which can be used to solve +problems in the field of structural bioinformatics. If you are a +bioinformatician, software engineer or a researcher working in this field, +chances are you may find something useful here. Our package consists of a few +major components: +1. Core class library - object-oriented, granular, with an emphasis on design +and clean interfaces. +2. Application framework - console applications ("protocols"), which consume +objects from the core library in order to build something executable (and +hopefully useful). +3. Test framework - ensures that the library actually works. +""" +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/csb-toolbox/CSB/releases/download/R-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3f05924acaca6673f94fc430965eabfe59a0c9b2cbdda8c1cb50a43ffe83f254'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +sanity_check_commands = ['csb-%s -h' % x for x in [ + 'bfit', 'bfite', 'buildhmm', 'csfrag', 'embd', + 'hhfrag', 'hhsearch', 'precision', 'promix', 'test']] + +sanity_check_paths = { + 'files': ['bin/csb-%s' % x for x in [ + 'bfit', 'bfite', 'buildhmm', 'csfrag', 'embd', + 'hhfrag', 'hhsearch', 'precision', 'promix', 'test']], + 'dirs': ["lib/python%(pyshortver)s/site-packages"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb index a834588d69c..cedcf2c3299 100644 --- a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb @@ -20,11 +20,7 @@ dependencies = [ ] use_pip = True - -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} +sanity_pip_check = True exts_list = [ ('imagecodecs-lite', '2019.12.3', { diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb index b71cf40e64d..fb0579f0eba 100644 --- a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb @@ -20,11 +20,7 @@ dependencies = [ ] use_pip = True - -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} +sanity_pip_check = True exts_list = [ ('imagecodecs-lite', '2019.12.3', { diff --git a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.1.1.eb b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.1.1.eb index f48f472ab49..48a6e747e0b 100644 --- a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.1.1.eb +++ b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.1.1.eb @@ -1,4 +1,5 @@ -easyblock = "EB_CUDA" +easyblock = 'EB_CUDA' + name = 'CUDAcore' version = '11.1.1' local_nv_version = '455.32.00' @@ -19,6 +20,8 @@ checksums = [ '3eae6727086024925ebbcef3e9a45ad379d8490768fd00f9c2d8b6fd9cd8dd8f', 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: '023e571fe26ee829c98138dfc305a92279854aac7d184d255fd58c06c6af3c17', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '9ab1dbafba205c06bea8c88e38cdadb3038af19cb56e7b3ba734d3d7a84b8f02', } ] diff --git a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.2.1.eb b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.2.1.eb index de8d7013e52..a53802b8cda 100644 --- a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.2.1.eb +++ b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.2.1.eb @@ -20,6 +20,8 @@ checksums = [ '1da98cb897cc5f58a7445a4a66ca4f6926867706cb3af58a669cdcd8dc3d17c8', 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: 'b3e8b6cd76872deb3acd050d32e197bc1c655e142b169070f0f9753680461a3f', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '4b322fa6477d1a2cd2f2f526fa520c0f90bef2c264ef8435cb016bebb5456c5e', } ] diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb new file mode 100644 index 00000000000..be6d64350ba --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'CVXOPT' +version = '1.2.6' + +homepage = 'https://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['CVXOPT-1.2.1-fix-setup-py.patch'] +checksums = [ + 'a4c433706fd0ad9d47e7f222773a7f7601766fb8e74b633524b3c3fce29aa73e', # cvxopt-1.2.6.tar.gz + '85d8475098895e9af45f330489a712b5b944489c5fb4a6c67f59bef8fed4303d', # CVXOPT-1.2.1-fix-setup-py.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('GSL', '2.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' +preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' + +installopts = ' --no-binary cvxopt' + +sanity_check_commands = ['cd %(builddir)s/%(namelower)s-%(version)s && nosetests'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/CVXPY/CVXPY-1.0.24-foss-2019a.eb b/easybuild/easyconfigs/c/CVXPY/CVXPY-1.0.24-foss-2019a.eb index 59a151a50ff..914307acca2 100644 --- a/easybuild/easyconfigs/c/CVXPY/CVXPY-1.0.24-foss-2019a.eb +++ b/easybuild/easyconfigs/c/CVXPY/CVXPY-1.0.24-foss-2019a.eb @@ -25,23 +25,18 @@ use_pip = True exts_list = [ ('multiprocess', '0.70.8', { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiprocess'], 'checksums': ['fc6b2d8f33e7d437a82c6d1c2f1673ae20a271152a1ac6a18571d10308de027d'], }), ('osqp', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/o/osqp'], 'checksums': ['86d58b5a9f8f4dc6fd1dcb02fbb29be8c3bcae59b85620d174c88125d953707d'], }), ('ecos', '2.0.7.post1', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecos'], 'checksums': ['83e90f42b3f32e2a93f255c3cfad2da78dbd859119e93844c45d2fca20bdc758'], }), ('scs', '2.1.1-2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scs'], 'checksums': ['f816cfe3d4b4cff3ac2b8b96588c5960ddd2a3dc946bda6b09db04e7bc6577f2'], }), ('cvxpy', version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/cvxpy'], 'checksums': ['4aa7fc03707fccc673bd793572cc5b950ebd304c478cd9c0b6d53ccf7186a3f1'], }), ] diff --git a/easybuild/easyconfigs/c/CVXPY/CVXPY-1.0.28-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CVXPY/CVXPY-1.0.28-foss-2019b-Python-3.7.4.eb index b6b3a0269eb..1c4947b2def 100644 --- a/easybuild/easyconfigs/c/CVXPY/CVXPY-1.0.28-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CVXPY/CVXPY-1.0.28-foss-2019b-Python-3.7.4.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('dill', '0.3.1.1', { 'checksums': ['42d8ef819367516592a825746a18073ced42ca169ab1f5f4044134703e7a049c'], diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.18.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.18.0-foss-2019b-Python-3.7.4.eb index 371119ea24a..effffb013d2 100644 --- a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.18.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.18.0-foss-2019b-Python-3.7.4.eb @@ -27,8 +27,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('OWSLib', '0.19.2', { 'checksums': ['605a742d088f1ed9c946e824d0b3be94b5256931f8b230dae63e27a52c781b6d'], diff --git a/easybuild/easyconfigs/c/CatMAP/CatMAP-20170927-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CatMAP/CatMAP-20170927-intel-2017b-Python-2.7.14.eb index c2691c0a065..590f91c9206 100644 --- a/easybuild/easyconfigs/c/CatMAP/CatMAP-20170927-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CatMAP/CatMAP-20170927-intel-2017b-Python-2.7.14.eb @@ -1,11 +1,11 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'CatMAP' version = '20170927' local_commit_id = '5d3d6c0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://catmap.readthedocs.io/' +homepage = 'https://catmap.readthedocs.io/' description = """Catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used in catalyst screening.""" @@ -19,18 +19,14 @@ dependencies = [ ('MPC', '1.0.3', '-MPFR-3.1.6'), # for gmpy2 ] -exts_defaultclass = 'PythonPackage' - exts_list = [ ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], 'checksums': [ '04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c', # mpmath-1.0.0.tar.gz ], }), ('gmpy2', '2.0.8', { 'source_tmpl': 'gmpy2-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/g/gmpy2/'], 'checksums': [ 'dd233e3288b90f21b0bb384bcc7a7e73557bb112ccf0032ad52aa614eb373d3f', # gmpy2-2.0.8.zip ], @@ -44,11 +40,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CellRanger-ARC/CellRanger-ARC-2.0.0.eb b/easybuild/easyconfigs/c/CellRanger-ARC/CellRanger-ARC-2.0.0.eb new file mode 100644 index 00000000000..b25bef3b1fb --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger-ARC/CellRanger-ARC-2.0.0.eb @@ -0,0 +1,33 @@ +# The STAR binary included in this version has been vectorized with AVX +# hence it is not recommended for systems that do not support it. + +easyblock = 'Tarball' + +name = 'CellRanger-ARC' +version = '2.0.0' + +homepage = 'https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/' +homepage += 'what-is-cell-ranger-arc' +description = """Cell Ranger ARC is a set of analysis pipelines that process + Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a + variety of analyses pertaining to gene expression, chromatin accessibility and + their linkage. Furthermore, since the ATAC and gene expression measurements are on + the very same cell, we are able to perform analyses that link chromatin + accessibility and gene expression.""" + +toolchain = SYSTEM + +# Download manually from https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/downloads/latest +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8df19f10bbecdcfd7690a7554d8779fe60a0863fc1ad0129b1cdf1698bf6cb70'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ["bin/cellranger-arc"], + 'dirs': ["bin/rna", "bin/tenkit"], +} + +sanity_check_commands = ['cellranger-arc -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.0.0.eb b/easybuild/easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.0.0.eb new file mode 100644 index 00000000000..f27a87654f3 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.0.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'Tarball' + +name = 'CellRanger-ATAC' +version = '2.0.0' + +homepage = "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac" +description = """Cell Ranger ATAC is a set of analysis pipelines that process +Chromium Single Cell ATAC data.""" + +toolchain = SYSTEM + +# Download manually from https://support.10xgenomics.com/single-cell-atac/software/downloads/latest +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b5f3a1b1b9ab22399fdaa9c1105d7a0544ac4befe411caf26e9b2b97c44dcd3b'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ['bin/cellranger-atac', 'cellranger-atac'], + 'dirs': ['bin/atac', 'lib'], +} + +sanity_check_commands = ["cellranger-atac testrun --id=tiny"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..2bdcd3b5af5 --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Check' +version = '0.15.2' + +homepage = 'https://libcheck.github.io/check/' +description = """ +Check is a unit testing framework for C. It features a simple interface for +defining unit tests, putting little in the way of the developer. Tests are +run in a separate address space, so both assertion failures and code errors +that cause segmentation faults or other signals can be caught. Test results +are reportable in the following: Subunit, TAP, XML, and a generic logging +format.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +github_account = 'libcheck' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['998d355294bb94072f40584272cf4424571c396c631620ce463f6ea97aa67d2e'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-build-docs" + +sanity_check_paths = { + 'files': ['bin/checkmk', 'lib/libcheck.a', 'lib/libcheck.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb index eb2ad4d21fc..c6904d99cd1 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb @@ -23,11 +23,9 @@ use_pip = True exts_list = [ ('DendroPy', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/D/DendroPy'], 'checksums': ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'], }), ('checkm-genome', version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/checkm-genome'], 'checksums': ['ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e'], 'modulename': 'checkm', }), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb index f9d1358bff3..e714707c6e2 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb @@ -23,11 +23,9 @@ use_pip = True exts_list = [ ('DendroPy', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/D/DendroPy'], 'checksums': ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'], }), ('checkm-genome', version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/checkm-genome'], 'checksums': ['ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e'], 'modulename': 'checkm', }), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb index ff5822e1cf5..a86d3eb6269 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb @@ -23,11 +23,9 @@ use_pip = True exts_list = [ ('DendroPy', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/D/DendroPy'], 'checksums': ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'], }), ('checkm-genome', version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/checkm-genome'], 'checksums': ['ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e'], 'modulename': 'checkm', }), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb index 94908bb8e9d..3896c5c1e88 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb @@ -23,11 +23,9 @@ use_pip = True exts_list = [ ('DendroPy', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/D/DendroPy'], 'checksums': ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'], }), ('checkm-genome', version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/checkm-genome'], 'checksums': ['ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e'], 'modulename': 'checkm', }), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb index 2804a0da015..a37f08d8828 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb @@ -23,11 +23,9 @@ use_pip = True exts_list = [ ('DendroPy', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/D/DendroPy'], 'checksums': ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'], }), ('checkm-genome', version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/checkm-genome'], 'checksums': ['ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e'], 'modulename': 'checkm', }), diff --git a/easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b-Python-2.7.15.eb index a7dd12ec211..a23a9fec02b 100644 --- a/easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'Cheetah' version = '2.4.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://cheetahtemplate.org' +homepage = 'https://cheetahtemplate.org' description = "Cheetah is an open source template engine and code generation tool." toolchain = {'name': 'intel', 'version': '2018b'} @@ -15,11 +15,9 @@ use_pip = True exts_list = [ ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cheetah'], 'checksums': ['be308229f0c1e5e5af4f27d7ee06d90bb19e6af3059794e5fd536a6f29a9b550'], 'modulename': name, }), diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb index ef7462a07f6..037c1ef7f84 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb @@ -57,6 +57,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.18.4'), ('Python', '3.8.6'), + ('elfutils', '0.183'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb index 4d5f014edba..b4f7a627ae0 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb @@ -61,6 +61,7 @@ builddependencies = [ ('CMake', '3.13.3'), ('Python', '2.7.15'), ('libxml2', '2.9.8'), + ('elfutils', '0.185'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.2.0-2.31.1-CUDA-10.1.105.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.2.0-2.31.1-CUDA-10.1.105.eb index 674b649a548..0feb52f5047 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.2.0-2.31.1-CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.2.0-2.31.1-CUDA-10.1.105.eb @@ -61,6 +61,7 @@ builddependencies = [ ('CMake', '3.13.3'), ('Python', '2.7.15'), ('libxml2', '2.9.8'), + ('elfutils', '0.185'), ] # Set the c++ std for NVCC or the build fails on ppc64le looking for __ieee128 diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb index 8ac1c941d22..c65903e6ddb 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb @@ -61,6 +61,7 @@ builddependencies = [ ('CMake', '3.15.3'), ('Python', '2.7.16'), ('libxml2', '2.9.9'), + ('elfutils', '0.185'), ] # Set the c++ std for NVCC or the build fails on ppc64le looking for __ieee128 diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb index 015c81f782a..6d9f2a9a9ac 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb @@ -61,6 +61,7 @@ builddependencies = [ ('CMake', '3.15.3'), ('Python', '2.7.16'), ('libxml2', '2.9.9'), + ('elfutils', '0.185'), ] # Set the c++ std for NVCC or the build fails on ppc64le looking for __ieee128 diff --git a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb index 2c7c87e6d80..62cae3ecd76 100644 --- a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb +++ b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb @@ -3,13 +3,12 @@ easyblock = 'PythonPackage' name = 'ClusterShell' version = '1.7.3' -homepage = 'http://cea-hpc.github.io/clustershell/' +homepage = 'https://cea-hpc.github.io/clustershell/' description = """ClusterShell is an event-driven open source Python library, designed to run local or distant commands in parallel on server farms or on large Linux clusters.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('PyYAML', '3.12')] diff --git a/easybuild/easyconfigs/c/CompareM/CompareM-0.0.23-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CompareM/CompareM-0.0.23-foss-2018b-Python-2.7.15.eb index 956eeaa1be2..21456cd5417 100644 --- a/easybuild/easyconfigs/c/CompareM/CompareM-0.0.23-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CompareM/CompareM-0.0.23-foss-2018b-Python-2.7.15.eb @@ -16,8 +16,6 @@ dependencies = [ ('prodigal', '2.6.3'), ] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..235a1b9fcca --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-9.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "8.32" + +homepage = 'https://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text manipulation utilities of the + GNU operating system. These are the core utilities which are expected to exist on every operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['4458d8de7849df44ccab15e16b1548b285224dbba5f08fac070c1c0e0bcc4cfa'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CrossMap/CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CrossMap/CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb index 036ac9462e8..14f5d6572ee 100644 --- a/easybuild/easyconfigs/c/CrossMap/CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CrossMap/CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb @@ -12,7 +12,6 @@ description = """CrossMap is a program for genome coordinates conversion toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e20a4653e9fc313ac0f5a6cfc37b42e83c3cf2b42f9483706cfb9ec9ff72c74c'] diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb index e7d275c6ef7..498590b96ea 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb @@ -7,15 +7,15 @@ homepage = 'https://cupy.dev' description = "CuPy is an open-source array library accelerated with NVIDIA CUDA." toolchain = {'name': 'fosscuda', 'version': '2020b'} -# setup.py requirement Cython>=0.29.22. Build fails with 0.29.21 +# setup.py requirement Cython>=0.29.22. Build fails with 0.29.21 # after patching setup.py builddependencies = [('Cython', '0.29.22')] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), - ('NCCL', '2.8.3', '-CUDA-11.1.1', True), - ('cuTENSOR', '1.2.2.5', '-CUDA-11.1.1', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('cuTENSOR', '1.2.2.5', '-CUDA-%(cudaver)s', True), ] use_pip = True diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..99955038a6b --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeGUI' +version = '4.6' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube graphical report explorer. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '1871c6736121d94a22314cb5daa8f3cbb978b58bfe54f677c4c9c9693757d0c5', # cubegui-4.6.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.35'), + ('CubeLib', '4.6'), +] + +dependencies = [ + ('Qt5', '5.14.2'), +] + +sanity_check_paths = { + 'files': ['bin/cube', 'bin/cubegui-config', + 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], + 'dirs': ['include/cubegui', 'lib/cube-plugins'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a669ee8b3fb --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.6-GCCcore-10.2.0.eb @@ -0,0 +1,56 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.6' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '36eaffa7688db8b9304c9e48ca5dc4edc2cb66538aaf48657b9b5ccd7979385b', # cubelib-4.4.4.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..4b3c1d7de04 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.4.3' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['93fff6cc1e8b0780f0171ef5302a2e1a257f99b6383fbfc1b9b82f925ceff501'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/cubew-config', 'lib/libcube4w.a', 'lib/libcube4w.so'], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..2d3fc4b8b4e --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.6-GCCcore-10.2.0.eb @@ -0,0 +1,55 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.6' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = [ + '99fe58ce7ab13061ebfbc360aedaecc28099a30636c5269a42c0cbaf57149aa8', # cubew-4.6.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb b/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb index 090809599da..e6e5e054399 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb @@ -11,7 +11,6 @@ Cython is a source code translator based on the well-known Pyrex, but supports m toolchain = {'name': 'gimkl', 'version': '2.11.5'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.10')] diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb index 558454ebb95..322fefa2351 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb @@ -11,7 +11,6 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.11')] diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb index f7014694979..c4148fc4f94 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb @@ -22,7 +22,6 @@ but supports more cutting edge functionality and optimizations.""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306'] diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.25.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/Cython/Cython-0.25.2-intel-2018a-Python-3.6.4.eb index 0088b1d9ba2..a012c66eb17 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.25.2-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.25.2-intel-2018a-Python-3.6.4.eb @@ -22,7 +22,6 @@ but supports more cutting edge functionality and optimizations.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306'] diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-8.2.0-Python-2.7.15.eb b/easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-8.2.0-Python-2.7.15.eb index 146271c687a..f7eae296685 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-8.2.0-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-8.2.0-Python-2.7.15.eb @@ -27,7 +27,6 @@ docurls = [ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'] diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.10-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.10-foss-2017b-Python-2.7.14.eb index 583e8b74d38..22299376074 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.29.10-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.10-foss-2017b-Python-2.7.14.eb @@ -22,7 +22,6 @@ but supports more cutting edge functionality and optimizations.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['26229570d6787ff3caa932fe9d802960f51a89239b990d275ae845405ce43857'] diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.10-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.10-foss-2017b-Python-3.6.3.eb index 34336ea5bad..854c838c814 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.29.10-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.10-foss-2017b-Python-3.6.3.eb @@ -22,7 +22,6 @@ but supports more cutting edge functionality and optimizations.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['26229570d6787ff3caa932fe9d802960f51a89239b990d275ae845405ce43857'] diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.10-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.10-intel-2017b-Python-2.7.14.eb index 1f23260777c..d854098f2c0 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.29.10-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.10-intel-2017b-Python-2.7.14.eb @@ -22,7 +22,6 @@ but supports more cutting edge functionality and optimizations.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['26229570d6787ff3caa932fe9d802960f51a89239b990d275ae845405ce43857'] diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.10-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.10-intel-2017b-Python-3.6.3.eb index 5cec7691bca..e474ff57217 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.29.10-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.10-intel-2017b-Python-3.6.3.eb @@ -22,7 +22,6 @@ but supports more cutting edge functionality and optimizations.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['26229570d6787ff3caa932fe9d802960f51a89239b990d275ae845405ce43857'] diff --git a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb new file mode 100644 index 00000000000..990e0dcabec --- /dev/null +++ b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'canu' +version = '2.1.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://canu.readthedocs.io' +description = "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +github_account = 'marbl' +source_urls = ['https://github.com/marbl/canu/releases/download/v%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['18c030ada93286be90c364387879025c17001c8e445e64719c866bc6c7609b98'] + +builddependencies = [ + ('binutils', '2.34'), + ('git', '2.23.0', '-nodocs'), +] + +dependencies = [ + ('Java', '11', '', True), + ('Perl', '5.30.2'), + ('gnuplot', '5.2.8'), +] + +skipsteps = ['configure', 'install'] + +start_dir = 'src' + +buildopts = 'TARGET_DIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/canu', 'lib/libcanu.a'], + 'dirs': ['lib/site_perl', 'share'], +} +sanity_check_commands = [ + "canu -version", + "canu -options", +] + +modextrapaths = {'PERL5LIB': 'lib/site_perl'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/causalml/causalml-0.3.0-20180610-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/causalml/causalml-0.3.0-20180610-foss-2019a-Python-3.7.2.eb index 768dea625f5..c791f8432ee 100644 --- a/easybuild/easyconfigs/c/causalml/causalml-0.3.0-20180610-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/causalml/causalml-0.3.0-20180610-foss-2019a-Python-3.7.2.eb @@ -23,11 +23,9 @@ use_pip = True exts_list = [ ('setuptools', '41.2.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['66b86bbae7cc7ac2e867f52dc08a6bd064d938bac59dfec71b9b565dd36d6012'], }), ('xgboost', '0.82', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xgboost/'], 'checksums': ['ff5aaa039fb43aae331a916b392994c32696279d9b6b5840cc7c74e06f183a95'], }), (name, local_commit, { diff --git a/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb index b0f1c28f7ff..834575685e9 100644 --- a/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = "Climate Data Store API" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f25c5df8ab0ab4e571a7022cb7714f6b91452bc0923bee0d8d0069abae1ffa1b'] @@ -18,9 +17,4 @@ dependencies = [('Python', '3.6.6')] download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2019a.eb b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2019a.eb index 23125380aae..078a650616a 100644 --- a/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2019a.eb +++ b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2019a.eb @@ -8,7 +8,6 @@ description = "Climate Data Store API" toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f25c5df8ab0ab4e571a7022cb7714f6b91452bc0923bee0d8d0069abae1ffa1b'] diff --git a/easybuild/easyconfigs/c/cget/cget-0.1.6-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/cget/cget-0.1.6-foss-2018a-Python-3.6.4.eb index eec7eb5cfb2..1d047f48255 100644 --- a/easybuild/easyconfigs/c/cget/cget-0.1.6-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/cget/cget-0.1.6-foss-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ # Author: Jonas Demeulemeester # The Francis Crick Insitute, London, UK ## -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'cget' version = '0.1.6' @@ -21,23 +21,16 @@ dependencies = [ ('CMake', '3.10.2'), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True + exts_list = [ ('click', '6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['cc6a19da8ebff6e7074f731447ef7e112bd23adf3de5c597cf9989f2fd8defe9'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('cget', version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/cget/'], 'checksums': ['353bdb724c4fe5f180f5bb27eebc9e5c57e45b841eb612e5e22d26224443019b'], }), ] @@ -49,6 +42,4 @@ sanity_check_paths = { sanity_check_commands = ["cget --help"] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2017b-Python-3.6.3.eb index 74f930bf586..e8d5fea89f3 100644 --- a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = "configparser is a Python library that brings the updated configpa toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['configparser-%(version)s_no-backports-namespace.patch'] checksums = [ @@ -23,11 +22,6 @@ dependencies = [('Python', '3.6.3')] download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = [ ('python', "-c 'import configparser'"), ('python', "-c 'from backports import configparser'"), diff --git a/easybuild/easyconfigs/c/corner/corner-2.0.1-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/c/corner/corner-2.0.1-foss-2019a-Python-2.7.15.eb index d11c8ec3603..8442e6f392d 100644 --- a/easybuild/easyconfigs/c/corner/corner-2.0.1-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/corner/corner-2.0.1-foss-2019a-Python-2.7.15.eb @@ -10,7 +10,6 @@ description = """Make some beautiful corner plots.""" toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['102e22797ee75d1432b6dc66aa2850f61388996ece66fd6600508742d2a7b88f'] diff --git a/easybuild/easyconfigs/c/corner/corner-2.0.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/corner/corner-2.0.1-foss-2019a-Python-3.7.2.eb index 2658bc2433a..4a102c760cb 100644 --- a/easybuild/easyconfigs/c/corner/corner-2.0.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/corner/corner-2.0.1-foss-2019a-Python-3.7.2.eb @@ -10,7 +10,6 @@ description = """Make some beautiful corner plots.""" toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['102e22797ee75d1432b6dc66aa2850f61388996ece66fd6600508742d2a7b88f'] diff --git a/easybuild/easyconfigs/c/coverage/coverage-4.5.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/coverage/coverage-4.5.1-intel-2017b-Python-2.7.14.eb index 981becf369b..6ceacd72321 100644 --- a/easybuild/easyconfigs/c/coverage/coverage-4.5.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/coverage/coverage-4.5.1-intel-2017b-Python-2.7.14.eb @@ -11,7 +11,6 @@ description = """ Coverage.py is a tool for measuring code coverage of Python pr toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['56e448f051a201c5ebbaa86a5efd0ca90d327204d8b059ab25ad0f35fbfd79f1'] diff --git a/easybuild/easyconfigs/c/cram/cram-0.7-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/cram/cram-0.7-GCCcore-8.2.0.eb index 79661174d2a..5673ff4c0b8 100644 --- a/easybuild/easyconfigs/c/cram/cram-0.7-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/cram/cram-0.7-GCCcore-8.2.0.eb @@ -8,7 +8,6 @@ description = "Cram is a functional testing framework for command line applicati toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['7da7445af2ce15b90aad5ec4792f857cef5786d71f14377e9eb994d8b8337f2f'] diff --git a/easybuild/easyconfigs/c/csvkit/csvkit-1.0.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/csvkit/csvkit-1.0.4-GCCcore-8.2.0.eb index 176629166ae..d4e830dda2a 100644 --- a/easybuild/easyconfigs/c/csvkit/csvkit-1.0.4-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/csvkit/csvkit-1.0.4-GCCcore-8.2.0.eb @@ -19,10 +19,6 @@ use_pip = True fix_python_shebang_for = ['bin/*'] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - exts_list = [ ('pytimeparse', '1.1.8', { 'checksums': ['e86136477be924d7e670646a98561957e8ca7308d44841e21f5ddea757556a0a'], diff --git a/easybuild/easyconfigs/c/csvkit/csvkit-1.0.5-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/c/csvkit/csvkit-1.0.5-GCCcore-8.3.0-Python-3.7.4.eb index 148a9dfa9c5..3fd077f37e1 100644 --- a/easybuild/easyconfigs/c/csvkit/csvkit-1.0.5-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/csvkit/csvkit-1.0.5-GCCcore-8.3.0-Python-3.7.4.eb @@ -24,10 +24,6 @@ sanity_pip_check = True fix_python_shebang_for = ['bin/*'] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - exts_list = [ ('pytimeparse', '1.1.8', { 'checksums': ['e86136477be924d7e670646a98561957e8ca7308d44841e21f5ddea757556a0a'], diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.4.30-CUDA-11.0.2.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.4.30-CUDA-11.0.2.eb index 4f3f62ee5da..aa8ab0f86fb 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.4.30-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.4.30-CUDA-11.0.2.eb @@ -1,30 +1,29 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# # Author: Stephane Thiell ## name = 'cuDNN' version = '8.0.4.30' local_cuda_version = '11.0.2' - -local_cuda_version_major_minor = '.'.join(local_cuda_version.split('.')[:2]) - +local_cuda_version_majmin = '.'.join(local_cuda_version.split('.')[:2]) versionsuffix = '-CUDA-%s' % local_cuda_version homepage = 'https://developer.nvidia.com/cudnn' -description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for - deep neural networks.""" +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" toolchain = SYSTEM -# Nvidia developer registration required. -# Download link: https://developer.nvidia.com/rdp/cudnn-download -sources = ['%%(namelower)s-%s-linux-%%(cudnnarch)s-v%%(version)s.tgz' % local_cuda_version_major_minor] +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] +local_tarball_tmpl = '-'.join(['%%(namelower)s', local_cuda_version_majmin, 'linux', '%s', 'v%%(version)s.tgz']) +sources = [local_tarball_tmpl % '%(cudnnarch)s'] checksums = [ { - '%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % local_cuda_version_major_minor: + local_tarball_tmpl % 'x64': '38a81a28952e314e21577432b0bab68357ef9de7f6c8858f721f78df9ee60c35', - '%%(namelower)s-%s-linux-ppc64le-v%%(version)s.tgz' % local_cuda_version_major_minor: + local_tarball_tmpl % 'ppc64le': '8da8ed689b1a348182ddd3f59b6758a502e11dc6708c33f96e3b4a40e033d2e1', } ] diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.4.30-CUDA-11.1.1.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.4.30-CUDA-11.1.1.eb index b58d69f676b..bedbe9ded47 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.4.30-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.4.30-CUDA-11.1.1.eb @@ -1,30 +1,29 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Author: Stephane Thiell +# Author: Stephane Thiell ## name = 'cuDNN' version = '8.0.4.30' local_cuda_version = '11.1.1' - -local_cuda_version_major_minor = '.'.join(local_cuda_version.split('.')[:2]) - +local_cuda_version_majmin = '.'.join(local_cuda_version.split('.')[:2]) versionsuffix = '-CUDA-%s' % local_cuda_version homepage = 'https://developer.nvidia.com/cudnn' -description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for - deep neural networks.""" +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" toolchain = SYSTEM -# Nvidia developer registration required. -# Download link: https://developer.nvidia.com/rdp/cudnn-download -sources = ['%%(namelower)s-%s-linux-%%(cudnnarch)s-v%%(version)s.tgz' % local_cuda_version_major_minor] +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] +local_tarball_tmpl = '-'.join(['%%(namelower)s', local_cuda_version_majmin, 'linux', '%s', 'v%%(version)s.tgz']) +sources = [local_tarball_tmpl % '%(cudnnarch)s'] checksums = [ { - '%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % local_cuda_version_major_minor: + local_tarball_tmpl % 'x64': '8f4c662343afce5998ce963500fe3bb167e9a508c1a1a949d821a4b80fa9beab', - '%%(namelower)s-%s-linux-ppc64le-v%%(version)s.tgz' % local_cuda_version_major_minor: + local_tarball_tmpl % 'ppc64le': 'b4ddb51610cbae806017616698635a9914c3e1eb14259f3a39ee5c84e7106712', } ] diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.5.39-CUDA-11.1.1.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.5.39-CUDA-11.1.1.eb index e365d665d8f..b5e57943125 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.5.39-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.0.5.39-CUDA-11.1.1.eb @@ -1,8 +1,7 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# # Author: Stephane Thiell ## + name = 'cuDNN' version = '8.0.5.39' local_cuda_version = '11.1.1' @@ -15,8 +14,10 @@ a GPU-accelerated library of primitives for deep neural networks.""" toolchain = SYSTEM -# Nvidia developer registration required. -# Download link: https://developer.nvidia.com/rdp/cudnn-download +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] local_tarball_tmpl = '-'.join(['%%(namelower)s', local_cuda_version_majmin, 'linux', '%s', 'v%%(version)s.tgz']) sources = [local_tarball_tmpl % '%(cudnnarch)s'] checksums = [ diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.1.0.77-CUDA-11.2.1.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.1.0.77-CUDA-11.2.1.eb new file mode 100644 index 00000000000..d7303be234d --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.1.0.77-CUDA-11.2.1.eb @@ -0,0 +1,42 @@ +## +# Author: Robert Mijakovic +# reciPY derived from the reciPY for 8.0.5 with the updated version. +## + +name = 'cuDNN' +version = '8.1.0.77' +local_cuda_version = '11.2.1' +local_cuda_version_majmin = '.'.join(local_cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] +local_tarball_tmpl = '-'.join(['%%(namelower)s', local_cuda_version_majmin, 'linux', '%s', 'v%%(version)s.tgz']) +sources = [local_tarball_tmpl % '%(cudnnarch)s'] +checksums = [ + { + local_tarball_tmpl % 'x64': + 'dbe82faf071d91ba9bcf00480146ad33f462482dfee56caf4479c1b8dabe3ecb', + local_tarball_tmpl % 'ppc64le': + '0d3f8fa21959e9f94889841cc8445aecf41d2f3c557091b447313afb43034037', + local_tarball_tmpl % 'aarch64sbsa': + 'ba16ff486b68a8b50b69b32702612634954de529f39cfff68c12b8bfc1958499', + } +] + +dependencies = [('CUDAcore', local_cuda_version)] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.1.1.33-CUDA-11.2.1.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.1.1.33-CUDA-11.2.1.eb new file mode 100644 index 00000000000..c3f7912ec02 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.1.1.33-CUDA-11.2.1.eb @@ -0,0 +1,42 @@ +## +# Author: Robert Mijakovic +# reciPY derived from the reciPY for 8.0.5 with the updated version. +## + +name = 'cuDNN' +version = '8.1.1.33' +local_cuda_version = '11.2.1' +local_cuda_version_majmin = '.'.join(local_cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] +local_tarball_tmpl = '-'.join(['%%(namelower)s', local_cuda_version_majmin, 'linux', '%s', 'v%%(version)s.tgz']) +sources = [local_tarball_tmpl % '%(cudnnarch)s'] +checksums = [ + { + local_tarball_tmpl % 'x64': + '98a8784e92862f20018d20c281b30d4a0cd951f93694f6433ccf4ae9c502ba6a', + local_tarball_tmpl % 'ppc64le': + 'c3e535a5d633ad8f4d50be0b6f8efd084c6c6ed3525c07cbd89fc508b1d76c7a', + local_tarball_tmpl % 'aarch64sbsa': + '4f7e4f5698539659d51f28dff0da11e5445a5ae58439af1d8a8e9f2d93535245', + } +] + +dependencies = [('CUDAcore', local_cuda_version)] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.1.32-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.1.32-CUDA-11.3.1.eb new file mode 100644 index 00000000000..bad4ffe62ab --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.1.32-CUDA-11.3.1.eb @@ -0,0 +1,37 @@ +name = 'cuDNN' +version = '8.2.1.32' +local_cuda_version = '11.3.1' +local_cuda_version_majmin = '.'.join(local_cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] +local_tarball_tmpl = '-'.join(['%%(namelower)s', local_cuda_version_majmin, 'linux', '%s', 'v%%(version)s.tgz']) +sources = [local_tarball_tmpl % '%(cudnnarch)s'] +checksums = [ + { + local_tarball_tmpl % 'x64': + '39412acd9ef5dd27954b6b9f5df75bd381c5d7ceb7979af6c743a7f4521f9c77', + local_tarball_tmpl % 'ppc64le': + '4ee4f2afeaae34fdb06da8d4942a6802aae94ecc51f307292c45966eecbe5fb9', + local_tarball_tmpl % 'aarch64sbsa': + 'e3a0e570cb8ba01d5d45e6eb1ebe29ff22fd5fb8ad45bfe7a448f4f95065ec1e', + } +] + +dependencies = [('CUDAcore', local_cuda_version)] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb index 5ec79014491..affdced4aa7 100644 --- a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'custodian' version = '1.1.0' @@ -14,20 +14,11 @@ dependencies = [ ('PyYAML', '3.12', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ - ('monty', '0.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], - }), - ('custodian', version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/custodian/'], - }), + ('monty', '0.9.6'), + ('custodian', version), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-foss-2017a-Python-2.7.13.eb index ed0a83a4639..9e9908b3368 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-foss-2017a-Python-2.7.13.eb @@ -11,13 +11,12 @@ name = 'cutadapt' version = '1.14' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.""" toolchain = {'name': 'foss', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['f32990a8b2f8b53f8f4c723ada3d256a8e8476febdd296506764cc8e83397d3d'] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb index 72895a67815..20932fca790 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb @@ -11,13 +11,12 @@ name = 'cutadapt' version = '1.14' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. """ toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['f32990a8b2f8b53f8f4c723ada3d256a8e8476febdd296506764cc8e83397d3d'] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.15-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.15-foss-2016b-Python-3.5.2.eb index 46bf4c372f3..1b3054cfd9d 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.15-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.15-foss-2016b-Python-3.5.2.eb @@ -11,13 +11,12 @@ name = 'cutadapt' version = '1.15' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['ba96e98281dbc31e75f25d02bde65d6945f1b94bc4ea8a673dc0d3ba08cfdc09'] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb index 9f8d094d4ad..2225c69f28a 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb @@ -13,7 +13,7 @@ name = 'cutadapt' version = '1.16' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.""" @@ -27,15 +27,12 @@ use_pip = True exts_list = [ ('bz2file', '0.98', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], }), ('xopen', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], 'checksums': ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'], }), ] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb index d3fed465492..01589d38226 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb @@ -13,7 +13,7 @@ name = 'cutadapt' version = '1.16' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.""" @@ -27,11 +27,9 @@ use_pip = True exts_list = [ ('xopen', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], 'checksums': ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'], }), ] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2018a-Python-3.6.4.eb index cd3d36deb95..e61f31a9799 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2018a-Python-3.6.4.eb @@ -13,13 +13,12 @@ name = 'cutadapt' version = '1.16' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.""" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb index 3ddabadd1a7..81e07579e66 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb @@ -10,7 +10,7 @@ name = 'cutadapt' version = '1.16' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.""" @@ -24,15 +24,12 @@ use_pip = True exts_list = [ ('bz2file', '0.98', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], }), ('xopen', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], 'checksums': ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'], }), ] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb index e0e98c0a7c6..50b19e4925d 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb @@ -10,7 +10,7 @@ name = 'cutadapt' version = '1.16' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.""" @@ -24,11 +24,9 @@ use_pip = True exts_list = [ ('xopen', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], 'checksums': ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'], }), ] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2018a-Python-2.7.14.eb index 4c237f1a7ba..ef7a6062b3f 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2018a-Python-2.7.14.eb @@ -10,13 +10,12 @@ name = 'cutadapt' version = '1.16' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2018a-Python-3.6.4.eb index 6acf7f04f66..31ed84be440 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2018a-Python-3.6.4.eb @@ -10,13 +10,12 @@ name = 'cutadapt' version = '1.16' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.2.0.eb index dfaa4ee1a3a..5de1382d091 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.2.0.eb @@ -25,8 +25,6 @@ builddependencies = [('binutils', '2.31.1')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('bz2file', '0.98', { 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.3.0.eb index 45981bfb888..8ec464cbed7 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.3.0.eb @@ -26,8 +26,6 @@ builddependencies = [('binutils', '2.32')] use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('bz2file', '0.98', { 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-foss-2018b-Python-2.7.15.eb index 2c976ef5d66..b5a0cd91812 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-foss-2018b-Python-2.7.15.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('bz2file', '0.98', { 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-foss-2018b-Python-3.6.6.eb index 572669c51e0..a6b555bf0ee 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-foss-2018b-Python-3.6.6.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('xopen', '0.5.1', { 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb index 70485d9ea5f..cedd9622158 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb @@ -25,11 +25,9 @@ use_pip = True exts_list = [ ('xopen', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], 'checksums': ['17aabf9b19d09a426d96030a83ad003c97b26dba9d45bf5570d33088fcd533f9'], }), ] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb index 65f2550e40b..68c59a65a13 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb @@ -11,13 +11,12 @@ name = 'cutadapt' version = '1.9.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. """ toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb index 9397e22d2b5..9f1c640cae5 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb @@ -11,13 +11,12 @@ name = 'cutadapt' version = '1.9.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. """ toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb index a48d2fa83b1..0257e6760b9 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb @@ -13,7 +13,7 @@ name = 'cutadapt' version = '2.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.""" @@ -25,15 +25,12 @@ use_pip = True exts_list = [ ('xopen', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], }), ('dnaio', '0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/d/dnaio'], 'checksums': ['47e4449affad0981978fe986684fc0d9c39736f05a157f6cf80e54dae0a92638'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], 'checksums': ['09fd222a27cc1eeb571633f2bd54442ea9d4ff668ef1f475fd9d5253a7d315ef'], }), ] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-8.3.0-Python-3.7.4.eb index 2be556237ea..536b81b91b6 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-8.3.0-Python-3.7.4.eb @@ -26,8 +26,6 @@ dependencies = [('Python', '3.7.4')] use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('xopen', '0.8.4', { 'checksums': ['dcd8f5ef5da5564f514a990573a48a0c347ee1fdbb9b6374d31592819868f7ba'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.7-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.7-GCCcore-8.3.0-Python-3.7.4.eb index 3f898dc9bfd..fe747fa33da 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.7-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.7-GCCcore-8.3.0-Python-3.7.4.eb @@ -26,8 +26,6 @@ dependencies = [('Python', '3.7.4')] use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('xopen', '0.8.4', { 'checksums': ['dcd8f5ef5da5564f514a990573a48a0c347ee1fdbb9b6374d31592819868f7ba'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.8-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.8-GCCcore-8.3.0-Python-3.7.4.eb index f4b8cefa7ac..7993c64d0fa 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.8-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.8-GCCcore-8.3.0-Python-3.7.4.eb @@ -26,8 +26,6 @@ dependencies = [('Python', '3.7.4')] use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('xopen', '0.8.4', { 'checksums': ['dcd8f5ef5da5564f514a990573a48a0c347ee1fdbb9b6374d31592819868f7ba'], diff --git a/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-foss-2017b-Python-2.7.14.eb index ba32d65aacb..1aeaef26cf2 100644 --- a/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-foss-2017b-Python-2.7.14.eb @@ -15,7 +15,6 @@ interrupts (and other signals and errors) in Cython code.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['8107b67a0c5991f74b0e000c6fa9fe8efcb2a22c7ede5b017aac4c3e20fb7db2'] diff --git a/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-foss-2017b-Python-3.6.3.eb index b62034d7f6c..6bd8a544bd5 100644 --- a/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-foss-2017b-Python-3.6.3.eb @@ -15,7 +15,6 @@ interrupts (and other signals and errors) in Cython code.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['8107b67a0c5991f74b0e000c6fa9fe8efcb2a22c7ede5b017aac4c3e20fb7db2'] diff --git a/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-intel-2017b-Python-2.7.14.eb index ea49369531e..05f444dce64 100644 --- a/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-intel-2017b-Python-2.7.14.eb @@ -15,7 +15,6 @@ interrupts (and other signals and errors) in Cython code.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['8107b67a0c5991f74b0e000c6fa9fe8efcb2a22c7ede5b017aac4c3e20fb7db2'] diff --git a/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-intel-2017b-Python-3.6.3.eb index 56a6a9ed509..4dc73470bb9 100644 --- a/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/cysignals/cysignals-1.10.2-intel-2017b-Python-3.6.3.eb @@ -15,7 +15,6 @@ interrupts (and other signals and errors) in Cython code.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['8107b67a0c5991f74b0e000c6fa9fe8efcb2a22c7ede5b017aac4c3e20fb7db2'] diff --git a/easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-GCCcore-8.2.0-Python-3.7.2.eb index 711e79ca048..7c668c1ecb0 100644 --- a/easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-GCCcore-8.2.0-Python-3.7.2.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('toolz', '0.10.0', { 'checksums': ['08fdd5ef7c96480ad11c12d472de21acd32359996f69a5259299b540feba4560'], diff --git a/easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-foss-2018b-Python-3.6.6.eb index 0c5e816c259..abb8fe99b87 100644 --- a/easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-foss-2018b-Python-3.6.6.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('toolz', '0.10.0', { 'checksums': ['08fdd5ef7c96480ad11c12d472de21acd32359996f69a5259299b540feba4560'], diff --git a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.10.10-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.10.10-foss-2018b-Python-3.6.6.eb index 2fac33807b4..ec626968a98 100644 --- a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.10.10-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.10.10-foss-2018b-Python-3.6.6.eb @@ -18,19 +18,15 @@ use_pip = True exts_list = [ ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('humanfriendly', '4.16.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/humanfriendly/'], 'checksums': ['ed1e98ae056b597f15b41bddcc32b9f21e6ab4f3445f9faad1668675de759f7b'], }), ('coloredlogs', '10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/coloredlogs/'], 'checksums': ['b869a2dda3fa88154b9dd850e27828d8755bfab5a838a1c97fbc850c6e377c36'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/cyvcf2'], 'checksums': ['14a469567992c218d1f1b8ab76b93ec5c1bf56c9f071cf93a3affdaabc9268e0'], }), ] diff --git a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-foss-2019a.eb b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-foss-2019a.eb index 5a76cf08ff2..7f016e92e84 100644 --- a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-foss-2019a.eb +++ b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-foss-2019a.eb @@ -21,8 +21,6 @@ fix_python_shebang_for = ['bin/*'] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('monotonic', '1.5', { 'checksums': ['23953d55076df038541e648a53676fb24980f7a1be290cdda21300b3bc21dfb0'], diff --git a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-intel-2019a.eb b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-intel-2019a.eb index bd393254fe9..fa22d1e6fa5 100644 --- a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-intel-2019a.eb +++ b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-intel-2019a.eb @@ -21,8 +21,6 @@ fix_python_shebang_for = ['bin/*'] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('monotonic', '1.5', { 'checksums': ['23953d55076df038541e648a53676fb24980f7a1be290cdda21300b3bc21dfb0'], diff --git a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..51c770e09cc --- /dev/null +++ b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,51 @@ +name = 'DOLFIN' +version = '2019.1.0.post0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/fenics-project/dolfin' +description = """DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE + (Problem Solving Environment) for ordinary and partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True, 'packed-linker-options': True, 'openmp': True} + +bitbucket_account = 'fenics-project' +source_urls = [BITBUCKET_DOWNLOADS] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['61abdcdb13684ba2a3ba4afb7ea6c7907aa0896a46439d3af7e8848483d4392f'] + +builddependencies = [ + ('CMake', '3.15.3'), + ('pkg-config', '0.29.2'), + ('patchelf', '0.10'), + ('pybind11', '2.4.3', versionsuffix), +] +dependencies = [ + ('Python', '3.7.4'), + ('Boost', '1.71.0'), + ('FFC', '2019.1.0.post0', versionsuffix), + ('SCOTCH', '6.0.9'), + ('SuiteSparse', '5.6.0', '-METIS-5.1.0'), + ('CGAL', '4.14.1', versionsuffix), + ('PETSc', '3.12.4', versionsuffix), + ('SLEPc', '3.12.2', versionsuffix), + ('HDF5', '1.10.5'), + ('Trilinos', '12.12.1', versionsuffix), + ('zlib', '1.2.11'), + ('libxml2', '2.9.9'), + ('Eigen', '3.3.7', '', True), + ('PLY', '3.11', versionsuffix), + ('VTK', '8.2.0', versionsuffix), + ('petsc4py', '3.12.0', versionsuffix), + ('slepc4py', '3.12.0', versionsuffix), + ('SUNDIALS', '5.1.0'), + ('pkgconfig', '1.5.1', versionsuffix), +] + +# demos run as tests fail with 'bad X server connection', skipping for now +runtest = False + +# strip out too strict version requirement for pybind11 +preinstallopts = "sed -i 's/pybind11==[0-9.]*/pybind11/g' %(builddir)s/dolfin-%(version)s/python/setup.py && " + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/d/DeepSurv/DeepSurv-2.0.0-20180922-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/DeepSurv/DeepSurv-2.0.0-20180922-fosscuda-2018b-Python-3.6.6.eb index fa341e3de7e..8a371a2873d 100644 --- a/easybuild/easyconfigs/d/DeepSurv/DeepSurv-2.0.0-20180922-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/DeepSurv/DeepSurv-2.0.0-20180922-fosscuda-2018b-Python-3.6.6.eb @@ -25,31 +25,24 @@ use_pip = True exts_list = [ ('Bottleneck', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bottleneck/'], 'checksums': ['6efcde5f830aed64feafca0359b51db0e184c72af8ba6675b4a99f263922eb36'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('autograd', '1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/a/autograd/'], 'checksums': ['a08bfa6d539b7a56e7c9f4d0881044afbef5e75f324a394c2494de963ea4a47d'], }), ('lifelines', '0.20.4', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lifelines/'], 'checksums': ['efdf109b2f383c4125ca30414c13f88a9386f5d61d986bcb458cc41242f429bd'], }), ('logger', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/l/logger/'], 'checksums': ['4ecac57133c6376fa215f0fe6b4dc4d60e4d1ad8be005cab4e8a702df682f8b3'], }), ('Optunity', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/o/optunity/'], 'checksums': ['a83618dd37e014c5993e8877749e0ee17864d24783f19f5ebdeedb5525c0a65b'], }), ('tensorboard_logger', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard_logger/'], 'checksums': ['614eaf9b68f7ca9e5db5972f241034a24ea593b938fc8a7e5544444099edeae5'], }), ('Lasagne', 'a61b76f', { diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-8.2.0.eb index 4e3ff7f19b8..d0f954d1fbd 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-8.2.0.eb @@ -20,7 +20,6 @@ reading, writing, simulation, processing and manipulation of phylogenetic trees toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'] diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-8.3.0.eb index 0a5cb0830f9..d457534a09e 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-8.3.0.eb @@ -19,7 +19,6 @@ reading, writing, simulation, processing and manipulation of phylogenetic trees toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'] diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2018b-Python-2.7.15.eb index 421f316402b..f3f41571485 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2018b-Python-2.7.15.eb @@ -20,7 +20,6 @@ reading, writing, simulation, processing and manipulation of phylogenetic trees toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'] diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2019a.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2019a.eb index bd01f3948ae..5671d6245a4 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2019a.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2019a.eb @@ -19,7 +19,6 @@ reading, writing, simulation, processing and manipulation of phylogenetic trees toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'] diff --git a/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb b/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb new file mode 100644 index 00000000000..1076bd462aa --- /dev/null +++ b/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +# Includes some material from the BEAR Software team at the University of Birmingham. + +easyblock = 'CMakeMake' + +name = 'DosageConvertor' +version = '1.0.4' +local_hash = 'c53a377bb6e03cd697f528cd74d97eb0c9f56e8b' + +homepage = 'http://genome.sph.umich.edu/wiki/DosageConvertor' +description = """DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 + to other formats such as MaCH or PLINK. Please note that this tool CANNOT handle missing values in + the input files and may NOT work for non-Minimac3/4 VCF files.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +builddependencies = [ + ('CMake', '3.18.4') +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libStatGen', '1.0.15'), +] + +source_urls = ['https://github.com/Santy-8128/%(name)s/archive'] +sources = ['%s.tar.gz' % local_hash] +checksums = ['3ee1f3ef23d7e7c04295a5fa43c3b59811cc8fe778f0f69c9759c2624ae3aa47'] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = [ + '%%(name)s --vcfDose %%(builddir)s/%%(name)s-%s/test/TestDataImputedVCF.dose.vcf.gz --prefix output --format 1' + ' --info %%(builddir)s/%%(name)s-%s/test/TestDataImputedVCF.info --type plink' % (local_hash, local_hash) +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dSFMT/dSFMT-2.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/dSFMT/dSFMT-2.2.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6e45821bd89 --- /dev/null +++ b/easybuild/easyconfigs/d/dSFMT/dSFMT-2.2.5-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'dSFMT' +version = '2.2.5' + +homepage = 'https://github.com/MersenneTwister-Lab/dSFMT' +description = "Double precision SIMD-oriented Fast Mersenne Twister." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'MersenneTwister-Lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['dSFMT-2.2.5_autotools.patch'] +checksums = [ + 'b7bc498cd140b4808963b1ff9f33b42a491870f54775c1060ecad0e02bcaffb4', # v2.2.5.tar.gz + '1df9824414428cef26b0912bb03585a008ac1055dd526c58f483cd1cc5d11857', # dSFMT-2.2.5_autotools.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('Autoconf-archive', '2021.02.19'), +] + +preconfigopts = "autoreconf -i -f &&" + +local_libs = ['lib%%(name)s%s' % x for x in ['', '-11213', '-1279', '-132049', '-19937', '-216091', + '-2203', '-4253', '-44497', '-521', '-86243']] + +sanity_check_paths = { + 'files': ['include/dSFMT.h'] + ['lib/%s.%s' % (x, SHLIB_EXT) for x in local_libs], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dSFMT/dSFMT-2.2.5_autotools.patch b/easybuild/easyconfigs/d/dSFMT/dSFMT-2.2.5_autotools.patch new file mode 100644 index 00000000000..d5bd1beeac7 --- /dev/null +++ b/easybuild/easyconfigs/d/dSFMT/dSFMT-2.2.5_autotools.patch @@ -0,0 +1,256 @@ +Description: Use autotools to build shared library + This patch uses autoconf, automake, and libtool to build shared + and static libraries that enable the use of dSFMT by other packages. + All optimization flags of the upstream makefile are preserved, but + each flag is queried for compatibility with the compiler. Options + are provided for disabling the optimization flags, and for enabling + SSE2 or AltiVec support. Separate libraries are built for each of the + Mersenne exponents. The install target creates convenience symbolic + links to the development libraries for the primarily used Mersenne + exponent 19937. +Author: Peter Colberg +Forwarded: no +Last-Update: 2015-10-28 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- /dev/null ++++ b/Makefile.am +@@ -0,0 +1,103 @@ ++ACLOCAL_AMFLAGS = -I m4 ++ ++include_HEADERS = dSFMT.h ++ ++lib_LTLIBRARIES = libdSFMT-521.la libdSFMT-1279.la libdSFMT-2203.la \ ++ libdSFMT-4253.la libdSFMT-11213.la libdSFMT-19937.la \ ++ libdSFMT-44497.la libdSFMT-86243.la libdSFMT-132049.la \ ++ libdSFMT-216091.la ++ ++libdSFMT_CPPFLAGS = -DDSFMT_BUILDING_LIB -DDSFMT_DO_NOT_USE_OLD_NAMES ++libdSFMT_LDFLAGS = -version-info $(LIB_VERSION) ++ ++libdSFMT_521_la_SOURCES = dSFMT.c ++libdSFMT_521_la_CPPFLAGS = -DDSFMT_MEXP=521 $(libdSFMT_CPPFLAGS) ++libdSFMT_521_la_LDFLAGS = $(libdSFMT_LDFLAGS) ++ ++libdSFMT_1279_la_SOURCES = dSFMT.c ++libdSFMT_1279_la_CPPFLAGS = -DDSFMT_MEXP=1279 $(libdSFMT_CPPFLAGS) ++libdSFMT_1279_la_LDFLAGS = $(libdSFMT_LDFLAGS) ++ ++libdSFMT_2203_la_SOURCES = dSFMT.c ++libdSFMT_2203_la_CPPFLAGS = -DDSFMT_MEXP=2203 $(libdSFMT_CPPFLAGS) ++libdSFMT_2203_la_LDFLAGS = $(libdSFMT_LDFLAGS) ++ ++libdSFMT_4253_la_SOURCES = dSFMT.c ++libdSFMT_4253_la_CPPFLAGS = -DDSFMT_MEXP=4253 $(libdSFMT_CPPFLAGS) ++libdSFMT_4253_la_LDFLAGS = $(libdSFMT_LDFLAGS) ++ ++libdSFMT_11213_la_SOURCES = dSFMT.c ++libdSFMT_11213_la_CPPFLAGS = -DDSFMT_MEXP=11213 $(libdSFMT_CPPFLAGS) ++libdSFMT_11213_la_LDFLAGS = $(libdSFMT_LDFLAGS) ++ ++libdSFMT_19937_la_SOURCES = dSFMT.c ++libdSFMT_19937_la_CPPFLAGS = -DDSFMT_MEXP=19937 $(libdSFMT_CPPFLAGS) ++libdSFMT_19937_la_LDFLAGS = $(libdSFMT_LDFLAGS) ++ ++libdSFMT_44497_la_SOURCES = dSFMT.c ++libdSFMT_44497_la_CPPFLAGS = -DDSFMT_MEXP=44497 $(libdSFMT_CPPFLAGS) ++libdSFMT_44497_la_LDFLAGS = $(libdSFMT_LDFLAGS) ++ ++libdSFMT_86243_la_SOURCES = dSFMT.c ++libdSFMT_86243_la_CPPFLAGS = -DDSFMT_MEXP=86243 $(libdSFMT_CPPFLAGS) ++libdSFMT_86243_la_LDFLAGS = $(libdSFMT_LDFLAGS) ++ ++libdSFMT_132049_la_SOURCES = dSFMT.c ++libdSFMT_132049_la_CPPFLAGS = -DDSFMT_MEXP=132049 $(libdSFMT_CPPFLAGS) ++libdSFMT_132049_la_LDFLAGS = $(libdSFMT_LDFLAGS) ++ ++libdSFMT_216091_la_SOURCES = dSFMT.c ++libdSFMT_216091_la_CPPFLAGS = -DDSFMT_MEXP=216091 $(libdSFMT_CPPFLAGS) ++libdSFMT_216091_la_LDFLAGS = $(libdSFMT_LDFLAGS) ++ ++install-exec-hook: ++ cd $(DESTDIR)$(libdir) && if test -f libdSFMT-19937.la; then $(LN_S) -f libdSFMT-19937.la libdSFMT.la; fi ++ cd $(DESTDIR)$(libdir) && if test -f libdSFMT-19937.so; then $(LN_S) -f libdSFMT-19937.so libdSFMT.so; fi ++ cd $(DESTDIR)$(libdir) && if test -f libdSFMT-19937.a; then $(LN_S) -f libdSFMT-19937.a libdSFMT.a; fi ++ ++noinst_PROGRAMS = test-M521 test-M1279 test-M2203 test-M4253 \ ++ test-M11213 test-M19937 test-M44497 test-M86243 \ ++ test-M132049 test-M216091 ++ ++test_M521_SOURCES = test.c ++test_M521_CPPFLAGS = -DDSFMT_MEXP=521 ++test_M521_LDADD = libdSFMT-521.la ++ ++test_M1279_SOURCES = test.c ++test_M1279_CPPFLAGS = -DDSFMT_MEXP=1279 ++test_M1279_LDADD = libdSFMT-1279.la ++ ++test_M2203_SOURCES = test.c ++test_M2203_CPPFLAGS = -DDSFMT_MEXP=2203 ++test_M2203_LDADD = libdSFMT-2203.la ++ ++test_M4253_SOURCES = test.c ++test_M4253_CPPFLAGS = -DDSFMT_MEXP=4253 ++test_M4253_LDADD = libdSFMT-4253.la ++ ++test_M11213_SOURCES = test.c ++test_M11213_CPPFLAGS = -DDSFMT_MEXP=11213 ++test_M11213_LDADD = libdSFMT-11213.la ++ ++test_M19937_SOURCES = test.c ++test_M19937_CPPFLAGS = -DDSFMT_MEXP=19937 ++test_M19937_LDADD = libdSFMT-19937.la ++ ++test_M44497_SOURCES = test.c ++test_M44497_CPPFLAGS = -DDSFMT_MEXP=44497 ++test_M44497_LDADD = libdSFMT-44497.la ++ ++test_M86243_SOURCES = test.c ++test_M86243_CPPFLAGS = -DDSFMT_MEXP=86243 ++test_M86243_LDADD = libdSFMT-86243.la ++ ++test_M132049_SOURCES = test.c ++test_M132049_CPPFLAGS = -DDSFMT_MEXP=132049 ++test_M132049_LDADD = libdSFMT-132049.la ++ ++test_M216091_SOURCES = test.c ++test_M216091_CPPFLAGS = -DDSFMT_MEXP=216091 ++test_M216091_LDADD = libdSFMT-216091.la ++ ++check test: $(noinst_PROGRAMS) ++ ./check.sh test +--- /dev/null ++++ b/configure.ac +@@ -0,0 +1,109 @@ ++AC_PREREQ([2.69]) ++AC_INIT([dSFMT], [2.2.3]) ++AC_CONFIG_SRCDIR([dSFMT.h]) ++AC_CONFIG_MACRO_DIR([m4]) ++AM_INIT_AUTOMAKE([foreign]) ++LT_INIT ++ ++AC_PROG_CC_C99 ++AC_PROG_MAKE_SET ++AC_PROG_LN_S ++ ++AX_CHECK_COMPILE_FLAG([-Wall], ++ [AM_CFLAGS="$AM_CFLAGS -Wall"], ++ [], ++ [-Werror]) ++ ++AX_CHECK_COMPILE_FLAG([-Wmissing-prototypes], ++ [AM_CFLAGS="$AM_CFLAGS -Wmissing-prototypes"], ++ [], ++ [-Werror]) ++ ++AC_MSG_CHECKING([whether to enable debugging assertions]) ++AC_ARG_ENABLE([debug], ++ [AC_HELP_STRING([--enable-debug], [enable debugging assertions @<:@default=no@:>@])], ++ [enable_debug=$enableval], ++ [enable_debug=no]) ++AC_MSG_RESULT([$enable_debug]) ++ ++if test "$enable_debug" != "yes"; then ++ AC_DEFINE([NDEBUG], [1], [Define to disable debugging assertions]) ++fi ++ ++AC_MSG_CHECKING([whether to enable optimization flags]) ++AC_ARG_ENABLE([optimize], ++ [AC_HELP_STRING([--enable-optimize], [enable optimization flags @<:@default=yes@:>@])], ++ [enable_optimize=$enableval], ++ [enable_optimize=yes]) ++AC_MSG_RESULT([$enable_optimize]) ++ ++if test "$enable_optimize" = "yes"; then ++ AX_CHECK_COMPILE_FLAG([-finline-functions], ++ [AM_CFLAGS="$AM_CFLAGS -finline-functions"], ++ [], ++ [-Werror]) ++ ++ AX_CHECK_COMPILE_FLAG([-fomit-frame-pointer], ++ [AM_CFLAGS="$AM_CFLAGS -fomit-frame-pointer"], ++ [], ++ [-Werror]) ++ ++ AX_CHECK_COMPILE_FLAG([-fno-strict-aliasing], ++ [AM_CFLAGS="$AM_CFLAGS -fno-strict-aliasing"], ++ [], ++ [-Werror]) ++ ++ AX_CHECK_COMPILE_FLAG([--param=max-inline-insns-single=1800], ++ [AM_CFLAGS="$AM_CFLAGS --param=max-inline-insns-single=1800"], ++ [], ++ [-Werror]) ++ ++ AX_CHECK_COMPILE_FLAG([--param=inline-unit-growth=500], ++ [AM_CFLAGS="$AM_CFLAGS --param=inline-unit-growth=500"], ++ [], ++ [-Werror]) ++ ++ AX_CHECK_COMPILE_FLAG([--param=large-function-growth=900], ++ [AM_CFLAGS="$AM_CFLAGS --param=large-function-growth=900"], ++ [], ++ [-Werror]) ++fi ++ ++AC_MSG_CHECKING([whether to enable SSE2 support]) ++AC_ARG_ENABLE([sse2], ++ [AC_HELP_STRING([--enable-sse2], [enable SSE2 support @<:@default=no@:>@])], ++ [enable_sse2=$enableval], ++ [enable_sse2=no]) ++AC_MSG_RESULT([$enable_sse2]) ++ ++if test "$enable_sse2" = "yes"; then ++ AX_CHECK_COMPILE_FLAG([-msse2], ++ [AM_CFLAGS="$AM_CFLAGS -msse2"], ++ [AC_MSG_ERROR([Need C compiler that supports SSE2])], ++ [-Werror]) ++ AC_DEFINE([HAVE_SSE2], [1], [Define to enable SSE2 support]) ++fi ++ ++AC_MSG_CHECKING([whether to enable AltiVec support]) ++AC_ARG_ENABLE([altivec], ++ [AC_HELP_STRING([--enable-altivec], [enable AltiVec support @<:@default=no@:>@])], ++ [enable_altivec=$enableval], ++ [enable_altivec=no]) ++AC_MSG_RESULT([$enable_altivec]) ++ ++if test "$enable_altivec" = "yes"; then ++ AX_CHECK_COMPILE_FLAG([-mabi=altivec -maltivec], ++ [AM_CFLAGS="$AM_CFLAGS -mabi=altivec -maltivec"], ++ [AX_CHECK_COMPILE_FLAG([-faltivec -maltivec], ++ [AM_CFLAGS="$AM_CFLAGS -faltivec -maltivec"], ++ [AC_MSG_ERROR([Need C compiler that supports AltiVec])], ++ [-Werror])], ++ [-Werror]) ++ AC_DEFINE([HAVE_ALTIVEC], [1], [Define to enable AltiVec support]) ++fi ++ ++AC_SUBST([LIB_VERSION], [1:0:0]) ++AC_SUBST([AM_CFLAGS]) ++AC_CONFIG_HEADERS([config.h]) ++AC_CONFIG_FILES([Makefile]) ++AC_OUTPUT +--- a/dSFMT.c ++++ b/dSFMT.c +@@ -11,6 +11,10 @@ + * + * The new BSD License is applied to this software, see LICENSE.txt + */ ++#if defined(HAVE_CONFIG_H) ++# include "config.h" ++#endif ++ + #include + #include + #include +--- a/test.c ++++ b/test.c +@@ -1,3 +1,7 @@ ++#if defined(HAVE_CONFIG_H) ++# include "config.h" ++#endif ++ + #include + #include + #include diff --git a/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb index 35e592cb9c5..0e7a838fac9 100644 --- a/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'dammit' version = '0.3.2' @@ -12,9 +12,6 @@ description = """dammit is a simple de novo transcriptome annotator. It was born toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.13'), ('X11', '20170314'), @@ -31,36 +28,28 @@ dependencies = [ exts_list = [ ('cloudpickle', '0.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], 'checksums': ['5bb83eb466f0733dbd077e76cf1a15c404a94eb063cecc7049a1482fa1b11661'], }), ('pyinotify', '0.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyinotify'], 'checksums': ['9c998a5d7606ca835065cdabc013ae6c66eb9ea76a00a1e3bc6e0cfe2b4f71f4'], }), ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser'], 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), ('doit', '0.29.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/doit'], 'checksums': ['fcb479482644de3e83d6faed9b29373f1f38942b79b991a7432943a84416d5cd'], }), ('nose', '1.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose'], 'checksums': ['76bc63a4e2d5e5a0df77ca7d18f0f56e2c46cfb62b71103ba92a92c79fab1e03'], }), ('nose-capturestderr', '1.0', { 'modulename': 'nose_capturestderr', - 'source_urls': ['https://pypi.python.org/packages/source/n/nose-capturestderr'], 'checksums': ['8a05620bec5acaf006acfe59ad1225673350bba359e1b946ddba53206a3f8c98'], }), ('ficus', '0.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/f/ficus'], 'checksums': ['7dbd69a4aceb0406e53cf8ede98c039a03110b7b8860b64356554caf537b9324'], }), ('numexpr', '2.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numexpr'], 'checksums': ['6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705'], }), (name, version, { @@ -68,7 +57,6 @@ exts_list = [ 'dammit-0.3.2_nodocs.patch', 'dammit-0.3.2_py2busco.patch', ], - 'source_urls': ['https://pypi.python.org/packages/source/d/dammit'], 'checksums': [ '400bb9c6644c4edd5f7b8bf294c142e89baa148008b3aba39d2c5e89f99ff278', # dammit-0.3.2.tar.gz '79dc4da8a778d842f7614e287add044cc0a7138d5a43ec80b378ac715054ae3b', # dammit-0.3.2_nodocs.patch @@ -77,11 +65,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dask/dask-0.11.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/d/dask/dask-0.11.0-foss-2016a-Python-2.7.11.eb index f2f70c3e0ca..a0ec21e7145 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.11.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.11.0-foss-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.11.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -17,11 +17,9 @@ use_pip = False exts_list = [ ('toolz', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['e8451af61face57b7c5d09e71c0d27b8005f001ead56e9fdf470417e5cc6d479'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['ef32490c0b156584a71576dccec4dfe550a0cd81a9c131a4ee2e43c241b601c3'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-2.7.12.eb index 8f1becf303e..2becfa05f89 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-2.7.12.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.11.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('toolz', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['e8451af61face57b7c5d09e71c0d27b8005f001ead56e9fdf470417e5cc6d479'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['ef32490c0b156584a71576dccec4dfe550a0cd81a9c131a4ee2e43c241b601c3'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-3.5.2.eb index 147bafcedd3..976bb99c76f 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-3.5.2.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.11.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('toolz', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['e8451af61face57b7c5d09e71c0d27b8005f001ead56e9fdf470417e5cc6d479'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['ef32490c0b156584a71576dccec4dfe550a0cd81a9c131a4ee2e43c241b601c3'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.12.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/d/dask/dask-0.12.0-foss-2016b-Python-3.5.2.eb index bf99d38dd22..d8b8470ca94 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.12.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.12.0-foss-2016b-Python-3.5.2.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.12.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -17,11 +17,9 @@ use_pip = False exts_list = [ ('toolz', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['e8451af61face57b7c5d09e71c0d27b8005f001ead56e9fdf470417e5cc6d479'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['24e9c50181370761f8a0c82e233fa823a7eb9ae01de50ee73378fd46724f669e'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-2.7.12.eb index d26c182dfcd..c6a4a6aa86a 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-2.7.12.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.12.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -16,11 +16,9 @@ dependencies = [('Python', '2.7.12')] exts_list = [ ('toolz', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['e8451af61face57b7c5d09e71c0d27b8005f001ead56e9fdf470417e5cc6d479'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['24e9c50181370761f8a0c82e233fa823a7eb9ae01de50ee73378fd46724f669e'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-3.5.2.eb index 085206f8987..addaa5d4a80 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-3.5.2.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.12.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('toolz', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['e8451af61face57b7c5d09e71c0d27b8005f001ead56e9fdf470417e5cc6d479'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['24e9c50181370761f8a0c82e233fa823a7eb9ae01de50ee73378fd46724f669e'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.16.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/d/dask/dask-0.16.0-foss-2017b-Python-2.7.14.eb index 6a4d91211e6..98eb9612e25 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.16.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.16.0-foss-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.16.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['40d150b73e3366c9521e9dde206046a66906330074f87be901b1e1013ce6cb73'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.16.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/d/dask/dask-0.16.0-foss-2017b-Python-3.6.3.eb index 063c9d5d4b1..63343ee8207 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.16.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.16.0-foss-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.16.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['40d150b73e3366c9521e9dde206046a66906330074f87be901b1e1013ce6cb73'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.16.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/d/dask/dask-0.16.0-intel-2017b-Python-2.7.14.eb index 2d877a0c74c..4ad377003f2 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.16.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.16.0-intel-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.16.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['40d150b73e3366c9521e9dde206046a66906330074f87be901b1e1013ce6cb73'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.16.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/d/dask/dask-0.16.0-intel-2017b-Python-3.6.3.eb index 5b475879437..64def432cde 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.16.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.16.0-intel-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.16.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['40d150b73e3366c9521e9dde206046a66906330074f87be901b1e1013ce6cb73'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.17.0-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/d/dask/dask-0.17.0-foss-2017a-Python-2.7.13.eb index dc11a02cca8..0b9047017f8 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.17.0-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.17.0-foss-2017a-Python-2.7.13.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.17.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['4d2b0754d16ddc3f87026c1fc4fa3b589d7604a41d3f6510268f172abc1d0a5e'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.17.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/d/dask/dask-0.17.0-intel-2017a-Python-2.7.13.eb index fd04cd9fe47..e10c9e64fb3 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.17.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.17.0-intel-2017a-Python-2.7.13.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.17.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -16,18 +16,11 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['4d2b0754d16ddc3f87026c1fc4fa3b589d7604a41d3f6510268f172abc1d0a5e'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-0.17.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/d/dask/dask-0.17.0-intel-2017a-Python-3.6.1.eb index a9e3ef08a6d..6f9d2f1aac6 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.17.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.17.0-intel-2017a-Python-3.6.1.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.17.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -16,18 +16,11 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['4d2b0754d16ddc3f87026c1fc4fa3b589d7604a41d3f6510268f172abc1d0a5e'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-0.17.2-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/d/dask/dask-0.17.2-foss-2018a-Python-3.6.4.eb index 080e2976343..bda6fcec4cc 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.17.2-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.17.2-foss-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.17.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -14,8 +14,6 @@ dependencies = [('Python', '3.6.4')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('toolz', '0.9.0', { 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], diff --git a/easybuild/easyconfigs/d/dask/dask-0.17.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/d/dask/dask-0.17.2-intel-2018a-Python-3.6.4.eb index 2542c270404..3d87f343207 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.17.2-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.17.2-intel-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.17.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -14,8 +14,6 @@ dependencies = [('Python', '3.6.4')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('toolz', '0.9.0', { 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], diff --git a/easybuild/easyconfigs/d/dask/dask-0.19.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/dask/dask-0.19.4-foss-2018b-Python-3.6.6.eb index adc7b9c9ea9..dd7e62e0f03 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.19.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.19.4-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.19.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -19,56 +19,43 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), ('HeapDict', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/h/HeapDict'], 'checksums': ['40c9e3680616cfdf942f77429a3a9e0a76f31ce965d62f4ffbe63a83a5ef1b5a'], }), ('zict', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], 'checksums': ['63377f063086fc92e5c16e4d02162c571f6470b9e796cf3411ef9e815c96b799'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('tblib', '1.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], 'checksums': ['436e4200e63d92316551179dc540906652878df4ff39b43db30fcf6400444fe7'], }), ('sortedcontainers', '2.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], 'checksums': ['b74f2756fb5e23512572cc76f0fe0832fd86310f77dfee54335a35fb33f6b950'], }), ('psutil', '5.4.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['5b6322b167a5ba0c5463b4d30dfd379cd4ce245a1162ebf8fc7ab5c5ffae4f3b'], }), ('msgpack-python', '0.5.6', { 'modulename': 'msgpack', - 'source_urls': ['https://pypi.python.org/packages/source/s/msgpack-python'], 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], }), ('msgpack', '0.5.6', { - 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'], 'checksums': ['0ee8c8c85aa651be3aa0cd005b5931769eaa658c948ce79428766f1bd46ae2c3'], }), ('cloudpickle', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], 'checksums': ['f169a8523a40eb0a3452e1878aac31da6759409fbafa51dd50d89d4a6b42bcf1'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['fd86d49d415de5f3a0e8efa47bb8bc454fb2cc9b7871b7d7007c10636880cdae'], }), ('distributed', '1.23.3', { - 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], 'checksums': ['2d48a4de280fd7243ca76f9b12db5fe2486fc89dcdb510c77fa51f51733a04cc'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.19.4-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/dask/dask-0.19.4-fosscuda-2018b-Python-3.6.6.eb index 93d426b2d99..62bd8d30cf9 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.19.4-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.19.4-fosscuda-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.19.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -19,56 +19,43 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), ('HeapDict', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/h/HeapDict'], 'checksums': ['40c9e3680616cfdf942f77429a3a9e0a76f31ce965d62f4ffbe63a83a5ef1b5a'], }), ('zict', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], 'checksums': ['63377f063086fc92e5c16e4d02162c571f6470b9e796cf3411ef9e815c96b799'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('tblib', '1.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], 'checksums': ['436e4200e63d92316551179dc540906652878df4ff39b43db30fcf6400444fe7'], }), ('sortedcontainers', '2.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], 'checksums': ['b74f2756fb5e23512572cc76f0fe0832fd86310f77dfee54335a35fb33f6b950'], }), ('psutil', '5.4.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['5b6322b167a5ba0c5463b4d30dfd379cd4ce245a1162ebf8fc7ab5c5ffae4f3b'], }), ('msgpack-python', '0.5.6', { 'modulename': 'msgpack', - 'source_urls': ['https://pypi.python.org/packages/source/s/msgpack-python'], 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], }), ('msgpack', '0.5.6', { - 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'], 'checksums': ['0ee8c8c85aa651be3aa0cd005b5931769eaa658c948ce79428766f1bd46ae2c3'], }), ('cloudpickle', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], 'checksums': ['f169a8523a40eb0a3452e1878aac31da6759409fbafa51dd50d89d4a6b42bcf1'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['fd86d49d415de5f3a0e8efa47bb8bc454fb2cc9b7871b7d7007c10636880cdae'], }), ('distributed', '1.23.3', { - 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], 'checksums': ['2d48a4de280fd7243ca76f9b12db5fe2486fc89dcdb510c77fa51f51733a04cc'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.19.4-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/dask/dask-0.19.4-intel-2018b-Python-3.6.6.eb index 43afe540096..4a470989de6 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.19.4-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.19.4-intel-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'dask' version = '0.19.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -19,56 +19,43 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), ('HeapDict', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/h/HeapDict'], 'checksums': ['40c9e3680616cfdf942f77429a3a9e0a76f31ce965d62f4ffbe63a83a5ef1b5a'], }), ('zict', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], 'checksums': ['63377f063086fc92e5c16e4d02162c571f6470b9e796cf3411ef9e815c96b799'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('tblib', '1.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], 'checksums': ['436e4200e63d92316551179dc540906652878df4ff39b43db30fcf6400444fe7'], }), ('sortedcontainers', '2.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], 'checksums': ['b74f2756fb5e23512572cc76f0fe0832fd86310f77dfee54335a35fb33f6b950'], }), ('psutil', '5.4.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['5b6322b167a5ba0c5463b4d30dfd379cd4ce245a1162ebf8fc7ab5c5ffae4f3b'], }), ('msgpack-python', '0.5.6', { 'modulename': 'msgpack', - 'source_urls': ['https://pypi.python.org/packages/source/s/msgpack-python'], 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], }), ('msgpack', '0.5.6', { - 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'], 'checksums': ['0ee8c8c85aa651be3aa0cd005b5931769eaa658c948ce79428766f1bd46ae2c3'], }), ('cloudpickle', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], 'checksums': ['f169a8523a40eb0a3452e1878aac31da6759409fbafa51dd50d89d4a6b42bcf1'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['fd86d49d415de5f3a0e8efa47bb8bc454fb2cc9b7871b7d7007c10636880cdae'], }), ('distributed', '1.23.3', { - 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], 'checksums': ['2d48a4de280fd7243ca76f9b12db5fe2486fc89dcdb510c77fa51f51733a04cc'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb index e5a08d46bfb..ee298e89319 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb @@ -4,13 +4,12 @@ name = 'dask' version = '0.8.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6e936a59e1bed9e3e98d43b86052549bba2e7fcee134f9914e79dd063754e471'] @@ -20,9 +19,4 @@ download_dep_fail = True # can't use pip because version included with Python is too old use_pip = False -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb index b4b1a602309..65a54889b15 100644 --- a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb @@ -4,13 +4,12 @@ name = 'dask' version = '0.8.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6e936a59e1bed9e3e98d43b86052549bba2e7fcee134f9914e79dd063754e471'] @@ -19,9 +18,4 @@ dependencies = [('Python', '3.5.1')] download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb index 2a73f7da31b..3a20da198f1 100644 --- a/easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'dask' version = '1.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -20,64 +20,48 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), ('HeapDict', version, { - 'source_urls': ['https://pypi.python.org/packages/source/h/HeapDict'], 'checksums': ['40c9e3680616cfdf942f77429a3a9e0a76f31ce965d62f4ffbe63a83a5ef1b5a'], }), ('zict', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], 'checksums': ['63377f063086fc92e5c16e4d02162c571f6470b9e796cf3411ef9e815c96b799'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('tblib', '1.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], 'checksums': ['436e4200e63d92316551179dc540906652878df4ff39b43db30fcf6400444fe7'], }), ('sortedcontainers', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], }), ('psutil', '5.4.8', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['6e265c8f3da00b015d24b842bfeb111f856b13d24f2c57036582568dc650d6c3'], }), ('msgpack-python', '0.5.6', { 'modulename': 'msgpack', - 'source_urls': ['https://pypi.python.org/packages/source/s/msgpack-python'], 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], }), ('msgpack', '0.5.6', { - 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'], 'checksums': ['0ee8c8c85aa651be3aa0cd005b5931769eaa658c948ce79428766f1bd46ae2c3'], }), ('cloudpickle', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], 'checksums': ['f169a8523a40eb0a3452e1878aac31da6759409fbafa51dd50d89d4a6b42bcf1'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['a1fa4a3b2d7ce4dd0c68db4b68dadf2c283ff54d98bd72c556fc462000449ff7'], }), ('distributed', '1.25.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], 'checksums': ['7d892c7aeb28ba4903eef6735851e7c6e20baeb6a4b4c159c27cae53f4b8064e'], }), - ('docrep', '0.2.5', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docrep'], - }), + ('docrep', '0.2.5'), ('dask-jobqueue', '0.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask-jobqueue'], - 'modulename': 'dask_jobqueue', + 'modulename': 'dask_jobqueue' }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb index 7c031f4e0d4..e7ac0335d8e 100644 --- a/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'dask' version = '1.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -20,63 +20,47 @@ use_pip = True exts_list = [ ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), ('HeapDict', version, { - 'source_urls': ['https://pypi.python.org/packages/source/h/HeapDict'], 'checksums': ['40c9e3680616cfdf942f77429a3a9e0a76f31ce965d62f4ffbe63a83a5ef1b5a'], }), ('zict', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], 'checksums': ['63377f063086fc92e5c16e4d02162c571f6470b9e796cf3411ef9e815c96b799'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('tblib', '1.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], 'checksums': ['436e4200e63d92316551179dc540906652878df4ff39b43db30fcf6400444fe7'], }), ('sortedcontainers', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], }), ('psutil', '5.4.8', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['6e265c8f3da00b015d24b842bfeb111f856b13d24f2c57036582568dc650d6c3'], }), ('msgpack-python', '0.5.6', { 'modulename': 'msgpack', - 'source_urls': ['https://pypi.python.org/packages/source/s/msgpack-python'], 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], }), ('msgpack', '0.5.6', { - 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'], 'checksums': ['0ee8c8c85aa651be3aa0cd005b5931769eaa658c948ce79428766f1bd46ae2c3'], }), ('cloudpickle', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], 'checksums': ['f169a8523a40eb0a3452e1878aac31da6759409fbafa51dd50d89d4a6b42bcf1'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['a1fa4a3b2d7ce4dd0c68db4b68dadf2c283ff54d98bd72c556fc462000449ff7'], }), ('distributed', '1.25.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], 'checksums': ['7d892c7aeb28ba4903eef6735851e7c6e20baeb6a4b4c159c27cae53f4b8064e'], }), - ('docrep', '0.2.5', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docrep'], - }), + ('docrep', '0.2.5'), ('dask-jobqueue', '0.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask-jobqueue'], 'modulename': 'dask_jobqueue', }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/d/dask/dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb index 29a5a9da8b9..e232bf05604 100644 --- a/easybuild/easyconfigs/d/dask/dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/d/dask/dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'dask' version = '1.1.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/dask/dask/' +homepage = 'https://github.com/dask/dask/' description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.""" @@ -19,69 +19,53 @@ use_pip = True exts_list = [ ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('futures', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], 'modulename': 'concurrent.futures', }), ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), ('HeapDict', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/h/HeapDict'], 'checksums': ['40c9e3680616cfdf942f77429a3a9e0a76f31ce965d62f4ffbe63a83a5ef1b5a'], }), ('zict', '0.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], 'checksums': ['a7838b2f21bc06b7e3db5c64ffa6642255a5f7c01841660b3388a9840e101f99'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('tblib', '1.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], 'checksums': ['436e4200e63d92316551179dc540906652878df4ff39b43db30fcf6400444fe7'], }), ('sortedcontainers', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], }), ('psutil', '5.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], }), ('msgpack-python', '0.5.6', { 'modulename': 'msgpack', - 'source_urls': ['https://pypi.python.org/packages/source/s/msgpack-python'], 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], }), ('msgpack', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'], 'checksums': ['4008c72f5ef2b7936447dcb83db41d97e9791c83221be13d5e19db0796df1972'], }), ('cloudpickle', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], 'checksums': ['3ea6fd33b7521855a97819b3d645f92d51c8763d3ab5df35197cd8e96c19ba6f'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], 'checksums': ['7e9a3c053d8f503483d7357d5b8486c70250c4975b08b3d29f91ab7fc97736c3'], }), ('distributed', '1.26.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], 'checksums': ['b9ffc4c28eb7a6639b15fbb84cea847693b6f9ce7e71f3e2a3e3272467b5b0b8'], }), ] diff --git a/easybuild/easyconfigs/d/dask/dask-2.3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/d/dask/dask-2.3.0-foss-2019a-Python-3.7.2.eb index d20b11e1e4f..d8a59341019 100644 --- a/easybuild/easyconfigs/d/dask/dask-2.3.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/d/dask/dask-2.3.0-foss-2019a-Python-3.7.2.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('fsspec', '0.4.1', { 'checksums': ['e37d78590e7a9adb5b165c9c5d1b650f08017173b40eb1efbdc02d6bdb0c753b'], diff --git a/easybuild/easyconfigs/d/dask/dask-2.8.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/dask/dask-2.8.0-foss-2019b-Python-3.7.4.eb index 0b9566bb78a..fccf7f5f130 100644 --- a/easybuild/easyconfigs/d/dask/dask-2.8.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/dask/dask-2.8.0-foss-2019b-Python-3.7.4.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('fsspec', '0.6.0', { 'checksums': ['5108f9192b7b2c6a03e69d5084d5fc88c05d4312724a38efce37c9f3a6d360fa'], diff --git a/easybuild/easyconfigs/d/dask/dask-2.8.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/dask/dask-2.8.0-fosscuda-2019b-Python-3.7.4.eb index 2b841e88aa9..0320d92838b 100644 --- a/easybuild/easyconfigs/d/dask/dask-2.8.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/dask/dask-2.8.0-fosscuda-2019b-Python-3.7.4.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('fsspec', '0.6.0', { 'checksums': ['5108f9192b7b2c6a03e69d5084d5fc88c05d4312724a38efce37c9f3a6d360fa'], diff --git a/easybuild/easyconfigs/d/dask/dask-2.8.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/dask/dask-2.8.0-intel-2019b-Python-3.7.4.eb index 20a80482a56..52e659f7bf4 100644 --- a/easybuild/easyconfigs/d/dask/dask-2.8.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/dask/dask-2.8.0-intel-2019b-Python-3.7.4.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('fsspec', '0.6.0', { 'checksums': ['5108f9192b7b2c6a03e69d5084d5fc88c05d4312724a38efce37c9f3a6d360fa'], diff --git a/easybuild/easyconfigs/d/datamash/datamash-1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/datamash/datamash-1.5-GCCcore-10.2.0.eb new file mode 100755 index 00000000000..cfb866c453c --- /dev/null +++ b/easybuild/easyconfigs/d/datamash/datamash-1.5-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'datamash' +version = '1.5' + +homepage = 'https://www.gnu.org/software/datamash/' +description = "GNU datamash performs basic numeric, textual and statistical operations on input data files" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['226249d5fe54024f96404798778f45963a3041714229d4225cd5d9acdaba21ad'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/datamash'], + 'dirs': ['share/man'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb index f639521510b..c9fa8723a08 100644 --- a/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb @@ -10,14 +10,8 @@ description = """DEAP is a novel evolutionary computation framework for rapid pr toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.12')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-2.5.4-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/d/deepTools/deepTools-2.5.4-intel-2017b-Python-3.6.3.eb index 6fe404ffe07..456b852ee5b 100755 --- a/easybuild/easyconfigs/d/deepTools/deepTools-2.5.4-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/d/deepTools/deepTools-2.5.4-intel-2017b-Python-3.6.3.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'deepTools' version = '2.5.4' @@ -16,21 +16,15 @@ dependencies = [ ('matplotlib', '2.1.1', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ ('py2bit', '0.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py2bit'], 'checksums': ['8bf068f250b18144cf31984f7325424abc315082c1d18bf526ae424966a56249'], }), ('pyBigWig', '0.3.9', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyBigWig'], 'modulename': 'pyBigWig', 'checksums': ['34306213414a8d8974c4ffaac153b3d0a67ce0183514a93aede6c3d33b6f7947'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/deepTools'], 'checksums': ['327600d3b2c75c5095d6e5192ea162e52c2526f2a04ff296f3d946ef7cabbd28'], }), ] @@ -44,6 +38,4 @@ sanity_check_paths = { sanity_check_commands = ["python -c 'import deeptools'"] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-foss-2018b-Python-3.6.6.eb index 96f7f99ff0d..c10f645b09a 100755 --- a/easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-foss-2018b-Python-3.6.6.eb @@ -20,20 +20,16 @@ use_pip = True exts_list = [ ('py2bit', '0.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py2bit'], 'checksums': ['450555c40cba66957ac8c9a4b6afb625fb34c4bb41638de78c87661ff8b682ef'], }), ('pyBigWig', '0.3.17', { 'modulename': 'pyBigWig', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyBigWig'], 'checksums': ['41f64f802689ed72e15296a21a4b7abd3904780b2e4f8146fd29098fc836fd94'], }), ('deeptoolsintervals', '0.1.9', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deeptoolsintervals'], 'checksums': ['7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/deepTools'], 'checksums': ['514240f97e58bcfbf8c8b69ae9071d26569b491f089e1c1c46ba4866d335e322'], }), ] diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-intel-2019b-Python-3.7.4.eb index ce3518f3fcf..73a3d02afcd 100755 --- a/easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-intel-2019b-Python-3.7.4.eb @@ -17,8 +17,6 @@ dependencies = [ ('plotly.py', '4.4.1'), ] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-foss-2018b-Python-3.6.6.eb index 8780f5f56e1..0c68212527c 100644 --- a/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-foss-2018b-Python-3.6.6.eb @@ -15,11 +15,9 @@ use_pip = True exts_list = [ ('jsonpickle', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpickle/'], 'checksums': ['d43ede55b3d9b5524a8e11566ea0b11c9c8109116ef6a509a1b619d2041e7397'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/deepdiff/'], 'checksums': ['ecad8e16a96ffd27e8f40c9801a6ab16ec6a7e7e6e6859a7710ba4695f22702c'], }), ] diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-2.7.15.eb index aad14be90f9..6c9a95f7e96 100644 --- a/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-2.7.15.eb @@ -15,11 +15,9 @@ use_pip = True exts_list = [ ('jsonpickle', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpickle/'], 'checksums': ['d43ede55b3d9b5524a8e11566ea0b11c9c8109116ef6a509a1b619d2041e7397'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/deepdiff/'], 'checksums': ['ecad8e16a96ffd27e8f40c9801a6ab16ec6a7e7e6e6859a7710ba4695f22702c'], }), ] diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-3.6.6.eb index e89c0c39417..c4e4a8206bc 100644 --- a/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-3.6.6.eb @@ -15,11 +15,9 @@ use_pip = True exts_list = [ ('jsonpickle', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpickle/'], 'checksums': ['d43ede55b3d9b5524a8e11566ea0b11c9c8109116ef6a509a1b619d2041e7397'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/deepdiff/'], 'checksums': ['ecad8e16a96ffd27e8f40c9801a6ab16ec6a7e7e6e6859a7710ba4695f22702c'], }), ] diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-4.0.6-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-4.0.6-GCCcore-8.2.0-Python-3.7.2.eb index 78560569fa2..ed8173e83ab 100644 --- a/easybuild/easyconfigs/d/deepdiff/deepdiff-4.0.6-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-4.0.6-GCCcore-8.2.0-Python-3.7.2.eb @@ -14,8 +14,6 @@ dependencies = [('Python', '3.7.2')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('jsonpickle', '1.1', { 'checksums': ['625098cc8e5854b8c23b587aec33bc8e33e0e597636bfaca76152249c78fe5c1'], diff --git a/easybuild/easyconfigs/d/dijitso/dijitso-2019.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/dijitso/dijitso-2019.1.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..f8258dc5c56 --- /dev/null +++ b/easybuild/easyconfigs/d/dijitso/dijitso-2019.1.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'dijitso' +version = '2019.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/fenics-project/dijitso' +description = "dijitso is a Python module for distributed just-in-time shared library building." + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://bitbucket.org/fenics-project/dijitso/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['eaa45eec4457f3f865d72a926b7cba86df089410e78de04cd89b15bb405e8fd9'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/dijitso'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dijitso --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.0-GCCcore-8.2.0.eb index 2cff665bda2..78f6d669823 100644 --- a/easybuild/easyconfigs/d/dill/dill-0.3.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/d/dill/dill-0.3.0-GCCcore-8.2.0.eb @@ -11,7 +11,6 @@ description = """dill extends python's pickle module for serializing and de-seri toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['993409439ebf7f7902d9de93eaa2a395e0446ff773d29f13dc46646482f76906'] diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..77d9fa7b00a --- /dev/null +++ b/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'dill' +version = '0.3.4' + +homepage = 'https://pypi.org/project/dill/' +description = """dill extends python's pickle module for serializing and de-serializing python objects to the majority + of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse + of which is converting a byte stream back to on python object hierarchy.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_ZIP] +checksums = ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-2.7.12.eb index 5ba4ae87abc..bed279adb88 100644 --- a/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'distributed' version = '1.14.3' @@ -10,48 +10,28 @@ description = """Dask.distributed is a lightweight library for distributed compu toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ('dask', '0.12.0', versionsuffix), ] exts_list = [ - ('zict', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], - }), + ('zict', '0.1.0'), ('HeapDict', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/H/HeapDict'], 'modulename': 'heapdict', }), - ('tornado', '4.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], - }), - ('tblib', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], - }), + ('tornado', '4.4.2'), + ('tblib', '1.3.0'), ('psutil', '5.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'source_tmpl': 'psutil-%(version)s.zip', }), ('msgpack-python', '0.4.8', { - 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack-python'], 'modulename': 'msgpack', }), - ('locket', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/l/locket'], - }), - ('cloudpickle', '0.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], - }), - ('click', '6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], - }), + ('locket', '0.2.0'), + ('cloudpickle', '0.2.1'), + ('click', '6.6'), + (name, version), ] sanity_check_paths = { @@ -60,6 +40,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-3.5.2.eb index 914c58bac94..917eb7b5e6a 100644 --- a/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-3.5.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'distributed' version = '1.14.3' @@ -10,48 +10,28 @@ description = """Dask.distributed is a lightweight library for distributed compu toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.5.2'), ('dask', '0.12.0', versionsuffix), ] exts_list = [ - ('zict', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], - }), + ('zict', '0.1.0'), ('HeapDict', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/H/HeapDict'], 'modulename': 'heapdict', }), - ('tornado', '4.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], - }), - ('tblib', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], - }), + ('tornado', '4.4.2'), + ('tblib', '1.3.0'), ('psutil', '5.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'source_tmpl': 'psutil-%(version)s.zip', }), ('msgpack-python', '0.4.8', { - 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack-python'], 'modulename': 'msgpack', }), - ('locket', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/l/locket'], - }), - ('cloudpickle', '0.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], - }), - ('click', '6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], - }), + ('locket', '0.2.0'), + ('cloudpickle', '0.2.1'), + ('click', '6.6'), + (name, version), ] sanity_check_paths = { @@ -60,6 +40,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/distributed/distributed-1.21.6-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/d/distributed/distributed-1.21.6-intel-2018a-Python-3.6.4.eb index 0f15db1ddf7..bbf279528a4 100644 --- a/easybuild/easyconfigs/d/distributed/distributed-1.21.6-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/d/distributed/distributed-1.21.6-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'distributed' version = '1.21.6' @@ -10,9 +10,6 @@ description = """Dask.distributed is a lightweight library for distributed compu toolchain = {'name': 'intel', 'version': '2018a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.6.4'), ('dask', '0.17.2', versionsuffix), @@ -20,45 +17,35 @@ dependencies = [ exts_list = [ ('zict', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], 'checksums': ['63377f063086fc92e5c16e4d02162c571f6470b9e796cf3411ef9e815c96b799'], }), ('HeapDict', '1.0.0', { 'modulename': 'heapdict', - 'source_urls': ['https://pypi.python.org/packages/source/H/HeapDict'], 'checksums': ['40c9e3680616cfdf942f77429a3a9e0a76f31ce965d62f4ffbe63a83a5ef1b5a'], }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), ('tblib', '1.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], 'checksums': ['436e4200e63d92316551179dc540906652878df4ff39b43db30fcf6400444fe7'], }), ('psutil', '5.4.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['ebe293be36bb24b95cdefc5131635496e88b17fabbcf1e4bc9b5c01f5e489cfe'], }), ('msgpack-python', '0.5.6', { 'modulename': 'msgpack', - 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack-python'], 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], }), ('locket', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/l/locket'], 'checksums': ['1fee63c1153db602b50154684f5725564e63a0f6d09366a1cb13dffcec179fb4'], }), ('cloudpickle', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], 'checksums': ['b0e63dd89ed5285171a570186751bc9b84493675e99e12789e9a5dc5490ef554'], }), ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], 'checksums': ['f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], 'checksums': ['0fa6057c9b7aa0235ba240e7eb66ffbf5fc9d25a5c4b5cf1169d93bc582b8687'], }), ] @@ -68,6 +55,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dtcwt/dtcwt-0.12.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/d/dtcwt/dtcwt-0.12.0-foss-2018b-Python-2.7.15.eb index 95485b5fc15..fe2e3ca314d 100644 --- a/easybuild/easyconfigs/d/dtcwt/dtcwt-0.12.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/d/dtcwt/dtcwt-0.12.0-foss-2018b-Python-2.7.15.eb @@ -9,7 +9,6 @@ description = "Dual-Tree Complex Wavelet Transform library for Python" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['57213e75d882cd94c8f95aeda985f7afe40dc783fb9e094da8dfda1c581c9956'] diff --git a/easybuild/easyconfigs/d/dtcwt/dtcwt-0.12.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/dtcwt/dtcwt-0.12.0-intel-2019b-Python-3.7.4.eb index eb80043e11e..1218c0e6f4b 100644 --- a/easybuild/easyconfigs/d/dtcwt/dtcwt-0.12.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/dtcwt/dtcwt-0.12.0-intel-2019b-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "Dual-Tree Complex Wavelet Transform library for Python" toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['57213e75d882cd94c8f95aeda985f7afe40dc783fb9e094da8dfda1c581c9956'] diff --git a/easybuild/easyconfigs/d/dxpy/dxpy-0.266.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/d/dxpy/dxpy-0.266.1-intel-2018a-Python-2.7.14.eb index a436f72ddaf..171da7e1bf1 100644 --- a/easybuild/easyconfigs/d/dxpy/dxpy-0.266.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/d/dxpy/dxpy-0.266.1-intel-2018a-Python-2.7.14.eb @@ -18,56 +18,45 @@ use_pip = True exts_list = [ ('xattr', '0.6.4', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xattr'], 'checksums': ['f9dcebc99555634b697fa3dad8ea3047deb389c6f1928d347a0c49277a5c0e9e'], }), ('fusepy', '2.0.2', { 'modulename': 'fuse', 'patches': ['fusepy-2.0.2_fix-libfuse.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/f/fusepy'], 'checksums': [ 'aa5929d5464caed81406481a330dc975d1a95b9a41d0a98f095c7e18fe501bfc', # fusepy-2.0.2.tar.gz '746577897c80658b1871d7b7d54d9e0b2f58f3219fc6304c593bdcad80c86c88', # fusepy-2.0.2_fix-libfuse.patch ], }), ('backports.ssl_match_hostname', '3.5.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname'], 'checksums': ['502ad98707319f4a51fa2ca1c677bd659008d27ded9f6380c79e8932e38dcdf2'], }), ('futures', '3.0.4', { 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], 'checksums': ['19485d83f7bd2151c0aeaf88fbba3ee50dadfb222ffc3b66a344ef4952b782a3'], }), ('psutil', '5.4.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['5b6322b167a5ba0c5463b4d30dfd379cd4ce245a1162ebf8fc7ab5c5ffae4f3b'], }), ('beautifulsoup4', '4.4.1', { 'modulename': 'bs4', - 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], 'checksums': ['87d4013d0625d4789a4f56b8d79a04d5ce6db1152bb65f1d39744f7709a366b4'], }), ('python-magic', '0.4.6', { 'modulename': 'magic', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-magic'], 'checksums': ['903d3d3c676e2b1244892954e2bbbe27871a633385a9bfe81f1a81a7032df2fe'], }), ('websocket_client', '0.53.0', { 'modulename': 'websocket', - 'source_urls': ['https://pypi.python.org/packages/source/w/websocket_client'], 'checksums': ['c42b71b68f9ef151433d6dcc6a7cb98ac72d2ad1e3a74981ca22bc5d9134f166'], }), ('pycparser', '2.19', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser'], 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/d/dxpy'], 'checksums': ['b8f1ec7820da0938f5be7aff53cb8abbc6327eda8d01842006dbe2eb717ab70b'], }), ] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb new file mode 100644 index 00000000000..7d5757ab807 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2021.05.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +checksums = ['aea66a18e87574c7c292e852e45943e16f8bc3839f456635d1d610957840d146'] + +builddependencies = [ + ('Autotools', '20210128'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.9.5'), +] + +preconfigopts = './autogen.sh && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb new file mode 100644 index 00000000000..fcca817c0ea --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2021.05.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +checksums = ['aea66a18e87574c7c292e852e45943e16f8bc3839f456635d1d610957840d146'] + +builddependencies = [ + ('Autotools', '20210128'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.9.5'), +] + +preconfigopts = './autogen.sh && ' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb new file mode 100644 index 00000000000..eaf6f22dc12 --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb @@ -0,0 +1,64 @@ +# authors: Kenneth Hoste (Ghent University) +# George Tsouloupas +# Fotis Georgatos +# +# This work implements a part of the HPCBIOS project and is a component +# of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute +# +# Updated: Pavel Grochal (INUITS) +# +easyblock = 'ConfigureMake' + +name = 'EMBOSS' +version = '6.6.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://emboss.sourceforge.net/' +description = """EMBOSS is 'The European Molecular Biology Open Software Suite' +. EMBOSS is a free Open Source software analysis package specially developed + for the needs of the molecular biology (e.g. EMBnet) user community.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'kimrutherford' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_disable-embossupdate.patch'] +checksums = [ + ( + '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', + '85f53a19125735e4a49fc25620d507fd86bf189e49096578924fe04893f2f7a9', + ), + # EMBOSS-6.6.0.tar.gz + '7e0a7deffd76f60093be9c5253605f2d6d2e3b0c2d3c9365035cc6bda43eb46c', # EMBOSS-6.6.0_disable-embossupdate.patch +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('X11', '20201008'), + ('libharu', '2.3.0'), + ('Java', '13', '', True), +] + +configopts = " --with-hpdf=$EBROOTLIBHARU " + +# jemboss.jar does not build in a parallel build +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', + 'epcre', 'eplplot', 'ezlib', 'nucleus']] + + ['share/EMBOSS/jemboss/lib/jemboss.jar'], + 'dirs': [], +} +sanity_check_commands = [ + 'embossdata -h' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index 7633004625b..ae781439f40 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -39,7 +39,7 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } @@ -49,41 +49,32 @@ exts_list = [ # Python deps, order is important! ('olefile', '0.45.1', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/o/olefile/'], 'checksums': ['2b6575f5290de8ab1086f8c5490591f7e0885af682c7c1793bdaf6e64078d385'], }), ('Pillow', '4.3.0', { 'modulename': 'PIL', - 'source_urls': ['https://pypi.python.org/packages/source/p/Pillow/'], 'checksums': ['a97c715d44efd5b4aa8d739b8fad88b93ed79f1b33fc2822d5802043f3b1b527'], }), ('pyproj', '1.9.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyproj/'], 'checksums': ['53fa54c8fa8a1dfcd6af4bf09ce1aae5d4d949da63b90570ac5ec849efaf3ea8'], }), ('pyshp', '1.2.12', { 'modulename': 'shapefile', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyshp/'], 'checksums': ['8dcd65e0aa2aa2951527ddb7339ea6e69023543d8a20a73fc51e2829b9ed6179'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('OWSLib', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/o/OWSLib/'], 'checksums': ['ec95a5e93c145a5d84b0074b9ea27570943486552a669151140debf08a100554'], }), ('basemap', '1.1.0', { @@ -98,27 +89,21 @@ exts_list = [ }), ('netCDF4', '1.3.1', { 'modulename': 'netCDF4', - 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4/'], 'checksums': ['570ea59992aa6d98a9b672c71161d11ba5683f787da53446086077470a869957'], }), ('geoval', '0.1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/g/geoval/'], 'checksums': ['7da4a1879f78bb7aac2d41b5c1ee360ff74087bf857c81c532deb8cc31feb36e'], }), ('cdo', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cdo/'], 'checksums': ['b167efbbac7d0a6cbf74f5d211255705c73245f7c2590b6d9eb634347d8b2c1f'], }), ('Shapely', '1.6.4.post1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Shapely/'], 'checksums': ['30df7572d311514802df8dc0e229d1660bc4cbdcf027a8281e79c5fc2fcf02f2'], }), ('Cartopy', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/Cartopy/'], 'checksums': ['f23dffa101f43dd91e866a49ebb5f5048be2a24ab8a921a5c07edabde746d9a4'], }), ('dask', '0.17.4', { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask/'], 'checksums': ['c111475a3d1f8cba41c8094e1fb1831c65015390dcef0308042a11a9606a2f6d'], }), ('PyKE', '1.1.1', { @@ -127,11 +112,9 @@ exts_list = [ 'checksums': ['b0b294f435c6e6d2d4a80badf57d92cb66814dfe21e644a521901209e6a3f8ae'], }), ('cf_units', '1.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cf_units/'], 'checksums': ['abdd2a0937b958322f7ff7ec6866e80f08603c60aa06cef5766b6512c750028a'], }), ('pyugrid', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyugrid/'], 'checksums': ['eddadc1e88c0e801f780b1e6f636fbfc00e3d14cdab82b43300fde0918310053'], }), ('mo_pack', '0.2.0', { @@ -140,27 +123,21 @@ exts_list = [ 'checksums': ['4aa70e1f846b666670843bc2514435dedf7393203e88abaf74d48f8f2717a726'], }), ('cycler', '0.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('tornado', '4.5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['6d14e47eab0e15799cf3cdcc86b0b98279da68522caace2bd7ce644287685f0a'], }), ('matplotlib', '1.5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], 'checksums': ['a0a5dc39f785014f2088fed2c6d2d129f0444f71afbb9c44f7bdf1b14d86ebbc'], }), ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz/'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), ('scitools-iris', '2.0.0', { @@ -176,20 +153,16 @@ exts_list = [ 'checksums': ['c2e92d25d8bfd2ddff22ae47c4532c884678bac6ea0d935367eced051ae08bb3'], }), ('patsy', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy/'], 'checksums': ['e05f38d5c38c8d216f0cc2b765b1069b433c92d628b954fb2fee68d13e42883b'], }), ('statsmodels', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels/'], 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], }), ('cftime', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cftime/'], 'checksums': ['f62fe79ed2ad38f4211477e59f6f045c91278351f4ce7578e33ddf52fb121ea8'], }), ('nc-time-axis', '1.1.0', { 'modulename': 'nc_time_axis', - 'source_urls': ['https://pypi.python.org/packages/source/n/nc-time-axis/'], 'checksums': ['ea9d4f7f9e9189c96f7d320235ac6c4be7f63dc5aa256b3ee5d5cca5845e6e26'], }), # R extension diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.0.eb new file mode 100644 index 00000000000..e3711e34964 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.0.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.4.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/24/d8/e6ff16377875551c1c5f0cdbb72e59ba30e77745910b0d222359fba83397/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/fd/1f/c9f1022fa34b3316af75d8f92e08304a141dfc762ed7523f6dacf1ded16b/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/c2/73/c5b6b8b09d4efc01c5e0ddbe6accdb1aba2edd224e85f47bcf83862b45c1/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '3d3339df5a74e60639beb6cfe9f21f822f497738d5eab4d265fd5fa6af3c3c2f', # easybuild-framework-4.4.0.tar.gz + 'd35b63bfa5fe2b877ae82295fbadbd9b49ada3720c16d12cb0daa7da5d3d405b', # easybuild-easyblocks-4.4.0.tar.gz + '4a0b384e9eac19e61c60114e008c23da04d4aa1d52416e75c184f710292c41d0', # easybuild-easyconfigs-4.4.0.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/EnsEMBLCoreAPI/EnsEMBLCoreAPI-96.0-r20190601-foss-2019a-Perl-5.28.1.eb b/easybuild/easyconfigs/e/EnsEMBLCoreAPI/EnsEMBLCoreAPI-96.0-r20190601-foss-2019a-Perl-5.28.1.eb index faa347d727c..cd3c9251a4b 100644 --- a/easybuild/easyconfigs/e/EnsEMBLCoreAPI/EnsEMBLCoreAPI-96.0-r20190601-foss-2019a-Perl-5.28.1.eb +++ b/easybuild/easyconfigs/e/EnsEMBLCoreAPI/EnsEMBLCoreAPI-96.0-r20190601-foss-2019a-Perl-5.28.1.eb @@ -151,7 +151,6 @@ exts_list = [ 'checksums': ['bf6fdddc8fcc901c78adcfb61f56c393cd64d73ab320195ebae9e4a82976eab6'], }), ('Sereal', '4.007', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/Y/YV/YVES'], 'checksums': ['450e43072e8e5afc0402f81008ca9f1d3d8d4377ff8105cff10aef96be769a59'], }), diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..39bd4527161 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [('GLib', '2.66.1')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/earthengine-api/earthengine-api-0.1.143-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/e/earthengine-api/earthengine-api-0.1.143-intel-2018a-Python-2.7.14.eb index 186ce8f94c8..3ac92bfd89d 100644 --- a/easybuild/easyconfigs/e/earthengine-api/earthengine-api-0.1.143-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/earthengine-api/earthengine-api-0.1.143-intel-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'earthengine-api' version = '0.1.143' @@ -11,72 +11,53 @@ toolchain = {'name': 'intel', 'version': '2018a'} dependencies = [('Python', '2.7.14')] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - # let sanity check fail when auto-downloaded dependencies are detected when installing extensions -exts_download_dep_fail = True - exts_list = [ ('rsa', '3.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/r/rsa/'], 'checksums': ['25df4e10c263fb88b5ace923dd84bf9aa7f5019687b5e55382ffcdb8bede9db5'], }), ('pyasn1-modules', '0.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1-modules/'], 'checksums': ['a0cf3e1842e7c60fde97cb22d275eb6f9524f5c5250489e292529de841417547'], 'modulename': 'pyasn1_modules', }), ('httplib2', '0.11.3', { - 'source_urls': ['https://pypi.python.org/packages/source/h/httplib2/'], 'checksums': ['e71daed9a0e6373642db61166fa70beecc9bf04383477f84671348c02a04cbdf'], }), ('oauth2client', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/o/oauth2client/'], 'checksums': ['bd3062c06f8b10c6ef7a890b22c2740e5f87d61b6e1f4b1c90d069cdfc9dadb5'], }), ('cryptography', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('pyOpenSSL', '18.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyOpenSSL/'], 'checksums': ['6488f1423b00f73b7ad5167885312bb0ce410d3312eb212393795b53c8caa580'], 'modulename': 'OpenSSL', }), ('uritemplate', '3.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/u/uritemplate/'], 'checksums': ['c02643cebe23fc8adb5e6becffe201185bf06c40bda5c0b4028a93f1527d011d'], }), ('cachetools', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cachetools/'], 'checksums': ['90f1d559512fc073483fe573ef5ceb39bf6ad3d39edc98dc55178a2b2b176fa3'], }), ('google-auth', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/google-auth/'], 'checksums': ['1745c9066f698eac3da99cef082914495fb71bc09597ba7626efbbb64c4acc57'], 'modulename': 'google.auth', }), ('google-auth-httplib2', '0.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/g/google-auth-httplib2/'], 'checksums': ['098fade613c25b4527b2c08fa42d11f3c2037dda8995d86de0745228e965d445'], 'modulename': 'google_auth_httplib2', }), ('google-api-python-client', '1.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/g/google-api-python-client/'], 'checksums': ['e32d30563b90c4f88ff042d4d891b5e8ed1f6cdca0adab95e9c2ce2603087436'], 'modulename': 'googleapiclient', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/e/earthengine-api/'], 'checksums': ['fe0c192c91f97d1a4426709dcfb968a963c90019c07e88df12e54d8a93d5bcaf'], 'modulename': 'ee', }), diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-GCC-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-GCC-8.3.0-Python-3.7.4.eb index 84cba4bf94a..0f698ce4daa 100644 --- a/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-GCC-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-GCC-8.3.0-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "Lightweight, super fast library for sequence alignment using edit toolchain = {'name': 'GCC', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['81bc688e8fc69d657a6b5067e104a0924b0217b7ab54547155278935d09346e0'] diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-iccifort-2019.5.281-Python-3.7.4.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-iccifort-2019.5.281-Python-3.7.4.eb index e3737f126dc..a608a677bd9 100644 --- a/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-iccifort-2019.5.281-Python-3.7.4.eb +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-iccifort-2019.5.281-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "Lightweight, super fast library for sequence alignment using edit toolchain = {'name': 'iccifort', 'version': '2019.5.281'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['81bc688e8fc69d657a6b5067e104a0924b0217b7ab54547155278935d09346e0'] diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post2-iccifort-2020.1.217-Python-3.8.2.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post2-iccifort-2020.1.217-Python-3.8.2.eb index 32cb2e5e507..34a3f0eb26a 100644 --- a/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post2-iccifort-2020.1.217-Python-3.8.2.eb +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post2-iccifort-2020.1.217-Python-3.8.2.eb @@ -9,7 +9,6 @@ description = "Lightweight, super fast library for sequence alignment using edit toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['58c08103174a39cacc0cc01eee93a433b4382fbe85146a627986570d3b2ab79b'] diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb new file mode 100644 index 00000000000..536eecf0032 --- /dev/null +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb @@ -0,0 +1,56 @@ +# Eggnog DB installation instructions: +# 1. 'export EGGNOG_DATA_DIR=//eggnog-mapper-data' +# 2. run 'download_eggnog_data.py' +# 3. Check the expected DB version with 'emapper.py --version' + +easyblock = 'PythonPackage' + +name = 'eggnog-mapper' +version = '2.1.4' + +homepage = 'https://github.com/eggnogdb/eggnog-mapper' +description = """EggNOG-mapper is a tool for fast functional annotation of novel +sequences. It uses precomputed orthologous groups and phylogenies from the +eggNOG database (http://eggnog5.embl.de) to transfer functional information from +fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation +of novel genomes, transcriptomes or even metagenomic gene catalogs.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'eggnogdb' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['c131043eb3cf5c8f32a4f088dabcbe0eae8fbb3680c2a6ac997c3bcd2fa5f0f2'] + +dependencies = [ + ('Python', '3.8.6'), + ('Biopython', '1.78'), + ('HMMER', '3.3.2'), + ('DIAMOND', '2.0.7'), + ('prodigal', '2.6.3'), + ('wget', '1.20.3'), + ('MMseqs2', '13-45111'), + ('XlsxWriter', '1.4.0'), +] + +# strip out (too) strict version requirements for dependencies +preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/create_dbs.py', 'bin/download_eggnog_data.py', 'bin/emapper.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'download_eggnog_data.py --help', + 'create_dbs.py --help', + 'emapper.py --version | grep %(version)s', +] + +options = {'modulename': 'eggnogmapper'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.182-GCCcore-9.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.182-GCCcore-9.3.0.eb index 5a24eed75b7..4a282ada13a 100644 --- a/easybuild/easyconfigs/e/elfutils/elfutils-0.182-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.182-GCCcore-9.3.0.eb @@ -25,14 +25,13 @@ builddependencies = [ dependencies = [ ('binutils', '2.34'), ('bzip2', '1.0.8'), - ('cURL', '7.69.1'), ('libarchive', '3.4.2'), - ('libmicrohttpd', '0.9.71'), - ('SQLite', '3.31.1'), ('XZ', '5.2.5'), ('zstd', '1.4.4'), ] +configopts = "--disable-debuginfod --disable-libdebuginfod" + sanity_check_paths = { 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.so'], 'dirs': [] diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb index f0b29a4ce55..e51ac2c8641 100644 --- a/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb @@ -26,14 +26,13 @@ builddependencies = [ dependencies = [ ('binutils', '2.35'), ('bzip2', '1.0.8'), - ('cURL', '7.72.0'), ('libarchive', '3.4.3'), - ('libmicrohttpd', '0.9.73'), - ('SQLite', '3.33.0'), ('XZ', '5.2.5'), ('zstd', '1.4.5'), ] +configopts = "--disable-debuginfod --disable-libdebuginfod" + sanity_check_paths = { 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.so'], 'dirs': [] diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-10.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..7b641a05b2b --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-10.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.185' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['dc8d3e74ab209465e7f568e1b3bb9a5a142f8656e2b57d10049a73da2ae6b5a6'] + +builddependencies = [ + ('M4', '1.4.18'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('binutils', '2.36.1'), + ('bzip2', '1.0.8'), + ('libarchive', '3.5.1'), + ('XZ', '5.2.5'), + ('zstd', '1.4.9'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-8.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..005327328a4 --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-8.2.0.eb @@ -0,0 +1,43 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.185' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['dc8d3e74ab209465e7f568e1b3bb9a5a142f8656e2b57d10049a73da2ae6b5a6'] + +builddependencies = [ + ('M4', '1.4.18'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('binutils', '2.31.1'), + ('bzip2', '1.0.6'), + ('libarchive', '3.4.0'), + ('XZ', '5.2.4'), + ('zstd', '1.4.0'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-8.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..b7aad84465e --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-8.3.0.eb @@ -0,0 +1,43 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.185' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['dc8d3e74ab209465e7f568e1b3bb9a5a142f8656e2b57d10049a73da2ae6b5a6'] + +builddependencies = [ + ('M4', '1.4.18'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('binutils', '2.32'), + ('bzip2', '1.0.8'), + ('libarchive', '3.5.1'), + ('XZ', '5.2.4'), + ('zstd', '1.4.4'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb index fc0663e9cbd..fe0b1370391 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb @@ -11,7 +11,6 @@ It's designed for Bayesian parameter estimation and it's really sweet! """ toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'] diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb index 282aafc7937..b02aadb4da7 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb @@ -11,7 +11,6 @@ It's designed for Bayesian parameter estimation and it's really sweet! """ toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'] diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2019a.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2019a.eb index dea7d1cb766..93f20672b46 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2019a.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2019a.eb @@ -10,7 +10,6 @@ It's designed for Bayesian parameter estimation and it's really sweet! """ toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'] diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb index 9e386cfc73b..7de331b5ee2 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb @@ -11,7 +11,6 @@ It's designed for Bayesian parameter estimation and it's really sweet! """ toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'] diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb index 2b5fce09e27..280514c82a8 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb @@ -11,7 +11,6 @@ It's designed for Bayesian parameter estimation and it's really sweet! """ toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'] diff --git a/easybuild/easyconfigs/e/exiv2/exiv2-0.27.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/e/exiv2/exiv2-0.27.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..30c12719807 --- /dev/null +++ b/easybuild/easyconfigs/e/exiv2/exiv2-0.27.4-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'exiv2' +version = '0.27.4' + +homepage = 'https://exiv2.org' +description = "Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://exiv2.org/builds/'] +sources = ['%(name)s-%(version)s-Source.tar.gz'] +checksums = ['84366dba7c162af9a7603bcd6c16f40fe0e9af294ba2fd2f66ffffb9fbec904e'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('expat', '2.2.9'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/exiv2', 'lib/libexiv2.%s' % SHLIB_EXT, 'lib/libexiv2-xmp.a', 'lib/pkgconfig/exiv2.pc'], + 'dirs': ['include/exiv2', 'lib/cmake'], +} + +sanity_check_commands = ["exiv2 --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FALCON/FALCON-1.8.8-intel-2017b.eb b/easybuild/easyconfigs/f/FALCON/FALCON-1.8.8-intel-2017b.eb index 47a119aa912..1080b94926d 100644 --- a/easybuild/easyconfigs/f/FALCON/FALCON-1.8.8-intel-2017b.eb +++ b/easybuild/easyconfigs/f/FALCON/FALCON-1.8.8-intel-2017b.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'FALCON' # version is taken from https://github.com/PacificBiosciences/FALCON-integrate/releases @@ -75,12 +75,8 @@ components = [ }), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ ('networkx', '1.10', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['ced4095ab83b7451cec1172183eff419ed32e21397ea4e1971d92a5808ed6fb8'], }), ('pypeFLOW', '20170504', { @@ -119,6 +115,4 @@ sanity_check_commands = [ "cd %(builddir)s/FALCON-examples* && make -C run/synth0 test", ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FALCON/FALCON-1.8.8-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/f/FALCON/FALCON-1.8.8-intel-2019b-Python-2.7.16.eb index 1a8ba6bca64..3e8dd7255f9 100644 --- a/easybuild/easyconfigs/f/FALCON/FALCON-1.8.8-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/f/FALCON/FALCON-1.8.8-intel-2019b-Python-2.7.16.eb @@ -83,7 +83,6 @@ components = [ exts_list = [ ('networkx', '1.10', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['ced4095ab83b7451cec1172183eff419ed32e21397ea4e1971d92a5808ed6fb8'], }), ('pypeFLOW', '20170504', { diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.7.6-intel-2020b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.7.6-intel-2020b.eb new file mode 100644 index 00000000000..9b15ca6c7bf --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.7.6-intel-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.7.6' + +homepage = 'https://pages.nist.gov/fds-smv' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['FDS%(version)s.tar.gz'] +checksums = ['33432cc31d9f75d3904c2b89f197016bb5c73d6b108878d804ebf055d3cafdc1'] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +buildopts = 'impi_intel_linux_64 FFLAGS="$FFLAGS -fpp" FCOMPL="$FC" obj=fds' + +modextrapaths = {'PATH': 'Build'} + +sanity_check_paths = { + 'files': ['Build/fds'], + 'dirs': [], +} + +sanity_check_commands = [ + "fds 2>&1 | grep 'MPI Enabled;'", + "fds 2>&1 | grep 'OpenMP Enabled;'", +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FEniCS/FEniCS-2019.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FEniCS/FEniCS-2019.1.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..0bdebfafe97 --- /dev/null +++ b/easybuild/easyconfigs/f/FEniCS/FEniCS-2019.1.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,20 @@ +easyblock = 'Bundle' + +name = 'FEniCS' +version = '2019.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://fenicsproject.org/' +description = "FEniCS is a computing platform for solving partial differential equations (PDEs)." + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), + ('DOLFIN', '2019.1.0.post0', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FFC/FFC-2019.1.0.post0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FFC/FFC-2019.1.0.post0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..0417e381220 --- /dev/null +++ b/easybuild/easyconfigs/f/FFC/FFC-2019.1.0.post0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'FFC' +version = '2019.1.0.post0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/fenics-project/ffc' +description = "The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms." + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://bitbucket.org/fenics-project/ffc/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['306e1179630200a34202975a5369194939b3482eebfc34bc44ad74dab1f109e8'] + +dependencies = [ + ('Python', '3.7.4'), + ('UFL', '2019.1.0', versionsuffix), + ('FIAT', '2019.1.0', versionsuffix), + ('dijitso', '2019.1.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/ffc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["ffc --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.9-intel-2021a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.9-intel-2021a.eb new file mode 100644 index 00000000000..43ab2c8719c --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.9-intel-2021a.eb @@ -0,0 +1,26 @@ +name = 'FFTW' +version = '3.3.9' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bf2c7ce40b04ae811af714deb512510cc2c17b9ab9d6ddcf49fe4487eea7af3d'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# https://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails on AMD systems when configuring with --enable-avx-128-fma, +# because Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..49875a9e83d --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-10.3.0.eb @@ -0,0 +1,47 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '4.3.2' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://ffmpeg.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ab3a6d6a70358ba0a5f67f37f91f6656b7302b02e98e5b8c846c16763c99913a'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2') +] + +dependencies = [ + ('NASM', '2.15.05'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('x264', '20210414'), + ('LAME', '3.100'), + ('x265', '3.5'), + ('X11', '20210518'), + ('freetype', '2.10.4'), + ('fontconfig', '2.13.93'), + ('FriBidi', '1.0.10'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-2018.1.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/f/FIAT/FIAT-2018.1.0-foss-2018a-Python-3.6.4.eb index 408ee32f81f..4489db26844 100644 --- a/easybuild/easyconfigs/f/FIAT/FIAT-2018.1.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/f/FIAT/FIAT-2018.1.0-foss-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'FIAT' version = '2018.1.0' @@ -13,13 +13,10 @@ toolchain = {'name': 'foss', 'version': '2018a'} dependencies = [('Python', '3.6.4')] -exts_defaultclass = 'PythonPackage' -exts_download_dep_fail = True -exts_default_options = {'use_pip': True} +use_pip = True exts_list = [ ('sympy', '1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sympy/'], 'checksums': ['286ca070d72e250861dea7a21ab44f541cb2341e8268c70264cf8642dbd9225f'], }), (name, version, { @@ -34,11 +31,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-2019.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FIAT/FIAT-2019.1.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..8d72cb9f826 --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-2019.1.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'FIAT' +version = '2019.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/fenics-project/fiat' +description = """The FInite element Automatic Tabulator (FIAT) supports +generation of arbitrary order instances of the Lagrange elements on +lines, triangles, and tetrahedra. It is also capable of generating +arbitrary order instances of Jacobi-type quadrature rules on the same +element shapes.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['341a1046cbe0f5f2eb26630c2f71f378b0dca51daf9892a54a2ff193970371e9'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('sympy', '1.5.1', versionsuffix), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'FIAT'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..fce9fa2557d --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.6-GCCcore-10.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.6' + +homepage = 'https://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-%(version)s_fix-LDFLAGS.patch'] +checksums = [ + '9aac75ef9e9b7bd7b5338a4c0d4dd536e6c22ea7b15ea622aa1d8f1fa30d37ab', # fltk-1.3.6-source.tar.gz + 'f8af2414a1ee193a186b0d98d1e3567add0ee003f44ec64dce2ce2dfd6d95ebf', # FLTK-1.3.6_fix-LDFLAGS.patch +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +builddependencies = [ + ('binutils', '2.36.1') +] + +dependencies = [ + ('Mesa', '21.1.1'), + ('libGLU', '9.0.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('xprop', '1.2.5'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.6_fix-LDFLAGS.patch b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.6_fix-LDFLAGS.patch new file mode 100644 index 00000000000..48822194f04 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.6_fix-LDFLAGS.patch @@ -0,0 +1,14 @@ +pass down $LDFLAGS to make sure libraries (in particular libpng) is picked up from the right location +author: Miguel Dias Costa (National University of Singapore) +updated to 1.3.6: micketeer@gmail.com +--- makeinclude.in.orig 2021-07-02 03:27:44.304515018 +0200 ++++ makeinclude.in 2021-07-02 03:28:28.235425984 +0200 +@@ -91,7 +91,7 @@ + CAIROFLAGS = @CAIROFLAGS@ + DSOFLAGS = -L. @DSOFLAGS@ + LDFLAGS = $(OPTIM) @LDFLAGS@ +-LDLIBS = @LIBS@ ++LDLIBS = @LDFLAGS@ @LIBS@ + GLDLIBS = @GLLIBS@ @LIBS@ + LINKFLTK = @LINKFLTK@ + LINKFLTKGL = @LINKFLTKGL@ diff --git a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb index 8cbaecb343b..4cb227e1d23 100644 --- a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb @@ -31,74 +31,57 @@ use_pip = True exts_list = [ ('versioneer', '0.18', { - 'source_urls': ['https://pypi.python.org/packages/source/v/versioneer'], 'checksums': ['ead1f78168150011189521b479d3a0dd2f55c94f5b07747b484fd693c3fbf335'], }), ('indexed_gzip', '0.8.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/indexed_gzip'], 'checksums': ['4928b5d59e1cfa06d4eb5ac348c5696b380b2828a5a4f4fad9251c8685de66d9'], }), ('patsy', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['e05f38d5c38c8d216f0cc2b765b1069b433c92d628b954fb2fee68d13e42883b'], }), ('statsmodels', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], }), ('svgutils', '0.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/svgutils'], 'checksums': ['29dddbc378f92db74067b9800b6b0294b94c712a632b7140d6dd3d4e66692b74'], }), ('nilearn', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nilearn'], 'checksums': ['5049363eb6da2e7c35589477dfc79bf69929ca66de2d7ed2e9dc07acf78636f4'], }), # sklearn is a dummy module, actual dependency is resolved by scikit-learn stand-alone module... ('sklearn', '0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sklearn'], 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('niworkflows', '0.4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/niworkflows'], 'checksums': ['85d605549d3ef303de6689b84f6ff6d2c5490df9ea6dbdca5c4cbb4c8eef15f6'], }), ('nitime', '0.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nitime'], 'checksums': ['18bac8d62686f884f1ac8b8d4fdb3d644e38a8a6ece76073a576080bafcbc5e9'], }), ('num2words', '0.5.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/num2words'], 'checksums': ['ac4b5971b427611bc565c395e95289ba09b3b1c0fb041ad2538786dde816d664'], }), ('grabbit', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/g/grabbit'], 'checksums': ['96b8ff05a23c61af1321af262fc7b195f116132109f03dfb4f5994558885ea06'], }), ('pybids', '0.6.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pybids'], 'checksums': ['b3850c07af80145744586b6624b244263f46a65cdf078e414a77dba5b72aee7c'], 'modulename': 'bids', }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('duecredit', '0.6.4', { - 'source_urls': ['https://pypi.python.org/packages/source/d/duecredit'], 'checksums': ['f0168f4dd6649d9faa145e1b9e95d9da5f499a55c4f906eb6bb7e7e5213bdbea'], }), (name, version, { 'source_tmpl': 'fmriprep-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/f/fmriprep'], 'checksums': ['1013a59f172aaab60b4a6b016d9ee586b430f89042da879429d325a466f27773'], }), ] diff --git a/easybuild/easyconfigs/f/FSLeyes/FSLeyes-0.15.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FSLeyes/FSLeyes-0.15.0-intel-2017a-Python-2.7.13.eb index e4d7b3236a0..58b5999a778 100644 --- a/easybuild/easyconfigs/f/FSLeyes/FSLeyes-0.15.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/FSLeyes/FSLeyes-0.15.0-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'FSLeyes' version = '0.15.0' @@ -18,17 +18,12 @@ dependencies = [ ('Pillow', '4.3.0', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ ('MarkupSafe', '1.0', { 'modulename': 'markupsafe', - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['ddaa01a212cd6d641401cb01b605f4a4d9f37bfc93043d7f760ec70fb99ff9ff'], }), ('indexed-gzip', '0.6.0', { @@ -39,41 +34,28 @@ exts_list = [ }), ('PyOpenGL-accelerate', '3.1.1a1', { 'modulename': 'OpenGL_accelerate', - 'source_urls': ['https://pypi.python.org/packages/source/P/PyOpenGL-accelerate'], 'checksums': ['3d37af9f2565febf214e1da2a5fe019561992d34026ce2a5f51972e121b84cdd'], }), ('PyOpenGL', '3.1.1a1', { 'modulename': 'OpenGL', - 'source_urls': ['https://pypi.python.org/packages/source/P/PyOpenGL'], 'checksums': ['c96d909b359abe3271b746bacf7e6ba52935141e2406a8f90231e4e44dfa4075'], }), ('fsleyes-widgets', '0.0.6', { 'modulename': 'fsleyes_widgets', - 'source_urls': ['https://pypi.python.org/packages/source/f/fsleyes-widgets'], 'checksums': ['24029ae8b7b5dd917e643dfd8ba8385b28979833b6a977437fc3b0dbe45e3b1f'], }), ('fslpy', '1.2.0', { 'modulename': 'fsl', - 'source_urls': ['https://pypi.python.org/packages/source/f/fslpy'], 'checksums': ['3978c81773823046bfea7eb41aa273a00bbb01faddcc3621974d204ed2fcb8b6'], }), ('fsleyes-props', '1.2.1', { 'modulename': 'fsleyes_props', - 'source_urls': ['https://pypi.python.org/packages/source/f/fsleyes-props'], 'checksums': ['d18f186ede16bb7f96d838ecc8b933e84fb5e99dd3294af70cf727b72d6b0a3a'], }), (name, version, { 'source_tmpl': 'fsleyes-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/f/fsleyes'], 'checksums': ['e1feadd322b8cbd8714f239ebc3246a4317f26079116397f4b555d3aeb29fe02'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FastaIndex/FastaIndex-0.11rc7-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/f/FastaIndex/FastaIndex-0.11rc7-intel-2017b-Python-2.7.14.eb index bcc58e4c078..26a2a8358e8 100644 --- a/easybuild/easyconfigs/f/FastaIndex/FastaIndex-0.11rc7-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/f/FastaIndex/FastaIndex-0.11rc7-intel-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = "FastA index (.fai) handler compatible with samtools faidx" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c130a2146bb178ea4f9d228e0d360787046ab4cb0ab53b5b43711dd57e31aff7'] diff --git a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..d03c231209c --- /dev/null +++ b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'Filtlong' +version = '0.2.0' + +homepage = 'https://github.com/rrwick/Filtlong' +description = """Filtlong is a tool for filtering long reads by quality. It can take a set + of long reads and produce a smaller, better subset. It uses both read length (longer is better) + and read identity (higher is better) when choosing which reads pass the filter""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/rrwick/Filtlong/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a4afb925d7ced8d083be12ca58911bb16d5348754e7c2f6431127138338ee02a'] + +unpack_options = '--strip-components=1' + +parallel = 1 + +dependencies = [ + ('zlib', '1.2.11'), +] + +files_to_copy = ["*"] + +sanity_check_paths = { + 'files': ['bin/filtlong'], + 'dirs': [] +} + +sanity_check_commands = ["filtlong --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-foss-2019b-Python-3.7.4.eb index 2a2663f1ff1..efec904282a 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-foss-2019b-Python-3.7.4.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cligj', '0.5.0', { 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-fosscuda-2019b-Python-3.7.4.eb index b65b571c300..9238db7609a 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-fosscuda-2019b-Python-3.7.4.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cligj', '0.5.0', { 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-intel-2019b-Python-3.7.4.eb index a8f8d15ce0d..5bfa0fa72d0 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-intel-2019b-Python-3.7.4.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cligj', '0.5.0', { 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13.post1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13.post1-foss-2019a-Python-3.7.2.eb index f04bb062142..2492e930356 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13.post1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13.post1-foss-2019a-Python-3.7.2.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cligj', '0.5.0', { 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb index aa5228efe14..7b9a26bb66f 100644 --- a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'FireWorks' version = '1.4.2' @@ -15,40 +15,20 @@ dependencies = [ ('PyYAML', '3.12', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ - ('Flask', '0.12', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], - }), + ('Flask', '0.12'), ('Flask-paginate', '0.4.5', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask-paginate/'], 'source_tmpl': 'flask-paginate-%(version)s.zip', 'modulename': 'flask_paginate', }), - ('Jinja2', '2.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], - }), - ('Werkzeug', '0.12.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug/'], - }), - ('gunicorn', '19.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gunicorn/'], - }), - ('monty', '0.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], - }), - ('pymongo', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pymongo/'], - }), - ('FireWorks', version, { - 'source_urls': ['https://pypi.python.org/packages/source/F/FireWorks/'], - }), + ('Jinja2', '2.9.6'), + ('Werkzeug', '0.12.1'), + ('gunicorn', '19.7.1'), + ('monty', '0.9.6'), + ('pymongo', '3.4.0'), + ('FireWorks', version), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/f/Flask/Flask-1.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/Flask/Flask-1.0.2-foss-2018b-Python-3.6.6.eb index deed4c6a7db..5652f46aec9 100644 --- a/easybuild/easyconfigs/f/Flask/Flask-1.0.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/Flask/Flask-1.0.2-foss-2018b-Python-3.6.6.eb @@ -18,38 +18,26 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/f/flask/'], 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], }), ('Flask-Cors', '3.0.7', { - 'source_urls': ['https://pypi.python.org/packages/source/f/flask-cors/'], 'checksums': ['7e90bf225fdf163d11b84b59fb17594d0580a16b97ab4e1146b1fb2737c1cfec'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-8.3.0-Python-3.7.4.eb index 6e5effb420d..078a0a8d88d 100644 --- a/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-8.3.0-Python-3.7.4.eb @@ -20,19 +20,15 @@ use_pip = True exts_list = [ ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Werkzeug', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/Werkzeug'], 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/f/flask/'], 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], }), ('Flask-Cors', '3.0.8', { - 'source_urls': ['https://pypi.python.org/packages/source/f/flask-cors/'], 'checksums': ['72170423eb4612f0847318afff8c247b38bd516b7737adfc10d1c2cdbb382d16'], }), ] diff --git a/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb index a9546fc1c71..5fba1cae3ae 100644 --- a/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb @@ -23,41 +23,34 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } exts_list = [ ('regex', '2019.04.14', { - 'source_urls': ['https://pypi.python.org/packages/source/r/regex/'], 'checksums': ['d56ce4c7b1a189094b9bee3b81c4aeb3f1ba3e375e91627ec8561b6ab483d0a8'], }), ('colorama', '0.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], 'checksums': ['05eed71e2e327246ad6b38c540c4a3117230b19679b875190486ddd2d721422d'], }), ('colorlog', '4.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colorlog/'], 'checksums': ['3cf31b25cbc8f86ec01fef582ef3b840950dea414084ed19ab922c8b493f9b42'], }), ('pexpect', '4.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['9e2c1fd0e6ee3a49b28f95d4b33bc389c89b20af6a1255906e90ff1262ce62eb'], }), ('easydev', '0.9.37', { - 'source_urls': ['https://pypi.python.org/packages/source/e/easydev/'], 'checksums': ['38bd1a7e489673847e109c27f83f8e373e45907b70ea78eb2d38d96464f3a4e3'], }), ('colormap', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormap/'], 'checksums': ['c0193efe8f7d626cfc78225fc03a56513a4cfb8d3fc43856ccfb97b9646cc1b1'], }), ('colour', '0.1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colour/'], 'checksums': ['af20120fefd2afede8b001fbef2ea9da70ad7d49fafdb6489025dae8745c3aee'], }), ('ptyprocess', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], }), ] diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb index fbfc9e59789..6ab5c776527 100644 --- a/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb @@ -18,6 +18,9 @@ dependencies = [('Python', '3.8.6')] download_dep_fail = True use_pip = True +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + sanity_check_paths = { 'files': ['bin/flye'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/f/FreeFEM/FreeFEM-4.5-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FreeFEM/FreeFEM-4.5-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..efda497dcd7 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeFEM/FreeFEM-4.5-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,33 @@ +name = 'FreeFEM' +version = '4.5' +versionsuffix = '-Python-3.7.4' + +homepage = 'https://freefem.org' +description = """FreeFEM offers a fast interpolation algorithm and a language for the manipulation + of data on multiple meshes.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://github.com/FreeFem/FreeFem-sources/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5b2d4125c312da8fbedd49a72e742f18f35e0ae100c82fb493067dfad5d51432'] + +builddependencies = [ + ('Autotools', '20180311'), + ('flex', '2.6.4'), + ('Bison', '3.3.2'), + ('CMake', '3.15.3'), +] + +dependencies = [ + ('GSL', '2.6'), + ('HDF5', '1.10.5'), + ('SuiteSparse', '5.6.0', '-METIS-5.1.0'), + ('freeglut', '3.2.1'), + ('PETSc', '3.12.4', versionsuffix), + ('SLEPc', '3.12.2', versionsuffix), + ('NLopt', '2.6.1'), + ('ParMETIS', '4.0.3'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..a278d8bd820 --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.10' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7f1c687c7831499bcacae5e8675945a39bacbad16ecaa945e9454a32df653c01'] + +builddependencies = [ + ('Autotools', '20210128'), + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +configopts = '--disable-docs' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/faceswap/faceswap-20180212-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/f/faceswap/faceswap-20180212-foss-2017b-Python-3.6.3.eb index bae26d695f5..f9701820b7f 100644 --- a/easybuild/easyconfigs/f/faceswap/faceswap-20180212-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/f/faceswap/faceswap-20180212-foss-2017b-Python-3.6.3.eb @@ -29,23 +29,22 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_filter = ("python -c 'import %(ext_name)s'", '') +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} exts_list = [ ('scandir', '1.6', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir'], 'checksums': ['e0278a2d4bc6c0569aedbe66bf26c8ab5b2b08378b3289de49257f23ac624338'], }), ('dlib', '19.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/dlib'], 'checksums': ['33a9ec8b6e9fcf0538003d019d97968dc7601f2aaa60304a6146cf0f834259da'], 'buildopts': "--yes CMAKE_VERBOSE_MAKEFILE --no USE_SSE4_INSTRUCTIONS", }), ('face_recognition', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/face_recognition'], 'checksums': ['bc914d0e83b515113f5bffda26a5943b1edc36a6df4b3f0a38167f03e7924b40'], }), ('tqdm', '4.19.5', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tqdm'], 'checksums': ['df32e6f127dc0ccbc675eadb33f749abbcb8f174c5cb9ec49c0cdb73aa737377'], }), ] diff --git a/easybuild/easyconfigs/f/fastqsplitter/fastqsplitter-1.2.0-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/f/fastqsplitter/fastqsplitter-1.2.0-GCCcore-8.2.0-Python-3.7.2.eb index acc15f8d972..46e68f147fc 100644 --- a/easybuild/easyconfigs/f/fastqsplitter/fastqsplitter-1.2.0-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/f/fastqsplitter/fastqsplitter-1.2.0-GCCcore-8.2.0-Python-3.7.2.eb @@ -19,8 +19,6 @@ dependencies = [('Python', '3.7.2')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('xopen', '0.9.0', { 'checksums': ['1e3918c8a5cd2bd128ba05b3b883ee322349219c99c305e10114638478e3162a'], diff --git a/easybuild/easyconfigs/f/fbm/fbm-0.2.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/f/fbm/fbm-0.2.0-intel-2018a-Python-3.6.4.eb index 214b6a39201..8d3222ef373 100644 --- a/easybuild/easyconfigs/f/fbm/fbm-0.2.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/f/fbm/fbm-0.2.0-intel-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = "Exact methods for simulating fractional Brownian motion and fract toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['594a7facbab8629914afd8ea7e854324f0434a31aa02b6ef38ce2d60af7420b7'] @@ -18,9 +17,4 @@ dependencies = [('Python', '3.6.4')] download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/ffnet/ffnet-0.8.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/ffnet/ffnet-0.8.3-intel-2016a-Python-2.7.11.eb index 1b97ca13091..3481656bb29 100644 --- a/easybuild/easyconfigs/f/ffnet/ffnet-0.8.3-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/f/ffnet/ffnet-0.8.3-intel-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'ffnet' version = '0.8.3' @@ -10,25 +10,11 @@ description = """Feed-forward neural network solution for python""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [('Python', '2.7.11')] exts_list = [ - ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/f/ffnet/'], - }), + ('networkx', '1.11'), + (name, version), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..214dfa7e942 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-2.0-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'flatbuffers-python' +version = '2.0' + +homepage = 'https://github.com/google/flatbuffers/' +description = """Python Flatbuffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/f/flatbuffers'] +sources = [{'download_filename': 'flatbuffers-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['12158ab0272375eab8db2d663ae97370c33f152b27801fa6024e1d6105fd4dd2'] + +dependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'VERSION=%(version)s ' +options = {'modulename': 'flatbuffers'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..dce515f9d2f --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.0-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '2.0.0' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['9ddb9031798f4f8754d00fca2f1a68ecf9d0f83dfac7239af1311e4fd9a565c4'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('Ninja', '1.10.2'), + ('Python', '3.9.5'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb new file mode 100644 index 00000000000..36aad7de33d --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.3.2'), + ('help2man', '1.47.8'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.32', '', True), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb new file mode 100644 index 00000000000..7d4dffd6bd2 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.7.6'), + ('help2man', '1.48.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.36.1', '', True), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..69270abd8cc --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.2.1' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['freeglut-3.2.1_gcc10_fix-1.patch'] +checksums = [ + 'd4000e02102acaf259998c870e25214739d1f16f67f99cb35e4f46841399da68', # freeglut-3.2.1.tar.gz + 'f278467e03348b87d9b4ae69f491e503ab80c6d82433cf7468eac89b7f859d37', # freeglut-3.2.1_gcc10_fix-1.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('X11', '20210518'), + ('Mesa', '21.1.1'), + ('libGLU', '9.0.1'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.%s" ' % SHLIB_EXT +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fullrmc/fullrmc-3.2.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/f/fullrmc/fullrmc-3.2.0-intel-2018a-Python-2.7.14.eb index 44d4e5fdac6..1edca96433d 100644 --- a/easybuild/easyconfigs/f/fullrmc/fullrmc-3.2.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/f/fullrmc/fullrmc-3.2.0-intel-2018a-Python-2.7.14.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'fullrmc' version = '3.2.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://bachiraoun.github.io/fullrmc' +homepage = 'https://bachiraoun.github.io/fullrmc' description = """Reverse Monte Carlo (RMC) is probably best known for its applications in condensed matter physics and solid state chemistry. fullrmc which stands for FUndamental Library Language for Reverse Monte Carlo is different than traditional @@ -20,31 +20,22 @@ dependencies = [ ('VMD', '1.9.3', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_download_dep_fail = True - exts_list = [ ('pylocker', '0.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pylocker/'], 'checksums': ['482032ef2a66dfa1c285ec021260a8f46372051bdb7e8e73eb7d4da24d554c2b'], }), ('pyrep', '1.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyrep/'], 'checksums': ['e24d2b1cd95c1a490b8bf2ae62ecd355b528859833a593aa4d31cfcaa3ac147c'], }), ('pysimplelog', '0.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pysimplelog/'], 'checksums': ['c2d105a0b996c8f86f029d4fd53ee77c3c4715fb0378217f81e9343342bb454d'], }), ('pdbParser', '0.1.5', { 'modulename': 'pdbParser', 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pdbParser/'], 'checksums': ['1a5baa62d381bffa09d90335bb1c86941293e744bc12b6418833094e370d5085'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/f/fullrmc/'], 'checksums': ['4f53ccdb18d89500ad80dc517cf4cd08cbb796367c7be340d4f92a7ae445cec0'], }), ] diff --git a/easybuild/easyconfigs/f/futhark/futhark-0.19.5.eb b/easybuild/easyconfigs/f/futhark/futhark-0.19.5.eb new file mode 100644 index 00000000000..6bc2922e543 --- /dev/null +++ b/easybuild/easyconfigs/f/futhark/futhark-0.19.5.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'futhark' + +version = '0.19.5' + +homepage = 'https://futhark-lang.org/' + +description = """Futhark is a small programming language designed to be compiled to efficient parallel code. It + is a statically typed, data-parallel, and purely functional array language in the ML family, and comes + with a heavily optimising ahead-of-time compiler that presently generates GPU code via CUDA and OpenCL, + although the language itself is hardware-agnostic and can also run on multicore CPUs""" + + +toolchain = SYSTEM + +source_urls = ['https://futhark-lang.org/releases/'] +sources = ['%(name)s-%(version)s-linux-x86_64.tar.xz'] +checksums = ['4cb1ec38f961ece5e10210f1af45899dd45119141fbeceaba81cb24f3ba55035'] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb new file mode 100644 index 00000000000..6648c32dd2c --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCLAGS -fallow-argument-mismatch" ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb new file mode 100644 index 00000000000..318f3bb9b99 --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +patches = ['futile_intel_bug.patch'] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + 'e3681e6dda9364a1be4fba937423b8ac1774c3ebfd1ff04211482df25a188e95', # futile_intel_bug.patch +] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/futile/futile_intel_bug.patch b/easybuild/easyconfigs/f/futile/futile_intel_bug.patch new file mode 100644 index 00000000000..b42301263c8 --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile_intel_bug.patch @@ -0,0 +1,50 @@ +Patch to fix compilation with the Intel compiler. It replaces some 'use' +statements with 'import' in several interfaces. +author: Micael Oliveira (Max Planck Institute for the Structure and Dynamics of Matter) +diff -rup futile-1.8.3.orig/flib/fpython.f90 futile-1.8.3/flib/fpython.f90 +--- futile-1.8.3.orig/flib/fpython.f90 2019-08-29 17:04:28.319733800 +0200 ++++ futile-1.8.3/flib/fpython.f90 2019-08-29 17:04:34.895795372 +0200 +@@ -1,6 +1,7 @@ + module f_python + use f_precisions, only: f_address +- ++ use dictionaries ++ + implicit none + + !> Equivalent type than the numpy one, to be able +@@ -24,7 +25,7 @@ module f_python + + interface + subroutine f_python_initialize(iproc, nproc, igroup, ngroup) +- use dictionaries ++ import + implicit none + integer, intent(in) :: iproc, nproc, igroup, ngroup + end subroutine f_python_initialize +@@ -32,14 +33,14 @@ module f_python + + interface + subroutine f_python_finalize() +- use dictionaries ++ import + implicit none + end subroutine f_python_finalize + end interface + + interface + subroutine f_python_execute_dict(dict, status) +- use dictionaries ++ import + implicit none + type(dictionary), pointer :: dict + integer, intent(out) :: status +@@ -48,7 +49,7 @@ module f_python + + interface + subroutine f_python_execute(script, status) +- use dictionaries ++ import + implicit none + character(len = *), intent(in) :: script + integer, intent(out) :: status diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018a-Python-2.7.14.eb index e66b55c9344..a3e7e1894ab 100644 --- a/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018a-Python-2.7.14.eb @@ -4,20 +4,14 @@ name = 'future' version = '0.16.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://python-future.org/' +homepage = 'https://python-future.org/' description = "python-future is the missing compatibility layer between Python 2 and Python 3." toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'] dependencies = [('Python', '2.7.14')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-2.7.15.eb index f8095fa4931..3b12d21dc74 100644 --- a/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-2.7.15.eb @@ -4,20 +4,14 @@ name = 'future' version = '0.16.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://python-future.org/' +homepage = 'https://python-future.org/' description = "python-future is the missing compatibility layer between Python 2 and Python 3." toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'] dependencies = [('Python', '2.7.15')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb index 9bc47f6aaad..5664de55d60 100644 --- a/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb @@ -4,12 +4,11 @@ name = 'future' version = '0.16.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://python-future.org/' +homepage = 'https://python-future.org/' description = "python-future is the missing compatibility layer between Python 2 and Python 3." toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'] @@ -18,9 +17,4 @@ dependencies = [('Python', '3.6.6')] use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/f/future/future-0.16.0-intel-2017b-Python-2.7.14.eb index 2289eb549e7..fe4dc1a07fb 100644 --- a/easybuild/easyconfigs/f/future/future-0.16.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/f/future/future-0.16.0-intel-2017b-Python-2.7.14.eb @@ -4,20 +4,14 @@ name = 'future' version = '0.16.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://python-future.org/' +homepage = 'https://python-future.org/' description = "python-future is the missing compatibility layer between Python 2 and Python 3." toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'] dependencies = [('Python', '2.7.14')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/f/future/future-0.16.0-intel-2017b-Python-3.6.3.eb index caac34fa9f2..12ba08b6a74 100644 --- a/easybuild/easyconfigs/f/future/future-0.16.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/f/future/future-0.16.0-intel-2017b-Python-3.6.3.eb @@ -4,20 +4,14 @@ name = 'future' version = '0.16.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://python-future.org/' +homepage = 'https://python-future.org/' description = "python-future is the missing compatibility layer between Python 2 and Python 3." toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'] dependencies = [('Python', '3.6.3')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/f/future/future-0.16.0-intel-2018a-Python-2.7.14.eb index 5ae938aef0f..6d7c4dcfc82 100644 --- a/easybuild/easyconfigs/f/future/future-0.16.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/f/future/future-0.16.0-intel-2018a-Python-2.7.14.eb @@ -4,20 +4,14 @@ name = 'future' version = '0.16.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://python-future.org/' +homepage = 'https://python-future.org/' description = "python-future is the missing compatibility layer between Python 2 and Python 3." toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'] dependencies = [('Python', '2.7.14')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/future/future-0.16.0-intel-2018b-Python-2.7.15.eb index 085e54d041a..0e607df47e3 100644 --- a/easybuild/easyconfigs/f/future/future-0.16.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/f/future/future-0.16.0-intel-2018b-Python-2.7.15.eb @@ -4,20 +4,14 @@ name = 'future' version = '0.16.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://python-future.org/' +homepage = 'https://python-future.org/' description = "python-future is the missing compatibility layer between Python 2 and Python 3." toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'] dependencies = [('Python', '2.7.15')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb index 8c72aecfdc3..fe92d8a30d3 100644 --- a/easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ description = """The Genomic Association Tester (GAT) is a tool for computing th toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['e34d80169289e938aefbbebc4c50a3d5cdc8b38bab2cf63ae9716089bfda5968'] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index 6a349180e9b..b4164dbe26a 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'GC3Pie' version = '2.4.2' @@ -11,94 +11,53 @@ toolchain = SYSTEM osdependencies = [('python-devel', 'python-dev')] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] exts_list = [ - ('setuptools', '18.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), + ('setuptools', '18.1'), # required for paramiko - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), + ('ecdsa', '0.13'), # required for paramiko ('pycrypto', '2.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'modulename': 'Crypto', }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), + ('paramiko', '1.15.2'), ('PrettyTable', '0.7.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], 'source_tmpl': 'prettytable-%(version)s.tar.gz', }), ('pyCLI', 'devel', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], 'modulename': 'cli', }), - ('SQLAlchemy', '1.0.8', { - 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], - }), - ('parsedatetime', '1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], - }), - ('boto', '2.38.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], - }), + ('SQLAlchemy', '1.0.8'), + ('parsedatetime', '1.5'), + ('boto', '2.38.0'), # required for pbr - ('pip', '7.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), + ('pip', '7.1.0'), # required for python-novaclient - ('pbr', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), + ('pbr', '1.4.0'), # required for python-novaclient - ('Babel', '2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], - }), + ('Babel', '2.0'), # required for python-novaclient - ('simplejson', '3.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], - }), + ('simplejson', '3.8.0'), # required for python-novaclient - ('requests', '2.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), + ('requests', '2.7.0'), # required for python-novaclient - ('iso8601', '0.1.10', { - 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], - }), + ('iso8601', '0.1.10'), # required for python-novaclient - ('argparse', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), + ('argparse', '1.3.0'), # required for python-novaclient - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + ('six', '1.9.0'), ('python-novaclient', '2.23.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], 'modulename': 'novaclient', }), (name.lower(), version, { - 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], 'modulename': 'gc3libs', }), ] local_pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) -# on RHEL-based systems, some extensions get installed to lib, some to lib64 -modextrapaths = { - 'PYTHONPATH': ['lib/python%s/site-packages' % local_pyver, 'lib64/python%s/site-packages' % local_pyver], -} - sanity_check_paths = { 'files': ['bin/gc3utils'], 'dirs': [('lib/python%s/site-packages' % local_pyver, 'lib64/python%s/site-packages' % local_pyver)], diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.0.eb index 1bbbbf66d87..48a5fd436d2 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.0.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'GC3Pie' version = '2.5.0' @@ -20,114 +20,86 @@ dependencies = [ ('libffi', '3.2.1'), # required dep for PyNaCl ] -exts_defaultclass = 'PythonPackage' -exts_download_dep_fail = True - exts_list = [ ('setuptools', '21.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['bdf0b7660f6673868d60d929e267e583bddc0e9623c71197b1ad79610c2ebe93'], }), ('pyCLI', '2.0.3', { 'modulename': 'cli', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], 'checksums': ['bc53e6c5db031ae1c05d131641f153d22a201c5e82cc8c9324a945752efbb622'], }), ('prettytable', '0.7.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prettytable/'], 'checksums': ['2d5460dc9db74a32bcc8f9f67de68b2c4f4d2f01fa3bd518764c69156d9cacd9'], }), ('dictproxyhack', '1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/dictproxyhack/'], 'checksums': ['964eef82fba883d53783b08cbce90415380a5c26e5c2dba47548d1c3d0a591f8'], }), ('monotonic', '1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/m/monotonic/'], 'checksums': ['23953d55076df038541e648a53676fb24980f7a1be290cdda21300b3bc21dfb0'], }), ('humanfriendly', '4.16.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/humanfriendly/'], 'checksums': ['ed1e98ae056b597f15b41bddcc32b9f21e6ab4f3445f9faad1668675de759f7b'], }), ('coloredlogs', '10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/coloredlogs/'], 'checksums': ['b869a2dda3fa88154b9dd850e27828d8755bfab5a838a1c97fbc850c6e377c36'], }), ('blinker', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blinker/'], 'checksums': ['471aee25f3992bd325afa3772f1063dbdbbca947a041b8b89466dc00d606f8b6'], }), ('SQLAlchemy', '1.2.11', { - 'source_urls': ['https://pypi.python.org/packages/source/s/SQLAlchemy/'], 'checksums': ['ef6569ad403520ee13e180e1bfd6ed71a0254192a934ec1dbd3dbf48f4aa9524'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('docutils', '0.14', { 'source_tmpl': 'docutils-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/docutils/'], 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('python-daemon', '2.2.0', { 'modulename': 'daemon', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-daemon/'], 'checksums': ['aca149ebf7e73f10cd554b2df5c95295d49add8666348eff6195053ec307728c'], }), ('future', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'], }), ('parsedatetime', '2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], 'checksums': ['3d817c58fb9570d1eec1dd46fa9448cd644eeed4fb612684b02dfda3a79cb84b'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/PyNaCl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34/'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], }), ('cryptography', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6'], }), ('pyasn1', '0.4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['f58f2a3d12fd754aa123e9fa74fb7345333000a035f3921dbdaa08597aa53137'], }), ('paramiko', '2.4.1', { 'patches': ['paramiko-2.3.1-disable-gssapi-on-unsupported-version.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': [ '33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3', # paramiko-2.4.1.tar.gz # paramiko-2.3.1-disable-gssapi-on-unsupported-version.patch @@ -136,16 +108,13 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('gc3pie', version, { 'modulename': 'gc3libs', - 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], 'checksums': ['fc0114a35a5c1cea22f91e8eef180bbb0971294b8391b4ccdbf772a2969c8b59'], }), ] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.2.eb index b965e0031be..95f69b271e7 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.2.eb @@ -22,10 +22,6 @@ dependencies = [ use_pip = False -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - exts_list = [ ('setuptools', '41.0.1', { 'source_tmpl': 'setuptools-%(version)s.zip', diff --git a/easybuild/easyconfigs/g/GCC/GCC-8.4.0.eb b/easybuild/easyconfigs/g/GCC/GCC-8.4.0.eb new file mode 100644 index 00000000000..5e8a455fa7c --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-8.4.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '8.4.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', '2.36.1', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-9.4.0.eb b/easybuild/easyconfigs/g/GCC/GCC-9.4.0.eb new file mode 100644 index 00000000000..3375239519c --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-9.4.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '9.4.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', '2.36.1', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index c145d065992..65f6fc7c6cd 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -32,7 +32,9 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-9.3.0_nvptx_sm_35_default.patch', 'GCCcore-10.2.0_fix-has-include-Fortran.patch', + 'GCCcore-10.2.0_fix-ice-on-arm.patch', 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', ] checksums = [ @@ -45,7 +47,9 @@ checksums = [ 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705', # nvptx-tools-20180301.tar.gz '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCCcore-10.2.0_fix-has-include-Fortran.patch + '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278', # GCCcore-10.2.0_fix-ice-on-arm.patch # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962', ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0_fix-ice-on-arm.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0_fix-ice-on-arm.patch new file mode 100644 index 00000000000..8f7895ce85a --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0_fix-ice-on-arm.patch @@ -0,0 +1,72 @@ +From 510ff5def87c70836fdbf832228661ae28e524b6 Mon Sep 17 00:00:00 2001 +From: Jakub Jelinek +Date: Thu, 4 Mar 2021 19:38:08 +0100 +Subject: [PATCH] expand: Fix ICE in store_bit_field_using_insv [PR93235] + +The following testcase ICEs on aarch64. The problem is that +op0 is (subreg:HI (reg:HF ...) 0) and because we can't create a SUBREG of a +SUBREG and aarch64 doesn't have HImode insv, only SImode insv, +store_bit_field_using_insv tries to create (subreg:SI (reg:HF ...) 0) +which is not valid for the target and so gen_rtx_SUBREG ICEs. + +The following patch fixes it by punting if the to be created SUBREG +doesn't validate, callers of store_bit_field_using_insv can handle +the fallback. + +2021-03-04 Jakub Jelinek + + PR middle-end/93235 + * expmed.c (store_bit_field_using_insv): Return false of xop0 is a + SUBREG and a SUBREG to op_mode can't be created. + + * gcc.target/aarch64/pr93235.c: New test. + +(cherry picked from commit 0ad6de3883a1641f7ec0bd9cf56d41fa5b313dae) +--- + gcc/expmed.c | 13 ++++++++++--- + gcc/testsuite/gcc.target/aarch64/pr93235.c | 12 ++++++++++++ + 2 files changed, 22 insertions(+), 3 deletions(-) + create mode 100644 gcc/testsuite/gcc.target/aarch64/pr93235.c + +diff --git a/gcc/expmed.c b/gcc/expmed.c +index e7c03fbf92c04..96ced5c8c8b61 100644 +--- a/gcc/expmed.c ++++ b/gcc/expmed.c +@@ -625,9 +625,16 @@ store_bit_field_using_insv (const extraction_insn *insv, rtx op0, + /* If xop0 is a register, we need it in OP_MODE + to make it acceptable to the format of insv. */ + if (GET_CODE (xop0) == SUBREG) +- /* We can't just change the mode, because this might clobber op0, +- and we will need the original value of op0 if insv fails. */ +- xop0 = gen_rtx_SUBREG (op_mode, SUBREG_REG (xop0), SUBREG_BYTE (xop0)); ++ { ++ /* If such a SUBREG can't be created, give up. */ ++ if (!validate_subreg (op_mode, GET_MODE (SUBREG_REG (xop0)), ++ SUBREG_REG (xop0), SUBREG_BYTE (xop0))) ++ return false; ++ /* We can't just change the mode, because this might clobber op0, ++ and we will need the original value of op0 if insv fails. */ ++ xop0 = gen_rtx_SUBREG (op_mode, SUBREG_REG (xop0), ++ SUBREG_BYTE (xop0)); ++ } + if (REG_P (xop0) && GET_MODE (xop0) != op_mode) + xop0 = gen_lowpart_SUBREG (op_mode, xop0); + } +diff --git a/gcc/testsuite/gcc.target/aarch64/pr93235.c b/gcc/testsuite/gcc.target/aarch64/pr93235.c +new file mode 100644 +index 0000000000000..829ae13f199fc +--- /dev/null ++++ b/gcc/testsuite/gcc.target/aarch64/pr93235.c +@@ -0,0 +1,12 @@ ++/* PR middle-end/93235 */ ++/* { dg-do compile } */ ++/* { dg-options "-O2 -fno-strict-aliasing" } */ ++ ++struct sfp16 { __fp16 f; }; ++struct sfp16 ++foo (short x) ++{ ++ struct sfp16 a; ++ *(short*)&a.f = x; ++ return a; ++} diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb index 3bd40126295..abac9ee3662 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb @@ -32,6 +32,8 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-9.3.0_nvptx_sm_35_default.patch', + 'gcc-10.3.0_fix-ice-in-tsubst.patch', ] checksums = [ '8fcf994811ad4e5c7ac908e8cf62af2c1982319e5551f62ae72016064dacdf16', # gcc-10.3.0.tar.gz @@ -43,6 +45,8 @@ checksums = [ '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch + '74e6e019458aa2feb36ae3c45f45e164725ca5edd66f4fe9f873c8ee78c35717', # gcc-10.3.0_fix-ice-in-tsubst.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.4.0.eb new file mode 100644 index 00000000000..b8fc3a2b366 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.4.0.eb @@ -0,0 +1,51 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '8.4.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.1.2.tar.bz2', + 'mpfr-4.0.2.tar.bz2', + 'mpc-1.1.0.tar.gz', + 'isl-0.21.tar.bz2', +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-8.3.0_fix-xsmin-ppc.patch', +] +checksums = [ + '41e8b145832fc0b2b34c798ed25fb54a881b0cee4cd581b77c7dc92722c116a8', # gcc-8.4.0.tar.gz + '5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2', # gmp-6.1.2.tar.bz2 + 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc', # mpfr-4.0.2.tar.bz2 + '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz + 'd18ca11f8ad1a39ab6d03d3dcb3365ab416720fcb65b42d69f34f51bf0a0e859', # isl-0.21.tar.bz2 + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch + 'bea1bce8f50ea6d51b038309eb61dec00a8681fb653d211c539be80f184609a3', # GCCcore-8.3.0_fix-xsmin-ppc.patch +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.36.1'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb index 005eee83c5b..a0037cc1561 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb @@ -34,6 +34,7 @@ patches = [ 'GCCcore-8.3.0_fix-xsmin-ppc.patch', 'GCCcore-%(version)s_gmp-c99.patch', 'GCCcore-%(version)s_vect_broadcasts_masmintel.patch', + 'GCCcore-%(version)s_nvptx_sm_35_default.patch', ] checksums = [ '5258a9b6afe9463c2e56b9e8355b1a4bee125ca828b8078f910303bc2ef91fa6', # gcc-9.3.0.tar.gz @@ -47,6 +48,7 @@ checksums = [ 'bea1bce8f50ea6d51b038309eb61dec00a8681fb653d211c539be80f184609a3', # GCCcore-8.3.0_fix-xsmin-ppc.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch 'a32ac9c7d999a8b91bf93dba6a9d81b6ff58b3c89c425ff76090cbc90076685c', # GCCcore-9.3.0_vect_broadcasts_masmintel.patch + '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0_nvptx_sm_35_default.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0_nvptx_sm_35_default.patch new file mode 100644 index 00000000000..d8a6e0a57f4 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0_nvptx_sm_35_default.patch @@ -0,0 +1,67 @@ +From 383400a6078d75bbfa1216c9af2c37f7e88740c9 Mon Sep 17 00:00:00 2001 +From: Tom de Vries +Date: Fri, 9 Oct 2020 11:36:10 +0200 +Subject: [PATCH] [nvptx] Set -misa=sm_35 by default + +The nvptx-as assembler verifies the ptx code using ptxas, if there's any +in the PATH. + +The default in the nvptx port for -misa=sm_xx is sm_30, but the ptxas of the +latest cuda release (11.1) no longer supports sm_30. + +Consequently we cannot build gcc against that release (although we should +still be able to build without any cuda release). + +Fix this by setting -misa=sm_35 by default. + +Tested check-gcc on nvptx. + +Tested libgomp on x86_64-linux with nvpx accelerator. + +Both build again cuda 9.1. + +gcc/ChangeLog: + +2020-10-09 Tom de Vries + + PR target/97348 + * config/nvptx/nvptx.h (ASM_SPEC): Also pass -m to nvptx-as if + default is used. + * config/nvptx/nvptx.opt (misa): Init with PTX_ISA_SM35. +--- + gcc/config/nvptx/nvptx.h | 5 ++++- + gcc/config/nvptx/nvptx.opt | 3 ++- + 2 files changed, 6 insertions(+), 2 deletions(-) + +diff --git a/gcc/config/nvptx/nvptx.h b/gcc/config/nvptx/nvptx.h +index 6ebcc760771..17fe157058c 100644 +--- a/gcc/config/nvptx/nvptx.h ++++ b/gcc/config/nvptx/nvptx.h +@@ -29,7 +29,10 @@ + + #define STARTFILE_SPEC "%{mmainkernel:crt0.o}" + +-#define ASM_SPEC "%{misa=*:-m %*}" ++/* Default needs to be in sync with default for misa in nvptx.opt. ++ We add a default here to work around a hard-coded sm_30 default in ++ nvptx-as. */ ++#define ASM_SPEC "%{misa=*:-m %*; :-m sm_35}" + + #define TARGET_CPU_CPP_BUILTINS() \ + do \ +diff --git a/gcc/config/nvptx/nvptx.opt b/gcc/config/nvptx/nvptx.opt +index 75c3d54864e..d6910a96cf0 100644 +--- a/gcc/config/nvptx/nvptx.opt ++++ b/gcc/config/nvptx/nvptx.opt +@@ -59,6 +59,7 @@ Enum(ptx_isa) String(sm_30) Value(PTX_ISA_SM30) + EnumValue + Enum(ptx_isa) String(sm_35) Value(PTX_ISA_SM35) + ++; Default needs to be in sync with default in ASM_SPEC in nvptx.h. + misa= +-Target RejectNegative ToLower Joined Enum(ptx_isa) Var(ptx_isa_option) Init(PTX_ISA_SM30) ++Target RejectNegative ToLower Joined Enum(ptx_isa) Var(ptx_isa_option) Init(PTX_ISA_SM35) + Specify the version of the ptx ISA to use. +-- +2.27.0 + diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb new file mode 100644 index 00000000000..814431d3215 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb @@ -0,0 +1,58 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '9.4.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.1.0.tar.bz2', + 'mpc-1.2.1.tar.gz', + 'isl-0.24.tar.bz2', + 'newlib-4.1.0.tar.gz', + {'download_filename': 'd0524fb.tar.gz', 'filename': 'nvptx-tools-20210115.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + '07ea650894cde75ab0f7cfbee0e69832c8a789b01efa2de3bfba7569338e24cb', # gcc-9.4.0.tar.gz + 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 + 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 + '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz + 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 + 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz + '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch + '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.36.1'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/gcc-10.3.0_fix-ice-in-tsubst.patch b/easybuild/easyconfigs/g/GCCcore/gcc-10.3.0_fix-ice-in-tsubst.patch new file mode 100644 index 00000000000..56d2dce0e01 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/gcc-10.3.0_fix-ice-in-tsubst.patch @@ -0,0 +1,198 @@ +Fix for gcc being called from nvcc, see https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100102 +Combines: +* https://gcc.gnu.org/git/gitweb.cgi?p=gcc.git;h=fc930b3010bd0de899a3da3209eab20664ddb703 +* https://gcc.gnu.org/git/gitweb.cgi?p=gcc.git;h=a1b3484a8e6c53c8084723e3f1738d402374198e + +Patch prepared for EasyBuild by Simon Branford (University of Birmingham) + +From fc930b3010bd0de899a3da3209eab20664ddb703 Mon Sep 17 00:00:00 2001 +From: Patrick Palka +Date: Fri, 4 Jun 2021 13:46:53 -0400 +Subject: [PATCH] c++: tsubst_function_decl and excess arg levels [PR100102] + +Here, when instantiating the dependent alias template +duration::__is_harmonic with args={{T,U},{int}}, we find ourselves +substituting the function decl _S_gcd. Since we have more arg levels +than _S_gcd has parm levels, an old special case in tsubst_function_decl +causes us to unwantedly reduce args to its innermost level, yielding +args={int}, which leads to a nonsensical substitution into the decl +context and eventually a crash. + +The comment for this special case refers to three examples for which we +ought to see more arg levels than parm levels here, but none of the +examples actually demonstrate this. In the first example, when +defining S::f(U) parms_depth is 2 and args_depth is 1, and +later when instantiating say S::f both depths are 2. In the +second example, when substituting the template friend declaration +parms_depth is 2 and args_depth is 1, and later when instantiating f +both depths are 1. Finally, the third example is invalid since we can't +specialize a member template of an unspecialized class template like +that. + +Given that this reduction code seems no longer relevant for its +documented purpose and that it causes problems as in the PR, this patch +just removes it. Note that as far as bootstrap/regtest is concerned, +this code is dead; the below two tests would be the first to reach it. + + PR c++/100102 + +gcc/cp/ChangeLog: + + * pt.c (tsubst_function_decl): Remove old code for reducing + args when it has excess levels. + +gcc/testsuite/ChangeLog: + + * g++.dg/cpp0x/alias-decl-72.C: New test. + * g++.dg/cpp0x/alias-decl-72a.C: New test. + +(cherry picked from commit 5357ab75dedef403b0eebf9277d61d1cbeb5898f) +--- + gcc/cp/pt.c | 39 --------------------- + gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C | 9 +++++ + gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C | 9 +++++ + 3 files changed, 18 insertions(+), 39 deletions(-) + create mode 100644 gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C + create mode 100644 gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C + +diff --git a/gcc/cp/pt.c b/gcc/cp/pt.c +index 5a957141ba3..7ce9ac234f8 100644 +--- a/gcc/cp/pt.c ++++ b/gcc/cp/pt.c +@@ -13811,45 +13811,6 @@ tsubst_function_decl (tree t, tree args, tsubst_flags_t complain, + if (tree spec = retrieve_specialization (gen_tmpl, argvec, hash)) + return spec; + } +- +- /* We can see more levels of arguments than parameters if +- there was a specialization of a member template, like +- this: +- +- template struct S { template void f(); } +- template <> template void S::f(U); +- +- Here, we'll be substituting into the specialization, +- because that's where we can find the code we actually +- want to generate, but we'll have enough arguments for +- the most general template. +- +- We also deal with the peculiar case: +- +- template struct S { +- template friend void f(); +- }; +- template void f() {} +- template S; +- template void f(); +- +- Here, the ARGS for the instantiation of will be {int, +- double}. But, we only need as many ARGS as there are +- levels of template parameters in CODE_PATTERN. We are +- careful not to get fooled into reducing the ARGS in +- situations like: +- +- template struct S { template void f(U); } +- template template <> void S::f(int) {} +- +- which we can spot because the pattern will be a +- specialization in this case. */ +- int args_depth = TMPL_ARGS_DEPTH (args); +- int parms_depth = +- TMPL_PARMS_DEPTH (DECL_TEMPLATE_PARMS (DECL_TI_TEMPLATE (t))); +- +- if (args_depth > parms_depth && !DECL_TEMPLATE_SPECIALIZATION (t)) +- args = get_innermost_template_args (args, parms_depth); + } + else + { +diff --git a/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C +new file mode 100644 +index 00000000000..8009756dcba +--- /dev/null ++++ b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C +@@ -0,0 +1,9 @@ ++// PR c++/100102 ++// { dg-do compile { target c++11 } } ++ ++template struct ratio; ++template struct duration { ++ static constexpr int _S_gcd(); ++ template using __is_harmonic = ratio<_S_gcd>; ++ using type = __is_harmonic; ++}; +diff --git a/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C +new file mode 100644 +index 00000000000..a4443e18f9d +--- /dev/null ++++ b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C +@@ -0,0 +1,9 @@ ++// PR c++/100102 ++// { dg-do compile { target c++11 } } ++ ++template struct ratio; ++template struct duration { ++ static constexpr int _S_gcd(); ++ template using __is_harmonic = ratio<(duration::_S_gcd)()>; ++ using type = __is_harmonic; ++}; +-- +2.27.0 + +From a1b3484a8e6c53c8084723e3f1738d402374198e Mon Sep 17 00:00:00 2001 +From: Jason Merrill +Date: Mon, 31 May 2021 12:56:34 -0400 +Subject: [PATCH] c++: alias member template [PR100102] + +Patrick already fixed the primary cause of this bug. But while I was +looking at this testcase I noticed that with the qualified name k::o we +ended up with a plain FUNCTION_DECL, whereas without the k:: we got a +BASELINK. There seems to be no good reason not to return the BASELINK +in this case as well. + + PR c++/100102 + +gcc/cp/ChangeLog: + + * init.c (build_offset_ref): Return the BASELINK for a static + member function. + +gcc/testsuite/ChangeLog: + + * g++.dg/cpp0x/alias-decl-73.C: New test. +--- + gcc/cp/init.c | 2 +- + gcc/testsuite/g++.dg/cpp0x/alias-decl-73.C | 9 +++++++++ + 2 files changed, 10 insertions(+), 1 deletion(-) + create mode 100644 gcc/testsuite/g++.dg/cpp0x/alias-decl-73.C + +diff --git a/gcc/cp/init.c b/gcc/cp/init.c +index b1123287300..1b161d526f6 100644 +--- a/gcc/cp/init.c ++++ b/gcc/cp/init.c +@@ -2214,7 +2214,7 @@ build_offset_ref (tree type, tree member, bool address_p, + if (!ok) + return error_mark_node; + if (DECL_STATIC_FUNCTION_P (t)) +- return t; ++ return member; + member = t; + } + else +diff --git a/gcc/testsuite/g++.dg/cpp0x/alias-decl-73.C b/gcc/testsuite/g++.dg/cpp0x/alias-decl-73.C +new file mode 100644 +index 00000000000..aae778646dc +--- /dev/null ++++ b/gcc/testsuite/g++.dg/cpp0x/alias-decl-73.C +@@ -0,0 +1,9 @@ ++// PR c++/100102 ++// { dg-do compile { target c++11 } } ++ ++template using a = int; ++template struct k { ++ static long o(); ++ template using n = a; ++ n q; ++}; +-- +2.27.0 + diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb new file mode 100644 index 00000000000..f41af638de0 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb @@ -0,0 +1,67 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.2.1' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = [ + 'GDAL-3.0.0_fix-python-CC-CXX.patch', + 'GDAL-3.2.1_cpp-conformance.patch', +] +checksums = [ + '6c588b58fcb63ff3f288eb9f02d76791c0955ba9210d98c3abd879c770ae28ea', # gdal-3.2.1.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch + 'fdf6a84d16141ccc9bc4ce98a762357ba374dea87d1f2a41a1a23be80b7ca69d', # GDAL-3.2.1_cpp-conformance.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('netCDF', '4.7.4'), + ('expat', '2.2.9'), + ('GEOS', '3.9.1'), + ('SQLite', '3.33.0'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('JasPer', '2.0.24'), + ('LibTIFF', '4.1.0'), + ('zlib', '1.2.11'), + ('cURL', '7.72.0'), + ('PCRE2', '10.35'), + ('PROJ', '7.2.1'), + ('libgeotiff', '1.6.0'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('HDF', '4.2.15'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +prebuildopts = "env LDSHARED='icc -shared' " + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import osgeo.gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1_cpp-conformance.patch b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1_cpp-conformance.patch new file mode 100644 index 00000000000..1ddb40eb3e2 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1_cpp-conformance.patch @@ -0,0 +1,26 @@ +diff -ru gdal-3.2.1.orig/port/cpl_vsil_curl_class.h gdal-3.2.1/port/cpl_vsil_curl_class.h +--- gdal-3.2.1.orig/port/cpl_vsil_curl_class.h 2020-12-29 13:16:45.000000000 +0100 ++++ gdal-3.2.1/port/cpl_vsil_curl_class.h 2021-07-02 20:59:48.375889808 +0200 +@@ -681,6 +681,10 @@ + std::map children{}; + + void AsJSON(CPLJSONObject& oJSON) const; ++ ++ // Constructor must be defined after the class definition as Intel prohibits ++ // the use of its constructor while constructing its members. ++ Stats(); + }; + + Stats m_stats{}; +@@ -729,6 +733,11 @@ + static CPLString GetReportAsSerializedJSON(); + }; + ++// Constructor definition must be outside the class to work around Intel ++// preventing the use of the constructor while initializing members in the ++// default constructor. ++inline NetworkStatisticsLogger::Stats::Stats() = default; ++ + struct NetworkStatisticsFileSystem + { + inline explicit NetworkStatisticsFileSystem(const char* pszName) { diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb new file mode 100644 index 00000000000..dd20522630b --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.3.0' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] +checksums = [ + '190c8f4b56afc767f43836b2a5cd53cc52ee7fdc25eb78c6079c5a244e28efa7', # gdal-3.3.0.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('netCDF', '4.8.0'), + ('expat', '2.2.9'), + ('GEOS', '3.9.1'), + ('SQLite', '3.35.4'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('JasPer', '2.0.28'), + ('LibTIFF', '4.2.0'), + ('zlib', '1.2.11'), + ('cURL', '7.76.0'), + ('PCRE2', '10.36'), + ('PROJ', '8.0.1'), + ('libgeotiff', '1.6.0'), + ('SciPy-bundle', '2021.05'), + ('HDF5', '1.10.7'), + ('HDF', '4.2.15'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import osgeo.gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..a232a09da3b --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '10.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['aaa1223d534c9b700a8bec952d9748ee1977513f178727e1bee520ee000b4f29'] + +builddependencies = [ + ('binutils', '2.34'), + ('makeinfo', '6.7'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('expat', '2.2.9'), + ('Python', '3.8.2'), + ('ISL', '0.23'), + ('MPC', '1.1.0'), +] + +preconfigopts = "mkdir obj && cd obj && " +configure_cmd_prefix = '../' +prebuildopts = "cd obj && " +preinstallopts = prebuildopts + +configopts = '--with-system-zlib --with-system-readline --with-expat=$EBROOTEXPAT ' +configopts += '--with-python=$EBROOTPYTHON/bin/python --with-isl=$EBROOTISL --with-mpc=$EBROOTMPC ' +configopts += '--enable-tui --enable-plugins --disable-install-libbfd ' + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..6dc9fc92714 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-GCC-10.3.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.9.1' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7e630507dcac9dc07565d249a26f06a15c9f5b0c52dd29129a0e3d381d7e382a'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..757f093e125 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-iccifort-2020.4.304.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.9.1' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7e630507dcac9dc07565d249a26f06a15c9f5b0c52dd29129a0e3d381d7e382a'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..173f65d0fcf --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.2' + +homepage = 'https://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] +checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('freeglut', '3.2.1'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..81475a6718c --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.2' + +homepage = 'https://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] +checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +dependencies = [ + ('X11', '20210518'), + ('Mesa', '21.1.1'), + ('libGLU', '9.0.1'), + ('freeglut', '3.2.1'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLFW/GLFW-3.3.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GLFW/GLFW-3.3.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d4ec48aedb4 --- /dev/null +++ b/easybuild/easyconfigs/g/GLFW/GLFW-3.3.4-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'GLFW' +version = '3.3.4' + +homepage = 'https://www.glfw.org' +description = """GLFW is an Open Source, multi-platform library for OpenGL, +OpenGL ES and Vulkan development on the desktop""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['cc8ac1d024a0de5fd6f68c4133af77e1918261396319c24fd697775a6bc93b63'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210518'), +] + +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +sanity_check_paths = { + 'files': ['include/GLFW/glfw3.h', 'include/GLFW/glfw3native.h', + 'lib/libglfw3.a', 'lib/libglfw.%s' % SHLIB_EXT, 'lib/pkgconfig/glfw3.pc'], + 'dirs': ['include/GLFW', 'lib/cmake/glfw3', 'lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..15dc80e9694 --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '0.9.9.8' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'GLM-0.9.9.8_fix_missing_install.patch', +] +checksums = [ + '7d508ab72cb5d43227a3711420f06ff99b0a0cb63ee2f93631b162bfe1fe9592', # 0.9.9.8.tar.gz + '1cc199f9d66679b0b5e9a9fbe20bca0d9b15760fa172ca8759dd15bab35802ca', # GLM-0.9.9.8_fix_missing_install.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.68.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.68.