From 8bc277debe4394a8132680b6bac4f70c2d5934dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Apr 2024 20:37:39 +0200 Subject: [PATCH 001/414] adding easyconfigs: ABAQUS-2024-hotfix-2405.eb --- .../a/ABAQUS/ABAQUS-2024-hotfix-2405.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABAQUS/ABAQUS-2024-hotfix-2405.eb diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2024-hotfix-2405.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2024-hotfix-2405.eb new file mode 100644 index 00000000000..c40a1f45068 --- /dev/null +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2024-hotfix-2405.eb @@ -0,0 +1,33 @@ +name = 'ABAQUS' +version = '2024' +local_hotfix = '2405' +versionsuffix = '-hotfix-%s' % local_hotfix + +homepage = 'https://www.simulia.com/products/abaqus_fea.html' +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" + +toolchain = SYSTEM + +sources = [ + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-6.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-6.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-6.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-6.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-6.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.6-6.tar', + # hotfixes + '%%(version)s.FP.CFA.%s.Part_SIMULIA_EstPrd.Linux64.tar' % local_hotfix, +] +checksums = [ + {'2024.AM_SIM_Abaqus_Extend.AllOS.1-6.tar': 'a8fcd10541a90177aefe68f0dee2a675a56cb97e1fdf4fb7d864b41d594f8b19'}, + {'2024.AM_SIM_Abaqus_Extend.AllOS.2-6.tar': '6caffc60ee34351203ac4205b4fcdc7e9975842e35d3ce689b831f94929ddac4'}, + {'2024.AM_SIM_Abaqus_Extend.AllOS.3-6.tar': '3d3bc97c686af0c87c4b6e46ae330983ed515bcc180dd30a834811c458774347'}, + {'2024.AM_SIM_Abaqus_Extend.AllOS.4-6.tar': 'c62596bd99125475e97bdeccd71baaf7cb36322e8da4d0dd1e4029bac677be16'}, + {'2024.AM_SIM_Abaqus_Extend.AllOS.5-6.tar': 'ee3349b2407b5d8a315108656590f39890d82c47085235b847103e22fba96fea'}, + {'2024.AM_SIM_Abaqus_Extend.AllOS.6-6.tar': '482829b1c364966ae01a577233bddf6b377b8e3cd9b7f77dd95830d4636677d7'}, + {'2024.FP.CFA.2405.Part_SIMULIA_EstPrd.Linux64.tar': + '70231acf27506546174b896b6724f27a14673594b791eb62fb4c1e3b24ba1852'}, +] + +moduleclass = 'cae' From ff9ccd4cb6115a6cc7eef734ce580ffbe39997f6 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 25 Apr 2024 11:59:36 +0200 Subject: [PATCH 002/414] {phys}[iomkl/2022b] FDS 6.8.0 --- .../f/FDS/FDS-6.8.0-iomkl-2022b.eb | 44 +++++++++++++ .../f/FDS/FDS-6.8.0_intel_ompi.patch | 16 +++++ .../imkl-FFTW-2022.2.1-iompi-2022b.eb | 11 ++++ easybuild/easyconfigs/i/iomkl/iomkl-2022b.eb | 19 ++++++ easybuild/easyconfigs/i/iompi/iompi-2022b.eb | 18 +++++ .../OpenMPI-4.1.4-intel-compilers-2022.2.1.eb | 66 +++++++++++++++++++ .../OpenMPI/OpenMPI-4.1.4_intel_iso_c99.patch | 19 ++++++ 7 files changed, 193 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.8.0-iomkl-2022b.eb create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.8.0_intel_ompi.patch create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iompi-2022b.eb create mode 100755 easybuild/easyconfigs/i/iomkl/iomkl-2022b.eb create mode 100755 easybuild/easyconfigs/i/iompi/iompi-2022b.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-intel-compilers-2022.2.1.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_intel_iso_c99.patch diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.8.0-iomkl-2022b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.8.0-iomkl-2022b.eb new file mode 100644 index 00000000000..fb3b29dbf9c --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.8.0-iomkl-2022b.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.8.0' + +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': 'iomkl', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['FDS-%(version)s.tar.gz'] +patches = ['FDS-%(version)s_intel_ompi.patch'] +checksums = [ + {'FDS-6.8.0.tar.gz': 'd8213d706bb36300ca5fdc9a7884fa4610e2820338de23212dd19de75d8e0704'}, + {'FDS-6.8.0_intel_ompi.patch': '4c2cf6c72ed3e1e440d051a9018da05cb87b31512b74d1762d289aca461426b0'}, +] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +buildopts = 'impi_intel_linux_openmp &&' +buildopts += 'cd %(installdir)s/Build && ln -s fds_impi_intel_linux_openmp 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/FDS/FDS-6.8.0_intel_ompi.patch b/easybuild/easyconfigs/f/FDS/FDS-6.8.0_intel_ompi.patch new file mode 100644 index 00000000000..b2022787fc3 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.8.0_intel_ompi.patch @@ -0,0 +1,16 @@ +# Pacth for OpenMPI with iomkl toolchain +# April 25 2024 by B. Hajgato