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1e18bd348ba --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.68.0-GCCcore-10.3.0.eb @@ -0,0 +1,47 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.68.0' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['d229242481a201b84a0c66716de1752bca41db4133672cfcfb37c93eb6e54a27'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('cairo', '1.16.0'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('GLib', '2.68.2'), + ('libffi', '3.3'), + ('util-linux', '2.36'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb index ec4f6977d05..f2583a352cf 100644 --- a/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'GRIT' version = '2.0.5' @@ -9,20 +9,13 @@ description = """GRIT - A tool for the integrative analysis of RNA-seq type assa toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ] exts_list = [ - ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], - }), - ('pysam', '0.9.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pysam/'], - }), + ('networkx', '1.11'), + ('pysam', '0.9.1.4'), (name, version, { 'source_urls': ['https://github.com/nboley/grit/archive/'], 'source_tmpl': '%(version)s.tar.gz', @@ -30,8 +23,6 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/run_grit'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb index 2cc942771df..39f0d36db46 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb @@ -20,7 +20,7 @@ name = 'GROMACS' version = '2020.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.gromacs.org' +homepage = 'https://www.gromacs.org' description = """ GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-10.3.0.eb new file mode 100644 index 00000000000..c15f012d4ab --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.7' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb index f3f78a99363..c6e3c5bf573 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb @@ -24,7 +24,6 @@ use_pip = True exts_list = [ ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), (name, version, { diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb index 0fc790cf4ab..96d22c898b8 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb @@ -28,13 +28,12 @@ use_pip = True exts_list = [ ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), (name, version, { 'modulename': 'gtdbtk', - 'source_tmpl': 'gtdbtk-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/g/gtdbtk'], + 'source_tmpl': 'gtdbtk-%(version)s.tar.gz', 'checksums': ['8df3b941df5aa1a4bd0e0344da179d73f756a20b5f28610f3837efacbb019f4a'], }), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb index 5908768c7f5..89a5cfe9651 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb @@ -28,13 +28,12 @@ use_pip = True exts_list = [ ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), (name, version, { 'modulename': 'gtdbtk', - 'source_tmpl': 'gtdbtk-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/g/gtdbtk'], + 'source_tmpl': 'gtdbtk-%(version)s.tar.gz', 'checksums': ['8df3b941df5aa1a4bd0e0344da179d73f756a20b5f28610f3837efacbb019f4a'], }), ] diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..acb18837be2 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.33' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac2ac757f5942d318a311a54b0c80b5ef295f299c2a73c632f6bfb1ff49cc6da'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.68.0'), +] +dependencies = [ + ('ATK', '2.36.0'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.5'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e4d0f69b4ef --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.36.1'), +] +dependencies = [ + ('GLib', '2.68.2'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..30606a25022 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.6-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.6' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4a6b75b7ed8f58ca48da830b9fa00ed96d668d3ab4b1f723dcf902f78bde77f'] + +builddependencies = [ + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.68.0'), +] + +dependencies = [ + ('GLib', '2.68.2'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.2.0'), + ('X11', '20210518'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb index 1227d2ac3af..b8b39104441 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb @@ -21,6 +21,6 @@ dependencies = [ ] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += " -DGEANT4_INSTALL_DATA=OFF" +configopts += " -DCLHEP_ROOT_DIR=$EBROOTCLHEP -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb new file mode 100644 index 00000000000..26842544fe9 --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GenomeTools' +version = '1.6.1' + +homepage = 'http://genometools.org' +description = "A comprehensive software library for efficient processing of structured genome annotations." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'genometools' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.6.1_fix-GCC-10.patch'] +checksums = [ + '528ca143a7f1d42af8614d60ea1e5518012913a23526d82e434f0dad2e2d863f', # v1.6.1.tar.gz + '743c5f8e9b0b98efb30f0ea2c405022c4f1bac00743de60774fc16e2a4706135', # GenomeTools-1.6.1_fix-GCC-10.patch +] + +# GenomeTools-1.6.1 has the following libraries bundled with it: +# bzip2-1.0.6, cgilua-5.1.3, expat-2.0.1, lpeg-0.10.2, lua-5.1.5, luafilesystem-1.5.0, md5-1.2, +# samtools-0.1.18, sqlite-3.8.7.1, tre-0.8.0, zlib-1.2.8 +# +# Bundled libraries can be globally disabled with the option useshared=yes +# However, it is preferable to use the bundled libraries due to the very old versions of some of them + +dependencies = [('Pango', '1.47.0')] + +skipsteps = ['configure'] + +buildopts = 'useshared=no errorcheck=no cairo=yes threads=yes' +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/gt', 'bin/genometools-config', 'lib/libgenometools.a', 'lib/libgenometools.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1_fix-GCC-10.patch b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1_fix-GCC-10.patch new file mode 100644 index 00000000000..2c4edf1b749 --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1_fix-GCC-10.patch @@ -0,0 +1,88 @@ +From 51205942b1f41abdf841771deac4e0e35d7d5016 Mon Sep 17 00:00:00 2001 +From: Sascha Steinbiss +Date: Wed, 22 Apr 2020 21:59:57 +0200 +Subject: [PATCH 1/2] make sure to not ignore snprintf output + +GCC 10 will warn about the (here intended) silent string truncation +done by snprintf() unless the return value is handled. +Obviously this will break the build as we use -Werror. We +circumvent the problem by checking the output value and printing a +warning if we notice a truncation. +--- + src/ltr/ltrdigest_file_out_stream.c | 17 ++++++++++++----- + 1 file changed, 12 insertions(+), 5 deletions(-) + +diff --git a/src/ltr/ltrdigest_file_out_stream.c b/src/ltr/ltrdigest_file_out_stream.c +index 723b8cf9a..61325b693 100644 +--- a/src/ltr/ltrdigest_file_out_stream.c ++++ b/src/ltr/ltrdigest_file_out_stream.c +@@ -1,5 +1,5 @@ + /* +- Copyright (c) 2008-2015 Sascha Steinbiss ++ Copyright (c) 2008-2020 Sascha Steinbiss + Copyright (c) 2008-2013 Center for Bioinformatics, University of Hamburg + + Permission to use, copy, modify, and distribute this software for any +@@ -33,6 +33,7 @@ + #include "core/symbol.h" + #include "core/undef_api.h" + #include "core/unused_api.h" ++#include "core/warning_api.h" + #include "extended/extract_feature_sequence.h" + #include "extended/feature_node.h" + #include "extended/feature_node_iterator_api.h" +@@ -416,6 +417,8 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) + + if (!had_err) { + GtRange rng; ++ int ret = 0; ++ + ls->element.seqid = gt_calloc((size_t) ls->seqnamelen+1, sizeof (char)); + (void) snprintf(ls->element.seqid, + GT_MIN((size_t) gt_str_length(sdesc), +@@ -425,12 +428,16 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) + if (gt_str_length(sdesc) > (GtUword) ls->seqnamelen) + ls->element.seqid[ls->seqnamelen] = '\0'; + +- (void) gt_ltrelement_format_description(&ls->element, +- ls->seqnamelen, +- desc, +- (size_t) (GT_MAXFASTAHEADER-1)); ++ ret = gt_ltrelement_format_description(&ls->element, ++ ls->seqnamelen, ++ desc, ++ (size_t) (GT_MAXFASTAHEADER-1)); ++ if (ret < 0) { ++ gt_warning("FASTA header truncated: %s", desc); ++ } + gt_str_delete(sdesc); + ++ + /* output basic retrotransposon data */ + lltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.leftLTR); + rltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.rightLTR); + +From 30ae36037228dc4ed174e8462f3489638e6f5e76 Mon Sep 17 00:00:00 2001 +From: Sascha Steinbiss +Date: Wed, 22 Apr 2020 22:01:00 +0200 +Subject: [PATCH 2/2] declare hashmap type as extern + +This fixes a build issue with GCC 10. +Closes #941. +--- + src/mgth/metagenomethreader.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/mgth/metagenomethreader.h b/src/mgth/metagenomethreader.h +index 92f16d498..7f76fffb9 100644 +--- a/src/mgth/metagenomethreader.h ++++ b/src/mgth/metagenomethreader.h +@@ -221,7 +221,7 @@ typedef struct + } ParseStruct; + + /* specific access mode of queryhash */ +-DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp,,) ++DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp, extern,) + DECLARE_SAFE_DEREF(GtUword *, ulp) + + /* Funktion, mit der der Metagenomethreader gestartet wird diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb new file mode 100644 index 00000000000..280fb4af01f --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -0,0 +1,97 @@ +# author: Denis Kristak (INUITS) +easyblock = 'CMakePythonPackage' + +name = 'GenomeWorks' +version = '2021.02.2' +local_commit = '691380d' # corresponds to 2021.02.2 tag + +homepage = 'https://github.com/clara-parabricks/GenomeWorks' +description = "SDK for GPU accelerated genome assembly and analysis" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/clara-parabricks', + 'repo_name': name, + 'commit': local_commit, + 'recursive': True, + }, +}] +# no checksum for source tarball because it's created locally via 'git clone' +checksums = [None] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Autoconf', '2.69'), + ('matplotlib', '3.3.3'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), + ('tqdm', '4.56.2'), +] + +# add missing include to a file +preconfigopts = "sed -i'' 's/#include /#include \\n#include /g'" +preconfigopts += " %(builddir)s/GenomeWorks/3rdparty/spoa/src/alignment_engine.cpp && """ + +preconfigopts += "sed -i 's/==/>=/g' %(builddir)s/GenomeWorks/pygenomeworks/requirements.txt && " +preconfigopts += "sed -i 's/~=/>=/g' %(builddir)s/GenomeWorks/pygenomeworks/requirements.txt && " + +# instruction from GenomeWorks' readme +configopts = "-Dgw_cuda_gen_all_arch=OFF " +configopts += " -Dgw_build_shared=ON " + +# no test targets +skipsteps = ['test'] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +local_genomeworks_preinstallopts = "sed -i 's/[=~]=/>=/g' requirements.txt && " +local_genomeworks_preinstallopts += "export GW_INSTALL_DIR=%(installdir)s && " +local_genomeworks_preinstallopts += "export GW_VERSION=%(version)s && " +local_genomeworks_preinstallopts += "export GW_ROOT_DIR=%(builddir)s/GenomeWorks && " + +exts_list = [ + ('sortedcollections', '2.1.0', { + 'source_urls': [PYPI_SOURCE], + 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], + }), + ('genomeworks', version, { + 'sources': ['GenomeWorks-%(version)s.tar.gz'], + # no checksum for source tarball because it's created locally via 'git clone' + 'checksums': [None], + 'start_dir': 'pygenomeworks', + 'preinstallopts': local_genomeworks_preinstallopts, + }), +] + +sanity_check_paths = { + 'files': ['bin/cudamapper', 'bin/cudapoa', 'bin/genome_simulator', + 'lib/libgwbase.%s' % SHLIB_EXT, 'lib/libgwio.%s' % SHLIB_EXT], + 'dirs': ['benchmarks', 'docs', 'include/claraparabricks/genomeworks', + 'lib/python%(pyshortver)s/site-packages', 'samples', 'tests'], +} + +sanity_check_commands = [ + "cudamapper --help", + "cudapoa --help", + "genome_simulator --help", + "python -c 'import genomeworks'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.54.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.54.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..a2a09968f24 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.54.0-GCCcore-10.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.54.0' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0646bb97f6f4d10a763f4919c54fa28b4fbdd3dff8e7de3410431c81762cade0'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.4'), + ('libjpeg-turbo', '2.0.6'), + ('expat', '2.2.9'), + ('GLib', '2.68.2'), + ('cairo', '1.16.0'), + ('LibTIFF', '4.2.0'), +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +# Avoid race condition in build if too much parallelism is used +maxparallel = 4 + +postinstallcmds = [ + # build and install shared libs + "make so && make soinstall", + # install header files + "mkdir -p %(installdir)s/include/ghostscript", + "install -v -m644 base/*.h %(installdir)s/include/ghostscript", + "install -v -m644 psi/*.h %(installdir)s/include/ghostscript", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/ghostscript', 'include/ghostscript', 'share/man'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-foss-2018b-Python-3.6.6.eb index 58081899110..17b186b11a5 100644 --- a/easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-foss-2018b-Python-3.6.6.eb @@ -20,17 +20,14 @@ sanity_pip_check = True exts_list = [ ('smmap2', '2.0.4', { 'modulename': 'smmap', - 'source_urls': ['https://pypi.python.org/packages/source/s/smmap2'], 'checksums': ['dc216005e529d57007ace27048eb336dcecb7fc413cfb3b2f402bb25972b69c6'], }), ('gitdb2', '2.0.4', { 'modulename': 'gitdb', - 'source_urls': ['https://pypi.python.org/packages/source/g/gitdb2'], 'checksums': ['bb4c85b8a58531c51373c89f92163b92f30f81369605a67cd52d1fc21246c044'], }), (name, version, { 'modulename': 'git', - 'source_urls': ['https://pypi.python.org/packages/source/g/GitPython'], 'checksums': ['8237dc5bfd6f1366abeee5624111b9d6879393d84745a507de0fda86043b65a8'], }), ] diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-intel-2018b-Python-3.6.6.eb index b07de071cbd..dd6bdf7be39 100644 --- a/easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-intel-2018b-Python-3.6.6.eb @@ -20,17 +20,14 @@ sanity_pip_check = True exts_list = [ ('smmap2', '2.0.4', { 'modulename': 'smmap', - 'source_urls': ['https://pypi.python.org/packages/source/s/smmap2'], 'checksums': ['dc216005e529d57007ace27048eb336dcecb7fc413cfb3b2f402bb25972b69c6'], }), ('gitdb2', '2.0.4', { 'modulename': 'gitdb', - 'source_urls': ['https://pypi.python.org/packages/source/g/gitdb2'], 'checksums': ['bb4c85b8a58531c51373c89f92163b92f30f81369605a67cd52d1fc21246c044'], }), (name, version, { 'modulename': 'git', - 'source_urls': ['https://pypi.python.org/packages/source/g/GitPython'], 'checksums': ['8237dc5bfd6f1366abeee5624111b9d6879393d84745a507de0fda86043b65a8'], }), ] diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-2.1.15.eb b/easybuild/easyconfigs/g/GitPython/GitPython-2.1.15.eb index bc1ad3c9fbc..25c660fdef1 100644 --- a/easybuild/easyconfigs/g/GitPython/GitPython-2.1.15.eb +++ b/easybuild/easyconfigs/g/GitPython/GitPython-2.1.15.eb @@ -13,8 +13,6 @@ use_pip = False allow_system_deps = [('Python', SYS_PYTHON_VERSION)] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - # version are pick to be compatible with both Python 2 and 3 exts_list = [ ('setuptools', '44.1.1', { diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.0.3-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.0.3-GCCcore-8.2.0-Python-3.7.2.eb index 3ca21a5bd92..2546e2c54c5 100644 --- a/easybuild/easyconfigs/g/GitPython/GitPython-3.0.3-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.0.3-GCCcore-8.2.0-Python-3.7.2.eb @@ -16,8 +16,6 @@ dependencies = [ ('git', '2.21.0', '-nodocs'), ] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.0-GCCcore-8.3.0-Python-3.7.4.eb index 53ee774642a..ff5ef06167c 100644 --- a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.0-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('smmap', '3.0.1', { 'checksums': ['171484fe62793e3626c8b05dd752eb2ca01854b0c55a1efc0dc4210fccb65446'], diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.18-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.18-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3bbd7a94022 --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.18-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.18' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('git', '2.32.0', '-nodocs'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('smmap', '4.0.0', { + 'checksums': ['7e65386bd122d45405ddf795637b7f7d2b532e7e401d46bbe3fb49b9986d5182'], + }), + ('gitdb', '4.0.7', { + 'checksums': ['96bf5c08b157a666fec41129e6d327235284cca4c81e92109260f353ba138005'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['b838a895977b45ab6f0cc926a9045c8d1c44e2b653c1fcc39fe91f42c6e8f05b'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0.eb index 31ddec11593..5e124bc9382 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0.eb @@ -15,11 +15,7 @@ multi_deps = {'Python': ['3.7.4', '2.7.16']} builddependencies = [('binutils', '2.32')] use_pip = True - -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} +sanity_pip_check = True exts_list = [ ('configobj', '5.0.6', { diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..94a5cbb5961 --- /dev/null +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GnuTLS' +version = '3.7.2' + +homepage = 'https://www.gnutls.org' +description = """GnuTLS is a secure communications library implementing the SSL, TLS + and DTLS protocols and technologies around them. It provides a simple + C language application programming interface (API) to access the secure + communications protocols as well as APIs to parse and write X.509, PKCS #12, + OpenPGP and other required structures. It is aimed to be portable + and efficient with focus on security and interoperability.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.gnupg.org/ftp/gcrypt/gnutls/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['646e6c5a9a185faa4cea796d378a1ba8e1148dbb197ca6605f95986a25af2752'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('GMP', '6.2.1'), + ('nettle', '3.7.2'), + ('Guile', '2.2.7'), + ('libtasn1', '4.17.0'), + ('libidn', '1.36'), + ('p11-kit', '0.24.0'), +] + +configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " +configopts += "--with-guile-site-ccache-dir=%(installdir)s/lib/guile/site-ccache " +configopts += "--with-guile-extension-dir=%(installdir)s/lib/guile/extensions" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['certtool', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]], + 'dirs': ['include/gnutls', 'lib/guile'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/Go/Go-1.16.5.eb b/easybuild/easyconfigs/g/Go/Go-1.16.5.eb new file mode 100644 index 00000000000..1f3ed26df22 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.16.5.eb @@ -0,0 +1,25 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Tarball' + +name = 'Go' +version = '1.16.5' + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] +sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] +checksums = ['b12c23023b68de22f74c0524f10b753e7b08b1504cb7e417eccebdd3fae49061'] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +modextravars = {'GOROOT': '%(installdir)s'} +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb new file mode 100644 index 00000000000..da19daca513 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.36' + +homepage = 'https://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_GZ] +patches = [ + 'GraphicsMagick_pkgconfig_libtiff.patch' +] +checksums = [ + '1e6723c48c4abbb31197fadf8396b2d579d97e197123edc70a4f057f0533d563', # GraphicsMagick-1.3.36.tar.gz + '25b4c5361f30e23c809a078ac4b26e670d2b8341496323480037e2095d969294', # GraphicsMagick_pkgconfig_libtiff.patch +] + +builddependencies = [('Autotools', '20200321')] + +dependencies = [ + ('X11', '20201008'), + ('bzip2', '1.0.8'), + ('freetype', '2.10.3'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('LibTIFF', '4.1.0'), + ('libxml2', '2.9.10'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('Ghostscript', '9.53.3'), +] + +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + +sanity_check_paths = { + 'files': ['bin/gm', 'lib/libGraphicsMagick.a', 'lib/libGraphicsMagick++.a', + 'lib/libGraphicsMagickWand.a'], + 'dirs': ['include/GraphicsMagick', 'lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..82bbddffe8d --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.2-GCCcore-10.3.0.eb @@ -0,0 +1,90 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '2.47.2' +local_pyver_major = '3' + +homepage = 'https://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Graphviz-2.42.2_skip-install-data-hook.patch'] +checksums = [ + '0f55cc79326fc1ff37aacf1e26ac0cd0e8eb5656035a470c8fb8b103fb4d4af3', # graphviz-2.47.2.tar.gz + '3d06544c435a6255f6a8f3b36df3102060667b50ffd72e4942bbe546b9363859', # Graphviz-2.42.2_skip-install-data-hook.patch +] + +builddependencies = [ + ('Autotools', '20210128'), + ('binutils', '2.36.1'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('SWIG', '4.0.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.9.5'), + ('FriBidi', '1.0.10'), + ('Gdk-Pixbuf', '2.42.6'), + ('Ghostscript', '9.54.0'), + ('GTS', '0.7.6'), + ('libgd', '2.3.1'), + ('Pango', '1.48.5'), + ('Perl', '5.32.1'), + ('Qt5', '5.15.2'), + ('Tcl', '8.6.11'), + ('zlib', '1.2.11'), +] + +preconfigopts = './autogen.sh NOCONFIG && ' + +configopts = '--enable-python%s=yes ' % local_pyver_major +configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' +# Use ltdl from libtool in EB +configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' +configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' +# Override the hardcoded paths to Java libraries +configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' +configopts += '--with-javalibdir=$JAVA_HOME/lib' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +postinstallcmds = ['%(installdir)s/bin/dot -c'] # Writes plugin configuration + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acyclic', 'bcomps', 'ccomps', 'cluster', 'diffimg', 'dijkstra', 'dot', + 'dot_builtins', 'dotty', 'edgepaint', 'gc', 'gml2gv', 'graphml2gv', 'gv2gml', + 'gvcolor', 'gvedit', 'gvgen', 'gvmap', 'gvmap.sh', 'gvpack', 'gvpr', 'gxl2gv', + 'lefty', 'lneato', 'mm2gv', 'nop', 'prune', 'sccmap', 'tred', 'unflatten', + 'vimdot']] + + ['lib/%s.%s' % (x, SHLIB_EXT) for x in ['libcdt', 'libcgraph', 'libgvc', 'libgvpr', 'liblab_gamut', + 'libpathplan', 'libxdot']], + 'dirs': ['include', 'lib/graphviz', 'lib/graphviz/java', 'lib/graphviz/python%s' % local_pyver_major, + 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), + ('python', '-c "import gv"'), +] + +modextrapaths = { + 'CLASSPATH': 'lib/graphviz/java', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'PYTHONPATH': 'lib/graphviz/python%s' % local_pyver_major, + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GromacsWrapper/GromacsWrapper-0.8.0-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GromacsWrapper/GromacsWrapper-0.8.0-fosscuda-2019a-Python-3.7.2.eb index 2e4cfe0c039..a61b13d61d0 100644 --- a/easybuild/easyconfigs/g/GromacsWrapper/GromacsWrapper-0.8.0-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GromacsWrapper/GromacsWrapper-0.8.0-fosscuda-2019a-Python-3.7.2.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('numkit', '1.1.2', { 'checksums': ['cc7cabd8cd733d93f9b5d490d116ce22971a852f93894ed98db1a00311845fab'], diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb index 1694edd45c2..32ea2805a04 100644 --- a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb @@ -15,7 +15,7 @@ name = 'GroopM' version = '0.3.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ecogenomics.github.io/GroopM/' +homepage = 'https://ecogenomics.github.io/GroopM/' description = """ GroopM is a metagenomic binning toolset. It leverages spatio-temporal dynamics (differential coverage) to accurately (and almost automatically) extract population genomes from multi-sample metagenomic datasets. @@ -23,7 +23,6 @@ description = """ GroopM is a metagenomic binning toolset. It leverages spatio-t toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['48bdaeb9010e7d81785697a55edc394ef36c2646b310d625a24bec740f1b6080'] diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.2.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-2.2.7-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b9a0a805883 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-2.2.7-GCCcore-10.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '2.2.7' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['44b4c5fbbe257ccdebea18420212c9b3e90c3c86a54920d8554039fc6769a007'] + +builddependencies = [ + ('Autotools', '20210128'), + ('binutils', '2.36.1'), +] + +dependencies = [ + ('gc', '8.0.4'), + ('GMP', '6.2.1'), + ('libffi', '3.3'), + ('libunistring', '0.9.10'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/gappa/gappa-0.7.1-GCC-10.3.0.eb b/easybuild/easyconfigs/g/gappa/gappa-0.7.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..a11955c4f83 --- /dev/null +++ b/easybuild/easyconfigs/g/gappa/gappa-0.7.1-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'gappa' +version = '0.7.1' + +homepage = 'https://github.com/lczech/gappa' +description = """ +gappa is a collection of commands for working with phylogenetic data. Its main +focus are evolutionary placements of short environmental sequences on a +reference phylogenetic tree. Such data is typically produced by tools like +EPA-ng, RAxML-EPA or pplacer and usually stored in jplace files. +""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/lczech/gappa/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['87aa73763c0bf2a2fe3b19e54cee66ce4c335a5e0d35ab839334090175e4c58c'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('make', '4.3'), +] + +files_to_copy = ['bin/%(name)s'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gc/gc-8.0.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gc/gc-8.0.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..7d14129641f --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.0.4-GCCcore-10.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.0.4' +local_libatomic_version = '7.6.10' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a + garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + '436a0ddc67b1ac0b0405b61a9675bca9e075c8156f4debd1d06f3a56c7cd289d', # gc-8.0.4.tar.gz + '587edf60817f56daf1e1ab38a4b3c729b8e846ff67b4f62a6157183708f099af', # libatomic_ops-7.6.10.tar.gz +] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gdbgui/gdbgui-0.13.1.2-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/g/gdbgui/gdbgui-0.13.1.2-GCCcore-8.2.0-Python-3.7.2.eb index 779082e0d71..905d2d08e50 100644 --- a/easybuild/easyconfigs/g/gdbgui/gdbgui-0.13.1.2-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/gdbgui/gdbgui-0.13.1.2-GCCcore-8.2.0-Python-3.7.2.eb @@ -22,7 +22,6 @@ use_pip = True exts_list = [ ('greenlet', '0.4.15', { - 'source_urls': ['https://pypi.python.org/packages/source/g/greenlet/'], 'checksums': ['9416443e219356e3c31f1f918a91badf2e37acf297e2fa13d24d1cc2380f8fbc'], }), ('pygdbmi', '0.9.0.1', { @@ -31,27 +30,21 @@ exts_list = [ 'checksums': ['9c3b1757dd11d6d90a2bf47a22277f6c204646402950fa981daffe740c2493ad'], }), ('gevent', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gevent/'], 'checksums': ['1eb7fa3b9bd9174dfe9c3b59b7a09b768ecd496debfc4976a9530a3e15c990d1'], }), ('itsdangerous', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous/'], 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], }), ('Flask-Compress', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/flask-compress/'], 'checksums': ['468693f4ddd11ac6a41bca4eb5f94b071b763256d54136f77957cfee635badb3'], }), ('Flask-SocketIO', '2.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/f/flask-socketio/'], 'checksums': ['f49edfd3a44458fbb9f7a04a57069ffc0c37f000495194f943a25d370436bb69'], }), ('Flask', '0.12.4', { - 'source_urls': ['https://pypi.python.org/packages/source/f/flask/'], 'checksums': ['2ea22336f6d388b4b242bc3abf8a01244a8aa3e236e7407469ef78c16ba355dd'], }), ('Werkzeug', '0.15.4', { - 'source_urls': ['https://pypi.python.org/packages/source/w/werkzeug/'], 'checksums': ['a0b915f0815982fb2a09161cb8f31708052d0951c3ba433ccc5e1aa276507ca6'], }), ('socketio', '4.1.0', { diff --git a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb index 8cbf5d6df0e..a1725592b5e 100644 --- a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'gdc-client' version = '1.0.1' @@ -10,9 +10,6 @@ description = """The gdc-client provides several convenience functions over the toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ('libxslt', '1.1.29'), @@ -20,23 +17,16 @@ dependencies = [ ] exts_list = [ - ('setuptools', '19.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), + ('setuptools', '19.2'), ('parcel', '20160602', { 'source_urls': ['https://github.com/LabAdvComp/parcel/archive'], 'source_tmpl': 'd3b619584606ed5d2f127f9ba12df7b764ebe975.tar.gz', }), - ('lxml', '3.5.0b1', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lxml/'], - }), + ('lxml', '3.5.0b1'), ('PyYAML', '3.11', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyYAML'], 'modulename': 'yaml', }), - ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - }), + ('jsonschema', '2.5.1'), (name, version, { 'source_urls': ['https://github.com/NCI-GDC/gdc-client/archive'], 'source_tmpl': 'v%(version)s.tar.gz', @@ -44,8 +34,6 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/gdc-client'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-foss-2018a-Python-2.7.14.eb index 78f0f587530..6f8a9c490c8 100644 --- a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-foss-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'gdc-client' version = '1.3.0' @@ -10,9 +10,6 @@ description = """The gdc-client provides several convenience functions over the toolchain = {'name': 'foss', 'version': '2018a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.14'), ('libxslt', '1.1.32'), @@ -21,91 +18,70 @@ dependencies = [ exts_list = [ ('pyasn1', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1'], 'checksums': ['738c4ebd88a718e700ee35c8d129acce2286542daa80a82823a7073644f706ad'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi'], 'checksums': ['ab87dd91c0c4073758d07334c1e5f712ce8fe48f007b86f8238773963ee700a6'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyOpenSSL', '17.1.0', { 'modulename': 'OpenSSL', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyOpenSSL'], 'checksums': ['5a20a51d35104cd234d056861ace3e7a335aaf1f47fc96726c9e20ac1dc49563'], }), ('ndg-httpsclient', '0.4.2', { 'modulename': 'ndg', 'source_tmpl': 'ndg_httpsclient-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/n/ndg-httpsclient'], 'checksums': ['580987ef194334c50389e0d7de885fccf15605c13c6eecaabd8d6c43768eb8ac'], }), ('lxml', '3.5.0b1', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lxml'], 'checksums': ['2244fadf836c45249bc31a4a959cf606fbcd675b3db6ffb50311d9f94a25e28b'], }), ('PyYAML', '3.11', { 'modulename': 'yaml', - 'source_urls': ['https://pypi.python.org/packages/source/P/PyYAML'], 'checksums': ['c36c938a872e5ff494938b33b14aaa156cb439ec67548fcab3535bb78b0846e8'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], 'checksums': ['36673ac378feed3daa5956276a829699056523d7961027911f064b52255ead41'], }), ('cmd2', '0.6.8', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cmd2'], 'checksums': ['ac780d8c31fc107bf6b4edcbcea711de4ff776d59d89bb167f8819d2d83764a8'], }), ('termcolor', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('sortedcontainers', '1.5.9', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], 'checksums': ['844daced0f20d75c02ce53f373d048ea2e401ad8a7b3a4c43b2aa544b569efb3'], }), ('intervaltree', '2.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/i/intervaltree'], 'checksums': ['d5c45ce8874ef04303c02b66327793320aa2027cf25c89188f74be69beaa3c5f'], }), ('itsdangerous', '0.24', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['cbb3fcf8d3e33df861709ecaf89d9e6629cff0a217bc2848f1b41cd30d360519'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['6246e5fc98a505824113fb6aca993d45ea284a2bcffdc2c65d0c538e53e4abd3'], }), ('Flask', '0.10.1', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['4c83829ff83d408b5e1d4995472265411d2c414112298f2eb4b359d9e4563373'], }), ('progressbar', '2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/progressbar'], 'checksums': ['b2d38a729785149e65323381d2e6fca0a5e9615a6d8bcf10bfa8adedfc481254'], }), ('requests', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests'], 'checksums': ['7b7735efd3b1e2323dc9fcef060b380d05f5f18bd0f247f5e9e74a628279de66'], }), ('parcel', '20170814', { @@ -121,8 +97,6 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/gdc-client'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-foss-2018b-Python-2.7.15.eb index 9c12234049e..950db311626 100644 --- a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-foss-2018b-Python-2.7.15.eb @@ -1,5 +1,5 @@ # easybuild easyconfig -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'gdc-client' version = '1.3.0' @@ -11,11 +11,7 @@ description = """The gdc-client provides several convenience functions over toolchain = {'name': 'foss', 'version': '2018b'} -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True dependencies = [ ('Python', '2.7.15'), @@ -25,91 +21,70 @@ dependencies = [ exts_list = [ ('pyasn1', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1'], 'checksums': ['738c4ebd88a718e700ee35c8d129acce2286542daa80a82823a7073644f706ad'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi'], 'checksums': ['ab87dd91c0c4073758d07334c1e5f712ce8fe48f007b86f8238773963ee700a6'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyOpenSSL', '17.1.0', { 'modulename': 'OpenSSL', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyOpenSSL'], 'checksums': ['5a20a51d35104cd234d056861ace3e7a335aaf1f47fc96726c9e20ac1dc49563'], }), ('ndg-httpsclient', '0.4.2', { 'modulename': 'ndg', 'source_tmpl': 'ndg_httpsclient-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/n/ndg-httpsclient'], 'checksums': ['580987ef194334c50389e0d7de885fccf15605c13c6eecaabd8d6c43768eb8ac'], }), ('lxml', '3.5.0b1', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lxml'], 'checksums': ['2244fadf836c45249bc31a4a959cf606fbcd675b3db6ffb50311d9f94a25e28b'], }), ('PyYAML', '3.11', { 'modulename': 'yaml', - 'source_urls': ['https://pypi.python.org/packages/source/P/PyYAML'], 'checksums': ['c36c938a872e5ff494938b33b14aaa156cb439ec67548fcab3535bb78b0846e8'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], 'checksums': ['36673ac378feed3daa5956276a829699056523d7961027911f064b52255ead41'], }), ('cmd2', '0.6.8', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cmd2'], 'checksums': ['ac780d8c31fc107bf6b4edcbcea711de4ff776d59d89bb167f8819d2d83764a8'], }), ('termcolor', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('sortedcontainers', '1.5.9', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], 'checksums': ['844daced0f20d75c02ce53f373d048ea2e401ad8a7b3a4c43b2aa544b569efb3'], }), ('intervaltree', '2.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/i/intervaltree'], 'checksums': ['d5c45ce8874ef04303c02b66327793320aa2027cf25c89188f74be69beaa3c5f'], }), ('itsdangerous', '0.24', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['cbb3fcf8d3e33df861709ecaf89d9e6629cff0a217bc2848f1b41cd30d360519'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['6246e5fc98a505824113fb6aca993d45ea284a2bcffdc2c65d0c538e53e4abd3'], }), ('Flask', '0.10.1', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['4c83829ff83d408b5e1d4995472265411d2c414112298f2eb4b359d9e4563373'], }), ('progressbar', '2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/progressbar'], 'checksums': ['b2d38a729785149e65323381d2e6fca0a5e9615a6d8bcf10bfa8adedfc481254'], }), ('requests', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests'], 'checksums': ['7b7735efd3b1e2323dc9fcef060b380d05f5f18bd0f247f5e9e74a628279de66'], }), ('parcel', '20170814', { @@ -125,8 +100,6 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/gdc-client'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-intel-2017b-Python-2.7.14.eb index dfe329084e2..2ffbfdbdeef 100644 --- a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.3.0-intel-2017b-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'gdc-client' version = '1.3.0' @@ -10,9 +10,6 @@ description = """The gdc-client provides several convenience functions over the toolchain = {'name': 'intel', 'version': '2017b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.14'), ('libxslt', '1.1.32'), @@ -21,91 +18,70 @@ dependencies = [ exts_list = [ ('pyasn1', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1'], 'checksums': ['738c4ebd88a718e700ee35c8d129acce2286542daa80a82823a7073644f706ad'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi'], 'checksums': ['ab87dd91c0c4073758d07334c1e5f712ce8fe48f007b86f8238773963ee700a6'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyOpenSSL', '17.1.0', { 'modulename': 'OpenSSL', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyOpenSSL'], 'checksums': ['5a20a51d35104cd234d056861ace3e7a335aaf1f47fc96726c9e20ac1dc49563'], }), ('ndg-httpsclient', '0.4.2', { 'modulename': 'ndg', 'source_tmpl': 'ndg_httpsclient-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/n/ndg-httpsclient'], 'checksums': ['580987ef194334c50389e0d7de885fccf15605c13c6eecaabd8d6c43768eb8ac'], }), ('lxml', '3.5.0b1', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lxml'], 'checksums': ['2244fadf836c45249bc31a4a959cf606fbcd675b3db6ffb50311d9f94a25e28b'], }), ('PyYAML', '3.11', { 'modulename': 'yaml', - 'source_urls': ['https://pypi.python.org/packages/source/P/PyYAML'], 'checksums': ['c36c938a872e5ff494938b33b14aaa156cb439ec67548fcab3535bb78b0846e8'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], 'checksums': ['36673ac378feed3daa5956276a829699056523d7961027911f064b52255ead41'], }), ('cmd2', '0.6.8', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cmd2'], 'checksums': ['ac780d8c31fc107bf6b4edcbcea711de4ff776d59d89bb167f8819d2d83764a8'], }), ('termcolor', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('sortedcontainers', '1.5.9', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], 'checksums': ['844daced0f20d75c02ce53f373d048ea2e401ad8a7b3a4c43b2aa544b569efb3'], }), ('intervaltree', '2.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/i/intervaltree'], 'checksums': ['d5c45ce8874ef04303c02b66327793320aa2027cf25c89188f74be69beaa3c5f'], }), ('itsdangerous', '0.24', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], 'checksums': ['cbb3fcf8d3e33df861709ecaf89d9e6629cff0a217bc2848f1b41cd30d360519'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Werkzeug', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['6246e5fc98a505824113fb6aca993d45ea284a2bcffdc2c65d0c538e53e4abd3'], }), ('Flask', '0.10.1', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], 'checksums': ['4c83829ff83d408b5e1d4995472265411d2c414112298f2eb4b359d9e4563373'], }), ('progressbar', '2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/progressbar'], 'checksums': ['b2d38a729785149e65323381d2e6fca0a5e9615a6d8bcf10bfa8adedfc481254'], }), ('requests', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests'], 'checksums': ['7b7735efd3b1e2323dc9fcef060b380d05f5f18bd0f247f5e9e74a628279de66'], }), ('parcel', '20170814', { @@ -121,8 +97,6 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/gdc-client'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb index f6f38f5d9fe..f55afd7a8a7 100644 --- a/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb @@ -11,16 +11,10 @@ description = """The gdist module is a Cython interface to a C++ library (http:/ toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.11'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb index 5fdf478fc7e..63fe4e46948 100644 --- a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'gensim' version = '0.13.2' @@ -10,37 +10,18 @@ description = """Gensim is a Python library for topic modelling, document indexi toolchain = {'name': 'foss', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.11'), ('requests', '2.10.0', '-Python-%(pyver)s'), ] exts_list = [ - ('boto', '2.42.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/%(name)s'], - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - }), - ('bz2file', '0.98', { - 'source_urls': ['https://pypi.python.org/packages/source/b/%(name)s'], - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - }), - ('smart_open', '1.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/s/%(name)s'], - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/g/%(name)s'], - }), + ('boto', '2.42.0'), + ('bz2file', '0.98'), + ('smart_open', '1.3.4'), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-foss-2019b-Python-3.7.4.eb index b6e38576136..b6d2b53e5ce 100644 --- a/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-foss-2019b-Python-3.7.4.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('descartes', '1.1.0', { 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-fosscuda-2019b-Python-3.7.4.eb index 44fc1d3a24e..3fb9add57ca 100644 --- a/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-fosscuda-2019b-Python-3.7.4.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('descartes', '1.1.0', { 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.8.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.8.0-foss-2019a-Python-3.7.2.eb index 4012ee6c16a..e779532aa0e 100644 --- a/easybuild/easyconfigs/g/geopandas/geopandas-0.8.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.8.0-foss-2019a-Python-3.7.2.eb @@ -36,8 +36,6 @@ components = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('descartes', '1.1.0', { 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.8.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.8.1-intel-2019b-Python-3.7.4.eb index 82453c148d9..ffbe5e69ff2 100644 --- a/easybuild/easyconfigs/g/geopandas/geopandas-0.8.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.8.1-intel-2019b-Python-3.7.4.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('descartes', '1.1.0', { 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], diff --git a/easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a-Python-3.6.1.eb index 4b03e02aeed..a34d08f03f0 100644 --- a/easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a-Python-3.6.1.eb @@ -9,14 +9,8 @@ description = "geopy is a Python 2 and 3 client for several popular geocoding we toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.6.1')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..3c5929e8422 --- /dev/null +++ b/easybuild/easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'geopy' +version = '2.1.0' + +homepage = 'https://geopy.readthedocs.io/en/stable/' +description = """ +geopy is a Python client for several popular geocoding web services. +geopy makes it easy for Python developers to locate the coordinates of addresses, cities, countries, +and landmarks across the globe using third-party geocoders and other data sources. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [('Python', '3.8.6')] + +use_pip = True + +exts_list = [ + ('geographiclib', '1.50', { + 'checksums': ['12bd46ee7ec25b291ea139b17aa991e7ef373e21abd053949b75c0e9ca55c632'], + }), + (name, version, { + 'checksums': ['892b219413e7955587b029949af3a1949c6fbac9d5ad17b79d850718f6a9550f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/gexiv2/gexiv2-0.12.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gexiv2/gexiv2-0.12.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..98ca8f0e8d8 --- /dev/null +++ b/easybuild/easyconfigs/g/gexiv2/gexiv2-0.12.2-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MesonNinja' + +name = 'gexiv2' +version = '0.12.2' + +homepage = 'https://wiki.gnome.org/Projects/gexiv2' +description = "gexiv2 is a GObject wrapper around the Exiv2 photo metadata library." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://download-fallback.gnome.org/sources/gexiv2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['2322b552aca330eef79724a699c51a302345d5e074738578b398b7f2ff97944c'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), + ('Vala', '0.52.4'), +] + +dependencies = [ + ('exiv2', '0.27.4'), + ('GObject-Introspection', '1.68.0'), +] + +configopts = "-Dpython2_girdir=no -Dpython3_girdir=no " + +sanity_check_paths = { + 'files': ['lib/libgexiv2.%s' % SHLIB_EXT, 'lib/pkgconfig/gexiv2.pc'], + 'dirs': ['include/gexiv2'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/git/git-2.32.0-GCCcore-10.3.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.32.0-GCCcore-10.3.0-nodocs.eb new file mode 100644 index 00000000000..5559af9962b --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.32.0-GCCcore-10.3.0-nodocs.eb @@ -0,0 +1,44 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.32.0' +versionsuffix = '-nodocs' + +homepage = 'https://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['004697482b6e3b0ae9147580c32efd35869426227f1526f8eafa7950c31def94'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), +] + +dependencies = [ + ('cURL', '7.76.0'), + ('expat', '2.2.9'), + ('gettext', '0.21'), + ('Perl', '5.32.1'), + ('OpenSSL', '1.1', '', True), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['libexec/git-core', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f267bb08489 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +## +# Authors: +# * The Crick HPC team, uploaded by J. Sassmannshausen +# * Robert Mijakovic +## + +easyblock = 'ConfigureMake' + +name = 'glew' +version = '2.1.0' + +homepage = 'http://glew.sourceforge.net/' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['04de91e7e6763039bc11940095cd9c7f880baba82196a7765f727ac05a993c95'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Mesa', '21.1.1')] + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all' + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': ['', ] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb index 61dd4c138ad..32893834e0c 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb @@ -22,7 +22,8 @@ sources = ['%(name)s-%(version)s.tgz'] checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] builddependencies = [('binutils', '2.35')] -buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system dependencies = [ ('Mesa', '20.2.1'), ('X11', '20201008'), @@ -31,7 +32,7 @@ dependencies = [ skipsteps = ['configure'] preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' -install_cmd = 'make install.all' +install_cmd = 'make install.all ' + local_system sanity_check_paths = { 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb index b995d85444f..083e28d4575 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb @@ -22,7 +22,8 @@ sources = ['%(name)s-%(version)s.tgz'] checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] builddependencies = [('binutils', '2.35')] -buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system dependencies = [ ('Mesa', '20.2.1'), ('X11', '20201008'), @@ -31,7 +32,7 @@ dependencies = [ skipsteps = ['configure'] preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' -install_cmd = 'make install.all' +install_cmd = 'make install.all ' + local_system sanity_check_paths = { 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb index 77964f2f35f..cb58df1067b 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb @@ -22,7 +22,8 @@ sources = ['%(name)s-%(version)s.tgz'] checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] builddependencies = [('binutils', '2.35')] -buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system dependencies = [ ('Mesa', '20.2.1'), ('X11', '20201008'), @@ -31,7 +32,7 @@ dependencies = [ skipsteps = ['configure'] preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' -install_cmd = 'make install.all' +install_cmd = 'make install.all ' + local_system sanity_check_paths = { 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-foss-2017b-Python-2.7.14.eb index 2c15e2790ca..50825d35654 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-foss-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['dd233e3288b90f21b0bb384bcc7a7e73557bb112ccf0032ad52aa614eb373d3f'] @@ -23,9 +22,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-foss-2017b-Python-3.6.3.eb index 4d083bcc5da..524482cc437 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-foss-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['dd233e3288b90f21b0bb384bcc7a7e73557bb112ccf0032ad52aa614eb373d3f'] @@ -23,9 +22,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb index d82b9f3a9d4..6a5afa26f15 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb @@ -9,7 +9,6 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] dependencies = [ @@ -19,9 +18,4 @@ dependencies = [ ('MPC', '1.0.3'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017b-Python-2.7.14.eb index c6ca8e79258..eefb7932bc1 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['dd233e3288b90f21b0bb384bcc7a7e73557bb112ccf0032ad52aa614eb373d3f'] @@ -23,9 +22,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017b-Python-3.6.3.eb index 26fecadd685..36c6aaf5a29 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['dd233e3288b90f21b0bb384bcc7a7e73557bb112ccf0032ad52aa614eb373d3f'] @@ -23,9 +22,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2017b-Python-2.7.14.eb index 2243f092077..6a3f25cb29e 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['30b30707c782e4e355c920d1d998751ffc1b2189070a88a482f08c6e35511939'] @@ -23,9 +22,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2017b-Python-3.6.3.eb index 882e9f523f2..4e299ec38f1 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['30b30707c782e4e355c920d1d998751ffc1b2189070a88a482f08c6e35511939'] @@ -23,9 +22,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-intel-2017b-Python-2.7.14.eb index 4696caa86a5..fa9cee567e3 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-intel-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['30b30707c782e4e355c920d1d998751ffc1b2189070a88a482f08c6e35511939'] @@ -23,9 +22,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-intel-2017b-Python-3.6.3.eb index e9e38fa734b..68f03001efb 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-intel-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['30b30707c782e4e355c920d1d998751ffc1b2189070a88a482f08c6e35511939'] @@ -23,9 +22,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b4-GCC-8.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b4-GCC-8.3.0.eb index de42ebc2374..403786c77c5 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b4-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b4-GCC-8.3.0.eb @@ -8,7 +8,6 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'GCC', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9564deb6dcc7045749c0c5d73b23855ef6220c60b4cc6ffa4b1e0b1b1ee95eaf'] diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.3.0.eb new file mode 100644 index 00000000000..07b227f0f55 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.0b5' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8951bcfc61c0f40102b92a4777daf9eb85445b537c4d09086deb0e097190bef0'] + +dependencies = [ + ('Python', '3.9.5'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.8.4-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.8.4-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..1410bea3468 --- /dev/null +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.8.4-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'gmsh' +version = '4.8.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://gmsh.info/' +description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {"usempi": True} + +source_urls = ['https://gmsh.info/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] +checksums = ['760dbdc072eaa3c82d066c5ba3b06eacdd3304eb2a97373fe4ada9509f0b6ace'] + +builddependencies = [ + ('CMake', '3.12.1'), + ('SWIG', '3.0.12', versionsuffix), +] + +dependencies = [ + ('Python', '3.6.4'), + ('PETSc', '3.9.3'), + ('SLEPc', '3.9.2'), +] + +separate_build_dir = True + +configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' + +modextrapaths = {'PYTHONPATH': ['lib64']} + +sanity_check_paths = { + 'files': ['bin/gmsh', 'bin/onelab.py'], + 'dirs': [], +} + +sanity_check_commands = ["gmsh --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f4127746086 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.4.2' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['e57c75e1318133951d32a83bcdc4aff17fed28722c4e71f2305cfc2ae1cae7ba'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), + ('Autotools', '20210128'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('cairo', '1.16.0'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('libgd', '2.3.1'), + ('Pango', '1.48.5'), + ('libcerf', '1.17'), + ('X11', '20210518'), + ('Qt5', '5.15.2'), + ('Lua', '5.4.3'), +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.11.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.11.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..62636115c07 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.11.0-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.11.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['b4870bf121ff7795ba20d20bcdd8627b8e088f2d1dab299a031c1034eddc93d5'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..e29ea9698a3 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.9.1' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'gperftools' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['484a88279d2fa5753d7e9dea5f86954b64975f20e796a6ffaf2f3426a674a06a'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), +] + +dependencies = [ + ('libunwind', '1.4.0'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e7725eca757 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.9.1' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'gperftools' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['484a88279d2fa5753d7e9dea5f86954b64975f20e796a6ffaf2f3426a674a06a'] + +builddependencies = [ + ('Autotools', '20210128'), + ('binutils', '2.36.1'), +] + +dependencies = [ + ('libunwind', '1.4.0'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb index 7ff8e499d58..b957f235126 100644 --- a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb @@ -17,20 +17,16 @@ use_pip = True exts_list = [ ('psutil', '5.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], }), ('blessings', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blessings'], 'checksums': ['98e5854d805f50a5b58ac2333411b0482516a8210f23f43308baeb58d77c157d'], }), ('nvidia-ml-py', '7.352.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nvidia-ml-py'], 'checksums': ['b4a342ba52a51ff794af38279ce62f78b278ba5f50c13103af52c4f6113ff65e'], 'modulename': 'pynvml', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/g/gpustat'], 'checksums': ['2f43421dbcd9ebd8caf179aeb5f78ac123786033fb9a4310ce0f8e18b25eb03e'], }), ] diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb index 9291ce32844..9126544a48d 100644 --- a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb @@ -16,8 +16,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('psutil', '5.7.0', { 'checksums': ['685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e'], diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb index 7290bfdd17e..346cabf772e 100644 --- a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = """Simple Python interface for Graphviz""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] dependencies = [ @@ -17,9 +16,4 @@ dependencies = [ ('Graphviz', '2.38.0'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-2.7.12.eb index 365523c5299..3d13addde20 100644 --- a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = """Simple Python interface for Graphviz""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] dependencies = [ @@ -17,9 +16,4 @@ dependencies = [ ('Graphviz', '2.38.0'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-3.5.2.eb index 236bb554544..47c26978fe3 100644 --- a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-3.5.2.eb @@ -9,7 +9,6 @@ description = """Simple Python interface for Graphviz""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] dependencies = [ @@ -17,9 +16,4 @@ dependencies = [ ('Graphviz', '2.38.0'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.8.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/graphviz/graphviz-0.8.2-intel-2018a-Python-3.6.4.eb index 3fb259fe876..d066bb3b71c 100644 --- a/easybuild/easyconfigs/g/graphviz/graphviz-0.8.2-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/g/graphviz/graphviz-0.8.2-intel-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = """Simple Python interface for Graphviz""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['606741c028acc54b1a065b33045f8c89ee0927ea77273ec409ac988f2c3d1091'] @@ -18,9 +17,4 @@ dependencies = [ ('Graphviz', '2.40.1'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb index 4d08613ba52..76c7be899c2 100644 --- a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb @@ -15,7 +15,7 @@ checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] builddependencies = [ ('binutils', '2.35'), - ('makeinfo', '6.7'), + ('makeinfo', '6.7', '-minimal'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.3.0.eb index 95b41f84fdf..27917ff5cf2 100644 --- a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.3.0.eb @@ -1,6 +1,3 @@ -## -# Author: Robert Mijakovic -## easyblock = 'ConfigureMake' name = 'groff' @@ -18,7 +15,7 @@ checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] builddependencies = [ ('binutils', '2.36.1'), - ('makeinfo', '6.7'), + ('makeinfo', '6.7', '-minimal'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb index 5d17ecce652..dbcd9eff63f 100644 --- a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb @@ -15,7 +15,7 @@ checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] builddependencies = [ ('binutils', '2.34'), - ('makeinfo', '6.7'), + ('makeinfo', '6.7', '-minimal'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/gsport/gsport-1.4.2-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/g/gsport/gsport-1.4.2-GCCcore-8.3.0-Python-3.7.4.eb index 35bcb6b7f42..949f69f9b21 100644 --- a/easybuild/easyconfigs/g/gsport/gsport-1.4.2-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/gsport/gsport-1.4.2-GCCcore-8.3.0-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = """GSPORT command-line tool for accessing GenomeScan Customer Port toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b8b96ef8ab3f83ff05c56677879b8a374ef0292a050c947e5cd3f68c9026f8a1'] diff --git a/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb new file mode 100644 index 00000000000..7753fb4bfa7 --- /dev/null +++ b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb @@ -0,0 +1,114 @@ +easyblock = 'MakeCp' + +name = 'HAL' +version = '2.1' + +homepage = 'https://github.com/ComparativeGenomicsToolkit/hal' +description = """HAL is a structure to efficiently store and index multiple genome alignments +and ancestral reconstructions. HAL is a graph-based representation which +provides several advantages over matrix/block-based formats such as MAF, such as +improved scalability and the ability to perform queries with respect to an +arbitrary reference or subtree. + +This package includes the HAL API and several analysis and conversion tools +which are described below. HAL files are presently stored in either HDF5 or mmap +format, but we note that the tools and most of the API are format-independent, +so other databases could be implemented in the future. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +local_sonLib_datetime = '20210415' +local_sonLib_hash = '562a466e4570c93a647ffb10aa2628143b4ee9f4' + +sources = [ + { + 'source_urls': ['https://github.com/ComparativeGenomicsToolkit/hal/archive/refs/tags/'], + 'filename': 'release-V%(version)s.tar.gz', + 'extract_cmd': 'tar xvf %s && mv hal-release-V%(version)s hal' + }, + { + 'source_urls': ['https://github.com/ComparativeGenomicsToolkit/sonLib/archive/'], + 'download_filename': '%s.tar.gz' % local_sonLib_hash, + 'filename': 'sonLib-%s-%s.tar.gz' % (local_sonLib_datetime, local_sonLib_hash), + 'extract_cmd': 'tar xvf %s && mv sonLib-' + local_sonLib_hash + ' hal/sonLib' + }, +] +checksums = [ + '540255be1af55abf390359fe034b82d7e61bdf6c3277df3cc01259cd450994e5', # release-V2.1.tar.gz + # sonLib-20210415-562a466e4570c93a647ffb10aa2628143b4ee9f4.tar.gz + '3ef2b1dd7805b636afae104728c74e0dff2cfee3a68166836300eff4d0952109', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('Sibelia', '3.0.7'), + ('PyYAML', '5.3.1'), +] + +prebuildopts = 'pushd sonLib && make && popd && ' +buildopts = 'sonLibRootDir=$(pwd)/sonLib' + +files_to_copy = [ + (['bin/*', 'sonLib/bin/*'], 'bin'), + (['lib/*', 'sonLib/lib/*'], 'lib'), + (['sonLib/src/sonLib/*'], 'lib/python%(pyshortver)s/site-packages/sonLib'), + (['__init__.py', 'mutations', 'randgen', 'analysis', 'extract', 'modify', + 'phyloP', 'assemblyHub', 'extra', 'validate', 'blockViz', 'stats', 'maf', 'liftover'], + 'lib/python%(pyshortver)s/site-packages/hal') +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], +} +exts_list = [ + ('addict', '2.2.1', { + 'checksums': ['f22493f056032f50e4931a82444fcba8ef74c8fc994c5d06aa546a1433c2b8b0'], + }), + ('dill', '0.3.4', { + 'source_tmpl': 'dill-%(version)s.zip', + 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], + }), + ('enlighten', '1.10.1', { + 'checksums': ['3391916586364aedced5d6926482b48745e4948f822de096d32258ba238ea984'], + }), + ('websocket-client', '1.1.0', { + 'modulename': 'websocket', + 'checksums': ['b68e4959d704768fa20e35c9d508c8dc2bbc041fd8d267c0d7345cffe2824568'], + }), + ('blessed', '1.18.1', { + 'checksums': ['8b09936def6bc06583db99b65636b980075733e13550cb6af262ce724a55da23'], + }), + ('prefixed', '0.3.2', { + 'checksums': ['ca48277ba5fa8346dd4b760847da930c7b84416387c39e93affef086add2c029'], + }), + ('docker', '4.3.1', { + 'checksums': ['bad94b8dd001a8a4af19ce4becc17f41b09f228173ffe6a4e0355389eef142f2'], + }), + ('toil', '5.3.0', { + 'checksums': ['4ea8f703ee697c4b5ff506db545d0dbb6e4753fbfc61c4230f1eccba8f860e7c'], + }), + ('newick', '1.3.0', { + 'checksums': ['a34010de5047481277dfad76b29f3db525d539f34d876437a861da6a24fca0c8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/halValidate'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + "halValidate --help 2>&1 | grep 'halValidate v%(version)s'", + "python -c 'from sonLib.bioio import getTempFile'", + "python -c 'from hal.stats.halStats import getHalGenomes'" +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HDDM/HDDM-0.6.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/HDDM/HDDM-0.6.1-intel-2018b-Python-3.6.6.eb index 970dc7dfa17..351be47d36f 100644 --- a/easybuild/easyconfigs/h/HDDM/HDDM-0.6.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/HDDM/HDDM-0.6.1-intel-2018b-Python-3.6.6.eb @@ -25,15 +25,12 @@ exts_list = [ 'checksums': ['12765987a5d64eaf210b1a32053990a0a4cacf2458e93d9b35ebab239032a4b5'], }), ('kabuki', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kabuki'], 'checksums': ['3d5e727529b323b3f12ec583c05702e863e7d4b1f31a7ba6077058115eb066b1'], }), ('patsy', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/H/HDDM'], 'checksums': ['fe5a4fae962539041a450df5ab039ea14edc0bfd4d88dd8639c0030a375f0d21'], }), ] diff --git a/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-2.7.16.eb index 38f035485c5..9723a77e91a 100644 --- a/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-2.7.16.eb @@ -25,15 +25,12 @@ exts_list = [ 'checksums': ['12765987a5d64eaf210b1a32053990a0a4cacf2458e93d9b35ebab239032a4b5'], }), ('kabuki', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kabuki'], 'checksums': ['3d5e727529b323b3f12ec583c05702e863e7d4b1f31a7ba6077058115eb066b1'], }), ('patsy', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/H/HDDM'], 'checksums': ['da13c51db24816d77ee04ebe9f7adbe5e4304da8e11a58371c660477f80b7f99'], }), ] diff --git a/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb index 989ce387e07..ba801e78b97 100644 --- a/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb @@ -29,15 +29,12 @@ exts_list = [ ], }), ('kabuki', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kabuki'], 'checksums': ['3d5e727529b323b3f12ec583c05702e863e7d4b1f31a7ba6077058115eb066b1'], }), ('patsy', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/H/HDDM'], 'checksums': ['da13c51db24816d77ee04ebe9f7adbe5e4304da8e11a58371c660477f80b7f99'], }), ] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb index 6a9f6d507b9..bdb2cb878ee 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb @@ -15,7 +15,11 @@ toolchainopts = {'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459'] +patches = ['HDF-4.2.15_fix-aarch64.patch'] +checksums = [ + 'dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459', # hdf-4.2.15.tar.gz + '1b4341e309cccefc6ea4310c8f8b08cc3dfe1fa9609b7fa7aee80e4dac598473', # HDF-4.2.15_fix-aarch64.patch +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..869a6a796a2 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.15' + +homepage = 'https://www.hdfgroup.org/products/hdf4/' + +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['HDF-4.2.15_fix-aarch64.patch'] +checksums = [ + 'dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459', # hdf-4.2.15.tar.gz + '1b4341e309cccefc6ea4310c8f8b08cc3dfe1fa9609b7fa7aee80e4dac598473', # HDF-4.2.15_fix-aarch64.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '2.0.6'), + ('Szip', '2.1.1'), + ('zlib', '1.2.11'), + ('libtirpc', '1.3.2'), +] + +preconfigopts = "LIBS='-ltirpc' " +local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' +local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' +configopts = [ + # -fallow-argument-mismatch is required to compile with GCC 10.x + local_common_configopts + 'FFLAGS="$FFLAGS -fallow-argument-mismatch"', + # Cannot build shared libraries and Fortran... + # https://trac.osgeo.org/gdal/wiki/HDF#IncompatibilitywithNetCDFLibraries + # netcdf must be disabled to allow HDF to be used by GDAL + local_common_configopts + "--enable-shared --disable-fortran --disable-netcdf", +] + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', + 'lib/libmfhdf.%s' % SHLIB_EXT], + 'dirs': ['include/hdf'], +} + +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb index 1c3ae1022a6..fd6e6693977 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb @@ -15,7 +15,11 @@ toolchainopts = {'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459'] +patches = ['HDF-4.2.15_fix-aarch64.patch'] +checksums = [ + 'dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459', # hdf-4.2.15.tar.gz + '1b4341e309cccefc6ea4310c8f8b08cc3dfe1fa9609b7fa7aee80e4dac598473', # HDF-4.2.15_fix-aarch64.patch +] builddependencies = [ ('binutils', '2.34'), diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15_fix-aarch64.patch b/easybuild/easyconfigs/h/HDF/HDF-4.2.15_fix-aarch64.patch new file mode 100644 index 00000000000..ffd703095ba --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15_fix-aarch64.patch @@ -0,0 +1,302 @@ +fix installation of HDF on aarch64, fixes compilation problems like: +hdfi.h:1119:1: error: unknown type name 'No' + 1119 | No machine type has been defined. Your Makefile needs to have someing like + +cfr. https://src.fedoraproject.org/rpms/hdf/blob/rawhide/f/hdf-aarch64.patch +diff -ru hdf-4.2.15.orig/hdf/src/hconv.h hdf-4.2.15/hdf/src/hconv.h +--- hdf-4.2.15.orig/hdf/src/hconv.h 2020-03-03 17:40:50.000000000 +0000 ++++ hdf-4.2.15/hdf/src/hconv.h 2021-06-05 14:08:07.061188314 +0000 +@@ -59,7 +59,7 @@ + /* CONSTANT DEFINITIONS */ + /*****************************************************************************/ + /* Generally Big-Endian machines */ +-#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) ++#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) && !defined(__arm__) && !defined(__AARCH64EL__) + # define UI8_IN DFKnb1b /* Unsigned Integer, 8 bits */ + # define UI8_OUT DFKnb1b + # define SI16_IN DFKnb2b /* S = Signed */ +diff -ru hdf-4.2.15.orig/hdf/src/hdfi.h hdf-4.2.15/hdf/src/hdfi.h +--- hdf-4.2.15.orig/hdf/src/hdfi.h 2020-03-03 17:40:50.000000000 +0000 ++++ hdf-4.2.15/hdf/src/hdfi.h 2021-06-05 14:07:29.321474674 +0000 +@@ -75,6 +75,8 @@ + #define DFMT_IA64 0x4441 + #define DFMT_LINUX64 0x4441 + #define DFMT_POWERPC64 0x1111 ++#define DFMT_LINUXARM 0x4441 ++#define DFMT_LINUXAARCH64 0x4441 + + /* I/O library constants */ + #define UNIXUNBUFIO 1 +@@ -1115,6 +1117,44 @@ + + #endif /* IA64 */ + ++/* Linux AArch64 */ ++#if defined __aarch64__ ++ ++#ifdef GOT_MACHINE ++If you get an error on this line more than one machine type has been defined. ++Please check your Makefile. ++#endif ++#define GOT_MACHINE ++ ++#include /* for unbuffered i/o stuff */ ++#include ++#define DF_MT DFMT_LINUXAARCH64 ++typedef void VOID; ++typedef void *VOIDP; ++typedef char *_fcd; ++typedef char char8; ++typedef unsigned char uchar8; ++typedef char int8; ++typedef unsigned char uint8; ++typedef short int int16; ++typedef unsigned short int uint16; ++typedef int int32; ++typedef unsigned int uint32; ++typedef int intn; ++typedef unsigned int uintn; ++typedef int intf; /* size of INTEGERs in Fortran compiler */ ++typedef float float32; ++typedef double float64; ++typedef long hdf_pint_t; /* an integer the same size as a pointer */ ++#define FNAME_POST_UNDERSCORE ++#define _fcdtocp(desc) (desc) ++#ifdef HAVE_FMPOOL ++#define FILELIB PAGEBUFIO /* enable page buffering */ ++#else ++#define FILELIB UNIXBUFIO ++#endif ++#endif /* Linux AArch64 */ ++ + #ifndef GOT_MACHINE + No machine type has been defined. Your Makefile needs to have someing like + -DSUN or -DUNICOS in order for the HDF internal structures to be defined +diff -ru hdf-4.2.15.orig/mfhdf/fortran/jackets.c.in hdf-4.2.15/mfhdf/fortran/jackets.c.in +--- hdf-4.2.15.orig/mfhdf/fortran/jackets.c.in 2020-03-03 17:40:50.000000000 +0000 ++++ hdf-4.2.15/mfhdf/fortran/jackets.c.in 2021-06-05 14:10:46.759976563 +0000 +@@ -34,7 +34,7 @@ + + struct ncfils { /* This will be a common block from Fortran */ + double dd; +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + int ll; + #else + long ll; +@@ -65,7 +65,7 @@ + + struct ncfils { /* This will be a common block from Fortran */ + double dd; +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + int ll; + #else + long ll; +@@ -420,7 +420,7 @@ + } + #endif /* FORTRAN_HAS_NO_SHORT */ + +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + /* + * Convert multi-dimensional array of NCLONGs stored in ints to packed + * array of longs, in malloc'ed space. Returns pointer to longs or NULL +@@ -908,7 +908,7 @@ + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long longs = *(int *)value; +@@ -1022,7 +1022,7 @@ + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long *longs = itol (value, ncount, ndims); +@@ -1133,7 +1133,7 @@ + tmpbasis = nctypelen(NC_LONG); + else + #endif +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + if (datatype == NC_LONG) + tmpbasis = sizeof(int); + else +@@ -1190,7 +1190,7 @@ + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long *longs = itolg (value, ncount, nbasis, ndims); +@@ -1326,7 +1326,7 @@ + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long longs; +@@ -1468,7 +1468,7 @@ + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long iocount = dimprod (ncount, ndims); /* product of dimensions */ +@@ -1606,7 +1606,7 @@ + tmpbasis = nctypelen(NC_LONG); + else + #endif +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + if (datatype == NC_LONG) + tmpbasis = sizeof(int); + else +@@ -1677,7 +1677,7 @@ + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long iocount = dimprod (ncount, ndims); /* product of dimensions */ +@@ -1843,7 +1843,7 @@ + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + #ifdef HDF + if ((nc_type) *datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long *longs = itol (value, attlen, 1); +@@ -2008,7 +2008,7 @@ + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + /* EIP We need to use int buffer to read data in on the platforms where long is 8 bytes +diff -ru hdf-4.2.15.orig/mfhdf/libsrc/netcdf.h.in hdf-4.2.15/mfhdf/libsrc/netcdf.h.in +--- hdf-4.2.15.orig/mfhdf/libsrc/netcdf.h.in 2020-03-03 17:40:50.000000000 +0000 ++++ hdf-4.2.15/mfhdf/libsrc/netcdf.h.in 2021-06-05 14:11:19.389728978 +0000 +@@ -293,7 +293,7 @@ + /* + * Variables/attributes of type NC_LONG should use the C type 'nclong' + */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + /* + * LP64 (also known as 4/8/8) denotes long and pointer as 64 bit types. + * http://www.unix.org/version2/whatsnew/lp64_wp.html +diff -ru hdf-4.2.15.orig/mfhdf/libsrc/putget.c hdf-4.2.15/mfhdf/libsrc/putget.c +--- hdf-4.2.15.orig/mfhdf/libsrc/putget.c 2020-03-03 17:40:50.000000000 +0000 ++++ hdf-4.2.15/mfhdf/libsrc/putget.c 2021-06-05 14:11:54.279464243 +0000 +@@ -665,7 +665,7 @@ + case NC_SHORT : + return( xdr_NCvshort(xdrs, (unsigned)rem/2, (short *)values) ) ; + case NC_LONG : +-#if (_MIPS_SZLONG == 64) || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ ++#if (_MIPS_SZLONG == 64) || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + return( xdr_int(xdrs, (nclong *)values) ) ; + #else + return( xdr_long(xdrs, (nclong *)values) ) ; +diff -ru hdf-4.2.15.orig/mfhdf/libsrc/xdrposix.c hdf-4.2.15/mfhdf/libsrc/xdrposix.c +--- hdf-4.2.15.orig/mfhdf/libsrc/xdrposix.c 2020-03-03 17:40:50.000000000 +0000 ++++ hdf-4.2.15/mfhdf/libsrc/xdrposix.c 2021-06-05 14:13:41.138652587 +0000 +@@ -262,7 +262,7 @@ + + static bool_t xdrposix_getlong(); + static bool_t xdrposix_putlong(); +-#if (_MIPS_SZLONG == 64) || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ ++#if (_MIPS_SZLONG == 64) || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + static bool_t xdrposix_getint(); + static bool_t xdrposix_putint(); + #endif +@@ -276,7 +276,7 @@ + #if (defined __sun && defined _LP64) + static rpc_inline_t * xdrposix_inline(); + #else +-#if ((defined __x86_64__ ) && !(defined __sun && defined _LP64)) || defined __powerpc64__ ++#if ((defined __x86_64__ ) && !(defined __sun && defined _LP64)) || defined __powerpc64__|| defined __aarch64__ + static int32_t * xdrposix_inline(); + #else + static netlong * xdrposix_inline(); +@@ -302,9 +302,9 @@ + xdrposix_getpos, /* get offset in the stream */ + xdrposix_setpos, /* set offset in the stream */ + xdrposix_inline, /* prime stream for inline macros */ +-#if (defined __sun && defined _LP64) || defined __x86_64__ || defined __powerpc64__ ++#if (defined __sun && defined _LP64) || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + xdrposix_destroy, /* destroy stream */ +-#if !(defined __x86_64__) && !(defined __powerpc64__) || (defined __sun && defined _LP64) /* i.e. we are on SUN/Intel in 64-bit mode */ ++#if !(defined __x86_64__) && !(defined __powerpc64__) && !(defined __aarch64__) || (defined __sun && defined _LP64) /* i.e. we are on SUN/Intel in 64-bit mode */ + NULL, /* no xdr_control function defined */ + #endif + /* Solaris 64-bit (arch=v9 and arch=amd64) has 64 bits long and 32 bits int. */ +@@ -442,7 +442,7 @@ + long *lp; + { + unsigned char *up = (unsigned char *)lp ; +-#if (defined AIX5L64 || defined __powerpc64__ || (defined __hpux && __LP64__)) ++#if (defined AIX5L64 || defined __powerpc64__ || (defined __hpux && __LP64__)) || defined __aarch64__ + *lp = 0 ; + up += (sizeof(long) - 4) ; + #endif +@@ -560,7 +560,7 @@ + #if (defined __sun && defined _LP64) + static rpc_inline_t * + #else +-#if ((defined __x86_64__) && !(defined __sun && defined _LP64)) || defined __powerpc64__ ++#if ((defined __x86_64__) && !(defined __sun && defined _LP64)) || defined __powerpc64__ || defined __aarch64__ + static int32_t * + #else + static netlong * +@@ -581,7 +581,7 @@ + return (NULL); + } + +-#if (_MIPS_SZLONG == 64) || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ ++#if (_MIPS_SZLONG == 64) || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ || defined __aarch64__ + + static bool_t + xdrposix_getint(xdrs, lp) +diff -ru hdf-4.2.15.orig/mfhdf/ncgen/ncgen.l hdf-4.2.15/mfhdf/ncgen/ncgen.l +--- hdf-4.2.15.orig/mfhdf/ncgen/ncgen.l 2020-03-03 17:40:50.000000000 +0000 ++++ hdf-4.2.15/mfhdf/ncgen/ncgen.l 2021-06-05 14:14:02.448490344 +0000 +@@ -113,7 +113,7 @@ + yyerror(errstr); + } + +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || __powerpc64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || __powerpc64__ || defined __aarch64__ + if (dd < INT_MIN || dd > INT_MAX) + #else + if (dd < LONG_MIN || dd > LONG_MAX) +diff -ru hdf-4.2.15.orig/mfhdf/ncgen/ncgenyy.c hdf-4.2.15/mfhdf/ncgen/ncgenyy.c +--- hdf-4.2.15.orig/mfhdf/ncgen/ncgenyy.c 2020-03-03 17:40:50.000000000 +0000 ++++ hdf-4.2.15/mfhdf/ncgen/ncgenyy.c 2021-06-05 14:14:33.818251508 +0000 +@@ -991,7 +991,7 @@ + yyerror(errstr); + } + +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || __powerpc64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || __powerpc64__ || defined __aarch64__ + if (dd < INT_MIN || dd > INT_MAX) + #else + if (dd < LONG_MIN || dd > LONG_MAX) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-gompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-gompi-2021a.eb new file mode 100644 index 00000000000..6d97a0de1d3 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-gompi-2021a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.7' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iimpi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iimpi-2021a.eb new file mode 100644 index 00000000000..45eb03efa0e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iimpi-2021a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.7' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-foss-2020a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-foss-2020a.eb new file mode 100644 index 00000000000..6061ecdaa0b --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-foss-2020a.eb @@ -0,0 +1,50 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +# 2.2.1 - changes from Adam Huffman +## + +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.2.1' + +homepage = 'https://ccb.jhu.edu/software/%(namelower)s/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +sources = [{ + 'source_urls': ['https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi'], + 'download_filename': 'download', + 'filename': '%(namelower)s-%(version)s-source.zip', +}] +checksums = ['48e933330d4d8470d2b3dfe7ec3918f2e98a75f7381891e23b7df1fb4f135eb1'] + +dependencies = [ + ('NGS', '2.10.5'), + ('ncbi-vdb', '2.10.7'), +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +local_executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l', 'hisat2-repeat', 'extract_exons.py', + 'extract_splice_sites.py', 'hisat2_extract_exons.py', 'hisat2_extract_snps_haplotypes_UCSC.py', + 'hisat2_extract_snps_haplotypes_VCF.py', 'hisat2_extract_splice_sites.py', + 'hisat2_read_statistics.py', 'hisat2_simulate_reads.py'] +files_to_copy = [(local_executables, 'bin'), 'scripts', 'example'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables], + 'dirs': ['scripts', 'example'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.10.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.10.0-foss-2018a-Python-2.7.14.eb index 91530d6178d..a03f8010cbc 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.10.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.10.0-foss-2018a-Python-2.7.14.eb @@ -6,12 +6,11 @@ name = 'HTSeq' version = '0.10.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e119af03cf068e981d7e08c4bd6393fd635007b595541943615b72abd676e547'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.0-foss-2018b-Python-2.7.15.eb index 372691fb67f..c5a5b235878 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.0-foss-2018b-Python-2.7.15.eb @@ -6,12 +6,11 @@ name = 'HTSeq' version = '0.11.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['19145fd3359baa4a8dd5c93470aa0a77e16da3ffde8e4e10fa8df4191df5cd29'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.0-intel-2018b-Python-2.7.15.eb index db1f336b248..b9d1fb4d0dc 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.0-intel-2018b-Python-2.7.15.eb @@ -6,12 +6,11 @@ name = 'HTSeq' version = '0.11.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['19145fd3359baa4a8dd5c93470aa0a77e16da3ffde8e4e10fa8df4191df5cd29'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb index 80e3db3157e..cf623ae02f3 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb @@ -6,12 +6,11 @@ name = 'HTSeq' version = '0.11.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/%(name)s/' +homepage = 'https://www-huber.embl.de/users/anders/%(name)s/' description = "A framework to process and analyze data from high-throughput sequencing (HTS) assays" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['65c4c13968506c7df92e97124df96fdd041c4476c12a548d67350ba8b436bcfc'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019a-Python-3.7.2.eb index a7735548334..ef24be11d92 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019a-Python-3.7.2.eb @@ -12,7 +12,6 @@ description = """HTSeq is a Python library to facilitate processing and analysis toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['65c4c13968506c7df92e97124df96fdd041c4476c12a548d67350ba8b436bcfc'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb index c6a4660ec07..7c2e179796d 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = """HTSeq is a Python library to facilitate processing and analysis toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['65c4c13968506c7df92e97124df96fdd041c4476c12a548d67350ba8b436bcfc'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016a-Python-2.7.11.eb index 40ff5797bac..de952d1cf61 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016a-Python-2.7.11.eb @@ -4,12 +4,11 @@ name = 'HTSeq' version = '0.6.1p1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb index c7f13d0e1c7..5c8ac95883e 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb @@ -4,12 +4,11 @@ name = 'HTSeq' version = '0.6.1p1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb index 12d319ea7b1..519a5a4cdd1 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb @@ -4,12 +4,11 @@ name = 'HTSeq' version = '0.6.1p1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb index 0e056b9e6c1..dd3ba2daf66 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb @@ -6,12 +6,11 @@ name = 'HTSeq' version = '0.9.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb index 2d71d7cdc61..004427e98ad 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb @@ -6,12 +6,11 @@ name = 'HTSeq' version = '0.9.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb index c18aae96747..0436ac8ca2d 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb @@ -6,12 +6,11 @@ name = 'HTSeq' version = '0.9.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017a-Python-2.7.13.eb index d576c324cca..952dca4bf6c 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017a-Python-2.7.13.eb @@ -6,12 +6,11 @@ name = 'HTSeq' version = '0.9.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb index a2deee36ee5..107494e6648 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb @@ -6,12 +6,11 @@ name = 'HTSeq' version = '0.9.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb index ba86ce1fb54..042790bc765 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb @@ -6,12 +6,11 @@ name = 'HTSeq' version = '0.9.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2018a-Python-2.7.14.eb index ee5faa431ca..7f3b43c52a8 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2018a-Python-2.7.14.eb @@ -6,12 +6,11 @@ name = 'HTSeq' version = '0.9.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +homepage = 'https://www-huber.embl.de/users/anders/HTSeq/' description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..5662fb3cc49 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb @@ -0,0 +1,41 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '2.8.1' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b3f17394c5bccee456172b2b30ddec0bb87e9c5df38b4559a973d14ccd04509d'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('GObject-Introspection', '1.68.0'), + ('pkg-config', '0.29.2'), + ('Autotools', '20210128'), +] + +dependencies = [ + ('GLib', '2.68.2'), + ('ICU', '69.1'), + ('cairo', '1.16.0'), + ('freetype', '2.10.4'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-2.1.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-2.1.1-foss-2018a-Python-3.6.4.eb index d3b5bfdc270..98499b34897 100644 --- a/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-2.1.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-2.1.1-foss-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'HiCExplorer' version = '2.1.1' @@ -18,33 +18,25 @@ dependencies = [ ('h5py', '2.7.1', versionsuffix), ] -exts_defaultclass = 'PythonPackage' - exts_list = [ ('intervaltree', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/intervaltree'], 'checksums': ['aca5804b88f70cb49050c37b6de59090570f77a75aec1932966cf69f6a48810b'], }), ('pyBigWig', '0.3.11', { 'modulename': 'pyBigWig', - 'source_urls': ['https://pypi.python.org/packages/source/p/pybigwig'], 'checksums': ['408ebb40f01c72c77adde4d785a18dabc9abbe9020024e4296b8f6a51a662ae7'], }), ('future', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'], }), ('cooler', '0.7.6', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cooler'], 'checksums': ['434559940e933d355dbe14b8188a887eb7e866f0e60ed86e84034521bce81c45'], }), ('Jinja2', '2.10', { 'options': {'modulename': 'jinja2'}, - 'source_urls': ['https://pypi.python.org/packages/source/j/jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Unidecode', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/unidecode'], 'checksums': ['8c33dd588e0c9bc22a76eaa0c715a5434851f726131bd44a6c26471746efabf5'], }), (name, version, { @@ -54,11 +46,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.1-foss-2019a-Python-3.7.2.eb index 28ae5158f8c..482c96e0f61 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.1-foss-2019a-Python-3.7.2.eb @@ -17,8 +17,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cloudpickle', '1.2.2', { 'checksums': ['922401d7140e133253ff5fab4faa4a1166416066453a783b00b507dca93f8859'], @@ -28,9 +26,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.0-Python-3.7.4.eb index 3bc8867e84c..7961fe5553f 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.0-Python-3.7.4.eb @@ -22,8 +22,6 @@ sanity_pip_check = True preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cloudpickle', '1.2.2', { 'checksums': ['922401d7140e133253ff5fab4faa4a1166416066453a783b00b507dca93f8859'], diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.2-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.2-Python-3.7.4.eb index 41a1a33219f..3b3947919da 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.2-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.2-Python-3.7.4.eb @@ -22,8 +22,6 @@ sanity_pip_check = True preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cloudpickle', '1.2.2', { 'checksums': ['922401d7140e133253ff5fab4faa4a1166416066453a783b00b507dca93f8859'], diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb index a14bba096a4..1551eac081f 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb @@ -22,8 +22,6 @@ sanity_pip_check = True preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cloudpickle', '1.2.2', { 'checksums': ['922401d7140e133253ff5fab4faa4a1166416066453a783b00b507dca93f8859'], diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.19.1-fosscuda-2019b-TensorFlow-2.1.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.19.1-fosscuda-2019b-TensorFlow-2.1.0-Python-3.7.4.eb index 776accd1a8a..335d43a59be 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.19.1-fosscuda-2019b-TensorFlow-2.1.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.19.1-fosscuda-2019b-TensorFlow-2.1.0-Python-3.7.4.eb @@ -22,8 +22,6 @@ sanity_pip_check = True preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cloudpickle', '1.2.2', { 'checksums': ['922401d7140e133253ff5fab4faa4a1166416066453a783b00b507dca93f8859'], diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.19.5-fosscuda-2019b-TensorFlow-2.2.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.19.5-fosscuda-2019b-TensorFlow-2.2.0-Python-3.7.4.eb index 1f9c3d6b011..e1a185b60ef 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.19.5-fosscuda-2019b-TensorFlow-2.2.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.19.5-fosscuda-2019b-TensorFlow-2.2.0-Python-3.7.4.eb @@ -22,8 +22,6 @@ sanity_pip_check = True preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cloudpickle', '1.5.0', { 'checksums': ['820c9245cebdec7257211cbe88745101d5d6a042bca11336d78ebd4897ddbc82'], diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.20.3-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.20.3-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb index 2470b55fa5c..bbde301e1ba 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.20.3-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.20.3-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb @@ -25,8 +25,6 @@ sanity_pip_check = True preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cloudpickle', '1.5.0', { 'checksums': ['820c9245cebdec7257211cbe88745101d5d6a042bca11336d78ebd4897ddbc82'], diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2019b-PyTorch-1.7.1-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2019b-PyTorch-1.7.1-Python-3.7.4.eb index a1192b6d896..0f136a8a46e 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2019b-PyTorch-1.7.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2019b-PyTorch-1.7.1-Python-3.7.4.eb @@ -28,8 +28,6 @@ preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_W parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cloudpickle', '1.5.0', { 'checksums': ['820c9245cebdec7257211cbe88745101d5d6a042bca11336d78ebd4897ddbc82'], diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2019b-TensorFlow-2.4.1-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2019b-TensorFlow-2.4.1-Python-3.7.4.eb index d8204fbe121..4c74fefb0cd 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2019b-TensorFlow-2.4.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2019b-TensorFlow-2.4.1-Python-3.7.4.eb @@ -28,8 +28,6 @@ preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_W parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cloudpickle', '1.5.0', { 'checksums': ['820c9245cebdec7257211cbe88745101d5d6a042bca11336d78ebd4897ddbc82'], diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020a-TensorFlow-2.3.1-Python-3.8.2.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020a-TensorFlow-2.3.1-Python-3.8.2.eb index 819a73e57db..259da5ff2ea 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020a-TensorFlow-2.3.1-Python-3.8.2.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020a-TensorFlow-2.3.1-Python-3.8.2.eb @@ -18,7 +18,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.2'), ('PyYAML', '5.3'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb index fe80381811b..7335bc5ac23 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb @@ -17,7 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), ('PyYAML', '5.3.1'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('PyTorch', local_pt_version), ] diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb new file mode 100644 index 00000000000..450a4626c5f --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.22.0' +local_pt_version = '1.8.1' +versionsuffix = '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), + ('flatbuffers', '1.12.0'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('PyTorch', local_pt_version), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + 'checksums': ['ed7526eeb5a9aca8a8a49a04a41a4648cb7b0a265857875fc5d6a04a739fdb37'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.1-intel-2017b-Python-2.7.14.eb index b8e70cf6ddb..81736595fa3 100644 --- a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.1-intel-2017b-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'Hyperopt' version = '0.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://hyperopt.github.io/hyperopt/' +homepage = 'https://hyperopt.github.io/hyperopt/' description = """hyperopt is a Python library for optimizing over awkward search spaces with real-valued, discrete, and conditional dimensions.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = ['Hyperopt-%(version)s_networkx-2.0.patch'] checksums = [ @@ -20,9 +19,4 @@ checksums = [ dependencies = [('Python', '2.7.14')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-foss-2021a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-foss-2021a.eb new file mode 100644 index 00000000000..f9ac0c866bc --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-foss-2021a.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'Hypre' +version = '2.21.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e380f914fe7efe22afc44cdf553255410dc8a02a15b2e5ebd279ba88817feaf5'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-Python-3.7.4.eb index 73db8f1cc14..1527f6c2208 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-%(version)s_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-fosscuda-2019b-Python-3.7.4.eb index 868d0058df5..15bfa77a7b0 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-fosscuda-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'fosscuda', 'version': '2019b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-%(version)s_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2019b-Python-3.7.4.eb index f2a37cad24d..61281eb59b0 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-%(version)s_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intelcuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intelcuda-2019b-Python-3.7.4.eb index 55f3c6286dd..18c23430d89 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intelcuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intelcuda-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intelcuda', 'version': '2019b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-%(version)s_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb index a4fd2837f9b..a759fbde381 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.5.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': False} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.8.16' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16.eb index 82bab13bca2..68987816c02 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.5.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.8.16' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-3.5.1-HDF5-1.8.16.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-3.5.1-HDF5-1.8.16.eb index 57965666d90..97eb861f762 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-3.5.1-HDF5-1.8.16.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-3.5.1-HDF5-1.8.16.eb @@ -5,7 +5,7 @@ version = '2.5.0' local_hdf5ver = '1.8.16' versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % local_hdf5ver -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -13,7 +13,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-%%(version)s-foss-2016a-Python-%%(pyver)s-HDF5-%s.patch' % local_hdf5ver] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb index d698f5483cb..b8c3a264932 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.5.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'usempi': False} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.8.16' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb index 0aa5cf9552c..ce6fbd66a04 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.5.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.8.16' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb index 29e4e46d37c..b3c644fad1e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.6.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.10.0-patch1' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.17.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.17.eb index 85ca3937692..a63fcb1eea8 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.17.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.17.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.6.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.8.17' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.18.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.18.eb index 2b87f7e737b..3119b7b681c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.18.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.18.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.6.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.8.18' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb index 8d27e286ca2..6de6de69ee7 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.6.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.10.0-patch1' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.8.18.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.8.18.eb index 90fd5b8c4ff..8d27bae1805 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.8.18.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.8.18.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.6.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.8.18' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016a-Python-2.7.11.eb index c1fd6e9c2f3..a4ebabb46b7 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.6.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb index dfb2b5c70e4..cd706bf19fc 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.6.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.10.0-patch1' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb index dfb0e8ed57c..ebfedb8ac95 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.6.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.8.17' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb index dc578098d47..2ab8f46d813 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.6.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.8.18' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb index 4cfe67cf77e..356b9803743 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.6.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.10.0-patch1' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb index 7b7a55e6420..6641bfd28b3 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.6.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.8.17' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.18.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.18.eb index 017b0d4d895..454113bd034 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.18.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.18.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.6.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_hdf5ver = '1.8.18' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb index b781021a2a6..750cd5c3378 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.7.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb index 7c4fd9e0727..f735512f788 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.7.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.10.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.10.1.eb index d8147a0effb..d1a03b92d89 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.10.1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.10.1.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.7.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.8.19.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.8.19.eb index 46e6b441f2e..bbd05d071e6 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.8.19.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.8.19.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.7.0' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb index 804ee87fa7c..d5913a99fac 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb index d45cef772eb..ba26927393a 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb index 9edda058448..0cc8e6fce3b 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb @@ -5,7 +5,7 @@ version = '2.7.0' local_hdf5_ver = '1.10.0-patch1' versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % local_hdf5_ver -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -13,7 +13,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb index f4dfcfc6f13..500dd12e431 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb index da90cccec5c..02659597091 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] @@ -23,7 +22,7 @@ dependencies = [ ] # To really use mpi enabled hdf5 we now seem to need a configure step -# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +# Works with pip. Tested with examples in https://docs.h5py.org/en/stable/mpi.html preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' use_pip = True diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb index 7aaecb0ed9a..ea9719799ae 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] @@ -23,7 +22,7 @@ dependencies = [ ] # To really use mpi enabled hdf5 we now seem to need a configure step -# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +# Works with pip. Tested with examples in https://docs.h5py.org/en/stable/mpi.html preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' use_pip = True diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2018a-Python-2.7.14.eb index 9481b426d1e..67df54b75e0 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2018a-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2018a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2018a-Python-3.6.4.eb index 3738ca2994e..094413c9243 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2018a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-2.7.14.eb index c254f513aec..a24c532ca13 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'fosscuda', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-3.6.3.eb index 99997f9907c..14ad8d11b0e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'fosscuda', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-2.7.13.eb index a34bfde78b7..1e19d22ba43 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-2.7.13.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-3.6.1.eb index 356f080aeb3..747ef913987 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-3.6.1.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb index 6afc1986df9..0eb4b0197bf 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] @@ -23,7 +22,7 @@ dependencies = [ ] # To really use mpi enabled hdf5 we now seem to need a configure step -# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +# Works with pip. Tested with examples in https://docs.h5py.org/en/stable/mpi.html preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' use_pip = True diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb index 7331785ea92..22f1288d2bc 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] @@ -23,7 +22,7 @@ dependencies = [ ] # To really use mpi enabled hdf5 we now seem to need a configure step -# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +# Works with pip. Tested with examples in https://docs.h5py.org/en/stable/mpi.html preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' use_pip = True diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-2.7.14-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-2.7.14-serial.eb index cf973bfc81c..118544f0835 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-2.7.14-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-2.7.14-serial.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s-serial' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2018a'} toolchainopts = {'usempi': False} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-2.7.14.eb index 6e84c380db2..cde6e73f5a5 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2018a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-3.6.4.eb index 7bdf5d84c36..68fac412ca8 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'h5py' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.h5py.org/' +homepage = 'https://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2018a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-foss-2018b-Python-2.7.15.eb index edfee06ed27..5556de46d0e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-foss-2018b-Python-2.7.15.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-2.10.0_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-foss-2018b-Python-3.6.6.eb index abbf19bc43e..7a8d6cb77b6 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-foss-2018b-Python-3.6.6.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-2.10.0_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-2.7.15.eb index 3e967cfc11e..01260926373 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-2.7.15.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'fosscuda', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-2.10.0_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-3.6.6.eb index 381a19379ae..d0571d974a1 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-3.6.6.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'fosscuda', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-2.10.0_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-2.7.15-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-2.7.15-serial.eb index 2cd435e80b5..186dfc196e1 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-2.7.15-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-2.7.15-serial.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'usempi': False} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e626c65a8587921ebc7fb8d31a49addfdd0b9a9aa96315ea484c09803337b955'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-2.7.15.eb index 04f90e4b409..649d4a36ac7 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-2.7.15.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-2.10.0_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-3.6.6.eb index bb66bc7ff51..b73b6bc8104 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-intel-2018b-Python-3.6.6.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-2.10.0_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb index 5cdce347651..20e1f0893ab 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-2.10.0_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb index 78746893a61..8557b9463de 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'fosscuda', 'version': '2019a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-2.10.0_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb index 56cf5f3e8c3..00a242a42ce 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2019a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-2.10.0_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb index 50a43b74e30..716e056593e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intelcuda', 'version': '2019a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-2.10.0_avoid-mpi-init.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb new file mode 100644 index 00000000000..36656ead5b2 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.2.1' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['89474be911bfcdb34cbf0d98b8ec48b578c27a89fdb1ae4ee7513f1ef8d9249e'] + +builddependencies = [('pkgconfig', '1.5.4', '-python')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('HDF5', '1.10.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb index 52346888250..8ee9d1902b0 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb index 53cb823d426..95b33f19656 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb index 31352d991d6..f5191f7af56 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb index 0da051bd2d4..ce2aef97f03 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb index 5f36662beee..0ba26f75c63 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb index 88ee1a23f1f..b0ee3b3f289 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-intel-2016a-Python-2.7.11.eb index 225dbc580f5..ea6beb02ab9 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-intel-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb index 07257d88953..37a6b75aa02 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-intel-2016a-Python-2.7.11.eb index a03565acd71..c8a9f916228 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-intel-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb index bf815b89e8c..b690d69de80 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-intel-2016a-Python-2.7.11.eb index 4923d95a2f7..dfb850cb0b4 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-intel-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb index 96ce2681cdb..1c54dbe72e5 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-intel-2016b-Python-2.7.12.eb index 012fa0c7638..c344402bb0e 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb index 9b08399c6ed..453fefa5448 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb index 08cd609af5e..d7a2250529c 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb index 01b8d95ac1f..25073afd3d6 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb index 64e3b2fc18b..877aaf82531 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb index fbc85768bd6..41fb847fcf7 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb index cc811494ff7..2b63aacbecc 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ It uses the Torque resource manager to do node allocation.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime diff --git a/easybuild/easyconfigs/h/hdf5storage/hdf5storage-0.1.15-foss-2019a.eb b/easybuild/easyconfigs/h/hdf5storage/hdf5storage-0.1.15-foss-2019a.eb index bdac8f32bde..55f5f690421 100644 --- a/easybuild/easyconfigs/h/hdf5storage/hdf5storage-0.1.15-foss-2019a.eb +++ b/easybuild/easyconfigs/h/hdf5storage/hdf5storage-0.1.15-foss-2019a.eb @@ -14,7 +14,6 @@ description = """This Python package provides high level utilities to read/write toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = ['%(name)s-%(version)s.zip'] checksums = ['79d23ad4ca89b8824b4ff98764ff9403a9830caa7497cae75e001d2dfbbf4e8e'] diff --git a/easybuild/easyconfigs/h/hdf5storage/hdf5storage-0.1.15-fosscuda-2019a.eb b/easybuild/easyconfigs/h/hdf5storage/hdf5storage-0.1.15-fosscuda-2019a.eb index 69922e64076..4af2ac3c08f 100644 --- a/easybuild/easyconfigs/h/hdf5storage/hdf5storage-0.1.15-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/h/hdf5storage/hdf5storage-0.1.15-fosscuda-2019a.eb @@ -14,7 +14,6 @@ description = """This Python package provides high level utilities to read/write toolchain = {'name': 'fosscuda', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = ['%(name)s-%(version)s.zip'] checksums = ['79d23ad4ca89b8824b4ff98764ff9403a9830caa7497cae75e001d2dfbbf4e8e'] diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.4.0.eb new file mode 100644 index 00000000000..08d063f0300 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.8' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '8.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['528f6a81ad34cbc76aa7dce5a82f8b3d2078ef065271ab81fda033842018a8dc'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.32', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-9.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-9.4.0.eb new file mode 100644 index 00000000000..a3563b02d50 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-9.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.48.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '9.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['8361ff3c643fbd391064e97e5f54592ca28b880eaffbf566a68e0ad800d1a8ac'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.36.1', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb new file mode 100644 index 00000000000..d06d9b20df6 --- /dev/null +++ b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMake' + +name = 'hipify-clang' +version = '4.2.0' + +homepage = 'https://github.com/ROCm-Developer-Tools/HIPIFY' +description = """Hipify-clang is a clang-based tool for translating CUDA + sources into HIP sources. It translates CUDA source into an abstract syntax + tree, which is traversed by transformation matchers. After applying all the + matchers, the output HIP source is produced.""" + +toolchain = {'name': 'gcccuda', 'version': '2020b'} + +source_urls = ['https://github.com/ROCm-Developer-Tools/HIPIFY/archive/refs/tags/'] +sources = ['rocm-%(version)s.tar.gz'] +checksums = ['afdc82ae00e14e8e742be6cd47d8fb120d18fc52fe96cba8d8ac4c56176a432e'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Clang', '11.0.1'), + # ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), + # ('Python', '3.8.6'), +] + +# NOTE: The following configuration options are needed if building with tests +# (as activated by 'runtest' below), for these to work the above commented +# dependencies need to be uncommented. Currently testing is disabled due to a +# lack of 'llvm-lit'. +# configopts = '-DHIPIFY_CLANG_TESTS=1' +# configopts += ' -DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA' +# configopts += ' -DCUDA_DNN_ROOT_DIR=$EBROOTCUDNN' +# configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python' + +# runtest = 'test-hipify' + +# For some reason the executable is not placed in 'bin' +postinstallcmds = [ + 'mv %(installdir)s/%(namelower)s %(installdir)s/bin/.' +] + +sanity_check_commands = [('hipify-clang', '--version')] +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['include'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.2.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.2.0-intel-2017b-Python-2.7.14.eb index 196e35de8ec..1d26895793c 100644 --- a/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.2.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.2.0-intel-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = "hmmlearn is a set of algorithms for unsupervised learning and inf toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['694646f8302bc6402925a4b6892f3a5ccede06d25f22157c18cfbdecdb748361'] @@ -18,9 +17,4 @@ dependencies = [ ('scikit-learn', '0.19.1', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.2.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.2.0-intel-2018a-Python-3.6.4.eb index db043209eeb..9da202d38a1 100644 --- a/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.2.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.2.0-intel-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = "hmmlearn is a set of algorithms for unsupervised learning and inf toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['694646f8302bc6402925a4b6892f3a5ccede06d25f22157c18cfbdecdb748361'] diff --git a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb b/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb index 6fce3e5290c..94664ec45e6 100644 --- a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb +++ b/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb @@ -30,8 +30,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('tqdm', '4.46.0', { 'checksums': ['4733c4a10d0f2a4d098d801464bdaf5240c7dadd2a7fde4ee93b0a0efd9fb25e'], diff --git a/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb index 6ee1f2efcb9..61ddd2fe071 100644 --- a/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'hyperspy' version = '1.1.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://hyperspy.org/' +homepage = 'https://hyperspy.org/' description = """HyperSpy is an open source Python library which provides tools to facilitate the interactive data analysis of multi-dimensional datasets that can be described as multi-dimensional arrays of a given signal (e.g. a 2D array of spectra a.k.a spectrum image)""" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.5.2'), # provides dateutil, numpy, requests, scipy ('h5py', '2.6.0', versionsuffix + '-HDF5-1.8.18'), @@ -23,43 +20,20 @@ dependencies = [ exts_list = [ ('dill', '0.2.5', { - 'source_urls': ['https://pypi.python.org/packages/source/d/dill'], 'source_tmpl': 'dill-%(version)s.tgz', }), - ('ipyparallel', '5.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipyparallel'], - }), - ('natsort', '5.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/natsort'], - }), - ('requests', '2.12.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests'], - }), - ('mpmath', '0.19', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], - }), - ('sympy', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sympy'], - }), - ('tqdm', '4.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tqdm'], - }), - ('traits', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traits'], - }), - ('pyface', '5.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyface/'], - }), - ('traitsui', '5.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitsui'], - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/h/hyperspy'], - }), + ('ipyparallel', '5.2.0'), + ('natsort', '5.0.1'), + ('requests', '2.12.4'), + ('mpmath', '0.19'), + ('sympy', '1.0'), + ('tqdm', '4.10.0'), + ('traits', '4.6.0'), + ('pyface', '5.1.0'), + ('traitsui', '5.1.0'), + (name, version), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.23.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.23.4-GCCcore-8.2.0.eb index ad60febd74a..2db50f6cb6e 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.23.4-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.23.4-GCCcore-8.2.0.eb @@ -20,11 +20,9 @@ use_pip = True exts_list = [ ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/h/hypothesis/'], 'checksums': ['a9708beea61b45ee11de99aa61e06fe6d559aeccabe5017f9080522449727f18'], }), ] diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.39.3-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.39.3-intel-2018a-Python-3.6.4.eb index 8812771cb50..cf87b46675d 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.39.3-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.39.3-intel-2018a-Python-3.6.4.eb @@ -21,20 +21,16 @@ use_pip = True exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('attrs', '19.3.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], }), ('coverage', '5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/coverage'], 'checksums': ['280baa8ec489c4f542f8940f9c4c2181f0306a8ee1a54eceba071a449fb870a0'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/h/hypothesis/'], 'checksums': ['48978b121244e28c445007db1c3f5b2bbd5bbb8e8e8e9625b6c79860c520b7cb'], }), ] diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.44.2-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.44.2-GCCcore-8.3.0-Python-3.7.4.eb index 605d9b32417..cd1dd6b1a42 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.44.2-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.44.2-GCCcore-8.3.0-Python-3.7.4.eb @@ -18,8 +18,6 @@ dependencies = [('Python', '3.7.4')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('attrs', '19.3.0', { 'modulename': 'attr', diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb index b601f23494d..4b6e1ae560e 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb @@ -21,11 +21,9 @@ use_pip = True exts_list = [ ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/h/hypothesis/'], 'checksums': ['2187928e96bab144b89c6c19d08d61dc247bb1623e58e31bec1da7f71381fa9e'], }), ] diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb index 7bde035e223..b1327a5af40 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb @@ -21,11 +21,9 @@ use_pip = True exts_list = [ ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/h/hypothesis/'], 'checksums': ['2187928e96bab144b89c6c19d08d61dc247bb1623e58e31bec1da7f71381fa9e'], }), ] diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b02cdc76908 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '4.53.1' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ff4b9b8286437eb323a3e0a62adb00039c4207038c229c3f5f1eff6051e376b1'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ICU/ICU-69.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-69.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..74d55174995 --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-69.1-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '69.1' + +homepage = 'https://icu-project.org/' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['4cba7b7acd1d3c42c44bb0c14be6637098c7faf2b330ce876bc5f3b915d09745'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb new file mode 100644 index 00000000000..da2da4d12fb --- /dev/null +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb @@ -0,0 +1,28 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = "IOR" +version = "3.3.0" + +homepage = 'https://github.com/hpc/ior' +description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, + or HDF5 interfaces. """ + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = [('https://github.com/hpc/ior/archive')] +sources = ['%(version)s.tar.gz'] +checksums = ['701f2167f81ef963e227d4c036c4a947a98b5642b7c14c87c8ae657849891528'] + +builddependencies = [('Autotools', '20200321')] + +preconfigopts = "./bootstrap && " + +sanity_check_paths = { + 'files': ["bin/ior"], + 'dirs': ["share"] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2021a.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2021a.eb new file mode 100644 index 00000000000..21928503246 --- /dev/null +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2021a.eb @@ -0,0 +1,28 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = "IOR" +version = "3.3.0" + +homepage = 'https://github.com/hpc/ior' +description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, + or HDF5 interfaces. """ + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = [('https://github.com/hpc/ior/archive')] +sources = ['%(version)s.tar.gz'] +checksums = ['701f2167f81ef963e227d4c036c4a947a98b5642b7c14c87c8ae657849891528'] + +builddependencies = [('Autotools', '20210128')] + +preconfigopts = "./bootstrap && " + +sanity_check_paths = { + 'files': ["bin/ior"], + 'dirs': ["share"] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPy/IPy-0.83.eb b/easybuild/easyconfigs/i/IPy/IPy-0.83.eb index a69eafcc296..dc24990cfad 100644 --- a/easybuild/easyconfigs/i/IPy/IPy-0.83.eb +++ b/easybuild/easyconfigs/i/IPy/IPy-0.83.eb @@ -10,7 +10,6 @@ description = """Class and tools for handling of IPv4 and IPv6 addresses and net toolchain = SYSTEM sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] options = {'modulename': 'IPy'} diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb index 5a7a6fc6ee3..96b4f370a04 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '3.2.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -19,67 +19,30 @@ dependencies = [ ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ ('pysqlite', '2.8.1', { 'modulename': 'pysqlite2', - 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], - }), - ('requests', '2.9.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), - ('Pygments', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], - }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - }), - ('backports.ssl_match_hostname', '3.5.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], - }), - ('certifi', '2015.11.20.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - }), - ('backports_abc', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - }), - ('tornado', '4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], - }), - ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], - }), - ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], - }), - ('vcversioner', '2.16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], - }), - ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], - }), - ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - }), - ('mistune', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], - }), - ('ptyprocess', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - }), - ('terminado', '0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], }), + ('requests', '2.9.1'), + ('Pygments', '2.0.2'), + ('singledispatch', '3.4.0.3'), + ('backports.ssl_match_hostname', '3.5.0.1'), + ('certifi', '2015.11.20.1'), + ('backports_abc', '0.4'), + ('tornado', '4.3'), + ('MarkupSafe', '0.23'), + ('Jinja2', '2.8'), + ('vcversioner', '2.16.0.0'), + ('functools32', '3.2.3-2'), + ('jsonschema', '2.5.1'), + ('mistune', '0.7.1'), + ('ptyprocess', '0.5'), + ('terminado', '0.6'), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'modulename': 'IPython', }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb index b9c58c257f8..c0f94ca287c 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '3.2.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -19,67 +19,30 @@ dependencies = [ ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ ('pysqlite', '2.8.1', { 'modulename': 'pysqlite2', - 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], - }), - ('requests', '2.9.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), - ('Pygments', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], - }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - }), - ('backports.ssl_match_hostname', '3.5.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], - }), - ('certifi', '2015.11.20.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - }), - ('backports_abc', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - }), - ('tornado', '4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], - }), - ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], - }), - ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], - }), - ('vcversioner', '2.16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], - }), - ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], - }), - ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - }), - ('mistune', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], - }), - ('ptyprocess', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - }), - ('terminado', '0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], }), + ('requests', '2.9.1'), + ('Pygments', '2.0.2'), + ('singledispatch', '3.4.0.3'), + ('backports.ssl_match_hostname', '3.5.0.1'), + ('certifi', '2015.11.20.1'), + ('backports_abc', '0.4'), + ('tornado', '4.3'), + ('MarkupSafe', '0.23'), + ('Jinja2', '2.8'), + ('vcversioner', '2.16.0.0'), + ('functools32', '3.2.3-2'), + ('jsonschema', '2.5.1'), + ('mistune', '0.7.1'), + ('ptyprocess', '0.5'), + ('terminado', '0.6'), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'modulename': 'IPython', }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb index 86ef6979c54..e070628da42 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb @@ -3,13 +3,13 @@ # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '4.2.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -25,114 +25,52 @@ dependencies = [ ('testpath', '0.3', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ ('pysqlite', '2.8.2', { 'modulename': 'pysqlite2', - 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], - }), - ('requests', '2.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), - ('nbformat', '4.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - }), - ('Pygments', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], - }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - }), - ('backports.ssl_match_hostname', '3.5.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], - }), - ('certifi', '2016.2.28', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - }), - ('backports_abc', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - }), - ('tornado', '4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('requests', '2.10.0'), + ('nbformat', '4.0.1'), + ('Pygments', '2.1.3'), + ('singledispatch', '3.4.0.3'), + ('backports.ssl_match_hostname', '3.5.0.1'), + ('certifi', '2016.2.28'), + ('backports_abc', '0.4'), + ('tornado', '4.3'), ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.io/packages/source/M/MarkupSafe/'], 'modulename': 'markupsafe', }), - ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], - }), - ('vcversioner', '2.16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], - }), - ('jupyter_client', '4.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], - }), - ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], - }), - ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - }), - ('mistune', '0.7.2', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], - }), - ('ptyprocess', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - }), - ('terminado', '0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], - }), + ('Jinja2', '2.8'), + ('vcversioner', '2.16.0.0'), + ('jupyter_client', '4.2.2'), + ('functools32', '3.2.3-2'), + ('jsonschema', '2.5.1'), + ('mistune', '0.7.2'), + ('ptyprocess', '0.5.1'), + ('terminado', '0.6'), ('setuptools_scm', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', }), ('simplegeneric', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'source_tmpl': 'simplegeneric-%(version)s.zip', }), ('path.py', '8.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], 'modulename': 'path', }), - ('ipython_genutils', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], - }), - ('pathlib2', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], - }), - ('pickleshare', '0.7.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], - }), - ('traitlets', '4.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], - }), - ('notebook', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], - }), - ('jupyter_core', '4.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], - }), - ('ipykernel', '4.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], - }), - ('pexpect', '4.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], - }), - ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], - }), + ('ipython_genutils', '0.1.0'), + ('pathlib2', '2.1.0'), + ('pickleshare', '0.7.2'), + ('traitlets', '4.2.1'), + ('notebook', '4.2.0'), + ('jupyter_core', '4.1.0'), + ('ipykernel', '4.3.1'), + ('pexpect', '4.0.1'), + ('backports.shutil_get_terminal_size', '1.0.0'), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'modulename': 'IPython', }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-2.7.11.eb index 0789701c375..380b5d4f8d6 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-2.7.11.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '5.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -26,108 +26,46 @@ dependencies = [ # this is a bundle of Python packages # XXX: the wheel packages (testpath, entrypoints, path.py, prompt-toolkit) have # to be included as dependencies because bundling wheels does not work -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('requests', '2.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), - ('nbformat', '4.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - }), - ('Pygments', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], - }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - }), - ('certifi', '2016.2.28', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - }), - ('backports_abc', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - }), - ('tornado', '4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], - }), + ('nose', '1.3.7'), + ('requests', '2.10.0'), + ('nbformat', '4.0.1'), + ('Pygments', '2.1.3'), + ('singledispatch', '3.4.0.3'), + ('certifi', '2016.2.28'), + ('backports_abc', '0.4'), + ('tornado', '4.4'), ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'modulename': 'markupsafe', }), - ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], - }), - ('jupyter_client', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], - }), - ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], - }), - ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - }), - ('mistune', '0.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], - }), - ('ptyprocess', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - }), - ('terminado', '0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], - }), - ('setuptools', '24.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), + ('Jinja2', '2.8'), + ('jupyter_client', '4.3.0'), + ('functools32', '3.2.3-2'), + ('jsonschema', '2.5.1'), + ('mistune', '0.7.3'), + ('ptyprocess', '0.5.1'), + ('terminado', '0.6'), + ('setuptools', '24.0.3'), ('simplegeneric', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'source_tmpl': 'simplegeneric-%(version)s.zip', }), - ('ipython_genutils', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], - }), - ('pathlib2', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], - }), - ('pickleshare', '0.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], - }), - ('traitlets', '4.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], - }), - ('notebook', '4.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], - }), - ('jupyter_core', '4.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], - }), - ('ipykernel', '4.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], - }), - ('pexpect', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], - }), - ('nbconvert', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - }), - ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], - }), - ('decorator', '4.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), + ('ipython_genutils', '0.1.0'), + ('pathlib2', '2.1.0'), + ('pickleshare', '0.7.3'), + ('traitlets', '4.2.2'), + ('notebook', '4.2.1'), + ('jupyter_core', '4.1.0'), + ('ipykernel', '4.3.1'), + ('pexpect', '4.2.0'), + ('nbconvert', '4.2.0'), + ('backports.shutil_get_terminal_size', '1.0.0'), + ('decorator', '4.0.10'), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'patches': ['ipython-5.0.0_fix-test-paths-symlink.patch'], 'modulename': 'IPython', }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-3.5.1.eb index f78869f5b94..a404ba8cd0a 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-3.5.1.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '5.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -26,90 +26,40 @@ dependencies = [ # this is a bundle of Python packages # XXX: the wheel packages (testpath, entrypoints, path.py, prompt-toolkit) have # to be included as dependencies because bundling wheels does not work -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('requests', '2.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), - ('nbformat', '4.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - }), - ('Pygments', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], - }), - ('tornado', '4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], - }), + ('nose', '1.3.7'), + ('requests', '2.10.0'), + ('nbformat', '4.0.1'), + ('Pygments', '2.1.3'), + ('tornado', '4.4'), ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'modulename': 'markupsafe', }), - ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], - }), - ('jupyter_client', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], - }), - ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - }), - ('mistune', '0.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], - }), - ('ptyprocess', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - }), - ('terminado', '0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], - }), - ('setuptools', '24.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), + ('Jinja2', '2.8'), + ('jupyter_client', '4.3.0'), + ('jsonschema', '2.5.1'), + ('mistune', '0.7.3'), + ('ptyprocess', '0.5.1'), + ('terminado', '0.6'), + ('setuptools', '24.0.3'), ('simplegeneric', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'source_tmpl': 'simplegeneric-%(version)s.zip', }), - ('ipython_genutils', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], - }), - ('pickleshare', '0.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], - }), - ('traitlets', '4.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], - }), - ('notebook', '4.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], - }), - ('jupyter_core', '4.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], - }), - ('ipykernel', '4.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], - }), - ('pexpect', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], - }), - ('nbconvert', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - }), - ('decorator', '4.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), + ('ipython_genutils', '0.1.0'), + ('pickleshare', '0.7.3'), + ('traitlets', '4.2.2'), + ('notebook', '4.2.1'), + ('jupyter_core', '4.1.0'), + ('ipykernel', '4.3.1'), + ('pexpect', '4.2.0'), + ('nbconvert', '4.2.0'), + ('decorator', '4.0.10'), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'patches': ['ipython-5.0.0_fix-test-paths-symlink.patch'], 'modulename': 'IPython', }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb index ec7c04c10be..75911a799b5 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '5.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -26,116 +26,52 @@ dependencies = [ # this is a bundle of Python packages # XXX: the wheel packages (testpath, entrypoints, path.py, prompt-toolkit) have # to be included as dependencies because bundling wheels does not work -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('requests', '2.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), - ('nbformat', '4.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - }), + ('nose', '1.3.7'), + ('requests', '2.11.0'), + ('nbformat', '4.1.0'), ('Pygments', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'modulename': 'pygments', }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - }), - ('certifi', '2016.8.8', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - }), - ('backports_abc', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - }), - ('tornado', '4.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], - }), + ('singledispatch', '3.4.0.3'), + ('certifi', '2016.8.8'), + ('backports_abc', '0.4'), + ('tornado', '4.4.1'), ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'modulename': 'markupsafe', }), ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'modulename': 'jinja2', }), - ('jupyter_client', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], - }), - ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], - }), - ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - }), - ('mistune', '0.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], - }), - ('ptyprocess', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - }), - ('terminado', '0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], - }), - ('setuptools', '25.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), + ('jupyter_client', '4.3.0'), + ('functools32', '3.2.3-2'), + ('jsonschema', '2.5.1'), + ('mistune', '0.7.3'), + ('ptyprocess', '0.5.1'), + ('terminado', '0.6'), + ('setuptools', '25.2.0'), ('simplegeneric', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'source_tmpl': 'simplegeneric-%(version)s.zip', }), - ('ipython_genutils', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], - }), - ('pathlib2', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], - }), - ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], - }), - ('traitlets', '4.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], - }), - ('notebook', '4.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], - }), - ('jupyter_core', '4.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], - }), - ('ipykernel', '4.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], - }), - ('pexpect', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], - }), - ('nbconvert', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - }), - ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], - }), - ('decorator', '4.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), + ('ipython_genutils', '0.1.0'), + ('pathlib2', '2.1.0'), + ('pickleshare', '0.7.4'), + ('traitlets', '4.2.2'), + ('notebook', '4.2.2'), + ('jupyter_core', '4.1.1'), + ('ipykernel', '4.4.1'), + ('pexpect', '4.2.0'), + ('nbconvert', '4.2.0'), + ('backports.shutil_get_terminal_size', '1.0.0'), + ('decorator', '4.0.10'), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'patches': ['ipython-5.0.0_fix-test-paths-symlink.patch'], 'modulename': 'IPython', }), - ('ipywidgets', '5.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], - }), - ('widgetsnbextension', '1.2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], - }), + ('ipywidgets', '5.2.2'), + ('widgetsnbextension', '1.2.6'), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb index ad14e82e325..f03c2986039 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '5.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -26,116 +26,52 @@ dependencies = [ # this is a bundle of Python packages # XXX: the wheel packages (testpath, entrypoints, path.py, prompt-toolkit) have # to be included as dependencies because bundling wheels does not work -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('requests', '2.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), - ('nbformat', '4.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - }), + ('nose', '1.3.7'), + ('requests', '2.11.0'), + ('nbformat', '4.1.0'), ('Pygments', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'modulename': 'pygments', }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - }), - ('certifi', '2016.8.8', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - }), - ('backports_abc', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - }), - ('tornado', '4.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], - }), + ('singledispatch', '3.4.0.3'), + ('certifi', '2016.8.8'), + ('backports_abc', '0.4'), + ('tornado', '4.4.1'), ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'modulename': 'markupsafe', }), ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'modulename': 'jinja2', }), - ('jupyter_client', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], - }), - ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], - }), - ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - }), - ('mistune', '0.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], - }), - ('ptyprocess', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - }), - ('terminado', '0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], - }), - ('setuptools', '25.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), + ('jupyter_client', '4.3.0'), + ('functools32', '3.2.3-2'), + ('jsonschema', '2.5.1'), + ('mistune', '0.7.3'), + ('ptyprocess', '0.5.1'), + ('terminado', '0.6'), + ('setuptools', '25.2.0'), ('simplegeneric', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'source_tmpl': 'simplegeneric-%(version)s.zip', }), - ('ipython_genutils', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], - }), - ('pathlib2', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], - }), - ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], - }), - ('traitlets', '4.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], - }), - ('notebook', '4.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], - }), - ('jupyter_core', '4.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], - }), - ('ipykernel', '4.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], - }), - ('pexpect', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], - }), - ('nbconvert', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - }), - ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], - }), - ('decorator', '4.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), + ('ipython_genutils', '0.1.0'), + ('pathlib2', '2.1.0'), + ('pickleshare', '0.7.4'), + ('traitlets', '4.2.2'), + ('notebook', '4.2.2'), + ('jupyter_core', '4.1.1'), + ('ipykernel', '4.4.1'), + ('pexpect', '4.2.0'), + ('nbconvert', '4.2.0'), + ('backports.shutil_get_terminal_size', '1.0.0'), + ('decorator', '4.0.10'), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'patches': ['ipython-5.0.0_fix-test-paths-symlink.patch'], 'modulename': 'IPython', }), - ('ipywidgets', '5.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], - }), - ('widgetsnbextension', '1.2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], - }), + ('ipywidgets', '5.2.2'), + ('widgetsnbextension', '1.2.6'), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb index f205e1577f2..0c2022cf1a7 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '5.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -26,107 +26,49 @@ dependencies = [ # this is a bundle of Python packages # XXX: the wheel packages (testpath, entrypoints, path.py, prompt-toolkit) have # to be included as dependencies because bundling wheels does not work -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('requests', '2.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), - ('nbformat', '4.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - }), + ('nose', '1.3.7'), + ('requests', '2.11.0'), + ('nbformat', '4.1.0'), ('Pygments', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'modulename': 'pygments', }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - }), - ('certifi', '2016.8.8', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - }), - ('tornado', '4.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], - }), + ('singledispatch', '3.4.0.3'), + ('certifi', '2016.8.8'), + ('tornado', '4.4.1'), ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'modulename': 'markupsafe', }), ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'modulename': 'jinja2', }), - ('jupyter_client', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], - }), - ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - }), - ('mistune', '0.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], - }), - ('ptyprocess', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - }), - ('terminado', '0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], - }), - ('setuptools', '25.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), + ('jupyter_client', '4.3.0'), + ('jsonschema', '2.5.1'), + ('mistune', '0.7.3'), + ('ptyprocess', '0.5.1'), + ('terminado', '0.6'), + ('setuptools', '25.2.0'), ('simplegeneric', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'source_tmpl': 'simplegeneric-%(version)s.zip', }), - ('ipython_genutils', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], - }), - ('pathlib2', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], - }), - ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], - }), - ('traitlets', '4.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], - }), - ('notebook', '4.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], - }), - ('jupyter_core', '4.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], - }), - ('ipykernel', '4.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], - }), - ('pexpect', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], - }), - ('nbconvert', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - }), - ('decorator', '4.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), + ('ipython_genutils', '0.1.0'), + ('pathlib2', '2.1.0'), + ('pickleshare', '0.7.4'), + ('traitlets', '4.2.2'), + ('notebook', '4.2.2'), + ('jupyter_core', '4.1.1'), + ('ipykernel', '4.4.1'), + ('pexpect', '4.2.0'), + ('nbconvert', '4.2.0'), + ('decorator', '4.0.10'), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'patches': ['ipython-5.0.0_fix-test-paths-symlink.patch'], 'modulename': 'IPython', }), - ('ipywidgets', '5.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], - }), - ('widgetsnbextension', '1.2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], - }), + ('ipywidgets', '5.2.2'), + ('widgetsnbextension', '1.2.6'), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb index 01c5f93a200..6ee16052eb0 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '5.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -26,116 +26,53 @@ dependencies = [ # this is a bundle of Python packages # XXX: the wheel packages (testpath, entrypoints, path.py, prompt-toolkit) have # to be included as dependencies because bundling wheels does not work -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('requests', '2.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), - ('nbformat', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - }), + ('nose', '1.3.7'), + ('requests', '2.13.0'), + ('nbformat', '4.3.0'), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'modulename': 'pygments', }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - }), - ('certifi', '2017.1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - }), - ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - }), - ('tornado', '4.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], - }), + ('singledispatch', '3.4.0.3'), + ('certifi', '2017.1.23'), + ('backports_abc', '0.5'), + ('tornado', '4.4.2'), ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'modulename': 'markupsafe', }), ('Jinja2', '2.9.5', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'modulename': 'jinja2', }), - ('jupyter_client', '5.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], - }), - ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], - }), - ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - }), - ('mistune', '0.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], - }), - ('ptyprocess', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - }), - ('terminado', '0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], - }), + ('jupyter_client', '5.0.0'), + ('functools32', '3.2.3-2'), + ('jsonschema', '2.6.0'), + ('mistune', '0.7.3'), + ('ptyprocess', '0.5.1'), + ('terminado', '0.6'), ('simplegeneric', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'source_tmpl': 'simplegeneric-%(version)s.zip', }), - ('ipython_genutils', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], - }), - ('pathlib2', '2.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], - }), - ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], - }), - ('traitlets', '4.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], - }), - ('notebook', '4.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], - }), - ('jupyter_core', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], - }), - ('ipykernel', '4.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], - }), - ('pexpect', '4.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], - }), - ('pandocfilters', '1.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], - }), + ('ipython_genutils', '0.1.0'), + ('pathlib2', '2.2.1'), + ('pickleshare', '0.7.4'), + ('traitlets', '4.3.1'), + ('notebook', '4.4.1'), + ('jupyter_core', '4.3.0'), + ('ipykernel', '4.5.2'), + ('pexpect', '4.2.1'), + ('pandocfilters', '1.4.1'), ('nbconvert', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'use_pip': True, }), - ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], - }), - ('decorator', '4.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), + ('backports.shutil_get_terminal_size', '1.0.0'), + ('decorator', '4.0.11'), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'modulename': 'IPython', }), - ('ipywidgets', '5.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], - }), - ('widgetsnbextension', '1.2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], - }), + ('ipywidgets', '5.2.2'), + ('widgetsnbextension', '1.2.6'), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb index 0eed01f29d7..624cf7d60fd 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '5.3.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -19,116 +19,87 @@ dependencies = [ ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), ] -exts_defaultclass = 'PythonPackage' - exts_list = [ ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('requests', '2.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['5722cd09762faa01276230270ff16af7acf7c5c45d623868d9ba116f15791ce8'], }), ('nbformat', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['5febcce872672f1c97569e89323992bdcb8573fdad703f835e6521253191478b'], }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('certifi', '2017.4.17', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['f7527ebf7461582ce95f7a9e03dd141ce810d40590834f4ec20cddd54234c10a'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('tornado', '4.5', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['8861cce3c081557cfca2623507290ed647978ea275c29e2e3dfeeb63ca61e855'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['ddaa01a212cd6d641401cb01b605f4a4d9f37bfc93043d7f760ec70fb99ff9ff'], }), ('jupyter_client', '5.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['1fe573880b5ca4469ed0bece098f4b910c373d349e12525e1ea3566f5a14536b'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('mistune', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['8517af9f5cd1857bb83f9a23da75aa516d7538c32a2c5d5c56f3789a9e4cd22f'], }), ('ptyprocess', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['0530ce63a9295bfae7bd06edc02b6aa935619f486f0f1dc0972f516265ee81a6'], }), ('terminado', '0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['2c0ba1f624067dccaaead7d2247cfe029806355cef124dc2ccb53c83229f0126'], }), ('simplegeneric', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'source_tmpl': 'simplegeneric-%(version)s.zip', 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('scandir', '1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['c2612d1a487d80fb4701b4a91ca1b8f8a695b1ae820570815e85e8c8b23f1283'], }), ('pathlib2', '2.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['ce9007df617ef6b7bd8a31cd2089ed0c1fed1f7c23cf2bf1ba140b3dd563175d'], }), ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('notebook', '5.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['1cea3bbbd03c8e5842a1403347a8cc8134486b3ce081a2e5b1952a00ea66ed54'], }), ('jupyter_core', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['a96b129e1641425bf057c3d46f4f44adce747a7d60107e8ad771045c36514d40'], }), ('pexpect', '4.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['3d132465a75b57aa818341c6521392a06cc660feb3988d7f1074f39bd23c9a92'], }), ('pandocfilters', '1.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['ec8bcd100d081db092c57f93462b1861bcfa1286ef126f34da5cb1d969538acd'], }), ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], 'patches': ['configparser-3.5.0_no-backports-namespace.patch'], 'use_pip': True, 'checksums': [ @@ -138,71 +109,57 @@ exts_list = [ ], }), ('entrypoints', '0.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'source_tmpl': 'entrypoints-%(version)s-py2.py3-none-any.whl', 'unpack_sources': False, 'use_pip': True, 'checksums': ['0a0685962ee5ac303f470acbb659f0f97aef5b9deb6b85d059691c706ef6e45e'], }), ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], }), ('decorator', '4.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['953d6bf082b100f43229cf547f4f97f97e970f5ad645ee7601d55ff87afdfe76'], }), ('testpath', '0.3', { - 'source_urls': ['https://pypi.python.org/packages/py2.py3/t/testpath/'], 'source_tmpl': 'testpath-%(version)s-py2.py3-none-any.whl', 'unpack_sources': False, 'use_pip': True, 'checksums': ['f16b2cb3b03e1ada4fb0200b265a4446f92f3ba4b9d88ace34f51c54ab6d294e'], }), ('bleach', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44'], }), ('nbconvert', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'use_pip': True, 'checksums': ['847731bc39829d0eb1e15a450ac98c71730e3598e53683d4d76a3f3b3fc5017d'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'source_tmpl': 'wcwidth-%(version)s-py2.py3-none-any.whl', 'unpack_sources': False, 'use_pip': True, 'checksums': ['f4ebe71925af7b40a864553f761ed559b43544f8f71746c2d756c7fe788ade7c'], }), ('prompt-toolkit', '1.0.14', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'source_tmpl': 'prompt_toolkit-%(version)s-py2-none-any.whl', 'unpack_sources': False, 'use_pip': True, 'checksums': ['82c7f8e07d7a0411ff5367a5a8ff520f0112b9179f3e599ee8ad2ad9b943d911'], }), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['bf5e615e7d96dac5a61fbf98d9e2926d98aa55582681bea7e9382992a3f43c1d'], 'modulename': 'IPython', }), ('ipykernel', '4.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['2e1825aca4e2585b5adb7953ea16e53f53a62159ed49952a564b1e23507205db'], }), ('ipywidgets', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['833bfd14f70ef692724aec01d5adeae068cdab7c86123f37f7e9742a2988e648'], }), ('widgetsnbextension', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['566582a84642d0c0f78b756a954450a38a8743eeb8dad04b7cab3ca66f455e6f'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.7.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/i/IPython/IPython-5.7.0-foss-2018a-Python-2.7.14.eb index f91c4b82684..cd9c4c1c7ba 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.7.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.7.0-foss-2018a-Python-2.7.14.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '5.7.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -20,198 +20,148 @@ dependencies = [ ('matplotlib', '2.1.2', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') -exts_download_dep_fail = True - exts_list = [ ('pyzmq', '17.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], 'modulename': 'zmq', }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('futures', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], 'modulename': 'concurrent.futures', }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('mistune', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], }), ('ptyprocess', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('scandir', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['b2d55be869c4f716084a19b1e16932f0769711316ba62de941320bf2be84763d'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'use_pip': True, 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('pexpect', '4.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['9f8eb3277716a01faafaba553d629d3d60a1a624c7cf45daa600d2148c30020c'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), ('entrypoints', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], }), ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], }), ('testpath', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['0d5337839c788da5900df70f8e01015aec141aa3fe7936cb0d0a2953f7ac7609'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['8db43a7fb7619037c98626613ff08d03dda9d5d12c84814a4504c78c0da8323c'], 'modulename': 'IPython', }), ('ipykernel', '4.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], }), ('ipywidgets', '7.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['ab9869cda5af7ba449d8f707b29b7e97a7db97d6366805d6b733338f51096f54'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44'], }), ('nbconvert', '5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'use_pip': True, 'checksums': ['12b1a4671d4463ab73af6e4cbcc965b62254e05d182cd54995dda0d0ef9e2db9'], }), ('parso', '0.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['5815f3fe254e5665f3c5d6f54f086c2502035cb631a91341591b5a564203cffb'], }), ('jedi', '0.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('notebook', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'use_pip': True, 'checksums': ['7d6143d10e9b026df888e0b2936ceff1827ef2f2087646b4dd475c8dcef58606'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.7.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/i/IPython/IPython-5.7.0-intel-2018a-Python-2.7.14.eb index 2609d8d33a5..63fd33eef6a 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.7.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.7.0-intel-2018a-Python-2.7.14.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '5.7.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -20,198 +20,148 @@ dependencies = [ ('matplotlib', '2.1.2', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') -exts_download_dep_fail = True - exts_list = [ ('pyzmq', '17.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], 'modulename': 'zmq', }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('futures', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], 'modulename': 'concurrent.futures', }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('mistune', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], }), ('ptyprocess', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('scandir', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['b2d55be869c4f716084a19b1e16932f0769711316ba62de941320bf2be84763d'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'use_pip': True, 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('pexpect', '4.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['9f8eb3277716a01faafaba553d629d3d60a1a624c7cf45daa600d2148c30020c'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), ('entrypoints', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], }), ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], }), ('testpath', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['0d5337839c788da5900df70f8e01015aec141aa3fe7936cb0d0a2953f7ac7609'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['8db43a7fb7619037c98626613ff08d03dda9d5d12c84814a4504c78c0da8323c'], 'modulename': 'IPython', }), ('ipykernel', '4.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], }), ('ipywidgets', '7.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['ab9869cda5af7ba449d8f707b29b7e97a7db97d6366805d6b733338f51096f54'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44'], }), ('nbconvert', '5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'use_pip': True, 'checksums': ['12b1a4671d4463ab73af6e4cbcc965b62254e05d182cd54995dda0d0ef9e2db9'], }), ('parso', '0.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['5815f3fe254e5665f3c5d6f54f086c2502035cb631a91341591b5a564203cffb'], }), ('jedi', '0.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('notebook', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'use_pip': True, 'checksums': ['7d6143d10e9b026df888e0b2936ceff1827ef2f2087646b4dd475c8dcef58606'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-2.7.14.eb index cb290c7ccf7..cf4b1f08fc3 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '5.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -25,198 +25,150 @@ use_pip = True exts_list = [ ('pyzmq', '17.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('futures', '3.2.0', { 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('mistune', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], }), ('ptyprocess', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('scandir', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['b2d55be869c4f716084a19b1e16932f0769711316ba62de941320bf2be84763d'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('pexpect', '4.5.0', { - 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'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['0d5337839c788da5900df70f8e01015aec141aa3fe7936cb0d0a2953f7ac7609'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('ipykernel', '4.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], }), ('ipywidgets', '7.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['ab9869cda5af7ba449d8f707b29b7e97a7db97d6366805d6b733338f51096f54'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44'], }), ('nbconvert', '5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['12b1a4671d4463ab73af6e4cbcc965b62254e05d182cd54995dda0d0ef9e2db9'], }), ('parso', '0.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['5815f3fe254e5665f3c5d6f54f086c2502035cb631a91341591b5a564203cffb'], }), ('jedi', '0.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('notebook', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['7d6143d10e9b026df888e0b2936ceff1827ef2f2087646b4dd475c8dcef58606'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ('requests', '2.21.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-3.6.3.eb index ec3ab6ca94c..122faf58f1e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '5.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -25,189 +25,143 @@ use_pip = True exts_list = [ ('pyzmq', '17.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('mistune', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], }), ('ptyprocess', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('scandir', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['b2d55be869c4f716084a19b1e16932f0769711316ba62de941320bf2be84763d'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('pexpect', '4.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['9f8eb3277716a01faafaba553d629d3d60a1a624c7cf45daa600d2148c30020c'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), ('entrypoints', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], }), ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], }), ('testpath', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['0d5337839c788da5900df70f8e01015aec141aa3fe7936cb0d0a2953f7ac7609'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('ipykernel', '4.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], }), ('ipywidgets', '7.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['ab9869cda5af7ba449d8f707b29b7e97a7db97d6366805d6b733338f51096f54'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44'], }), ('nbconvert', '5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['12b1a4671d4463ab73af6e4cbcc965b62254e05d182cd54995dda0d0ef9e2db9'], }), ('parso', '0.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['5815f3fe254e5665f3c5d6f54f086c2502035cb631a91341591b5a564203cffb'], }), ('jedi', '0.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('notebook', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['7d6143d10e9b026df888e0b2936ceff1827ef2f2087646b4dd475c8dcef58606'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ('requests', '2.21.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb index 2fcc937bde5..2979a0a544b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '5.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -24,204 +24,155 @@ use_pip = True exts_list = [ ('Pygments', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('pexpect', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], }), ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), ('pathlib2', '2.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), ('pickleshare', '0.7.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ptyprocess', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('parso', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['68406ebd7eafe17f8e40e15a84b56848eccbf27d7c1feb89e93d8fca395706db'], }), ('jedi', '0.13.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], }), ('testpath', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), ('defusedxml', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], }), ('nbconvert', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('ipywidgets', '7.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['a3e224f430163f767047ab9a042fc55adbcab0c24bbe6cf9f306c4f89fdf0ba3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '3.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['3fdf7f77adcf649c9911387df51254b813185e32b2c6619f690b593a617e19fa'], }), ('pyrsistent', '0.14.11', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyrsistent/'], 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('vcversioner', '2.16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], }), ('jsonschema', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('pyzmq', '18.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['b30c339eb58355f51f4f54dd61d785f1ff58c86bca1c3a5916977631d121867b'], }), ('entrypoints', '0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('mistune', '0.8.4', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('futures', '3.2.0', { 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('jupyter_client', '5.2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['b5f9cb06105c1d2d30719db5ffb3ea67da60919fb68deaefa583deccd8813551'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('ipykernel', '4.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['699103c8e64886e3ec7053f2a6aa83bb90426063526f63a818732ff385202bad'], }), ('prometheus_client', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], 'checksums': ['1b38b958750f66f208bcd9ab92a633c0c994d8859c831f7abc1f46724fcee490'], }), ('notebook', '5.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['d908673a4010787625c8952e91a22adf737db031f2aa0793ad92f6558918a74a'], }), ('widgetsnbextension', '3.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['fa618be8435447a017fd1bf2c7ae922d0428056cfc7449f7a8641edf76b48265'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2019a-Python-2.7.15.eb index 5e78353b3a6..11e5b337899 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2019a-Python-2.7.15.eb @@ -24,48 +24,37 @@ use_pip = True exts_list = [ ('Pygments', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], }), ('pexpect', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], }), ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), ('pathlib2', '2.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), ('pickleshare', '0.7.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ptyprocess', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], # installation with pip fails with BackendUnavailable error, # see also https://github.com/pypa/pip/issues/6164 'use_pip': False, @@ -73,123 +62,95 @@ exts_list = [ }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('parso', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['68406ebd7eafe17f8e40e15a84b56848eccbf27d7c1feb89e93d8fca395706db'], }), ('jedi', '0.13.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], }), ('testpath', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], # installation with pip fails with BackendUnavailable error, # see also https://github.com/pypa/pip/issues/6164 'use_pip': False, 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), ('defusedxml', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], }), ('nbconvert', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('ipywidgets', '7.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['a3e224f430163f767047ab9a042fc55adbcab0c24bbe6cf9f306c4f89fdf0ba3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '3.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['3fdf7f77adcf649c9911387df51254b813185e32b2c6619f690b593a617e19fa'], }), ('pyrsistent', '0.14.11', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyrsistent/'], 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('vcversioner', '2.16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], }), ('jsonschema', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('pyzmq', '18.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['b30c339eb58355f51f4f54dd61d785f1ff58c86bca1c3a5916977631d121867b'], }), ('entrypoints', '0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], # installation with pip fails with BackendUnavailable error, # see also https://github.com/pypa/pip/issues/6164 'use_pip': False, 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('mistune', '0.8.4', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], # installation with pip fails with BackendUnavailable error, # see also https://github.com/pypa/pip/issues/6164 'use_pip': False, @@ -197,47 +158,36 @@ exts_list = [ }), ('futures', '3.2.0', { 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('jupyter_client', '5.2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['b5f9cb06105c1d2d30719db5ffb3ea67da60919fb68deaefa583deccd8813551'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('ipykernel', '4.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['699103c8e64886e3ec7053f2a6aa83bb90426063526f63a818732ff385202bad'], }), ('prometheus_client', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], 'checksums': ['1b38b958750f66f208bcd9ab92a633c0c994d8859c831f7abc1f46724fcee490'], }), ('notebook', '5.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['d908673a4010787625c8952e91a22adf737db031f2aa0793ad92f6558918a74a'], }), ('widgetsnbextension', '3.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['fa618be8435447a017fd1bf2c7ae922d0428056cfc7449f7a8641edf76b48265'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2017b-Python-2.7.14.eb index 99e1b41b36b..41b7e0740be 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '5.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -25,198 +25,150 @@ use_pip = True exts_list = [ ('pyzmq', '17.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('futures', '3.2.0', { 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('mistune', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], }), ('ptyprocess', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('scandir', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['b2d55be869c4f716084a19b1e16932f0769711316ba62de941320bf2be84763d'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('pexpect', '4.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['9f8eb3277716a01faafaba553d629d3d60a1a624c7cf45daa600d2148c30020c'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), ('entrypoints', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], }), ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], }), ('testpath', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['0d5337839c788da5900df70f8e01015aec141aa3fe7936cb0d0a2953f7ac7609'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('ipykernel', '4.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], }), ('ipywidgets', '7.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['ab9869cda5af7ba449d8f707b29b7e97a7db97d6366805d6b733338f51096f54'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44'], }), ('nbconvert', '5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['12b1a4671d4463ab73af6e4cbcc965b62254e05d182cd54995dda0d0ef9e2db9'], }), ('parso', '0.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['5815f3fe254e5665f3c5d6f54f086c2502035cb631a91341591b5a564203cffb'], }), ('jedi', '0.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('notebook', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['7d6143d10e9b026df888e0b2936ceff1827ef2f2087646b4dd475c8dcef58606'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ('requests', '2.21.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2017b-Python-3.6.3.eb index 14022adba43..ef2aa9dec03 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '5.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -25,189 +25,143 @@ use_pip = True exts_list = [ ('pyzmq', '17.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('mistune', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], }), ('ptyprocess', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('scandir', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['b2d55be869c4f716084a19b1e16932f0769711316ba62de941320bf2be84763d'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), ('pickleshare', '0.7.4', { - 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'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('ipykernel', '4.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], }), ('ipywidgets', '7.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['ab9869cda5af7ba449d8f707b29b7e97a7db97d6366805d6b733338f51096f54'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '2.1.3', { - 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A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -24,208 +24,158 @@ use_pip = True exts_list = [ ('Pygments', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], }), ('pexpect', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], }), ('scandir', '1.9.0', { - 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'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('vcversioner', '2.16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], }), ('jsonschema', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('pyzmq', '18.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['b30c339eb58355f51f4f54dd61d785f1ff58c86bca1c3a5916977631d121867b'], }), ('entrypoints', '0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('mistune', '0.8.4', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('futures', '3.2.0', { 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('jupyter_client', '5.2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['b5f9cb06105c1d2d30719db5ffb3ea67da60919fb68deaefa583deccd8813551'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('ipykernel', '4.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['699103c8e64886e3ec7053f2a6aa83bb90426063526f63a818732ff385202bad'], }), ('prometheus_client', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], 'checksums': ['1b38b958750f66f208bcd9ab92a633c0c994d8859c831f7abc1f46724fcee490'], }), ('notebook', '5.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['d908673a4010787625c8952e91a22adf737db031f2aa0793ad92f6558918a74a'], }), ('widgetsnbextension', '3.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['fa618be8435447a017fd1bf2c7ae922d0428056cfc7449f7a8641edf76b48265'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2019a-Python-2.7.15.eb index caefb7c724d..736d8ed311b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2019a-Python-2.7.15.eb @@ -24,48 +24,37 @@ use_pip = True exts_list = [ ('Pygments', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], }), ('pexpect', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], }), ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), ('pathlib2', '2.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), ('pickleshare', '0.7.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ptyprocess', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], # installation with pip fails with BackendUnavailable error, # see also https://github.com/pypa/pip/issues/6164 'use_pip': False, @@ -73,123 +62,95 @@ exts_list = [ }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('parso', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['68406ebd7eafe17f8e40e15a84b56848eccbf27d7c1feb89e93d8fca395706db'], }), ('jedi', '0.13.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], }), ('testpath', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], # installation with pip fails with BackendUnavailable error, # see also https://github.com/pypa/pip/issues/6164 'use_pip': False, 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), ('defusedxml', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], }), ('nbconvert', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('ipywidgets', '7.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['a3e224f430163f767047ab9a042fc55adbcab0c24bbe6cf9f306c4f89fdf0ba3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '3.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['3fdf7f77adcf649c9911387df51254b813185e32b2c6619f690b593a617e19fa'], }), ('pyrsistent', '0.14.11', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyrsistent/'], 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('vcversioner', '2.16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], }), ('jsonschema', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('pyzmq', '18.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['b30c339eb58355f51f4f54dd61d785f1ff58c86bca1c3a5916977631d121867b'], }), ('entrypoints', '0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], # installation with pip fails with BackendUnavailable error, # see also https://github.com/pypa/pip/issues/6164 'use_pip': False, 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('mistune', '0.8.4', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], # installation with pip fails with BackendUnavailable error, # see also https://github.com/pypa/pip/issues/6164 'use_pip': False, @@ -197,47 +158,36 @@ exts_list = [ }), ('futures', '3.2.0', { 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('jupyter_client', '5.2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['b5f9cb06105c1d2d30719db5ffb3ea67da60919fb68deaefa583deccd8813551'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('ipykernel', '4.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['699103c8e64886e3ec7053f2a6aa83bb90426063526f63a818732ff385202bad'], }), ('prometheus_client', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], 'checksums': ['1b38b958750f66f208bcd9ab92a633c0c994d8859c831f7abc1f46724fcee490'], }), ('notebook', '5.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['d908673a4010787625c8952e91a22adf737db031f2aa0793ad92f6558918a74a'], }), ('widgetsnbextension', '3.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['fa618be8435447a017fd1bf2c7ae922d0428056cfc7449f7a8641edf76b48265'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-2.7.14.eb index a196af4552f..ed44354bc6e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '5.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -25,198 +25,150 @@ use_pip = True exts_list = [ ('pyzmq', '17.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('futures', '3.2.0', { 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('mistune', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], }), ('ptyprocess', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('scandir', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['b2d55be869c4f716084a19b1e16932f0769711316ba62de941320bf2be84763d'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('pexpect', '4.5.0', { - 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'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['0d5337839c788da5900df70f8e01015aec141aa3fe7936cb0d0a2953f7ac7609'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('ipykernel', '4.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], }), ('ipywidgets', '7.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['ab9869cda5af7ba449d8f707b29b7e97a7db97d6366805d6b733338f51096f54'], }), ('Send2Trash', '1.5.0', { - 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'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-3.6.3.eb index 5ed8b5e99b9..1b36d7e6f0c 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '5.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -25,189 +25,143 @@ use_pip = True exts_list = [ ('pyzmq', '17.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('backports_abc', '0.5', { - 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'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('ipykernel', '4.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], }), ('ipywidgets', '7.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['ab9869cda5af7ba449d8f707b29b7e97a7db97d6366805d6b733338f51096f54'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44'], }), ('nbconvert', '5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['12b1a4671d4463ab73af6e4cbcc965b62254e05d182cd54995dda0d0ef9e2db9'], }), ('parso', '0.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['5815f3fe254e5665f3c5d6f54f086c2502035cb631a91341591b5a564203cffb'], }), ('jedi', '0.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('notebook', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['7d6143d10e9b026df888e0b2936ceff1827ef2f2087646b4dd475c8dcef58606'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ('requests', '2.21.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb index 7dec9dbe500..5077c7fd854 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '5.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -24,204 +24,155 @@ use_pip = True exts_list = [ ('Pygments', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('pexpect', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], }), ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), ('pathlib2', '2.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), ('pickleshare', '0.7.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ptyprocess', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('parso', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['68406ebd7eafe17f8e40e15a84b56848eccbf27d7c1feb89e93d8fca395706db'], }), ('jedi', '0.13.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], }), ('testpath', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), ('defusedxml', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], }), ('nbconvert', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('ipywidgets', '7.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['a3e224f430163f767047ab9a042fc55adbcab0c24bbe6cf9f306c4f89fdf0ba3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '3.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['3fdf7f77adcf649c9911387df51254b813185e32b2c6619f690b593a617e19fa'], }), ('pyrsistent', '0.14.11', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyrsistent/'], 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('vcversioner', '2.16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], }), ('jsonschema', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('pyzmq', '18.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['b30c339eb58355f51f4f54dd61d785f1ff58c86bca1c3a5916977631d121867b'], }), ('entrypoints', '0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('mistune', '0.8.4', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('futures', '3.2.0', { 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('jupyter_client', '5.2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['b5f9cb06105c1d2d30719db5ffb3ea67da60919fb68deaefa583deccd8813551'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('ipykernel', '4.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['699103c8e64886e3ec7053f2a6aa83bb90426063526f63a818732ff385202bad'], }), ('prometheus_client', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], 'checksums': ['1b38b958750f66f208bcd9ab92a633c0c994d8859c831f7abc1f46724fcee490'], }), ('notebook', '5.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['d908673a4010787625c8952e91a22adf737db031f2aa0793ad92f6558918a74a'], }), ('widgetsnbextension', '3.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['fa618be8435447a017fd1bf2c7ae922d0428056cfc7449f7a8641edf76b48265'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intelcuda-2017b-Python-2.7.14.eb index 91321c9b42b..bc48e5307c6 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intelcuda-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '5.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -25,198 +25,150 @@ use_pip = True exts_list = [ ('pyzmq', '17.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), ('futures', '3.2.0', { 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('mistune', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], }), ('ptyprocess', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('scandir', '1.7', { - 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'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intelcuda-2017b-Python-3.6.3.eb index 8db4970d877..477e48720d2 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intelcuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intelcuda-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '5.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -25,189 +25,143 @@ use_pip = True exts_list = [ ('pyzmq', '17.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('backports_abc', '0.5', { - 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'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), ('entrypoints', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], }), ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], }), ('testpath', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['0d5337839c788da5900df70f8e01015aec141aa3fe7936cb0d0a2953f7ac7609'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('ipykernel', '4.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], }), ('ipywidgets', '7.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], 'checksums': ['ab9869cda5af7ba449d8f707b29b7e97a7db97d6366805d6b733338f51096f54'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44'], }), ('nbconvert', '5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['12b1a4671d4463ab73af6e4cbcc965b62254e05d182cd54995dda0d0ef9e2db9'], }), ('parso', '0.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['5815f3fe254e5665f3c5d6f54f086c2502035cb631a91341591b5a564203cffb'], }), ('jedi', '0.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('notebook', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['7d6143d10e9b026df888e0b2936ceff1827ef2f2087646b4dd475c8dcef58606'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ('requests', '2.21.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('widgetsnbextension', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-6.2.1-foss-2017a-Python-3.6.4.eb b/easybuild/easyconfigs/i/IPython/IPython-6.2.1-foss-2017a-Python-3.6.4.eb index 91106440ae5..5a5fa86a6a4 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-6.2.1-foss-2017a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-6.2.1-foss-2017a-Python-3.6.4.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '6.2.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -19,154 +19,116 @@ dependencies = [ ('ZeroMQ', '4.2.2'), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('ipython', version, { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['51c158a6c8b899898d1c91c6b51a34110196815cc905f9be0fa5878e19355608'], 'modulename': 'IPython', }), ('pexpect', '4.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['8e287b171dbaf249d0b06b5f2e88cb7e694651d2d0b8c15bccb83170d3c55575'], }), ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ptyprocess', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], }), ('simplegeneric', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'source_tmpl': 'simplegeneric-%(version)s.zip', 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('jedi', '0.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97'], }), ('parso', '0.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['5815f3fe254e5665f3c5d6f54f086c2502035cb631a91341591b5a564203cffb'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('testpath', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['0d5337839c788da5900df70f8e01015aec141aa3fe7936cb0d0a2953f7ac7609'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Send2Trash', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['725fbce571dffe0b640e2f1788d52c3c544b510f9d8f69b2597c8c2555bc8441'], }), ('bleach', '2.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['38fc8cbebea4e787d8db55d6f324820c7f74362b70db9142c1ac7920452d1a19'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('pyzmq', '16.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['bc23fad15d6da82081e89ea0b254a7b6efe6d1c4c58edb16f28e4b4d880086b2'], 'modulename': 'zmq', }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('entrypoints', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'use_pip': True, 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'use_pip': True, 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('mistune', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], }), ('nbconvert', '5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'use_pip': True, 'checksums': ['12b1a4671d4463ab73af6e4cbcc965b62254e05d182cd54995dda0d0ef9e2db9'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('tornado', '4.5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['6d14e47eab0e15799cf3cdcc86b0b98279da68522caace2bd7ce644287685f0a'], }), ('jupyter_client', '5.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'use_pip': True, 'checksums': ['83d5e23132f0d8f79ccd3939f53fb9fa97f88a896a85114dc48d0e86909b06c4'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('ipykernel', '4.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['dedc199df6a38725c732986dfa606c245fb8fe0fe999b33a0c305b73d80c6774'], }), ('notebook', '5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'use_pip': True, 'checksums': ['380bbed63117accbb13e42d01d06153c72da6a386f75c81ae4c174eaa11e738b'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-6.3.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/IPython/IPython-6.3.1-intel-2018a-Python-3.6.4.eb index 3d0e1b7dbaf..fcd8cea053e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-6.3.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-6.3.1-intel-2018a-Python-3.6.4.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '6.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -20,161 +20,120 @@ dependencies = [ ('matplotlib', '2.1.2', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - # let sanity check fail when auto-downloaded dependencies are detected when installing extensions -exts_download_dep_fail = True - exts_list = [ ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['a6ac981381b3f5f604b37a293369963485200e3639fb0404fa76092383c10c41'], }), ('pexpect', '4.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['9f8eb3277716a01faafaba553d629d3d60a1a624c7cf45daa600d2148c30020c'], }), ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ptyprocess', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('parso', '0.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['5815f3fe254e5665f3c5d6f54f086c2502035cb631a91341591b5a564203cffb'], }), ('jedi', '0.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97'], }), ('testpath', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['0d5337839c788da5900df70f8e01015aec141aa3fe7936cb0d0a2953f7ac7609'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('pyzmq', '17.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], }), ('entrypoints', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'use_pip': True, 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'use_pip': True, 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('mistune', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], }), ('nbconvert', '5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'use_pip': True, 'checksums': ['12b1a4671d4463ab73af6e4cbcc965b62254e05d182cd54995dda0d0ef9e2db9'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'use_pip': True, 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('ipykernel', '4.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], }), ('notebook', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'use_pip': True, 'checksums': ['7d6143d10e9b026df888e0b2936ceff1827ef2f2087646b4dd475c8dcef58606'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-6.4.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/IPython/IPython-6.4.0-foss-2018a-Python-3.6.4.eb index d2dc56365f8..d0f13c2b77d 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-6.4.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-6.4.0-foss-2018a-Python-3.6.4.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '6.4.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -20,161 +20,120 @@ dependencies = [ ('matplotlib', '2.1.2', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - # let sanity check fail when auto-downloaded dependencies are detected when installing extensions -exts_download_dep_fail = True - exts_list = [ ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['eca537aa61592aca2fef4adea12af8e42f5c335004dfa80c78caf80e8b525e5c'], }), ('pexpect', '4.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['9f8eb3277716a01faafaba553d629d3d60a1a624c7cf45daa600d2148c30020c'], }), ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], }), ('ptyprocess', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('parso', '0.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['5815f3fe254e5665f3c5d6f54f086c2502035cb631a91341591b5a564203cffb'], }), ('jedi', '0.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97'], }), ('testpath', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['0d5337839c788da5900df70f8e01015aec141aa3fe7936cb0d0a2953f7ac7609'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('pyzmq', '17.0.0', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], }), ('entrypoints', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'use_pip': True, 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'use_pip': True, 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('mistune', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], }), ('nbconvert', '5.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'use_pip': True, 'checksums': ['12b1a4671d4463ab73af6e4cbcc965b62254e05d182cd54995dda0d0ef9e2db9'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('tornado', '5.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], }), ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'use_pip': True, 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('ipykernel', '4.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], }), ('notebook', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'use_pip': True, 'checksums': ['7d6143d10e9b026df888e0b2936ceff1827ef2f2087646b4dd475c8dcef58606'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.2.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/IPython/IPython-7.2.0-foss-2018b-Python-3.6.6.eb index dcaf71e0dd7..f285649bd87 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.2.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.2.0-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '7.2.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -24,150 +24,114 @@ use_pip = True exts_list = [ ('Pygments', '2.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['82666aac15622bd7bb685a4ee7f6625dd716da3ef7473620c192c0168aae64fc'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['6a9496209b76463f1dec126ab928919aaf1f55b38beb9219af3fe202f6bbdd12'], }), ('pexpect', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], }), ('pickleshare', '0.7.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '2.0.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['fd17048d8335c1e6d5ee403c3569953ba3eb8555d710bfc548faf0712666ea39'], }), ('ptyprocess', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('parso', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['35704a43a3c113cce4de228ddb39aab374b8004f4f2407d070b6a2ca784ce8a2'], }), ('jedi', '0.13.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], }), ('testpath', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '3.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['48d39675b80a75f6d1c3bdbffec791cf0bbbab665cf01e20da701c77de278718'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('pyzmq', '17.1.2', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['a72b82ac1910f2cf61a49139f4974f994984475f771b0faa730839607eeedddf'], }), ('entrypoints', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('mistune', '0.8.4', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], }), ('defusedxml', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], }), ('nbconvert', '5.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['a8a2749f972592aa9250db975304af6b7337f32337e523a2c995cc9e12c07807'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('ipykernel', '5.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['0fc0bf97920d454102168ec2008620066878848fcfca06c22b669696212e292f'], }), ('prometheus_client', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], 'checksums': ['046cb4fffe75e55ff0e6dfd18e2ea16e54d86cc330f369bebcc683475c8b68a9'], }), ('notebook', '5.7.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['91705b109fc785198faed892489cddb233265564d5e2dad5e4f7974af05ee8dd'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.2.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/IPython/IPython-7.2.0-fosscuda-2018b-Python-3.6.6.eb index 33dfb20ba39..60942ce84a8 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.2.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.2.0-fosscuda-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '7.2.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -24,154 +24,117 @@ use_pip = True exts_list = [ ('Pygments', '2.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['82666aac15622bd7bb685a4ee7f6625dd716da3ef7473620c192c0168aae64fc'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['6a9496209b76463f1dec126ab928919aaf1f55b38beb9219af3fe202f6bbdd12'], }), ('pexpect', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], }), ('pickleshare', '0.7.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '2.0.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['fd17048d8335c1e6d5ee403c3569953ba3eb8555d710bfc548faf0712666ea39'], }), ('ptyprocess', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('parso', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['35704a43a3c113cce4de228ddb39aab374b8004f4f2407d070b6a2ca784ce8a2'], }), ('jedi', '0.13.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], }), ('testpath', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '3.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['48d39675b80a75f6d1c3bdbffec791cf0bbbab665cf01e20da701c77de278718'], }), ('vcversioner', '2.16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('pyzmq', '17.1.2', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['a72b82ac1910f2cf61a49139f4974f994984475f771b0faa730839607eeedddf'], }), ('entrypoints', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('mistune', '0.8.4', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], }), ('defusedxml', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], }), ('nbconvert', '5.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['a8a2749f972592aa9250db975304af6b7337f32337e523a2c995cc9e12c07807'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('ipykernel', '5.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['0fc0bf97920d454102168ec2008620066878848fcfca06c22b669696212e292f'], }), ('prometheus_client', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], 'checksums': ['046cb4fffe75e55ff0e6dfd18e2ea16e54d86cc330f369bebcc683475c8b68a9'], }), ('notebook', '5.7.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['91705b109fc785198faed892489cddb233265564d5e2dad5e4f7974af05ee8dd'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.2.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/IPython/IPython-7.2.0-intel-2018b-Python-3.6.6.eb index e9836a1ec77..95ad2bcf6ae 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.2.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.2.0-intel-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'IPython' version = '7.2.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ipython.org/index.html' +homepage = 'https://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. @@ -24,150 +24,114 @@ use_pip = True exts_list = [ ('Pygments', '2.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], 'checksums': ['82666aac15622bd7bb685a4ee7f6625dd716da3ef7473620c192c0168aae64fc'], }), ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), ('ipython', version, { 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['6a9496209b76463f1dec126ab928919aaf1f55b38beb9219af3fe202f6bbdd12'], }), ('pexpect', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], }), ('pickleshare', '0.7.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], }), ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('prompt_toolkit', '2.0.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], 'checksums': ['fd17048d8335c1e6d5ee403c3569953ba3eb8555d710bfc548faf0712666ea39'], }), ('ptyprocess', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), ('parso', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], 'checksums': ['35704a43a3c113cce4de228ddb39aab374b8004f4f2407d070b6a2ca784ce8a2'], }), ('jedi', '0.13.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], }), ('testpath', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], }), ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], }), ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), ('bleach', '3.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], 'checksums': ['48d39675b80a75f6d1c3bdbffec791cf0bbbab665cf01e20da701c77de278718'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), ('pyzmq', '17.1.2', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], 'checksums': ['a72b82ac1910f2cf61a49139f4974f994984475f771b0faa730839607eeedddf'], }), ('entrypoints', '0.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], }), ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('mistune', '0.8.4', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], }), ('defusedxml', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], }), ('nbconvert', '5.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], 'checksums': ['a8a2749f972592aa9250db975304af6b7337f32337e523a2c995cc9e12c07807'], }), ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), ('ipykernel', '5.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['0fc0bf97920d454102168ec2008620066878848fcfca06c22b669696212e292f'], }), ('prometheus_client', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], 'checksums': ['046cb4fffe75e55ff0e6dfd18e2ea16e54d86cc330f369bebcc683475c8b68a9'], }), ('notebook', '5.7.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], 'checksums': ['91705b109fc785198faed892489cddb233265564d5e2dad5e4f7974af05ee8dd'], }), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..27ff87d5da0 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb @@ -0,0 +1,163 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '7.25.0' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('ZeroMQ', '4.3.4'), +] + +use_pip = True + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['54bbd1fe3882457aaf28ae060a5ccdef97f212a741754e420028d4ec5c2291dc'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '3.0.19', { + 'checksums': ['08360ee3a3148bdb5163621709ee322ec34fc4375099afa4bbf751e9b7b7fa4f'], + }), + ('traitlets', '5.0.5', { + 'checksums': ['178f4ce988f69189f7e523337a3e11d91c786ded9360174a3d9ca83e79bc5396'], + }), + ('parso', '0.8.2', { + 'checksums': ['12b83492c6239ce32ff5eed6d3639d6a536170723c6f3f1506869f1ace413398'], + }), + ('jedi', '0.18.0', { + 'checksums': ['92550a404bad8afed881a137ec9a461fed49eca661414be45059329614ed0707'], + }), + ('testpath', '0.5.0', { + 'use_pip': False, + 'checksums': ['1acf7a0bcd3004ae8357409fc33751e16d37ccc650921da1094a86581ad1e417'], + }), + ('Send2Trash', '1.7.1', { + 'checksums': ['17730aa0a33ab82ed6ca76be3bb25f0433d0014f1ccf63c979bab13a5b9db2b2'], + }), + ('bleach', '3.3.0', { + 'checksums': ['98b3170739e5e83dd9dc19633f074727ad848cbedb6026708c8ac2d3b697a433'], + }), + ('pandocfilters', '1.4.3', { + 'checksums': ['bc63fbb50534b4b1f8ebe1860889289e8af94a23bff7445259592df25a3906eb'], + }), + ('pyzmq', '22.1.0', { + 'modulename': 'zmq', + 'checksums': ['7040d6dd85ea65703904d023d7f57fab793d7ffee9ba9e14f3b897f34ff2415d'], + }), + ('entrypoints', '0.3', { + 'use_pip': False, + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('jupyter_core', '4.7.1', { + 'checksums': ['79025cb3225efcd36847d0840f3fc672c0abd7afd0de83ba8a1d3837619122b4'], + }), + ('nbformat', '5.1.3', { + 'checksums': ['b516788ad70771c6250977c1374fcca6edebe6126fd2adb5a69aa5c2356fd1c8'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('nest_asyncio', '1.5.1', { + 'checksums': ['afc5a1c515210a23c461932765691ad39e8eba6551c055ac8d5546e69250d0aa'], + }), + ('nbclient', '0.5.3', { + 'checksums': ['db17271330c68c8c88d46d72349e24c147bb6f34ec82d8481a8f025c4d26589c'], + }), + ('nbconvert', '6.1.0', { + 'checksums': ['d22a8ff202644d31db254d24d52c3a96c82156623fcd7c7f987bba2612303ec9'], + }), + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('terminado', '0.10.1', { + 'checksums': ['89d5dac2f4e2b39758a0ff9a3b643707c95a020a6df36e70583b88297cd59cbe'], + }), + ('jupyter_client', '6.1.12', { + 'checksums': ['c4bca1d0846186ca8be97f4d2fa6d2bae889cce4892a167ffa1ba6bd1f73e782'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('ipykernel', '6.0.0', { + 'checksums': ['65433238970dc6414a3ebca6f7a819fed0551efba9ac1da816ada778eb47ec65'], + }), + ('prometheus_client', '0.11.0', { + 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], + }), + ('ipywidgets', '7.6.3', { + 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.10.3', { + 'checksums': ['80799306fa42752a3592e9fda3bac7ecc8c56a2a13f26932c922b8c064378437'], + }), + ('jupyterlab_widgets', '1.0.0', { + 'checksums': ['5c1a29a84d3069208cb506b10609175b249b6486d6b1cbae8fcde2a11584fb78'], + }), + ('argon2-cffi', '20.1.0', { + 'modulename': 'argon2', + 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], + }), + ('notebook', '6.4.0', { + 'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + ('matplotlib-inline', '0.1.2', { + 'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'], + }), + ('debugpy', '1.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['8e3002cfb2ebf570f19fd060950e459a071630f6767f7e44804ac5a67ef57baf'], + }), +] + +modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/IPython', + 'share/jupyter' + ], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "NOSE_EXCLUDE='system_interrupt' iptest", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-foss-2019a-Python-3.7.2.eb index 6d5add901db..3acf58bfcb9 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-foss-2019a-Python-3.7.2.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ipython_genutils', '0.2.0', { 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb index 131686b09e9..008c9513048 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ipython_genutils', '0.2.0', { 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-intel-2019a-Python-3.7.2.eb index 4a41ad0d23c..1d307717884 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-intel-2019a-Python-3.7.2.eb @@ -24,8 +24,6 @@ dependencies = [ use_pip = True check_ldshared = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ipython_genutils', '0.2.0', { 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb index bf03798c488..55da438aac4 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ipython_genutils', '0.2.0', { 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.9.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/IPython/IPython-7.9.0-fosscuda-2019b-Python-3.7.4.eb index 60e8d2fa85b..c97ad548e22 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.9.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.9.0-fosscuda-2019b-Python-3.7.4.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ipython_genutils', '0.2.0', { 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.9.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/IPython/IPython-7.9.0-intel-2019b-Python-3.7.4.eb index ced88645a1c..6ef3a8bf461 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.9.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.9.0-intel-2019b-Python-3.7.4.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ipython_genutils', '0.2.0', { 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb new file mode 100644 index 00000000000..51142541134 --- /dev/null +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb @@ -0,0 +1,68 @@ +easyblock = 'Bundle' + +name = 'IRkernel' +version = '1.2' +versionsuffix = '-R-%(rver)s-Python-%(pyver)s' + +homepage = 'https://irkernel.github.io' +description = """The R kernel for the 'Jupyter' environment executes R code + which the front-end (Jupyter Notebook or other front-ends) submits to the + kernel via the network.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('R', '4.0.0'), + ('Python', '3.8.2'), + ('IPython', '7.15.0', '-Python-%(pyver)s'), + ('ZeroMQ', '4.3.2'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.rstudio.com/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('repr', '1.1.3', { + 'checksums': ['531b43d413b51cbc96e3b9162493c975d9395bb9532e500ad51cd99b36a53562'], + }), + ('IRdisplay', '1.0', { + 'checksums': ['8967ec58656ede561d20ab07dd9ef27de088c0ea099e325242b3860a63964b96'], + }), + ('pbdZMQ', '0.3-5', { + 'checksums': ['4d8088b3365d612a661f0078bcba50357cb3a7ec04a699348b4312fd6fd811ed'], + }), + (name, version, { + 'checksums': ['5fb4dbdb741d05043120a8be0eb73f054b607d9854f314bd79cfec08d219ff91'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +# IPython notebook looks for the json kernel file in kernels/IRkernel +# We start the kernel with default bitmapType 'cairo'. This is a more sensible default +# for headless nodes. See https://github.com/IRkernel/IRkernel/issues/388 +local_kerneldir = '%(installdir)s/IRkernel' +postinstallcmds = [ + 'mkdir -p %s/kernels/ir' % local_kerneldir, + 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir), + ('sed -i \'s/"IRkernel::main()"/"options(bitmapType=\\x27cairo\\x27); IRkernel::main()"/g\'' + ' %s/kernels/ir/kernel.json') % local_kerneldir +] + +modextravars = {'JUPYTER_PATH': local_kerneldir} + +sanity_check_paths = { + 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], + 'dirs': [name], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-9.3.0.eb b/easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e2973d809d4 --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-9.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.23' + +homepage = 'http://isl.gforge.inria.fr/' +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['http://isl.gforge.inria.fr/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d'] + +builddependencies = [('binutils', '2.34')] +dependencies = [('GMP', '6.2.0')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f2d23dbd601 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.11-14' + +homepage = 'https://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/ImageMagick/ImageMagick/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dfa5aa3f7f289f12c2f9ee6c7c19b02ae857b4eec02f40298f60f5c11048a016'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20210518'), + ('Ghostscript', '9.54.0'), + ('JasPer', '2.0.28'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.2.0'), + ('LittleCMS', '2.12'), +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', + 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb index 21d9d474c7a..56433fb0b9c 100644 --- a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'i-cisTarget' version = '20160602' # corresponds to f8be714885560ddabdb1612cf9921a348ffac468 @@ -10,23 +10,14 @@ description = """An integrative genomics method for the prediction of regulatory toolchain = {'name': 'intel', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ # airspeed requires this specific version of cachetools - ('cachetools', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cachetools/'], - }), - ('airspeed', '0.5.4dev-20150515', { - 'source_urls': ['https://pypi.python.org/packages/source/a/airspeed/'], - }), + ('cachetools', '0.8.0'), + ('airspeed', '0.5.4dev-20150515'), ('bx-python', '0.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bx-python/'], 'modulename': 'bx', }), ('Wand', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Wand/'], 'modulename': 'wand.image', }), # i-cisTarget sources are not freely available, contact lcbtools@ls.kuleuven.be @@ -46,8 +37,6 @@ dependencies = [ ('Kent_tools', '20130806', '-linux.x86_64', True), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ctx-convert', 'ctx-db2r', 'ctx-gt', 'ctx-r2db', 'ctx-rcc']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/i/igv-reports/igv-reports-0.9.8-GCC-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/i/igv-reports/igv-reports-0.9.8-GCC-8.3.0-Python-3.7.4.eb index bab993f1798..f499243d4e1 100644 --- a/easybuild/easyconfigs/i/igv-reports/igv-reports-0.9.8-GCC-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/igv-reports/igv-reports-0.9.8-GCC-8.3.0-Python-3.7.4.eb @@ -10,7 +10,6 @@ within a browser with "file" protocol.""" toolchain = {'name': 'GCC', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ae0ecac0f24e86b9858720fe0eac7d424bf79449f56446f99a2312cb4fb739b3'] diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.3.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/imageio/imageio-2.3.0-intel-2018a-Python-3.6.4.eb index 53d9a829e59..fa71ba39d0a 100644 --- a/easybuild/easyconfigs/i/imageio/imageio-2.3.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/imageio/imageio-2.3.0-intel-2018a-Python-3.6.4.eb @@ -10,7 +10,6 @@ description = """Imageio is a Python library that provides an easy interface to toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c4fd5183c342d47fdc2e98552d14e3f24386021bbc3efedd1e3b579d7d249c07'] diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.5.0-foss-2019a.eb b/easybuild/easyconfigs/i/imageio/imageio-2.5.0-foss-2019a.eb index e599b650616..272e5ff1e53 100644 --- a/easybuild/easyconfigs/i/imageio/imageio-2.5.0-foss-2019a.eb +++ b/easybuild/easyconfigs/i/imageio/imageio-2.5.0-foss-2019a.eb @@ -9,7 +9,6 @@ description = """Imageio is a Python library that provides an easy interface to toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['42e65aadfc3d57a1043615c92bdf6319b67589e49a0aae2b985b82144aceacad'] diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2019b-Python-3.7.4.eb index 946658ae697..b4e4fe4e223 100644 --- a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """Imageio is a Python library that provides an easy interface to toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-intel-2019b-Python-3.7.4.eb index c7f5e3531fa..04af67b06c4 100644 --- a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-intel-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """Imageio is a Python library that provides an easy interface to toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb index 6f8572780e1..184c06fb3e6 100644 --- a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ description = """imbalanced-learn is a Python package offering a number of re-sa toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'imblearn'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb index 399d48b06bd..9e5f22c70e3 100644 --- a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb @@ -10,7 +10,6 @@ description = """imbalanced-learn is a Python package offering a number of re-sa toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'imblearn'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.3.3-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.3.3-foss-2018a-Python-3.6.4.eb index 6c2d9d58ed3..f349199d745 100644 --- a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.3.3-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.3.3-foss-2018a-Python-3.6.4.eb @@ -10,7 +10,6 @@ description = """imbalanced-learn is a Python package offering a number of re-sa toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e49550da4c98771afd0aa49db7710ab0d85e766754bad9fb767567c367d2b2e4'] @@ -21,9 +20,4 @@ dependencies = [ options = {'modulename': 'imblearn'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb index 4c7a6ab1e30..7123a22afac 100644 --- a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ description = """imbalanced-learn is a Python package offering a number of re-sa toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5bd9e86e40ce4001a57426541d7c79b18143cbd181e3330c1a3e5c5c43287083'] @@ -24,9 +23,4 @@ download_dep_fail = True options = {'modulename': 'imblearn'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.2.8-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.2.8-foss-2018b-Python-3.6.6.eb index 573a44b437e..3d651817f9b 100644 --- a/easybuild/easyconfigs/i/imgaug/imgaug-0.2.8-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.2.8-foss-2018b-Python-3.6.6.eb @@ -23,11 +23,9 @@ use_pip = True exts_list = [ ('Shapely', '1.6.4.post2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Shapely/'], 'checksums': ['c4b87bb61fc3de59fc1f85e71a79b0c709dc68364d9584473697aad4aa13240f'], }), ('imageio', '2.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imageio/'], 'checksums': ['42e65aadfc3d57a1043615c92bdf6319b67589e49a0aae2b985b82144aceacad'], }), (name, version, { diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2019b-Python-3.7.4.eb index 329b54c4fcf..de30c641737 100644 --- a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2019b-Python-3.7.4.eb @@ -21,7 +21,6 @@ dependencies = [ ('imageio', '2.9.0', versionsuffix), ] -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['imgaug-0.4.0_openvc_requirement.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb new file mode 100644 index 00000000000..8f55b4abbfa --- /dev/null +++ b/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'inline' +version = '0.3.19' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/inline' +description = """Functionality to dynamically define R functions and S4 methods + with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling + conventions.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'] + +dependencies = [ + ('R', '4.0.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['inline'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ipyparallel/ipyparallel-6.2.2-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/ipyparallel/ipyparallel-6.2.2-foss-2018a-Python-3.6.4.eb index efb8866ff67..877d4c77a6c 100644 --- a/easybuild/easyconfigs/i/ipyparallel/ipyparallel-6.2.2-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/ipyparallel/ipyparallel-6.2.2-foss-2018a-Python-3.6.4.eb @@ -10,7 +10,6 @@ description = """ipyparallel is a Python package and collection toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['02b225966d5c20f12b1fba0b6b10aa5d352a6b492e075f137ff0ff6e95b9358e'] @@ -23,9 +22,4 @@ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb index 48e2b67b7ee..f0757066dd6 100644 --- a/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'ipyrad' version = '0.6.15' @@ -10,9 +10,6 @@ description = """ipyrad is an interactive toolkit for assembly and analysis of r toolchain = {'name': 'intel', 'version': '2017a'} -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - dependencies = [ ('Python', '2.7.13'), ('h5py', '2.7.0', versionsuffix), @@ -22,77 +19,37 @@ dependencies = [ ] exts_list = [ - ('imagesize', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize'], - }), - ('alabaster', '0.7.10', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster'], - }), - ('Babel', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel'], - }), - ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer'], - }), - ('docutils', '0.13.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], - }), - ('Sphinx', '1.5.5', { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx'], - }), - ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], - }), - ('jupyter', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter'], - }), - ('ipyparallel', '6.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipyparallel'], - }), - ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings'], - }), - ('html5lib', '0.999999999', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib'], - }), - ('bleach', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bleach'], - }), + ('imagesize', '0.7.1'), + ('alabaster', '0.7.10'), + ('Babel', '2.4.0'), + ('snowballstemmer', '1.2.1'), + ('docutils', '0.13.1'), + ('Sphinx', '1.5.5'), + ('networkx', '1.11'), + ('jupyter', '1.0.0'), + ('ipyparallel', '6.0.2'), + ('webencodings', '0.5.1'), + ('html5lib', '0.999999999'), + ('bleach', '2.0.0'), ('jupyter-console', '5.1.0', { 'modulename': 'jupyter_console', - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_console'], 'source_tmpl': 'jupyter_console-%(version)s.tar.gz', }), - ('qtconsole', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/q/qtconsole'], - }), + ('qtconsole', '4.3.0'), ('futures', '3.1.1', { 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], - }), - ('arrow', '0.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/arrow'], - }), - ('colormath', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath'], - }), - ('multipledispatch', '0.4.9', { - 'source_urls': ['https://pypi.python.org/packages/source/m/multipledispatch'], }), + ('arrow', '0.10.0'), + ('colormath', '2.1.1'), + ('multipledispatch', '0.4.9'), ('pypng', '0.0.18', { 'modulename': 'png', - 'source_urls': ['https://pypi.python.org/packages/source/p/pypng'], }), ('olefile', '0.44', { - 'source_urls': ['https://pypi.python.org/packages/source/o/olefile'], 'source_tmpl': 'olefile-%(version)s.zip', }), - ('reportlab', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/reportlab'], - }), - ('toyplot', '0.14.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toyplot'], - }), + ('reportlab', '3.4.0'), + ('toyplot', '0.14.0'), (name, version, { 'source_urls': ['https://github.com/dereneaton/ipyrad/archive/'], 'source_tmpl': '%(version)s.tar.gz', @@ -104,6 +61,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.16.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.16.0.eb new file mode 100644 index 00000000000..dacdf0697b8 --- /dev/null +++ b/easybuild/easyconfigs/i/ispc/ispc-1.16.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'ispc' +version = '1.16.0' + +homepage = 'https://ispc.github.io/ , https://github.com/ispc/ispc/' +description = """Intel SPMD Program Compilers; An open-source compiler for high-performance + SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, + with extensions for 'single program, multiple data' (SPMD) programming. + Under the SPMD model, the programmer writes a program that generally appears + to be a regular serial program, though the execution model is actually that + a number of program instances execute in parallel on the hardware.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/ispc/ispc/releases/download/v%(version)s/'] +sources = ['ispc-v%(version)s-linux.tar.gz'] +checksums = ['71a20e75ee1b952d8096a842368244111a0a727454d4a42043de10eadf02e740'] + +sanity_check_paths = { + 'files': ['bin/ispc'], + 'dirs': [] +} + +sanity_check_commands = ["ispc --help"] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_292-OpenJDK.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_292-OpenJDK.eb new file mode 100644 index 00000000000..0f8bb10be87 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_292-OpenJDK.eb @@ -0,0 +1,41 @@ +name = 'Java' +local_java_version = '8' +local_patch_version = '292' +local_build_version = '10' +version = '1.%s.0_%s' % (local_java_version, local_patch_version) +versionsuffix = '-OpenJDK' + +homepage = 'https://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_jdk_version = 'jdk%su%s-b%s' % (local_java_version, local_patch_version, local_build_version) +source_urls = ['https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/%s' % local_jdk_version] + +local_tarball_version = '%su%sb%s' % (local_java_version, local_patch_version, local_build_version) +local_tarball_tmpl = '_'.join( + ['OpenJDK%sU-jdk' % local_java_version, '%s', 'linux', 'hotspot', '%s.tar.gz' % local_tarball_version] +) + +sources = [ + { + 'filename': local_tarball_tmpl % '%(jdkarch)s', + # extract and remove dangling symlinks, + # issue https://github.com/adoptium/adoptium-support/issues/298 + 'extract_cmd': "tar xzf %%s && unlink %s/jre/lib/*/server/libjsig.debuginfo" % local_jdk_version, + } +] +checksums = [ + { + local_tarball_tmpl % 'x64': + '0949505fcf42a1765558048451bb2a22e84b3635b1a31dd6191780eeccaa4ada', + local_tarball_tmpl % 'ppc64le': + '7ecf00e57033296fd23201477a64dc13a1356b16a635907e104d079ddb544e4b', + local_tarball_tmpl % 'aarch64': + 'a29edaf66221f7a51353d3f28e1ecf4221268848260417bc562d797e514082a8', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.3.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.3.2-intel-2018a-Python-3.6.4.eb index 3dee7acee08..a5024698103 100644 --- a/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.3.2-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.3.2-intel-2018a-Python-3.6.4.eb @@ -20,11 +20,9 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('symengine', '0.3.1.dev0', { @@ -35,20 +33,16 @@ exts_list = [ }), ('jitcxde-common', '1.3.0', { 'source_tmpl': 'jitcxde_common-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/j/jitcxde-common'], 'checksums': ['db9ff40b3a73d05b95f28eee89a00dedbdf398f3d9d4eda4edd70c26d5f5ed49'], 'modulename': 'jitcxde_common', }), ('jitcdde', '1.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jitcdde'], 'checksums': ['68e9fcc2bb0da764fc17c77666e2de6cecbaf480003086a775a241a308f9669a'], }), ('jitcsde', '1.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jitcsde'], 'checksums': ['863cf30483e124dbba6c8f31496ae21b0507ba7f07952df5566bb9842f17d009'], }), ('jitcode', version, { - 'source_urls': ['https://pypi.python.org/packages/source/j/jitcode'], 'checksums': ['84348cfecba84e3865a864259e9c98417e4facdcb2963d1fe27565c6994ea7c2'], }), ] diff --git a/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.4.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.4.0-foss-2019a-Python-3.7.2.eb index 34bf107599e..8e2199795c0 100644 --- a/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.4.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.4.0-foss-2019a-Python-3.7.2.eb @@ -21,34 +21,27 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('Jinja2', '2.10.1', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['065c4f02ebe7f7cf559e49ee5a95fb800a9e4528727aec6f24402a5374c65013'], }), ('symengine', '0.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/symengine'], 'checksums': ['54c553692ca94262377923d5064ac89da84e12de4ef63f2b1db5b7850ac9d1c2'], 'preinstallopts': "export SymEngine_DIR=$EBROOTSYMENGINE/lib/cmake/symengine && ", }), ('jitcxde-common', '1.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jitcxde-common'], 'source_tmpl': 'jitcxde_common-%(version)s.tar.gz', 'checksums': ['dbdfc7121d5f8ea44f680d6d24a8406477381e9db94ce72dc77924f7ccdac219'], 'modulename': 'jitcxde_common', }), ('jitcdde', '1.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jitcdde'], 'checksums': ['68e9fcc2bb0da764fc17c77666e2de6cecbaf480003086a775a241a308f9669a'], }), ('jitcsde', version, { - 'source_urls': ['https://pypi.python.org/packages/source/j/jitcsde'], 'checksums': ['2697740a8921adab68fd54563c6693eb57bdf498f1ff44e382562dad43dc0794'], }), ('jitcode', version, { - 'source_urls': ['https://pypi.python.org/packages/source/j/jitcode'], 'checksums': ['01dca542b24252d038e3fe601192362a32e7c0ab3184591b46b00b549cb36868'], }), ] diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..55046992818 --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.4' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['e34a628a8142643b976c7233ef381457efad79468c67cb1ae0b83a33d7493999'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), + ('binutils', '2.36.1'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..13e61332cf5 --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20210128'), + ('binutils', '2.36.1'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.6.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.6.1-foss-2016a-Python-3.5.1.eb index 4f7acfa8c4c..34edefbc45c 100755 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.6.1-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.6.1-foss-2016a-Python-3.5.1.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'JupyterHub' version = '0.6.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://jupyter.org' +homepage = 'https://jupyter.org' description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.""" @@ -16,26 +16,13 @@ dependencies = [ ('configurable-http-proxy', '1.3.0', '-nodejs-4.4.7'), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ - ('SQLAlchemy', '1.0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], - }), - ('requests', '2.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), - ('pamela', '0.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pamela/'], - }), - ('jupyterhub', version, { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyterhub/'], - }), + ('SQLAlchemy', '1.0.13'), + ('requests', '2.10.0'), + ('pamela', '0.2.1'), + ('jupyterhub', version), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/jupyterhub'], 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.8.1-foss-2017a-Python-3.6.4.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.8.1-foss-2017a-Python-3.6.4.eb index adf98f2603e..092ffde901b 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.8.1-foss-2017a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.8.1-foss-2017a-Python-3.6.4.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'JupyterHub' version = '0.8.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://jupyter.org' +homepage = 'https://jupyter.org' description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.""" @@ -16,75 +16,60 @@ dependencies = [ ('configurable-http-proxy', '3.1.1', '-nodejs-8.9.4'), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ ('pamela', '0.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pamela/'], 'checksums': [ '1e198446a6cdd87704aa0def7621d62e7c20b0e6068e2788b9a866a8355e5d6b', # pamela-0.3.0.tar.gz ], }), ('SQLAlchemy', '1.1.15', { - 'source_urls': ['https://pypi.python.org/packages/source/s/SQLAlchemy/'], 'checksums': [ '8b79a5ed91cdcb5abe97b0045664c55c140aec09e5dd5c01303e23de5fe7a95a', # SQLAlchemy-1.1.15.tar.gz ], }), ('alembic', '0.9.7', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alembic/'], 'checksums': [ '46f4849c6dce69f54dd5001b3215b6a983dee6b17512efee10e237fa11f20cfa', # alembic-0.9.7.tar.gz ], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': [ '9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e', # requests-2.18.4.tar.gz ], }), ('python-oauth2', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/python-oauth2/'], 'modulename': 'oauth2', 'checksums': [ '5583b5cea3e6cc154800f7a04a061fc7673cb12c75ad9413e607d4472d062d28', # python-oauth2-1.0.1.tar.gz ], }), ('Mako', '1.0.7', { - 'source_urls': ['https://pypi.python.org/packages/source/m/Mako/'], 'checksums': [ '4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae', # Mako-1.0.7.tar.gz ], }), ('python-editor', '1.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/python_editor/'], 'modulename': 'editor', 'checksums': [ 'a3c066acee22a1c94f63938341d4fb374e3fdd69366ed6603d7b24bed1efc565', # python-editor-1.0.3.tar.gz ], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': [ 'cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f', # urllib3-1.22.tar.gz ], }), ('certifi', '2018.1.18', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': [ 'edbc3f203427eef571f79a7692bb160a2b0f7ccaa31953e99bd17e307cf63f7d', # certifi-2018.1.18.tar.gz ], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': [ '84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae', # chardet-3.0.4.tar.gz ], }), ('jupyterhub', version, { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyterhub/'], 'use_pip': True, 'checksums': [ '100cf18d539802807a45450d38fefbb376cf1c810f3b1b31be31638829a5c69c', # jupyterhub-0.8.1.tar.gz @@ -92,8 +77,6 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/jupyterhub'], 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-1.2.5-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-1.2.5-foss-2019b-Python-3.7.4.eb index 56acd57e7fe..8a0e96f90f8 100644 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-1.2.5-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-1.2.5-foss-2019b-Python-3.7.4.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('json5', '0.8.5', { 'checksums': ['124b0f0da1ed2ff3bfe3a3e9b8630abd3c650852465cb52c15ef60b8e82a73b0'], diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-1.2.5-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-1.2.5-fosscuda-2019b-Python-3.7.4.eb index 39620523bfc..b7666ab4e2c 100644 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-1.2.5-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-1.2.5-fosscuda-2019b-Python-3.7.4.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('json5', '0.8.5', { 'checksums': ['124b0f0da1ed2ff3bfe3a3e9b8630abd3c650852465cb52c15ef60b8e82a73b0'], diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6a8b7a7bec4 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '3.0.16' + +homepage = "https://jupyter.org/" +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('IPython', '7.25.0'), +] + +use_pip = True +sanity_pip_check = True + + +exts_list = [ + ('anyio', '3.2.1', { + 'checksums': ['07968db9fa7c1ca5435a133dc62f988d84ef78e1d9b22814a59d1c62618afbc5'], + }), + ('json5', '0.9.6', { + 'checksums': ['9175ad1bc248e22bb8d95a8e8d765958bf0008fef2fe8abab5bc04e0f1ac8302'], + }), + ('jupyter_server', '1.9.0', { + 'checksums': ['7d19006380f6217458a9db309b54e3dab87ced6c06329c61823907bef2a6f51b'], + }), + ('requests-unixsocket', '0.2.0', { + 'checksums': ['9e5c1a20afc3cf786197ae59c79bcdb0e7565f218f27df5f891307ee8817c1ea'], + }), + ('sniffio', '1.2.0', { + 'checksums': ['c4666eecec1d3f50960c6bdf61ab7bc350648da6c126e3cf6898d8cd4ddcd3de'], + }), + ('websocket-client', '1.1.0', { + 'modulename': 'websocket', + 'checksums': ['b68e4959d704768fa20e35c9d508c8dc2bbc041fd8d267c0d7345cffe2824568'], + }), + ('nbclassic', '0.3.1', { + 'checksums': ['f920f8d09849bea7950e1017ff3bd101763a8d68f565a51ce053572e65aa7947'], + }), + ('jupyterlab_server', '2.6.0', { + 'checksums': ['f300adf6bb0a952bebe9c807a3b2a345d62da39b476b4f69ea0dc6b5f3f6b97d'], + }), + (name, version, { + 'patches': ['%(name)s-1.2.5_set-app-path-for-easybuild.patch'], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': [ + '7ad4fbe1f6d38255869410fd151a8b15692a663ca97c0a8146b3f5c40e275c23', # jupyterlab-3.0.16.tar.gz + # JupyterLab-1.2.5_set-app-path-for-easybuild.patch + 'a219b1071f37f848f7e79c6800149c0b2386a2b748be43288bc32af8e7dab668', + ], + }), +] + +sanity_check_commands = ["jupyter lab --help"] + +modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/joypy/joypy-0.2.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/j/joypy/joypy-0.2.2-intel-2019b-Python-3.7.4.eb index d014690d4ec..1f45fdd646f 100644 --- a/easybuild/easyconfigs/j/joypy/joypy-0.2.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/j/joypy/joypy-0.2.2-intel-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = "Joyplots in Python with matplotlib & pandas" toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a12598e75f4d40d72a26f7eeae6b74f4ced05c49af147ace8e3a229ab7b20395'] diff --git a/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb index 418b1b87b0e..e4caa7a3144 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/k/Keras/Keras-1.1.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/k/Keras/Keras-1.1.0-intel-2016b-Python-3.5.2.eb index 503271be943..f3ec6602cbe 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-1.1.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-1.1.0-intel-2016b-Python-3.5.2.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb index b4756636047..38517b82d4a 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ @@ -23,9 +22,4 @@ dependencies = [ # it defaults to Tensorflow modextravars = {'KERAS_BACKEND': 'theano'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb index d338fae1c93..fe9cca652e8 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ @@ -23,9 +22,4 @@ dependencies = [ # it defaults to Tensorflow modextravars = {'KERAS_BACKEND': 'theano'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.5-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.5-intel-2017a-Python-3.6.1.eb index 105d38b643c..1ebcf74410d 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.0.5-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.5-intel-2017a-Python-3.6.1.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ @@ -23,9 +22,4 @@ dependencies = [ # it defaults to Tensorflow modextravars = {'KERAS_BACKEND': 'theano'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.8-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.8-intel-2017a-Python-3.6.1.eb index 94353499b77..5375bb29c12 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.0.8-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.8-intel-2017a-Python-3.6.1.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['899dc6aaed366f20100b9f80cf1093ea5b43eecc74afd1dc63a4e48dfa776ab9'] @@ -24,9 +23,4 @@ dependencies = [ # it defaults to Tensorflow modextravars = {'KERAS_BACKEND': 'theano'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.1.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/k/Keras/Keras-2.1.1-intel-2017b-Python-2.7.14.eb index e46bd07b49e..8d05874c88a 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.1.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.1.1-intel-2017b-Python-2.7.14.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f0ca2458c60d9711edf4291230b31795307ad3781cb6232ff4792b53c8f55123'] @@ -24,9 +23,4 @@ dependencies = [ # it defaults to Tensorflow modextravars = {'KERAS_BACKEND': 'theano'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.1.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/k/Keras/Keras-2.1.1-intel-2017b-Python-3.6.3.eb index 4497a241dd9..cf369f270fd 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.1.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.1.1-intel-2017b-Python-3.6.3.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f0ca2458c60d9711edf4291230b31795307ad3781cb6232ff4792b53c8f55123'] @@ -24,9 +23,4 @@ dependencies = [ # it defaults to Tensorflow modextravars = {'KERAS_BACKEND': 'theano'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.1.2-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/k/Keras/Keras-2.1.2-foss-2017b-Python-3.6.3.eb index 53f860a3393..67884b95d4e 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.1.2-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.1.2-foss-2017b-Python-3.6.3.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3ee56fc129d9d00b1916046e50056047836f97ada59df029e5661fb34442d5e8'] @@ -22,9 +21,4 @@ dependencies = [ ('PyYAML', '3.12', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.1.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/k/Keras/Keras-2.1.2-intel-2017b-Python-2.7.14.eb index 6e923277120..b5f4a19c517 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.1.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.1.2-intel-2017b-Python-2.7.14.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3ee56fc129d9d00b1916046e50056047836f97ada59df029e5661fb34442d5e8'] @@ -24,9 +23,4 @@ dependencies = [ # it defaults to Tensorflow modextravars = {'KERAS_BACKEND': 'theano'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.1.3-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/k/Keras/Keras-2.1.3-foss-2017b-Python-3.6.3.eb index ba440fc26bf..5ce027bee39 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.1.3-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.1.3-foss-2017b-Python-3.6.3.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['7ca3a381523bad40a6922e88951a316664cb088fd01cea07e5ec8ada3327e3c7'] @@ -22,9 +21,4 @@ dependencies = [ ('PyYAML', '3.12', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.1.3-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/k/Keras/Keras-2.1.3-intel-2017b-Python-3.6.3.eb index d7415098906..8197ec299e6 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.1.3-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.1.3-intel-2017b-Python-3.6.3.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['7ca3a381523bad40a6922e88951a316664cb088fd01cea07e5ec8ada3327e3c7'] @@ -22,9 +21,4 @@ dependencies = [ ('PyYAML', '3.12', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-foss-2018a-Python-3.6.4.eb index 7c9225e089c..c45a56e5dee 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-foss-2018a-Python-3.6.4.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5b8499d157af217f1a5ee33589e774127ebc3e266c833c22cb5afbb0ed1734bf'] @@ -22,9 +21,4 @@ dependencies = [ ('PyYAML', '3.12', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb index 4bd4c8b5e66..54960920311 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb @@ -23,23 +23,15 @@ use_pip = True exts_list = [ ('Keras-Applications', '1.0.4', { 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], 'checksums': ['8c95300328630ae74fb0828b6fa38269a25c0228a02f1e5181753bfd48961f49'], }), ('Keras-Preprocessing', '1.0.2', { 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], 'checksums': ['f5306554d2b454d825b36f35e327744f5477bd2ae21017f1a93b2097bed6757e'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras'], 'checksums': ['5b8499d157af217f1a5ee33589e774127ebc3e266c833c22cb5afbb0ed1734bf'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb index de38ea3229f..fc1262f42b7 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb @@ -23,23 +23,15 @@ use_pip = True exts_list = [ ('Keras-Applications', '1.0.4', { 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], 'checksums': ['8c95300328630ae74fb0828b6fa38269a25c0228a02f1e5181753bfd48961f49'], }), ('Keras-Preprocessing', '1.0.2', { 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], 'checksums': ['f5306554d2b454d825b36f35e327744f5477bd2ae21017f1a93b2097bed6757e'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras'], 'checksums': ['5b8499d157af217f1a5ee33589e774127ebc3e266c833c22cb5afbb0ed1734bf'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.2-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.2-fosscuda-2018b-Python-2.7.15.eb index ffdfdc5aadd..c79fd20a93d 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.2.2-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.2-fosscuda-2018b-Python-2.7.15.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['468d98da104ec5c3dbb10c2ef6bb345ab154f6ca2d722d4c250ef4d6105de17a'] @@ -22,9 +21,4 @@ dependencies = [ ('PyYAML', '3.13', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-foss-2018b-Python-3.6.6.eb index f173c2453d9..e7d0779559c 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.2.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-foss-2018b-Python-3.6.6.eb @@ -22,17 +22,14 @@ use_pip = True exts_list = [ ('Keras-Applications', '1.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['a03af60ddc9c5afdae4d5c9a8dd4ca857550e0b793733a5072e0725829b87017'], }), ('Keras-Preprocessing', '1.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras'], 'checksums': ['90b610a3dbbf6d257b20a079eba3fdf2eed2158f64066a7c6f7227023fd60bc9'], }), ] diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.4-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-foss-2019a-Python-3.7.2.eb index be48acdf0a0..4fb22a51c05 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.2.4-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-foss-2019a-Python-3.7.2.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['90b610a3dbbf6d257b20a079eba3fdf2eed2158f64066a7c6f7227023fd60bc9'] @@ -25,9 +24,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2018b-Python-3.6.6.eb index 1f73707b820..5bce5f37a64 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['90b610a3dbbf6d257b20a079eba3fdf2eed2158f64066a7c6f7227023fd60bc9'] @@ -27,9 +26,4 @@ download_dep_fail = True fix_python_shebang_for = ['bin/conv-template', 'bin/from-template'] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2019a-Python-3.7.2.eb index 1854e8a770a..557817a33bf 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2019a-Python-3.7.2.eb @@ -10,7 +10,6 @@ capable of running on top of either TensorFlow or Theano.""" toolchain = {'name': 'fosscuda', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['90b610a3dbbf6d257b20a079eba3fdf2eed2158f64066a7c6f7227023fd60bc9'] @@ -27,9 +26,4 @@ download_dep_fail = True fix_python_shebang_for = ['bin/conv-template', 'bin/from-template'] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.4-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-intel-2018a-Python-3.6.4.eb index 55e4b9aef57..62bd40154fe 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.2.4-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-intel-2018a-Python-3.6.4.eb @@ -23,17 +23,14 @@ use_pip = True exts_list = [ ('Keras-Applications', '1.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['a03af60ddc9c5afdae4d5c9a8dd4ca857550e0b793733a5072e0725829b87017'], }), ('Keras-Preprocessing', '1.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras'], 'checksums': ['90b610a3dbbf6d257b20a079eba3fdf2eed2158f64066a7c6f7227023fd60bc9'], }), ] diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.3.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/k/Keras/Keras-2.3.1-foss-2019b-Python-3.7.4.eb index 38be4d4d534..0f78ffba4ea 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.3.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.3.1-foss-2019b-Python-3.7.4.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Keras_Applications', '1.0.8', { 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.3.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/k/Keras/Keras-2.3.1-fosscuda-2019b-Python-3.7.4.eb index fe0159bc009..8388c69f669 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.3.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.3.1-fosscuda-2019b-Python-3.7.4.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Keras_Applications', '1.0.8', { 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], diff --git a/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb index 92bba843cd1..6313c8ad1e2 100644 --- a/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb @@ -6,7 +6,7 @@ # Adam Huffman # The Francis Crick Institute -easyblock = "Bundle" +easyblock = "PythonBundle" name = 'khmer' version = '2.1.1' @@ -17,20 +17,15 @@ description = """ In-memory nucleotide sequence k-mer counting, filtering, graph toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.13'), ] exts_list = [ ('bz2file', '0.98', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], }), ('screed', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/screed'], 'checksums': ['5db69f8c413a984ade62eb8344a6eb2be26555d74be86d38512673c1cf621b91'], }), ('khmer', '2.1.1', { @@ -46,6 +41,4 @@ sanity_check_paths = { 'dirs': ["lib/python%(pyshortver)s/site-packages/khmer-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kwant/kwant-1.4.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/k/kwant/kwant-1.4.1-foss-2019a-Python-3.7.2.eb index 020ebca00b8..d2f369dc5f1 100644 --- a/easybuild/easyconfigs/k/kwant/kwant-1.4.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/k/kwant/kwant-1.4.1-foss-2019a-Python-3.7.2.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('mpmath', '1.1.0', { 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], diff --git a/easybuild/easyconfigs/k/kwant/kwant-1.4.1-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/k/kwant/kwant-1.4.1-intel-2019a-Python-3.7.2.eb index 8639a9f1327..5f213270dff 100644 --- a/easybuild/easyconfigs/k/kwant/kwant-1.4.1-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/k/kwant/kwant-1.4.1-intel-2019a-Python-3.7.2.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('mpmath', '1.1.0', { 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..62f298edf85 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), +] + +dependencies = [('ncurses', '6.2')] + +preconfigopts = "autoconf && " + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.26.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.26.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..01d38679892 --- /dev/null +++ b/easybuild/easyconfigs/l/LDC/LDC-1.26.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeNinja' + +name = 'LDC' +version = '1.26.0' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s'] +sources = ['ldc-%(version)s-src.tar.gz'] +checksums = ['c18f4c76869f0196b459dcd6196c7eaea1b097cc422cf3771de394f6c0ef7474'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('Ninja', '1.10.2'), + # building LDC from source required LDC 0.17.x + ('LDC', '0.17.6', '-%(arch)s', True), +] + +dependencies = [ + ('LLVM', '11.1.0'), +] + +configopts = "-DLLVM_ROOT_DIR=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/ldc2', 'bin/ldmd2'], + 'dirs': ['include/d', 'lib'], +} + +sanity_check_commands = [ + "ldc2 --help", + "ldmd2 --help", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.24-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.24-GCCcore-9.3.0.eb index 0c8d372d0a2..3ea274e0802 100644 --- a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.24-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.24-GCCcore-9.3.0.eb @@ -9,11 +9,12 @@ description = """LIBSVM is an integrated software for support vector classificat toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -source_urls = [homepage] -sources = [SOURCELOWER_TAR_GZ] +github_account = 'cjlin1' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%s.tar.gz' % version.replace('.', '')] patches = ['LIBSVM-3.23_shared_lib.patch'] checksums = [ - 'd5881a201a4e6227bf8e2f5de7d6eeaef481c6c2bb9540aeca547737844f8696', # libsvm-3.24.tar.gz + '3ba1ac74ee08c4dd57d3a9e4a861ffb57dab88c6a33fd53eac472fc84fbb2a8f', # v324.tar.gz 'c0ede89365949644f5d7f11382a3f176fd76317c7f5ae5769226ff7c3a801fe6', # LIBSVM-3.23_shared_lib.patch ] diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-11.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-11.1.0-GCCcore-10.3.0.eb index 1796d4bfc1d..cdaefd6f34a 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-11.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-11.1.0-GCCcore-10.3.0.eb @@ -20,7 +20,7 @@ checksums = ['ce8508e318a01a63d4e8b3090ab2ded3c598a50258cc49e2625b9120d4c03ea5'] builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), - ('Python', '3.9.5'), + ('Python', '3.9.5', '-bare'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-0.9.14-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/l/LMfit/LMfit-0.9.14-intel-2018b-Python-2.7.15.eb index 7f74ec070bb..6ab7ea33e0f 100644 --- a/easybuild/easyconfigs/l/LMfit/LMfit-0.9.14-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/l/LMfit/LMfit-0.9.14-intel-2018b-Python-2.7.15.eb @@ -14,8 +14,6 @@ dependencies = [('Python', '2.7.15')] use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('asteval', '0.9.12', { 'checksums': ['38f3b0592cae7e7f65adc687e37aad1824a8e518245603a29ec33258277e779b'], diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-0.9.9-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/l/LMfit/LMfit-0.9.9-intel-2018a-Python-3.6.4.eb index 97a9a7abe39..5bbc13fd540 100644 --- a/easybuild/easyconfigs/l/LMfit/LMfit-0.9.9-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/l/LMfit/LMfit-0.9.9-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'LMfit' version = '0.9.9' @@ -11,26 +11,14 @@ toolchain = {'name': 'intel', 'version': '2018a'} dependencies = [('Python', '3.6.4')] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ ('asteval', '0.9.12', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asteval'], 'checksums': ['38f3b0592cae7e7f65adc687e37aad1824a8e518245603a29ec33258277e779b'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/l/lmfit'], 'source_tmpl': 'lmfit-%(version)s.tar.gz', 'checksums': ['eee9fa534dc3c494a4d7dd3e0cd243792bbc6cb409805440282a4b5fdab50ea1'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.0-intel-2019b-Python-3.7.4.eb index 15624a318d8..13b4e27db87 100644 --- a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.0-intel-2019b-Python-3.7.4.eb @@ -17,8 +17,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('asteval', '0.9.18', { 'checksums': ['5d64e18b8a72c2c7ae8f9b70d1f80b68bbcaa98c1c0d7047c35489d03209bc86'], diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb new file mode 100644 index 00000000000..3e119826309 --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.0.2' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = """Lmfit provides a high-level interface to non-linear optimization +and curve fitting problems for Python""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asteval', '0.9.23', { + 'checksums': ['f5096a924b1d2f147e70327245d95fc8f534dbe94277b6828ce2a8c049d3a438'], + }), + ('uncertainties', '3.1.5', { + 'checksums': ['9122c1e7e074196883b4a7a946e8482807b2f89675cb5e3798b87e0608ede903'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['67090ce56685cf7f92bd7358a1e7d4ad862b3758988109ec440e9825e5184b45'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb new file mode 100644 index 00000000000..2c4a3881ddc --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.0.2' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = """Lmfit provides a high-level interface to non-linear optimization +and curve fitting problems for Python""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asteval', '0.9.23', { + 'checksums': ['f5096a924b1d2f147e70327245d95fc8f534dbe94277b6828ce2a8c049d3a438'], + }), + ('uncertainties', '3.1.5', { + 'checksums': ['9122c1e7e074196883b4a7a946e8482807b2f89675cb5e3798b87e0608ede903'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['67090ce56685cf7f92bd7358a1e7d4ad862b3758988109ec440e9825e5184b45'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LTR_retriever/LTR_retriever-2.9.0-foss-2020b.eb b/easybuild/easyconfigs/l/LTR_retriever/LTR_retriever-2.9.0-foss-2020b.eb new file mode 100644 index 00000000000..35d99a92ae2 --- /dev/null +++ b/easybuild/easyconfigs/l/LTR_retriever/LTR_retriever-2.9.0-foss-2020b.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'Tarball' + +name = 'LTR_retriever' +version = '2.9.0' + +homepage = 'https://github.com/oushujun/LTR_retriever' +description = """LTR_retriever is a highly accurate and sensitive program for + identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also + included in this package. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'oushujun' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e2d94f6179c33990a77fa9fdcefb842c8481b4c30833c9c12cbbe54cb3fdda73'] + +dependencies = [ + ('Perl', '5.32.0'), + ('BLAST+', '2.11.0'), + ('RepeatMasker', '4.1.2-p1'), + ('HMMER', '3.3.2'), + ('CD-HIT', '4.8.1'), + ('TRF', '4.09.1'), +] + +sanity_check_paths = { + 'files': ['LTR_retriever'], + 'dirs': ['bin', 'database'], +} + +sanity_check_commands = [("%(name)s -h 2>&1 | grep 'Usage: LTR_retriever'", '')] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.12-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.12-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..42476101d66 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.12-GCCcore-10.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.12' + +homepage = 'https://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['18663985e864100455ac3e507625c438c3710354d85e5cbb7cd4043e11fe10f5'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('libjpeg-turbo', '2.0.6')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.4.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.4.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d751c559192 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.4.3-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +name = 'Lua' +version = '5.4.3' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f8612276169e3bfcbcfb8f226195bfc6e466fe13042f1076cbde92b7ec96bbfb'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('libreadline', '8.1'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6cb69512262 --- /dev/null +++ b/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'MakeCp' + +name = 'libStatGen' +version = '1.0.15' +_hash = 'ff4f2fc' + +homepage = "https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen" +description = """Useful set of classes for creating statistical genetic programs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'statgen' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % _hash, 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['68acb15b6c85f07b0dbf3f8b7a2a99a88fc97d3e29e80bebab82bd2a8e09121e'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +runtest = 'test' + +files_to_copy = [ + (['libStatGen.a'], 'lib'), + ('include'), +] + +sanity_check_paths = { + 'files': ['lib/libStatGen.a', 'include/VcfFile.h', 'include/SamFile.h', 'include/BamIndex.h', 'include/Cigar.h'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..076fa063db8 --- /dev/null +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.112' +local_libversion = '1.0.1' + +homepage = 'https://pagure.io/libaio' +description = "Asynchronous input/output library that uses the kernels native interface." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] + +builddependencies = [('binutils', '2.36.1')] + +files_to_copy = [ + (["src/libaio.a", "src/libaio.%s.%s" % (SHLIB_EXT, local_libversion)], "lib"), + (["src/libaio.h"], "include"), +] + +postinstallcmds = ["cd %%(installdir)s/lib; ln -s libaio.%s.%s libaio.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT)] + +sanity_check_paths = { + 'files': ['lib/libaio.a', 'lib/libaio.%s.%s' % (SHLIB_EXT, local_libversion), 'include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..85bd90476f0 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-8.3.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.5.1' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['9015d109ec00bb9ae1a384b172bf2fc1dff41e2c66e5a9eeddf933af9db37f5a'] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +builddependencies = [ + ('binutils', '2.32'), + ('XZ', '5.2.4'), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.17-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.17-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e8ac5205b1a --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.17-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '1.17' + +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['b1916b292cb37f2d0d0b699fbcf0fe260cca97ec7266ea20ff0c5cd8ef2eaab4'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('Perl', '5.32.1'), # required for pod2html +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb new file mode 100644 index 00000000000..f8db3f095f4 --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '4.4.0' + +homepage = 'https://github.com/sunqm/libcint' +description = """libcint is an open source library for analytical Gaussian integrals.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/sunqm/libcint/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_remove_pyscftest.patch'] +checksums = [ + '39a831e9131395e7ac312608981495aed3e44d0511b0700b2a1fb163b32c89c1', # v4.4.0.tar.gz + '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d', # libcint-4.4.0_remove_pyscftest.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + # Python with numpy only required for 'make test' + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +separate_build_dir = False # Must use the same directory for tests + +configopts = '-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on' + +buildopts = "VERBOSE=1" + +runtest = 'test ' + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/libcint.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2021a.eb b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2021a.eb new file mode 100644 index 00000000000..acf85af6d68 --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2021a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '4.4.0' + +homepage = 'https://github.com/sunqm/libcint' +description = """libcint is an open source library for analytical Gaussian integrals.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/sunqm/libcint/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_remove_pyscftest.patch'] +checksums = [ + '39a831e9131395e7ac312608981495aed3e44d0511b0700b2a1fb163b32c89c1', # v4.4.0.tar.gz + '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d', # libcint-4.4.0_remove_pyscftest.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + # Python with numpy only required for 'make test' + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +separate_build_dir = False # Must use the same directory for tests + +configopts = '-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on' + +buildopts = "VERBOSE=1" + +runtest = 'test ' + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/libcint.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libcint/libcint-4.4.0_remove_pyscftest.patch b/easybuild/easyconfigs/l/libcint/libcint-4.4.0_remove_pyscftest.patch new file mode 100644 index 00000000000..d66fee600f1 --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-4.4.0_remove_pyscftest.patch @@ -0,0 +1,18 @@ +Remove single test with circular dependency on PySCF. +Author: micketeer@gmail.com +--- testsuite/test_3c2e.py.orig 2021-06-14 13:15:11.316287035 +0200 ++++ testsuite/test_3c2e.py 2021-06-14 13:11:51.777769636 +0200 +@@ -307,9 +307,10 @@ + ): + test_int3c2e_sph(*f) + if "--quick" not in sys.argv: +- for f in (('cint3c2e', 'cint3c2e_sph', 4412.363002589966, 1, 10), +- ): +- test_int3c2e_spinor(*f) ++# for f in (('cint3c2e', 'cint3c2e_sph', 4412.363002589966, 1, 10), ++# ): ++# test_int3c2e_spinor(*f) ++ pass + + # for f in (('cint2c2e_sph', 'cint2e_sph', 782.3104849606677, 1, 10), + # ('cint2c2e_ip1_sph', 'cint2e_ip1_sph', 394.6515972715189, 3, 10), diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f5cd050faa3 --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.8' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['0cd80cb040b75cbe77fadd45c48282ebab82d845c597ce11ee5e8cb9c1efeabb'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210518'), + ('Mesa', '21.1.1'), +] + +configopts = '-Degl=no --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb index 308b71928cf..6428a4e759b 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb @@ -14,26 +14,40 @@ deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. """ +# The psm3 provider (enabled by default) requires an AVX capable system to run toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} github_account = 'ofiwg' source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] sources = [SOURCE_TAR_BZ2] -patches = ['%(name)s-%(version)s_fix-psm3-multiep-default.patch'] +patches = [ + '%(name)s-%(version)s_fix-psm3-multiep-default.patch', + '%(name)s-%(version)s_disable-psm3-avx-config.patch', +] checksums = [ 'db3c8e0a495e6e9da6a7436adab905468aedfbd4579ee3da5232a5c111ba642c', # libfabric-1.12.1.tar.bz2 # libfabric-1.12.1_fix-psm3-multiep-default.patch '298ba67bc04472bc627e642525dd4333fe18f80774814ae86c8e18437ada4e7d', + # libfabric-1.12.1_disable-psm3-avx-config.patch + '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', ] builddependencies = [ ('binutils', '2.36.1'), ('pkg-config', '0.29.2'), + ('Autotools', '20210128'), +] + +dependencies = [ + ('numactl', '2.0.14'), ] osdependencies = [OS_PKG_IBVERBS_DEV] +# Regenerate build files +preconfigopts = "autoreconf -f -i &&" + # Disable deprecated "sockets" provider configopts = "--disable-sockets " @@ -42,6 +56,8 @@ configopts = "--disable-sockets " # osdependencies.append(('libnl3-devel', 'libnl3-dev')) configopts += "--disable-usnic " +buildopts = "V=1" + sanity_check_paths = { 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1_disable-psm3-avx-config.patch b/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1_disable-psm3-avx-config.patch new file mode 100644 index 00000000000..cf39627a5e3 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1_disable-psm3-avx-config.patch @@ -0,0 +1,90 @@ +The AVX/AVX2 detection seems to be based on compiler instead of CPU capabilities +which can lead to broken binaries as result of the build (eg AVX2 binaries in Intel IvyBridge) +Completetly disable this detection as it is already set by EasyBuild +author: Alex Domingo (Vrije Universiteit Brussel) +--- prov/psm3/configure.m4.orig 2021-06-18 23:47:26.752607000 +0200 ++++ prov/psm3/configure.m4 2021-06-18 23:47:47.015363000 +0200 +@@ -88,45 +88,45 @@ + ]) + CFLAGS=$save_CFLAGS + +- AC_MSG_CHECKING([for -mavx support]) +- save_CFLAGS=$CFLAGS +- CFLAGS="$PSM3_STRIP_OPTFLAGS -mavx -O0" +- AC_LINK_IFELSE( +- [AC_LANG_PROGRAM( +- [[#include ]], +- [[unsigned long long _a[4] = {1ULL,2ULL,3ULL,4ULL}; +- __m256i vA = _mm256_loadu_si256((__m256i *)_a); +- __m256i vB; +- _mm256_store_si256(&vB, vA); +- return 0;]]) +- ],[ +- AC_MSG_RESULT([yes]) +- PSM3_ARCH_CFLAGS="-mavx" +- ],[ +- psm3_happy=0 +- AC_MSG_RESULT([no]) +- AC_MSG_NOTICE([psm3 requires minimum of avx instruction set to build]) +- ]) +- CFLAGS=$save_CFLAGS ++dnl AC_MSG_CHECKING([for -mavx support]) ++dnl save_CFLAGS=$CFLAGS ++dnl CFLAGS="$PSM3_STRIP_OPTFLAGS -mavx -O0" ++dnl AC_LINK_IFELSE( ++dnl [AC_LANG_PROGRAM( ++dnl [[#include ]], ++dnl [[unsigned long long _a[4] = {1ULL,2ULL,3ULL,4ULL}; ++dnl __m256i vA = _mm256_loadu_si256((__m256i *)_a); ++dnl __m256i vB; ++dnl _mm256_store_si256(&vB, vA); ++dnl return 0;]]) ++dnl ],[ ++dnl AC_MSG_RESULT([yes]) ++dnl PSM3_ARCH_CFLAGS="-mavx" ++dnl ],[ ++dnl psm3_happy=0 ++dnl AC_MSG_RESULT([no]) ++dnl AC_MSG_NOTICE([psm3 requires minimum of avx instruction set to build]) ++dnl ]) ++dnl CFLAGS=$save_CFLAGS + +- AC_MSG_CHECKING([for -mavx2 support]) +- save_CFLAGS=$CFLAGS +- CFLAGS="$PSM3_STRIP_OPTFLAGS -mavx2 -O0" +- AC_LINK_IFELSE( +- [AC_LANG_PROGRAM( +- [[#include ]], +- [[unsigned long long _a[4] = {1ULL,2ULL,3ULL,4ULL}; +- __m256i vA = _mm256_loadu_si256((__m256i *)_a); +- __m256i vB = _mm256_add_epi64(vA, vA); +- (void)vB; +- return 0;]]) +- ],[ +- AC_MSG_RESULT([yes]) +- PSM3_ARCH_CFLAGS="-mavx2" +- ],[ +- AC_MSG_RESULT([no]) +- ]) +- CFLAGS=$save_CFLAGS ++dnl AC_MSG_CHECKING([for -mavx2 support]) ++dnl save_CFLAGS=$CFLAGS ++dnl CFLAGS="$PSM3_STRIP_OPTFLAGS -mavx2 -O0" ++dnl AC_LINK_IFELSE( ++dnl [AC_LANG_PROGRAM( ++dnl [[#include ]], ++dnl [[unsigned long long _a[4] = {1ULL,2ULL,3ULL,4ULL}; ++dnl __m256i vA = _mm256_loadu_si256((__m256i *)_a); ++dnl __m256i vB = _mm256_add_epi64(vA, vA); ++dnl (void)vB; ++dnl return 0;]]) ++dnl ],[ ++dnl AC_MSG_RESULT([yes]) ++dnl PSM3_ARCH_CFLAGS="-mavx2" ++dnl ],[ ++dnl AC_MSG_RESULT([no]) ++dnl ]) ++dnl CFLAGS=$save_CFLAGS + + AS_IF([test x$with_psm3_rv = xno], + [psm3_CPPFLAGS="$psm3_CPPFLAGS -URNDV_MOD"], diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..2226dccada8 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.1-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.1' + +homepage = 'https://libgd.github.io/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e904a35fd3379ddb2d7c64f929b7cbdf0422863646dae252be0029b9e47c9fe3'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('fontconfig', '2.13.93'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.6.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.6.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d7a0715af4a --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.6.0-GCCcore-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.6.0' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['9311017e5284cffb86f2c7b7a9df1fb5ebcdc61c30468fb2e6bca36e4272ebca'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('PROJ', '8.0.1'), + ('libjpeg-turbo', '2.0.6'), + ('zlib', '1.2.11'), + ('SQLite', '3.35.4'), + ('LibTIFF', '4.2.0'), + ('cURL', '7.76.0'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-2.7.14.eb index 284524975d2..d89cdf21119 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-2.7.14.eb @@ -22,7 +22,6 @@ exts_list = [ (name, version, { 'buildcmd': 'build_ext', 'modulename': 'pygpu', - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'], }), diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-3.6.3.eb index 276518b694c..d3dd24dc63b 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-3.6.3.eb @@ -22,7 +22,6 @@ exts_list = [ (name, version, { 'buildcmd': 'build_ext', 'modulename': 'pygpu', - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'], }), diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-2.7.14.eb index 6d45e16e3b4..457f3f176aa 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-2.7.14.eb @@ -22,7 +22,6 @@ exts_list = [ (name, version, { 'buildcmd': 'build_ext', 'modulename': 'pygpu', - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'], }), diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-3.6.3.eb index 6be15556e91..24677ed2c6c 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-3.6.3.eb @@ -22,7 +22,6 @@ exts_list = [ (name, version, { 'buildcmd': 'build_ext', 'modulename': 'pygpu', - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'], }), diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb index 97742e3f66c..c76c0d9b051 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb @@ -33,7 +33,6 @@ exts_list = [ (name, version, { 'buildcmd': 'build_ext', 'modulename': 'pygpu', - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], }), diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb index 01eff92c58c..5b798cd4a45 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb @@ -33,7 +33,6 @@ exts_list = [ (name, version, { 'buildcmd': 'build_ext', 'modulename': 'pygpu', - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], }), diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb index f0a678a0df3..21aa4a17f7d 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('Mako', '1.1.3'), - ('NCCL', '2.8.3', '-CUDA-11.1.1', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] build_type = 'Release' @@ -35,7 +35,6 @@ exts_list = [ (name, version, { 'buildcmd': 'build_ext', 'modulename': 'pygpu', - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], }), diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..507b4b404b1 --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , +# Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Modified for foss-2016b by: +# Adam Huffman +# The Francis Crick Institute +# +# Updated: Pavel Grochal (INUITS) +# + +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'https://github.com/libharu/libharu/' +description = """libHaru is a free, cross platform, open source library for +generating PDF files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# 'https://github.com/libharu/libharu/archive/' +source_urls = [GITHUB_SOURCE] +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] + +dependencies = [('libpng', '1.6.37')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': ['if', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..21350c7724d --- /dev/null +++ b/easybuild/easyconfigs/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-8.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libmicrohttpd' +version = '0.9.73' + +homepage = 'https://www.gnu.org/software/libmicrohttpd/' + +description = """ + GNU libmicrohttpd is a small C library that is supposed to make it easy to run + an HTTP server as part of another application. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libmicrohttpd/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a37b2f1b88fd1bfe74109586be463a434d34e773530fc2a74364cfcf734c032e'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [('cURL', '7.63.0')] + +sanity_check_paths = { + 'files': ['include/microhttpd.h', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'share/man/man3/%(name)s.3'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..5fa17a10951 --- /dev/null +++ b/easybuild/easyconfigs/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-8.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libmicrohttpd' +version = '0.9.73' + +homepage = 'https://www.gnu.org/software/libmicrohttpd/' + +description = """ + GNU libmicrohttpd is a small C library that is supposed to make it easy to run + an HTTP server as part of another application. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libmicrohttpd/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a37b2f1b88fd1bfe74109586be463a434d34e773530fc2a74364cfcf734c032e'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [('cURL', '7.66.0')] + +sanity_check_paths = { + 'files': ['include/microhttpd.h', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'share/man/man3/%(name)s.3'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..afc526ef5ff --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.17.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.17.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..edb3934eb01 --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.17.0-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.17.0' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and + some other packages. It was written by Fabio Fiorina, and has been shipped as + part of GnuTLS for some time but is now a proper GNU package.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ece7551cea7922b8e10d7ebc70bc2248d1fdd73351646a2d6a8d68a9421c45a5'] + +builddependencies = [('binutils', '2.36.1')] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1ae268c656d --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.2-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.2' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['e24eb88b8ce7db3b7ca6eb80115dd1284abc5ec32a8deccfed2224fc2532b9fd'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.36.1') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..97b950d3568 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.10' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['eb8fb2c3e4b6e2d336608377050892b54c3c983b646c561836550863003c05d7'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..33d60c749bc --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '4.3.4' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'libxc-%(version)s_lm-fix.patch', + 'libxc-%(version)s_fix-CMakeLists.patch', + 'libxc-%(version)s_fix-timeout.patch', +] +checksums = [ + 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch + '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch + 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Perl', '5.32.1'), +] + +separate_build_dir = True + +parallel = 1 + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info', 'bin/xc-threshold'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..5b25d77dc2d --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '4.3.4' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'libxc-%(version)s_rename-F03.patch', + 'libxc-%(version)s_lm-fix.patch', + 'libxc-%(version)s_fix-CMakeLists.patch', + 'libxc-%(version)s_fix-timeout.patch', +] +checksums = [ + 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + 'e494be3ca2026998f2dd7c6b03a4e662f204fd3d963271e588f9f0d5739e76b5', # libxc-4.3.4_rename-F03.patch + 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch + '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch + 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Perl', '5.32.1'), +] + +separate_build_dir = True + +# rename *.F03 source file since Intel Fortran compiler doesn't like that extension +# also requires patch file to rename file in CMakeLists.txt and src/Makefile.in +preconfigopts = "mv ../libxc-%(version)s/src/libxc_master.F03 ../libxc-%(version)s/src/libxc_master_F03.F90 && " + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info', 'bin/xc-threshold'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb new file mode 100644 index 00000000000..8246e8aaa30 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb @@ -0,0 +1,48 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'libxc' +version = '5.1.5' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['02e4615a22dc3ec87a23efbd3d9be5bfad2445337140bad1720699571c45c3f9'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Perl', '5.32.1'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..9886c92eddb --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '5.1.5' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['02e4615a22dc3ec87a23efbd3d9be5bfad2445337140bad1720699571c45c3f9'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Perl', '5.32.1'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.22.8-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.22.8-fosscuda-2019a-Python-3.7.2.eb index 543dc6d7ac3..89538a82d55 100644 --- a/easybuild/easyconfigs/l/lifelines/lifelines-0.22.8-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.22.8-fosscuda-2019a-Python-3.7.2.eb @@ -22,11 +22,9 @@ use_pip = True exts_list = [ ('autograd', '1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/autograd/'], 'checksums': ['a15d147577e10de037de3740ca93bfa3b5a7cdfbc34cfb9105429c3580a33ec4'], }), ('autograd-gamma', '0.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/autograd-gamma/'], 'checksums': ['3b4349cb415bd6e28dd2fac5055e34de1b6c87fe711757a0e42a84bd650fba35'], }), (name, version, { diff --git a/easybuild/easyconfigs/l/limix/limix-2.0.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/l/limix/limix-2.0.4-foss-2018b-Python-3.6.6.eb index 341bd02e222..706885a92f7 100644 --- a/easybuild/easyconfigs/l/limix/limix-2.0.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/l/limix/limix-2.0.4-foss-2018b-Python-3.6.6.eb @@ -35,8 +35,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pytest-runner', '4.5.1', { 'modulename': False, diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb new file mode 100644 index 00000000000..c52483a837d --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '8.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['M4-1.4.18_glibc_2.28.patch'] +checksums = [ + 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz + 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.32', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb new file mode 100644 index 00000000000..6e539babe63 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '9.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.36.1', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19.eb new file mode 100644 index 00000000000..33d745de5e0 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' + +description = """ + GNU M4 is an implementation of the traditional Unix macro processor. It is + mostly SVR4 compatible although it has some extensions (for example, handling + more than 9 positional parameters to macros). GNU M4 also has built-in + functions for including files, running shell commands, doing arithmetic, etc. +""" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.1.20160309-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.1.20160309-intel-2017b-Python-2.7.14.eb index f740dc4a177..6070c4675e2 100644 --- a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.1.20160309-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.1.20160309-intel-2017b-Python-2.7.14.eb @@ -19,7 +19,6 @@ description = "Model Based Analysis for ChIP-Seq data" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2008ba838f83f34f8e0fddefe2a3a0159f4a740707c68058f815b31ddad53d26'] diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-foss-2017b-Python-2.7.14.eb index 4e896fa00bf..4a50c5ac87f 100644 --- a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-foss-2017b-Python-2.7.14.eb @@ -19,7 +19,6 @@ description = "Model Based Analysis for ChIP-Seq data" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6ee9381bda61bacf65e2e31bde267cbcd61a1304457f8a00a0eb7632dd12419b'] diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2017b-Python-2.7.14.eb index a8a101b6fb2..1bb839ef9e3 100644 --- a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2017b-Python-2.7.14.eb @@ -19,7 +19,6 @@ description = "Model Based Analysis for ChIP-Seq data" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6ee9381bda61bacf65e2e31bde267cbcd61a1304457f8a00a0eb7632dd12419b'] diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2019a-Python-2.7.15.eb index fb9e95d7359..35e222c950d 100644 --- a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2019a-Python-2.7.15.eb @@ -19,7 +19,6 @@ description = "Model Based Analysis for ChIP-Seq data" toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6ee9381bda61bacf65e2e31bde267cbcd61a1304457f8a00a0eb7632dd12419b'] diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb index 5fa730a4a18..0d27db777e1 100644 --- a/easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb @@ -11,7 +11,6 @@ description = "Model Based Analysis for ChIP-Seq data" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a3d8c5885e3e2cb6ffd46fe292841f7d74fdbaaf549105c77e48a2b96e479741'] diff --git a/easybuild/easyconfigs/m/MAJIQ/MAJIQ-1.1.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/MAJIQ/MAJIQ-1.1.1-intel-2018a-Python-3.6.4.eb index 84309f61af5..81950b656a7 100644 --- a/easybuild/easyconfigs/m/MAJIQ/MAJIQ-1.1.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/MAJIQ/MAJIQ-1.1.1-intel-2018a-Python-3.6.4.eb @@ -29,7 +29,6 @@ use_pip = True exts_list = [ ('numpy', '1.14.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'source_tmpl': 'numpy-%(version)s.zip', 'patches': ['numpy-1.12.0-mkl.patch'], 'checksums': [ @@ -41,23 +40,18 @@ exts_list = [ 'pretestopts': "export KMP_INIT_AT_FORK=FALSE && ", }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('psutil', '5.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil/'], 'checksums': ['e2467e9312c2fa191687b89ff4bc2ad8843be4af6fb4dc95a7cc5f7d7a327b18'], }), ('quicksect', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/q/quicksect/'], 'checksums': ['c236f629e76ba6d6d3585b9583b34590e555965698aa3b44c9ff762dd4fb8f63'], }), ('SQLAlchemy', '1.2.5', { - 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], 'checksums': ['249000654107a420a40200f1e0b555a79dfd4eff235b2ff60bc77714bd045f2d'], }), (name, version, { diff --git a/easybuild/easyconfigs/m/MATLAB/README.md b/easybuild/easyconfigs/m/MATLAB/README.md index c9eda0180d2..3c49f974385 100644 --- a/easybuild/easyconfigs/m/MATLAB/README.md +++ b/easybuild/easyconfigs/m/MATLAB/README.md @@ -1,36 +1,41 @@ -This example uses Matlab 2018a and MATLAB-2018a.eb -Steps to install Matlab: -* Install the appropriate Java install which requires manual download. See Java documentation for install. -* Matlab needs a "File Installation Key". There are a few options available: - * Your Matlab license should have a "`File Installation Key`" in under "`Advanced Options`" in the "`Install and Activate`" tab of your "`License Center`". - This will only install the products associated with this license. - * If you need to install all of the toolboxes to support multiple licenses Mathworks can enable a "`All Product File Installation Key`". - This will install all of the client products but will not install server products like MDCS. - A second manual installation on top of the first will be required. - * If you have a server product key, like MDCS, the "`File Installation Key`" may not install client products like Matlab Compilers. - A second manual installation on top of the first will be required. -* Edit the easyconfig file (`MATLAB-2018a.eb`). - * Update the version of Java to match the version installed in step 1. - * Add the following three lines - ``` - # This string could be really long - key = 'XXXXX-XXXXX-XXXXX-XXXXX-XXXXX-XXXXX' - license_server = '' - license_server_port = '' - ``` -* Download both ISO files from Mathworks. -* Create the tar file needed for install. - ``` - $ mkdir R2018a - $ mount -o loop,ro R2018a_glnxa64_dvd1.iso /mnt/ - $ rsync -avHlP /mnt/ R2018a/ - $ umount /mnt - $ mount -o loop,ro R2018a_glnxa64_dvd2.iso /mnt/ - $ rsync -avHlP /mnt/ R2018a/ - $ umount /mnt - $ tar -zcvf /my/easybuild/download/path/matlab-2018a.tar.gz R2018a - ``` -* Install with EasyBuild - ``` - $ eb MATLAB-2018a.eb -r - ``` +# Source preparation + +Download all ISO files from Mathworks. +Newer easyconfigs use the ISO files directly and unpack them with the `7z` command. +Older versions repackaged the ISOs as a tarball, e.g: +``` +$ mkdir R2018a +$ mount -o loop,ro R2018a_glnxa64_dvd1.iso /mnt/ +$ rsync -avHlP /mnt/ R2018a/ +$ umount /mnt +$ mount -o loop,ro R2018a_glnxa64_dvd2.iso /mnt/ +$ rsync -avHlP /mnt/ R2018a/ +$ umount /mnt +$ tar -zcvf /my/easybuild/download/path/matlab-2018a.tar.gz R2018a +``` + +# License + +* Your Matlab license should have a "`File Installation Key`" under "`Advanced Options`" in the "`Install and Activate`" tab of your "`License Center`". + This will only install the products associated with this license. +* If you need to install all of the toolboxes to support multiple licenses Mathworks can enable a "`All Product File Installation Key`". + This will install all of the client products but will not install server products like MDCS. + A second manual installation on top of the first will be required. +* If you have a server product key, like MDCS, the "`File Installation Key`" may not install client products like Matlab Compilers. + A second manual installation on top of the first will be required. + +To use the license information for an installation, either +* specify the environment variables + ``` + export EB_MATLAB_KEY=XXXXX-XXXXX-XXXXX-XXXXX-XXXXX-XXXXX + export EB_MATLAB_LICENSE_SERVER= + export EB_MATLAB_LICENSE_SERVER_PORT= + ``` +* modify the easyconfig directly + ``` + key = 'XXXXX-XXXXX-XXXXX-XXXXX-XXXXX-XXXXX' + license_server = '' + license_server_port = '' + ``` +and then install as normal, e.g. `eb MATLAB-2021a.eb` + diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2021a.3.eb b/easybuild/easyconfigs/m/MCR/MCR-R2021a.3.eb new file mode 100644 index 00000000000..36a442b08b3 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2021a.3.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'MCR' +version = 'R2021a' # runtime version 9.10 +local_update = '3' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['2e6b74db52de2eb5567e163435d9a0267519b412e3f77e1fcb94b3135a5cb838'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb index 15c988fe00f..18682ece38c 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb @@ -21,10 +21,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - exts_list = [ ('GridDataFormats', '0.4.0', { 'modulename': 'gridData', diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb index 3e34beac879..99aba5cebee 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb @@ -21,10 +21,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - exts_list = [ ('GridDataFormats', '0.4.0', { 'modulename': 'gridData', diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d6ae24de238 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,41 @@ +## +# Author: Robert Mijakovic +## +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +# We use 32bit for indices and 64bit for content +patches = ['%(name)s-%(version)s-use-doubles.patch'] + +checksums = [ + '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2', # source + '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67', # patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb new file mode 100644 index 00000000000..876e969d182 --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +version = '13-45111' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['6444bb682ebf5ced54b2eda7a301fa3e933c2a28b7661f96ef5bdab1d53695a2'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [('bzip2', '1.0.8')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE' + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MPC/MPC-1.1.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..1ef1d746c85 --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.1.0-GCCcore-9.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.1.0' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e'] + +builddependencies = [('binutils', '2.34')] +dependencies = [ + ('GMP', '6.2.0'), + ('MPFR', '4.0.2'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb new file mode 100644 index 00000000000..a79a8570985 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb @@ -0,0 +1,30 @@ +## +# Author: Robert Mijakovic +## +name = 'MUMPS' +version = '5.4.0' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['c613414683e462da7c152c131cebf34f937e79b30571424060dd673368bbf627'] + +dependencies = [ + ('SCOTCH', '6.1.0'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb index aa1648fa036..b5f62ea3ce5 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.12')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb index 92bfc1f2e0b..a3a9321a285 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.12')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb index 998e83cb614..dd2609b7d9b 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.13')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb index 6d556cd86fa..5938dec3139 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.13')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb index 16ec8b1aa98..4399beafd44 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.14')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb index c705394e03b..6d0c44eaf47 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.14')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb index ff45921f9e8..1ede0b6c152 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.15')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb index 092a64f05b2..7f10fa840a9 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.14')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb index fc3215a0712..09232aedd66 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.14')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb index 4366ca55fea..503946a005f 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.15')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb index eb6febf4b63..264e3ff8728 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '3.6.6')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb index 2208f39b88d..37963681be4 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.14')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb index e95ac36a974..c2d5d2d7976 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.14')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb index 426de8784bc..ca2d4c65982 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.14')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb index f1310f736ff..fd7be55e6b9 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '3.6.4')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb index 031d3d2df99..4f663621b21 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.15')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb index 2fd2e1001b0..1136f24547a 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.14')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb index 5a0ec8a6856..718022f8b7b 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb @@ -13,8 +13,6 @@ dependencies = [('Python', '2.7.14')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.8-GCCcore-8.2.0.eb index 9ec7a294e9b..78059a8fb9b 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.8-GCCcore-8.2.0.eb @@ -3,12 +3,11 @@ easyblock = 'PythonPackage' name = 'Mako' version = '1.0.8' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['04092940c0df49b01f43daea4f5adcecd0e50ef6a4b222be5ac003d5d84b2843'] diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.1.0-GCCcore-8.3.0.eb index da3f63619ee..8db740cc361 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.1.0-GCCcore-8.3.0.eb @@ -3,12 +3,11 @@ easyblock = 'PythonPackage' name = 'Mako' version = '1.1.0' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a36919599a9b7dc5d86a7a8988f23a9a3a3d083070023bab23d64f7f1d1e0a4b'] diff --git a/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..aa73c698f49 --- /dev/null +++ b/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +# Author: Jasper Grimm + +easyblock = 'ConfigureMake' + +name = 'MbedTLS' +version = '2.26.0' + +homepage = 'https://tls.mbed.org/' +description = "An open source, portable, easy to use, readable and flexible SSL library." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ARMmbed' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['37949e823c7e1f6695fc56858578df355da0770c284b1c1304cfc8b396d539cd'] + +builddependencies = [ + ('binutils', '2.35'), + # Perl, Python only needed for test suite + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +skipsteps = ['configure'] + +buildopts = 'SHARED=ON PYTHON=python' + +runtest = 'check' + +installopts = 'DESTDIR=%(installdir)s' + +local_bins = ['bin/%%(namelower)s_%s' % x for x in ['aescrypt2', 'cert_app', 'ecdsa', 'ssl_client2']] +local_libs = ['lib/libmbed%s.%s' % (x, SHLIB_EXT) for x in ['crypto', 'tls', 'x509']] + +sanity_check_paths = { + 'files': local_bins + local_libs, + 'dirs': [], +} +sanity_check_commands = [ + "%(namelower)s_hello", + "%(namelower)s_selftest", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2019b-Python-3.7.4.eb index 9791ff7f863..fdf79733a24 100644 --- a/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2019b-Python-3.7.4.eb @@ -13,7 +13,6 @@ description = """MedPy is a library and script collection for medical image proc toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f8a94937dbb947ab069e767862dc6b86896b153c41ce8ed9369c7d79c0033a88'] diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-5.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-5.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..0553bb5242d --- /dev/null +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-5.8-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +## +# Author: Robert Mijakovic +## +easyblock = "PythonPackage" + +name = 'Mercurial' +version = '5.8' + +homepage = 'https://www.mercurial-scm.org' +description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects +of any size and offers an easy and intuitive interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.mercurial-scm.org/release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fc5d6a8f6478d88ef83cdd0ab6d86ad68ee722bbdf4964e6a0b47c3c6ba5309f'] + +dependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_commands = ["hg --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.1-foss-2019a-Python-3.7.2.eb index 2760fb6a1d8..ed8c4f716b8 100644 --- a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.1-foss-2019a-Python-3.7.2.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('imageio', '2.6.1', { 'checksums': ['f44eb231b9df485874f2ffd22dfd0c3c711e7de076516b9374edea5c65bc67ae'], diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2020b.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2020b.eb new file mode 100644 index 00000000000..a0ef1f5ec72 --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2020b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MrBayes' +version = '3.2.7' + +homepage = "https://nbisweden.github.io/MrBayes/" +description = """MrBayes is a program for Bayesian inference and model choice across + a wide range of phylogenetic and evolutionary models.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://github.com/NBISweden/MrBayes/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['39d9eb269969b501268d5c27f77687c6eaa2c71ccf15c724e6f330fc405f24b9'] + +dependencies = [ + ('libreadline', '8.0'), + ('beagle-lib', '3.1.2'), +] + +configopts = "--with-mpi --with-readline --with-beagle=$EBROOTBEAGLEMINLIB " + +sanity_check_paths = { + 'files': ['bin/mb'], + 'dirs': ['share'] +} + +sanity_check_commands = ["mb -help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompic-2019b.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompic-2019b.eb new file mode 100644 index 00000000000..a3a837f406c --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompic-2019b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MrBayes' +version = '3.2.7' + +homepage = "https://nbisweden.github.io/MrBayes/" +description = """MrBayes is a program for Bayesian inference and model choice across + a wide range of phylogenetic and evolutionary models.""" + +toolchain = {'name': 'gompic', 'version': '2019b'} + +source_urls = ['https://github.com/NBISweden/MrBayes/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['39d9eb269969b501268d5c27f77687c6eaa2c71ccf15c724e6f330fc405f24b9'] + +dependencies = [ + ('libreadline', '8.0'), + ('beagle-lib', '3.1.2'), +] + +configopts = "--with-mpi --with-readline --with-beagle=$EBROOTBEAGLEMINLIB " + +sanity_check_paths = { + 'files': ['bin/mb'], + 'dirs': ['share'] +} + +sanity_check_commands = ["mb -help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb index 0be8df4a6a2..be9f2342596 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb @@ -5,13 +5,13 @@ # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'MultiQC' version = '0.9' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -25,44 +25,22 @@ dependencies = [ ('matplotlib', '2.0.0', versionsuffix), ] -exts_defaultclass = 'PythonPackage' - exts_list = [ - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('pyparsing', '2.1.9', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('pytz', '2016.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], - }), - ('cycler', '0.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], - }), + ('six', '1.10.0'), + ('pyparsing', '2.1.9'), + ('pytz', '2016.6.1'), + ('cycler', '0.10.0'), ('python-dateutil', '2.5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'modulename': 'dateutil', }), - ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], - }), - ('click', '6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], - }), + ('MarkupSafe', '0.23'), + ('click', '6.6'), ('PyYAML', '3.12', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyyaml'], 'modulename': 'yaml', }), - ('simplejson', '3.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], - }), - ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], - }), - ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], - }), + ('simplejson', '3.8.2'), + ('Jinja2', '2.8'), + ('multiqc', version), ] modextrapaths = { diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-foss-2017b-Python-2.7.14.eb index f25cf11e016..4f5a16fe6c2 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-foss-2017b-Python-2.7.14.eb @@ -11,7 +11,7 @@ name = 'MultiQC' version = '1.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -30,25 +30,21 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': [ 'a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665', # MarkupSafe-1.0.tar.gz ], }), ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': [ 'f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b', # click-6.7.tar.gz ], }), ('simplejson', '3.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': [ '01a22d49ddd9a168b136f26cac87d9a335660ce07aa5c630b8e3607d6f4325e7', # simplejson-3.11.1.tar.gz ], }), ('Jinja2', '2.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': [ 'ddaa01a212cd6d641401cb01b605f4a4d9f37bfc93043d7f760ec70fb99ff9ff', # Jinja2-2.9.6.tar.gz ], @@ -56,67 +52,56 @@ exts_list = [ # networkx 1.x is required, spectra does not support networkx 2.x yet # see also https://github.com/ewels/MultiQC/issues/592 ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], 'checksums': [ '0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8', # networkx-1.11.tar.gz ], }), ('colormath', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], 'checksums': [ '003a2b2d9c1f43aa7d90addf1863fb2d822463c839b1166ae3092950792f9707', # colormath-2.1.1.tar.gz ], }), ('spectra', '0.0.8', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], 'checksums': [ '851b88c9c0bba84e0be1fce5b9c02a7b4ef139a2b3e590b0d082d679e19f0759', # spectra-0.0.8.tar.gz ], }), ('certifi', '2017.7.27.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': [ '40523d2efb60523e113b44602298f0960e900388cf3bb6043f645cf57ea9e3f5', # certifi-2017.7.27.1.tar.gz ], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': [ 'cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f', # urllib3-1.22.tar.gz ], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': [ '84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae', # chardet-3.0.4.tar.gz ], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': [ '9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e', # requests-2.18.4.tar.gz ], }), ('Markdown', '2.6.9', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], 'checksums': [ '73af797238b95768b3a9b6fe6270e250e5c09d988b8e5b223fd5efa4e06faf81', # Markdown-2.6.9.tar.gz ], }), ('future', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': [ 'e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb', # future-0.16.0.tar.gz ], }), ('lzstring', '1.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], 'checksums': [ 'd54dd5a5f86837ccfc1343cc9f1cb0674d2d6ebd4b49f6408c35104f0a996cb4', # lzstring-1.0.3.tar.gz ], }), ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], 'checksums': [ '63544cc06c235a4a8ec5eb17425bf660c497cefe9d81cb8f6e621e53fddb5a0c', # multiqc-1.2.tar.gz ], diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-foss-2017b-Python-3.6.3.eb index 57791d14c90..8f30630fd64 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-foss-2017b-Python-3.6.3.eb @@ -11,7 +11,7 @@ name = 'MultiQC' version = '1.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -30,25 +30,21 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': [ 'a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665', # MarkupSafe-1.0.tar.gz ], }), ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': [ 'f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b', # click-6.7.tar.gz ], }), ('simplejson', '3.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': [ '01a22d49ddd9a168b136f26cac87d9a335660ce07aa5c630b8e3607d6f4325e7', # simplejson-3.11.1.tar.gz ], }), ('Jinja2', '2.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': [ 'ddaa01a212cd6d641401cb01b605f4a4d9f37bfc93043d7f760ec70fb99ff9ff', # Jinja2-2.9.6.tar.gz ], @@ -56,67 +52,56 @@ exts_list = [ # networkx 1.x is required, spectra does not support networkx 2.x yet # see also https://github.com/ewels/MultiQC/issues/592 ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], 'checksums': [ '0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8', # networkx-1.11.tar.gz ], }), ('colormath', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], 'checksums': [ '003a2b2d9c1f43aa7d90addf1863fb2d822463c839b1166ae3092950792f9707', # colormath-2.1.1.tar.gz ], }), ('spectra', '0.0.8', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], 'checksums': [ '851b88c9c0bba84e0be1fce5b9c02a7b4ef139a2b3e590b0d082d679e19f0759', # spectra-0.0.8.tar.gz ], }), ('certifi', '2017.7.27.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': [ '40523d2efb60523e113b44602298f0960e900388cf3bb6043f645cf57ea9e3f5', # certifi-2017.7.27.1.tar.gz ], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': [ 'cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f', # urllib3-1.22.tar.gz ], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': [ '84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae', # chardet-3.0.4.tar.gz ], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': [ '9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e', # requests-2.18.4.tar.gz ], }), ('Markdown', '2.6.9', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], 'checksums': [ '73af797238b95768b3a9b6fe6270e250e5c09d988b8e5b223fd5efa4e06faf81', # Markdown-2.6.9.tar.gz ], }), ('future', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': [ 'e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb', # future-0.16.0.tar.gz ], }), ('lzstring', '1.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], 'checksums': [ 'd54dd5a5f86837ccfc1343cc9f1cb0674d2d6ebd4b49f6408c35104f0a996cb4', # lzstring-1.0.3.tar.gz ], }), ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], 'checksums': [ '63544cc06c235a4a8ec5eb17425bf660c497cefe9d81cb8f6e621e53fddb5a0c', # multiqc-1.2.tar.gz ], diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-intel-2017b-Python-2.7.14.eb index e549011c360..eccd39ecd73 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-intel-2017b-Python-2.7.14.eb @@ -11,7 +11,7 @@ name = 'MultiQC' version = '1.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -30,25 +30,21 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': [ 'a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665', # MarkupSafe-1.0.tar.gz ], }), ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': [ 'f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b', # click-6.7.tar.gz ], }), ('simplejson', '3.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': [ '01a22d49ddd9a168b136f26cac87d9a335660ce07aa5c630b8e3607d6f4325e7', # simplejson-3.11.1.tar.gz ], }), ('Jinja2', '2.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': [ 'ddaa01a212cd6d641401cb01b605f4a4d9f37bfc93043d7f760ec70fb99ff9ff', # Jinja2-2.9.6.tar.gz ], @@ -56,67 +52,56 @@ exts_list = [ # networkx 1.x is required, spectra does not support networkx 2.x yet # see also https://github.com/ewels/MultiQC/issues/592 ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], 'checksums': [ '0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8', # networkx-1.11.tar.gz ], }), ('colormath', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], 'checksums': [ '003a2b2d9c1f43aa7d90addf1863fb2d822463c839b1166ae3092950792f9707', # colormath-2.1.1.tar.gz ], }), ('spectra', '0.0.8', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], 'checksums': [ '851b88c9c0bba84e0be1fce5b9c02a7b4ef139a2b3e590b0d082d679e19f0759', # spectra-0.0.8.tar.gz ], }), ('certifi', '2017.7.27.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': [ '40523d2efb60523e113b44602298f0960e900388cf3bb6043f645cf57ea9e3f5', # certifi-2017.7.27.1.tar.gz ], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': [ 'cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f', # urllib3-1.22.tar.gz ], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': [ '84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae', # chardet-3.0.4.tar.gz ], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': [ '9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e', # requests-2.18.4.tar.gz ], }), ('Markdown', '2.6.9', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], 'checksums': [ '73af797238b95768b3a9b6fe6270e250e5c09d988b8e5b223fd5efa4e06faf81', # Markdown-2.6.9.tar.gz ], }), ('future', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': [ 'e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb', # future-0.16.0.tar.gz ], }), ('lzstring', '1.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], 'checksums': [ 'd54dd5a5f86837ccfc1343cc9f1cb0674d2d6ebd4b49f6408c35104f0a996cb4', # lzstring-1.0.3.tar.gz ], }), ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], 'checksums': [ '63544cc06c235a4a8ec5eb17425bf660c497cefe9d81cb8f6e621e53fddb5a0c', # multiqc-1.2.tar.gz ], diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-intel-2017b-Python-3.6.3.eb index 1351af2fa56..7595eb785c4 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.2-intel-2017b-Python-3.6.3.eb @@ -11,7 +11,7 @@ name = 'MultiQC' version = '1.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -30,25 +30,21 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': [ 'a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665', # MarkupSafe-1.0.tar.gz ], }), ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': [ 'f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b', # click-6.7.tar.gz ], }), ('simplejson', '3.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': [ '01a22d49ddd9a168b136f26cac87d9a335660ce07aa5c630b8e3607d6f4325e7', # simplejson-3.11.1.tar.gz ], }), ('Jinja2', '2.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': [ 'ddaa01a212cd6d641401cb01b605f4a4d9f37bfc93043d7f760ec70fb99ff9ff', # Jinja2-2.9.6.tar.gz ], @@ -56,67 +52,56 @@ exts_list = [ # networkx 1.x is required, spectra does not support networkx 2.x yet # see also https://github.com/ewels/MultiQC/issues/592 ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], 'checksums': [ '0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8', # networkx-1.11.tar.gz ], }), ('colormath', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], 'checksums': [ '003a2b2d9c1f43aa7d90addf1863fb2d822463c839b1166ae3092950792f9707', # colormath-2.1.1.tar.gz ], }), ('spectra', '0.0.8', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], 'checksums': [ '851b88c9c0bba84e0be1fce5b9c02a7b4ef139a2b3e590b0d082d679e19f0759', # spectra-0.0.8.tar.gz ], }), ('certifi', '2017.7.27.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': [ '40523d2efb60523e113b44602298f0960e900388cf3bb6043f645cf57ea9e3f5', # certifi-2017.7.27.1.tar.gz ], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': [ 'cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f', # urllib3-1.22.tar.gz ], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': [ '84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae', # chardet-3.0.4.tar.gz ], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': [ '9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e', # requests-2.18.4.tar.gz ], }), ('Markdown', '2.6.9', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], 'checksums': [ '73af797238b95768b3a9b6fe6270e250e5c09d988b8e5b223fd5efa4e06faf81', # Markdown-2.6.9.tar.gz ], }), ('future', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': [ 'e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb', # future-0.16.0.tar.gz ], }), ('lzstring', '1.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], 'checksums': [ 'd54dd5a5f86837ccfc1343cc9f1cb0674d2d6ebd4b49f6408c35104f0a996cb4', # lzstring-1.0.3.tar.gz ], }), ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], 'checksums': [ '63544cc06c235a4a8ec5eb17425bf660c497cefe9d81cb8f6e621e53fddb5a0c', # multiqc-1.2.tar.gz ], diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-foss-2017b-Python-2.7.14.eb index 7cdb42b91e0..da4038258a6 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-foss-2017b-Python-2.7.14.eb @@ -11,7 +11,7 @@ name = 'MultiQC' version = '1.6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -30,64 +30,49 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b'], }), ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('networkx', '2.2', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], }), ('colormath', '3.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], }), ('spectra', '0.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], }), ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('requests', '2.20.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ea881206e59f41dbd0bd445437d792e43906703fff75ca8ff43ccdb11f33f263'], }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('lzstring', '1.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], }), ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], 'checksums': ['1e9f0480b7f6590a4ac159f69c1ee6c04aed0e3c156538b4994e3df451a6244e'], }), ] diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-foss-2017b-Python-3.6.3.eb index dc0f4d1a53e..933da977ad0 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-foss-2017b-Python-3.6.3.eb @@ -11,7 +11,7 @@ name = 'MultiQC' version = '1.6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -30,64 +30,49 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b'], }), ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('networkx', '2.2', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], }), ('colormath', '3.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], }), ('spectra', '0.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], }), ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('requests', '2.20.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ea881206e59f41dbd0bd445437d792e43906703fff75ca8ff43ccdb11f33f263'], }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('lzstring', '1.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], }), ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], 'checksums': ['1e9f0480b7f6590a4ac159f69c1ee6c04aed0e3c156538b4994e3df451a6244e'], }), ] diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-intel-2017b-Python-2.7.14.eb index afb6ce491ad..e8d305c28cc 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-intel-2017b-Python-2.7.14.eb @@ -11,7 +11,7 @@ name = 'MultiQC' version = '1.6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -30,64 +30,49 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b'], }), ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('networkx', '2.2', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], }), ('colormath', '3.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], }), ('spectra', '0.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], }), ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('requests', '2.20.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ea881206e59f41dbd0bd445437d792e43906703fff75ca8ff43ccdb11f33f263'], }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('lzstring', '1.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], }), ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], 'checksums': ['1e9f0480b7f6590a4ac159f69c1ee6c04aed0e3c156538b4994e3df451a6244e'], }), ] diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-intel-2017b-Python-3.6.3.eb index ae87908c63a..8f5d102e428 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.6-intel-2017b-Python-3.6.3.eb @@ -11,7 +11,7 @@ name = 'MultiQC' version = '1.6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -30,64 +30,49 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b'], }), ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('networkx', '2.2', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], }), ('colormath', '3.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], }), ('spectra', '0.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], }), ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('requests', '2.20.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ea881206e59f41dbd0bd445437d792e43906703fff75ca8ff43ccdb11f33f263'], }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('lzstring', '1.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], }), ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], 'checksums': ['1e9f0480b7f6590a4ac159f69c1ee6c04aed0e3c156538b4994e3df451a6244e'], }), ] diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb index ac31b168d25..6214f17bce5 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb @@ -14,7 +14,7 @@ name = 'MultiQC' version = '1.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -33,68 +33,52 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('networkx', '2.2', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], }), ('colormath', '3.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], }), ('spectra', '0.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], }), ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('idna', '2.8', { - 'source_urls': ['https://pypi.io/packages/source/i/idna'], 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], }), ('requests', '2.21.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('lzstring', '1.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], }), ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], 'patches': ['%(namelower)s-%(version)s_allow-matplotlib-3-for-python-3.patch'], 'checksums': [ '02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68', # multiqc-1.7.tar.gz diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-2.7.15.eb index c4edccfdf8f..67d868a77a3 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-2.7.15.eb @@ -14,7 +14,7 @@ name = 'MultiQC' version = '1.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -33,68 +33,52 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('networkx', '2.2', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], }), ('colormath', '3.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], }), ('spectra', '0.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], }), ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('idna', '2.8', { - 'source_urls': ['https://pypi.io/packages/source/i/idna'], 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], }), ('requests', '2.21.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('lzstring', '1.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], }), ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], 'checksums': ['02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68'], }), ] diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-3.6.6.eb index 4b63d8b400f..035a57aad93 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-3.6.6.eb @@ -14,7 +14,7 @@ name = 'MultiQC' version = '1.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. @@ -33,68 +33,52 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('networkx', '2.2', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], }), ('colormath', '3.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], }), ('spectra', '0.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], }), ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('idna', '2.8', { - 'source_urls': ['https://pypi.io/packages/source/i/idna'], 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], }), ('requests', '2.21.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('lzstring', '1.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], }), ('multiqc', version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], 'patches': ['%(namelower)s-%(version)s_allow-matplotlib-3-for-python-3.patch'], 'checksums': [ '02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68', # multiqc-1.7.tar.gz diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-foss-2019b-Python-3.7.4.eb index 8fb28c980d0..fe42e8bb1a0 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-foss-2019b-Python-3.7.4.eb @@ -32,8 +32,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('simplejson', '3.17.0', { 'checksums': ['2b4b2b738b3b99819a17feaf118265d0753d5536049ea570b3c43b51c4701e81'], diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb index a2347c8e202..e007484e77b 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb @@ -31,8 +31,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('networkx', '2.2', { 'source_tmpl': 'networkx-%(version)s.zip', diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb index e089f8aff21..18d8daa1430 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb @@ -32,8 +32,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('simplejson', '3.17.0', { 'checksums': ['2b4b2b738b3b99819a17feaf118265d0753d5536049ea570b3c43b51c4701e81'], diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.9-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.9-foss-2019b-Python-3.7.4.eb index a4d54bd20e6..b12ced0ca57 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.9-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.9-foss-2019b-Python-3.7.4.eb @@ -32,8 +32,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('simplejson', '3.17.0', { 'checksums': ['2b4b2b738b3b99819a17feaf118265d0753d5536049ea570b3c43b51c4701e81'], diff --git a/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11-MariaDB-10.1.14.eb b/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11-MariaDB-10.1.14.eb index 29f0ba0198f..2a955d4eade 100644 --- a/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11-MariaDB-10.1.14.eb +++ b/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11-MariaDB-10.1.14.eb @@ -8,7 +8,6 @@ description = """MySQL database connector for Python""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] local_mariadb_ver = '10.1.14' @@ -24,9 +23,4 @@ prebuildopts = "sed -i 's/static = False/static = True/g' site.cfg && " options = {'modulename': 'MySQLdb'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11.eb index 69281bf6075..494981377f7 100644 --- a/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """MySQL database connector for Python""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] dependencies = [ @@ -22,9 +21,4 @@ prebuildopts = "sed -i 's/static = False/static = True/g' site.cfg && " options = {'modulename': 'MySQLdb'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mahotas/mahotas-1.4.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mahotas/mahotas-1.4.3-intel-2016b-Python-2.7.12.eb index dd39e28312d..501d93dfa3c 100644 --- a/easybuild/easyconfigs/m/mahotas/mahotas-1.4.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/mahotas/mahotas-1.4.3-intel-2016b-Python-2.7.12.eb @@ -4,19 +4,13 @@ name = 'mahotas' version = '1.4.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://mahotas.readthedocs.io/' +homepage = 'https://mahotas.readthedocs.io/' description = "Mahotas is a computer vision and image processing library for Python" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.12')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0-minimal.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0-minimal.eb new file mode 100644 index 00000000000..bd55c1413d1 --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0-minimal.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '6.7' +versionsuffix = '-minimal' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project. + +This is a minimal build with very basic functionality. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('Perl', '5.32.0', '-minimal'), +] + +configopts = '--disable-perl-xs --disable-perl-api-texi-build --disable-pod-simple-texinfo-tests ' + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb index 9af1d073ea3..f24d92de956 100644 --- a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb @@ -13,6 +13,7 @@ sources = ['texinfo-%(version)s.tar.xz'] checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] builddependencies = [('binutils', '2.35')] +dependencies = [('Perl', '5.32.0')] sanity_check_paths = { 'files': ['bin/makeinfo'], diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.3.0-minimal.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.3.0-minimal.eb new file mode 100644 index 00000000000..4a65b76f6a5 --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.3.0-minimal.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '6.7' +versionsuffix = '-minimal' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project. + +This is a minimal build with very basic functionality. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] + +builddependencies = [ + ('binutils', '2.36.1'), +] +dependencies = [ + ('Perl', '5.32.1', '-minimal'), +] + +configopts = '--disable-perl-xs --disable-perl-api-texi-build --disable-pod-simple-texinfo-tests ' + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.3.0.eb index 442dd922d7e..1565fd80722 100644 --- a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.3.0.eb @@ -13,6 +13,7 @@ sources = ['texinfo-%(version)s.tar.xz'] checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] builddependencies = [('binutils', '2.36.1')] +dependencies = [('Perl', '5.32.1')] sanity_check_paths = { 'files': ['bin/makeinfo'], diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0-minimal.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0-minimal.eb new file mode 100644 index 00000000000..d8bc53de55d --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0-minimal.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '6.7' +versionsuffix = '-minimal' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project. + +This is a minimal build with very basic functionality. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] + +builddependencies = [ + ('binutils', '2.34'), +] +dependencies = [ + ('Perl', '5.30.2', '-minimal'), +] + +configopts = '--disable-perl-xs --disable-perl-api-texi-build --disable-pod-simple-texinfo-tests ' + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb index 99e1d30eb2c..400f61cb376 100644 --- a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb @@ -13,6 +13,7 @@ sources = ['texinfo-%(version)s.tar.xz'] checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] builddependencies = [('binutils', '2.34')] +dependencies = [('Perl', '5.30.2')] sanity_check_paths = { 'files': ['bin/makeinfo'], diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb index aef74b24d0a..4587e8e91df 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb @@ -34,6 +34,11 @@ dependencies = [ ('zlib', '1.2.11'), ] +# workaround for bug in Boost 1.74.0 triggered by use of -Wundef, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/13337 +# and https://github.com/boostorg/type_traits/issues/107 +configopts = "-DBoost_NO_BOOST_CMAKE=ON" + buildopts = "FLAGS='-I$EBROOTPYTHON/include -L$EBROOTPYTHON/lib -lpython ' " # following are necessary should anyone try to make manta compatible with python3 diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb new file mode 100644 index 00000000000..a949307ab3a --- /dev/null +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'mapDamage' +version = '2.2.1' +versionsuffix = '-R-%(rver)s' + +github_account = 'ginolhac' + +homepage = 'https://ginolhac.github.io/mapDamage/' +description = """mapDamage2 is a computational framework written in Python and + R, which tracks and quantifies DNA damage patterns among ancient DNA + sequencing reads generated by Next-Generation Sequencing platforms.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c'] + +dependencies = [ + ('Python', '3.8.6'), + ('seqtk', '1.3'), + ('Pysam', '0.16.0.1'), + ('R', '4.0.4'), + ('inline', '0.3.19', versionsuffix), + ('RcppGSL', '0.3.8', versionsuffix), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2016b-Python-2.7.12.eb index 88cd996e394..3439269fbd7 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2016b-Python-2.7.12.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.4.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ('freetype', '2.7'), @@ -23,20 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'patches': [('matplotlib-1.4.3_Qhull-intel-fix.patch')], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb index 45139a59609..c210d1a053c 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -1,18 +1,15 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.1' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'foss', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - local_freetype_ver = '2.6.3' versionsuffix = '-Python-%%(pyver)s-freetype-%s' % local_freetype_ver @@ -25,20 +22,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.9.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb index 4f26fc7f9fc..df47452a98c 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'foss', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.11'), ('freetype', '2.6.2'), @@ -23,20 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.9.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-3.5.1.eb index 6a4796ee51e..3efff0233ae 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-3.5.1.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'foss', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.5.1'), ('freetype', '2.6.2'), @@ -23,20 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.9.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb index b493596c9d2..53507b1ca3a 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -1,18 +1,15 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.1' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - local_freetype_ver = '2.6.3' versionsuffix = '-Python-%%(pyver)s-freetype-%s' % local_freetype_ver @@ -25,20 +22,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.9.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb index ae04912d989..f9786b5eb6f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.11'), ('freetype', '2.6.2'), @@ -23,20 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.9.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb index bf02ecb3887..4017bde8c2f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb @@ -1,20 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s"', '') - dependencies = [ ('Python', '3.5.1'), ('freetype', '2.6.2'), @@ -24,20 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.9.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-2.7.12.eb index d8442b82e4e..438465f70f9 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-2.7.12.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ('freetype', '2.6.5'), @@ -23,20 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.9.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-3.5.2.eb index 0d702d4024e..0ad608f3b6c 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-3.5.2.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.5.2'), ('freetype', '2.6.5'), @@ -23,20 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.9.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.12.eb index 5d6c476df04..3c131201e9a 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.12.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'foss', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ('freetype', '2.6.5'), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-2.7.12.eb index fd54071fa52..1cf88a1bb92 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-2.7.12.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ('freetype', '2.6.5'), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-3.5.2.eb index f0c4475b110..80174e38d3c 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-3.5.2.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.5.2'), ('freetype', '2.6.5'), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-2.7.12.eb index 695b612c0ff..fdc34ced52d 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-2.7.12.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'foss', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ('freetype', '2.7'), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-3.5.2.eb index 479ce28d384..3f33cb99d5e 100755 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-3.5.2.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'foss', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.5.2'), ('freetype', '2.7'), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-2.7.12.eb index b6faf82671e..2e54d9cd522 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-2.7.12.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ('freetype', '2.7'), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-3.5.2.eb index e64cc6e2126..3249f240931 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-3.5.2.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '1.5.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.5.2'), ('freetype', '2.7'), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb index 4ef9e7db5dd..c269f3d7d63 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'foss', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ('freetype', '2.7'), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb index 341407799bd..325a7b7edbc 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.12'), ('freetype', '2.7.1'), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb index 8344d6309df..cfdc98252de 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.13'), ('Tkinter', '%(pyver)s', versionsuffix), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb index 378d25f433d..9e45efa1135 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.0.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.6.1'), ('Tkinter', '%(pyver)s', versionsuffix), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb index ddda873ec7d..8897d8dbe57 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.0.2' @@ -6,16 +6,13 @@ versionsuffix = '-Python-%(pyver)s' local_libpng_ver = '1.6.29' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'foss', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.13'), ('Tkinter', '%(pyver)s', versionsuffix), @@ -26,23 +23,14 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['0ffbc44faa34a8b1704bc108c451ecf87988f900ef7ce757b8e2e84383121ff1'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-3.6.1.eb index fb633263fd4..4f612b2ec3a 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-3.6.1.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.0.2' @@ -6,16 +6,13 @@ versionsuffix = '-Python-%(pyver)s' local_libpng_ver = '1.6.29' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'foss', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.6.1'), ('Tkinter', '%(pyver)s', versionsuffix), @@ -26,23 +23,14 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['0ffbc44faa34a8b1704bc108c451ecf87988f900ef7ce757b8e2e84383121ff1'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-Qt-4.8.7.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-Qt-4.8.7.eb index 983539b0609..d09865fe0d1 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-Qt-4.8.7.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-Qt-4.8.7.eb @@ -1,20 +1,17 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.0.2' local_qtver = '4.8.7' versionsuffix = '-Python-%%(pyver)s-Qt-%s' % local_qtver -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.13'), ('Tkinter', '%(pyver)s', '-Python-%(pyver)s'), @@ -26,21 +23,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-libpng-1.6.29.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-libpng-1.6.29.eb index 719439ea1be..1789fb091d5 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-libpng-1.6.29.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-libpng-1.6.29.eb @@ -1,20 +1,17 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.0.2' local_libpng_ver = '1.6.29' versionsuffix = '-Python-%%(pyver)s-libpng-%s' % local_libpng_ver -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.13'), ('Tkinter', '%(pyver)s', '-Python-%(pyver)s'), @@ -24,21 +21,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb index eb41c1fa5a9..1850b9cbceb 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.0.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.13'), ('Tkinter', '%(pyver)s', versionsuffix), @@ -23,21 +20,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-3.6.1-libpng-1.6.29.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-3.6.1-libpng-1.6.29.eb index 037d5f95957..e925eb89af6 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-3.6.1-libpng-1.6.29.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-3.6.1-libpng-1.6.29.eb @@ -1,20 +1,17 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.0.2' local_libpng_ver = '1.6.29' versionsuffix = '-Python-%%(pyver)s-libpng-%s' % local_libpng_ver -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.6.1'), ('Tkinter', '%(pyver)s', '-Python-%(pyver)s'), @@ -24,21 +21,11 @@ dependencies = [ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-2.7.14.eb index e5265edba7a..88acc865612 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-2.7.14.eb @@ -24,21 +24,17 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': [ 'cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8', # cycler-0.10.0.tar.gz ], }), ('subprocess32', '3.2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], }), ('backports.functools_lru_cache', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['31f235852f88edc1558d428d890663c49eb4514ffec9f3650e7f3c9e4a12e36f'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': [ '4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387', # matplotlib-2.1.0.tar.gz ], diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-3.6.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-3.6.2.eb index 9edbe70af0e..cc9f62ed0b1 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-3.6.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-3.6.2.eb @@ -4,7 +4,7 @@ name = 'matplotlib' version = '2.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" @@ -24,13 +24,11 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': [ 'cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8', # cycler-0.10.0.tar.gz ], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': [ '4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387', # matplotlib-2.1.0.tar.gz ], diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-3.6.3.eb index 5dc94ea0f36..ab1c61c8754 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-foss-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'matplotlib' version = '2.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" @@ -24,13 +24,11 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': [ 'cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8', # cycler-0.10.0.tar.gz ], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': [ '4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387', # matplotlib-2.1.0.tar.gz ], diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb index 6f6fd9ac513..5f8af19fef3 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb @@ -24,21 +24,17 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': [ 'cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8', # cycler-0.10.0.tar.gz ], }), ('subprocess32', '3.2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], }), ('backports.functools_lru_cache', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['31f235852f88edc1558d428d890663c49eb4514ffec9f3650e7f3c9e4a12e36f'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': [ '4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387', # matplotlib-2.1.0.tar.gz ], diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb index 231087a3445..f0b7527d7e7 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'matplotlib' version = '2.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" @@ -24,13 +24,11 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': [ 'cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8', # cycler-0.10.0.tar.gz ], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': [ '4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387', # matplotlib-2.1.0.tar.gz ], diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intel-2017b-Python-2.7.14.eb index 6e328e1e884..db78fdc1a7e 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intel-2017b-Python-2.7.14.eb @@ -24,19 +24,15 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], }), ('backports.functools_lru_cache', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['31f235852f88edc1558d428d890663c49eb4514ffec9f3650e7f3c9e4a12e36f'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intel-2017b-Python-3.6.3.eb index 2add37c2172..729f63842fa 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intel-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'matplotlib' version = '2.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" @@ -24,11 +24,9 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb index 320248830c6..be7e7c735cf 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb @@ -24,19 +24,15 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], }), ('backports.functools_lru_cache', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['31f235852f88edc1558d428d890663c49eb4514ffec9f3650e7f3c9e4a12e36f'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb index 880da7a1a20..48c16e20d7e 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'matplotlib' version = '2.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" @@ -24,11 +24,9 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-foss-2017b-Python-3.6.3.eb index 6b94183a28a..92f119e4a35 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-foss-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'matplotlib' version = '2.1.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" @@ -24,11 +24,9 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['659f5e1aa0e0f01488c61eff47560c43b8be511c6a29293d7f3896ae17bd8b23'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-intel-2017b-Python-2.7.14.eb index ac5e3d5a751..0afbba6a98b 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-intel-2017b-Python-2.7.14.eb @@ -24,19 +24,15 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], }), ('backports.functools_lru_cache', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['31f235852f88edc1558d428d890663c49eb4514ffec9f3650e7f3c9e4a12e36f'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['659f5e1aa0e0f01488c61eff47560c43b8be511c6a29293d7f3896ae17bd8b23'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-intel-2017b-Python-3.6.3.eb index 1ab348e78b2..bfea5a039e5 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.1-intel-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'matplotlib' version = '2.1.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" @@ -24,11 +24,9 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['659f5e1aa0e0f01488c61eff47560c43b8be511c6a29293d7f3896ae17bd8b23'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-foss-2018a-Python-2.7.14.eb index d1162827d82..6cfbd305555 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-foss-2018a-Python-2.7.14.eb @@ -28,30 +28,21 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], }), ('backports.functools_lru_cache', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['31f235852f88edc1558d428d890663c49eb4514ffec9f3650e7f3c9e4a12e36f'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['725a3f12739d133adfa381e1b33bd70c6f64db453bfc536e148824816e568894'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - postinstallcmds = [ 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-foss-2018a-Python-3.6.4.eb index 36e01fb68c1..dd3bf2e19af 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-foss-2018a-Python-3.6.4.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.1.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'foss', 'version': '2018a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - builddependencies = [ ('pkg-config', '0.29.2'), ] @@ -29,26 +26,17 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['725a3f12739d133adfa381e1b33bd70c6f64db453bfc536e148824816e568894'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - # use non-interactive plotting backend as default # see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend modextravars = {'MPLBACKEND': 'Agg'} diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-intel-2018a-Python-2.7.14.eb index 98eae338dd0..1871b6c7160 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-intel-2018a-Python-2.7.14.eb @@ -28,30 +28,21 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], }), ('backports.functools_lru_cache', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['31f235852f88edc1558d428d890663c49eb4514ffec9f3650e7f3c9e4a12e36f'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['725a3f12739d133adfa381e1b33bd70c6f64db453bfc536e148824816e568894'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - postinstallcmds = [ 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-intel-2018a-Python-3.6.4.eb index f087c6f6a8b..4578d6b3b4f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-intel-2018a-Python-3.6.4.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.1.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'intel', 'version': '2018a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - builddependencies = [ ('pkg-config', '0.29.2'), ] @@ -29,26 +26,17 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['725a3f12739d133adfa381e1b33bd70c6f64db453bfc536e148824816e568894'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - # use non-interactive plotting backend as default # see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend modextravars = {'MPLBACKEND': 'Agg'} diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-iomkl-2018.02-Python-3.6.4.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-iomkl-2018.02-Python-3.6.4.eb index 8e03c503470..10c46a3eeab 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-iomkl-2018.02-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-iomkl-2018.02-Python-3.6.4.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.1.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'iomkl', 'version': '2018.02'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - builddependencies = [ ('pkg-config', '0.29.2'), ] @@ -29,26 +26,17 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['725a3f12739d133adfa381e1b33bd70c6f64db453bfc536e148824816e568894'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - # use non-interactive plotting backend as default # see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend modextravars = {'MPLBACKEND': 'Agg'} diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-iomkl-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-iomkl-2018a-Python-3.6.4.eb index 95253729053..2eaa036b3ef 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-iomkl-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.2-iomkl-2018a-Python-3.6.4.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.1.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" toolchain = {'name': 'iomkl', 'version': '2018a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - builddependencies = [ ('pkg-config', '0.29.2'), ] @@ -29,26 +26,17 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['725a3f12739d133adfa381e1b33bd70c6f64db453bfc536e148824816e568894'], 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - # use non-interactive plotting backend as default # see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend modextravars = {'MPLBACKEND': 'Agg'} diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-foss-2018b-Python-2.7.15.eb index fca86bf5796..427c0c175cc 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-foss-2018b-Python-2.7.15.eb @@ -28,34 +28,24 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], }), ('backports.functools_lru_cache', '1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['9d98697f088eb1b0fa451391f91afb5e3ebde16bbdb272819fd091151fda4f1a'], }), ('kiwisolver', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['7355bf757ecacd5f0ac9dd9523c8e1a1103faadf8d33c22664178e17533f8ce5'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - postinstallcmds = [ 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-fosscuda-2018b-Python-2.7.15.eb index 5adb106a325..02538daed30 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-fosscuda-2018b-Python-2.7.15.eb @@ -28,34 +28,24 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], }), ('backports.functools_lru_cache', '1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['9d98697f088eb1b0fa451391f91afb5e3ebde16bbdb272819fd091151fda4f1a'], }), ('kiwisolver', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['7355bf757ecacd5f0ac9dd9523c8e1a1103faadf8d33c22664178e17533f8ce5'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - postinstallcmds = [ 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-2.7.15.eb index 92251b47076..eca81898f4b 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-2.7.15.eb @@ -28,34 +28,24 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], }), ('backports.functools_lru_cache', '1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['9d98697f088eb1b0fa451391f91afb5e3ebde16bbdb272819fd091151fda4f1a'], }), ('kiwisolver', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['7355bf757ecacd5f0ac9dd9523c8e1a1103faadf8d33c22664178e17533f8ce5'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - postinstallcmds = [ 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb index 49477f77634..461c0d6dc68 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'matplotlib' version = '2.2.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://matplotlib.org' +homepage = 'https://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" @@ -28,17 +28,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['7355bf757ecacd5f0ac9dd9523c8e1a1103faadf8d33c22664178e17533f8ce5'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-foss-2019a-Python-2.7.15.eb index 422da228dc9..d78569296a2 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-foss-2019a-Python-2.7.15.eb @@ -29,25 +29,20 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.5.4', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], }), ('backports.functools_lru_cache', '1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['9d98697f088eb1b0fa451391f91afb5e3ebde16bbdb272819fd091151fda4f1a'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['029620799e581802961ac1dcff5cb5d3ee2f602e0db9c0f202a90495b37d2126'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-foss-2019b-Python-2.7.16.eb index 743083ff3f8..4e9294a62c7 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-foss-2019b-Python-2.7.16.eb @@ -29,25 +29,20 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.5.4', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], }), ('backports.functools_lru_cache', '1.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['029620799e581802961ac1dcff5cb5d3ee2f602e0db9c0f202a90495b37d2126'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-fosscuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-fosscuda-2019a-Python-2.7.15.eb index b022407dce8..d1cf5e10e05 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-fosscuda-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-fosscuda-2019a-Python-2.7.15.eb @@ -29,25 +29,20 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.5.4', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], }), ('backports.functools_lru_cache', '1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['9d98697f088eb1b0fa451391f91afb5e3ebde16bbdb272819fd091151fda4f1a'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['029620799e581802961ac1dcff5cb5d3ee2f602e0db9c0f202a90495b37d2126'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-fosscuda-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-fosscuda-2019b-Python-2.7.16.eb index 4d82f6fea3e..d5391abe0c4 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-fosscuda-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-fosscuda-2019b-Python-2.7.16.eb @@ -29,25 +29,20 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.5.4', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], }), ('backports.functools_lru_cache', '1.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['029620799e581802961ac1dcff5cb5d3ee2f602e0db9c0f202a90495b37d2126'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019a-Python-2.7.15.eb index 74eebe09a83..171b339aded 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019a-Python-2.7.15.eb @@ -32,25 +32,20 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.5.4', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], }), ('backports.functools_lru_cache', '1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['9d98697f088eb1b0fa451391f91afb5e3ebde16bbdb272819fd091151fda4f1a'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['029620799e581802961ac1dcff5cb5d3ee2f602e0db9c0f202a90495b37d2126'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-2.7.16.eb index 56d52183922..4b5972c33cc 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-2.7.16.eb @@ -29,25 +29,20 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.5.4', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], }), ('backports.functools_lru_cache', '1.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['029620799e581802961ac1dcff5cb5d3ee2f602e0db9c0f202a90495b37d2126'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intelcuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intelcuda-2019a-Python-2.7.15.eb index a83dc1b3bac..59abb29e47d 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intelcuda-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intelcuda-2019a-Python-2.7.15.eb @@ -32,25 +32,20 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('subprocess32', '3.5.4', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], }), ('backports.functools_lru_cache', '1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], 'checksums': ['9d98697f088eb1b0fa451391f91afb5e3ebde16bbdb272819fd091151fda4f1a'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['029620799e581802961ac1dcff5cb5d3ee2f602e0db9c0f202a90495b37d2126'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2019b-Python-2.7.16.eb index bdc0ebdeeee..6a22b61740f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2019b-Python-2.7.16.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-foss-2018b-Python-3.6.6.eb index 1e3f6deaf03..a8927f95f73 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-foss-2018b-Python-3.6.6.eb @@ -28,26 +28,18 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b4e2333c98a7c2c1ff6eb930cd2b57d4b818de5437c5048802096b32f66e65f9'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = [ """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, "python -c 'from mpl_toolkits.mplot3d import Axes3D'", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-fosscuda-2018b-Python-3.6.6.eb index 73c50ddbafa..3da528f23cf 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-fosscuda-2018b-Python-3.6.6.eb @@ -28,26 +28,18 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b4e2333c98a7c2c1ff6eb930cd2b57d4b818de5437c5048802096b32f66e65f9'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = [ """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, "python -c 'from mpl_toolkits.mplot3d import Axes3D'", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-intel-2018b-Python-3.6.6.eb index b610702b334..5df40c93efd 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-intel-2018b-Python-3.6.6.eb @@ -28,26 +28,18 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b4e2333c98a7c2c1ff6eb930cd2b57d4b818de5437c5048802096b32f66e65f9'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = [ """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, "python -c 'from mpl_toolkits.mplot3d import Axes3D'", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-iomkl-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-iomkl-2018b-Python-3.6.6.eb index d0941261e89..8374839c668 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-iomkl-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-iomkl-2018b-Python-3.6.6.eb @@ -28,26 +28,18 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b4e2333c98a7c2c1ff6eb930cd2b57d4b818de5437c5048802096b32f66e65f9'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = [ """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, "python -c 'from mpl_toolkits.mplot3d import Axes3D'", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.2-foss-2018b-Python-3.6.6.eb index 4adb7ebbb42..04eb94f123d 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.2-foss-2018b-Python-3.6.6.eb @@ -28,26 +28,18 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['c94b792af431f6adb6859eb218137acd9a35f4f7442cea57e4a59c54751c36af'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = [ """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, "python -c 'from mpl_toolkits.mplot3d import Axes3D'", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb index 256dd216e5b..ef4889bc341 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb @@ -29,17 +29,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['e1d33589e32f482d0a7d1957bf473d43341115d40d33f578dad44432e47df7b7'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb index 300c4cace6a..d9e588224a2 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb @@ -29,17 +29,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['e1d33589e32f482d0a7d1957bf473d43341115d40d33f578dad44432e47df7b7'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb index bb7a81858a6..fe24e490059 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['e1d33589e32f482d0a7d1957bf473d43341115d40d33f578dad44432e47df7b7'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb index ae73925a06b..8ab7e3c0583 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['e1d33589e32f482d0a7d1957bf473d43341115d40d33f578dad44432e47df7b7'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-foss-2019b-Python-3.7.4.eb index af9997193d9..6184af6f4e4 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-foss-2019b-Python-3.7.4.eb @@ -29,17 +29,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['1febd22afe1489b13c6749ea059d392c03261b2950d1d45c17e3aed812080c93'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-fosscuda-2019b-Python-3.7.4.eb index 1269ff4f0f6..5fc0dd6e949 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-fosscuda-2019b-Python-3.7.4.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-intel-2019b-Python-3.7.4.eb index 6db9f9313e1..5ac1873c3fc 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-intel-2019b-Python-3.7.4.eb @@ -31,17 +31,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['1febd22afe1489b13c6749ea059d392c03261b2950d1d45c17e3aed812080c93'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb index b57ab849cd6..f7d180895f2 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-fosscuda-2020a-Python-3.8.2.eb index 0def9b61390..89128f86756 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-fosscuda-2020a-Python-3.8.2.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intel-2020a-Python-3.8.2.eb index 9b8d59a1fb2..80e9967b664 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intel-2020a-Python-3.8.2.eb @@ -31,17 +31,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intelcuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intelcuda-2020a-Python-3.8.2.eb index cd09f2ce059..c9161554e13 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intelcuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intelcuda-2020a-Python-3.8.2.eb @@ -31,17 +31,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb index ed77f16aee6..4a49f2dc220 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb index 8fb868afaca..06ed98ff905 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb index d05fd348d94..a79ad305774 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb index f20755abf93..845af2bf736 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], }), ] diff --git a/easybuild/easyconfigs/m/mayavi/mayavi-4.4.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mayavi/mayavi-4.4.4-intel-2016a-Python-2.7.11.eb index bf81b4b97a2..b5d1ea2f4e3 100644 --- a/easybuild/easyconfigs/m/mayavi/mayavi-4.4.4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/mayavi/mayavi-4.4.4-intel-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'mayavi' version = '4.4.4' @@ -15,39 +15,17 @@ dependencies = [ ('PyQt', '4.11.4', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ - ('configobj', '5.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configobj/'], - }), - ('Pygments', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], - }), - ('traits', '4.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traits/'], - }), - ('pyface', '5.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyface/'], - }), - ('traitsui', '5.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitsui/'], - }), - ('apptools', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/apptools/'], - }), - ('envisage', '4.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source//envisage/'], - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/mayavi/'], - }), + ('configobj', '5.0.6'), + ('Pygments', '2.1.3'), + ('traits', '4.5.0'), + ('pyface', '5.1.0'), + ('traitsui', '5.1.0'), + ('apptools', '4.4.0'), + ('envisage', '4.5.1'), + (name, version), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/mayavi2'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/m/mayavi/mayavi-4.6.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/mayavi/mayavi-4.6.2-foss-2018b-Python-3.6.6.eb index b9dd9ac0457..5f7375b34d4 100644 --- a/easybuild/easyconfigs/m/mayavi/mayavi-4.6.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/mayavi/mayavi-4.6.2-foss-2018b-Python-3.6.6.eb @@ -19,8 +19,6 @@ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('configobj', '5.0.6', { 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], diff --git a/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-2.7.15.eb index 8cdba03e817..b30f60d4f7f 100644 --- a/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-2.7.15.eb @@ -20,8 +20,6 @@ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('configobj', '5.0.6', { 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], diff --git a/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb index 7b97300ef57..1dd1fb23c70 100644 --- a/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb @@ -20,8 +20,6 @@ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('configobj', '5.0.6', { 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], diff --git a/easybuild/easyconfigs/m/medImgProc/medImgProc-2.5.7-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/medImgProc/medImgProc-2.5.7-foss-2019b-Python-3.7.4.eb index 478c74f4e41..b9c05184d58 100644 --- a/easybuild/easyconfigs/m/medImgProc/medImgProc-2.5.7-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/medImgProc/medImgProc-2.5.7-foss-2019b-Python-3.7.4.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('trimesh', '3.6.15', { 'checksums': ['9444160957f094769c87a4d2a48051ad1e7c4e29272d063fe832e961e5014be3'], diff --git a/easybuild/easyconfigs/m/medaka/medaka-0.11.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/medaka/medaka-0.11.4-foss-2018b-Python-3.6.6.eb index f8c2d9d1ea9..a014e950e34 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-0.11.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-0.11.4-foss-2018b-Python-3.6.6.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('sortedcontainers', '2.1.0', { 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], diff --git a/easybuild/easyconfigs/m/medaka/medaka-0.12.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/medaka/medaka-0.12.0-foss-2018b-Python-3.6.6.eb index 0f31bee417f..5a37a7b8c16 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-0.12.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-0.12.0-foss-2018b-Python-3.6.6.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('sortedcontainers', '2.1.0', { 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], diff --git a/easybuild/easyconfigs/m/medaka/medaka-0.4.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/medaka/medaka-0.4.3-foss-2018b-Python-3.6.6.eb index f25832e0824..ad1c2cdf4fc 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-0.4.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-0.4.3-foss-2018b-Python-3.6.6.eb @@ -23,23 +23,15 @@ use_pip = True exts_list = [ ('sortedcontainers', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers/'], 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], }), ('intervaltree', '3.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/intervaltree/'], 'checksums': ['cb4f61c81dcb4fea6c09903f3599015a83c9bdad1f0bbd232495e6681e19e273'], }), (name, version, { 'preinstallopts': "sed -i'.orig' 's/==.*//g' requirements.txt && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/medaka/'], 'checksums': ['429cbb41db3f70b1238fa48ff98d4354426b4180f99a7117bde9a843cf35f770'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb index 550726dfa89..b1a1a776145 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb @@ -31,8 +31,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('mappy', '2.17', { 'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'], diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.1.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/medaka/medaka-1.1.3-foss-2019b-Python-3.7.4.eb index 060438597e9..5054f1ae8cc 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.1.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.1.3-foss-2019b-Python-3.7.4.eb @@ -31,8 +31,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('mappy', '2.17', { 'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'], diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.2.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/medaka/medaka-1.2.0-foss-2019b-Python-3.7.4.eb index 250921ccf9e..efe71e22c3d 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.2.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.2.0-foss-2019b-Python-3.7.4.eb @@ -36,8 +36,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('mappy', '2.17', { 'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'], diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..82d2fd618e1 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,81 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.4.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2019b'} + +builddependencies = [('Autotools', '20180311')] + +dependencies = [ + ('Python', '3.7.4'), # includes cffi + # TensorFlow 2.2.2 required by medaka 1.4.3, see requirements.txt + ('TensorFlow', '2.2.2', versionsuffix), + ('Biopython', '1.75', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + # Pysam 0.16.0.1 is strictly required, see requirements.txt + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.10'), + ('minimap2', '2.17'), + ('HTSlib', '1.10.2'), # for tabix, bgzip + ('Racon', '1.4.13'), + ('spoa', '4.0.0'), + ('networkx', '2.4', versionsuffix), + ('edlib', '1.3.8.post1', versionsuffix), + ('pyspoa', '0.0.4', versionsuffix), + ('ont-fast5-api', '3.3.0', versionsuffix), + ('pyfaidx', '0.5.9.5', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('mappy', '2.20', { + 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], + }), + ('parasail', '1.2.4', { + 'checksums': ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'], + }), + ('isal', '0.10.0', { + 'checksums': ['3f89471065c2837d1235877dbdcdbd8b7649068723026b0582010fa106a71ff3'], + }), + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + ('whatshap', '1.1', { + 'checksums': ['4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + (name, version, { + 'patches': ['medaka-1.4.3_use-SAMtools-dep.patch'], + 'checksums': [ + '59997b5fdaff6f2040f2df2d3d3eb2d6d1805916a720e8275309caf4d2d4b8a5', # medaka-1.4.3.tar.gz + '06b1d8344035ebcfaf1893e62f37db9b4cab0053ad7a073113630872d44be33e', # medaka-1.4.3_use-SAMtools-dep.patch + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["medaka --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3_use-SAMtools-dep.patch b/easybuild/easyconfigs/m/medaka/medaka-1.4.3_use-SAMtools-dep.patch new file mode 100644 index 00000000000..05bc22d1e1f --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3_use-SAMtools-dep.patch @@ -0,0 +1,48 @@ +use SAMtools provided as dependency rather than building libhts.a from scratch + +author: Kenneth Hoste (HPC-UGent) +--- medaka-1.4.3/build.py.orig 2021-06-21 19:06:16.000000000 +0200 ++++ medaka-1.4.3/build.py 2021-06-24 17:38:34.231762728 +0200 +@@ -3,12 +3,8 @@ + + from cffi import FFI + +-#samver is pulled from this file in the Makefile +-samver = "1.11" +-htslib_dir=os.path.join('submodules', 'samtools-{}'.format(samver), 'htslib-{}'.format(samver)) +- + libraries=['m', 'z', 'lzma', 'bz2', 'pthread', 'curl', 'crypto'] +-library_dirs=[htslib_dir] ++library_dirs=[] + src_dir='src' + + ffibuilder = FFI() +@@ -27,14 +23,14 @@ + """, + libraries=libraries, + library_dirs=library_dirs, +- include_dirs=[src_dir, htslib_dir], ++ include_dirs=[src_dir], + sources=[ + os.path.join(src_dir, x) for x in ( + 'medaka_bamiter.c', 'medaka_common.c', 'medaka_counts.c', + 'fastrle.c', 'medaka_trimbam.c', 'medaka_pytrimbam.c', + 'medaka_rnn_variants.c')], + extra_compile_args=['-std=c99', '-msse3', '-O3'], +- extra_objects=['libhts.a'] ++ extra_objects=[os.path.join(os.getenv('EBROOTSAMTOOLS'), 'lib', 'libhts.a')] + ) + + cdef = [] +--- medaka-1.4.3/setup.py.orig 2021-06-24 18:53:32.019117378 +0200 ++++ medaka-1.4.3/setup.py 2021-06-24 18:54:04.229468742 +0200 +@@ -165,9 +165,6 @@ + }, + scripts=['scripts/medaka_consensus', 'scripts/medaka_variant', 'scripts/medaka_haploid_variant', 'scripts/mini_align', 'scripts/hdf2tf.py'], + zip_safe=False, +- cmdclass={ +- 'build_ext': HTSBuild +- }, + ) + + if os.environ.get('MEDAKA_BINARIES') is not None: diff --git a/easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-foss-2019a.eb b/easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-foss-2019a.eb index 4e87d93e218..ea58b0bc6ae 100644 --- a/easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-foss-2019a.eb +++ b/easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-foss-2019a.eb @@ -10,7 +10,6 @@ description = """memory-profiler is a Python module for monitoring memory consum toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'pic': True} -source_urls = [PYPI_SOURCE] sources = ['memory_profiler-%(version)s.tar.gz'] checksums = ['5fa47b274c929dd2cbcd9190afb62fec110701251d2ac2d301caaf545c81afc1'] diff --git a/easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-intel-2019a.eb b/easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-intel-2019a.eb index d2820e6f231..275a23b7394 100644 --- a/easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-intel-2019a.eb +++ b/easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-intel-2019a.eb @@ -10,7 +10,6 @@ description = """memory-profiler is a Python module for monitoring memory consum toolchain = {'name': 'intel', 'version': '2019a'} toolchainopts = {'pic': True} -source_urls = [PYPI_SOURCE] sources = ['memory_profiler-%(version)s.tar.gz'] checksums = ['5fa47b274c929dd2cbcd9190afb62fec110701251d2ac2d301caaf545c81afc1'] diff --git a/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb index cda151feb88..c93e70b843d 100644 --- a/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = "meshio is a tool for reading/writing various mesh formats represe toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ @@ -20,15 +19,9 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ - ('appdirs', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], - }), - ('requests', '2.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), - ('pipdated', '0.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pipdated'], - }), + ('appdirs', '1.4.0'), + ('requests', '2.13.0'), + ('pipdated', '0.1.4'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/meshio/meshio-2.0.2-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/meshio/meshio-2.0.2-intel-2018a-Python-2.7.14.eb index 6eb1e3b3da7..0783adb8df3 100644 --- a/easybuild/easyconfigs/m/meshio/meshio-2.0.2-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/meshio/meshio-2.0.2-intel-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'meshio' version = '2.0.2' @@ -15,26 +15,18 @@ dependencies = [ ('VTK', '8.1.0', versionsuffix), ] -exts_download_dep_fail = True - -exts_defaultclass = 'PythonPackage' exts_list = [ ('appdirs', '1.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), ('pipdate', '0.2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pipdate'], 'checksums': ['1b9d58d5a5d890aa34eddc4a4224d3704e2ae9185ed77b161c6ab686c1d03094'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/meshio'], 'checksums': ['c852bcd14f1e5d1eb52739773f24a15d68057fcfbb7083c71c88cee6a4d5a647'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/meshio-convert'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/m/meshio/meshio-2.0.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/meshio/meshio-2.0.2-intel-2018a-Python-3.6.4.eb index 7f71f1c9813..5930c996595 100644 --- a/easybuild/easyconfigs/m/meshio/meshio-2.0.2-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/meshio/meshio-2.0.2-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'meshio' version = '2.0.2' @@ -15,26 +15,18 @@ dependencies = [ ('VTK', '8.1.0', versionsuffix), ] -exts_download_dep_fail = True - -exts_defaultclass = 'PythonPackage' exts_list = [ ('appdirs', '1.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), ('pipdate', '0.2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pipdate'], 'checksums': ['1b9d58d5a5d890aa34eddc4a4224d3704e2ae9185ed77b161c6ab686c1d03094'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/meshio'], 'checksums': ['c852bcd14f1e5d1eb52739773f24a15d68057fcfbb7083c71c88cee6a4d5a647'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/meshio-convert'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-foss-2019a-Python-3.7.2.eb index 5baf9b33228..464c52ebda3 100644 --- a/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-foss-2019a-Python-3.7.2.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('np_utils', '0.5.11.1', { 'checksums': ['5b75f329eb686923a467ee7ce6e3210051ea09953a6cdd8620908290eb546f9b'], diff --git a/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-fosscuda-2019a-Python-3.7.2.eb index 1c4b61b7336..b3092e1572f 100644 --- a/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-fosscuda-2019a-Python-3.7.2.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('np_utils', '0.5.11.1', { 'checksums': ['5b75f329eb686923a467ee7ce6e3210051ea09953a6cdd8620908290eb546f9b'], diff --git a/easybuild/easyconfigs/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb new file mode 100644 index 00000000000..205c6e8881d --- /dev/null +++ b/easybuild/easyconfigs/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'microctools' +local_commit = 'f642925' +version = '0.1.0-20201209' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/ilyamaclean/microctools' +description = "Various worker functions for microclimc package" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/ilyamaclean/microctools/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['8b6c0b784301bb61f0a67f6abb118fc49a15841902015833efc32373cfe3f515'] + +dependencies = [ + ('R', '4.0.4'), + ('rgdal', '1.5-23', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb index cc883fdc728..c077e4e423a 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ description = """A small wrapper for core parts of EIgen, c++ library for linear toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] dependencies = [ ('Boost', '1.60.0', versionsuffix), diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016b-Python-2.7.12.eb index b281fdb6096..41ca0907dfa 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ description = """A small wrapper for core parts of EIgen, c++ library for linear toolchain = {'name': 'foss', 'version': '2016b'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] dependencies = [ ('Boost', '1.61.0', versionsuffix), diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb index 32173fca1a7..7ba65e73099 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ description = """A small wrapper for core parts of EIgen, c++ library for linear toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] dependencies = [ ('Boost', '1.60.0', versionsuffix), diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb index e3b513572f9..032912e1502 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb @@ -11,7 +11,6 @@ description = """A small wrapper for core parts of EIgen, c++ library for linear toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] dependencies = [ ('Boost', local_boostver, '-Python-%(pyver)s'), diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12.eb index ee0afa54ae6..68b343a562a 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ description = """A small wrapper for core parts of EIgen, c++ library for linear toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] dependencies = [ ('Boost', '1.61.0', versionsuffix), diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..5cff5bf900c --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.20' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['f9eff90a7f14f999df93dff6ed4e3428277edbbd6bda6bdb1800e8d57c9135e3'] + +builddependencies = [('binutils', '2.35')] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/modred/modred-2.0.2-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/modred/modred-2.0.2-foss-2016b-Python-3.5.2.eb index d45b071d802..b8cb769e049 100644 --- a/easybuild/easyconfigs/m/modred/modred-2.0.2-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/m/modred/modred-2.0.2-foss-2016b-Python-3.5.2.eb @@ -9,14 +9,8 @@ description = """Compute modal decompositions and reduced-order models, easily, toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.5.2')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mordecai/mordecai-2.0.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/mordecai/mordecai-2.0.1-foss-2018a-Python-3.6.4.eb index 76e6b2cd9f7..d47fc2db302 100644 --- a/easybuild/easyconfigs/m/mordecai/mordecai-2.0.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/mordecai/mordecai-2.0.1-foss-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'mordecai' version = '2.0.1' @@ -12,10 +12,6 @@ information.""" toolchain = {'name': 'foss', 'version': '2018a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_download_dep_fail = True - dependencies = [ ('Python', '3.6.4'), ('h5py', '2.7.1', versionsuffix), @@ -25,77 +21,59 @@ dependencies = [ exts_list = [ ('cymem', '1.31.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cymem'], 'checksums': ['f06d9b50da0474d7405674d8101c319d89a17d33792d6d429fe3d5c64f0d9df1'], }), ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], }), ('cytoolz', '0.9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cytoolz'], 'checksums': ['84cc06fa40aa310f2df79dd440fc5f84c3e20f01f9f7783fc9c38d0a11ba00e5'], }), ('dill', '0.2.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/dill'], 'checksums': ['624dc244b94371bb2d6e7f40084228a2edfff02373fe20e018bef1ee92fdd5b3'], }), ('msgpack', '0.5.6', { - 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'], 'checksums': ['0ee8c8c85aa651be3aa0cd005b5931769eaa658c948ce79428766f1bd46ae2c3'], }), ('msgpack-numpy', '0.4.3.1', { 'modulename': 'msgpack_numpy', - 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack-numpy'], 'checksums': ['31fd5dd009bbee7f8b107db8c859e3a0a2793acc196f25ffbbae1e71b4c63ca5'], }), ('murmurhash', '0.28.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/murmurhash'], 'checksums': ['651137ed3e1169342c9edade454f3beb7fcdf28d4ad1ac232725237eaf442d9a'], }), ('plac', '0.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/plac'], 'checksums': ['ba3f719a018175f0a15a6b04e6cc79c25fd563d348aacd320c3644d2a9baf89b'], }), ('preshed', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/preshed'], 'checksums': ['7b99ace606143a922163a7ff7ad4969b296288f5b20b9c9bda328caec3b92f71'], }), ('regex', '2017.04.05', { - 'source_urls': ['https://pypi.python.org/packages/source/r/regex'], 'checksums': ['d811874ed669165fe1059a54f860db5c6ab5f48100bf4945d915fd2f877b2531'], }), ('tqdm', '4.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tqdm'], 'checksums': ['60bbaa6700e87a250f6abcbbd7ddb33243ad592240ba46afce5305b15b406fad'], }), ('wrapt', '1.10.11', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt'], 'checksums': ['d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6'], }), ('thinc', '6.10.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/thinc'], 'checksums': ['6e89d60f6165685837ebaff6a978ea9ca2b6c8c551a0886125c27de42e8fcf04'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ('editdistance', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/e/editdistance'], 'checksums': ['c765db6f8817d38922e4a50be4b9ab338b2c539377b6fcf0bca11dea72eeb8c1'], }), ('elasticsearch', '5.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/e/elasticsearch'], 'checksums': ['e754c688e20fe73160fb6f7f5b63f2a71c78788dc9e6908950681d3a39b56e85'], }), ('elasticsearch-dsl', '5.3.0', { 'modulename': 'elasticsearch_dsl', - 'source_urls': ['https://pypi.python.org/packages/source/e/elasticsearch-dsl'], 'checksums': ['de81b2322cde9bf1171c8a41d80596cdadd433b88b93daa09060af3a512523a7'], }), ('spacy', '2.0.12', { - 'source_urls': ['https://pypi.python.org/packages/source/s/spacy'], 'checksums': ['b220ebee412c19613c26b2c1870b60473834bd686cec49553ce5f184164d3359'], }), ('en_core_web_lg', '2.0.0', { @@ -104,7 +82,6 @@ exts_list = [ }), (name, version, { 'patches': ['mordecai-2.0.1_fix_bad_path_handling.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/m/mordecai'], 'checksums': [ 'c417f343eac29eccc8af0b5cacb47da8d17bfc4dd4187d3fa193828622b5372c', # mordecai-2.0.1.tar.gz # mordecai-2.0.1_fix_bad_path_handling.patch @@ -121,8 +98,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - modextravars = {'OMPI_MCA_mpi_warn_on_fork': '0'} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/motionSegmentation/motionSegmentation-2.7.9-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/motionSegmentation/motionSegmentation-2.7.9-foss-2019b-Python-3.7.4.eb index 17c8581f27b..967937f5578 100644 --- a/easybuild/easyconfigs/m/motionSegmentation/motionSegmentation-2.7.9-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/motionSegmentation/motionSegmentation-2.7.9-foss-2019b-Python-3.7.4.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('trimesh', '3.6.15', { 'checksums': ['9444160957f094769c87a4d2a48051ad1e7c4e29272d063fe832e961e5014be3'], diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2017a-Python-2.7.13-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2017a-Python-2.7.13-timed-pingpong.eb index 979db51cf47..a430ae4af1f 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2017a-Python-2.7.13-timed-pingpong.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2017a-Python-2.7.13-timed-pingpong.eb @@ -11,7 +11,6 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['mpi4py-1.3.1_%s.patch' % local_label] checksums = [ diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.0-intel-2018a-Python-2.7.14-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.0-intel-2018a-Python-2.7.14-timed-pingpong.eb index fcd163d27ba..a997e4fb5a7 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.0-intel-2018a-Python-2.7.14-timed-pingpong.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.0-intel-2018a-Python-2.7.14-timed-pingpong.eb @@ -11,7 +11,6 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['mpi4py-%%(version)s_%s.patch' % local_label] checksums = [ diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.2-gompi-2019a-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.2-gompi-2019a-timed-pingpong.eb index 2a5f9297ce9..dd8e9c61a68 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.2-gompi-2019a-timed-pingpong.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.2-gompi-2019a-timed-pingpong.eb @@ -11,7 +11,6 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'gompi', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['mpi4py-3.0.0_%s.patch' % local_label] checksums = [ diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.2-iimpi-2019a-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.2-iimpi-2019a-timed-pingpong.eb index 1e469d6c68e..7c4832ed0b2 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.2-iimpi-2019a-timed-pingpong.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.2-iimpi-2019a-timed-pingpong.eb @@ -11,7 +11,6 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'iimpi', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['mpi4py-3.0.0_%s.patch' % local_label] checksums = [ diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/mpmath/mpmath-1.0.0-foss-2018b-Python-2.7.15.eb index d7bb04f5256..b5f628a6036 100644 --- a/easybuild/easyconfigs/m/mpmath/mpmath-1.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mpmath/mpmath-1.0.0-foss-2018b-Python-2.7.15.eb @@ -10,7 +10,7 @@ name = 'mpmath' version = '1.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://mpmath.org/' +homepage = 'https://mpmath.org/' description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, with either real or complex @@ -19,7 +19,6 @@ description = """mpmath can be used as an arbitrary-precision substitute for Pyt toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'] @@ -31,9 +30,4 @@ use_pip = True runtest = 'python -c "import mpmath; mpmath.runtests();"' -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-1.0.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/mpmath/mpmath-1.0.0-intel-2018a-Python-2.7.14.eb index cf7bf09fb3e..8d63a9dbc20 100644 --- a/easybuild/easyconfigs/m/mpmath/mpmath-1.0.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/mpmath/mpmath-1.0.0-intel-2018a-Python-2.7.14.eb @@ -10,7 +10,7 @@ name = 'mpmath' version = '1.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://mpmath.org/' +homepage = 'https://mpmath.org/' description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, with either real or complex @@ -19,7 +19,6 @@ description = """mpmath can be used as an arbitrary-precision substitute for Pyt toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'] @@ -31,9 +30,4 @@ use_pip = True runtest = 'python -c "import mpmath; mpmath.runtests();"' -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb index d3d580bc0a1..76de20a4b67 100644 --- a/easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb @@ -21,8 +21,6 @@ check_ldshared = True use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pyrsistent', '0.15.2', { 'checksums': ['16692ee739d42cf5e39cef8d27649a8c1fdb7aa99887098f1460057c5eb75c3a'], diff --git a/easybuild/easyconfigs/m/mygene/mygene-3.1.0-intel-2019a.eb b/easybuild/easyconfigs/m/mygene/mygene-3.1.0-intel-2019a.eb index fc7866f964b..77e657a845c 100644 --- a/easybuild/easyconfigs/m/mygene/mygene-3.1.0-intel-2019a.eb +++ b/easybuild/easyconfigs/m/mygene/mygene-3.1.0-intel-2019a.eb @@ -20,19 +20,11 @@ use_pip = True exts_list = [ ('biothings_client', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/biothings_client/'], 'checksums': ['9e86d0c106eb5b175b603b52aff82330598d25d4468a5ddc3ba7c23072b1dad4'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/mygene'], - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'checksums': ['307305d83b5f9c0722dd8a78642d59c0d9d7742e60f548040819274a330d53af'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb index a1fa67726eb..419ae8f501e 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """A mpi4py based random pair pingpong network stress test.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_vsc_base_ver = '2.4.17' diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb index a615b7a8b7d..33e55e75ec8 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = """A mpi4py based random pair pingpong network stress test.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb index a1ef8e5b6d9..321116d715d 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb @@ -9,7 +9,6 @@ description = """A mpi4py based random pair pingpong network stress test.""" toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb index e56d7c03b57..e26533855e6 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb @@ -9,7 +9,6 @@ description = """A mpi4py based random pair pingpong network stress test.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb index 1c4b167ac58..7c14b8aa091 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """A mpi4py based random pair pingpong network stress test.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb index 3d740d96c75..5c72b2d9539 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb @@ -9,7 +9,6 @@ description = """A mpi4py based random pair pingpong network stress test.""" toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] diff --git a/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb b/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb index bd652ff3b64..1d71b690422 100644 --- a/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb +++ b/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'mypy' version = '0.4.5' @@ -8,14 +8,10 @@ description = """Optional static typing for Python""" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [('Python', '3.5.2')] exts_list = [ ('typed-ast', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typed-ast'], 'modulename': 'typed_ast', }), (name, version, { @@ -24,8 +20,6 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/mypy'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-foss-2016a-Python-2.7.11.eb index 292d557dbaf..38c76e8391c 100644 --- a/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """Python interface to MySQL""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ @@ -22,9 +21,4 @@ prebuildopts = "sed -i 's/static = False/static = True/g' site.cfg && " options = {'modulename': 'MySQLdb'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-intel-2016a-Python-2.7.11.eb index 3cd081ee974..6814b8c68d0 100644 --- a/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-intel-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """Python interface to MySQL""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ @@ -22,9 +21,4 @@ prebuildopts = "sed -i 's/static = False/static = True/g' site.cfg && " options = {'modulename': 'MySQLdb'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb new file mode 100644 index 00000000000..cbf8532c70e --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -0,0 +1,25 @@ +name = 'NCCL' +version = '2.8.3' +local_gcc_ver = '10.2.0' +local_cuda_version = '11.1.1' +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': local_gcc_ver} + +builddependencies = [('GCC', local_gcc_ver, '', True)] +dependencies = [('CUDAcore', local_cuda_version, '', True)] + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +patches = ['NCCL-2.8.3_fix-isend-irecv.patch'] +checksums = [ + '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6', # v2.8.3-1.tar.gz + '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92', # NCCL-2.8.3_fix-isend-irecv.patch +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb new file mode 100644 index 00000000000..50bb04e3b90 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -0,0 +1,25 @@ +name = 'NCCL' +version = '2.8.3' +local_gcc_ver = '9.3.0' +local_cuda_version = '11.0.2' +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': local_gcc_ver} + +builddependencies = [('GCC', local_gcc_ver, '', True)] +dependencies = [('CUDAcore', local_cuda_version, '', True)] + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +patches = ['NCCL-2.8.3_fix-isend-irecv.patch'] +checksums = [ + '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6', # v2.8.3-1.tar.gz + '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92', # NCCL-2.8.3_fix-isend-irecv.patch +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3_fix-isend-irecv.patch b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3_fix-isend-irecv.patch new file mode 100644 index 00000000000..31b057ecd54 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3_fix-isend-irecv.patch @@ -0,0 +1,46 @@ +Fix hang in corner cases of alltoallv using point to point send/recv. +Extracted from https://github.com/NVIDIA/nccl/commit/911d61f214d45c98df1ee8c0ac23c33fb94b63de + +Extracted by: Alexander Grund (TU Dresden) + +diff --git a/src/group.cc b/src/group.cc +index 78a74b65c..43a93284f 100644 +--- a/src/group.cc ++++ b/src/group.cc +@@ -233,7 +233,7 @@ ncclResult_t ncclGroupEnd() { + // schedule delta 0, +1, -1, +2, -2, ... + // also make sure we don't do 0 twice, nor +n/2 and -n/2 if n is even. + for (int d=0; d<=nRanks/4; d++) { +- int deltas[4] = { d, (nRanks-d)%nRanks, nRanks/2-d, nRanks-(nRanks/2-d) }; ++ int deltas[4] = { d, (nRanks-d)%nRanks, nRanks/2-d, (nRanks-(nRanks/2-d))%nRanks }; + int index = 0; + int delta = deltas[index]; + sched_delta: +@@ -258,6 +258,10 @@ ncclResult_t ncclGroupEnd() { + ssize_t sendbytes = totSendBytes-sendOffset; + if (recvbytes > recvChunkSize) { recvbytes = recvChunkSize; } else { recvRemaining = 0; } + if (sendbytes > sendChunkSize) { sendbytes = sendChunkSize; } else { sendRemaining = 0; } ++ // 0-bytes send/recv are considered as syncs. Make sure we only add syncs when requested ++ // (total size == 0), otherwise set size to -1 so that the kernel skips the operation. ++ if (sendbytes == 0 && totSendBytes != 0) sendbytes = -1; ++ if (recvbytes == 0 && totRecvBytes != 0) recvbytes = -1; + if (sendbytes >= 0 || recvbytes >= 0) { + NCCLCHECKGOTO(scheduleSendRecv(comm, delta, channelId, + recvbytes, recv ? ((char*)(recv->buff)) + recvOffset : NULL, +diff --git a/src/misc/utils.cc b/src/misc/utils.cc +index b231eb19a..79e61704d 100644 +--- a/src/misc/utils.cc ++++ b/src/misc/utils.cc +@@ -67,10 +67,10 @@ ncclResult_t getHostName(char* hostname, int maxlen, const char delim) { + } + + uint64_t getHash(const char* string, int n) { +- // Based on DJB2, result = result * 33 + char ++ // Based on DJB2a, result = result * 33 ^ char + uint64_t result = 5381; + for (int c = 0; c < n; c++) { +- result = ((result << 5) + result) + string[c]; ++ result = ((result << 5) + result) ^ string[c]; + } + return result; + } diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-CUDA-11.3.1.eb new file mode 100644 index 00000000000..1bc204ed7ce --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-CUDA-11.3.1.eb @@ -0,0 +1,43 @@ +## +# Author: Robert Mijakovic +## +easyblock = "MakeCp" + +name = 'NCCL' +version = '2.9.9' +local_cuda_version = '11.3.1' +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = SYSTEM + +local_cuda_version_major_minor = '.'.join(local_cuda_version.split('.')[:2]) + +# Download from https://developer.nvidia.com/nccl/nccl-download (after log in) +sources = ['%%(namelower)s_%%(version)s-1+cuda%s_%%(arch)s.txz' % local_cuda_version_major_minor] +checksums = [ + { + '%%(namelower)s_%%(version)s-1+cuda%s_aarch64.txz' % local_cuda_version_major_minor: + 'b3291328990785807ba01d20a730bed86fbf84d28194da7e8194c9503d0eaefe', + '%%(namelower)s_%%(version)s-1+cuda%s_ppc64le.txz' % local_cuda_version_major_minor: + '11dec74b9397c100588dcc96a8c23ffc89567523d47047bcf5d12f625c1c13b6', + '%%(namelower)s_%%(version)s-1+cuda%s_x86_64.txz' % local_cuda_version_major_minor: + '59df720e039fd8a765ceb94749e0a8ca9d7bb3dd9bec4867f500e8f0325262c8', + } +] + +dependencies = [('CUDAcore', local_cuda_version)] + +skipsteps = ['build'] + +files_to_copy = ['lib', 'include'] + +sanity_check_paths = { + 'files': ['lib/libnccl.%s' % SHLIB_EXT, 'lib/libnccl_static.a', 'include/nccl.h'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.1.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.1.1-foss-2019b-Python-3.7.4.eb index b369e5e6ea1..0fffbe06f83 100644 --- a/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.1.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.1.1-foss-2019b-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "NGSpeciesID is a tool for clustering and consensus forming of tar toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['97e463a5cfd696b9d3c4aeb9a5c9f9de3c10872bf36ec1b98dafd8f0c3a1425c'] diff --git a/easybuild/easyconfigs/n/NINJA/NINJA-0.97-cluster_only-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NINJA/NINJA-0.97-cluster_only-GCC-10.2.0.eb new file mode 100644 index 00000000000..62d086e7a85 --- /dev/null +++ b/easybuild/easyconfigs/n/NINJA/NINJA-0.97-cluster_only-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'NINJA' +version = '0.97-cluster_only' + +homepage = 'https://github.com/TravisWheelerLab/NINJA' +description = "Nearly Infinite Neighbor Joining Application." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'cstd': 'gnu++11', 'openmp': True, 'opt': True} + +github_account = 'TravisWheelerLab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b9b948c698efc3838e63817f732ead35c08debe1c0ae36b5c74df7d26ca4c4b6'] + +start_dir = name +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +files_to_copy = [(['%(name)s/Ninja'], 'bin'), 'NINJA/README', 'README.md', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/Ninja'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.3.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.3.eb new file mode 100644 index 00000000000..28520bd94b1 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.3.eb @@ -0,0 +1,74 @@ +## +# Author: Andreas Herten < a.herten@fz-juelich.de>, Robert Mijakovic +## +name = 'NVHPC' +version = '21.3' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +# By downloading, you accept the HPC SDK Software License Agreement (https://docs.nvidia.com/hpc-sdk/eula/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +local_tarball_tmpl = 'nvhpc_2021_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + '88e0dbf8fcdd06a2ba06aacf65ae1625b8683688f6593ed3bf8ce129ce1b17b7', + local_tarball_tmpl % 'ppc64le': + '08cd0cd6c80d633f107b44f88685ada7f014fbf6eac19ef5ae4a7952cabe4037', + local_tarball_tmpl % 'x86_64': + '391d5604a70f61bdd4ca6a3e4692f6f2391948990c8a35c395b6867341890031', + } +] + +local_gccver = '10.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.36.1', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.14', '', ('GCCcore', local_gccver)) +] + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/21.3/cuda/) +# for NVHPC 21.3, those are: 11.2, 11.0, 10.2; +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="10.2" (for example) +default_cuda_version = '11.2' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDAcore as a dependency, for example +# dependencies = [('CUDAcore', '11.0.2')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb new file mode 100644 index 00000000000..722a853a9a9 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb @@ -0,0 +1,74 @@ +## +# Author: Robert Mijakovic +## +name = 'NVHPC' +version = '21.5' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +# By downloading, you accept the HPC SDK Software License Agreement (https://docs.nvidia.com/hpc-sdk/eula/index.html) +accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +local_tarball_tmpl = 'nvhpc_2021_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + '1a1748cd7cf538199d92ab3b1208935fa4a62708ba21125aeadb328ddc7380d4', + local_tarball_tmpl % 'ppc64le': + '4674931a5ce28724308cb9cebd546eefa3f0646d3d08adbea28ba5ad27f0c163', + local_tarball_tmpl % 'x86_64': + '21989e52c58a6914743631c8200de1fec7e10b3449c6c1833f3032ee74b85f8e', + } +] + +local_gccver = '10.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.36.1', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.14', '', ('GCCcore', local_gccver)) +] + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/21.5/cuda/) +# for NVHPC 21.5, those are: 11.3, 11.0, 10.2; +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '11.3' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDAcore as a dependency, for example +# dependencies = [('CUDAcore', '11.3.1')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.10.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.10.1-intel-2019b-Python-3.7.4.eb index 16c326a454b..ec069496fae 100644 --- a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.10.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.10.1-intel-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = "Comparing runs of Oxford Nanopore sequencing data and alignments" toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['552334d8048165374a3c3090ff75cb8177ee2e518770b53aeedf7fc9a6d6bc07'] diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-intel-2019b-Python-3.7.4.eb index 90e1afe4371..27668d84f2f 100644 --- a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-intel-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = "Filtering and trimming of Oxford Nanopore Sequencing data" toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0f833be4fbbbad20c1cb85dacc28ae6009ab1edc68f3dcf61ae7e74e33b5f653'] diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.28.4-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.28.4-intel-2019b-Python-3.7.4.eb index 4846e23b396..1a88aabd364 100644 --- a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.28.4-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.28.4-intel-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = "Plotting suite for long read sequencing data and alignments" toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ede9fff91deeccdd5056839dcefba3a8091732e576cce30e08e36e51f35d2317'] diff --git a/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb new file mode 100644 index 00000000000..daf63dd2f9c --- /dev/null +++ b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb @@ -0,0 +1,57 @@ +easyblock = 'CMakeMake' + +name = 'Nektar++' +version = '5.0.1' + +homepage = 'https://www.nektar.info' +description = """Nektar++ is a tensor product based finite element package +designed to allow one to construct efficient classical low polynomial order +h-type solvers (where h is the size of the finite element) as well as higher +p-order piecewise polynomial order solvers.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +source_urls = ['https://www.nektar.info/downloads/file'] +sources = [{'download_filename': 'nektar-5-0-1-tar-xz', 'filename': '%(namelower)s-%(version)s.tar.xz'}] +checksums = ['d38401321250e21a29a73dd491e05ca077dd177a32c222c961693b3189542d06'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.74.0'), + ('HDF5', '1.10.7'), + ('METIS', '5.1.0'), + ('PETSc', '3.14.4'), + ('VTK', '9.0.1'), +] + +preconfigopts = 'export OPENBLAS_HOME=$EBROOTOPENBLAS LAPACK_DIR=$EBROOTOPENBLAS BLAS_DIR=$EBROOTOPENBLAS && ' + +configopts = '-DNEKTAR_USE_OPENBLAS=True ' + +sanity_check_paths = { + 'files': ['bin/%s' % x + for x in ['AcousticSolver', 'AddModeTo2DFld', 'ADRSolver', 'Aliasing', 'APESolver', 'CardiacEPSolver', + 'CFLStep', 'CollectionsUnitTests', 'CollectionTiming', 'CompressibleBL', + 'CompressibleFlowSolver', 'Deriv3DHomo1D', 'Deriv3DHomo1D_SingleMode', 'Deriv3DHomo2D', + 'DiffusionSolver', 'DiffusionSolverTimeInt', 'DummySolver', 'ErrorStream', + 'ExtractMeanModeFromHomo1DFld', 'ExtractSurface2DCFS', 'ExtractSurface3DCFS', 'FieldConvert', + 'Fld2DTo2D5', 'Fld2Tecplot', 'FldAddFalknerSkanBL', 'FoundationDemo', 'HDGHelmholtz1D', + 'HDGHelmholtz2D', 'HDGHelmholtz3D', 'HDGHelmholtz3DHomo1D', 'Helmholtz1D', 'Helmholtz2D', + 'Helmholtz3D', 'Helmholtz3DHomo1D', 'Helmholtz3DHomo2D', 'IncNavierStokesSolver', + 'LibUtilitiesUnitTests', 'LinearAlgebraUnitTests', 'LinearElasticSolver', + 'LocalRegionsUnitTests', 'LocProject', 'MMFDiffusion', 'MMFSolver', 'NekMesh', 'NodalDemo', + 'NonLinearEnergy', 'PartitionAnalyse', 'PostProcHDG2D', 'PostProcHDG3D', 'PrePacing', + 'PulseWaveSolver', 'ShallowWaterSolver', 'StdEquiToCoeff2D', 'StdProject', + 'SteadyAdvectionDiffusionReaction2D', 'Tester', 'TimeIntegrationDemo', 'UnitTests']] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) + for x in ['Collections', 'FieldUtils', 'GlobalMapping', 'LibUtilities', 'LocalRegions', + 'MultiRegions', 'NekMeshUtils', 'SolverUtils', 'SpatialDomains', 'StdRegions']], + 'dirs': ['include/nektar++', 'lib/nektar++/cmake'], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/n/NeuroKit/NeuroKit-0.2.7-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/NeuroKit/NeuroKit-0.2.7-intel-2018a-Python-3.6.4.eb index acb7d1ee1dc..86600d4bb65 100644 --- a/easybuild/easyconfigs/n/NeuroKit/NeuroKit-0.2.7-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/n/NeuroKit/NeuroKit-0.2.7-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'NeuroKit' version = '0.2.7' @@ -19,15 +19,10 @@ dependencies = [ ('CVXOPT', '1.2.1', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('future', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'], }), ('nolds', '0.4.1', { @@ -36,27 +31,21 @@ exts_list = [ 'checksums': ['019897002a72324a06f5baf5e3d0514b9d8ef247a7dbd66f4a4d3b76ecca6a3b'], }), ('bioread', '1.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bioread'], 'checksums': ['aa9ed6a32511dcd9d98c5a7b7c531293fde1b15c211c716be7d9399abeafb731'], }), ('shortuuid', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/shortuuid'], 'checksums': ['d08fd398f40f8baf87e15eef8355e92fa541bca4eb8465fefab7ee22f92711b9'], }), ('bidict', '0.17.3', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bidict'], 'checksums': ['265699b30ec6bda7f145f27c5ae63ce9ecca355fa92c6b1df4ed42b3c9638c43'], }), ('biosppy', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/b/biosppy'], 'checksums': ['39315a105eb8a1a46a9c641a683a2dbbd25cb0617786e96230ef82bae2e3fa7e'], }), ('mne', '0.16.2', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mne'], 'checksums': ['c166b19aed189409c23af25b29038cbdd4ea55349212057fda575cc24a6e19d9'], }), ('sklearn', '0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sklearn'], 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], }), (name, version, { @@ -66,11 +55,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.1.0-intel-2017a-Python-2.7.13.eb index 83d74f5756a..d3cd92e1052 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.1.0-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'NiBabel' version = '2.1.0' @@ -17,13 +17,9 @@ dependencies = [ ('Pillow', '4.3.0', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ ('pydicom', '0.9.9', { 'modulename': 'dicom', - 'source_urls': ['https://pypi.python.org/packages/source/p/pydicom'], 'start_dir': 'source', 'checksums': [ '09b82896319d9b0e5e95dae64875c37413b6ca9b974f4bb785564875f617236a', # pydicom-0.9.9.tar.gz @@ -31,7 +27,6 @@ exts_list = [ }), ('NiBabel', '2.1.0', { 'source_tmpl': 'nibabel-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], 'checksums': [ '9cc37ed9107319aca79177e3fed422da9677606bd72cf5697f14fc5a4b3a2738', # nibabel-2.1.0.tar.gz ], @@ -43,6 +38,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.2.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.2.1-intel-2018a-Python-3.6.4.eb index 038074e7031..439a462003d 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.2.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.2.1-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'NiBabel' version = '2.2.1' @@ -18,18 +18,13 @@ dependencies = [ ] # raise an error when auto-downloading of dependency packages is detected -exts_download_dep_fail = True - -exts_defaultclass = 'PythonPackage' exts_list = [ ('pydicom', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pydicom'], 'start_dir': 'source', 'checksums': ['26988f7b38456702d18468642d06e710a68efd0ca281e3c410910b7b03205264'], }), (name, version, { 'source_tmpl': 'nibabel-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], 'checksums': ['a857cb6c0b55bd1f812314f0eab11956b48ab435310e44e75c52cf020d0aad98'], }), ] @@ -39,6 +34,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb index 9434fafcc82..90e02caefd5 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb @@ -26,7 +26,6 @@ exts_list = [ 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], }), ('nibabel', version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], 'checksums': ['bf34aeb0f7ca52dc528ae4f842607cea307b334163857ff1d64d43068f637ada'], }), ] diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb index 8b4b5660029..0423416995f 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb @@ -26,7 +26,6 @@ exts_list = [ 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], }), ('nibabel', version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], 'checksums': ['bf34aeb0f7ca52dc528ae4f842607cea307b334163857ff1d64d43068f637ada'], }), ] diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2018b-Python-3.6.6.eb index 39160c2c1a0..5fc64ff6f32 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'NiBabel' version = '2.3.0' @@ -17,12 +17,8 @@ dependencies = [ ('Pillow', '5.3.0', versionsuffix), ] -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True -exts_defaultclass = 'PythonPackage' exts_list = [ ('pydicom', '1.2.0', { 'source_tmpl': 'v%(version)s.tar.gz', @@ -30,7 +26,6 @@ exts_list = [ 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], }), ('nibabel', version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], 'checksums': ['bf34aeb0f7ca52dc528ae4f842607cea307b334163857ff1d64d43068f637ada'], }), ] @@ -40,6 +35,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb index 55de0ad583a..123f3e3d6af 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb @@ -26,7 +26,6 @@ exts_list = [ 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], }), ('nibabel', version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], 'checksums': ['bf34aeb0f7ca52dc528ae4f842607cea307b334163857ff1d64d43068f637ada'], }), ] diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb index 6280675c29e..b0d0883c8a7 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb @@ -26,7 +26,6 @@ exts_list = [ 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], }), ('nibabel', version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], 'checksums': ['bf34aeb0f7ca52dc528ae4f842607cea307b334163857ff1d64d43068f637ada'], }), ] diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-foss-2019a.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-foss-2019a.eb index f027faccf5f..7a21bf07943 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-foss-2019a.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-foss-2019a.eb @@ -27,11 +27,9 @@ exts_list = [ 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], }), ('bz2file', '0.98', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], }), ('nibabel', version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], 'checksums': ['dd0c41715d0391c724e2828bba2c16690dbd6aafbca8e920ee8448ed0086e4c1'], }), ] diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-intel-2019a.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-intel-2019a.eb index 7c443e522cc..1c17845f85a 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-intel-2019a.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-intel-2019a.eb @@ -27,11 +27,9 @@ exts_list = [ 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], }), ('bz2file', '0.98', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], }), ('nibabel', version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], 'checksums': ['dd0c41715d0391c724e2828bba2c16690dbd6aafbca8e920ee8448ed0086e4c1'], }), ] diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.5.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.5.1-foss-2018b-Python-3.6.6.eb index 39dac3e2e45..8f24c9b2550 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.5.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.5.1-foss-2018b-Python-3.6.6.eb @@ -26,11 +26,9 @@ exts_list = [ 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], }), ('bz2file', '0.98', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], }), ('nibabel', version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], 'checksums': ['83ecac4773ece02c49c364d99b465644c17cc66f1719560117e74991d9eb566b'], }), ] diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.1.0-foss-2019b-Python-3.7.4.eb index acb1cb7a728..4328074d64e 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.1.0-foss-2019b-Python-3.7.4.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pydicom', '1.4.2', { 'checksums': ['9488495a9f3e202d1219f7cb165aee0de31efd512d938c0226d34147ce860391'], diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.1.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.1.0-intel-2019b-Python-3.7.4.eb index 2ceca673437..5dc4153b5e5 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.1.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.1.0-intel-2019b-Python-3.7.4.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pydicom', '1.4.2', { 'checksums': ['9488495a9f3e202d1219f7cb165aee0de31efd512d938c0226d34147ce860391'], diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb new file mode 100644 index 00000000000..cf9d4e90463 --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '3.2.1' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Pillow', '8.0.1'), + ('pydicom', '2.1.2'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['4d2ff9426b740011a1c916b54fc25da9348282e727eaa2ea163f42e00f1fc29e'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2017b-Python-2.7.14.eb index c1562a71ec8..4ff4cb1eb50 100644 --- a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2017b-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'Nilearn' version = '0.5.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://nilearn.github.io/' +homepage = 'https://nilearn.github.io/' description = """Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['https://pypi.python.org/packages/source/n/nilearn'] sources = [SOURCELOWER_TAR_GZ] checksums = ['18b763d641e6903bdf8512e0ec5cdc14133fb4679e9a15648415e9be62c81b56'] @@ -22,9 +21,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2017b-Python-3.6.3.eb index b776e446b8b..3920dc8b31c 100644 --- a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2017b-Python-3.6.3.eb @@ -4,12 +4,11 @@ name = 'Nilearn' version = '0.5.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://nilearn.github.io/' +homepage = 'https://nilearn.github.io/' description = """Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['https://pypi.python.org/packages/source/n/nilearn'] sources = [SOURCELOWER_TAR_GZ] checksums = ['18b763d641e6903bdf8512e0ec5cdc14133fb4679e9a15648415e9be62c81b56'] @@ -22,9 +21,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2019a.eb b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2019a.eb index b8d068d580d..02ce2ab36d6 100644 --- a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2019a.eb +++ b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-foss-2019a.eb @@ -3,12 +3,11 @@ easyblock = 'PythonPackage' name = 'Nilearn' version = '0.5.2' -homepage = 'http://nilearn.github.io/' +homepage = 'https://nilearn.github.io/' description = """Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.""" toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = ['https://pypi.python.org/packages/source/n/nilearn'] sources = [SOURCELOWER_TAR_GZ] checksums = ['18b763d641e6903bdf8512e0ec5cdc14133fb4679e9a15648415e9be62c81b56'] @@ -22,9 +21,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2017b-Python-2.7.14.eb index a346c4cf2f9..a1566d13e4e 100644 --- a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2017b-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'Nilearn' version = '0.5.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://nilearn.github.io/' +homepage = 'https://nilearn.github.io/' description = """Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = ['https://pypi.python.org/packages/source/n/nilearn'] sources = [SOURCELOWER_TAR_GZ] checksums = ['18b763d641e6903bdf8512e0ec5cdc14133fb4679e9a15648415e9be62c81b56'] @@ -22,9 +21,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2017b-Python-3.6.3.eb index 5830765b0d4..64b461e7745 100644 --- a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2017b-Python-3.6.3.eb @@ -4,12 +4,11 @@ name = 'Nilearn' version = '0.5.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://nilearn.github.io/' +homepage = 'https://nilearn.github.io/' description = """Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = ['https://pypi.python.org/packages/source/n/nilearn'] sources = [SOURCELOWER_TAR_GZ] checksums = ['18b763d641e6903bdf8512e0ec5cdc14133fb4679e9a15648415e9be62c81b56'] @@ -22,9 +21,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2019a.eb b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2019a.eb index 4bec97468ec..db265bf1265 100644 --- a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2019a.eb +++ b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.5.2-intel-2019a.eb @@ -3,12 +3,11 @@ easyblock = 'PythonPackage' name = 'Nilearn' version = '0.5.2' -homepage = 'http://nilearn.github.io/' +homepage = 'https://nilearn.github.io/' description = """Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.""" toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = ['https://pypi.python.org/packages/source/n/nilearn'] sources = [SOURCELOWER_TAR_GZ] checksums = ['18b763d641e6903bdf8512e0ec5cdc14133fb4679e9a15648415e9be62c81b56'] @@ -22,9 +21,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nim/Nim-1.4.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/Nim/Nim-1.4.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c273fe29677 --- /dev/null +++ b/easybuild/easyconfigs/n/Nim/Nim-1.4.8-GCCcore-10.3.0.eb @@ -0,0 +1,17 @@ +name = 'Nim' +version = '1.4.8' + +homepage = 'https://nim-lang.org/' +description = "Nim is a systems and applications programming language." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://nim-lang.org/download/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b798c577411d7d95b8631261dbb3676e9d1afd9e36740d044966a0555b41441a'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('libreadline', '8.1')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb index cfd71248ed2..fe62223f1a7 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb index 82f318c76b7..afa160c1017 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-10.3.0.eb index 55f2ace9bbc..7b32691b617 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-10.3.0.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-foss-2018a.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-foss-2018a.eb index b04a1d2f4e6..69dd62f6f59 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-foss-2018a.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-foss-2018a.eb @@ -23,4 +23,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-foss-2018b.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-foss-2018b.eb index 31d55f73a3b..8fce93a4792 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-foss-2018b.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-foss-2018b.eb @@ -23,4 +23,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb index ae099f03205..792c317c671 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb @@ -23,4 +23,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-intel-2017b.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-intel-2017b.eb index 3475dab343d..b2af47781c4 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-intel-2017b.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-intel-2017b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} source_urls = ['https://github.com/ninja-build/ninja/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['86b8700c3d0880c2b44c2ff67ce42774aaf8c28cbf57725cb881569288c1c6f4'] builddependencies = [('Python', '2.7.14')] @@ -22,4 +23,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-intel-2018a.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-intel-2018a.eb index e05212d7d47..fecffd5a9c2 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-intel-2018a.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-intel-2018a.eb @@ -23,4 +23,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb index 887f01adbf6..610bae2282b 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.3.0.eb index f714daab9dc..74b3f1baf2e 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.3.0.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-foss-2018b.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-foss-2018b.eb index 5ea2081b987..3b3f397954a 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-foss-2018b.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-foss-2018b.eb @@ -23,4 +23,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.0.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.0.2-intel-2018a-Python-3.6.4.eb index 79e777a9adf..92920264ec9 100644 --- a/easybuild/easyconfigs/n/Nipype/Nipype-1.0.2-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.0.2-intel-2018a-Python-3.6.4.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Nipype' version = '1.0.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://nipy.org/nipype' +homepage = 'https://nipy.org/nipype' description = """Nipype is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow.""" @@ -17,83 +17,62 @@ dependencies = [ ] # raise an error when auto-downloading of dependency packages is detected -exts_download_dep_fail = True - -exts_defaultclass = 'PythonPackage' exts_list = [ ('networkx', '2.1', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1'], }), ('traits', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traits'], 'checksums': ['5d82345e0a34b88e394964eea1be47419530027aef7f0b20ad315b6ec6c68370'], }), ('future', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'], }), ('packaging', '17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging'], 'checksums': ['f019b770dd64e585a99714f1fd5e01c7a8f11b45635aa953fd41c689a657375b'], }), ('pydot', '1.2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pydot'], 'checksums': ['92d2e2d15531d00710f2d6fb5540d2acabc5399d464f2f20d5d21073af241eb6'], }), ('pydotplus', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pydotplus'], 'checksums': ['91e85e9ee9b85d2391ead7d635e3d9c7f5f44fd60a60e59b13e2403fa66505c4'], }), ('pluggy', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy'], 'checksums': ['7f8ae7f5bdf75671a718d2daf0a64b7885f74510bcd98b1a0bb420eb9a9d0cff'], }), ('more-itertools', '4.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools'], 'checksums': ['c9ce7eccdcb901a2c75d326ea134e0886abfbea5f93e91cc95de9507c0816c44'], 'modulename': 'more_itertools', }), ('attrs', '17.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], 'checksums': ['1c7960ccfd6a005cd9f7ba884e6316b5e430a3f1a6c37c5f87d8b43f83b54ec9'], 'modulename': 'attr', }), ('py', '1.5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py'], 'checksums': ['29c9fab495d7528e80ba1e343b958684f4ace687327e6f789a94bf3d1915f881'], }), ('pytest', '3.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest'], 'checksums': ['54713b26c97538db6ff0703a12b19aeaeb60b5e599de542e7fca0ec83b9038e8'], }), ('funcsigs', version, { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], 'checksums': ['f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b'], }), ('isodate', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/isodate'], 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], }), ('rdflib', '4.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/r/rdflib'], 'checksums': ['da1df14552555c5c7715d8ce71c08f404c988c58a1ecd38552d0da4fc261280d'], }), ('prov', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prov'], 'checksums': ['96a74efa1b3324961ff66246539ed7bdc06245dcbeef538688c755a0ad5777ee'], }), ('simplejson', '3.14.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson'], 'checksums': ['1ebbd84c2d7512f7ba65df0b9cc3cbc1bbd6ef9eab39fc9389dfe7e3681f7bd2'], }), ('nipype', version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/nipype'], 'checksums': ['1ed65f3e97fd0f82c418ad48af2107050e86d9e39eea4d22381ad7df932bf1ec'], }), ] @@ -105,6 +84,4 @@ sanity_check_paths = { sanity_check_commands = ["python -c 'import nipype.interfaces'"] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.1.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.1.3-foss-2018b-Python-3.6.6.eb index 2d230224feb..cf198644a0b 100644 --- a/easybuild/easyconfigs/n/Nipype/Nipype-1.1.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.1.3-foss-2018b-Python-3.6.6.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Nipype' version = '1.1.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://nipy.org/nipype' +homepage = 'https://nipy.org/nipype' description = """Nipype is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow.""" @@ -16,109 +16,81 @@ dependencies = [ ('NiBabel', '2.3.0', versionsuffix), ] -# raise an error when auto-downloading of dependency packages is detected -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True -exts_defaultclass = 'PythonPackage' exts_list = [ ('networkx', '2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], }), ('traits', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traits'], 'checksums': ['5d82345e0a34b88e394964eea1be47419530027aef7f0b20ad315b6ec6c68370'], }), ('future', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'], }), ('packaging', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging'], 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], }), ('pydot', '1.2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pydot'], 'checksums': ['92d2e2d15531d00710f2d6fb5540d2acabc5399d464f2f20d5d21073af241eb6'], }), ('pydotplus', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pydotplus'], 'checksums': ['91e85e9ee9b85d2391ead7d635e3d9c7f5f44fd60a60e59b13e2403fa66505c4'], }), ('pluggy', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy'], 'checksums': ['95eb8364a4708392bae89035f45341871286a333f749c3141c20573d2b3876e1'], }), ('more-itertools', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools'], 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], 'modulename': 'more_itertools', }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('py', '1.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py'], 'checksums': ['06a30435d058473046be836d3fc4f27167fd84c45b99704f2fb5509ef61f9af1'], }), ('atomicwrites', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites'], 'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'], }), ('pytest', '3.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest'], 'checksums': ['9332147e9af2dcf46cd7ceb14d5acadb6564744ddff1fe8c17f0ce60ece7d9a2'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('isodate', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/isodate'], 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], }), ('rdflib', '4.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/r/rdflib'], 'checksums': ['da1df14552555c5c7715d8ce71c08f404c988c58a1ecd38552d0da4fc261280d'], }), ('prov', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prov'], 'checksums': ['96a74efa1b3324961ff66246539ed7bdc06245dcbeef538688c755a0ad5777ee'], }), ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), ('pytest-forked', '0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest-forked'], 'checksums': ['e4500cd0509ec4a26535f7d4112a8cc0f17d3a41c29ffd4eab479d2a55b30805'], 'modulename': 'pytest_forked', }), ('apipkg', '1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/a/apipkg'], 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], }), ('execnet', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/e/execnet'], 'checksums': ['a7a84d5fa07a089186a329528f127c9d73b9de57f1a1131b82bb5320ee651f6a'], }), ('pytest-xdist', '1.23.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest-xdist'], 'checksums': ['1ef0d05c905cfa0c5442c90e9e350e65c6ada120e33a00a066ca51c89f5f869a'], 'modulename': 'xdist', }), ('nipype', version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/nipype'], 'checksums': ['c14856f3d4823aa5d63d0c19e8f04d70c74e156361ce607d86694046bab06806'], }), ] @@ -130,6 +102,4 @@ sanity_check_paths = { sanity_check_commands = ["python -c 'import nipype.interfaces'"] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.4.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.4.2-intel-2019b-Python-3.7.4.eb index 0a5649643cc..06e6c7e2fa2 100644 --- a/easybuild/easyconfigs/n/Nipype/Nipype-1.4.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.4.2-intel-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('traits', '6.0.0', { 'checksums': ['dbcd70166feca434130a1193284d5819ca72ffbc8dbce8deeecc0cebb41a3bfb'], diff --git a/easybuild/easyconfigs/n/Nsight-Compute/Nsight-Compute-2021.2.0.eb b/easybuild/easyconfigs/n/Nsight-Compute/Nsight-Compute-2021.2.0.eb new file mode 100644 index 00000000000..a140a490abb --- /dev/null +++ b/easybuild/easyconfigs/n/Nsight-Compute/Nsight-Compute-2021.2.0.eb @@ -0,0 +1,30 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Binary' + +name = 'Nsight-Compute' +version = '2021.2.0' + +homepage = 'https://developer.nvidia.com/nsight-compute' +description = """NVIDIA® Nsight™ Compute is an interactive kernel profiler for CUDA applications. It provides detailed +performance metrics and API debugging via a user interface and a command line tool. In addition, its baseline feature +allows users to compare results within the tool. Nsight Compute provides a customizable and data-driven user interface +and fast metric collection, which can be extended with rules-based analysis scripts for post-processing results. The +rules-based guided analysis helps isolate and fix memory throughput, compute, and occupancy inefficiencies in the target +application.""" + +toolchain = SYSTEM + +# Download requires login https://developer.nvidia.com/gameworksdownload#?dn=nsight-compute-2021-2-0 +sources = ['%(namelower)s-linux-%(version)s.15-30066266.run'] +checksums = ['fd058676115b8003ec2370a2bf199fbd6c6346811c4b4e3e1707f6ad044032b1'] + +install_cmd = 'sh ' + sources[0] + ' --target %(builddir)s --nox11 -- -noprompt --targetpath=%(installdir)s' + +sanity_check_paths = { + 'files': ['ncu', 'ncu-ui'], + 'dirs': ['docs'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.12.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.12.1-intel-2019b-Python-3.7.4.eb index 404fa547a91..d498c497f7c 100644 --- a/easybuild/easyconfigs/n/nanoget/nanoget-1.12.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.12.1-intel-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = "Functions to extract information from Oxford Nanopore sequencing toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['37af88a4f09214c791b32f47f60c731fd4706fd63cf131aa5a13440afd034e60'] diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-0.23.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/nanomath/nanomath-0.23.1-intel-2019b-Python-3.7.4.eb index 91ba82fa2d3..94ea2e9a035 100644 --- a/easybuild/easyconfigs/n/nanomath/nanomath-0.23.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/nanomath/nanomath-0.23.1-intel-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = "A few simple math function for other Oxford Nanopore processing s toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['54a7edb3b458194014a35122968a7bc70cf9076de2f65f4a8b00638f71b06011'] diff --git a/easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb index 3ab16635b60..a10b13bc47a 100644 --- a/easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'nanonet' version = '2.0.0' @@ -9,9 +9,6 @@ description = "Nanonet provides recurrent neural network basecalling for Oxford toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.13'), ('h5py', '2.7.1', versionsuffix), @@ -23,25 +20,21 @@ dependencies = [ exts_list = [ ('myriad', '0.1.4', { 'source_tmpl': 'myriad-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/m/myriad'], 'checksums': [ 'ae1d836f0e9c37b90b94c185555e485e2c7e36458a4709e39e4aefc3945fdfd5', # myriad-0.1.4.zip ], }), ('pathtools', '0.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathtools'], 'checksums': [ '7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0', # pathtools-0.1.2.tar.gz ], }), ('argh', '0.26.2', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argh'], 'checksums': [ 'e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65', # argh-0.26.2.tar.gz ], }), ('watchdog', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/w/watchdog'], 'checksums': [ '7e65882adb7746039b6f3876ee174952f8eaaa34491ba34333ddf1fe35de4162', # watchdog-0.8.3.tar.gz ], @@ -62,6 +55,4 @@ sanity_check_paths = { } sanity_check_commands = ["nanonet2d --help"] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nd2reader/nd2reader-3.0.6-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/nd2reader/nd2reader-3.0.6-intel-2017b-Python-2.7.14.eb index de57fb3d43a..07b2429eefb 100755 --- a/easybuild/easyconfigs/n/nd2reader/nd2reader-3.0.6-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/nd2reader/nd2reader-3.0.6-intel-2017b-Python-2.7.14.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'nd2reader' version = '3.0.6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.lighthacking.nl/nd2reader/' +homepage = 'https://www.lighthacking.nl/nd2reader/' description = "nd2reader is a pure-Python package that reads images produced by NIS Elements 4.0+." toolchain = {'name': 'intel', 'version': '2017b'} @@ -14,25 +14,13 @@ dependencies = [ ('PIMS', '0.4.1', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ ('xmltodict', '0.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xmltodict'], 'checksums': ['8f8d7d40aa28d83f4109a7e8aa86e67a4df202d9538be40c0cb1d70da527b0df'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/nd2reader'], 'checksums': ['3aad2a5a7aa9454f8e4e02e5acbb1f5d7d8ab4023265eb848ff5c3c7d9b6788b'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2021a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2021a.eb new file mode 100644 index 00000000000..dea496162d8 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2021a.eb @@ -0,0 +1,25 @@ +name = 'netCDF-Fortran' +version = '4.5.3' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c6da30c2fe7e4e614c1dff4124e857afbd45355c6798353eccfa60c0702b495a'] + +builddependencies = [ + ('M4', '1.4.18'), +] + +dependencies = [('netCDF', '4.8.0')] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2021a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2021a.eb new file mode 100644 index 00000000000..73da2be4e9c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2021a.eb @@ -0,0 +1,25 @@ +name = 'netCDF-Fortran' +version = '4.5.3' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c6da30c2fe7e4e614c1dff4124e857afbd45355c6798353eccfa60c0702b495a'] + +builddependencies = [ + ('M4', '1.4.18'), +] + +dependencies = [('netCDF', '4.8.0')] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.8.0-gompi-2021a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.0-gompi-2021a.eb new file mode 100644 index 00000000000..3ac7a6c6dca --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.0-gompi-2021a.eb @@ -0,0 +1,37 @@ +name = 'netCDF' +version = '4.8.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['aff58f02b1c3e91dc68f989746f652fe51ff39e6270764e484920cb8db5ad092'] + +builddependencies = [ + ('Autotools', '20210128'), + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('cURL', '7.76.0'), + ('Szip', '2.1.1'), +] + +# HDF5 version detection is missed in netCDF 4.8.0 when HDF5_C_LIBRARY, HDF5_INCLUDE_DIR, and HDF5_HL_LIBRARY are set +local_hdf5_version_fix = '-DHDF5_VERSION=$EBVERSIONHDF5' + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF %s " % local_hdf5_version_fix, + "-DBUILD_SHARED_LIBS=ON %s " % local_hdf5_version_fix, +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.8.0-iimpi-2021a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.0-iimpi-2021a.eb new file mode 100644 index 00000000000..549b2dec3a0 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.0-iimpi-2021a.eb @@ -0,0 +1,37 @@ +name = 'netCDF' +version = '4.8.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['aff58f02b1c3e91dc68f989746f652fe51ff39e6270764e484920cb8db5ad092'] + +builddependencies = [ + ('Autotools', '20210128'), + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('cURL', '7.76.0'), + ('Szip', '2.1.1'), +] + +# HDF5 version detection is missed in netCDF 4.8.0 when HDF5_C_LIBRARY, HDF5_INCLUDE_DIR, and HDF5_HL_LIBRARY are set +local_hdf5_version_fix = '-DHDF5_VERSION=$EBVERSIONHDF5' + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF %s " % local_hdf5_version_fix, + "-DBUILD_SHARED_LIBS=ON %s " % local_hdf5_version_fix, +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb index f010055ca79..46b4ff64b8a 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb @@ -20,7 +20,6 @@ use_pip = True exts_list = [ ('cftime', '1.0.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cftime'], 'checksums': ['2c81d4879a2c1753961d647e55e0125039ddeda195944c3d526f2cf087dfb7bb'], }), (name, version, { diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.2-intel-2019a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.2-intel-2019a.eb index 709b075d7ca..4fc7c4335cb 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.2-intel-2019a.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.2-intel-2019a.eb @@ -9,8 +9,6 @@ description = """Python/numpy interface to netCDF.""" toolchain = {'name': 'intel', 'version': '2019a'} toolchainopts = {'usempi': True} -source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] - multi_deps = {'Python': ['3.7.2', '2.7.15']} dependencies = [ @@ -21,8 +19,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cftime', '1.0.3.4', { 'checksums': ['dd74d0d470baf1c50e31335215793a5e78436903e34b4f151fa9ccbf3a6cc20c'], diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-2.7.16.eb index 7154348ded3..37d4474c410 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-2.7.16.eb @@ -21,7 +21,6 @@ use_pip = True exts_list = [ ('cftime', '1.1.1.2', { - 'source_urls': [PYPI_SOURCE], 'checksums': ['35711b5ec3928b9e724817bfa1b7325da205788ee04eae9166cbcd96ea7976a6'], }), (name, version, { diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-3.7.4.eb index 121a9cd86ac..0f650015307 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-3.7.4.eb @@ -21,12 +21,11 @@ use_pip = True exts_list = [ ('cftime', '1.1.1.2', { - 'source_urls': [PYPI_SOURCE], 'checksums': ['35711b5ec3928b9e724817bfa1b7325da205788ee04eae9166cbcd96ea7976a6'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], 'checksums': [ '2a3ca855848f4bbf07fac366da77a681fcead18c0a8813d91d46302f562dc3be', # netCDF4-1.5.3.tar.gz diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2020a-Python-3.8.2.eb index 996188f2e02..10182b3ace2 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2020a-Python-3.8.2.eb @@ -26,8 +26,8 @@ exts_list = [ }), (name, version, { 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], - 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'checksums': [ '2a3ca855848f4bbf07fac366da77a681fcead18c0a8813d91d46302f562dc3be', # netCDF4-1.5.3.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-intel-2019b-Python-3.7.4.eb index 1f821612c7d..c336f452529 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-intel-2019b-Python-3.7.4.eb @@ -22,8 +22,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cftime', '1.1.1.2', { 'checksums': ['35711b5ec3928b9e724817bfa1b7325da205788ee04eae9166cbcd96ea7976a6'], diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-intel-2020a-Python-3.8.2.eb index 6afaf088731..ed8b4bfed50 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-intel-2020a-Python-3.8.2.eb @@ -26,8 +26,8 @@ exts_list = [ }), (name, version, { 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], - 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'checksums': [ '2a3ca855848f4bbf07fac366da77a681fcead18c0a8813d91d46302f562dc3be', # netCDF4-1.5.3.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb index b7343ccf1ab..4970fc65904 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb @@ -27,8 +27,8 @@ exts_list = [ }), (name, version, { 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], - 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'checksums': [ 'd957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd', # netCDF4-1.5.5.1.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb index 01db361cc5d..4877a912839 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb @@ -25,8 +25,8 @@ exts_list = [ }), (name, version, { 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], - 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'checksums': [ 'd957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd', # netCDF4-1.5.5.1.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb index 00b1f150440..5babd145291 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb @@ -10,16 +10,10 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.12'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb index afc809e5852..9949b8983ea 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb index 162c58702cb..522e9c9a40e 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2017b-Python-2.7.14.eb index b26759a0b6e..f83ccd3af5b 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2017b-Python-2.7.14.eb @@ -10,15 +10,9 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['b3e0144d5fe6b7479b694e1b598a5545a38f3fc6f1e3c09173eb30f0c7a5770e'] dependencies = [('Python', '2.7.14')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/networkx/networkx-2.0-intel-2017b-Python-2.7.14.eb index 4e9c1319f8e..203a6847c37 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.0-intel-2017b-Python-2.7.14.eb @@ -10,15 +10,9 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['cd5ff8f75d92c79237f067e2f0876824645d37f017cfffa5b7c9678cae1454aa'] dependencies = [('Python', '2.7.14')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/networkx/networkx-2.1-intel-2017b-Python-2.7.14.eb index 96f37545bbc..7b0e6b5eda8 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.1-intel-2017b-Python-2.7.14.eb @@ -10,15 +10,9 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1'] dependencies = [('Python', '2.7.14')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-2.7.15.eb index 08818a0b7d6..e27a207ffea 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-2.7.15.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.6.6.eb index 89256354661..773f3e26619 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] @@ -19,9 +18,4 @@ dependencies = [('Python', '3.6.6')] use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019a-Python-2.7.15.eb index 37aaee48c4e..98d24fe1c16 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019a-Python-2.7.15.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019b-Python-2.7.16.eb index d61e7b42be6..bcc93a611c9 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019b-Python-2.7.16.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-2.7.15.eb index 3e2537f6828..7154af778f1 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-2.7.15.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] @@ -19,9 +18,4 @@ dependencies = [('Python', '2.7.15')] use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.6.6.eb index 74fc5505732..9a21f7f6cda 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] @@ -19,9 +18,4 @@ dependencies = [('Python', '3.6.6')] use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.3-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/n/networkx/networkx-2.3-foss-2019a-Python-3.7.2.eb index c39af502105..ede655a36d1 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.3-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.3-foss-2019a-Python-3.7.2.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['8311ddef63cf5c5c5e7c1d0212dd141d9a1fe3f474915281b73597ed5f1d4e3d'] diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/n/networkx/networkx-2.3-intel-2019a-Python-3.7.2.eb index 6f812aa169d..238dc1f5815 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.3-intel-2019a-Python-3.7.2.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['8311ddef63cf5c5c5e7c1d0212dd141d9a1fe3f474915281b73597ed5f1d4e3d'] diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019a-Python-3.7.2.eb index 15d45d83108..bab34889d85 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019a-Python-3.7.2.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019b-Python-3.7.4.eb index 416da59ab61..e0396f3d02c 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.4-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/networkx/networkx-2.4-fosscuda-2019b-Python-3.7.4.eb index 0c35f1395b7..927c8afa638 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.4-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.4-fosscuda-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'fosscuda', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.4-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/n/networkx/networkx-2.4-intel-2019a-Python-3.7.2.eb index 4f3f65bb68f..de4256226ba 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.4-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.4-intel-2019a-Python-3.7.2.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.4-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/networkx/networkx-2.4-intel-2019b-Python-3.7.4.eb index bd04c05b771..7e46a5d4335 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.4-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.4-intel-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """NetworkX is a Python package for the creation, manipulation, an toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] diff --git a/easybuild/easyconfigs/n/nglview/nglview-2.7.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/n/nglview/nglview-2.7.0-intel-2019a-Python-3.7.2.eb index 1614c1c0148..5b155bb8507 100644 --- a/easybuild/easyconfigs/n/nglview/nglview-2.7.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/n/nglview/nglview-2.7.0-intel-2019a-Python-3.7.2.eb @@ -17,8 +17,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('widgetsnbextension', '3.5.1', { 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..deaf600ec19 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '14.17.0' # LTS on 2021-06-03 +local_libversion = '83' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://%(name)s.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-argument-list-too-long.patch'] +checksums = [ + '6114e82d3256136dc85a509d835442fbdf2f8430dcd8bfa7c304097344d06fb7', # node-v14.17.0.tar.gz + # nodejs-14.17.0_fix-argument-list-too-long.patch + 'b0eac4b478a9268c8902ec701f99e1445eeba2a70927bfacdeb5ba243e668550', +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), +] + +configopts = [ + '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library + '--shared --with-intl=none', # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +postinstallcmds = [ + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'dirs': ['lib/node_modules', 'include/node'] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_fix-argument-list-too-long.patch b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_fix-argument-list-too-long.patch new file mode 100644 index 00000000000..6f9440fdccf --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_fix-argument-list-too-long.patch @@ -0,0 +1,121 @@ +From d6fb5d77ef21b6f9f3d3d50d73a0512956c7e453 Mon Sep 17 00:00:00 2001 +From: Daniel Bevenius +Date: Mon, 31 May 2021 08:46:45 +0200 +Subject: [PATCH] tools: fix execvp: printf: Argument list too long + +When statically linking quictls/openssl 3.0.0alpha17 there are a number +of architectures that error with the following message: + +execvp: printf: Argument list too long + +This commit adds a patch provided in +https://github.com/nodejs/node/issues/9137 to see if this will address +this issue. + +Refs: https://github.com/nodejs/node/issues/9137#issuecomment-825940168 +--- + tools/gyp/pylib/gyp/generator/make.py | 74 +++++++++++++++++++++++++-- + 1 file changed, 69 insertions(+), 5 deletions(-) + +diff --git a/tools/gyp/pylib/gyp/generator/make.py b/tools/gyp/pylib/gyp/generator/make.py +index d163ae3135a7..2ce1c30137c5 100644 +--- a/tools/gyp/pylib/gyp/generator/make.py ++++ b/tools/gyp/pylib/gyp/generator/make.py +@@ -155,6 +155,31 @@ def CalculateGeneratorInputInfo(params): + quiet_cmd_link = LINK($(TOOLSET)) $@ + cmd_link = $(LINK.$(TOOLSET)) -o $@ $(GYP_LDFLAGS) $(LDFLAGS.$(TOOLSET)) -Wl,--start-group $(LD_INPUTS) $(LIBS) -Wl,--end-group + ++# Note: this does not handle spaces in paths ++define xargs ++ $(1) $(word 1,$(2)) ++$(if $(word 2,$(2)),$(call xargs,$(1),$(wordlist 2,$(words $(2)),$(2)))) ++endef ++ ++define write-to-file ++ @: >$(1) ++$(call xargs,@printf "%s\\n" >>$(1),$(2)) ++endef ++ ++OBJ_FILE_LIST := ar-file-list ++ ++define create_archive ++ rm -f $(1) $(1).$(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crs $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ ++define create_thin_archive ++ rm -f $(1) $(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crsT $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ + # We support two kinds of shared objects (.so): + # 1) shared_library, which is just bundling together many dependent libraries + # into a link line. +@@ -199,6 +224,31 @@ def CalculateGeneratorInputInfo(params): + quiet_cmd_alink_thin = AR($(TOOLSET)) $@ + cmd_alink_thin = rm -f $@ && $(AR.$(TOOLSET)) crsT $@ $(filter %.o,$^) + ++# Note: this does not handle spaces in paths ++define xargs ++ $(1) $(word 1,$(2)) ++$(if $(word 2,$(2)),$(call xargs,$(1),$(wordlist 2,$(words $(2)),$(2)))) ++endef ++ ++define write-to-file ++ @: >$(1) ++$(call xargs,@printf "%s\\n" >>$(1),$(2)) ++endef ++ ++OBJ_FILE_LIST := ar-file-list ++ ++define create_archive ++ rm -f $(1) $(1).$(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crs $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ ++define create_thin_archive ++ rm -f $(1) $(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crsT $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ + # Due to circular dependencies between libraries :(, we wrap the + # special "figure out circular dependencies" flags around the entire + # input list during linking. +@@ -1766,14 +1816,28 @@ def WriteTarget( + self.flavor not in ("mac", "openbsd", "netbsd", "win") + and not self.is_standalone_static_library + ): +- self.WriteDoCmd( ++ if self.flavor in ('linux', 'android'): ++ self.WriteMakeRule( + [self.output_binary], + link_deps, +- "alink_thin", +- part_of_all, +- postbuilds=postbuilds, +- ) ++ actions = ['$(call create_thin_archive,$@,$^)'] ++ ) ++ else: ++ self.WriteDoCmd( ++ [self.output_binary], ++ link_deps, ++ "alink_thin", ++ part_of_all, ++ postbuilds=postbuilds, ++ ) + else: ++ if self.flavor in ('linux', 'android'): ++ self.WriteMakeRule( ++ [self.output_binary], ++ link_deps, ++ actions = ['$(call create_archive,$@,$^)'] ++ ) ++ else: + self.WriteDoCmd( + [self.output_binary], + link_deps, diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-2.7.11.eb index ced9988f351..ec0d0e98ac0 100644 --- a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """Parameterized testing with any Python test framework.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.11')] diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.1.eb index 6c5140ef8ce..690eca6ac9d 100644 --- a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.1.eb @@ -9,7 +9,6 @@ description = """Parameterized testing with any Python test framework.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.5.1')] diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb index 971304f89cb..95afc4f2dd7 100644 --- a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb @@ -9,7 +9,6 @@ description = """Parameterized testing with any Python test framework.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.5.2')] diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb index 7877603edbd..b2ea3a101fb 100644 --- a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb @@ -9,16 +9,10 @@ description = """Parameterized testing with any Python test framework.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.6.1')] options = {'modulename': 'nose_parameterized'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..09a6c114e34 --- /dev/null +++ b/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'nsync' +version = '1.24.0' + +homepage = 'https://github.com/google/nsync' +description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/google/nsync/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['47a6eb2a295be5121a1904a6a775722338a20dc02ee3eec4169ed2c3f203617a'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('Ninja', '1.10.2'), +] + +sanity_check_paths = { + 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.36.0_fix-LLVM-11.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.36.0_fix-LLVM-11.patch new file mode 100644 index 00000000000..b7d54335a7c --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.36.0_fix-LLVM-11.patch @@ -0,0 +1,36 @@ +fix build on top of LLVM 11.x, +see also https://github.com/numba/llvmlite/issues/639 +diff --git a/ffi/custom_passes.cpp b/ffi/custom_passes.cpp +index 5758aad..860df2d 100644 +--- a/ffi/custom_passes.cpp ++++ b/ffi/custom_passes.cpp +@@ -400,7 +400,7 @@ struct RefPrunePass : public FunctionPass { + // LLVM 9 postdomtree.dominates takes basic blocks + if ( domtree.dominates(incref, decref) + && postdomtree.dominates(decref->getParent(), incref->getParent()) ){ +-#elif LLVM_VERSION_MAJOR == 10 ++#elif LLVM_VERSION_MAJOR == 11 + // LLVM 10 postdomtree.dominates can handle instructions + if ( domtree.dominates(incref, decref) + && postdomtree.dominates(decref, incref) ){ +diff --git a/ffi/transforms.cpp b/ffi/transforms.cpp +index 23bfd72..2eac2e9 100644 +--- a/ffi/transforms.cpp ++++ b/ffi/transforms.cpp +@@ -6,6 +6,7 @@ + + extern "C" { + ++ /* + namespace llvm { + inline PassManagerBuilder *unwrap(LLVMPassManagerBuilderRef P) { + return reinterpret_cast(P); +@@ -15,7 +16,7 @@ namespace llvm { + return reinterpret_cast(P); + } + } +- ++ */ + + API_EXPORT(LLVMPassManagerBuilderRef) + LLVMPY_PassManagerBuilderCreate() diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb index c02c1fdb846..98bcce96006 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb @@ -1,18 +1,15 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'numba' version = '0.24.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://numba.pydata.org/' +homepage = 'https://numba.pydata.org/' description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" toolchain = {'name': 'intel', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.11'), ('LLVM', '3.7.1'), @@ -20,12 +17,9 @@ dependencies = [ exts_list = [ ('llvmlite', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'patches': ['llvmlite-0.9.0_fix-ffi-Makefile.patch'], }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], - }), + (name, version), ] sanity_check_paths = { @@ -33,6 +27,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb index cf37952ede2..761d02f84cc 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb @@ -1,18 +1,15 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'numba' version = '0.24.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://numba.pydata.org/' +homepage = 'https://numba.pydata.org/' description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" toolchain = {'name': 'intel', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.5.1'), ('LLVM', '3.7.1'), @@ -20,12 +17,9 @@ dependencies = [ exts_list = [ ('llvmlite', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'patches': ['llvmlite-0.9.0_fix-ffi-Makefile.patch'], }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], - }), + (name, version), ] sanity_check_paths = { @@ -33,6 +27,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.26.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.26.0-intel-2016a-Python-2.7.11.eb index 2fb043b333d..9b62dd833b9 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.26.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.26.0-intel-2016a-Python-2.7.11.eb @@ -1,18 +1,15 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'numba' version = '0.26.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://numba.pydata.org/' +homepage = 'https://numba.pydata.org/' description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" toolchain = {'name': 'intel', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.11'), ('LLVM', '3.7.1'), @@ -20,12 +17,9 @@ dependencies = [ exts_list = [ ('llvmlite', '0.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'patches': ['llvmlite-0.11.0_fix-ffi-Makefile.patch'], }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], - }), + (name, version), ] sanity_check_paths = { @@ -33,6 +27,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb index 838ace2ac5b..9b087fe9db9 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb @@ -1,30 +1,23 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'numba' version = '0.32.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://numba.pydata.org/' +homepage = 'https://numba.pydata.org/' description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.13'), ('LLVM', '4.0.0'), ] exts_list = [ - ('llvmlite', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], - }), + ('llvmlite', '0.17.1'), + (name, version), ] sanity_check_paths = { @@ -32,6 +25,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb index 4a0b29f8e1b..9130424b1cf 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'numba' version = '0.37.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://numba.pydata.org/' +homepage = 'https://numba.pydata.org/' description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" @@ -21,7 +21,6 @@ use_pip = True exts_list = [ ('llvmlite', '0.22.0', { 'patches': ['llvmlite-0.22.0_fix-ffi-Makefile.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'checksums': [ 'a0a875f3d502f41f4a24444aa98fbf076a6bf36e2a0b3b4481b22e1c4a3acdc2', # llvmlite-0.22.0.tar.gz # llvmlite-0.22.0_fix-ffi-Makefile.patch @@ -29,11 +28,9 @@ exts_list = [ ], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], 'checksums': ['c62121b2d384d8b4d244ef26c1cf8bb5cb819278a80b893bf41918ad6d391258'], }), ] diff --git a/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb index 1aa6703b4f3..6078000e2c7 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'numba' version = '0.37.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://numba.pydata.org/' +homepage = 'https://numba.pydata.org/' description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" @@ -21,7 +21,6 @@ use_pip = True exts_list = [ ('llvmlite', '0.22.0', { 'patches': ['llvmlite-0.22.0_fix-ffi-Makefile.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'checksums': [ 'a0a875f3d502f41f4a24444aa98fbf076a6bf36e2a0b3b4481b22e1c4a3acdc2', # llvmlite-0.22.0.tar.gz # llvmlite-0.22.0_fix-ffi-Makefile.patch @@ -29,11 +28,9 @@ exts_list = [ ], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], 'checksums': ['c62121b2d384d8b4d244ef26c1cf8bb5cb819278a80b893bf41918ad6d391258'], }), ] diff --git a/easybuild/easyconfigs/n/numba/numba-0.37.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/numba/numba-0.37.0-intel-2017b-Python-2.7.14.eb index ac710d551a6..604509e21cb 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.37.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.37.0-intel-2017b-Python-2.7.14.eb @@ -1,19 +1,16 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'numba' version = '0.37.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://numba.pydata.org/' +homepage = 'https://numba.pydata.org/' description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'pic': True} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.14'), ('LLVM', '5.0.1'), @@ -22,7 +19,6 @@ dependencies = [ exts_list = [ ('llvmlite', '0.22.0', { 'patches': ['llvmlite-0.22.0_fix-ffi-Makefile.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'checksums': [ # llvmlite-0.22.0.tar.gz 'a0a875f3d502f41f4a24444aa98fbf076a6bf36e2a0b3b4481b22e1c4a3acdc2', @@ -31,7 +27,6 @@ exts_list = [ ], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], 'checksums': ['c62121b2d384d8b4d244ef26c1cf8bb5cb819278a80b893bf41918ad6d391258'], }), ] @@ -41,6 +36,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.37.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/numba/numba-0.37.0-intel-2018a-Python-3.6.4.eb index 24ba2ad1bb8..b5e446c0d57 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.37.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.37.0-intel-2018a-Python-3.6.4.eb @@ -1,21 +1,17 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'numba' version = '0.37.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://numba.pydata.org/' +homepage = 'https://numba.pydata.org/' description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" toolchain = {'name': 'intel', 'version': '2018a'} toolchainopts = {'pic': True} -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True dependencies = [ ('Python', '3.6.4'), @@ -25,7 +21,6 @@ dependencies = [ exts_list = [ ('llvmlite', '0.22.0', { 'patches': ['llvmlite-0.22.0_fix-ffi-Makefile.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'checksums': [ 'a0a875f3d502f41f4a24444aa98fbf076a6bf36e2a0b3b4481b22e1c4a3acdc2', # llvmlite-0.22.0.tar.gz # llvmlite-0.22.0_fix-ffi-Makefile.patch @@ -33,7 +28,6 @@ exts_list = [ ], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], 'checksums': ['c62121b2d384d8b4d244ef26c1cf8bb5cb819278a80b893bf41918ad6d391258'], }), ] @@ -43,6 +37,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.39.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/numba/numba-0.39.0-foss-2018b-Python-3.6.6.eb index c8f822fac9f..6f85d4ef147 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.39.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.39.0-foss-2018b-Python-3.6.6.eb @@ -22,7 +22,6 @@ sanity_pip_check = True exts_list = [ ('llvmlite', '0.26.0', { - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'patches': ['llvmlite-0.26.0_fix-ffi-Makefile.patch'], 'checksums': [ '13e84fe6ebb0667233074b429fd44955f309dead3161ec89d9169145dbad2ebf', # llvmlite-0.26.0.tar.gz @@ -31,7 +30,6 @@ exts_list = [ ], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], 'checksums': ['07749d1ddac8c4c0ce8b22bf3dec52ef2fd4922174c71447126807f5f8dc2bae'], }), ] diff --git a/easybuild/easyconfigs/n/numba/numba-0.43.1-intel-2019a.eb b/easybuild/easyconfigs/n/numba/numba-0.43.1-intel-2019a.eb index ee011f39d6a..b675aa0d16d 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.43.1-intel-2019a.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.43.1-intel-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'numba' version = '0.43.1' -homepage = 'http://numba.pydata.org/' +homepage = 'https://numba.pydata.org/' description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" @@ -24,7 +24,6 @@ check_ldshared = True exts_list = [ ('llvmlite', '0.28.0', { - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'patches': ['llvmlite-0.26.0_fix-ffi-Makefile.patch'], 'checksums': [ 'a189c0cd8a80e8bbd002a1e422b1efcc2bceab2cb63b961f2d03ab711c3ba45b', # llvmlite-0.28.0.tar.gz @@ -33,7 +32,6 @@ exts_list = [ ], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], 'checksums': ['e7789d473f332a17e40166d2960826d821edd75d148b4ed340a893a334b46fae'], }), ] diff --git a/easybuild/easyconfigs/n/numba/numba-0.46.0-foss-2019a.eb b/easybuild/easyconfigs/n/numba/numba-0.46.0-foss-2019a.eb index af15581f182..3a2a378d439 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.46.0-foss-2019a.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.46.0-foss-2019a.eb @@ -25,7 +25,6 @@ use_pip = True exts_list = [ ('llvmlite', '0.30.0', { 'patches': ['llvmlite-0.30.0_fix-ffi-Makefile.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'checksums': [ '4eaa398d4cafb76e2d8f30ca6ab875039a1023c91e7a690c6ddec20e58bb9a07', # llvmlite-0.30.0.tar.gz '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', @@ -33,7 +32,6 @@ exts_list = [ ], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], 'checksums': ['c2cbaeae60f80805290fff50175028726fae12692404a36babd3326730fbceee'], }), ] diff --git a/easybuild/easyconfigs/n/numba/numba-0.47.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/numba/numba-0.47.0-foss-2019b-Python-3.7.4.eb index 088706c24e3..381906d47c6 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.47.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.47.0-foss-2019b-Python-3.7.4.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('llvmlite', '0.31.0', { 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], diff --git a/easybuild/easyconfigs/n/numba/numba-0.47.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/numba/numba-0.47.0-fosscuda-2019b-Python-3.7.4.eb index 64e3c5bf161..40fe3407e15 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.47.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.47.0-fosscuda-2019b-Python-3.7.4.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('llvmlite', '0.31.0', { 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], diff --git a/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb new file mode 100644 index 00000000000..bd578f812fd --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.53.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('LLVM', '11.0.0'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + +exts_list = [ + ('llvmlite', '0.36.0', { + 'patches': ['llvmlite-0.36.0_fix-LLVM-11.patch'], + 'preinstallopts': local_llvmlite_preinstallopts, + 'checksums': [ + '765128fdf5f149ed0b889ffbe2b05eb1717f8e20a5c87fa2b4018fbcce0fcfc9', # llvmlite-0.36.0.tar.gz + '17ebf3e8eaea2dd820bf4e089983d5743656613eb6313c1ffed30c58e8d66be4', # llvmlite-0.36.0_fix-LLVM-11.patch + ], + }), + (name, version, { + 'checksums': ['9cd4e5216acdc66c4e9dab2dfd22ddb5bef151185c070d4a3cd8e78638aff5b0'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb new file mode 100644 index 00000000000..c8466673edd --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.53.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('LLVM', '11.0.0'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + +exts_list = [ + ('llvmlite', '0.36.0', { + 'patches': ['llvmlite-0.36.0_fix-LLVM-11.patch'], + 'preinstallopts': local_llvmlite_preinstallopts, + 'checksums': [ + '765128fdf5f149ed0b889ffbe2b05eb1717f8e20a5c87fa2b4018fbcce0fcfc9', # llvmlite-0.36.0.tar.gz + '17ebf3e8eaea2dd820bf4e089983d5743656613eb6313c1ffed30c58e8d66be4', # llvmlite-0.36.0_fix-LLVM-11.patch + ], + }), + (name, version, { + 'checksums': ['9cd4e5216acdc66c4e9dab2dfd22ddb5bef151185c070d4a3cd8e78638aff5b0'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb index b83a080a7d8..485576f1421 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb @@ -11,7 +11,6 @@ description = """NumPy is the fundamental package for scientific computing with toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] patches = ['numpy-1.12.0-mkl.patch'] diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/numpy/numpy-1.13.0-intel-2017a-Python-2.7.13.eb index d0c0134be72..6b437738049 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.13.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.13.0-intel-2017a-Python-2.7.13.eb @@ -11,7 +11,6 @@ description = """NumPy is the fundamental package for scientific computing with toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] patches = [ diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.13.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/n/numpy/numpy-1.13.1-intel-2017a-Python-3.6.1.eb index f74e6368fc6..4af7c369ed9 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.13.1-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.13.1-intel-2017a-Python-3.6.1.eb @@ -11,7 +11,6 @@ description = """NumPy is the fundamental package for scientific computing with toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] patches = ['numpy-1.12.0-mkl.patch'] checksums = [ diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d8de7f18054 --- /dev/null +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'nvtop' +version = '1.2.1' + +homepage = 'https://github.com/Syllo/nvtop' +description = 'htop-like GPU usage monitor' + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/Syllo/nvtop/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9b9d8159b95be5cbd9bf6904b44c212e820f17c9009e36e5cfeac43bbb059340'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('CUDAcore', '11.1.1', '', True), + ('ncurses', '6.2'), +] + +separate_build_dir = True + +configopts = '-DNVML_INCLUDE_DIRS=$EBROOTCUDA/include -DNVML_LIBRARIES=$EBROOTCUDA/lib64/stubs/libnvidia-ml.so' + +sanity_check_paths = { + 'files': ['bin/nvtop'], + 'dirs': [], +} + +sanity_check_commands = ["nvtop --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..45cc9a4c8f6 --- /dev/null +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'nvtop' +version = '1.2.1' + +homepage = 'https://github.com/Syllo/nvtop' +description = 'htop-like GPU usage monitor' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/Syllo/nvtop/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9b9d8159b95be5cbd9bf6904b44c212e820f17c9009e36e5cfeac43bbb059340'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +# Note: software dlopen's libraries from the OS installed drivers, thus no specific CUDA dependency. +dependencies = [ + ('ncurses', '6.2'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/nvtop'], + 'dirs': [], +} + +sanity_check_commands = ["nvtop --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb index 06458378d20..750808c0834 100644 --- a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb @@ -11,7 +11,6 @@ description = """The OBITools programs aims to help you to manipulate various da toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..765db865588 --- /dev/null +++ b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'OBITools3' +version = '3.0.1b8' + +homepage = 'https://metabarcoding.org/obitools3' +description = """A package for the management of analyses and data in DNA metabarcoding.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['33e10ffced0ef34829d6929180d5012afd6857ae87de420f65d789ebe2bb7741'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +preinstallopts = "sed -i \"s|get_python_lib()|get_python_lib(prefix='%(installdir)s')|g\" setup.py &&" + +fix_python_shebang_for = ['bin/obi'] + +sanity_check_paths = { + 'files': ['bin/obi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "obi --help", + "obi --version", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0849295e0d1 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.6' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['55972289ce66080bb48622110c3189a36e88a12917635f049b37685b9d3bbcb0'] + +builddependencies = [ + ('binutils', '2.35'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb new file mode 100644 index 00000000000..672d136bce4 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.7.1' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TGZ] +checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a59b3c5ca9d --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '2.3' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['36957428d37c40d35b6b45208f050fb5cfe23c54e874189778a24b0e9219c7e3'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.6', '-tools'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb new file mode 100644 index 00000000000..3da5bd86b42 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb @@ -0,0 +1,78 @@ +name = 'Octave' +version = '6.2.0' + +homepage = 'https://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['457d1fda8634a839e2fd7cfc55b98bd56f36b6ae73d31bb9df43dde3012caa7c'] + +builddependencies = [ + ('Bison', '3.7.1'), + ('flex', '2.6.4'), + ('Autotools', '20200321'), + ('gperf', '3.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20201008'), + ('PCRE', '8.44'), + ('ncurses', '6.2'), + ('libreadline', '8.0'), + ('arpack-ng', '3.8.0'), + ('cURL', '7.72.0'), + ('FLTK', '1.3.5'), + ('fontconfig', '2.13.92'), + ('freetype', '2.10.3'), + ('GLPK', '4.65'), + ('GL2PS', '1.4.2'), + ('gnuplot', '5.4.1'), + ('Java', '11', '', True), + ('zlib', '1.2.11'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('Qhull', '2020.2'), + ('Qt5', '5.14.2'), + ('HDF5', '1.10.7'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('texinfo', '6.7'), + ('libsndfile', '1.0.28'), + ('GraphicsMagick', '1.3.36'), +] + +configopts = '--disable-docs ' +# correct for both GCC and Intel compilers +configopts += '--enable-fortran-calling-convention=gfortran' + +local_pkg_url = 'https://downloads.sourceforge.net/' +local_pkg_url += 'project/octave/Octave%20Forge%20Packages/Individual%20Package%20Releases/' +exts_default_options = {'source_urls': [local_pkg_url]} + +exts_list = [ + ('control', '3.2.0', { + 'checksums': ['faf1d510d16ab46e4fa91a1288f4a7839ee05469c33e4698b7a007a0bb965e3e'], + }), + ('general', '2.1.1', { + 'checksums': ['fbd09409950c8b95e02ccb3895ec78f52cc8589a08a65d8c512a7cacf567bb4a'], + }), + ('io', '2.6.3', { + 'checksums': ['6bc63c6498d79cada01a6c4446f793536e0bb416ddec2a5201dd8d741d459e10'], + }), + ('signal', '1.4.1', { + 'checksums': ['d978600f8b8f61339b986136c9862cad3e8f7015f84132f214bf63e9e281aeaa'], + }), + ('statistics', '1.4.2', { + 'checksums': ['7976814f837508e70367548bfb0a6d30aa9e447d4e3a66914d069efb07876247'], + }), + ('struct', '1.0.17', { + 'checksums': ['0137bbb5df650f29104f6243502f3a2302aaaa5e42ea9f02d8a3943aaf668433'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.17.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.17.1-foss-2019b-Python-3.7.4.eb index 1e13a0db681..faa08f6edfc 100644 --- a/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.17.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.17.1-foss-2019b-Python-3.7.4.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cloudpickle', '1.3.0', { 'checksums': ['38af54d0e7705d87a287bdefe1df00f936aadb1f629dca383e825cca927fa753'], diff --git a/easybuild/easyconfigs/o/OpenMM-PLUMED/OpenMM-PLUMED-1.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenMM-PLUMED/OpenMM-PLUMED-1.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..681660bc2e2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM-PLUMED/OpenMM-PLUMED-1.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'OpenMM-PLUMED' +version = '1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/openmm/openmm-plumed/' +description = """This project provides a connection between OpenMM and +PLUMED. It allows you to bias or analyze an OpenMM simulation based on +collective variables.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +# https://github.com/openmm/openmm-plumed/archive/refs/tags/v1.0.tar.gz +github_account = 'openmm' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['97cbffab7a452a3c8f0b00c301c9a796b752ee73e30dc5c1b2435678dd7c73ed'] + +builddependencies = [ + ('CMake', '3.16.4'), + ('SWIG', '4.0.1'), +] +dependencies = [ + ('Python', '3.8.2'), + ('OpenMM', '7.4.2', versionsuffix), + ('PLUMED', '2.6.0', versionsuffix), +] + +separate_build_dir = True + +configopts = '-DPLUMED_INCLUDE_DIR="$EBROOTPLUMED/include/plumed" ' +configopts += '-DPLUMED_LIBRARY_DIR="$EBROOTPLUMED/lib" ' +configopts += '-DOPENMM_DIR="$EBROOTOPENMM" ' + +installopts = ' && make -f python/CMakeFiles/PythonInstall.dir/build.make python/PlumedPluginWrapper.cpp' +installopts += ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['include/PlumedForce.h', 'include/PlumedKernels.h', + 'lib/libOpenMMPlumed.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/openmmplumed.py'], + 'dirs': [], +} + +sanity_check_commands = ['python -c "from openmmplumed import PlumedForce"'] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-foss-2019b-Python-3.7.4.eb index b06b11d3d8b..9d7dc617480 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-foss-2019b-Python-3.7.4.eb @@ -9,7 +9,7 @@ name = 'OpenMM' version = '7.4.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://openmm.org' +homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." toolchain = {'name': 'foss', 'version': '2019b'} diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-intel-2019b-Python-3.7.4.eb index acdb4b56917..2b8131164e8 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-intel-2019b-Python-3.7.4.eb @@ -9,7 +9,7 @@ name = 'OpenMM' version = '7.4.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://openmm.org' +homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." toolchain = {'name': 'intel', 'version': '2019b'} diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.2-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.2-intel-2020a-Python-3.8.2.eb index 58d781963e7..6a35d086519 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.2-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.2-intel-2020a-Python-3.8.2.eb @@ -9,7 +9,7 @@ name = 'OpenMM' version = '7.4.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://openmm.org' +homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." toolchain = {'name': 'intel', 'version': '2020a'} diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb index 04383ac6bc9..fb7a82f5637 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'OpenMM' version = '7.5.0' -homepage = 'http://openmm.org' +homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020a-Python-3.8.2.eb index d6fb9a71439..06732f1e2bb 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020a-Python-3.8.2.eb @@ -9,7 +9,7 @@ name = 'OpenMM' version = '7.5.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://openmm.org' +homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." toolchain = {'name': 'fosscuda', 'version': '2020a'} diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..a7be917c4fd --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb @@ -0,0 +1,64 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.0' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_path_to_nvcc.patch'] +checksums = [ + '516748b4f1ae936c4d70cc6401174fc9384244c65cd3aef27bc2c53eac6d6de5', # 7.5.0.tar.gz + '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SWIG', '4.0.2'), +] + +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020a-Python-3.8.2.eb index c690fc0e944..1578c538644 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020a-Python-3.8.2.eb @@ -9,7 +9,7 @@ name = 'OpenMM' version = '7.5.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://openmm.org' +homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." toolchain = {'name': 'intel', 'version': '2020a'} diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb index 07e2f420389..0620868684e 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'OpenMM' version = '7.5.0' -homepage = 'http://openmm.org' +homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." toolchain = {'name': 'intel', 'version': '2020b'} diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb index 95e6d6ba503..077d51b2f9e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,12 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['36f10daa3f1b1d37530f686bf7f70966b2a13c0bc6e2e05aebc7e85e3d21b10d'] +patches = ['OpenMPI-4.0.1_add-support-for-ucx-1.7.patch'] +checksums = [ + '36f10daa3f1b1d37530f686bf7f70966b2a13c0bc6e2e05aebc7e85e3d21b10d', # openmpi-4.0.0.tar.gz + # OpenMPI-4.0.1_add-support-for-ucx-1.7.patch + '3c5ce8fe164869f309821a4528bbd8a4c087bc748dadf589850482bbccf8890c', +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb index 85d5af984cd..dc12c1ff8ed 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb @@ -8,7 +8,17 @@ toolchain = {'name': 'GCC', 'version': '8.3.0-2.32'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['e55e213fe09a214ab9f2c722acfd8bf7b39bbc1800e4b7a464d38df15e707f59'] +patches = [ + 'OpenMPI-4.0.1_add-support-for-ucx-1.7.patch', + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', +] +checksums = [ + 'e55e213fe09a214ab9f2c722acfd8bf7b39bbc1800e4b7a464d38df15e707f59', # openmpi-4.0.1.tar.gz + # OpenMPI-4.0.1_add-support-for-ucx-1.7.patch + '3c5ce8fe164869f309821a4528bbd8a4c087bc748dadf589850482bbccf8890c', + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1_add-support-for-ucx-1.7.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1_add-support-for-ucx-1.7.patch new file mode 100644 index 00000000000..012ebc677d0 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1_add-support-for-ucx-1.7.patch @@ -0,0 +1,407 @@ +From 47ec3e4d2bd30d3feaaca3989124452fca60f5d6 Mon Sep 17 00:00:00 2001 +From: Nathan Hjelm +Date: Thu, 26 Sep 2019 08:57:00 -0700 +Subject: [PATCH 1/3] btl/uct: add support for OpenUCX v1.8 API changes + +OpenUCX broke the UCT API again in v1.8. This commit updates +btl/uct to fix compilation with current OpenUCX master +(future v1.8). Further changes will likely be needed for +the final release. + +Signed-off-by: Nathan Hjelm +(cherry picked from commit 526775dfd7ad75c308532784de4fb3ffed25458f) +--- + opal/mca/btl/uct/btl_uct.h | 4 ++ + opal/mca/btl/uct/btl_uct_amo.c | 4 +- + opal/mca/btl/uct/btl_uct_component.c | 82 +++++++++++++++++++++++++++- + opal/mca/btl/uct/btl_uct_rdma.c | 4 +- + opal/mca/btl/uct/btl_uct_rdma.h | 14 +++++ + opal/mca/btl/uct/btl_uct_tl.c | 6 ++ + 6 files changed, 107 insertions(+), 7 deletions(-) + +diff --git a/opal/mca/btl/uct/btl_uct.h b/opal/mca/btl/uct/btl_uct.h +index 38756794430..73640103c07 100644 +--- a/opal/mca/btl/uct/btl_uct.h ++++ b/opal/mca/btl/uct/btl_uct.h +@@ -85,6 +85,10 @@ struct mca_btl_uct_module_t { + /** array containing the am_tl and rdma_tl */ + mca_btl_uct_tl_t *comm_tls[2]; + ++#if UCT_API > UCT_VERSION(1, 7) ++ uct_component_h uct_component; ++#endif ++ + /** registration cache */ + mca_rcache_base_module_t *rcache; + +diff --git a/opal/mca/btl/uct/btl_uct_amo.c b/opal/mca/btl/uct/btl_uct_amo.c +index f7d02326884..72398ce7369 100644 +--- a/opal/mca/btl/uct/btl_uct_amo.c ++++ b/opal/mca/btl/uct/btl_uct_amo.c +@@ -110,7 +110,7 @@ int mca_btl_uct_afop (struct mca_btl_base_module_t *btl, struct mca_btl_base_end + mca_btl_uct_uct_completion_release (comp); + } + +- uct_rkey_release (&rkey); ++ mca_btl_uct_rkey_release (uct_btl, &rkey); + + return rc; + } +@@ -184,7 +184,7 @@ int mca_btl_uct_acswap (struct mca_btl_base_module_t *btl, struct mca_btl_base_e + mca_btl_uct_uct_completion_release (comp); + } + +- uct_rkey_release (&rkey); ++ mca_btl_uct_rkey_release (uct_btl, &rkey); + + return rc; + } +diff --git a/opal/mca/btl/uct/btl_uct_component.c b/opal/mca/btl/uct/btl_uct_component.c +index f968cb9c31c..538872860f9 100644 +--- a/opal/mca/btl/uct/btl_uct_component.c ++++ b/opal/mca/btl/uct/btl_uct_component.c +@@ -314,7 +314,12 @@ ucs_status_t mca_btl_uct_am_handler (void *arg, void *data, size_t length, unsig + return UCS_OK; + } + ++#if UCT_API > UCT_VERSION(1, 7) ++static int mca_btl_uct_component_process_uct_md (uct_component_h component, uct_md_resource_desc_t *md_desc, ++ char **allowed_ifaces) ++#else + static int mca_btl_uct_component_process_uct_md (uct_md_resource_desc_t *md_desc, char **allowed_ifaces) ++#endif + { + mca_rcache_base_resources_t rcache_resources; + uct_tl_resource_desc_t *tl_desc; +@@ -348,8 +353,14 @@ static int mca_btl_uct_component_process_uct_md (uct_md_resource_desc_t *md_desc + + md = OBJ_NEW(mca_btl_uct_md_t); + ++ ++#if UCT_API > UCT_VERSION(1, 7) ++ uct_md_config_read (component, NULL, NULL, &uct_config); ++ uct_md_open (component, md_desc->md_name, uct_config, &md->uct_md); ++#else + uct_md_config_read (md_desc->md_name, NULL, NULL, &uct_config); + uct_md_open (md_desc->md_name, uct_config, &md->uct_md); ++#endif + uct_config_release (uct_config); + + uct_md_query (md->uct_md, &md_attr); +@@ -375,6 +386,10 @@ static int mca_btl_uct_component_process_uct_md (uct_md_resource_desc_t *md_desc + return OPAL_ERR_NOT_AVAILABLE; + } + ++#if UCT_API > UCT_VERSION(1, 7) ++ module->uct_component = component; ++#endif ++ + mca_btl_uct_component.modules[mca_btl_uct_component.module_count++] = module; + + /* NTH: a registration cache shouldn't be necessary when using UCT but there are measurable +@@ -400,6 +415,42 @@ static int mca_btl_uct_component_process_uct_md (uct_md_resource_desc_t *md_desc + return OPAL_SUCCESS; + } + ++#if UCT_API > UCT_VERSION(1, 7) ++static int mca_btl_uct_component_process_uct_component (uct_component_h component, char **allowed_ifaces) ++{ ++ uct_component_attr_t attr = {.field_mask = UCT_COMPONENT_ATTR_FIELD_NAME | ++ UCT_COMPONENT_ATTR_FIELD_MD_RESOURCE_COUNT}; ++ ucs_status_t ucs_status; ++ int rc; ++ ++ ucs_status = uct_component_query (component, &attr); ++ if (UCS_OK != ucs_status) { ++ return OPAL_ERROR; ++ } ++ ++ BTL_VERBOSE(("processing uct component %s", attr.name)); ++ ++ attr.md_resources = calloc (attr.md_resource_count, sizeof (*attr.md_resources)); ++ attr.field_mask |= UCT_COMPONENT_ATTR_FIELD_MD_RESOURCES; ++ ucs_status = uct_component_query (component, &attr); ++ if (UCS_OK != ucs_status) { ++ return OPAL_ERROR; ++ } ++ ++ for (int i = 0 ; i < attr.md_resource_count ; ++i) { ++ rc = mca_btl_uct_component_process_uct_md (component, attr.md_resources + i, ++ allowed_ifaces); ++ if (OPAL_SUCCESS != rc) { ++ break; ++ } ++ } ++ ++ free (attr.md_resources); ++ ++ return OPAL_SUCCESS; ++} ++#endif /* UCT_API > UCT_VERSION(1, 7) */ ++ + /* + * UCT component initialization: + * (1) read interface list from kernel and compare against component parameters +@@ -415,6 +466,7 @@ static mca_btl_base_module_t **mca_btl_uct_component_init (int *num_btl_modules, + struct mca_btl_base_module_t **base_modules; + uct_md_resource_desc_t *resources; + unsigned resource_count; ++ ucs_status_t ucs_status; + char **allowed_ifaces; + int rc; + +@@ -431,10 +483,32 @@ static mca_btl_base_module_t **mca_btl_uct_component_init (int *num_btl_modules, + return NULL; + } + +- uct_query_md_resources (&resources, &resource_count); +- + mca_btl_uct_component.module_count = 0; + ++#if UCT_API > UCT_VERSION(1, 7) ++ uct_component_h *components; ++ unsigned num_components; ++ ++ ucs_status = uct_query_components(&components, &num_components); ++ if (UCS_OK != ucs_status) { ++ BTL_ERROR(("could not query UCT components")); ++ return NULL; ++ } ++ ++ /* generate all suitable btl modules */ ++ for (unsigned i = 0 ; i < num_components ; ++i) { ++ rc = mca_btl_uct_component_process_uct_component (components[i], allowed_ifaces); ++ if (OPAL_SUCCESS != rc) { ++ break; ++ } ++ } ++ ++ uct_release_component_list (components); ++ ++#else /* UCT 1.6 and older */ ++ ++ uct_query_md_resources (&resources, &resource_count); ++ + /* generate all suitable btl modules */ + for (unsigned i = 0 ; i < resource_count ; ++i) { + rc = mca_btl_uct_component_process_uct_md (resources + i, allowed_ifaces); +@@ -443,9 +517,11 @@ static mca_btl_base_module_t **mca_btl_uct_component_init (int *num_btl_modules, + } + } + +- opal_argv_free (allowed_ifaces); + uct_release_md_resource_list (resources); + ++#endif /* UCT_API > UCT_VERSION(1, 7) */ ++ ++ opal_argv_free (allowed_ifaces); + mca_btl_uct_modex_send (); + + /* pass module array back to caller */ +diff --git a/opal/mca/btl/uct/btl_uct_rdma.c b/opal/mca/btl/uct/btl_uct_rdma.c +index 2d2d1c3f04b..9ee9530f260 100644 +--- a/opal/mca/btl/uct/btl_uct_rdma.c ++++ b/opal/mca/btl/uct/btl_uct_rdma.c +@@ -132,7 +132,7 @@ int mca_btl_uct_get (mca_btl_base_module_t *btl, mca_btl_base_endpoint_t *endpoi + + BTL_VERBOSE(("get issued. status = %d", ucs_status)); + +- uct_rkey_release (&rkey); ++ mca_btl_uct_rkey_release (uct_btl, &rkey); + + return OPAL_LIKELY(UCS_OK == ucs_status) ? OPAL_SUCCESS : OPAL_ERR_RESOURCE_BUSY; + } +@@ -237,7 +237,7 @@ int mca_btl_uct_put (mca_btl_base_module_t *btl, mca_btl_base_endpoint_t *endpoi + mca_btl_uct_uct_completion_release (comp); + } + +- uct_rkey_release (&rkey); ++ mca_btl_uct_rkey_release (uct_btl, &rkey); + + return OPAL_LIKELY(UCS_OK == ucs_status) ? OPAL_SUCCESS : OPAL_ERR_RESOURCE_BUSY; + } +diff --git a/opal/mca/btl/uct/btl_uct_rdma.h b/opal/mca/btl/uct/btl_uct_rdma.h +index e9b0d6b19dc..609fec91f52 100644 +--- a/opal/mca/btl/uct/btl_uct_rdma.h ++++ b/opal/mca/btl/uct/btl_uct_rdma.h +@@ -55,8 +55,22 @@ static inline int mca_btl_uct_get_rkey (mca_btl_uct_module_t *module, + return rc; + } + ++#if UCT_API > UCT_VERSION(1, 7) ++ ucs_status = uct_rkey_unpack (module->uct_component, (void *) remote_handle, rkey); ++#else + ucs_status = uct_rkey_unpack ((void *) remote_handle, rkey); ++#endif + return (UCS_OK == ucs_status) ? OPAL_SUCCESS : OPAL_ERROR; + } + ++static inline void mca_btl_uct_rkey_release (mca_btl_uct_module_t *uct_btl, uct_rkey_bundle_t *rkey) ++{ ++#if UCT_API > UCT_VERSION(1, 7) ++ uct_rkey_release (uct_btl->uct_component, rkey); ++#else ++ (void) uct_btl; ++ uct_rkey_release (rkey); ++#endif ++} ++ + #endif /* !defined(BTL_UCT_RDMA_H) */ +diff --git a/opal/mca/btl/uct/btl_uct_tl.c b/opal/mca/btl/uct/btl_uct_tl.c +index a711a41ce99..dcf00f23524 100644 +--- a/opal/mca/btl/uct/btl_uct_tl.c ++++ b/opal/mca/btl/uct/btl_uct_tl.c +@@ -516,7 +516,13 @@ static int mca_btl_uct_evaluate_tl (mca_btl_uct_module_t *module, mca_btl_uct_tl + * come up with a better estimate. */ + + /* UCT bandwidth is in bytes/sec, BTL is in MB/sec */ ++#if UCT_API > UCT_VERSION(1, 7) ++ module->super.btl_bandwidth = (uint32_t) ((MCA_BTL_UCT_TL_ATTR(tl, 0).bandwidth.dedicated + ++ MCA_BTL_UCT_TL_ATTR(tl, 0).bandwidth.shared / ++ (opal_process_info.num_local_peers + 1)) / 1048576.0); ++#else + module->super.btl_bandwidth = (uint32_t) (MCA_BTL_UCT_TL_ATTR(tl, 0).bandwidth / 1048576.0); ++#endif + /* TODO -- figure out how to translate UCT latency to us */ + module->super.btl_latency = 1; + } + +From 55e01220cd213ff2b24950becc49c764dd62de17 Mon Sep 17 00:00:00 2001 +From: Nathan Hjelm +Date: Tue, 5 Nov 2019 12:52:42 -0800 +Subject: [PATCH 2/3] btl/uct: fix compilation for UCX 1.7.0 + +Ref #7128 + +Signed-off-by: Nathan Hjelm +(cherry picked from commit a3026c016a6a8be379f62585b6ddc070175c8106) +--- + opal/mca/btl/uct/btl_uct.h | 3 ++- + opal/mca/btl/uct/btl_uct_component.c | 14 +++++++------- + opal/mca/btl/uct/btl_uct_rdma.h | 4 ++-- + opal/mca/btl/uct/btl_uct_tl.c | 2 +- + 4 files changed, 12 insertions(+), 11 deletions(-) + +diff --git a/opal/mca/btl/uct/btl_uct.h b/opal/mca/btl/uct/btl_uct.h +index 73640103c07..0e4ec9a9498 100644 +--- a/opal/mca/btl/uct/btl_uct.h ++++ b/opal/mca/btl/uct/btl_uct.h +@@ -12,6 +12,7 @@ + * All rights reserved. + * Copyright (c) 2015-2018 Los Alamos National Security, LLC. All rights + * reserved. ++ * Copyright (c) 2019 Google, LLC. All rights reserved. + * $COPYRIGHT$ + * + * Additional copyrights may follow +@@ -85,7 +86,7 @@ struct mca_btl_uct_module_t { + /** array containing the am_tl and rdma_tl */ + mca_btl_uct_tl_t *comm_tls[2]; + +-#if UCT_API > UCT_VERSION(1, 7) ++#if UCT_API >= UCT_VERSION(1, 7) + uct_component_h uct_component; + #endif + +diff --git a/opal/mca/btl/uct/btl_uct_component.c b/opal/mca/btl/uct/btl_uct_component.c +index 538872860f9..bff160736bc 100644 +--- a/opal/mca/btl/uct/btl_uct_component.c ++++ b/opal/mca/btl/uct/btl_uct_component.c +@@ -314,7 +314,7 @@ ucs_status_t mca_btl_uct_am_handler (void *arg, void *data, size_t length, unsig + return UCS_OK; + } + +-#if UCT_API > UCT_VERSION(1, 7) ++#if UCT_API >= UCT_VERSION(1, 7) + static int mca_btl_uct_component_process_uct_md (uct_component_h component, uct_md_resource_desc_t *md_desc, + char **allowed_ifaces) + #else +@@ -354,7 +354,7 @@ static int mca_btl_uct_component_process_uct_md (uct_md_resource_desc_t *md_desc + md = OBJ_NEW(mca_btl_uct_md_t); + + +-#if UCT_API > UCT_VERSION(1, 7) ++#if UCT_API >= UCT_VERSION(1, 7) + uct_md_config_read (component, NULL, NULL, &uct_config); + uct_md_open (component, md_desc->md_name, uct_config, &md->uct_md); + #else +@@ -386,7 +386,7 @@ static int mca_btl_uct_component_process_uct_md (uct_md_resource_desc_t *md_desc + return OPAL_ERR_NOT_AVAILABLE; + } + +-#if UCT_API > UCT_VERSION(1, 7) ++#if UCT_API >= UCT_VERSION(1, 7) + module->uct_component = component; + #endif + +@@ -415,7 +415,7 @@ static int mca_btl_uct_component_process_uct_md (uct_md_resource_desc_t *md_desc + return OPAL_SUCCESS; + } + +-#if UCT_API > UCT_VERSION(1, 7) ++#if UCT_API >= UCT_VERSION(1, 7) + static int mca_btl_uct_component_process_uct_component (uct_component_h component, char **allowed_ifaces) + { + uct_component_attr_t attr = {.field_mask = UCT_COMPONENT_ATTR_FIELD_NAME | +@@ -449,7 +449,7 @@ static int mca_btl_uct_component_process_uct_component (uct_component_h componen + + return OPAL_SUCCESS; + } +-#endif /* UCT_API > UCT_VERSION(1, 7) */ ++#endif /* UCT_API >= UCT_VERSION(1, 7) */ + + /* + * UCT component initialization: +@@ -485,7 +485,7 @@ static mca_btl_base_module_t **mca_btl_uct_component_init (int *num_btl_modules, + + mca_btl_uct_component.module_count = 0; + +-#if UCT_API > UCT_VERSION(1, 7) ++#if UCT_API >= UCT_VERSION(1, 7) + uct_component_h *components; + unsigned num_components; + +@@ -519,7 +519,7 @@ static mca_btl_base_module_t **mca_btl_uct_component_init (int *num_btl_modules, + + uct_release_md_resource_list (resources); + +-#endif /* UCT_API > UCT_VERSION(1, 7) */ ++#endif /* UCT_API >= UCT_VERSION(1, 7) */ + + opal_argv_free (allowed_ifaces); + mca_btl_uct_modex_send (); +diff --git a/opal/mca/btl/uct/btl_uct_rdma.h b/opal/mca/btl/uct/btl_uct_rdma.h +index 609fec91f52..ab790371afe 100644 +--- a/opal/mca/btl/uct/btl_uct_rdma.h ++++ b/opal/mca/btl/uct/btl_uct_rdma.h +@@ -55,7 +55,7 @@ static inline int mca_btl_uct_get_rkey (mca_btl_uct_module_t *module, + return rc; + } + +-#if UCT_API > UCT_VERSION(1, 7) ++#if UCT_API >= UCT_VERSION(1, 7) + ucs_status = uct_rkey_unpack (module->uct_component, (void *) remote_handle, rkey); + #else + ucs_status = uct_rkey_unpack ((void *) remote_handle, rkey); +@@ -65,7 +65,7 @@ static inline int mca_btl_uct_get_rkey (mca_btl_uct_module_t *module, + + static inline void mca_btl_uct_rkey_release (mca_btl_uct_module_t *uct_btl, uct_rkey_bundle_t *rkey) + { +-#if UCT_API > UCT_VERSION(1, 7) ++#if UCT_API >= UCT_VERSION(1, 7) + uct_rkey_release (uct_btl->uct_component, rkey); + #else + (void) uct_btl; +diff --git a/opal/mca/btl/uct/btl_uct_tl.c b/opal/mca/btl/uct/btl_uct_tl.c +index dcf00f23524..e69c769b41f 100644 +--- a/opal/mca/btl/uct/btl_uct_tl.c ++++ b/opal/mca/btl/uct/btl_uct_tl.c +@@ -516,7 +516,7 @@ static int mca_btl_uct_evaluate_tl (mca_btl_uct_module_t *module, mca_btl_uct_tl + * come up with a better estimate. */ + + /* UCT bandwidth is in bytes/sec, BTL is in MB/sec */ +-#if UCT_API > UCT_VERSION(1, 7) ++#if UCT_API >= UCT_VERSION(1, 7) + module->super.btl_bandwidth = (uint32_t) ((MCA_BTL_UCT_TL_ATTR(tl, 0).bandwidth.dedicated + + MCA_BTL_UCT_TL_ATTR(tl, 0).bandwidth.shared / + (opal_process_info.num_local_peers + 1)) / 1048576.0); diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch new file mode 100644 index 00000000000..be24bd287a3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch @@ -0,0 +1,346 @@ +If --with-pmi is given OpenMPI will always search for a PMIx in the same directory and the system first +before honoring a potential --with-pmix option. +This patch removes that. +See https://github.com/open-mpi/ompi/issues/9105 + +Author: Alexander Grund (TU Dresden) + +--- a/configure 2021-06-29 13:14:03.339401816 +0200 ++++ b/configure 2021-06-29 13:16:01.366946769 +0200 +@@ -13333,336 +13333,6 @@ + fi + fi + +- # check for pmix lib installed by slurm */ +- slurm_pmix_found=no +- +- +- +- +- # Is the private index set? If not, set it. +- if test "x$opal_scope_index" = "x"; then +- opal_scope_index=1 +- fi +- +- # First, check to see if any of these variables are already set. +- # This is a simple sanity check to ensure we're not already +- # overwriting pre-existing variables (that have a non-empty +- # value). It's not a perfect check, but at least it's something. +- for opal_var in opal_external_pmix_save_CPPFLAGS opal_external_pmix_save_LDFLAGS opal_external_pmix_save_LIBS; do +- opal_str="opal_str=\"\$$opal_var\"" +- eval $opal_str +- +- if test "x$opal_str" != "x"; then +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Found configure shell variable clash at line $LINENO!" >&5 +-$as_echo "$as_me: WARNING: Found configure shell variable clash at line $LINENO!" >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: OPAL_VAR_SCOPE_PUSH called on \"$opal_var\"," >&5 +-$as_echo "$as_me: WARNING: OPAL_VAR_SCOPE_PUSH called on \"$opal_var\"," >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: but it is already defined with value \"$opal_str\"" >&5 +-$as_echo "$as_me: WARNING: but it is already defined with value \"$opal_str\"" >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: This usually indicates an error in configure." >&5 +-$as_echo "$as_me: WARNING: This usually indicates an error in configure." >&2;} +- as_fn_error $? "Cannot continue" "$LINENO" 5 +- fi +- done +- +- # Ok, we passed the simple sanity check. Save all these names so +- # that we can unset them at the end of the scope. +- opal_str="opal_scope_$opal_scope_index=\"opal_external_pmix_save_CPPFLAGS opal_external_pmix_save_LDFLAGS opal_external_pmix_save_LIBS\"" +- eval $opal_str +- unset opal_str +- +- env | grep opal_scope +- opal_scope_index=`expr $opal_scope_index + 1` +- +- opal_external_pmix_happy=no +- +- # Make sure we have the headers and libs in the correct location +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for pmix.h in $check_pmi_install_dir" >&5 +-$as_echo_n "checking for pmix.h in $check_pmi_install_dir... " >&6; } +- files=`ls $check_pmi_install_dir/pmix.h 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_header_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for pmix.h in $check_pmi_install_dir/include" >&5 +-$as_echo_n "checking for pmix.h in $check_pmi_install_dir/include... " >&6; } +- files=`ls $check_pmi_install_dir/include/pmix.h 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_header_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- opal_external_pmix_header_happy=no +-fi +-fi +- +- if test "$opal_external_pmix_header_happy" = "yes"; then : +- if test -n "$check_pmi_lib_dir"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking libpmix.* in $check_pmi_lib_dir" >&5 +-$as_echo_n "checking libpmix.* in $check_pmi_lib_dir... " >&6; } +- files=`ls $check_pmi_lib_dir/libpmix.* 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- pmix_ext_install_libdir=$check_pmi_lib_dir +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking libpmix.* in $check_pmi_lib_dir/lib64" >&5 +-$as_echo_n "checking libpmix.* in $check_pmi_lib_dir/lib64... " >&6; } +- files=`ls $check_pmi_lib_dir/lib64/libpmix.* 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- pmix_ext_install_libdir=$check_pmi_lib_dir/lib64 +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking libpmix.* in $check_pmi_lib_dir/lib" >&5 +-$as_echo_n "checking libpmix.* in $check_pmi_lib_dir/lib... " >&6; } +- files=`ls $check_pmi_lib_dir/lib/libpmix.* 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- pmix_ext_install_libdir=$check_pmi_lib_dir/lib +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- as_fn_error $? "Cannot continue" "$LINENO" 5 +-fi +-fi +-fi +-else +- # check for presence of lib64 directory - if found, see if the +- # desired library is present and matches our build requirements +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking libpmix.* in $check_pmi_install_dir/lib64" >&5 +-$as_echo_n "checking libpmix.* in $check_pmi_install_dir/lib64... " >&6; } +- files=`ls $check_pmi_install_dir/lib64/libpmix.* 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- pmix_ext_install_libdir=$check_pmi_install_dir/lib64 +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking libpmix.* in $check_pmi_install_dir/lib" >&5 +-$as_echo_n "checking libpmix.* in $check_pmi_install_dir/lib... " >&6; } +- files=`ls $check_pmi_install_dir/lib/libpmix.* 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- pmix_ext_install_libdir=$check_pmi_install_dir/lib +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- as_fn_error $? "Cannot continue" "$LINENO" 5 +-fi +-fi +-fi +- +- # check the version +- opal_external_pmix_save_CPPFLAGS=$CPPFLAGS +- opal_external_pmix_save_LDFLAGS=$LDFLAGS +- opal_external_pmix_save_LIBS=$LIBS +- +- # if the pmix_version.h file does not exist, then +- # this must be from a pre-1.1.5 version OMPI does +- # NOT support anything older than v1.2.5 +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking PMIx version" >&5 +-$as_echo_n "checking PMIx version... " >&6; } +- CPPFLAGS="-I$check_pmi_install_dir/include $CPPFLAGS" +- if test "x`ls $check_pmi_install_dir/include/pmix_version.h 2> /dev/null`" = "x"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: version file not found - assuming v1.1.4" >&5 +-$as_echo "version file not found - assuming v1.1.4" >&6; } +- opal_external_pmix_version_found=1 +- opal_external_pmix_happy=no +- opal_external_pmix_version=internal +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: version file found" >&5 +-$as_echo "version file found" >&6; } +- opal_external_pmix_version_found=0 +-fi +- +- # if it does exist, then we need to parse it to find +- # the actual release series +- if test "$opal_external_pmix_version_found" = "0"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking version 4x" >&5 +-$as_echo_n "checking version 4x... " >&6; } +- cat confdefs.h - <<_ACEOF >conftest.$ac_ext +-/* end confdefs.h. */ +- +- #include +- #if (PMIX_VERSION_MAJOR < 4L) +- #error "not version 4 or above" +- #endif +- +-int +-main () +-{ +- +- ; +- return 0; +-} +-_ACEOF +-if ac_fn_c_try_cpp "$LINENO"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_version=4x +- opal_external_pmix_version_found=1 +- opal_external_pmix_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +-fi +-rm -f conftest.err conftest.i conftest.$ac_ext +-fi +- +- if test "$opal_external_pmix_version_found" = "0"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking version 3x or above" >&5 +-$as_echo_n "checking version 3x or above... " >&6; } +- cat confdefs.h - <<_ACEOF >conftest.$ac_ext +-/* end confdefs.h. */ +- +- #include +- #if (PMIX_VERSION_MAJOR != 3L) +- #error "not version 3" +- #endif +- +-int +-main () +-{ +- +- ; +- return 0; +-} +-_ACEOF +-if ac_fn_c_try_cpp "$LINENO"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_version=3x +- opal_external_pmix_version_found=1 +- opal_external_pmix_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +-fi +-rm -f conftest.err conftest.i conftest.$ac_ext +-fi +- +- if test "$opal_external_pmix_version_found" = "0"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking version 2x" >&5 +-$as_echo_n "checking version 2x... " >&6; } +- cat confdefs.h - <<_ACEOF >conftest.$ac_ext +-/* end confdefs.h. */ +- +- #include +- #if (PMIX_VERSION_MAJOR != 2L) +- #error "not version 2" +- #endif +- +-int +-main () +-{ +- +- ; +- return 0; +-} +-_ACEOF +-if ac_fn_c_try_cpp "$LINENO"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_version=2x +- opal_external_pmix_version_found=1 +- opal_external_pmix_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +-fi +-rm -f conftest.err conftest.i conftest.$ac_ext +-fi +- +- if test "$opal_external_pmix_version_found" = "0"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking version 1x" >&5 +-$as_echo_n "checking version 1x... " >&6; } +- cat confdefs.h - <<_ACEOF >conftest.$ac_ext +-/* end confdefs.h. */ +- +- #include +- #if (PMIX_VERSION_MAJOR != 1L && PMIX_VERSION_MINOR != 2L) +- #error "not version 1.2.x" +- #endif +- +-int +-main () +-{ +- +- ; +- return 0; +-} +-_ACEOF +-if ac_fn_c_try_cpp "$LINENO"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_version=1x +- opal_external_pmix_version_found=1 +- opal_external_have_pmix1=1 +- opal_external_pmix_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +-fi +-rm -f conftest.err conftest.i conftest.$ac_ext +-fi +- +- if test "x$opal_external_pmix_version" = "x"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: External PMIx support detected, but version" >&5 +-$as_echo "$as_me: WARNING: External PMIx support detected, but version" >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: information of the external lib could not" >&5 +-$as_echo "$as_me: WARNING: information of the external lib could not" >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: be detected" >&5 +-$as_echo "$as_me: WARNING: be detected" >&2;} +- opal_external_pmix_happy=no +-fi +- +- CPPFLAGS=$opal_external_pmix_save_CPPFLAGS +- LDFLAGS=$opal_external_pmix_save_LDFLAGS +- LIBS=$opal_external_pmix_save_LIBS +- +-fi +- if test "$opal_external_pmix_happy" = "yes"; then : +- opal_enable_pmix=yes +-else +- opal_enable_pmix=no +-fi +- +- +- # Unwind the index +- opal_scope_index=`expr $opal_scope_index - 1` +- opal_scope_test=`expr $opal_scope_index \> 0` +- if test "$opal_scope_test" = "0"; then +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: OPAL_VAR_SCOPE_POP popped too many OPAL configure scopes." >&5 +-$as_echo "$as_me: WARNING: OPAL_VAR_SCOPE_POP popped too many OPAL configure scopes." >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: This usually indicates an error in configure." >&5 +-$as_echo "$as_me: WARNING: This usually indicates an error in configure." >&2;} +- as_fn_error $? "Cannot continue" "$LINENO" 5 +- fi +- +- # Get the variable names from that index +- opal_str="opal_str=\"\$opal_scope_$opal_scope_index\"" +- eval $opal_str +- +- # Iterate over all the variables and unset them all +- for opal_var in $opal_str; do +- unset $opal_var +- done +- +- +- + # since support was explicitly requested, then we should error out + # if we didn't find the required support + { $as_echo "$as_me:${as_lineno-$LINENO}: checking can PMI support be built" >&5 diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb index bf4fb7c22ec..258fb6469ea 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb @@ -8,7 +8,17 @@ toolchain = {'name': 'GCC', 'version': '9.2.0-2.32'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['662805870e86a1471e59739b0c34c6f9004e0c7a22db068562d5388ec4421904'] +patches = [ + 'OpenMPI-4.0.1_add-support-for-ucx-1.7.patch', + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', +] +checksums = [ + '662805870e86a1471e59739b0c34c6f9004e0c7a22db068562d5388ec4421904', # openmpi-4.0.2.tar.gz + # OpenMPI-4.0.1_add-support-for-ucx-1.7.patch + '3c5ce8fe164869f309821a4528bbd8a4c087bc748dadf589850482bbccf8890c', + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb index e094a645860..e51943031bb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb @@ -8,7 +8,12 @@ toolchain = {'name': 'GCC', 'version': '9.3.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb index a8dc23189a4..9fcc5c0ce5a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb @@ -8,7 +8,12 @@ toolchain = {'name': 'gcccuda', 'version': '2020a'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb index 283308daf5e..85a80cef61d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb @@ -8,7 +8,12 @@ toolchain = {'name': 'iccifort', 'version': '2020.1.217'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb index 9775ccaefff..c19688551ab 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb @@ -8,7 +8,12 @@ toolchain = {'name': 'iccifortcuda', 'version': '2020a'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb index 15b78eb63ec..de69437e30c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -8,7 +8,12 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb index 128123c01bd..6f35c379b0b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb @@ -8,7 +8,12 @@ toolchain = {'name': 'GCC', 'version': '9.3.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb index b83f21c664b..245532a13ea 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -8,7 +8,12 @@ toolchain = {'name': 'gcccuda', 'version': '2020b'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb index b132e94d87d..6083f480cda 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -8,7 +8,12 @@ toolchain = {'name': 'iccifort', 'version': '2020.4.304'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb new file mode 100644 index 00000000000..98875b6d1cf --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb @@ -0,0 +1,37 @@ +name = 'OpenMPI' +version = '4.0.6' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '8f2d159d2d846979b1380e9552f56e4365f5ec71d54a05077ddb244719d70fc3', # openmpi-4.0.6.tar.gz + # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch + '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.4.1'), + ('libevent', '2.1.12'), + ('UCX', '1.10.0'), + ('libfabric', '1.12.1'), + ('PMIx', '3.2.3'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch new file mode 100644 index 00000000000..1472eae0dd1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch @@ -0,0 +1,351 @@ +If --with-pmi is given OpenMPI will always search for a PMIx in the same directory and the system first +before honoring a potential --with-pmix option. +This patch removes that. +See https://github.com/open-mpi/ompi/issues/9105 + +Author: Alexander Grund (TU Dresden) + +diff -ur a/configure b/configure +--- a/configure 2021-06-14 22:53:22.000000000 +0200 ++++ b/configure 2021-07-01 18:16:23.062505971 +0200 +@@ -13441,340 +13441,6 @@ + fi + fi + +- # check for pmix lib installed by slurm */ +- slurm_pmix_found=no +- +- +- +- +- # Is the private index set? If not, set it. +- if test "x$opal_scope_index" = "x"; then +- opal_scope_index=1 +- fi +- +- # First, check to see if any of these variables are already set. +- # This is a simple sanity check to ensure we're not already +- # overwriting pre-existing variables (that have a non-empty +- # value). It's not a perfect check, but at least it's something. +- for opal_var in opal_external_pmix_save_CPPFLAGS opal_external_pmix_save_LDFLAGS opal_external_pmix_save_LIBS; do +- opal_str="opal_str=\"\$$opal_var\"" +- eval $opal_str +- +- if test "x$opal_str" != "x"; then +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Found configure shell variable clash at line $LINENO!" >&5 +-$as_echo "$as_me: WARNING: Found configure shell variable clash at line $LINENO!" >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: OPAL_VAR_SCOPE_PUSH called on \"$opal_var\"," >&5 +-$as_echo "$as_me: WARNING: OPAL_VAR_SCOPE_PUSH called on \"$opal_var\"," >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: but it is already defined with value \"$opal_str\"" >&5 +-$as_echo "$as_me: WARNING: but it is already defined with value \"$opal_str\"" >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: This usually indicates an error in configure." >&5 +-$as_echo "$as_me: WARNING: This usually indicates an error in configure." >&2;} +- as_fn_error $? "Cannot continue" "$LINENO" 5 +- fi +- done +- +- # Ok, we passed the simple sanity check. Save all these names so +- # that we can unset them at the end of the scope. +- opal_str="opal_scope_$opal_scope_index=\"opal_external_pmix_save_CPPFLAGS opal_external_pmix_save_LDFLAGS opal_external_pmix_save_LIBS\"" +- eval $opal_str +- unset opal_str +- +- env | grep opal_scope +- opal_scope_index=`expr $opal_scope_index + 1` +- +- opal_external_pmix_happy=no +- +- # Make sure we have the headers and libs in the correct location +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for pmix.h in $check_pmi_install_dir" >&5 +-$as_echo_n "checking for pmix.h in $check_pmi_install_dir... " >&6; } +- files=`ls $check_pmi_install_dir/pmix.h 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_header_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for pmix.h in $check_pmi_install_dir/include" >&5 +-$as_echo_n "checking for pmix.h in $check_pmi_install_dir/include... " >&6; } +- files=`ls $check_pmi_install_dir/include/pmix.h 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_header_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- opal_external_pmix_header_happy=no +-fi +-fi +- +- if test "$opal_external_pmix_header_happy" = "yes"; then : +- if test -n "$check_pmi_lib_dir"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking libpmix.* in $check_pmi_lib_dir" >&5 +-$as_echo_n "checking libpmix.* in $check_pmi_lib_dir... " >&6; } +- files=`ls $check_pmi_lib_dir/libpmix.* 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- pmix_ext_install_libdir=$check_pmi_lib_dir +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking libpmix.* in $check_pmi_lib_dir/lib64" >&5 +-$as_echo_n "checking libpmix.* in $check_pmi_lib_dir/lib64... " >&6; } +- files=`ls $check_pmi_lib_dir/lib64/libpmix.* 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- pmix_ext_install_libdir=$check_pmi_lib_dir/lib64 +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking libpmix.* in $check_pmi_lib_dir/lib" >&5 +-$as_echo_n "checking libpmix.* in $check_pmi_lib_dir/lib... " >&6; } +- files=`ls $check_pmi_lib_dir/lib/libpmix.* 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- pmix_ext_install_libdir=$check_pmi_lib_dir/lib +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- as_fn_error $? "Cannot continue" "$LINENO" 5 +-fi +-fi +-fi +-else +- # check for presence of lib64 directory - if found, see if the +- # desired library is present and matches our build requirements +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking libpmix.* in $check_pmi_install_dir/lib64" >&5 +-$as_echo_n "checking libpmix.* in $check_pmi_install_dir/lib64... " >&6; } +- files=`ls $check_pmi_install_dir/lib64/libpmix.* 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- pmix_ext_install_libdir=$check_pmi_install_dir/lib64 +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking libpmix.* in $check_pmi_install_dir/lib" >&5 +-$as_echo_n "checking libpmix.* in $check_pmi_install_dir/lib... " >&6; } +- files=`ls $check_pmi_install_dir/lib/libpmix.* 2> /dev/null | wc -l` +- if test "$files" -gt 0; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- pmix_ext_install_libdir=$check_pmi_install_dir/lib +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +- as_fn_error $? "Cannot continue" "$LINENO" 5 +-fi +-fi +-fi +- +- # check the version +- opal_external_pmix_save_CPPFLAGS=$CPPFLAGS +- opal_external_pmix_save_LDFLAGS=$LDFLAGS +- opal_external_pmix_save_LIBS=$LIBS +- +- # if the pmix_version.h file does not exist, then +- # this must be from a pre-1.1.5 version OMPI does +- # NOT support anything older than v1.2.5 +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking PMIx version" >&5 +-$as_echo_n "checking PMIx version... " >&6; } +- CPPFLAGS="-I$check_pmi_install_dir/include $CPPFLAGS" +- if test "x`ls $check_pmi_install_dir/include/pmix_version.h 2> /dev/null`" = "x"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: version file not found - assuming v1.1.4" >&5 +-$as_echo "version file not found - assuming v1.1.4" >&6; } +- opal_external_pmix_version_found=1 +- opal_external_pmix_happy=no +- opal_external_pmix_version=internal +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: version file found" >&5 +-$as_echo "version file found" >&6; } +- opal_external_pmix_version_found=0 +-fi +- +- # if it does exist, then we need to parse it to find +- # the actual release series +- if test "$opal_external_pmix_version_found" = "0"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking version 4x" >&5 +-$as_echo_n "checking version 4x... " >&6; } +- cat confdefs.h - <<_ACEOF >conftest.$ac_ext +-/* end confdefs.h. */ +- +- #include +- #if (PMIX_VERSION_MAJOR < 4L) +- #error "not version 4 or above" +- #endif +- +-int +-main () +-{ +- +- ; +- return 0; +-} +-_ACEOF +-if ac_fn_c_try_cpp "$LINENO"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_version=4x +- opal_external_pmix_version_major=4 +- opal_external_pmix_version_found=1 +- opal_external_pmix_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +-fi +-rm -f conftest.err conftest.i conftest.$ac_ext +-fi +- +- if test "$opal_external_pmix_version_found" = "0"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking version 3x or above" >&5 +-$as_echo_n "checking version 3x or above... " >&6; } +- cat confdefs.h - <<_ACEOF >conftest.$ac_ext +-/* end confdefs.h. */ +- +- #include +- #if (PMIX_VERSION_MAJOR != 3L) +- #error "not version 3" +- #endif +- +-int +-main () +-{ +- +- ; +- return 0; +-} +-_ACEOF +-if ac_fn_c_try_cpp "$LINENO"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_version=3x +- opal_external_pmix_version_major=3 +- opal_external_pmix_version_found=1 +- opal_external_pmix_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +-fi +-rm -f conftest.err conftest.i conftest.$ac_ext +-fi +- +- if test "$opal_external_pmix_version_found" = "0"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking version 2x" >&5 +-$as_echo_n "checking version 2x... " >&6; } +- cat confdefs.h - <<_ACEOF >conftest.$ac_ext +-/* end confdefs.h. */ +- +- #include +- #if (PMIX_VERSION_MAJOR != 2L) +- #error "not version 2" +- #endif +- +-int +-main () +-{ +- +- ; +- return 0; +-} +-_ACEOF +-if ac_fn_c_try_cpp "$LINENO"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_version=2x +- opal_external_pmix_version_major=2 +- opal_external_pmix_version_found=1 +- opal_external_pmix_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +-fi +-rm -f conftest.err conftest.i conftest.$ac_ext +-fi +- +- if test "$opal_external_pmix_version_found" = "0"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking version 1x" >&5 +-$as_echo_n "checking version 1x... " >&6; } +- cat confdefs.h - <<_ACEOF >conftest.$ac_ext +-/* end confdefs.h. */ +- +- #include +- #if (PMIX_VERSION_MAJOR != 1L && PMIX_VERSION_MINOR != 2L) +- #error "not version 1.2.x" +- #endif +- +-int +-main () +-{ +- +- ; +- return 0; +-} +-_ACEOF +-if ac_fn_c_try_cpp "$LINENO"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5 +-$as_echo "found" >&6; } +- opal_external_pmix_version=1x +- opal_external_pmix_version_major=1 +- opal_external_pmix_version_found=1 +- opal_external_have_pmix1=1 +- opal_external_pmix_happy=yes +-else +- { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +-$as_echo "not found" >&6; } +-fi +-rm -f conftest.err conftest.i conftest.$ac_ext +-fi +- +- if test "x$opal_external_pmix_version" = "x"; then : +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: External PMIx support detected, but version" >&5 +-$as_echo "$as_me: WARNING: External PMIx support detected, but version" >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: information of the external lib could not" >&5 +-$as_echo "$as_me: WARNING: information of the external lib could not" >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: be detected" >&5 +-$as_echo "$as_me: WARNING: be detected" >&2;} +- opal_external_pmix_happy=no +-fi +- +- CPPFLAGS=$opal_external_pmix_save_CPPFLAGS +- LDFLAGS=$opal_external_pmix_save_LDFLAGS +- LIBS=$opal_external_pmix_save_LIBS +- +-fi +- if test "$opal_external_pmix_happy" = "yes"; then : +- opal_enable_pmix=yes +-else +- opal_enable_pmix=no +-fi +- +- +- # Unwind the index +- opal_scope_index=`expr $opal_scope_index - 1` +- opal_scope_test=`expr $opal_scope_index \> 0` +- if test "$opal_scope_test" = "0"; then +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: OPAL_VAR_SCOPE_POP popped too many OPAL configure scopes." >&5 +-$as_echo "$as_me: WARNING: OPAL_VAR_SCOPE_POP popped too many OPAL configure scopes." >&2;} +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: This usually indicates an error in configure." >&5 +-$as_echo "$as_me: WARNING: This usually indicates an error in configure." >&2;} +- as_fn_error $? "Cannot continue" "$LINENO" 5 +- fi +- +- # Get the variable names from that index +- opal_str="opal_str=\"\$opal_scope_$opal_scope_index\"" +- eval $opal_str +- +- # Iterate over all the variables and unset them all +- for opal_var in $opal_str; do +- unset $opal_var +- done +- +- +- + # since support was explicitly requested, then we should error out + # if we didn't find the required support + { $as_echo "$as_me:${as_lineno-$LINENO}: checking can PMI support be built" >&5 diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index c80283a7154..fda533d6ab2 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -8,11 +8,16 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch'] +patches = [ + 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch' +] checksums = [ '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a', # openmpi-4.1.0.tar.gz # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb index bee50ce527f..2728bb55635 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb @@ -11,11 +11,16 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch'] +patches = [ + 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', + 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' +] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', + # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch + '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..a78f76fc48b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + 'OpenPGM-5.2.122-pkgconfig_includes.patch', + 'OpenPGM-5.2.122-python3-compliant.patch' +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenPIV/OpenPIV-0.21.8-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenPIV/OpenPIV-0.21.8-intel-2019b-Python-3.7.4.eb index c1b23a80831..a062c1ba00f 100644 --- a/easybuild/easyconfigs/o/OpenPIV/OpenPIV-0.21.8-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenPIV/OpenPIV-0.21.8-intel-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('python-utils', '2.4.0', { 'checksums': ['f21fc09ff58ea5ebd1fd2e8ef7f63e39d456336900f26bdc9334a03a3f7d8089'], diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb index d4a12b797dc..a49a797ca06 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb @@ -2,6 +2,7 @@ easyblock = 'EB_OpenSSL_wrapper' name = 'OpenSSL' version = '1.1' +minimum_openssl_version = '1.1.1' homepage = 'https://www.openssl.org/' description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, @@ -14,12 +15,14 @@ toolchainopts = {'pic': True} osdependencies = ['perl'] # This easyconfig will wrap the OpenSSL installation in the host system. -# If the system provides the required binary, header files, and libraries for this -# version of OpenSSL, the installation directory of this module will be populated with -# symlinks to the system files. If the host system does not have this version -# of OpenSSL (or with the option wrap_system_openssl = False), EasyBuild will -# fall back to the following component list, which will be build and installed as -# usual. +# If the system provides the required binary, header files, and libraries for +# this version of OpenSSL, the installation directory of this module will be +# populated with symlinks to the system files. The minimum required version of +# OpenSSL can be finely controled with 'minimum_openssl_version' (defaults to +# easyconfig version). +# If the host system does not have this version of OpenSSL (or with the option +# wrap_system_openssl = False), EasyBuild will fall back to the following +# component list, which will be build and installed as usual. components = [ (name, '1.1.1k', { diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..2811d67607e --- /dev/null +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('h5py', '2.10.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + 'modulename': 'progressbar', + }), + (name, version, { + 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], + }), +] + +sanity_check_paths = { + 'files': ['bin/compress_fast5', 'bin/fast5_subset', 'bin/multi_to_single_fast5', 'bin/single_to_multi_fast5'], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb new file mode 100644 index 00000000000..a8d05c6400f --- /dev/null +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '3.3.0' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + 'modulename': 'progressbar', + }), + (name, version, { + 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], + }), +] + +sanity_check_paths = { + 'files': ['bin/compress_fast5', 'bin/fast5_subset', 'bin/multi_to_single_fast5', 'bin/single_to_multi_fast5'], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..b4a6b8321bc --- /dev/null +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '3.3.0' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + 'modulename': 'progressbar', + }), + (name, version, { + 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], + }), +] + +sanity_check_paths = { + 'files': ['bin/compress_fast5', 'bin/fast5_subset', 'bin/multi_to_single_fast5', 'bin/single_to_multi_fast5'], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/openkim-models/openkim-models-20210128-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210128-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..f1ab75253ab --- /dev/null +++ b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210128-GCCcore-10.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMake' + +name = 'openkim-models' +version = '20210128' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +OpenKIM is an API and a collection of interatomic models (potentials) for +atomistic simulations. It is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild installs the models. The API itself is in the kim-api +package. + """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('kim-api', '2.2.1'), +] + +source_urls = ['https://s3.openkim.org/archives/collection/'] +sources = ['openkim-models-2021-01-28.txz'] +checksums = ['8824adee02ae4583bd378cc81140fbb49515c5965708ee98d856d122d48dd95f'] + +separate_build_dir = True +abs_path_compilers = True # Otherwise some KIM-API magic breaks cmake. +configopts = '-DKIM_API_INSTALL_COLLECTION=SYSTEM ' +configopts += '-DKIM_API_PORTABLE_MODEL_INSTALL_PREFIX=%(installdir)s/lib/kim-api/portable-models ' +configopts += '-DKIM_API_SIMULATOR_MODEL_INSTALL_PREFIX=%(installdir)s/lib/kim-api/simulator-models ' +configopts += '-DKIM_API_MODEL_DRIVER_INSTALL_PREFIX=%(installdir)s/lib/kim-api/model-drivers ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/kim-api/model-drivers', 'lib/kim-api/portable-models', 'lib/kim-api/simulator-models'] +} + +modextravars = { + 'KIM_API_MODEL_DRIVERS_DIR': '%(installdir)s/lib/kim-api/model-drivers', + 'KIM_API_PORTABLE_MODELS_DIR': '%(installdir)s/lib/kim-api/portable-models', + 'KIM_API_SIMULATOR_MODELS_DIR': '%(installdir)s/lib/kim-api/simulator-models', +} + + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-2.6.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-2.6.2-GCCcore-8.2.0.eb index 982a8b75714..26616ea3d81 100644 --- a/easybuild/easyconfigs/o/openpyxl/openpyxl-2.6.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-2.6.2-GCCcore-8.2.0.eb @@ -21,15 +21,12 @@ use_pip = True exts_list = [ ('et_xmlfile', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/e/et_xmlfile'], 'checksums': ['614d9722d572f6246302c4491846d2c393c199cfa4edc9af593437691683335b'], }), ('jdcal', '1.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/e/j/jdcal'], 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/o/openpyxl'], 'checksums': ['1d2af392cef8c8227bd2ac3ebe3a28b25aba74fd4fa473ce106065f0b73bfe2e'], }), ] diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb index 60da7c2c8d1..484d0c4ee7a 100644 --- a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb @@ -22,15 +22,12 @@ sanity_pip_check = True exts_list = [ ('et_xmlfile', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/e/et_xmlfile'], 'checksums': ['614d9722d572f6246302c4491846d2c393c199cfa4edc9af593437691683335b'], }), ('jdcal', '1.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/e/j/jdcal'], 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/o/openpyxl'], 'checksums': ['547a9fc6aafcf44abe358b89ed4438d077e9d92e4f182c87e2dc294186dc4b64'], }), ] diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..fdcf96e3727 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0.1-GCCcore-10.3.0.eb @@ -0,0 +1,47 @@ +## +# Author: Robert Mijakovic +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '6.0.0.1' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3cd7ed50c65b0d21d66e46d0ba34cd171178af4bbf9d94e693915c1aca1e287f'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +start_dir = 'src' + +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb index 67c60ea6119..3b57bb0e828 100644 --- a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb @@ -29,7 +29,7 @@ exts_defaultclass = 'PythonPackage' exts_list = [ ('pysnptools', '0.3.13', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pysnptools'], + 'source_urls': [PYPI_SOURCE], 'checksums': ['158f05cb72687772c61bd306c166a7bfc40f158beb1d473e04711daa7bd1d152'], 'use_pip': True, }), diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..4e8554240a6 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +checksums = ['1037628d854edfeded3d847150d3e8fbd3774e8146407ce32f5021c80f6299be'] + +builddependencies = [ + ('binutils', '2.35'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PHLAT/PHLAT-1.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PHLAT/PHLAT-1.1-foss-2018b-Python-2.7.15.eb index a058916b4d3..9118d9736cb 100644 --- a/easybuild/easyconfigs/p/PHLAT/PHLAT-1.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PHLAT/PHLAT-1.1-foss-2018b-Python-2.7.15.eb @@ -44,7 +44,6 @@ exts_default_options = { exts_list = [ # version 0.8.3 is recommended: the developers report a compatibility issue with 0.9+ ('pysam', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pysam'], 'checksums': ['343e91a1882278455ef9a5f3c9fc4921c37964341785bf22432381d18e6d115e'], }), ] diff --git a/easybuild/easyconfigs/p/PIMS/PIMS-0.4.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PIMS/PIMS-0.4.1-intel-2017b-Python-2.7.14.eb index 0d3361efe01..0a087a579ee 100755 --- a/easybuild/easyconfigs/p/PIMS/PIMS-0.4.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PIMS/PIMS-0.4.1-intel-2017b-Python-2.7.14.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'PIMS' version = '0.4.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://soft-matter.github.io/pims' +homepage = 'https://soft-matter.github.io/pims' description = "PIMS is a lazy-loading interface to sequential data with numpy-like slicing." toolchain = {'name': 'intel', 'version': '2017b'} @@ -15,30 +15,21 @@ dependencies = [ ('scikit-image', '0.13.1', versionsuffix), ('FFmpeg', '3.4.1'), ] - -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ ('slicerator', '0.9.8', { - 'source_urls': ['https://pypi.python.org/packages/source/s/slicerator'], 'checksums': ['b91dd76a415fd8872185cbd6fbf1922fe174359053d4694983fc719e4a0f5667'], }), ('imageio', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imageio'], 'checksums': ['6dd95300d3d64713a2649334390fd9cf96712013172afd6e73b008e00934a73f'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('tqdm', '4.19.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tqdm'], 'checksums': ['a6fd7479f3fb0ba653290e61d97917b2621c51cc8e31dc19963b5002904abaa1'], }), ('moviepy', '0.2.3.2', { 'patches': ['moviepy-0.2.3.2_avoid-hardcoding.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/m/moviepy'], 'checksums': [ 'c733967656fa4be4c37ec48af72b63ab2991455aa862321437a013705797c4ab', # moviepy-0.2.3.2.tar.gz # moviepy-0.2.3.2_avoid-hardcoding.patch @@ -46,25 +37,15 @@ exts_list = [ ], }), ('av', '0.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/av'], 'checksums': ['bb6a6abcae38087efe6eb4f8b29dcfbbb7b161b3177babb89fa754d9053e901c'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/P/PIMS'], 'checksums': ['6a53a155e900b44e71127a1e1fccbfbaed7eec3c2b52497c40c23a05f334c9dd'], }), ('pims_nd2', '1.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pims_nd2'], 'checksums': ['bc426802087b5a34c7ec020ca62c8bc6e01f635433eec40bdc50c33533f17b85'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..1f356250624 --- /dev/null +++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'PLY' +version = '3.11' +versionsuffix = "-Python-%(pyver)s" + +homepage = "https://www.dabeaz.com/ply/" +description = """PLY is yet another implementation of lex and yacc for Python.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [('Python', '3.7.4')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/POT/POT-0.5.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/POT/POT-0.5.1-intel-2018b-Python-3.6.6.eb index 8fa9aca152f..125b353a752 100644 --- a/easybuild/easyconfigs/p/POT/POT-0.5.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/POT/POT-0.5.1-intel-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ description = """POT (Python Optimal Transport) is a Python library provide seve toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3f8584b153e9850a83267b1b3f88e43ae0e5f68ae57ee79da9390bc19a93f836'] @@ -22,11 +21,6 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - options = {'modulename': 'ot'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-8.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-8.0.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..9b222a4f22e --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-8.0.1-GCCcore-10.3.0.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '8.0.1' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e0463a8068898785ca75dd49a261d3d28b07d0a88f3b657e8e0089e16a0375fa'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.36.1'), +] + +dependencies = [ + ('SQLite', '3.35.4'), + ('LibTIFF', '4.2.0'), + ('cURL', '7.76.0'), +] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb index 405769bd638..f2c00964235 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb @@ -4,7 +4,7 @@ name = 'PSI4' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.psicode.org/' +homepage = 'https://www.psicode.org/' description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel.""" diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb new file mode 100644 index 00000000000..34640f7529c --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb new file mode 100644 index 00000000000..df8ca360b55 --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.48.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.48.5-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b3485ec6566 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.48.5-GCCcore-10.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.48.5' + +homepage = 'https://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['501e74496173c02dcd024ded7fbb3f09efd37e2a488e248aa40799424dbb3b2a'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('GObject-Introspection', '1.68.0'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210518'), + ('GLib', '2.68.2'), + ('cairo', '1.16.0'), + ('HarfBuzz', '2.8.1'), + ('FriBidi', '1.0.10'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb new file mode 100644 index 00000000000..f74f7c6ef0d --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.18.4')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParmEd/ParmEd-3.2.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/ParmEd/ParmEd-3.2.0-intel-2019b-Python-3.7.4.eb index 8758cd51a01..b07771c557d 100644 --- a/easybuild/easyconfigs/p/ParmEd/ParmEd-3.2.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/ParmEd/ParmEd-3.2.0-intel-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """ParmEd is a general tool for aiding in investigations of biomol toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0c178994af736b16df3c8eaa9c54a0ac98425129c8f0228563acc094e7c6f40f'] diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb new file mode 100644 index 00000000000..865360a39d3 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb @@ -0,0 +1,26 @@ +name = 'Perl' +version = '5.30.2' +versionsuffix = '-minimal' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +This is a minimal build without any modules. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['66db7df8a91979eb576fac91743644da878244cf8ee152f02cd6f5cd7a731689'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb new file mode 100644 index 00000000000..882c2de9022 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb @@ -0,0 +1,26 @@ +name = 'Perl' +version = '5.32.0' +versionsuffix = '-minimal' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +This is a minimal build without any modules. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 76d0b56cf8b..515872cd4ae 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -1761,10 +1761,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], }), - ('IO::Compress::Bzip2', '2.096', { + ('IO::Compress::Bzip2', '2.093', { 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], - 'checksums': ['9d219fd5df4b490b5d2f847921e3cb1c3392758fa0bae9b05a8992b3620ba572'], + 'checksums': ['5f8f5d06913f16c16759cc4e06749692208b8947910ffedd2c00a74ed0d60ba2'], }), ('JSON::XS', '4.03', { 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb new file mode 100644 index 00000000000..123f7022a08 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb @@ -0,0 +1,26 @@ +name = 'Perl' +version = '5.32.1' +versionsuffix = '-minimal' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +This is a minimal build without any modules. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['03b693901cd8ae807231b1787798cf1f2e0b8a56218d07b7da44f784a7caeb2c'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb index 3ca90e1c265..66b41381b24 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '3.2.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_freetype_ver = '2.6.3' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11-freetype-2.6.3.eb index 8a6c2159860..2c27d15fd3d 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '3.2.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_freetype_ver = '2.6.3' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb index 085a2ad2893..5300e0785be 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '3.2.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-foss-2016b-Python-3.5.2.eb index ae5f4b8993f..b88a5582948 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-foss-2016b-Python-3.5.2.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '3.4.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0ee9975c05602e755ff5000232e0335ba30d507f6261922a658ee11b1cec36d1'] @@ -26,9 +25,4 @@ dependencies = [ options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-2.7.12.eb index 4667d2c7a63..855a1ace0bb 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-2.7.12.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '3.4.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2-freetype-2.6.5.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2-freetype-2.6.5.eb index 2681aedaedd..038a88fe1d2 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2-freetype-2.6.5.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2-freetype-2.6.5.eb @@ -3,13 +3,12 @@ easyblock = 'PythonPackage' name = 'Pillow' version = '3.4.2' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] local_freetype_ver = '2.6.5' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2.eb index a95d247bb56..7787dadb5a8 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '3.4.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb index f4cf66d2ef6..f01b7255b51 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '4.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb index 7e73af7e4a9..af7d05f60cc 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '4.1.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.2.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.2.1-intel-2017a-Python-3.6.1.eb index 0b05e830a73..8c93178b94d 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-4.2.1-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.2.1-intel-2017a-Python-3.6.1.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '4.2.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c724f65870e545316f9e82e4c6d608ab5aa9dd82d5185e5b2e72119378740073'] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-foss-2017b-Python-3.6.3.eb index 0aee4b354d4..e96ed1920b1 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-foss-2017b-Python-3.6.3.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '4.3.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a97c715d44efd5b4aa8d739b8fad88b93ed79f1b33fc2822d5802043f3b1b527'] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-intel-2017a-Python-2.7.13.eb index 9da668b52e3..a02cbcd2f55 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-intel-2017a-Python-2.7.13.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '4.3.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a97c715d44efd5b4aa8d739b8fad88b93ed79f1b33fc2822d5802043f3b1b527'] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-intel-2017b-Python-2.7.14.eb index 493136f03d5..31740a6b54c 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.3.0-intel-2017b-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '4.3.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a97c715d44efd5b4aa8d739b8fad88b93ed79f1b33fc2822d5802043f3b1b527'] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb index 3aeb1eb1247..141061b70ab 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '5.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['12f29d6c23424f704c66b5b68c02fe0b571504459605cfe36ab8158359b0e1bb'] @@ -28,9 +27,4 @@ use_pip = True options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb index 344c5ec4acd..7f514d1ca72 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '5.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['12f29d6c23424f704c66b5b68c02fe0b571504459605cfe36ab8158359b0e1bb'] @@ -28,9 +27,4 @@ use_pip = True options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2018a-Python-3.6.4.eb index 94fd5fba8cb..07edb7270d9 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2018a-Python-3.6.4.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '5.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['12f29d6c23424f704c66b5b68c02fe0b571504459605cfe36ab8158359b0e1bb'] @@ -25,9 +24,4 @@ dependencies = [ options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2017b-Python-2.7.14.eb index 5234e5a0ba2..00bd15a0d6d 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2017b-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '5.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['12f29d6c23424f704c66b5b68c02fe0b571504459605cfe36ab8158359b0e1bb'] @@ -25,9 +24,4 @@ dependencies = [ options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2017b-Python-3.6.3.eb index 48128a92517..7c27558699b 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2017b-Python-3.6.3.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '5.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['12f29d6c23424f704c66b5b68c02fe0b571504459605cfe36ab8158359b0e1bb'] @@ -25,9 +24,4 @@ dependencies = [ options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2018a-Python-2.7.14.eb index 494b389bd5a..f70a139e43c 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2018a-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '5.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['12f29d6c23424f704c66b5b68c02fe0b571504459605cfe36ab8158359b0e1bb'] @@ -25,9 +24,4 @@ dependencies = [ options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2018a-Python-3.6.4.eb index 3c42ad1e44d..cc1563ed105 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2018a-Python-3.6.4.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '5.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['12f29d6c23424f704c66b5b68c02fe0b571504459605cfe36ab8158359b0e1bb'] @@ -25,9 +24,4 @@ dependencies = [ options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2018b-Python-2.7.15.eb index b48c38b0c50..bdf64498773 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2018b-Python-2.7.15.eb @@ -10,7 +10,6 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2018b-Python-3.6.6.eb index 95581efaab0..7b8e18ea4bf 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2018b-Python-3.6.6.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '5.3.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] @@ -28,9 +27,4 @@ use_pip = True options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-fosscuda-2018b-Python-3.6.6.eb index 5eb352d99d1..11844dec9a9 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-fosscuda-2018b-Python-3.6.6.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '5.3.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] @@ -28,9 +27,4 @@ use_pip = True options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2018b-Python-3.6.6.eb index 575c84290d5..688e8b62b4c 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2018b-Python-3.6.6.eb @@ -4,13 +4,12 @@ name = 'Pillow' version = '5.3.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] @@ -28,9 +27,4 @@ use_pip = True options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb index 243c594905c..02e02a6573a 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb @@ -3,13 +3,12 @@ easyblock = 'PythonPackage' name = 'Pillow' version = '6.0.0' -homepage = 'http://pillow.readthedocs.org/' +homepage = 'https://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['809c0a2ce9032cbcd7b5313f71af4bdc5c8c771cb86eb7559afd954cab82ebb5'] @@ -30,9 +29,4 @@ use_pip = True options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb index 3ae7feddea1..13dee61b577 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb @@ -9,7 +9,6 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['bf4e972a88f8841d8fdc6db1a75e0f8d763e66e3754b03006cbc3854d89f1cb1'] @@ -30,9 +29,4 @@ use_pip = True options = {'modulename': 'PIL'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..198aa646f08 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '8.2.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a787ab10d7bb5494e5f76536ac460741788f1fbce851068d73a87ca7c35fc3e1'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.2.0'), + ('freetype', '2.10.4') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pingouin/Pingouin-0.3.8-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/Pingouin/Pingouin-0.3.8-foss-2019b-Python-3.7.4.eb index 391315203bc..3932f6a7c24 100644 --- a/easybuild/easyconfigs/p/Pingouin/Pingouin-0.3.8-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/Pingouin/Pingouin-0.3.8-foss-2019b-Python-3.7.4.eb @@ -21,12 +21,8 @@ dependencies = [ ('xarray', '0.15.1', versionsuffix), ] -sanity_pip_check = True use_pip = True - -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} +sanity_pip_check = True exts_list = [ ('littleutils', '0.2.2', { diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.14-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/Pint/Pint-0.14-GCCcore-8.3.0-Python-3.7.4.eb index 75a70ab4798..4ea9e03d2e8 100644 --- a/easybuild/easyconfigs/p/Pint/Pint-0.14-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/Pint/Pint-0.14-GCCcore-8.3.0-Python-3.7.4.eb @@ -12,7 +12,6 @@ conversions from and to different units.""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9aa450ebb9d722ed03fa9a450104cfd16c479b49f862d547c6f77320de597f72'] diff --git a/easybuild/easyconfigs/p/PlasmaPy/PlasmaPy-0.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PlasmaPy/PlasmaPy-0.3.1-foss-2020a-Python-3.8.2.eb index da10ab98a5f..61f915312bf 100644 --- a/easybuild/easyconfigs/p/PlasmaPy/PlasmaPy-0.3.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PlasmaPy/PlasmaPy-0.3.1-foss-2020a-Python-3.8.2.eb @@ -25,23 +25,18 @@ sanity_pip_check = True exts_list = [ ('colorama', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], }), ('uncertainties', '3.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/u/uncertainties/'], 'checksums': ['ba07c17a8a78cb58a47cd373079c7ea459f8b26cd474e29163b6ba0d72856a1e'], }), ('asteval', '0.9.18', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asteval/'], 'checksums': ['5d64e18b8a72c2c7ae8f9b70d1f80b68bbcaa98c1c0d7047c35489d03209bc86'], }), ('lmfit', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lmfit/'], 'checksums': ['d249eb756899360f4d2a544c9458f47fc8f765ac22c09e099530585fd64e286e'], }), ('plasmapy', version, { - 'source_urls': ['https://pypi.python.org/packages/source/P/plasmapy/'], 'checksums': ['d2af2dd4de77797c5d26e2ae2ca894619f18c117f61aba5ffcb8e3eaff319fed'], }), ] diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompi-2019b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompi-2019b.eb new file mode 100644 index 00000000000..b8b59e7c6e4 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompi-2019b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = "1.12.1" + +homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompi', 'version': '2019b'} + +source_urls = ['https://parallel-netcdf.github.io/Release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56f5afaa0ddc256791c405719b6436a83b92dcd5be37fe860dea103aee8250a2'] + +builddependencies = [ + ('Autotools', '20180311'), + ('Perl', '5.30.0'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompi-2020a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompi-2020a.eb index 2c6249dfbfb..1e8e0989213 100644 --- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompi-2020a.eb +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompi-2020a.eb @@ -14,6 +14,7 @@ checksums = ['56f5afaa0ddc256791c405719b6436a83b92dcd5be37fe860dea103aee8250a2'] builddependencies = [ ('Autotools', '20180311'), + ('Perl', '5.30.2'), ] preconfigopts = "autoreconf -f -i && " diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompic-2019b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompic-2019b.eb new file mode 100644 index 00000000000..2d23016617e --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompic-2019b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = "1.12.1" + +homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompic', 'version': '2019b'} + +source_urls = ['https://parallel-netcdf.github.io/Release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56f5afaa0ddc256791c405719b6436a83b92dcd5be37fe860dea103aee8250a2'] + +builddependencies = [ + ('Autotools', '20180311'), + ('Perl', '5.30.0'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompic-2020a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompic-2020a.eb index e1444b0dc7f..a57028784ce 100644 --- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompic-2020a.eb +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-gompic-2020a.eb @@ -14,6 +14,7 @@ checksums = ['56f5afaa0ddc256791c405719b6436a83b92dcd5be37fe860dea103aee8250a2'] builddependencies = [ ('Autotools', '20180311'), + ('Perl', '5.30.2'), ] preconfigopts = "autoreconf -f -i && " diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-iimpi-2020a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-iimpi-2020a.eb index 83f2e4c9279..21567908664 100644 --- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-iimpi-2020a.eb +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.1-iimpi-2020a.eb @@ -14,6 +14,7 @@ checksums = ['56f5afaa0ddc256791c405719b6436a83b92dcd5be37fe860dea103aee8250a2'] builddependencies = [ ('Autotools', '20180311'), + ('Perl', '5.30.2'), ] preconfigopts = "autoreconf -f -i && " diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompi-2020b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompi-2020b.eb new file mode 100644 index 00000000000..2132d9c00f2 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompi-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = "1.12.2" + +homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://parallel-netcdf.github.io/Release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ef1411875b07955f519a5b03278c31e566976357ddfc74c2493a1076e7d7c74'] + +builddependencies = [ + ('Autotools', '20200321'), + ('Perl', '5.32.0'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompic-2020b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompic-2020b.eb new file mode 100644 index 00000000000..fc395be7898 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompic-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = "1.12.2" + +homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = ['https://parallel-netcdf.github.io/Release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ef1411875b07955f519a5b03278c31e566976357ddfc74c2493a1076e7d7c74'] + +builddependencies = [ + ('Autotools', '20200321'), + ('Perl', '5.32.0'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/ProjectQ/ProjectQ-0.4.2-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/ProjectQ/ProjectQ-0.4.2-intel-2018b-Python-3.6.6.eb index f4d389c23d8..8102e563dc2 100644 --- a/easybuild/easyconfigs/p/ProjectQ/ProjectQ-0.4.2-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/ProjectQ/ProjectQ-0.4.2-intel-2018b-Python-3.6.6.eb @@ -20,32 +20,25 @@ use_pip = True exts_list = [ ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('py', '1.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694'], }), ('pluggy', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['8ddc32f03971bfdf900a81961a48ccf2fb677cf7715108f85295c67405798616'], }), ('more-itertools', '5.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('attrs', '18.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], 'modulename': 'attr', }), ('atomicwrites', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('projectq', version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/projectq/'], 'checksums': ['45a45fb51f6961754fee0cb2baabcc2969fa8c882b8288627a6bbdfe2f695717'], }), ] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb index 07596366dc6..3a973ddf495 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb @@ -19,12 +19,8 @@ local_preinstallopts = './configure.py --cuda-root="$EBROOTCUDA" --boost-inc-dir local_preinstallopts += '--boost-lib-dir="$EBROOTBOOST/lib" --no-use-shipped-boost ' local_preinstallopts += '--boost-python-libname=boost_python38 && ' -sanity_pip_check = True use_pip = True - -exts_default_options = { - 'source_tmpl': SOURCELOWER_TAR_GZ, -} +sanity_pip_check = True exts_list = [ ('appdirs', '1.4.4', { @@ -34,6 +30,7 @@ exts_list = [ 'checksums': ['50f2d5b2196a18950fa1397d5ad7ea52daa5985e6196bfd06ba608a7caf93d07'], }), (name, version, { + 'source_tmpl': SOURCELOWER_TAR_GZ, 'preinstallopts': local_preinstallopts, 'checksums': ['effa3b99b55af67f3afba9b0d1b64b4a0add4dd6a33bdd6786df1aa4cc8761a5'], }), diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.16.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.16.1-foss-2017b-Python-3.6.3.eb index 1c6580e7d3a..8491e6a9bb6 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.16.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.16.1-foss-2017b-Python-3.6.3.eb @@ -4,12 +4,11 @@ name = 'PyCairo' version = '1.16.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://cairographics.org/pycairo/' +homepage = 'https://cairographics.org/pycairo/' description = """Python bindings for the cairo library""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['47a14a6a2f8dadb649229f099ac712a5f3d0a22e14877165a203d8a0de09ad63'] diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.16.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.16.2-intel-2017b-Python-2.7.14.eb index 3a1ce49f1c1..cf936105177 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.16.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.16.2-intel-2017b-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'PyCairo' version = '1.16.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://cairographics.org/pycairo/' +homepage = 'https://cairographics.org/pycairo/' description = """Python bindings for the cairo library""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['49a3cf8737c009852e97289d43e952bf228d8df53a7ddb840d4deeb4d0cc1ea7'] diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb index d47b6f39603..6ab6482505f 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb @@ -9,7 +9,6 @@ description = """Python bindings for the cairo library""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['abd42a4c9c2069febb4c38fe74bfc4b4a9d3a89fea3bc2e4ba7baff7a20f783f'] diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-foss-2018b-Python-2.7.15.eb index 62e8cb82747..267d1e773c4 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-foss-2018b-Python-2.7.15.eb @@ -4,12 +4,11 @@ name = 'PyCairo' version = '1.18.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://cairographics.org/pycairo/' +homepage = 'https://cairographics.org/pycairo/' description = """Python bindings for the cairo library""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['abd42a4c9c2069febb4c38fe74bfc4b4a9d3a89fea3bc2e4ba7baff7a20f783f'] diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-foss-2018b-Python-3.6.6.eb index dc9bc6eae40..dfac6894a03 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-foss-2018b-Python-3.6.6.eb @@ -4,12 +4,11 @@ name = 'PyCairo' version = '1.18.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://cairographics.org/pycairo/' +homepage = 'https://cairographics.org/pycairo/' description = """Python bindings for the cairo library""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['abd42a4c9c2069febb4c38fe74bfc4b4a9d3a89fea3bc2e4ba7baff7a20f783f'] diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-intel-2018a-Python-2.7.14.eb index a33106c77c2..31c31e8131d 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-intel-2018a-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """Python bindings for the cairo library""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['abd42a4c9c2069febb4c38fe74bfc4b4a9d3a89fea3bc2e4ba7baff7a20f783f'] diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.2-GCCcore-8.3.0.eb index bb316cef9a5..e5b43bd9c15 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.2-GCCcore-8.3.0.eb @@ -8,7 +8,6 @@ description = """Python bindings for the cairo library""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['dcb853fd020729516e8828ad364084e752327d4cff8505d20b13504b32b16531'] diff --git a/easybuild/easyconfigs/p/PyCifRW/PyCifRW-4.4.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PyCifRW/PyCifRW-4.4.2-GCCcore-8.3.0.eb index f16b4e671b8..e97f9f012a2 100644 --- a/easybuild/easyconfigs/p/PyCifRW/PyCifRW-4.4.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PyCifRW/PyCifRW-4.4.2-GCCcore-8.3.0.eb @@ -9,7 +9,6 @@ description = """PyCIFRW provides support for reading and writing CIF toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a1b6ca0098c9c986b80a50f6cf05122ad65434a18b97a1120f83304ba485acc7'] @@ -24,9 +23,4 @@ options = {'modulename': 'CifFile'} sanity_pip_check = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyDatastream/PyDatastream-0.5.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/PyDatastream/PyDatastream-0.5.1-intel-2018a-Python-3.6.4.eb index a9c4cd97c8a..e25439bd82e 100644 --- a/easybuild/easyconfigs/p/PyDatastream/PyDatastream-0.5.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/PyDatastream/PyDatastream-0.5.1-intel-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = "Lightweight SOAP client" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1e2d639260870b5f818e48b31afc849722b3372342c945261d65bd0474716c23'] @@ -21,9 +20,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyFMI/PyFMI-2.4.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyFMI/PyFMI-2.4.0-intel-2018b-Python-2.7.15.eb index 1cc7f2b7109..fe034eebf5c 100644 --- a/easybuild/easyconfigs/p/PyFMI/PyFMI-2.4.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyFMI/PyFMI-2.4.0-intel-2018b-Python-2.7.15.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'PyFMI' version = '2.4.0' @@ -22,15 +22,11 @@ dependencies = [ ('lxml', '4.2.5', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - # PyFMI needs specific version of numpy and scipy, therefore matplotlib and Assimulo as well. exts_list = [ ('numpy', '1.6.2', { 'patches': ['numpy-1.6.2_distutils_multiple-lib-dirs.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ 'e2236a4d514b8b74cdb4aa73093e55de6585a5289a2b7ce5328b9bbd980b212b', # numpy-1.6.2.zip # numpy-1.6.2_distutils_multiple-lib-dirs.patch @@ -39,7 +35,6 @@ exts_list = [ }), ('scipy', '0.10.1', { 'patches': ['scipy-0.10.1_qhull-icc.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': [ '77cc5c48e3f0c07b8137135538cdb99d596d3cc5c498bb0031fb5ff22eae4aa7', # scipy-0.10.1.tar.gz '9344603548a6be64b3b3aa36cf6cb1a2c8084b4ccb57808deb5895b62c265535', # scipy-0.10.1_qhull-icc.patch @@ -48,17 +43,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('matplotlib', '1.5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['a0a5dc39f785014f2088fed2c6d2d129f0444f71afbb9c44f7bdf1b14d86ebbc'], }), ('Assimulo', '2.9', { 'patches': ['Assimulo-2.9_fix-python-buildopts.patch', 'Assimulo-2.9_fix-intel_i8_r8.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/A/Assimulo/'], 'checksums': [ 'e61f5278618f3c2c920c0ef758eae0ae9a0538240d0ceaaae06b5dadff35aa2e', # Assimulo-2.9.zip # Assimulo-2.9_fix-python-buildopts.patch @@ -68,20 +60,8 @@ exts_list = [ }), (name, version, { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/P/PyFMI/'], 'checksums': ['ae1e194667d9148879b70bb40520855c0984c4116140d8362414046b8f1a00b8'], }), ] -exts_download_dep_fail = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyFR/PyFR-1.9.0-intelcuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyFR/PyFR-1.9.0-intelcuda-2019b-Python-3.7.4.eb index 13e853f147f..84f9e6b8097 100644 --- a/easybuild/easyconfigs/p/PyFR/PyFR-1.9.0-intelcuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyFR/PyFR-1.9.0-intelcuda-2019b-Python-3.7.4.eb @@ -30,7 +30,6 @@ sanity_pip_check = True exts_list = [ ('gimmik', '2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s'], 'checksums': ['36ec13aff705e787b856ae236211d1826ceaa4b22d52d4d98ff72642bb4021a3'], }), (name, version, { diff --git a/easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb b/easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb new file mode 100644 index 00000000000..21040014286 --- /dev/null +++ b/easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'PyFoam' +version = '2020.5' + +homepage = 'http://openfoamwiki.net/index.php/Contrib/PyFoam' +description = "A Python library to control OpenFOAM-runs and manipulate OpenFOAM-data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1965041e96349719b77371961e569d179ca19c1386a8dedc6d9f774ac5353ada'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': name} + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ["bin/pyFoam%s.py" % x for x in ('Execute', 'Runner', 'Version')], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyFoam%s.py --help" % x for x in ('Execute', 'Runner', 'Version')] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.7.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.7.1-foss-2019b-Python-3.7.4.eb index dc4f2c39891..7818cef938d 100644 --- a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.7.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.7.1-foss-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = """PyGEOS is a C/Python library with vectorized geometry functions toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['d2d549f2ffba5ed29cdf499f7e6b390603f964021892c94e567810c5ee3296a1'] @@ -22,8 +21,8 @@ dependencies = [ ('GEOS', '3.8.0', versionsuffix), ] -sanity_pip_check = True use_pip = True +sanity_pip_check = True download_dep_fail = True moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.8-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.8-foss-2020a-Python-3.8.2.eb index f2cc39b052a..af63cbc2cc2 100644 --- a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.8-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.8-foss-2020a-Python-3.8.2.eb @@ -21,8 +21,8 @@ dependencies = [ ('GEOS', '3.8.1', versionsuffix), ] -sanity_pip_check = True use_pip = True +sanity_pip_check = True download_dep_fail = True moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.2.0-Python-3.7.2.eb index 71eb3bef743..1fb4c9b5698 100644 --- a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.2.0-Python-3.7.2.eb @@ -9,7 +9,6 @@ description = """Python Bindings for GLib/GObject/GIO/GTK+""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2acb0daf2b3a23a90f52066cc23d1053339fee2f5f7f4275f8baa3704ae0c543'] diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.3.0-Python-2.7.16.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.3.0-Python-2.7.16.eb index 61683154fc6..2c6919a1327 100644 --- a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.3.0-Python-2.7.16.eb +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.3.0-Python-2.7.16.eb @@ -10,7 +10,6 @@ libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2acb0daf2b3a23a90f52066cc23d1053339fee2f5f7f4275f8baa3704ae0c543'] diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.3.0-Python-3.7.4.eb index 8512620cc26..defcda5fc8b 100644 --- a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -10,7 +10,6 @@ libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2acb0daf2b3a23a90f52066cc23d1053339fee2f5f7f4275f8baa3704ae0c543'] diff --git a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.2.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.2.0-foss-2016a-Python-2.7.11.eb index df162eee90c..417cf0dd34f 100644 --- a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.2.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.2.0-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """PyGWAS is a library for running Genome Wide Association studies toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2fd4264b92697efab7a09f815f004015554b3e46c74c81d8ed1bec8d2f20f9c9'] diff --git a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.3.1-foss-2016a-Python-2.7.11.eb index 072a19fea41..ddf01059a2e 100644 --- a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.3.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.3.1-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """PyGWAS is a library for running Genome Wide Association studies toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c87c578e848ce4e0b72d1f4b30b8c3d8ca6942ed19a7fbdb6ca886a490f5b4bb'] diff --git a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.4.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.4.0-foss-2016a-Python-2.7.11.eb index a64d2ef2c44..dc776b7ef12 100644 --- a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.4.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.4.0-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """PyGWAS is a library for running Genome Wide Association studies toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['77d011083748459f1002d42895bd9741a5493a785c851be18aa7cc78a3bc7f7e'] diff --git a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.5.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.5.0-foss-2016a-Python-2.7.11.eb index 8eb0cc148d4..60bf51fce23 100644 --- a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.5.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.5.0-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """PyGWAS is a library for running Genome Wide Association studies toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b7ac1d64ecb11d2a85acd58931d90b4e58668055ffd8a5308f87cf940d40989c'] diff --git a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.6.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.6.1-foss-2016a-Python-2.7.11.eb index d11451ee37d..63da035bb78 100644 --- a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.6.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.6.1-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """PyGWAS is a library for running Genome Wide Association studies toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2070933b6ed37388cb8a7d7eb1aecb10421f004a7ed901a65e0919e6dd52bba1'] diff --git a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.6.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.6.1-intel-2016a-Python-2.7.11.eb index 4eb1eee5fef..a90b86fd14b 100644 --- a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.6.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.6.1-intel-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """PyGWAS is a library for running Genome Wide Association studies toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2070933b6ed37388cb8a7d7eb1aecb10421f004a7ed901a65e0919e6dd52bba1'] diff --git a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.7.1-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.7.1-foss-2017a-Python-2.7.13.eb index da5f467f349..4c73228e535 100644 --- a/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.7.1-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PyGWAS/PyGWAS-1.7.1-foss-2017a-Python-2.7.13.eb @@ -9,7 +9,6 @@ description = """PyGWAS is a library for running Genome Wide Association studies toolchain = {'name': 'foss', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c125af69bcae6b531b17fa8277d678c2bdc14eed1a6a3db50d0814b940be7a49'] diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-foss-2019b-Python-3.7.4.eb index 1c2ce140ea7..6a074c06b64 100644 --- a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-foss-2019b-Python-3.7.4.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('xarray', '0.15.1', { 'checksums': ['64e3138d87b641e22fe7a003c94abc685896b247b63e434505c1e6b38c91a8fb'], diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-intel-2019b-Python-3.7.4.eb index c95bf45e282..4d706c55886 100644 --- a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-intel-2019b-Python-3.7.4.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('xarray', '0.15.1', { 'checksums': ['64e3138d87b641e22fe7a003c94abc685896b247b63e434505c1e6b38c91a8fb'], diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2020.2.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2020.2.2-fosscuda-2019b-Python-3.7.4.eb index 7d86554ef7a..2db674bea2c 100644 --- a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2020.2.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2020.2.2-fosscuda-2019b-Python-3.7.4.eb @@ -17,8 +17,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('appdirs', '1.4.4', { 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-GCCcore-8.2.0.eb index bce63c784d8..3dcf9f45025 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-GCCcore-8.2.0.eb @@ -19,7 +19,6 @@ description = """PyOpenGL is the most common cross platform Python binding to Op toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c96d909b359abe3271b746bacf7e6ba52935141e2406a8f90231e4e44dfa4075'] diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.12.eb index e76b799546b..88631b69de0 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.12.eb @@ -20,7 +20,6 @@ description = """PyOpenGL is the most common cross platform Python binding to Op toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2018a-Python-2.7.14.eb index 0a6c698ebca..592b58681a0 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2018a-Python-2.7.14.eb @@ -20,7 +20,6 @@ description = """PyOpenGL is the most common cross platform Python binding to Op toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c96d909b359abe3271b746bacf7e6ba52935141e2406a8f90231e4e44dfa4075'] diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb index cd4aac12db5..0cbaaa8dc24 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """PyOpenGL is the most common cross platform Python binding to Op toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2017b-Python-2.7.14.eb index 71dab44f0c8..0497e2d0588 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """PyOpenGL is the most common cross platform Python binding to Op toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-foss-2018b-Python-2.7.15.eb index 08392a6c723..a208f296fd2 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-foss-2018b-Python-2.7.15.eb @@ -20,7 +20,6 @@ description = """PyOpenGL is the most common cross platform Python binding to Op toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ac73b4c0b433be02d6a55b9ed768acf07003a92a3315ba9d62bc8f8da5f0c291'] diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-intel-2018a-Python-2.7.14.eb index 44c15149da2..b5168595329 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-intel-2018a-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """PyOpenGL is the most common cross platform Python binding to Op toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ac73b4c0b433be02d6a55b9ed768acf07003a92a3315ba9d62bc8f8da5f0c291'] diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-8.3.0.eb index 2b6326c9a17..6d4a3afaf34 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-8.3.0.eb @@ -19,7 +19,6 @@ description = """PyOpenGL is the most common cross platform Python binding to Op toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4107ba0d0390da5766a08c242cf0cf3404c377ed293c5f6d701e457c57ba3424'] diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb index 2fc24f0a12a..d50e24ff287 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'PyQt5' version = '5.15.1' @@ -18,6 +18,8 @@ dependencies = [ default_easyblock = 'PythonPackage' +use_pip = True + local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " @@ -32,7 +34,6 @@ local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/si local_sipver = '5.4.0' components = [ ('SIP', local_sipver, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], 'start_dir': 'sip-%s' % local_sipver, @@ -40,21 +41,18 @@ components = [ 'options': {'modulename': 'PyQt5.sip'}, }), ('PyQt-builder', '1.5.0', { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.8.1', { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], 'easyblock': 'Binary', @@ -63,7 +61,6 @@ components = [ 'install_cmd': local_setup_env + local_pyqt5_sip_install, }), ('PyQtWebEngine', version, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], 'easyblock': 'ConfigureMakePythonPackage', @@ -74,6 +71,8 @@ components = [ }), ] +sanity_pip_check = True + sanity_check_paths = { 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb index 2122c835fca..1005bfa8e3e 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'PyQt5' version = '5.15.1' @@ -19,6 +19,8 @@ dependencies = [ default_easyblock = 'PythonPackage' +use_pip = True + local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " @@ -33,7 +35,6 @@ local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/si local_sipver = '5.4.0' components = [ ('SIP', local_sipver, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], 'start_dir': 'sip-%s' % local_sipver, @@ -41,21 +42,18 @@ components = [ 'options': {'modulename': 'PyQt5.sip'}, }), ('PyQt-builder', '1.5.0', { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.8.1', { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], 'easyblock': 'Binary', @@ -64,7 +62,6 @@ components = [ 'install_cmd': local_setup_env + local_pyqt5_sip_install, }), ('PyQtWebEngine', version, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], 'easyblock': 'ConfigureMakePythonPackage', @@ -75,6 +72,8 @@ components = [ }), ] +sanity_pip_check = True + sanity_check_paths = { 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb index b5e094b367b..6922b10ac8f 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb @@ -22,30 +22,24 @@ use_pip = True exts_list = [ # PyRETIS requires more recent setuptools due to use of find_namespace_packages (added in setuptools v40.1.0) ('setuptools', '41.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['79d30254b6fe7a8e672e43cd85f13a9f3f2a50080bc81d851143e2219ef0dcb1'], }), # PyRETIS requires Cython 0.29.* ('Cython', '0.29.6', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6c5d33f1b5c864382fbce810a8fd9e015447869ae42e98e6301e977b8165e7ae'], }), ('colorama', '0.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], 'checksums': ['05eed71e2e327246ad6b38c540c4a3117230b19679b875190486ddd2d721422d'], }), ('tqdm', '4.31.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tqdm/'], 'checksums': ['e22977e3ebe961f72362f6ddfb9197cc531c9737aaf5f607ef09740c849ecd05'], }), ('sphinx-bootstrap-theme', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx-bootstrap-theme/'], 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], }), (name, version, { 'source_tmpl': 'pyretis-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyretis'], 'checksums': ['fbacc3c69d0c57e279992a4d01e80f84af3fd191a7bdfebd032391133c540d07'], }), ] diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb index 4d7a3a189ef..26ec09dd274 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb @@ -22,16 +22,13 @@ use_pip = True exts_list = [ ('colorama', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], }), ('sphinx-bootstrap-theme', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx-bootstrap-theme/'], 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], }), (name, version, { 'source_tmpl': 'pyretis-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyretis'], 'checksums': ['b4b842a83f39e97a9bbf2d9797f53823b9e741b479b5a6744aeb42daf1c7ad2b'], }), ] diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb index a2105a15bef..466dd1fe7e3 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb @@ -22,16 +22,13 @@ use_pip = True exts_list = [ ('colorama', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], }), ('sphinx-bootstrap-theme', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx-bootstrap-theme/'], 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], }), (name, version, { 'source_tmpl': 'pyretis-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyretis'], 'checksums': ['b4b842a83f39e97a9bbf2d9797f53823b9e741b479b5a6744aeb42daf1c7ad2b'], }), ] diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-foss-2020b.eb b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-foss-2020b.eb new file mode 100644 index 00000000000..d83b01a8132 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-foss-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMakeCp' + +name = 'PySCF' +version = '1.7.6' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1805819557cf78fb5938a2141a429c74dabb3ba664b60420032584d7a876c2ab'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy, scipy + ('h5py', '3.1.0'), + ('libcint', '4.4.0'), + ('libxc', '4.3.4'), + ('XCFun', '2.1.1'), +] + +start_dir = 'pyscf/lib' + +separate_build_dir = True + +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" + +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +files_to_copy = ['pyscf'] + +sanity_check_paths = { + 'files': ['pyscf/__init__.py'], + 'dirs': ['pyscf/data', 'pyscf/lib'], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-foss-2021a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-foss-2021a.eb new file mode 100644 index 00000000000..9a7c7e573c0 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMakeCp' + +name = 'PySCF' +version = '1.7.6' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1805819557cf78fb5938a2141a429c74dabb3ba664b60420032584d7a876c2ab'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy, scipy + ('h5py', '3.2.1'), + ('libcint', '4.4.0'), + ('libxc', '5.1.5'), + ('XCFun', '2.1.1'), +] + +start_dir = 'pyscf/lib' + +separate_build_dir = True + +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" + +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +files_to_copy = ['pyscf'] + +sanity_check_paths = { + 'files': ['pyscf/__init__.py'], + 'dirs': ['pyscf/data', 'pyscf/lib'], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.0.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.0.0-intel-2018a-Python-3.6.4.eb index 26a3e56c544..40a42970cfb 100644 --- a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.0.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.0.0-intel-2018a-Python-3.6.4.eb @@ -10,7 +10,6 @@ description = """Python interface to Stan, a package for Bayesian inference toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['b85301b960d5991918b40bd64a4e9321813657a9fc028e0f39edce7220a309eb'] diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.3.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.3.2-foss-2019b-Python-3.7.4.eb index fb5cae3268d..293c0902301 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.3.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.3.2-foss-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ ('RDFlib', '4.2.2'), ] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.4.2-foss-2019b-Python-3.7.4-PyTorch-1.4.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.4.2-foss-2019b-Python-3.7.4-PyTorch-1.4.0.eb index 9335a70d935..b67fa2f46bf 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.4.2-foss-2019b-Python-3.7.4-PyTorch-1.4.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.4.2-foss-2019b-Python-3.7.4-PyTorch-1.4.0.eb @@ -21,8 +21,6 @@ dependencies = [ ('RDFlib', '4.2.2'), ] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb new file mode 100644 index 00000000000..20dd004271e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb @@ -0,0 +1,316 @@ +name = 'PyTorch' +version = '1.3.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +local_pytorchthirdpartydir = 'pytorch-%(version)s/third_party' +local_extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' + +source_urls = ['https://github.com/pytorch/pytorch/archive'] + +# PyTorch pulls in a bunch of submodules that are not releases. We download the submodule revisions from their repos. +# determine commit of additional sources via https://github.com/pytorch/pytorch/tree/v1.3.1/third_party +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], + 'download_filename': 'ca528e32fea9ca8f2b16053cff17160290fc84ce.tar.gz', + 'filename': 'gloo-20190930.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'gloo'), + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'googletest'), + }, + { + 'source_urls': ['https://github.com/pybind/pybind11/archive'], + 'download_filename': '25abf7efba0b2990f5a6dfb0a31bc65c0f2f4d17.tar.gz', + 'filename': 'pybind11-20190204.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'pybind11'), + }, + { + 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], + 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', + 'filename': 'clang-cindex-python3-20170330.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'pybind11/tools/clang'), + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': '89fe1695edf9ee14c22f815f24bac45577a4f135.tar.gz', + 'filename': 'cpuinfo-20190117.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'cpuinfo'), + }, + { + 'source_urls': ['https://github.com/onnx/onnx/archive'], + 'download_filename': '034921bd574cc84906b7996c07873454b7dd4135.tar.gz', + 'filename': 'onnx-20190926.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx'), + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': 'e776aa0275e293707b6a0901e0e8d8a8a3679508.tar.gz', + 'filename': 'benchmark-20180525.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx/third_party/benchmark'), + }, + { + 'source_urls': ['https://github.com/pybind/pybind11/archive'], + 'download_filename': '09f082940113661256310e3f4811aa7261a9fa05.tar.gz', + 'filename': 'pybind11-20170919.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx/third_party/pybind11'), + }, + { + 'source_urls': ['https://github.com/onnx/onnx-tensorrt/archive'], + 'download_filename': 'cb3d8066f20e6bca306454934d09d6abd826264a.tar.gz', + 'filename': 'onnx-tensorrt-20190425.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx-tensorrt'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], + 'download_filename': '13da0b4c21d17f94150713366420baaf1b5a46f4.tar.gz', + 'filename': 'pthreadpool-20181008.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'pthreadpool'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], + 'download_filename': 'b742d1143724d646cd0f914646f1240eacf5bd73.tar.gz', + 'filename': 'FXdiv-20181016.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'FXdiv'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/psimd/archive'], + 'download_filename': '90a938f30ba414ada2f4b00674ee9631d7d85e19.tar.gz', + 'filename': 'psimd-20180906.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'psimd'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FP16/archive'], + 'download_filename': 'febbb1c163726b5db24bed55cc9dc42529068997.tar.gz', + 'filename': 'FP16-20181128.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'FP16'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/NNPACK/archive'], + 'download_filename': 'c039579abe21f5756e0f0e45e8e767adccc11852.tar.gz', + 'filename': 'NNPACK-20190323.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'NNPACK'), + }, + { + 'source_urls': ['https://github.com/shibatch/sleef/archive'], + 'download_filename': '7f523de651585fe25cade462efccca647dcc8d02.tar.gz', + 'filename': 'sleef-20190730.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'sleef'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/PeachPy/archive'], + 'download_filename': '07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz', + 'filename': 'PeachPy-20180219.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'python-peachpy'), + }, + { + 'source_urls': ['https://github.com/pytorch/QNNPACK/archive'], + 'download_filename': '7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz', + 'filename': 'QNNPACK-20190828.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'QNNPACK'), + }, + { + 'source_urls': ['https://github.com/pytorch/fbgemm/archive'], + 'download_filename': '60e318d48dd72a22a1f63fa625387d4b7363bd23.tar.gz', + 'filename': 'fbgemm-20200521.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm'), + }, + { + 'source_urls': ['https://github.com/asmjit/asmjit/archive'], + 'download_filename': '4da474ac9aa2689e88d5e40a2f37628f302d7e3c.tar.gz', + 'filename': 'asmjit-20190814.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm/third_party/asmjit'), + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': 'd5e37adf1406cf899d7d9ec1d317c47506ccb970.tar.gz', + 'filename': 'cpuinfo-20190201.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm/third_party/cpuinfo'), + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '0fc5466dbb9e623029b1ada539717d10bd45e99e.tar.gz', + 'filename': 'googletest-20180920.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm/third_party/googletest'), + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': '505be96ab23056580a3a2315abba048f4428b04e.tar.gz', + 'filename': 'benchmark-20180606.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'benchmark'), + }, + { + 'source_urls': ['https://github.com/eigenteam/eigen-git-mirror/archive'], + 'download_filename': 'd41dc4dd74acce21fb210e7625d5d135751fa9e5.tar.gz', + 'filename': 'eigen-20190126.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'eigen'), + }, + { + 'source_urls': ['https://github.com/google/gemmlowp/archive'], + 'download_filename': '3fb5c176c17c765a3492cd2f0321b0dab712f350.tar.gz', + 'filename': 'gemmlowp-20181127.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'gemmlowp/gemmlowp'), + }, + { + 'source_urls': ['https://github.com/NVlabs/cub/archive'], + 'download_filename': '285aeebaa34b0e8a7670867a2e66c1a52d998d6a.tar.gz', + 'filename': 'cub-20170829.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'cub'), + }, + { + 'source_urls': ['https://github.com/houseroad/foxi/archive'], + 'download_filename': '8f74bc4df3a4cfc69b1a3eadf62aa29d9961c72d.tar.gz', + 'filename': 'foxi-20190424.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'foxi'), + }, + { + 'source_urls': ['https://github.com/intel/ideep/archive'], + 'download_filename': '78eafa5d231924e3d525d4dc46de880015257618.tar.gz', + 'filename': 'ideep-20190912.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'ideep'), + }, + { + 'source_urls': ['https://github.com/intel/tbb/archive'], + 'download_filename': 'a51a90bc609bb73db8ea13841b5cf7aa4344d4a9.tar.gz', + 'filename': 'tbb-20181009.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'tbb'), + }, + { + 'source_urls': ['https://github.com/intel/mkl-dnn/archive'], + 'download_filename': '0125f28c61c1f822fd48570b4c1066f96fcb9b2e.tar.gz', + 'filename': 'mkl-dnn-20190905.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'ideep/mkl-dnn'), + }, +] +patches = [ + '%(name)s-1.2.0_fix-findAVX.patch', + '%(name)s-1.2.0_disable-tests-ppc64le.patch', + '%(name)s-1.2.0_add-cuda11-support.patch', + 'PyTorch-1.3.1_add-jit-support-for-cuda11.patch', + 'PyTorch-1.3.1_add-Python3.8-compat.patch', + 'PyTorch-1.3.1_add-support-for-cuda11.patch', + 'PyTorch-1.3.1_add-support-for-cudnn8.patch', + 'PyTorch-1.3.1_fix-build-on-AVX512-cpus.patch', + 'PyTorch-1.3.1_fix-for-nccl-error.patch', + '%(name)s-%(version)s_fix-missing-sleef_h.patch', + 'PyTorch-1.3.1_skip-nccl-error-tests.patch', + '%(name)s-1.4.0_fix-missing-source-dir.patch', + 'PyTorch-1.6.0_fix-test-cuda.patch', + 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', +] +checksums = [ + 'ab6feb5044f7d36f6e93dce4668d8c593e89d34aca7023fd99a38d215ca9dfc0', # v1.3.1.tar.gz + '1354079f38459bc8f322d1f5808eb5c57059a473e77489e981fb5debeadf0ad0', # gloo-20190930.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + '1a1ccf8779332a7d6d0db9034d42df188867cbaf52eb71d74451f79aa8ce2040', # pybind11-20190204.tar.gz + '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz + 'b84c49b4bdc12b0e8f1bff365dcefd50e5a2a25eeef8c928aeb2dab9fda4d599', # cpuinfo-20190117.tar.gz + 'eaa2d4b70aa0003fdab136ae26b5e0aebabcf6421df7fef69fec9ce005a09586', # onnx-20190926.tar.gz + 'c7682e9007ddfd94072647abab3e89ffd9084089460ae47d67060974467b58bf', # benchmark-20180525.tar.gz + '02407529fd8431cf627d45638b4d9a6c02b8aa5bf50d73b8fa12217918c57ff4', # pybind11-20170919.tar.gz + '1a98c6fece7878c88b59ffe651b427c15b4929c801a09655cd14ca44553787c3', # onnx-tensorrt-20190425.tar.gz + '90ab4f60ae0e99c0172dd5201dccc6de6c8f384a21b3d959588f4c1e00beec0f', # pthreadpool-20181008.tar.gz + '07625551202a1f35fe5e826669ad495962b26f6a139290e90b321c5996f002ef', # FXdiv-20181016.tar.gz + 'afd27417c6df1c85f79a68361055dd3adc292174913c39c1f58b698b9cfd7926', # psimd-20180906.tar.gz + '3e71681e0a67cd28552aa0bbb78ec6a6bd238216df15336dc1326280f7958de2', # FP16-20181128.tar.gz + '2c276e6cc9e3fb7a79bc337662aba738a638975381bac6d393254ec288d6269e', # NNPACK-20190323.tar.gz + '8cb5fae822077ca9cbc14dcc7bba9a3a35ad519284fc5169f9a176672c63860a', # sleef-20190730.tar.gz + '13100c3deed300bbf16f87d8af3539f432462bfef9d38f0c7e3e387dc2e88676', # PeachPy-20180219.tar.gz + '0d752bd75f46ce4d7c6f0a60b0d6c0e5918a7b4683c825284f8db3706dd24f76', # QNNPACK-20190828.tar.gz + '5669f25fe8b550a44edbaf35bb7bb4a549474940f6b3291d988ffac5cc6a2d4f', # fbgemm-20200521.tar.gz + 'a6de3e1604b46b2e37ae31c0896e90f4962e887e0a3bcf1bd2fb8cc55a5c59cf', # asmjit-20190814.tar.gz + '3f2dc1970f397a0e59db72f9fca6ff144b216895c1d606f6c94a507c1e53a025', # cpuinfo-20190201.tar.gz + 'e99b904983d08ac8e9bddb5b0d21196b78ad9499e3c5d12192cee2ddd2b7515c', # googletest-20180920.tar.gz + '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz + '2ec954f18cec50a7063a7358ce555f7e11788a7f6d4e7e597d83687dc2f3b989', # eigen-20190126.tar.gz + 'fdd6f08bdb33d33f4df516ffb91730fdb163479c19502cfc983083fd9cf43bfa', # gemmlowp-20181127.tar.gz + '7224b03af4acbc54525105bb42e3ecd75c66a3a5b47e8a725ab008467c4109f9', # cub-20170829.tar.gz + 'b444b4428adc4befc777d9a1af2fd9bbf5f5a2339913668357196c5133e9cc7b', # foxi-20190424.tar.gz + 'b8fb8b4871cc3da4bded01c476957a08f51949c20f834f39f90f9e10811d6dfe', # ideep-20190912.tar.gz + ('dc0a8d8d96cb8765782aa6ac1b509ad4db955d9bbb58fa5cc2265f0292756d72', + 'be111cf161b587812fa3b106fe550efb6f129b8b0b702fef32fac23af9580e5e'), # tbb-20181009.tar.gz + ('d16c64ab2ce654f0a21e51f933ae9ee480a8873717d0bd10e0f2a2f658a7095b', + 'bf096e6b3f17925ebe7802e0fa7dcc246319210b6ea3645b3ed52899a474fafc'), # mkl-dnn-20190905.tar.gz + '001c9bf604aebe4b39ccad15332a71130b07b780c539ceca84d6c64cd6fc8a68', # PyTorch-1.2.0_fix-findAVX.patch + 'c4183bcb29a8bcbadea0341e93a3a32afdf860aa31331b768e787d899183da92', # PyTorch-1.2.0_disable-tests-ppc64le.patch + '5a8289ced3ea448c61b2c417bb6118cb73da67eb6b9a58ac14376c65f7151906', # PyTorch-1.2.0_add-cuda11-support.patch + # PyTorch-1.3.1_add-jit-support-for-cuda11.patch + '3dfff6835b0edeae2ad91f36ea5e9ee9dcdef82f5bf27aca27b8db98fed15939', + '2a743d0fc52a6f7239e6750a7cd59148417546b45a0b10ad1a15e526b94c4434', # PyTorch-1.3.1_add-Python3.8-compat.patch + 'e379846cb0bccb7e6143bf21b1fa517771842c7ca165cb35d60e507edd38b6ce', # PyTorch-1.3.1_add-support-for-cuda11.patch + '2560bf24f40aa981c9d3802313b67c4d2378082a9fdd919c499de10793da7e64', # PyTorch-1.3.1_add-support-for-cudnn8.patch + 'daf8e2c49a5ecab37c583f9cc97688f4264d420adba23192b72184f268558676', # PyTorch-1.3.1_fix-build-on-AVX512-cpus.patch + '064801bf29f07524a93d17fc0ca6004adc4a506232b33077ac43bdbe3f3a9f7d', # PyTorch-1.3.1_fix-for-nccl-error.patch + '1337647ff64a1208d1e401fc84052d0bc6174b133cec2f3521319cb593f524fa', # PyTorch-1.3.1_fix-missing-sleef_h.patch + '5743ac23a0d0f40373baeb026bb5656a84ca1417fcce10be8370ec3f4c9e80a6', # PyTorch-1.3.1_skip-nccl-error-tests.patch + '797987fb9c9bf9f1d75a1be878ddf9f418f9524006b0985ca8e6d65d4e2b6998', # PyTorch-1.4.0_fix-missing-source-dir.patch + 'adf21e77dbc5e60fd46fe21fceb908633b0da7d4fc9b6a3ea7f7cfb0c4a44678', # PyTorch-1.6.0_fix-test-cuda.patch + # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch + '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '4.53.1'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +excluded_tests = { + '': [ + # https://github.com/pytorch/pytorch/issues/42498 + 'cpp_extensions', + # Precision issues. Maybe actual failures or "just" the new cuDNN + 'nn', + ], + 'POWER': [ + # https://github.com/pytorch/pytorch/issues/41186 + 'autograd', + # https://github.com/pytorch/pytorch/issues/41400 + 'jit', + # https://github.com/pytorch/pytorch/issues/41469 + 'nn', + # Sporadically fails for unknown reason. Fixed in newer versions + 'torch', + # Unknown + 'cuda', + ], +} + +# OpenMP causes e.g. torch.matmul to return invalid results at least on POWER +# See e.g. https://github.com/pytorch/pytorch/issues/3716#issuecomment-387776917 +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-Python3.8-compat.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-Python3.8-compat.patch new file mode 100644 index 00000000000..b46187678ae --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-Python3.8-compat.patch @@ -0,0 +1,751 @@ +From 86c64440c9169d94bffb58b523da1db00c896703 Mon Sep 17 00:00:00 2001 +From: vishwakftw +Date: Thu, 7 Nov 2019 09:18:38 -0800 +Subject: [PATCH] Make PyTorch Python 3.8 compatible (#29302) + +Summary: +PEP 590 modifies the `tp_print` offset to `tp_vectorcall_offset` - which requires a Py_ssize_t object. +Passing a nullptr caused compatibility issues for Python 3.8. + +Changelog: +- Modify all occurrences of `nullptr /* tp_print */` to 0 /* tp_vectorcall_offset */ +- Minor formatting changes +Pull Request resolved: https://github.com/pytorch/pytorch/pull/29302 + +Test Plan: +- Local fresh build with Python 3.8 completed successfully. + +Fixes https://github.com/pytorch/pytorch/issues/28060. +Fixes https://github.com/pytorch/pytorch/issues/29162. + +Supersedes https://github.com/pytorch/pytorch/pull/28364 + +Differential Revision: D18372022 + +Pulled By: ezyang + +fbshipit-source-id: 8e9a15b0d0f72101ccc69bd489f5efa216b880bb +--- + .../templates/python_torch_functions.cpp | 2 +- + torch/csrc/Device.cpp | 46 +++++++-------- + torch/csrc/Dtype.cpp | 54 ++++++++--------- + torch/csrc/Generator.cpp | 2 +- + torch/csrc/Layout.cpp | 58 +++++++++---------- + torch/csrc/MemoryFormat.cpp | 2 +- + torch/csrc/PtrWrapper.cpp | 20 +++---- + torch/csrc/QScheme.cpp | 2 +- + torch/csrc/Size.cpp | 48 +++++++-------- + torch/csrc/TypeInfo.cpp | 4 +- + torch/csrc/autograd/python_engine.cpp | 20 +++---- + torch/csrc/autograd/python_function.cpp | 26 ++++----- + .../csrc/autograd/python_legacy_variable.cpp | 18 +++--- + torch/csrc/autograd/python_variable.cpp | 26 ++++----- + torch/csrc/cuda/Event.cpp | 2 +- + torch/csrc/cuda/Stream.cpp | 2 +- + torch/csrc/generic/Storage.cpp | 22 +++---- + 17 files changed, 177 insertions(+), 177 deletions(-) + +diff --git a/tools/autograd/templates/python_torch_functions.cpp b/tools/autograd/templates/python_torch_functions.cpp +index 935a01f6cc10d..9d10f0324647d 100644 +--- a/tools/autograd/templates/python_torch_functions.cpp ++++ b/tools/autograd/templates/python_torch_functions.cpp +@@ -489,7 +489,7 @@ static PyTypeObject THPVariableFunctions = { + 0, /* tp_basicsize */ + 0, /* tp_itemsize */ + 0, /* tp_dealloc */ +- 0, /* tp_print */ ++ 0, /* tp_vectorcall_offset */ + 0, /* tp_getattr */ + 0, /* tp_setattr */ + 0, /* tp_reserved */ +diff --git a/torch/csrc/Device.cpp b/torch/csrc/Device.cpp +index 6bdfcb47570d8..d24530feb61f0 100644 +--- a/torch/csrc/Device.cpp ++++ b/torch/csrc/Device.cpp +@@ -181,39 +181,39 @@ PyTypeObject THPDeviceType = { + "torch.device", /* tp_name */ + sizeof(THPDevice), /* tp_basicsize */ + 0, /* tp_itemsize */ +- nullptr, /* tp_dealloc */ +- nullptr, /* tp_print */ +- nullptr, /* tp_getattr */ +- nullptr, /* tp_setattr */ +- nullptr, /* tp_reserved */ ++ nullptr, /* tp_dealloc */ ++ 0, /* tp_vectorcall_offset */ ++ nullptr, /* tp_getattr */ ++ nullptr, /* tp_setattr */ ++ nullptr, /* tp_reserved */ + (reprfunc)THPDevice_repr, /* tp_repr */ +- nullptr, /* tp_as_number */ +- nullptr, /* tp_as_sequence */ +- nullptr, /* tp_as_mapping */ ++ nullptr, /* tp_as_number */ ++ nullptr, /* tp_as_sequence */ ++ nullptr, /* tp_as_mapping */ + (hashfunc)THPDevice_hash, /* tp_hash */ +- nullptr, /* tp_call */ ++ nullptr, /* tp_call */ + (reprfunc)THPDevice_str, /* tp_str */ +- nullptr, /* tp_getattro */ +- nullptr, /* tp_setattro */ +- nullptr, /* tp_as_buffer */ ++ nullptr, /* tp_getattro */ ++ nullptr, /* tp_setattro */ ++ nullptr, /* tp_as_buffer */ + Py_TPFLAGS_DEFAULT, /* tp_flags */ + nullptr, /* tp_doc */ +- nullptr, /* tp_traverse */ +- nullptr, /* tp_clear */ ++ nullptr, /* tp_traverse */ ++ nullptr, /* tp_clear */ + (richcmpfunc)THPDevice_rc, /* tp_richcompare */ + 0, /* tp_weaklistoffset */ +- nullptr, /* tp_iter */ +- nullptr, /* tp_iternext */ ++ nullptr, /* tp_iter */ ++ nullptr, /* tp_iternext */ + THPDevice_methods, /* tp_methods */ +- nullptr, /* tp_members */ ++ nullptr, /* tp_members */ + THPDevice_properties, /* tp_getset */ +- nullptr, /* tp_base */ +- nullptr, /* tp_dict */ +- nullptr, /* tp_descr_get */ +- nullptr, /* tp_descr_set */ ++ nullptr, /* tp_base */ ++ nullptr, /* tp_dict */ ++ nullptr, /* tp_descr_get */ ++ nullptr, /* tp_descr_set */ + 0, /* tp_dictoffset */ +- nullptr, /* tp_init */ +- nullptr, /* tp_alloc */ ++ nullptr, /* tp_init */ ++ nullptr, /* tp_alloc */ + THPDevice_pynew, /* tp_new */ + }; + +diff --git a/torch/csrc/Dtype.cpp b/torch/csrc/Dtype.cpp +index dc3c7c44ac9d6..c0a084712f847 100644 +--- a/torch/csrc/Dtype.cpp ++++ b/torch/csrc/Dtype.cpp +@@ -61,40 +61,40 @@ PyTypeObject THPDtypeType = { + "torch.dtype", /* tp_name */ + sizeof(THPDtype), /* tp_basicsize */ + 0, /* tp_itemsize */ +- nullptr, /* tp_dealloc */ +- nullptr, /* tp_print */ +- nullptr, /* tp_getattr */ +- nullptr, /* tp_setattr */ +- nullptr, /* tp_reserved */ ++ nullptr, /* tp_dealloc */ ++ 0, /* tp_vectorcall_offset */ ++ nullptr, /* tp_getattr */ ++ nullptr, /* tp_setattr */ ++ nullptr, /* tp_reserved */ + (reprfunc)THPDtype_repr, /* tp_repr */ +- nullptr, /* tp_as_number */ +- nullptr, /* tp_as_sequence */ +- nullptr, /* tp_as_mapping */ +- nullptr, /* tp_hash */ +- nullptr, /* tp_call */ +- nullptr, /* tp_str */ +- nullptr, /* tp_getattro */ +- nullptr, /* tp_setattro */ +- nullptr, /* tp_as_buffer */ ++ nullptr, /* tp_as_number */ ++ nullptr, /* tp_as_sequence */ ++ nullptr, /* tp_as_mapping */ ++ nullptr, /* tp_hash */ ++ nullptr, /* tp_call */ ++ nullptr, /* tp_str */ ++ nullptr, /* tp_getattro */ ++ nullptr, /* tp_setattro */ ++ nullptr, /* tp_as_buffer */ + Py_TPFLAGS_DEFAULT, /* tp_flags */ + nullptr, /* tp_doc */ +- nullptr, /* tp_traverse */ +- nullptr, /* tp_clear */ +- nullptr, /* tp_richcompare */ ++ nullptr, /* tp_traverse */ ++ nullptr, /* tp_clear */ ++ nullptr, /* tp_richcompare */ + 0, /* tp_weaklistoffset */ +- nullptr, /* tp_iter */ +- nullptr, /* tp_iternext */ ++ nullptr, /* tp_iter */ ++ nullptr, /* tp_iternext */ + THPDtype_methods, /* tp_methods */ +- nullptr, /* tp_members */ ++ nullptr, /* tp_members */ + THPDtype_properties, /* tp_getset */ +- nullptr, /* tp_base */ +- nullptr, /* tp_dict */ +- nullptr, /* tp_descr_get */ +- nullptr, /* tp_descr_set */ ++ nullptr, /* tp_base */ ++ nullptr, /* tp_dict */ ++ nullptr, /* tp_descr_get */ ++ nullptr, /* tp_descr_set */ + 0, /* tp_dictoffset */ +- nullptr, /* tp_init */ +- nullptr, /* tp_alloc */ +- nullptr, /* tp_new */ ++ nullptr, /* tp_init */ ++ nullptr, /* tp_alloc */ ++ nullptr, /* tp_new */ + }; + + void THPDtype_init(PyObject *module) +diff --git a/torch/csrc/Generator.cpp b/torch/csrc/Generator.cpp +index 2d7458dd99016..7ffe1b231b2b2 100644 +--- a/torch/csrc/Generator.cpp ++++ b/torch/csrc/Generator.cpp +@@ -182,7 +182,7 @@ PyTypeObject THPGeneratorType = { + sizeof(THPGenerator), /* tp_basicsize */ + 0, /* tp_itemsize */ + (destructor)THPGenerator_dealloc, /* tp_dealloc */ +- nullptr, /* tp_print */ ++ 0, /* tp_vectorcall_offset */ + nullptr, /* tp_getattr */ + nullptr, /* tp_setattr */ + nullptr, /* tp_reserved */ +diff --git a/torch/csrc/Layout.cpp b/torch/csrc/Layout.cpp +index 5bbd30d82ab23..552ca6121078b 100644 +--- a/torch/csrc/Layout.cpp ++++ b/torch/csrc/Layout.cpp +@@ -32,40 +32,40 @@ PyTypeObject THPLayoutType = { + "torch.layout", /* tp_name */ + sizeof(THPLayout), /* tp_basicsize */ + 0, /* tp_itemsize */ +- nullptr, /* tp_dealloc */ +- nullptr, /* tp_print */ +- nullptr, /* tp_getattr */ +- nullptr, /* tp_setattr */ +- nullptr, /* tp_reserved */ ++ nullptr, /* tp_dealloc */ ++ 0, /* tp_vectorcall_offset */ ++ nullptr, /* tp_getattr */ ++ nullptr, /* tp_setattr */ ++ nullptr, /* tp_reserved */ + (reprfunc)THPLayout_repr, /* tp_repr */ +- nullptr, /* tp_as_number */ +- nullptr, /* tp_as_sequence */ +- nullptr, /* tp_as_mapping */ +- nullptr, /* tp_hash */ +- nullptr, /* tp_call */ +- nullptr, /* tp_str */ +- nullptr, /* tp_getattro */ +- nullptr, /* tp_setattro */ +- nullptr, /* tp_as_buffer */ ++ nullptr, /* tp_as_number */ ++ nullptr, /* tp_as_sequence */ ++ nullptr, /* tp_as_mapping */ ++ nullptr, /* tp_hash */ ++ nullptr, /* tp_call */ ++ nullptr, /* tp_str */ ++ nullptr, /* tp_getattro */ ++ nullptr, /* tp_setattro */ ++ nullptr, /* tp_as_buffer */ + Py_TPFLAGS_DEFAULT, /* tp_flags */ + nullptr, /* tp_doc */ +- nullptr, /* tp_traverse */ +- nullptr, /* tp_clear */ +- nullptr, /* tp_richcompare */ ++ nullptr, /* tp_traverse */ ++ nullptr, /* tp_clear */ ++ nullptr, /* tp_richcompare */ + 0, /* tp_weaklistoffset */ +- nullptr, /* tp_iter */ +- nullptr, /* tp_iternext */ +- nullptr, /* tp_methods */ +- nullptr, /* tp_members */ +- nullptr, /* tp_getset */ +- nullptr, /* tp_base */ +- nullptr, /* tp_dict */ +- nullptr, /* tp_descr_get */ +- nullptr, /* tp_descr_set */ ++ nullptr, /* tp_iter */ ++ nullptr, /* tp_iternext */ ++ nullptr, /* tp_methods */ ++ nullptr, /* tp_members */ ++ nullptr, /* tp_getset */ ++ nullptr, /* tp_base */ ++ nullptr, /* tp_dict */ ++ nullptr, /* tp_descr_get */ ++ nullptr, /* tp_descr_set */ + 0, /* tp_dictoffset */ +- nullptr, /* tp_init */ +- nullptr, /* tp_alloc */ +- nullptr, /* tp_new */ ++ nullptr, /* tp_init */ ++ nullptr, /* tp_alloc */ ++ nullptr, /* tp_new */ + }; + + void THPLayout_init(PyObject *module) +diff --git a/torch/csrc/MemoryFormat.cpp b/torch/csrc/MemoryFormat.cpp +index 54ce6aad1240d..85d8750c659ca 100644 +--- a/torch/csrc/MemoryFormat.cpp ++++ b/torch/csrc/MemoryFormat.cpp +@@ -33,7 +33,7 @@ PyTypeObject THPMemoryFormatType = { + sizeof(THPMemoryFormat), /* tp_basicsize */ + 0, /* tp_itemsize */ + nullptr, /* tp_dealloc */ +- nullptr, /* tp_print */ ++ 0, /* tp_vectorcall_offset */ + nullptr, /* tp_getattr */ + nullptr, /* tp_setattr */ + nullptr, /* tp_reserved */ +diff --git a/torch/csrc/PtrWrapper.cpp b/torch/csrc/PtrWrapper.cpp +index 407c40ea8e025..aa48c49949b9b 100644 +--- a/torch/csrc/PtrWrapper.cpp ++++ b/torch/csrc/PtrWrapper.cpp +@@ -53,11 +53,11 @@ static void THPWrapper_dealloc(THPWrapper* self) + + PyTypeObject THPWrapperType = { + PyVarObject_HEAD_INIT(nullptr, 0) +- "torch._C._PtrWrapper", /* tp_name */ +- sizeof(THPWrapper), /* tp_basicsize */ +- 0, /* tp_itemsize */ +- (destructor)THPWrapper_dealloc, /* tp_dealloc */ +- nullptr, /* tp_print */ ++ "torch._C._PtrWrapper", /* tp_name */ ++ sizeof(THPWrapper), /* tp_basicsize */ ++ 0, /* tp_itemsize */ ++ (destructor)THPWrapper_dealloc, /* tp_dealloc */ ++ 0, /* tp_vectorcall_offset */ + nullptr, /* tp_getattr */ + nullptr, /* tp_setattr */ + nullptr, /* tp_reserved */ +@@ -71,12 +71,12 @@ PyTypeObject THPWrapperType = { + nullptr, /* tp_getattro */ + nullptr, /* tp_setattro */ + nullptr, /* tp_as_buffer */ +- Py_TPFLAGS_DEFAULT, /* tp_flags */ +- nullptr, /* tp_doc */ ++ Py_TPFLAGS_DEFAULT, /* tp_flags */ ++ nullptr, /* tp_doc */ + nullptr, /* tp_traverse */ + nullptr, /* tp_clear */ + nullptr, /* tp_richcompare */ +- 0, /* tp_weaklistoffset */ ++ 0, /* tp_weaklistoffset */ + nullptr, /* tp_iter */ + nullptr, /* tp_iternext */ + nullptr, /* tp_methods */ +@@ -86,10 +86,10 @@ PyTypeObject THPWrapperType = { + nullptr, /* tp_dict */ + nullptr, /* tp_descr_get */ + nullptr, /* tp_descr_set */ +- 0, /* tp_dictoffset */ ++ 0, /* tp_dictoffset */ + nullptr, /* tp_init */ + nullptr, /* tp_alloc */ +- THPWrapper_pynew, /* tp_new */ ++ THPWrapper_pynew, /* tp_new */ + }; + + bool THPWrapper_init(PyObject *module) +diff --git a/torch/csrc/QScheme.cpp b/torch/csrc/QScheme.cpp +index eb73652a6a408..274ccf890df3c 100644 +--- a/torch/csrc/QScheme.cpp ++++ b/torch/csrc/QScheme.cpp +@@ -43,7 +43,7 @@ PyTypeObject THPQSchemeType = { + sizeof(THPQScheme), /* tp_basicsize */ + 0, /* tp_itemsize */ + nullptr, /* tp_dealloc */ +- nullptr, /* tp_print */ ++ 0, /* tp_vectorcall_offset */ + nullptr, /* tp_getattr */ + nullptr, /* tp_setattr */ + nullptr, /* tp_reserved */ +diff --git a/torch/csrc/Size.cpp b/torch/csrc/Size.cpp +index 15902d9b09667..d02d016876b67 100644 +--- a/torch/csrc/Size.cpp ++++ b/torch/csrc/Size.cpp +@@ -186,39 +186,39 @@ PyTypeObject THPSizeType = { + "torch.Size", /* tp_name */ + sizeof(THPSize), /* tp_basicsize */ + 0, /* tp_itemsize */ +- nullptr, /* tp_dealloc */ +- nullptr, /* tp_print */ +- nullptr, /* tp_getattr */ +- nullptr, /* tp_setattr */ +- nullptr, /* tp_reserved */ ++ nullptr, /* tp_dealloc */ ++ 0, /* tp_vectorcall_offset */ ++ nullptr, /* tp_getattr */ ++ nullptr, /* tp_setattr */ ++ nullptr, /* tp_reserved */ + (reprfunc)THPSize_repr, /* tp_repr */ +- nullptr, /* tp_as_number */ ++ nullptr, /* tp_as_number */ + &THPSize_as_sequence, /* tp_as_sequence */ + &THPSize_as_mapping, /* tp_as_mapping */ +- nullptr, /* tp_hash */ +- nullptr, /* tp_call */ +- nullptr, /* tp_str */ +- nullptr, /* tp_getattro */ +- nullptr, /* tp_setattro */ +- nullptr, /* tp_as_buffer */ ++ nullptr, /* tp_hash */ ++ nullptr, /* tp_call */ ++ nullptr, /* tp_str */ ++ nullptr, /* tp_getattro */ ++ nullptr, /* tp_setattro */ ++ nullptr, /* tp_as_buffer */ + Py_TPFLAGS_DEFAULT, /* tp_flags */ + nullptr, /* tp_doc */ +- nullptr, /* tp_traverse */ +- nullptr, /* tp_clear */ +- nullptr, /* tp_richcompare */ ++ nullptr, /* tp_traverse */ ++ nullptr, /* tp_clear */ ++ nullptr, /* tp_richcompare */ + 0, /* tp_weaklistoffset */ +- nullptr, /* tp_iter */ +- nullptr, /* tp_iternext */ ++ nullptr, /* tp_iter */ ++ nullptr, /* tp_iternext */ + THPSize_methods, /* tp_methods */ +- nullptr, /* tp_members */ +- nullptr, /* tp_getset */ ++ nullptr, /* tp_members */ ++ nullptr, /* tp_getset */ + &PyTuple_Type, /* tp_base */ +- nullptr, /* tp_dict */ +- nullptr, /* tp_descr_get */ +- nullptr, /* tp_descr_set */ ++ nullptr, /* tp_dict */ ++ nullptr, /* tp_descr_get */ ++ nullptr, /* tp_descr_set */ + 0, /* tp_dictoffset */ +- nullptr, /* tp_init */ +- nullptr, /* tp_alloc */ ++ nullptr, /* tp_init */ ++ nullptr, /* tp_alloc */ + THPSize_pynew, /* tp_new */ + }; + +diff --git a/torch/csrc/TypeInfo.cpp b/torch/csrc/TypeInfo.cpp +index 8fd9a0b49c701..56d668e1ae972 100644 +--- a/torch/csrc/TypeInfo.cpp ++++ b/torch/csrc/TypeInfo.cpp +@@ -193,7 +193,7 @@ PyTypeObject THPFInfoType = { + sizeof(THPFInfo), /* tp_basicsize */ + 0, /* tp_itemsize */ + nullptr, /* tp_dealloc */ +- nullptr, /* tp_print */ ++ 0, /* tp_vectorcall_offset */ + nullptr, /* tp_getattr */ + nullptr, /* tp_setattr */ + nullptr, /* tp_reserved */ +@@ -243,7 +243,7 @@ PyTypeObject THPIInfoType = { + sizeof(THPIInfo), /* tp_basicsize */ + 0, /* tp_itemsize */ + nullptr, /* tp_dealloc */ +- nullptr, /* tp_print */ ++ 0, /* tp_vectorcall_offset */ + nullptr, /* tp_getattr */ + nullptr, /* tp_setattr */ + nullptr, /* tp_reserved */ +diff --git a/torch/csrc/autograd/python_engine.cpp b/torch/csrc/autograd/python_engine.cpp +index 26f1a412bb86b..0b40ce3e98814 100644 +--- a/torch/csrc/autograd/python_engine.cpp ++++ b/torch/csrc/autograd/python_engine.cpp +@@ -255,11 +255,11 @@ static struct PyMethodDef THPEngine_methods[] = { + + PyTypeObject THPEngineType = { + PyVarObject_HEAD_INIT(nullptr, 0) +- "torch._C._EngineBase", /* tp_name */ +- sizeof(THPEngine), /* tp_basicsize */ +- 0, /* tp_itemsize */ ++ "torch._C._EngineBase", /* tp_name */ ++ sizeof(THPEngine), /* tp_basicsize */ ++ 0, /* tp_itemsize */ + nullptr, /* tp_dealloc */ +- nullptr, /* tp_print */ ++ 0, /* tp_vectorcall_offset */ + nullptr, /* tp_getattr */ + nullptr, /* tp_setattr */ + nullptr, /* tp_reserved */ +@@ -273,25 +273,25 @@ PyTypeObject THPEngineType = { + nullptr, /* tp_getattro */ + nullptr, /* tp_setattro */ + nullptr, /* tp_as_buffer */ +- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ +- nullptr, /* tp_doc */ ++ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ ++ nullptr, /* tp_doc */ + nullptr, /* tp_traverse */ + nullptr, /* tp_clear */ + nullptr, /* tp_richcompare */ +- 0, /* tp_weaklistoffset */ ++ 0, /* tp_weaklistoffset */ + nullptr, /* tp_iter */ + nullptr, /* tp_iternext */ +- THPEngine_methods, /* tp_methods */ ++ THPEngine_methods, /* tp_methods */ + nullptr, /* tp_members */ + nullptr, /* tp_getset */ + nullptr, /* tp_base */ + nullptr, /* tp_dict */ + nullptr, /* tp_descr_get */ + nullptr, /* tp_descr_set */ +- 0, /* tp_dictoffset */ ++ 0, /* tp_dictoffset */ + nullptr, /* tp_init */ + nullptr, /* tp_alloc */ +- THPEngine_new /* tp_new */ ++ THPEngine_new /* tp_new */ + }; + + static void child_atfork() { +diff --git a/torch/csrc/autograd/python_function.cpp b/torch/csrc/autograd/python_function.cpp +index 517bb068f7803..df17cb194a84e 100644 +--- a/torch/csrc/autograd/python_function.cpp ++++ b/torch/csrc/autograd/python_function.cpp +@@ -1063,11 +1063,11 @@ static struct PyMethodDef THPFunction_methods[] = { + + PyTypeObject THPFunctionType = { + PyVarObject_HEAD_INIT(nullptr, 0) +- "torch._C._FunctionBase", /* tp_name */ +- sizeof(THPFunction), /* tp_basicsize */ +- 0, /* tp_itemsize */ +- (destructor)THPFunction_dealloc, /* tp_dealloc */ +- nullptr, /* tp_print */ ++ "torch._C._FunctionBase", /* tp_name */ ++ sizeof(THPFunction), /* tp_basicsize */ ++ 0, /* tp_itemsize */ ++ (destructor)THPFunction_dealloc, /* tp_dealloc */ ++ 0, /* tp_vectorcall_offset */ + nullptr, /* tp_getattr */ + nullptr, /* tp_setattr */ + nullptr, /* tp_reserved */ +@@ -1082,24 +1082,24 @@ PyTypeObject THPFunctionType = { + nullptr, /* tp_setattro */ + nullptr, /* tp_as_buffer */ + Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE | Py_TPFLAGS_HAVE_GC, /* tp_flags */ +- nullptr, /* tp_doc */ +- (traverseproc)THPFunction_traverse, /* tp_traverse */ +- (inquiry)THPFunction_clear, /* tp_clear */ ++ nullptr, /* tp_doc */ ++ (traverseproc)THPFunction_traverse, /* tp_traverse */ ++ (inquiry)THPFunction_clear, /* tp_clear */ + nullptr, /* tp_richcompare */ +- 0, /* tp_weaklistoffset */ ++ 0, /* tp_weaklistoffset */ + nullptr, /* tp_iter */ + nullptr, /* tp_iternext */ +- THPFunction_methods, /* tp_methods */ ++ THPFunction_methods, /* tp_methods */ + nullptr, /* tp_members */ +- THPFunction_properties, /* tp_getset */ ++ THPFunction_properties, /* tp_getset */ + nullptr, /* tp_base */ + nullptr, /* tp_dict */ + nullptr, /* tp_descr_get */ + nullptr, /* tp_descr_set */ +- 0, /* tp_dictoffset */ ++ 0, /* tp_dictoffset */ + nullptr, /* tp_init */ + nullptr, /* tp_alloc */ +- THPFunction_new /* tp_new */ ++ THPFunction_new /* tp_new */ + }; + + bool THPFunction_initModule(PyObject *module) +diff --git a/torch/csrc/autograd/python_legacy_variable.cpp b/torch/csrc/autograd/python_legacy_variable.cpp +index c57975bbda77b..c27579d40c6e3 100644 +--- a/torch/csrc/autograd/python_legacy_variable.cpp ++++ b/torch/csrc/autograd/python_legacy_variable.cpp +@@ -90,11 +90,11 @@ static PyObject *THPVariable_pynew(PyTypeObject* type, PyObject *args, PyObject + + PyTypeObject THPLegacyVariableType = { + PyVarObject_HEAD_INIT(nullptr, 0) +- "torch._C._LegacyVariableBase", /* tp_name */ +- 0, /* tp_basicsize */ +- 0, /* tp_itemsize */ ++ "torch._C._LegacyVariableBase", /* tp_name */ ++ 0, /* tp_basicsize */ ++ 0, /* tp_itemsize */ + nullptr, /* tp_dealloc */ +- nullptr, /* tp_print */ ++ 0, /* tp_vectorcall_offset */ + nullptr, /* tp_getattr */ + nullptr, /* tp_setattr */ + nullptr, /* tp_reserved */ +@@ -108,12 +108,12 @@ PyTypeObject THPLegacyVariableType = { + nullptr, /* tp_getattro */ + nullptr, /* tp_setattro */ + nullptr, /* tp_as_buffer */ +- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ +- nullptr, /* tp_doc */ ++ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ ++ nullptr, /* tp_doc */ + nullptr, /* tp_traverse */ + nullptr, /* tp_clear */ + nullptr, /* tp_richcompare */ +- 0, /* tp_weaklistoffset */ ++ 0, /* tp_weaklistoffset */ + nullptr, /* tp_iter */ + nullptr, /* tp_iternext */ + nullptr, /* tp_methods */ +@@ -123,10 +123,10 @@ PyTypeObject THPLegacyVariableType = { + nullptr, /* tp_dict */ + nullptr, /* tp_descr_get */ + nullptr, /* tp_descr_set */ +- 0, /* tp_dictoffset */ ++ 0, /* tp_dictoffset */ + nullptr, /* tp_init */ + nullptr, /* tp_alloc */ +- THPVariable_pynew /* tp_new */ ++ THPVariable_pynew /* tp_new */ + }; + + void init_legacy_variable(PyObject *module) { +diff --git a/torch/csrc/autograd/python_variable.cpp b/torch/csrc/autograd/python_variable.cpp +index cd97099780eb6..a77a00d0b35f4 100644 +--- a/torch/csrc/autograd/python_variable.cpp ++++ b/torch/csrc/autograd/python_variable.cpp +@@ -541,18 +541,18 @@ static PyMethodDef extra_methods[] = { + + PyTypeObject THPVariableType = { + PyVarObject_HEAD_INIT(nullptr, 0) +- "torch._C._TensorBase", /* tp_name */ +- sizeof(THPVariable), /* tp_basicsize */ +- 0, /* tp_itemsize */ +- (destructor)THPVariable_dealloc, /* tp_dealloc */ +- nullptr, /* tp_print */ ++ "torch._C._TensorBase", /* tp_name */ ++ sizeof(THPVariable), /* tp_basicsize */ ++ 0, /* tp_itemsize */ ++ (destructor)THPVariable_dealloc, /* tp_dealloc */ ++ 0, /* tp_vectorcall_offset */ + nullptr, /* tp_getattr */ + nullptr, /* tp_setattr */ + nullptr, /* tp_reserved */ + nullptr, /* tp_repr */ + nullptr, /* tp_as_number */ + nullptr, /* tp_as_sequence */ +- &THPVariable_as_mapping, /* tp_as_mapping */ ++ &THPVariable_as_mapping, /* tp_as_mapping */ + nullptr, /* tp_hash */ + nullptr, /* tp_call */ + nullptr, /* tp_str */ +@@ -560,24 +560,24 @@ PyTypeObject THPVariableType = { + nullptr, /* tp_setattro */ + nullptr, /* tp_as_buffer */ + Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE | Py_TPFLAGS_HAVE_GC, /* tp_flags */ +- nullptr, /* tp_doc */ +- (traverseproc)THPVariable_traverse, /* tp_traverse */ +- (inquiry)THPVariable_clear, /* tp_clear */ ++ nullptr, /* tp_doc */ ++ (traverseproc)THPVariable_traverse, /* tp_traverse */ ++ (inquiry)THPVariable_clear, /* tp_clear */ + nullptr, /* tp_richcompare */ +- 0, /* tp_weaklistoffset */ ++ 0, /* tp_weaklistoffset */ + nullptr, /* tp_iter */ + nullptr, /* tp_iternext */ + nullptr, /* tp_methods */ + nullptr, /* tp_members */ +- THPVariable_properties, /* tp_getset */ ++ THPVariable_properties, /* tp_getset */ + nullptr, /* tp_base */ + nullptr, /* tp_dict */ + nullptr, /* tp_descr_get */ + nullptr, /* tp_descr_set */ +- 0, /* tp_dictoffset */ ++ 0, /* tp_dictoffset */ + nullptr, /* tp_init */ + nullptr, /* tp_alloc */ +- THPVariable_pynew /* tp_new */ ++ THPVariable_pynew /* tp_new */ + }; + + namespace torch { namespace autograd { +diff --git a/torch/csrc/cuda/Event.cpp b/torch/csrc/cuda/Event.cpp +index 6615dbd4c417b..c19e57db4c1b3 100644 +--- a/torch/csrc/cuda/Event.cpp ++++ b/torch/csrc/cuda/Event.cpp +@@ -164,7 +164,7 @@ PyTypeObject THCPEventType = { + sizeof(THCPEvent), /* tp_basicsize */ + 0, /* tp_itemsize */ + (destructor)THCPEvent_dealloc, /* tp_dealloc */ +- 0, /* tp_print */ ++ 0, /* tp_vectorcall_offset */ + 0, /* tp_getattr */ + 0, /* tp_setattr */ + 0, /* tp_reserved */ +diff --git a/torch/csrc/cuda/Stream.cpp b/torch/csrc/cuda/Stream.cpp +index bbe4b0eeadaa3..761b68efb6bfd 100644 +--- a/torch/csrc/cuda/Stream.cpp ++++ b/torch/csrc/cuda/Stream.cpp +@@ -126,7 +126,7 @@ PyTypeObject THCPStreamType = { + sizeof(THCPStream), /* tp_basicsize */ + 0, /* tp_itemsize */ + (destructor)THCPStream_dealloc, /* tp_dealloc */ +- 0, /* tp_print */ ++ 0, /* tp_vectorcall_offset */ + 0, /* tp_getattr */ + 0, /* tp_setattr */ + 0, /* tp_reserved */ +diff --git a/torch/csrc/generic/Storage.cpp b/torch/csrc/generic/Storage.cpp +index 5faac8f25596d..e39d1c4b576bc 100644 +--- a/torch/csrc/generic/Storage.cpp ++++ b/torch/csrc/generic/Storage.cpp +@@ -235,30 +235,30 @@ static PyMappingMethods THPStorage_(mappingmethods) = { + // TODO: implement equality + PyTypeObject THPStorageType = { + PyVarObject_HEAD_INIT(nullptr, 0) +- "torch._C." THPStorageBaseStr, /* tp_name */ +- sizeof(THPStorage), /* tp_basicsize */ +- 0, /* tp_itemsize */ +- (destructor)THPStorage_(dealloc), /* tp_dealloc */ +- nullptr, /* tp_print */ ++ "torch._C." THPStorageBaseStr, /* tp_name */ ++ sizeof(THPStorage), /* tp_basicsize */ ++ 0, /* tp_itemsize */ ++ (destructor)THPStorage_(dealloc), /* tp_dealloc */ ++ 0, /* tp_vectorcall_offset */ + nullptr, /* tp_getattr */ + nullptr, /* tp_setattr */ + nullptr, /* tp_reserved */ + nullptr, /* tp_repr */ + nullptr, /* tp_as_number */ + nullptr, /* tp_as_sequence */ +- &THPStorage_(mappingmethods), /* tp_as_mapping */ ++ &THPStorage_(mappingmethods), /* tp_as_mapping */ + nullptr, /* tp_hash */ + nullptr, /* tp_call */ + nullptr, /* tp_str */ + nullptr, /* tp_getattro */ + nullptr, /* tp_setattro */ + nullptr, /* tp_as_buffer */ +- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ +- nullptr, /* tp_doc */ ++ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ ++ nullptr, /* tp_doc */ + nullptr, /* tp_traverse */ + nullptr, /* tp_clear */ + nullptr, /* tp_richcompare */ +- 0, /* tp_weaklistoffset */ ++ 0, /* tp_weaklistoffset */ + nullptr, /* tp_iter */ + nullptr, /* tp_iternext */ + nullptr, /* will be assigned in init */ /* tp_methods */ +@@ -268,10 +268,10 @@ PyTypeObject THPStorageType = { + nullptr, /* tp_dict */ + nullptr, /* tp_descr_get */ + nullptr, /* tp_descr_set */ +- 0, /* tp_dictoffset */ ++ 0, /* tp_dictoffset */ + nullptr, /* tp_init */ + nullptr, /* tp_alloc */ +- THPStorage_(pynew), /* tp_new */ ++ THPStorage_(pynew), /* tp_new */ + }; + + static struct PyMemberDef THPStorage_(members)[] = { diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-jit-support-for-cuda11.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-jit-support-for-cuda11.patch new file mode 100644 index 00000000000..8bf1b9c91f6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-jit-support-for-cuda11.patch @@ -0,0 +1,32 @@ +Add SM 8 for nvrtc 11 so it can JIT compile to SM 8.0 directly instead of to 7.x first +and the having the CUDA driver compile for SM 8.0 again. + +Author: Alexander Grund (TU Dresden) +diff --git a/torch/csrc/jit/fuser/cuda/fused_kernel.cpp b/torch/csrc/jit/fuser/cuda/fused_kernel.cpp +index 4f2f7ebb9b..b2d310316f 100644 +--- a/torch/csrc/jit/fuser/cuda/fused_kernel.cpp ++++ b/torch/csrc/jit/fuser/cuda/fused_kernel.cpp +@@ -51,16 +51,15 @@ static void getMajorMinor( + minor = 0; + } else if (nvrtc_major <= 9 && prop->major >= 7) { // 9 supports 3-7.2 + major = 7; +- if (prop->major == 7 && prop->minor <= 2) +- minor = prop->minor; +- else +- minor = 0; ++ minor = (prop->major == 7 && prop->minor <= 2) ? prop->minor : 0; + } else if (nvrtc_major <= 10 && prop->major >= 7) { // 10 supports 3-7.5 + major = 7; +- if (prop->major == 7 && prop->minor <= 5) +- minor = prop->minor; +- else +- minor = 0; ++ minor = (prop->major == 7 && prop->minor <= 5) ? prop->minor : 0; ++ } else if ( ++ nvrtc_major == 11 && nvrtc_minor == 0 && ++ prop->major >= 8) { // 11.0 supports 3.5-8.0 ++ major = 8; ++ minor = 0; + } + } + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-support-for-cuda11.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-support-for-cuda11.patch new file mode 100644 index 00000000000..3c4b8923cf3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-support-for-cuda11.patch @@ -0,0 +1,273 @@ +Add support for CUDA 11 and CCC 8.0 using various changes from upstream (PyTorch 1.6+) + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/utils/cpp_extension.py b/torch/utils/cpp_extension.py +index 98ad0f4f7d..99b5a706ee 100644 +--- a/torch/utils/cpp_extension.py ++++ b/torch/utils/cpp_extension.py +@@ -963,7 +963,7 @@ def _get_cuda_arch_flags(cflags=None): + ]) + + supported_arches = ['3.5', '3.7', '5.0', '5.2', '5.3', '6.0', '6.1', '6.2', +- '7.0', '7.2', '7.5'] ++ '7.0', '7.2', '7.5', '8.0'] + valid_arch_strings = supported_arches + [s + "+PTX" for s in supported_arches] + + # The default is sm_30 for CUDA 9.x and 10.x +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 909d6b914a..f1e1e2e37e 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -502,6 +502,8 @@ if(NOT APPLE AND UNIX) + list(APPEND Caffe2_DEPENDENCY_LIBS dl) + endif() + ++add_definitions(-DTHRUST_IGNORE_DEPRECATED_CPP_DIALECT -DCUB_IGNORE_DEPRECATED_CPP_DIALECT) ++ + # Prefix path to Caffe2 headers. + # If a directory containing installed Caffe2 headers was inadvertently + # added to the list of include directories, prefixing +diff --git a/aten/src/ATen/native/sparse/cuda/SparseCUDABlas.cu b/aten/src/ATen/native/sparse/cuda/SparseCUDABlas.cu +index e13d383221..2be3fd2b73 100644 +--- a/aten/src/ATen/native/sparse/cuda/SparseCUDABlas.cu ++++ b/aten/src/ATen/native/sparse/cuda/SparseCUDABlas.cu +@@ -2,14 +2,29 @@ + #include + #include + #include ++#include + + #include + + #include + +-namespace at { namespace native { namespace sparse { namespace cuda { ++// LIMITATION (cusparseSpMM): ++// The generic APIs are available on all platforms on CUDA 11.0 ++// For CUDA 10.1+ it is available for all platforms except Windows. ++// Using these APIs in any other systems will result in compile-time or run-time failures. ++// Their support will be extended in the next releases. ++ ++#if defined(__CUDACC__) && (CUSPARSE_VERSION >= 11000 || (!defined(_MSC_VER) && CUSPARSE_VERSION >= 10301)) ++#define IS_SPMM_AVAILABLE() 1 ++#else ++#define IS_SPMM_AVAILABLE() 0 ++#endif ++ ++#if IS_SPMM_AVAILABLE() ++#include ++#endif + +-#if (!((CUSPARSE_VER_MAJOR >= 10) && (CUSPARSE_VER_MINOR >= 2))) ++#if !defined(CUSPARSE_VERSION) || (CUSPARSE_VERSION < 10100) + std::string cusparseGetErrorString(cusparseStatus_t status) { + switch(status) + { +@@ -66,7 +81,9 @@ inline cusparseHandle_t setCUDASparseStream() { + return handle; + } + +-void Xcoo2csr(const int *coorowind, int64_t nnz, int64_t m, int *csrrowptr) { ++namespace at { namespace native { namespace sparse { namespace cuda { ++ ++ void Xcoo2csr(const int *coorowind, int64_t nnz, int64_t m, int *csrrowptr) { + TORCH_CHECK((m <= INT_MAX) && (nnz <= INT_MAX), + "cusparseXcoo2csr only supports m, nnz with the bound [val] <= ", + INT_MAX); +@@ -106,6 +123,116 @@ void adjustLd(char transb, int64_t m, int64_t n, int64_t k, int64_t *ldb, int64_ + } + } + ++#if IS_SPMM_AVAILABLE() ++ ++template ++void csrmm2( ++ char transa, char transb, ++ int64_t m, int64_t n, int64_t k, int64_t nnz, ++ T alpha, T *csrvala, int *csrrowptra, int *csrcolinda, ++ T *b, int64_t ldb, T beta, T *c, int64_t ldc) ++{ ++ static_assert(std::is_same::value || std::is_same::value, "csrmm2 only supports float and double value types"); ++ constexpr auto cusparse_value_type = std::is_same::value ? CUDA_R_32F : CUDA_R_64F; ++ ++ if (csrvala == nullptr || b == nullptr || c == nullptr) return; ++ ++ cusparseOperation_t opa = convertTransToCusparseOperation(transa); ++ cusparseOperation_t opb = convertTransToCusparseOperation(transb); ++ ++ // cusparseSpMM actually supports int64_t. ++ // In order to support int64 here, index pointers csrrowptra, csrcolinda have to be passed as int64_t. ++ TORCH_CHECK((m <= INT_MAX) && (n <= INT_MAX) && (k <= INT_MAX) && (nnz <= INT_MAX) && (ldb <= INT_MAX) && (ldc <= INT_MAX), ++ "At the moment, cusparseSpMM only supports m, n, k, nnz, ldb, ldc with the bound [val] <= ", INT_MAX, ".", ++ "If you need this, please file an issue on GitHub." ++ ); ++ ++ int64_t ma = m, ka = k; ++ if (transa != 'n') std::swap(ma, ka); ++ ++ cusparseSpMatDescr_t descA; ++ CUSPARSE_CHECK(cusparseCreateCsr( ++ &descA, /* output */ ++ ma, ka, nnz, /* rows, cols, number of non zero elements */ ++ csrrowptra, /* row offsets of the sparse matrix, size = rows +1 */ ++ csrcolinda, /* column indices of the sparse matrix, size = nnz */ ++ csrvala, /* values of the sparse matrix, size = nnz */ ++ CUSPARSE_INDEX_32I, /* data type of row offsets index */ ++ CUSPARSE_INDEX_32I, /* data type of col indices */ ++ CUSPARSE_INDEX_BASE_ZERO, /* base index of row offset and col indes */ ++ cusparse_value_type /* data type of values */ ++ )); ++ ++ int64_t kb = k, nb = n; ++ if (transb != 'n') std::swap(kb, nb); ++ ++ cusparseDnMatDescr_t descB; ++ CUSPARSE_CHECK(cusparseCreateDnMat( ++ &descB, /* output */ ++ kb, nb, ldb, /* rows, cols, leading dimension */ ++ b, /* values */ ++ cusparse_value_type, /* data type of values */ ++ CUSPARSE_ORDER_COL /* memory layout, ONLY column-major is supported now */ ++ )); ++ ++ cusparseDnMatDescr_t descC; ++ CUSPARSE_CHECK(cusparseCreateDnMat( ++ &descC, /* output */ ++ m, n, ldc, /* rows, cols, leading dimension */ ++ c, /* values */ ++ cusparse_value_type, /* data type of values */ ++ CUSPARSE_ORDER_COL /* memory layout, ONLY column-major is supported now */ ++ )); ++ ++ ++ auto handle = at::cuda::getCurrentCUDASparseHandle(); ++ ++ // cusparseSpMM_bufferSize returns the bufferSize that can be used by cusparseSpMM ++ size_t bufferSize; ++ CUSPARSE_CHECK(cusparseSpMM_bufferSize( ++ handle, opa, opb, ++ &alpha, ++ descA, descB, ++ &beta, ++ descC, ++ cusparse_value_type, /* data type in which the computation is executed */ ++ CUSPARSE_CSRMM_ALG1, /* default computing algorithm for CSR sparse matrix format */ ++ &bufferSize /* output */ ++ )); ++ ++ auto& allocator = *c10::cuda::CUDACachingAllocator::get(); ++ auto dataPtr = allocator.allocate(bufferSize); ++ ++ CUSPARSE_CHECK(cusparseSpMM( ++ handle, opa, opb, ++ &alpha, ++ descA, descB, ++ &beta, ++ descC, ++ cusparse_value_type, /* data type in which the computation is executed */ ++ CUSPARSE_CSRMM_ALG1, /* default computing algorithm for CSR sparse matrix format */ ++ dataPtr.get() /* external buffer */ ++ )); ++ ++ CUSPARSE_CHECK(cusparseDestroySpMat(descA)); ++ CUSPARSE_CHECK(cusparseDestroyDnMat(descB)); ++ CUSPARSE_CHECK(cusparseDestroyDnMat(descC)); ++ ++ // TODO: Proper fix is to create real descriptor classes ++} ++template void csrmm2( ++ char transa, char transb, ++ int64_t m, int64_t n, int64_t k, int64_t nnz, ++ float alpha, float *csrvala, int *csrrowptra, int *csrcolinda, ++ float *b, int64_t ldb, float beta, float *c, int64_t ldc); ++template void csrmm2( ++ char transa, char transb, ++ int64_t m, int64_t n, int64_t k, int64_t nnz, ++ double alpha, double *csrvala, int *csrrowptra, int *csrcolinda, ++ double *b, int64_t ldb, double beta, double *c, int64_t ldc); ++ ++#else ++ + /* Level 3 */ + void Scsrmm2(char transa, char transb, int64_t m, int64_t n, int64_t k, int64_t nnz, float alpha, float *csrvala, int *csrrowptra, int *csrcolinda, float *b, int64_t ldb, float beta, float *c, int64_t ldc) + { +@@ -153,6 +280,37 @@ void Dcsrmm2(char transa, char transb, int64_t m, int64_t n, int64_t k, int64_t + // TODO: Proper fix is to create real descriptor classes + } + ++// T can only be float or double ++template ++void csrmm2( ++ char transa, char transb, ++ int64_t m, int64_t n, int64_t k, int64_t nnz, ++ T alpha, T *csrvala, int *csrrowptra, int *csrcolinda, ++ T *b, int64_t ldb, T beta, T *c, int64_t ldc) ++{ ++ TORCH_INTERNAL_ASSERT(false, "cusparse csr MM only supports data type of float and double."); ++} ++ ++template<> void csrmm2( ++ char transa, char transb, ++ int64_t m, int64_t n, int64_t k, int64_t nnz, ++ float alpha, float *csrvala, int *csrrowptra, int *csrcolinda, ++ float *b, int64_t ldb, float beta, float *c, int64_t ldc) ++{ ++ Scsrmm2(transa, transb, m, n, k, nnz, alpha, csrvala, csrrowptra, csrcolinda, b, ldb, beta, c, ldc); ++} ++ ++template<> void csrmm2( ++ char transa, char transb, ++ int64_t m, int64_t n, int64_t k, int64_t nnz, ++ double alpha, double *csrvala, int *csrrowptra, int *csrcolinda, ++ double *b, int64_t ldb, double beta, double *c, int64_t ldc) ++{ ++ Dcsrmm2(transa, transb, m, n, k, nnz, alpha, csrvala, csrrowptra, csrcolinda, b, ldb, beta, c, ldc); ++} ++ ++#endif ++ + /* format conversion */ + void CreateIdentityPermutation(int64_t nnz, int *P) { + TORCH_CHECK((nnz <= INT_MAX), +diff --git a/aten/src/ATen/native/sparse/cuda/SparseCUDABlas.cuh b/aten/src/ATen/native/sparse/cuda/SparseCUDABlas.cuh +index ed800fcb93..1979f3af4c 100644 +--- a/aten/src/ATen/native/sparse/cuda/SparseCUDABlas.cuh ++++ b/aten/src/ATen/native/sparse/cuda/SparseCUDABlas.cuh +@@ -7,12 +7,8 @@ namespace at { namespace native { namespace sparse { namespace cuda { + AT_CUDA_API void Xcoo2csr(const int *coorowind, int64_t nnz, int64_t m, int *csrrowptr); + + /* Level 3 */ +-AT_CUDA_API void Scsrmm2(char transa, char transb, int64_t m, int64_t n, int64_t k, int64_t nnz, float alpha, float *csrvala, int *csrrowptra, int *csrcolinda, float *b, int64_t ldb, float beta, float *c, int64_t ldc); +-AT_CUDA_API void Dcsrmm2(char transa, char transb, int64_t m, int64_t n, int64_t k, int64_t nnz, double alpha, double *csrvala, int *csrrowptra, int *csrcolinda, double *b, int64_t ldb, double beta, double *c, int64_t ldc); +- +-// overloaded version +-inline void csrmm2(char transa, char transb, int64_t m, int64_t n, int64_t k, int64_t nnz, float alpha, float *csrvala, int *csrrowptra, int *csrcolinda, float *b, int64_t ldb, float beta, float *c, int64_t ldc) { Scsrmm2(transa, transb, m, n, k, nnz, alpha, csrvala, csrrowptra, csrcolinda, b, ldb, beta, c, ldc); } +-inline void csrmm2(char transa, char transb, int64_t m, int64_t n, int64_t k, int64_t nnz, double alpha, double *csrvala, int *csrrowptra, int *csrcolinda, double *b, int64_t ldb, double beta, double *c, int64_t ldc) { Dcsrmm2(transa, transb, m, n, k, nnz, alpha, csrvala, csrrowptra, csrcolinda, b, ldb, beta, c, ldc); } ++template ++AT_CUDA_API void csrmm2(char transa, char transb, int64_t m, int64_t n, int64_t k, int64_t nnz, T alpha, T *csrvala, int *csrrowptra, int *csrcolinda, T *b, int64_t ldb, T beta, T *c, int64_t ldc); + + /* format conversion */ + AT_CUDA_API void CreateIdentityPermutation(int64_t nnz, int *P); +diff --git a/caffe2/utils/GpuDefs.cuh b/caffe2/utils/GpuDefs.cuh +index 73c8cfdf26..d24cc6f58c 100644 +--- a/caffe2/utils/GpuDefs.cuh ++++ b/caffe2/utils/GpuDefs.cuh +@@ -7,16 +7,9 @@ namespace caffe2 { + + // Static definition of GPU warp size for unrolling and code generation + +-#ifdef __CUDA_ARCH__ +-#if __CUDA_ARCH__ <= 750 +-constexpr int kWarpSize = 32; +-#else +-#error Unknown __CUDA_ARCH__; please define parameters for compute capability +-#endif // __CUDA_ARCH__ types +-#elif defined(__HIP_PLATFORM_HCC__) ++#if defined(__HIP_PLATFORM_HCC__) + constexpr int kWarpSize = warpSize; // = 64 (Defined in hip_runtime.h) + #else +-// dummy value for host compiler + constexpr int kWarpSize = 32; + #endif // __CUDA_ARCH__ + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-support-for-cudnn8.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-support-for-cudnn8.patch new file mode 100644 index 00000000000..efaf24e25cb --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_add-support-for-cudnn8.patch @@ -0,0 +1,238 @@ +Collect various commits from upstream PyTorch 1.6+ to allow building against cuDNN 8. + +Author: Alexander Grund (TU Dresden) + +diff --git a/cmake/public/cuda.cmake b/cmake/public/cuda.cmake +index 8e3a0ca873..84adf901ad 100644 +--- a/cmake/public/cuda.cmake ++++ b/cmake/public/cuda.cmake +@@ -133,7 +133,11 @@ endif() + # ---[ Extract versions + if(CAFFE2_USE_CUDNN) + # Get cuDNN version +- file(READ ${CUDNN_INCLUDE_PATH}/cudnn.h CUDNN_HEADER_CONTENTS) ++ if(EXISTS ${CUDNN_INCLUDE_PATH}/cudnn_version.h) ++ file(READ ${CUDNN_INCLUDE_PATH}/cudnn_version.h CUDNN_HEADER_CONTENTS) ++ else() ++ file(READ ${CUDNN_INCLUDE_PATH}/cudnn.h CUDNN_HEADER_CONTENTS) ++ endif() + string(REGEX MATCH "define CUDNN_MAJOR * +([0-9]+)" + CUDNN_VERSION_MAJOR "${CUDNN_HEADER_CONTENTS}") + string(REGEX REPLACE "define CUDNN_MAJOR * +([0-9]+)" "\\1" +diff --git a/caffe2/operators/rnn/recurrent_op_cudnn.cc b/caffe2/operators/rnn/recurrent_op_cudnn.cc +index 8f69944dcf..3679c9d2a7 100644 +--- a/caffe2/operators/rnn/recurrent_op_cudnn.cc ++++ b/caffe2/operators/rnn/recurrent_op_cudnn.cc +@@ -99,7 +99,7 @@ void RecurrentBaseOp::initialize( + // RNN setup + { + #if CUDNN_VERSION_MIN(7, 0, 0) +- CUDNN_ENFORCE(cudnnSetRNNDescriptor( ++ CUDNN_ENFORCE(cudnnSetRNNDescriptor_v6( + cudnn_wrapper_.inline_cudnn_handle(), + rnnDesc_, + hiddenSize, +diff --git a/caffe2/operators/conv_op_cudnn.cc b/caffe2/operators/conv_op_cudnn.cc +index 285a74cf41bb3..cfbebcfe601c4 100644 +--- a/caffe2/operators/conv_op_cudnn.cc ++++ b/caffe2/operators/conv_op_cudnn.cc +@@ -751,15 +751,28 @@ bool CudnnConvOp::DoRunWithType() { + } + } else { + // Get the convolution algorithm based on the workspace limit. +- CUDNN_ENFORCE(cudnnGetConvolutionForwardAlgorithm( ++ constexpr int nalgo = CUDNN_CONVOLUTION_FWD_ALGO_COUNT; ++ int valid_algos; ++ cudnnConvolutionFwdAlgoPerf_t algos[nalgo]; ++ CUDNN_ENFORCE(cudnnGetConvolutionForwardAlgorithm_v7( + cudnn_wrapper_.inline_cudnn_handle(), + bottom_desc_, + filter_desc_, + conv_desc_, + top_desc_, +- CUDNN_CONVOLUTION_FWD_SPECIFY_WORKSPACE_LIMIT, +- cudnn_ws_nbytes_limit_, +- &algo_)); ++ nalgo, ++ &valid_algos, ++ algos)); ++ bool found = false; ++ for (int i = 0; i < valid_algos; i++) { ++ auto a = algos[i]; ++ if (a.memory <= cudnn_ws_nbytes_limit_) { ++ algo_ = a.algo; ++ found = true; ++ break; ++ } ++ } ++ CAFFE_ENFORCE(found, "Unable to find algorithms for cuDNN forward"); + } + for (int step = 0; step < 2; ++step) { + cudnnStatus_t _status = cudnnGetConvolutionForwardWorkspaceSize( +@@ -1164,15 +1177,28 @@ bool CudnnConvGradientOp::DoRunWithType() { + } + } else { + // choose backward algorithm for filter +- CUDNN_ENFORCE(cudnnGetConvolutionBackwardFilterAlgorithm( ++ constexpr int nalgo = CUDNN_CONVOLUTION_BWD_FILTER_ALGO_COUNT; ++ int valid_algos; ++ cudnnConvolutionBwdFilterAlgoPerf_t algos[nalgo]; ++ CUDNN_ENFORCE(cudnnGetConvolutionBackwardFilterAlgorithm_v7( + cudnn_wrapper_.inline_cudnn_handle(), + bottom_desc_, + top_desc_, + bwd_filter_conv_desc_, + filter_desc_, +- CUDNN_CONVOLUTION_BWD_FILTER_SPECIFY_WORKSPACE_LIMIT, +- cudnn_ws_nbytes_limit_, +- &bwd_filter_algo_)); ++ nalgo, ++ &valid_algos, ++ algos)); ++ bool found = false; ++ for (int i = 0; i < valid_algos; i++) { ++ auto a = algos[i]; ++ if (a.memory <= cudnn_ws_nbytes_limit_) { ++ bwd_filter_algo_ = a.algo; ++ found = true; ++ break; ++ } ++ } ++ CAFFE_ENFORCE(found, "Unable to find algorithms for cuDNN backward filter"); + } + // Pick dX algo if needed + if (OutputSize() == 3 || (no_bias_ && (OutputSize() == 2))) { +@@ -1252,15 +1278,28 @@ bool CudnnConvGradientOp::DoRunWithType() { + bwd_data_conv_desc_, kComputeTypesToTry[bestAlgoIndex]); + } + } else { +- CUDNN_ENFORCE(cudnnGetConvolutionBackwardDataAlgorithm( ++ constexpr int nalgo = CUDNN_CONVOLUTION_BWD_DATA_ALGO_COUNT; ++ int valid_algos; ++ cudnnConvolutionBwdDataAlgoPerf_t algos[nalgo]; ++ CUDNN_ENFORCE(cudnnGetConvolutionBackwardDataAlgorithm_v7( + cudnn_wrapper_.inline_cudnn_handle(), + filter_desc_, + top_desc_, + bwd_data_conv_desc_, + bottom_desc_, +- CUDNN_CONVOLUTION_BWD_DATA_SPECIFY_WORKSPACE_LIMIT, +- cudnn_ws_nbytes_limit_, +- &bwd_data_algo_)); ++ nalgo, ++ &valid_algos, ++ algos)); ++ bool found = false; ++ for (int i = 0; i < valid_algos; i++) { ++ auto a = algos[i]; ++ if (a.memory <= cudnn_ws_nbytes_limit_) { ++ bwd_data_algo_ = a.algo; ++ found = true; ++ break; ++ } ++ } ++ CAFFE_ENFORCE(found, "Unable to find algorithms for cuDNN backward data"); + } + } + +diff --git a/caffe2/operators/conv_transpose_op_cudnn.cc b/caffe2/operators/conv_transpose_op_cudnn.cc +index c00e43eadc476..d432e4d30780f 100644 +--- a/caffe2/operators/conv_transpose_op_cudnn.cc ++++ b/caffe2/operators/conv_transpose_op_cudnn.cc +@@ -356,15 +356,28 @@ bool CudnnConvTransposeOp::RunOnDevice() { + return data_perf_stat[0].algo; + }); + } else { +- CUDNN_ENFORCE(cudnnGetConvolutionBackwardDataAlgorithm( ++ constexpr int nalgo = CUDNN_CONVOLUTION_BWD_DATA_ALGO_COUNT; ++ int valid_algos; ++ cudnnConvolutionBwdDataAlgoPerf_t algos[nalgo]; ++ CUDNN_ENFORCE(cudnnGetConvolutionBackwardDataAlgorithm_v7( + cudnn_wrapper_.inline_cudnn_handle(), + filter_desc_, + bottom_desc_, + conv_desc_, + top_desc_, +- CUDNN_CONVOLUTION_BWD_DATA_SPECIFY_WORKSPACE_LIMIT, +- cudnn_ws_nbytes_limit_, +- &bwd_data_algo_)); ++ nalgo, ++ &valid_algos, ++ algos)); ++ bool found = false; ++ for (int i = 0; i < valid_algos; i++) { ++ auto a = algos[i]; ++ if (a.memory <= cudnn_ws_nbytes_limit_) { ++ bwd_data_algo_ = a.algo; ++ found = true; ++ break; ++ } ++ } ++ CAFFE_ENFORCE(found, "Unable to find algorithms for cuDNN backward data"); + } + + size_t bwd_data_ws_size; +@@ -661,25 +674,55 @@ bool CudnnConvTransposeGradientOp::RunOnDevice() { + }); + } else { + // choose backward algorithm for filter +- CUDNN_ENFORCE(cudnnGetConvolutionBackwardFilterAlgorithm( ++ { ++ constexpr int nalgo = CUDNN_CONVOLUTION_BWD_FILTER_ALGO_COUNT; ++ int valid_algos; ++ cudnnConvolutionBwdFilterAlgoPerf_t algos[nalgo]; ++ CUDNN_ENFORCE(cudnnGetConvolutionBackwardFilterAlgorithm_v7( + cudnn_wrapper_.inline_cudnn_handle(), + top_desc_, + bottom_desc_, + conv_desc_, + filter_desc_, +- CUDNN_CONVOLUTION_BWD_FILTER_SPECIFY_WORKSPACE_LIMIT, +- cudnn_ws_nbytes_limit_, +- &bwd_filter_algo_)); ++ nalgo, ++ &valid_algos, ++ algos)); ++ bool found = false; ++ for (int i = 0; i < valid_algos; i++) { ++ auto a = algos[i]; ++ if (a.memory <= cudnn_ws_nbytes_limit_) { ++ bwd_filter_algo_ = a.algo; ++ found = true; ++ break; ++ } ++ } ++ CAFFE_ENFORCE(found, "Unable to find algorithms for cuDNN backward filter"); ++ } + // choose backward algo for data +- CUDNN_ENFORCE(cudnnGetConvolutionForwardAlgorithm( ++ { ++ constexpr int nalgo = CUDNN_CONVOLUTION_FWD_ALGO_COUNT; ++ int valid_algos; ++ cudnnConvolutionFwdAlgoPerf_t algos[nalgo]; ++ CUDNN_ENFORCE(cudnnGetConvolutionForwardAlgorithm_v7( + cudnn_wrapper_.inline_cudnn_handle(), + top_desc_, + filter_desc_, + conv_desc_, + bottom_desc_, +- CUDNN_CONVOLUTION_FWD_SPECIFY_WORKSPACE_LIMIT, +- cudnn_ws_nbytes_limit_, +- &algo_)); ++ nalgo, ++ &valid_algos, ++ algos)); ++ bool found = false; ++ for (int i = 0; i < valid_algos; i++) { ++ auto a = algos[i]; ++ if (a.memory <= cudnn_ws_nbytes_limit_) { ++ algo_ = a.algo; ++ found = true; ++ break; ++ } ++ } ++ CAFFE_ENFORCE(found, "Unable to find algorithms for cuDNN forward"); ++ } + } + // get workspace for backwards filter algorithm + size_t bwd_filter_ws_size, fwd_ws_size; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_fix-build-on-AVX512-cpus.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_fix-build-on-AVX512-cpus.patch new file mode 100644 index 00000000000..2b5d2e06be3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_fix-build-on-AVX512-cpus.patch @@ -0,0 +1,26 @@ +Do not compile FBGEMM code with `-masm=intel` flag by default, because it would emit invalid assembly for `_mm512_mul_ps` + +From https://github.com/pytorch/FBGEMM/commit/74a084677397ea17dc80ebc129b826e29f2b0761 + +diff -aur pytorch-1.3.1-orig/third_party/fbgemm/CMakeLists.txt pytorch-1.3.1/third_party/fbgemm/CMakeLists.txt +--- pytorch-1.3.1-orig/third_party/fbgemm/CMakeLists.txt 2021-06-28 09:32:41.565226195 +0200 ++++ pytorch-1.3.1/third_party/fbgemm/CMakeLists.txt 2021-06-28 09:34:43.822720790 +0200 +@@ -112,10 +112,16 @@ if(MSVC) + target_compile_options(fbgemm_avx512 PRIVATE "/arch:AVX512") + else(MSVC) + target_compile_options(fbgemm_avx2 PRIVATE +- "-m64" "-mavx2" "-mf16c" "-mfma" "-masm=intel") ++ "-m64" "-mavx2" "-mf16c" "-mfma") + target_compile_options(fbgemm_avx512 PRIVATE + "-m64" "-mavx2" "-mfma" "-mavx512f" "-mavx512bw" "-mavx512dq" +- "-mavx512vl" "-masm=intel") ++ "-mavx512vl") ++ set_source_files_properties(src/FbgemmFP16UKernelsAvx2.cc ++ PROPERTIES COMPILE_FLAGS "-masm=intel") ++ set_source_files_properties(src/FbgemmFP16UKernelsAvx512.cc ++ PROPERTIES COMPILE_FLAGS "-masm=intel") ++ set_source_files_properties(src/FbgemmFP16UKernelsAvx512_256.cc ++ PROPERTIES COMPILE_FLAGS "-masm=intel") + endif(MSVC) + + if(USE_SANITIZER) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_fix-for-nccl-error.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_fix-for-nccl-error.patch new file mode 100644 index 00000000000..1717a75cc67 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_fix-for-nccl-error.patch @@ -0,0 +1,75 @@ +From 34c502e2f6e3e7d441b6eb023468e8e1dac57ada Mon Sep 17 00:00:00 2001 +From: Michael Carilli +Date: Thu, 31 Oct 2019 18:23:17 -0700 +Subject: [PATCH] Making torch/csrc/cuda nccl usage safe for nccl 2.5 + +--- + torch/csrc/cuda/nccl.cpp | 4 ++-- + torch/csrc/cuda/python_nccl.cpp | 6 +++--- + 2 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/torch/csrc/cuda/nccl.cpp b/torch/csrc/cuda/nccl.cpp +index f421d1c6fe73d..40b4ce8ae1b56 100644 +--- a/torch/csrc/cuda/nccl.cpp ++++ b/torch/csrc/cuda/nccl.cpp +@@ -236,10 +236,10 @@ void broadcast( + ncclDataType_t data_type = _get_data_type(tensors[0]); + int64_t numel = tensors[0].numel(); + +- AutoNcclGroup nccl_group_guard; + const auto comms = user_comms.empty() ? _get_communicators(tensors) + : ArrayRef(user_comms); + ++ AutoNcclGroup nccl_group_guard; + at::cuda::OptionalCUDAGuard device_guard; + for (size_t i = 0, num_tensors = tensors.size(); i < num_tensors; i++) { + int device = tensors[i].get_device(); +@@ -282,10 +282,10 @@ void reduce( + ncclDataType_t data_type = _get_data_type(inputs[0]); + + const auto count = inputs[0].numel(); +- AutoNcclGroup nccl_group_guard; + auto comms_ref = user_comms.empty() ? _get_communicators(inputs) + : ArrayRef(user_comms); + ++ AutoNcclGroup nccl_group_guard; + at::cuda::OptionalCUDAGuard device_guard; + for (size_t i = 0; i < len; i++) { + int device = inputs[i].device().index(); +diff --git a/torch/csrc/cuda/python_nccl.cpp b/torch/csrc/cuda/python_nccl.cpp +index 3601134322f39..8aeba37528a30 100644 +--- a/torch/csrc/cuda/python_nccl.cpp ++++ b/torch/csrc/cuda/python_nccl.cpp +@@ -191,9 +191,9 @@ PyObject* THCPModule_nccl_all_reduce(PyObject* self, PyObject* args) { + ncclDataType_t data_type = _get_data_type(inputs[0]); + + int64_t count = inputs[0].numel(); +- AutoNcclGroup nccl_group_guard; + auto comms = user_comms.empty() ? _get_communicators(inputs) + : ArrayRef(user_comms); ++ AutoNcclGroup nccl_group_guard; + at::cuda::OptionalCUDAGuard device_guard; + for (size_t i = 0; i < len; i++) { + int device = inputs[i].get_device(); +@@ -270,9 +270,9 @@ PyObject* THCPModule_nccl_all_gather(PyObject* self, PyObject* args) { + ncclDataType_t data_type = _get_data_type(inputs[0]); + + int64_t count = inputs[0].numel(); +- AutoNcclGroup nccl_group_guard; + auto comms = user_comms.empty() ? _get_communicators(inputs) + : ArrayRef(user_comms); ++ AutoNcclGroup nccl_group_guard; + at::cuda::OptionalCUDAGuard device_guard; + for (size_t i = 0; i < len; i++) { + int device = inputs[i].get_device(); +@@ -332,9 +332,9 @@ PyObject* THCPModule_nccl_reduce_scatter(PyObject* self, PyObject* args) { + ncclDataType_t data_type = _get_data_type(inputs[0]); + + int64_t count = inputs[0].numel() / len; +- AutoNcclGroup nccl_group_guard; + auto comms = user_comms.empty() ? _get_communicators(inputs) + : ArrayRef(user_comms); ++ AutoNcclGroup nccl_group_guard; + at::cuda::OptionalCUDAGuard device_guard; + for (size_t i = 0; i < len; i++) { + int device = inputs[i].get_device(); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_skip-nccl-error-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_skip-nccl-error-tests.patch new file mode 100644 index 00000000000..03736e23156 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1_skip-nccl-error-tests.patch @@ -0,0 +1,43 @@ +Some NCCL error tests fail with e.g. +"CUDA error: uncorrectable NVLink error detected during the execution" + +See https://github.com/pytorch/pytorch/issues/58155 and https://github.com/pytorch/pytorch/issues/59552 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_c10d.py b/test/test_c10d.py +index f03b34e790..a4fd1c2be7 100644 +--- a/test/test_c10d.py ++++ b/test/test_c10d.py +@@ -3054,26 +3054,31 @@ class CommTest(MultiProcessTestCase): + + @requires_nccl() + @skip_if_not_multigpu ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_clean_exit(self): + self._test_nccl_errors_blocking(lambda : sys.exit(0)) + + @requires_nccl() + @skip_if_not_multigpu ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_nonzero_exit(self): + self._test_nccl_errors_blocking(lambda : sys.exit(1)) + + @requires_nccl() + @skip_if_not_multigpu ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_abort(self): + self._test_nccl_errors_blocking(lambda : os.abort()) + + @requires_nccl() + @skip_if_not_multigpu ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_sigkill(self): + self._test_nccl_errors_blocking(lambda : os.kill(os.getpid(), signal.SIGKILL)) + + @requires_nccl() + @skip_if_not_multigpu ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_sigterm(self): + self._test_nccl_errors_blocking(lambda : os.kill(os.getpid(), signal.SIGTERM)) + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..5483fb70434 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb @@ -0,0 +1,348 @@ +name = 'PyTorch' +version = '1.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020a'} + +# PyTorch pulls in a bunch of submodules that are not releases. +# We download the submodule revisions from their repos. +# The list is generated by easybuild-framework/easybuild/scripts/createSubmoduleDeps.sh +local_extract_cmd_pattern = 'tar -C pytorch-%%(version)s/third_party/%s --strip-components=1 -xf %%s' + +source_urls = ['https://github.com/pytorch/pytorch/archive'] +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'source_urls': ['https://github.com/Maratyszcza/FP16/archive'], + 'download_filename': '4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz', + 'filename': 'FP16-20200514.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'FP16', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], + 'download_filename': 'b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz', + 'filename': 'FXdiv-20200417.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'FXdiv', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/NNPACK/archive'], + 'download_filename': '24b55303f5cf65d75844714513a0d1b1409809bd.tar.gz', + 'filename': 'NNPACK-20191007.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'NNPACK', + }, + { + 'source_urls': ['https://github.com/pytorch/QNNPACK/archive'], + 'download_filename': '7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz', + 'filename': 'QNNPACK-20190828.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'QNNPACK', + }, + { + 'source_urls': ['https://github.com/google/XNNPACK/archive'], + 'download_filename': '1b354636b5942826547055252f3b359b54acff95.tar.gz', + 'filename': 'XNNPACK-20200323.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'XNNPACK', + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': '505be96ab23056580a3a2315abba048f4428b04e.tar.gz', + 'filename': 'benchmark-20180606.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'benchmark', + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': '63b254577ed77a8004a9be6ac707f3dccc4e1fd9.tar.gz', + 'filename': 'cpuinfo-20200611.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'cpuinfo', + }, + { + 'source_urls': ['https://github.com/NVlabs/cub/archive'], + 'download_filename': 'd106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz', + 'filename': 'cub-20200512.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'cub', + }, + { + 'source_urls': ['https://github.com/eigenteam/eigen-git-mirror/archive'], + 'download_filename': 'd41dc4dd74acce21fb210e7625d5d135751fa9e5.tar.gz', + 'filename': 'eigen-20190125.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'eigen', + }, + { + 'source_urls': ['https://github.com/pytorch/fbgemm/archive'], + 'download_filename': '1d710393d5b7588f5de3b83f51c22bbddf095229.tar.gz', + 'filename': 'fbgemm-20200914.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm', + }, + { + 'source_urls': ['https://github.com/asmjit/asmjit/archive'], + 'download_filename': '9057aa30b620f0662ff51e2230c126a345063064.tar.gz', + 'filename': 'asmjit-20200429.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/asmjit', + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': 'd5e37adf1406cf899d7d9ec1d317c47506ccb970.tar.gz', + 'filename': 'cpuinfo-20190201.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/cpuinfo', + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '0fc5466dbb9e623029b1ada539717d10bd45e99e.tar.gz', + 'filename': 'googletest-20180925.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/googletest', + }, + { + 'source_urls': ['https://github.com/fmtlib/fmt/archive'], + 'download_filename': 'cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz', + 'filename': 'fmt-20200806.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fmt', + }, + { + 'source_urls': ['https://github.com/houseroad/foxi/archive'], + 'download_filename': '4aba696ec8f31794fd42880346dc586486205e0a.tar.gz', + 'filename': 'foxi-20200922.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'foxi', + }, + { + 'source_urls': ['https://github.com/google/gemmlowp/archive'], + 'download_filename': '3fb5c176c17c765a3492cd2f0321b0dab712f350.tar.gz', + 'filename': 'gemmlowp-20181126.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'gemmlowp/gemmlowp', + }, + { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], + 'download_filename': '3dc0328fe6a9d47bd47c0c6ca145a0d8a21845c6.tar.gz', + 'filename': 'gloo-20200918.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'gloo', + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'googletest', + }, + { + 'source_urls': ['https://github.com/intel/ideep/archive'], + 'download_filename': 'ba885200dbbc1f144c7b58eba487378eb324f281.tar.gz', + 'filename': 'ideep-20200915.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'ideep', + }, + { + 'source_urls': ['https://github.com/intel/mkl-dnn/archive'], + 'download_filename': '5ef631a030a6f73131c77892041042805a06064f.tar.gz', + 'filename': 'mkl-dnn-20200909.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'ideep/mkl-dnn', + }, + { + 'source_urls': ['https://github.com/onnx/onnx/archive'], + 'download_filename': 'a82c6a7010e2e332d8f74ad5b0c726fd47c85376.tar.gz', + 'filename': 'onnx-20200531.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'onnx', + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': 'e776aa0275e293707b6a0901e0e8d8a8a3679508.tar.gz', + 'filename': 'benchmark-20180525.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'onnx/third_party/benchmark', + }, + { + 'source_urls': ['https://github.com/onnx/onnx-tensorrt/archive'], + 'download_filename': 'c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz', + 'filename': 'onnx-tensorrt-20190916.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'onnx-tensorrt', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/psimd/archive'], + 'download_filename': '072586a71b55b7f8c584153d223e95687148a900.tar.gz', + 'filename': 'psimd-20200517.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'psimd', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], + 'download_filename': '029c88620802e1361ccf41d1970bd5b07fd6b7bb.tar.gz', + 'filename': 'pthreadpool-20200615.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'pthreadpool', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/PeachPy/archive'], + 'download_filename': '07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz', + 'filename': 'PeachPy-20180218.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'python-peachpy', + }, + { + 'source_urls': ['https://github.com/shibatch/sleef/archive'], + 'download_filename': '7f523de651585fe25cade462efccca647dcc8d02.tar.gz', + 'filename': 'sleef-20190730.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'sleef', + }, + { + 'source_urls': ['https://github.com/01org/tbb/archive'], + 'download_filename': 'a51a90bc609bb73db8ea13841b5cf7aa4344d4a9.tar.gz', + 'filename': 'tbb-20181009.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tbb', + }, + { + 'source_urls': ['https://github.com/pytorch/tensorpipe/archive'], + 'download_filename': '95ff9319161fcdb3c674d2bb63fac3e94095b343.tar.gz', + 'filename': 'tensorpipe-20200928.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe', + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/googletest', + }, + { + 'source_urls': ['https://github.com/google/libnop/archive'], + 'download_filename': 'aa95422ea8c409e3f078d2ee7708a5f59a8b9fa2.tar.gz', + 'filename': 'libnop-20200723.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/libnop', + }, + { + 'source_urls': ['https://github.com/libuv/libuv/archive'], + 'download_filename': '02a9e1be252b623ee032a3137c0b0c94afbe6809.tar.gz', + 'filename': 'libuv-20200419.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/libuv', + }, +] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_fix_altivec_defines.patch', + 'PyTorch-1.7.0_fix_test_DistributedDataParallel.patch', + 'PyTorch-1.7.0_fix-fbgemm-not-implemented-issue.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_add-jit-support-for-cuda11.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.7.1_detect-max-ccc-from-nvrtc.patch', + 'PyTorch-1.7.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch', + 'PyTorch-1.7.1_complex32.patch', + 'PyTorch-1.7.1_bypass-nan-compare.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.7.1_fix-err-variable.patch', + 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.7.1_el8_ppc64le.patch', + 'PyTorch-1.7.1_run-large-tests-on-GPU.patch', + 'PyTorch-1.7.1_disable-failing-cuda-11.2-tests.patch', +] +checksums = [ + 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz + '90f20492621d5ed80b442aa682ff92d7ccf333ac8fac4a10e7e02afb159f3c13', # FP16-20200514.tar.gz + '9ccf554541666b5c089ad5dd465141d671c99971f36d72f313652f5c49ffce14', # FXdiv-20200417.tar.gz + '1f11dbbfad78d0a4c39fe94e52a28c0821cb25f9880420bb304f6302f73fe002', # NNPACK-20191007.tar.gz + '0d752bd75f46ce4d7c6f0a60b0d6c0e5918a7b4683c825284f8db3706dd24f76', # QNNPACK-20190828.tar.gz + 'b55a6ef3a0b4c0d3c39ad5578eb4fa9a7b2d7ee1ef06592b8a808a59a8e6589b', # XNNPACK-20200323.tar.gz + '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz + '18a99130ced1eaacab2ba8f75a1435f9955aab54fa0436b60468f020876ee902', # cpuinfo-20200611.tar.gz + 'd87f6737be1b544c299340b64b9303c1d6ec0447b49b3aaf6642838b4f8280d7', # cub-20200512.tar.gz + '2ec954f18cec50a7063a7358ce555f7e11788a7f6d4e7e597d83687dc2f3b989', # eigen-20190125.tar.gz + 'e7e495fee65a73fa40cf1644f5b9496a6498c7a4209ce4b6b4d7d80f3d3941a4', # fbgemm-20200914.tar.gz + '5c7ecb03ede09a38fa9bcf2527a0f1454cd67a34c0e6fd939ae4d93b276ce982', # asmjit-20200429.tar.gz + '3f2dc1970f397a0e59db72f9fca6ff144b216895c1d606f6c94a507c1e53a025', # cpuinfo-20190201.tar.gz + 'e99b904983d08ac8e9bddb5b0d21196b78ad9499e3c5d12192cee2ddd2b7515c', # googletest-20180925.tar.gz + '0654ea5a1899f373fee87ae00ca3478aef227c3cf23916572421c6ce25d274bc', # fmt-20200806.tar.gz + '10a3774a2ebef7a09dd5c9a6b7bfdc9d3e4eb153711572864d4cc560637727c3', # foxi-20200922.tar.gz + 'fdd6f08bdb33d33f4df516ffb91730fdb163479c19502cfc983083fd9cf43bfa', # gemmlowp-20181126.tar.gz + '9c6bace1c2af3ee186a84c791ba61a6ba92ecbe8a3990839d895771219a73ebc', # gloo-20200918.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + 'f205584378d9b0b6aeae9558b9d578469235f4e394e71b44ead616881e5fb210', # ideep-20200915.tar.gz + '4234ce25fd8bb64899493bb21c2473559d6bcfe098309fe74e351945475da930', # mkl-dnn-20200909.tar.gz + 'c3bf8cc8091b24c43aa205a1f2037a518d249eb5997bea7f543b7fc880e80e21', # onnx-20200531.tar.gz + 'c7682e9007ddfd94072647abab3e89ffd9084089460ae47d67060974467b58bf', # benchmark-20180525.tar.gz + '314cde420a7cf692bdb6877bc6af6bc514805f6cdb8bee90f32566ed08d94b1c', # onnx-tensorrt-20190916.tar.gz + 'f6c4dab91ae9a03b3019e7cab0572743afd0e1b6e75b97fcca50259c737c924e', # psimd-20200517.tar.gz + 'd13818a10a645d557202aa005606337b2a0cdf690e5655253800ab11abb0c076', # pthreadpool-20200615.tar.gz + '13100c3deed300bbf16f87d8af3539f432462bfef9d38f0c7e3e387dc2e88676', # PeachPy-20180218.tar.gz + '8cb5fae822077ca9cbc14dcc7bba9a3a35ad519284fc5169f9a176672c63860a', # sleef-20190730.tar.gz + # checksum for original download of tbb-20181009.tar.gz from https://github.com/intel/tbb/archive + ('dc0a8d8d96cb8765782aa6ac1b509ad4db955d9bbb58fa5cc2265f0292756d72', + # checksum for download of tbb-20181009.tar.gz from https://github.com/01org/tbb/archive + 'be111cf161b587812fa3b106fe550efb6f129b8b0b702fef32fac23af9580e5e'), + '0039658ffed8d4ff21575651a6f5258853cf8e1ca8bf564822b51f94da28b7fd', # tensorpipe-20200928.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + '9ee3f3b1efc629dbc3703ece3892e7e05c7048eed7031d06020e38bb30bee3ab', # libnop-20200723.tar.gz + '5ca4e9091f3231d8ad8801862dc4e851c23af89c69141d27723157776f7291e7', # libuv-20200419.tar.gz + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + '98a32023292772984aa53ef739e444ec8b20617b72bd7593c62e884f5d8b2e6c', # PyTorch-1.7.0_fix_altivec_defines.patch + # PyTorch-1.7.0_fix_test_DistributedDataParallel.patch + '5e70e6aecb1916bb8369b8d3f5e4b3cbf7e2b7a015f8099eea330b42775e25c5', + # PyTorch-1.7.0_fix-fbgemm-not-implemented-issue.patch + '97febb91ae2d051db9541e1e4c5924c77555ab73ee49ad7d62ef3e4714110297', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + # PyTorch-1.7.0_increase-distributed-test-timeout.patch + '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_add-jit-support-for-cuda11.patch + '7a5a6ca64196f5fe0dc954d387e188695a683cc37790da67f903c52a5dd5a1e7', + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + # PyTorch-1.7.1_detect-max-ccc-from-nvrtc.patch + '96241088dbfcd4db93bd5faadecabce6259a495ffd24b75101444cd0e164c12b', + '12be5139e4e7aeec214bb38b123b09b391cd1ca72ce5ded6e61590cfae801824', # PyTorch-1.7.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch + 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', + '6028bff2be720cf70acad2129db60fd10872e02c9e460c72bb274228cf90b320', # PyTorch-1.7.1_complex32.patch + '0943496231b6857801e2424e561d03897a6982d098cba5b6967017b391a7e977', # PyTorch-1.7.1_bypass-nan-compare.patch + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + 'abb79e7ffd10be87adfb62e79131c50079c32470031ac22b12b273cfae85ca4c', # PyTorch-1.7.1_fix-err-variable.patch + # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch + '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', + '2a94a9cc009f02469b843fc65a6ee2cb01873f783568b8bcc83c33ba8e6b1a58', # PyTorch-1.7.1_el8_ppc64le.patch + # PyTorch-1.7.1_run-large-tests-on-GPU.patch + '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', + # PyTorch-1.7.1_disable-failing-cuda-11.2-tests.patch + '2a9df4face04798f51eee0db83d28a905ea7ac53569cf25ed9f049b0a547702e', +] + +builddependencies = [ + ('CMake', '3.16.4'), + ('hypothesis', '5.6.0', versionsuffix), +] +dependencies = [ + ('Ninja', '1.10.0'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.2'), + ('protobuf', '3.13.0'), + ('protobuf-python', '3.13.0', versionsuffix), + ('pybind11', '2.4.3', versionsuffix), + ('SciPy-bundle', '2020.03', '-Python-3.8.2'), + ('typing-extensions', '3.7.4.3', versionsuffix), + ('PyYAML', '5.3'), + ('MPFR', '4.0.2'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.2.2'), + ('Pillow', '7.0.0', versionsuffix), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +excluded_tests = { + '': [ + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! + # https://github.com/pytorch/pytorch/issues/43209 + 'test_quantization', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index c841f628150..5b00155d13b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -30,7 +30,7 @@ dependencies = [ ('Pillow', '8.0.1'), ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), ('magma', '2.5.4'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) @@ -245,6 +245,7 @@ patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_add-jit-support-for-cuda11.patch', 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', 'PyTorch-1.7.1_detect-max-ccc-from-nvrtc.patch', 'PyTorch-1.7.1_dont-use-gpu-ccc-in-test.patch', @@ -307,6 +308,8 @@ checksums = [ # PyTorch-1.7.0_increase-distributed-test-timeout.patch '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_add-jit-support-for-cuda11.patch + '7a5a6ca64196f5fe0dc954d387e188695a683cc37790da67f903c52a5dd5a1e7', # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', # PyTorch-1.7.1_detect-max-ccc-from-nvrtc.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1_add-jit-support-for-cuda11.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1_add-jit-support-for-cuda11.patch new file mode 100644 index 00000000000..1e84cfadd28 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1_add-jit-support-for-cuda11.patch @@ -0,0 +1,32 @@ +Add SM 8 for nvrtc 11 so it can JIT compile to SM 8.0 directly instead of to 7.x first +and the having the CUDA driver compile for SM 8.0 again. + +Author: Alexander Grund (TU Dresden) +diff --git a/torch/csrc/jit/codegen/fuser/cuda/fused_kernel.cpp b/torch/csrc/jit/codegen/fuser/cuda/fused_kernel.cpp +index 4f2f7ebb9b..b2d310316f 100644 +--- a/torch/csrc/jit/codegen/fuser/cuda/fused_kernel.cpp ++++ b/torch/csrc/jit/codegen/fuser/cuda/fused_kernel.cpp +@@ -51,16 +51,15 @@ static void getMajorMinor( + minor = 0; + } else if (nvrtc_major <= 9 && prop->major >= 7) { // 9 supports 3-7.2 + major = 7; +- if (prop->major == 7 && prop->minor <= 2) +- minor = prop->minor; +- else +- minor = 0; ++ minor = (prop->major == 7 && prop->minor <= 2) ? prop->minor : 0; + } else if (nvrtc_major <= 10 && prop->major >= 7) { // 10 supports 3-7.5 + major = 7; +- if (prop->major == 7 && prop->minor <= 5) +- minor = prop->minor; +- else +- minor = 0; ++ minor = (prop->major == 7 && prop->minor <= 5) ? prop->minor : 0; ++ } else if ( ++ nvrtc_major == 11 && nvrtc_minor == 0 && ++ prop->major >= 8) { // 11.0 supports 3.5-8.0 ++ major = 8; ++ minor = 0; + } + } + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.0_correct-skip-tests-decorators.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.0_correct-skip-tests-decorators.patch index 89cbeae0759..7216af42688 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.0_correct-skip-tests-decorators.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.0_correct-skip-tests-decorators.patch @@ -96,7 +96,7 @@ Fixed to apply to PyTorch 1.8.0 by Simon Branford (University of Birmingham) # stft is currently warning that it requires return-complex while an upgrader is written + @onlyOnCPUAndCUDA -+ @skipCPUIfNoMkl ++ @skipIf(not TEST_MKL, "Test requires MKL") def test_stft_requires_complex(self, device): x = torch.rand(100) y = x.stft(10, pad_mode='constant') diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index f8827697e06..1d96d37ea37 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -19,22 +19,38 @@ sources = [{ patches = [ 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', - 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', + 'PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch', + 'PyTorch-1.8.1_fix-arange-on-VSX.patch', + 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_fix-vsx-vector-functions.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch - # PyTorch-1.7.0_increase-distributed-test-timeout.patch - '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch # PyTorch-1.8.0_correct-skip-tests-decorators.patch - '4b2fe7616217dd6fd12d667cb1439dde58f84bf234fbf3e6026c4665fc697a2e', + 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', + # PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch + 'a5bc86837c59a36d59311be9cbd0c6d86ea6be235c2a7ffb400b89c758b28490', + 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch + # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch + '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + 'a8fcb63cf963dc743e8b0a96b966f18d8edde6a4e76365d6de56aa2c71ce6d3f', # PyTorch-1.8.1_fix-vsx-vector-functions.patch + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch + 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -61,6 +77,10 @@ dependencies = [ ] excluded_tests = { + 'POWER': [ + # https://github.com/pytorch/pytorch/issues/57617 + 'test_autograd', + ], '': [ # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', @@ -70,7 +90,7 @@ excluded_tests = { ] } -runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' sanity_check_commands = ["python -c 'import caffe2.python'"] tests = ['PyTorch-check-cpp-extension.py'] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb new file mode 100644 index 00000000000..b7c08cd3003 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -0,0 +1,127 @@ +name = 'PyTorch' +version = '1.8.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', + 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_fix-arange-on-VSX.patch', + 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_fix-testnn-on-A100.patch', + 'PyTorch-1.8.1_fix-vsx-vector-functions.patch', + 'PyTorch-1.8.1_honor_shared_cupti-setting.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.8.1_limit_world_size_for_zero_redundancy_opt_test.patch', + 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', + 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', + 'PyTorch-1.8.1_skip-nccl-error-tests.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch + '18ecad081a8c940add64040ad9698d3273366acf738a8a44eab1c793d3f49950', + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch + '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', + # PyTorch-1.8.0_correct-skip-tests-decorators.patch + 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', + 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch + # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch + '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + '241561a0497dd27adffd71b8b0815be1fe924800f4ee336d95e0cc3881fac98b', # PyTorch-1.8.1_fix-testnn-on-A100.patch + 'a8fcb63cf963dc743e8b0a96b966f18d8edde6a4e76365d6de56aa2c71ce6d3f', # PyTorch-1.8.1_fix-vsx-vector-functions.patch + # PyTorch-1.8.1_honor_shared_cupti-setting.patch + 'a6459fe544f9e2b61ab09ba54e8db5b294176ffdbf41c99e0d0b678e1e617b8f', + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + # PyTorch-1.8.1_limit_world_size_for_zero_redundancy_opt_test.patch + 'c3488fa24405eac6e2e36fbdf94e877bd39fd177e92fb3a0b6bbd5c8b7ddc7bc', + # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch + 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', + # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch + '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', + '33704164ad2da7426a6c21482389826345b92690d37cbf938896eef421a62575', # PyTorch-1.8.1_skip-nccl-error-tests.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + 'POWER': [ + # https://github.com/pytorch/pytorch/issues/57617 + 'test_autograd', + ], + '': [ + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! + # https://github.com/pytorch/pytorch/issues/43209 + 'test_quantization', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch new file mode 100644 index 00000000000..279f4de0cae --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch @@ -0,0 +1,38 @@ +From 614d0228c3ef8cc7251b2593f4cda537d73cb84e Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Wed, 19 May 2021 17:51:06 +0200 +Subject: [PATCH] Only sync CUDA if the operation is run on GPU + +This fixes test failures when PyTorch is build without CUDA +--- + test/test_torch.py | 10 ++++++---- + 1 file changed, 6 insertions(+), 4 deletions(-) + +diff --git a/test/test_torch.py b/test/test_torch.py +index f071ffed0235b..3bc9234daf255 100644 +--- a/test/test_torch.py ++++ b/test/test_torch.py +@@ -7289,8 +7289,9 @@ def test_multinomial_invalid(self, device): + def test(probs): + with self.assertRaisesRegex(RuntimeError, + 'probability tensor contains either `inf`, `nan` or element < 0'): +- torch.multinomial(probs.to(device), 2) +- torch.cuda.synchronize() ++ out = torch.multinomial(probs.to(device), 2) ++ if out.is_cuda: ++ torch.cuda.synchronize() + + test(torch.tensor([1., -1., 1.])) + test(torch.tensor([1., inf, 1.])) +@@ -7301,8 +7302,9 @@ def test_multinomial_invalid_distribution(self, device): + def test(probs, replacement): + with self.assertRaisesRegex(RuntimeError, + r"invalid multinomial distribution \(sum of probabilities <= 0\)"): +- torch.multinomial(probs, 2, replacement) +- torch.cuda.synchronize() ++ out = torch.multinomial(probs, 2, replacement) ++ if out.is_cuda: ++ torch.cuda.synchronize() + + x = torch.zeros(3, device=device) + y = torch.zeros(3, 3, device=device) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch new file mode 100644 index 00000000000..a5c0731da64 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch @@ -0,0 +1,22 @@ +Disable a part of a test which uses the current GPUs CUDA compute capability +This will fail if the GPU is newer than what nvcc supports. +See https://github.com/pytorch/pytorch/issues/51950 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_cpp_extensions_jit.py b/test/test_cpp_extensions_jit.py +index efda7cb2cf..64607346c8 100644 +--- a/test/test_cpp_extensions_jit.py ++++ b/test/test_cpp_extensions_jit.py +@@ -181,11 +181,9 @@ class TestCppExtensionJIT(common.TestCase): + # - With/without '+PTX' + + n = torch.cuda.device_count() +- capabilities = {torch.cuda.get_device_capability(i) for i in range(n)} + # expected values is length-2 tuple: (list of ELF, list of PTX) + # note: there should not be more than one PTX value + archflags = { +- '': (['{}{}'.format(capability[0], capability[1]) for capability in capabilities], None), + "Maxwell+Tegra;6.1": (['53', '61'], None), + "Pascal 3.5": (['35', '60', '61'], None), + "Volta": (['70'], ['70']), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-arange-on-VSX.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-arange-on-VSX.patch new file mode 100644 index 00000000000..c37c62d3412 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-arange-on-VSX.patch @@ -0,0 +1,84 @@ +From 308226bf119f9e9a432c624dd26caa9842dd334c Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Wed, 19 May 2021 13:22:33 +0200 +Subject: [PATCH] Fix arange functions for VSX specializations of Vec256 + +Need a templated 2nd parameter to support e.g. double steps even for int vectors +--- + aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h | 3 ++- + aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h | 3 ++- + aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h | 3 ++- + aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h | 3 ++- + aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h | 3 ++- + 5 files changed, 10 insertions(+), 5 deletions(-) + +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h +index cfa0914a5e6bc..949201a44cbbb 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h +@@ -141,7 +141,8 @@ class Vec256 { + vec_sel(a._vec0, b._vec0, mask._vecb0), + vec_sel(a._vec1, b._vec1, mask._vecb1)}; + } +- static Vec256 arange(double base = 0., double step = 1.) { ++ template ++ static Vec256 arange(double base = 0., step_t step = static_cast(1)) { + return Vec256(base, base + step, base + 2 * step, base + 3 * step); + } + +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h +index 586f32e8a853d..3d2c47603fc97 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h +@@ -135,7 +135,8 @@ class Vec256 { + vec_sel(a._vec1, b._vec1, mask._vecb1)}; + } + +- static Vec256 arange(float base = 0.f, float step = 1.f) { ++ template ++ static Vec256 arange(float base = 0.f, step_t step = static_cast(1)) { + return Vec256( + base, + base + step, +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h +index 4eb580052c2de..2ede5dde3cdfd 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h +@@ -201,7 +201,8 @@ class Vec256 { + vec_sel(a._vec1, b._vec1, mask._vecb1)}; + } + +- static Vec256 arange(int16_t base = 0, int16_t step = 1) { ++ template ++ static Vec256 arange(int16_t base = 0, step_t step = static_cast(1)) { + return Vec256( + base, + base + step, +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h +index 8df4de480e955..00f3847e10e66 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h +@@ -154,7 +154,8 @@ class Vec256 { + vec_sel(a._vec1, b._vec1, mask._vecb1)}; + } + +- static Vec256 arange(int32_t base = 0.f, int32_t step = 1.f) { ++ template ++ static Vec256 arange(int32_t base = 0.f, step_t step = static_cast(1)) { + return Vec256( + base, + base + step, +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h +index 0887c0dc1df3a..b57a0ffce79b8 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h +@@ -116,7 +116,8 @@ class Vec256 { + vec_sel(a._vec0, b._vec0, mask._vecb0), + vec_sel(a._vec1, b._vec1, mask._vecb1)}; + } +- static Vec256 arange(int64_t base = 0., int64_t step = 1.) { ++ template ++ static Vec256 arange(int64_t base = 0., step_t step = static_cast(1)) { + return Vec256(base, base + step, base + 2 * step, base + 3 * step); + } + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch new file mode 100644 index 00000000000..95af9f0c356 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch @@ -0,0 +1,226 @@ +From: Alexander Grund +Date: Tue, 18 May 2021 15:08:41 +0200 +Subject: [PATCH 1/2] Fix usage of TORCH_INTERNAL_ASSERT with message + +Using only a string as the argument for TORCH_INTERNAL_ASSERT will never +trigger a failure as a string is always a truethy value. +This hides actual bugs and makes users and devs think all worked while +it did not. +Change to use TORCH_INTERNAL_ASSERT(false, "msg") + +Subject: [PATCH 2/2] Add missing skip decorator for +test_preserve_bundled_inputs_methods + +This test uses optimize_for_mobile which requires NNPACK to work + +diff --git a/aten/src/ATen/native/BinaryOps.cpp b/aten/src/ATen/native/BinaryOps.cpp +index c4edadb03e..e889cd03a8 100644 +--- a/aten/src/ATen/native/BinaryOps.cpp ++++ b/aten/src/ATen/native/BinaryOps.cpp +@@ -106,6 +106,7 @@ Tensor& add_relu_impl( + max_val = std::numeric_limits::max(); + } else { + TORCH_INTERNAL_ASSERT( ++ false, + "Unsupported datatype for add_relu:", self.dtype().name()); + } + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag.cpp +index 050fdce2ca..7e72263917 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag.cpp +@@ -780,6 +780,7 @@ class QEmbeddingBag final { + include_last_offset); + } else { + TORCH_INTERNAL_ASSERT( ++ false, + "Currently only support 8-bit embedding_bag quantization"); + } + } +@@ -808,6 +809,7 @@ class QEmbedding final { + + } else { + TORCH_INTERNAL_ASSERT( ++ false, + "Currently only support 8-bit embedding quantization"); + } + return output; +diff --git a/aten/src/ATen/native/quantized/cpu/qnnpack_utils.h b/aten/src/ATen/native/quantized/cpu/qnnpack_utils.h +index 6de646acfe..66341c959d 100644 +--- a/aten/src/ATen/native/quantized/cpu/qnnpack_utils.h ++++ b/aten/src/ATen/native/quantized/cpu/qnnpack_utils.h +@@ -131,6 +131,7 @@ struct PackedConvWeightsQnnp : public ConvPackedParamsBase { + + if (conv_p.per_channel && conv_p.ukernel_type == pytorch_qnnp_ukernel_type_xzp_gemm) { + TORCH_INTERNAL_ASSERT( ++ false, + "Per channel quantized weights are not supported for XZP kernels"); + } + +@@ -140,6 +141,7 @@ struct PackedConvWeightsQnnp : public ConvPackedParamsBase { + static_cast(calloc(1, sizeof(struct pytorch_qnnp_operator))); + if (convolution == nullptr) { + TORCH_INTERNAL_ASSERT( ++ false, + "failed to allocate %zu bytes for pytorch_qnnp_operator structure", + sizeof(struct pytorch_qnnp_operator)); + } +@@ -406,7 +408,7 @@ std::pair, at::Tensor> make_zero_points_and_scales_tensor( + 128); + } + } else { +- TORCH_INTERNAL_ASSERT("Unsupported quantization scheme."); ++ TORCH_INTERNAL_ASSERT(false, "Unsupported quantization scheme."); + } + at:: Tensor weight_scales = + at::empty( +@@ -423,7 +425,7 @@ std::pair, at::Tensor> make_zero_points_and_scales_tensor( + weight_contig.q_per_channel_scales()[i].item(); + } + } else { +- TORCH_INTERNAL_ASSERT("Unsupported quantization scheme."); ++ TORCH_INTERNAL_ASSERT(false, "Unsupported quantization scheme."); + } + for (int i = num_output_channels; i < num_output_channels_padded; ++i) { + weight_scales_data[i] = 1.f; +diff --git a/test/test_mobile_optimizer.py b/test/test_mobile_optimizer.py +index 11ef019a26..7b5ac1a239 100644 +--- a/test/test_mobile_optimizer.py ++++ b/test/test_mobile_optimizer.py +@@ -269,6 +269,9 @@ class TestOptimizer(TestCase): + bi_module_lint_list = generate_mobile_module_lints(bi_module) + self.assertEqual(len(bi_module_lint_list), 0) + ++ @unittest.skipUnless(torch.backends.xnnpack.enabled, ++ " XNNPACK must be enabled for these tests." ++ " Please build with USE_XNNPACK=1.") + def test_preserve_bundled_inputs_methods(self): + class MyBundledInputModule(torch.nn.Module): + def __init__(self): +diff --git a/torch/csrc/jit/api/module.cpp b/torch/csrc/jit/api/module.cpp +index 38592b80b9..8f9508321b 100644 +--- a/torch/csrc/jit/api/module.cpp ++++ b/torch/csrc/jit/api/module.cpp +@@ -305,7 +305,7 @@ void Module::train(bool on) { + if (auto slot = m._ivalue()->type()->findAttributeSlot("training")) { + m._ivalue()->setSlot(*slot, on); + } else { +- TORCH_INTERNAL_ASSERT("'training' attribute not found"); ++ TORCH_INTERNAL_ASSERT(false, "'training' attribute not found"); + } + } + } +diff --git a/torch/csrc/jit/passes/quantization/insert_quant_dequant.cpp b/torch/csrc/jit/passes/quantization/insert_quant_dequant.cpp +index 53a13b6cf1..93c2b5a7da 100644 +--- a/torch/csrc/jit/passes/quantization/insert_quant_dequant.cpp ++++ b/torch/csrc/jit/passes/quantization/insert_quant_dequant.cpp +@@ -304,6 +304,7 @@ Node* insertEmbeddingBagOps(Node* observer, const std::string& op_name) { + quant_fn = "quantized::embedding_bag_byte_rowwise_offsets"; + } else { + TORCH_INTERNAL_ASSERT( ++ false, + "Graph Mode Quantization currently supports 4-bit and 8-bit embedding bag quantization."); + } + +diff --git a/torch/csrc/jit/passes/vulkan_rewrite.cpp b/torch/csrc/jit/passes/vulkan_rewrite.cpp +index 4e381c47da..63c64ecd07 100644 +--- a/torch/csrc/jit/passes/vulkan_rewrite.cpp ++++ b/torch/csrc/jit/passes/vulkan_rewrite.cpp +@@ -225,21 +225,25 @@ script::Module vulkanOptimizeForMobile( + + void vulkanInsertPrePackedOps(std::shared_ptr& graph) { + TORCH_INTERNAL_ASSERT( ++ false, + "Vulkan is not enabled. Please build with USE_VULKAN=1"); + } + + void vulkanInsertPrePackedOps(script::Module& module) { + TORCH_INTERNAL_ASSERT( ++ false, + "Vulkan is not enabled. Please build with USE_VULKAN=1"); + } + + void vulkanFusePrePackedConvWithClamp(script::Module& module) { + TORCH_INTERNAL_ASSERT( ++ false, + "Vulkan is not enabled. Please build with USE_VULKAN=1"); + } + + void vulkanFoldPrePackingOps(script::Module& m) { + TORCH_INTERNAL_ASSERT( ++ false, + "Vulkan is not enabled. Please build with USE_VULKAN=1"); + } + +@@ -247,6 +251,7 @@ script::Module vulkanOptimizeForMobile( + const script::Module& module, + const std::vector& preserved_methods) { + TORCH_INTERNAL_ASSERT( ++ false, + "Mobile optimizaiton only available with Vulkan at the moment. " + "Vulkan is not enabled. Please build with USE_VULKAN=1"); + return module; +diff --git a/torch/csrc/jit/passes/xnnpack_rewrite.cpp b/torch/csrc/jit/passes/xnnpack_rewrite.cpp +index 3be480068c..2289f028ae 100644 +--- a/torch/csrc/jit/passes/xnnpack_rewrite.cpp ++++ b/torch/csrc/jit/passes/xnnpack_rewrite.cpp +@@ -405,21 +405,25 @@ script::Module optimizeForMobile( + + void insertPrePackedOps(std::shared_ptr& graph) { + TORCH_INTERNAL_ASSERT( ++ false, + "XNNPACK is not enabled. Please build with USE_XNNPACK=1"); + } + + void insertPrePackedOps(script::Module& module) { + TORCH_INTERNAL_ASSERT( ++ false, + "XNNPACK is not enabled. Please build with USE_XNNPACK=1"); + } + + void fusePrePackedLinearConvWithClamp(script::Module& module) { + TORCH_INTERNAL_ASSERT( ++ false, + "XNNPACK is not enabled. Please build with USE_XNNPACK=1"); + } + + void FoldPrePackingOps(script::Module& m) { + TORCH_INTERNAL_ASSERT( ++ false, + "XNNPACK is not enabled. Please build with USE_XNNPACK=1"); + } + +@@ -428,6 +432,7 @@ script::Module optimizeForMobile( + const std::set& blocklist, + const std::vector& preserved_methods) { + TORCH_INTERNAL_ASSERT( ++ false, + "Mobile optimization only available with XNNPACK at the moment. " + "XNNPACK is not enabled. Please build with USE_XNNPACK=1"); + return module; +diff --git a/torch/csrc/jit/runtime/register_ops_utils.cpp b/torch/csrc/jit/runtime/register_ops_utils.cpp +index 537716e1ad..3bcff0af55 100644 +--- a/torch/csrc/jit/runtime/register_ops_utils.cpp ++++ b/torch/csrc/jit/runtime/register_ops_utils.cpp +@@ -182,7 +182,7 @@ IValue tensorToListRecursive( + } else if (inner_result.isBool()) { + result.emplace_back(inner_result.toBool()); + } else { +- TORCH_INTERNAL_ASSERT("Unknown return type for tensorToListRecursive"); ++ TORCH_INTERNAL_ASSERT(false, "Unknown return type for tensorToListRecursive"); + } + + data += strides[cur_dim] * element_size; +diff --git a/torch/lib/c10d/ProcessGroup.cpp b/torch/lib/c10d/ProcessGroup.cpp +index 7909bfa7c9..9e2a51f291 100644 +--- a/torch/lib/c10d/ProcessGroup.cpp ++++ b/torch/lib/c10d/ProcessGroup.cpp +@@ -43,7 +43,7 @@ std::string opTypeToString(OpType opType) { + case OpType::UNKNOWN: + return "UNKNOWN"; + default: +- TORCH_INTERNAL_ASSERT("Unknown op type!"); ++ TORCH_INTERNAL_ASSERT(false, "Unknown op type!"); + } + return "UNKNOWN"; + } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-testnn-on-A100.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-testnn-on-A100.patch new file mode 100644 index 00000000000..7e1cc8f6d45 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-testnn-on-A100.patch @@ -0,0 +1,66 @@ +Fix test failures due to use of native TF32 types on A100 GPUs. +See https://github.com/pytorch/pytorch/issues/52278. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_nn.py b/test/test_nn.py +index 533cff9ea4..fd2654a06c 100644 +--- a/test/test_nn.py ++++ b/test/test_nn.py +@@ -10079,12 +10079,11 @@ def add_test(test, decorator=None): + add(cuda_test_name + '_cdouble', test_cdouble) + + else: +- if tf32_is_not_fp32() and test.with_tf32: +- +- def with_tf32_off(self, test=test, kwargs=kwargs): +- with tf32_off(): +- test.test_cuda(self, **kwargs) ++ def with_tf32_off(self, test=test, kwargs=kwargs): ++ with tf32_off(): ++ test.test_cuda(self, **kwargs) + ++ if tf32_is_not_fp32() and test.with_tf32: + add(cuda_test_name + '_fp32', with_tf32_off) + + def with_tf32_on(self, test=test, kwargs=kwargs): +@@ -10093,7 +10092,7 @@ def add_test(test, decorator=None): + + add(cuda_test_name + '_tf32', with_tf32_on) + else: +- add(cuda_test_name, lambda self, test=test, kwargs=kwargs: test.test_cuda(self, **kwargs)) ++ add(cuda_test_name, with_tf32_off) + + for test_params in module_tests + new_module_tests: + # TODO: CUDA is not implemented yet +diff --git a/torch/testing/_internal/common_nn.py b/torch/testing/_internal/common_nn.py +index ee75a6985a..f890838686 100644 +--- a/torch/testing/_internal/common_nn.py ++++ b/torch/testing/_internal/common_nn.py +@@ -3692,7 +3692,7 @@ new_module_tests = [ + check_gradgrad=False, + desc='gelu_activation', + with_tf32=True, +- tf32_precision=0.01, ++ tf32_precision=0.05, + ), + dict( + module_name='TransformerDecoderLayer', +@@ -3704,7 +3704,7 @@ new_module_tests = [ + check_gradgrad=False, + desc='relu_activation', + with_tf32=True, +- tf32_precision=0.01, ++ tf32_precision=0.05, + ), + dict( + module_name='TransformerDecoderLayer', +@@ -3717,7 +3717,7 @@ new_module_tests = [ + check_gradgrad=False, + desc='gelu_activation', + with_tf32=True, +- tf32_precision=0.01, ++ tf32_precision=0.05, + ), + dict( + module_name='Transformer', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-vsx-vector-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-vsx-vector-functions.patch new file mode 100644 index 00000000000..8d063418ebe --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix-vsx-vector-functions.patch @@ -0,0 +1,330 @@ +This fixes multiple bugs introduced by the VSX optimized code in https://github.com/pytorch/pytorch/pull/41541 + +- min/max/clamp now consistently return nan when any value is NaN as on other architectures +- The non-complex angle functions return PI for negative values now +- The complex angle functions have been corrected and optimized +- The float32-log function implementation returned a wrong result when inf was passed (and maybe other inputs), replaced by the sleef function just as for float64 + +See https://github.com/pytorch/pytorch/pull/59382 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_complex_double_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_complex_double_vsx.h +index f62ac36850..ed511c45ed 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_complex_double_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_complex_double_vsx.h +@@ -236,17 +236,14 @@ class Vec256 { + // angle = atan2(b/a) + // auto b_a = _mm256_permute_pd(values, 0x05); // b a + // return Sleef_atan2d4_u10(values, b_a); // 90-angle angle +- auto ret = el_swapped(); +- for (int i = 0; i < 2; i++) { +- ret._vec0[i] = std::atan2(_vec0[i], ret._vec0[i]); +- ret._vec1[i] = std::atan2(_vec1[i], ret._vec0[i]); +- } ++ Vec256 ret; ++ ret._vec0[0] = std::atan2(_vec0[1], _vec0[0]); ++ ret._vec1[0] = std::atan2(_vec1[1], _vec1[0]); + return ret; + } + + Vec256 angle() const { +- auto a = angle_().el_swapped(); +- return a & vd_real_mask; ++ return angle_() & vd_real_mask; + } + + Vec256 real_() const { +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_complex_float_vsx.h +index cb9b4c90fb..4e6433b093 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_complex_float_vsx.h +@@ -357,17 +357,16 @@ class Vec256 { + // angle = atan2(b/a) + // auto b_a = _mm256_permute_ps(values, 0xB1); // b a + // return Sleef_atan2f8_u10(values, b_a); // 90-angle angle +- auto ret = el_swapped(); +- for (int i = 0; i < 4; i++) { +- ret._vec0[i] = std::atan2(_vec0[i], ret._vec0[i]); +- ret._vec1[i] = std::atan2(_vec1[i], ret._vec0[i]); ++ Vec256 ret; ++ for (int i = 0; i < 4; i += 2) { ++ ret._vec0[i] = std::atan2(_vec0[i + 1], _vec0[i]); ++ ret._vec1[i] = std::atan2(_vec1[i + 1], _vec1[i]); + } + return ret; + } + + Vec256 angle() const { +- auto a = angle_().el_swapped(); +- return a & real_mask; ++ return angle_() & real_mask; + } + + Vec256 sin() const { +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h +index f4fa4faa80..3ea237ac32 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h +@@ -53,6 +53,16 @@ class Vec256 { + return _vec1; + } + ++ Vec256 _nor() const { ++ return {vec_nor(_vec0, _vec0), vec_nor(_vec1, _vec1)}; ++ } ++ ++ Vec256 _isnan() const { ++ auto x = *this; ++ auto ret = (x == x); ++ return ret._nor(); ++ } ++ + int zero_mask() const { + auto cmp = (*this == vd_zero); + return (cmp._vecb0[0] & 1) | (cmp._vecb0[1] & 2) | (cmp._vecb1[0] & 4) | +@@ -249,7 +259,8 @@ class Vec256 { + } + + Vec256 angle() const { +- return Vec256{0}; ++ auto tmp = blendv(Vec256(0), Vec256(c10::pi), *this < Vec256(0)); ++ return blendv(tmp, *this, _isnan()); + } + Vec256 real() const { + return *this; +@@ -367,8 +378,8 @@ class Vec256 { + DEFINE_MEMBER_OP(operator-, double, vec_sub) + DEFINE_MEMBER_OP(operator*, double, vec_mul) + DEFINE_MEMBER_OP(operator/, double, vec_div) +- DEFINE_MEMBER_OP(maximum, double, vec_max) +- DEFINE_MEMBER_OP(minimum, double, vec_min) ++ DEFINE_MEMBER_OP(maximum, double, vec_max_nan2) ++ DEFINE_MEMBER_OP(minimum, double, vec_min_nan2) + DEFINE_MEMBER_OP(operator&, double, vec_and) + DEFINE_MEMBER_OP(operator|, double, vec_or) + DEFINE_MEMBER_OP(operator^, double, vec_xor) +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h +index 2a1a87aa72..5bcf818232 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h +@@ -282,7 +282,8 @@ class Vec256 { + } + + Vec256 angle() const { +- return Vec256{0}; ++ auto tmp = blendv(Vec256(0), Vec256(c10::pi), *this < Vec256(0)); ++ return blendv(tmp, *this, _isnan()); + } + Vec256 real() const { + return *this; +@@ -340,54 +341,16 @@ class Vec256 { + } + + Vec256 C10_ALWAYS_INLINE log() const { +- auto temp = *this; +- auto invalid_mask = temp < zero; +- // cut off denormalized stuff +- auto x = temp.maximum(min_norm_pos); +- vint32 imm0 = vec_sr(vint32(x._vec0), vu_23); +- vint32 imm1 = vec_sr(vint32(x._vec1), vu_23); +- // keep only the fractional part +- x = x & inv_mant_mask; +- x = x | half; +- imm0 = imm0 - v0x7f; +- imm1 = imm1 - v0x7f; +- Vec256 ex; +- ex._vec0 = vec_float(imm0); +- ex._vec1 = vec_float(imm1); +- ex = ex + one; +- auto mask = x < cephes_SQRTHF; +- auto t = x & mask; +- x = x - one; +- ex = ex - (mask & one); +- x = x + t; +- auto z = x * x; +- auto y = x.madd(log_p0, log_p1); +- y = y.madd(x, log_p2); +- y = y.madd(x, log_p3); +- y = y.madd(x, log_p4); +- y = y.madd(x, log_p5); +- y = y.madd(x, log_p6); +- y = y.madd(x, log_p7); +- y = y.madd(x, log_p8); +- y = y * x * z; +- y = ex.madd(log_q1, y); +- y = y - z * half; +- x = x + y; +- x = ex.madd(log_q2, x); +- // negative arg will be NAN +- x = blendv(x, v_nan, invalid_mask); +- // zero is -inf +- x = blendv(x, min_inf, (temp == zero)); +- return x; ++ return {Sleef_logf4_u10vsx(_vec0), Sleef_logf4_u10vsx(_vec1)}; + } + Vec256 C10_ALWAYS_INLINE log10() const { +- return log() * log10e_inv; ++ return {Sleef_log10f4_u10vsx(_vec0), Sleef_log10f4_u10vsx(_vec1)}; + } + Vec256 C10_ALWAYS_INLINE log1p() const { +- return ((*this) + one).log(); ++ return {Sleef_log1pf4_u10vsx(_vec0), Sleef_log1pf4_u10vsx(_vec1)}; + } + Vec256 C10_ALWAYS_INLINE log2() const { +- return log() * log2e_inv; ++ return {Sleef_log2f4_u10vsx(_vec0), Sleef_log2f4_u10vsx(_vec1)}; + } + Vec256 C10_ALWAYS_INLINE ceil() const { + return {vec_ceil(_vec0), vec_ceil(_vec1)}; +@@ -653,8 +616,8 @@ class Vec256 { + DEFINE_MEMBER_OP(operator-, float, vec_sub) + DEFINE_MEMBER_OP(operator*, float, vec_mul) + DEFINE_MEMBER_OP(operator/, float, vec_div) +- DEFINE_MEMBER_OP(maximum, float, vec_max) +- DEFINE_MEMBER_OP(minimum, float, vec_min) ++ DEFINE_MEMBER_OP(maximum, float, vec_max_nan2) ++ DEFINE_MEMBER_OP(minimum, float, vec_min_nan2) + DEFINE_MEMBER_OP(operator&, float, vec_and) + DEFINE_MEMBER_OP(operator|, float, vec_or) + DEFINE_MEMBER_OP(operator^, float, vec_xor) +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h +index 33460abe2a..f9d33febdf 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h +@@ -287,7 +287,7 @@ class Vec256 { + int16_t& operator[](int idx) = delete; + + Vec256 angle() const { +- return Vec256{0}; ++ return blendv(Vec256(0), Vec256(c10::pi), *this < Vec256(0)); + } + Vec256 real() const { + return *this; +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h +index 2ee2318f03..3fd92551e2 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h +@@ -218,7 +218,7 @@ class Vec256 { + int32_t& operator[](int idx) = delete; + + Vec256 angle() const { +- return Vec256{0}; ++ return blendv(Vec256(0), Vec256(c10::pi), *this < Vec256(0)); + } + Vec256 real() const { + return *this; +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h +index d752f71c9a..e628aeac54 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h +@@ -170,7 +170,7 @@ class Vec256 { + int64_t& operator[](int idx) = delete; + + Vec256 angle() const { +- return Vec256{0}; ++ return blendv(Vec256(0), Vec256(c10::pi), *this < Vec256(0)); + } + Vec256 real() const { + return *this; +diff --git a/aten/src/ATen/cpu/vec256/vsx/vsx_helpers.h b/aten/src/ATen/cpu/vec256/vsx/vsx_helpers.h +index 61a572e1ab..716fa2c128 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vsx_helpers.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vsx_helpers.h +@@ -85,6 +85,69 @@ vec_sldw_aux(const vfloat32& vec_in0, const vfloat32& vec_in1) { + + #define vec_not(a) vec_nor(a, a) + ++// Vectorized min/max which return a if any operand is nan ++template ++C10_ALWAYS_INLINE T vec_min_nan(const T& a, const T& b) { ++ return vec_min(a, b); ++} ++template ++C10_ALWAYS_INLINE T vec_max_nan(const T& a, const T& b) { ++ return vec_max(a, b); ++} ++ ++// Specializations for float/double taken from Eigen ++template<> ++C10_ALWAYS_INLINE vfloat32 vec_min_nan(const vfloat32& a, const vfloat32& b) ++{ ++ // NOTE: about 10% slower than vec_min, but consistent with std::min and SSE regarding NaN ++ vfloat32 ret; ++ __asm__ ("xvcmpgesp %x0,%x1,%x2\n\txxsel %x0,%x1,%x2,%x0" : "=&wa" (ret) : "wa" (a), "wa" (b)); ++ return ret; ++} ++// Specializations for float/double taken from Eigen ++template<> ++C10_ALWAYS_INLINE vfloat32 vec_max_nan(const vfloat32& a, const vfloat32& b) ++{ ++ // NOTE: about 10% slower than vec_max, but consistent with std::min and SSE regarding NaN ++ vfloat32 ret; ++ __asm__ ("xvcmpgtsp %x0,%x2,%x1\n\txxsel %x0,%x1,%x2,%x0" : "=&wa" (ret) : "wa" (a), "wa" (b)); ++ return ret; ++} ++ ++template<> ++C10_ALWAYS_INLINE vfloat64 vec_min_nan(const vfloat64& a, const vfloat64& b) ++{ ++ // NOTE: about 10% slower than vec_min, but consistent with std::min and SSE regarding NaN ++ vfloat64 ret; ++ __asm__ ("xvcmpgedp %x0,%x1,%x2\n\txxsel %x0,%x1,%x2,%x0" : "=&wa" (ret) : "wa" (a), "wa" (b)); ++ return ret; ++} ++template<> ++C10_ALWAYS_INLINE vfloat64 vec_max_nan(const vfloat64& a, const vfloat64& b) ++{ ++ // NOTE: about 10% slower than vec_max, but consistent with std::max and SSE regarding NaN ++ vfloat64 ret; ++ __asm__ ("xvcmpgtdp %x0,%x2,%x1\n\txxsel %x0,%x1,%x2,%x0" : "=&wa" (ret) : "wa" (a), "wa" (b)); ++ return ret; ++} ++ ++// Vectorizes min/max function which returns nan if any side is nan ++#define C10_VSX_VEC_NAN_PROPAG(name, type, btype, func) \ ++ C10_ALWAYS_INLINE type name(const type& a, const type& b) { \ ++ type tmp = func(a, b); \ ++ btype nan_a = vec_cmpne(a, a); \ ++ btype nan_b = vec_cmpne(b, b); \ ++ tmp = vec_sel(tmp, a, nan_a); \ ++ return vec_sel(tmp, b, nan_b); \ ++ } ++ ++C10_VSX_VEC_NAN_PROPAG(vec_min_nan2, vfloat32, vbool32, vec_min) ++C10_VSX_VEC_NAN_PROPAG(vec_max_nan2, vfloat32, vbool32, vec_max) ++C10_VSX_VEC_NAN_PROPAG(vec_min_nan2, vfloat64, vbool64, vec_min) ++C10_VSX_VEC_NAN_PROPAG(vec_max_nan2, vfloat64, vbool64, vec_max) ++ ++#undef C10_VSX_VEC_NAN_PROPAG ++ + #define DEFINE_MEMBER_UNARY_OP(op, op_type, func) \ + Vec256 C10_ALWAYS_INLINE op() const { \ + return Vec256{func(_vec0), func(_vec1)}; \ +@@ -137,20 +200,22 @@ vec_sldw_aux(const vfloat32& vec_in0, const vfloat32& vec_in1) { + const Vec256& min, \ + const Vec256& max) { \ + return Vec256{ \ +- vec_min(max.vec0(), vec_max(a.vec0(), min.vec0())), \ +- vec_min(max.vec1(), vec_max(a.vec1(), min.vec1()))}; \ ++ vec_min_nan(vec_max_nan(a.vec0(), min.vec0()), max.vec0()), \ ++ vec_min_nan(vec_max_nan(a.vec1(), min.vec1()), max.vec1())}; \ + } \ + template <> \ + Vec256 C10_ALWAYS_INLINE clamp_min( \ + const Vec256& a, const Vec256& min) { \ + return Vec256{ \ +- vec_max(a.vec0(), min.vec0()), vec_max(a.vec1(), min.vec1())}; \ ++ vec_max_nan(a.vec0(), min.vec0()), \ ++ vec_max_nan(a.vec1(), min.vec1())}; \ + } \ + template <> \ + Vec256 C10_ALWAYS_INLINE clamp_max( \ + const Vec256& a, const Vec256& max) { \ + return Vec256{ \ +- vec_min(a.vec0(), max.vec0()), vec_min(a.vec1(), max.vec1())}; \ ++ vec_min_nan(a.vec0(), max.vec0()), \ ++ vec_min_nan(a.vec1(), max.vec1())}; \ + } + + #define DEFINE_REINTERPRET_CAST_FUNCS( \ diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_honor_shared_cupti-setting.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_honor_shared_cupti-setting.patch new file mode 100644 index 00000000000..2a514dd6153 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_honor_shared_cupti-setting.patch @@ -0,0 +1,33 @@ +PyTorch always uses the statically built CUPTI when found which completely breaks C++ exception handling +Change this to prefer the shared CUPTI + +See https://github.com/pytorch/pytorch/issues/57744 + +Author: Alexander Grund (TU Dresden) + +diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake +index 06464e799a..4bea90c0b4 100644 +--- a/cmake/Dependencies.cmake ++++ b/cmake/Dependencies.cmake +@@ -1816,16 +1816,16 @@ if(USE_KINETO) + message(STATUS " KINETO_LIBRARY_TYPE = ${KINETO_LIBRARY_TYPE}") + message(STATUS " CUDA_SOURCE_DIR = ${CUDA_SOURCE_DIR}") + +- if(EXISTS ${CUDA_SOURCE_DIR}/extras/CUPTI/lib64/libcupti_static.a) +- set(CUDA_cupti_LIBRARY "${CUDA_SOURCE_DIR}/extras/CUPTI/lib64/libcupti_static.a") +- elseif(EXISTS ${CUDA_SOURCE_DIR}/lib64/libcupti_static.a) +- set(CUDA_cupti_LIBRARY "${CUDA_SOURCE_DIR}/lib64/libcupti_static.a") +- elseif(USE_CUPTI_SO) ++ if(USE_CUPTI_SO) + if(EXISTS ${CUDA_SOURCE_DIR}/extras/CUPTI/lib64/libcupti.so) + set(CUDA_cupti_LIBRARY "${CUDA_SOURCE_DIR}/extras/CUPTI/lib64/libcupti.so") + elseif(EXISTS ${CUDA_SOURCE_DIR}/lib64/libcupti.so) + set(CUDA_cupti_LIBRARY "${CUDA_SOURCE_DIR}/lib64/libcupti.so") + endif() ++ elseif(EXISTS ${CUDA_SOURCE_DIR}/extras/CUPTI/lib64/libcupti_static.a) ++ set(CUDA_cupti_LIBRARY "${CUDA_SOURCE_DIR}/extras/CUPTI/lib64/libcupti_static.a") ++ elseif(EXISTS ${CUDA_SOURCE_DIR}/lib64/libcupti_static.a) ++ set(CUDA_cupti_LIBRARY "${CUDA_SOURCE_DIR}/lib64/libcupti_static.a") + endif() + + if(EXISTS ${CUDA_SOURCE_DIR}/extras/CUPTI/include) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_increase-distributed-test-timeout.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_increase-distributed-test-timeout.patch new file mode 100644 index 00000000000..c82f2fc6d30 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_increase-distributed-test-timeout.patch @@ -0,0 +1,18 @@ +It seems the timeout for the distributed tests is set to low and spurious failures can be seen +Increase it by a factor of 3 similar to torch/testing/_internal/distributed/distributed_test.py + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_distributed.py b/torch/testing/_internal/common_distributed.py +index 4f36b31a23..fbd2b9364a 100644 +--- a/torch/testing/_internal/common_distributed.py ++++ b/torch/testing/_internal/common_distributed.py +@@ -160,7 +160,7 @@ def skip_if_win32(): + "This unit test case is not supportted on Windows platform", + ) + +-TIMEOUT_DEFAULT = 100 ++TIMEOUT_DEFAULT = 300 + TIMEOUT_OVERRIDE = {"test_ddp_uneven_inputs": 400} + + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_limit_world_size_for_zero_redundancy_opt_test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_limit_world_size_for_zero_redundancy_opt_test.patch new file mode 100644 index 00000000000..e43c2824b1e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_limit_world_size_for_zero_redundancy_opt_test.patch @@ -0,0 +1,20 @@ +Some tests fail when run with anything but 2 GPUs and others when run with anything but 2 or 4 GPUs. +So limit to 2 GPUs. + +See https://github.com/pytorch/pytorch/issues/59548 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/optim/test_zero_redundancy_optimizer.py b/test/distributed/optim/test_zero_redundancy_optimizer.py +index 06f1b4f484..bc82f6c304 100644 +--- a/test/distributed/optim/test_zero_redundancy_optimizer.py ++++ b/test/distributed/optim/test_zero_redundancy_optimizer.py +@@ -233,7 +233,7 @@ class TestZeroRedundancyOptimizerSingleRank(TestZeroRedundancyOptimizer): + class TestZeroRedundancyOptimizerDistributed(TestZeroRedundancyOptimizer): + @property + def world_size(self): +- return max(2, torch.cuda.device_count()) ++ return 2 + + @skip_if_rocm + def test_step(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch new file mode 100644 index 00000000000..8c9019778f3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch @@ -0,0 +1,31 @@ +The complex gradient checks fail in PPC for some reason, so skip those. +See https://github.com/pytorch/pytorch/issues/57617 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 101a86c8d6..dfd80568e8 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -25,7 +25,7 @@ from torch.testing._internal.common_utils import \ + random_symmetric_matrix, random_symmetric_psd_matrix, + random_symmetric_pd_matrix, make_nonzero_det, + random_fullrank_matrix_distinct_singular_value, set_rng_seed, +- TEST_WITH_ROCM, IS_WINDOWS, IS_MACOS, make_tensor, TEST_SCIPY, ++ TEST_WITH_ROCM, IS_WINDOWS, IS_MACOS, IS_PPC, make_tensor, TEST_SCIPY, + torch_to_numpy_dtype_dict, slowTest, TEST_WITH_ASAN) + + from distutils.version import LooseVersion +@@ -1967,6 +1967,12 @@ op_db: List[OpInfo] = [ + dtypesIfROCM=all_types_and_complex_and(torch.bool), + decorators=(precisionOverride({torch.float16: 1e-2, + torch.bfloat16: 1e-2}),), ++ skips=( ++ # Complex grad check fails on PPC ++ SkipInfo('TestGradients', 'test_fn_grad', ++ device_type='cpu', dtypes=[torch.complex128], ++ active_if=IS_PPC), ++ ), + safe_casts_outputs=True, + supports_complex_to_float=True, + test_inplace_grad=False), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip-nccl-error-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip-nccl-error-tests.patch new file mode 100644 index 00000000000..90c97c07488 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip-nccl-error-tests.patch @@ -0,0 +1,62 @@ +Some NCCL error tests fail with e.g. +"CUDA error: uncorrectable NVLink error detected during the execution" + +See https://github.com/pytorch/pytorch/issues/58155 and https://github.com/pytorch/pytorch/issues/59552 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/test_c10d.py b/test/distributed/test_c10d.py +index e2985df527..3f973a4adb 100644 +--- a/test/distributed/test_c10d.py ++++ b/test/distributed/test_c10d.py +@@ -4321,36 +4321,42 @@ class NcclErrorHandlingTest(MultiProcessTestCase): + @requires_nccl() + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_clean_exit(self): + self._test_nccl_errors_blocking(lambda: sys.exit(0)) + + @requires_nccl() + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_nonzero_exit(self): + self._test_nccl_errors_blocking(lambda: sys.exit(1)) + + @requires_nccl() + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_abort(self): + self._test_nccl_errors_blocking(lambda: os.abort()) + + @requires_nccl() + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_sigkill(self): + self._test_nccl_errors_blocking(lambda: os.kill(os.getpid(), signal.SIGKILL)) + + @requires_nccl() + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_sigterm(self): + self._test_nccl_errors_blocking(lambda: os.kill(os.getpid(), signal.SIGTERM)) + + @requires_nccl() + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_blocking_wait_with_barrier(self): + os.environ["NCCL_BLOCKING_WAIT"] = "1" + store = c10d.FileStore(self.file_name, self.world_size) +@@ -4396,6 +4402,7 @@ class NcclErrorHandlingTest(MultiProcessTestCase): + + @requires_nccl() + @skip_if_lt_x_gpu(3) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_timeout(self): + store = c10d.FileStore(self.file_name, self.world_size) + os.environ["NCCL_BLOCKING_WAIT"] = "1" diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch new file mode 100644 index 00000000000..8311b224812 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch @@ -0,0 +1,17 @@ +Skip a failing test due to some internal asserts. +See https://github.com/pytorch/pytorch/issues/59436. + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/distributed/rpc/dist_autograd_test.py b/torch/testing/_internal/distributed/rpc/dist_autograd_test.py +index 3d405c3191..75397047b5 100644 +--- a/torch/testing/_internal/distributed/rpc/dist_autograd_test.py ++++ b/torch/testing/_internal/distributed/rpc/dist_autograd_test.py +@@ -2285,6 +2285,7 @@ class TensorPipeDistAutogradTest(RpcAgentTestFixture): + return self.next_stage.rpc_sync().forward(input) + + @skip_if_lt_x_gpu(4) ++ @unittest.skip("Test fails") + def test_dist_autograd_sync_streams(self): + + options = self.rpc_backend_options diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb new file mode 100644 index 00000000000..d614502526d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -0,0 +1,92 @@ +name = 'PyTorch' +version = '1.9.0' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch', + 'PyTorch-1.8.1_fix-arange-on-VSX.patch', + 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', + 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + # PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch + 'a5bc86837c59a36d59311be9cbd0c6d86ea6be235c2a7ffb400b89c758b28490', + 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch + # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch + '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch + 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', + '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + # PyTorch-1.9.0_skip-lstm-serialization-test.patch + '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), +] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..ede9dfd996c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -0,0 +1,124 @@ +name = 'PyTorch' +version = '1.9.0' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_fix-arange-on-VSX.patch', + 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', + 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', + 'PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch', + 'PyTorch-1.9.0_fix-testnn-on-A100.patch', + 'PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', + 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', + 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', + 'PyTorch-1.9.0_skip-nccl-error-tests.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch + # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch + '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch + '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', + # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch + 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', + # PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch + 'edb180d6967c507c147400a64422ff4499bcd5519f9be8d332890c317359dbad', + '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch + # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch + '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', + '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + # PyTorch-1.9.0_increase-test-cuda-tolerance.patch + '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', + # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch + '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.9.0_skip-lstm-serialization-test.patch + '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', + '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch new file mode 100644 index 00000000000..c43ff64d7a1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch @@ -0,0 +1,31 @@ +Avoid some failing tests due to the used libm which may cause overflows for very large complex inputs. +See https://github.com/pytorch/pytorch/issues/60259 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_unary_ufuncs.py b/test/test_unary_ufuncs.py +index 29f62c234e..1916ffa682 100644 +--- a/test/test_unary_ufuncs.py ++++ b/test/test_unary_ufuncs.py +@@ -542,7 +542,7 @@ class TestUnaryUfuncs(TestCase): + torch.nan_to_num(x, out=out, nan=nan, posinf=posinf, neginf=neginf) + self.assertEqual(result, out) + +- @dtypes(torch.cfloat, torch.cdouble) ++ @dtypes(torch.cdouble) + def test_complex_edge_values(self, device, dtype): + # sqrt Test Reference: https://github.com/pytorch/pytorch/pull/47424 + x = torch.tensor(0. - 1.0e+20j, dtype=dtype, device=device) +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index fd45a76efa..37684d91ac 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -4095,7 +4095,7 @@ op_db: List[OpInfo] = [ + skips=( + SkipInfo('TestUnaryUfuncs', 'test_reference_numerics_extremal', + device_type='cpu', dtypes=[torch.cfloat, torch.cdouble]), +- SkipInfo('TestUnaryUfuncs', 'test_reference_numerics_normal', ++ SkipInfo('TestUnaryUfuncs', 'test_reference_numerics_hard', + device_type='cpu', dtypes=[torch.cfloat, torch.cdouble]), + SkipInfo('TestUnaryUfuncs', 'test_reference_numerics_extremal', + device_type='cuda', dtypes=[torch.cfloat, torch.cdouble], diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch new file mode 100644 index 00000000000..a0c8cce654c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch @@ -0,0 +1,26 @@ +Those tests require 2 GPUs, not 1. + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/distributed/rpc/rpc_test.py b/torch/testing/_internal/distributed/rpc/rpc_test.py +index 825a4c68ee..5a3a6541c1 100644 +--- a/torch/testing/_internal/distributed/rpc/rpc_test.py ++++ b/torch/testing/_internal/distributed/rpc/rpc_test.py +@@ -5864,7 +5864,7 @@ class TensorPipeAgentCudaRpcTest(RpcAgentTestFixture): + + rpc.shutdown() + +- @skip_if_lt_x_gpu(1) ++ @skip_if_lt_x_gpu(2) + def test_devices_option_mismatch(self): + with self.assertRaisesRegex( + RuntimeError, +@@ -5885,7 +5885,7 @@ class TensorPipeAgentCudaRpcTest(RpcAgentTestFixture): + + rpc.shutdown() + +- @skip_if_lt_x_gpu(1) ++ @skip_if_lt_x_gpu(2) + def test_devices_option_mismatch_reverse(self): + with self.assertRaisesRegex( + RuntimeError, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-testnn-on-A100.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-testnn-on-A100.patch new file mode 100644 index 00000000000..782b8315fcf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-testnn-on-A100.patch @@ -0,0 +1,68 @@ +Fix test failures due to use of native TF32 types on A100 GPUs. +See https://github.com/pytorch/pytorch/issues/52278. +Increase TF32 tolerance to allow tests to pass. +See https://github.com/pytorch/pytorch/pull/60451. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_nn.py b/test/test_nn.py +index 533cff9ea4..fd2654a06c 100644 +--- a/test/test_nn.py ++++ b/test/test_nn.py +@@ -10079,12 +10079,11 @@ def add_test(test, decorator=None): + add(cuda_test_name + '_cdouble', test_cdouble) + + else: +- if tf32_is_not_fp32() and test.with_tf32: +- +- def with_tf32_off(self, test=test, kwargs=kwargs): +- with tf32_off(): +- test.test_cuda(self, **kwargs) ++ def with_tf32_off(self, test=test, kwargs=kwargs): ++ with tf32_off(): ++ test.test_cuda(self, **kwargs) + ++ if tf32_is_not_fp32() and test.with_tf32: + add(cuda_test_name + '_fp32', with_tf32_off) + + def with_tf32_on(self, test=test, kwargs=kwargs): +@@ -10093,7 +10092,7 @@ def add_test(test, decorator=None): + + add(cuda_test_name + '_tf32', with_tf32_on) + else: +- add(cuda_test_name, lambda self, test=test, kwargs=kwargs: test.test_cuda(self, **kwargs)) ++ add(cuda_test_name, with_tf32_off) + + for test_params in module_tests + new_module_tests: + # TODO: CUDA is not implemented yet +diff --git a/torch/testing/_internal/common_nn.py b/torch/testing/_internal/common_nn.py +index ad4a0390d4..3d1c8d6838 100644 +--- a/torch/testing/_internal/common_nn.py ++++ b/torch/testing/_internal/common_nn.py +@@ -2381,7 +2381,7 @@ new_module_tests = [ + input_size=(2, 3, 6, 5, 4), + cudnn=True, + with_tf32=True, +- tf32_precision=0.005, ++ tf32_precision=0.05, + ), + dict( + fullname='Conv3d_pad_same', +@@ -2390,7 +2390,7 @@ new_module_tests = [ + input_size=(2, 3, 6, 5, 4), + cudnn=True, + with_tf32=True, +- tf32_precision=0.005, ++ tf32_precision=0.05, + ), + dict( + fullname='Conv3d_pad_same_dilated', +@@ -2399,7 +2399,7 @@ new_module_tests = [ + input_size=(2, 3, 6, 5, 4), + cudnn=True, + with_tf32=True, +- tf32_precision=0.005, ++ tf32_precision=0.05, + ), + dict( + module_name='ConvTranspose3d', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch new file mode 100644 index 00000000000..9714663ac14 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch @@ -0,0 +1,101 @@ +From 63c753573d726ae37cac2783fa0f6a3fd1c30e59 Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Thu, 15 Apr 2021 14:40:39 +0200 +Subject: [PATCH] Fix segmentation fault due to access to destroyed + CudaIPCGlobalEntities instance + +There is an instance of the static destruction order fiasco where cuda_ipc_global_entities +may be accessed after it is destroyed. See #51961 + +This change uses a flag and avoids accesses to the destroyed class when it is set to false. +--- + torch/csrc/CudaIPCTypes.cpp | 23 ++++++++++++++++++++++- + 1 file changed, 22 insertions(+), 1 deletion(-) + +diff --git a/torch/csrc/CudaIPCTypes.cpp b/torch/csrc/CudaIPCTypes.cpp +index be2095d9654c6..9146150c04002 100644 +--- a/torch/csrc/CudaIPCTypes.cpp ++++ b/torch/csrc/CudaIPCTypes.cpp +@@ -25,6 +25,13 @@ void warnProducerTerminatedBeforeSharedTensorsReleased() { + } + + struct CudaIPCGlobalEntities { ++ // This class is used as a singleton (see cuda_ipc_global_entities) ++ // This variable is used to track its lifetime to avoid accessing it ++ // after it was destroyed which would lead to segmentation faults ++ // Note that a trvial type is used which doesn't suffer from construction ++ // and destruction order issues ++ static bool alive; ++ + std::mutex ref_counters_mutex_; + std::atomic sync_events_used_; + std::map> +@@ -32,18 +39,14 @@ struct CudaIPCGlobalEntities { + std::shared_ptr next_available_ref_counters_file_; + CudaIPCSentDataLimbo CudaIPCSentDataLimbo_; + // NOLINTNEXTLINE(cppcoreguidelines-pro-type-member-init) +- CudaIPCGlobalEntities() : ref_counters_files_() {} ++ CudaIPCGlobalEntities() { alive = true; } + ~CudaIPCGlobalEntities() { + CudaIPCSentDataLimbo_.collect(); +- // Clear shared blocks to avoid releasing shared blocks after +- // ~CudaIPCGlobalEntities is done since circular references causes the +- // destructor of ~CudaIPCSentData to access the cuda_ipc_global_entities +- // again. +- CudaIPCSentDataLimbo_.clear_shared_blocks(); + safe_clean_current_file(); + if (next_available_ref_counters_file_) { + warnProducerTerminatedBeforeSharedTensorsReleased(); + } ++ alive = false; + } + void safe_clean_current_file() { + std::lock_guard lock(ref_counters_mutex_); +@@ -54,6 +62,7 @@ struct CudaIPCGlobalEntities { + } + }; + ++bool CudaIPCGlobalEntities::alive = false; + CudaIPCGlobalEntities cuda_ipc_global_entities; + + CudaIPCSentDataLimbo::~CudaIPCSentDataLimbo() { +@@ -108,6 +117,9 @@ void CudaIPCSentDataLimbo::add(std::unique_ptr shared_block) { + void CudaIPCSentDataDelete(void* ptr) { + std::unique_ptr sent_data( + static_cast(ptr)); ++ if(!CudaIPCGlobalEntities::alive) { ++ return; ++ } + if (sent_data->counter_value() > 0) { + cuda_ipc_global_entities.CudaIPCSentDataLimbo_.add(std::move(sent_data)); + } +@@ -115,6 +127,9 @@ void CudaIPCSentDataDelete(void* ptr) { + } + + void ReturnRefCounter(const std::string& handle, uint64_t offset /* unused */) { ++ if(!CudaIPCGlobalEntities::alive) { ++ return; ++ } + std::lock_guard lock( + cuda_ipc_global_entities.ref_counters_mutex_); + auto& map = cuda_ipc_global_entities.ref_counters_files_; +@@ -185,6 +200,9 @@ CudaIPCSentData::~CudaIPCSentData() { + if (event_sync_required_) { + at::cuda::CUDAGuard device_guard(device_.index()); + cudaEventDestroy(event_); ++ if(!CudaIPCGlobalEntities::alive) { ++ return; ++ } + cuda_ipc_global_entities.sync_events_used_ --; + } + } catch (...) { /* No throw */ +@@ -239,6 +257,9 @@ at::DataPtr GetNewRefCountedSentData(void* data, at::Device device) { + } + + bool CudaIPCCollect() { ++ if(!CudaIPCGlobalEntities::alive) { ++ return true; ++ } + bool freed_memory = cuda_ipc_global_entities.CudaIPCSentDataLimbo_.collect(); + if (cuda_ipc_global_entities.CudaIPCSentDataLimbo_.size() == 0) { + cuda_ipc_global_entities.safe_clean_current_file(); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-vsx-vector-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-vsx-vector-functions.patch new file mode 100644 index 00000000000..a3c3e0b0b85 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-vsx-vector-functions.patch @@ -0,0 +1,342 @@ +This fixes multiple bugs introduced by the VSX optimized code in https://github.com/pytorch/pytorch/pull/41541 + +- min/max/clamp now consistently return nan when any value is NaN as on other architectures +- The non-complex angle functions return PI for negative values now +- The complex angle functions have been corrected and optimized +- The float32-log function implementation returned a wrong result when inf was passed (and maybe other inputs), replaced by the sleef function just as for float64 + +See https://github.com/pytorch/pytorch/pull/59382 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_complex_double_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_complex_double_vsx.h +index f62ac36850..ed511c45ed 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_complex_double_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_complex_double_vsx.h +@@ -236,17 +236,14 @@ class Vec256 { + // angle = atan2(b/a) + // auto b_a = _mm256_permute_pd(values, 0x05); // b a + // return Sleef_atan2d4_u10(values, b_a); // 90-angle angle +- auto ret = el_swapped(); +- for (int i = 0; i < 2; i++) { +- ret._vec0[i] = std::atan2(_vec0[i], ret._vec0[i]); +- ret._vec1[i] = std::atan2(_vec1[i], ret._vec0[i]); +- } ++ Vec256 ret; ++ ret._vec0[0] = std::atan2(_vec0[1], _vec0[0]); ++ ret._vec1[0] = std::atan2(_vec1[1], _vec1[0]); + return ret; + } + + Vec256 angle() const { +- auto a = angle_().el_swapped(); +- return a & vd_real_mask; ++ return angle_() & vd_real_mask; + } + + Vec256 real_() const { +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_complex_float_vsx.h +index cb9b4c90fb..4e6433b093 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_complex_float_vsx.h +@@ -357,17 +357,16 @@ class Vec256 { + // angle = atan2(b/a) + // auto b_a = _mm256_permute_ps(values, 0xB1); // b a + // return Sleef_atan2f8_u10(values, b_a); // 90-angle angle +- auto ret = el_swapped(); +- for (int i = 0; i < 4; i++) { +- ret._vec0[i] = std::atan2(_vec0[i], ret._vec0[i]); +- ret._vec1[i] = std::atan2(_vec1[i], ret._vec0[i]); ++ Vec256 ret; ++ for (int i = 0; i < 4; i += 2) { ++ ret._vec0[i] = std::atan2(_vec0[i + 1], _vec0[i]); ++ ret._vec1[i] = std::atan2(_vec1[i + 1], _vec1[i]); + } + return ret; + } + + Vec256 angle() const { +- auto a = angle_().el_swapped(); +- return a & real_mask; ++ return angle_() & real_mask; + } + + Vec256 sin() const { +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h +index f4fa4faa80..3ea237ac32 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_double_vsx.h +@@ -249,7 +259,8 @@ class Vec256 { + } + + Vec256 angle() const { +- return Vec256{0}; ++ auto tmp = blendv(Vec256(0), Vec256(c10::pi), *this < Vec256(0)); ++ return blendv(tmp, *this, isnan()); + } + Vec256 real() const { + return *this; +@@ -367,8 +378,8 @@ class Vec256 { + DEFINE_MEMBER_OP(operator-, double, vec_sub) + DEFINE_MEMBER_OP(operator*, double, vec_mul) + DEFINE_MEMBER_OP(operator/, double, vec_div) +- DEFINE_MEMBER_OP(maximum, double, vec_max) +- DEFINE_MEMBER_OP(minimum, double, vec_min) ++ DEFINE_MEMBER_OP(maximum, double, vec_max_nan2) ++ DEFINE_MEMBER_OP(minimum, double, vec_min_nan2) + DEFINE_MEMBER_OP(operator&, double, vec_and) + DEFINE_MEMBER_OP(operator|, double, vec_or) + DEFINE_MEMBER_OP(operator^, double, vec_xor) +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h +index 2a1a87aa72..5bcf818232 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_float_vsx.h +@@ -282,7 +282,8 @@ class Vec256 { + } + + Vec256 angle() const { +- return Vec256{0}; ++ auto tmp = blendv(Vec256(0), Vec256(c10::pi), *this < Vec256(0)); ++ return blendv(tmp, *this, isnan()); + } + Vec256 real() const { + return *this; +@@ -340,54 +341,16 @@ class Vec256 { + } + + Vec256 C10_ALWAYS_INLINE log() const { +- auto temp = *this; +- auto invalid_mask = temp < zero; +- // cut off denormalized stuff +- auto x = temp.maximum(min_norm_pos); +- vint32 imm0 = vec_sr(vint32(x._vec0), vu_23); +- vint32 imm1 = vec_sr(vint32(x._vec1), vu_23); +- // keep only the fractional part +- x = x & inv_mant_mask; +- x = x | half; +- imm0 = imm0 - v0x7f; +- imm1 = imm1 - v0x7f; +- Vec256 ex; +- ex._vec0 = vec_float(imm0); +- ex._vec1 = vec_float(imm1); +- ex = ex + one; +- auto mask = x < cephes_SQRTHF; +- auto t = x & mask; +- x = x - one; +- ex = ex - (mask & one); +- x = x + t; +- auto z = x * x; +- auto y = x.madd(log_p0, log_p1); +- y = y.madd(x, log_p2); +- y = y.madd(x, log_p3); +- y = y.madd(x, log_p4); +- y = y.madd(x, log_p5); +- y = y.madd(x, log_p6); +- y = y.madd(x, log_p7); +- y = y.madd(x, log_p8); +- y = y * x * z; +- y = ex.madd(log_q1, y); +- y = y - z * half; +- x = x + y; +- x = ex.madd(log_q2, x); +- // negative arg will be NAN +- x = blendv(x, v_nan, invalid_mask); +- // zero is -inf +- x = blendv(x, min_inf, (temp == zero)); +- return x; ++ return {Sleef_logf4_u10vsx(_vec0), Sleef_logf4_u10vsx(_vec1)}; + } + Vec256 C10_ALWAYS_INLINE log10() const { +- return log() * log10e_inv; ++ return {Sleef_log10f4_u10vsx(_vec0), Sleef_log10f4_u10vsx(_vec1)}; + } + Vec256 C10_ALWAYS_INLINE log1p() const { +- return ((*this) + one).log(); ++ return {Sleef_log1pf4_u10vsx(_vec0), Sleef_log1pf4_u10vsx(_vec1)}; + } + Vec256 C10_ALWAYS_INLINE log2() const { +- return log() * log2e_inv; ++ return {Sleef_log2f4_u10vsx(_vec0), Sleef_log2f4_u10vsx(_vec1)}; + } + Vec256 C10_ALWAYS_INLINE ceil() const { + return {vec_ceil(_vec0), vec_ceil(_vec1)}; +@@ -593,27 +593,7 @@ class Vec256 { + } + + Vec256 C10_ALWAYS_INLINE pow(const Vec256& exp) const { +- auto x = *this; +- auto sign_bit = (*this) & sign_mask; +- // |b| +- auto exp_abs = exp.abs(); +- auto exp_trunc = exp.trunc(); +- Vec256 odd_mask; +- odd_mask._vecb0 = (vec_signed(exp._vec0) & vi_1) != vi_0; +- odd_mask._vecb1 = (vec_signed(exp._vec1) & vi_1) != vi_0; +- // using ln fuction +- auto temp = (abs().log() * exp).exp(); +- +- // is odd or even check from Sleef +- auto is_int = (exp == exp_trunc) | (exp_abs >= vcheck); +- auto is_odd = odd_mask & is_int & (exp_abs < vcheck); +- // if even then then pow result should be absolute +- auto temp_sign = temp | sign_bit; // copy_sign +- auto out = blendv(temp, temp_sign, is_odd); +- // x<0 and y != N, then NAN +- auto out1 = blendv(out, v_nan, ((exp.floor() != exp) & (x < zero))); +- // y = 0 then 1 +- return blendv(out1, one, (exp_abs == zero)); ++ return {Sleef_powf4_u10vsx(_vec0, b._vec0), Sleef_powf4_u10vsx(_vec1, b._vec1)}; + } + + Vec256 fmod(const Vec256& b) const { +@@ -653,8 +616,8 @@ class Vec256 { + DEFINE_MEMBER_OP(operator-, float, vec_sub) + DEFINE_MEMBER_OP(operator*, float, vec_mul) + DEFINE_MEMBER_OP(operator/, float, vec_div) +- DEFINE_MEMBER_OP(maximum, float, vec_max) +- DEFINE_MEMBER_OP(minimum, float, vec_min) ++ DEFINE_MEMBER_OP(maximum, float, vec_max_nan2) ++ DEFINE_MEMBER_OP(minimum, float, vec_min_nan2) + DEFINE_MEMBER_OP(operator&, float, vec_and) + DEFINE_MEMBER_OP(operator|, float, vec_or) + DEFINE_MEMBER_OP(operator^, float, vec_xor) +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h +index 33460abe2a..f9d33febdf 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_int16_vsx.h +@@ -287,7 +287,7 @@ class Vec256 { + int16_t& operator[](int idx) = delete; + + Vec256 angle() const { +- return Vec256{0}; ++ return blendv(Vec256(0), Vec256(c10::pi), *this < Vec256(0)); + } + Vec256 real() const { + return *this; +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h +index 2ee2318f03..3fd92551e2 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_int32_vsx.h +@@ -218,7 +218,7 @@ class Vec256 { + int32_t& operator[](int idx) = delete; + + Vec256 angle() const { +- return Vec256{0}; ++ return blendv(Vec256(0), Vec256(c10::pi), *this < Vec256(0)); + } + Vec256 real() const { + return *this; +diff --git a/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h b/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h +index d752f71c9a..e628aeac54 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vec256_int64_vsx.h +@@ -170,7 +170,7 @@ class Vec256 { + int64_t& operator[](int idx) = delete; + + Vec256 angle() const { +- return Vec256{0}; ++ return blendv(Vec256(0), Vec256(c10::pi), *this < Vec256(0)); + } + Vec256 real() const { + return *this; +diff --git a/aten/src/ATen/cpu/vec256/vsx/vsx_helpers.h b/aten/src/ATen/cpu/vec256/vsx/vsx_helpers.h +index 61a572e1ab..716fa2c128 100644 +--- a/aten/src/ATen/cpu/vec256/vsx/vsx_helpers.h ++++ b/aten/src/ATen/cpu/vec256/vsx/vsx_helpers.h +@@ -85,6 +85,69 @@ vec_sldw_aux(const vfloat32& vec_in0, const vfloat32& vec_in1) { + + #define vec_not(a) vec_nor(a, a) + ++// Vectorized min/max which return a if any operand is nan ++template ++C10_ALWAYS_INLINE T vec_min_nan(const T& a, const T& b) { ++ return vec_min(a, b); ++} ++template ++C10_ALWAYS_INLINE T vec_max_nan(const T& a, const T& b) { ++ return vec_max(a, b); ++} ++ ++// Specializations for float/double taken from Eigen ++template<> ++C10_ALWAYS_INLINE vfloat32 vec_min_nan(const vfloat32& a, const vfloat32& b) ++{ ++ // NOTE: about 10% slower than vec_min, but consistent with std::min and SSE regarding NaN ++ vfloat32 ret; ++ __asm__ ("xvcmpgesp %x0,%x1,%x2\n\txxsel %x0,%x1,%x2,%x0" : "=&wa" (ret) : "wa" (a), "wa" (b)); ++ return ret; ++} ++// Specializations for float/double taken from Eigen ++template<> ++C10_ALWAYS_INLINE vfloat32 vec_max_nan(const vfloat32& a, const vfloat32& b) ++{ ++ // NOTE: about 10% slower than vec_max, but consistent with std::min and SSE regarding NaN ++ vfloat32 ret; ++ __asm__ ("xvcmpgtsp %x0,%x2,%x1\n\txxsel %x0,%x1,%x2,%x0" : "=&wa" (ret) : "wa" (a), "wa" (b)); ++ return ret; ++} ++ ++template<> ++C10_ALWAYS_INLINE vfloat64 vec_min_nan(const vfloat64& a, const vfloat64& b) ++{ ++ // NOTE: about 10% slower than vec_min, but consistent with std::min and SSE regarding NaN ++ vfloat64 ret; ++ __asm__ ("xvcmpgedp %x0,%x1,%x2\n\txxsel %x0,%x1,%x2,%x0" : "=&wa" (ret) : "wa" (a), "wa" (b)); ++ return ret; ++} ++template<> ++C10_ALWAYS_INLINE vfloat64 vec_max_nan(const vfloat64& a, const vfloat64& b) ++{ ++ // NOTE: about 10% slower than vec_max, but consistent with std::max and SSE regarding NaN ++ vfloat64 ret; ++ __asm__ ("xvcmpgtdp %x0,%x2,%x1\n\txxsel %x0,%x1,%x2,%x0" : "=&wa" (ret) : "wa" (a), "wa" (b)); ++ return ret; ++} ++ ++// Vectorizes min/max function which returns nan if any side is nan ++#define C10_VSX_VEC_NAN_PROPAG(name, type, btype, func) \ ++ C10_ALWAYS_INLINE type name(const type& a, const type& b) { \ ++ type tmp = func(a, b); \ ++ btype nan_a = vec_cmpne(a, a); \ ++ btype nan_b = vec_cmpne(b, b); \ ++ tmp = vec_sel(tmp, a, nan_a); \ ++ return vec_sel(tmp, b, nan_b); \ ++ } ++ ++C10_VSX_VEC_NAN_PROPAG(vec_min_nan2, vfloat32, vbool32, vec_min) ++C10_VSX_VEC_NAN_PROPAG(vec_max_nan2, vfloat32, vbool32, vec_max) ++C10_VSX_VEC_NAN_PROPAG(vec_min_nan2, vfloat64, vbool64, vec_min) ++C10_VSX_VEC_NAN_PROPAG(vec_max_nan2, vfloat64, vbool64, vec_max) ++ ++#undef C10_VSX_VEC_NAN_PROPAG ++ + #define DEFINE_MEMBER_UNARY_OP(op, op_type, func) \ + Vec256 C10_ALWAYS_INLINE op() const { \ + return Vec256{func(_vec0), func(_vec1)}; \ +@@ -137,20 +200,22 @@ vec_sldw_aux(const vfloat32& vec_in0, const vfloat32& vec_in1) { + const Vec256& min, \ + const Vec256& max) { \ + return Vec256{ \ +- vec_min(max.vec0(), vec_max(a.vec0(), min.vec0())), \ +- vec_min(max.vec1(), vec_max(a.vec1(), min.vec1()))}; \ ++ vec_min_nan(vec_max_nan(a.vec0(), min.vec0()), max.vec0()), \ ++ vec_min_nan(vec_max_nan(a.vec1(), min.vec1()), max.vec1())}; \ + } \ + template <> \ + Vec256 C10_ALWAYS_INLINE clamp_min( \ + const Vec256& a, const Vec256& min) { \ + return Vec256{ \ +- vec_max(a.vec0(), min.vec0()), vec_max(a.vec1(), min.vec1())}; \ ++ vec_max_nan(a.vec0(), min.vec0()), \ ++ vec_max_nan(a.vec1(), min.vec1())}; \ + } \ + template <> \ + Vec256 C10_ALWAYS_INLINE clamp_max( \ + const Vec256& a, const Vec256& max) { \ + return Vec256{ \ +- vec_min(a.vec0(), max.vec0()), vec_min(a.vec1(), max.vec1())}; \ ++ vec_min_nan(a.vec0(), max.vec0()), \ ++ vec_min_nan(a.vec1(), max.vec1())}; \ + } + + #define DEFINE_REINTERPRET_CAST_FUNCS( \ diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_increase-test-cuda-tolerance.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_increase-test-cuda-tolerance.patch new file mode 100644 index 00000000000..a94b6b0e08c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_increase-test-cuda-tolerance.patch @@ -0,0 +1,27 @@ +Relax test tolerance to avoid failure with A100s +See https://github.com/pytorch/pytorch/pull/60458 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_cuda.py b/test/test_cuda.py +index 6f35cbf2ff..10ce9d8e12 100644 +--- a/test/test_cuda.py ++++ b/test/test_cuda.py +@@ -2307,7 +2307,7 @@ torch.cuda.synchronize() + self.assertTrue(scaler.get_scale() == 1.0) + + for c, s in zip(mod_control.parameters(), mod_scaling.parameters()): +- self.assertTrue(torch.allclose(c, s, atol=atol)) ++ self.assertEqual(c, s, atol=atol, rtol=1e-05) + + # Compares no scaling + no autocasting against scaling + autocasting. + def test_grad_scaling_autocast(self): +@@ -2359,7 +2359,7 @@ torch.cuda.synchronize() + if (not scaler.is_enabled()) or (i != skip_iter): + optimizer.step() + +- self._run_scaling_case(run, unskipped=3, skipped=1) ++ self._run_scaling_case(run, unskipped=3, skipped=1, atol=1e-5) + + def test_grad_scaling_clipping_separate_unscale(self): + def run(data, model, optimizer, scaler, loss_fn, skip_iter, try_scaling_api): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch new file mode 100644 index 00000000000..93a3e1f0f2c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch @@ -0,0 +1,47 @@ +From 414dea09876ad2e6b4a4c726285e78f198852476 Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Tue, 22 Jun 2021 16:36:51 +0200 +Subject: [PATCH] Increase tolerance for some distributed tests to 5e-5 + +On A100 GPUs 10 tests fail due to slightly higher deviations. +This fixes those. +--- + test/distributed/test_c10d_common.py | 2 +- + test/distributed/test_c10d_nccl.py | 4 ++-- + 2 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/test/distributed/test_c10d_common.py b/test/distributed/test_c10d_common.py +index a25ef9a046bf5..520c00927d71b 100644 +--- a/test/distributed/test_c10d_common.py ++++ b/test/distributed/test_c10d_common.py +@@ -376,7 +376,7 @@ def update_parameters(model): + len(list(model.parameters())), len(list(ddp_model.parameters())) + ) + for i, j in zip(model.parameters(), ddp_model.parameters()): +- self.assertEqual(i, j) ++ self.assertEqual(i, j, rtol=1.3e-06, atol=5e-5) + + # Shuffle the input so that DDP input is different + torch.manual_seed(1337 + iteration) +diff --git a/test/distributed/test_c10d_nccl.py b/test/distributed/test_c10d_nccl.py +index a22cfa0352ec2..e905c6b1bb060 100644 +--- a/test/distributed/test_c10d_nccl.py ++++ b/test/distributed/test_c10d_nccl.py +@@ -1134,7 +1134,7 @@ def step_model(model, input, target): + ) + for i, j in zip(model.parameters(), ddp_model.parameters()): + # TODO(#38095): Replace assertEqualIgnoreType. See issue #38095 +- self.assertEqualIgnoreType(i.grad, j.grad) ++ self.assertEqualIgnoreType(i.grad, j.grad, rtol=1.3e-06, atol=5e-5) + + # Shuffle the input so that DDP input is different + torch.manual_seed(1337 + iteration) +@@ -1777,7 +1777,7 @@ def _test_ddp_checkpointing( + for i, j in zip(model.parameters(), ddp_model.parameters()): + self.assertTrue(i.grad is not None) + self.assertTrue(j.grad is not None) +- self.assertEqual(i.grad, j.grad) ++ self.assertEqual(i.grad, j.grad, rtol=1.3e-06, atol=5e-5) + + # DDP works as expect when layer is checkpointed only once + @requires_nccl() diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch new file mode 100644 index 00000000000..c360a459f01 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch @@ -0,0 +1,20 @@ +Some tests fail when run with anything but 2 GPUs and others when run with anything but 2 or 4 GPUs. +So limit to 2 GPUs. + +See https://github.com/pytorch/pytorch/issues/59548 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/optim/test_zero_redundancy_optimizer.py b/test/distributed/optim/test_zero_redundancy_optimizer.py +index 06f1b4f484..bc82f6c304 100644 +--- a/test/distributed/optim/test_zero_redundancy_optimizer.py ++++ b/test/distributed/optim/test_zero_redundancy_optimizer.py +@@ -233,7 +233,7 @@ class TestZeroRedundancyOptimizerSingleRank(TestZeroRedundancyOptimizer): + class TestZeroRedundancyOptimizerDistributed(TestZeroRedundancyOptimizer): + @property + def world_size(self): +- return min(4, max(2, torch.cuda.device_count())) ++ return 2 + + @skip_if_rocm + def test_step(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-lstm-serialization-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-lstm-serialization-test.patch new file mode 100644 index 00000000000..ecd4f781e17 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-lstm-serialization-test.patch @@ -0,0 +1,25 @@ +This test fails due to use of AVX512 instructions by FBGEMM (on Skylake and up) +See https://github.com/pytorch/pytorch/issues/59098 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/quantization/test_backward_compatibility.py b/test/quantization/test_backward_compatibility.py +index f4e8518de5..4a21337d9f 100644 +--- a/test/quantization/test_backward_compatibility.py ++++ b/test/quantization/test_backward_compatibility.py +@@ -2,6 +2,7 @@ + + import sys + import os ++import unittest + + # torch + import torch +@@ -216,6 +217,7 @@ class TestSerialization(TestCase): + # TODO: graph mode quantized conv3d module + ++ @unittest.skip("Test fails on AVX512") + @override_qengines + def test_lstm(self): + class LSTMModule(torch.nn.Module): + def __init__(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-nccl-error-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-nccl-error-tests.patch new file mode 100644 index 00000000000..8a987b45b0e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-nccl-error-tests.patch @@ -0,0 +1,86 @@ +Some NCCL error tests fail with e.g. +"CUDA error: uncorrectable NVLink error detected during the execution" + +See https://github.com/pytorch/pytorch/issues/58155 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/distributed/distributed_test.py b/torch/testing/_internal/distributed/distributed_test.py +index 1230f6fcda..8b84a679d2 100644 +--- a/torch/testing/_internal/distributed/distributed_test.py ++++ b/torch/testing/_internal/distributed/distributed_test.py +@@ -6050,6 +6050,7 @@ class DistributedTest: + @require_backends_available({"gloo", "nccl"}) + @skip_if_rocm + @skip_if_lt_x_gpu(int(os.environ["WORLD_SIZE"])) ++ @unittest.skip("Broken on recent NCCL") + def test_monitored_barrier_allreduce_hang(self): + # tests expected behavior when nonzero rank hangs and we want to + # report first timed out rank. +@@ -6060,6 +6061,7 @@ class DistributedTest: + @require_backends_available({"gloo", "nccl"}) + @skip_if_rocm + @skip_if_lt_x_gpu(int(os.environ["WORLD_SIZE"])) ++ @unittest.skip("Broken on recent NCCL") + def test_monitored_barrier_allreduce_hang_wait_all_ranks(self): + # tests expected behavior when nonzero rank hangs and we want to + # report all timed out ranks. +diff --git a/test/distributed/test_c10d_nccl.py b/test/distributed/test_c10d_nccl.py +index 0209755460..79f50ee2d0 100644 +--- a/test/distributed/test_c10d_nccl.py ++++ b/test/distributed/test_c10d_nccl.py +@@ -1940,6 +1940,7 @@ class NcclErrorHandlingTest(MultiProcessTestCase): + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) + @skip_if_rocm ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_clean_exit(self): + self._test_nccl_errors_blocking(lambda: sys.exit(0)) + +@@ -1948,6 +1949,7 @@ class NcclErrorHandlingTest(MultiProcessTestCase): + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) + @skip_if_rocm ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_nonzero_exit(self): + self._test_nccl_errors_blocking(lambda: sys.exit(1)) + +@@ -1956,6 +1958,7 @@ class NcclErrorHandlingTest(MultiProcessTestCase): + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) + @skip_if_rocm ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_abort(self): + self._test_nccl_errors_blocking(lambda: os.abort()) + +@@ -1964,6 +1967,7 @@ class NcclErrorHandlingTest(MultiProcessTestCase): + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) + @skip_if_rocm ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_sigkill(self): + self._test_nccl_errors_blocking(lambda: os.kill(os.getpid(), signal.SIGKILL)) + +@@ -1972,6 +1976,7 @@ class NcclErrorHandlingTest(MultiProcessTestCase): + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) + @skip_if_rocm ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_sigterm(self): + self._test_nccl_errors_blocking(lambda: os.kill(os.getpid(), signal.SIGTERM)) + +@@ -1979,6 +1984,7 @@ class NcclErrorHandlingTest(MultiProcessTestCase): + @requires_nccl() + @requires_nccl_version(2400, "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_blocking_wait_with_barrier(self): + store = c10d.FileStore(self.file_name, self.world_size) + process_group = c10d.ProcessGroupNCCL( +@@ -2024,6 +2030,7 @@ class NcclErrorHandlingTest(MultiProcessTestCase): + @with_nccl_blocking_wait + @requires_nccl() + @skip_if_lt_x_gpu(3) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_timeout(self): + store = c10d.FileStore(self.file_name, self.world_size) diff --git a/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0-Python-2.7.16.eb b/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0-Python-2.7.16.eb index 246347a9e78..3f5b19fcde0 100644 --- a/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0-Python-2.7.16.eb +++ b/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0-Python-2.7.16.eb @@ -9,7 +9,6 @@ description = "A Variant Call Format reader for Python." toolchain = {'name': 'GCC', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'] diff --git a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intel-2019b-Python-3.7.4.eb index a9fe93659b2..a2392553843 100644 --- a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intel-2019b-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "PyWavelets is open source wavelet transform software for Python." toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'] diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2016a-Python-2.7.11.eb index 1898bceb6d1..a1fb064f04d 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2016b-Python-2.7.12.eb index 647a8747ca4..9d0b1d36ec1 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2017b-Python-2.7.14.eb index 63dfbd0450d..d8b50aef171 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2017b-Python-3.6.3.eb index 56748ad856d..4c7123990a0 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2018a-Python-2.7.14.eb index d991f7f0c87..d5e6d282392 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2018a-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2018a-Python-3.6.4.eb index cec8fe9b1fc..ee3bc3b7af9 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-foss-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-2.7.14.eb index 0413cca4381..48b8040a254 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'fosscuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -23,9 +22,4 @@ download_dep_fail = True options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-3.6.3.eb index 0aaa6640869..6a4388d848d 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'fosscuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -23,9 +22,4 @@ download_dep_fail = True options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-2.7.12.eb index 142b448ffd0..47ba4b60cc9 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb index ab85ee09074..cef5cce3ccd 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb index f670e65fd2d..f472c656259 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.eb index 10b6ba3ac95..9650ec327bb 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017b-Python-2.7.14.eb index 95b101ebb9e..95fc8069286 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017b-Python-3.6.3.eb index ea0e7706fd3..413984a5fe1 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2018a-Python-2.7.14.eb index a3a95779357..80d53122e8c 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2018a-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2018a-Python-3.6.4.eb index 9bbd5c5834e..e29a126efba 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb index 675ef0e7283..31b69d74377 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb @@ -8,7 +8,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-foss-2018b-Python-3.6.6.eb index 9f13df6db8a..b2c3b935c60 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-foss-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-2.7.15.eb index f710b4901e3..8bb513d5d09 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-2.7.15.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb index 33906e08e06..74550b0a3a0 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb index d9ec29b77b8..573b55a70e2 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'] @@ -23,9 +22,4 @@ use_pip = True options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-3.6.6.eb index b0a6eec3183..c870d14c8a0 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'] @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13.eb index d199e60a2fb..3bc6570c2fe 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13.eb @@ -8,7 +8,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'] diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb index c9e5dc94be2..33fceacbe02 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb @@ -8,7 +8,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['436bc774ecf7c103814098159fbb84c2715d25980175292c648f2da143909f95'] @@ -25,9 +24,4 @@ download_dep_fail = True options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1.2-GCCcore-8.3.0.eb index c5f190c7631..5cb32be4880 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1.2-GCCcore-8.3.0.eb @@ -8,7 +8,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['01adf0b6c6f61bd11af6e10ca52b7d4057dd0be0343eb9283c878cf3af56aee4'] @@ -25,9 +24,4 @@ download_dep_fail = True options = {'modulename': 'yaml'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.4.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..5acea098c90 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.4.1-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '5.4.1' + +homepage = "https://github.com/yaml/pyyaml" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['607774cbba28732bfa802b54baa7484215f530991055bb562efbed5b2f20a45e'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('libyaml', '0.2.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'yaml'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.43.0.5-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.43.0.5-GCCcore-8.3.0-Python-3.7.4.eb index 4a900c434f9..0846664118f 100644 --- a/easybuild/easyconfigs/p/PycURL/PycURL-7.43.0.5-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PycURL/PycURL-7.43.0.5-GCCcore-8.3.0-Python-3.7.4.eb @@ -19,7 +19,6 @@ dependencies = [ ('cURL', '7.66.0'), ] -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['ec7dd291545842295b7b56c12c90ffad2976cc7070c98d7b1517b7b6cd5994b3'] diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-2.7.11.eb index 29f7e2e571d..8b8e0eee463 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-2.7.11.eb @@ -4,13 +4,12 @@ name = 'Pygments' version = '2.1.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pygments.org/' +homepage = 'https://pygments.org/' description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb index 85869f21eaa..2175e280735 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb @@ -4,13 +4,12 @@ name = 'Pygments' version = '2.1.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pygments.org/' +homepage = 'https://pygments.org/' description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-2.7.15.eb index 38ca18f985a..17ace7eb8aa 100644 --- a/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-2.7.15.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Pyomo' version = '5.5.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.pyomo.org/' +homepage = 'https://www.pyomo.org/' description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models. """ @@ -12,40 +12,24 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [('Python', '2.7.15')] -exts_defaultclass = 'PythonPackage' - -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('appdirs', '1.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), ('ply', '3.11', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ply'], 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], }), ('PyUtilib', '5.6.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyutilib'], 'checksums': ['6a21fccfe691c39566c0bb19b5c9aa11bca8b076aa6f1dbf21c11711f5105191'], # use setuptools: pip fails due to missing __init__.py files # see: https://github.com/PyUtilib/pyutilib/issues/39 'use_pip': False, }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyomo'], 'checksums': ['6079a7a24d148b1c725d5364de1e0fa99e2e9c284ba223517e0955ef2b8f3ea1'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb index b0785c43d77..cf1f1e6d781 100644 --- a/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'Pyomo' version = '5.5.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.pyomo.org/' +homepage = 'https://www.pyomo.org/' description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models. """ @@ -16,29 +16,20 @@ use_pip = True exts_list = [ ('appdirs', '1.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), ('ply', '3.11', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ply'], 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], }), ('PyUtilib', '5.6.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyutilib'], 'checksums': ['6a21fccfe691c39566c0bb19b5c9aa11bca8b076aa6f1dbf21c11711f5105191'], # use setuptools: pip fails due to missing __init__.py files # see: https://github.com/PyUtilib/pyutilib/issues/39 'use_pip': False, }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyomo'], 'checksums': ['6079a7a24d148b1c725d5364de1e0fa99e2e9c284ba223517e0955ef2b8f3ea1'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb index 0a1e3fec180..a6f93596747 100644 --- a/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ description = """Pyro means PYthon Remote Objects. It is a library that enables toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] options = {'modulename': 'Pyro4'} @@ -19,9 +18,4 @@ dependencies = [ ('Python', '2.7.11'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb index d8682d26e19..5fe62ef7c4e 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb @@ -6,7 +6,7 @@ # Modified by: Robert Qiao , Exequiel Sepulveda # @ adelaide.edu.au/phoenix -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Pysam' version = '0.10.0' @@ -25,13 +25,8 @@ dependencies = [ ('cURL', '7.49.1'), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ ('Cython', '0.25.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306'], }), ('pysam', version, { @@ -41,13 +36,4 @@ exts_list = [ }), ] -modextrapaths = { - 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb index 93e0a909562..4f71583f038 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb @@ -6,7 +6,7 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Pysam' version = '0.9.1.4' @@ -27,27 +27,12 @@ dependencies = [ ('cURL', '7.49.1'), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ - ('Cython', '0.25.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), + ('Cython', '0.25.1'), ('pysam', version, { 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], }), ] -modextrapaths = { - 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/pysam-%(version)s-py%(pyshortver)s-linux-x86_64.egg'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pysolar/Pysolar-0.7-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pysolar/Pysolar-0.7-intel-2017b-Python-3.6.3.eb index a79ff06bbc8..99be9df970b 100644 --- a/easybuild/easyconfigs/p/Pysolar/Pysolar-0.7-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pysolar/Pysolar-0.7-intel-2017b-Python-3.6.3.eb @@ -4,21 +4,15 @@ name = 'Pysolar' version = '0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pysolar.org/' +homepage = 'https://pysolar.org/' description = """Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth by the sun.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['f12288b3b918fc564f0180411334355b77ff0a70257250ee2e2fc06b612dbe2c'] dependencies = [('Python', '3.6.3')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Pysolar/Pysolar-0.7-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/Pysolar/Pysolar-0.7-intel-2018a-Python-3.6.4.eb index 3bb6e037a85..ceb8e77bf10 100644 --- a/easybuild/easyconfigs/p/Pysolar/Pysolar-0.7-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/Pysolar/Pysolar-0.7-intel-2018a-Python-3.6.4.eb @@ -4,13 +4,12 @@ name = 'Pysolar' version = '0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pysolar.org/' +homepage = 'https://pysolar.org/' description = """Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth by the sun.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['f12288b3b918fc564f0180411334355b77ff0a70257250ee2e2fc06b612dbe2c'] @@ -18,9 +17,4 @@ dependencies = [('Python', '3.6.4')] download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-GCCcore-8.2.0-Python-3.7.2.eb index 8021bc8a267..eeb4619b9e1 100644 --- a/easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-GCCcore-8.2.0-Python-3.7.2.eb @@ -4,13 +4,12 @@ name = 'Pysolar' version = '0.8' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pysolar.org/' +homepage = 'https://pysolar.org/' description = """Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth by the sun.""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['548c05177acd2845143d9624e670635cd3e5c3a63782449ca35e090ca755c617'] diff --git a/easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-intel-2018b-Python-3.6.6.eb index 35b28a9d42b..6dc525a1668 100644 --- a/easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-intel-2018b-Python-3.6.6.eb @@ -4,13 +4,12 @@ name = 'Pysolar' version = '0.8' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pysolar.org/' +homepage = 'https://pysolar.org/' description = """Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth by the sun.""" toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['548c05177acd2845143d9624e670635cd3e5c3a63782449ca35e090ca755c617'] @@ -19,9 +18,4 @@ dependencies = [('Python', '3.6.6')] download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb index 08355556150..a46c9232e80 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.10' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -32,15 +32,9 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '7.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '16.0'), + ('pip', '7.0.1'), + ('nose', '1.3.6'), ('numpy', local_numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % local_numpyversion, 'download')], 'patches': ['numpy-1.8.0-mkl.patch'], @@ -48,74 +42,41 @@ exts_list = [ ('scipy', local_scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % local_scipyversion, 'download')], }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('pbr', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], }), + ('paycheck', '1.0.2'), + ('argparse', '1.3.0'), + ('pbr', '1.0.1'), + ('lockfile', '0.10.2'), ('Cython', '0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'source_tmpl': 'cython-%(version)s.tar.gz', }), - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + ('six', '1.9.0'), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), + ('decorator', '3.4.2'), ('arff', '2.0.2', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.14', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('mock', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2015.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.16.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('ecdsa', '0.13'), + ('paramiko', '1.15.2'), + ('pyparsing', '2.0.3'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.14'), + ('mock', '1.0.1'), + ('pytz', '2015.4'), + ('pandas', '0.16.1'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 49ce885a5f2..8a05e2167e7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.11' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -33,15 +33,9 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '18.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '7.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '18.7.1'), + ('pip', '7.1.2'), + ('nose', '1.3.7'), ('numpy', local_numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % local_numpyversion, 'download')], 'patches': ['numpy-1.8.0-mkl.patch'], @@ -49,89 +43,49 @@ exts_list = [ ('scipy', local_scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % local_scipyversion, 'download')], }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('pbr', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2'), + ('argparse', '1.4.0'), + ('pbr', '1.8.1'), + ('lockfile', '0.12.2'), + ('Cython', '0.23.4'), + ('six', '1.10.0'), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), + ('decorator', '4.0.4'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2015.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('ecdsa', '0.13'), + ('paramiko', '1.16.0'), + ('pyparsing', '2.0.6'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('funcsigs', '0.4'), + ('mock', '1.3.0'), + ('pytz', '2015.7'), + ('pandas', '0.17.1'), ('enum34', '1.1.2', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; # cfr. https://github.com/scott-griffiths/bitstring/issues/159 - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), - ('virtualenv', '14.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], - }), + ('virtualenv', '14.0.5'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb index b25b8045796..3500d735705 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.11' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -33,15 +33,9 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '18.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '7.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '18.7.1'), + ('pip', '7.1.2'), + ('nose', '1.3.7'), ('numpy', local_numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % local_numpyversion, 'download')], 'patches': [ @@ -52,84 +46,46 @@ exts_list = [ ('scipy', local_scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % local_scipyversion, 'download')], }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('pbr', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2'), + ('argparse', '1.4.0'), + ('pbr', '1.8.1'), + ('lockfile', '0.12.2'), + ('Cython', '0.23.4'), + ('six', '1.10.0'), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), + ('decorator', '4.0.4'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2015.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('ecdsa', '0.13'), + ('paramiko', '1.16.0'), + ('pyparsing', '2.0.6'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('funcsigs', '0.4'), + ('mock', '1.3.0'), + ('pytz', '2015.7'), + ('pandas', '0.17.1'), ('enum34', '1.1.2', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; # cfr. https://github.com/scott-griffiths/bitstring/issues/159 - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb index 978699a66af..7e4c2985498 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.11' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -33,15 +33,9 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '18.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '7.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '18.7.1'), + ('pip', '7.1.2'), + ('nose', '1.3.7'), ('numpy', local_numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % local_numpyversion, 'download')], 'patches': [ @@ -52,89 +46,49 @@ exts_list = [ ('scipy', local_scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % local_scipyversion, 'download')], }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('pbr', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2'), + ('argparse', '1.4.0'), + ('pbr', '1.8.1'), + ('lockfile', '0.12.2'), + ('Cython', '0.23.4'), + ('six', '1.10.0'), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), + ('decorator', '4.0.4'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2015.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('ecdsa', '0.13'), + ('paramiko', '1.16.0'), + ('pyparsing', '2.0.6'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('funcsigs', '0.4'), + ('mock', '1.3.0'), + ('pytz', '2015.7'), + ('pandas', '0.17.1'), ('enum34', '1.1.2', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; # cfr. https://github.com/scott-griffiths/bitstring/issues/159 - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), - ('virtualenv', '14.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], - }), + ('virtualenv', '14.0.5'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 834dd4e2cb5..20efcbef9b2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -3,7 +3,7 @@ version = '2.7.11' versionsuffix = '-libX11-1.6.3' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,15 +35,9 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '18.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '7.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '18.7.1'), + ('pip', '7.1.2'), + ('nose', '1.3.7'), ('numpy', local_numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % local_numpyversion, 'download')], 'patches': [ @@ -54,89 +48,49 @@ exts_list = [ ('scipy', local_scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % local_scipyversion, 'download')], }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('pbr', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2'), + ('argparse', '1.4.0'), + ('pbr', '1.8.1'), + ('lockfile', '0.12.2'), + ('Cython', '0.23.4'), + ('six', '1.10.0'), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), + ('decorator', '4.0.4'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2015.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('ecdsa', '0.13'), + ('paramiko', '1.16.0'), + ('pyparsing', '2.0.6'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('funcsigs', '0.4'), + ('mock', '1.3.0'), + ('pytz', '2015.7'), + ('pandas', '0.17.1'), ('enum34', '1.1.2', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; # cfr. https://github.com/scott-griffiths/bitstring/issues/159 - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), - ('virtualenv', '14.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], - }), + ('virtualenv', '14.0.5'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index aaeff362509..a761ffb29d7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.11' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -33,15 +33,9 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '18.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '7.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '18.7.1'), + ('pip', '7.1.2'), + ('nose', '1.3.7'), ('numpy', local_numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % local_numpyversion, 'download')], 'patches': [ @@ -52,89 +46,49 @@ exts_list = [ ('scipy', local_scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % local_scipyversion, 'download')], }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('pbr', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2'), + ('argparse', '1.4.0'), + ('pbr', '1.8.1'), + ('lockfile', '0.12.2'), + ('Cython', '0.23.4'), + ('six', '1.10.0'), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), + ('decorator', '4.0.4'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2015.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('ecdsa', '0.13'), + ('paramiko', '1.16.0'), + ('pyparsing', '2.0.6'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('funcsigs', '0.4'), + ('mock', '1.3.0'), + ('pytz', '2015.7'), + ('pandas', '0.17.1'), ('enum34', '1.1.2', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; # cfr. https://github.com/scott-griffiths/bitstring/issues/159 - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), - ('virtualenv', '14.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], - }), + ('virtualenv', '14.0.5'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb index c96e277c8f9..9d8994b1c56 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb @@ -3,7 +3,7 @@ name = 'Python' version = '2.7.11' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,15 +35,9 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '18.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '7.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '18.7.1'), + ('pip', '7.1.2'), + ('nose', '1.3.7'), ('numpy', local_numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % local_numpyversion, 'download')], 'patches': ['numpy-1.8.0-mkl.patch'], @@ -51,89 +45,49 @@ exts_list = [ ('scipy', local_scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % local_scipyversion, 'download')], }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('pbr', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2'), + ('argparse', '1.4.0'), + ('pbr', '1.8.1'), + ('lockfile', '0.12.2'), + ('Cython', '0.23.4'), + ('six', '1.10.0'), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), + ('decorator', '4.0.4'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2015.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('ecdsa', '0.13'), + ('paramiko', '1.16.0'), + ('pyparsing', '2.0.6'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('funcsigs', '0.4'), + ('mock', '1.3.0'), + ('pytz', '2015.7'), + ('pandas', '0.17.1'), ('enum34', '1.1.2', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; # cfr. https://github.com/scott-griffiths/bitstring/issues/159 - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), - ('virtualenv', '14.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], - }), + ('virtualenv', '14.0.5'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb index f624ce412fa..a142023c82b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.11' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -33,15 +33,9 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '18.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '7.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '18.7.1'), + ('pip', '7.1.2'), + ('nose', '1.3.7'), ('numpy', local_numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % local_numpyversion, 'download')], 'patches': ['numpy-1.8.0-mkl.patch'], @@ -49,89 +43,49 @@ exts_list = [ ('scipy', local_scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % local_scipyversion, 'download')], }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('pbr', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2'), + ('argparse', '1.4.0'), + ('pbr', '1.8.1'), + ('lockfile', '0.12.2'), + ('Cython', '0.23.4'), + ('six', '1.10.0'), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), + ('decorator', '4.0.4'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2015.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('ecdsa', '0.13'), + ('paramiko', '1.16.0'), + ('pyparsing', '2.0.6'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('funcsigs', '0.4'), + ('mock', '1.3.0'), + ('pytz', '2015.7'), + ('pandas', '0.17.1'), ('enum34', '1.1.2', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; # cfr. https://github.com/scott-griffiths/bitstring/issues/159 - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), - ('virtualenv', '14.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], - }), + ('virtualenv', '14.0.5'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb index c7948e385b3..016bc5c4749 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.12' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -33,133 +33,106 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated May 28th 2015 exts_list = [ ('setuptools', '23.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['4e269d36ba2313e6236f384b36eb97b3433cf99a16b94c74cca7eee2b311f2be'], }), ('pip', '8.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['4d24b03ffa67638a3fa931c09fd9e0273ffa904e95ebebe7d4b1a54c93d7b732'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.11.1', { 'patches': ['numpy-1.8.0-mkl.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ 'dc4082c43979cc856a2bf352a8297ea109ccb3244d783ae067eb2ee5b0d577cd', # numpy-1.11.1.tar.gz '3c72a669be7a8c2810e0ff372eb356a473a847e1a4b9e5cd6eec7107bfccb051', # numpy-1.8.0-mkl.patch ], }), ('scipy', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['9c4cd2f8013cc4084230a0e858d7642963dbadfd76494d2fad3b0b29bebb38ac'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['e7bd2044aaac5a6ea87a87b2ecc73b310bb6efe5026031e33067ea3c2efc3507'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['186428c270309e6fdfe2d5ab0949ab21ae5f7dea831eab96701b86bd666af39c'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.24', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['6de44d8c482128efc12334641347a9c3e5098d807dd3c69e867fa8f84ec2a3f1'], }), ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a'], }), ('dateutil', '2.5.3', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['1408fdb07c6a1fa9997567ce3fcee6a337b39a503d80699e0f213de4aa4b32ed'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b'], }), ('decorator', '4.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['9c6e98edcb33499881b86ede07d9968c81ab7c769e28e9af24075f0a5379f070'], }), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['be6b5b76698d5fca1f24d75c98ed9c0ff5e24eb0d985d01cfd26c08a70f9654e'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('cryptography', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['bb149540ed90c4b2171bf694fe6991d6331bc149ae623c8ff419324f4222d128'], }), ('paramiko', '2.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['261afe9246c2494e50bbeab55e50934348e91d1189803123459e0c81cda70fac'], }), ('pyparsing', '2.1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['b9ace99b581174d7ca98891a7bc57fd08892b94f17922645d90835f7b9b54a56'], }), ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['9656a169cb83da34d732b0eb72b39373d48774aee009a3d1272b7ea2ce109cde'], }), ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['a1f5c9fcf75ac2579b9995c843dade33009543c04f218ff7c007b3c81695bd19'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2016.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], 'checksums': ['c823de61ff40d1996fe087cec343e0503881ca641b897e0f9b86c7683a0bfee1'], }), ('pandas', '0.18.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['d2e483692c7915916dffd1b83256ea9761b4224c8d45646ceddf48b977ee77b2'], }), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['fab40f32d9ad298fba04a260f3073505a16d52539a84843cf8c8369d4fd17167'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb index 83057093839..4c909ec5e37 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.12' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -31,103 +31,54 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '23.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '8.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '23.1.0'), + ('pip', '8.1.2'), + ('nose', '1.3.7'), ('numpy', '1.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'patches': ['numpy-1.8.0-mkl.patch'], }), - ('scipy', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('scipy', '0.17.1'), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('pbr', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.24', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], }), + ('paycheck', '1.0.2'), + ('pbr', '1.10.0'), + ('lockfile', '0.12.2'), + ('Cython', '0.24'), + ('six', '1.10.0'), ('dateutil', '2.5.3', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '4.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), + ('decorator', '4.0.10'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('cryptography', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - }), - ('paramiko', '2.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2016.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.18.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('ecdsa', '0.13'), + ('cryptography', '1.4'), + ('paramiko', '2.0.1'), + ('pyparsing', '2.1.5'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('funcsigs', '1.0.2'), + ('mock', '2.0.0'), + ('pytz', '2016.4'), + ('pandas', '0.18.1'), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], - }), - ('virtualenv', '15.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), + ('virtualenv', '15.0.2'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb index bfb67d268a2..17e8f481781 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.12' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -31,106 +31,55 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '23.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '8.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '23.1.0'), + ('pip', '8.1.2'), + ('nose', '1.3.7'), ('numpy', '1.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'patches': ['numpy-1.8.0-mkl.patch'], }), - ('scipy', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('scipy', '0.17.1'), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('pbr', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.24', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], }), + ('paycheck', '1.0.2'), + ('pbr', '1.10.0'), + ('lockfile', '0.12.2'), + ('Cython', '0.24'), + ('six', '1.10.0'), ('dateutil', '2.5.3', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '4.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), + ('decorator', '4.0.10'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('cryptography', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - }), - ('paramiko', '2.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2016.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.18.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('ecdsa', '0.13'), + ('cryptography', '1.4'), + ('paramiko', '2.0.1'), + ('pyparsing', '2.1.5'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('funcsigs', '1.0.2'), + ('mock', '2.0.0'), + ('pytz', '2016.4'), + ('pandas', '0.18.1'), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], - }), - ('virtualenv', '15.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], - }), - ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], }), + ('virtualenv', '15.0.2'), + ('docopt', '0.6.2'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb index 84c7c48c9e3..8b83e77fb18 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.13' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -34,20 +34,16 @@ exts_list = [ # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, # see https://github.com/pypa/setuptools/issues/980 ('setuptools', '33.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['6b20352ed60ba08c43b3611bdb502286f7a869fbfcf472f40d7279f1e77de145'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.12.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'source_tmpl': '%(name)s-%(version)s.zip', 'patches': ['numpy-1.12.0-mkl.patch'], 'checksums': [ @@ -56,131 +52,104 @@ exts_list = [ ], }), ('scipy', '0.19.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['4190d34bf9a09626cd42100bbb12e3d96b2daf1a8a3244e991263eb693732122'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['0ccd2db529afd070df815b1521f01401d43de03941170f8a800e7531faba265d'], }), ('Cython', '0.25.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306'], }), ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a'], }), ('dateutil', '2.6.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['62a2f8df3d66f878373fd0072eacf4ee52194ba302e00082828e0d263b0418d2'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b'], }), ('decorator', '4.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['953d6bf082b100f43229cf547f4f97f97e970f5ad645ee7601d55ff87afdfe76'], }), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['be6b5b76698d5fca1f24d75c98ed9c0ff5e24eb0d985d01cfd26c08a70f9654e'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['323524312bb467565ebca7e50c8ae5e9674e544951d28a2904a50012a8828190'], }), ('paramiko', '2.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['5fae49bed35e2e3d45c4f7b0db2d38b9ca626312d91119b3991d0ecf8125e310'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.5', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['59d8ad52dd3116fcb6635e175751b250dc783fb011adba539558bd764e5d628b'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['f5c056e8f62d45ba8215e5cb8f50dfccb198b4b9fbea8500674f3443e4689589'], }), ('pandas', '0.19.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['6f0f4f598c2b16746803c8bafef7c721c57e4844da752d36240c0acf97658014'], }), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb index 50c1f3a97cc..73b08e8b434 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.13' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -34,20 +34,16 @@ exts_list = [ # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, # see https://github.com/pypa/setuptools/issues/980 ('setuptools', '33.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['6b20352ed60ba08c43b3611bdb502286f7a869fbfcf472f40d7279f1e77de145'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.12.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'source_tmpl': '%(name)s-%(version)s.zip', 'patches': ['numpy-1.12.0-mkl.patch'], 'checksums': [ @@ -56,131 +52,104 @@ exts_list = [ ], }), ('scipy', '0.19.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['4190d34bf9a09626cd42100bbb12e3d96b2daf1a8a3244e991263eb693732122'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['0ccd2db529afd070df815b1521f01401d43de03941170f8a800e7531faba265d'], }), ('Cython', '0.25.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306'], }), ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a'], }), ('dateutil', '2.6.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['62a2f8df3d66f878373fd0072eacf4ee52194ba302e00082828e0d263b0418d2'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b'], }), ('decorator', '4.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['953d6bf082b100f43229cf547f4f97f97e970f5ad645ee7601d55ff87afdfe76'], }), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['be6b5b76698d5fca1f24d75c98ed9c0ff5e24eb0d985d01cfd26c08a70f9654e'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['323524312bb467565ebca7e50c8ae5e9674e544951d28a2904a50012a8828190'], }), ('paramiko', '2.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['5fae49bed35e2e3d45c4f7b0db2d38b9ca626312d91119b3991d0ecf8125e310'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.5', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['59d8ad52dd3116fcb6635e175751b250dc783fb011adba539558bd764e5d628b'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['f5c056e8f62d45ba8215e5cb8f50dfccb198b4b9fbea8500674f3443e4689589'], }), ('pandas', '0.19.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['6f0f4f598c2b16746803c8bafef7c721c57e4844da752d36240c0acf97658014'], }), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2017b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2017b.eb index d62b529c93f..f8e12526bbb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2017b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.14' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,181 +35,142 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '36.5.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['ce2007c1cea3359870b80657d634253a0765b0c7dc5a988d77ba803fc86f2c64'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.1', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ 'c9b0283776085cb2804efff73e9955ca279ba4edafd58d3ead70b61d209c4fbb', # numpy-1.13.1.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.26.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['c2e63c4794161135adafa8aa4a855d6068073f421c83ffacc39369497a189dd5'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['d04bb2425086c3fe86f7bc48915290b13e798497839fbb18ab7f6dffcf98cc3a'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['ff94ae65379914ec3c960de731381f49092057b6dd1d24d18842ead5a2eb2277'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.2', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], 'checksums': ['f5c056e8f62d45ba8215e5cb8f50dfccb198b4b9fbea8500674f3443e4689589'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2018a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2018a.eb index fa4673554b4..63dca7fb3fe 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2018a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.14' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,195 +35,151 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ '3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb', # numpy-1.14.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('python-dateutil', '2.6.1', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('liac-arff', '2.1.1', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.19', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['200d8686011d470b5e4de207d803445deee427455cd0cb7c982b68cf82524f81'], }), ('enum34', '1.1.6', { - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34/'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], 'modulename': 'enum', }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.22.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['44a94091dd71f05922eec661638ec1a35f26d573c119aa2fad964f10a2880e6c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2017b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2017b.eb index dd15a316151..62d64a358ee 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2017b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.14' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,181 +35,142 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '36.5.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['ce2007c1cea3359870b80657d634253a0765b0c7dc5a988d77ba803fc86f2c64'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.1', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ 'c9b0283776085cb2804efff73e9955ca279ba4edafd58d3ead70b61d209c4fbb', # numpy-1.13.1.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.26.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['c2e63c4794161135adafa8aa4a855d6068073f421c83ffacc39369497a189dd5'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['d04bb2425086c3fe86f7bc48915290b13e798497839fbb18ab7f6dffcf98cc3a'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['ff94ae65379914ec3c960de731381f49092057b6dd1d24d18842ead5a2eb2277'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.2', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], 'checksums': ['f5c056e8f62d45ba8215e5cb8f50dfccb198b4b9fbea8500674f3443e4689589'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2018a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2018a.eb index 1dd07ddb2cd..79f3142203e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2018a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.14' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,195 +35,151 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ '3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb', # numpy-1.14.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('python-dateutil', '2.6.1', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('liac-arff', '2.1.1', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.19', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['200d8686011d470b5e4de207d803445deee427455cd0cb7c982b68cf82524f81'], }), ('enum34', '1.1.6', { - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34/'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], 'modulename': 'enum', }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.22.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['44a94091dd71f05922eec661638ec1a35f26d573c119aa2fad964f10a2880e6c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2017b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2017b.eb index b4a56e3c4a3..a9d3712ce44 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2017b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.14' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,181 +35,142 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '36.5.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['ce2007c1cea3359870b80657d634253a0765b0c7dc5a988d77ba803fc86f2c64'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.1', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ 'c9b0283776085cb2804efff73e9955ca279ba4edafd58d3ead70b61d209c4fbb', # numpy-1.13.1.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.26.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['c2e63c4794161135adafa8aa4a855d6068073f421c83ffacc39369497a189dd5'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 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['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['d04bb2425086c3fe86f7bc48915290b13e798497839fbb18ab7f6dffcf98cc3a'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['ff94ae65379914ec3c960de731381f49092057b6dd1d24d18842ead5a2eb2277'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.2', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], 'checksums': ['f5c056e8f62d45ba8215e5cb8f50dfccb198b4b9fbea8500674f3443e4689589'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018.01.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018.01.eb index ca6fe0d6c5b..bbffc80bbfa 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018.01.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018.01.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.14' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,180 +35,141 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '37.0.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['0b95db16abf74d435217f17774245fce1ea5a583e5ae8098d98f4ab0145491e3'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.3', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ '36ee86d5adbabc4fa2643a073f93d5504bdfed37a149a3a49f4dde259f35a750', # numpy-1.13.3.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['68a26c353627163d74ee769d4749f2ee243866e9dac43c93bb33ebd8fbed1199'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.21.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['5cd5cb30e72eeaf202f0e5e180780b897570e889d2db328c689a5a263405c559'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018a.eb index 713ed6a6e46..532b3259a64 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.14' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,195 +35,151 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ '3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb', # numpy-1.14.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('python-dateutil', '2.6.1', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('liac-arff', '2.1.1', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('enum34', '1.1.6', { - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34/'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], 'modulename': 'enum', }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.22.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['44a94091dd71f05922eec661638ec1a35f26d573c119aa2fad964f10a2880e6c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-intelcuda-2017b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-intelcuda-2017b.eb index 0fb57307a81..809a152aa1d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-intelcuda-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-intelcuda-2017b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.14' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,181 +35,142 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '36.5.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['ce2007c1cea3359870b80657d634253a0765b0c7dc5a988d77ba803fc86f2c64'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.1', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ 'c9b0283776085cb2804efff73e9955ca279ba4edafd58d3ead70b61d209c4fbb', # numpy-1.13.1.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.26.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['c2e63c4794161135adafa8aa4a855d6068073f421c83ffacc39369497a189dd5'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['d04bb2425086c3fe86f7bc48915290b13e798497839fbb18ab7f6dffcf98cc3a'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['ff94ae65379914ec3c960de731381f49092057b6dd1d24d18842ead5a2eb2277'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.2', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], 'checksums': ['f5c056e8f62d45ba8215e5cb8f50dfccb198b4b9fbea8500674f3443e4689589'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-iomkl-2018a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-iomkl-2018a.eb index 28d678ded65..2fc8fa47172 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-iomkl-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-iomkl-2018a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.14' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,195 +35,151 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ '3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb', # numpy-1.14.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('python-dateutil', '2.6.1', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('liac-arff', '2.1.1', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('enum34', '1.1.6', { - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34/'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], 'modulename': 'enum', }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.22.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['44a94091dd71f05922eec661638ec1a35f26d573c119aa2fad964f10a2880e6c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-foss-2018b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-foss-2018b.eb index c94fbe693ae..88e0bab42e0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-foss-2018b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.15' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,194 +35,149 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '39.2.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['f7cddbb5f5c640311eb00eab6e849f7701fa70bf6a183fc8a2c33dd1d1672fb2'], }), ('pip', '10.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['f2bd08e0cd1b06e10218feaf6fef299f473ba706582eb3bd9d52203fdbd7ee68'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': ['a4a433b3a264dbc9aa9c7c241e87c0358a503ea6394f8737df1683c7c9a102ac'], }), ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['a9c27eb8f0e24e786e544b2dbaedb729c9d8546342b5a6818d8eda098ad4340d'], }), ('Cython', '0.28.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['1aae6d6e9858888144cea147eb5e677830f45faaff3d305d77378c3cba55f526'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': 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['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['c06425302f2cf668f1bba7a0a03f3c1d34d4ebeef2c72003da308b3947c7f749'], }), ('pandas', '0.23.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['50b52af2af2e15f4aeb2fe196da073a8c131fa02e433e105d95ce40016df5690'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], }), ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb index bd7285d48d0..e3e2ebf9bb6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.15' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,198 +35,152 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '39.2.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['f7cddbb5f5c640311eb00eab6e849f7701fa70bf6a183fc8a2c33dd1d1672fb2'], }), ('pip', '10.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['f2bd08e0cd1b06e10218feaf6fef299f473ba706582eb3bd9d52203fdbd7ee68'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': ['a4a433b3a264dbc9aa9c7c241e87c0358a503ea6394f8737df1683c7c9a102ac'], }), ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['a9c27eb8f0e24e786e544b2dbaedb729c9d8546342b5a6818d8eda098ad4340d'], }), ('Cython', '0.28.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['1aae6d6e9858888144cea147eb5e677830f45faaff3d305d77378c3cba55f526'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], }), ('liac-arff', '2.2.2', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['f4b60475e7473c4c42665f106ef87fe94fbf1e4cac7571903153ad38c3167c69'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34/'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['c06425302f2cf668f1bba7a0a03f3c1d34d4ebeef2c72003da308b3947c7f749'], }), ('pandas', '0.23.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['50b52af2af2e15f4aeb2fe196da073a8c131fa02e433e105d95ce40016df5690'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], }), ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb index 407c1189a17..15d04666405 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.15' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,202 +35,156 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '39.2.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['f7cddbb5f5c640311eb00eab6e849f7701fa70bf6a183fc8a2c33dd1d1672fb2'], }), ('pip', '10.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['f2bd08e0cd1b06e10218feaf6fef299f473ba706582eb3bd9d52203fdbd7ee68'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.5', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ 'a4a433b3a264dbc9aa9c7c241e87c0358a503ea6394f8737df1683c7c9a102ac', # numpy-1.14.5.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['a9c27eb8f0e24e786e544b2dbaedb729c9d8546342b5a6818d8eda098ad4340d'], }), ('Cython', '0.28.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['1aae6d6e9858888144cea147eb5e677830f45faaff3d305d77378c3cba55f526'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], }), ('liac-arff', '2.2.2', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['f4b60475e7473c4c42665f106ef87fe94fbf1e4cac7571903153ad38c3167c69'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34/'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['c06425302f2cf668f1bba7a0a03f3c1d34d4ebeef2c72003da308b3947c7f749'], }), ('pandas', '0.23.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['50b52af2af2e15f4aeb2fe196da073a8c131fa02e433e105d95ce40016df5690'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], }), ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb index 49edecd5c92..f1171547154 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.15' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -35,202 +35,156 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '39.2.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['f7cddbb5f5c640311eb00eab6e849f7701fa70bf6a183fc8a2c33dd1d1672fb2'], }), ('pip', '10.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['f2bd08e0cd1b06e10218feaf6fef299f473ba706582eb3bd9d52203fdbd7ee68'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.5', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ 'a4a433b3a264dbc9aa9c7c241e87c0358a503ea6394f8737df1683c7c9a102ac', # numpy-1.14.5.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['a9c27eb8f0e24e786e544b2dbaedb729c9d8546342b5a6818d8eda098ad4340d'], }), ('Cython', '0.28.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['1aae6d6e9858888144cea147eb5e677830f45faaff3d305d77378c3cba55f526'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], }), ('liac-arff', '2.2.2', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['f4b60475e7473c4c42665f106ef87fe94fbf1e4cac7571903153ad38c3167c69'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('enum34', '1.1.6', { 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34/'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['c06425302f2cf668f1bba7a0a03f3c1d34d4ebeef2c72003da308b3947c7f749'], }), ('pandas', '0.23.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['50b52af2af2e15f4aeb2fe196da073a8c131fa02e433e105d95ce40016df5690'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], }), ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index aac8bcc2c07..669d110cb5a 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.5.1' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -34,89 +34,53 @@ osdependencies = [('openssl-devel', 'libssl-dev')] # order is important! # package versions updated Feb 25th 2016 exts_list = [ - ('setuptools', '20.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '8.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '20.1.1'), + ('pip', '8.0.2'), + ('nose', '1.3.7'), ('numpy', local_numpyversion, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'patches': [ 'numpy-1.8.0-mkl.patch', 'numpy-%s-sse42.patch' % local_numpyversion, ], }), - ('scipy', local_scipyversion, { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('scipy', local_scipyversion), + ('blist', '1.3.6'), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': [ 'paycheck-1.0.2_setup-open-README-utf8.patch', ], }), - ('pbr', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + ('pbr', '1.8.1'), + ('lockfile', '0.12.2'), + ('Cython', '0.23.4'), + ('six', '1.10.0'), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'patches': [ 'deap-1.0.2_setup-open-README-utf8.patch', ], }), - ('decorator', '4.0.9', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), + ('decorator', '4.0.9'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('pandas', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('ecdsa', '0.13'), + ('paramiko', '1.16.0'), + ('pyparsing', '2.1.0'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('pandas', '0.17.1'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb index 0f528e01582..cd99efac014 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.5.2' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -32,92 +32,52 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '23.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '8.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '23.1.0'), + ('pip', '8.1.2'), + ('nose', '1.3.7'), ('numpy', '1.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'patches': ['numpy-1.8.0-mkl.patch'], }), - ('scipy', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('scipy', '0.17.1'), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': [ 'paycheck-1.0.2_setup-open-README-utf8.patch', ], }), - ('pbr', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.24', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + ('pbr', '1.10.0'), + ('lockfile', '0.12.2'), + ('Cython', '0.24'), + ('six', '1.10.0'), ('dateutil', '2.5.3', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'patches': [ 'deap-1.0.2_setup-open-README-utf8.patch', ], }), - ('decorator', '4.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), + ('decorator', '4.0.10'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('cryptography', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - }), - ('paramiko', '2.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('pandas', '0.18.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], - }), - ('virtualenv', '15.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), + ('ecdsa', '0.13'), + ('cryptography', '1.4'), + ('paramiko', '2.0.1'), + ('pyparsing', '2.1.5'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('pandas', '0.18.1'), + ('virtualenv', '15.0.2'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb index 2fc712658f2..a1af6dd6780 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.5.2' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -32,92 +32,52 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '23.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '8.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '23.1.0'), + ('pip', '8.1.2'), + ('nose', '1.3.7'), ('numpy', '1.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'patches': ['numpy-1.8.0-mkl.patch'], }), - ('scipy', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('scipy', '0.17.1'), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': [ 'paycheck-1.0.2_setup-open-README-utf8.patch', ], }), - ('pbr', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.24', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + ('pbr', '1.10.0'), + ('lockfile', '0.12.2'), + ('Cython', '0.24'), + ('six', '1.10.0'), ('dateutil', '2.5.3', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'patches': [ 'deap-1.0.2_setup-open-README-utf8.patch', ], }), - ('decorator', '4.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), + ('decorator', '4.0.10'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('cryptography', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - }), - ('paramiko', '2.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('pandas', '0.18.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], - }), - ('virtualenv', '15.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), + ('ecdsa', '0.13'), + ('cryptography', '1.4'), + ('paramiko', '2.0.1'), + ('pyparsing', '2.1.5'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('pandas', '0.18.1'), + ('virtualenv', '15.0.2'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb index 198569f10b5..9d2b25dbd08 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.5.2' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -32,92 +32,52 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '23.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '8.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), + ('setuptools', '23.1.0'), + ('pip', '8.1.2'), + ('nose', '1.3.7'), ('numpy', '1.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'patches': ['numpy-1.8.0-mkl.patch'], }), - ('scipy', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), + ('scipy', '0.17.1'), + ('blist', '1.3.6'), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': [ 'paycheck-1.0.2_setup-open-README-utf8.patch', ], }), - ('pbr', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.24', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), + ('pbr', '1.10.0'), + ('lockfile', '0.12.2'), + ('Cython', '0.24'), + ('six', '1.10.0'), ('dateutil', '2.5.3', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'patches': [ 'deap-1.0.2_setup-open-README-utf8.patch', ], }), - ('decorator', '4.0.10', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), + ('decorator', '4.0.10'), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('cryptography', '1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - }), - ('paramiko', '2.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('pandas', '0.18.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], - }), - ('virtualenv', '15.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), + ('ecdsa', '0.13'), + ('cryptography', '1.4'), + ('paramiko', '2.0.1'), + ('pyparsing', '2.1.5'), + ('netifaces', '0.10.4'), + ('netaddr', '0.7.18'), + ('pandas', '0.18.1'), + ('virtualenv', '15.0.2'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.1-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.1-foss-2017a.eb index 8556dd37ec0..942219e9294 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.1-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.1-foss-2017a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.1' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -41,21 +41,17 @@ exts_list = [ # see https://github.com/pypa/setuptools/issues/980 ('setuptools', '33.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6b20352ed60ba08c43b3611bdb502286f7a869fbfcf472f40d7279f1e77de145'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.12.1', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ 'a65266a4ad6ec8936a1bc85ce51f8600634a31a258b722c9274a80ff189d9542', # numpy-1.12.1.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch @@ -63,20 +59,17 @@ exts_list = [ }), ('scipy', '0.19.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['4190d34bf9a09626cd42100bbb12e3d96b2daf1a8a3244e991263eb693732122'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -84,30 +77,25 @@ exts_list = [ ], }), ('pbr', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['0ccd2db529afd070df815b1521f01401d43de03941170f8a800e7531faba265d'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.25.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306'], }), ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a'], }), ('dateutil', '2.6.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['62a2f8df3d66f878373fd0072eacf4ee52194ba302e00082828e0d263b0418d2'], }), ('deap', '1.0.2', { 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': [ 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz # deap-1.0.2_setup-open-README-utf8.patch @@ -115,65 +103,51 @@ exts_list = [ ], }), ('decorator', '4.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['953d6bf082b100f43229cf547f4f97f97e970f5ad645ee7601d55ff87afdfe76'], }), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['be6b5b76698d5fca1f24d75c98ed9c0ff5e24eb0d985d01cfd26c08a70f9654e'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['323524312bb467565ebca7e50c8ae5e9674e544951d28a2904a50012a8828190'], }), ('paramiko', '2.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['5fae49bed35e2e3d45c4f7b0db2d38b9ca626312d91119b3991d0ecf8125e310'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.5', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['59d8ad52dd3116fcb6635e175751b250dc783fb011adba539558bd764e5d628b'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('pandas', '0.19.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['6f0f4f598c2b16746803c8bafef7c721c57e4844da752d36240c0acf97658014'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb index 54e00a2f5ee..c246a6b1ee6 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.1' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -45,21 +45,17 @@ exts_list = [ # see https://github.com/pypa/setuptools/issues/980 ('setuptools', '33.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6b20352ed60ba08c43b3611bdb502286f7a869fbfcf472f40d7279f1e77de145'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.12.1', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ 'a65266a4ad6ec8936a1bc85ce51f8600634a31a258b722c9274a80ff189d9542', # numpy-1.12.1.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch @@ -67,20 +63,17 @@ exts_list = [ }), ('scipy', '0.19.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['4190d34bf9a09626cd42100bbb12e3d96b2daf1a8a3244e991263eb693732122'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -88,30 +81,25 @@ exts_list = [ ], }), ('pbr', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['0ccd2db529afd070df815b1521f01401d43de03941170f8a800e7531faba265d'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.25.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306'], }), ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a'], }), ('dateutil', '2.6.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['62a2f8df3d66f878373fd0072eacf4ee52194ba302e00082828e0d263b0418d2'], }), ('deap', '1.0.2', { 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': [ 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz # deap-1.0.2_setup-open-README-utf8.patch @@ -119,65 +107,51 @@ exts_list = [ ], }), ('decorator', '4.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['953d6bf082b100f43229cf547f4f97f97e970f5ad645ee7601d55ff87afdfe76'], }), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['be6b5b76698d5fca1f24d75c98ed9c0ff5e24eb0d985d01cfd26c08a70f9654e'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['323524312bb467565ebca7e50c8ae5e9674e544951d28a2904a50012a8828190'], }), ('paramiko', '2.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['5fae49bed35e2e3d45c4f7b0db2d38b9ca626312d91119b3991d0ecf8125e310'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.5', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['59d8ad52dd3116fcb6635e175751b250dc783fb011adba539558bd764e5d628b'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('pandas', '0.19.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['6f0f4f598c2b16746803c8bafef7c721c57e4844da752d36240c0acf97658014'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.2-foss-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.2-foss-2017b.eb index 15f55337da3..8a1d887b9a1 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.2-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.2-foss-2017b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.2' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -41,42 +41,34 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '36.3.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['e9fa391c1183b40fc6a1298bee02d554743f23c805a3b75dbb18def0f0755fb1'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.1', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ 'c9b0283776085cb2804efff73e9955ca279ba4edafd58d3ead70b61d209c4fbb', # numpy-1.13.1.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -84,30 +76,25 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.26.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['c2e63c4794161135adafa8aa4a855d6068073f421c83ffacc39369497a189dd5'], }), ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.0.2', { 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': [ 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz # deap-1.0.2_setup-open-README-utf8.patch @@ -115,99 +102,77 @@ exts_list = [ ], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.19', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['d04bb2425086c3fe86f7bc48915290b13e798497839fbb18ab7f6dffcf98cc3a'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['ff94ae65379914ec3c960de731381f49092057b6dd1d24d18842ead5a2eb2277'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2017b.eb index 35db963a049..7bfa572ace5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2017b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.2' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -45,42 +45,34 @@ ulimit_unlimited = True exts_list = [ ('setuptools', '36.3.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['e9fa391c1183b40fc6a1298bee02d554743f23c805a3b75dbb18def0f0755fb1'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.1', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ 'c9b0283776085cb2804efff73e9955ca279ba4edafd58d3ead70b61d209c4fbb', # numpy-1.13.1.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -88,30 +80,25 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.26.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['c2e63c4794161135adafa8aa4a855d6068073f421c83ffacc39369497a189dd5'], }), ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.0.2', { 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': [ 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz # deap-1.0.2_setup-open-README-utf8.patch @@ -119,99 +106,77 @@ exts_list = [ ], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.19', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), ('cryptography', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['d04bb2425086c3fe86f7bc48915290b13e798497839fbb18ab7f6dffcf98cc3a'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['ff94ae65379914ec3c960de731381f49092057b6dd1d24d18842ead5a2eb2277'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2018.00.eb b/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2018.00.eb index 851f669a66c..f2e3ee7476b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2018.00.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2018.00.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.2' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -45,42 +45,34 @@ ulimit_unlimited = True exts_list = [ ('setuptools', '36.3.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['e9fa391c1183b40fc6a1298bee02d554743f23c805a3b75dbb18def0f0755fb1'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.1', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ 'c9b0283776085cb2804efff73e9955ca279ba4edafd58d3ead70b61d209c4fbb', # numpy-1.13.1.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -88,30 +80,25 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.26.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['c2e63c4794161135adafa8aa4a855d6068073f421c83ffacc39369497a189dd5'], }), ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.0.2', { 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': [ 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz # deap-1.0.2_setup-open-README-utf8.patch @@ -119,99 +106,77 @@ exts_list = [ ], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.19', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['d04bb2425086c3fe86f7bc48915290b13e798497839fbb18ab7f6dffcf98cc3a'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['ff94ae65379914ec3c960de731381f49092057b6dd1d24d18842ead5a2eb2277'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.3-foss-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.3-foss-2017b.eb index 2c9b541d58c..971a41dc778 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.3-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.3-foss-2017b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.3' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -41,42 +41,34 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '36.6.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['62074589522a798da243f47348f38020d55b6c945652e2f2c09d3a96299812b7'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.3', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ '36ee86d5adbabc4fa2643a073f93d5504bdfed37a149a3a49f4dde259f35a750', # numpy-1.13.3.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -84,30 +76,25 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.27.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['e6840a2ba2704f4ffb40e454c36f73aeb440a4005453ee8d7ff6a00d812ba176'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.0.2', { 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': [ 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz # deap-1.0.2_setup-open-README-utf8.patch @@ -115,103 +102,80 @@ exts_list = [ ], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.19', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), ('cryptography', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['2699ed21e1f73dd1bdb7b0b22a517295de07809d535b23e200dd22166037fe6f'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['fa6b4f5c9d88f27c60fd9578146ff24e99d4b9f63391ff1343305bfd766c4660'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb index 52314a666e7..4ba48e9fbda 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.3' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -41,42 +41,34 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '36.6.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['62074589522a798da243f47348f38020d55b6c945652e2f2c09d3a96299812b7'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.3', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ '36ee86d5adbabc4fa2643a073f93d5504bdfed37a149a3a49f4dde259f35a750', # numpy-1.13.3.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -84,30 +76,25 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.27.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['e6840a2ba2704f4ffb40e454c36f73aeb440a4005453ee8d7ff6a00d812ba176'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.0.2', { 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': [ 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz # deap-1.0.2_setup-open-README-utf8.patch @@ -115,103 +102,80 @@ exts_list = [ ], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.19', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), ('cryptography', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['2699ed21e1f73dd1bdb7b0b22a517295de07809d535b23e200dd22166037fe6f'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['fa6b4f5c9d88f27c60fd9578146ff24e99d4b9f63391ff1343305bfd766c4660'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2017b.eb index f3cd8404395..3fb4a2f7fb9 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2017b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.3' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -49,42 +49,34 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '36.6.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['62074589522a798da243f47348f38020d55b6c945652e2f2c09d3a96299812b7'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.3', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ '36ee86d5adbabc4fa2643a073f93d5504bdfed37a149a3a49f4dde259f35a750', # numpy-1.13.3.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -92,30 +84,25 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.27.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['e6840a2ba2704f4ffb40e454c36f73aeb440a4005453ee8d7ff6a00d812ba176'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.0.2', { 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': [ 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz # deap-1.0.2_setup-open-README-utf8.patch @@ -123,103 +110,80 @@ exts_list = [ ], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.19', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), ('cryptography', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['2699ed21e1f73dd1bdb7b0b22a517295de07809d535b23e200dd22166037fe6f'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['fa6b4f5c9d88f27c60fd9578146ff24e99d4b9f63391ff1343305bfd766c4660'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2018.01.eb b/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2018.01.eb index c339251c900..1784aa46116 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2018.01.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2018.01.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.3' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -45,42 +45,34 @@ ulimit_unlimited = True exts_list = [ ('setuptools', '37.0.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['0b95db16abf74d435217f17774245fce1ea5a583e5ae8098d98f4ab0145491e3'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.3', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ '36ee86d5adbabc4fa2643a073f93d5504bdfed37a149a3a49f4dde259f35a750', # numpy-1.13.3.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -88,129 +80,100 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.19', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), ('cryptography', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['68a26c353627163d74ee769d4749f2ee243866e9dac43c93bb33ebd8fbed1199'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.21.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['5cd5cb30e72eeaf202f0e5e180780b897570e889d2db328c689a5a263405c559'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb index 64a6eddec81..b9fbee6941a 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.3' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -49,42 +49,34 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '36.6.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['62074589522a798da243f47348f38020d55b6c945652e2f2c09d3a96299812b7'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.13.3', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ '36ee86d5adbabc4fa2643a073f93d5504bdfed37a149a3a49f4dde259f35a750', # numpy-1.13.3.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -92,30 +84,25 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.27.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': ['e6840a2ba2704f4ffb40e454c36f73aeb440a4005453ee8d7ff6a00d812ba176'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.0.2', { 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': [ 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz # deap-1.0.2_setup-open-README-utf8.patch @@ -123,103 +110,80 @@ exts_list = [ ], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.19', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), ('cryptography', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['2699ed21e1f73dd1bdb7b0b22a517295de07809d535b23e200dd22166037fe6f'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['fa6b4f5c9d88f27c60fd9578146ff24e99d4b9f63391ff1343305bfd766c4660'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2017a.eb index c22d06e30fd..11e26ac5dfa 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2017a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.4' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -36,19 +36,16 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '36.6.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': [ '62074589522a798da243f47348f38020d55b6c945652e2f2c09d3a96299812b7', # setuptools-36.6.0.zip ], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': [ '09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d', # pip-9.0.1.tar.gz ], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': [ 'f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98', # nose-1.3.7.tar.gz ], @@ -56,34 +53,29 @@ exts_list = [ ('numpy', '1.13.3', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'checksums': [ '36ee86d5adbabc4fa2643a073f93d5504bdfed37a149a3a49f4dde259f35a750', # numpy-1.13.3.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '0.19.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], 'checksums': [ 'a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6', # scipy-0.19.1.tar.gz ], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': [ '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3', # blist-1.3.6.tar.gz ], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': [ '6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81', # mpi4py-2.0.0.tar.gz ], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -91,32 +83,28 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': [ '05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1', # pbr-3.1.1.tar.gz ], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 'checksums': [ '6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799', # lockfile-0.12.2.tar.gz ], }), ('Cython', '0.27.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], 'checksums': [ 'e6840a2ba2704f4ffb40e454c36f73aeb440a4005453ee8d7ff6a00d812ba176', # Cython-0.27.1.tar.gz ], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': [ '70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9', # six-1.11.0.tar.gz ], }), ('dateutil', '2.6.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-%(name)s'], 'checksums': [ '891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca', # python-dateutil-2.6.1.tar.gz ], @@ -124,7 +112,6 @@ exts_list = [ ('deap', '1.0.2', { 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': [ 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz # deap-1.0.2_setup-open-README-utf8.patch @@ -132,137 +119,112 @@ exts_list = [ ], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': [ '7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5', # decorator-4.1.2.tar.gz ], }), ('arff', '2.1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-%(name)s'], 'checksums': [ 'b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817', # liac-arff-2.1.1.tar.gz ], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': [ 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz ], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': [ '64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa', # ecdsa-0.13.tar.gz ], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('pycparser', '2.19', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('cryptography', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': [ '2699ed21e1f73dd1bdb7b0b22a517295de07809d535b23e200dd22166037fe6f', # cryptography-2.1.1.tar.gz ], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': [ 'fa6b4f5c9d88f27c60fd9578146ff24e99d4b9f63391ff1343305bfd766c4660', # paramiko-2.3.1.tar.gz ], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': [ '0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04', # pyparsing-2.2.0.tar.gz ], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], 'checksums': [ '0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0', # netifaces-0.10.6.tar.gz ], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], 'checksums': [ '38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd', # netaddr-0.7.19.tar.gz ], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.20.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], 'checksums': [ 'a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66', # pandas-0.20.3.tar.gz ], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], 'checksums': [ '02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a', # virtualenv-15.1.0.tar.gz ], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], 'checksums': [ '49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491', # docopt-0.6.2.tar.gz ], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], 'checksums': [ '7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085', # joblib-0.11.tar.gz ], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2018a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2018a.eb index 4f08b0a0fc5..c43db2642f3 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2018a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.4' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -36,40 +36,33 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ '3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb', # numpy-1.14.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -78,157 +71,120 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('python-dateutil', '2.6.1', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('liac-arff', '2.1.1', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyasn1', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['d258b0a71994f7770599835249cece1caef3c70def868c4915e6e5ca49b67d15'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.22.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['44a94091dd71f05922eec661638ec1a35f26d573c119aa2fad964f10a2880e6c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.1.18', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['edbc3f203427eef571f79a7692bb160a2b0f7ccaa31953e99bd17e307cf63f7d'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-fosscuda-2018a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-fosscuda-2018a.eb index 8581febb506..94c58b2575d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-fosscuda-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-fosscuda-2018a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.4' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -36,40 +36,33 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ '3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb', # numpy-1.14.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -78,157 +71,120 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('python-dateutil', '2.6.1', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('liac-arff', '2.1.1', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyasn1', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['d258b0a71994f7770599835249cece1caef3c70def868c4915e6e5ca49b67d15'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.22.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['44a94091dd71f05922eec661638ec1a35f26d573c119aa2fad964f10a2880e6c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.1.18', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['edbc3f203427eef571f79a7692bb160a2b0f7ccaa31953e99bd17e307cf63f7d'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-golf-2018a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-golf-2018a.eb index 507536807b2..137b45aebf1 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-golf-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-golf-2018a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.4' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -36,36 +36,29 @@ exts_download_dep_fail = True exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ '3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb', # numpy-1.14.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -74,157 +67,120 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('python-dateutil', '2.6.1', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('liac-arff', '2.1.1', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyasn1', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['d258b0a71994f7770599835249cece1caef3c70def868c4915e6e5ca49b67d15'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.22.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['44a94091dd71f05922eec661638ec1a35f26d573c119aa2fad964f10a2880e6c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.1.18', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['edbc3f203427eef571f79a7692bb160a2b0f7ccaa31953e99bd17e307cf63f7d'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-iimkl-2018a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-iimkl-2018a.eb index a43ff71136c..735f5d7fa26 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-iimkl-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-iimkl-2018a.eb @@ -38,170 +38,131 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ '3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb', # numpy-1.14.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('python-dateutil', '2.6.1', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('liac-arff', '2.1.1', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyasn1', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['d258b0a71994f7770599835249cece1caef3c70def868c4915e6e5ca49b67d15'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.22.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['44a94091dd71f05922eec661638ec1a35f26d573c119aa2fad964f10a2880e6c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.1.18', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['edbc3f203427eef571f79a7692bb160a2b0f7ccaa31953e99bd17e307cf63f7d'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-intel-2018a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-intel-2018a.eb index c1f1806f987..8ae78fba582 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-intel-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-intel-2018a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.4' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -44,40 +44,33 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ '3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb', # numpy-1.14.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -86,157 +79,120 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('python-dateutil', '2.6.1', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('liac-arff', '2.1.1', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyasn1', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['d258b0a71994f7770599835249cece1caef3c70def868c4915e6e5ca49b67d15'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.22.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['44a94091dd71f05922eec661638ec1a35f26d573c119aa2fad964f10a2880e6c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.1.18', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['edbc3f203427eef571f79a7692bb160a2b0f7ccaa31953e99bd17e307cf63f7d'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018.02.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018.02.eb index 5fb0e4bfa03..5e8c94bc8af 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018.02.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018.02.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.4' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -44,40 +44,33 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ '3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb', # numpy-1.14.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -86,157 +79,120 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('python-dateutil', '2.6.1', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('liac-arff', '2.1.1', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyasn1', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['d258b0a71994f7770599835249cece1caef3c70def868c4915e6e5ca49b67d15'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.22.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['44a94091dd71f05922eec661638ec1a35f26d573c119aa2fad964f10a2880e6c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.1.18', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['edbc3f203427eef571f79a7692bb160a2b0f7ccaa31953e99bd17e307cf63f7d'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018a.eb index 72c86103c1a..fe6c59a65d3 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018a.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.4' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -44,40 +44,33 @@ ulimit_unlimited = True exts_list = [ ('setuptools', '38.4.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], }), ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ '3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb', # numpy-1.14.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -86,157 +79,120 @@ exts_list = [ ], }), ('pbr', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], }), ('Cython', '0.27.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('python-dateutil', '2.6.1', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], }), ('liac-arff', '2.1.1', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.6', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f'], }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('cryptography', '2.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['e4d967371c5b6b2e67855066471d844c5d52d210c36c28d49a8507b96e2c5291'], }), ('pyasn1', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['d258b0a71994f7770599835249cece1caef3c70def868c4915e6e5ca49b67d15'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['486f637f0a33a4792e0e567be37426c287efaa8c4c4a45e3216f9ce7fd70b1fc'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.6', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2017.3', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], }), ('pandas', '0.22.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['44a94091dd71f05922eec661638ec1a35f26d573c119aa2fad964f10a2880e6c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.1.18', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['edbc3f203427eef571f79a7692bb160a2b0f7ccaa31953e99bd17e307cf63f7d'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb index 41b1f536bfa..12fec72b854 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.6' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -45,36 +45,29 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '40.0.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['012adb8e25fbfd64c652e99e7bab58799a3aaf05d39ab38561f69190a909015f'], }), ('pip', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['a0e11645ee37c90b40c46d607070c4fd583e2cd46231b1c06e389c5e814eed76'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.15.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': ['f28e73cf18d37a413f7d5de35d024e6b98f14566a10d82100f9dc491a7d449f9'], }), ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -83,160 +76,122 @@ exts_list = [ ], }), ('pbr', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['1b8be50d938c9bb75d0eaf7eda111eec1bf6dc88a62a6412e33bf077457e0f45'], }), ('Cython', '0.28.5', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['b64575241f64f6ec005a4d4137339fb0ba5e156e826db2fdb5f458060d9979e0'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], }), ('liac-arff', '2.3', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['21b1b17c082cacd7b554bf9a42f6de61d2bf02feef6eb31ec36b5486c31b2ae9'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('cryptography', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6'], }), ('pyasn1', '0.4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['f58f2a3d12fd754aa123e9fa74fb7345333000a035f3921dbdaa08597aa53137'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['ffb9ef1de172603304d9d2819af6f5ece76f2e85ec10692a524dd876e72bf277'], }), ('pandas', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['e9f04885cf11704669f3a731ea6ac00bbc7dea16137aa4394ef7c272cdb9d008'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.8.13', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['4c1d68a1408dd090d2f3a869aa94c3947cc1d967821d1ed303208c9f41f0f2f4'], }), ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], }), ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb index afdc17f51a5..1a8381a2516 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.6' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -44,37 +44,30 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '40.0.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['012adb8e25fbfd64c652e99e7bab58799a3aaf05d39ab38561f69190a909015f'], }), ('pip', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['a0e11645ee37c90b40c46d607070c4fd583e2cd46231b1c06e389c5e814eed76'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.15.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': ['f28e73cf18d37a413f7d5de35d024e6b98f14566a10d82100f9dc491a7d449f9'], }), ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz # paycheck-1.0.2_setup-open-README-utf8.patch @@ -82,160 +75,122 @@ exts_list = [ ], }), ('pbr', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['1b8be50d938c9bb75d0eaf7eda111eec1bf6dc88a62a6412e33bf077457e0f45'], }), ('Cython', '0.28.5', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['b64575241f64f6ec005a4d4137339fb0ba5e156e826db2fdb5f458060d9979e0'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], }), ('liac-arff', '2.3', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['21b1b17c082cacd7b554bf9a42f6de61d2bf02feef6eb31ec36b5486c31b2ae9'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('cryptography', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6'], }), ('pyasn1', '0.4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['f58f2a3d12fd754aa123e9fa74fb7345333000a035f3921dbdaa08597aa53137'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['ffb9ef1de172603304d9d2819af6f5ece76f2e85ec10692a524dd876e72bf277'], }), ('pandas', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['e9f04885cf11704669f3a731ea6ac00bbc7dea16137aa4394ef7c272cdb9d008'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.8.13', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['4c1d68a1408dd090d2f3a869aa94c3947cc1d967821d1ed303208c9f41f0f2f4'], }), ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], }), ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb index 7a60c8e36e6..66fcd7c7d83 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.6' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -45,40 +45,33 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '40.0.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['012adb8e25fbfd64c652e99e7bab58799a3aaf05d39ab38561f69190a909015f'], }), ('pip', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['a0e11645ee37c90b40c46d607070c4fd583e2cd46231b1c06e389c5e814eed76'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.15.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ 'f28e73cf18d37a413f7d5de35d024e6b98f14566a10d82100f9dc491a7d449f9', # numpy-1.15.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -87,160 +80,122 @@ exts_list = [ ], }), ('pbr', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['1b8be50d938c9bb75d0eaf7eda111eec1bf6dc88a62a6412e33bf077457e0f45'], }), ('Cython', '0.28.5', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['b64575241f64f6ec005a4d4137339fb0ba5e156e826db2fdb5f458060d9979e0'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], }), ('liac-arff', '2.3', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['21b1b17c082cacd7b554bf9a42f6de61d2bf02feef6eb31ec36b5486c31b2ae9'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('cryptography', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6'], }), ('pyasn1', '0.4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['f58f2a3d12fd754aa123e9fa74fb7345333000a035f3921dbdaa08597aa53137'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['ffb9ef1de172603304d9d2819af6f5ece76f2e85ec10692a524dd876e72bf277'], }), ('pandas', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['e9f04885cf11704669f3a731ea6ac00bbc7dea16137aa4394ef7c272cdb9d008'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.8.13', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['4c1d68a1408dd090d2f3a869aa94c3947cc1d967821d1ed303208c9f41f0f2f4'], }), ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], }), ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb index 1a6d8c0f4ea..f83de9fb536 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb @@ -1,7 +1,7 @@ name = 'Python' version = '3.6.6' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" @@ -45,40 +45,33 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '40.0.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['012adb8e25fbfd64c652e99e7bab58799a3aaf05d39ab38561f69190a909015f'], }), ('pip', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['a0e11645ee37c90b40c46d607070c4fd583e2cd46231b1c06e389c5e814eed76'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.15.0', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ 'f28e73cf18d37a413f7d5de35d024e6b98f14566a10d82100f9dc491a7d449f9', # numpy-1.15.0.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -87,160 +80,122 @@ exts_list = [ ], }), ('pbr', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['1b8be50d938c9bb75d0eaf7eda111eec1bf6dc88a62a6412e33bf077457e0f45'], }), ('Cython', '0.28.5', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['b64575241f64f6ec005a4d4137339fb0ba5e156e826db2fdb5f458060d9979e0'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], }), ('liac-arff', '2.3', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['21b1b17c082cacd7b554bf9a42f6de61d2bf02feef6eb31ec36b5486c31b2ae9'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('cryptography', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6'], }), ('pyasn1', '0.4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['f58f2a3d12fd754aa123e9fa74fb7345333000a035f3921dbdaa08597aa53137'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['ffb9ef1de172603304d9d2819af6f5ece76f2e85ec10692a524dd876e72bf277'], }), ('pandas', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['e9f04885cf11704669f3a731ea6ac00bbc7dea16137aa4394ef7c272cdb9d008'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.8.13', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['4c1d68a1408dd090d2f3a869aa94c3947cc1d967821d1ed303208c9f41f0f2f4'], }), ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], }), ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.0-foss-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.7.0-foss-2018b.eb index dd711c7c728..e4f783cd76f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.7.0-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.7.0-foss-2018b.eb @@ -25,7 +25,7 @@ dependencies = [ ('SQLite', '3.24.0'), ('XZ', '5.2.4'), ('GMP', '6.1.2'), # required for pycrypto - ('libffi', '3.2.1'), # required for cryptography + ('libffi', '3.2.1'), # OS dependency should be preferred if the OS version is more recent then this version, # it's nice to have an up to date OpenSSL for security reasons; # Python 3.7.0 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) @@ -49,28 +49,22 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '39.2.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['f7cddbb5f5c640311eb00eab6e849f7701fa70bf6a183fc8a2c33dd1d1672fb2'], }), ('pip', '10.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['f2bd08e0cd1b06e10218feaf6fef299f473ba706582eb3bd9d52203fdbd7ee68'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': ['a4a433b3a264dbc9aa9c7c241e87c0358a503ea6394f8737df1683c7c9a102ac'], }), ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { @@ -78,7 +72,6 @@ exts_list = [ 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -87,160 +80,122 @@ exts_list = [ ], }), ('pbr', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['a9c27eb8f0e24e786e544b2dbaedb729c9d8546342b5a6818d8eda098ad4340d'], }), ('Cython', '0.28.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['1aae6d6e9858888144cea147eb5e677830f45faaff3d305d77378c3cba55f526'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], }), ('liac-arff', '2.2.2', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['f4b60475e7473c4c42665f106ef87fe94fbf1e4cac7571903153ad38c3167c69'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('cryptography', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['c06425302f2cf668f1bba7a0a03f3c1d34d4ebeef2c72003da308b3947c7f749'], }), ('pandas', '0.23.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['9cd3614b4e31a0889388ff1bd19ae857ad52658b33f776065793c293a29cf612'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], }), ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.0-intel-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.7.0-intel-2018b.eb index 23e412a0637..6630711317f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.7.0-intel-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.7.0-intel-2018b.eb @@ -25,7 +25,7 @@ dependencies = [ ('SQLite', '3.24.0'), ('XZ', '5.2.4'), ('GMP', '6.1.2'), # required for pycrypto - ('libffi', '3.2.1'), # required for cryptography + ('libffi', '3.2.1'), # OS dependency should be preferred if the OS version is more recent then this version, # it's nice to have an up to date OpenSSL for security reasons; # Python 3.7.0 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) @@ -49,32 +49,26 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '39.2.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['f7cddbb5f5c640311eb00eab6e849f7701fa70bf6a183fc8a2c33dd1d1672fb2'], }), ('pip', '10.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['f2bd08e0cd1b06e10218feaf6fef299f473ba706582eb3bd9d52203fdbd7ee68'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.5', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ 'a4a433b3a264dbc9aa9c7c241e87c0358a503ea6394f8737df1683c7c9a102ac', # numpy-1.14.5.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { @@ -82,7 +76,6 @@ exts_list = [ 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -91,160 +84,122 @@ exts_list = [ ], }), ('pbr', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['a9c27eb8f0e24e786e544b2dbaedb729c9d8546342b5a6818d8eda098ad4340d'], }), ('Cython', '0.28.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['1aae6d6e9858888144cea147eb5e677830f45faaff3d305d77378c3cba55f526'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], }), ('liac-arff', '2.2.2', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['f4b60475e7473c4c42665f106ef87fe94fbf1e4cac7571903153ad38c3167c69'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('cryptography', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['c06425302f2cf668f1bba7a0a03f3c1d34d4ebeef2c72003da308b3947c7f749'], }), ('pandas', '0.23.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['9cd3614b4e31a0889388ff1bd19ae857ad52658b33f776065793c293a29cf612'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], }), ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.0-iomkl-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.7.0-iomkl-2018b.eb index f96302a955a..8d1ca735282 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.7.0-iomkl-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.7.0-iomkl-2018b.eb @@ -25,7 +25,7 @@ dependencies = [ ('SQLite', '3.24.0'), ('XZ', '5.2.4'), ('GMP', '6.1.2'), # required for pycrypto - ('libffi', '3.2.1'), # required for cryptography + ('libffi', '3.2.1'), # OS dependency should be preferred if the OS version is more recent then this version, # it's nice to have an up to date OpenSSL for security reasons; # Python 3.7.0 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) @@ -49,32 +49,26 @@ buildopts = 'LDFLAGS="$LDFLAGS -lssp"' exts_list = [ ('setuptools', '39.2.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['f7cddbb5f5c640311eb00eab6e849f7701fa70bf6a183fc8a2c33dd1d1672fb2'], }), ('pip', '10.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'checksums': ['f2bd08e0cd1b06e10218feaf6fef299f473ba706582eb3bd9d52203fdbd7ee68'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('numpy', '1.14.5', { 'patches': ['numpy-1.12.0-mkl.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'checksums': [ 'a4a433b3a264dbc9aa9c7c241e87c0358a503ea6394f8737df1683c7c9a102ac', # numpy-1.14.5.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], }), ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '3.0.0', { @@ -82,7 +76,6 @@ exts_list = [ 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'checksums': [ '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz @@ -91,160 +84,122 @@ exts_list = [ ], }), ('pbr', '4.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['a9c27eb8f0e24e786e544b2dbaedb729c9d8546342b5a6818d8eda098ad4340d'], }), ('Cython', '0.28.3', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['1aae6d6e9858888144cea147eb5e677830f45faaff3d305d77378c3cba55f526'], }), ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], }), ('liac-arff', '2.2.2', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['f4b60475e7473c4c42665f106ef87fe94fbf1e4cac7571903153ad38c3167c69'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), ('cryptography', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], }), ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], }), ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], }), ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], }), ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], }), ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['c06425302f2cf668f1bba7a0a03f3c1d34d4ebeef2c72003da308b3947c7f749'], }), ('pandas', '0.23.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['9cd3614b4e31a0889388ff1bd19ae857ad52658b33f776065793c293a29cf612'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], }), ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], }), ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], }), ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb index 614b1aaca14..9fbf771c28e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('SQLite', '3.27.2'), ('XZ', '5.2.4'), ('GMP', '6.1.2'), # required for pycrypto - ('libffi', '3.2.1'), # required for cryptography + ('libffi', '3.2.1'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.7.4-GCCcore-8.3.0.eb index aa755e46fb8..a85008caeef 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.7.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.7.4-GCCcore-8.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('SQLite', '3.29.0'), ('XZ', '5.2.4'), ('GMP', '6.1.2'), # required for pycrypto - ('libffi', '3.2.1'), # required for cryptography + ('libffi', '3.2.1'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb index ef76f05fa6f..f3b5d1b0640 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('SQLite', '3.31.1'), ('XZ', '5.2.5'), ('GMP', '6.2.0'), # required for pycrypto - ('libffi', '3.3'), # required for cryptography + ('libffi', '3.3'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index 74d7a4c7022..602f3f5c329 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('SQLite', '3.33.0'), ('XZ', '5.2.5'), ('GMP', '6.2.0'), # required for pycrypto - ('libffi', '3.3'), # required for cryptography + ('libffi', '3.3'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb new file mode 100644 index 00000000000..e96cf3a75bc --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb @@ -0,0 +1,34 @@ +name = 'Python' +version = '3.9.5' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['e0fbd5b6e1ee242524430dee3c91baf4cbbaba4a72dd1674b90fda87b713c7ab'] + +builddependencies = [ + ('UnZip', '6.0'), +] + +dependencies = [ + ('binutils', '2.36.1'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('SQLite', '3.35.4'), + ('XZ', '5.2.5'), + ('libffi', '3.3'), + ('OpenSSL', '1.1', '', True), +] + +install_pip = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb index 73460e65a1e..4ba357afee6 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ('SQLite', '3.35.4'), ('XZ', '5.2.5'), ('GMP', '6.2.1'), # required for pycrypto - ('libffi', '3.3'), # required for cryptography + ('libffi', '3.3'), ('OpenSSL', '1.1', '', True), ] diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d6be9457006 --- /dev/null +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.0-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'p11-kit' +version = '0.24.0' + +homepage = 'https://p11-glue.freedesktop.org/p11-kit.html' +description = """Provides a way to load and enumerate PKCS#11 modules. + Provides a standard configuration setup for installing + PKCS#11 modules in such a way that they're discoverable. + Also solves problems with coordinating the use of PKCS#11 + by different components or libraries living in the same process.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/p11-glue/p11-kit/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['81e6140584f635e4e956a1b93a32239acf3811ff5b2d3a5c6094e94e99d2c685'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('libtasn1', '4.17.0'), + ('libffi', '3.3'), +] + +preconfigopts = "bashcompdir=%(installdir)s/share/bash-completions " + +configopts = "--without-systemd" + +sanity_check_paths = { + 'files': ['bin/p11-kit', 'bin/trust'] + + ['lib/libp11-kit.%s' % SHLIB_EXT], + 'dirs': ['include/p11-kit-1/p11-kit'], +} + +sanity_check_commands = ["p11-kit --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas-datareader/pandas-datareader-0.7.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/pandas-datareader/pandas-datareader-0.7.0-intel-2018a-Python-3.6.4.eb index 89c224069b6..29d64d72643 100644 --- a/easybuild/easyconfigs/p/pandas-datareader/pandas-datareader-0.7.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/pandas-datareader/pandas-datareader-0.7.0-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'pandas-datareader' version = '0.7.0' @@ -14,29 +14,16 @@ dependencies = [ ('lxml', '4.2.0', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('wrapt', '1.10.11', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt/'], 'checksums': ['d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas-datareader/'], 'checksums': ['7dee3fe6fa483c8c2ee4f1af91a65b542c5446d75a6fc25c832cad1ffca8ef0b'], 'modulename': 'pandas_datareader', }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-2.7.11.eb index 9fd43e27cf1..6f9a6395bd1 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-2.7.11.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.11')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-3.5.1.eb index a23b70abdac..82241e9431e 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-3.5.1.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.5.1')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb index 69e84f6fa3e..7dc3b62da10 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.11')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb index a3d2dbb5d14..143b07bdc3f 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.5.1')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-2.7.12.eb index 127a463ca2e..984f541a6b2 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-2.7.12.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.12')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-3.5.2.eb index 11324cd1bf1..552d2d08be1 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-3.5.2.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.5.2')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-2.7.12.eb index d10a536e673..2dfb2c718d0 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-2.7.12.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.12')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-3.5.2.eb index 66017ec4037..c1ddca89451 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-3.5.2.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.5.2')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-2.7.12.eb index 8829139b1b7..03aee14035e 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-2.7.12.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.12')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-3.5.2.eb index 823a55912c7..9042197f139 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-3.5.2.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.5.2')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-2.7.12.eb index 2d89267d1db..9ac0360c54d 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-2.7.12.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.12')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-3.5.2.eb index 15fd3118b30..c8d42334c33 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-3.5.2.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.5.2')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb index ea5b45bce17..a5754dff826 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb @@ -10,14 +10,8 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.6.1')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.21.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pandas/pandas-0.21.0-intel-2017a-Python-2.7.13.eb index d94937fb35b..c7c25dbc505 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.21.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.21.0-intel-2017a-Python-2.7.13.eb @@ -10,15 +10,9 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5cd5cb30e72eeaf202f0e5e180780b897570e889d2db328c689a5a263405c559'] dependencies = [('Python', '2.7.13')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.21.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pandas/pandas-0.21.0-intel-2017b-Python-3.6.3.eb index ee2db00b242..88733a95740 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.21.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.21.0-intel-2017b-Python-3.6.3.eb @@ -10,15 +10,9 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5cd5cb30e72eeaf202f0e5e180780b897570e889d2db328c689a5a263405c559'] dependencies = [('Python', '3.6.3')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20210622-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20210622-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1d3574e98be --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20210622-GCCcore-10.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20210622' + +homepage = 'https://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7b33279bf71e76c52c393081d2db69057dd320be019759c4e704841a6761ec86'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Perl', '5.32.1')] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +sanity_check_commands = ["parallel --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.12-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.12-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..af356f8b6c1 --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.12-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.12' + +homepage = 'https://github.com/NixOS/patchelf' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['3dca33fb862213b3541350e1da262249959595903f559eae0fbc68966e9c3f56'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb index d128f00a079..9c236158ead 100644 --- a/easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ description = """path.py is a Python library implementing path objects as first- toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = ['path.py-%(version)s-py2.py3-none-any.whl'] dependencies = [ diff --git a/easybuild/easyconfigs/p/pauvre/pauvre-0.1923-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pauvre/pauvre-0.1923-intel-2019b-Python-3.7.4.eb index a05913d919d..b76af7e135e 100644 --- a/easybuild/easyconfigs/p/pauvre/pauvre-0.1923-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pauvre/pauvre-0.1923-intel-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = "Tools for plotting Oxford Nanopore and other long-read data" toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f898ac728a66525bda8f5bd49607abad35946a48bc1cca7e1c5af5908eb8866d'] diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.12.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.12.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..d03cb403d19 --- /dev/null +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.12.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'petsc4py' +version = '3.12.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/petsc/petsc4py' +description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." + +toolchain = {'name': 'foss', 'version': '2019b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1a02fa0336c27583aabf399124ac0610ef20452cf6b837a1082f7788f17fadad'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('PETSc', '3.12.4', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from petsc4py import PETSc'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.9.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.9.1-foss-2018a-Python-3.6.4.eb index 308ac6d4e40..92a55d85084 100644 --- a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.9.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.9.1-foss-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = "petsc4py are Python bindings for PETSc, the Portable, Extensible toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0ccee912216f100d9b08637e036df00e043a530303ff8afd7c3ac7c454681fb9'] @@ -21,10 +20,6 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} sanity_check_commands = ["python -c 'from petsc4py import PETSc'"] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/phono3py/phono3py-1.12.5.35-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/phono3py/phono3py-1.12.5.35-intel-2017b-Python-2.7.14.eb index 6219aa2e7b1..4f520c4add6 100644 --- a/easybuild/easyconfigs/p/phono3py/phono3py-1.12.5.35-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/phono3py/phono3py-1.12.5.35-intel-2017b-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'phono3py' version = '1.12.5.35' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phono3py/' +homepage = 'https://atztogo.github.io/phono3py/' description = "phono3py calculates phonon-phonon interaction and related properties using the supercell approach." toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['dd98ff25393c836fa99f53bc39da2692c64e0a3ad7ff8d1a35eb3673cbec7f95'] diff --git a/easybuild/easyconfigs/p/phono3py/phono3py-1.12.7.55-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/phono3py/phono3py-1.12.7.55-foss-2018a-Python-2.7.14.eb index 527c1c78739..abb186b5e42 100644 --- a/easybuild/easyconfigs/p/phono3py/phono3py-1.12.7.55-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/phono3py/phono3py-1.12.7.55-foss-2018a-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'phono3py' version = '1.12.7.55' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phono3py/' +homepage = 'https://atztogo.github.io/phono3py/' description = "phono3py calculates phonon-phonon interaction and related properties using the supercell approach." toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9b1b28a1b6b0b127aa7b9f4c388617f5e5c3ba2a06d2b83795ffd1d030f6218a'] diff --git a/easybuild/easyconfigs/p/phono3py/phono3py-1.12.7.55-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/phono3py/phono3py-1.12.7.55-intel-2018a-Python-2.7.14.eb index cfdf6c1bd7b..2744b21318f 100644 --- a/easybuild/easyconfigs/p/phono3py/phono3py-1.12.7.55-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/phono3py/phono3py-1.12.7.55-intel-2018a-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'phono3py' version = '1.12.7.55' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phono3py/' +homepage = 'https://atztogo.github.io/phono3py/' description = "phono3py calculates phonon-phonon interaction and related properties using the supercell approach." toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9b1b28a1b6b0b127aa7b9f4c388617f5e5c3ba2a06d2b83795ffd1d030f6218a'] diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.10.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.10.1-intel-2016a-Python-2.7.11.eb index 28aab3077e6..5aed720857d 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-1.10.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.10.1-intel-2016a-Python-2.7.11.eb @@ -4,12 +4,11 @@ name = 'phonopy' version = '1.10.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phonopy/' +homepage = 'https://atztogo.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.12.2.20-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.12.2.20-intel-2017b-Python-2.7.14.eb index e8ad84e2385..89fecb4498b 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-1.12.2.20-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.12.2.20-intel-2017b-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'phonopy' version = '1.12.2.20' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phonopy/' +homepage = 'https://atztogo.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4328ec2cf8bb7b04c4149e03a40c0979625f68a2a057c9b38b00afbd92463117'] diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.12.6.66-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.12.6.66-foss-2018a-Python-2.7.14.eb index 83c86dfb211..fff9e1b08a9 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-1.12.6.66-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.12.6.66-foss-2018a-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'phonopy' version = '1.12.6.66' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phonopy/' +homepage = 'https://atztogo.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9b81ba2b1dc10a21e1e4e5f6e354b6049af340118df3c4649ccb018fd949eb5e'] diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.12.6.66-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.12.6.66-intel-2018a-Python-2.7.14.eb index 07efc5c08a1..25e742651a3 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-1.12.6.66-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.12.6.66-intel-2018a-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'phonopy' version = '1.12.6.66' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phonopy/' +homepage = 'https://atztogo.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9b81ba2b1dc10a21e1e4e5f6e354b6049af340118df3c4649ccb018fd949eb5e'] diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.13.0.64-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.13.0.64-intel-2018a-Python-2.7.14.eb index 5af7be4d019..b5797cacfa8 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-1.13.0.64-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.13.0.64-intel-2018a-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'phonopy' version = '1.13.0.64' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phonopy/' +homepage = 'https://atztogo.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['cdb5d53b046429c2b2136d04e1741200d06416461aa549ba6f636d45ee743590'] diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018b-Python-2.7.15.eb index 4d5d1b46ccc..6798bcc9fd9 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018b-Python-2.7.15.eb @@ -4,12 +4,11 @@ name = 'phonopy' version = '1.14.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phonopy/' +homepage = 'https://atztogo.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['022fa8c30fa4afb128a81a35cfa537265c65a4ac19865dc67ba63adf5986b7a2'] diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.0.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.0.0-intel-2018a-Python-2.7.14.eb index ec0fc78b950..2557f745f6b 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.0.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.0.0-intel-2018a-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'phonopy' version = '2.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phonopy/' +homepage = 'https://atztogo.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['46baf7c4571fe75374071674727c2beb0388cf57073e0623d8457f04b1c54495'] diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.2.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.2.0-intel-2019a-Python-3.7.2.eb index 3199100f6ce..b29d4f065eb 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.2.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.2.0-intel-2019a-Python-3.7.2.eb @@ -4,12 +4,11 @@ name = 'phonopy' version = '2.2.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phonopy/' +homepage = 'https://atztogo.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a4d307e78325cd52b4bc524a2872102632f22a1257809bfaf313ed02eb44970b'] diff --git a/easybuild/easyconfigs/p/phototonic/phototonic-2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/phototonic/phototonic-2.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b6ca79a78c0 --- /dev/null +++ b/easybuild/easyconfigs/p/phototonic/phototonic-2.1-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'phototonic' +version = '2.1' + +homepage = 'https://github.com/oferkv/phototonic' +description = "Phototonic is an image viewer and organizer" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/oferkv/phototonic/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a8b2dbc81750efabb65a4732b1704641afd4a4f772ef9c90817871ca2a52f5ef'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Qt5', '5.15.2'), + ('exiv2', '0.27.4'), + ('expat', '2.2.9'), + ('zlib', '1.2.11'), +] + +prebuildopts = "qmake && " + +files_to_copy = [(['phototonic'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/phototonic'], + 'dirs': [], +} + +sanity_check_commands = [ + "QT_QPA_PLATFORM=offscreen phototonic --help 2>&1 | grep 'Phototonic v%(version)s image viewer'", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/picard/picard-2.25.5-Java-13.eb b/easybuild/easyconfigs/p/picard/picard-2.25.5-Java-13.eb new file mode 100644 index 00000000000..dde956fdf6b --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.25.5-Java-13.eb @@ -0,0 +1,54 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.10.1: +# Adam Huffman +# The Francis Crick Institute +# 2.18.11: +# Jonas Demeulemeester +# The Francis Crick Institute +# 2.21.1 +# Pavel Grochal (INUITS) +# 2.25.1 +# J. Sassmannshausen (GSTT) +# 2.25.5 +# Erica Bianco (HPCNow!) +## + +easyblock = 'JAR' + +name = 'picard' +version = '2.25.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = [{ + 'filename': '%(name)s-%(version)s.jar', + 'download_filename': '%(name)s.jar', +}] +checksums = ['f7fa9784b84d384abfcbd77076f5ceab7b2797dc863ac35fd41470daa3efe3a5'] + +postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] + +dependencies = [('Java', '13')] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pip/pip-8.0.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pip/pip-8.0.2-intel-2016a-Python-2.7.11.eb index 7bc4eae5a19..8f045a74bfa 100644 --- a/easybuild/easyconfigs/p/pip/pip-8.0.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pip/pip-8.0.2-intel-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """The PyPA recommended tool for installing Python packages.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016a-Python-2.7.11.eb index 32c9404b007..60c86bcce15 100644 --- a/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """The PyPA recommended tool for installing Python packages.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016b-Python-2.7.12.eb index 77fa36d059e..4dfcd1e99c3 100644 --- a/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = """The PyPA recommended tool for installing Python packages.""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2016b-Python-2.7.12.eb index ffdebb21219..c82d0e3aeeb 100644 --- a/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = """The PyPA recommended tool for installing Python packages.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-2.7.11.eb index 6bd0a5f2557..7146cd46046 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-2.7.11.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-3.5.1.eb index f7eb516df75..2ca9c2557fe 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-3.5.1.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-2.7.12.eb index 3a5591472cd..2cd285ca257 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-2.7.12.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-3.5.2.eb index 6ed59909cb4..28cdcd0ef7e 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-3.5.2.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016a-Python-2.7.11.eb index 5b4ecdd7897..f95418fafa0 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016a-Python-2.7.11.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-2.7.12.eb index fc557311840..9a344bdd773 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-2.7.12.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-3.5.2.eb index 2846411c026..0970859a5c8 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-3.5.2.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb index 8424a0b36f0..6236490e80d 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-3.6.1.eb index 061822f16c3..9ec5a70a4e1 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-3.6.1.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-2.7.14.eb index 05a89d482df..9df84f58c63 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-3.6.3.eb index 0541ac57e11..04abb6ab8c9 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-3.6.3.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-2.7.14.eb index 6e9c3b9162f..fd4f6b983d5 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'fosscuda', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-3.6.3.eb index 8190e84270a..0e7129ba121 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-3.6.3.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'fosscuda', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb index a03a4dac397..e599b6ba333 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb index 2ac3d71f687..5c420abfa68 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-2.7.14.eb index e0c07d8bde6..e9c917995d3 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-3.6.3.eb index 86f7de3311a..9bc525f9aa9 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-3.6.3.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018a-Python-2.7.14.eb index 3389349d323..6e7252465f0 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018a-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2018a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018a-Python-3.6.4.eb index 579525fdad3..e1b288765ab 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018a-Python-3.6.4.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2018a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018b-Python-2.7.15.eb index 64853e89b19..eb98bc950df 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018b-Python-2.7.15.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018b-Python-3.6.6.eb index 570a876d8f0..94f2ef2a8f5 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-foss-2018b-Python-3.6.6.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-2.7.15.eb index 0a034197a7c..f654aa82c0a 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-2.7.15.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'fosscuda', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-3.6.6.eb index 6cd22620ed3..97d0ad30541 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-3.6.6.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'fosscuda', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018a-Python-2.7.14.eb index 910d24f5a9a..97cd5f4a352 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018a-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'intel', 'version': '2018a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018a-Python-3.6.4.eb index 5040ff474ca..c595b5446a5 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018a-Python-3.6.4.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'intel', 'version': '2018a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018b-Python-2.7.15.eb index 58469f964c4..92f68f67918 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018b-Python-2.7.15.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018b-Python-3.6.6.eb index 96e300236ae..c0aadc344d1 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-intel-2018b-Python-3.6.6.eb @@ -4,13 +4,12 @@ name = 'pkgconfig' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/matze/pkgconfig' +homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb index f7ba3e761c5..854336b2ebc 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb @@ -9,7 +9,6 @@ description = """pkgconfig is a Python module to interface with the pkg-config c toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['97bfe3d981bab675d5ea3ef259045d7919c93897db7d3b59d4e8593cba8d354f'] diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.4-GCCcore-10.3.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.4-GCCcore-10.3.0-python.eb new file mode 100644 index 00000000000..221e398e9d7 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.4-GCCcore-10.3.0-python.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.5.4' +versionsuffix = '-python' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c34503829fd226822fd93c902b1cf275516908a023a24be0a02ba687f3a00399'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('pkg-config', '0.29.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/plc/plc-3.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/plc/plc-3.0.1-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..0924f87d0ce --- /dev/null +++ b/easybuild/easyconfigs/p/plc/plc-3.0.1-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,65 @@ +easyblock = 'Waf' + +name = 'plc' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pla.esac.esa.int/pla/#home' + +description = """ + plc is the public Planck Likelihood Code. + It provides C and Fortran libraries that allow + users to compute the log likelihoods of the temperature, + polarization, and lensing maps. Optionally, it also provides a python version of this library, + as well as tools to modify the predetermined options for some likelihoods + (e.g. changing the high-ell and low-ell lmin and lmax values of the temperature). +""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://pla.esac.esa.int/pla/aio'] +sources = ['product-action?COSMOLOGY.FILE_ID=COM_Likelihood_Code-v3.0_R3.01.tar.gz'] +checksums = ['ea641f7ba6a1cdc6b6271079b2bb70613944260e7de57d53fee2516b77d68c8d'] + +dependencies = [ + ('Python', '3.7.4'), + ('CFITSIO', '3.47'), + ('cURL', '7.66.0'), + ('astropy', '4.0.1', versionsuffix), +] + +configopts = "--gcc " # Do not test for gcc and only use gcc +configopts += "--gfortran " # Do not test for gfortran and use gfortran +configopts += "--lapack_link=\"${LIBLAPACK}\" " +configopts += "--cfitsio_prefix=${EBROOTCFITSIO} " # location of the EB cfitsio install +configopts += "--extra_lib=curl " # not having curl in extra lib will fail to build the examples +configopts += "--extra_lib=m " # not having -lm will fail the build.. +configopts += "--extra_libpath=${EBROOTCURL}/lib " # -''- + +unpack_options = '--strip 3' +buildininstalldir = 'true' + +modextravars = { + 'CLIK_PATH': '%(installdir)s', + 'CLIK_DATA': 'share/clik', + 'CLIK_PLUGIN': 'rel2015', +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python/site-packages' +} + +sanity_check_paths = { + 'files': [ + 'lib/libclik_f90.%s' % SHLIB_EXT, + 'lib/libclik.%s' % SHLIB_EXT, + 'lib/python/site-packages/clik/__init__.py', + 'include/clik.h', + ], + 'dirs': [ + 'bin', + 'share', + ], +} + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.1.0-intel-2019a.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.1.0-intel-2019a.eb index cc2a6cf2ecc..bf5a5965a10 100644 --- a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.1.0-intel-2019a.eb +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.1.0-intel-2019a.eb @@ -12,8 +12,6 @@ multi_deps = {'Python': ['3.7.2', '2.7.15']} use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('retrying', '1.3.3', { 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb index bc4a11ccdf6..01c235ad79b 100644 --- a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb @@ -12,8 +12,6 @@ multi_deps = {'Python': ['3.7.4', '2.7.16']} use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('retrying', '1.3.3', { 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], diff --git a/easybuild/easyconfigs/p/poretools/poretools-0.6.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/poretools/poretools-0.6.0-intel-2018a-Python-2.7.14.eb index 6b8fb0240f3..2b0d254024c 100644 --- a/easybuild/easyconfigs/p/poretools/poretools-0.6.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/poretools/poretools-0.6.0-intel-2018a-Python-2.7.14.eb @@ -4,12 +4,11 @@ name = 'poretools' version = '0.6.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://poretools.readthedocs.io/en/latest/' +homepage = 'https://poretools.readthedocs.io/en/latest/' description = "A toolkit for working with nanopore sequencing data from Oxford Nanopore." toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4d22e45f1e080fb5131dad47c72391f37d08abe9e70b7266ca6ef971c9ec0fb2'] diff --git a/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-foss-2017b-Python-2.7.14.eb index 5cc114278ca..79d9505eef6 100644 --- a/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-foss-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = "This Python package provides a wrapper to the C++ Parma Polyhedra toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b962914d5814edab320d00c11ca396b70c4ce1e67db7a6d59c4b0a3772a16836'] @@ -27,9 +26,4 @@ download_dep_fail = True options = {'modulename': 'ppl'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-foss-2017b-Python-3.6.3.eb index 84d357998c0..517922cff59 100644 --- a/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-foss-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = "This Python package provides a wrapper to the C++ Parma Polyhedra toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b962914d5814edab320d00c11ca396b70c4ce1e67db7a6d59c4b0a3772a16836'] @@ -27,9 +26,4 @@ download_dep_fail = True options = {'modulename': 'ppl'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-intel-2017b-Python-2.7.14.eb index 8c75d9d9e36..f03995d0852 100644 --- a/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-intel-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = "This Python package provides a wrapper to the C++ Parma Polyhedra toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b962914d5814edab320d00c11ca396b70c4ce1e67db7a6d59c4b0a3772a16836'] @@ -27,9 +26,4 @@ download_dep_fail = True options = {'modulename': 'ppl'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-intel-2017b-Python-3.6.3.eb index 90259287789..a6852abd494 100644 --- a/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/pplpy/pplpy-0.8.4-intel-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = "This Python package provides a wrapper to the C++ Parma Polyhedra toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b962914d5814edab320d00c11ca396b70c4ce1e67db7a6d59c4b0a3772a16836'] @@ -27,9 +26,4 @@ download_dep_fail = True options = {'modulename': 'ppl'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb index 035c739fdd7..159ee493783 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ description = """prompt_toolkit is a Python library for building powerful intera toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = ['prompt_toolkit-%(version)s-py2-none-any.whl'] dependencies = [ diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.17.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.17.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c20dd1e402f --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.17.3-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.17.3' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = [{'download_filename': 'protobuf-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['72804ea5eaa9c22a090d2803813e280fb273b62d5ae497aaf3553d141c4fdd7b'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('protobuf', version) +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.17.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.17.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..17daeb0172d --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.17.3-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '3.17.3' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c6003e1d2e7fefa78a3039f19f383b4f3a61e81be8c19356f85b6461998ad3db'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +srcdir = 'cmake' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018a-Python-2.7.14.eb index 28524de5229..7b6cacca6eb 100644 --- a/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018a-Python-2.7.14.eb @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('psutil', '5.4.8', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['6e265c8f3da00b015d24b842bfeb111f856b13d24f2c57036582568dc650d6c3'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/psrecord'], 'checksums': ['e656230c09370a964a18f647264e9d81465c71765ed0dc02e6659fa498f53994'], }), ] diff --git a/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018a-Python-3.6.4.eb index 72bd8d20cbd..7cbc5de649a 100644 --- a/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018a-Python-3.6.4.eb @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('psutil', '5.4.8', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['6e265c8f3da00b015d24b842bfeb111f856b13d24f2c57036582568dc650d6c3'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/psrecord'], 'checksums': ['e656230c09370a964a18f647264e9d81465c71765ed0dc02e6659fa498f53994'], }), ] diff --git a/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018b-Python-2.7.15.eb index 039c8b78df2..77b5f64da81 100644 --- a/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018b-Python-2.7.15.eb @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('psutil', '5.4.8', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['6e265c8f3da00b015d24b842bfeb111f856b13d24f2c57036582568dc650d6c3'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/psrecord'], 'checksums': ['e656230c09370a964a18f647264e9d81465c71765ed0dc02e6659fa498f53994'], }), ] diff --git a/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018b-Python-3.6.6.eb index d11a2f3d552..460b5979e53 100644 --- a/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/psrecord/psrecord-1.1-intel-2018b-Python-3.6.6.eb @@ -16,11 +16,9 @@ use_pip = True exts_list = [ ('psutil', '5.4.8', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['6e265c8f3da00b015d24b842bfeb111f856b13d24f2c57036582568dc650d6c3'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/psrecord'], 'checksums': ['e656230c09370a964a18f647264e9d81465c71765ed0dc02e6659fa498f53994'], }), ] diff --git a/easybuild/easyconfigs/p/psutil/psutil-4.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/psutil/psutil-4.2.0-intel-2016a-Python-2.7.11.eb index 4ad57c66abb..2751e1f4d68 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-4.2.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-4.2.0-intel-2016a-Python-2.7.11.eb @@ -9,16 +9,10 @@ description = """A cross-platform process and system utilities module for Python toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.11'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psutil/psutil-4.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/psutil/psutil-4.3.0-foss-2016a-Python-2.7.11.eb index 1230de05aa2..0552bfa8462 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-4.3.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-4.3.0-foss-2016a-Python-2.7.11.eb @@ -9,16 +9,10 @@ description = """A cross-platform process and system utilities module for Python toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.11'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psutil/psutil-4.3.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/psutil/psutil-4.3.0-intel-2016a-Python-2.7.11.eb index c74074ba5c7..e078f5978bf 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-4.3.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-4.3.0-intel-2016a-Python-2.7.11.eb @@ -9,16 +9,10 @@ description = """A cross-platform process and system utilities module for Python toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.11'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.4.3-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/psutil/psutil-5.4.3-intel-2017b-Python-2.7.14.eb index 47295f5806c..cb98883ea32 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.4.3-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.4.3-intel-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """A cross-platform process and system utilities module for Python toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e2467e9312c2fa191687b89ff4bc2ad8843be4af6fb4dc95a7cc5f7d7a327b18'] @@ -17,9 +16,4 @@ dependencies = [ ('Python', '2.7.14'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.4.7-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/psutil/psutil-5.4.7-foss-2018b-Python-2.7.15.eb index d635689fc33..1f5597506ec 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.4.7-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.4.7-foss-2018b-Python-2.7.15.eb @@ -9,7 +9,6 @@ description = """A cross-platform process and system utilities module for Python toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5b6322b167a5ba0c5463b4d30dfd379cd4ce245a1162ebf8fc7ab5c5ffae4f3b'] @@ -17,9 +16,4 @@ dependencies = [ ('Python', '2.7.15'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.4.7-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/psutil/psutil-5.4.7-foss-2018b-Python-3.6.6.eb index 80961af0389..1acd849ccfa 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.4.7-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.4.7-foss-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = """A cross-platform process and system utilities module for Python toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5b6322b167a5ba0c5463b4d30dfd379cd4ce245a1162ebf8fc7ab5c5ffae4f3b'] @@ -17,9 +16,4 @@ dependencies = [ ('Python', '3.6.6'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb index 55bc2e064ce..0f8574e4808 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb @@ -9,7 +9,6 @@ description = """A cross-platform process and system utilities module for Python toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'] @@ -20,9 +19,4 @@ dependencies = [ ('Python', '2.7.15'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.6.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.6.3-GCCcore-8.2.0.eb index 4d6f6f8039a..d0107809c6e 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.6.3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.6.3-GCCcore-8.2.0.eb @@ -8,7 +8,6 @@ description = """A cross-platform process and system utilities module for Python toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['863a85c1c0a5103a12c05a35e59d336e1d665747e531256e061213e2e90f63f3'] @@ -19,9 +18,4 @@ multi_deps = {'Python': ['3.7.2', '2.7.15']} builddependencies = [('binutils', '2.31.1')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb index 948a2bd8f64..5c768e00371 100644 --- a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = "Psycopg is the most popular PostgreSQL adapter for the Python pro toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ @@ -17,9 +16,4 @@ dependencies = [ ('PostgreSQL', '9.6.2', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb index 3ac0511ce13..48e7171a32c 100644 --- a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb @@ -9,7 +9,6 @@ description = "Psycopg is the most popular PostgreSQL adapter for the Python pro toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ @@ -17,9 +16,4 @@ dependencies = [ ('PostgreSQL', '9.6.2', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.8.3-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.8.3-foss-2019a-Python-3.7.2.eb index bec2f5629c7..80179990ea3 100644 --- a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.8.3-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.8.3-foss-2019a-Python-3.7.2.eb @@ -12,7 +12,6 @@ description = "Psycopg is the most popular PostgreSQL adapter for the Python pro toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['897a6e838319b4bf648a574afb6cabcb17d0488f8c7195100d48d872419f4457'] @@ -24,9 +23,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/ptemcee/ptemcee-1.0.0-foss-2019a.eb b/easybuild/easyconfigs/p/ptemcee/ptemcee-1.0.0-foss-2019a.eb index 4029a825784..e522e9a9d2e 100644 --- a/easybuild/easyconfigs/p/ptemcee/ptemcee-1.0.0-foss-2019a.eb +++ b/easybuild/easyconfigs/p/ptemcee/ptemcee-1.0.0-foss-2019a.eb @@ -11,7 +11,6 @@ description = """ptemcee, pronounced "tem-cee", is fork of Daniel Foreman-Mackey toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['58e7c1d9a477acd808668b5caa5cb4d61fc5f6cd1df02a391d0d04cd14453739'] diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb index 28062167da6..62450799bc5 100644 --- a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb @@ -8,7 +8,6 @@ description = "py-cpuinfo gets CPU info with pure Python." toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2cf6426f776625b21d1db8397d3297ef7acfa59018f02a8779123f3190f18500'] diff --git a/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-2.7.11.eb index 7bd9dcc8b81..c904135dbf6 100644 --- a/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-2.7.11.eb @@ -4,12 +4,11 @@ name = 'py' version = '1.4.31' versionsuffix = '-Python-%(pyver)s' -homepage = ' http://pylib.readthedocs.org/' +homepage = ' https://pylib.readthedocs.org/' description = """library with cross-python path, ini-parsing, io, code, log facilities""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb index 80574f22544..d10bc52ce3e 100644 --- a/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb @@ -4,12 +4,11 @@ name = 'py' version = '1.4.31' versionsuffix = '-Python-%(pyver)s' -homepage = ' http://pylib.readthedocs.org/' +homepage = ' https://pylib.readthedocs.org/' description = """library with cross-python path, ini-parsing, io, code, log facilities""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pyABC/pyABC-0.10.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyABC/pyABC-0.10.4-foss-2019b-Python-3.7.4.eb index adddee8bf7f..e270bc7f013 100644 --- a/easybuild/easyconfigs/p/pyABC/pyABC-0.10.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pyABC/pyABC-0.10.4-foss-2019b-Python-3.7.4.eb @@ -37,8 +37,6 @@ dependencies = [ github_account = 'icb-dcm' -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.0.33-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.0.33-GCCcore-8.2.0-Python-3.7.2.eb index 216f1677a14..38a765755fe 100644 --- a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.0.33-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.0.33-GCCcore-8.2.0-Python-3.7.2.eb @@ -20,11 +20,9 @@ use_pip = True exts_list = [ ('humanize', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/humanize'], 'checksums': ['a43f57115831ac7c70de098e6ac46ac13be00d69abbf60bdcac251344785bb19'], }), ('htsget', '0.2.5', { - 'source_urls': ['https://pypi.python.org/packages/source/h/htsget'], 'checksums': ['d383dc36f699bd921f760f5500c8ed251e5f8358a7cc219c6c89c35d103e8045'], }), (name, version, { diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb index 7d4e1487f16..c45d367bff5 100644 --- a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -20,11 +20,9 @@ use_pip = True exts_list = [ ('humanize', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/humanize'], 'checksums': ['a43f57115831ac7c70de098e6ac46ac13be00d69abbf60bdcac251344785bb19'], }), ('htsget', '0.2.5', { - 'source_urls': ['https://pypi.python.org/packages/source/h/htsget'], 'checksums': ['d383dc36f699bd921f760f5500c8ed251e5f8358a7cc219c6c89c35d103e8045'], }), (name, version, { diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb index 0b8b5f96536..0d5101849ac 100644 --- a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -20,11 +20,9 @@ use_pip = True exts_list = [ ('humanize', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/humanize'], 'checksums': ['a43f57115831ac7c70de098e6ac46ac13be00d69abbf60bdcac251344785bb19'], }), ('htsget', '0.2.5', { - 'source_urls': ['https://pypi.python.org/packages/source/h/htsget'], 'checksums': ['d383dc36f699bd921f760f5500c8ed251e5f8358a7cc219c6c89c35d103e8045'], }), (name, version, { diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-foss-2018b-Python-3.6.6.eb index 1ede2aa1ed2..a8a8c298b26 100644 --- a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-foss-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ description = """A pythonic wrapper around FFTW, the FFT library, presenting a u toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['05ea28dede4c3aaaf5c66f56eb0f71849d0d50f5bc0f53ca0ffa69534af14926'] diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb index dd407dfc5a3..e4c849db54c 100644 --- a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb @@ -9,7 +9,6 @@ description = """A pythonic wrapper around FFTW, the FFT library, presenting a u toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['05ea28dede4c3aaaf5c66f56eb0f71849d0d50f5bc0f53ca0ffa69534af14926'] diff --git a/easybuild/easyconfigs/p/pyScaf/pyScaf-0.12a4-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pyScaf/pyScaf-0.12a4-intel-2017b-Python-2.7.14.eb index 20d12c8e46f..b88734fe360 100644 --- a/easybuild/easyconfigs/p/pyScaf/pyScaf-0.12a4-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pyScaf/pyScaf-0.12a4-intel-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = "pyScaf orders contigs from genome assemblies utilising several ty toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3ce3f6fe80bd058831b6a38a56d464ef10f3ebbdd6bc3dcb0d7f127c0b2c1b36'] diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-foss-2018b-Python-3.6.6.eb index 4c3b5e773c2..a79fedc3d22 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-foss-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = "pybedtools wraps and extends BEDTools and offers feature-level ma toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['518a2311bd33f29cf2ee8fc1a028dda8c8e380c9fc83fcb0fbaa206933174b50'] @@ -19,9 +18,4 @@ dependencies = [ ('Pysam', '0.15.1', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-intel-2017b-Python-2.7.14.eb index 99fb1e344e8..afacfac2371 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-intel-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = "pybedtools wraps and extends BEDTools and offers feature-level ma toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['pybedtools-%(version)s_fix-errors-icc.patch'] checksums = [ @@ -23,9 +22,4 @@ dependencies = [ ('Pysam', '0.13', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-intel-2018a-Python-2.7.14.eb index ac8522ed9d4..9a5c6257b9b 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.7.10-intel-2018a-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = "pybedtools wraps and extends BEDTools and offers feature-level ma toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['pybedtools-%(version)s_fix-errors-icc.patch'] checksums = [ @@ -23,9 +22,4 @@ dependencies = [ ('Pysam', '0.14.1', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.0-foss-2019a.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.0-foss-2019a.eb index 20a3717ea3d..d490e7c915f 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.0-foss-2019a.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.0-foss-2019a.eb @@ -8,7 +8,6 @@ description = "pybedtools wraps and extends BEDTools and offers feature-level ma toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4eebd2cd1764ee1c604fd881703c3e329195485350b987b7fb8db42d232984f6'] @@ -22,9 +21,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.0-intel-2019a.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.0-intel-2019a.eb index f87fcdb8030..f54825adb7f 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.0-intel-2019a.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.0-intel-2019a.eb @@ -8,7 +8,6 @@ description = "pybedtools wraps and extends BEDTools and offers feature-level ma toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4eebd2cd1764ee1c604fd881703c3e329195485350b987b7fb8db42d232984f6'] @@ -22,9 +21,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.1-foss-2019b.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.1-foss-2019b.eb index c77991c957c..8665fb4a4a5 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.1-foss-2019b.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.1-foss-2019b.eb @@ -8,7 +8,6 @@ description = "pybedtools wraps and extends BEDTools and offers feature-level ma toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c035e078617f94720eb627e20c91f2377a7bd9158a137872a6ac88f800898593'] diff --git a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.0-foss-2019b-Python-3.7.4.eb index 9f82c2f729f..e428fc8a298 100644 --- a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.0-foss-2019b-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "Tools for working with the MSCOCO dataset" toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['cbb8c2fbab80450a67ee9879c63b0bc8a69e58dd9a0153d55de404c0d383a94b'] diff --git a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.0-fosscuda-2019b-Python-3.7.4.eb index 6b9a19ff6aa..1c365ba93f6 100644 --- a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.0-fosscuda-2019b-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "Tools for working with the MSCOCO dataset" toolchain = {'name': 'fosscuda', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['cbb8c2fbab80450a67ee9879c63b0bc8a69e58dd9a0153d55de404c0d383a94b'] diff --git a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.1-foss-2019b-Python-3.7.4.eb index 8831ba2ca49..0d5c39fc2a0 100644 --- a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.1-foss-2019b-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "Official APIs for the MS-COCO dataset" toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1c06e73a85ed9874c1174d47064524b9fb2759b95a6997437775652f20c1711f'] diff --git a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.1-fosscuda-2019b-Python-3.7.4.eb index 04e039b4f51..fafec958937 100644 --- a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.1-fosscuda-2019b-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "Tools for working with the MSCOCO dataset" toolchain = {'name': 'fosscuda', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1c06e73a85ed9874c1174d47064524b9fb2759b95a6997437775652f20c1711f'] diff --git a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.5.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.5.0-intel-2018a-Python-3.6.4.eb index 1eda301f1c0..f83608a8fae 100644 --- a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.5.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.5.0-intel-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = """pycodestyle is a tool to check your Python code against some of toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e40a936c9a450ad81df37f549d676d127b1b66000a6c500caa2b085bc0ca976c'] @@ -21,9 +20,4 @@ download_dep_fail = True use_pip = True sanity_pip_check = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.6.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.6.1-GCCcore-8.3.0-Python-3.7.4.eb index a223a1117bb..601330edab4 100644 --- a/easybuild/easyconfigs/p/pydantic/pydantic-1.6.1-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.6.1-GCCcore-8.3.0-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = """Data validation and settings management using Python type hinti toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['54122a8ed6b75fe1dd80797f8251ad2063ea348a03b77218d73ea9fe19bd4e73'] diff --git a/easybuild/easyconfigs/p/pydot/pydot-1.4.1-foss-2019b.eb b/easybuild/easyconfigs/p/pydot/pydot-1.4.1-foss-2019b.eb index 2cf3b80824d..8adb24c3c31 100644 --- a/easybuild/easyconfigs/p/pydot/pydot-1.4.1-foss-2019b.eb +++ b/easybuild/easyconfigs/p/pydot/pydot-1.4.1-foss-2019b.eb @@ -8,7 +8,6 @@ description = """Python interface to Graphviz's Dot language.""" toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['d49c9d4dd1913beec2a997f831543c8cbd53e535b1a739e921642fe416235f01'] diff --git a/easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb index 44fd59e0faf..dc4e50e9ec3 100644 --- a/easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb @@ -9,7 +9,6 @@ description = "PyEnchant is a spellchecking library for Python, based on the exc toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ @@ -19,9 +18,4 @@ dependencies = [ options = {'modulename': 'enchant'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..19c8302c793 --- /dev/null +++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pyfaidx' +version = '0.5.9.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pyfaidx' +description = "pyfaidx: efficient pythonic random access to fasta subsequences" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9965644c5bd62bedc0ff7f336cbb2baef6406a36b4ec5c786b199872ce46192b'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [('Python', '3.7.4')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/faidx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["faidx --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyfits/pyfits-3.5-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pyfits/pyfits-3.5-intel-2018b-Python-2.7.15.eb index 8dd3a793050..48cf5dbf541 100644 --- a/easybuild/easyconfigs/p/pyfits/pyfits-3.5-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pyfits/pyfits-3.5-intel-2018b-Python-2.7.15.eb @@ -15,8 +15,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('d2to1', '0.2.12.post1', { 'checksums': ['49ef2d16862b3efdc81fc5c32eac373b984945cde5fc02bb01a0a11ff03dd825'], diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb index fff50e2e31f..9b5c672dad3 100644 --- a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb @@ -38,7 +38,6 @@ exts_default_options = { exts_list = [ ('cloudpickle', '1.6.0', { - 'sources': ['%(name)s-%(version)s.tar.gz'], 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], }), ('dill', '0.3.3', { diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.5-foss-2019b.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.5-foss-2019b.eb index 092ecb1ddc4..f8f4af931ce 100644 --- a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.5-foss-2019b.eb +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.5-foss-2019b.eb @@ -10,7 +10,6 @@ graph data structure and layout algorithms.""" toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['50a829a305dc5a0fd1f9590748b19fece756093b581ac91e00c2c27c651d319d'] diff --git a/easybuild/easyconfigs/p/pygrib/pygrib-2.0.4-foss-2019a.eb b/easybuild/easyconfigs/p/pygrib/pygrib-2.0.4-foss-2019a.eb index de0ff66be7f..e4eba561032 100644 --- a/easybuild/easyconfigs/p/pygrib/pygrib-2.0.4-foss-2019a.eb +++ b/easybuild/easyconfigs/p/pygrib/pygrib-2.0.4-foss-2019a.eb @@ -8,7 +8,6 @@ description = "Python interface for reading and writing GRIB data" toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c3a828c1121c686814c2cfe281a7a3be196a22b9754306bf61c3fd65c31f1fcd'] diff --git a/easybuild/easyconfigs/p/pyhdf/pyhdf-0.10.1-foss-2019a.eb b/easybuild/easyconfigs/p/pyhdf/pyhdf-0.10.1-foss-2019a.eb index 77950afa2d4..0e2adf137b6 100644 --- a/easybuild/easyconfigs/p/pyhdf/pyhdf-0.10.1-foss-2019a.eb +++ b/easybuild/easyconfigs/p/pyhdf/pyhdf-0.10.1-foss-2019a.eb @@ -8,7 +8,6 @@ description = "Python wrapper around the NCSA HDF version 4 library" toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c939cf92487c37da61b41867b4ab032711ccde407340f7ef7d18917631cf62b2'] diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.2.5-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.2.5-intel-2019a-Python-3.7.2.eb index bf5144b1784..f2291201b08 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.2.5-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.2.5-intel-2019a-Python-3.7.2.eb @@ -26,8 +26,6 @@ dependencies = [ check_ldshared = True use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('h5io', '0.1.1', { 'checksums': ['3412b962a418b38312bcbe2ac41404258bb1adbf6fdaed3b1ca17fcd7f6f5f70'], diff --git a/easybuild/easyconfigs/p/pylift/pylift-0.1.5-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pylift/pylift-0.1.5-foss-2019b-Python-3.7.4.eb index fd7f5a85c54..550cd419071 100644 --- a/easybuild/easyconfigs/p/pylift/pylift-0.1.5-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pylift/pylift-0.1.5-foss-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """ pylift is an uplift library that provides, primarily: toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['bf855996abfd65125cde40b378393766c379694a4b814cdecb1cadd743392730'] diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb index 42d0b6df4c9..dc94b3f35ee 100644 --- a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'pymatgen-db' version = '0.6.5' @@ -15,24 +15,11 @@ dependencies = [ ('pymatgen', '4.7.3', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ - ('smoqe', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], - }), + ('smoqe', '0.1.3'), ('pymatgen-db', '0.6.5', { 'modulename': 'matgendb', - 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen-db/'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2017.10.16-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2017.10.16-intel-2017b-Python-2.7.14.eb index 4824d46203a..26762b188fd 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-2017.10.16-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2017.10.16-intel-2017b-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'pymatgen' version = '2017.10.16' @@ -17,96 +17,67 @@ dependencies = [ ('spglib-python', '1.10.0.2', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b'], }), ('itsdangerous', '0.24', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous/'], 'checksums': ['cbb3fcf8d3e33df861709ecaf89d9e6629cff0a217bc2848f1b41cd30d360519'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['ddaa01a212cd6d641401cb01b605f4a4d9f37bfc93043d7f760ec70fb99ff9ff'], }), ('Werkzeug', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug/'], 'checksums': ['903a7b87b74635244548b30d30db4c8947fe64c5198f58899ddcd3a13c23bb26'], }), ('Flask', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], 'checksums': ['49f44461237b69ecd901cc7ce66feea0319b9158743dd27a2899962ab214dac1'], }), ('monty', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], 'checksums': ['86d9686ff92f0e97fffc74bc9d91c68d2b904915fe7976ff8673bee6fa961b17'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('sympy', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sympy/'], 'checksums': ['ac5b57691bc43919dcc21167660a57cc51797c28a4301a6144eff07b751216a4'], }), ('palettable', '3.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/palettable/'], 'checksums': ['4c6f6531b93d97eb0bf4d707160626261de11470c47e2d017ac6bb569b5308aa'], }), ('tabulate', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['b9b4d2fc712c1e3b8f2970edf6d83fd8a329d0148de78bbe2755a79a96c190fa'], }), ('PyDispatcher', '2.0.5', { 'modulename': 'pydispatch', - 'source_urls': ['https://pypi.python.org/packages/source/P/PyDispatcher/'], 'checksums': ['5570069e1b1769af1fe481de6dd1d3a388492acddd2cdad7a3bde145615d5caf'], }), ('ruamel.yaml', '0.15.34', { - 'source_urls': ['https://pypi.python.org/packages/source/r/ruamel.yaml/'], 'use_pip': True, 'checksums': ['f1e29054c6e477963e302b007b6cd1d6c7a58c38d78fabe64fde9ce170d2d1fd'], }), ('certifi', '2017.7.27.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['40523d2efb60523e113b44602298f0960e900388cf3bb6043f645cf57ea9e3f5'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), ('ruamel.ordereddict', '0.4.13', { - 'source_urls': ['https://pypi.python.org/packages/source/r/ruamel.ordereddict/'], 'use_pip': True, 'checksums': ['bf0a198c8ce5d973c24e5dba12d3abc254996788ca6ad8448eabc6aa710db149'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], 'checksums': ['f05ce838c7fe9cc37aae85083f45bf9503eda1292aa1d778bfcd4b5b3018cb1b'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -sanity_check_paths = { - 'files': ['bin/pmg'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2017.10.16-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2017.10.16-intel-2017b-Python-3.6.3.eb index 25d8b874323..e82d9d14698 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-2017.10.16-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2017.10.16-intel-2017b-Python-3.6.3.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'pymatgen' version = '2017.10.16' @@ -17,91 +17,63 @@ dependencies = [ ('spglib-python', '1.10.0.2', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ ('click', '6.7', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b'], }), ('itsdangerous', '0.24', { - 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous/'], 'checksums': ['cbb3fcf8d3e33df861709ecaf89d9e6629cff0a217bc2848f1b41cd30d360519'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('Jinja2', '2.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['ddaa01a212cd6d641401cb01b605f4a4d9f37bfc93043d7f760ec70fb99ff9ff'], }), ('Werkzeug', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug/'], 'checksums': ['903a7b87b74635244548b30d30db4c8947fe64c5198f58899ddcd3a13c23bb26'], }), ('Flask', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], 'checksums': ['49f44461237b69ecd901cc7ce66feea0319b9158743dd27a2899962ab214dac1'], }), ('monty', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], 'checksums': ['86d9686ff92f0e97fffc74bc9d91c68d2b904915fe7976ff8673bee6fa961b17'], }), ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], }), ('sympy', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sympy/'], 'checksums': ['ac5b57691bc43919dcc21167660a57cc51797c28a4301a6144eff07b751216a4'], }), ('palettable', '3.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/palettable/'], 'checksums': ['4c6f6531b93d97eb0bf4d707160626261de11470c47e2d017ac6bb569b5308aa'], }), ('tabulate', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['b9b4d2fc712c1e3b8f2970edf6d83fd8a329d0148de78bbe2755a79a96c190fa'], }), ('PyDispatcher', '2.0.5', { 'modulename': 'pydispatch', - 'source_urls': ['https://pypi.python.org/packages/source/P/PyDispatcher/'], 'checksums': ['5570069e1b1769af1fe481de6dd1d3a388492acddd2cdad7a3bde145615d5caf'], }), ('ruamel.yaml', '0.15.34', { - 'source_urls': ['https://pypi.python.org/packages/source/r/ruamel.yaml/'], 'use_pip': True, 'checksums': ['f1e29054c6e477963e302b007b6cd1d6c7a58c38d78fabe64fde9ce170d2d1fd'], }), ('certifi', '2017.7.27.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['40523d2efb60523e113b44602298f0960e900388cf3bb6043f645cf57ea9e3f5'], }), ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], 'checksums': ['f05ce838c7fe9cc37aae85083f45bf9503eda1292aa1d778bfcd4b5b3018cb1b'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -sanity_check_paths = { - 'files': ['bin/pmg'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index f6c2197ee20..b157ad44f04 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -10,7 +10,6 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb index 6b8241e929e..9d167112278 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb index ff5f953560c..d4a5530e7f0 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,6 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb index ac2c4ca2a31..b36ffaff925 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'pymatgen' version = '4.7.3' @@ -17,40 +17,17 @@ dependencies = [ ('spglib-python', '1.9.9.38', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ - ('Flask', '0.12', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], - }), + ('Flask', '0.12'), ('Flask-paginate', '0.4.5', { - 'source_urls': ['https://pypi.python.org/packages/source/F/Flask-paginate/'], 'source_tmpl': 'flask-paginate-%(version)s.zip', 'modulename': 'flask_paginate', }), - ('gunicorn', '19.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gunicorn/'], - }), - ('monty', '0.9.6', { - 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], - }), - ('mpmath', '0.19', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], - }), - ('sympy', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sympy/'], - }), - ('pymatgen', version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], - }), + ('gunicorn', '19.7.1'), + ('monty', '0.9.6'), + ('mpmath', '0.19'), + ('sympy', '1.0'), + ('pymatgen', version), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymemcache/pymemcache-2.1.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/pymemcache/pymemcache-2.1.1-foss-2018a-Python-3.6.4.eb index 38a467158dc..73182861f9b 100644 --- a/easybuild/easyconfigs/p/pymemcache/pymemcache-2.1.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/pymemcache/pymemcache-2.1.1-foss-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = 'A comprehensive, fast, pure-Python memcached client.' toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['24634565e4cdf9c625a3c89ac69650812cc3986f4159a56814c932f027605a9c'] diff --git a/easybuild/easyconfigs/p/pymemcache/pymemcache-2.1.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/pymemcache/pymemcache-2.1.1-intel-2018a-Python-3.6.4.eb index 52627b626a4..d88d045f332 100644 --- a/easybuild/easyconfigs/p/pymemcache/pymemcache-2.1.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/pymemcache/pymemcache-2.1.1-intel-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = 'A comprehensive, fast, pure-Python memcached client.' toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['24634565e4cdf9c625a3c89ac69650812cc3986f4159a56814c932f027605a9c'] diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-2.1.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-2.1.3-GCCcore-8.2.0.eb index 685038ea87f..9d887f1f97b 100644 --- a/easybuild/easyconfigs/p/pyproj/pyproj-2.1.3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/pyproj/pyproj-2.1.3-GCCcore-8.2.0.eb @@ -8,7 +8,6 @@ description = "Python interface to PROJ4 library for cartographic transformation toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['99c52788b01a7bb9a88024bf4d40965c0a66a93d654600b5deacf644775f424d'] diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-2.4.2-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyproj/pyproj-2.4.2-GCCcore-8.3.0-Python-3.7.4.eb index 781d238a032..b4443b86cda 100644 --- a/easybuild/easyconfigs/p/pyproj/pyproj-2.4.2-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pyproj/pyproj-2.4.2-GCCcore-8.3.0-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "Python interface to PROJ4 library for cartographic transformation toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2821f7fdfe4d2c5916e71f80d0f4029d82785f477a11223e70de2db39a1f26dd'] diff --git a/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2016a-Python-2.7.11.eb index a162402911d..d6dc2e76f43 100644 --- a/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ description = """Debugger capable of attaching to and injecting code into python toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pysndfx/pysndfx-0.3.6-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pysndfx/pysndfx-0.3.6-foss-2019b-Python-3.7.4.eb index 0d53be51dfc..1f9d89ba2f0 100644 --- a/easybuild/easyconfigs/p/pysndfx/pysndfx-0.3.6-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pysndfx/pysndfx-0.3.6-foss-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """A lightweight Python wrapper for SoX - Sound eXchange. toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ce168812963e398e849ad60aa1dc74e78f452ce0c948679367b2627459f39c9c'] diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb new file mode 100644 index 00000000000..6e7e7a5935e --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonPackage' + +name = 'pyspoa' +version = '0.0.8' + +homepage = 'https://github.com/nanoporetech/pyspoa' +description = "Python bindings to spoa." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [ + { + 'source_urls': ['https://github.com/nanoporetech/pyspoa/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'pyspoa-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/USCiLab/cereal/archive/'], + 'download_filename': '3e4d1b8.tar.gz', + 'filename': 'cereal-20200423.tar.gz', + }, +] +patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] +checksums = [ + 'a1e630ef30a42d8e8c076d914261d0d34060631d64694569d52c1a2be5deada7', # pyspoa-0.0.8.tar.gz + '284cd14c1e60b36c966bcc8ce650d0b798b8a836d6c379e021e0da0dbe6ddf38', # cereal-20200423.tar.gz + 'a98c82ae8346b48952b171675f9df7ab1c95ea5421afcf5bcd778c01c5ee5a52', # pyspoa-0.0.8_use-spoa-dep.patch +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('pybind11', '2.6.0'), + ('spoa', '4.0.7'), +] + +download_dep_fail = True + +preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " +# strip out cmake requirements, since we provide that as proper dependency +preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " + +use_pip = True + +options = {'modulename': 'spoa'} + +sanity_pip_check = True + +sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8_use-spoa-dep.patch b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8_use-spoa-dep.patch new file mode 100644 index 00000000000..b31bfee8fa6 --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8_use-spoa-dep.patch @@ -0,0 +1,22 @@ +use spoa dependency provided through EasyBuild + +author: Kenneth Hoste (HPC-UGent) +--- pyspoa-0.0.8/setup.py.orig 2021-05-25 19:13:24.688407374 +0200 ++++ pyspoa-0.0.8/setup.py 2021-05-25 19:13:25.878395003 +0200 +@@ -94,14 +94,14 @@ + 'spoa', + ['pyspoa.cpp'], + include_dirs=[ +- 'src/include/spoa', ++ os.path.join(os.getenv('EBROOTSPOA'), 'include/spoa'), + 'src/vendor/cereal/include', + get_pybind_include(), + get_pybind_include(user=True), + ], + language='c++', + extra_objects=[ +- 'src/build/lib/libspoa.a' ++ os.path.join(os.getenv('EBROOTSPOA'), 'lib64/libspoa.a'), + ], + + ), diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.8.2-foss-2016a-Python-2.7.11.eb index 0387ef7b1e9..68e107d0425 100644 --- a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.8.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.8.2-foss-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ description = """pysqlite is an interface to the SQLite 3.x embedded relational toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pystran/pystran-2017.04.20-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pystran/pystran-2017.04.20-intel-2017b-Python-2.7.14.eb index 40cb335795a..264433e1777 100644 --- a/easybuild/easyconfigs/p/pystran/pystran-2017.04.20-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pystran/pystran-2017.04.20-intel-2017b-Python-2.7.14.eb @@ -5,7 +5,7 @@ version = '2017.04.20' local_commit = '0d79ca83184a6a5edb252b57f4a6869eb3eba431' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stijnvanhoey.github.io/pystran/' +homepage = 'https://stijnvanhoey.github.io/pystran/' description = """Toolset of dynamical model STRucture ANalysis algorithms""" toolchain = {'name': 'intel', 'version': '2017b'} @@ -22,15 +22,9 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ ('numexpr', '2.6.5', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/n/numexpr/'], + 'source_urls': [PYPI_SOURCE], 'checksums': ['f8ad8014085628eab91bc82fb9d10cf9ab8e04ede4884e4a1061445d395b36bb'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..5fda9670815 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'pytest-xdist' +version = '2.3.0' + +homepage = 'https://github.com/pytest-dev/pytest-xdist' +description = """xdist: pytest distributed testing plugin + +The pytest-xdist plugin extends pytest with some unique test execution modes: + + * test run parallelization: if you have multiple CPUs or hosts you + can use those for a combined test run. This allows to speed up + development or to use special resources of remote machines. + + * --looponfail: run your tests repeatedly in a subprocess. After + each run pytest waits until a file in your project changes and + then re-runs the previously failing tests. This is repeated + until all tests pass after which again a full run is + performed. + + * Multi-Platform coverage: you can specify different Python + interpreters or different platforms and run tests in parallel on + all of them. + +Before running tests remotely, pytest efficiently “rsyncs” your +program source code to the remote place. All test results are reported +back and displayed to your local terminal. You may specify different +Python versions and interpreters.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('apipkg', '1.5', { + 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], + }), + ('execnet', '1.9.0', { + 'checksums': ['8f694f3ba9cc92cab508b152dcfe322153975c29bda272e2fd7f3f00f36e47c5'], + }), + ('pytest-forked', '1.3.0', { + 'checksums': ['6aa9ac7e00ad1a539c41bec6d21011332de671e938c7637378ec9710204e37ca'], + }), + (name, version, { + 'modulename': 'xdist', + 'checksums': ['e8ecde2f85d88fbcadb7d28cb33da0fa29bca5cf7d5967fa89fc0e97e5299ea5'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-2.7.11.eb index a816b7e71ea..c27799cd38f 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-2.7.11.eb @@ -4,12 +4,11 @@ name = 'pytest' version = '3.0.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-3.5.1.eb index 85ae51712a4..f62a7135bc0 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-3.5.1.eb @@ -4,12 +4,11 @@ name = 'pytest' version = '3.0.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.8.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/pytest/pytest-3.8.0-foss-2018a-Python-3.6.4.eb index 152fd2bbe83..99ded67f1af 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-3.8.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-3.8.0-foss-2018a-Python-3.6.4.eb @@ -1,47 +1,37 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'pytest' version = '3.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'foss', 'version': '2018a'} dependencies = [('Python', '3.6.4')] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('py', '1.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['06a30435d058473046be836d3fc4f27167fd84c45b99704f2fb5509ef61f9af1'], }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('pluggy', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['95eb8364a4708392bae89035f45341871286a333f749c3141c20573d2b3876e1'], }), ('atomicwrites', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'], }), ('more-itertools', '4.3.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['a8a07f84e680482eb51e244370aaf2caa6301ef265f37c2bdefb3dd3b663f99d'], }), ] @@ -51,6 +41,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.8.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/pytest/pytest-3.8.0-intel-2018a-Python-3.6.4.eb index 5a12f094cb0..3ba9495c955 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-3.8.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-3.8.0-intel-2018a-Python-3.6.4.eb @@ -1,47 +1,37 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'pytest' version = '3.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'intel', 'version': '2018a'} dependencies = [('Python', '3.6.4')] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('py', '1.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['06a30435d058473046be836d3fc4f27167fd84c45b99704f2fb5509ef61f9af1'], }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('pluggy', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['95eb8364a4708392bae89035f45341871286a333f749c3141c20573d2b3876e1'], }), ('atomicwrites', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'], }), ('more-itertools', '4.3.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['a8a07f84e680482eb51e244370aaf2caa6301ef265f37c2bdefb3dd3b663f99d'], }), ] @@ -51,6 +41,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2017b-Python-2.7.14.eb index bcea787ae84..cb419b0f4ea 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '3.8.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'foss', 'version': '2017b'} @@ -15,37 +15,29 @@ use_pip = True exts_list = [ ('py', '1.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694'], }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('pluggy', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['447ba94990e8014ee25ec853339faf7b0fc8050cdc3289d4d71f7f410fb90095'], }), ('atomicwrites', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'], }), ('more-itertools', '4.3.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], }), ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['9332147e9af2dcf46cd7ceb14d5acadb6564744ddff1fe8c17f0ce60ece7d9a2'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2017b-Python-3.6.3.eb index cab83137239..86aa5eb6ae3 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '3.8.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'foss', 'version': '2017b'} @@ -15,37 +15,29 @@ use_pip = True exts_list = [ ('py', '1.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694'], }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('pluggy', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['447ba94990e8014ee25ec853339faf7b0fc8050cdc3289d4d71f7f410fb90095'], }), ('atomicwrites', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'], }), ('more-itertools', '4.3.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], }), ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['9332147e9af2dcf46cd7ceb14d5acadb6564744ddff1fe8c17f0ce60ece7d9a2'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2018b-Python-3.6.6.eb index 0f4f37e15d7..b3653f57051 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '3.8.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'foss', 'version': '2018b'} @@ -15,37 +15,29 @@ use_pip = True exts_list = [ ('py', '1.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694'], }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('pluggy', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['447ba94990e8014ee25ec853339faf7b0fc8050cdc3289d4d71f7f410fb90095'], }), ('atomicwrites', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'], }), ('more-itertools', '4.3.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], }), ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['9332147e9af2dcf46cd7ceb14d5acadb6564744ddff1fe8c17f0ce60ece7d9a2'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2017b-Python-2.7.14.eb index 3cf3c32991f..4d1eabc73e2 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '3.8.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'intel', 'version': '2017b'} @@ -15,37 +15,29 @@ use_pip = True exts_list = [ ('py', '1.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694'], }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('pluggy', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['447ba94990e8014ee25ec853339faf7b0fc8050cdc3289d4d71f7f410fb90095'], }), ('atomicwrites', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'], }), ('more-itertools', '4.3.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], }), ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['9332147e9af2dcf46cd7ceb14d5acadb6564744ddff1fe8c17f0ce60ece7d9a2'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2017b-Python-3.6.3.eb index 5c05962d2d3..d2dd4e9adef 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '3.8.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'intel', 'version': '2017b'} @@ -15,37 +15,29 @@ use_pip = True exts_list = [ ('py', '1.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694'], }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('pluggy', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['447ba94990e8014ee25ec853339faf7b0fc8050cdc3289d4d71f7f410fb90095'], }), ('atomicwrites', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'], }), ('more-itertools', '4.3.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], }), ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['9332147e9af2dcf46cd7ceb14d5acadb6564744ddff1fe8c17f0ce60ece7d9a2'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-2.7.15.eb index af0b5a81385..8801bfdae5b 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '3.8.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'intel', 'version': '2018b'} @@ -15,37 +15,29 @@ use_pip = True exts_list = [ ('py', '1.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694'], }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('pluggy', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['447ba94990e8014ee25ec853339faf7b0fc8050cdc3289d4d71f7f410fb90095'], }), ('atomicwrites', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'], }), ('more-itertools', '4.3.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], }), ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['9332147e9af2dcf46cd7ceb14d5acadb6564744ddff1fe8c17f0ce60ece7d9a2'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-3.6.6.eb index a3813148956..9a04d817e7c 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '3.8.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'intel', 'version': '2018b'} @@ -15,37 +15,29 @@ use_pip = True exts_list = [ ('py', '1.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694'], }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('pluggy', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['447ba94990e8014ee25ec853339faf7b0fc8050cdc3289d4d71f7f410fb90095'], }), ('atomicwrites', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'], }), ('more-itertools', '4.3.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], }), ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), ('pathlib2', '2.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['9332147e9af2dcf46cd7ceb14d5acadb6564744ddff1fe8c17f0ce60ece7d9a2'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb index afa87efe8b5..896b4722668 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '4.3.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'foss', 'version': '2018b'} @@ -15,29 +15,23 @@ use_pip = True exts_list = [ ('py', '1.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('pluggy', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], }), ('atomicwrites', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['067a1d4bf827ffdd56ad21bd46674703fce77c5957f6c1eef731f6146bfcef1c'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb index 00903c9ef46..d03c8388314 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '4.3.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'intel', 'version': '2018b'} @@ -15,29 +15,23 @@ use_pip = True exts_list = [ ('py', '1.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('attrs', '18.2.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], }), ('pluggy', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], }), ('atomicwrites', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['067a1d4bf827ffdd56ad21bd46674703fce77c5957f6c1eef731f6146bfcef1c'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb index 502bedc4461..523f63a9bd8 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '4.4.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'foss', 'version': '2018b'} @@ -15,37 +15,29 @@ use_pip = True exts_list = [ ('py', '1.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('pluggy', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], }), ('atomicwrites', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('scandir', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], }), ('pathlib2', '2.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['f21d2f1fb8200830dcbb5d8ec466a9c9120e20d8b53c7585d180125cce1d297a'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb index 103ad368022..a6d417ca666 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '4.4.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'foss', 'version': '2018b'} @@ -15,37 +15,29 @@ use_pip = True exts_list = [ ('py', '1.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('pluggy', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], }), ('atomicwrites', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('scandir', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], }), ('pathlib2', '2.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['f21d2f1fb8200830dcbb5d8ec466a9c9120e20d8b53c7585d180125cce1d297a'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb index 0898a7655d0..b6481deebf1 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '4.4.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'intel', 'version': '2018b'} @@ -15,37 +15,29 @@ use_pip = True exts_list = [ ('py', '1.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('pluggy', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], }), ('atomicwrites', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('scandir', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], }), ('pathlib2', '2.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['f21d2f1fb8200830dcbb5d8ec466a9c9120e20d8b53c7585d180125cce1d297a'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb index 9698a8bafd9..79453f76e3f 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'pytest' version = '4.4.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' +homepage = 'https://pytest.org' description = """pytest: simple powerful testing with Python""" toolchain = {'name': 'intel', 'version': '2018b'} @@ -15,37 +15,29 @@ use_pip = True exts_list = [ ('py', '1.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('attrs', '19.1.0', { 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('pluggy', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], }), ('atomicwrites', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('scandir', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], }), ('pathlib2', '2.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], 'checksums': ['f21d2f1fb8200830dcbb5d8ec466a9c9120e20d8b53c7585d180125cce1d297a'], }), ] diff --git a/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2018b-Python-3.6.6.eb index d20f86e290b..666224aa914 100644 --- a/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = 'Python extension for computing string edit distances and similari toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['033a11de5e3d19ea25c9302d11224e1a1898fe5abd23c61c7c360c25195e3eb1'] @@ -22,9 +21,4 @@ use_pip = True options = {'modulename': 'Levenshtein'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2019b-Python-3.7.4.eb index 2200977a737..3c4da336322 100644 --- a/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2019b-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = 'Python extension for computing string edit distances and similari toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['033a11de5e3d19ea25c9302d11224e1a1898fe5abd23c61c7c360c25195e3eb1'] diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.7.1.post6-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.7.1.post6-foss-2018b-Python-3.6.6.eb index 04580fa31cf..51dfe2949fb 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.7.1.post6-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.7.1.post6-foss-2018b-Python-3.6.6.eb @@ -4,13 +4,12 @@ name = 'python-igraph' version = '0.7.1.post6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://igraph.org/python' +homepage = 'https://igraph.org/python' description = """Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a5ea42790a077eadb3d1e8f82edc47516fea4a2b26bbf52bfc148370fe0fe676'] diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.7.1.post6-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.7.1.post6-intel-2017b-Python-2.7.14.eb index df84cbfd0b2..2354a04ed80 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.7.1.post6-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.7.1.post6-intel-2017b-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'python-igraph' version = '0.7.1.post6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://igraph.org/python' +homepage = 'https://igraph.org/python' description = """Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a5ea42790a077eadb3d1e8f82edc47516fea4a2b26bbf52bfc148370fe0fe676'] diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2019b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2019b.eb index 0ad316f281c..15bf0636f34 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2019b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2019b.eb @@ -22,8 +22,6 @@ dependencies = [ use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('texttable', '1.6.2', { 'checksums': ['eff3703781fbc7750125f50e10f001195174f13825a92a45e9403037d539b4f4'], diff --git a/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb index e71c606f3fe..b3f71b6a46b 100644 --- a/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('javabridge', '1.0.18', { 'checksums': ['d6d27dad4331fd1f4cc4a82aedd168bbc3d57641def8f055e137ae3cad521737'], diff --git a/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb index 88b782286f1..5b7b69e1ac7 100644 --- a/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ply', '3.11', { 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], diff --git a/easybuild/easyconfigs/q/QML/QML-0.2.10-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/q/QML/QML-0.2.10-intel-2017a-Python-2.7.13.eb index 19b0dc9a7dd..7bd5c096d0e 100644 --- a/easybuild/easyconfigs/q/QML/QML-0.2.10-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/q/QML/QML-0.2.10-intel-2017a-Python-2.7.13.eb @@ -4,14 +4,13 @@ name = "QML" version = "0.2.10" versionsuffix = "-Python-%(pyver)s" -homepage = "http://www.qmlcode.org" +homepage = "https://www.qmlcode.org" description = """QML is a Python2/3-compatible toolkit for representation learning of properties of molecules and solids.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s-fix-setup.py.patch'] checksums = [ diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb index 595f99f75e4..f3b210b0ca5 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb @@ -24,7 +24,6 @@ use_pip = True exts_list = [ ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), (name, version, { diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb index 8cf4516a862..cef7ad2f682 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb @@ -28,7 +28,6 @@ use_pip = True exts_list = [ ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), (name, version, { diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb index 5ff4f1c58e1..01960475b5e 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb @@ -28,7 +28,6 @@ use_pip = True exts_list = [ ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), (name, version, { diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb index 0904642e34f..87ae71af604 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb @@ -28,7 +28,6 @@ use_pip = True exts_list = [ ('simplejson', '3.17.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson'], 'checksums': ['2b4b2b738b3b99819a17feaf118265d0753d5536049ea570b3c43b51c4701e81'], }), (name, version, { diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..f55d1c11a28 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.11.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.11.1-foss-2019a-Python-3.7.2.eb index 2bd87c6d1e3..48ea3c1d3c9 100644 --- a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.11.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.11.1-foss-2019a-Python-3.7.2.eb @@ -32,8 +32,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('marshmallow', '2.20.0', { 'checksums': ['6f027308cddb25b74f8245b833a355e65b21b362f38773b40325ff9b5da6c959'], @@ -113,9 +111,4 @@ postinstallcmds = [ "echo %s > %%(installdir)s/lib/python%%(pyshortver)s/site-packages/qiskit/providers/aer/VERSION.txt" % local_aerver, ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'quantum' diff --git a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.12.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.12.0-foss-2019a-Python-3.7.2.eb index 622b440ec50..4a10029c3fb 100644 --- a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.12.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.12.0-foss-2019a-Python-3.7.2.eb @@ -32,8 +32,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('marshmallow', '2.20.2', { 'checksums': ['a339159e422a055269f5625df51fbdc7fb20512cfffa08451cd5727783ddca39'], diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb index 818ca0cb63a..09588551870 100644 --- a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -10,7 +10,6 @@ It provides support for PyQt5, PyQt4, PySide2 and PySide.""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2db72c44b55d0fe1407be8fba35c838ad0d6d3bb81f23007886dc1fc0f459c8d'] diff --git a/easybuild/easyconfigs/q/Quandl/Quandl-3.4.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/q/Quandl/Quandl-3.4.2-intel-2018a-Python-3.6.4.eb index a4545ac1843..238eebf24fd 100644 --- a/easybuild/easyconfigs/q/Quandl/Quandl-3.4.2-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/q/Quandl/Quandl-3.4.2-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Quandl' version = '3.4.2' @@ -11,33 +11,19 @@ toolchain = {'name': 'intel', 'version': '2018a'} dependencies = [('Python', '3.6.4')] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('inflection', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/inflection'], 'checksums': ['18ea7fb7a7d152853386523def08736aa8c32636b047ade55f7578c4edeb16ca'], }), ('more-itertools', '4.3.0', { 'modulename': 'more_itertools', - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools'], 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/Q/Quandl'], 'checksums': ['1c76204d4d6e33840f90f1747a14024162e34b747527938b4868655ae980d75b'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/Quandl/Quandl-3.4.8-foss-2019a.eb b/easybuild/easyconfigs/q/Quandl/Quandl-3.4.8-foss-2019a.eb index 1facbac87df..aca1be24330 100644 --- a/easybuild/easyconfigs/q/Quandl/Quandl-3.4.8-foss-2019a.eb +++ b/easybuild/easyconfigs/q/Quandl/Quandl-3.4.8-foss-2019a.eb @@ -14,8 +14,6 @@ dependencies = [('SciPy-bundle', '2019.03')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('inflection', '0.3.1', { 'checksums': ['18ea7fb7a7d152853386523def08736aa8c32636b047ade55f7578c4edeb16ca'], diff --git a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb new file mode 100644 index 00000000000..fad68609ddd --- /dev/null +++ b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'Quandl' +version = '3.6.1' + +homepage = 'https://pypi.python.org/pypi/Quandl' +description = "A Python library for Quandl’s RESTful API." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('inflection', '0.5.1', { + 'checksums': ['1a29730d366e996aaacffb2f1f1cb9593dc38e2ddd30c91250c6dde09ea9b417'], + }), + ('more-itertools', '8.8.0', { + 'checksums': ['83f0308e05477c68f56ea3a888172c78ed5d5b3c282addb67508e7ba6c8f813a'], + }), + ('pyOpenSSL', '19.1.0', { + 'modulename': 'OpenSSL', + 'checksums': ['9a24494b2602aaf402be5c9e30a0b82d4a5c67528fe8fb475e3f3bc00dd69507'], + }), + ('ndg-httpsclient', '0.5.1', { + 'modulename': 'ndg', + 'source_tmpl': 'ndg_httpsclient-%(version)s.tar.gz', + 'checksums': ['d72faed0376ab039736c2ba12e30695e2788c4aa569c9c3e3d72131de2592210'], + }), + (name, version, { + 'checksums': ['84414e5f8e870a9c8a9392e9dc639d50e839c5f5e07737a09bb57dd8b14b264b'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb index 8fafd046ad5..74d36c967cb 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb @@ -18,12 +18,12 @@ source_urls = [ ] sources = [ 'qe-%(version)s-ReleasePack.tgz', - # to be uncommented once qe-gipaw-6.7 is released - # {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}, + {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)sMaX.tar.gz'}, {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, ] checksums = [ '8f06ea31ae52ad54e900a2f51afd5c70f78096d9dcf39c86c2b17dccb1ec9c87', # qe-6.7-ReleasePack.tgz + '95d2ed2f4d27f044dba171bdf8c1913a67ebc8846ed3463462828f2d414a2a61', # qe-gipaw-%(version)s.tar.gz '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz ] @@ -35,7 +35,7 @@ dependencies = [ # The third party packages should be installed separately and added as # dependencies. The exception is w90, which is force built -buildopts = 'all gwl xspectra couple epw w90' # gipaw +buildopts = "all gwl xspectra couple epw gipaw w90" # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb new file mode 100644 index 00000000000..43a880080ad --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +## +name = 'QuantumESPRESSO' +version = '6.7' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s.0/', + 'https://github.com/dceresoli/qe-gipaw/archive/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + {'filename': 'qe-gipaw-%(version)sMaX.tar.gz', 'download_filename': '%(version)sMaX.tar.gz'}, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + '8f06ea31ae52ad54e900a2f51afd5c70f78096d9dcf39c86c2b17dccb1ec9c87', # qe-6.7-ReleasePack.tgz + '95d2ed2f4d27f044dba171bdf8c1913a67ebc8846ed3463462828f2d414a2a61', # qe-gipaw-6.7MaX.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('ELPA', '2020.11.001'), + ('libxc', '4.3.4'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb new file mode 100644 index 00000000000..5438527c158 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb @@ -0,0 +1,44 @@ +name = 'QuantumESPRESSO' +version = '6.7' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s.0/', + 'https://github.com/dceresoli/qe-gipaw/archive/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)sMaX.tar.gz'}, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + '8f06ea31ae52ad54e900a2f51afd5c70f78096d9dcf39c86c2b17dccb1ec9c87', # qe-6.7-ReleasePack.tgz + '95d2ed2f4d27f044dba171bdf8c1913a67ebc8846ed3463462828f2d414a2a61', # qe-gipaw-%(version)s.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('ELPA', '2021.05.001'), + ('libxc', '5.1.5'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb index f0ce9341f07..d52fb661c17 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb @@ -18,12 +18,12 @@ source_urls = [ ] sources = [ 'qe-%(version)s-ReleasePack.tgz', - # to be uncommented once qe-gipaw-6.7 is released - # {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}, + {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)sMaX.tar.gz'}, {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, ] checksums = [ '8f06ea31ae52ad54e900a2f51afd5c70f78096d9dcf39c86c2b17dccb1ec9c87', # qe-6.7-ReleasePack.tgz + '95d2ed2f4d27f044dba171bdf8c1913a67ebc8846ed3463462828f2d414a2a61', # qe-gipaw-%(version)s.tar.gz '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz ] @@ -35,7 +35,7 @@ dependencies = [ # The third party packages should be installed separately and added as # dependencies. The exception is w90, which is force built -buildopts = 'all gwl xspectra couple epw w90' # gipaw +buildopts = "all gwl xspectra couple epw gipaw w90" # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb new file mode 100644 index 00000000000..90cb839d1f7 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb @@ -0,0 +1,44 @@ +name = 'QuantumESPRESSO' +version = '6.7' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s.0/', + 'https://github.com/dceresoli/qe-gipaw/archive/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)sMaX.tar.gz'}, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + '8f06ea31ae52ad54e900a2f51afd5c70f78096d9dcf39c86c2b17dccb1ec9c87', # qe-6.7-ReleasePack.tgz + '95d2ed2f4d27f044dba171bdf8c1913a67ebc8846ed3463462828f2d414a2a61', # qe-gipaw-%(version)s.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('ELPA', '2021.05.001'), + ('libxc', '5.1.5'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb index 3b9f1fb9c16..d35f44ab478 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb @@ -18,12 +18,12 @@ source_urls = [ ] sources = [ 'qe-%(version)s-ReleasePack.tgz', - # to be uncommented once qe-gipaw-6.7 is released - # {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}, + {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)sMaX.tar.gz'}, {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, ] checksums = [ '8f06ea31ae52ad54e900a2f51afd5c70f78096d9dcf39c86c2b17dccb1ec9c87', # qe-6.7-ReleasePack.tgz + '95d2ed2f4d27f044dba171bdf8c1913a67ebc8846ed3463462828f2d414a2a61', # qe-gipaw-%(version)s.tar.gz '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz ] @@ -35,7 +35,7 @@ dependencies = [ # The third party packages should be installed separately and added as # dependencies. The exception is w90, which is force built -buildopts = 'all gwl xspectra couple epw w90' # gipaw +buildopts = "all gwl xspectra couple epw gipaw w90" # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2019b-Python-3.7.4.eb index ae575a11817..fd863b4268e 100644 --- a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = "qcat is a Python command-line tool for demultiplexing Oxford Nano toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['56f225321a48eef43e2b83a33cbbb47bf1b1edcd569f3db4d088a1bc0199e20a'] diff --git a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-intel-2019b-Python-3.7.4.eb index 178471d0b1f..79306a20120 100644 --- a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-intel-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = "qcat is a Python command-line tool for demultiplexing Oxford Nano toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['56f225321a48eef43e2b83a33cbbb47bf1b1edcd569f3db4d088a1bc0199e20a'] diff --git a/easybuild/easyconfigs/q/qpth/qpth-0.0.13-20190626-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/qpth/qpth-0.0.13-20190626-foss-2019a-Python-3.7.2.eb index ff8b2feef70..12b271e5bb1 100644 --- a/easybuild/easyconfigs/q/qpth/qpth-0.0.13-20190626-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/q/qpth/qpth-0.0.13-20190626-foss-2019a-Python-3.7.2.eb @@ -23,7 +23,6 @@ use_pip = True exts_list = [ ('block', '0.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/block'], 'checksums': ['8de2c9e37959f3851f1e7b7475ab797d1de4ec3e825352cdde0fcd01ec1c7c67'], }), (name, version, { diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..81525546aa6 --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'https://sourceforge.net/projects/qrupdate/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_makeconf.patch'] +checksums = [ + 'e2a1c711dc8ebc418e21195833814cb2f84b878b90a2774365f0166402308e08', # qrupdate-1.1.2.tar.gz + '4aa0e61a18bd14c76048f7b2f1f52875f7bac4bc3426ce9a37dfdb5b2b0d2379', # qrupdate-1.1.2_makeconf.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb index 2bb0ece82c1..79229f933da 100644 --- a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb @@ -19,6 +19,7 @@ dependencies = [ ('muParser', '2.3.2'), ('Rmath', '%(rver)s'), ('X11', '20201008'), + ('rgdal', '1.5-23', versionsuffix), ] default_easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index f4c74e7d9bf..42178857455 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2846,6 +2846,42 @@ exts_list = [ ('semPLS', '1.0-10', { 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 6b48ef208c5..d988cd20cce 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2856,6 +2856,42 @@ exts_list = [ ('semPLS', '1.0-10', { 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 4d3fed4c0ca..1f05e7f1af3 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -1728,7 +1728,7 @@ exts_list = [ 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], 'checksums': [ 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz - '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch ], }), ('diveRsity', '1.9.90', { @@ -2151,7 +2151,8 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], @@ -2881,6 +2882,42 @@ exts_list = [ ('semPLS', '1.0-10', { 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 8eac804505c..f56ea3e03bf 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2155,7 +2155,8 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], @@ -2886,6 +2887,42 @@ exts_list = [ ('semPLS', '1.0-10', { 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb new file mode 100644 index 00000000000..b6cddf6beef --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -0,0 +1,2932 @@ +## +# Author: Robert Mijakovic +## +name = 'R' +version = '4.0.5' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['0a3ee079aa772e131fe5435311ab627fcbccb5a50cabc54292e6f62046f1ffef'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.9'), +] +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('PCRE2', '10.35'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.5'), # for plottting in R + ('LibTIFF', '4.1.0'), + ('Java', '11', '', True), + ('Tk', '8.6.10'), # for tcltk + ('cURL', '7.72.0'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.0'), # for igraph + ('NLopt', '2.6.2'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '67.1'), # for rJava & gdsfmt + ('HDF5', '1.10.7'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.10-35'), # for animation + ('GLPK', '4.65'), # for Rglpk + ('nodejs', '12.19.0'), # for V8 (required by rstan) + ('GDAL', '3.2.1') # for sf + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 07 Apr 2021 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9.1', { + 'checksums': ['99e02a955935040bf0834d44d1dc10a3794c8260fd072d3aff3e15ab249e0ac9'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.6', { + 'checksums': ['c9f24756bc000f7a989bd4f9aa93d57f7739dcde77946703f8bb32332a35f012'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '4.0.4', { + 'checksums': ['22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5'], + }), + ('bnlearn', '4.6.1', { + 'checksums': ['e4544465af3330e53e4777079c448585a8a97be2d3862a5264169007c20daeaf'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.16', { + 'checksums': ['e7dea648ee018e2c8c8834084051c76f7e8b2b42067772c62035a941c32457a9'], + }), + ('formatR', '1.8', { + 'checksums': ['df7885827149e186b2b902fd01a18d1a514e50f9912f38c308949e2847f10613'], + }), + ('gtools', '3.8.2', { + 'checksums': ['503ba60a41f3c61b8129c25de62c74dab29761d2e661d4addd106e2e02f1dcde'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.1', { + 'checksums': ['e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917'], + }), + ('highr', '0.8', { + 'checksums': ['4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-16', { + 'checksums': ['c796c8b987ed1bd9dfddd593e17312ed681fc4fa3a1ecfe51da2def0ac1e50df'], + }), + ('kernlab', '0.9-29', { + 'checksums': ['c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f'], + }), + ('mime', '0.10', { + 'checksums': ['783233a15a817a7530d140e9825565a661aa4bdea7c635d11b9c74faa33be3f7'], + }), + ('xfun', '0.22', { + 'checksums': ['3e717b0eb8100f01c84e2d69c2618f9e54b801a44eef5a2ce4c030c123b8a347'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-3', { + 'checksums': ['b1f92be633243185ab86e880a1e1ac5a4dd3c535d01ebd187a4872d0a8c6f194'], + }), + ('NLP', 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('tensorA', '0.36.2', { + 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], + }), + ('EasyABC', '1.5', { + 'checksums': ['1dd7b1383a7c891cafb34d9cec65d92f1511a336cff1b219e63c0aa791371b9f'], + }), + ('whisker', '0.4', { + 'checksums': ['7a86595be4f1029ec5d7152472d11b16175737e2777134e296ae97341bf8fba8'], + }), + ('roxygen2', '7.1.1', { + 'checksums': ['bdc55ded037d4366f4d25a0d69e880dacc0fa22bee20f595d45855eef8548861'], + }), + ('git2r', '0.28.0', { + 'checksums': ['ce6d148d21d2c87757e98ef4474b2d09faded9b9b866f046bd26d4ca925e55f2'], + }), + ('rversions', '2.0.2', { + 'checksums': ['3523f4b7393365341d429500b01ba3a224056e89d134635b81dfb4918ba2173e'], + }), + ('xopen', '1.0.0', { + 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], + }), + ('sessioninfo', '1.1.1', { + 'checksums': ['166b04678448a7decd50f24afabe5e2ad613e3c55b180ef6e8dd7a870a1dae48'], + }), + ('rcmdcheck', '1.3.3', { + 'checksums': ['1ab679eb1976d74cd3be5bcad0af7fcc673dbdfd4406bbce32591c8fddfb93b4'], + }), + ('remotes', '2.3.0', { + 'checksums': ['677d676b60288196c4329fcd00747041f0221d241920e918bd1bf6b610316538'], + }), + ('clisymbols', '1.2.0', { + 'checksums': ['0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.1', { + 'checksums': ['b14aaf4e910a9d2d6c65c93e645f0b0159c00898e669f917f83c03dfedb1dfea'], + }), + ('gh', '1.2.1', { + 'checksums': ['00cfbf7a48a0587d651233dd661092fdc52f70ec592e6f98470e891c160eaa9b'], + }), + ('credentials', '1.3.0', { + 'checksums': ['c119ec26fd97b977c3b0cd1eb8fad3c59b84df6262c3adbf5ee9f3d6c9903ff1'], + }), + ('gert', '1.3.0', { + 'checksums': ['071229134517b47ef710fc5586a27458be308daef21cc8c2f603492ed21507ba'], + }), + ('usethis', '2.0.1', { + 'checksums': ['ef269e7a3190791bc77ff1d5cb11f20cb594adedb334805f88db5451f3ffd6c8'], + }), + ('rex', '1.2.0', { + 'checksums': ['06b491f1469078862e40543fd74e1d38b2e0fb61fdf01c8083add4b11ac2eb54'], + }), + ('covr', '3.5.1', { + 'checksums': ['a54cfc3623ea56084158ac5d7fe33f216f45191f6dcddab9c9ed4ec1d9d8ac6c'], + }), + ('devtools', '2.4.0', { + 'checksums': ['728e4f6556efc0af504a44e20cf5dd84819189ade3e0cd5ab075cf031aa19324'], + }), + ('Rook', '1.1-1', { + 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + }), + ('Cairo', '1.5-12.2', { + 'checksums': ['dd524105c83b82b5c3b3ee2583ef90d4cafa54b0c29817dac48b425b79f90f92'], + }), + ('RMTstat', '0.3', { + 'checksums': ['81eb4c5434d04cb66c749a434c33ceb1c07d92ba79765d4e9233c13a092ec2da'], + }), + ('Lmoments', '1.3-1', { + 'checksums': ['7c9d489a08f93fa5877e2f233ab9732e0d1b2761596b3f6ac91f2295e41a865d'], + }), + ('distillery', '1.2', { + 'checksums': ['1eb129b019b5fe9a4599c3e902ecc222c7aa3ff0602b45ee25495c086e82d082'], + }), + ('extRemes', '2.1', { + 'checksums': ['2d760b8d9db81fa70ac20735c10ef612908cea39cc779cc71b171afaebc8c9ac'], + }), + ('tkrplot', '0.0-25', { + 'checksums': ['21ae0e869e024838b9bf42a0c06d55672a2683453dc9218327409086a611ed5c'], + }), + ('misc3d', '0.9-0', { + 'checksums': ['a1e9291d625bd1312bae5b0e26d48b9362f66a8a0fabbf48891ba1d2432e4e82'], + }), + ('multicool', '0.1-11', { + 'checksums': ['1c907e64af2ac39facdf431a5691e69649f64af1f50e198ae39da5bf30026476'], + }), + ('plot3D', '1.3', { + 'checksums': ['b9e4ec2789e34ad249318900e186868650e1a33466b385cb492a45466db3dfc9'], + }), + ('plot3Drgl', '1.0.1', { + 'checksums': ['466d428d25c066c9c96d892f24da930513d42b1bdf76d3b53628c3ba13c3e48a'], + }), + ('OceanView', '1.0.5', { + 'checksums': ['c16e1bed97f4ede46dc017fdd6bd7575d925b57bd2601317bd3ad2357609f885'], + }), + ('ks', '1.12.0', { + 'checksums': ['e6affe52bbfe73e31387462c57dfe56058c5d64f54e5c7b7c794187c6936cee9'], + }), + ('logcondens', '2.1.5', { + 'checksums': ['72e61abc1f3eb28830266fbe5b0da0999eb5520586000a3024e7c26be93c02eb'], + }), + ('Iso', '0.0-18.1', { + 'checksums': ['2fa5f78a7603cbae94a5e38e791938596a053d48c609a7c120a19cbb7d93c66f'], + }), + ('penalized', '0.9-51', { + 'checksums': ['eaa80dca99981fb9eb576261f30046cfe492d014cc2bf286c447b03a92e299fd'], + }), + ('clusterRepro', '0.9', { + 'checksums': ['940d84529ff429b315cf4ad25700f93e1156ccacee7b6c38e4bdfbe2d4c6f868'], + }), + ('data.tree', '1.0.0', { + 'checksums': ['40674c90a5bd00f5185db9adbd221c6f1114043e69095249f5fa8b3044af3f5e'], + }), + ('influenceR', '0.1.0', { + 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], + }), + ('visNetwork', '2.0.9', { + 'checksums': ['5e0b3dc3a91e66e0a359433f03cc856d04b981b0f9ad228d8fa9c96b7fcaa420'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.6.1', { + 'checksums': ['be4e4c520a3692902ce405e8225aef9f3d5f0cd11fcde614f6541e981b63673d'], + }), + ('randomForestSRC', '2.11.0', { + 'checksums': ['6295fa43bb20bd5248e30a3239259185acfb4c2b6219be9c7a9306031a1c3744'], + }), + ('sm', '2.2-5.6', { + 'checksums': ['b890cd7ebe8ed711ab4a3792c204c4ecbe9e6ca1fd5bbc3925eba5833a839c30'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-8', { + 'checksums': ['40e204909100b7338619ae23cd87e0a4058e581c286da2327f36dbb3834b84a2'], + }), + ('matrixcalc', '1.0-3', { + 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], + }), + ('arm', '1.11-2', { + 'checksums': ['8385be32f6b6b6f1b32df15f42073b191d714d870bbb4f95875b64aff6112bbf'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('servr', '0.21', { + 'checksums': ['3fc0da063dd04b796a49ce62bf8e69d5854679520da90cc92ee3fc0a0b2ad389'], + }), + ('rgexf', '0.16.0', { + 'checksums': ['2a671df9ac70cfefd4092754317cb28e32a33df345b80e1975bf838e838245ee'], + }), + ('sem', '3.1-11', { + 'checksums': ['33b1ad7695db13af8cdd214f5d388db494528b433c61c7ad89970cefcc8b430e'], + }), + ('network', '1.16.1', { + 'checksums': ['eb6435794cacc81abe1664391e8dcf1c10112bbb76fff9016dd6dbb8e83efeb1'], + }), + ('rle', '0.9.2', { + 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], + }), + ('statnet.common', '4.4.1', { + 'checksums': ['4ecf2b84718d7fb60f196215b4cf6f52cd6b26cc9148a6da6981b26e885509fd'], + }), + ('sna', '2.6', { + 'checksums': ['3a016550d9f424a0613c3f5b0b680dbd3a1f20a343173d39a96034340ad9202a'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.4.1', { + 'checksums': ['78ef9eae464d52c5247998b9514a81b178419b857b1a6c00d885e3ae6c03a886'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('BDgraph', '2.63', { + 'checksums': ['cc474e1315a04f67fbf14461d35004c899d031c31f18be7d3db076dbf66a0617'], + }), + ('pbapply', '1.4-3', { + 'checksums': ['8fe6287535be766b5a688810e2cc1ca4e668ac6b42b6e832473fe5701133eb21'], + }), + ('graphlayouts', '0.7.1', { + 'checksums': ['380f8ccb0b08735694e83f661fd56a0d592a78448ae91b89c290ba8582d66717'], + }), + ('tweenr', '1.0.2', { + 'checksums': ['1805f575da6705ca4e5ec1c4605222fc826ba806d9ff9af41770294fe08ff69f'], + }), + ('ggforce', '0.3.3', { + 'checksums': ['2a283bb409da6b96929863a926b153bcc59b2c6f00551805db1d1d43e5929f2f'], + }), + ('tidygraph', '1.2.0', { + 'checksums': ['057d6c42fc0144109f3ace7f5058cca7b2fe493c761daa991448b23f86b6129f'], + }), + ('ggraph', '2.0.5', { + 'checksums': ['e36ad49dba92ee8652e18b1fb197be0ceb9f0a2f8faee2194453a62578449654'], + }), + ('qgraph', '1.6.9', { + 'checksums': ['b125a9c1b505632da8b404811c8d6d667736f229d95994ca7913beacabc36b94'], + }), + ('HWxtest', '1.1.9', { + 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], + 'checksums': [ + 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + ], + }), + ('diveRsity', '1.9.90', { + 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], + }), + ('doSNOW', '1.0.19', { + 'checksums': ['4cd2d080628482f4c6ecab593313d7e42516f5ff13fbf9f90e461fcad0580738'], + }), + ('geepack', '1.3-2', { + 'checksums': ['99b53e40f7e5fda7422b143e6fee16513e2f880cb04a97cd403e98c4760670a6'], + }), + ('biom', '0.3.12', { + 'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'], + }), + ('pim', '2.0.2', { + 'checksums': ['1195dbdbd67348dfef4b6fc34fcec643da685ebe58d34bbe049ab121aca9944f'], + }), + ('minpack.lm', '1.2-1', { + 'checksums': ['14cb7dba3ef2b46da0479b46d46c76198e129a31f6157cd8b37f178adb15d5a3'], + }), + ('rootSolve', '1.8.2.1', { + 'checksums': ['488451182663197ae4513e46e24f72cadb2297d35a58a3007a0dbf1bf0833031'], + }), + ('diagram', '1.6.5', { + 'checksums': ['e9c03e7712e0282c5d9f2b760bafe2aac9e99a9723578d9e6369d60301f574e4'], + }), + ('FME', '1.3.6.1', { + 'checksums': ['ae0c69f75614e2ef9f2096c205c7f8eb90485c6311213762c1416ece4036be18'], + }), + ('bmp', '0.3', { + 'checksums': ['bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649'], + }), + ('tiff', '0.1-8', { + 'checksums': ['4b7482f70d8ecef9596b766ef1c64102c8b09208cb769c39d9e4db81cb3ba1a2'], + }), + ('readbitmap', '0.1.5', { + 'checksums': ['737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291'], + }), + ('imager', '0.42.8', { + 'checksums': ['8515ed79a03d15a4b68e7d39d02d3cb222615bc78bf9b5902824a669e848f4cf'], + }), + ('signal', '0.7-6', { + 'checksums': ['6b60277b07cf0167f8272059b128cc82f27a9bab1fd33d74c2a9e1f2abca5def'], + }), + ('tuneR', '1.3.3', { + 'checksums': ['bdc3c2017b162d2ba0a249e80361a4f47202e763c21aecfc57380a482a3a692b'], + }), + ('pastecs', '1.3.21', { + 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], + }), + ('audio', '0.1-7', { + 'checksums': ['52e0397a45325aa9586ec68b94ab9e505bdefaf2a588d634fcb57a6a11659c74'], + }), + ('fftw', '1.0-6', { + 'checksums': ['397ef5ec354b919884f74fba4202bfc13ad11a70b16285c41677aad1d3b170ce'], + }), + ('seewave', '2.1.6', { + 'checksums': ['84a0a0035737574a65f371fa4a20a1a3a66de195efe41975f21be8fb001e7088'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('sf', '0.9-8', { + 'checksums': ['11570a6578701faef0b2a481f6722e8f4e7750eac958c4c7aec65abfa078cf24'], + }), + ('oce', '1.4-0', { + 'checksums': ['3b341448001164dc62b54a26c8f86adf50e68705ddc47615b290b950da734408'], + }), + ('ineq', '0.2-13', { + 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], + }), + ('soundecology', '1.3.3', { + 'checksums': 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['f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c'], + }), + ('energy', '1.7-8', { + 'checksums': ['de08e8de037bb30068bbf0c1880b153a586d342304681f4ba103ab808c7f4789'], + }), + ('compositions', '2.0-1', { + 'checksums': ['84a291308faf858e5a9d9570135c2da5e57b0887f407903485fa85d09da61a0f'], + }), + ('clustree', '0.4.3', { + 'checksums': ['5ff3afc3fb3e1d20d033328935084de574250d29545c0a5b69180fe4846fbe53'], + }), + ('plotly', '4.9.3', { + 'checksums': ['d44d1a16d96de28bc2d36f1c897384215eeec44d109546c6e9c2707db0880120'], + }), + ('tweedie', '2.3.3', { + 'checksums': ['a032cad512dac37a8619e6f66cb513eb82a88a5a2ffbe91e92c2d44d1756d0d9'], + }), + ('RcppGSL', '0.3.8', { + 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], + }), + ('mvabund', '4.1.9', { + 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.2.3', { + 'checksums': ['154bf7e65452186841036a2a7f2af89664965a63040ff0bee33f8b3fab8c0e4b'], + }), + ('grpreg', '3.3.1', { + 'checksums': ['f07e202d9da45fe7cb82dd1c6a760c04cc83b4e32aeae2bb40b979fab95305a5'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('ergm', '3.11.0', { + 'checksums': ['4e5506b44badc2343be3657acbf2bca51b47d7c187ff499d5a5e70a9811fe9f2'], + }), + ('networkDynamic', '0.10.1', { + 'checksums': ['22eed8d9dea8d70877c1619eb2bc3f1ac5142ce3db6fd6eb3e0879ca56b76ca0'], + }), + ('tergm', '3.7.0', { + 'checksums': ['afd2b160bda691127f8fc57c4caff61f688cc03e71e622f8e833b2a26dc635df'], + }), + ('ergm.count', '3.4.0', { + 'checksums': ['7c24c79d0901c18991cce907306a1531cca676ae277c6b0a0e4962ad27c36baf'], + }), + ('tsna', '0.3.1', { + 'checksums': ['bba4b5e04ba647784581a2137f653f60b4c83cfd726c399556054c5a6d2cbd95'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.5-0', { + 'checksums': ['795ffd3d62bf14d3ecb3f5307bd329cd75798cf4b270ff0e768bc71a35de0ace'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.15', { + 'checksums': ['73d20ff1abd752a9d8267eea9d97be58818554ffe072923810db576c449ecbc2'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.32.0.1', { + 'checksums': ['86161b81e4aecf0243b17cabcd1f887cf4b9104918d91c804810be603d50ab66'], + }), + ('mlegp', '3.1.8', { + 'checksums': ['eac1df085a608451828575028ca05b78dc6b5035da14cabc141bfee5ef986de9'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.6', { + 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.1', { + 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.2.0', { + 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), + ('cobs', '1.3-4', { + 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.5', { + 'checksums': ['9c41ca817104ab076bfd62cccac7d024658ebf4a11dcd91654f0588868aa8d74'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.7-3.1', { + 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0-1', { + 'checksums': ['9fc1f7432a40d8911393701ca33e2ad64356c3bd12128f01dd216399b16e3d93'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.17', { + 'checksums': ['792857b2ebd408d6523424d2f6bb7297e241d4b28ab32372f6a9240c8cd554f3'], + }), + ('BMA', '3.18.14', { + 'checksums': ['3bc0fd44001c5817dc6a8eda9fb266967407f8a05ac0a5c05b10c87df462cb23'], + }), + ('BCEE', '1.3.0', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-58', { + 'checksums': ['2ab6662eaa1103a7b633477e8ebd266b262ed54fac6f9326b160067a2ded9ce7'], + }), + ('bdsmatrix', '1.3-4', { + 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.19.3', { + 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.4', { + 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.9', { + 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '3.0', { + 'checksums': ['ada4e1f8cbb08ba8ff16275ec5f9a453857e0cab63b70d42753989ab4c716b7b'], + }), + ('bbmle', '1.0.23.1', { + 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('terra', '1.1-4', { + 'checksums': ['6f6929d6bc7757281c7e314b43875d79b5bcfd1174d62d3462509b82752950ef'], + }), + ('rasterVis', '0.50.1', { + 'checksums': ['fc40c2a375f3f133d95ca88f53e014ae7b1e5236c8bdca841cb3dae629f575ba'], + }), + ('tictoc', '1.0', { + 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], + }), + ('ISOcodes', '2021.02.24', { + 'checksums': ['152769bcb4ae99d06a767384541c2000c94990a2c6983780837f85e885b539a6'], + }), + ('stopwords', '2.2', { + 'checksums': ['b66bccc786200c6ec600be8340e2801bbc7ee787fa5c5a15bc201306861706b9'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0.1', { + 'checksums': ['1fedbb913bc13c790d2fabfe4edda0a987db3a078bea8c0ca9b777d20af08662'], + }), + ('topicmodels', '0.2-12', { + 'checksums': ['afd83a4381bf39e470446ebefd41ed03f314be400c1b2f702a4b1060eb8fd1b4'], + }), + ('tidytext', '0.3.0', { + 'checksums': ['7d36be1e504f751c33dc2239751a600bd4ff05af24a0b9cdd549aff909778bc5'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.2.1', { + 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-11', { + 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.4.1', { + 'checksums': ['bc21fb6b4a93a7e95ee1be57e4e787d731895fb8b4743c26b30b43adee475b50'], + }), + ('RcppParallel', '5.0.3', { + 'checksums': ['71121138f25fcc97885b14545b7e7eb92e5f3953aec15e7df3822ae26d8e0c46'], + }), + ('StanHeaders', '2.21.0-7', { + 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], + }), + ('V8', '3.4.0', { + 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + }), + ('rstan', '2.21.2', { + 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.0', { + 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.1', { + 'checksums': ['506e684071332dac62005c709833d419f4944a85478e2f4395f218ac314f5e66'], + }), + ('corrplot', '0.84', { + 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], + }), + ('rstatix', '0.7.0', { + 'checksums': ['a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.4.0', { + 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.1.1', { + 'checksums': ['cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481'], + }), + ('leiden', '0.3.7', { + 'checksums': ['770994d2d763c195b53e3e09a987188cbf844fbb3bca2d175e46798663b13892'], + }), + ('future.apply', '1.7.0', { + 'checksums': ['2ffa6adb55f239918ce9679b7eac8dcc4bf2e6bed35c9cbedf4bf90d906345db'], + }), + ('sctransform', '0.3.2', { + 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], + }), + ('packrat', '0.6.0', { + 'checksums': ['d99d3474baa264cd255a2e60623a1c2a7b30809d352208015c88d992dc169605'], + }), + ('shinyjs', '2.0.0', { + 'checksums': ['c2cdd9fab41f6b46bb41b288cd9b3fb3a7fe9627b664e3a58a0cb5dd4c19f8ff'], + }), + ('colourpicker', '1.1.0', { + 'checksums': ['2dfbb6262d187d3b17357ff9c22670ced3621feda5b2a2a500558478e4d551e2'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), + ('findpython', '1.0.7', { + 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], + }), + ('argparse', '2.0.3', { + 'checksums': ['d26139c610ea0adf8d6632699cd34c4595ae3e7963bfc7a00cb3b7504f2059b0'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), + ('qqman', '0.1.4', { + 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'], + }), + ('rstantools', '2.1.1', { + 'checksums': ['c95b15de8ec577eeb24bb5206e7b685d882f88b5e6902efda924b7217f463d2d'], + }), + ('bayesplot', '1.8.0', { + 'checksums': ['a605f9929e681593a3ef3ca9c836e713314994aaea00f359f71cfc42d151c948'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('rsconnect', '0.8.16', { + 'checksums': ['3f728c6a5153dca28f69b9355ae9d18c5f7e70d12495c0c047eef673c1053116'], + }), + ('shinystan', '2.5.0', { + 'checksums': ['45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1'], + }), + ('optimx', '2020-4.2', { + 'checksums': ['6381c25c322287fc98ab1b2965d3f68c9a92c587c76aca1d33fd6428b2167101'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('projpred', '2.0.2', { + 'checksums': ['af0a9fb53f706090fe81b6381b27b0b6bd3f7ae1e1e44b0ada6f40972b09a55b'], + }), + ('brms', '2.15.0', { + 'checksums': ['c11701d1d8758590b74bb845b568b736e4455a81b114c7dfde0b27b7bd1bcc2f'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.0', { + 'checksums': ['b423df43e9c4bb8ffafe2de88b93fdcf3a90f964f136580ea1b849a83dba7400'], + }), + ('mcmcse', '1.4-1', { + 'checksums': ['6b181f56d60ddf55c9c08a2468ef9ffe3ec8a1b16cfa9a7742c3872597f85d17'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.6.2', { + 'checksums': ['4264f28e37855188675f6b08530752606dba3d761b36c1e7cca96a75f8208390'], + }), + ('drugCombo', '1.1.1', { + 'checksums': ['9fdc3a7cf63552c32f1c7573258fc4ceacdaf5c475fe79aa4ca8c9226b9f8a38'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.0.1', { + 'checksums': ['a3bb9bdc7a4a79ea38482df3f8cbb6e9082332a0d894eeb4b3dc816344cec0e4'], + }), + ('maxlike', '0.1-8', { + 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + }), + ('coxme', '2.2-16', { + 'checksums': ['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.2', { + 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'], + }), + ('ENMeval', '0.3.1', { + 'checksums': ['e7f20c1b4d7ede82a3aca86e3ce3fc4ae46337f812dfc171b499c2558b0183d0'], + }), + ('plotmo', '3.6.0', { + 'checksums': ['c05afcc442f9542868beea5c3c40fb93b049f9b61c42725b2a1e2bc750c241e3'], + }), + ('earth', '5.3.0', { + 'checksums': ['05ace806271a74b3ddf8718a93237fe2a8550a8659ebd87f8079c0bda5e02437'], + }), + ('mda', '0.5-2', { + 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], + }), + ('biomod2', '3.4.6', { + 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'], + }), + ('poLCA', '1.4.1', { + 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], + }), + ('PermAlgo', '1.1', { + 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.12', { + 'checksums': ['9acdf912f0e7a68a5b6a7946d5ebb0c2007b3d6cd2e39075eddae2b586354e89'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.3', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-1', { + 'checksums': ['e8abadc5614f132edc3fb9cb1c82ce4dacc1315b727fbd49db7399aee24115ba'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-19', { + 'checksums': ['6c7eed2d238ab4d8ebcd624e05a68849fa57bf2929b893bcd1a0990b5fcc304d'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.4.0', { + 'checksums': ['49459e76412037b3d8021bd83ee93d140bc3e715a2a2282a347ef60061900514'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-8', { + 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], + }), + ('gWidgets2tcltk', '1.0-6', { + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.2', { + 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], + }), + ('ie2misc', '0.8.6', { + 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '2.1', { + 'checksums': ['088d291339a4d8d9396cdb956889ac571fd9e834c6e3c3d51621a8c3f0eb9f32'], + }), + ('lmom', '2.8', { + 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], + }), + ('gld', '2.6.2', { + 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], + }), + ('DescTools', '0.99.40', { + 'checksums': ['53954f0477eac77328efac562716c8b078e76b5ad5edf0227ba2624aa2b8c7dd'], + }), + ('orthopolynom', '1.0-5', { + 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], + }), + ('gaussquad', '1.0-2', { + 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], + }), + ('nlsem', '0.8', { + 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.0', { + 'checksums': ['b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1'], + }), + ('tableone', '0.12.0', { + 'checksums': ['6a5cc16f7d2303c8f42b8adcad0fc41e1ba74f24ada4e7ad3a16effb63d3575e'], + }), + ('jstable', '1.0.2', { + 'checksums': ['0d7ffa8ecd1b2df05cf1256406152d211eabfa660bf1cc13bada1d75dfdd6d13'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.2', { + 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], + }), + ('sensemakr', '0.1.3', { + 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-5', { + 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], + }), + ('blavaan', '0.3-15', { + 'checksums': ['f73ead024bc3b65bdb0c5e5cd5458845158914eb579c07be2fd697a3573ebe6f'], + }), + ('metafor', '2.4-0', { + 'checksums': ['b64a678b762e91f1e0a6360b15e79fe19159b243c9f40ad9cc0be833bb4ba9ac'], + }), + ('fmri', '1.9.6', { + 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], + }), + ('AnalyzeFMRI', '1.1-23', { + 'checksums': ['4237ca4ffe812e614349cdffa2668de4eda5697d73ea208df0c60808daa29444'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.4', { + 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], + }), + ('DEoptim', '2.2-5', { + 'checksums': ['ae12dedcd4a43994e811e7285f8c12bfdb688e7c99d65515cf7e8cb6db13955a'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2013.9-1', { + 'checksums': ['1a1a399682a06a5fea3934985ebb1334005676c6a2a22d06f3c91c3923432908'], + }), + ('Rvmmin', '2018-4.17', { + 'checksums': ['d53ba7ab06596a47990caf101a50935b2b34402f9dd8414f098a873026ff1f56'], + }), + ('Rcgmin', '2013-2.21', { + 'checksums': ['a824a09c32d7565a3e30607c71333506d5b7197478fbe8b43f8a77dad6c12f0a'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '1.3.0', { + 'patches': ['DMCfun-1.3.0_fix-parallel-detect.patch'], + 'checksums': [ + '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz + # DMCfun-1.3.0_fix-parallel-detect.patch + '67259a76722717f29577d7a25c822a4fb9c1b5ce45699d02aa53ab0ffa1d0b2a', + ], + }), + ('miceadds', '3.11-6', { + 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], + }), + ('visdat', '0.5.3', { + 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('naniar', '0.6.0', { + 'checksums': ['9c93c64f51dd8c3002c930c276ef57651e91c8db12f885a03113753c604e7e54'], + }), + ('stringdist', '0.9.6.3', { + 'checksums': ['cd6d98f982e9ae7c4154a040c3a3f959bce19abf0229d64d22efef41f85b3f1b'], + }), + ('image.binarization', '0.1.1', { + 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], + }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), + ('lslx', '0.6.10', { + 'checksums': ['adc2b2a621625b52165245ab2f3a0bfba4f4db64fcc6ad48a3e5b219c3bd2fa1'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.6.2', { + 'checksums': ['b65201c730e10b0a80d1dd788e0c370372a1f22f314f2e49ce4dc63cb3ffd992'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb new file mode 100644 index 00000000000..ad61d8b44d6 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -0,0 +1,2950 @@ +## +# Author: Robert Mijakovic +## +name = 'R' +version = '4.0.5' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['0a3ee079aa772e131fe5435311ab627fcbccb5a50cabc54292e6f62046f1ffef'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.9'), +] +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('PCRE2', '10.35'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.5'), # for plottting in R + ('LibTIFF', '4.1.0'), + ('Java', '11', '', True), + ('Tk', '8.6.10'), # for tcltk + ('cURL', '7.72.0'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.0'), # for igraph + ('NLopt', '2.6.2'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '67.1'), # for rJava & gdsfmt + ('HDF5', '1.10.7'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.10-35'), # for animation + ('GLPK', '4.65'), # for Rglpk + ('nodejs', '12.19.0'), # for V8 (required by rstan) + ('GDAL', '3.2.1'), # for sf + ('pocl', '1.6'), # for OpenCL support (particularly on POWER) + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +# replace hardcoded CUDA compute capabilitites in liquidSVM +local_cuda_cc = [c.replace('.', '') for c in cuda_compute_capabilities] +local_cuda_arch = "-arch sm_%s" % local_cuda_cc[0] +local_cuda_gencode = ' '.join(['-gencode=arch=compute_%s,code=sm_%s' % (c, c) for c in local_cuda_cc]) +local_liquidSVM_sed = "sed -i 's/-arch sm_30/%s %s/' src/Makevars.in" % (local_cuda_arch, local_cuda_gencode) + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 07 Apr 2021 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9.1', { + 'checksums': ['99e02a955935040bf0834d44d1dc10a3794c8260fd072d3aff3e15ab249e0ac9'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.6', { + 'checksums': ['c9f24756bc000f7a989bd4f9aa93d57f7739dcde77946703f8bb32332a35f012'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '4.0.4', { + 'checksums': ['22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5'], + }), + ('bnlearn', '4.6.1', { + 'checksums': ['e4544465af3330e53e4777079c448585a8a97be2d3862a5264169007c20daeaf'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.16', { + 'checksums': ['e7dea648ee018e2c8c8834084051c76f7e8b2b42067772c62035a941c32457a9'], + }), + ('formatR', '1.8', { + 'checksums': ['df7885827149e186b2b902fd01a18d1a514e50f9912f38c308949e2847f10613'], + }), + ('gtools', '3.8.2', { + 'checksums': ['503ba60a41f3c61b8129c25de62c74dab29761d2e661d4addd106e2e02f1dcde'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.1', { + 'checksums': ['e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917'], + }), + ('highr', '0.8', { + 'checksums': ['4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-16', { + 'checksums': ['c796c8b987ed1bd9dfddd593e17312ed681fc4fa3a1ecfe51da2def0ac1e50df'], + }), + ('kernlab', '0.9-29', { + 'checksums': ['c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f'], + }), + ('mime', '0.10', { + 'checksums': ['783233a15a817a7530d140e9825565a661aa4bdea7c635d11b9c74faa33be3f7'], + }), + ('xfun', '0.22', { + 'checksums': ['3e717b0eb8100f01c84e2d69c2618f9e54b801a44eef5a2ce4c030c123b8a347'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-3', { + 'checksums': ['b1f92be633243185ab86e880a1e1ac5a4dd3c535d01ebd187a4872d0a8c6f194'], + }), + ('NLP', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '5.4.7', { + 'checksums': ['45f5a666caee5bebd3160922b8655295a25e37f624741f6574365e4ac5a14c23'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('segmented', '1.3-3', { + 'checksums': ['1e1cc37ca6ac1bfa10daa1f057a1f97a7e54f6d398308efcc7f8e0062e350398'], + }), + ('som', '0.3-5.1', { + 'checksums': ['a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9'], + }), + ('SuppDists', '1.1-9.5', { + 'checksums': ['680b67145c07d44e200275e08e48602fe19cd99fb106c05422b3f4a244c071c4'], + }), + ('stabledist', '0.7-1', { + 'checksums': ['06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69'], + }), + ('survivalROC', '1.0.3', { + 'checksums': ['1449e7038e048e6ad4d3f7767983c0873c9c7a7637ffa03a4cc7f0e25c31cd72'], + }), + ('pspline', '1.0-18', { + 'checksums': ['f71cf293bd5462e510ac5ad16c4a96eda18891a0bfa6447dd881c65845e19ac7'], + }), + ('timeDate', '3043.102', { + 'checksums': ['377cba03cddab8c6992e31d0683c1db3a73afa9834eee3e95b3b0723f02d7473'], + }), + ('longmemo', '1.1-2', { + 'checksums': ['7964e982287427dd58f98e1144e468ae0cbd572d25a4bea6ca9ae9c7522f3207'], + }), + ('ADGofTest', '0.3', { + 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], + }), + ('MASS', '7.3-53.1', { + 'checksums': ['e45b1eb97ee32db9a3a211ce42b972094827d93ef2f48bda653c121f08314465'], + }), + ('pixmap', '0.4-12', { + 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], + }), + ('lattice', '0.20-41', { + 'checksums': ['54ca557f0cb33df60eb10b883c2ed2847e061ddd57ed9b5dd7695149609d57b5'], + }), + ('sp', '1.4-5', { + 'checksums': ['6beeb216d540475cdead5f2c72d6c7ee400fe2423c1882d72cf57f6df58f09da'], 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+ ('rex', '1.2.0', { + 'checksums': ['06b491f1469078862e40543fd74e1d38b2e0fb61fdf01c8083add4b11ac2eb54'], + }), + ('covr', '3.5.1', { + 'checksums': ['a54cfc3623ea56084158ac5d7fe33f216f45191f6dcddab9c9ed4ec1d9d8ac6c'], + }), + ('devtools', '2.4.0', { + 'checksums': ['728e4f6556efc0af504a44e20cf5dd84819189ade3e0cd5ab075cf031aa19324'], + }), + ('Rook', '1.1-1', { + 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + }), + ('Cairo', '1.5-12.2', { + 'checksums': ['dd524105c83b82b5c3b3ee2583ef90d4cafa54b0c29817dac48b425b79f90f92'], + }), + ('RMTstat', '0.3', { + 'checksums': ['81eb4c5434d04cb66c749a434c33ceb1c07d92ba79765d4e9233c13a092ec2da'], + }), + ('Lmoments', '1.3-1', { + 'checksums': ['7c9d489a08f93fa5877e2f233ab9732e0d1b2761596b3f6ac91f2295e41a865d'], + }), + ('distillery', '1.2', { + 'checksums': ['1eb129b019b5fe9a4599c3e902ecc222c7aa3ff0602b45ee25495c086e82d082'], + }), + ('extRemes', '2.1', { + 'checksums': ['2d760b8d9db81fa70ac20735c10ef612908cea39cc779cc71b171afaebc8c9ac'], + }), + ('tkrplot', '0.0-25', { + 'checksums': ['21ae0e869e024838b9bf42a0c06d55672a2683453dc9218327409086a611ed5c'], + }), + ('misc3d', '0.9-0', { + 'checksums': ['a1e9291d625bd1312bae5b0e26d48b9362f66a8a0fabbf48891ba1d2432e4e82'], + }), + ('multicool', '0.1-11', { + 'checksums': ['1c907e64af2ac39facdf431a5691e69649f64af1f50e198ae39da5bf30026476'], + }), + ('plot3D', '1.3', { + 'checksums': ['b9e4ec2789e34ad249318900e186868650e1a33466b385cb492a45466db3dfc9'], + }), + ('plot3Drgl', '1.0.1', { + 'checksums': ['466d428d25c066c9c96d892f24da930513d42b1bdf76d3b53628c3ba13c3e48a'], + }), + ('OceanView', '1.0.5', { + 'checksums': ['c16e1bed97f4ede46dc017fdd6bd7575d925b57bd2601317bd3ad2357609f885'], + }), + ('ks', '1.12.0', { + 'checksums': ['e6affe52bbfe73e31387462c57dfe56058c5d64f54e5c7b7c794187c6936cee9'], + }), + ('logcondens', '2.1.5', { + 'checksums': ['72e61abc1f3eb28830266fbe5b0da0999eb5520586000a3024e7c26be93c02eb'], + }), + ('Iso', '0.0-18.1', { + 'checksums': ['2fa5f78a7603cbae94a5e38e791938596a053d48c609a7c120a19cbb7d93c66f'], + }), + ('penalized', '0.9-51', { + 'checksums': ['eaa80dca99981fb9eb576261f30046cfe492d014cc2bf286c447b03a92e299fd'], + }), + ('clusterRepro', '0.9', { + 'checksums': ['940d84529ff429b315cf4ad25700f93e1156ccacee7b6c38e4bdfbe2d4c6f868'], + }), + ('data.tree', '1.0.0', { + 'checksums': ['40674c90a5bd00f5185db9adbd221c6f1114043e69095249f5fa8b3044af3f5e'], + }), + ('influenceR', '0.1.0', { + 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], + }), + ('visNetwork', '2.0.9', { + 'checksums': ['5e0b3dc3a91e66e0a359433f03cc856d04b981b0f9ad228d8fa9c96b7fcaa420'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.6.1', { + 'checksums': ['be4e4c520a3692902ce405e8225aef9f3d5f0cd11fcde614f6541e981b63673d'], + }), + ('randomForestSRC', '2.11.0', { + 'checksums': ['6295fa43bb20bd5248e30a3239259185acfb4c2b6219be9c7a9306031a1c3744'], + }), + ('sm', '2.2-5.6', { + 'checksums': ['b890cd7ebe8ed711ab4a3792c204c4ecbe9e6ca1fd5bbc3925eba5833a839c30'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-8', { + 'checksums': ['40e204909100b7338619ae23cd87e0a4058e581c286da2327f36dbb3834b84a2'], + }), + ('matrixcalc', '1.0-3', { + 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], + }), + ('arm', '1.11-2', { + 'checksums': ['8385be32f6b6b6f1b32df15f42073b191d714d870bbb4f95875b64aff6112bbf'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('servr', '0.21', { + 'checksums': ['3fc0da063dd04b796a49ce62bf8e69d5854679520da90cc92ee3fc0a0b2ad389'], + }), + ('rgexf', '0.16.0', { + 'checksums': ['2a671df9ac70cfefd4092754317cb28e32a33df345b80e1975bf838e838245ee'], + }), + ('sem', '3.1-11', { + 'checksums': ['33b1ad7695db13af8cdd214f5d388db494528b433c61c7ad89970cefcc8b430e'], + }), + ('network', '1.16.1', { + 'checksums': ['eb6435794cacc81abe1664391e8dcf1c10112bbb76fff9016dd6dbb8e83efeb1'], + }), + ('rle', '0.9.2', { + 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], + }), + ('statnet.common', '4.4.1', { + 'checksums': ['4ecf2b84718d7fb60f196215b4cf6f52cd6b26cc9148a6da6981b26e885509fd'], + }), + ('sna', '2.6', { + 'checksums': ['3a016550d9f424a0613c3f5b0b680dbd3a1f20a343173d39a96034340ad9202a'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.4.1', { + 'checksums': ['78ef9eae464d52c5247998b9514a81b178419b857b1a6c00d885e3ae6c03a886'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('BDgraph', '2.63', { + 'checksums': ['cc474e1315a04f67fbf14461d35004c899d031c31f18be7d3db076dbf66a0617'], + }), + ('pbapply', '1.4-3', { + 'checksums': ['8fe6287535be766b5a688810e2cc1ca4e668ac6b42b6e832473fe5701133eb21'], + }), + ('graphlayouts', '0.7.1', { + 'checksums': ['380f8ccb0b08735694e83f661fd56a0d592a78448ae91b89c290ba8582d66717'], + }), + ('tweenr', '1.0.2', { + 'checksums': ['1805f575da6705ca4e5ec1c4605222fc826ba806d9ff9af41770294fe08ff69f'], + }), + ('ggforce', '0.3.3', { + 'checksums': ['2a283bb409da6b96929863a926b153bcc59b2c6f00551805db1d1d43e5929f2f'], + }), + ('tidygraph', '1.2.0', { + 'checksums': ['057d6c42fc0144109f3ace7f5058cca7b2fe493c761daa991448b23f86b6129f'], + }), + ('ggraph', '2.0.5', { + 'checksums': ['e36ad49dba92ee8652e18b1fb197be0ceb9f0a2f8faee2194453a62578449654'], + }), + ('qgraph', '1.6.9', { + 'checksums': ['b125a9c1b505632da8b404811c8d6d667736f229d95994ca7913beacabc36b94'], + }), + ('HWxtest', '1.1.9', { + 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], + 'checksums': [ + 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + ], + }), + ('diveRsity', '1.9.90', { + 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], + }), + ('doSNOW', '1.0.19', { + 'checksums': ['4cd2d080628482f4c6ecab593313d7e42516f5ff13fbf9f90e461fcad0580738'], + }), + ('geepack', '1.3-2', { + 'checksums': ['99b53e40f7e5fda7422b143e6fee16513e2f880cb04a97cd403e98c4760670a6'], + }), + ('biom', '0.3.12', { + 'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'], + }), + ('pim', '2.0.2', { + 'checksums': ['1195dbdbd67348dfef4b6fc34fcec643da685ebe58d34bbe049ab121aca9944f'], + }), + ('minpack.lm', '1.2-1', { + 'checksums': ['14cb7dba3ef2b46da0479b46d46c76198e129a31f6157cd8b37f178adb15d5a3'], + }), + ('rootSolve', '1.8.2.1', { + 'checksums': 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('pastecs', '1.3.21', { + 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], + }), + ('audio', '0.1-7', { + 'checksums': ['52e0397a45325aa9586ec68b94ab9e505bdefaf2a588d634fcb57a6a11659c74'], + }), + ('fftw', '1.0-6', { + 'checksums': ['397ef5ec354b919884f74fba4202bfc13ad11a70b16285c41677aad1d3b170ce'], + }), + ('seewave', '2.1.6', { + 'checksums': ['84a0a0035737574a65f371fa4a20a1a3a66de195efe41975f21be8fb001e7088'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('sf', '0.9-8', { + 'checksums': ['11570a6578701faef0b2a481f6722e8f4e7750eac958c4c7aec65abfa078cf24'], + }), + ('oce', '1.4-0', { + 'checksums': ['3b341448001164dc62b54a26c8f86adf50e68705ddc47615b290b950da734408'], + }), + ('ineq', '0.2-13', { + 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], + }), + ('soundecology', '1.3.3', { + 'checksums': 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('ranger', '0.12.1', { + 'checksums': ['fc308e0ac06718272799928e1a19612de16b05bde481d8f38e11a101df5425ef'], + }), + ('hexbin', '1.28.2', { + 'checksums': ['6241f8d3a6c6be2c1c693c3ddb99554bc103e3c6cf602d0c2787c0ce6fd1702d'], + }), + ('pryr', '0.1.4', { + 'checksums': ['d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b'], + }), + ('moments', '0.14', { + 'checksums': ['2a3b81e60dafdd092d2bdd3513d7038855ca7d113dc71df1229f7518382a3e39'], + }), + ('laeken', '0.5.1', { + 'checksums': ['1aa94a1768969eb999f7a41212af2d8b2943b43a68a92f99c9f77929e19439a5'], + }), + ('VIM', '6.1.0', { + 'checksums': ['1f9eb2ad9b18b7a0435e6074d031b7b5bc7143ff4251514ba20a38a53de00aa9'], + }), + ('smoother', '1.1', { + 'checksums': ['91b55b82f805cfa1deedacc0a4e844a2132aa59df593f3b05676954cf70a195b'], + }), + ('dynamicTreeCut', '1.63-1', { + 'checksums': ['831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9'], + }), + ('beeswarm', '0.3.1', { + 'checksums': ['525e61e71206feab28885d90a0311a09a2ebc66a730016d984e770eeaf7f4fcb'], + }), + ('vipor', '0.4.5', { + 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], + }), + ('ggbeeswarm', '0.6.0', { + 'checksums': ['bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333'], + }), + ('shinydashboard', '0.7.1', { + 'checksums': ['51a49945c6b8a684111a2ba4b2a5964e3a50610286ce0378e37ae02316620a4e'], + }), + ('rrcov', '1.5-5', { + 'checksums': ['1f7f07558e347e7d1f1adff68631764670bc672777a7d990901c4fa94cc0e629'], + }), + ('WriteXLS', '6.3.0', { + 'checksums': ['0b1d987abe4b08f6a32003b77d1cfc2eefdc5a478382e77ca0da98bccf6e526b'], + }), + ('bst', '0.3-23', { + 'checksums': ['70957f1db8800bf0d628a9e6f72b7273329786dd119427790b326844591aa0f3'], + }), + ('pamr', '1.56.1', { + 'checksums': ['d0e527f2336ee4beee91eefb2a8f0dfa96413d9b5a5841d6fc7ff821e67c9779'], + }), + ('WeightSVM', '1.7-5', { + 'checksums': ['dd895fe3a400897cea18d9de3e406e040efca9f84495739757b52570c98f820a'], + }), + ('mpath', '0.4-2.19', { + 'checksums': ['fa0d92984910b8f556677850e3d899bc675724f0e2a3a73629d2700040335afe'], + }), + ('timereg', '1.9.8', { + 'checksums': ['00b200764743e7074d1697ddbe8534ca7599e26ef20c34020fa1f6a29fa6bb18'], + }), + ('peperr', '1.3', { + 'checksums': ['64d30b0ec09bf9b8f7b6edce67dd0f9e0e3dbe665fec8f5411f74142e53e9f5d'], + }), + ('heatmap3', '1.1.9', { + 'checksums': ['594c33947b2be2cc8a592075f41a0df2398c892add7d63a15c613a5eeb8fdb69'], + }), + ('GlobalOptions', '0.1.2', { + 'checksums': ['47890699668cfa9900a829c51f8a32e02a7a7764ad07cfac972aad66f839753e'], + }), + ('circlize', '0.4.12', { + 'checksums': ['b3b60caa5292cf980cf474c85f59582f6862925631a4da86a78eac05903252f4'], + }), + ('GetoptLong', '1.0.5', { + 'checksums': ['8c237986ed3dfb72d956ad865ef7768644eebf144675ad66140acfd1aca9d701'], + }), + ('dendextend', '1.14.0', { + 'checksums': ['3789461bc474e146b077ad26566b1fa05be32fc7e57ab1fb5e78bdabcc797858'], + }), + ('RInside', '0.2.16', { + 'checksums': ['7ae4ade128ea05f37068d59e610822ff0b277f9d39d8900f7eb31759ad5a2a0e'], + }), + ('limSolve', '1.5.6', { + 'checksums': ['b97ea9930383634c8112cdbc42f71c4e93fe0e7bfaa8f401921835cb44cb49a0'], + }), + ('dbplyr', '2.1.1', { + 'checksums': ['aba4cf47b85ab240fd3ec4cd8d512f6e1958201e151577c1a2ebc3d6ebc5bc08'], + }), + ('modelr', '0.1.8', { + 'checksums': ['825ba77d95d60cfb94920bec910872ca2ffe7790a44148b2992be2759cb361c4'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('reprex', '2.0.0', { + 'checksums': ['905377fcc644a485e97caffda3b077f6b3ad8fda09c0bbf378c422e13feb96d1'], + }), + ('selectr', '0.4-2', { + 'checksums': ['5588aed05f3f5ee63c0d29953ef53da5dac7afccfdd04b7b22ef24e1e3b0c127'], + }), + ('rvest', '1.0.0', { + 'checksums': ['a358bf258a91b3362b3736fb5f957c12e98cddf21b6066fb2abdd26ecd665713'], + }), + ('tidyverse', '1.3.0', { + 'checksums': ['6d8acb81e994f9bef5e4dcf908bcea3786d108adcf982628235b6c8c80f6fe09'], + }), + ('R.rsp', '0.44.0', { + 'checksums': ['8969075bdcabd43bad40eef6b82223e119426279fded041163fd41e55cee3a59'], + }), + ('listenv', '0.8.0', { + 'checksums': ['fd2aaf3ff2d8d546ce33d1cb38e68401613975117c1f9eb98a7b41facf5c485f'], + }), + ('globals', '0.14.0', { + 'checksums': ['203dbccb829ca9cc6aedb6f5e79cb126ea31f8dd379dff9111ec66e3628c32f3'], + }), + ('parallelly', '1.24.0', { + 'checksums': ['e6e69f4bf8c717b78fbf7c5507887fbd7efa7aada7b19a680eaf7eef59bf04f4'], + }), + ('future', '1.21.0', { + 'checksums': ['909e6602068eba543a6d2e464b911123cc29efdb600a7000eff0e5624ff0d12d'], + }), + ('gdistance', '1.3-6', { + 'checksums': ['2ccabeb2f8cf44630c0bd2da79815fe357b812737ebece1bed8f90b27c126a24'], + }), + ('vioplot', '0.3.6', { + 'checksums': ['d758c24da9b305dd4855266d360a4ceccf54ea793a236c2b7a0e36fe52cd7597'], + }), + ('emulator', '1.2-20', { + 'checksums': ['7cabf2cf74d879ad9dbaed8fdee54a5c94a8658a0645c021d160b2ef712ce287'], + }), + ('gmm', '1.6-6', { + 'checksums': ['b1b321ad1b4a4a14a2825a2c3eb939ce2f2bcef995247a1d638eca250e59739b'], + }), + ('tmvtnorm', '1.4-10', { + 'checksums': ['1a9f35e9b4899672e9c0b263affdc322ecb52ec198b2bb015af9d022faad73f0'], + }), + ('IDPmisc', '1.1.20', { + 'checksums': ['bcb9cd7b8097e5089d1936286ef310ac2030ea7791350df706382ba470afc67f'], + }), + ('gap', '1.2.2', { + 'checksums': ['9c66a52b371b282b20295676bdd86a11d59a6fb2acddb19170376e1a5c65b834'], + }), + ('qrnn', '2.0.5', { + 'checksums': ['3bd83ee8bd83941f9defdab1b5573d0ceca02bf06759a67665e5b9358ff92f52'], + }), + ('TMB', '1.7.19', { + 'checksums': ['9a30063aafc2762c8cbc3564f5afa0a5127ff55a6f348a68e45ada571a82d26e'], + }), + ('glmmTMB', '1.0.2.1', { + 'checksums': ['4b0923027bbe2a304282273fa626044063c195f4eee8d2fea88d85df598765a8'], + }), + ('gmp', '0.6-2', { + 'checksums': ['6bfcb45b3f1e7da27d8773f911027355cab371d150c3dabf7dbaf8fba85b7f0e'], + }), + ('ROI', '1.0-0', { + 'checksums': ['b0d87fb4ed2137d982734f3c5cdc0305aabe6e80f95de29655d02a9e82a0a341'], + }), + ('Rglpk', '0.6-4', { + 'checksums': ['a28dbc3130b9618d6ed2ef718d2c55df8ed8c44a47161097c53fe15fa3bfbfa6'], + }), + ('ROI.plugin.glpk', '1.0-0', { + 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], + }), + ('spaMM', '3.7.34', { + 'checksums': ['109b1b12590c30020c0b3fe2ef9f2adf11509e7a81be728d70ce76075d18ef62'], + }), + ('qgam', '1.3.2', { + 'checksums': ['273a40d0bfdc340c049bcb85aea83acd887868d8a69c0062b8399e0b24137a52'], + }), + ('DHARMa', '0.4.0', { + 'checksums': ['d38fe3673410abf8ebc0b68309b9098b519d0f93513a95cdd310bb8a6ee683b9'], + }), + ('mvnfast', '0.2.5.1', { + 'checksums': ['6393f4d2c3f67ec2d633975320309b83e9c240b59e78c0d46de70ec6378870a4'], + }), + ('bridgesampling', '1.0-0', { + 'checksums': ['9e182e15ba4e0a0fefd6edc58f1939fd971dd5c53c444ca9c1820bb2c1de90ab'], + }), + ('BayesianTools', '0.1.7', { + 'checksums': ['af49389bdeb794da3c39e1d63f59e6219438ecb8613c5ef523b00c6fed5a600c'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.5', { + 'checksums': ['50ff06d5e24d38b5d5d62f84582861bd353b82363e37623f95529b520504adbf'], + }), + ('dummies', '1.5.6', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '1.1.2', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3.1', { + 'checksums': ['052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.5', { + 'checksums': ['d042d448671355d0664d37fd64dc90932eb780e6494c479d4431d1faae2071a1'], + }), + ('Rssa', '1.0.3', { + 'checksums': ['d3dc8a22c428148b955d84b703ca0bf3993318a86b067edfe4c4de271b3054ea'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.32', { + 'checksums': ['23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1'], + }), + ('DistributionUtils', '0.6-0', { + 'checksums': ['7443d6cd154760d55b6954142908eae30385672c4f3f838dd49876ec2f297823'], + }), + ('gapfill', '0.9.6-1', { + 'checksums': ['22f04755873e34a9077bb1b1de8d16f5bc56cb8c395c4f797f9ad0b209b1b996'], + }), + ('gee', '4.13-20', { + 'checksums': ['53014cee059bd87dc22f9679dfbf18fe6813b9ab41dfe90361921159edfbf798'], + }), + ('Matching', '4.9-7', { + 'checksums': ['1956ecb5ebe1c88e2112cd277ae5c2ab4b8d8f60743e6e856a2c2e40aa05fc6d'], + }), + ('MatchIt', '4.1.0', { + 'checksums': ['b34767cbb8cfb70c6b781849d5430b11480fac43af0a2d53460a1c57c7997ba1'], + }), + ('RItools', '0.1-17', { + 'checksums': ['75654780e9ca39cb3c43acfaca74080ad74de50f92c5e36e95694aafdfdc0cea'], + }), + ('optmatch', '0.9-13', { + 'checksums': ['f8f327faa95c808773376570793bbabdbc185a6c7fcdce3b96a09c998134d0d8'], + }), + ('SPAtest', '3.1.2', { + 'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'], + }), + ('SKAT', '2.0.1', { + 'checksums': ['c8637cf5786b926f6bbef3f4ef1d3af5130cc0cfd9094d4835839724b2d0e8c7'], + }), + ('GillespieSSA', '0.6.1', { + 'checksums': ['272e9b6b26001d166fd7ce8d04f32831ba23c676075fbd1e922e27ba2c962052'], + }), + ('startupmsg', '0.9.6', { + 'checksums': ['1d60ff13bb260630f797bde66a377a5d4cd65d78ae81a3936dc4374572ec786e'], + }), + ('distr', '2.8.0', { + 'checksums': ['bb7df05d6b946bcdbbec2e3397c7c7e349b537cabfcbb13a34bcf6312a71ceb7'], + }), + ('distrEx', '2.8.0', { + 'checksums': ['b064cde7d63ce93ec9969c8c4463c1e327758b6f8ea7765217d77f9ba9d590bf'], + }), + ('KODAMA', '1.5', { + 'checksums': ['8ecf53732c1be2bd1e111b3c6de65b66caf28360306e683fe945dc76d4c267dd'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-2', { + 'checksums': ['e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179'], + }), + ('dtw', '1.22-3', { + 'checksums': ['df7cf9adf613422ddb22a160597eb5f5475ab6c67c0d790092edb7f72ba98f00'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.3', { + 'checksums': ['f5eafab17f2d4a8a2a83821ad3e96ae7c26b62bbce9de414484c657383c7b42e'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-3', { + 'checksums': ['776d5456e14398e44b78b3d7db526559bb7a3537e546a29c88aa192141c756de'], + }), + ('reticulate', '1.18', { + 'checksums': ['b33f855a58f446eefbe38df8a1a4865390f5d4ebd64b2c72266baaee64628513'], + }), + ('hdf5r', '1.3.3', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['a0f83cbf21563e81dbd1a1bd8379623ed0c9c4df4e094c75013abfd7a5271545'], + }), + ('DTRreg', '1.7', { + 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], + }), + ('pulsar', '0.3.7', { + 'checksums': ['78c9f7e3b2bf8a8d16a81d6ee43bb05b0c360219be473d920c8c8ccb2aba4e3d'], + }), + ('bayesm', '3.1-4', { + 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + }), + ('gsl', '2.1-6', { + 'checksums': ['f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c'], + }), + ('energy', '1.7-8', { + 'checksums': ['de08e8de037bb30068bbf0c1880b153a586d342304681f4ba103ab808c7f4789'], + }), + ('compositions', '2.0-1', { + 'checksums': ['84a291308faf858e5a9d9570135c2da5e57b0887f407903485fa85d09da61a0f'], + }), + ('clustree', '0.4.3', { + 'checksums': ['5ff3afc3fb3e1d20d033328935084de574250d29545c0a5b69180fe4846fbe53'], + }), + ('plotly', '4.9.3', { + 'checksums': ['d44d1a16d96de28bc2d36f1c897384215eeec44d109546c6e9c2707db0880120'], + }), + ('tweedie', '2.3.3', { + 'checksums': ['a032cad512dac37a8619e6f66cb513eb82a88a5a2ffbe91e92c2d44d1756d0d9'], + }), + ('RcppGSL', '0.3.8', { + 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], + }), + ('mvabund', '4.1.9', { + 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.2.3', { + 'checksums': ['154bf7e65452186841036a2a7f2af89664965a63040ff0bee33f8b3fab8c0e4b'], + }), + ('grpreg', '3.3.1', { + 'checksums': ['f07e202d9da45fe7cb82dd1c6a760c04cc83b4e32aeae2bb40b979fab95305a5'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('ergm', '3.11.0', { + 'checksums': ['4e5506b44badc2343be3657acbf2bca51b47d7c187ff499d5a5e70a9811fe9f2'], + }), + ('networkDynamic', '0.10.1', { + 'checksums': ['22eed8d9dea8d70877c1619eb2bc3f1ac5142ce3db6fd6eb3e0879ca56b76ca0'], + }), + ('tergm', '3.7.0', { + 'checksums': ['afd2b160bda691127f8fc57c4caff61f688cc03e71e622f8e833b2a26dc635df'], + }), + ('ergm.count', '3.4.0', { + 'checksums': ['7c24c79d0901c18991cce907306a1531cca676ae277c6b0a0e4962ad27c36baf'], + }), + ('tsna', '0.3.1', { + 'checksums': ['bba4b5e04ba647784581a2137f653f60b4c83cfd726c399556054c5a6d2cbd95'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.5-0', { + 'checksums': ['795ffd3d62bf14d3ecb3f5307bd329cd75798cf4b270ff0e768bc71a35de0ace'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.15', { + 'checksums': ['73d20ff1abd752a9d8267eea9d97be58818554ffe072923810db576c449ecbc2'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + # Replace hardcoded CUDA compute capabilities with settings from EB + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': local_liquidSVM_sed + " && LIQUIDSVM_TARGET='empty'", + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.32.0.1', { + 'checksums': ['86161b81e4aecf0243b17cabcd1f887cf4b9104918d91c804810be603d50ab66'], + }), + ('mlegp', '3.1.8', { + 'checksums': ['eac1df085a608451828575028ca05b78dc6b5035da14cabc141bfee5ef986de9'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.6', { + 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.1', { + 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.2.0', { + 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), + ('cobs', '1.3-4', { + 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.5', { + 'checksums': ['9c41ca817104ab076bfd62cccac7d024658ebf4a11dcd91654f0588868aa8d74'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.7-3.1', { + 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0-1', { + 'checksums': ['9fc1f7432a40d8911393701ca33e2ad64356c3bd12128f01dd216399b16e3d93'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.17', { + 'checksums': ['792857b2ebd408d6523424d2f6bb7297e241d4b28ab32372f6a9240c8cd554f3'], + }), + ('BMA', '3.18.14', { + 'checksums': ['3bc0fd44001c5817dc6a8eda9fb266967407f8a05ac0a5c05b10c87df462cb23'], + }), + ('BCEE', '1.3.0', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-58', { + 'checksums': ['2ab6662eaa1103a7b633477e8ebd266b262ed54fac6f9326b160067a2ded9ce7'], + }), + ('bdsmatrix', '1.3-4', { + 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.19.3', { + 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.4', { + 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.9', { + 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '3.0', { + 'checksums': ['ada4e1f8cbb08ba8ff16275ec5f9a453857e0cab63b70d42753989ab4c716b7b'], + }), + ('bbmle', '1.0.23.1', { + 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('terra', '1.1-4', { + 'checksums': ['6f6929d6bc7757281c7e314b43875d79b5bcfd1174d62d3462509b82752950ef'], + }), + ('rasterVis', '0.50.1', { + 'checksums': ['fc40c2a375f3f133d95ca88f53e014ae7b1e5236c8bdca841cb3dae629f575ba'], + }), + ('tictoc', '1.0', { + 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], + }), + ('ISOcodes', '2021.02.24', { + 'checksums': ['152769bcb4ae99d06a767384541c2000c94990a2c6983780837f85e885b539a6'], + }), + ('stopwords', '2.2', { + 'checksums': ['b66bccc786200c6ec600be8340e2801bbc7ee787fa5c5a15bc201306861706b9'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0.1', { + 'checksums': ['1fedbb913bc13c790d2fabfe4edda0a987db3a078bea8c0ca9b777d20af08662'], + }), + ('topicmodels', '0.2-12', { + 'checksums': ['afd83a4381bf39e470446ebefd41ed03f314be400c1b2f702a4b1060eb8fd1b4'], + }), + ('tidytext', '0.3.0', { + 'checksums': ['7d36be1e504f751c33dc2239751a600bd4ff05af24a0b9cdd549aff909778bc5'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.2.1', { + 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-11', { + 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.4.1', { + 'checksums': ['bc21fb6b4a93a7e95ee1be57e4e787d731895fb8b4743c26b30b43adee475b50'], + }), + ('RcppParallel', '5.0.3', { + 'checksums': ['71121138f25fcc97885b14545b7e7eb92e5f3953aec15e7df3822ae26d8e0c46'], + }), + ('StanHeaders', '2.21.0-7', { + 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], + }), + ('V8', '3.4.0', { + 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + }), + ('rstan', '2.21.2', { + 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.0', { + 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.1', { + 'checksums': ['506e684071332dac62005c709833d419f4944a85478e2f4395f218ac314f5e66'], + }), + ('corrplot', '0.84', { + 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], + }), + ('rstatix', '0.7.0', { + 'checksums': ['a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.4.0', { + 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.1.1', { + 'checksums': ['cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481'], + }), + ('leiden', '0.3.7', { + 'checksums': ['770994d2d763c195b53e3e09a987188cbf844fbb3bca2d175e46798663b13892'], + }), + ('future.apply', '1.7.0', { + 'checksums': ['2ffa6adb55f239918ce9679b7eac8dcc4bf2e6bed35c9cbedf4bf90d906345db'], + }), + ('sctransform', '0.3.2', { + 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], + }), + ('packrat', '0.6.0', { + 'checksums': ['d99d3474baa264cd255a2e60623a1c2a7b30809d352208015c88d992dc169605'], + }), + ('shinyjs', '2.0.0', { + 'checksums': ['c2cdd9fab41f6b46bb41b288cd9b3fb3a7fe9627b664e3a58a0cb5dd4c19f8ff'], + }), + ('colourpicker', '1.1.0', { + 'checksums': ['2dfbb6262d187d3b17357ff9c22670ced3621feda5b2a2a500558478e4d551e2'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), + ('findpython', '1.0.7', { + 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], + }), + ('argparse', '2.0.3', { + 'checksums': ['d26139c610ea0adf8d6632699cd34c4595ae3e7963bfc7a00cb3b7504f2059b0'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), + ('qqman', '0.1.4', { + 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'], + }), + ('rstantools', '2.1.1', { + 'checksums': ['c95b15de8ec577eeb24bb5206e7b685d882f88b5e6902efda924b7217f463d2d'], + }), + ('bayesplot', '1.8.0', { + 'checksums': ['a605f9929e681593a3ef3ca9c836e713314994aaea00f359f71cfc42d151c948'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('rsconnect', '0.8.16', { + 'checksums': ['3f728c6a5153dca28f69b9355ae9d18c5f7e70d12495c0c047eef673c1053116'], + }), + ('shinystan', '2.5.0', { + 'checksums': ['45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1'], + }), + ('optimx', '2020-4.2', { + 'checksums': ['6381c25c322287fc98ab1b2965d3f68c9a92c587c76aca1d33fd6428b2167101'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('projpred', '2.0.2', { + 'checksums': ['af0a9fb53f706090fe81b6381b27b0b6bd3f7ae1e1e44b0ada6f40972b09a55b'], + }), + ('brms', '2.15.0', { + 'checksums': ['c11701d1d8758590b74bb845b568b736e4455a81b114c7dfde0b27b7bd1bcc2f'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.0', { + 'checksums': ['b423df43e9c4bb8ffafe2de88b93fdcf3a90f964f136580ea1b849a83dba7400'], + }), + ('mcmcse', '1.4-1', { + 'checksums': ['6b181f56d60ddf55c9c08a2468ef9ffe3ec8a1b16cfa9a7742c3872597f85d17'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.6.2', { + 'checksums': ['4264f28e37855188675f6b08530752606dba3d761b36c1e7cca96a75f8208390'], + }), + ('drugCombo', '1.1.1', { + 'checksums': ['9fdc3a7cf63552c32f1c7573258fc4ceacdaf5c475fe79aa4ca8c9226b9f8a38'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.0.1', { + 'checksums': ['a3bb9bdc7a4a79ea38482df3f8cbb6e9082332a0d894eeb4b3dc816344cec0e4'], + }), + ('maxlike', '0.1-8', { + 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + }), + ('coxme', '2.2-16', { + 'checksums': ['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.2', { + 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'], + }), + ('ENMeval', '0.3.1', { + 'checksums': ['e7f20c1b4d7ede82a3aca86e3ce3fc4ae46337f812dfc171b499c2558b0183d0'], + }), + ('plotmo', '3.6.0', { + 'checksums': ['c05afcc442f9542868beea5c3c40fb93b049f9b61c42725b2a1e2bc750c241e3'], + }), + ('earth', '5.3.0', { + 'checksums': ['05ace806271a74b3ddf8718a93237fe2a8550a8659ebd87f8079c0bda5e02437'], + }), + ('mda', '0.5-2', { + 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], + }), + ('biomod2', '3.4.6', { + 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'], + }), + ('poLCA', '1.4.1', { + 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], + }), + ('PermAlgo', '1.1', { + 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.12', { + 'checksums': ['9acdf912f0e7a68a5b6a7946d5ebb0c2007b3d6cd2e39075eddae2b586354e89'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.3', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-1', { + 'checksums': ['e8abadc5614f132edc3fb9cb1c82ce4dacc1315b727fbd49db7399aee24115ba'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-19', { + 'checksums': ['6c7eed2d238ab4d8ebcd624e05a68849fa57bf2929b893bcd1a0990b5fcc304d'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.4.0', { + 'checksums': ['49459e76412037b3d8021bd83ee93d140bc3e715a2a2282a347ef60061900514'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-8', { + 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], + }), + ('gWidgets2tcltk', '1.0-6', { + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.2', { + 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], + }), + ('ie2misc', '0.8.6', { + 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '2.1', { + 'checksums': ['088d291339a4d8d9396cdb956889ac571fd9e834c6e3c3d51621a8c3f0eb9f32'], + }), + ('lmom', '2.8', { + 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], + }), + ('gld', '2.6.2', { + 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], + }), + ('DescTools', '0.99.40', { + 'checksums': ['53954f0477eac77328efac562716c8b078e76b5ad5edf0227ba2624aa2b8c7dd'], + }), + ('orthopolynom', '1.0-5', { + 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], + }), + ('gaussquad', '1.0-2', { + 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], + }), + ('nlsem', '0.8', { + 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.0', { + 'checksums': ['b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1'], + }), + ('tableone', '0.12.0', { + 'checksums': ['6a5cc16f7d2303c8f42b8adcad0fc41e1ba74f24ada4e7ad3a16effb63d3575e'], + }), + ('jstable', '1.0.2', { + 'checksums': ['0d7ffa8ecd1b2df05cf1256406152d211eabfa660bf1cc13bada1d75dfdd6d13'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.2', { + 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], + }), + ('sensemakr', '0.1.3', { + 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-5', { + 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], + }), + ('blavaan', '0.3-15', { + 'checksums': ['f73ead024bc3b65bdb0c5e5cd5458845158914eb579c07be2fd697a3573ebe6f'], + }), + ('metafor', '2.4-0', { + 'checksums': ['b64a678b762e91f1e0a6360b15e79fe19159b243c9f40ad9cc0be833bb4ba9ac'], + }), + ('fmri', '1.9.6', { + 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], + }), + ('AnalyzeFMRI', '1.1-23', { + 'checksums': ['4237ca4ffe812e614349cdffa2668de4eda5697d73ea208df0c60808daa29444'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.4', { + 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], + }), + ('DEoptim', '2.2-5', { + 'checksums': ['ae12dedcd4a43994e811e7285f8c12bfdb688e7c99d65515cf7e8cb6db13955a'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2013.9-1', { + 'checksums': ['1a1a399682a06a5fea3934985ebb1334005676c6a2a22d06f3c91c3923432908'], + }), + ('Rvmmin', '2018-4.17', { + 'checksums': ['d53ba7ab06596a47990caf101a50935b2b34402f9dd8414f098a873026ff1f56'], + }), + ('Rcgmin', '2013-2.21', { + 'checksums': ['a824a09c32d7565a3e30607c71333506d5b7197478fbe8b43f8a77dad6c12f0a'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '1.3.0', { + 'patches': ['DMCfun-1.3.0_fix-parallel-detect.patch'], + 'checksums': [ + '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz + # DMCfun-1.3.0_fix-parallel-detect.patch + '67259a76722717f29577d7a25c822a4fb9c1b5ce45699d02aa53ab0ffa1d0b2a', + ], + }), + ('miceadds', '3.11-6', { + 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], + }), + ('visdat', '0.5.3', { + 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('naniar', '0.6.0', { + 'checksums': ['9c93c64f51dd8c3002c930c276ef57651e91c8db12f885a03113753c604e7e54'], + }), + ('stringdist', '0.9.6.3', { + 'checksums': ['cd6d98f982e9ae7c4154a040c3a3f959bce19abf0229d64d22efef41f85b3f1b'], + }), + ('image.binarization', '0.1.1', { + 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], + }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), + ('lslx', '0.6.10', { + 'checksums': ['adc2b2a621625b52165245ab2f3a0bfba4f4db64fcc6ad48a3e5b219c3bd2fa1'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.6.2', { + 'checksums': ['b65201c730e10b0a80d1dd788e0c370372a1f22f314f2e49ce4dc63cb3ffd992'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), + # Specific packages for GPUs + ('OpenCL', '0.2-1', { + 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], + }), + ('RViennaCL', '1.7.1.8', { + 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb new file mode 100644 index 00000000000..c3e0f54a993 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -0,0 +1,2965 @@ +name = 'R' +version = '4.1.0' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_identify-flexiblas-in-configure.patch'] +checksums = [ + 'e8e68959d7282ca147360fc9644ada9bd161bab781bab14d33b8999a95182781', # R-4.1.0.tar.gz + '2c6720e2e144ae4fe00842daab0ebba72241080603e0ff1a6ca758738041b257', # R-4.1.0_identify-flexiblas-in-configure.patch +] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.11'), +] +dependencies = [ + ('X11', '20210518'), + ('Mesa', '21.1.1'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.35.4'), + ('PCRE2', '10.36'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.6'), # for plottting in R + ('LibTIFF', '4.2.0'), + ('Java', '11', '', True), + ('Tk', '8.6.11'), # for tcltk + ('cURL', '7.76.0'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.1'), # for igraph + ('NLopt', '2.7.0'), # for nloptr + ('FFTW', '3.3.9'), # for fftw + ('libsndfile', '1.0.31'), # for seewave + ('ICU', '69.1'), # for rJava & gdsfmt + ('HDF5', '1.10.7'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.0.11-14'), # for animation + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '14.17.0'), # for V8 (required by rstan) + ('GDAL', '3.3.0'), # for sf + ('libgit2', '1.1.0'), + ('OpenSSL', '1.1', '', True), +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 3rd June 2021 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9.1', { + 'checksums': ['99e02a955935040bf0834d44d1dc10a3794c8260fd072d3aff3e15ab249e0ac9'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.6', { + 'checksums': ['c9f24756bc000f7a989bd4f9aa93d57f7739dcde77946703f8bb32332a35f012'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '4.0.4', { + 'checksums': ['22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5'], + }), + ('bnlearn', '4.6.1', { + 'checksums': ['e4544465af3330e53e4777079c448585a8a97be2d3862a5264169007c20daeaf'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.16', { + 'checksums': ['e7dea648ee018e2c8c8834084051c76f7e8b2b42067772c62035a941c32457a9'], + }), + ('formatR', '1.11', { + 'checksums': ['bd81662d09cf363652761e63ba5969c71be4dd5ae6fc9098f440d6729254a30c'], + }), + ('gtools', '3.8.2', { + 'checksums': ['503ba60a41f3c61b8129c25de62c74dab29761d2e661d4addd106e2e02f1dcde'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.1', { + 'checksums': ['e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917'], + }), + ('xfun', '0.23', { + 'checksums': ['ec8528e85ea7e7f3dad0148359cdb0b10c8dc586bb99d4ab20b3fb24ed850e37'], + }), + ('highr', '0.9', { + 'checksums': ['beff11390d936c90fdcc00e7ed0eb72220f3de403a51b56659e3d3e0b6d8ed4d'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-16', { + 'checksums': ['c796c8b987ed1bd9dfddd593e17312ed681fc4fa3a1ecfe51da2def0ac1e50df'], + }), + ('kernlab', '0.9-29', { + 'checksums': ['c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f'], + }), + ('mime', '0.10', { + 'checksums': ['783233a15a817a7530d140e9825565a661aa4bdea7c635d11b9c74faa33be3f7'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-3', { + 'checksums': ['b1f92be633243185ab86e880a1e1ac5a4dd3c535d01ebd187a4872d0a8c6f194'], + }), + ('NLP', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '5.4.7', { + 'checksums': ['45f5a666caee5bebd3160922b8655295a25e37f624741f6574365e4ac5a14c23'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('segmented', '1.3-4', { + 'checksums': ['8276bfbb3e5c1d7a9a61098f72ac9b2b0f52c89ae9f9b715f76b22303cc3902d'], + }), + ('som', '0.3-5.1', { + 'checksums': ['a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9'], + }), + ('SuppDists', '1.1-9.5', { + 'checksums': ['680b67145c07d44e200275e08e48602fe19cd99fb106c05422b3f4a244c071c4'], + }), + ('stabledist', '0.7-1', { + 'checksums': ['06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69'], + }), + ('survivalROC', '1.0.3', { + 'checksums': ['1449e7038e048e6ad4d3f7767983c0873c9c7a7637ffa03a4cc7f0e25c31cd72'], + }), + ('pspline', '1.0-18', { + 'checksums': ['f71cf293bd5462e510ac5ad16c4a96eda18891a0bfa6447dd881c65845e19ac7'], + }), + ('timeDate', '3043.102', { + 'checksums': ['377cba03cddab8c6992e31d0683c1db3a73afa9834eee3e95b3b0723f02d7473'], + }), + ('longmemo', '1.1-2', { + 'checksums': ['7964e982287427dd58f98e1144e468ae0cbd572d25a4bea6ca9ae9c7522f3207'], + }), + ('ADGofTest', '0.3', { + 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], + }), + ('MASS', '7.3-54', { + 'checksums': ['b800ccd5b5c2709b1559cf5eab126e4935c4f8826cf7891253432bb6a056e821'], + }), + ('pixmap', '0.4-12', { + 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], + }), + ('lattice', '0.20-44', { + 'checksums': ['57b908e3c7ada08a38ad857ee44f44fdf9cfa59d5d9500bda2ccc9c7e96cdb9b'], + }), + ('sp', '1.4-5', { + 'checksums': ['6beeb216d540475cdead5f2c72d6c7ee400fe2423c1882d72cf57f6df58f09da'], + }), + ('pkgconfig', '2.0.3', { + 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], + }), + ('rlang', '0.4.11', { + 'checksums': ['740e926b20b00788a7ea64cb92ddfdc94cdf256b05b0c57059edf7292511d5dd'], + }), + ('ellipsis', '0.3.2', { + 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], + }), + ('digest', '0.6.27', { + 'checksums': ['f485f75122907da24c41d4a62c91a232f0c371befd2f77e973342a1bef00253f'], + }), + ('glue', '1.4.2', { + 'checksums': ['9f7354132a26e9a876428fa87629b9aaddcd558f9932328e6ac065b95b8ef7ad'], + }), + ('vctrs', '0.3.8', { + 'checksums': ['7f4e8b75eda115e69dddf714f0643eb889ad61017cdc13af24389aab2a2d1bb1'], + }), + ('lifecycle', '1.0.0', { + 'checksums': ['03334ab213f2ad49a49e184e73f2051e04d35d43f562db903e68243cd2ec0f8e'], + }), + ('hms', '1.1.0', { + 'checksums': ['e8599af260c3e8963ef183a98ca334b3f102a4595dde38e7c3c930a161e1b4ce'], + }), + ('prettyunits', '1.1.1', { + 'checksums': 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('distillery', '1.2-1', { + 'checksums': ['4b88f0b34e472b9134ad403fb32283424f1883a5943e52c55f1fe05995efb5fa'], + }), + ('extRemes', '2.1-1', { + 'checksums': ['5a1927bb21f178ec5a3e3f862d792e690e45c16c88190e64e83aa1fb9e3ffa02'], + }), + ('tkrplot', '0.0-25', { + 'checksums': ['21ae0e869e024838b9bf42a0c06d55672a2683453dc9218327409086a611ed5c'], + }), + ('misc3d', '0.9-0', { + 'checksums': ['a1e9291d625bd1312bae5b0e26d48b9362f66a8a0fabbf48891ba1d2432e4e82'], + }), + ('multicool', '0.1-11', { + 'checksums': ['1c907e64af2ac39facdf431a5691e69649f64af1f50e198ae39da5bf30026476'], + }), + ('plot3D', '1.4', { + 'checksums': ['d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0'], + }), + ('plot3Drgl', '1.0.2', { + 'checksums': ['aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496'], + }), + ('OceanView', '1.0.5', { + 'checksums': ['c16e1bed97f4ede46dc017fdd6bd7575d925b57bd2601317bd3ad2357609f885'], + }), + ('ks', '1.13.1', { + 'checksums': ['9a3a5756861e77cdb499a369164cce91dc32f3edf3c6eecada78c3f17bf4277e'], + }), + ('logcondens', '2.1.5', { + 'checksums': ['72e61abc1f3eb28830266fbe5b0da0999eb5520586000a3024e7c26be93c02eb'], + }), + ('Iso', '0.0-18.1', { + 'checksums': ['2fa5f78a7603cbae94a5e38e791938596a053d48c609a7c120a19cbb7d93c66f'], + }), + ('penalized', '0.9-51', { + 'checksums': ['eaa80dca99981fb9eb576261f30046cfe492d014cc2bf286c447b03a92e299fd'], + }), + ('clusterRepro', '0.9', { + 'checksums': ['940d84529ff429b315cf4ad25700f93e1156ccacee7b6c38e4bdfbe2d4c6f868'], + }), + ('data.tree', '1.0.0', { + 'checksums': ['40674c90a5bd00f5185db9adbd221c6f1114043e69095249f5fa8b3044af3f5e'], + }), + ('influenceR', '0.1.0', { + 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], + }), + ('visNetwork', '2.0.9', { + 'checksums': ['5e0b3dc3a91e66e0a359433f03cc856d04b981b0f9ad228d8fa9c96b7fcaa420'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.6.1', { + 'checksums': ['be4e4c520a3692902ce405e8225aef9f3d5f0cd11fcde614f6541e981b63673d'], + }), + ('randomForestSRC', '2.11.0', { + 'checksums': ['6295fa43bb20bd5248e30a3239259185acfb4c2b6219be9c7a9306031a1c3744'], + }), + ('sm', '2.2-5.6', { + 'checksums': ['b890cd7ebe8ed711ab4a3792c204c4ecbe9e6ca1fd5bbc3925eba5833a839c30'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-8', { + 'checksums': ['40e204909100b7338619ae23cd87e0a4058e581c286da2327f36dbb3834b84a2'], + }), + ('matrixcalc', '1.0-4', { + 'checksums': ['94c5831104a6c501ad8436039ff1ddb871fc79e85b1073e9ac497fce1dd2a045'], + }), + ('arm', '1.11-2', { + 'checksums': ['8385be32f6b6b6f1b32df15f42073b191d714d870bbb4f95875b64aff6112bbf'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('servr', '0.22', { + 'checksums': ['309c55bb86cbcb130dcd45f4563149fc2777096a4d5c7cfe73b9148ddc9ad4ee'], + }), + ('rgexf', '0.16.0', { + 'checksums': ['2a671df9ac70cfefd4092754317cb28e32a33df345b80e1975bf838e838245ee'], + }), + ('sem', '3.1-11', { + 'checksums': ['33b1ad7695db13af8cdd214f5d388db494528b433c61c7ad89970cefcc8b430e'], + }), + ('network', '1.16.1', { + 'checksums': ['eb6435794cacc81abe1664391e8dcf1c10112bbb76fff9016dd6dbb8e83efeb1'], + }), + ('rle', '0.9.2', { + 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], + }), + ('statnet.common', '4.4.1', { + 'checksums': ['4ecf2b84718d7fb60f196215b4cf6f52cd6b26cc9148a6da6981b26e885509fd'], + }), + ('sna', '2.6', { + 'checksums': ['3a016550d9f424a0613c3f5b0b680dbd3a1f20a343173d39a96034340ad9202a'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.4.1', { + 'checksums': ['78ef9eae464d52c5247998b9514a81b178419b857b1a6c00d885e3ae6c03a886'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('BDgraph', '2.64', { + 'checksums': ['243f3af3724552049f8f4f55dd425e3313adab95e1128ae4d6551d96005fdf5e'], + }), + ('graphlayouts', '0.7.1', { + 'checksums': ['380f8ccb0b08735694e83f661fd56a0d592a78448ae91b89c290ba8582d66717'], + }), + ('tweenr', '1.0.2', { + 'checksums': ['1805f575da6705ca4e5ec1c4605222fc826ba806d9ff9af41770294fe08ff69f'], + }), + ('ggforce', '0.3.3', { + 'checksums': ['2a283bb409da6b96929863a926b153bcc59b2c6f00551805db1d1d43e5929f2f'], + }), + ('tidygraph', '1.2.0', { + 'checksums': ['057d6c42fc0144109f3ace7f5058cca7b2fe493c761daa991448b23f86b6129f'], + }), + ('ggraph', '2.0.5', { + 'checksums': ['e36ad49dba92ee8652e18b1fb197be0ceb9f0a2f8faee2194453a62578449654'], + }), + ('qgraph', '1.6.9', { + 'checksums': 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('tuneR', '1.3.3', { + 'checksums': ['bdc3c2017b162d2ba0a249e80361a4f47202e763c21aecfc57380a482a3a692b'], + }), + ('pastecs', '1.3.21', { + 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], + }), + ('audio', '0.1-7', { + 'checksums': ['52e0397a45325aa9586ec68b94ab9e505bdefaf2a588d634fcb57a6a11659c74'], + }), + ('fftw', '1.0-6', { + 'checksums': ['397ef5ec354b919884f74fba4202bfc13ad11a70b16285c41677aad1d3b170ce'], + }), + ('seewave', '2.1.6', { + 'checksums': ['84a0a0035737574a65f371fa4a20a1a3a66de195efe41975f21be8fb001e7088'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('sf', '0.9-8', { + 'checksums': ['11570a6578701faef0b2a481f6722e8f4e7750eac958c4c7aec65abfa078cf24'], + }), + ('oce', '1.4-0', { + 'checksums': ['3b341448001164dc62b54a26c8f86adf50e68705ddc47615b290b950da734408'], + }), + ('ineq', '0.2-13', { + 'checksums': 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('tclust', '1.4-2', { + 'checksums': ['95dcd07dbd16383f07f5cea8561e7f3bf314e4a7483879841103b149fc8c65d9'], + }), + ('ranger', '0.12.1', { + 'checksums': ['fc308e0ac06718272799928e1a19612de16b05bde481d8f38e11a101df5425ef'], + }), + ('hexbin', '1.28.2', { + 'checksums': ['6241f8d3a6c6be2c1c693c3ddb99554bc103e3c6cf602d0c2787c0ce6fd1702d'], + }), + ('pryr', '0.1.4', { + 'checksums': ['d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b'], + }), + ('moments', '0.14', { + 'checksums': ['2a3b81e60dafdd092d2bdd3513d7038855ca7d113dc71df1229f7518382a3e39'], + }), + ('laeken', '0.5.1', { + 'checksums': ['1aa94a1768969eb999f7a41212af2d8b2943b43a68a92f99c9f77929e19439a5'], + }), + ('VIM', '6.1.0', { + 'checksums': ['1f9eb2ad9b18b7a0435e6074d031b7b5bc7143ff4251514ba20a38a53de00aa9'], + }), + ('smoother', '1.1', { + 'checksums': ['91b55b82f805cfa1deedacc0a4e844a2132aa59df593f3b05676954cf70a195b'], + }), + ('dynamicTreeCut', '1.63-1', { + 'checksums': 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+ }), + ('WeightSVM', '1.7-5', { + 'checksums': ['dd895fe3a400897cea18d9de3e406e040efca9f84495739757b52570c98f820a'], + }), + ('mpath', '0.4-2.19', { + 'checksums': ['fa0d92984910b8f556677850e3d899bc675724f0e2a3a73629d2700040335afe'], + }), + ('timereg', '2.0.0', { + 'checksums': ['2a68711ae4a80fd16a06d8de8e90692d9c986459d6253cc0a5add4e48e46170c'], + }), + ('peperr', '1.3', { + 'checksums': ['64d30b0ec09bf9b8f7b6edce67dd0f9e0e3dbe665fec8f5411f74142e53e9f5d'], + }), + ('heatmap3', '1.1.9', { + 'checksums': ['594c33947b2be2cc8a592075f41a0df2398c892add7d63a15c613a5eeb8fdb69'], + }), + ('GlobalOptions', '0.1.2', { + 'checksums': ['47890699668cfa9900a829c51f8a32e02a7a7764ad07cfac972aad66f839753e'], + }), + ('circlize', '0.4.12', { + 'checksums': ['b3b60caa5292cf980cf474c85f59582f6862925631a4da86a78eac05903252f4'], + }), + ('GetoptLong', '1.0.5', { + 'checksums': ['8c237986ed3dfb72d956ad865ef7768644eebf144675ad66140acfd1aca9d701'], + }), + ('dendextend', '1.15.1', { + 'checksums': ['ad0241921d9be0aa80b839f2f0371bb6ba16f9b40f54d04704434ac132e1c47d'], + }), + ('RInside', '0.2.16', { + 'checksums': ['7ae4ade128ea05f37068d59e610822ff0b277f9d39d8900f7eb31759ad5a2a0e'], + }), + ('limSolve', '1.5.6', { + 'checksums': ['b97ea9930383634c8112cdbc42f71c4e93fe0e7bfaa8f401921835cb44cb49a0'], + }), + ('dbplyr', '2.1.1', { + 'checksums': ['aba4cf47b85ab240fd3ec4cd8d512f6e1958201e151577c1a2ebc3d6ebc5bc08'], + }), + ('modelr', '0.1.8', { + 'checksums': ['825ba77d95d60cfb94920bec910872ca2ffe7790a44148b2992be2759cb361c4'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('reprex', '2.0.0', { + 'checksums': ['905377fcc644a485e97caffda3b077f6b3ad8fda09c0bbf378c422e13feb96d1'], + }), + ('selectr', '0.4-2', { + 'checksums': ['5588aed05f3f5ee63c0d29953ef53da5dac7afccfdd04b7b22ef24e1e3b0c127'], + }), + ('rvest', '1.0.0', { + 'checksums': ['a358bf258a91b3362b3736fb5f957c12e98cddf21b6066fb2abdd26ecd665713'], + }), + ('dtplyr', '1.1.0', { + 'checksums': ['99681b7285d7d5086e5595ca6bbeebf7f4e2ee358a32b694cd9d35916cdfc732'], + }), + ('gargle', '1.1.0', { + 'checksums': ['7ce429638a3e3286e78f801636b3671400c0ea1647a159fa4d7c91f27f4bc20f'], + }), + ('googledrive', '1.0.1', { + 'checksums': ['9a06078e9e0d6949fcc2a3fb8583e975d73a033b5a34f064b2bcf6ec39a07e61'], + }), + ('ids', '1.0.1', { + 'checksums': ['b6212a186063c23116c5cbd3cca65dbb8977dd737261e4526ebee8f64852cfe8'], + }), + ('googlesheets4', '0.3.0', { + 'checksums': ['621137d078d89a91f59e61a2be83f3bcfbef2e6db9c623b1485940f51b3b6111'], + }), + ('tidyverse', '1.3.1', { + 'checksums': ['83cf95109d4606236274f5a8ec2693855bf75d3a1b3bc1ab4426dcc275ed6632'], + }), + ('R.rsp', '0.44.0', { + 'checksums': ['8969075bdcabd43bad40eef6b82223e119426279fded041163fd41e55cee3a59'], + }), + ('listenv', '0.8.0', { + 'checksums': ['fd2aaf3ff2d8d546ce33d1cb38e68401613975117c1f9eb98a7b41facf5c485f'], + }), + ('globals', '0.14.0', { + 'checksums': ['203dbccb829ca9cc6aedb6f5e79cb126ea31f8dd379dff9111ec66e3628c32f3'], + }), + ('parallelly', '1.25.0', { + 'checksums': ['91cb7cc18a814b5a587fc868c965eef554f92751f1f1b4d01fb808d550f3ac29'], + }), + ('future', '1.21.0', { + 'checksums': ['909e6602068eba543a6d2e464b911123cc29efdb600a7000eff0e5624ff0d12d'], + }), + ('gdistance', '1.3-6', { + 'checksums': ['2ccabeb2f8cf44630c0bd2da79815fe357b812737ebece1bed8f90b27c126a24'], + }), + ('vioplot', '0.3.6', { + 'checksums': ['d758c24da9b305dd4855266d360a4ceccf54ea793a236c2b7a0e36fe52cd7597'], + }), + ('emulator', '1.2-21', { + 'checksums': ['9b50b2c1e673dbc5e846a4fa72e8bd03434add9f659bde6d7b0c4f1bbd713346'], + }), + ('gmm', '1.6-6', { + 'checksums': ['b1b321ad1b4a4a14a2825a2c3eb939ce2f2bcef995247a1d638eca250e59739b'], + }), + ('tmvtnorm', '1.4-10', { + 'checksums': ['1a9f35e9b4899672e9c0b263affdc322ecb52ec198b2bb015af9d022faad73f0'], + }), + ('IDPmisc', '1.1.20', { + 'checksums': ['bcb9cd7b8097e5089d1936286ef310ac2030ea7791350df706382ba470afc67f'], + }), + ('gap', '1.2.3-1', { + 'checksums': ['343ae58ca91e75147ae3961285c3413bdf6dedf7cb4743a822a6c5b16d1b89e7'], + }), + ('qrnn', '2.0.5', { + 'checksums': ['3bd83ee8bd83941f9defdab1b5573d0ceca02bf06759a67665e5b9358ff92f52'], + }), + ('TMB', '1.7.20', { + 'checksums': ['67a830705e4d3a9de4f0db31424f5e9a1e40b8ce30ec5ceb9124b3b810bb8a93'], + }), + ('glmmTMB', '1.0.2.1', { + 'checksums': ['4b0923027bbe2a304282273fa626044063c195f4eee8d2fea88d85df598765a8'], + }), + ('gmp', '0.6-2', { + 'checksums': ['6bfcb45b3f1e7da27d8773f911027355cab371d150c3dabf7dbaf8fba85b7f0e'], + }), + ('ROI', '1.0-0', { + 'checksums': ['b0d87fb4ed2137d982734f3c5cdc0305aabe6e80f95de29655d02a9e82a0a341'], + }), + ('Rglpk', '0.6-4', { + 'checksums': ['a28dbc3130b9618d6ed2ef718d2c55df8ed8c44a47161097c53fe15fa3bfbfa6'], + }), + ('ROI.plugin.glpk', '1.0-0', { + 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], + }), + ('spaMM', '3.8.0', { + 'checksums': ['a77fea8e6bc6212a3cc7c9f8287c5517feb28a035ce7f7ac28b4c1088702ace7'], + }), + ('qgam', '1.3.3', { + 'checksums': ['9a68fe4e74f4188862f7c01d682d50ffadd96ce7b98383404472309c87e3a26f'], + }), + ('DHARMa', '0.4.1', { + 'checksums': ['f031c08174d4d863af3fe7a7cbcee8d52ba3f6369f93324ef5c1d00361c20cb7'], + }), + ('mvnfast', '0.2.7', { + 'checksums': ['b67d50936c9a466977669ef6bb7b23df8e7c90a820ac916328c20e41ef8e0b72'], + }), + ('bridgesampling', '1.1-2', { + 'checksums': ['54ecd39aa2e36d4d521d3d36425f9fe56a3f8547df6048c814c5931d790f3e6b'], + }), + ('BayesianTools', '0.1.7', { + 'checksums': ['af49389bdeb794da3c39e1d63f59e6219438ecb8613c5ef523b00c6fed5a600c'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.5', { + 'checksums': ['50ff06d5e24d38b5d5d62f84582861bd353b82363e37623f95529b520504adbf'], + }), + ('dummies', '1.5.6', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '1.1.2', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3.1', { + 'checksums': ['052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.5', { + 'checksums': ['d042d448671355d0664d37fd64dc90932eb780e6494c479d4431d1faae2071a1'], + }), + ('Rssa', '1.0.3', { + 'checksums': ['d3dc8a22c428148b955d84b703ca0bf3993318a86b067edfe4c4de271b3054ea'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.32', { + 'checksums': ['23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1'], + }), + ('DistributionUtils', '0.6-0', { + 'checksums': ['7443d6cd154760d55b6954142908eae30385672c4f3f838dd49876ec2f297823'], + }), + ('gapfill', '0.9.6-1', { + 'checksums': ['22f04755873e34a9077bb1b1de8d16f5bc56cb8c395c4f797f9ad0b209b1b996'], + }), + ('gee', '4.13-20', { + 'checksums': ['53014cee059bd87dc22f9679dfbf18fe6813b9ab41dfe90361921159edfbf798'], + }), + ('Matching', '4.9-9', { + 'checksums': ['9c92737348f1e0b23c2d44775989f0a8b84563833c400255eeb702b673439a48'], + }), + ('MatchIt', '4.2.0', { + 'checksums': ['ed64baefa618b3360b962376c001820ef540736376268d5f385dfbadef13483c'], + }), + ('RItools', '0.1-17', { + 'checksums': ['75654780e9ca39cb3c43acfaca74080ad74de50f92c5e36e95694aafdfdc0cea'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.0', { + 'checksums': ['b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1'], + }), + ('optmatch', '0.9-14', { + 'checksums': ['ba0cfd976a9c50ae62afd372b6910bcedc98c6a0bbc5893cd97d8df9259a5ced'], + }), + ('SPAtest', '3.1.2', { + 'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'], + }), + ('SKAT', '2.0.1', { + 'checksums': ['c8637cf5786b926f6bbef3f4ef1d3af5130cc0cfd9094d4835839724b2d0e8c7'], + }), + ('GillespieSSA', '0.6.1', { + 'checksums': ['272e9b6b26001d166fd7ce8d04f32831ba23c676075fbd1e922e27ba2c962052'], + }), + ('startupmsg', '0.9.6', { + 'checksums': ['1d60ff13bb260630f797bde66a377a5d4cd65d78ae81a3936dc4374572ec786e'], + }), + ('distr', '2.8.0', { + 'checksums': ['bb7df05d6b946bcdbbec2e3397c7c7e349b537cabfcbb13a34bcf6312a71ceb7'], + }), + ('distrEx', '2.8.0', { + 'checksums': ['b064cde7d63ce93ec9969c8c4463c1e327758b6f8ea7765217d77f9ba9d590bf'], + }), + ('KODAMA', '1.6', { + 'checksums': ['304e42d7053a6d02c6b88012e4d5465c229461add04aa05fa7b8168ad2990c7a'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-2', { + 'checksums': ['e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179'], + }), + ('dtw', '1.22-3', { + 'checksums': ['df7cf9adf613422ddb22a160597eb5f5475ab6c67c0d790092edb7f72ba98f00'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.3', { + 'checksums': ['f5eafab17f2d4a8a2a83821ad3e96ae7c26b62bbce9de414484c657383c7b42e'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-5', { + 'checksums': ['2e34969e53fcdccaf003d65b24ed28ab2e8ae281ed7b06ff4e0bff02e0de39dd'], + }), + ('reticulate', '1.20', { + 'checksums': ['7019404c8097821f38577c44f9630132c9ae0f9b148dc1950047d2d1c062c82b'], + }), + ('hdf5r', '1.3.3', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['a0f83cbf21563e81dbd1a1bd8379623ed0c9c4df4e094c75013abfd7a5271545'], + }), + ('DTRreg', '1.7', { + 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], + }), + ('pulsar', '0.3.7', { + 'checksums': ['78c9f7e3b2bf8a8d16a81d6ee43bb05b0c360219be473d920c8c8ccb2aba4e3d'], + }), + ('bayesm', '3.1-4', { + 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + }), + ('gsl', '2.1-6', { + 'checksums': ['f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c'], + }), + ('energy', '1.7-8', { + 'checksums': ['de08e8de037bb30068bbf0c1880b153a586d342304681f4ba103ab808c7f4789'], + }), + ('compositions', '2.0-1', { + 'checksums': ['84a291308faf858e5a9d9570135c2da5e57b0887f407903485fa85d09da61a0f'], + }), + ('clustree', '0.4.3', { + 'checksums': ['5ff3afc3fb3e1d20d033328935084de574250d29545c0a5b69180fe4846fbe53'], + }), + ('plotly', '4.9.3', { + 'checksums': ['d44d1a16d96de28bc2d36f1c897384215eeec44d109546c6e9c2707db0880120'], + }), + ('tweedie', '2.3.3', { + 'checksums': ['a032cad512dac37a8619e6f66cb513eb82a88a5a2ffbe91e92c2d44d1756d0d9'], + }), + ('RcppGSL', '0.3.8', { + 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], + }), + ('mvabund', '4.1.12', { + 'checksums': ['c1af39dbfd048c9bb367765ee266be49622e1a5d964186920a2d47bec4e6f780'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.3.0', { + 'checksums': ['de615707da13d78be3d6ff77651fd19e229f2cd702031616a95bcbce3e2f4432'], + }), + ('grpreg', '3.3.1', { + 'checksums': ['f07e202d9da45fe7cb82dd1c6a760c04cc83b4e32aeae2bb40b979fab95305a5'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('ergm', '3.11.0', { + 'checksums': ['4e5506b44badc2343be3657acbf2bca51b47d7c187ff499d5a5e70a9811fe9f2'], + }), + ('networkDynamic', '0.10.1', { + 'checksums': ['22eed8d9dea8d70877c1619eb2bc3f1ac5142ce3db6fd6eb3e0879ca56b76ca0'], + }), + ('tergm', '3.7.0', { + 'checksums': ['afd2b160bda691127f8fc57c4caff61f688cc03e71e622f8e833b2a26dc635df'], + }), + ('ergm.count', '3.4.0', { + 'checksums': ['7c24c79d0901c18991cce907306a1531cca676ae277c6b0a0e4962ad27c36baf'], + }), + ('tsna', '0.3.3', { + 'checksums': ['bd5663557ab6a27deda21096e3ab549095d52d57a8f47b878706756acebfb286'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.5-0', { + 'checksums': ['795ffd3d62bf14d3ecb3f5307bd329cd75798cf4b270ff0e768bc71a35de0ace'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.15', { + 'checksums': ['73d20ff1abd752a9d8267eea9d97be58818554ffe072923810db576c449ecbc2'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.32.1.3', { + 'checksums': ['08f3388651a2fbdcf51e82867e5cd125c82c6a8e758256d34cbfb25fd6a64f9b'], + }), + ('mlegp', '3.1.8', { + 'checksums': ['eac1df085a608451828575028ca05b78dc6b5035da14cabc141bfee5ef986de9'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.6', { + 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.1', { + 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.2.1', { + 'checksums': ['6b078da4a47904194bfe29e2c3b6fbbf6e3ad190e33979f840a3ea366c708616'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), + ('cobs', '1.3-4', { + 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.5', { + 'checksums': ['9c41ca817104ab076bfd62cccac7d024658ebf4a11dcd91654f0588868aa8d74'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.7-3.1', { + 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0-1', { + 'checksums': ['9fc1f7432a40d8911393701ca33e2ad64356c3bd12128f01dd216399b16e3d93'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.19', { + 'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'], + }), + ('BMA', '3.18.15', { + 'checksums': ['4be0d52f433503631e9574944067f613bafba129ebe27396bcfccb3b95992b1a'], + }), + ('BCEE', '1.3.0', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-59', { + 'checksums': ['55ce3496acb64e56a21f3e21e94ee31ede9304891a12ffca6df8b18997dc9079'], + }), + ('bdsmatrix', '1.3-4', { + 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.19.3', { + 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.4', { + 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.9', { + 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '3.0', { + 'checksums': ['ada4e1f8cbb08ba8ff16275ec5f9a453857e0cab63b70d42753989ab4c716b7b'], + }), + ('bbmle', '1.0.23.1', { + 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('terra', '1.2-10', { + 'checksums': ['2d0e6b8ccba18195df9cdad70f1c55c1747ff873b996d0f68d891dc05ce5594c'], + }), + ('rasterVis', '0.50.2', { + 'checksums': ['b94f671d2b7d3b9efb4456bb654fd1615e31e89e9f21d12ef5e8cbd2b931873a'], + }), + ('tictoc', '1.0.1', { + 'checksums': ['a09a1535c417ddf6637bbbda5fca6edab6c7f7b252a64e57e99d4d0748712705'], + }), + ('ISOcodes', '2021.02.24', { + 'checksums': ['152769bcb4ae99d06a767384541c2000c94990a2c6983780837f85e885b539a6'], + }), + ('stopwords', '2.2', { + 'checksums': ['b66bccc786200c6ec600be8340e2801bbc7ee787fa5c5a15bc201306861706b9'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0.1', { + 'checksums': ['1fedbb913bc13c790d2fabfe4edda0a987db3a078bea8c0ca9b777d20af08662'], + }), + ('topicmodels', '0.2-12', { + 'checksums': ['afd83a4381bf39e470446ebefd41ed03f314be400c1b2f702a4b1060eb8fd1b4'], + }), + ('tidytext', '0.3.1', { + 'checksums': ['30b96058d69733a5f49cff4ff471605f47deb549a40d4517dcdffc7f4b534fa0'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.3.0', { + 'checksums': ['0af71dc25ebbd2b03136c44d33359e67811e5d3b262c91791f87a5c890d7103a'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-13', { + 'checksums': ['7186d23e561818f3e1f01376a4fb2af9ccee775ce5afc1e3175f3b07a81db515'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.4.1', { + 'checksums': ['bc21fb6b4a93a7e95ee1be57e4e787d731895fb8b4743c26b30b43adee475b50'], + }), + ('RcppParallel', '5.1.4', { + 'checksums': ['76b545a6878c55edba780183fd89a76fe723b7f19709c5243495dcf3d54eea82'], + }), + ('StanHeaders', '2.21.0-7', { + 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], + }), + ('V8', '3.4.2', { + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['210643473ca8bf423fae34ce72ceb37a3e44c3315ec4abae59a77f077542d2ed'], + }), + ('rstan', '2.21.2', { + 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.1', { + 'checksums': ['0f30a5d8d11ebb52b3275d0950901efc232fc4640fcc0e92ebb16fbaac66f5de'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.1', { + 'checksums': ['506e684071332dac62005c709833d419f4944a85478e2f4395f218ac314f5e66'], + }), + ('corrplot', '0.88', { + 'checksums': ['bfd14d28ea0009843bb27ec4d65d2b0deb75c66414146fa5b9248a7e9b8e09e8'], + }), + ('rstatix', '0.7.0', { + 'checksums': ['a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.4.0', { + 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.1.1', { + 'checksums': ['cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481'], + }), + ('leiden', '0.3.8', { + 'checksums': ['811f8084f64baf4df8cdc5fdac45c150a2831e7daade0577311ffdfb3491606b'], + }), + ('future.apply', '1.7.0', { + 'checksums': ['2ffa6adb55f239918ce9679b7eac8dcc4bf2e6bed35c9cbedf4bf90d906345db'], + }), + ('sctransform', '0.3.2', { + 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], + }), + ('packrat', '0.6.0', { + 'checksums': ['d99d3474baa264cd255a2e60623a1c2a7b30809d352208015c88d992dc169605'], + }), + ('colourpicker', '1.1.0', { + 'checksums': ['2dfbb6262d187d3b17357ff9c22670ced3621feda5b2a2a500558478e4d551e2'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), + ('findpython', '1.0.7', { + 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], + }), + ('argparse', '2.0.3', { + 'checksums': ['d26139c610ea0adf8d6632699cd34c4595ae3e7963bfc7a00cb3b7504f2059b0'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), + ('qqman', '0.1.8', { + 'checksums': ['58da8317df8d726d1fde4805919da5d64f880894a423ee20937cafb479b9d8a8'], + }), + ('rstantools', '2.1.1', { + 'checksums': ['c95b15de8ec577eeb24bb5206e7b685d882f88b5e6902efda924b7217f463d2d'], + }), + ('bayesplot', '1.8.0', { + 'checksums': ['a605f9929e681593a3ef3ca9c836e713314994aaea00f359f71cfc42d151c948'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('rsconnect', '0.8.18', { + 'checksums': ['743b78f3b290312c519bee6fd13f18afa38b0a1161d8a3dc7baec8f7a2097205'], + }), + ('shinystan', '2.5.0', { + 'checksums': ['45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1'], + }), + ('optimx', '2020-4.2', { + 'checksums': ['6381c25c322287fc98ab1b2965d3f68c9a92c587c76aca1d33fd6428b2167101'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('projpred', '2.0.2', { + 'checksums': ['af0a9fb53f706090fe81b6381b27b0b6bd3f7ae1e1e44b0ada6f40972b09a55b'], + }), + ('brms', '2.15.0', { + 'checksums': ['c11701d1d8758590b74bb845b568b736e4455a81b114c7dfde0b27b7bd1bcc2f'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.1', { + 'checksums': ['285335dbe29b6898641e1151ab2f06acf76c6f4d6fbeadd66d151c25d7e38a74'], + }), + ('mcmcse', '1.4-1', { + 'checksums': ['6b181f56d60ddf55c9c08a2468ef9ffe3ec8a1b16cfa9a7742c3872597f85d17'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.6.2', { + 'checksums': ['4264f28e37855188675f6b08530752606dba3d761b36c1e7cca96a75f8208390'], + }), + ('drugCombo', '1.1.1', { + 'checksums': ['9fdc3a7cf63552c32f1c7573258fc4ceacdaf5c475fe79aa4ca8c9226b9f8a38'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.1.1', { + 'checksums': ['48474f396c4a91e257490025ede6a998883683e8020a898fff5d4e23a3764bfd'], + }), + ('maxlike', '0.1-8', { + 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + }), + ('coxme', '2.2-16', { + 'checksums': ['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.2', { + 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'], + }), + ('ENMeval', '2.0.0', { + 'checksums': ['2a2dad01f5ae4605513115d317834d673e88a6dee38f77d0b8febfa832a8c901'], + }), + ('plotmo', '3.6.0', { + 'checksums': ['c05afcc442f9542868beea5c3c40fb93b049f9b61c42725b2a1e2bc750c241e3'], + }), + ('earth', '5.3.0', { + 'checksums': ['05ace806271a74b3ddf8718a93237fe2a8550a8659ebd87f8079c0bda5e02437'], + }), + ('mda', '0.5-2', { + 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], + }), + ('biomod2', '3.4.6', { + 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'], + }), + ('poLCA', '1.4.1', { + 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], + }), + ('PermAlgo', '1.1', { + 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.13', { + 'checksums': ['90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.3', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-1', { + 'checksums': ['e8abadc5614f132edc3fb9cb1c82ce4dacc1315b727fbd49db7399aee24115ba'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-19', { + 'checksums': ['6c7eed2d238ab4d8ebcd624e05a68849fa57bf2929b893bcd1a0990b5fcc304d'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.4.0', { + 'checksums': ['49459e76412037b3d8021bd83ee93d140bc3e715a2a2282a347ef60061900514'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-8', { + 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], + }), + ('gWidgets2tcltk', '1.0-6', { + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.2', { + 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], + }), + ('ie2misc', '0.8.6', { + 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '2.1', { + 'checksums': ['088d291339a4d8d9396cdb956889ac571fd9e834c6e3c3d51621a8c3f0eb9f32'], + }), + ('lmom', '2.8', { + 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], + }), + ('gld', '2.6.2', { + 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], + }), + ('DescTools', '0.99.41', { + 'checksums': ['b138261fd8d37ddb2e23ba84edecb3968a4751eb7694bfdb2a8d782fec53e520'], + }), + ('orthopolynom', '1.0-5', { + 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], + }), + ('gaussquad', '1.0-2', { + 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], + }), + ('nlsem', '0.8', { + 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], + }), + ('tableone', '0.12.0', { + 'checksums': ['6a5cc16f7d2303c8f42b8adcad0fc41e1ba74f24ada4e7ad3a16effb63d3575e'], + }), + ('jstable', '1.0.2', { + 'checksums': ['0d7ffa8ecd1b2df05cf1256406152d211eabfa660bf1cc13bada1d75dfdd6d13'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.2', { + 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], + }), + ('sensemakr', '0.1.3', { + 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-5', { + 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], + }), + ('blavaan', '0.3-15', { + 'checksums': ['f73ead024bc3b65bdb0c5e5cd5458845158914eb579c07be2fd697a3573ebe6f'], + }), + ('mathjaxr', '1.4-0', { + 'checksums': ['ba57378236d593a39c5839054adc5473526de0c8f05b7eeb87c99438496ddc67'], + }), + ('metafor', '3.0-1', { + 'checksums': ['902424c442da7a9843c12e3f969aae4fac8ed74421c3256fc29f4b63cf7be7e4'], + }), + ('fmri', '1.9.6', { + 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], + }), + ('AnalyzeFMRI', '1.1-23', { + 'checksums': ['4237ca4ffe812e614349cdffa2668de4eda5697d73ea208df0c60808daa29444'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.4', { + 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], + }), + ('DEoptim', '2.2-6', { + 'checksums': ['8c63397d83a067212d003ef3e639fd81f5f00bf61e3c271b4e4999031a69e2e1'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2013.9-1', { + 'checksums': ['1a1a399682a06a5fea3934985ebb1334005676c6a2a22d06f3c91c3923432908'], + }), + ('Rvmmin', '2018-4.17.1', { + 'checksums': ['55000ac4ff57d42f172c46c7d6b0a603da3b65866d6440d6b32bac4d2b81814e'], + }), + ('Rcgmin', '2013-2.21', { + 'checksums': ['a824a09c32d7565a3e30607c71333506d5b7197478fbe8b43f8a77dad6c12f0a'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '1.3.0', { + 'patches': ['DMCfun-1.3.0_fix-parallel-detect.patch'], + 'checksums': [ + '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz + # DMCfun-1.3.0_fix-parallel-detect.patch + '67259a76722717f29577d7a25c822a4fb9c1b5ce45699d02aa53ab0ffa1d0b2a', + ], + }), + ('miceadds', '3.11-6', { + 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], + }), + ('visdat', '0.5.3', { + 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('norm', '1.0-9.5', { + 'checksums': ['305cbf007f3905cfd535ed9bf5ae3e2995e228cc8883d6482e5d3a2f02814106'], + }), + ('naniar', '0.6.1', { + 'checksums': ['d546ca15bf6c224f3103eb1441abef91d34feebb7320c2398d598f5d50177450'], + }), + ('stringdist', '0.9.6.3', { + 'checksums': ['cd6d98f982e9ae7c4154a040c3a3f959bce19abf0229d64d22efef41f85b3f1b'], + }), + ('image.binarization', '0.1.1', { + 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], + }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), + ('lslx', '0.6.10', { + 'checksums': ['adc2b2a621625b52165245ab2f3a0bfba4f4db64fcc6ad48a3e5b219c3bd2fa1'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.8.0', { + 'checksums': ['28ff1c2dbddcafc6ed6c30154f46074aa0c8974757466680529b71a5f3e463ec'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), + ('cubelyr', '1.0.1', { + 'checksums': ['740a34100592b2c6b7bc89a31bddccf4c8fd95720caf68f530104f17aada77bc'], + }), + ('broom.mixed', '0.2.6', { + 'checksums': ['51ad18c65596fd3354427181a22255258738d64ef62a08c045da046ca36da8a0'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.1.0_identify-flexiblas-in-configure.patch b/easybuild/easyconfigs/r/R/R-4.1.0_identify-flexiblas-in-configure.patch new file mode 100644 index 00000000000..4731a8a8758 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.1.0_identify-flexiblas-in-configure.patch @@ -0,0 +1,12 @@ +Make R identify -lflexiblas as being for FlexiBLAS, so that it is not reported as a generic BLAS +Patch by Simon Branford (University of Birmingham) +--- configure.orig 2021-06-03 17:38:35.653766000 +0100 ++++ configure 2021-06-03 17:40:25.970132472 +0100 +@@ -55457,6 +55457,7 @@ + *-latlas*) r_blas=ATLAS ;; + *-lgoto*) r_blas=Goto ;; + *-lopenblas*) r_blas=OpenBLAS ;; ++ *-lflexiblas*) r_blas=FlexiBLAS ;; + *-lacml*) r_blas=ACML ;; + *-lmkl*) r_blas=MKL ;; + *-lsgemm*) r_blas=PhiPack ;; diff --git a/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.3-intel-2016b-Python-2.7.12.eb index b11e63c0268..31218bfb00a 100644 --- a/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.3-intel-2016b-Python-2.7.12.eb @@ -11,7 +11,6 @@ description = """A general purpose classical simulation package that can be used toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['https://pypi.python.org/packages/source/r/RASPA2/'] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-GCC-10.2.0-pthreads-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-GCC-10.2.0-pthreads-avx2.eb new file mode 100644 index 00000000000..0d508c30443 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-GCC-10.2.0-pthreads-avx2.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.12' +versionsuffix = '-pthreads-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105'] + +buildopts = '-f Makefile.AVX2.PTHREADS.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-PTHREADS-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-PTHREADS-AVX2 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +sanity_check_commands = ["raxmlHPC -%s" % x for x in ['h', 'v']] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb index 7f3482ebb6d..5015d25f856 100644 --- a/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb @@ -17,24 +17,19 @@ use_pip = True exts_list = [ ('ply', '3.11', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ply/'], 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], }), ('appdirs', '1.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs/'], 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), ('PyUtilib', '5.6.5', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyUtilib/'], 'checksums': ['4730084624be98f2c326da88f3852831c6aa919e11babab2c34b0299c8f5ce2a'], }), ('Pyomo', '5.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pyomo/'], 'checksums': ['449be9a4c9b3caee7c89dbe5f0e4e5ad0eaeef8be110a860641cd249986e362c'], 'modulename': 'pyomo', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/r/rbfopt/'], 'source_tmpl': 'rbfopt-%(version)s.tar.gz', 'checksums': ['fdcef4ca8272f3467d38fb061ce362fc372cc3494f5e75e84c91c9bdeb0db295'], }), diff --git a/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2019a.eb b/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2019a.eb index 818094b26f6..d45802b02eb 100644 --- a/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2019a.eb +++ b/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2019a.eb @@ -21,25 +21,20 @@ use_pip = True exts_list = [ ('ply', '3.11', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ply/'], 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], }), ('appdirs', '1.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs/'], 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), ('PyUtilib', '5.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyUtilib/'], 'checksums': ['b9cff12af85e3b3d4af528294d26f5c7b105cfe9d124223d7910ed8a0b93b1d4'], }), ('Pyomo', '5.6.6', { 'modulename': 'pyomo', - 'source_urls': ['https://pypi.python.org/packages/source/P/Pyomo/'], 'checksums': ['813e14a604b9d3ac63bdd0880c07f5f4e1b8f0a8a10345f1b42bee762219c001'], }), (name, version, { 'source_tmpl': 'rbfopt-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/r/rbfopt/'], 'checksums': ['fdcef4ca8272f3467d38fb061ce362fc372cc3494f5e75e84c91c9bdeb0db295'], }), ] diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-4.2.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-4.2.2-GCCcore-8.3.0.eb index 93a5d0807da..d4cbd10a82c 100644 --- a/easybuild/easyconfigs/r/RDFlib/RDFlib-4.2.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-4.2.2-GCCcore-8.3.0.eb @@ -13,8 +13,6 @@ builddependencies = [('binutils', '2.32')] multi_deps = {'Python': ['2.7.16', '3.7.4']} -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-4.2.2-foss-2019a.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-4.2.2-foss-2019a.eb index 17fa1b5fe4c..c1c887f5a09 100644 --- a/easybuild/easyconfigs/r/RDFlib/RDFlib-4.2.2-foss-2019a.eb +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-4.2.2-foss-2019a.eb @@ -11,8 +11,6 @@ toolchain = {'name': 'foss', 'version': '2019a'} multi_deps = {'Python': ['2.7.15', '3.7.2']} -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/r/RE2/RE2-2021-06-01-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2021-06-01-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c1e9c7de09c --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2021-06-01-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = "CMakeMake" + +name = 'RE2' +version = '2021-06-01' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['26155e050b10b5969e986dab35654247a3b1b295e0532880b5a9c13c0a700ceb'] + +builddependencies = { + ('CMake', '3.18.4'), + ('binutils', '2.35'), +} + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RECON/RECON-1.08-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RECON/RECON-1.08-GCC-10.2.0.eb new file mode 100644 index 00000000000..cc485eefd28 --- /dev/null +++ b/easybuild/easyconfigs/r/RECON/RECON-1.08-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'RECON' +version = '1.08' + +homepage = 'https://www.repeatmasker.org/RepeatModeler/' +description = """Patched version of RECON to be used with RepeatModeler.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.repeatmasker.org/RepeatModeler/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8'] + +dependencies = [('Perl', '5.32.0')] + +start_dir = 'src' + +buildopts = 'CC="$CC"' + +local_bins = ['edgeredef', 'eledef', 'eleredef', 'famdef', 'imagespread'] +local_scripts = ['scripts/%s' % x for x in ['MSPCollect.pl', 'recon.pl']] + +files_to_copy = [ + (['src/%s' % x for x in local_bins], 'bin'), + 'scripts', 'COPYRIGHT', 'LICENSE', '00README', +] + +postinstallcmds = ["sed -i 's|$path = \"\"|$path = \"%(installdir)s/bin\"|g' %(installdir)s/scripts/recon.pl"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + local_scripts, + 'dirs': [], +} + +sanity_check_commands = [("recon.pl 2>&1 | grep 'usage: recon seq_name_list_file MSP_file integer'", '')] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb new file mode 100644 index 00000000000..857bf922ee0 --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb @@ -0,0 +1,63 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'RMBlast' +version = '2.11.0' + +homepage = 'https://www.repeatmasker.org/RMBlast.html' +description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary + difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' + for use with RepeatMasker and RepeatModeler.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +# RMBlast is distributed as a patch that applies on top of BLAST+ +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [('https://www.repeatmasker.org/isb-%(version)s+-%(namelower)s.patch.gz', 2)] +checksums = [ + 'd88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954', # ncbi-blast-2.11.0+-src.tar.gz + '0fc27781c2ea2f17645247e2f3775b5d18c56f0b62761a865347be745ea4f6be', # isb-2.11.0+-rmblast.patch.gz +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('PCRE', '8.44'), + ('Boost', '1.74.0'), + ('GMP', '6.2.0'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), +] + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +prebuildopts = "sed -i 's/LIBS =/LIBS = $(BLAST_THIRD_PARTY_LIBS)/' src/app/rmblastn/Makefile.rmblastn.app && " + +sanity_check_paths = { + 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb b/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb new file mode 100644 index 00000000000..fa1a05370aa --- /dev/null +++ b/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonPackage' + +name = 'RagTag' +version = '2.0.1' + +homepage = 'https://github.com/malonge/RagTag' +description = """RagTag is a collection of software tools for scaffolding and +improving modern genome assemblies. Tasks include: homology-based misassembly +correction, homology-based assembly scaffolding and patching, and scaffold +merging. RagTag also provides command line utilities for working with common +genome assembly file formats.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/malonge/RagTag/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ragtag-2.0.1-scripts.patch'] +checksums = [ + 'fc3022d744cabdc2f492c0aa353af7c07fc71efd1b07c5ca5d333601868862c4', # v2.0.1.tar.gz + '01d1623fade21fb838904334fc2afc93351e66241c612939c619714658f43687', # ragtag-2.0.1-scripts.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Pysam', '0.16.0.1'), + ('networkx', '2.5'), + ('MUMmer', '4.0.0beta2'), + ('minimap2', '2.18'), + ('unimap', '0.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/ragtag.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'ragtag.py updategff --help', + # Ragtag exec()s these commands + 'nucmer --help', + 'minimap2 --help', + 'unimap --help', +] + +options = {'modulename': 'ragtag_utilities'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RagTag/ragtag-2.0.1-scripts.patch b/easybuild/easyconfigs/r/RagTag/ragtag-2.0.1-scripts.patch new file mode 100644 index 00000000000..ec538d831b1 --- /dev/null +++ b/easybuild/easyconfigs/r/RagTag/ragtag-2.0.1-scripts.patch @@ -0,0 +1,20 @@ +Binary files RagTag-old/.git/index and RagTag/.git/index differ +diff -ruN RagTag-old/setup.py RagTag/setup.py +--- RagTag-old/setup.py 2021-06-23 15:39:09.445353653 +0200 ++++ RagTag/setup.py 2021-06-23 15:38:48.621474180 +0200 +@@ -8,7 +8,7 @@ + with open("README.md", "r") as fh: + long_description = fh.read() + +-scripts = glob.glob("*.p*") ++scripts = glob.glob("ragtag*.p*") + + version = get_ragtag_version()[1:] + +@@ -37,4 +37,4 @@ + python_requires='>=3.6', + scripts=scripts, + zip_safe=True +-) +\ No newline at end of file ++) diff --git a/easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb b/easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb new file mode 100644 index 00000000000..d86d97d9b04 --- /dev/null +++ b/easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Ragout' +version = '2.3' + +homepage = 'https://github.com/fenderglass/Ragout' +description = """Ragout (Reference-Assisted Genome Ordering UTility) is a tool +for chromosome-level scaffolding using multiple references. Given initial +assembly fragments (contigs/scaffolds) and one or multiple related references +(complete or draft), it produces a chromosome-scale assembly (as a set of +scaffolds).""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'fenderglass' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['69d50a7ff49f03821e0143449ee0dc3e80c73e2c24568cad71948a5492613bca'] + +dependencies = [ + ('Python', '3.8.6'), + ('Sibelia', '3.0.7'), + ('HAL', '2.1'), + ('networkx', '2.5'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_commands = ['ragout --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.6.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.6.0-intel-2018b-Python-3.6.6.eb index ded6150d638..53c293e0811 100644 --- a/easybuild/easyconfigs/r/Raysect/Raysect-0.6.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.6.0-intel-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ description = """Raysect is an OOP ray-tracing framework for Python""" toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['04aca4fdaa4d0802409922cc396934d6eb62da261cfacd7ab7b0a19380253cc6'] diff --git a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb new file mode 100644 index 00000000000..1d6a13798f2 --- /dev/null +++ b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb @@ -0,0 +1,31 @@ +easyblock = 'RPackage' + +name = 'RcppGSL' +version = '0.3.8' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/RcppGSL' +description = """The 'RcppGSL' package provides an easy-to-use interface + between 'GSL' data structures and R using concepts from 'Rcpp' which is itself + a package that eases the interfaces between R and C++.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'] + +dependencies = [ + ('R', '4.0.4'), + ('GSL', '2.6'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['RcppGSL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb index 37be512a83b..7cd54d733cf 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb @@ -13,8 +13,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] req_py_majver = 3 req_py_minver = 6 -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb index 77a03ef8b4b..a8e5fb9d649 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb @@ -13,8 +13,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] req_py_majver = 3 req_py_minver = 6 -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb index a672d19e378..e325322041c 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb @@ -13,8 +13,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] req_py_majver = 3 req_py_minver = 6 -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb index 134f250ccc0..897caab22e8 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb @@ -13,8 +13,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] req_py_majver = 3 req_py_minver = 6 -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb index 9fa373cba0c..5fa93291a41 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb @@ -13,8 +13,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] req_py_majver = 3 req_py_minver = 6 -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb new file mode 100644 index 00000000000..be6da2fe133 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.6.2' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.1.2', { + 'use_pip': False, + 'checksums': ['eb5df6b9ab0af50fe1098a52fd439b04730b6e066887ff7497357b9ebd19f79b'], + }), + ('setuptools', '53.0.0', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['1b18ef17d74ba97ac9c0e4b4265f123f07a8ae85d9cd093949fa056d3eeeead5'], + }), + ('reframe', version, { + 'prebuildopts': ('./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ' + 'PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH '), + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], + 'use_pip': False, + 'checksums': ['b4725e434f4cd721ca825a56a652e67aa77e7af5ed7ca00f281747585827060d'], + }), +] + +postinstallcmds = [ + 'cp -r tutorials %(installdir)s', + 'mkdir -p %(installdir)s/share/man/man1 %(installdir)s/share/man/man8', + 'cp docs/man/man1/reframe.1 %(installdir)s/share/man/man1', + 'cp docs/man/man8/reframe.settings.8 %(installdir)s/share/man/man8', + 'cp -r share/completions %(installdir)s/share/completions' +] + +sanity_check_paths = { + 'files': ['bin/reframe', 'share/man/man1/reframe.1', + 'share/man/man8/reframe.settings.8', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['lib', 'tutorials', 'external'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions +modextrapaths = { + 'PATH': 'bin', + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/RegTools/RegTools-0.4.2-foss-2020b.eb b/easybuild/easyconfigs/r/RegTools/RegTools-0.4.2-foss-2020b.eb new file mode 100644 index 00000000000..3e591219097 --- /dev/null +++ b/easybuild/easyconfigs/r/RegTools/RegTools-0.4.2-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'RegTools' +version = '0.4.2' + +homepage = 'https://regtools.readthedocs.org' +description = """RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a +regulatory and splicing context.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/griffithlab/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['47b52015c4d36d064f1ebf36c8481f6119b9e993df3c078d1e2925c45d2e72d0'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +# required by included scripts +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), # required by create_IGVsessions.py script + ('R', '4.0.3'), +] + +# 'make install' is not supported... +install_cmd = "mkdir %(installdir)s/bin && cp -a regtools %(installdir)s/bin/ && " +install_cmd += "cp -a %(builddir)s/regtools-%(version)s/scripts %(installdir)s/" + +sanity_check_paths = { + 'files': ['bin/regtools'], + 'dirs': ['scripts'], +} + +sanity_check_commands = ["regtools --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb new file mode 100644 index 00000000000..726cafbe039 --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb @@ -0,0 +1,53 @@ +easyblock = 'Tarball' + +name = 'RepeatMasker' +version = '4.1.2-p1' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://www.repeatmasker.org/%(name)s'] +sources = [ + SOURCE_TAR_GZ, + # optional but recommended: RepBase RepeatMasker Edition + # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php + # { + # 'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz', + # 'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1", + # }, +] +checksums = [ + '4be54bf6c050422b211e24a797feb06fd7954c8b4ee6f3ece94cb6faaf6b0e96', # RepeatMasker-4.1.2-p1.tar.gz + # 'd7fa3bcd55703da14aa456fdc25c0487f171ad34ddfef886f847552993b32d34', # RepBaseRepeatMaskerEdition-20181026.tar.gz +] + +dependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0'), + ('TRF', '4.09.1'), + ('h5py', '3.1.0'), + # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match + ('HMMER', '3.3.2'), + ('RMBlast', '2.11.0'), +] + +local_default_search_engine = 'RMBlast' + +preinstall_cmd = './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +preinstall_cmd += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +preinstall_cmd += '-default_search_engine %s' % local_default_search_engine.lower() +# preinstall_cmd += '-libdir="RepeatMasker/Libraries" + +sanity_check_paths = { + 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], + 'dirs': ['Libraries', 'util'], +} + +sanity_check_commands = ['RepeatMasker -help'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb new file mode 100644 index 00000000000..1b471ca34da --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'RepeatScout' +version = '1.0.6' + +homepage = 'https://www.repeatmasker.org/' +description = """De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and + tested with our multiple sequence version of RepeatScout ( 1.0.6 )""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.repeatmasker.org'] +sources = ['RepeatScout-%(version)s.tar.gz'] +checksums = ['31a44cf648d78356aec585ee5d3baf936d01eaba43aed382d9ac2d764e55b716'] + +dependencies = [ + ('Perl', '5.32.0'), + ('TRF', '4.09.1'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i -e 's|mkdir|mkdir -p|g' -e 's|VERSION = .*|VERSION = %(version)s|g' Makefile &&" + +installopts = 'INSTDIR="%(installdir)s"' + +sanity_check_paths = { + 'files': [name, 'build_lmer_table', 'README'], + 'dirs': [], +} + +sanity_check_commands = [("RepeatScout 2>&1 | grep 'Usage:\nRepeatScout'", '')] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rtree/Rtree-0.8.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/r/Rtree/Rtree-0.8.3-intel-2018a-Python-2.7.14.eb index e63a0ad1bf5..44d6685bdef 100755 --- a/easybuild/easyconfigs/r/Rtree/Rtree-0.8.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/r/Rtree/Rtree-0.8.3-intel-2018a-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'Rtree' version = '0.8.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://toblerity.org/rtree/' +homepage = 'https://toblerity.org/rtree/' description = """Rtree is a ctypes Python wrapper of libspatialindex that provides a number of advanced spatial indexing features for the spatially curious Python user.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6cb9cf3000963ea6a3db777a597baee2bc55c4fc891e4f1967f262cc96148649'] @@ -19,9 +18,4 @@ dependencies = [ ('libspatialindex', '1.8.5'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f02f5356791 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-10.3.0.eb @@ -0,0 +1,164 @@ +name = 'Ruby' +version = '3.0.1' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['369825db2199f6aeef16b408df6a04ebaddb664fb9af0ec8c686b0ce7ab77727'] + +builddependencies = [('binutils', '2.36.1')] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# !! order of packages is important !! +# some packages have dependencies with minimum and maximum version requirements +# each version is picked as high as possible to fullfill all requirements +# packages updated on 2021-07-02 +exts_list = [ + ('ffi', '1.15.3', { + 'checksums': ['98d5c5c4281c9c0466acc60cf0e79124bf3c311417fd97e7473e41722953fbf1'], + }), + ('childprocess', '4.1.0', { + 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], + }), + ('json', '2.5.1', { + 'checksums': ['918d8c41dacb7cfdbe0c7bbd6014a5372f0cf1c454ca150e9f4010fe80cc3153'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.21.0', { + 'checksums': ['f9394457cb1dd5ca1b7bdc0dfbbd8f56f5cde40f45f96bc90f0f895a87e41b77'], + }), + ('arr-pm', '0.0.11', { + 'checksums': ['f1ab088421276f446da1971c5071defd1504855ec46e196815fa43cd62d61a9f'], + }), + ('clamp', '1.3.2', { + 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], + }), + ('multipart-post', '2.1.1', { + 'checksums': ['d2dd7aa957650e0d99e0513cd388401b069f09528441b87d884609c8e94ffcfd'], + }), + ('ruby2_keywords', '0.0.4', { + 'checksums': ['3ae3189c2e1d2f60204dcceedf890ff49dd28979771e2576016a3ee73b668e97'], + }), + ('faraday-net_http', '1.0.1', { + 'checksums': ['3245ce406ebb77b40e17a77bfa66191dda04be2fd4e13a78d8a4305854d328ba'], + }), + ('faraday', '1.3.0', { + 'checksums': ['7f06817ba823ddeabf4dd85ca5e0f63e234527f564a03f09f6c7127951d3bac2'], + }), + ('faraday_middleware', '1.0.0', { + 'checksums': ['19e808539681bbf2e65df30dfbe27bb402bde916a1dceb4c7496dbe8de14334a'], + }), + ('highline', '2.0.3', { + 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.2.5', { + 'checksums': ['13a8fc3921ce4df8e04fb65f1037251decb08d74757b41163688bd1c1feccd39'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.15.0', { + 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], + }), + ('public_suffix', '4.0.6', { + 'checksums': ['a99967c7b2d1d2eb00e1142e60de06a1a6471e82af574b330e9af375e87c0cf7'], + }), + ('addressable', '2.7.0', { + 'checksums': ['5e9b62fe1239091ea9b2893cd00ffe1bcbdd9371f4e1d35fac595c98c5856cbb'], + }), + ('concurrent-ruby', '1.1.9', { + 'checksums': ['0ec0846d991c38f355b4228ad8ea77aa69c3fdaa320cd574dafedc10c4688a5b'], + }), + ('i18n', '1.8.10', { + 'checksums': ['ca24e52fdd6ad7af419241eef8c41e65ef4e3499c6b252df13f697919eb24e3c'], + }), + ('minitest', '5.14.4', { + 'checksums': ['f4716634d71b3ffb627cd63ba4f6f0f77c7a3f17353b1bdf52c8a7f2e0e4e7a7'], + }), + ('thread_safe', '0.3.6', { + 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], + }), + ('tzinfo', '1.1.0', { + 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], + }), + ('zeitwerk', '2.4.2', { + 'checksums': ['f4d6279b0ef0cb35c9e1bddbcecd6b148df82f1cf7b8023ac03d6625f567869c'], + }), + ('activesupport', '5.0.7.2', { + 'checksums': ['f75cc67fb08421bdf4c2a383a47d9b3b02ce5eec4749704b1286fb0c12c98bad'], + }), + ('gh', '0.18.0', { + 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], + }), + ('launchy', '2.5.0', { + 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], + }), + ('ethon', '0.14.0', { + 'checksums': ['10e267a39d7e2a92d944e5681ba46dbd211b5b5b6cf9b51afb769b8417247ead'], + }), + ('typhoeus', '1.4.0', { + 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], + }), + ('websocket', '1.2.9', { + 'checksums': ['884b12dee993217795bb5f58acc89c0121c88bdc99df4d1636c0505dca352b36'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.4.4', { + 'checksums': ['bf3a658875f70c1467fe7a3b302b795f074c84b28db6e4a2bd6b1ad6d12a2255'], + }), + ('rspec-support', '3.10.2', { + 'checksums': ['74315f89069fbaf2a710e2117340373b77ee45eceb026de87e0cad9dd5154596'], + }), + ('rspec-mocks', '3.10.2', { + 'checksums': ['93fc76e312c3d19cacc1cb2eb64bf82731de2e216295cf2b4d0ce31ba77923b4'], + }), + ('rspec-expectations', '3.10.1', { + 'checksums': ['27acf5d5df13f8cc8f7158001ebf572513bcec3d45404ba76e0a8998895ce9eb'], + }), + ('rspec-core', '3.10.1', { + 'checksums': ['ac9abdc9577a3a34e9e92815603da8343931055ab4fba1c2a49de6dd3b749673'], + }), + ('rspec', '3.10.0', { + 'checksums': ['b870b43d49ae4a4e063b94976d2742b0854ec10458c425d569b5556ee5898ab7'], + }), + ('rack', '2.2.3', { + 'checksums': ['2638e7eb6689a5725c7e16f30cc4aa4e31694dc3ca30d790952526781bd0bb44'], + }), + ('rack-protection', '2.1.0', { + 'checksums': ['1f523c16e5b32f139c8f6f1e3b3eb53aaa7a69bc79a30f3e80f8a93c89242a95'], + }), + ('tilt', '2.0.10', { + 'checksums': ['9b664f0e9ae2b500cfa00f9c65c34abc6ff1799cf0034a8c0a0412d520fac866'], + }), + ('mustermann', '1.1.1', { + 'checksums': ['0a21cfe505869cce9ce17998db5260344e78df81ae857c07a62143fd30299531'], + }), + ('sinatra', '2.1.0', { + 'checksums': ['f323e4446f3e2a132dcaaa134f89caddb29dd88370317f4f32faf5797f1ea535'], + }), + ('rack-test', '1.1.0', { + 'checksums': ['154161f40f162b1c009a655b7b0c5de3a3102cc6d7d2e94b64e1f46ace800866'], + }), + ('bundler', '2.2.21', { + 'checksums': ['3c8dc5e0cf66d385a9b33751e54986290d42023c5e1bba2b5df094917b6e234a'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb index 112305de8b9..313e5b7e910 100644 --- a/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ # This is not upstream version, but artic tweaked one, which is exactly required. ('Porechop', '0.3.2pre', { diff --git a/easybuild/easyconfigs/r/rapidtide/rapidtide-1.8.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/r/rapidtide/rapidtide-1.8.0-intel-2019a-Python-3.7.2.eb index 10c76f78836..a3c52bc806f 100644 --- a/easybuild/easyconfigs/r/rapidtide/rapidtide-1.8.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/r/rapidtide/rapidtide-1.8.0-intel-2019a-Python-3.7.2.eb @@ -31,11 +31,9 @@ fix_python_shebang_for = ['bin/*'] exts_list = [ ('patsy', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), ('statsmodels', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], }), (name, version, { diff --git a/easybuild/easyconfigs/r/retworkx/retworkx-0.9.0-foss-2021a.eb b/easybuild/easyconfigs/r/retworkx/retworkx-0.9.0-foss-2021a.eb new file mode 100644 index 00000000000..db7f66dde6f --- /dev/null +++ b/easybuild/easyconfigs/r/retworkx/retworkx-0.9.0-foss-2021a.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'retworkx' +version = '0.9.0' + +homepage = 'https://github.com/Qiskit/retworkx' +description = """retworkx is a general purpose graph library for python3 written in Rust to take advantage of the +performance and safety that Rust provides. It was built as a replacement for qiskit's previous (and current) +networkx usage (hence the name) but is designed to provide a high performance general purpose graph library for any +python application. The project was originally started to build a faster directed graph to use as the underlying data +structure for the DAG at the center of qiskit-terra's transpiler, but it has since grown to cover all the graph usage +in Qiskit and other applications.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f32269410471b93c1504c5e43db283509513848ef0547a945135c89f906b6304'] + +builddependencies = [ + ('Rust', '1.52.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rgdal/rgdal-1.5-23-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/rgdal/rgdal-1.5-23-foss-2020b-R-4.0.4.eb new file mode 100644 index 00000000000..c0c6e75fd59 --- /dev/null +++ b/easybuild/easyconfigs/r/rgdal/rgdal-1.5-23-foss-2020b-R-4.0.4.eb @@ -0,0 +1,32 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'RPackage' + +name = 'rgdal' +version = '1.5-23' +versionsuffix = '-R-%(rver)s' + +homepage = "https://rgdal.r-forge.r-project.org/" +description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and + access to projection/transformation operations from the 'PROJ.4' library.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['9ca5744b946e7a3c4ca26598612bf54e550d3a0c5811d56e22c30b73f83ccb6e'] + +dependencies = [ + ('R', '4.0.4'), + ('GDAL', '3.2.1'), +] + +sanity_check_paths = { + 'files': ['rgdal/R/rgdal'], + 'dirs': [], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-20200529-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-20200529-intel-2019b-Python-3.7.4.eb index ede9f792dcc..14d69982ce3 100644 --- a/easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-20200529-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-20200529-intel-2019b-Python-3.7.4.eb @@ -30,7 +30,6 @@ exts_list = [ 'checksums': ['a3d50157a274decab87589ad78b9e41e9f3d34eb27a7d50cc6e7ef34def98b44'], }), ('pymbar', '3.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['b079a7d0b9fbc8a92850277b664bb582991ef5ac399b3607e695569148f6c784'], }), ('openmmtools', '0.19.0', { diff --git a/easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-intel-2019b-Python-3.7.4.eb index 2a8891a4f82..7d4e36ca94d 100644 --- a/easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-intel-2019b-Python-3.7.4.eb @@ -29,7 +29,6 @@ exts_list = [ 'checksums': ['a3d50157a274decab87589ad78b9e41e9f3d34eb27a7d50cc6e7ef34def98b44'], }), ('pymbar', '3.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['b079a7d0b9fbc8a92850277b664bb582991ef5ac399b3607e695569148f6c784'], }), ('openmmtools', '0.19.0', { diff --git a/easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.12-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.12-intel-2019a-Python-3.7.2.eb index e9800204cc0..553c7127cd5 100644 --- a/easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.12-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.12-intel-2019a-Python-3.7.2.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cligj', '0.5.0', { 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], diff --git a/easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.24-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.24-foss-2019b-Python-3.7.4.eb index 28a6c274b6d..762952cbb66 100644 --- a/easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.24-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.24-foss-2019b-Python-3.7.4.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('snuggs', '1.4.7', { 'checksums': ['501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b'], diff --git a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb index bf84cbd7b91..f8c58014097 100644 --- a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb @@ -4,14 +4,14 @@ name = 'rnaQUAST' version = '1.5.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://cab.spbu.ru/software/rnaquast/' +homepage = 'https://cab.spbu.ru/software/rnaquast/' description = """rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://cab.spbu.ru/files/rnaquast/release%(version)s/'] +source_urls = ['https://cab.spbu.ru/files/rnaquast/release%(version)s/'] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['7286cd766127c65de032e7c4d38ff874a217bee29dadff7f5dbad5785a550d79'] @@ -29,29 +29,25 @@ postinstallcmds = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } exts_list = [ ('simplejson', '3.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], }), ('argh', '0.26.2', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argh'], 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], }), ('argcomplete', '1.9.5', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argcomplete'], 'checksums': ['94423d1a56cdec2ef47699e02c9a48cf8827b9c4465b836c0cefb30afe85e59a'], }), ('pyfaidx', '0.5.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyfaidx'], 'checksums': ['9ac22bdc7b9c5d995d32eb9dc278af9ba970481636ec75c0d687d38c26446caa'], }), ('gffutils', '0.9', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gffutils/'], 'checksums': ['e1b0bf2b422ec3491be13d77bf7baf71d274abd844e8f8b6c1217a95b236218b'], }), ] diff --git a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.0-foss-2020a-Python-3.8.2.eb index afaf20d3d31..7b587b5cdec 100644 --- a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.0-foss-2020a-Python-3.8.2.eb @@ -29,33 +29,28 @@ postinstallcmds = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } exts_list = [ ('joblib', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['7ad866067ac1fdec27d51c8678ea760601b70e32ff1881d4dc8e1171f2b64b24'], }), ('simplejson', '3.17.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], }), ('argh', '0.26.2', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argh'], 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], }), ('argcomplete', '1.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argcomplete'], 'checksums': ['de0e1282330940d52ea92a80fea2e4b9e0da1932aaa570f84d268939d1897b04'], }), ('pyfaidx', '0.5.9.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyfaidx'], 'checksums': ['73e740eaa45c097a09e543450f88d5ed06c0ece4b6936dad7e71077f67797b74'], }), ('gffutils', '0.10.1', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gffutils/'], 'checksums': ['a8fc39006d7aa353147238160640e2210b168f7849cb99896be3fc9441e351cb'], }), ] diff --git a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb index e078d87dbe5..f96103a11dc 100644 --- a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb @@ -12,7 +12,6 @@ description = """root_numpy is a Python extension module that provides an effici toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = [ '5842bbcde92133f60a61f56e9f0a875a0dbc2a567cc65a9ac141ecd72e416878', # root_numpy-4.8.0.tar.gz diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.7.9-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.7.9-foss-2016b-Python-2.7.12.eb index ec57b0aef7a..4759a647c49 100644 --- a/easybuild/easyconfigs/r/rpy2/rpy2-2.7.9-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.7.9-foss-2016b-Python-2.7.12.eb @@ -12,7 +12,6 @@ graphical libraries, as well as R-like structures and functions. """ toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['39e661949ddad0b3ee9c2ac0b85252c54cf8ccb4ed799f07f4d741e72cb64ba1'] @@ -21,9 +20,4 @@ dependencies = [ ('R', '3.3.1'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.8.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.8.2-intel-2017a-Python-2.7.13.eb index 327e3428b01..b1af303931d 100644 --- a/easybuild/easyconfigs/r/rpy2/rpy2-2.8.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.8.2-intel-2017a-Python-2.7.13.eb @@ -10,7 +10,6 @@ graphical libraries, as well as R-like structures and functions. """ toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2c1a313df4e64236dcfe1078ce847b8e3c180656c894928d3a4b391aacb9b24c'] @@ -21,9 +20,4 @@ dependencies = [ ('R', '3.4.0', '-X11-20170314'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-3.2.6-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/rpy2/rpy2-3.2.6-foss-2019b-Python-3.7.4.eb index 0d8095c5c9a..0f523377344 100644 --- a/easybuild/easyconfigs/r/rpy2/rpy2-3.2.6-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/rpy2/rpy2-3.2.6-foss-2019b-Python-3.7.4.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('simplegeneric', '0.8.1', { 'source_tmpl': '%(name)s-%(version)s.zip', @@ -39,11 +37,6 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = [ "pytest --pyargs rpy2 " # Disable tests which requires X11 present othewise it crashes with diff --git a/easybuild/easyconfigs/s/SALib/SALib-1.1.3-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/SALib/SALib-1.1.3-intel-2017b-Python-2.7.14.eb index ef70bc92669..6ac432be301 100644 --- a/easybuild/easyconfigs/s/SALib/SALib-1.1.3-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/SALib/SALib-1.1.3-intel-2017b-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'SALib' version = '1.1.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://SALib.github.io/SALib/' +homepage = 'https://SALib.github.io/SALib/' description = """Sensitivity Analysis Library in Python (Numpy). Contains Sobol, Morris, Fractional Factorial and FAST methods.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a69334cba08d1e1b2d73380da9d247d331acb9fc071fe3cc273095ef7286113d'] diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb index 45b05158e7e..4bb5584e658 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pyzmq', '18.1.0', { 'modulename': 'zmq', diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb new file mode 100644 index 00000000000..1b0ac4abc44 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb @@ -0,0 +1,22 @@ +## +# Author: Robert Mijakovic +## +name = 'SCOTCH' +version = '6.1.0' + +homepage = 'https://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gforge.inria.fr/frs/download.php/file/38352/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] +checksums = ['a3bc3fa3b243fcb52f8d68de4272562a0328afb18a96f535724d284e36730485'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.1.0.post1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.1.0.post1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..560936b94a0 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.1.0.post1-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '4.1.0.post1' + +homepage = 'https://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ecb062482b9d80319b56758c0341eb717735437f86a575bac3552804428bd73e'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/sconsign'], + 'dirs': [], +} + +sanity_check_commands = ["scons --help"] + +sanity_pip_check = True + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb index d74aa67bcc7..f137d101fa2 100644 --- a/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb @@ -30,10 +30,6 @@ dependencies = [ ('Trinity', '2.9.1', versionsuffix), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.35.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.35.0-foss-2019b-Python-3.7.4.eb index 8705f5f7835..6e1f5d06b99 100644 --- a/easybuild/easyconfigs/s/SHAP/SHAP-0.35.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.35.0-foss-2019b-Python-3.7.4.eb @@ -23,7 +23,6 @@ download_dep_fail = True sanity_pip_check = True use_pip = True -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['6b9a2a3636918b9cdce4d3c599786b38353fbdca49147b5407a75aee398b1018'] diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb new file mode 100644 index 00000000000..92977478d53 --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.6' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +checksums = ['2c220390ef63d001f8ab02c380087187ea02ad2bfc5956e05ecaa0725a6f9942'] + +builddependencies = [ + ('binutils', '2.35'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.6.0-GCC-8.2.0-2.31.1-Perl-5.28.1-Python-3.7.2.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.6.0-GCC-8.2.0-2.31.1-Perl-5.28.1-Python-3.7.2.eb index b957dbd9b3e..2bf04f1c7b1 100644 --- a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.6.0-GCC-8.2.0-2.31.1-Perl-5.28.1-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.6.0-GCC-8.2.0-2.31.1-Perl-5.28.1-Python-3.7.2.eb @@ -48,7 +48,6 @@ exts_list = [ ('DB_File', '1.852', { 'preconfigopts': "DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ", 'runtest': 'test', - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], 'checksums': ['3ab7957523b6da39c55cb2ec4e677d88aa4034fd0b2f40788781a58e7d078391'], }), diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..9f221d63902 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.3.0.eb @@ -0,0 +1,24 @@ +name = 'SWIG' +version = '4.0.2' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d53be9730d8d58a16bf0cbd1f8ac0c0c3e1090573168bfa151b01eb47fa906fc'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('zlib', '1.2.11'), + ('PCRE', '8.44'), +] + +configopts = '--without-alllang --with-boost=no' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a.eb index d4eeb11b53d..9f346722668 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'SciPy-bundle' version = '2019.03' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = "Bundle of Python packages for scientific software" toolchain = {'name': 'intel', 'version': '2019a'} @@ -20,7 +20,6 @@ check_ldshared = True # package versions updated Mar 15th 2019 exts_list = [ ('numpy', '1.16.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'source_tmpl': '%(name)s-%(version)s.zip', 'patches': [ 'numpy-1.12.0-mkl.patch', @@ -33,19 +32,16 @@ exts_list = [ ], }), ('scipy', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c'], }), ('mpi4py', '3.0.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], 'checksums': ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'], }), ('pandas', '0.24.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], }), ('mpmath', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intelcuda-2019a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intelcuda-2019a.eb index 180c9ecebd3..61d470b58a9 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intelcuda-2019a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intelcuda-2019a.eb @@ -20,7 +20,6 @@ check_ldshared = True # package versions updated Mar 15th 2019 exts_list = [ ('numpy', '1.16.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'source_tmpl': '%(name)s-%(version)s.zip', 'patches': [ 'numpy-1.12.0-mkl.patch', @@ -33,7 +32,6 @@ exts_list = [ ], }), ('scipy', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c'], }), ('mpi4py', '3.0.1', { @@ -41,11 +39,9 @@ exts_list = [ 'checksums': ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'], }), ('pandas', '0.24.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], }), ('mpmath', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb index ead229b0905..0e04cea1f7a 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb @@ -20,7 +20,6 @@ sanity_pip_check = True # order is important! exts_list = [ ('numpy', '1.17.3', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'source_tmpl': '%(name)s-%(version)s.zip', 'patches': ['numpy-1.12.0-mkl.patch'], 'checksums': [ @@ -29,7 +28,6 @@ exts_list = [ ], }), ('scipy', '1.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['2643cfb46d97b7797d1dbdb6f3c23fe3402904e3c90e6facfe6a9b98d808c1b5'], }), ('mpi4py', '3.0.2', { @@ -37,11 +35,9 @@ exts_list = [ 'checksums': ['f8d629d1e3e3b7b89cb99d0e3bc5505e76cc42089829807950d5c56606ed48e0'], }), ('pandas', '0.25.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['52da74df8a9c9a103af0a72c9d5fdc8e0183a90884278db7f386b5692a2220a4'], }), ('mpmath', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019b-Python-2.7.16.eb index 06924d8aadb..d583430b6e3 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019b-Python-2.7.16.eb @@ -21,7 +21,6 @@ sanity_pip_check = True exts_list = [ ('numpy', '1.16.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'patches': ['numpy-1.12.0-mkl.patch'], 'checksums': [ '8bb452d94e964b312205b0de1238dd7209da452343653ab214b5d681780e7a0c', @@ -29,7 +28,6 @@ exts_list = [ ], }), ('scipy', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['a4331e0b8dab1ff75d2c67b5158a8bb9a83c799d7140094dda936d876c7cfbb1'], }), ('mpi4py', '3.0.2', { @@ -37,11 +35,9 @@ exts_list = [ 'checksums': ['f8d629d1e3e3b7b89cb99d0e3bc5505e76cc42089829807950d5c56606ed48e0'], }), ('pandas', '0.24.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], }), ('mpmath', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019b-Python-3.7.4.eb index 75141f103fd..895d0f46d07 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019b-Python-3.7.4.eb @@ -19,7 +19,6 @@ use_pip = True # order is important! exts_list = [ ('numpy', '1.17.3', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'source_tmpl': '%(name)s-%(version)s.zip', 'patches': ['numpy-1.12.0-mkl.patch'], 'checksums': [ @@ -28,7 +27,6 @@ exts_list = [ ], }), ('scipy', '1.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['2643cfb46d97b7797d1dbdb6f3c23fe3402904e3c90e6facfe6a9b98d808c1b5'], }), ('mpi4py', '3.0.2', { @@ -36,11 +34,9 @@ exts_list = [ 'checksums': ['f8d629d1e3e3b7b89cb99d0e3bc5505e76cc42089829807950d5c56606ed48e0'], }), ('pandas', '0.25.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['52da74df8a9c9a103af0a72c9d5fdc8e0183a90884278db7f386b5692a2220a4'], }), ('mpmath', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intelcuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intelcuda-2019b-Python-3.7.4.eb index 8f227716c41..7af08a51737 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intelcuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intelcuda-2019b-Python-3.7.4.eb @@ -20,7 +20,6 @@ sanity_pip_check = True # order is important! exts_list = [ ('numpy', '1.17.3', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'source_tmpl': '%(name)s-%(version)s.zip', 'patches': ['numpy-1.12.0-mkl.patch'], 'checksums': [ @@ -29,7 +28,6 @@ exts_list = [ ], }), ('scipy', '1.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], 'checksums': ['2643cfb46d97b7797d1dbdb6f3c23fe3402904e3c90e6facfe6a9b98d808c1b5'], }), ('mpi4py', '3.0.2', { @@ -37,11 +35,9 @@ exts_list = [ 'checksums': ['f8d629d1e3e3b7b89cb99d0e3bc5505e76cc42089829807950d5c56606ed48e0'], }), ('pandas', '0.25.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], 'checksums': ['52da74df8a9c9a103af0a72c9d5fdc8e0183a90884278db7f386b5692a2220a4'], }), ('mpmath', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb index cb732c6888a..7157731622e 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb @@ -25,12 +25,15 @@ exts_list = [ 'patches': [ 'numpy-1.20.3_skip-ppc-long-complex-test.patch', 'numpy-1.20.3_xfail-test-nan.patch', + 'numpy-1.20.3_fix-target-test-ccompiler-opt.patch', ], 'checksums': [ 'e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69', # numpy-1.20.3.zip # numpy-1.20.3_skip-ppc-long-complex-test.patch '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4', 'f0ce961f7d79551598e23050d92f46e827e300f6a7e5a6112e58efcc10385d4d', # numpy-1.20.3_xfail-test-nan.patch + # numpy-1.20.3_fix-target-test-ccompiler-opt.patch + '3d84e8b7d48387778974a5f6ae342a690ab5989547206b6add9d9667f8d7572a', ], }), ('scipy', '1.6.3', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-target-test-ccompiler-opt.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-target-test-ccompiler-opt.patch new file mode 100644 index 00000000000..ee866e86597 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-target-test-ccompiler-opt.patch @@ -0,0 +1,33 @@ +From 6f2f26e08c6e0d476593c82ad31d13847f30cbf4 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= +Date: Sun, 28 Mar 2021 10:00:14 +0200 +Subject: [PATCH] BUG: Fix test_ccompiler_opt when path contains dots + +Fix test_ccompiler_opt not to be confused by dots occurring on the path +to the temporary directory, by using only the source file's basename +when grabbing options. Otherwise, the test can fail with mismatches +such as: + + E AssertionError: 'sources_status' returns different targets than the compiled targets + E ['AVX512F', 'AVX2'] != ['(20 2/TEMP/TMPB0YHSCAI/TEST_TARGETS AVX512F)', '(20 2/TEMP/TMPB0YHSCAI/TEST_TARGETS AVX2)'] + +This is because our TMPDIR value includes numpy version, i.e. 1.20.2. +The splitting happens on the first dot that is part of the directory +path rather than test filename. +--- + numpy/distutils/tests/test_ccompiler_opt.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/numpy/distutils/tests/test_ccompiler_opt.py b/numpy/distutils/tests/test_ccompiler_opt.py +index 287a683c8d6..d2b0a4c581a 100644 +--- a/numpy/distutils/tests/test_ccompiler_opt.py ++++ b/numpy/distutils/tests/test_ccompiler_opt.py +@@ -112,7 +112,7 @@ def get_targets(self, targets, groups, **kwargs): + gflags = {} + fake_objects = opt.try_dispatch([file]) + for source, flags in fake_objects: +- gtar = source.split('.')[1:-1] ++ gtar = path.basename(source).split('.')[1:-1] + glen = len(gtar) + if glen == 0: + gtar = "baseline" diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-intel-2018a-Python-2.7.14.eb index eb9a049ab77..15e903bfcf2 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-intel-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Scoary' version = '1.6.16' @@ -18,23 +18,15 @@ dependencies = [ ('Tkinter', '%(pyver)s', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - -exts_download_dep_fail = True - exts_list = [ ('ete3', '3.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ete3'], 'checksums': ['870a3d4b496a36fbda4b13c7c6b9dfa7638384539ae93551ec7acb377fb9c385'], }), ('argparse', '1.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse'], 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], }), (name, version, { 'source_tmpl': 'scoary-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/s/scoary'], 'checksums': ['f433343422c5805a70a20f7fe83851490ae3cdf07745c65680de5feea40a6dca'], }), ] @@ -44,6 +36,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompic-2020b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompic-2020b.eb new file mode 100644 index 00000000000..e3bc0ac5298 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompic-2020b.eb @@ -0,0 +1,57 @@ +# # +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Alexander Grund +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'Score-P' +version = '7.0' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['68f24a68eb6f94eaecf500e17448f566031946deab74f2cba072ee8368af0996'] + +dependencies = [ + ('CubeLib', '4.6'), + ('CubeWriter', '4.6'), + ('libunwind', '1.4.0'), + ('OPARI2', '2.0.6'), + ('OTF2', '2.3'), + # Hardware counter support (optional): + ('PAPI', '6.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'cuda_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.0-foss-2019b-Python-3.7.4.eb index c918b44bea7..e2ecac6185a 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.0-foss-2019b-Python-3.7.4.eb @@ -14,7 +14,6 @@ description = """ Seaborn is a Python visualization library based on matplotlib. toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['59fe414e138d7d5ea08b0feb01b86caf4682e36fa748e3987730523a89aecbb9'] diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.0-intel-2019b-Python-3.7.4.eb index 1a2676f3791..8305ee75433 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.0-intel-2019b-Python-3.7.4.eb @@ -14,7 +14,6 @@ description = """ Seaborn is a Python visualization library based on matplotlib. toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['59fe414e138d7d5ea08b0feb01b86caf4682e36fa748e3987730523a89aecbb9'] diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb index e80e2daca5c..44dffd9d940 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb @@ -9,13 +9,12 @@ name = 'Seaborn' version = '0.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ @@ -23,9 +22,4 @@ dependencies = [ ('matplotlib', '1.5.3', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.8.1-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.8.1-foss-2017a-Python-2.7.13.eb index 68432892ddd..b9c21ec81ea 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.8.1-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.8.1-foss-2017a-Python-2.7.13.eb @@ -4,13 +4,12 @@ name = 'Seaborn' version = '0.8.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'foss', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['6702978b903d0284446e935916b980dfebae4063c18ad8eb6e8f9e76d0257eae'] @@ -19,9 +18,4 @@ dependencies = [ ('matplotlib', '2.0.2', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.8.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.8.1-intel-2018a-Python-2.7.14.eb index 634b6c0f83a..1c9ab96e23e 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.8.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.8.1-intel-2018a-Python-2.7.14.eb @@ -4,13 +4,12 @@ name = 'Seaborn' version = '0.8.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['6702978b903d0284446e935916b980dfebae4063c18ad8eb6e8f9e76d0257eae'] @@ -21,9 +20,4 @@ dependencies = [ download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2017b-Python-2.7.14.eb index 4d2479c1b8e..8a963210091 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2017b-Python-2.7.14.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2017b-Python-3.6.3.eb index 04e3944c2a8..f9daf4f3406 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2017b-Python-3.6.3.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-2.7.15.eb index f7dbb662709..93032476826 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-2.7.15.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-3.6.6.eb index 6c5c6eff5b5..19ccdec8b60 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-3.6.6.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2019a-Python-2.7.15.eb index 5372abd89b4..775482fc508 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2019a-Python-2.7.15.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2019a-Python-3.7.2.eb index 61c0fc8943a..b316b889440 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2019a-Python-3.7.2.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-fosscuda-2017b-Python-2.7.14.eb index 9896c9844f7..32f29c0a54d 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-fosscuda-2017b-Python-2.7.14.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'fosscuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-fosscuda-2017b-Python-3.6.3.eb index ac01b045957..d1e9f1de9eb 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-fosscuda-2017b-Python-3.6.3.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'fosscuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2017b-Python-2.7.14.eb index 58863599926..0a727a96d6c 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2017b-Python-2.7.14.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2017b-Python-3.6.3.eb index 2fd97e4924c..48298c5a2cd 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2017b-Python-3.6.3.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018a-Python-2.7.14.eb index ff61bb9233c..1a1d9751eec 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018a-Python-2.7.14.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018a-Python-3.6.4.eb index ebe3b1ca83e..3a3b1bb2621 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018a-Python-3.6.4.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-2.7.15.eb index debe3ec3068..257ac512af1 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-2.7.15.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-3.6.6.eb index 61fdbde00d4..5665bec0859 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-3.6.6.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2019a-Python-2.7.15.eb index d44108752ff..ff6e188dc68 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2019a-Python-2.7.15.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2019a-Python-3.7.2.eb index ea4d73d82a1..4b9d9493c53 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2019a-Python-3.7.2.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intelcuda-2017b-Python-2.7.14.eb index 8f9f122fb52..33c4ff1bb4d 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intelcuda-2017b-Python-2.7.14.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intelcuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intelcuda-2017b-Python-3.6.3.eb index 8b22c8f4a22..298c9313762 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intelcuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intelcuda-2017b-Python-3.6.3.eb @@ -8,13 +8,12 @@ name = 'Seaborn' version = '0.9.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +homepage = 'https://stanford.edu/~mwaskom/software/seaborn/' description = """ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. """ toolchain = {'name': 'intelcuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] @@ -26,9 +25,4 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2019b-Python-2.7.16.eb index 613f68e2c49..a479accde43 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2019b-Python-2.7.16.eb @@ -14,7 +14,6 @@ description = """ Seaborn is a Python visualization library based on matplotlib. toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['da33aa8c20a9a342ce73831d02831a10413f54a05471c7f31edf34f225d456ae'] @@ -26,11 +25,6 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_pip_check = True moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb new file mode 100644 index 00000000000..c5786632482 --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.1.96' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('gperftools', '2.9.1'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5198f31c3bb25e685e9e68355a3bf67a1db23c9e8bdccc33dc015f496a44df7a'], +} + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'separate_build_dir': True, + 'start_dir': '%(namelower)s-%(version)s', + }), + ('sentencepiece', version, { + 'easyblock': 'PythonPackage', + 'start_dir': '%(namelower)s-%(version)s/python', + 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/'] + +sanity_check_paths = { + 'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] + + ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] + + ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'], +} + +sanity_check_commands = [ + 'spm_train --help', + "python -c 'import sentencepiece'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d65645b9dd5 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'SCons' +name = 'Serf' +version = '1.3.9' + +homepage = 'https://serf.apache.org/' +description = """The serf library is a high performance C-based HTTP client library + built upon the Apache Portable Runtime (APR) library""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Serf-%(version)s_python3_scons.patch'] +checksums = [ + '549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc', # serf-1.3.9.tar.bz2 + 'db401893bfb464ddcf369b543cacb9a165a21f8ff9bf1a819e4b61550bb9d3d0', # Serf-1.3.9_python3_scons.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), + ('SCons', '4.1.0.post1'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('OpenSSL', '1.1', '', True), +] + +buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" + +sanity_check_paths = { + 'files': ['include/serf-1/serf.h'] + + ['lib/libserf-1.%s' % x for x in ['a', 'so']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb new file mode 100644 index 00000000000..331b937181f --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb @@ -0,0 +1,60 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.0.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} + +exts_list = [ + ('spatstat.utils', '2.2-0', { + 'checksums': ['5ad87e524285621dc4ef75c941eba933d980125293ee8f2bef5b7db02f63d7ab'], + }), + ('spatstat.data', '2.1-0', { + 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], + }), + ('spatstat.geom', '2.2-0', { + 'checksums': ['70b063a7f317f531b2afb3afaedb047fce81b39ee481a4067962529d6069634c'], + }), + ('spatstat.sparse', '2.0-0', { + 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], + }), + ('spatstat.core', '2.2-0', { + 'checksums': ['0ecbc1ae688c8d4f41db3efa6253ac8db5c432ef714240d01a2b195950d65253'], + }), + ('Matrix', '1.3-4', { + 'checksums': ['ab42179d44545e99bbdf44bb6d04cab051dd2aba552b1f6edd51ed71b55f6c39'], + }), + ('SeuratObject', '4.0.2', { + 'checksums': ['64ee97a221ccaa0bbdc1890da9d3e9cf5b3b9fab037095cfb757db5bbb69cb1c'], + }), + (name, version, { + 'checksums': ['75d98696d0cee22eac5154ac26ef94accde5a5b0a140f3bdd60265322d9edfc9'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-GCC-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-GCC-8.3.0-Python-3.7.4.eb index b3392c28308..8b6dbbe911c 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-GCC-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-GCC-8.3.0-Python-3.7.4.eb @@ -10,7 +10,6 @@ It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from wh toolchain = {'name': 'GCC', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e21a9fe1a416463ff11ae037766fe410526c95700b9e545372475d2361cc951e'] diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-foss-2019a-Python-3.7.2.eb index 7a0b7af72c3..33370fee5b2 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-foss-2019a-Python-3.7.2.eb @@ -10,7 +10,6 @@ It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from wh toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e21a9fe1a416463ff11ae037766fe410526c95700b9e545372475d2361cc951e'] diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-iccifort-2019.5.281-Python-3.7.4.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-iccifort-2019.5.281-Python-3.7.4.eb index 310dd34740f..be8a389cef0 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-iccifort-2019.5.281-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.7.0-iccifort-2019.5.281-Python-3.7.4.eb @@ -10,7 +10,6 @@ It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from wh toolchain = {'name': 'iccifort', 'version': '2019.5.281'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e21a9fe1a416463ff11ae037766fe410526c95700b9e545372475d2361cc951e'] diff --git a/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb b/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb new file mode 100644 index 00000000000..4ee05dcdc08 --- /dev/null +++ b/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = "CMakeMake" + +name = 'Sibelia' +version = '3.0.7' + +homepage = 'http://bioinf.spbau.ru/en/%(namelower)s' +description = """Sibelia: A comparative genomics tool: It assists biologists in analysing + the genomic variations that correlate with pathogens, or the genomic changes that help + microorganisms adapt in different environments. Sibelia will also be helpful for the + evolutionary and genome rearrangement studies for multiple strains of microorganisms.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [('http://sourceforge.net/projects/%(namelower)s-bio/files/', 'download')] +sources = ['%(name)s-%(version)s-Source.tar.gz'] +patches = ['Sibelia-3.0.7-indeces.patch'] +checksums = [ + '114d076dd9f381d7e856ea54414e8a53e9f6bad28d75bb530ee511584f53070e', # Sibelia-3.0.7-Source.tar.gz + 'c20badf609d38b10be26c0f4a6517f6805684d6fb24fe0d34f4794c9c365529e', # Sibelia-3.0.7-indeces.patch +] + +builddependencies = [('CMake', '3.18.4')] + +start_dir = 'src' + +separate_build_dir = True + +prebuildopts = 'sed -i.bak "s#gcc#$CC#g" ../Sibelia-%(version)s-Source/src/lagan/src/Makefile && ' +prebuildopts += 'sed -i.bak "s#g++#$CXX#g" ../Sibelia-%(version)s-Source/src/lagan/src/Makefile && ' +prebuildopts += 'sed -i.bak "s#gcc#$CC#g" ../Sibelia-%(version)s-Source/src/lagan/src/glocal/Makefile && ' +prebuildopts += 'sed -i.bak "s#g++#$CXX#g" ../Sibelia-%(version)s-Source/src/lagan/src/glocal/Makefile && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['C-%(name)s.py', '%(name)s', 'snpEffAnnotate.py']], + 'dirs': [''], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-indeces.patch b/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-indeces.patch new file mode 100644 index 00000000000..51a9e9a4ef3 --- /dev/null +++ b/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-indeces.patch @@ -0,0 +1,119 @@ +Fix 'indices redeclared' linker error, use the provided CC and CFLAGS instead of the hard-coded ones + +Author: Jakub Zárybnický + +diff -ruN Sibelia-old/src/lagan/src/fchaos.c Sibelia/src/lagan/src/fchaos.c +--- Sibelia-old/src/lagan/src/fchaos.c 2021-06-24 12:01:17.431513317 +0200 ++++ Sibelia/src/lagan/src/fchaos.c 2021-06-24 12:04:34.334513210 +0200 +@@ -29,7 +29,7 @@ + int offset; + } match; + +-extern int indeces[256]; ++int indeces[256]; + + + void remElem(LList* tbf, int i); +diff -ruN Sibelia-old/src/lagan/src/glocal/Makefile Sibelia/src/lagan/src/glocal/Makefile +--- Sibelia-old/src/lagan/src/glocal/Makefile 2021-06-24 12:01:17.431513317 +0200 ++++ Sibelia/src/lagan/src/glocal/Makefile 2021-06-24 12:05:56.331688662 +0200 +@@ -1,7 +1,5 @@ +-CC = g++ +-OPTFLAGS = + CFLAGS = $(OPTFLAGS) -O3 -w +-CLINKER = g++ ++CLINKER = $(CXX) + # LIBDIR = -L/usr/local/lib + MLIB = -lm + INCDIR = -I. +diff -ruN Sibelia-old/src/lagan/src/Makefile Sibelia/src/lagan/src/Makefile +--- Sibelia-old/src/lagan/src/Makefile 2021-06-24 12:01:17.430513328 +0200 ++++ Sibelia/src/lagan/src/Makefile 2021-06-24 12:09:40.773449864 +0200 +@@ -1,6 +1,3 @@ +-CC = gcc $(CFLAGS) +-CPP = g++ $(CFLAGS) +-CFLAGS = -O3 -w + TRGT_DIR = .. + + all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay +@@ -9,46 +6,46 @@ + rm -f *.o *~ utils/*~ mlagan.purify core + (cd glocal; $(MAKE) clean) + ../anchors: anchors.c skiplist.c +- $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c + ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG + ../order: order.c diagmatrix.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c + ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG + ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG + ../utils/bin2mf: utils/bin2mf.c +- $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c + ../utils/bin2bl: utils/bin2bl.c +- $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c + ../utils/cextract: utils/cextract.c +- $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c + ../utils/cstat: utils/cstat.c +- $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c + ../utils/contigorder: utils/contigorder.c +- $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c + ../utils/getbounds: utils/getbounds.c +- $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c + ../utils/getcontigpos: utils/getcontigpos.c +- $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c + ../utils/getlength: utils/getlength.c +- $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c + ../utils/getoverlap: utils/getoverlap.c +- $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c + ../utils/rc: utils/rc.c +- $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c + ../utils/seqmerge: utils/seqmerge.c +- $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c + ../utils/scorealign: utils/scorealign.c +- $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm + ../utils/scorecontigs: utils/scorecontigs.c +- $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm + ../utils/fa2xfa: utils/fa2xfa.c +- $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c + ../utils/overlay: utils/overlay.c +- $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c ++ $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c + ../utils/Glue: utils/Glue.cpp +- $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp ++ $(CXX) $(CFLAGS) $(CXXFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp + ../utils/dotplot: utils/dotplot.cpp +- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp ++ $(CXX) $(CFLAGS) $(CXXFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp +diff -ruN Sibelia-old/src/lagan/src/thrtrie.h Sibelia/src/lagan/src/thrtrie.h +--- Sibelia-old/src/lagan/src/thrtrie.h 2021-06-24 12:01:17.436513266 +0200 ++++ Sibelia/src/lagan/src/thrtrie.h 2021-06-24 12:04:34.334513210 +0200 +@@ -2,7 +2,7 @@ + #define MAX_DEGEN 2 + + +-int indeces[256]; ++extern int indeces[256]; + + typedef struct PrevHits { + int* inds1; diff --git a/easybuild/easyconfigs/s/SimPEG/SimPEG-0.3.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.3.1-intel-2016b-Python-2.7.12.eb index d9e07f44c50..eafbad5b735 100644 --- a/easybuild/easyconfigs/s/SimPEG/SimPEG-0.3.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.3.1-intel-2016b-Python-2.7.12.eb @@ -4,14 +4,13 @@ name = 'SimPEG' version = '0.3.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://simpeg.xyz' +homepage = 'https://simpeg.xyz' description = """Simulation and Parameter Estimation in Geophysics: a python package for simulation and gradient based parameter estimation in the context of geophysical applications.""" toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] dependencies = [ ('Python', '2.7.12'), diff --git a/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb index 973bfb387a1..35d4801c28d 100644 --- a/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb @@ -33,8 +33,6 @@ use_pip = True # required because we're building Python packages using Intel compilers on top of Python built with GCC check_ldshared = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('squarify', '0.4.2', { 'checksums': ['d149d81fc76c4272251649e4f6f1bfe3f2db7cb13ba51fd22a80c4f70786d331'], diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb index ade62e1b626..0e81ab6be6c 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'Spark' version = '2.2.0' versionsuffix = '-Hadoop-2.6-Java-%(javaver)s-Python-%(pyver)s' -homepage = 'http://spark.apache.org' +homepage = 'https://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'intel', 'version': '2017b'} @@ -24,9 +24,10 @@ dependencies = [ exts_defaultclass = 'PythonPackage' +exts_default_options = {'source_urls': [PYPI_SOURCE]} + exts_list = [ ('py4j', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py4j'], 'checksums': ['b49a28c6bd96d334a39c15c3ce52225585332eff5e2659c7dc7aa223aa8bd454'], }), ('pyspark', version, { diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb index d82c33b1f66..23510072e38 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb @@ -33,7 +33,6 @@ exts_default_options = { exts_list = [ ('py4j', '0.10.8.1', { 'source_tmpl': 'py4j-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/py4j'], 'checksums': ['8329bb156a0cf37be9642a2a060dbdb627b5fcb827919be65d95102daccca274'], }), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb index 8fc9c0cab45..6fa3caf6ede 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb @@ -26,8 +26,8 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { - 'download_dep_fail': True, 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, 'use_pip': True, } diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb index 5007e91244f..387340456d0 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb @@ -33,7 +33,6 @@ exts_default_options = { exts_list = [ ('py4j', '0.10.8.1', { 'source_tmpl': 'py4j-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/py4j'], 'checksums': ['8329bb156a0cf37be9642a2a060dbdb627b5fcb827919be65d95102daccca274'], }), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb index cff8677c4a2..cd360504934 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb @@ -33,7 +33,6 @@ exts_default_options = { exts_list = [ ('py4j', '0.10.8.1', { 'source_tmpl': 'py4j-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/py4j'], 'checksums': ['8329bb156a0cf37be9642a2a060dbdb627b5fcb827919be65d95102daccca274'], }), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb index 855d0669d32..f8644c9fdea 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb @@ -29,6 +29,7 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } @@ -37,7 +38,6 @@ exts_list = [ # Spark requires this version specifically ('py4j', '0.10.7', { 'source_tmpl': 'py4j-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/py4j'], 'checksums': ['721189616b3a7d28212dfb2e7c6a1dd5147b03105f1fc37ff2432acd0e863fa5'], }), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb index 6ae5535e4df..acff4d94720 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb @@ -26,13 +26,13 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } exts_list = [ ('py4j', '0.10.9', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['36ec57f43ff8ced260a18aa9a4e46c3500a730cac8860e259cbaa546c2b9db2f'], }), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb index ec3723f625c..b090aaef033 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb @@ -32,7 +32,6 @@ exts_default_options = { exts_list = [ ('py4j', '0.10.9', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['36ec57f43ff8ced260a18aa9a4e46c3500a730cac8860e259cbaa546c2b9db2f'], }), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb index 5d026d55f62..a6e616bd811 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb @@ -26,13 +26,13 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } exts_list = [ ('py4j', '0.10.9.2', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], }), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index d006f6a9321..71ff15224de 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -25,13 +25,13 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } exts_list = [ ('py4j', '0.10.9.2', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], }), ] diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb index cad99052f5a..1f4bff57863 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Sphinx' version = '1.4.8' @@ -12,9 +12,6 @@ description = """Sphinx is a tool that makes it easy to create intelligent and b toolchain = {'name': 'foss', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.11'), ('Pygments', '2.1.3', '-Python-%(pyver)s'), @@ -22,37 +19,23 @@ dependencies = [ ] exts_list = [ - ('imagesize', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], - }), + ('imagesize', '0.7.1'), ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.io/packages/source/M/MarkupSafe/'], 'modulename': 'markupsafe', }), ('Docutils', '0.12', { 'source_tmpl': 'docutils-%(version)s.tar.gz', 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], }), - ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], - }), - ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], - }), - ('Babel', '2.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], - }), - ('alabaster', '0.7.8', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], - }), + ('Jinja2', '2.8'), + ('snowballstemmer', '1.2.1'), + ('Babel', '2.3.4'), + ('alabaster', '0.7.8'), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' % version], }), # sphinx_rtd_theme depends on Sphinx, and should be there to make the tests work - ('sphinx_rtd_theme', '0.1.10a0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], - }), + ('sphinx_rtd_theme', '0.1.10a0'), ] # Sphinx unit tests *after* installing extensions @@ -66,6 +49,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb index bfe74494209..33d4e013a97 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Sphinx' version = '1.4.8' @@ -12,9 +12,6 @@ description = """Sphinx is a tool that makes it easy to create intelligent and b toolchain = {'name': 'foss', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.5.1'), ('Pygments', '2.1.3', '-Python-%(pyver)s'), @@ -22,37 +19,23 @@ dependencies = [ ] exts_list = [ - ('imagesize', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], - }), + ('imagesize', '0.7.1'), ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.io/packages/source/M/MarkupSafe/'], 'modulename': 'markupsafe', }), ('Docutils', '0.12', { 'source_tmpl': 'docutils-%(version)s.tar.gz', 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], }), - ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], - }), - ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], - }), - ('Babel', '2.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], - }), - ('alabaster', '0.7.8', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], - }), + ('Jinja2', '2.8'), + ('snowballstemmer', '1.2.1'), + ('Babel', '2.3.4'), + ('alabaster', '0.7.8'), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' % version], }), # sphinx_rtd_theme depends on Sphinx, and should be there to make the tests work - ('sphinx_rtd_theme', '0.1.10a0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], - }), + ('sphinx_rtd_theme', '0.1.10a0'), ] # Sphinx unit tests *after* installing extensions @@ -66,6 +49,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-2.7.14.eb index 19cb7ea3777..ee6b6cf10eb 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-2.7.14.eb @@ -18,27 +18,22 @@ use_pip = True exts_list = [ ('packaging', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('sphinxcontrib-websupport', '1.1.0', { 'modulename': 'sphinxcontrib.websupport', - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], # can't use pip here because it doesn't support namespaces # cfr. https://github.com/pypa/pip/issues/1924 'use_pip': False, }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('imagesize', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], }), ('Docutils', '0.14', { @@ -47,35 +42,27 @@ exts_list = [ 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], }), ('Babel', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], }), ('alabaster', '0.7.12', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), ('typing', '3.6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], }), ('sphinx_rtd_theme', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], }), ('numpydoc', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], }), ] diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-3.6.3.eb index e5ebc21dbed..7beeebfdb11 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-3.6.3.eb @@ -18,27 +18,22 @@ use_pip = True exts_list = [ ('packaging', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('sphinxcontrib-websupport', '1.1.0', { 'modulename': 'sphinxcontrib.websupport', - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], # can't use pip here because it doesn't support namespaces # cfr. https://github.com/pypa/pip/issues/1924 'use_pip': False, }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('imagesize', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], }), ('Docutils', '0.14', { @@ -47,35 +42,27 @@ exts_list = [ 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], }), ('Babel', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], }), ('alabaster', '0.7.12', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), ('typing', '3.6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], }), ('sphinx_rtd_theme', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], }), ('numpydoc', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], }), ] diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018a-Python-3.6.4.eb index 3ce69c9fae6..26353b88ff6 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018a-Python-3.6.4.eb @@ -18,27 +18,22 @@ use_pip = True exts_list = [ ('packaging', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('sphinxcontrib-websupport', '1.1.0', { 'modulename': 'sphinxcontrib.websupport', - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], # can't use pip here because it doesn't support namespaces # cfr. https://github.com/pypa/pip/issues/1924 'use_pip': False, }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('imagesize', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], }), ('Docutils', '0.14', { @@ -47,35 +42,27 @@ exts_list = [ 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], }), ('Babel', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], }), ('alabaster', '0.7.12', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), ('typing', '3.6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], }), ('sphinx_rtd_theme', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], }), ('numpydoc', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], }), ] diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018b-Python-2.7.15.eb index 3e555e83c63..48ab09d940f 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018b-Python-2.7.15.eb @@ -18,27 +18,22 @@ use_pip = True exts_list = [ ('packaging', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('sphinxcontrib-websupport', '1.1.0', { 'modulename': 'sphinxcontrib.websupport', - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], # can't use pip here because it doesn't support namespaces # cfr. https://github.com/pypa/pip/issues/1924 'use_pip': False, }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('imagesize', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], }), ('Docutils', '0.14', { @@ -47,35 +42,27 @@ exts_list = [ 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], }), ('Babel', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], }), ('alabaster', '0.7.12', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), ('typing', '3.6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], }), ('sphinx_rtd_theme', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], }), ('numpydoc', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], }), ] diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018b-Python-3.6.6.eb index a8f1704ce4f..b184ab2543f 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2018b-Python-3.6.6.eb @@ -18,27 +18,22 @@ use_pip = True exts_list = [ ('packaging', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('sphinxcontrib-websupport', '1.1.0', { 'modulename': 'sphinxcontrib.websupport', - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], # can't use pip here because it doesn't support namespaces # cfr. https://github.com/pypa/pip/issues/1924 'use_pip': False, }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('imagesize', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], }), ('Docutils', '0.14', { @@ -47,35 +42,27 @@ exts_list = [ 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], }), ('Babel', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], }), ('alabaster', '0.7.12', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), ('typing', '3.6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], }), ('sphinx_rtd_theme', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], }), ('numpydoc', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], }), ] diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-2.7.14.eb index c43976b768c..7c0ed56194b 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-2.7.14.eb @@ -18,27 +18,22 @@ use_pip = True exts_list = [ ('packaging', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('sphinxcontrib-websupport', '1.1.0', { 'modulename': 'sphinxcontrib.websupport', - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], # can't use pip here because it doesn't support namespaces # cfr. https://github.com/pypa/pip/issues/1924 'use_pip': False, }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('imagesize', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], }), ('Docutils', '0.14', { @@ -47,35 +42,27 @@ exts_list = [ 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], }), ('Babel', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], }), ('alabaster', '0.7.12', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), ('typing', '3.6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], }), ('sphinx_rtd_theme', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], }), ('numpydoc', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], }), ] diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-3.6.3.eb index 30615223fa9..dd11a90c3cf 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-3.6.3.eb @@ -18,27 +18,22 @@ use_pip = True exts_list = [ ('packaging', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('sphinxcontrib-websupport', '1.1.0', { 'modulename': 'sphinxcontrib.websupport', - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], # can't use pip here because it doesn't support namespaces # cfr. https://github.com/pypa/pip/issues/1924 'use_pip': False, }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('imagesize', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], }), ('Docutils', '0.14', { @@ -47,35 +42,27 @@ exts_list = [ 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], }), ('Babel', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], }), ('alabaster', '0.7.12', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), ('typing', '3.6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], }), ('sphinx_rtd_theme', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], }), ('numpydoc', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], }), ] diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2018b-Python-3.6.6.eb index e21f7196125..fd715d0ba3e 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2018b-Python-3.6.6.eb @@ -18,27 +18,22 @@ use_pip = True exts_list = [ ('packaging', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], }), ('MarkupSafe', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), ('sphinxcontrib-websupport', '1.1.0', { 'modulename': 'sphinxcontrib.websupport', - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], # can't use pip here because it doesn't support namespaces # cfr. https://github.com/pypa/pip/issues/1924 'use_pip': False, }), ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], }), ('imagesize', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], }), ('Docutils', '0.14', { @@ -47,35 +42,27 @@ exts_list = [ 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], }), ('Babel', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], }), ('alabaster', '0.7.12', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), ('typing', '3.6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], }), ('sphinx_rtd_theme', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], }), ('numpydoc', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], }), ] diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.3-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.3-intel-2018a-Python-3.6.4.eb index a9564d630b7..c9cc143096c 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.3-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.3-intel-2018a-Python-3.6.4.eb @@ -18,25 +18,20 @@ use_pip = True exts_list = [ ('packaging', '19.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0c98a5d0be38ed775798ece1b9727178c4469d9c3b4ada66e8e6b7849f8732af'], }), ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('sphinxcontrib-websupport', '1.1.0', { 'modulename': 'sphinxcontrib.websupport', - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], 'use_pip': False, 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], }), ('Pygments', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], }), ('imagesize', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], }), ('Docutils', '0.14', { @@ -45,43 +40,33 @@ exts_list = [ 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], }), ('Babel', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], }), ('alabaster', '0.7.12', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), ('typing', '3.6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'checksums': ['c4cb17ba44acffae3d3209646b6baec1e215cad3065e852c68cc569d4df1b9f8'], }), ('sphinx_rtd_theme', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], }), ('numpydoc', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], }), ('sphinx-bootstrap-theme', '0.6.5', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx-bootstrap-theme'], 'checksums': ['82936109a05b84029052e7efb1756161c3b4c27ae18512a90234d50fe608cba7'], }), ('sphinx-gallery', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/sphinx-gallery'], 'checksums': ['b49356b5516cc7dab67b1b378f6bf8146fe2372ee73d5e1ea2c483a2e3f4f182'], }), ] diff --git a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb index 9ffb9501007..4fb2abe7280 100644 --- a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb @@ -9,14 +9,8 @@ description = "SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('Python', '2.7.12')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb index e2776528bdd..8b43dbae92c 100644 --- a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb @@ -9,14 +9,8 @@ description = "SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('Python', '3.6.1')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-foss-2017b-Python-3.6.3.eb index 9b64aceca53..87e0bc9a61d 100644 --- a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-foss-2017b-Python-3.6.3.eb @@ -9,15 +9,9 @@ description = "SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['fdd8eeb4df1f482a18048364bc0508fbee381c930146330e4e3bc8f5574ca9a9'] dependencies = [('Python', '3.6.3')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-foss-2018a-Python-3.6.4.eb index 3b573113c8b..47e0de45015 100644 --- a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-foss-2018a-Python-3.6.4.eb @@ -9,15 +9,9 @@ description = "SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['fdd8eeb4df1f482a18048364bc0508fbee381c930146330e4e3bc8f5574ca9a9'] dependencies = [('Python', '3.6.4')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-intel-2017b-Python-3.6.3.eb index 9c356eb576b..28a5a537358 100644 --- a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-2.1.0-intel-2017b-Python-3.6.3.eb @@ -9,15 +9,9 @@ description = "SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['fdd8eeb4df1f482a18048364bc0508fbee381c930146330e4e3bc8f5574ca9a9'] dependencies = [('Python', '3.6.3')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-3.1.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/Spyder/Spyder-3.1.4-intel-2017a-Python-2.7.13.eb index de450126b37..51abde2506c 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-3.1.4-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-3.1.4-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Spyder' version = '3.1.4' @@ -16,92 +16,46 @@ dependencies = [ ('PyZMQ', '16.0.2', versionsuffix + '-zmq4'), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ - ('qtconsole', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/q/qtconsole'], - }), - ('rope', '0.10.5', { - 'source_urls': ['https://pypi.python.org/packages/source/r/rope'], - }), - ('jedi', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi'], - }), - ('pyflakes', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyflakes'], - }), - ('Sphinx', '1.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Sphinx'], - }), - ('Pygments', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], - }), - ('pylint', '1.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pylint'], - }), - ('pep8', '1.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pep8'], - }), - ('psutil', '5.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], - }), - ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], - }), - ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], - }), - ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - }), - ('nbformat', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - }), + ('qtconsole', '4.3.0'), + ('rope', '0.10.5'), + ('jedi', '0.10.2'), + ('pyflakes', '1.5.0'), + ('Sphinx', '1.6.1'), + ('Pygments', '2.2.0'), + ('pylint', '1.7.1'), + ('pep8', '1.7.0'), + ('psutil', '5.2.2'), + ('ipython_genutils', '0.2.0'), + ('traitlets', '4.3.2'), + ('jsonschema', '2.6.0'), + ('nbformat', '4.3.0'), ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], 'patches': ['configparser-3.5.0_no-backports-namespace.patch'], 'use_pip': True, }), ('entrypoints', '0.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], 'source_tmpl': 'entrypoints-%(version)s-py2.py3-none-any.whl', 'unpack_sources': False, 'use_pip': True, }), - ('pandocfilters', '1.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], - }), + ('pandocfilters', '1.4.1'), ('testpath', '0.3', { - 'source_urls': ['https://pypi.python.org/packages/py2.py3/t/testpath/'], 'source_tmpl': 'testpath-%(version)s-py2.py3-none-any.whl', 'unpack_sources': False, 'use_pip': True, }), ('nbconvert', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert'], 'use_pip': True, }), ('QtAwesome', '0.4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/Q/QtAwesome'], 'prebuildopts': "rm -r qtawesome/tests/__pycache__ && ", }), - ('pickleshare', '0.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare'], - }), - ('QtPy', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/Q/QtPy'], - }), - ('chardet', '3.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet'], - }), - ('numpydoc', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc'], - }), - (name.lower(), version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/spyder'], - }), + ('pickleshare', '0.7.4'), + ('QtPy', '1.2.1'), + ('chardet', '3.0.3'), + ('numpydoc', '0.6.0'), + (name.lower(), version), ] sanity_check_paths = { @@ -109,6 +63,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-3.3.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/Spyder/Spyder-3.3.1-foss-2018a-Python-3.6.4.eb index 5da587c3913..8a074fda18c 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-3.3.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-3.3.1-foss-2018a-Python-3.6.4.eb @@ -28,98 +28,75 @@ use_pip = True exts_list = [ ('pyzmq', '17.1.2', { 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq'], 'checksums': ['a72b82ac1910f2cf61a49139f4974f994984475f771b0faa730839607eeedddf'], }), ('psutil', '5.4.7', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['5b6322b167a5ba0c5463b4d30dfd379cd4ce245a1162ebf8fc7ab5c5ffae4f3b'], }), ('cloudpickle', '0.5.6', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], 'checksums': ['0390ecb3731ac035d74c34651460f4a683e9ef7443861712b8d56c20c2f92113'], }), ('spyder-kernels', '0.2.6', { 'modulename': 'spyder_kernels', - 'source_urls': ['https://pypi.python.org/packages/source/s/spyder-kernels'], 'checksums': ['26c8e9f78f90ac107ee72ccf78b2550d65d437010990aaf30396d0f90af3282c'], }), ('QtPy', '1.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/Q/QtPy'], 'checksums': ['c0c2a0a1425b2c166737ef219904be1b04567a1eff94c2ed146f033a2afb383b'], }), ('QtAwesome', '0.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/Q/QtAwesome'], 'checksums': ['f415688877b65822d65cb2d9e9e198b37992f4e0ce7778439d14fbea6b4fb4ac'], }), ('lazy-object-proxy', '1.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lazy-object-proxy'], 'checksums': ['eb91be369f945f10d3a49f5f9be8b3d0b93a4c2be8f8a5b83b0571b8123e0a7a'], }), ('typed-ast', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typed-ast'], 'checksums': ['57fe287f0cdd9ceaf69e7b71a2e94a24b5d268b35df251a88fef5cc241bf73aa'], }), ('wrapt', '1.10.11', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt'], 'checksums': ['d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6'], }), ('astroid', '2.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/a/astroid'], 'checksums': ['c7013d119ec95eb626f7a2011f0b63d0c9a095df9ad06d8507b37084eada1a8d'], }), ('isort', '4.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/i/isort'], 'checksums': ['b9c40e9750f3d77e6e4d441d8b0266cf555e7cdabdcff33c4fd06366ca761ef8'], }), ('mccabe', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mccabe'], 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], }), ('pylint', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pylint'], 'checksums': ['31142f764d2a7cd41df5196f9933b12b7ee55e73ef12204b648ad7e556c119fb'], }), ('pycodestyle', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycodestyle'], 'checksums': ['cbfca99bd594a10f674d0cd97a3d802a1fdef635d4361e1a2658de47ed261e3a'], }), ('jeepney', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jeepney'], 'checksums': ['6089412a5de162c04747f0220f6b2223b8ba660acd041e52a76426ca550e3c70'], }), ('SecretStorage', '3.1.0', { 'source_tmpl': 'SecretStorage-%(version)s-py3-none-any.whl', - 'source_urls': ['https://pypi.python.org/packages/source/S/SecretStorage'], 'unpack_sources': False, 'checksums': ['20196abd1a9d1310df7573d58ca6e7ed9292218c98ca3638eea07beb16080343'], }), ('keyrings.alt', '3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/keyrings.alt'], 'checksums': ['b59c86b67b9027a86e841a49efc41025bcc3b1b0308629617b66b7011e52db5a'], }), ('keyring', '16.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/keyring'], 'checksums': ['a86499736e2e6555618606c2fbc98147e803fa276f990ddba7011eb29a01b5ad'], }), ('pyflakes', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyflakes'], 'checksums': ['9a7662ec724d0120012f6e29d6248ae3727d821bba522a0e6b356eff19126a49'], }), ('qtconsole', '4.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/q/qtconsole'], 'checksums': ['faa529167b22412ea51ea44f20728a602415734d2229721d1194cea47cb730fa'], }), ('rope', '0.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/rope'], 'checksums': ['a108c445e1cd897fe19272ab7877d172e7faf3d4148c80e7d20faba42ea8f7b2'], }), ('docutils', '0.14', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('spyder', version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/spyder'], 'checksums': ['992d74f07961df9a9b9aa495fa2d87832699ada5323850dc3e26ac0ff640b170'], }), ] diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb index 984f055278b..7f224de1bb0 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb @@ -27,94 +27,72 @@ use_pip = True exts_list = [ ('psutil', '5.4.8', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['6e265c8f3da00b015d24b842bfeb111f856b13d24f2c57036582568dc650d6c3'], }), ('cloudpickle', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], 'checksums': ['f169a8523a40eb0a3452e1878aac31da6759409fbafa51dd50d89d4a6b42bcf1'], }), ('spyder-kernels', '0.4.2', { 'modulename': 'spyder_kernels', - 'source_urls': ['https://pypi.python.org/packages/source/s/spyder-kernels'], 'checksums': ['a13cefb569ef9f63814cb5fcf3d0db66e09d2d7e6cc68c703d5118b2d7ba062b'], }), ('QtPy', '1.5.2', { - 'source_urls': ['https://pypi.python.org/packages/source/Q/QtPy'], 'checksums': ['4c690f90586c82c1210bb6fdf5e9ee4d1228809421dc6a349c5afacc27caabcd'], }), ('QtAwesome', '0.5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/Q/QtAwesome'], 'checksums': ['8dfd8bcac56caa6d81639fc43db673b62aeca6129f4c8e9b1da17a32c0d309fd'], }), ('lazy-object-proxy', '1.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lazy-object-proxy'], 'checksums': ['eb91be369f945f10d3a49f5f9be8b3d0b93a4c2be8f8a5b83b0571b8123e0a7a'], }), ('typed-ast', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typed-ast'], 'checksums': ['57fe287f0cdd9ceaf69e7b71a2e94a24b5d268b35df251a88fef5cc241bf73aa'], }), ('wrapt', '1.10.11', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt'], 'checksums': ['d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6'], }), ('astroid', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/astroid'], 'checksums': ['35b032003d6a863f5dcd7ec11abd5cd5893428beaa31ab164982403bcb311f22'], }), ('isort', '4.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/i/isort'], 'checksums': ['b9c40e9750f3d77e6e4d441d8b0266cf555e7cdabdcff33c4fd06366ca761ef8'], }), ('mccabe', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mccabe'], 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], }), ('pylint', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pylint'], 'checksums': ['689de29ae747642ab230c6d37be2b969bf75663176658851f456619aacf27492'], }), ('pycodestyle', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycodestyle'], 'checksums': ['cbfca99bd594a10f674d0cd97a3d802a1fdef635d4361e1a2658de47ed261e3a'], }), ('jeepney', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jeepney'], 'checksums': ['6089412a5de162c04747f0220f6b2223b8ba660acd041e52a76426ca550e3c70'], }), ('SecretStorage', '3.1.0', { 'source_tmpl': 'SecretStorage-%(version)s-py3-none-any.whl', - 'source_urls': ['https://pypi.python.org/packages/source/S/SecretStorage'], 'unpack_sources': False, 'checksums': ['20196abd1a9d1310df7573d58ca6e7ed9292218c98ca3638eea07beb16080343'], }), ('keyrings.alt', '3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/keyrings.alt'], 'checksums': ['b59c86b67b9027a86e841a49efc41025bcc3b1b0308629617b66b7011e52db5a'], }), ('keyring', '17.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/keyring'], 'checksums': ['d3744d22e398c19405d819d3c2d3bb82dc05a96513f577411c8847bb207dc289'], }), ('pyflakes', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyflakes'], 'checksums': ['9a7662ec724d0120012f6e29d6248ae3727d821bba522a0e6b356eff19126a49'], }), ('qtconsole', '4.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/q/qtconsole'], 'checksums': ['bc1ba15f50c29ed50f1268ad823bb6543be263c18dd093b80495e9df63b003ac'], }), ('rope', '0.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/rope'], 'checksums': ['a108c445e1cd897fe19272ab7877d172e7faf3d4148c80e7d20faba42ea8f7b2'], }), ('docutils', '0.14', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('spyder', version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/spyder'], 'checksums': ['ab3a30321d3142bf6c98f71cea3a6d65b4b6f67d4b77c4966249e8547bb9bbfa'], }), ] diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb new file mode 100644 index 00000000000..17cdbfec0d0 --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'MakeCp' + +name = 'Subread' +version = '2.0.2' + +# HTTPS is not valid +homepage = 'http://%(namelower)s.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] + +checksums = [ # source subread-2.0.2-source.tar.gz + '0b64bd51f39f8d322c4594697fa5f0f64fbe60283113eadadff9f4268f897079'] + +start_dir = 'src' + +prebuildopts = "sed -i 's/-mtune=core2//g' Makefile.Linux && " +prebuildopts += "sed -i 's/-mtune=core2//g' longread-one/Makefile && " + +buildopts = " -f Makefile.Linux" + +files_to_copy = ['bin'] + +local_binaries_list = [ + 'exactSNP', 'featureCounts', 'subindel', 'subjunc', 'sublong', 'subread-align', 'subread-buildindex', +] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_binaries_list], + 'dirs': ['bin/utilities'], +} + +sanity_check_commands = [ + 'cd %(builddir)s/%(namelower)s-%(version)s-source/test && bash test_all.sh' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..31cf4364801 --- /dev/null +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.1-GCCcore-10.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'Subversion' +version = '1.14.1' + +homepage = 'https://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [ + 'https://apache.belnet.be/%(namelower)s', + 'http://www.eu.apache.org/dist/%(namelower)s', + 'http://www.us.apache.org/dist/%(namelower)s', + 'https://archive.apache.org/dist/%(namelower)s', +] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Subversion-1.12.0-no_swig.patch'] +checksums = [ + '2c5da93c255d2e5569fa91d92457fdb65396b0666fad4fd59b22e154d986e1a9', # subversion-1.14.1.tar.bz2 + '539ea2118f958d152d78438c81649eb727ff0b2e8491295702ee98e1f922041f', # Subversion-1.12.0-no_swig.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('SQLite', '3.35.4'), + ('zlib', '1.2.11'), + ('lz4', '1.9.3'), + ('utf8proc', '2.6.1'), + ('Serf', '1.3.9'), +] + +preconfigopts = './autogen.sh && ' + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-lz4=$EBROOTLZ4 --with-serf=$EBROOTSERF" + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0.eb new file mode 100644 index 00000000000..3dd8e4852c7 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0.eb @@ -0,0 +1,29 @@ +name = 'SuiteSparse' +version = '5.10.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SunPy/SunPy-1.1.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/SunPy/SunPy-1.1.3-foss-2019b-Python-3.7.4.eb index 4fb9edd00c8..e019ba06766 100644 --- a/easybuild/easyconfigs/s/SunPy/SunPy-1.1.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/SunPy/SunPy-1.1.3-foss-2019b-Python-3.7.4.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('semantic_version', '2.8.5', { 'checksums': ['d2cb2de0558762934679b9a104e82eca7af448c9f4974d1f3eeccff651df8a54'], diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.1.24-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scVelo/scVelo-0.1.24-foss-2019b-Python-3.7.4.eb index 2d3a114bfe9..f4af465f0ba 100644 --- a/easybuild/easyconfigs/s/scVelo/scVelo-0.1.24-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.1.24-foss-2019b-Python-3.7.4.eb @@ -32,8 +32,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('numpy-groupies', '0.9.10', { 'modulename': 'numpy_groupies', diff --git a/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.1.8-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.1.8-foss-2017a-Python-2.7.13.eb index 59830df41bd..cdea0cac2c4 100644 --- a/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.1.8-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.1.8-foss-2017a-Python-2.7.13.eb @@ -4,13 +4,12 @@ name = 'scikit-allel' version = '1.1.8' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-allel.readthedocs.io/en/latest/' +homepage = 'https://scikit-allel.readthedocs.io/en/latest/' description = """This package provides utilities for exploratory analysis of large scale genetic variation data. It is based on numpy, scipy and other general-purpose Python scientific libraries.""" toolchain = {'name': 'foss', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['974e2fc354ddf838c8c9b8d945cf62a3c9f325c5b384cd4dea841275651b060c'] diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-foss-2018b-Python-3.6.6.eb index d55ae34a15c..149c40bad36 100755 --- a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-foss-2018b-Python-3.6.6.eb @@ -17,8 +17,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('packaging', '20.0', { 'checksums': ['fe1d8331dfa7cc0a883b49d75fc76380b2ab2734b220fbb87d774e4fd4b851f8'], @@ -32,9 +30,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-intel-2018b-Python-3.6.6.eb index bcecf9b0486..149eb07dced 100755 --- a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-intel-2018b-Python-3.6.6.eb @@ -17,8 +17,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('packaging', '20.0', { 'checksums': ['fe1d8331dfa7cc0a883b49d75fc76380b2ab2734b220fbb87d774e4fd4b851f8'], @@ -32,9 +30,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-GCCcore-10.3.0.eb new file mode 100755 index 00000000000..ee134af8db3 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.11.1' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('distro', '1.5.0', { + 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], + }), + (name, version, { + 'modulename': 'skbuild', + 'checksums': ['da40dfd69b2456fad1349a894b90180b43712152b8a85d2a00f4ae2ce8ac9a5c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-cuda/scikit-cuda-0.5.3-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scikit-cuda/scikit-cuda-0.5.3-fosscuda-2019b-Python-3.7.4.eb index 7ef29af2355..357221532a1 100644 --- a/easybuild/easyconfigs/s/scikit-cuda/scikit-cuda-0.5.3-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scikit-cuda/scikit-cuda-0.5.3-fosscuda-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """SciKit-cuda, a.k.a. skcuda, provides Python interfaces to many toolchain = {'name': 'fosscuda', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['46e05613d25bbc988c63bfbdbd6adf0e0fa2cdba0827f0c5595d77d9f45aa3ba'] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb index ec8ebe2866a..883c6340169 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb @@ -23,8 +23,6 @@ dependencies = [ # can't use pip because version included with Python is too old use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('networkx', '1.11', { 'checksums': ['0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8'], diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016b-Python-3.5.2.eb index 264bbcdb917..ba74430e1d9 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016b-Python-3.5.2.eb @@ -20,8 +20,6 @@ dependencies = [ # can't use pip because version included with Python is too old use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('networkx', '1.11', { 'checksums': ['0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8'], diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb index d82e7ccabd9..89b89e3705e 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb @@ -20,8 +20,6 @@ dependencies = [ # can't use pip because version included with Python is too old use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('networkx', '1.11', { 'checksums': ['0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8'], diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb index fa512106f24..d7dc19735da 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb @@ -20,8 +20,6 @@ dependencies = [ # can't use pip because version included with Python is too old use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('networkx', '1.11', { 'checksums': ['0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8'], diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-foss-2017b-Python-3.6.3.eb index 99c5451eb88..46a43350082 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-foss-2017b-Python-3.6.3.eb @@ -21,17 +21,14 @@ use_pip = True exts_list = [ ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8'], }), ('PyWavelets', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyWavelets'], 'checksums': ['3c5cece36d4e17d395be6e9ac6b80ce7b774a1f71c251756c6163e63b6d878dc'], 'modulename': 'pywt', }), (name, version, { 'modulename': 'skimage', - 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'checksums': ['77a636bdc08c7668a15951894548c527f0c8c5c2abc86cb850de17551af51e3e'], }), ] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-2.7.13.eb index ade71b9e4e0..a56cb970f11 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-2.7.13.eb @@ -21,17 +21,14 @@ use_pip = True exts_list = [ ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8'], }), ('PyWavelets', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyWavelets'], 'checksums': ['3c5cece36d4e17d395be6e9ac6b80ce7b774a1f71c251756c6163e63b6d878dc'], 'modulename': 'pywt', }), (name, version, { 'modulename': 'skimage', - 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'checksums': ['77a636bdc08c7668a15951894548c527f0c8c5c2abc86cb850de17551af51e3e'], }), ] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-3.6.1.eb index 8d123edf5bb..0bf92945d63 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-3.6.1.eb @@ -21,17 +21,14 @@ use_pip = True exts_list = [ ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8'], }), ('PyWavelets', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyWavelets'], 'checksums': ['3c5cece36d4e17d395be6e9ac6b80ce7b774a1f71c251756c6163e63b6d878dc'], 'modulename': 'pywt', }), (name, version, { 'modulename': 'skimage', - 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'checksums': ['77a636bdc08c7668a15951894548c527f0c8c5c2abc86cb850de17551af51e3e'], }), ] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2017b-Python-3.6.3.eb index 68aa4534f6d..d7ccd9fe3f2 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2017b-Python-3.6.3.eb @@ -21,17 +21,14 @@ use_pip = True exts_list = [ ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8'], }), ('PyWavelets', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyWavelets'], 'checksums': ['3c5cece36d4e17d395be6e9ac6b80ce7b774a1f71c251756c6163e63b6d878dc'], 'modulename': 'pywt', }), (name, version, { 'modulename': 'skimage', - 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'checksums': ['353879ddf7483f4621872c49cd9bc8a0ad1c3154ac0670b70799922f4cb899e8'], }), ] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2018a-Python-3.6.4.eb index 6951f582412..16720a0e379 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2018a-Python-3.6.4.eb @@ -22,17 +22,14 @@ dependencies = [ exts_list = [ ('networkx', '2.1', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1'], }), ('PyWavelets', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyWavelets'], 'checksums': ['3c5cece36d4e17d395be6e9ac6b80ce7b774a1f71c251756c6163e63b6d878dc'], 'modulename': 'pywt', }), (name, version, { 'modulename': 'skimage', - 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'checksums': ['353879ddf7483f4621872c49cd9bc8a0ad1c3154ac0670b70799922f4cb899e8'], }), ] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-intel-2017b-Python-2.7.14.eb index 290969539cd..ea8c9932f6d 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-intel-2017b-Python-2.7.14.eb @@ -21,17 +21,14 @@ use_pip = True exts_list = [ ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8'], }), ('PyWavelets', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyWavelets'], 'checksums': ['3c5cece36d4e17d395be6e9ac6b80ce7b774a1f71c251756c6163e63b6d878dc'], 'modulename': 'pywt', }), (name, version, { 'modulename': 'skimage', - 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'checksums': ['353879ddf7483f4621872c49cd9bc8a0ad1c3154ac0670b70799922f4cb899e8'], }), ] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.0-intel-2018a-Python-3.6.4.eb index 83c40110ece..6d217a678b0 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.0-intel-2018a-Python-3.6.4.eb @@ -21,12 +21,10 @@ use_pip = True exts_list = [ ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8'], }), (name, version, { 'modulename': 'skimage', - 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'checksums': ['325f75eb80fbc5371136e37f323445309ca9f65b6c6f718d0d0e2189e5de1224'], }), ] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-foss-2018b-Python-3.6.6.eb index 27ef73db649..762a70e7d14 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-foss-2018b-Python-3.6.6.eb @@ -22,17 +22,14 @@ dependencies = [ exts_list = [ ('networkx', '2.1', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1'], }), ('PyWavelets', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyWavelets'], 'checksums': ['3c5cece36d4e17d395be6e9ac6b80ce7b774a1f71c251756c6163e63b6d878dc'], 'modulename': 'pywt', }), (name, version, { 'modulename': 'skimage', - 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'checksums': ['86a9b3b4f74f231e0a6bcfd3235dcf3f0118df25dac21201da5e064d681e2c50'], }), ] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-fosscuda-2018b-Python-3.6.6.eb index 85bd9ea6d45..806897df994 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-fosscuda-2018b-Python-3.6.6.eb @@ -22,17 +22,14 @@ dependencies = [ exts_list = [ ('networkx', '2.1', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1'], }), ('PyWavelets', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyWavelets'], 'checksums': ['3c5cece36d4e17d395be6e9ac6b80ce7b774a1f71c251756c6163e63b6d878dc'], 'modulename': 'pywt', }), (name, version, { 'modulename': 'skimage', - 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'checksums': ['86a9b3b4f74f231e0a6bcfd3235dcf3f0118df25dac21201da5e064d681e2c50'], }), ] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-intel-2018b-Python-3.6.6.eb index a3b1f6b90fe..3b28980ae6e 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-intel-2018b-Python-3.6.6.eb @@ -22,17 +22,14 @@ dependencies = [ exts_list = [ ('networkx', '2.1', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], 'checksums': ['64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1'], }), ('PyWavelets', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/PyWavelets'], 'checksums': ['3c5cece36d4e17d395be6e9ac6b80ce7b774a1f71c251756c6163e63b6d878dc'], 'modulename': 'pywt', }), (name, version, { 'modulename': 'skimage', - 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'checksums': ['86a9b3b4f74f231e0a6bcfd3235dcf3f0118df25dac21201da5e064d681e2c50'], }), ] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.15.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.15.0-foss-2019a-Python-3.7.2.eb index 23a5fb7a45f..22c50645cb5 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.15.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.15.0-foss-2019a-Python-3.7.2.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('networkx', '2.3', { 'source_tmpl': '%(name)s-%(version)s.zip', diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-foss-2019b-Python-3.7.4.eb index d76bd474417..0dbed27697c 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-foss-2019b-Python-3.7.4.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('networkx', '2.4', { 'checksums': ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'], diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-fosscuda-2019b-Python-3.7.4.eb index 2fb7b5f261f..ea6c0a2c473 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-fosscuda-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('networkx', '2.4', { 'checksums': ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'], diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-intel-2019b-Python-3.7.4.eb index b426d2a3c14..f4dbbf7f82f 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-intel-2019b-Python-3.7.4.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('networkx', '2.4', { 'checksums': ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'], diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-foss-2017a-Python-2.7.13.eb index c5755d9fadf..1ed1213ac89 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-foss-2017a-Python-2.7.13.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.16.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-2.7.11.eb index 7a34f126ed0..8fe71c5bfc2 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.17.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-3.5.1.eb index 9c2111d9465..e99325e0e85 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-3.5.1.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.17.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb index 1a4d008ab8d..099134c32c3 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.17.1' versionsuffix = '-Python-%(pyver)s-freetype-2.6.3' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb index 50d044b41ce..35bc1afd248 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.17.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb index f49a608d871..33acf76f514 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.17.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb index 948220fce8b..a7ba8e27b7b 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.17.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-2.7.12.eb index cedad0e0ae1..ba519e0c076 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-2.7.12.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.18' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-3.5.2.eb index a4cbd226228..9ae23481d88 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-3.5.2.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.18' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-2.7.12.eb index 9e8395819b8..c2e689912e1 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-2.7.12.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.18.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-3.5.2.eb index dd9bbeb576e..507a4c0edae 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-3.5.2.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.18.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-2.7.12.eb index ad5177d70b7..0c7247f9fd8 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-2.7.12.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.18.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-3.5.2.eb index 8d85cb18f49..77f6b74d0d4 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-3.5.2.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.18.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb index 388e0e3afa8..f2f57767c32 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.18.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb index af24f8502f6..77df65e8e21 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.18.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.2-intel-2017a-Python-3.6.1.eb index 680d9601f6f..cb00faff30d 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.2-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.2-intel-2017a-Python-3.6.1.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.18.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.0-intel-2017a-Python-3.6.1.eb index 327753864db..5042218e3d7 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.0-intel-2017a-Python-3.6.1.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['24f5cb67559e0df27827b1804b197431c08880d2ec9285724fac90906830021f'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017a-Python-2.7.13.eb index bd204035f3b..28292c0e61f 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017a-Python-2.7.13.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-2.7.14.eb index de44a56868f..f9784ecae14 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-3.6.3.eb index 014815b715c..d65a04cd1f0 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2018a-Python-3.6.4.eb index afaa1891c7c..d7006e76012 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-2.7.14.eb index 39796a374ab..bf700ed32ac 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'fosscuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-3.6.3.eb index 2b326084577..90b520d3f03 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'fosscuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2017b-Python-2.7.14.eb index e9bba457669..a7e4ed4be5b 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2017b-Python-3.6.3.eb index b5bb8144fa8..e0277aa24f3 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2018a-Python-3.6.4.eb index a6d836d4110..ccf5d6928f8 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-2.7.14.eb index 19c6ac62205..2486d13666c 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intelcuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-3.6.3.eb index fb028dc3c82..d6741d721d0 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.19.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intelcuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-2.7.15.eb index 3b8faa9e1b2..8d90cc6e2de 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.20.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-3.6.6.eb index ed4dabda6d3..4e05d8a4372 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.20.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-fosscuda-2018b-Python-3.6.6.eb index 87691aa1220..20c56853367 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-fosscuda-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.20.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-2.7.15.eb index 11f5ae28a67..250569f1947 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.20.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-3.6.6.eb index 601b4a0aff9..7f683fc3d19 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.20.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-2.7.15.eb index 2c34a989744..daaa5cb0221 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.20.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['bc5bc7c7ee2572a1edcb51698a6caf11fae554194aaab9a38105d9ec419f29e6'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-3.6.6.eb index 192a4e462ce..d4b9194208e 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'scikit-learn' version = '0.20.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['bc5bc7c7ee2572a1edcb51698a6caf11fae554194aaab9a38105d9ec419f29e6'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb index c685c2a82e1..389795b2f3b 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'scikit-learn' version = '0.20.3' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -11,7 +11,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c503802a81de18b8b4d40d069f5e363795ee44b1605f38bc104160ca3bfe2c41'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb index 74d63aee085..3a6ebf41d92 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb @@ -11,7 +11,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'fosscuda', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c503802a81de18b8b4d40d069f5e363795ee44b1605f38bc104160ca3bfe2c41'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a.eb index 6652590033a..4dd97d73904 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'scikit-learn' version = '0.20.3' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. @@ -11,7 +11,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c503802a81de18b8b4d40d069f5e363795ee44b1605f38bc104160ca3bfe2c41'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-intel-2019b-Python-2.7.16.eb index 1cd644e8d9b..267ae359715 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-intel-2019b-Python-2.7.16.eb @@ -13,7 +13,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['dfa8a3f33907614030cdfbc8b6f553dacbecaf09f922244f128af3060a137cfc'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-foss-2019b-Python-3.7.4.eb index 0210ca25374..3a0f857875f 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-foss-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['eb9b8ebf59eddd8b96366428238ab27d05a19e89c5516ce294abc35cea75d003'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-fosscuda-2019b-Python-3.7.4.eb index cfec6455342..a9136c92a18 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-fosscuda-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'fosscuda', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['eb9b8ebf59eddd8b96366428238ab27d05a19e89c5516ce294abc35cea75d003'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-intel-2019b-Python-3.7.4.eb index 7b7abf9f344..d454ae26dc9 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.21.3-intel-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['eb9b8ebf59eddd8b96366428238ab27d05a19e89c5516ce294abc35cea75d003'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.24.2-foss-2021a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.24.2-foss-2021a.eb new file mode 100644 index 00000000000..096bd82d8a5 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.24.2-foss-2021a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.24.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d14701a12417930392cd3898e9646cf5670c190b933625ebe7511b1f7d7b8736'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'sklearn'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb index db2ac3007b9..d98e8fda9f2 100644 --- a/easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb @@ -23,17 +23,14 @@ use_pip = True exts_list = [ ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('liac-arff', '2.4.0', { 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff'], 'checksums': ['47afcd1fd248b2892f66075987422d0576fc2c2fd0811d0cbd32f2135b065df5'], }), ('python-louvain', '0.13', { 'modulename': 'community', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-louvain'], 'checksums': ['b4938f20063bc53e68d5b182dcea0634dfb63a0e3489f929d4083c24a920b2fe'], }), (name, version, { diff --git a/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.5.2-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.5.2-intel-2018b-Python-3.6.6.eb index eeb8892d7d5..30e3adac8b5 100755 --- a/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.5.2-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.5.2-intel-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ description = """Scikit-Optimize, or skopt, is a simple and efficient library to toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1d7657a4b8ef9aa6d81e49b369c677c584e83269f11710557741d3b3f8fa0a75'] @@ -26,9 +25,4 @@ options = {'modulename': 'skopt'} download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.7.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.7.4-foss-2019b-Python-3.7.4.eb index f82e415a699..978f2b5a91a 100755 --- a/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.7.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.7.4-foss-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """Scikit-Optimize, or skopt, is a simple and efficient library to toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['d193b9505d04dc0aade256f10b08124a5e5679fe8c3e90c09ff9e3a60d9f1752'] diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.17.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scipy/scipy-0.17.0-intel-2016a-Python-2.7.11.eb index abaaff05460..3dda0f75599 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.17.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.17.0-intel-2016a-Python-2.7.11.eb @@ -2,14 +2,13 @@ name = 'scipy' version = '0.17.0' versionsuffix = '-Python-2.7.11' -homepage = 'http://www.scipy.org' +homepage = 'https://www.scipy.org' description = """SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb index 523cf018d91..0eafa5ab727 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb @@ -2,14 +2,13 @@ name = 'scipy' version = '0.19.0' versionsuffix = '-Python-3.5.2' -homepage = 'http://www.scipy.org' +homepage = 'https://www.scipy.org' description = """SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python.""" toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] dependencies = [ diff --git a/easybuild/easyconfigs/s/scipy/scipy-1.4.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scipy/scipy-1.4.1-foss-2019b-Python-3.7.4.eb index 85622b36c98..e3ac0cf9ab3 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-1.4.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-1.4.1-foss-2019b-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = """SciPy is a collection of mathematical algorithms and convenienc toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'pic': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['scipy-1.4.1-fix-pthread.patch'] checksums = [ diff --git a/easybuild/easyconfigs/s/scipy/scipy-1.4.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scipy/scipy-1.4.1-fosscuda-2019b-Python-3.7.4.eb index e73aa803e91..d195067492a 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-1.4.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-1.4.1-fosscuda-2019b-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = """SciPy is a collection of mathematical algorithms and convenienc toolchain = {'name': 'fosscuda', 'version': '2019b'} toolchainopts = {'pic': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['scipy-1.4.1-fix-pthread.patch'] checksums = [ diff --git a/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb index 1372c5db1ed..3f708f068cf 100644 --- a/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb @@ -9,14 +9,8 @@ description = """The scp.py module uses a paramiko transport to send and recieve toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.12')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb index f78369388fa..42d38ea65d4 100644 --- a/easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb @@ -9,7 +9,6 @@ description = """The scp.py module uses a paramiko transport to send and recieve toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4320ad188d3b8216352fb6c3647e0080ca14ced217735afc053256f86cd65159'] @@ -18,9 +17,4 @@ dependencies = [('Python', '2.7.15')] download_dep_fail = True use_pip = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scp/scp-0.13.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/scp/scp-0.13.2-intel-2018b-Python-2.7.15.eb index 20b81c1155f..8f44e51eb96 100644 --- a/easybuild/easyconfigs/s/scp/scp-0.13.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/scp/scp-0.13.2-intel-2018b-Python-2.7.15.eb @@ -9,7 +9,6 @@ description = """The scp.py module uses a paramiko transport to send and recieve toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ef9d6e67c0331485d3db146bf9ee9baff8a48f3eb0e6c08276a8584b13bf34b3'] diff --git a/easybuild/easyconfigs/s/segmentation-models/segmentation-models-1.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/segmentation-models/segmentation-models-1.0.1-foss-2019b-Python-3.7.4.eb index d62622e77f4..7cd76667701 100644 --- a/easybuild/easyconfigs/s/segmentation-models/segmentation-models-1.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/segmentation-models/segmentation-models-1.0.1-foss-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('imageio', '2.8.0', { 'checksums': ['fb5fd6d3d17126bbaac9af29fe340e2c97a196eb9416d4f28c0e543744a152cf'], diff --git a/easybuild/easyconfigs/s/segmentation-models/segmentation-models-1.0.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/segmentation-models/segmentation-models-1.0.1-fosscuda-2019b-Python-3.7.4.eb index cea076aeec9..e9f282c4924 100644 --- a/easybuild/easyconfigs/s/segmentation-models/segmentation-models-1.0.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/segmentation-models/segmentation-models-1.0.1-fosscuda-2019b-Python-3.7.4.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('imageio', '2.8.0', { 'checksums': ['fb5fd6d3d17126bbaac9af29fe340e2c97a196eb9416d4f28c0e543744a152cf'], diff --git a/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb index 3eab596a57a..0efcbbb6af4 100644 --- a/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb @@ -10,7 +10,6 @@ description = """Python and C library for Source Extraction and Photometry. toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a35704cffadbd042f931899a5564c539835fa7049d0cafff407d7ec7727d3aaa'] @@ -21,9 +20,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'astro' diff --git a/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb index 31bc313c363..825a360185b 100644 --- a/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb @@ -10,7 +10,6 @@ description = """Python and C library for Source Extraction and Photometry. toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a35704cffadbd042f931899a5564c539835fa7049d0cafff407d7ec7727d3aaa'] @@ -21,9 +20,4 @@ dependencies = [ use_pip = True download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'astro' diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.2.0.eb new file mode 100644 index 00000000000..de96dba8af8 --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'seqtk' +version = '1.3' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563'] + +dependencies = [('zlib', '1.2.11')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BINDIR=%(installdir)s/bin/' + +sanity_check_paths = { + 'files': ['bin/seqtk'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb index d6752459e10..2e3fc828b3e 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb @@ -8,7 +8,6 @@ description = """Download, build, install, upgrade, and uninstall Python package toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-41.0.1-py3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-41.0.1-py3.eb index 1060e249efa..c3a7da0c5ef 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-41.0.1-py3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-41.0.1-py3.eb @@ -9,7 +9,6 @@ description = """Easily download, build, install, upgrade, and uninstall Python toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] checksums = ['a222d126f5471598053c9a77f4b5d4f26eaa1f150ad6e01dcf1a42e185d05613'] diff --git a/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb index 5495126d2a2..c8c72fb14ab 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('hdf5plugin', '2.3.1', { 'checksums': ['2f6d886012c37bf7e8e002173dd6b16e6879b8e0e9f7d2f2ef9f79db97ed28d2'], diff --git a/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb index 954f9158ed7..690129aaddf 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('hdf5plugin', '2.3.1', { 'checksums': ['2f6d886012c37bf7e8e002173dd6b16e6879b8e0e9f7d2f2ef9f79db97ed28d2'], diff --git a/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2018b-Python-3.6.6.eb index 91ddc59f674..fe0f59c310b 100644 --- a/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = "SimPy is a process-based discrete-event simulation framework base toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['d09625b9b01f34242ae100fe6bdb6c9508da181a08419ab00cc2bd47c7ec0f43'] diff --git a/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2019a.eb b/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2019a.eb index c69ea372378..5e4a5568e5b 100644 --- a/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2019a.eb +++ b/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2019a.eb @@ -8,7 +8,6 @@ description = "SimPy is a process-based discrete-event simulation framework base toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['d09625b9b01f34242ae100fe6bdb6c9508da181a08419ab00cc2bd47c7ec0f43'] diff --git a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.12.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.12.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..ebd9bf791ba --- /dev/null +++ b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.12.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'slepc4py' +version = '3.12.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/slepc/slepc4py' +description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations." + +toolchain = {'name': 'foss', 'version': '2019b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['6310a641ebe4b02a547a9f8a9a3c72d44c9fb05b7a5c0c3a9bf6e6a3f1ff07ce'] + +dependencies = [ + ('Python', '3.7.4'), + ('SLEPc', '3.12.2', versionsuffix), + ('petsc4py', '3.12.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from slepc4py import SLEPc'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.9.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.9.0-foss-2018a-Python-3.6.4.eb index cdfa23022a9..fe048686c21 100644 --- a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.9.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.9.0-foss-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Pr toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['67ed4ffed36c076448d6a0148edfad65d6610b9838df97c79f6fc5d7ec06b90b'] @@ -19,9 +18,4 @@ dependencies = [ ('petsc4py', '3.9.1', versionsuffix), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-2.7.15.eb index 25a140232a1..0cd1ea1935d 100644 --- a/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-2.7.15.eb @@ -17,7 +17,6 @@ use_pip = True exts_list = [ ('psutil', '5.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], }), (name, version, { diff --git a/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb index 06a7ce25c3a..fee9a4b5a61 100644 --- a/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb @@ -17,7 +17,6 @@ use_pip = True exts_list = [ ('psutil', '5.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], }), (name, version, { diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-5.2.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/snakemake/snakemake-5.2.2-intel-2018a-Python-3.6.4.eb index 78ee9925827..1ed07da2007 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-5.2.2-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-5.2.2-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'snakemake' version = '5.2.2' @@ -14,43 +14,31 @@ dependencies = [ ('PyYAML', '3.12', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('docutils', '0.14', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('datrie', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/datrie'], 'checksums': ['7a11371cc2dbbad71d6dfef57ced6e8b384bb377eeb847c63d58f8dc8e8b2023'], }), ('appdirs', '1.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), ('ConfigArgParse', '0.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/ConfigArgParse'], 'checksums': ['e6441aa58e23d3d122055808e5e2220fd742dff6e1e51082d2a4e4ed145dd788'], }), ('ratelimiter', '1.2.0.post0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/ratelimiter'], 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], }), ('wrapt', '1.10.11', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt'], 'checksums': ['d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/snakemake'], 'checksums': ['adffe7e24b4a613a9e8bf0a2a320b3cea236d86afb9132bb0bbbc08b8e35a3a3'], }), ] @@ -62,6 +50,4 @@ sanity_check_paths = { sanity_check_commands = ['snakemake --help'] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-foss-2018b-Python-3.6.6.eb index 786160ef2b1..87768d27331 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-foss-2018b-Python-3.6.6.eb @@ -19,35 +19,27 @@ use_pip = True exts_list = [ ('docutils', '0.14', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('datrie', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/datrie'], 'checksums': ['7a11371cc2dbbad71d6dfef57ced6e8b384bb377eeb847c63d58f8dc8e8b2023'], }), ('appdirs', '1.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), ('ConfigArgParse', '0.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/ConfigArgParse'], 'checksums': ['e6441aa58e23d3d122055808e5e2220fd742dff6e1e51082d2a4e4ed145dd788'], }), ('ratelimiter', '1.2.0.post0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/ratelimiter'], 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], }), ('wrapt', '1.10.11', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt'], 'checksums': ['d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/snakemake'], 'checksums': ['ff48ec6b227d9f1fb125c646c071a4f105ac62a3dfadec3d4eb70e1c5fef403e'], }), ] diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-intel-2018b-Python-3.6.6.eb index 1d04771ecef..f4f76fa7de2 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-intel-2018b-Python-3.6.6.eb @@ -19,35 +19,27 @@ use_pip = True exts_list = [ ('docutils', '0.14', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('jsonschema', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], }), ('datrie', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/datrie'], 'checksums': ['7a11371cc2dbbad71d6dfef57ced6e8b384bb377eeb847c63d58f8dc8e8b2023'], }), ('appdirs', '1.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), ('ConfigArgParse', '0.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/ConfigArgParse'], 'checksums': ['e6441aa58e23d3d122055808e5e2220fd742dff6e1e51082d2a4e4ed145dd788'], }), ('ratelimiter', '1.2.0.post0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/ratelimiter'], 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], }), ('wrapt', '1.10.11', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt'], 'checksums': ['d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/snakemake'], 'checksums': ['ff48ec6b227d9f1fb125c646c071a4f105ac62a3dfadec3d4eb70e1c5fef403e'], }), ] diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-5.7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/snakemake/snakemake-5.7.1-foss-2019a-Python-3.7.2.eb index 23bc59ed412..6a96b3fee22 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-5.7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-5.7.1-foss-2019a-Python-3.7.2.eb @@ -16,8 +16,6 @@ dependencies = [ ('GitPython', '3.0.3', versionsuffix), ] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb new file mode 100644 index 00000000000..f3814608665 --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.0' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['2b177440eb4a2c3bbfc8f50d4adf9e405f3dcfc05a31a55c96f773f07832af34'] + +dependencies = [ + ('Java', '13', '', True), + ('Python', '3.8.2'), + ('Perl', '5.30.2'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0-Java-13.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0-Java-13.eb index eb6fcd69eee..b945a1fda66 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-5.0-Java-13.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0-Java-13.eb @@ -12,7 +12,7 @@ toolchain = SYSTEM source_urls = ['https://snpeff.blob.core.windows.net/versions/'] sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] -checksums = ['448cdae47247fde506e259938b195511f531f85ab2cd66a06cedf85fe215c7c7'] +checksums = ['2b177440eb4a2c3bbfc8f50d4adf9e405f3dcfc05a31a55c96f773f07832af34'] dependencies = [('Java', '13')] diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..1932103b688 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['94d056e48e7e6fe2e6fe4161471e774ac03221a6225fd83d551d3184220c1edf'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb new file mode 100644 index 00000000000..61912e520f1 --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '4.0.7' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] +sources = ['spoa-v%(version)s.tar.gz'] +checksums = ['f7a8cd039e4aabea1481e123387fedaa8f87e55418a3649408a615f5c6b1b9a4'] + +builddependencies = [('CMake', '3.18.4')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a', 'lib/pkgconfig/spoa-1.pc'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.10.1-foss-2019a.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.10.1-foss-2019a.eb index ffa1316dd70..fccb9fee5e2 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.10.1-foss-2019a.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.10.1-foss-2019a.eb @@ -19,11 +19,9 @@ use_pip = True exts_list = [ ('patsy', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/statsmodels'], 'checksums': ['320659a80f916c2edf9dfbe83512d9004bb562b72eedb7d9374562038697fa10'], }), ] diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.11.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.11.0-foss-2019b-Python-3.7.4.eb index 5761bd098e5..d7d94385fd7 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.11.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.11.0-foss-2019b-Python-3.7.4.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('patsy', '0.5.1', { 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.11.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.11.0-intel-2019b-Python-3.7.4.eb index 3e9236311a1..5fa24cf275c 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.11.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.11.0-intel-2019b-Python-3.7.4.eb @@ -20,11 +20,9 @@ use_pip = True exts_list = [ ('patsy', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], 'checksums': ['0a8ee8fc091d9ef1db68f01e6e0079acc0f41671dfbac463131939ca573f8c71'], }), ] diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-foss-2017a-Python-2.7.13.eb index 7b53b41d1c7..74e35c5471e 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-foss-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'statsmodels' version = '0.6.1' @@ -10,29 +10,17 @@ and perform statistical tests.""" toolchain = {'name': 'foss', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [('Python', '2.7.13')] exts_list = [ ('patsy', '0.4.1', { 'source_tmpl': 'patsy-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['dc1cc280045b0e6e50c04706fd1e26d2a00ea400aa112f88e8142f88b0b7d3d4'], }), (name, version, { 'source_tmpl': 'statsmodels-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/statsmodels'], 'checksums': ['4313dd4cbf1ebadef3661f6efd895132b615016e9bee560b5fdfd80c74dd422f'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb index 56756a24071..18357cae266 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'statsmodels' version = '0.6.1' @@ -10,28 +10,15 @@ description = """Statsmodels is a Python package that provides a complement to s toolchain = {'name': 'intel', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '3.5.1'), ] exts_list = [ ('patsy', '0.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'source_tmpl': 'patsy-%(version)s.zip', }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], - }), + (name, version), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb index 484c222815b..e7c87dfaec5 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'statsmodels' version = '0.6.1' @@ -10,27 +10,15 @@ and perform statistical tests.""" toolchain = {'name': 'intel', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [('Python', '3.5.2')] exts_list = [ ('patsy', '0.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'source_tmpl': 'patsy-%(version)s.zip', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/statsmodels'], 'source_tmpl': 'statsmodels-%(version)s.zip', }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb index 85483b00055..2deb3d02413 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'statsmodels' version = '0.8.0' @@ -10,27 +10,15 @@ and perform statistical tests.""" toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [('Python', '2.7.13')] exts_list = [ ('patsy', '0.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'source_tmpl': 'patsy-%(version)s.zip', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/statsmodels'], 'source_tmpl': 'statsmodels-%(version)s.tar.gz', }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb index 9806418887c..5dd27444f93 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb @@ -17,11 +17,9 @@ use_pip = True exts_list = [ ('patsy', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], }), ] diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-3.6.6.eb index 544ee34951d..170293116d3 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-3.6.6.eb @@ -18,11 +18,9 @@ sanity_pip_check = True exts_list = [ ('patsy', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], }), ] diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb index 15441771e45..5402334e416 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb @@ -17,11 +17,9 @@ use_pip = True exts_list = [ ('patsy', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], }), ] diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-3.6.6.eb index cc86de528d4..0633921b2f6 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-3.6.6.eb @@ -19,11 +19,9 @@ use_pip = True exts_list = [ ('patsy', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], }), ] diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2019b-Python-2.7.16.eb index a4dbfea47c1..bc30eca0f39 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2019b-Python-2.7.16.eb @@ -18,7 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ ('patsy', '0.5.1', { 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], diff --git a/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.3-foss-2018b-Python-2.7.15.eb index a270b6a4483..10969e4b873 100644 --- a/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.3-foss-2018b-Python-2.7.15.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Pympler', '0.6', { 'checksums': ['c262ceca4dac67b8b523956833c52443420eabc3321a07185990b358b8ba13a7'], diff --git a/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019a-Python-3.7.2.eb index 0a2298f761d..03da2dccc86 100644 --- a/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019a-Python-3.7.2.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Pympler', '0.7', { 'checksums': ['7a11e739125a9ce8bf868ded67238a40e8a7bf979bc03005eb8126182e5e274e'], diff --git a/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019b-Python-3.7.4.eb index 40a9f143072..ff027b67acb 100644 --- a/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019b-Python-3.7.4.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Pympler', '0.7', { 'checksums': ['7a11e739125a9ce8bf868ded67238a40e8a7bf979bc03005eb8126182e5e274e'], diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb index 1ee4a4a0bc6..d60f5e1642a 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'sympy' version = '1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://sympy.org/' +homepage = 'https://sympy.org/' description = """SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy @@ -12,7 +12,6 @@ description = """SymPy is a Python library for symbolic mathematics. It aims to toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # patch to fix tests diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb index 1c13652bc7d..5ad99612b2c 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'sympy' version = '1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://sympy.org/' +homepage = 'https://sympy.org/' description = """SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy @@ -12,7 +12,6 @@ description = """SymPy is a Python library for symbolic mathematics. It aims to toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # patch to fix tests diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/sympy/sympy-1.3-foss-2018b-Python-2.7.15.eb index e76c8f72d68..3848d9a8df8 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.3-foss-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'sympy' version = '1.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://sympy.org/' +homepage = 'https://sympy.org/' description = """ SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as @@ -14,7 +14,6 @@ description = """ toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['sympy-%(version)s_allpython.patch'] @@ -35,9 +34,4 @@ use_pip = True runtest = 'python setup.py test' -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/sympy/sympy-1.3-foss-2018b-Python-3.6.6.eb index d39f249b7f4..7cc0d6ba6ac 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.3-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'sympy' version = '1.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://sympy.org/' +homepage = 'https://sympy.org/' description = """ SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as @@ -14,7 +14,6 @@ description = """ toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['sympy-%(version)s_allpython.patch'] @@ -34,9 +33,4 @@ use_pip = True runtest = 'python setup.py test' -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/sympy/sympy-1.3-intel-2018a-Python-2.7.14.eb index f4430068361..351ba641a5f 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.3-intel-2018a-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'sympy' version = '1.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://sympy.org/' +homepage = 'https://sympy.org/' description = """SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy @@ -12,7 +12,6 @@ description = """SymPy is a Python library for symbolic mathematics. It aims to toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['sympy-%(version)s_allpython.patch'] @@ -33,9 +32,4 @@ use_pip = True runtest = 'python setup.py test' -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.3-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/sympy/sympy-1.3-intel-2018a-Python-3.6.4.eb index feff7186115..a6529ce4e1c 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.3-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.3-intel-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'sympy' version = '1.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://sympy.org/' +homepage = 'https://sympy.org/' description = """SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy @@ -12,7 +12,6 @@ description = """SymPy is a Python library for symbolic mathematics. It aims to toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['sympy-%(version)s_allpython.patch'] @@ -29,9 +28,4 @@ use_pip = True runtest = 'python setup.py test' -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb index 717aecb5894..04e303c151e 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'sympy' version = '1.4' -homepage = 'http://sympy.org/' +homepage = 'https://sympy.org/' description = """SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy @@ -11,7 +11,6 @@ description = """SymPy is a Python library for symbolic mathematics. It aims to toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['sympy-1.3_allpython.patch'] checksums = [ @@ -30,9 +29,4 @@ use_pip = True runtest = 'python setup.py test' -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb index 58f9fd8cb47..f5d112ca364 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'sympy' version = '1.4' -homepage = 'http://sympy.org/' +homepage = 'https://sympy.org/' description = """SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy @@ -11,7 +11,6 @@ description = """SymPy is a Python library for symbolic mathematics. It aims to toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = [ 'sympy-1.3_allpython.patch', @@ -35,9 +34,4 @@ use_pip = True runtest = 'python setup.py test' -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb index 9b1e7b6a9d1..0c153932260 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = """SymPy is a Python library for symbolic mathematics. It aims to toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['%(name)s-%(version)s_allpython.patch'] checksums = [ diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.8-foss-2021a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.8-foss-2021a.eb new file mode 100644 index 00000000000..15c25b4cfcd --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.8-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.8' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1ca588a9f6ce6a323c5592f9635159c2093572826668a1022c75c75bdf0297cb'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('gmpy2', '2.1.0b5'), +] + +download_dep_fail = True +use_pip = True + +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/TEToolkit/TEToolkit-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/TEToolkit/TEToolkit-1.5.1-foss-2016a-Python-2.7.11.eb index 0b342a93605..716f4766c83 100644 --- a/easybuild/easyconfigs/t/TEToolkit/TEToolkit-1.5.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/t/TEToolkit/TEToolkit-1.5.1-foss-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ Elements and other highly repetitive regions""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['22c13ca45bccc89e9d9bf48d59ae6db1fa4c634def64fc56ba9bffd23aa689ac'] diff --git a/easybuild/easyconfigs/t/TVB-deps/TVB-deps-20160618-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/TVB-deps/TVB-deps-20160618-intel-2016a-Python-2.7.11.eb index e4bb6126b7f..e4486a55a28 100644 --- a/easybuild/easyconfigs/t/TVB-deps/TVB-deps-20160618-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/t/TVB-deps/TVB-deps-20160618-intel-2016a-Python-2.7.11.eb @@ -1,10 +1,10 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'TVB-deps' version = '20160618' # date of most recent updated package included in this bundle (psutil) versionsuffix = '-Python-%(pyver)s' -homepage = 'http://thevirtualbrain.org' +homepage = 'https://thevirtualbrain.org' description = """Bundle of dependency Python packages for TVB (The Virtual Brain)""" toolchain = {'name': 'intel', 'version': '2016a'} @@ -21,66 +21,29 @@ dependencies = [ ('numba', '0.26.0', versionsuffix), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - exts_list = [ - ('APScheduler', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/APScheduler/'], - }), + ('APScheduler', '3.2.0'), ('BeautifulSoup', '3.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/B/BeautifulSoup/'], 'modulename': 'BeautifulSoup', }), - ('CherryPy', '6.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/C/CherryPy/'], - }), - ('Genshi', '0.7', { - 'source_urls': ['https://pypi.python.org/packages/source/G/Genshi/'], - }), - ('cfflib', '2.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cfflib/'], - }), - ('FormEncode', '1.3.0a1', { - 'source_urls': ['https://pypi.python.org/packages/source/F/FormEncode/'], - }), + ('CherryPy', '6.0.1'), + ('Genshi', '0.7'), + ('cfflib', '2.0.5'), + ('FormEncode', '1.3.0a1'), ('minixsv', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/minixsv/'], 'source_tmpl': 'minixsv-%(version)s.zip', }), - ('mod_pywebsocket', '0.7.9', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mod_pywebsocket/'], - }), - ('networkx', '1.11', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], - }), - ('numexpr', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numexpr/'], - }), - ('psutil', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil/'], - }), - ('simplejson', '3.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], - }), + ('mod_pywebsocket', '0.7.9'), + ('networkx', '1.11'), + ('numexpr', '2.6.0'), + ('psutil', '4.3.0'), + ('simplejson', '3.8.2'), # versions of SQLAlchemy & sqlalchemy-migrate are fixed to old versions by TVB, probably with good reason - ('SQLAlchemy', '0.7.8', { - 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], - }), + ('SQLAlchemy', '0.7.8'), ('sqlalchemy-migrate', '0.7.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sqlalchemy-migrate/'], 'modulename': 'migrate', }), - ('gdist', '1.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gdist/'], - }), + ('gdist', '1.0.3'), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-foss-2019a-Python-3.7.2-PyTorch-1.2.0.eb b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-foss-2019a-Python-3.7.2-PyTorch-1.2.0.eb index e5752ccc2d5..ef27f6cf9d6 100644 --- a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-foss-2019a-Python-3.7.2-PyTorch-1.2.0.eb +++ b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-foss-2019a-Python-3.7.2-PyTorch-1.2.0.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('patsy', '0.5.1', { 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], diff --git a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2-PyTorch-1.2.0.eb b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2-PyTorch-1.2.0.eb index 1f2fbec877a..4152866075f 100644 --- a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2-PyTorch-1.2.0.eb +++ b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2-PyTorch-1.2.0.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('patsy', '0.5.1', { 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-foss-2016b-Python-2.7.12.eb index 258e36d48a4..5ff1d1ce4e8 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-foss-2016b-Python-2.7.12.eb @@ -13,7 +13,6 @@ local_pymaj = '2' local_pymin = '7' local_pymajmin = local_pymaj + local_pymin -source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(py)s-cp%(py)smu-manylinux1_x86_64.whl' % {'py': local_pymajmin}, ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-foss-2016b-Python-3.5.2.eb index dfaf926882b..98420b89cfc 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-foss-2016b-Python-3.5.2.eb @@ -13,7 +13,6 @@ local_pymaj = '3' local_pymin = '5' local_pymajmin = local_pymaj + local_pymin -source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(py)s-cp%(py)sm-manylinux1_x86_64.whl' % {'py': local_pymajmin}, ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-intel-2016b-Python-2.7.12.eb index 014e8defc26..c4a6bbf80ed 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-intel-2016b-Python-2.7.12.eb @@ -13,7 +13,6 @@ local_pymaj = '2' local_pymin = '7' local_pymajmin = local_pymaj + local_pymin -source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(py)s-cp%(py)smu-manylinux1_x86_64.whl' % {'py': local_pymajmin}, ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-intel-2016b-Python-3.5.2.eb index 2add626957f..d2d05927dfd 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-0.12.1-intel-2016b-Python-3.5.2.eb @@ -13,7 +13,6 @@ local_pymaj = '3' local_pymin = '5' local_pymajmin = local_pymaj + local_pymin -source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(py)s-cp%(py)sm-manylinux1_x86_64.whl' % {'py': local_pymajmin}, ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.0.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.0.1-intel-2016b-Python-2.7.12.eb index 88c22926286..48ad719af57 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.0.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.0.1-intel-2016b-Python-2.7.12.eb @@ -13,7 +13,6 @@ local_pymaj = '2' local_pymin = '7' local_pymajmin = local_pymaj + local_pymin -source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(py)s-cp%(py)smu-manylinux1_x86_64.whl' % {'py': local_pymajmin}, ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.0.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.0.1-intel-2016b-Python-3.5.2.eb index f97458a49e3..7be521a3bba 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.0.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.0.1-intel-2016b-Python-3.5.2.eb @@ -13,7 +13,6 @@ local_pymaj = '3' local_pymin = '5' local_pymajmin = local_pymaj + local_pymin -source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(py)s-cp%(py)sm-manylinux1_x86_64.whl' % {'py': local_pymajmin}, ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.1.0-intel-2017a-Python-2.7.13.eb index c71e1361b40..df25331b2e9 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.1.0-intel-2017a-Python-2.7.13.eb @@ -13,7 +13,6 @@ local_pymaj = '2' local_pymin = '7' local_pymajmin = local_pymaj + local_pymin -source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(py)s-cp%(py)smu-manylinux1_x86_64.whl' % {'py': local_pymajmin}, ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.1.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.1.0-intel-2017a-Python-3.6.1.eb index 906ac7bdbf6..587950bee87 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.1.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.1.0-intel-2017a-Python-3.6.1.eb @@ -13,7 +13,6 @@ local_pymaj = '3' local_pymin = '6' local_pymajmin = local_pymaj + local_pymin -source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(py)s-cp%(py)sm-manylinux1_x86_64.whl' % {'py': local_pymajmin}, ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.0-fosscuda-2018b-Python-2.7.15.eb index 4ba81f2cdf5..48b7dd4053d 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.0-fosscuda-2018b-Python-2.7.15.eb @@ -37,41 +37,36 @@ dependencies = [ cuda_compute_capabilities = ['3.0', '3.2', '3.5', '3.7', '5.0', '6.0', '7.0'] +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} exts_list = [ ('absl-py', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], 'checksums': ['6fcc3c04dc881fd93d793674a42ee8c73155570eda8f8b90c4477c8522478b7b'], 'modulename': 'absl', }), ('astor', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], }), ('gast', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], 'checksums': ['7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930'], }), ('grpcio', '1.15.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], 'checksums': ['15a5fc23ba2e5f30758fbb8763f79a764e3de1ffcb92c2ccd46f45ffa63910d2'], 'modulename': 'grpc', }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('tensorboard', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], 'source_tmpl': 'tensorboard-%(version)s-py2-none-any.whl', 'checksums': ['64edbe66864e02719f85708ae01efe3448af964c042a502fd2046cc87a3b1f12'], 'unpack_sources': False, }), ('termcolor', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.1-foss-2018b-Python-3.6.6.eb index 350831c8065..70a9827e6d8 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.1-foss-2018b-Python-3.6.6.eb @@ -31,41 +31,36 @@ dependencies = [ ('protobuf-python', '3.6.0', versionsuffix), ] +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} exts_list = [ ('absl-py', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], 'checksums': ['6fcc3c04dc881fd93d793674a42ee8c73155570eda8f8b90c4477c8522478b7b'], 'modulename': 'absl', }), ('astor', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], }), ('gast', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], 'checksums': ['7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930'], }), ('grpcio', '1.15.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], 'checksums': ['15a5fc23ba2e5f30758fbb8763f79a764e3de1ffcb92c2ccd46f45ffa63910d2'], 'modulename': 'grpc', }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('tensorboard', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'checksums': ['e4ea6ac2e47bf715b915f08a186e6205fa097318bd73f0b265d437b1d7834484'], 'unpack_sources': False, }), ('termcolor', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.1-fosscuda-2018b-Python-2.7.15.eb index 41398d0b9fa..059456a6805 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.1-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.10.1-fosscuda-2018b-Python-2.7.15.eb @@ -37,41 +37,36 @@ dependencies = [ cuda_compute_capabilities = ['3.0', '3.2', '3.5', '3.7', '5.0', '6.0', '7.0'] +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} exts_list = [ ('absl-py', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], 'checksums': ['6fcc3c04dc881fd93d793674a42ee8c73155570eda8f8b90c4477c8522478b7b'], 'modulename': 'absl', }), ('astor', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], }), ('gast', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], 'checksums': ['7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930'], }), ('grpcio', '1.15.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], 'checksums': ['15a5fc23ba2e5f30758fbb8763f79a764e3de1ffcb92c2ccd46f45ffa63910d2'], 'modulename': 'grpc', }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('tensorboard', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], 'source_tmpl': 'tensorboard-%(version)s-py2-none-any.whl', 'checksums': ['64edbe66864e02719f85708ae01efe3448af964c042a502fd2046cc87a3b1f12'], 'unpack_sources': False, }), ('termcolor', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.11.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.11.0-foss-2018b-Python-3.6.6.eb index 4cf76834c18..01cc13ab3a9 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.11.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.11.0-foss-2018b-Python-3.6.6.eb @@ -24,49 +24,39 @@ use_pip = True exts_list = [ ('absl-py', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], 'checksums': ['6fcc3c04dc881fd93d793674a42ee8c73155570eda8f8b90c4477c8522478b7b'], 'modulename': 'absl', }), ('astor', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], }), ('gast', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], 'checksums': ['7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930'], }), ('grpcio', '1.15.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], 'checksums': ['15a5fc23ba2e5f30758fbb8763f79a764e3de1ffcb92c2ccd46f45ffa63910d2'], 'modulename': 'grpc', }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('tensorboard', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'unpack_sources': False, 'checksums': ['e4ea6ac2e47bf715b915f08a186e6205fa097318bd73f0b265d437b1d7834484'], }), ('termcolor', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Keras-Applications', '1.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['a03af60ddc9c5afdae4d5c9a8dd4ca857550e0b793733a5072e0725829b87017'], 'modulename': 'keras_applications', }), ('Keras-Preprocessing', '1.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], 'modulename': 'keras_preprocessing', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-foss-2018b-Python-3.6.6.eb index b51a5031b9d..15245b95bcc 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-foss-2018b-Python-3.6.6.eb @@ -34,49 +34,39 @@ exts_list = [ 'modulename': 'google.protobuf', }), ('absl-py', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], 'checksums': ['87519e3b91a3d573664c6e2ee33df582bb68dca6642ae3cf3a4361b1c0a4e9d6'], 'modulename': 'absl', }), ('astor', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], }), ('gast', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], 'checksums': ['7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930'], }), ('grpcio', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], 'checksums': ['0cc5f2d3ee21c642d8982f197c83053fd3a8cbcd6a60240d8c87c6c256b10d57'], 'modulename': 'grpc', }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('tensorboard', version, { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'checksums': ['ca275a7e39797946930d7d4460999369b73968e8191f2256e23bfb7924004d59'], 'unpack_sources': False, }), ('termcolor', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Keras-Applications', '1.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['a03af60ddc9c5afdae4d5c9a8dd4ca857550e0b793733a5072e0725829b87017'], 'modulename': 'keras_applications', }), ('Keras-Preprocessing', '1.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], 'modulename': 'keras_preprocessing', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb index 839e916589c..c75d7a67970 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb @@ -37,49 +37,39 @@ exts_list = [ 'modulename': 'google.protobuf', }), ('absl-py', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], 'checksums': ['87519e3b91a3d573664c6e2ee33df582bb68dca6642ae3cf3a4361b1c0a4e9d6'], 'modulename': 'absl', }), ('astor', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], }), ('gast', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], 'checksums': ['7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930'], }), ('grpcio', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], 'checksums': ['0cc5f2d3ee21c642d8982f197c83053fd3a8cbcd6a60240d8c87c6c256b10d57'], 'modulename': 'grpc', }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('tensorboard', version, { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], 'source_tmpl': 'tensorboard-%(version)s-py2-none-any.whl', 'unpack_sources': False, 'checksums': ['537603db949e10d2f5f201d88b073f3f8fb4e4c311d5541e1d4518aa59aa8daa'], }), ('termcolor', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Keras-Applications', '1.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['a03af60ddc9c5afdae4d5c9a8dd4ca857550e0b793733a5072e0725829b87017'], 'modulename': 'keras_applications', }), ('Keras-Preprocessing', '1.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], 'modulename': 'keras_preprocessing', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb index 15c68ed4e6e..fe2784739ad 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb @@ -36,49 +36,39 @@ exts_list = [ 'modulename': 'google.protobuf', }), ('absl-py', '0.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], 'checksums': ['87519e3b91a3d573664c6e2ee33df582bb68dca6642ae3cf3a4361b1c0a4e9d6'], 'modulename': 'absl', }), ('astor', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], }), ('gast', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], 'checksums': ['7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930'], }), ('grpcio', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], 'checksums': ['0cc5f2d3ee21c642d8982f197c83053fd3a8cbcd6a60240d8c87c6c256b10d57'], 'modulename': 'grpc', }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('tensorboard', version, { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'unpack_sources': False, 'checksums': ['ca275a7e39797946930d7d4460999369b73968e8191f2256e23bfb7924004d59'], }), ('termcolor', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Keras-Applications', '1.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['a03af60ddc9c5afdae4d5c9a8dd4ca857550e0b793733a5072e0725829b87017'], 'modulename': 'keras_applications', }), ('Keras-Preprocessing', '1.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], 'modulename': 'keras_preprocessing', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb index 05b73431a7c..576544b8554 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb @@ -34,55 +34,44 @@ exts_list = [ 'modulename': 'google.protobuf', }), ('absl-py', '0.7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], 'checksums': ['8718189e4bd6013bf79910b9d1cb0a76aecad8ce664f78e1144980fabdd2cd23'], 'modulename': 'absl', }), ('astor', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], }), ('gast', '0.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], 'checksums': ['fe939df4583692f0512161ec1c880e0a10e71e6a232da045ab8edd3756fbadf0'], }), ('grpcio', '1.19.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], 'checksums': ['2ddbca16c2e7b3f2ffc6e34c7cfa6886fb01de9f156ad3f77b72ad652d632097'], 'modulename': 'grpc', }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('tensorboard', '1.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'checksums': ['82c9c711b76949b7b3794fc319dc3d3b0fad25f7c0c5260ec4a8371b02d23da6'], 'unpack_sources': False, }), ('termcolor', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('Werkzeug', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Keras-Applications', '1.0.7', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['60607b2b98868983e5153bf1cc6aa468ba73adc93bc977a90edaa4bc595e69fa'], 'modulename': 'keras_applications', }), ('Keras-Preprocessing', '1.0.9', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['5e3700117981c2db762e512ed6586638124fac5842170701628088a11aeb51ac'], 'modulename': 'keras_preprocessing', }), ('tensorflow-estimator', '1.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow-estimator'], 'source_tmpl': 'tensorflow_estimator-1.13.0-py2.py3-none-any.whl', 'unpack_sources': False, }), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb index a46fdedca19..040263d7fa2 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb @@ -22,11 +22,8 @@ dependencies = [ ('h5py', '2.9.0'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('protobuf-python', '3.6.1', { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb index 8b353ed51ae..574f0ddf817 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb @@ -24,11 +24,8 @@ dependencies = [ ('NCCL', '2.4.2'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('protobuf-python', '3.6.1', { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb index b45ba1102ab..e6fb23204ac 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb @@ -22,11 +22,8 @@ dependencies = [ ('h5py', '2.9.0'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ # tensorboard 1.14.0 has requirement setuptools>=41.0.0 diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-fosscuda-2019a-Python-3.7.2.eb index d5954f6bf81..4e9a7567cc5 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-fosscuda-2019a-Python-3.7.2.eb @@ -23,11 +23,8 @@ dependencies = [ ('NCCL', '2.4.2'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ # tensorboard 1.14.0 has requirement setuptools>=41.0.0 diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.0-foss-2019b-Python-3.7.4.eb index 9f9f2544785..c00c39afbbb 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.0-foss-2019b-Python-3.7.4.eb @@ -24,11 +24,8 @@ dependencies = [ ('h5py', '2.10.0', versionsuffix), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Keras-Preprocessing', '1.1.0', { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.0-fosscuda-2019b-Python-3.7.4.eb index 1fd5a54d703..3e1979bbeb6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.0-fosscuda-2019b-Python-3.7.4.eb @@ -26,11 +26,8 @@ dependencies = [ ('NCCL', '2.4.8'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Keras-Preprocessing', '1.1.0', { @@ -118,6 +115,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.2-foss-2019b-Python-3.7.4.eb index 77544972806..62c34323ea5 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.2-foss-2019b-Python-3.7.4.eb @@ -24,11 +24,8 @@ dependencies = [ ('h5py', '2.10.0', versionsuffix), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Keras-Preprocessing', '1.1.0', { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.2-fosscuda-2019b-Python-3.7.4.eb index 6af7e534de8..fd870f0622f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.2-fosscuda-2019b-Python-3.7.4.eb @@ -26,11 +26,8 @@ dependencies = [ ('NCCL', '2.4.8'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Keras-Preprocessing', '1.1.0', { @@ -117,6 +114,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.5-fosscuda-2019b-Python-3.7.4-nompi.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.5-fosscuda-2019b-Python-3.7.4-nompi.eb index 67b9d74d07a..58db0b940e9 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.5-fosscuda-2019b-Python-3.7.4-nompi.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.5-fosscuda-2019b-Python-3.7.4-nompi.eb @@ -26,11 +26,8 @@ dependencies = [ ('NCCL', '2.4.8'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Keras-Preprocessing', '1.1.2', { @@ -117,6 +114,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.5-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.5-fosscuda-2019b-Python-3.7.4.eb index 904e58df939..46344dd1796 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.5-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.15.5-fosscuda-2019b-Python-3.7.4.eb @@ -26,11 +26,8 @@ dependencies = [ ('NCCL', '2.4.8'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Keras-Preprocessing', '1.1.2', { @@ -117,6 +114,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.0-intel-2017a-Python-3.6.1.eb index f06d40d782a..c3799878d6c 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.0-intel-2017a-Python-3.6.1.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'TensorFlow' version = '1.2.0' @@ -13,9 +13,6 @@ local_pymaj = '3' local_pymin = '6' local_pymajmin = local_pymaj + local_pymin -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '%s.%s.1' % (local_pymaj, local_pymin)), ('protobuf-python', '3.3.0', versionsuffix), @@ -24,10 +21,8 @@ dependencies = [ exts_list = [ ('backports.weakref', '1.0rc1', { 'modulename': 'backports.weakref', - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.weakref'], }), ('tensorflow', version, { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow'], 'source_tmpl': 'tensorflow-%%(version)s-cp%(py)s-cp%(py)sm-manylinux1_x86_64.whl' % {'py': local_pymajmin}, 'checksums': ['a3835274cddd9c5b5a752e39b34c31a2d3d80e0ebcb5488e2dafaf3d614391d1'], 'use_pip': True, @@ -40,6 +35,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb index 8168a4acde1..3bf1060dd25 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'TensorFlow' version = '1.2.1' @@ -10,9 +10,6 @@ description = "An open-source software library for Machine Intelligence" toolchain = {'name': 'foss', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - local_pymaj = '3' local_pymin = '5' local_pymajmin = local_pymaj + local_pymin @@ -27,11 +24,9 @@ dependencies = [ exts_list = [ ('backports.weakref', '1.0rc1', { 'modulename': 'backports.weakref', - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.weakref'], 'checksums': ['8813bf712a66b3d8b85dc289e1104ed220f1878cf981e2fe756dfaabe9a82892'], }), ('Werkzeug', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/w/Werkzeug'], 'checksums': ['903a7b87b74635244548b30d30db4c8947fe64c5198f58899ddcd3a13c23bb26'], }), ('bleach', '2.0.0', { @@ -56,6 +51,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-Python-3.5.2.eb index 7367ac20c03..ab3e62b4313 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-Python-3.5.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'TensorFlow' version = '1.2.1' @@ -9,9 +9,6 @@ description = "An open-source software library for Machine Intelligence" toolchain = {'name': 'foss', 'version': '2016b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - local_pymaj = '3' local_pymin = '5' local_pymajmin = local_pymaj + local_pymin @@ -24,11 +21,9 @@ dependencies = [ exts_list = [ ('backports.weakref', '1.0rc1', { 'modulename': 'backports.weakref', - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.weakref'], 'checksums': ['8813bf712a66b3d8b85dc289e1104ed220f1878cf981e2fe756dfaabe9a82892'], }), ('Werkzeug', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/w/Werkzeug'], 'checksums': ['903a7b87b74635244548b30d30db4c8947fe64c5198f58899ddcd3a13c23bb26'], }), ('bleach', '2.0.0', { @@ -40,7 +35,6 @@ exts_list = [ 'checksums': ['0ac8a81e658167da95d063a9279c9c1b2699f37c7c4153256a458b3a43860e33'], }), ('tensorflow', version, { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow'], 'source_tmpl': 'tensorflow-%%(version)s-cp%(py)s-cp%(py)sm-manylinux1_x86_64.whl' % {'py': local_pymajmin}, 'checksums': ['d42e7a5c522bff59f0d3f5e28fca3dda11bad981a7aa4d777d1f1684700d2a06'], 'use_pip': True, @@ -53,6 +47,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017a-Python-2.7.13.eb index 5adc30fd14b..c6665a67b2c 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'TensorFlow' version = '1.3.0' @@ -18,18 +18,13 @@ dependencies = [ ('protobuf-python', '3.4.0', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ ('backports.weakref', '1.0.post1', { 'modulename': 'backports.weakref', - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.weakref'], 'checksums': ['bc4170a29915f8b22c9e7c4939701859650f2eb84184aee80da329ac0b9825c2'], }), ('tensorflow', version, { 'source_tmpl': 'tensorflow-%%(version)s-cp%(py)s-cp%(py)smu-manylinux1_x86_64.whl' % {'py': local_pymajmin}, - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow'], 'unpack_sources': False, 'use_pip': True, 'checksums': ['0bf3866115184d97993d702f2f47cd557fa5a26b6661aa94aa16c05e4a545cfb'], @@ -41,6 +36,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017a-Python-3.6.1.eb index 6ad96e1e738..ad907aad025 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017a-Python-3.6.1.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'TensorFlow' version = '1.3.0' @@ -18,18 +18,13 @@ dependencies = [ ('protobuf-python', '3.4.0', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ ('backports.weakref', '1.0.post1', { 'modulename': 'backports.weakref', - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.weakref'], 'checksums': ['bc4170a29915f8b22c9e7c4939701859650f2eb84184aee80da329ac0b9825c2'], }), ('tensorflow', version, { 'source_tmpl': 'tensorflow-%%(version)s-cp%(py)s-cp%(py)sm-manylinux1_x86_64.whl' % {'py': local_pymajmin}, - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow'], 'unpack_sources': False, 'use_pip': True, 'checksums': ['a535a4a32aaaf5c59dc582ed472f321a86bf1786d17931c017c0ec7c8f1a1c02'], @@ -41,6 +36,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017b-Python-3.6.3.eb index 66ac7c02368..92f6526af1e 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.3.0-intel-2017b-Python-3.6.3.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'TensorFlow' version = '1.3.0' @@ -18,18 +18,13 @@ dependencies = [ ('protobuf-python', '3.4.0', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - exts_list = [ ('backports.weakref', '1.0.post1', { 'modulename': 'backports.weakref', - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.weakref'], 'checksums': ['bc4170a29915f8b22c9e7c4939701859650f2eb84184aee80da329ac0b9825c2'], }), ('tensorflow', version, { 'source_tmpl': 'tensorflow-%%(version)s-cp%(py)s-cp%(py)sm-manylinux1_x86_64.whl' % {'py': local_pymajmin}, - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow'], 'unpack_sources': False, 'use_pip': True, 'checksums': ['a535a4a32aaaf5c59dc582ed472f321a86bf1786d17931c017c0ec7c8f1a1c02'], @@ -41,6 +36,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.0-foss-2019a-Python-3.7.2.eb index cc83c753e7b..faf2b6b3df7 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.0-foss-2019a-Python-3.7.2.eb @@ -12,7 +12,6 @@ toolchainopts = {'usempi': True} builddependencies = [ ('Bazel', '0.26.1'), - ('protobuf', '3.7.1'), # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.21.0', '-nodocs'), ] @@ -20,13 +19,11 @@ dependencies = [ ('Python', '3.7.2'), ('SciPy-bundle', '2019.03'), ('h5py', '2.9.0'), + ('protobuf', '3.7.1'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ # tensorboard 2.0.0 has requirement setuptools>=41.0.0 @@ -128,6 +125,7 @@ exts_list = [ 'TensorFlow-1.14.0_swig-env.patch', 'TensorFlow-1.13.1_lrt-flag.patch', 'TensorFlow-1.14.0_fix-mpi-undeclared-inclusion.patch', + 'TensorFlow-2.0.0_fix-ambiguous-configurable-attribute.patch', 'TensorFlow-2.0.0_fix-build-tf-lite-avx512.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', @@ -138,6 +136,8 @@ exts_list = [ 'b388be35f2581786bcd533b1bfa375165d7f35e38a3aab74570019312816bf1b', # TensorFlow-1.13.1_lrt-flag.patch # TensorFlow-1.14.0_fix-mpi-undeclared-inclusion.patch '09e5fdce89588074b3c2abb6a4705b1f141b43395c960660320cf1cb79cd1ef4', + # TensorFlow-2.0.0_fix-ambiguous-configurable-attribute.patch + '04f8f792204b2d6a302ef57d5181b57d6dc95ba0a5b2f888a78d3ff518830b42', # TensorFlow-2.0.0_fix-build-tf-lite-avx512.patch 'ee65c8e34b62644f426054b67386734b8bf51c43ac0da4d51331b4ba191fad17', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.0-fosscuda-2019b-Python-3.7.4.eb index 7173464f038..dd3ac573691 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.0-fosscuda-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ toolchainopts = {'usempi': True} builddependencies = [ ('Bazel', '0.26.1'), - ('protobuf', '3.10.0'), # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.23.0', '-nodocs'), ] @@ -35,6 +34,7 @@ dependencies = [ ('nsync', '1.24.0'), ('SQLite', '3.29.0'), ('PCRE', '8.43'), + ('protobuf', '3.10.0'), ('protobuf-python', '3.10.0', versionsuffix), ('libpng', '1.6.37'), ('snappy', '1.1.7'), @@ -42,11 +42,8 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Markdown', '3.1.1', { @@ -139,6 +136,7 @@ exts_list = [ 'TensorFlow-1.13.1_lrt-flag.patch', 'TensorFlow-1.14.0_fix-mpi-undeclared-inclusion.patch', 'TensorFlow-1.14.0_fix-cuda-build.patch', + 'TensorFlow-2.0.0_fix-ambiguous-configurable-attribute.patch', 'TensorFlow-2.0.0_fix-build-tf-lite-avx512.patch', 'TensorFlow-2.0.0_fix-system-flatbuffers.patch', 'TensorFlow-2.0.0_fix-system-nasm.patch', @@ -154,6 +152,8 @@ exts_list = [ '09e5fdce89588074b3c2abb6a4705b1f141b43395c960660320cf1cb79cd1ef4', # TensorFlow-1.14.0_fix-cuda-build.patch '92afeee76520a63dc638c2cd4adaf2e7429411068ea4be96718255f67f113e43', + # TensorFlow-2.0.0_fix-ambiguous-configurable-attribute.patch + '04f8f792204b2d6a302ef57d5181b57d6dc95ba0a5b2f888a78d3ff518830b42', # TensorFlow-2.0.0_fix-build-tf-lite-avx512.patch 'ee65c8e34b62644f426054b67386734b8bf51c43ac0da4d51331b4ba191fad17', # TensorFlow-2.0.0_fix-system-flatbuffers.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.0_fix-ambiguous-configurable-attribute.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.0_fix-ambiguous-configurable-attribute.patch new file mode 100644 index 00000000000..6c8cdb61f82 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.0_fix-ambiguous-configurable-attribute.patch @@ -0,0 +1,24 @@ +Passing no_gcp_support leads to an ambiguous attribute. Remove! + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/core/platform/default/build_config.bzl b/tensorflow/core/platform/default/build_config.bzl +index 6404fde5504..d7cac0ae90b 100644 +--- a/tensorflow/core/platform/default/build_config.bzl ++++ b/tensorflow/core/platform/default/build_config.bzl +@@ -695,7 +695,5 @@ def tf_additional_cloud_op_deps(): + "//tensorflow:ios": [], + "//tensorflow:linux_s390x": [], + "//tensorflow:windows": [], +- "//tensorflow:api_version_2": [], +- "//tensorflow:windows_and_api_version_2": [], + "//tensorflow:no_gcp_support": [], + "//conditions:default": [ +@@ -711,7 +710,5 @@ def tf_additional_cloud_kernel_deps(): + "//tensorflow:ios": [], + "//tensorflow:linux_s390x": [], + "//tensorflow:windows": [], +- "//tensorflow:api_version_2": [], +- "//tensorflow:windows_and_api_version_2": [], + "//tensorflow:no_gcp_support": [], + "//conditions:default": [ diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.1-foss-2019a-Python-3.7.2.eb index a5bc827e864..c455d2871c9 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.1-foss-2019a-Python-3.7.2.eb @@ -12,7 +12,6 @@ toolchainopts = {'usempi': True} builddependencies = [ ('Bazel', '0.26.1'), - ('protobuf', '3.7.1'), # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.21.0', '-nodocs'), ] @@ -20,13 +19,11 @@ dependencies = [ ('Python', '3.7.2'), ('SciPy-bundle', '2019.03'), ('h5py', '2.9.0'), + ('protobuf', '3.7.1'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ # tensorboard 2.0.0 has requirement setuptools>=41.0.0 @@ -128,6 +125,7 @@ exts_list = [ 'TensorFlow-1.14.0_swig-env.patch', 'TensorFlow-1.13.1_lrt-flag.patch', 'TensorFlow-1.14.0_fix-mpi-undeclared-inclusion.patch', + 'TensorFlow-2.0.0_fix-ambiguous-configurable-attribute.patch', 'TensorFlow-2.0.0_fix-build-tf-lite-avx512.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', @@ -138,6 +136,8 @@ exts_list = [ 'b388be35f2581786bcd533b1bfa375165d7f35e38a3aab74570019312816bf1b', # TensorFlow-1.13.1_lrt-flag.patch # TensorFlow-1.14.0_fix-mpi-undeclared-inclusion.patch '09e5fdce89588074b3c2abb6a4705b1f141b43395c960660320cf1cb79cd1ef4', + # TensorFlow-2.0.0_fix-ambiguous-configurable-attribute.patch + '04f8f792204b2d6a302ef57d5181b57d6dc95ba0a5b2f888a78d3ff518830b42', # TensorFlow-2.0.0_fix-build-tf-lite-avx512.patch 'ee65c8e34b62644f426054b67386734b8bf51c43ac0da4d51331b4ba191fad17', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.1-fosscuda-2019b-Python-3.7.4.eb index 7bbd2bfce7a..9f5eade9895 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.0.1-fosscuda-2019b-Python-3.7.4.eb @@ -12,7 +12,6 @@ toolchainopts = {'usempi': True} builddependencies = [ ('Bazel', '0.26.1'), - ('protobuf', '3.10.0'), # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.23.0', '-nodocs'), ] @@ -35,6 +34,7 @@ dependencies = [ ('nsync', '1.24.0'), ('SQLite', '3.29.0'), ('PCRE', '8.43'), + ('protobuf', '3.10.0'), ('protobuf-python', '3.10.0', versionsuffix), ('libpng', '1.6.37'), ('snappy', '1.1.7'), @@ -42,11 +42,8 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Markdown', '3.1.1', { @@ -139,6 +136,7 @@ exts_list = [ 'TensorFlow-1.13.1_lrt-flag.patch', 'TensorFlow-1.14.0_fix-mpi-undeclared-inclusion.patch', 'TensorFlow-1.14.0_fix-cuda-build.patch', + 'TensorFlow-2.0.0_fix-ambiguous-configurable-attribute.patch', 'TensorFlow-2.0.0_fix-build-tf-lite-avx512.patch', 'TensorFlow-2.0.0_fix-system-flatbuffers.patch', 'TensorFlow-2.0.0_fix-system-nasm.patch', @@ -154,6 +152,8 @@ exts_list = [ '09e5fdce89588074b3c2abb6a4705b1f141b43395c960660320cf1cb79cd1ef4', # TensorFlow-1.14.0_fix-cuda-build.patch '92afeee76520a63dc638c2cd4adaf2e7429411068ea4be96718255f67f113e43', + # TensorFlow-2.0.0_fix-ambiguous-configurable-attribute.patch + '04f8f792204b2d6a302ef57d5181b57d6dc95ba0a5b2f888a78d3ff518830b42', # TensorFlow-2.0.0_fix-build-tf-lite-avx512.patch 'ee65c8e34b62644f426054b67386734b8bf51c43ac0da4d51331b4ba191fad17', # TensorFlow-2.0.0_fix-system-flatbuffers.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-foss-2019b-Python-3.7.4.eb index 5fba7ffeeed..47e1c7f158b 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-foss-2019b-Python-3.7.4.eb @@ -43,11 +43,8 @@ dependencies = [ ('scipy', '1.4.1', versionsuffix), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Markdown', '3.1.1', { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb index d21c85292bd..093b3db3573 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb @@ -45,11 +45,8 @@ dependencies = [ ('scipy', '1.4.1', versionsuffix), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Markdown', '3.1.1', { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb index 60127614918..d2d8abc9c80 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb @@ -45,11 +45,8 @@ dependencies = [ ('scipy', '1.4.1', versionsuffix), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Markdown', '3.2.1', { @@ -121,6 +118,9 @@ exts_list = [ 'unpack_sources': False, 'checksums': ['d09dacdd127f2579cea8d5af21f4a918036b8ae246adc82f26b61f91cc247dc2'], }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), ('gast', '0.3.3', { 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], }), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb index c6e8b97aecb..a4e33b621ba 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb @@ -47,11 +47,8 @@ dependencies = [ ('scipy', '1.4.1', versionsuffix), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('Markdown', '3.2.1', { @@ -123,6 +120,9 @@ exts_list = [ 'unpack_sources': False, 'checksums': ['d09dacdd127f2579cea8d5af21f4a918036b8ae246adc82f26b61f91cc247dc2'], }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), ('gast', '0.3.3', { 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], }), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.2-foss-2019b-Python-3.7.4.eb index c66b375190c..33d60128d6d 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.2-foss-2019b-Python-3.7.4.eb @@ -45,6 +45,7 @@ dependencies = [ ('scipy', '1.4.1', versionsuffix), ] +sanity_pip_check = True use_pip = True exts_list = [ @@ -117,6 +118,9 @@ exts_list = [ 'unpack_sources': False, 'checksums': ['d09dacdd127f2579cea8d5af21f4a918036b8ae246adc82f26b61f91cc247dc2'], }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), ('gast', '0.3.3', { 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], }), @@ -152,6 +156,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2019b-Python-3.7.4.eb index c57db0e910d..c56c5eb1216 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2019b-Python-3.7.4.eb @@ -40,11 +40,8 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2019b-Python-3.7.4.eb index aad5fc0bbb3..8fdbe840c0c 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2019b-Python-3.7.4.eb @@ -42,11 +42,8 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb index 1275e8528b5..1d255bd3b4b 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb @@ -19,7 +19,7 @@ builddependencies = [ ] dependencies = [ ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.2'), ('h5py', '2.10.0', versionsuffix), ('cURL', '7.69.1'), @@ -119,8 +119,8 @@ exts_list = [ 'unpack_sources': False, 'checksums': ['b75e034300ccb169403cf2695adf3368da68863aeb0c14c3760064c713d5c486'], }), - ('astor', '0.8.0', { - 'checksums': ['37a6eed8b371f1228db08234ed7f6cfdc7817a3ed3824797e20cbb11dc2a7862'], + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], }), ('gast', '0.3.3', { 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fix-alias-violation-in-absl.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fix-alias-violation-in-absl.patch new file mode 100644 index 00000000000..7ab8bd93fee --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fix-alias-violation-in-absl.patch @@ -0,0 +1,26 @@ +The behavior relied on by Abseil is unsupported by GCC and leads to misoptimizations. +See https://github.com/tensorflow/tensorflow/issues/47179 + +Author: Alexander Grund + +diff --git a/third_party/com_google_absl_fix_mac_and_nvcc_build.patch b/third_party/com_google_absl_fix_mac_and_nvcc_build.patch +index 6301119ab2c..0b8b4838726 100644 +--- a/third_party/com_google_absl_fix_mac_and_nvcc_build.patch ++++ b/third_party/com_google_absl_fix_mac_and_nvcc_build.patch +@@ -1,3 +1,16 @@ ++diff --git a/absl/container/internal/container_memory.h b/absl/container/internal/container_memory.h ++index d24b0f8..f8847b5 100644 ++--- a/absl/container/internal/container_memory.h +++++ b/absl/container/internal/container_memory.h ++@@ -338,7 +338,7 @@ struct map_slot_policy { ++ // If pair and pair are layout-compatible, we can accept one ++ // or the other via slot_type. We are also free to access the key via ++ // slot_type::key in this case. ++- using kMutableKeys = memory_internal::IsLayoutCompatible; +++ using kMutableKeys = std::false_type; ++ ++ public: ++ static value_type& element(slot_type* slot) { return slot->value; } + diff --git a/absl/container/internal/compressed_tuple.h b/absl/container/internal/compressed_tuple.h + index 4bfe92f..01db713 100644 + --- a/absl/container/internal/compressed_tuple.h diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index 1e90ae6d021..b3b7e485294 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -43,11 +43,10 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True + # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d exts_list = [ @@ -129,6 +128,9 @@ exts_list = [ 'unpack_sources': False, 'checksums': ['5b7b7bf2debe19a8794adacc43e8ba6459daa4efaf54d3302623994a359b17f0'], }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), ('gast', '0.3.3', { 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], }), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb index 44857f51abf..55b550b6e69 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb @@ -118,6 +118,9 @@ exts_list = [ 'unpack_sources': False, 'checksums': ['5b7b7bf2debe19a8794adacc43e8ba6459daa4efaf54d3302623994a359b17f0'], }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), ('gast', '0.3.3', { 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], }), @@ -154,9 +157,9 @@ exts_list = [ 'TensorFlow-2.4.0_add-missing-llvm-deps.patch', 'TensorFlow-2.4.0_fix-absl-on-power.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1-fix-alias-violation-in-absl.patch', 'TensorFlow-2.4.1_fix-min-priority-test.patch', 'TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch', - 'TensorFlow-2.4.1_skip-unique-string-test.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -213,12 +216,12 @@ exts_list = [ 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', # TensorFlow-2.4.0_dont-use-var-lock.patch 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1-fix-alias-violation-in-absl.patch + '33744bbf4ccbd5995e5e12336eb571c849ccbbc0e493fee8a3cf03bc7d5a0919', # TensorFlow-2.4.1_fix-min-priority-test.patch '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', # TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch 'f384cd97e004673ae530b6e5cc826f8fddb46646991f1a228fc07b2aac87ee80', - # TensorFlow-2.4.1_skip-unique-string-test.patch - '4a39ac39123019c51cbec2415958fd30ed98587a151c99b55f04644c2ba90863', ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 9a4a9e1ad3a..7693cdd06a7 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -18,8 +18,8 @@ builddependencies = [ ('pkgconfig', '1.5.1', '-python'), # For h5py ] dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), - ('NCCL', '2.8.3', '-CUDA-11.1.1', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.6'), # Next 2 are for h5py ('SciPy-bundle', '2020.11'), @@ -129,6 +129,9 @@ exts_list = [ 'unpack_sources': False, 'checksums': ['5b7b7bf2debe19a8794adacc43e8ba6459daa4efaf54d3302623994a359b17f0'], }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), ('gast', '0.3.3', { 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], }), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1_skip-unique-string-test.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1_skip-unique-string-test.patch deleted file mode 100644 index 5cfa86e78e8..00000000000 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1_skip-unique-string-test.patch +++ /dev/null @@ -1,35 +0,0 @@ -This test fails on some cascade lake systems returning random values for tf_idx - -This seems to be solved for 2020b so ignore the test for now as the use case is probably rare. - -Author: Alexander Grund (TU Dresden) - -diff --git a/tensorflow/python/kernel_tests/unique_op_test.py b/tensorflow/python/kernel_tests/unique_op_test.py -index 436fef8171f..f10534358ef 100644 ---- a/tensorflow/python/kernel_tests/unique_op_test.py -+++ b/tensorflow/python/kernel_tests/unique_op_test.py -@@ -18,6 +18,8 @@ from __future__ import absolute_import - from __future__ import division - from __future__ import print_function - -+import unittest -+ - import numpy as np - - from tensorflow.python.framework import dtypes -@@ -48,6 +50,7 @@ class UniqueTest(test.TestCase): - for i in range(len(x)): - self.assertEqual(x[i], tf_y[tf_idx[i]]) - -+ @unittest.skip("Fails on cascade lake?") - def testString(self): - indx = np.random.randint(65, high=122, size=7000) - x = [chr(i) for i in indx] -@@ -133,6 +136,7 @@ class UniqueWithCountsTest(test.TestCase): - for value, count in zip(tf_y, tf_count): - self.assertEqual(count, np.sum(x == value)) - -+ @unittest.skip("Fails on cascade lake?") - def testString(self): - indx = np.random.randint(65, high=122, size=7000) - x = [chr(i) for i in indx] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fix-alias-violation-in-absl.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fix-alias-violation-in-absl.patch new file mode 100644 index 00000000000..427f7555ecb --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fix-alias-violation-in-absl.patch @@ -0,0 +1,26 @@ +The behavior relied on by Abseil is unsupported by GCC and leads to misoptimizations. +See https://github.com/tensorflow/tensorflow/issues/47179 + +Author: Alexander Grund + +diff --git a/third_party/absl/com_google_absl_fix_mac_and_nvcc_build.patch b/third_party/absl/com_google_absl_fix_mac_and_nvcc_build.patch +index 6301119ab2c..0b8b4838726 100644 +--- a/third_party/absl/com_google_absl_fix_mac_and_nvcc_build.patch ++++ b/third_party/absl/com_google_absl_fix_mac_and_nvcc_build.patch +@@ -1,3 +1,16 @@ ++diff --git a/absl/container/internal/container_memory.h b/absl/container/internal/container_memory.h ++index d24b0f8..f8847b5 100644 ++--- a/absl/container/internal/container_memory.h +++++ b/absl/container/internal/container_memory.h ++@@ -338,7 +338,7 @@ struct map_slot_policy { ++ // If pair and pair are layout-compatible, we can accept one ++ // or the other via slot_type. We are also free to access the key via ++ // slot_type::key in this case. ++- using kMutableKeys = memory_internal::IsLayoutCompatible; +++ using kMutableKeys = std::false_type; ++ ++ public: ++ static value_type& element(slot_type* slot) { return slot->value; } + diff --git a/absl/container/internal/compressed_tuple.h b/absl/container/internal/compressed_tuple.h + index 4bfe92f..01db713 100644 + --- a/absl/container/internal/compressed_tuple.h diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb new file mode 100644 index 00000000000..015fdb2f972 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -0,0 +1,211 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.5.0' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.14.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.28.0', '-nodocs'), + ('pybind11', '2.6.0'), + ('pkgconfig', '1.5.1', '-python'), # For h5py +] +dependencies = [ + ('Python', '3.8.6'), + ('h5py', '3.1.0'), + ('cURL', '7.72.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.2.0'), + ('ICU', '67.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.33.0'), + ('PCRE', '8.44'), + ('protobuf-python', '3.14.0'), + ('flatbuffers-python', '1.12'), + ('typing-extensions', '3.7.4.3'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('google-auth', '1.30.0', { + 'modulename': 'google.auth', + 'checksums': ['9ad25fba07f46a628ad4d0ca09f38dcb262830df2ac95b217f9b0129c9e42206'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.4', { + 'checksums': ['09832c6e75032f93818edf1affe4746121d640c625a5bef9b5c96af676e98eee'], + }), + ('Werkzeug', '2.0.0', { + 'checksums': ['3389bbfe6d40c6dd25e6d3f974155163c8b3de5bbda6a89342d4ab93fae80ba0'], + }), + ('absl-py', '0.12.0', { + 'modulename': 'absl', + 'checksums': ['b44f68984a5ceb2607d135a615999b93924c771238a63920d17d3387b0d229d5'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.34.1', { + 'modulename': 'grpc', + 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': SOURCE_PY3_WHL, # Requires Rust to build, take the dummy for now + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e167460085b6528956b33bab1c970c989cdce47a6616273880733f5e7bde452e'], + }), + ('tensorboard_plugin_wit', '1.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard_plugin_profile', '2.4.0', { + 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow_estimator', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.3.1', { + 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], + }), + ('keras_nightly', '2.5.0.dev2021032900', { + 'modulename': 'keras', + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-default-shell-env.patch', + 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + ], + 'checksums': [ + '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.5.0_add-default-shell-env.patch + '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', + # TensorFlow-2.5.0_add-protobuf-deps.patch + '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', + # TensorFlow-2.5.0_disable-avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..5e6c23ac575 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -0,0 +1,225 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.5.0' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.14.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.28.0', '-nodocs'), + ('pybind11', '2.6.0'), + ('pkgconfig', '1.5.1', '-python'), # For h5py +] +dependencies = [ + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('Python', '3.8.6'), + ('h5py', '3.1.0'), + ('cURL', '7.72.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.2.0'), + ('ICU', '67.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.33.0'), + ('PCRE', '8.44'), + ('protobuf-python', '3.14.0'), + ('flatbuffers-python', '1.12'), + ('typing-extensions', '3.7.4.3'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('google-auth', '1.30.0', { + 'modulename': 'google.auth', + 'checksums': ['9ad25fba07f46a628ad4d0ca09f38dcb262830df2ac95b217f9b0129c9e42206'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.4', { + 'checksums': ['09832c6e75032f93818edf1affe4746121d640c625a5bef9b5c96af676e98eee'], + }), + ('Werkzeug', '2.0.0', { + 'checksums': ['3389bbfe6d40c6dd25e6d3f974155163c8b3de5bbda6a89342d4ab93fae80ba0'], + }), + ('absl-py', '0.12.0', { + 'modulename': 'absl', + 'checksums': ['b44f68984a5ceb2607d135a615999b93924c771238a63920d17d3387b0d229d5'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.34.1', { + 'modulename': 'grpc', + 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': SOURCE_PY3_WHL, # Requires Rust to build, take the dummy for now + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e167460085b6528956b33bab1c970c989cdce47a6616273880733f5e7bde452e'], + }), + ('tensorboard_plugin_wit', '1.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard_plugin_profile', '2.4.0', { + 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow_estimator', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.3.1', { + 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], + }), + ('keras_nightly', '2.5.0.dev2021032900', { + 'modulename': 'keras', + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_fix-min-priority-test.patch', + 'TensorFlow-2.5.0_add-default-shell-env.patch', + 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', + ], + 'checksums': [ + '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_fix-min-priority-test.patch + '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', + # TensorFlow-2.5.0_add-default-shell-env.patch + '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', + # TensorFlow-2.5.0_add-protobuf-deps.patch + '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', + # TensorFlow-2.5.0_disable-avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch + 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' + '-benchmark-test,-v1only'), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_add-default-shell-env.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_add-default-shell-env.patch new file mode 100644 index 00000000000..bb24bde8931 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_add-default-shell-env.patch @@ -0,0 +1,90 @@ +Make TensorFlow use the environment as set by EasyBuild + +From https://github.com/tensorflow/tensorflow/pull/44549 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/core/kernels/mlir_generated/build_defs.bzl b/tensorflow/core/kernels/mlir_generated/build_defs.bzl +index f03d2b1670d..592d2ece255 100644 +--- a/tensorflow/core/kernels/mlir_generated/build_defs.bzl ++++ b/tensorflow/core/kernels/mlir_generated/build_defs.bzl +@@ -156,6 +156,7 @@ def _gen_kernel_bin_impl(ctx): + "--enable_ftz=%s" % (ctx.attr.data_type == "f32"), + "--cpu_codegen=%s" % ctx.attr.cpu_codegen, + ], ++ use_default_shell_env = True, + mnemonic = "compile", + ) + compilation_outputs = cc_common.create_compilation_outputs( +diff --git a/third_party/flatbuffers/build_defs.bzl b/third_party/flatbuffers/build_defs.bzl +index d409f836cb0..754db3f5d86 100644 +--- a/third_party/flatbuffers/build_defs.bzl ++++ b/third_party/flatbuffers/build_defs.bzl +@@ -394,6 +394,7 @@ def _concat_flatbuffer_py_srcs_impl(ctx): + ctx.attr.deps[0].files.to_list()[0].path, + ctx.outputs.out.path, + ), ++ use_default_shell_env = True, + ) + + _concat_flatbuffer_py_srcs = rule( +diff --git a/third_party/mlir/tblgen.bzl b/third_party/mlir/tblgen.bzl +index c0127ed1f16..9234f997093 100644 +--- a/third_party/mlir/tblgen.bzl ++++ b/third_party/mlir/tblgen.bzl +@@ -153,6 +153,7 @@ def _gentbl_rule_impl(ctx): + inputs = trans_srcs, + executable = ctx.executable.tblgen, + arguments = [args], ++ use_default_shell_env = True, + ) + + return [DefaultInfo()] +diff --git a/third_party/nccl/build_defs.bzl.tpl b/third_party/nccl/build_defs.bzl.tpl +index ceb65e3b632..4bf2dfcb719 100644 +--- a/third_party/nccl/build_defs.bzl.tpl ++++ b/third_party/nccl/build_defs.bzl.tpl +@@ -100,6 +100,7 @@ def _device_link_impl(ctx): + "--output-file=%s" % cubin.path, + ] + [file.path for file in inputs], + mnemonic = "nvlink", ++ use_default_shell_env = True, + ) + cubins.append(cubin) + images.append("--image=profile=%s,file=%s" % (arch, cubin.path)) +@@ -125,6 +126,7 @@ def _device_link_impl(ctx): + arguments = arguments_list + images, + tools = [bin2c], + mnemonic = "fatbinary", ++ use_default_shell_env = True, + ) + + # Generate the source file #including the headers generated above. +@@ -203,6 +205,7 @@ def _prune_relocatable_code_impl(ctx): + executable = ctx.file._nvprune, + arguments = arguments, + mnemonic = "nvprune", ++ use_default_shell_env = True, + ) + output.append(outputs) + +@@ -236,6 +239,7 @@ def _merge_archive_impl(ctx): + inputs = ctx.files.srcs, # + ctx.files._crosstool, + outputs = [ctx.outputs.out], + command = "echo -e \"%s\" | %s -M" % (mri_script, cc_toolchain.ar_executable), ++ use_default_shell_env = True, + ) + + _merge_archive = rule( +diff --git a/third_party/systemlibs/grpc.bazel.generate_cc.bzl b/third_party/systemlibs/grpc.bazel.generate_cc.bzl +index 1534e526fd1..cd7304a9515 100644 +--- a/third_party/systemlibs/grpc.bazel.generate_cc.bzl ++++ b/third_party/systemlibs/grpc.bazel.generate_cc.bzl +@@ -140,6 +140,7 @@ def generate_cc_impl(ctx): + outputs = out_files, + executable = ctx.executable._protoc, + arguments = arguments, ++ use_default_shell_env = True, + ) + + return struct(files = depset(out_files)) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_add-protobuf-deps.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_add-protobuf-deps.patch new file mode 100644 index 00000000000..61a9faf62bb --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_add-protobuf-deps.patch @@ -0,0 +1,27 @@ +The com_google_googleapis dependency calls the protobuf_deps function which isn't there yet for the +system protobuf. So add a dummy which does nothing which is enough for this use case. + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/workspace2.bzl b/tensorflow/workspace2.bzl +index 059a5921ff5..b7df2535f3b 100644 +--- a/tensorflow/workspace2.bzl ++++ b/tensorflow/workspace2.bzl +@@ -570,6 +570,7 @@ def _tf_repositories(): + system_build_file = "//third_party/systemlibs:protobuf.BUILD", + system_link_files = { + "//third_party/systemlibs:protobuf.bzl": "protobuf.bzl", ++ "//third_party/systemlibs:protobuf_deps.bzl": "protobuf_deps.bzl", + }, + urls = [ + "https://storage.googleapis.com/mirror.tensorflow.org/github.com/protocolbuffers/protobuf/archive/v3.9.2.zip", +diff --git a/third_party/systemlibs/protobuf_deps.bzl b/third_party/systemlibs/protobuf_deps.bzl +new file mode 100644 +index 00000000000..8699b840ed4 +--- /dev/null ++++ b/third_party/systemlibs/protobuf_deps.bzl +@@ -0,0 +1,4 @@ ++"""Stub version of @com_google_protobuf//:protobuf_deps.bzl necessary for TF system libs""" ++ ++def protobuf_deps(): ++ pass diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_add-support-for-large-core-systems.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_add-support-for-large-core-systems.patch new file mode 100644 index 00000000000..673d76d12cd --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_add-support-for-large-core-systems.patch @@ -0,0 +1,32 @@ +Enhance NumSchedulableCPUs to allow for nodes with more than 1024 cores +See https://github.com/tensorflow/tensorflow/issues/49833 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/core/platform/default/port.cc b/tensorflow/core/platform/default/port.cc +index 8c8c8641b2c..e648f99c7f4 100644 +--- a/tensorflow/core/platform/default/port.cc ++++ b/tensorflow/core/platform/default/port.cc +@@ -71,9 +71,19 @@ string JobName() { + + int NumSchedulableCPUs() { + #if defined(__linux__) && !defined(__ANDROID__) +- cpu_set_t cpuset; +- if (sched_getaffinity(0, sizeof(cpu_set_t), &cpuset) == 0) { +- return CPU_COUNT(&cpuset); ++ for(int ncpus = 1024; ncpus < std::numeric_limits::max() / 2; ncpus *= 2) { ++ size_t setsize = CPU_ALLOC_SIZE(ncpus); ++ cpu_set_t* mask = CPU_ALLOC(ncpus); ++ if (!mask) ++ break; ++ if (sched_getaffinity(0, setsize, mask) == 0) { ++ int result = CPU_COUNT_S(setsize, mask); ++ CPU_FREE(mask); ++ return result; ++ } ++ CPU_FREE(mask); ++ if (errno != EINVAL) ++ break; + } + perror("sched_getaffinity"); + #endif diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_disable-avx512-extensions.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_disable-avx512-extensions.patch new file mode 100644 index 00000000000..bbfad786fff --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_disable-avx512-extensions.patch @@ -0,0 +1,19 @@ +(Some of the) AVX512 extensions to Eigen introduced by TensorFlow are broken and return wrong values. +So disable them for now to keep AVX512 in the other code parts working. +See https://github.com/tensorflow/tensorflow/issues/49944 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/eigen3/unsupported/Eigen/CXX11/FixedPoint b/third_party/eigen3/unsupported/Eigen/CXX11/FixedPoint +index 67cb111db80..0f3593b6c78 100644 +--- a/third_party/eigen3/unsupported/Eigen/CXX11/FixedPoint ++++ b/third_party/eigen3/unsupported/Eigen/CXX11/FixedPoint +@@ -31,7 +31,7 @@ + #include "src/FixedPoint/FixedPointTypes.h" + + // Use optimized implementations whenever available +-#if defined (EIGEN_VECTORIZE_AVX512DQ) || defined (EIGEN_VECTORIZE_AVX512BW) ++#if 0 + #include "src/FixedPoint/PacketMathAVX512.h" + #include "src/FixedPoint/TypeCastingAVX512.h" + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch new file mode 100644 index 00000000000..c4e6aca62ad --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch @@ -0,0 +1,31 @@ +From 18f954796326c9b227b655f1acc325bb76a423d6 Mon Sep 17 00:00:00 2001 +From: "A. Unique TensorFlower" +Date: Thu, 29 Apr 2021 11:06:40 -0700 +Subject: [PATCH] Fix alignment issue in sparse_matmul_op_test (#46460) + +The class relies on over-aligned members, but is constructed via non-aligned +`new`. Here we add Eigen's custom-aligned `new` operator to ensure proper +alignment. This is a no-op in c++17. + +Fixes #46460. + +PiperOrigin-RevId: 371159511 +Change-Id: Ic46030a2021575299f4ef6b404b87e6f9205c6ad +--- + tensorflow/core/kernels/sparse_matmul_op_test.cc | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/tensorflow/core/kernels/sparse_matmul_op_test.cc b/tensorflow/core/kernels/sparse_matmul_op_test.cc +index a0f07d4c4deb1..aec5807bb834b 100644 +--- a/tensorflow/core/kernels/sparse_matmul_op_test.cc ++++ b/tensorflow/core/kernels/sparse_matmul_op_test.cc +@@ -317,6 +317,9 @@ class SparseMatmulOpTest : public ::testing::Test { + // bfloat16 representation of data3 + EIGEN_ALIGN_MAX float data3_bfloat16[kMaxPacketSize]; + EIGEN_ALIGN_MAX float ref[kMaxPacketSize]; ++ ++ public: ++ EIGEN_MAKE_ALIGNED_OPERATOR_NEW + }; + + TEST_F(SparseMatmulOpTest, BroadcastPacketTest) { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch new file mode 100644 index 00000000000..5d80e47df8f --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch @@ -0,0 +1,37 @@ +The comment is not true, the function actually takes the arguments as it should +Hence just redefine the function + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h b/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h +index 916edd561ff..9c8025dac49 100644 +--- a/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h ++++ b/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h +@@ -122,26 +122,7 @@ inline int32x4_t vpaddq_s32(int32x4_t a, int32x4_t b) { + #endif // !__aarch64__ + + #ifdef __ARM_FEATURE_DOTPROD +-// The vdotq_lane_s32 takes int8x8t for the rhs parameter, whereas the actual +-// instruction selects from between 4 32-bit (4x8-bit packed) sub-registers, an +-// unusual interpretation of "lane". +-inline int32x4_t vdotq_four_lane_s32(int32x4_t acc, int8x16_t lhs, +- int8x16_t rhs, const int lane) { +- switch (lane) { +- case 0: +- return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_low_s8(rhs)), 0); +- case 1: +- return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_low_s8(rhs)), 1); +- case 2: +- return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_high_s8(rhs)), +- 0); +- case 3: +- default: +- return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_high_s8(rhs)), +- 1); +- } +-} +- ++#define vdotq_four_lane_s32 vdotq_lane_s32 + #else + + inline int32x4_t vdotq_s32(int32x4_t acc, int8x16_t lhs, int8x16_t rhs) { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch new file mode 100644 index 00000000000..4e40a81b147 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch @@ -0,0 +1,45 @@ +TensorFlow adds some GPU tests twice increasing the runtime of the test suite. +This filters out the test part meant for CPU. + +See https://github.com/tensorflow/tensorflow/issues/47081 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl +index a4be1fea8bb..2343b8985f8 100644 +--- a/tensorflow/tensorflow.bzl ++++ b/tensorflow/tensorflow.bzl +@@ -1116,19 +1116,20 @@ def tf_gpu_cc_test( + args = [], + kernels = [], + linkopts = []): +- tf_cc_test( +- name = name, +- size = size, +- srcs = srcs, +- args = args, +- data = data, +- extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), +- kernels = kernels, +- linkopts = linkopts, +- linkstatic = linkstatic, +- tags = tags, +- deps = deps, +- ) ++ if 'gpu' not in tags: ++ tf_cc_test( ++ name = name, ++ size = size, ++ srcs = srcs, ++ args = args, ++ data = data, ++ extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), ++ kernels = kernels, ++ linkopts = linkopts, ++ linkstatic = linkstatic, ++ tags = tags, ++ deps = deps, ++ ) + tf_cc_test( + name = name, + size = size, diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb index c127bf92619..f2ab32773d4 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.11')] diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb index bb0c6b10ffd..de5f0369f9c 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.5.1')] diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb index ce6dc2f2056..7599824a873 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.5.2')] diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb index 6119fbb5768..baebe56791c 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.13')] diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb index 3bd29d98766..5e7ba8dcb94 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.6.1')] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.0-intel-2017b-Python-2.7.14.eb index 486eeef6153..41b65c186c5 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.0-intel-2017b-Python-2.7.14.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['7bc82e4fcaac023cac23c390b30d5df81bc09d33568812df75b0bd2b86d2fa8f'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.0-intel-2017b-Python-3.6.3.eb index da5f7d672d4..60fc4485acb 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.0-intel-2017b-Python-3.6.3.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['7bc82e4fcaac023cac23c390b30d5df81bc09d33568812df75b0bd2b86d2fa8f'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.1-foss-2017b-Python-3.6.3.eb index ad2d4532bad..ac4d31ac4ca 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.1-foss-2017b-Python-3.6.3.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['88d8aba1fe2b6b75eacf455d01bc7e31e838c5a0fb8c13dde2d9472495ff4662'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.1-intel-2017b-Python-3.6.3.eb index f118c860389..dbb31133e8f 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.1-intel-2017b-Python-3.6.3.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['88d8aba1fe2b6b75eacf455d01bc7e31e838c5a0fb8c13dde2d9472495ff4662'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-foss-2018a-Python-3.6.4.eb index 5f24dec59fc..aa6ed5cbc89 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-foss-2018a-Python-3.6.4.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-2.7.14.eb index f1bd26f1a67..6589dfa80c2 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-2.7.14.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'fosscuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-3.6.3.eb index f424f5723ad..6e535883387 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-3.6.3.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'fosscuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2018b-Python-2.7.15.eb index 4cf64203fa6..f9d314c2999 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2018b-Python-2.7.15.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intel-2018a-Python-3.6.4.eb index 830007f0463..96f84a9b30b 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intel-2018a-Python-3.6.4.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-2.7.14.eb index 2188089c17a..6126330865e 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-2.7.14.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'intelcuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-3.6.3.eb index 71d31c573e7..e80b7495e44 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-3.6.3.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'intelcuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.3-foss-2018b-Python-3.6.6.eb index 4107192174f..f76dab05a50 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.3-foss-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['637f3b34d40ef5e0d54dd4c40618475aaa085c26d2491e925c98e2ad4bc2115a'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.3-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.3-fosscuda-2018b-Python-3.6.6.eb index 46c7130178c..41cec9c8d22 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.3-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.3-fosscuda-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['637f3b34d40ef5e0d54dd4c40618475aaa085c26d2491e925c98e2ad4bc2115a'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb index cefdcc58151..ce8b519f248 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] dependencies = [('Python', '3.6.4')] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2019a.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2019a.eb index e535b680782..7086dec72ed 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2019a.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2019a.eb @@ -9,7 +9,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2019b-Python-3.7.4.eb index 3887a6a01bf..303a3a9cb8d 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb index 781edd4bef1..453b7b96a9f 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019a.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019a.eb index 1e92a7db651..bfd58509c62 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019a.eb @@ -9,7 +9,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'fosscuda', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019b-Python-3.7.4.eb index 0782d56c46e..d4a8d97c714 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'fosscuda', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-intel-2019b-Python-3.7.4.eb index e5c903dcbe5..8d7493afed3 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-intel-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] diff --git a/easybuild/easyconfigs/t/TinyDB/TinyDB-3.15.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/TinyDB/TinyDB-3.15.2-GCCcore-8.3.0.eb index 7a1a08ec46f..2e2c6cba620 100644 --- a/easybuild/easyconfigs/t/TinyDB/TinyDB-3.15.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/TinyDB/TinyDB-3.15.2-GCCcore-8.3.0.eb @@ -11,7 +11,6 @@ description = """TinyDB is a lightweight document oriented database optimized fo toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['f273d9b6d8b1b5e1d094a6eb8b72851b39b81099293344132c73332b60e3b893'] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.11-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..67cd20e4235 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.11-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.11' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] +checksums = [ + '5228a8187a7f70fa0791ef0f975270f068ba9557f57456f51eb02d9d4ea31282', # tk8.6.11-src.tar.gz + '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d', # Tk-8.6.4_different-prefix-with-tcl.patch +] + +builddependencies = [('binutils', '2.36.1')] +dependencies = [ + ('Tcl', version), + ('X11', '20210518'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/ToFu/ToFu-1.3.17-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/t/ToFu/ToFu-1.3.17-foss-2018a-Python-2.7.14.eb index 970490c54c2..78538287933 100644 --- a/easybuild/easyconfigs/t/ToFu/ToFu-1.3.17-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/t/ToFu/ToFu-1.3.17-foss-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'ToFu' version = '1.3.17' @@ -16,42 +16,26 @@ dependencies = [ ('MDSplus', '7.46.1'), ] -# raise an error when auto-downloading of dependency packages is detected -exts_download_dep_fail = True - -exts_defaultclass = 'PythonPackage' exts_list = [ ('docutils', '0.14', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('Polygon2', '2.0.8', { 'modulename': 'Polygon', - 'source_urls': ['https://pypi.python.org/packages/source/p/polygon2'], 'checksums': ['4ae3b027483daf1e967a96bceca18481d57cfa30480c579c3bac32f5c3fe9c84'], }), ('zope.interface', '4.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/z/zope.interface'], 'checksums': ['57c38470d9f57e37afb460c399eb254e7193ac7fb8042bd09bdc001981a9c74c'], }), ('DateTime', '4.2', { 'modulename': 'DateTime', - 'source_urls': ['https://pypi.python.org/packages/source/d/datetime'], 'checksums': ['b3d91011caff312274a629b35abd6eb67038f8f92423ad3d9e071c0bf8823226'], }), ('tofu', version, { - 'source_urls': ['https://pypi.python.org/packages/source/t/tofu'], 'checksums': ['263afa286cda0ae70272268548bf344a4dd68a76f4a3de04dfd57deffdfe4169'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["python -c 'import tofu.geom'"] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/ToFu/ToFu-1.3.17-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/ToFu/ToFu-1.3.17-foss-2018a-Python-3.6.4.eb index c880bfc08f9..71df9026ef3 100644 --- a/easybuild/easyconfigs/t/ToFu/ToFu-1.3.17-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/t/ToFu/ToFu-1.3.17-foss-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'ToFu' version = '1.3.17' @@ -16,42 +16,26 @@ dependencies = [ ('MDSplus', '7.46.1'), ] -# raise an error when auto-downloading of dependency packages is detected -exts_download_dep_fail = True - -exts_defaultclass = 'PythonPackage' exts_list = [ ('docutils', '0.14', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('Polygon3', '3.0.8', { 'modulename': 'Polygon', - 'source_urls': ['https://pypi.python.org/packages/source/p/polygon3'], 'checksums': ['382aecaf1b550134aa71cc9c0f880a244e0ac5273e05bf898f5a6cde5bff9e2c'], }), ('zope.interface', '4.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/z/zope.interface'], 'checksums': ['57c38470d9f57e37afb460c399eb254e7193ac7fb8042bd09bdc001981a9c74c'], }), ('DateTime', '4.2', { 'modulename': 'DateTime', - 'source_urls': ['https://pypi.python.org/packages/source/d/datetime'], 'checksums': ['b3d91011caff312274a629b35abd6eb67038f8f92423ad3d9e071c0bf8823226'], }), ('tofu', version, { - 'source_urls': ['https://pypi.python.org/packages/source/t/tofu'], 'checksums': ['263afa286cda0ae70272268548bf344a4dd68a76f4a3de04dfd57deffdfe4169'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["python -c 'import tofu.geom'"] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2019b-Python-3.7.4.eb index a9674c0df46..c5910bd996b 100644 --- a/easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2019b-Python-3.7.4.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pyfaidx', '0.5.8', { 'checksums': ['58f0ff57a875af7e69a12cf1e7086efa4976919ac4dcebbc5f3def6fd4881d0d'], diff --git a/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..fc3261b7435 --- /dev/null +++ b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'tabixpp' +version = '1.1.0' + +homepage = 'https://github.com/ekg/tabixpp' +description = """C++ wrapper to tabix indexer""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1.0_use-external-HTSlib.patch'] +checksums = [ + '56c8f1b07190aba5e1d0b738e380e726d380f0ad8b2d0df133200b0ab1f8ed88', # v1.1.0.tar.gz + '65496b6e042cf54290386a33cf0de26cb1160b3ddb35216765999d790b99cab4', # tabixpp-1.1.0_use-external-HTSlib.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('HTSlib', '1.12'), + ('PCRE', '8.44'), +] + +skipsteps = ['configure'] + +preinstallopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/tabix++', 'lib/libtabixpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb index d8f225d930a..fa4ffd50081 100644 --- a/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('Boost', '1.74.0'), ] -separate_build_dir = True +configopts = "-DBoost_NO_BOOST_CMAKE=ON" buildopts = "&& mkdir -p %(installdir)s/bin" buildopts += " && cp -a {alignments-filter,binner,taxator,taxknife,unittest_ncbitaxonomy} %(installdir)s/bin/" diff --git a/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-gompi-2019a.eb b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-gompi-2019a.eb index 0d1c5cd9f4b..a8a059fa02d 100644 --- a/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-gompi-2019a.eb +++ b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-gompi-2019a.eb @@ -22,7 +22,7 @@ dependencies = [ ('Boost', '1.70.0'), ] -separate_build_dir = True +configopts = "-DBoost_NO_BOOST_CMAKE=ON" buildopts = "&& mkdir -p %(installdir)s/bin" buildopts += " && cp -a {alignments-filter,binner,taxator,taxknife,unittest_ncbitaxonomy} %(installdir)s/bin/" diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb new file mode 100644 index 00000000000..5083f889388 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'tensorboardX' +version = '2.2' +local_pytorch_ver = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_ver + +homepage = 'https://github.com/lanpa/tensorboardX' +description = "Tensorboard for PyTorch." + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'lanpa' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['dff39191ca26bce9c5c82b9a013558e8c17602d17279f70270ca3341f127c4cf'] + +# tensorboardX v2.x works with tensorboards generated with TensorFlow 2, +# but TensorFlow is not needed to use tensorboardX +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('protobuf-python', '3.14.0'), + ('PyTorch', local_pytorch_ver), + ('torchvision', '0.8.2', versionsuffix), +] + +options = {'modulename': '%(name)s'} + +use_pip = True +download_dep_fail = True + +postinstallcmds = ["cp -r %s %%(installdir)s" % d for d in ['docs', 'examples', 'tests']] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'docs', 'examples', 'tests'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 00000000000..e398062f1db --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'tensorboardX' +version = '2.2' +local_pytorch_ver = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_ver + +homepage = 'https://github.com/lanpa/tensorboardX' +description = "Tensorboard for PyTorch." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +github_account = 'lanpa' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['dff39191ca26bce9c5c82b9a013558e8c17602d17279f70270ca3341f127c4cf'] + +# tensorboardX v2.x works with tensorboards generated with TensorFlow 2, +# but TensorFlow is not needed to use tensorboardX +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('protobuf-python', '3.14.0'), + ('PyTorch', local_pytorch_ver), + ('torchvision', '0.8.2', versionsuffix), +] + +options = {'modulename': '%(name)s'} + +use_pip = True +download_dep_fail = True + +postinstallcmds = ["cp -r %s %%(installdir)s" % d for d in ['docs', 'examples', 'tests']] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'docs', 'examples', 'tests'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.2a-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tmux/tmux-3.2a-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f56ae998243 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.2a-GCCcore-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.2a' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['551553a4f82beaa8dadc9256800bcc284d7c000081e47aa6ecbb6ff36eacd05f'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Bison', '3.7.6'), + ('make', '4.3'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.2'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0-Python-3.7.4.eb index 8b5ea20b4ca..ea932956b96 100644 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0-Python-3.7.4.eb @@ -11,7 +11,6 @@ description = "Data loaders and abstractions for text and NLP" toolchain = {'name': 'fosscuda', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['7f22e24e9b939fff56b9118c78dc07aafec8dcc67164de15b9b5ed339e4179c6'] diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 00000000000..e9c3ae26bc1 --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,42 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.8.1' +local_pytorch_version = '1.7.1' +local_python_suffix = '-Python-%(pyver)s' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['128f3c9ea6d774fca26d838f71b86adf32c2978ab092882454df598be5e8ce37'] + +builddependencies = [ + ('RE2', '2021-06-01'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SentencePiece', '0.1.96'), + ('tqdm', '4.56.2'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.1.5'), +] + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/BuildExtension/d' setup.py &&" + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.3.0-foss-2019a-Python-3.7.2.eb index 936e9edb9bc..e43b9e5a451 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.3.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.3.0-foss-2019a-Python-3.7.2.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'torchvision' version = '0.3.0' versionsuffix = '-Python-%(pyver)s' @@ -21,12 +19,4 @@ dependencies = [ ('PyTorch', '1.1.0', versionsuffix), ] -use_pip = True -download_dep_fail = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/torchvision'], -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-foss-2019b-Python-3.7.4.eb index d4f94e16fa9..7a502458099 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-foss-2019b-Python-3.7.4.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'torchvision' version = '0.4.2' versionsuffix = '-Python-%(pyver)s' @@ -21,8 +19,4 @@ dependencies = [ ('PyTorch', '1.3.1', versionsuffix), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb index fff03c08a58..61327c3ba06 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'torchvision' version = '0.4.2' versionsuffix = '-Python-%(pyver)s' @@ -21,12 +19,7 @@ dependencies = [ ('PyTorch', '1.3.1', versionsuffix), ] -use_pip = True -download_dep_fail = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/torchvision'], -} +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2020b-PyTorch-1.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2020b-PyTorch-1.3.1.eb new file mode 100644 index 00000000000..32ef599a467 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2020b-PyTorch-1.3.1.eb @@ -0,0 +1,26 @@ +name = 'torchvision' +version = '0.4.2' +local_pytorch_version = '1.3.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1184a27eab85c9e784bacc6f9d6fec99e168ab4eda6047ef9f709e7fdb22d8f9'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('PyTorch', local_pytorch_version), +] + +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb index 5ba49db6ea4..9f8c7d66e55 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'torchvision' version = '0.5.0' versionsuffix = '-Python-%(pyver)s-PyTorch-1.4.0' @@ -21,11 +19,7 @@ dependencies = [ ('PyTorch', '1.4.0', '-Python-%(pyver)s'), ] -use_pip = True -download_dep_fail = True - -preinstallopts = 'export TORCH_CUDA_ARCH_LIST="3.5 3.7 5.2 6.0 6.1 7.0 7.2 7.5" && ' - -sanity_pip_check = True +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-foss-2019b-Python-3.7.4-PyTorch-1.6.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-foss-2019b-Python-3.7.4-PyTorch-1.6.0.eb index 2eec86a3001..24afca0a3d9 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-foss-2019b-Python-3.7.4-PyTorch-1.6.0.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-foss-2019b-Python-3.7.4-PyTorch-1.6.0.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'torchvision' version = '0.7.0' local_pytorch_version = '1.6.0' @@ -22,9 +20,4 @@ dependencies = [ ('PyTorch', local_pytorch_version, '-Python-%(pyver)s'), ] -use_pip = True -download_dep_fail = True - -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0-imkl.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0-imkl.eb index 023053c5f9b..50c81de1d15 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0-imkl.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0-imkl.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'torchvision' version = '0.7.0' local_pytorch_version = '1.6.0' @@ -22,11 +20,7 @@ dependencies = [ ('PyTorch', local_pytorch_version, '-Python-%(pyver)s-imkl'), ] -use_pip = True -download_dep_fail = True - -preinstallopts = 'export TORCH_CUDA_ARCH_LIST="3.5 3.7 5.2 6.0 6.1 7.0 7.2 7.5" && ' - -sanity_pip_check = True +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0.eb index a96311750f8..754a6fedcfc 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'torchvision' version = '0.7.0' local_pytorch_version = '1.6.0' @@ -22,11 +20,7 @@ dependencies = [ ('PyTorch', local_pytorch_version, '-Python-%(pyver)s'), ] -use_pip = True -download_dep_fail = True - -preinstallopts = 'export TORCH_CUDA_ARCH_LIST="3.5 3.7 5.2 6.0 6.1 7.0 7.2 7.5" && ' - -sanity_pip_check = True +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-foss-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-foss-2020b-PyTorch-1.7.1.eb new file mode 100644 index 00000000000..081b0a52121 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-foss-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,26 @@ +name = 'torchvision' +version = '0.8.2' +local_pytorch_version = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9a866c3c8feb23b3221ce261e6153fc65a98ce9ceaa71ccad017016945c178bf'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('PyTorch', local_pytorch_version), +] + +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2019b-Python-3.7.4-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2019b-Python-3.7.4-PyTorch-1.7.1.eb index 231c9d75148..b4598a88526 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2019b-Python-3.7.4-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2019b-Python-3.7.4-PyTorch-1.7.1.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'torchvision' version = '0.8.2' local_pytorch_version = '1.7.1' @@ -22,13 +20,7 @@ dependencies = [ ('PyTorch', local_pytorch_version, '-Python-%(pyver)s'), ] -use_pip = True -download_dep_fail = True - # Defaults. Can be changed with --cuda-compute-capabilities cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] -preinstallopts = 'export TORCH_CUDA_ARCH_LIST="%(cuda_cc_semicolon_sep)s" && ' - -sanity_pip_check = True moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb index bbec243ce6a..8d0b69baaf0 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'torchvision' version = '0.8.2' local_pytorch_version = '1.7.1' @@ -22,13 +20,7 @@ dependencies = [ ('PyTorch', local_pytorch_version), ] -use_pip = True -download_dep_fail = True - # Defaults. Can be changed with --cuda-compute-capabilities cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] -preinstallopts = 'export TORCH_CUDA_ARCH_LIST="%(cuda_cc_semicolon_sep)s" && ' - -sanity_pip_check = True moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb new file mode 100644 index 00000000000..c07d776f192 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb @@ -0,0 +1,26 @@ +name = 'torchvision' +version = '0.9.1' +local_pytorch_version = '1.8.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['79964773729880e0eee0e6af13f336041121d4cc8491a3e2c0e5f184cac8a718'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('PyTorch', local_pytorch_version), +] + +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.24.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.24.0-foss-2016a-Python-3.5.1.eb index 16009eca3be..e9a2e1cd91c 100644 --- a/easybuild/easyconfigs/t/tqdm/tqdm-4.24.0-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.24.0-foss-2016a-Python-3.5.1.eb @@ -9,15 +9,9 @@ description = """A fast, extensible progress bar for Python and CLI""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['60bbaa6700e87a250f6abcbbd7ddb33243ad592240ba46afce5305b15b406fad'] dependencies = [('Python', '3.5.1')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.24.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.24.0-foss-2018b-Python-2.7.15.eb index 5e57b3dcdd7..2dbe4c7342b 100644 --- a/easybuild/easyconfigs/t/tqdm/tqdm-4.24.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.24.0-foss-2018b-Python-2.7.15.eb @@ -9,15 +9,9 @@ description = """A fast, extensible progress bar for Python and CLI""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['60bbaa6700e87a250f6abcbbd7ddb33243ad592240ba46afce5305b15b406fad'] dependencies = [('Python', '2.7.15')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.29.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.29.0-intel-2018a-Python-3.6.4.eb index ee6b43f3820..a73394395b6 100644 --- a/easybuild/easyconfigs/t/tqdm/tqdm-4.29.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.29.0-intel-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = """A fast, extensible progress bar for Python and CLI""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['79420109a762f82e20e8ecdc3b3bc1bc6c6536884a8de5fa86a50eb99386376a'] @@ -17,9 +16,4 @@ dependencies = [('Python', '3.6.4')] download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.32.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.32.1-GCCcore-8.2.0.eb index 622bddc719a..26a46ceff3a 100644 --- a/easybuild/easyconfigs/t/tqdm/tqdm-4.32.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.32.1-GCCcore-8.2.0.eb @@ -8,7 +8,6 @@ description = """A fast, extensible progress bar for Python and CLI""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0a860bf2683fdbb4812fe539a6c22ea3f1777843ea985cb8c3807db448a0f7ab'] diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-GCCcore-8.3.0.eb index d95da7be450..6cb0bb9b79c 100644 --- a/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-GCCcore-8.3.0.eb @@ -8,7 +8,6 @@ description = """A fast, extensible progress bar for Python and CLI""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4789ccbb6fc122b5a6a85d512e4e41fc5acad77216533a6f2b8ce51e0f265c23'] @@ -16,8 +15,8 @@ builddependencies = [('binutils', '2.32')] multi_deps = {'Python': ['2.7.16', '3.7.4']} -sanity_pip_check = True use_pip = True +sanity_pip_check = True download_dep_fail = True moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-foss-2018b-Python-3.6.6.eb index dba5399a8f6..57610e2917f 100755 --- a/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-foss-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = """Instantly make your loops show a smart progress meter.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4789ccbb6fc122b5a6a85d512e4e41fc5acad77216533a6f2b8ce51e0f265c23'] @@ -21,9 +20,4 @@ dependencies = [ ('Python', '3.6.6'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-intel-2018b-Python-3.6.6.eb index 48105765623..dc2eafcf5cc 100755 --- a/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.41.1-intel-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = """Instantly make your loops show a smart progress meter.""" toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4789ccbb6fc122b5a6a85d512e4e41fc5acad77216533a6f2b8ce51e0f265c23'] @@ -21,9 +20,4 @@ dependencies = [ ('Python', '3.6.6'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb index d4b6a58b781..bcc2d0056bf 100644 --- a/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb @@ -13,7 +13,6 @@ description = "Python library containing T-SNE algorithms." toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'openmp': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['%(name)s-%(version)s_fix-setup-py-imkl.patch'] checksums = [ diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.10.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.10.0.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..04328b49f82 --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.10.0.0-GCCcore-10.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '3.10.0.0' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions – Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-8.3.0-Python-3.7.4.eb index 572e0c607e1..819238efc1f 100644 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-8.3.0-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = 'Typing Extensions – Backported and Experimental Type Hints for toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = ['typing_extensions-%(version)s.tar.gz'] checksums = ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'] diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..53bb3739ac1 --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '3.7.4.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = "Typing Extensions – Backported and Experimental Type Hints for Python" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'] + +builddependencies = [ + ('binutils', '2.34'), +] +dependencies = [ + ('Python', '3.8.2'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..e34d13f9868 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -0,0 +1,42 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.10.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['ucx-%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_link_against_existing_UCX_libs.patch', +] +checksums = [ + 'b885e24b1b94724c03cb213c355381e98df1e2d1fd7f633cf8055b6dd05db92d', # ucx-1.10.0.tar.gz + # UCX-CUDA-1.10.0_link_against_existing_UCX_libs.patch + '794cb5b6476ca3aca6e0156b19e833696c816e3e4b874ad4d0b3b6a7a9c14e1b', +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('UCX', version), + ('CUDAcore', '11.3.1', '', True), + ('GDRCopy', '2.2'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0_link_against_existing_UCX_libs.patch b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0_link_against_existing_UCX_libs.patch new file mode 100644 index 00000000000..65a2d96c34b --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0_link_against_existing_UCX_libs.patch @@ -0,0 +1,65 @@ +Make CUDA/ROCm plugins link against the existing ucs/ucm/uct libraries. + +Åke Sandgren, Mikael Öhman 2021-06-26 +diff -ru ucx-1.10.0.orig/configure.ac ucx-1.10.0/configure.ac +--- ucx-1.10.0.orig/configure.ac 2021-06-26 02:05:59.632558898 +0200 ++++ ucx-1.10.0/configure.ac 2021-06-26 02:08:39.330081752 +0200 +@@ -29,13 +29,13 @@ + AC_GNU_SOURCE + AC_CONFIG_HEADERS([config.h]) + +-AC_CHECK_PROG(GITBIN, git, yes) +-AS_IF([test x"${GITBIN}" = x"yes"], +- [# remove preceding "refs/heads/" (11 characters) for symbolic ref +- AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) +- AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], +- [AC_SUBST(SCM_BRANCH, "") +- AC_SUBST(SCM_VERSION, "0000000")]) ++#AC_CHECK_PROG(GITBIN, git, yes) ++#AS_IF([test x"${GITBIN}" = x"yes"], ++# [# remove preceding "refs/heads/" (11 characters) for symbolic ref ++# AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) ++# AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], ++# [AC_SUBST(SCM_BRANCH, "") ++# AC_SUBST(SCM_VERSION, "0000000")]) + + AH_TOP([ + #ifndef UCX_CONFIG_H +diff -ru ucx-1.10.0.orig/src/ucm/cuda/Makefile.am ucx-1.10.0/src/ucm/cuda/Makefile.am +--- ucx-1.10.0.orig/src/ucm/cuda/Makefile.am 2021-06-26 02:05:59.640558874 +0200 ++++ ucx-1.10.0/src/ucm/cuda/Makefile.am 2021-06-26 02:09:06.221001406 +0200 +@@ -9,7 +9,7 @@ + module_LTLIBRARIES = libucm_cuda.la + libucm_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libucm_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) +-libucm_cuda_la_LIBADD = ../libucm.la ++libucm_cuda_la_LIBADD = -lucm + libucm_cuda_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(patsubst %, -Xlinker %, $(CUDA_LDFLAGS)) \ + -version-info $(SOVERSION) +diff -ru ucx-1.10.0.orig/src/uct/cuda/gdr_copy/Makefile.am ucx-1.10.0/src/uct/cuda/gdr_copy/Makefile.am +--- ucx-1.10.0.orig/src/uct/cuda/gdr_copy/Makefile.am 2021-06-26 02:05:59.654558833 +0200 ++++ ucx-1.10.0/src/uct/cuda/gdr_copy/Makefile.am 2021-06-26 02:21:05.451894680 +0200 +@@ -8,7 +8,7 @@ + module_LTLIBRARIES = libuct_cuda_gdrcopy.la + libuct_cuda_gdrcopy_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) $(GDR_COPY_CPPFLAGS) + libuct_cuda_gdrcopy_la_CFLAGS = $(BASE_CFLAGS) +-libuct_cuda_gdrcopy_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ ++libuct_cuda_gdrcopy_la_LIBADD = -lucs \ + $(top_builddir)/src/uct/cuda/libuct_cuda.la + libuct_cuda_gdrcopy_la_LDFLAGS = $(CUDA_LDFLAGS) $(GDR_COPY_LDFLAGS) -version-info $(SOVERSION) + +diff -ru ucx-1.10.0.orig/src/uct/cuda/Makefile.am ucx-1.10.0/src/uct/cuda/Makefile.am +--- ucx-1.10.0.orig/src/uct/cuda/Makefile.am 2021-06-26 02:05:59.654558833 +0200 ++++ ucx-1.10.0/src/uct/cuda/Makefile.am 2021-06-26 02:16:59.322587865 +0200 +@@ -10,8 +10,8 @@ + module_LTLIBRARIES = libuct_cuda.la + libuct_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libuct_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) +-libuct_cuda_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la ++libuct_cuda_la_LIBADD = -lucs \ ++ -luct + libuct_cuda_la_LDFLAGS = $(CUDA_LDFLAGS) -version-info $(SOVERSION) + + noinst_HEADERS = \ diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-10.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..2b44e28db6d --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-10.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.28' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/', + 'https://sources.easybuild.io/u/UDUNITS/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['590baec83161a3fd62c00efa66f6113cec8a7c461e3f61a5182167e0cc5d579e'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('expat', '2.2.9')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/u/UFL/UFL-2019.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/u/UFL/UFL-2019.1.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..e7f433a362e --- /dev/null +++ b/easybuild/easyconfigs/u/UFL/UFL-2019.1.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'UFL' +version = '2019.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/fenics-project/ufl' +description = """The Unified Form Language (UFL) is a domain specific language + for declaration of finite element discretizations of variational forms. + More precisely, it defines a flexible interface for choosing finite element + spaces and defining expressions for weak forms in a notation close to + mathematical notation.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://bitbucket.org/fenics-project/ufl/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['213a56bfa2edb0365909fa6f110f970e582b10a3f5f1fd9a0e85254f1eefaa11'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.0-foss-2018b-Python-3.6.6.eb index dc614276640..81321cb4564 100644 --- a/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.0-foss-2018b-Python-3.6.6.eb @@ -19,11 +19,9 @@ use_pip = True exts_list = [ ('regex', '2019.02.07', { - 'source_urls': ['https://pypi.python.org/packages/source/r/regex'], 'checksums': ['4a1a1d963f462c13722b34ef1f82c4707091b0a3fb9b5fd79b6670c38b734095'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), (name, version, { diff --git a/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2019b-Python-3.7.4.eb index de8ea9fac13..a498ee54b96 100644 --- a/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2019b-Python-3.7.4.eb @@ -19,7 +19,6 @@ use_pip = True exts_list = [ ('regex', '2020.4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['295badf61a51add2d428a46b8580309c520d8b26e769868b922750cf3ce67142'], }), (name, version, { diff --git a/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2020a-Python-3.8.2.eb index ee4960aaaa3..32bc21349d7 100644 --- a/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2020a-Python-3.8.2.eb @@ -19,7 +19,6 @@ use_pip = True exts_list = [ ('regex', '2020.4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['295badf61a51add2d428a46b8580309c520d8b26e769868b922750cf3ce67142'], }), (name, version, { diff --git a/easybuild/easyconfigs/u/Unidecode/Unidecode-1.1.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/u/Unidecode/Unidecode-1.1.1-GCCcore-8.3.0-Python-3.7.4.eb index 58c43462c4d..e666e8f2f65 100644 --- a/easybuild/easyconfigs/u/Unidecode/Unidecode-1.1.1-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/u/Unidecode/Unidecode-1.1.1-GCCcore-8.3.0-Python-3.7.4.eb @@ -9,7 +9,6 @@ description = "Python library for lossy ASCII transliterations of Unicode text ( toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2b6aab710c2a1647e928e36d69c21e76b453cd455f4e2621000e54b2a9b8cce8'] diff --git a/easybuild/easyconfigs/u/umis/umis-1.0.3-intel-2019a.eb b/easybuild/easyconfigs/u/umis/umis-1.0.3-intel-2019a.eb index 597dd1a07d3..68eeca960c4 100644 --- a/easybuild/easyconfigs/u/umis/umis-1.0.3-intel-2019a.eb +++ b/easybuild/easyconfigs/u/umis/umis-1.0.3-intel-2019a.eb @@ -25,15 +25,12 @@ use_pip = True exts_list = [ ('regex', '2019.06.08', { - 'source_urls': ['https://pypi.python.org/packages/source/r/regex/'], 'checksums': ['84daedefaa56320765e9c4d43912226d324ef3cc929f4d75fa95f8c579a08211'], }), ('toolz', '0.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz/'], 'checksums': ['08fdd5ef7c96480ad11c12d472de21acd32359996f69a5259299b540feba4560'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/u/umis'], 'checksums': ['7535affabe6665370a8c9a8fef26d1fad3289441118ef607a29bbc7e9047fb49'], }), ] diff --git a/easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c03b77d5dbe --- /dev/null +++ b/easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'unimap' +version = '0.1' + +homepage = 'https://github.com/lh3/unimap' +description = """Unimap is a fork of minimap2 optimized for assembly-to-reference +alignment. It integrates the minigraph chaining algorithm and can align through +long INDELs (up to 100kb by default) much faster than minimap2. Unimap is a +better fit for resolving segmental duplications and is recommended over minimap2 +for alignment between high-quality assemblies. + +Unimap does not replace minimap2 for other types of alignment. It drops the +support of multi-part index and short-read mapping. Its long-read alignment is +different from minimap2 but is not necessarily better. Unimap is more of a +specialized minimap2 at the moment.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/lh3/unimap/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d5d7831e1fa78c943a96ef78ba22ec88eebf39368bdb135c30554f052f0dbc5c'] + +builddependencies = [('binutils', '2.35')] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "unimap --help", + "cd %(builddir)s/unimap-%(version)s && unimap -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..025e8cde284 --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.6.1' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4c06a9dc4017e8a2438ef80ee371d45868bda2237a98b26554de7a95406b283b'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VAtools/VAtools-3.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/v/VAtools/VAtools-3.0.1-foss-2018b-Python-3.6.6.eb index 0a8d80ecae0..a5e44ea7e60 100644 --- a/easybuild/easyconfigs/v/VAtools/VAtools-3.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/v/VAtools/VAtools-3.0.1-foss-2018b-Python-3.6.6.eb @@ -19,20 +19,16 @@ use_pip = True exts_list = [ ('vcfpy', '0.12.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/vcfpy'], 'checksums': ['2ce36cdad9b7853e0be056070336d6f664d8b6e17f51125d25d0cc172219e6e0'], }), ('gtfparse', '1.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/g/gtfparse'], 'checksums': ['2f27aa2b87eb43d613edabf27f9c11147dc595c8683b440ac1d88e9acdb85873'], }), ('testfixtures', '6.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testfixtures'], 'checksums': ['1ff15abd7c93a25c25e707e15bc245fb3d5723e43ce114e8fd6f72cff17926c8'], }), (name, version, { 'source_tmpl': 'vatools-%(version)s-py3-none-any.whl', - 'source_urls': ['https://pypi.python.org/packages/source/v/vatools/'], 'checksums': ['d26f775df7e7ee8d84eb0857ac1a1226200ce92ecda9ad8d7dd2cb13d3b19de4'], }), ] diff --git a/easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb index 2143c42d364..05ad2eafb08 100644 --- a/easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb @@ -26,57 +26,44 @@ use_pip = True exts_list = [ ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('tabulate', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate'], 'checksums': ['8af07a39377cee1103a5c8b3330a421c2d99b9141e9cc5ddd2e3263fea416943'], }), ('sortedcontainers', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], }), ('intervaltree', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/intervaltree'], 'checksums': ['aca5804b88f70cb49050c37b6de59090570f77a75aec1932966cf69f6a48810b'], }), ('args', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/args'], 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], }), ('clint', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/clint'], 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], }), ('cyvcf2', '0.10.8', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cyvcf2'], 'checksums': ['62d950c940977243ab5d2d6e6eabad5fb0deb12012e8e0d2611da03384f118d9'], }), ('Unidecode', '0.04.21', { - 'source_urls': ['https://pypi.python.org/packages/source/U/Unidecode'], 'checksums': ['280a6ab88e1f2eb5af79edff450021a0d3f0448952847cd79677e55e58bad051'], }), ('regex', '2019.02.21', { - 'source_urls': ['https://pypi.python.org/packages/source/r/regex'], 'checksums': ['587bd4cad11c7294f89799c45778abca271d7c6668a0e85c41a6dbfa8096f9bb'], }), ('awesome-slugify', '1.6.5', { - 'source_urls': ['https://pypi.python.org/packages/source/a/awesome-slugify'], 'checksums': ['bbdec3fa2187917473a2efad092b57f7125a55f841a7cf6a1773178d32ccfd71'], 'modulename': 'slugify', }), ('yahmm', '1.1.3', { 'source_tmpl': 'yahmm-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/y/yahmm'], 'checksums': ['fe3614ef96da9410468976756fb93dc8235485242c05df01d8e5ed356a7dfb43'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/V/VCF-kit'], 'checksums': ['e44319bc057ff4f90cc3a777bb6b1794e5dc3dcf56fe2753fee199f782fed6b6'], 'preinstallopts': "sed -i 's/==[0-9.]*//g' requirements.txt && ", 'modulename': 'vcfkit', diff --git a/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb new file mode 100644 index 00000000000..b53ccb6277c --- /dev/null +++ b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +name = 'VEP' +version = '103.1' + +homepage = 'https://www.ensembl.org/info/docs/tools/vep' +description = """Variant Effect Predictor (VEP) determines the effect of your + variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, + transcripts, and protein sequence, as well as regulatory regions. + Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently + used routines in VEP.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/'] +sources = ['%(version)s.tar.gz'] +checksums = ['3512a2c3514f7c10b0348b45bf9fe621dc691100e43f14bec48842b1e11bbf8b'] + +dependencies = [ + ('Perl', '5.32.0'), + ('Archive-Zip', '1.68'), + ('DBD-mysql', '4.050'), + ('BioPerl', '1.7.8'), + ('Bio-DB-HTS', '3.01'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('Bio::EnsEMBL::XS', '2.3.2', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], + 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb new file mode 100644 index 00000000000..e2b6645847e --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -0,0 +1,60 @@ +## +# Author: Robert Mijakovic +## +name = 'VMD' +version = '1.9.4a51' + +homepage = 'https://www.ks.uiuc.edu/Research/vmd' +description = """VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular + systems using 3-D graphics and built-in scripting.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', + 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', + 'https://webclu.bio.wzw.tum.de/stride/' +] +sources = [ + 'vmd-%(version)s.src.tar.gz', + {'filename': 'stride.tar.gz', 'extract_cmd': "tar -C vmd-%(version)s/lib/stride -xf %s"}, +] +patches = [ + ('VMD-1.9.3_plugins.patch'), + ('VMD-1.9.3_surf_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_surf_bad_printfs.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_MAX_AT_IN_RES.patch', 'vmd-%(version)s'), + ('VMD-%(version)s_configure.patch', 'vmd-%(version)s'), + ('VMD-%(version)s_extra_colors.patch', 'vmd-%(version)s'), +] +checksums = [ + 'b1c40b21111f5bab56d43d5e442c468d327159b07915af2ec175ba6b12842e5c', # vmd-1.9.4a51.src.tar.gz + '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz + '85760d6ae838e2b09801e34b36b484532383f7aaf2e8634b3ef808002a92baa3', # VMD-1.9.3_plugins.patch + 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch + 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch + 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch + 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch + 'dc9fc419e2e938f42d2e4784b0c9c7429317893f08d3ed170f949c3ee3aec062', # VMD-1.9.4a51_configure.patch + '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4a51_extra_colors.patch +] + +dependencies = [ + ('Tcl', '8.6.10'), + ('Tk', '8.6.10'), + ('FLTK', '1.3.5'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('Mesa', '20.2.1'), + ('netCDF', '4.7.4'), + ('FFmpeg', '4.3.1'), + ('ImageMagick', '7.0.10-35'), + ('ACTC', '1.1'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('POV-Ray', '3.7.0.8'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb new file mode 100644 index 00000000000..854dade5cbe --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -0,0 +1,61 @@ +## +# Author: Robert Mijakovic +## +name = 'VMD' +version = '1.9.4a51' + +homepage = 'https://www.ks.uiuc.edu/Research/vmd' +description = """VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular + systems using 3-D graphics and built-in scripting.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', + 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', + 'https://webclu.bio.wzw.tum.de/stride/' +] +sources = [ + 'vmd-%(version)s.src.tar.gz', + {'filename': 'stride.tar.gz', 'extract_cmd': "tar -C vmd-%(version)s/lib/stride -xf %s"}, +] +patches = [ + ('VMD-1.9.3_plugins.patch'), + ('VMD-1.9.3_surf_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_surf_bad_printfs.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_MAX_AT_IN_RES.patch', 'vmd-%(version)s'), + ('VMD-%(version)s_configure.patch', 'vmd-%(version)s'), + ('VMD-%(version)s_extra_colors.patch', 'vmd-%(version)s'), +] +checksums = [ + 'b1c40b21111f5bab56d43d5e442c468d327159b07915af2ec175ba6b12842e5c', # vmd-1.9.4a51.src.tar.gz + '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz + '85760d6ae838e2b09801e34b36b484532383f7aaf2e8634b3ef808002a92baa3', # VMD-1.9.3_plugins.patch + 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch + 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch + 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch + 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch + 'dc9fc419e2e938f42d2e4784b0c9c7429317893f08d3ed170f949c3ee3aec062', # VMD-1.9.4a51_configure.patch + '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4a51_extra_colors.patch +] + +dependencies = [ + ('Tcl', '8.6.10'), + ('Tk', '8.6.10'), + ('FLTK', '1.3.5'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('Mesa', '20.2.1'), + ('netCDF', '4.7.4'), + ('FFmpeg', '4.3.1'), + ('ImageMagick', '7.0.10-35'), + ('ACTC', '1.1'), + ('OptiX', '6.5.0', '', True), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('POV-Ray', '3.7.0.8'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51_configure.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51_configure.patch new file mode 100644 index 00000000000..b0432661c4e --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51_configure.patch @@ -0,0 +1,177 @@ +--- configure 2021-05-10 14:04:56.826893000 +0200 ++++ configure 2021-05-10 14:08:01.893394000 +0200 +@@ -497,17 +497,16 @@ + + $arch_cc = "cc"; + $arch_ccpp = "CC"; +-$arch_nvcc = "/usr/local/cuda-10.2/bin/nvcc"; ++$arch_nvcc = "$ENV{'EBROOTCUDA'}/bin/nvcc"; + $arch_nvccflags = "-lineinfo --ptxas-options=-v " . +- "-gencode arch=compute_30,code=compute_30 " . +- "-gencode arch=compute_30,code=sm_35 " . +- "-gencode arch=compute_30,code=sm_37 " . + "-gencode arch=compute_50,code=compute_50 " . + "-gencode arch=compute_50,code=sm_50 " . + "-gencode arch=compute_60,code=compute_60 " . + "-gencode arch=compute_60,code=sm_60 " . + "-gencode arch=compute_70,code=compute_70 " . + "-gencode arch=compute_70,code=sm_70 " . ++ "-gencode arch=compute_75,code=sm_75 " . ++ "-gencode arch=compute_80,code=sm_80 " . + "--ftz=true "; + # "-gencode arch=compute_75,code=sm_75 " . + $arch_gcc = "gcc"; +@@ -633,17 +632,17 @@ + # location of Mesa library and include files; basically does the same + # as OpenGL. This is based on the default instructions from the Mesa + # README; the include files should by default be in /usr/local/include/GL. +-$mesa_dir = "$vmd_library_dir/Mesa"; ++$mesa_dir = $ENV{'EBROOTMESA'}; + $mesa_include = "-I$mesa_dir/include"; + $mesa_library = "-L$mesa_dir/lib_$config_arch"; + #$mesa_libs = "-lMesaGL -lMesaGLU"; +-$mesa_libs = "-lMesaGL"; ++$mesa_libs = "-lGL -lGLU"; + $mesa_defines = "-DUSELINEAXES -DVMDMESA -DVMDOPENGL"; + @mesa_cc = (); + @mesa_cu = (); +-@mesa_ccpp = @opengl_ccpp; +-@mesa_h = @opengl_h; +-@mesa_extra = @opengl_extra; ++@mesa_ccpp = (); ++@mesa_h = (); ++@mesa_extra = (); + + + # +@@ -719,10 +718,10 @@ + + ################ FLTK GUI + $fltk_defines = "-DVMDGUI -DVMDFLTK"; +-$fltk_dir = "$vmd_library_dir/fltk"; ++$fltk_dir = $ENV{'EBROOTFLTK'}; + $fltk_include = "-I$fltk_dir/include"; + $fltk_library = "-L$fltk_dir/$config_arch"; +-$fltk_libs = "-lfltk -lX11"; ++$fltk_libs = "-lfltk -lX11 -lXfixes -lXcursor -lXinerama"; + #@fltk_cc = ('forms_ui.c'); + @fltk_cu = (); + @fltk_ccpp = ( 'ColorFltkMenu.C', +@@ -764,7 +763,6 @@ + $stock_tcl_include_dir=$ENV{"TCL_INCLUDE_DIR"} || "$vmd_library_dir/tcl/include"; + $stock_tcl_library_dir=$ENV{"TCL_LIBRARY_DIR"} || "$vmd_library_dir/tcl/lib_$config_arch"; + +- + # location of Tk (for TK option) + #$stock_tk_include_dir=$ENV{"TK_INCLUDE_DIR"} || "/usr/local/include"; + #$stock_tk_library_dir=$ENV{"TK_LIBRARY_DIR"} || "/usr/local/lib"; +@@ -782,8 +780,8 @@ + if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; } + $tcl_library = "-L$stock_tcl_library_dir"; + if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; } +-$tcl_libs = "-ltcl8.5"; +-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; } ++$tcl_libs = "-ltcl8.6"; ++if ($config_tk) { $tcl_libs = "-ltk8.6 -lX11 " . $tcl_libs; } + + @tcl_cc = (); + @tcl_cu = (); +@@ -992,7 +990,7 @@ + # This option enables the use of CUDA GPU acceleration functions. + ####################### + $cuda_defines = "-DVMDCUDA -DMSMPOT_CUDA"; +-$cuda_dir = "/usr/local/cuda-10.2"; ++$cuda_dir = "$ENV{'CUDA_HOME'}"; + $cuda_include = ""; + $cuda_library = ""; + $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart_static -lrt"; +@@ -1201,7 +1199,7 @@ + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-5.0.1-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-5.1.0-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-6.0.0-linux64"; +-$liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-6.5.0-linux64"; ++$liboptix_dir = "$ENV{'EBROOTOPTIX'}"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-7.0.0-linux64"; + + # NCSA Blue Waters +@@ -1356,7 +1354,7 @@ + die "LIBPNG option requires ZLIB!"; + } + $libpng_defines = "-DVMDLIBPNG"; +-$libpng_dir = "/Projects/vmd/vmd/lib/libpng"; ++$libpng_dir = "$ENV{'EBROOTLIBPNG'}"; + $libpng_include = "-I$libpng_dir/include"; + $libpng_library = "-L$libpng_dir/lib_$config_arch"; + $libpng_libs = "-lpng16"; +@@ -1384,7 +1382,7 @@ + # OPTIONAL COMPONENT: Data compresssion library + # This may be commented out if not required. + $zlib_defines = "-DVMDZLIB"; +-$zlib_dir = "/Projects/vmd/vmd/lib/zlib"; ++$zlib_dir = "$ENV{'EBROOTZLIB'}"; + $zlib_include = "-I$zlib_dir/include"; + $zlib_library = "-L$zlib_dir/lib_$config_arch"; + $zlib_libs = "-lz"; +@@ -1575,7 +1573,7 @@ + # primitives. + ####################### + $actc_defines = "-DVMDACTC"; +-$actc_dir = "$vmd_library_dir/actc"; ++$actc_dir = "$ENV{'EBROOTACTC'}"; + $actc_include = "-I$actc_dir/include"; + $actc_library = "-L$actc_dir/lib_$config_arch"; + $actc_libs = "-lactc"; +@@ -1590,7 +1588,7 @@ + # OPTIONAL COMPONENT: NetCDF I/O Library (Used by cdfplugin) + ####################### + $netcdf_defines = ""; +-$netcdf_dir = "$vmd_library_dir/netcdf"; ++$netcdf_dir = "$ENV{'EBROOTNETCDF'}"; + $netcdf_include = "-I$netcdf_dir/include"; + $netcdf_library = "-L$netcdf_dir/lib_$config_arch"; + $netcdf_libs = "-lnetcdf"; +@@ -1648,7 +1646,7 @@ + $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$conda_root/lib/python3.7/config-3.7m-x86_64-linux-gnu"; + $stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "$conda_root/lib/python3.7/site-packages/numpy/core/include/numpy"; + $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$conda_root/lib/python-3.7/site-packages/numpy/core/include"; +- $python_libs = "-fno-lto -lpython3.7m -lpthread"; ++ $python_libs = "$ENV{'PYTHON_LIBRARIES'}" || "-fno-lto -lpython3.7m -lpthread"; + } else { + # $stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "/usr/local/include"; + # $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib"; +@@ -1659,7 +1657,7 @@ + # $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib"; + $stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "$vmd_library_dir/numpy/lib_$config_arch/include"; + $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include"; +- $python_libs = "-lpython2.5 -lpthread"; ++ $python_libs = "$ENV{'PYTHON_LIBRARIES'}" || "-lpython2.5 -lpthread"; + } + + $python_defines = "-DVMDPYTHON"; +@@ -2573,7 +2571,7 @@ + + if ($config_cuda) { + $arch_nvccflags .= " --machine 64 -O3 $cuda_include"; +- $cuda_library = "-L/usr/local/cuda-10.2/lib64"; ++ $cuda_library = "-L/$ENV{'EBROOTCUDA'}/lib64"; + } + + $arch_lex = "flex"; # has problems with vendor lex +@@ -2583,7 +2581,7 @@ + # they likely serve no useful purpose going forward. + if (!$config_opengl_dispatch) { + $opengl_dep_libs = "-L/usr/X11R6/lib64 -lGL -lX11"; +- $mesa_libs = "-lMesaGL -L/usr/X11R6/lib64 -lXext -lX11"; ++ $mesa_libs = "-lGL -lGLU -L/usr/X11R6/lib64 -lXext -lX11"; + } + + # this is to make tcl happy +@@ -3763,7 +3761,7 @@ + + .cu.ptx: + \$(ECHO) "Compiling " \$< " --> " \$*.ptx " ..."; \\ +- \$(NVCC) \$(DEFINES) --use_fast_math $liboptix_include -gencode arch=compute_30,code=compute_30 -ptx \$< $arch_coptout$vmd_arch_dir/\$\@ ++ \$(NVCC) \$(DEFINES) --use_fast_math $liboptix_include -gencode arch=compute_80,code=compute_80 -ptx \$< $arch_coptout$vmd_arch_dir/\$\@ + + .y.o: + diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51_extra_colors.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51_extra_colors.patch new file mode 100644 index 00000000000..26e9ba954db --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51_extra_colors.patch @@ -0,0 +1,46 @@ +Add some additional colors, e.g. to allow for color blind compatible rendering. +Bob Dröge, 2020-06-23 +--- src/Scene.C.orig 2020-06-23 09:37:41.000000000 +0200 ++++ src/Scene.C 2020-06-23 09:40:59.000000000 +0200 +@@ -63,7 +63,10 @@ + ,"yellow2", "yellow3", "green2", "green3", + "cyan2", "cyan3", "blue2", "blue3", + "violet", "violet2", "magenta", "magenta2", +- "red2", "red3", "orange2", "orange3" ++ "red2", "red3", "orange2", "orange3", ++ "matisse", "flamenco", "forest_green", "punch", ++ "wisteria", "spicy_mix", "orchid", "gray2", ++ "lime_pie", "java" + #endif + + }; +@@ -89,7 +92,17 @@ + 0.27f, 0.00f, 0.98f, 0.45f, 0.00f, 0.90f, // violet + 0.90f, 0.00f, 0.90f, 1.00f, 0.00f, 0.66f, // magenta + 0.98f, 0.00f, 0.23f, 0.81f, 0.00f, 0.00f, // red +- 0.89f, 0.35f, 0.00f, 0.96f, 0.72f, 0.00f // orange ++ 0.89f, 0.35f, 0.00f, 0.96f, 0.72f, 0.00f, // orange ++ 0.1f, 0.5f, 0.7f, // MPL1, matisse ++ 1.0f, 0.5f, 0.1f, // MPL2, flamenco ++ 0.2f, 0.6f, 0.2f, // MPL3, forest green ++ 0.8f, 0.2f, 0.2f, // MPL4, punch ++ 0.6f, 0.4f, 0.7f, // MPL5, wisteria ++ 0.5f, 0.3f, 0.3f, // MPL6, spicy mix ++ 0.9f, 0.5f, 0.8f, // MPL7, orchid ++ 0.5f, 0.5f, 0.5f, // MPL8, gray ++ 0.7f, 0.7f, 0.1f, // MPL9, key lime pie ++ 0.1f, 0.7f, 0.8f // MPL10, java + #endif + + }; +--- src/Scene.h.orig 2020-06-23 09:37:45.000000000 +0200 ++++ src/Scene.h 2020-06-23 09:42:21.000000000 +0200 +@@ -37,7 +37,7 @@ + #define DISP_LIGHTS 4 + + // total number of colors defined here +-#define REGCLRS 33 ++#define REGCLRS 43 + #define EXTRACLRS 1 + #define VISCLRS (REGCLRS - EXTRACLRS) + #define MAPCLRS 1024 diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb new file mode 100644 index 00000000000..b6987d9bb81 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb @@ -0,0 +1,87 @@ +## +# Authors:: +# * Fotis Georgatos +# * Robert Mijakovic +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '9.0.1' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + '1b39a5e191c282861e7af4101eaa8585969a2de05f5646c9199a161213a622c7', # VTK-9.0.1.tar.gz + '3f8bfdadd66e0b541bc5580340481abf92bec100b09d787283632ab590b1ce1c', # VTKData-9.0.1.tar.gz + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('XZ', '5.2.5'), + ('libGLU', '9.0.1'), + ('X11', '20210518'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/Vala/Vala-0.52.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/v/Vala/Vala-0.52.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..27224518e26 --- /dev/null +++ b/easybuild/easyconfigs/v/Vala/Vala-0.52.4-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Vala' +version = '0.52.4' + +homepage = 'https://wiki.gnome.org/Projects/Vala' +description = """Vala is a programming language using modern high level abstractions without imposing additional runtime +requirements and without using a different ABI compared to applications and libraries written in C.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://download.gnome.org/sources/vala/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ecde520e5160e659ee699f8b1cdc96065edbd44bbd08eb48ef5f2506751fdf31'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('Graphviz', '2.47.2'), +] + +dependencies = [ + ('GLib', '2.68.2'), +] + +sanity_check_paths = { + 'files': ['bin/vala', 'bin/valac', 'bin/valadoc', 'lib/libvala-%%(version_major_minor)s.%s' % SHLIB_EXT, + 'lib/libvaladoc-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/vala-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "vala --help", + "valac --help", + "valadoc --help", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/v/variant_tools/variant_tools-3.1.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/v/variant_tools/variant_tools-3.1.3-foss-2019b-Python-3.7.4.eb index 557ad9b9f3f..fffdd7c285b 100644 --- a/easybuild/easyconfigs/v/variant_tools/variant_tools-3.1.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/v/variant_tools/variant_tools-3.1.3-foss-2019b-Python-3.7.4.eb @@ -24,7 +24,6 @@ dependencies = [ ('HDF5', '1.10.5'), ] -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c5afa8a2129205492786700c93a117504b2162aa6df3d5d10ff575cc946a923c'] diff --git a/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb index b8c46f56c23..f6ac894247e 100644 --- a/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb @@ -10,7 +10,6 @@ description = """ Load data from a VCF (variant call format) file into numpy arr toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['vcfnp-%(version)s_numpy_setup.patch'] checksums = [ diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.17-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.17-intel-2016a-Python-2.7.11.eb index bf597beacdf..118643ad859 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.17-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.17-intel-2016a-Python-2.7.11.eb @@ -11,7 +11,6 @@ and fancylogger (logging functionality).""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] dependencies = [ ('Python', '2.7.11'), @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'vsc.utils.fancylogger'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1-intel-2016a-Python-2.7.11.eb index 0894c451e20..d48dec3c7ab 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1-intel-2016a-Python-2.7.11.eb @@ -11,7 +11,6 @@ and fancylogger (logging functionality).""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] builddependencies = [('vsc-install', '0.10.6', versionsuffix)] dependencies = [ @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'vsc.utils.fancylogger'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1-intel-2016b-Python-2.7.12.eb index 4663f7299c9..0f37a9f9d36 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1-intel-2016b-Python-2.7.12.eb @@ -11,7 +11,6 @@ and fancylogger (logging functionality).""" toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] builddependencies = [('vsc-install', '0.10.11', versionsuffix)] dependencies = [ @@ -20,9 +19,4 @@ dependencies = [ options = {'modulename': 'vsc.utils.fancylogger'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1.eb index 17ac60fe31d..cc0ea34734a 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1.eb @@ -10,7 +10,6 @@ description = """Basic Python libraries used by UGent's HPC group""" toolchain = SYSTEM sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] # install as zipped egg to make sure that tools that use this as a dependency are responsive install_target = 'easy_install' diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb index 9903d5c491d..b035e621abc 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb @@ -10,7 +10,6 @@ description = """Basic Python libraries used by UGent's HPC group""" toolchain = SYSTEM sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] # install as zipped egg to make sure that tools that use this as a dependency are responsive install_target = 'easy_install' diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.0.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.0.eb index f83d8082014..4e09cc07bc0 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.0.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.0.eb @@ -9,7 +9,6 @@ description = """Basic Python libraries used by UGent's HPC group""" # purposely built with system compilers & Python toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2eae538f9b5d0f28deab780fbfaffab4035dc28ef7464e7ac8261082108332cd'] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.1.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.1.eb index d2e276a174f..6df321ce5aa 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.1.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.1.eb @@ -9,7 +9,6 @@ description = """Basic Python libraries used by UGent's HPC group""" # purposely built with system compilers & Python toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['7dbd3888302af73b6e6cc6fba1cc1aaa78d955ea38c8430f9d69ffde6ffcfdeb'] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.3.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.3.eb index 0df67a869ba..50342783265 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.3.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.3.eb @@ -9,7 +9,6 @@ description = """Basic Python libraries used by UGent's HPC group""" # purposely built with system compilers & Python toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9e102ca9d94ab97c2b974c63708dab7ea4dbaa3144787f06455e16445b92f204'] diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016a-Python-2.7.11.eb index a3bd950894c..c45b28cb6f3 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016a-Python-2.7.11.eb @@ -11,7 +11,6 @@ description = """vsc-install provides shared setuptools functions and classes fo toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] dependencies = [ ('Python', '2.7.11'), @@ -19,9 +18,4 @@ dependencies = [ options = {'modulename': 'vsc.install'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016b-Python-2.7.12.eb index cac40f2de54..2710ad90d9f 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016b-Python-2.7.12.eb @@ -11,7 +11,6 @@ description = """vsc-install provides shared setuptools functions and classes fo toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] dependencies = [ ('Python', '2.7.12'), @@ -19,9 +18,4 @@ dependencies = [ options = {'modulename': 'vsc.install'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb index 7002f832800..c2c9c833716 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb @@ -10,7 +10,6 @@ description = """Shared setuptools functions and classes for python libraries de toolchain = SYSTEM sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] options = {'modulename': 'vsc.install'} diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb index 04bc9bb8b25..712a8d993e0 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb @@ -10,7 +10,6 @@ description = """Shared setuptools functions and classes for python libraries de toolchain = SYSTEM sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] options = {'modulename': 'vsc.install'} diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6-intel-2016a-Python-2.7.11.eb index 9f063999d7d..239248a2339 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6-intel-2016a-Python-2.7.11.eb @@ -11,7 +11,6 @@ description = """vsc-install provides shared setuptools functions and classes fo toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] dependencies = [ ('Python', '2.7.11'), @@ -19,9 +18,4 @@ dependencies = [ options = {'modulename': 'vsc.install'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6.eb index 522465ed3bc..c3bd8287f58 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6.eb @@ -10,7 +10,6 @@ description = """Shared setuptools functions and classes for python libraries de toolchain = SYSTEM sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] options = {'modulename': 'vsc.install'} diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.1.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.1.eb index 55ad4211d58..f57fcec50d0 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.1.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.1.eb @@ -9,7 +9,6 @@ description = """Shared setuptools functions and classes for python libraries de # purposely built with system compilers & Python toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['afbec5532f9f692c49fbefe8656975547b515eb8eb01c6ba8b85dd7af07cc1f4'] diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.2.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.2.eb index 53930a69547..46d314e777d 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.2.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.2.eb @@ -9,7 +9,6 @@ description = """Shared setuptools functions and classes for python libraries de # purposely built with system compilers & Python toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c03ce30a54cc5be53acc55addb027d67be58386bebdd9d2274ed6429b1fc0512'] diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.18-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.18-intel-2016a-Python-2.7.11.eb index a3123a79e4f..e141936115c 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.18-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.18-intel-2016a-Python-2.7.11.eb @@ -11,7 +11,6 @@ description = """vsc-install provides shared setuptools functions and classes fo toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] dependencies = [ ('Python', '2.7.11'), @@ -19,9 +18,4 @@ dependencies = [ options = {'modulename': 'vsc.install'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb index 8d5708b6689..2109513f82b 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb @@ -9,7 +9,6 @@ description = """VSC-tools is a set of Python libraries and scripts that are com # we build this to work with every python version toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] builddependencies = [('vsc-install', '0.10.26')] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb index 00c08f8f51e..6dcba6d8e0c 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb @@ -8,7 +8,6 @@ description = """VSC-tools is a set of Python libraries and scripts that are com toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = ['vsc-mympirun-%(version)s.tar.gz'] dependencies = [ diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb index f584edb6581..aee2e9f5e38 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb @@ -9,7 +9,6 @@ description = """VSC-tools is a set of Python libraries and scripts that are com # we build this to work with every python version toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b5b08e6291a68802d29c344d5807e4c2a1945375055b57c819721151775789f0'] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb index 0dd4cf7cf3c..7cdd6f28572 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb @@ -9,7 +9,6 @@ description = """VSC-tools is a set of Python libraries and scripts that are com # we build this to work with every python version toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a6ef244a80e29ddb1197c1d1bfac6f7b9a0092abb44c4cff789db42e27a3e1ad'] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.4.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.4.eb index 89003144f39..a2738e3ea44 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.4.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.4.eb @@ -9,7 +9,6 @@ description = """VSC-tools is a set of Python libraries and scripts that are com # we build this to work with every python version toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a12da9dad02df01bef87789563d02e13562309d822e87eb654480887c9bed1a7'] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.5.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.5.eb index 708bf81e8e0..bfa777cfc32 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.5.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.5.eb @@ -9,7 +9,6 @@ description = """VSC-tools is a set of Python libraries and scripts that are com # we build this to work with every python version toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1b27ec04e5e63e30dfb14993f3dd74de7225540a85bf9c7a0fd626043d3d21cf'] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.6.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.6.eb index 04914211361..567d8503a39 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.6.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.6.eb @@ -9,7 +9,6 @@ description = """VSC-tools is a set of Python libraries and scripts that are com # we build this to work with every python version toolchain = SYSTEM -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['7502dfe4ecbcc167cb33be042b9c7a8faec2d6197050fe5be7e3c1fdcb08f839'] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb index 6c0eb1fe001..d7df9b15a48 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb @@ -17,44 +17,35 @@ use_pip = False exts_list = [ ('setuptools', '39.2.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['f7cddbb5f5c640311eb00eab6e849f7701fa70bf6a183fc8a2c33dd1d1672fb2'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('pbr', '5.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['8c361cc353d988e4f5b998555c88098b9d5964c2e11acf7b0d21925a66bb5824'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('IPy', '1.00', { 'modulename': 'IPy', - 'source_urls': ['https://pypi.python.org/packages/source/i/IPy'], 'checksums': ['2f2bf658a858d43868d8a4352b3889cf78c66e2ce678b300dcf518c9149ba621'], }), ('vsc-install', '0.12.7', { 'modulename': 'vsc.install', - 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-install'], 'checksums': ['f1d0796aa6201c0d7e1c6bde591153be1b8bde2f04860494272432c1d30f18f5'], }), ('vsc-base', '2.9.2', { 'modulename': 'vsc.utils', - 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-base'], 'checksums': ['55803ce00f29bc0eb8b4e37518b21368b4c0f4cdb37c3a168912fc815fd88f15'], }), (name, version, { # don't check for import of vsc.mympirun, since that may fail if vsc-base is picked up from the OS 'modulename': 'vsc', - 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-mympirun'], 'checksums': ['497433504860328934db5777200a2107561b83d524515418f908da77b5fec83b'], }), ] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.9.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.9.eb index 31193b749e1..e28b7b6b09f 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.9.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.9.eb @@ -17,44 +17,35 @@ use_pip = False exts_list = [ ('setuptools', '41.0.1', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['a222d126f5471598053c9a77f4b5d4f26eaa1f150ad6e01dcf1a42e185d05613'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('pbr', '5.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['9b321c204a88d8ab5082699469f52cc94c5da45c51f114113d01b3d993c24cdf'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '3.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['83657d894c90d5681d62155c82bda9c1187827525880eda8ff5df4ec813437c3'], }), ('IPy', '1.00', { 'modulename': 'IPy', - 'source_urls': ['https://pypi.python.org/packages/source/i/IPy'], 'checksums': ['2f2bf658a858d43868d8a4352b3889cf78c66e2ce678b300dcf518c9149ba621'], }), ('vsc-install', '0.12.7', { 'modulename': 'vsc.install', - 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-install'], 'checksums': ['f1d0796aa6201c0d7e1c6bde591153be1b8bde2f04860494272432c1d30f18f5'], }), ('vsc-base', '2.9.6', { 'modulename': 'vsc.utils', - 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-base'], 'checksums': ['a62158022c36b5b456771ee8145d9ea3d299b301240e9724d04052e6aa0400b3'], }), (name, version, { # don't check for import of vsc.mympirun, since that may fail if vsc-base is picked up from the OS 'modulename': 'vsc', - 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-mympirun'], 'checksums': ['6773ac481071d5c68c7ddb51321980f4ab1e13cf4354785019931374258a68f4'], }), ] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.1.0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.1.0.eb index c97b9c5b87b..e62fa0b9fee 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.1.0.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.1.0.eb @@ -14,8 +14,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ # must be setuptools < 42.0 (required by vsc-install) ('setuptools', '41.6.0', { diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.0.eb index 3c9a0d992fc..8fe2795aa36 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.0.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.0.eb @@ -14,8 +14,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('setuptools', '41.6.0', { 'source_tmpl': '%(name)s-%(version)s.zip', diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.2.eb index fa0895720f3..1cb1a314425 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.2.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.2.eb @@ -14,8 +14,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ # must be setuptools < 42.0 (required by vsc-install) ('setuptools', '41.6.0', { diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.3.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.3.eb index bebe9773716..0082fe9c0ce 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.3.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.3.eb @@ -14,8 +14,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('setuptools', '41.6.0', { 'source_tmpl': '%(name)s-%(version)s.zip', diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.4.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.4.eb index b323c820f66..d9fa907edcb 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.4.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.4.eb @@ -14,8 +14,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('setuptools', '41.6.0', { 'source_tmpl': '%(name)s-%(version)s.zip', diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.5.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.5.eb index c3f7d830c63..f25dcdd66cb 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.5.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.5.eb @@ -14,8 +14,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] use_pip = False -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('setuptools', '41.6.0', { 'source_tmpl': '%(name)s-%(version)s.zip', diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.6.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.6.eb new file mode 100644 index 00000000000..6bf1b1d2541 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.6.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'vsc-mympirun' +version = '5.2.6' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """mympirun is a tool to make it easier for users of HPC clusters to +run MPI programs with good performance.""" + +# we build this to work with every python version +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +use_pip = False + +exts_list = [ + ('setuptools', '41.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6afa61b391dcd16cb8890ec9f66cc4015a8a31a6e1c2b4e0c464514be1a3d722'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('pbr', '5.6.0', { + 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '4.0.3', { + 'checksums': ['7d3fbbde18228f4ff2f1f119a45cdffa458b4c0dee32eb4d2bb2f82554bac7bc'], + }), + ('IPy', '1.01', { + 'modulename': 'IPy', + 'checksums': ['edeca741dea2d54aca568fa23740288c3fe86c0f3ea700344571e9ef14a7cc1a'], + }), + ('vsc-install', '0.17.15', { + 'modulename': 'vsc.install', + 'checksums': ['c846236ea98eb112727ca62164978d5fc984eeabafd82c043f39f963aaa6a975'], + }), + ('vsc-base', '3.3.1', { + 'modulename': 'vsc.utils', + 'checksums': ['f7a671c84aefe896278f4aacb6e7e5553e56f14be16fab79a55730b5d6983e61'], + }), + (name, version, { + 'modulename': 'vsc', + 'checksums': ['6dd08211211a093cf11305d187d4b088eb68082f5aed916e719a22acf2252472'], + }), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mypmirun', 'bin/mympisanity', 'bin/mytasks'], + 'dirs': ['bin/fake'], +} +sanity_check_commands = ["mympirun --help"] + +# can't enable 'pip check' since pip may not be installed in OS +sanity_pip_check = False + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WISExome/WISExome-20180517-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/w/WISExome/WISExome-20180517-intel-2018a-Python-2.7.14.eb index f1e24621d2f..51a61c21a68 100644 --- a/easybuild/easyconfigs/w/WISExome/WISExome-20180517-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/w/WISExome/WISExome-20180517-intel-2018a-Python-2.7.14.eb @@ -28,18 +28,18 @@ postinstallcmds = [ exts_defaultclass = 'PythonPackage' exts_filter = ("python -c 'import %(ext_name)s'", '') - -# let sanity check fail when auto-downloaded dependencies are detected when installing extensions -exts_download_dep_fail = True +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} exts_list = [ ('pyliftover', '0.3', { 'source_tmpl': 'pyliftover-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyliftover/'], 'checksums': ['8feaa3106e55705291feb70bb82be0861d7ba2306911a3ad42ceed1a2df19299'], }), ('xlwt', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlwt/'], 'checksums': ['c59912717a9b28f1a3c2a98fd60741014b06b043936dcecbc113eaaada156c88'], }), ] diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2021a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2021a.eb new file mode 100644 index 00000000000..a843cbf4b70 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +# The -fallow-argument-mismatch allows MPI communication calls to be +# called with arrays of different types at different places in the +# code. This otherwise cause an error in GCC 10.X +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2021a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2021a.eb new file mode 100644 index 00000000000..5aecb5e2c34 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2021a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb new file mode 100644 index 00000000000..1cdcd817b63 --- /dev/null +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'WhatsHap' +version = '1.1' + +homepage = 'https://whatshap.readthedocs.io' +description = """WhatsHap is a software for phasing genomic variants using DNA +sequencing reads, also called read-based phasing or haplotype assembly. It is +especially suitable for long reads, but works also well with short reads.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Pysam', '0.16.0.1'), + ('networkx', '2.5'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), + ('Yasm', '1.3.0'), + ('pyfaidx', '0.5.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('isal', '0.10.0', { + 'checksums': ['3f89471065c2837d1235877dbdcdbd8b7649068723026b0582010fa106a71ff3'], + }), + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f'], + }), +] + + +sanity_check_paths = { + 'files': ['bin/whatshap'], + 'dirs': ['bin', 'lib'], +} + +sanity_check_commands = [ + 'whatshap --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/wandb/wandb-0.8.30-gcccuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/w/wandb/wandb-0.8.30-gcccuda-2019b-Python-3.7.4.eb index e8ba9f475a0..49a9c4a6657 100644 --- a/easybuild/easyconfigs/w/wandb/wandb-0.8.30-gcccuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/w/wandb/wandb-0.8.30-gcccuda-2019b-Python-3.7.4.eb @@ -22,8 +22,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('nvidia-ml-py3', '7.352.0', { 'modulename': 'pynvml', diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-2.7.11.eb index c66afc64449..db17f6d61a2 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-3.5.1.eb index 765f8143906..a59a7cef7e3 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-3.5.1.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-2.7.14.eb index 99ca22f0fbc..520fc977d75 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-3.6.3.eb index 7fdd33839b0..e990e963051 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2018a-Python-3.6.4.eb index 906906d619e..9d15888ad25 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-2.7.14.eb index dbdf2b5273e..38c807a33da 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'fosscuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-3.6.3.eb index 22b2b003051..f1a65ebc6f5 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'fosscuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2017b-Python-2.7.14.eb index a1d870aaabe..5e8742b89bc 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2017b-Python-3.6.3.eb index 4b748731023..fa928563cff 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2018a-Python-3.6.4.eb index eca8da6c2b8..23a2a1ec082 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intel-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-2.7.14.eb index d6564ddf387..befe2392c58 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'intelcuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-3.6.3.eb index fd45223ab46..2005094e092 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-3.6.3.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'intelcuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.31.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/w/wheel/wheel-0.31.0-foss-2018a-Python-3.6.4.eb index 8b9b07f21a2..8ec9ca1cd44 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.31.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.31.0-foss-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1ae8153bed701cb062913b72429bcf854ba824f973735427681882a688cb55ce'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.31.0-fosscuda-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/w/wheel/wheel-0.31.0-fosscuda-2018a-Python-2.7.14.eb index 27a60bdaa8e..079977d3916 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.31.0-fosscuda-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.31.0-fosscuda-2018a-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'fosscuda', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1ae8153bed701cb062913b72429bcf854ba824f973735427681882a688cb55ce'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.31.0-fosscuda-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/w/wheel/wheel-0.31.0-fosscuda-2018a-Python-3.6.4.eb index 4580b77ffce..07fb4a286da 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.31.0-fosscuda-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.31.0-fosscuda-2018a-Python-3.6.4.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'fosscuda', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1ae8153bed701cb062913b72429bcf854ba824f973735427681882a688cb55ce'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.31.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/w/wheel/wheel-0.31.0-intel-2018a-Python-2.7.14.eb index 78d6bde284d..c1851a4e50e 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.31.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.31.0-intel-2018a-Python-2.7.14.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1ae8153bed701cb062913b72429bcf854ba824f973735427681882a688cb55ce'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.31.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/w/wheel/wheel-0.31.1-foss-2018b-Python-3.6.6.eb index 9e7e4167cc4..0fde2069f42 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.31.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.31.1-foss-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0a2e54558a0628f2145d2fc822137e322412115173e8a2ddbe1c9024338ae83c'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-2.7.15.eb index b75e54dc46e..00f2478467b 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-2.7.15.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0a2e54558a0628f2145d2fc822137e322412115173e8a2ddbe1c9024338ae83c'] diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb index 331611679eb..e4d95fa291f 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb @@ -9,7 +9,6 @@ description = """A built-package format for Python.""" toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0a2e54558a0628f2145d2fc822137e322412115173e8a2ddbe1c9024338ae83c'] diff --git a/easybuild/easyconfigs/w/wrf-python/wrf-python-1.2.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.2.0-intel-2018a-Python-3.6.4.eb index a45954e8af7..44f82d89915 100644 --- a/easybuild/easyconfigs/w/wrf-python/wrf-python-1.2.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.2.0-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'wrf-python' version = '1.2.0' @@ -20,41 +20,25 @@ dependencies = [ ('PROJ', '5.0.0'), # required for Cartopy ] -exts_defaultclass = 'PythonPackage' -exts_default_options = {'use_pip': True} - -exts_download_dep_fail = True - +use_pip = True exts_list = [ ('wrapt', '1.10.11', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt'], 'checksums': ['d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/w/wrf-python'], 'checksums': ['7520cec5027c6397930ae9d780f076c01f0ea563bc9fff45b91767ebb0865755'], 'modulename': 'wrf', }), ('Shapely', '1.6.4.post2', { - 'source_urls': ['https://pypi.python.org/packages/source/S/Shapely'], 'checksums': ['c4b87bb61fc3de59fc1f85e71a79b0c709dc68364d9584473697aad4aa13240f'], }), ('pyshp', '1.2.12', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyshp'], 'checksums': ['8dcd65e0aa2aa2951527ddb7339ea6e69023543d8a20a73fc51e2829b9ed6179'], 'modulename': 'shapefile', }), ('Cartopy', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cartopy'], 'checksums': ['f23dffa101f43dd91e866a49ebb5f5048be2a24ab8a921a5c07edabde746d9a4'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.1-intel-2018b-Python-3.6.6.eb index b78844dd5a1..ee7eb420832 100644 --- a/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.1-intel-2018b-Python-3.6.6.eb @@ -24,25 +24,20 @@ use_pip = True exts_list = [ ('wrapt', '1.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt'], 'checksums': ['4aea003270831cceb8a90ff27c4031da6ead7ec1886023b80ce0dfe0adf61533'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/w/wrf-python'], 'checksums': ['24af2618b5bf436830d780af3366c423fc540244ba644307ca71633020d052a2'], 'modulename': 'wrf', }), ('Shapely', '1.6.4.post2', { - 'source_urls': ['https://pypi.python.org/packages/source/S/Shapely'], 'checksums': ['c4b87bb61fc3de59fc1f85e71a79b0c709dc68364d9584473697aad4aa13240f'], }), ('pyshp', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyshp'], 'checksums': ['e65c7f24d372b97d0920b864bbeb78322bb37b83f2606e2a2212631d5d51e5c0'], 'modulename': 'shapefile', }), ('Cartopy', '0.17.0', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cartopy'], 'checksums': ['424bd9e9ddef6e48cbdee694ce589ec431be8591f15b6cb93cb2b333a29b2c61'], }), ] diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb index 0b30943ecb8..2a615753735 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb @@ -2,7 +2,7 @@ name = 'wxPython' version = '4.0.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.wxpython.org' +homepage = 'https://www.wxpython.org' description = """wxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. @@ -12,7 +12,6 @@ description = """wxPython is a GUI toolkit for the Python programming language. toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = [PYPI_SOURCE] sources = ['%(name)s-%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_fix_install_path.patch', diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb index 1c22af4a243..523bd6e843a 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb @@ -2,7 +2,7 @@ name = 'wxPython' version = '4.0.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.wxpython.org' +homepage = 'https://www.wxpython.org' description = """wxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. @@ -12,7 +12,6 @@ description = """wxPython is a GUI toolkit for the Python programming language. toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = [PYPI_SOURCE] sources = ['%(name)s-%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_fix_install_path.patch', diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.7.post2-GCC-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.7.post2-GCC-8.3.0-Python-3.7.4.eb index 3e0a622be56..f6bb1f01b41 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.7.post2-GCC-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.7.post2-GCC-8.3.0-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = """wxPython is a GUI toolkit for the Python programming language. toolchain = {'name': 'GCC', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = ['%(name)s-%(version)s.tar.gz'] patches = [ '%(name)s-4.0.4_fix_install_path.patch', diff --git a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c9423b441d3 --- /dev/null +++ b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'XCFun' +version = '2.1.1' + +homepage = 'https://xcfun.readthedocs.io' +description = """Arbitrary order exchange-correlation functional library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/dftlibs/xcfun/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8b602df74c7be83d501532565deafd1b7881946d94789122f24c309a669298ab'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] + +separate_build_dir = True +build_type = 'release' + +modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} + +sanity_check_paths = { + 'files': ['lib/libxcfun.%s' % SHLIB_EXT], + 'dirs': ['include/XCFun'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b4e94d5e324 --- /dev/null +++ b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'XCFun' +version = '2.1.1' + +homepage = 'https://xcfun.readthedocs.io' +description = """Arbitrary order exchange-correlation functional library""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/dftlibs/xcfun/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8b602df74c7be83d501532565deafd1b7881946d94789122f24c309a669298ab'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1') +] + +separate_build_dir = True +build_type = 'release' + +modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} + +sanity_check_paths = { + 'files': ['lib/libxcfun.%s' % SHLIB_EXT], + 'dirs': ['include/XCFun'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb index da4a0e2bda9..5f17fb82cdd 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb @@ -10,15 +10,9 @@ description = """XGBoost is an optimized distributed gradient boosting library d toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['ebc4e2bf8c8266212e342ff8ec4f6ae469e8c41a05d099b6778de8424ce32563'] dependencies = [('Python', '2.7.12')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb index a979a43a6fd..c1d0c449ee7 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb @@ -10,15 +10,9 @@ description = """XGBoost is an optimized distributed gradient boosting library d toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['ebc4e2bf8c8266212e342ff8ec4f6ae469e8c41a05d099b6778de8424ce32563'] dependencies = [('Python', '3.5.2')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb index 6269db2cd46..e07fe10748d 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb @@ -10,15 +10,9 @@ description = """XGBoost is an optimized distributed gradient boosting library d toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['ebc4e2bf8c8266212e342ff8ec4f6ae469e8c41a05d099b6778de8424ce32563'] dependencies = [('Python', '3.6.1')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.72.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.72.1-intel-2017b-Python-2.7.14.eb index fb39496f69c..739b57374f3 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.72.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.72.1-intel-2017b-Python-2.7.14.eb @@ -10,15 +10,9 @@ description = """XGBoost is an optimized distributed gradient boosting library d toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['a4be2482694351b6610f1d8faf79eb049ca572aec80c8ba00c7020b8d44d8c1d'] dependencies = [('Python', '2.7.14')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.90-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.90-foss-2019b-Python-3.7.4.eb index 1b7edbe2ade..e834f33cebb 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.90-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.90-foss-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ description = """XGBoost is an optimized distributed gradient boosting library d toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['d69f90d61a63e8889fd39a31ad00c629bac1ca627f8406b9b6d4594c9e29ab84'] diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb index cebce458cbf..3fb7c1d49dd 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb @@ -1,7 +1,8 @@ easyblock = 'MakeCp' name = 'XGBoost' -version = '20171120' # commit: 8817769 +version = '20171120' +local_commit = '8817769' versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/dmlc/xgboost' @@ -10,12 +11,17 @@ description = """XGBoost is an optimized distributed gradient boosting library d toolchain = {'name': 'intel', 'version': '2017b'} -# source tarball needs to be created manually, -# because of lack of proper releases & use of git submodules -# - git clone --recursive https://github.com/dmlc/xgboost -# - cd xgboost && git reset --hard && cd - -# - tar cfvz xgboost-.tar.gz xgboost -sources = [SOURCELOWER_TAR_GZ] +sources = [{ + 'filename': SOURCELOWER_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/dmlc', + 'repo_name': 'xgboost', + 'commit': local_commit, + 'recursive': True, + }, +}] +# can't include reliable checksum because source tarball is created via git, commit ID should be sufficient +checksums = [None] builddependencies = [('CMake', '3.9.5')] dependencies = [('Java', '1.8.0_152', '', True)] diff --git a/easybuild/easyconfigs/x/XMDS2/XMDS2-2.2.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/x/XMDS2/XMDS2-2.2.3-foss-2018b-Python-2.7.15.eb index 2273f23104a..6ea139f4f92 100644 --- a/easybuild/easyconfigs/x/XMDS2/XMDS2-2.2.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/x/XMDS2/XMDS2-2.2.3-foss-2018b-Python-2.7.15.eb @@ -25,15 +25,12 @@ use_pip = True exts_list = [ ('Cheetah', '2.4.4', { 'modulename': 'Cheetah', - 'source_urls': ['https://pypi.python.org/packages/source/c/Cheetah/'], 'checksums': ['be308229f0c1e5e5af4f27d7ee06d90bb19e6af3059794e5fd536a6f29a9b550'], }), ('pyparsing', '2.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['f353aab21fd474459d97b709e527b5571314ee5f067441dc9f88e33eecd96592'], }), ('Markdown', '3.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/Markdown/'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('xmds', version, { diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.11-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..da8a33a8547 --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.11-GCCcore-10.3.0.eb @@ -0,0 +1,110 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '1.20.11' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), + ('Python', '3.9.5'), +] + +dependencies = [ + ('X11', '20210518'), + ('pixman', '0.40.0'), + ('libdrm', '2.4.106'), + ('Mesa', '21.1.1'), + ('nettle', '3.7.2'), + ('libunwind', '1.4.0'), + ('XZ', '5.2.5'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['e5b687029e44d0bd3ccd254a4da6a5cbfc40350aa8b43fcca16ef6e9b9bb9f22'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.3.2', { + 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], + }), + ('font-misc-misc', '1.1.2', { + 'preconfigopts': local_font_misc_preconfigopts, + 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], + }), + ('xkbcomp', '1.4.5', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['e88a4d86b9925ea1e8685dd5ea29c815abafb8ddf19bf5f1a1e0650839252c23'], + }), + ('xkeyboard-config', '2.32', { + 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], + 'checksums': ['88effbe680cb5d5b0f566e5f6aa27927aaa7f7e709f43a6af64f83eb44accece'], + 'configopts': '--with-xkb-rules-symlink=xorg', + }), + ('xauth', '1.1', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['e9fce796c8c5c9368594b9e8bbba237fb54b6615f5fd60e8d0a5b3c52a92c5ef'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual/xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + '4e9341c96f5ed0f6b9491ed732c501303479d3fe21da280c768a1822d7e5d352', # xorg-server-1.20.11.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.10.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/x/xarray/xarray-0.10.0-intel-2017b-Python-2.7.14.eb index b59eeb290bd..01bd5bbe83d 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.10.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.10.0-intel-2017b-Python-2.7.14.eb @@ -11,15 +11,9 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['af1449e8df84a6eb09eb1d56c1dc5ac7f24a9563d4f2b9391ff364dc0c62344c'] dependencies = [('Python', '2.7.14')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.10.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/x/xarray/xarray-0.10.0-intel-2017b-Python-3.6.3.eb index 1b39d30e90d..747ed2705fe 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.10.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.10.0-intel-2017b-Python-3.6.3.eb @@ -11,15 +11,9 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['af1449e8df84a6eb09eb1d56c1dc5ac7f24a9563d4f2b9391ff364dc0c62344c'] dependencies = [('Python', '3.6.3')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.10.3-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/x/xarray/xarray-0.10.3-intel-2018a-Python-3.6.4.eb index b6f7a2d47bd..cbe7981e544 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.10.3-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.10.3-intel-2018a-Python-3.6.4.eb @@ -11,15 +11,9 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['72fafe29ba00633483aed39e405442226ef66d2ddc1021a39527ae1522b7067a'] dependencies = [('Python', '3.6.4')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.10.4-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/x/xarray/xarray-0.10.4-intel-2018a-Python-3.6.4.eb index 0fcfb30be90..3269b24525b 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.10.4-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.10.4-intel-2018a-Python-3.6.4.eb @@ -11,15 +11,9 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['64c2d07b75b8ea1320cba521818a2f09107f5f46514d50ff5ef1c4d5da90aaf1'] dependencies = [('Python', '3.6.4')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.10.8-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/x/xarray/xarray-0.10.8-intel-2018a-Python-3.6.4.eb index 620308843b9..7f291fb290a 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.10.8-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.10.8-intel-2018a-Python-3.6.4.eb @@ -11,15 +11,9 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6a1f2c5dc5f639f8343f70ed08d0afbb477a3867298ef38f0d9bf4aafa0fb750'] dependencies = [('Python', '3.6.4')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.12.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/x/xarray/xarray-0.12.1-foss-2018b-Python-3.6.6.eb index 69e7829bc10..ed449460877 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.12.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.12.1-foss-2018b-Python-3.6.6.eb @@ -11,7 +11,6 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ac09a819e791be208ae33fa7ecee19d0fe7b5479906f927d358a61957ce27e10'] diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.12.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/x/xarray/xarray-0.12.1-intel-2018b-Python-3.6.6.eb index 5411f6e6d09..a068e32408f 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.12.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.12.1-intel-2018b-Python-3.6.6.eb @@ -11,7 +11,6 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ac09a819e791be208ae33fa7ecee19d0fe7b5479906f927d358a61957ce27e10'] diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.13.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/x/xarray/xarray-0.13.0-intel-2019a-Python-3.7.2.eb index 336be934588..61b6d7cba93 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.13.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.13.0-intel-2019a-Python-3.7.2.eb @@ -11,7 +11,6 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['80e5746ffdebb96b997dba0430ff02d98028ef3828e6db6106cbbd6d62e32825'] diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.15.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/x/xarray/xarray-0.15.1-foss-2019b-Python-3.7.4.eb index da26a94c8b9..dd90e1e414a 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.15.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.15.1-foss-2019b-Python-3.7.4.eb @@ -11,7 +11,6 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['64e3138d87b641e22fe7a003c94abc685896b247b63e434505c1e6b38c91a8fb'] diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.15.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/x/xarray/xarray-0.15.1-intel-2019b-Python-3.7.4.eb index 3fab1bea5b8..f632a7030b7 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.15.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.15.1-intel-2019b-Python-3.7.4.eb @@ -11,7 +11,6 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2019b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['64e3138d87b641e22fe7a003c94abc685896b247b63e434505c1e6b38c91a8fb'] diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-2.7.13.eb index 10d17b9e1ff..87c912ffa21 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-2.7.13.eb @@ -11,14 +11,8 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '2.7.13')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb index aba02b5499c..aff0f83d248 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb @@ -11,14 +11,8 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('Python', '3.6.1')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/x/xarray/xarray-0.9.6-intel-2017a-Python-2.7.13.eb index d49636fa5c5..5d8b8974846 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.9.6-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.9.6-intel-2017a-Python-2.7.13.eb @@ -11,15 +11,9 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f649a41d43b5a6c64bdcbd57e994932656b689f9593a86dd0be95778a2b47494'] dependencies = [('Python', '2.7.13')] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xonsh/xonsh-0.3.2-intel-2016a.eb b/easybuild/easyconfigs/x/xonsh/xonsh-0.3.2-intel-2016a.eb index 929f6e1b155..0ecfbdcb40d 100644 --- a/easybuild/easyconfigs/x/xonsh/xonsh-0.3.2-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xonsh/xonsh-0.3.2-intel-2016a.eb @@ -1,40 +1,26 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'xonsh' version = '0.3.2' -homepage = 'http://xon.sh/' +homepage = 'https://xon.sh/' description = """Xonsh is a Python-ish, BASHwards-looking shell language and command prompt.""" toolchain = {'name': 'intel', 'version': '2016a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - dependencies = [('Python', '3.5.1')] exts_list = [ - ('ply', '3.8', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ply/'], - }), - ('wcwidth', '0.1.6', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], - }), + ('ply', '3.8'), + ('wcwidth', '0.1.6'), ('prompt-toolkit', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt-toolkit/'], 'source_tmpl': 'prompt_toolkit-%(version)s.tar.gz', 'modulename': 'prompt_toolkit', }), - ('Pygments', '2.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/x/xonsh/'], - }), + ('Pygments', '2.1.3'), + (name, version), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/xonsh'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..734dff0fa72 --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.5' + +homepage = "https://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://ftp.x.org/archive/individual/app/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b7bf6b6be6cf23e7966a153fc84d5901c14f01ee952fbd9d930aa48e2385d670'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210518'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-8.3.0.eb index 0b940765ef6..6cff5283e8f 100644 --- a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-8.3.0.eb @@ -13,7 +13,6 @@ of a convolutional neural network.""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.11-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d5a8fe3c3ac --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.8.11-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Z3' +version = '4.8.11' + +homepage = 'https://github.com/Z3Prover/z3' +description = """ + Z3 is a theorem prover from Microsoft Research. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/Z3Prover/z3/archive/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['99e912b9af76a17f8827f89afcf4da117736f3877a8bbdd737c548c6541009d7'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = '-DZ3_USE_LIB_GMP=ON -DZ3_LINK_TIME_OPTIMIZATION=ON ' + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..37cef2c3bb4 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.4' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.36'), +] + +configopts = '--with-pic --with-pgm --with-libsodium ' + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.1.4-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/z/zarr/zarr-2.1.4-foss-2017a-Python-2.7.13.eb index b5c64ad1505..d107160cc98 100644 --- a/easybuild/easyconfigs/z/zarr/zarr-2.1.4-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/z/zarr/zarr-2.1.4-foss-2017a-Python-2.7.13.eb @@ -1,17 +1,15 @@ -easyblock = "Bundle" +easyblock = "PythonBundle" name = 'zarr' version = '2.1.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://zarr.readthedocs.io/en/stable/' +homepage = 'https://zarr.readthedocs.io/en/stable/' description = """Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing.""" toolchain = {'name': 'foss', 'version': '2017a'} -exts_defaultclass = 'PythonPackage' - dependencies = [ ('Python', '2.7.13'), ] @@ -19,30 +17,19 @@ dependencies = [ exts_list = [ ('asciitree', '0.3.3', { 'source_tmpl': 'asciitree-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/A/asciitree/'], 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], }), ('fasteners', '0.14.1', { 'source_tmpl': 'fasteners-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/F/fasteners/'], 'checksums': ['427c76773fe036ddfa41e57d89086ea03111bbac57c55fc55f3006d027107e18'], }), ('numcodecs', '0.5.3', { 'source_tmpl': 'numcodecs-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/N/numcodecs/'], 'checksums': ['6f62f9225919b2cc951c7fe7fdeb616e46ebeda4623481602218df0759814acf'], }), (name, version, { - 'source_urls': [PYPI_SOURCE], 'checksums': ['2eb998752184a5f4976d65e643678bf866094220285ab51a926aa2ce9fc630a3'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb new file mode 100644 index 00000000000..6c89bf42f36 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '8.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.32', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb new file mode 100644 index 00000000000..670d5940075 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '9.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [ + ('binutils', '2.36.1', '', True), +] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/%(name)s.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/setup.py b/setup.py index 375c1c355b1..5947b9e5a02 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.4.0' +VERSION = '4.4.1' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f0fad481ac4..4a937e0793d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -34,7 +34,7 @@ import sys import tempfile from distutils.version import LooseVersion -from unittest import TestCase, TestLoader, main +from unittest import TestCase, TestLoader, main, skip import easybuild.main as eb_main import easybuild.tools.options as eboptions @@ -68,65 +68,209 @@ single_tests_ok = True +def is_pr(): + """Return true if run in a pull request CI""" + # $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR + travis_pr_test = re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST', '')) + + # when testing a PR in GitHub Actions, $GITHUB_EVENT_NAME will be set to 'pull_request' + github_pr_test = os.environ.get('GITHUB_EVENT_NAME') == 'pull_request' + return travis_pr_test or github_pr_test + + +def get_target_branch(): + """Return the target branch of a pull request""" + # target branch should be anything other than 'master'; + # usually is 'develop', but could also be a release branch like '3.7.x' + target_branch = os.environ.get('GITHUB_BASE_REF', None) + if not target_branch: + target_branch = os.environ.get('TRAVIS_BRANCH', None) + if not target_branch: + raise RuntimeError("Did not find a target branch") + return target_branch + + +def skip_if_not_pr_to_non_main_branch(): + if not is_pr(): + return skip("Only run for pull requests") + if get_target_branch() == "main": + return skip("Not run for pull requests against main") + return lambda func: func + + +def get_eb_files_from_diff(diff_filter): + """Return the files changed on HEAD relative to the current target branch""" + target_branch = get_target_branch() + + # relocate to top-level directory of repository to run 'git diff' command + top_dir = os.path.dirname(os.path.dirname(get_paths_for('easyconfigs')[0])) + cwd = change_dir(top_dir) + + # first determine the 'merge base' between target branch and PR branch + # cfr. https://git-scm.com/docs/git-merge-base + cmd = "git merge-base %s HEAD" % target_branch + out, ec = run_cmd(cmd, simple=False, log_ok=False) + if ec == 0: + merge_base = out.strip() + print("Merge base for %s and HEAD: %s" % (target_branch, merge_base)) + else: + msg = "Failed to determine merge base (ec: %s, output: '%s'), " + msg += "falling back to specifying target branch %s" + print(msg % (ec, out, target_branch)) + merge_base = target_branch + + # determine list of changed files using 'git diff' and merge base determined above + cmd = "git diff --name-only --diff-filter=%s %s..HEAD --" % (diff_filter, merge_base) + out, _ = run_cmd(cmd, simple=False) + files = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith('.eb')] + + change_dir(cwd) + return files + + class EasyConfigTest(TestCase): """Baseclass for easyconfig testcases.""" - # make sure that the EasyBuild installation is still known even if we purge an EB module - if os.getenv('EB_SCRIPT_PATH') is None: - eb_path = which('eb') - if eb_path is not None: - os.environ['EB_SCRIPT_PATH'] = eb_path - - # initialize configuration (required for e.g. default modules_tool setting) - eb_go = eboptions.parse_options() - config.init(eb_go.options, eb_go.get_options_by_section('config')) - build_options = { - 'check_osdeps': False, - 'external_modules_metadata': {}, - 'force': True, - 'local_var_naming_check': 'error', - 'optarch': 'test', - 'robot_path': get_paths_for("easyconfigs")[0], - 'silent': True, - 'suffix_modules_path': GENERAL_CLASS, - 'valid_module_classes': config.module_classes(), - 'valid_stops': [x[0] for x in EasyBlock.get_steps()], - } - config.init_build_options(build_options=build_options) - set_tmpdir() - del eb_go + @classmethod + def setUpClass(cls): + """Setup environment for all tests. Called once!""" + # make sure that the EasyBuild installation is still known even if we purge an EB module + if os.getenv('EB_SCRIPT_PATH') is None: + eb_path = which('eb') + if eb_path is not None: + os.environ['EB_SCRIPT_PATH'] = eb_path + + # initialize configuration (required for e.g. default modules_tool setting) + eb_go = eboptions.parse_options(args=[]) # Ignore cmdline args as those are meant for the unittest framework + config.init(eb_go.options, eb_go.get_options_by_section('config')) + build_options = { + 'check_osdeps': False, + 'external_modules_metadata': {}, + 'force': True, + 'local_var_naming_check': 'error', + 'optarch': 'test', + 'robot_path': get_paths_for("easyconfigs")[0], + 'silent': True, + 'suffix_modules_path': GENERAL_CLASS, + 'valid_module_classes': config.module_classes(), + 'valid_stops': [x[0] for x in EasyBlock.get_steps()], + } + config.init_build_options(build_options=build_options) + set_tmpdir() - # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains - TMPDIR = tempfile.mkdtemp() - os.environ['MODULEPATH'] = TMPDIR - write_file(os.path.join(TMPDIR, 'craype-test'), '#%Module\n') + # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains + cls.TMPDIR = tempfile.mkdtemp() + os.environ['MODULEPATH'] = cls.TMPDIR + write_file(os.path.join(cls.TMPDIR, 'craype-test'), '#%Module\n') - log = fancylogger.getLogger("EasyConfigTest", fname=False) + log = fancylogger.getLogger("EasyConfigTest", fname=False) - # make sure a logger is present for main - eb_main._log = log - ordered_specs = None - parsed_easyconfigs = [] + # make sure a logger is present for main + eb_main._log = log - def process_all_easyconfigs(self): - """Process all easyconfigs and resolve inter-easyconfig dependencies.""" + cls._ordered_specs = None + cls._parsed_easyconfigs = [] + cls._parsed_all_easyconfigs = False + cls._changed_ecs = None # ECs changed in a PR + + @classmethod + def tearDownClass(cls): + """Cleanup after running all tests""" + shutil.rmtree(cls.TMPDIR) + + @classmethod + def parse_all_easyconfigs(cls): + """Parse all easyconfigs.""" + if cls._parsed_all_easyconfigs: + return # all available easyconfig files easyconfigs_path = get_paths_for("easyconfigs")[0] specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) - - # parse all easyconfigs if they haven't been already - if not EasyConfigTest.parsed_easyconfigs: - for spec in specs: - EasyConfigTest.parsed_easyconfigs.extend(process_easyconfig(spec)) - + parsed_specs = set(ec['spec'] for ec in cls._parsed_easyconfigs) + for spec in specs: + if spec not in parsed_specs: + cls._parsed_easyconfigs.extend(process_easyconfig(spec)) + cls._parsed_all_easyconfigs = True + + @classmethod + def resolve_all_dependencies(cls): + """Resolve dependencies between easyconfigs""" + # Parse all easyconfigs if not done yet + cls.parse_all_easyconfigs() # filter out external modules - for ec in EasyConfigTest.parsed_easyconfigs: + for ec in cls._parsed_easyconfigs: for dep in ec['dependencies'][:]: if dep.get('external_module', False): ec['dependencies'].remove(dep) + cls._ordered_specs = resolve_dependencies( + cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True) + + def _get_changed_easyconfigs(self): + """Gather all added or modified easyconfigs""" + # get list of changed easyconfigs + changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M') + added_ecs_filenames = get_eb_files_from_diff(diff_filter='A') + if changed_ecs_filenames: + print("\nList of changed easyconfig files in this PR:\n\t%s" % '\n\t'.join(changed_ecs_filenames)) + if added_ecs_filenames: + print("\nList of added easyconfig files in this PR:\n\t%s" % '\n\t'.join(added_ecs_filenames)) + EasyConfigTest._changed_ecs_filenames = changed_ecs_filenames + EasyConfigTest._added_ecs_filenames = added_ecs_filenames + + # grab parsed easyconfigs for changed easyconfig files + changed_ecs = [] + for ec_fn in changed_ecs_filenames + added_ecs_filenames: + match = None + for ec in self.parsed_easyconfigs: + if os.path.basename(ec['spec']) == ec_fn: + match = ec['ec'] + break - EasyConfigTest.ordered_specs = resolve_dependencies( - EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True) + if match: + changed_ecs.append(match) + else: + # if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR... + # so as a last resort, try to find the easyconfig file in __archive__ + easyconfigs_path = get_paths_for("easyconfigs")[0] + specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn)) + if len(specs) == 1: + ec = process_easyconfig(specs[0])[0] + changed_ecs.append(ec['ec']) + else: + raise RuntimeError("Failed to find parsed easyconfig for %s" + " (and could not isolate it in easyconfigs archive either)" % ec_fn) + EasyConfigTest._changed_ecs = changed_ecs + + @property + def parsed_easyconfigs(self): + # parse all easyconfigs if they haven't been already + EasyConfigTest.parse_all_easyconfigs() + return EasyConfigTest._parsed_easyconfigs + + @property + def ordered_specs(self): + # Resolve dependencies if not done + if EasyConfigTest._ordered_specs is None: + EasyConfigTest.resolve_all_dependencies() + return EasyConfigTest._ordered_specs + + @property + def changed_ecs_filenames(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._changed_ecs_filenames + + @property + def added_ecs_filenames(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._added_ecs_filenames + + @property + def changed_ecs(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._changed_ecs def test_dep_graph(self): """Unit test that builds a full dependency graph.""" @@ -136,10 +280,7 @@ def test_dep_graph(self): (hn, fn) = tempfile.mkstemp(suffix='.dot') os.close(hn) - if EasyConfigTest.ordered_specs is None: - self.process_all_easyconfigs() - - dep_graph(fn, EasyConfigTest.ordered_specs) + dep_graph(fn, self.ordered_specs) remove_file(fn) else: @@ -152,10 +293,7 @@ def test_conflicts(self): print("(skipped conflicts test)") return - if EasyConfigTest.ordered_specs is None: - self.process_all_easyconfigs() - - self.assertFalse(check_conflicts(EasyConfigTest.ordered_specs, modules_tool(), check_inter_ec_conflicts=False), + self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False), "No conflicts detected") def check_dep_vars(self, gen, dep, dep_vars): @@ -212,6 +350,12 @@ def check_dep_vars(self, gen, dep, dep_vars): if all(ec.startswith('Boost.Python-%s-' % boost_ver) for ec in ecs): dep_vars.pop(key) + # filter out Perl with -minimal versionsuffix which are only used in makeinfo-minimal + if dep == 'Perl': + minimal_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -minimal')] + if len(minimal_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != minimal_vsuff_vars[0]) + # filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains if dep in ['FFTW', 'imkl']: serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] @@ -315,11 +459,13 @@ def check_dep_vars(self, gen, dep, dep_vars): # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 ('2.2.0;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'Horovod-0.19.5-', 'decona-0.1.2-', 'NGSpeciesID-0.1.1.1-']), + # medaka 1.4.3 depends on TensorFlow 2.2.2 + ('2.2.2;', ['medaka-1.4.3-']), ], - # medaka 1.1.* and 1.2.* requires Pysam 0.16.0.1, + # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 - 'Pysam': [('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'decona-0.1.2-', + 'Pysam': [('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', 'NGSpeciesID-0.1.1.1-'])], } if dep in old_dep_versions and len(dep_vars) > 1: @@ -537,11 +683,8 @@ def test_dep_versions_per_toolchain_generation(self): This is enforced to try and limit the chance of running into conflicts when multiple modules built with the same toolchain are loaded together. """ - if EasyConfigTest.ordered_specs is None: - self.process_all_easyconfigs() - - ecs_by_full_mod_name = dict((ec['full_mod_name'], ec) for ec in EasyConfigTest.parsed_easyconfigs) - if len(ecs_by_full_mod_name) != len(EasyConfigTest.parsed_easyconfigs): + ecs_by_full_mod_name = dict((ec['full_mod_name'], ec) for ec in self.parsed_easyconfigs) + if len(ecs_by_full_mod_name) != len(self.parsed_easyconfigs): self.fail('Easyconfigs with duplicate full_mod_name found') # Cache already determined dependencies @@ -569,12 +712,12 @@ def get_deps_for(ec): # restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a) # and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x - for pattern in ['201[89][ab]', '20[2-9][0-9][ab]', r'GCCcore-[7-9]\.[0-9]']: + for pattern in ['20(1[89]|[2-9][0-9])[ab]', r'GCCcore-([7-9]|[1-9][0-9])\.[0-9]']: all_deps = {} regex = re.compile(r'^.*-(?P%s).*\.eb$' % pattern) # collect variants for all dependencies of easyconfigs that use a toolchain that matches - for ec in EasyConfigTest.ordered_specs: + for ec in self.ordered_specs: ec_file = os.path.basename(ec['spec']) # take into account software which also follows a {a,b} versioning scheme @@ -609,10 +752,7 @@ def get_deps_for(ec): def test_sanity_check_paths(self): """Make sure specified sanity check paths adher to the requirements.""" - if not EasyConfigTest.parsed_easyconfigs: - self.process_all_easyconfigs() - - for ec in EasyConfigTest.parsed_easyconfigs: + for ec in self.parsed_easyconfigs: ec_scp = ec['ec']['sanity_check_paths'] if ec_scp != {}: # if sanity_check_paths is specified (i.e., non-default), it must adher to the requirements @@ -627,11 +767,8 @@ def test_r_libs_site_env_var(self): """Make sure $R_LIBS_SITE is being updated, rather than $R_LIBS.""" # cfr. https://github.com/easybuilders/easybuild-easyblocks/pull/2326 - if not EasyConfigTest.parsed_easyconfigs: - self.process_all_easyconfigs() - r_libs_ecs = [] - for ec in EasyConfigTest.parsed_easyconfigs: + for ec in self.parsed_easyconfigs: for key in ('modextrapaths', 'modextravars'): if 'R_LIBS' in ec['ec'][key]: r_libs_ecs.append(ec['spec']) @@ -656,7 +793,8 @@ def test_easyconfig_locations(self): if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) - def check_sha256_checksums(self, changed_ecs): + @skip_if_not_pr_to_non_main_branch() + def test_pr_sha256_checksums(self): """Make sure changed easyconfigs have SHA256 checksums in place.""" # list of software for which checksums can not be required, @@ -676,7 +814,7 @@ def check_sha256_checksums(self, changed_ecs): # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__; # therefore, we need to reset 'sources' to an empty list here if Bundle is used... # likewise for 'patches' and 'checksums' - for ec in changed_ecs: + for ec in self.changed_ecs: if ec['easyblock'] in ['Bundle', 'PythonBundle', 'EB_OpenSSL_wrapper']: ec['sources'] = [] ec['patches'] = [] @@ -684,14 +822,15 @@ def check_sha256_checksums(self, changed_ecs): # filter out deprecated easyconfigs retained_changed_ecs = [] - for ec in changed_ecs: + for ec in self.changed_ecs: if not ec['deprecated']: retained_changed_ecs.append(ec) checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) - def check_python_packages(self, changed_ecs, added_ecs_filenames): + @skip_if_not_pr_to_non_main_branch() + def test_pr_python_packages(self): """Several checks for easyconfigs that install (bundles of) Python packages.""" # These packages do not support installation with 'pip' @@ -706,13 +845,15 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): r'Mako-1.0.4.*Python-2.7.12.*', # no pip 9.x or newer for configparser easyconfigs using a 2016a or 2016b toolchain r'configparser-3.5.0.*-2016[ab].*', + # mympirun is installed with system Python, pip may not be installed for system Python + r'vsc-mympirun.*', ] failing_checks = [] python_default_urls = PythonPackage.extra_options()['source_urls'][0] - for ec in changed_ecs: + for ec in self.changed_ecs: with ec.disable_templating(): ec_fn = os.path.basename(ec.path) @@ -782,7 +923,7 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn # This is only a failure for newly added ECs, not for existing ECS # As that would probably break many ECs - if ec_fn in added_ecs_filenames: + if ec_fn in self.added_ecs_filenames: failing_checks.append(msg) else: print('\nNote: Failed non-critical check: ' + msg) @@ -802,11 +943,12 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): if failing_checks: self.fail('\n'.join(failing_checks)) - def check_R_packages(self, changed_ecs): + @skip_if_not_pr_to_non_main_branch() + def test_pr_R_packages(self): """Several checks for easyconfigs that install (bundles of) R packages.""" failing_checks = [] - for ec in changed_ecs: + for ec in self.changed_ecs: ec_fn = os.path.basename(ec.path) exts_defaultclass = ec.get('exts_defaultclass') if exts_defaultclass == 'RPackage' or ec.name == 'R': @@ -822,7 +964,8 @@ def check_R_packages(self, changed_ecs): seen_exts.add(ext_name) self.assertFalse(failing_checks, '\n'.join(failing_checks)) - def check_sanity_check_paths(self, changed_ecs): + @skip_if_not_pr_to_non_main_branch() + def test_pr_sanity_check_paths(self): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # some generic easyblocks already have a decent customised sanity_check_paths, @@ -832,12 +975,12 @@ def check_sanity_check_paths(self, changed_ecs): 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, - # CESM-deps: Python + Perl + netCDF + ESMF + git - bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC'] + # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co + bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS'] failing_checks = [] - for ec in changed_ecs: + for ec in self.changed_ecs: easyblock = ec.get('easyblock') @@ -850,7 +993,8 @@ def check_sanity_check_paths(self, changed_ecs): self.assertFalse(failing_checks, '\n'.join(failing_checks)) - def check_https(self, changed_ecs): + @skip_if_not_pr_to_non_main_branch() + def test_pr_https(self): """Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://).""" whitelist = [ @@ -872,11 +1016,25 @@ def check_https(self, changed_ecs): # https:// has outdated SSL configurations 'http://faculty.scs.illinois.edu', ] + # Cache: Mapping of already checked HTTP urls to whether the HTTPS variant works + checked_urls = dict() + + def check_https_url(http_url): + """Check if the https url works""" + http_url = http_url.rstrip('/') # Remove trailing slashes + https_url_works = checked_urls.get(http_url) + if https_url_works is None: + https_url = http_url.replace('http://', 'https://') + try: + https_url_works = bool(urlopen(https_url, timeout=5)) + except Exception: + https_url_works = False + checked_urls[http_url] = https_url_works http_regex = re.compile('http://[^"\'\n]+', re.M) failing_checks = [] - for ec in changed_ecs: + for ec in self.changed_ecs: ec_fn = os.path.basename(ec.path) # skip whitelisted easyconfigs @@ -892,111 +1050,11 @@ def check_https(self, changed_ecs): if any(http_url.startswith(x) for x in url_whitelist): continue - https_url = http_url.replace('http://', 'https://') - try: - https_url_works = bool(urlopen(https_url, timeout=5)) - except Exception: - https_url_works = False - - if https_url_works: + if check_https_url(http_url): failing_checks.append("Found http:// URL in %s, should be https:// : %s" % (ec_fn, http_url)) if failing_checks: self.fail('\n'.join(failing_checks)) - def test_changed_files_pull_request(self): - """Specific checks only done for the (easyconfig) files that were changed in a pull request.""" - def get_eb_files_from_diff(diff_filter): - - # first determine the 'merge base' between target branch and PR branch - # cfr. https://git-scm.com/docs/git-merge-base - cmd = "git merge-base %s HEAD" % target_branch - out, ec = run_cmd(cmd, simple=False, log_ok=False) - if ec == 0: - merge_base = out.strip() - print("Merge base for %s and HEAD: %s" % (target_branch, merge_base)) - else: - msg = "Failed to determine merge base (ec: %s, output: '%s'), " - msg += "falling back to specifying target branch %s" - print(msg % (ec, out, target_branch)) - merge_base = target_branch - - # determine list of changed files using 'git diff' and merge base determined above - cmd = "git diff --name-only --diff-filter=%s %s..HEAD --" % (diff_filter, merge_base) - out, _ = run_cmd(cmd, simple=False) - return [os.path.basename(f) for f in out.strip().split('\n') if f.endswith('.eb')] - - # $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR - travis_pr_test = re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST', '(none)')) - - # when testing a PR in GitHub Actions, $GITHUB_EVENT_NAME will be set to 'pull_request' - github_pr_test = os.environ.get('GITHUB_EVENT_NAME') == 'pull_request' - - if travis_pr_test or github_pr_test: - - # target branch should be anything other than 'master'; - # usually is 'develop', but could also be a release branch like '3.7.x' - if travis_pr_test: - target_branch = os.environ.get('TRAVIS_BRANCH', None) - else: - target_branch = os.environ.get('GITHUB_BASE_REF', None) - - if target_branch is None: - self.assertTrue(False, "Failed to determine target branch for current pull request.") - - if target_branch != 'main': - - if not EasyConfigTest.parsed_easyconfigs: - self.process_all_easyconfigs() - - # relocate to top-level directory of repository to run 'git diff' command - top_dir = os.path.dirname(os.path.dirname(get_paths_for('easyconfigs')[0])) - cwd = change_dir(top_dir) - - # get list of changed easyconfigs - changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M') - added_ecs_filenames = get_eb_files_from_diff(diff_filter='A') - if changed_ecs_filenames: - print("\nList of changed easyconfig files in this PR:\n\t%s" % '\n\t'.join(changed_ecs_filenames)) - if added_ecs_filenames: - print("\nList of added easyconfig files in this PR:\n\t%s" % '\n\t'.join(added_ecs_filenames)) - - change_dir(cwd) - - # grab parsed easyconfigs for changed easyconfig files - changed_ecs = [] - for ec_fn in changed_ecs_filenames + added_ecs_filenames: - match = None - for ec in EasyConfigTest.parsed_easyconfigs: - if os.path.basename(ec['spec']) == ec_fn: - match = ec['ec'] - break - - if match: - changed_ecs.append(match) - else: - # if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR... - # so as a last resort, try to find the easyconfig file in __archive__ - easyconfigs_path = get_paths_for("easyconfigs")[0] - specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn)) - if len(specs) == 1: - ec = process_easyconfig(specs[0])[0] - changed_ecs.append(ec['ec']) - else: - error_msg = "Failed to find parsed easyconfig for %s" % ec_fn - error_msg += " (and could not isolate it in easyconfigs archive either)" - self.assertTrue(False, error_msg) - - # run checks on changed easyconfigs - self.check_sha256_checksums(changed_ecs) - self.check_python_packages(changed_ecs, added_ecs_filenames) - self.check_R_packages(changed_ecs) - self.check_sanity_check_paths(changed_ecs) - self.check_https(changed_ecs) - - def test_zzz_cleanup(self): - """Dummy test to clean up global temporary directory.""" - shutil.rmtree(self.TMPDIR) - def template_easyconfig_test(self, spec): """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" @@ -1012,7 +1070,7 @@ def template_easyconfig_test(self, spec): ec = ecs[0]['ec'] # cache the parsed easyconfig, to avoid that it is parsed again - EasyConfigTest.parsed_easyconfigs.append(ecs[0]) + EasyConfigTest._parsed_easyconfigs.append(ecs[0]) else: self.assertTrue(False, "easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) @@ -1109,8 +1167,30 @@ def template_easyconfig_test(self, spec): if requires_binutils: # dependencies() returns both build and runtime dependencies # in some cases, binutils can also be a runtime dep (e.g. for Clang) + # Also using GCC directly as a build dep is also allowed (it includes the correct binutils) dep_names = [d['name'] for d in ec.dependencies()] - self.assertTrue('binutils' in dep_names, "binutils is a build dep in %s: %s" % (spec, dep_names)) + self.assertTrue('binutils' in dep_names or 'GCC' in dep_names, + "binutils or GCC is a build dep in %s: %s" % (spec, dep_names)) + + # make sure that OpenSSL wrapper is used rather than OS dependency, + # for easyconfigs using a 2021a (sub)toolchain or more recent common toolchain version + osdeps = ec['osdependencies'] + if osdeps: + # check whether any entry in osdependencies related to OpenSSL + openssl_osdep = False + for osdep in osdeps: + if isinstance(osdep, string_type): + osdep = [osdep] + if any('libssl' in x for x in osdep) or any('openssl' in x for x in osdep): + openssl_osdep = True + + if openssl_osdep: + tcname = ec['toolchain']['name'] + tcver = LooseVersion(ec['toolchain']['version']) + + gcc_subtc_2021a = tcname in ('GCCcore', 'GCC') and tcver > LooseVersion('10.3') + if gcc_subtc_2021a or (tcname in ('foss', 'gompi', 'iimpi', 'intel') and tcver >= LooseVersion('2021')): + self.assertFalse(openssl_osdep, "OpenSSL should not be listed as OS dependency in %s" % spec) src_cnt = len(ec['sources']) patch_checksums = ec['checksums'][src_cnt:] @@ -1248,7 +1328,7 @@ def template_easyconfig_test(self, spec): single_tests_ok = True and prev_single_tests_ok -def suite(): +def suite(loader=None): """Return all easyblock initialisation tests.""" def make_inner_test(spec_path): def innertest(self): @@ -1259,11 +1339,11 @@ def innertest(self): # define new inner functions that can be added as class methods to InitTest easyconfigs_path = get_paths_for('easyconfigs')[0] cnt = 0 - for (subpath, _, specs) in os.walk(easyconfigs_path, topdown=True): + for (subpath, dirs, specs) in os.walk(easyconfigs_path, topdown=True): # ignore archived easyconfigs - if '__archive__' in subpath: - continue + if '__archive__' in dirs: + dirs.remove('__archive__') for spec in specs: if spec.endswith('.eb') and spec != 'TEMPLATE.eb': @@ -1275,7 +1355,9 @@ def innertest(self): setattr(EasyConfigTest, innertest.__name__, innertest) print("Found %s easyconfigs..." % cnt) - return TestLoader().loadTestsFromTestCase(EasyConfigTest) + if not loader: + loader = TestLoader() + return loader.loadTestsFromTestCase(EasyConfigTest) if __name__ == '__main__': diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index 5664050d22e..ec27d234b46 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -57,9 +57,11 @@ def test_style_conformance(self): self.assertEqual(result, 0, "Found code style errors (and/or warnings): %s" % result) -def suite(): +def suite(loader=None): """Return all style tests for easyconfigs.""" - return TestLoader().loadTestsFromTestCase(StyleTest) + if not loader: + loader = TestLoader() + return loader.loadTestsFromTestCase(StyleTest) if __name__ == '__main__': diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 9571d7ccdaf..3d204108c36 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -32,9 +32,9 @@ """ import os import shutil -import sys import tempfile import unittest +from unittest import main import easybuild.tools.build_log # noqa initialize EasyBuild logging, so we can disable it import test.easyconfigs.easyconfigs as e @@ -46,17 +46,24 @@ fancylogger.setLogLevelError() # make sure no deprecated behaviour is triggered -os.environ['EASYBUILD_DEPRECATED'] = '10000' +# os.environ['EASYBUILD_DEPRECATED'] = '10000' -os.environ['EASYBUILD_TMP_LOGDIR'] = tempfile.mkdtemp(prefix='easyconfigs_test_') -# call suite() for each module and then run them all -SUITE = unittest.TestSuite([x.suite() for x in [e, s]]) -res = unittest.TextTestRunner().run(SUITE) +class EasyConfigsTestSuite(unittest.TestSuite): + def __init__(self, loader): + # call suite() for each module and then run them all + super(EasyConfigsTestSuite, self).__init__([x.suite(loader) for x in [e, s]]) -shutil.rmtree(os.environ['EASYBUILD_TMP_LOGDIR']) -del os.environ['EASYBUILD_TMP_LOGDIR'] + def run(self, *args, **kwargs): + os.environ['EASYBUILD_TMP_LOGDIR'] = tempfile.mkdtemp(prefix='easyconfigs_test_') + super(EasyConfigsTestSuite, self).run(*args, **kwargs) + shutil.rmtree(os.environ['EASYBUILD_TMP_LOGDIR']) + del os.environ['EASYBUILD_TMP_LOGDIR'] -if not res.wasSuccessful(): - sys.stderr.write("ERROR: Not all tests were successful.\n") - sys.exit(2) + +def load_tests(loader, tests, pattern): + return EasyConfigsTestSuite(loader) + + +if __name__ == '__main__': + main()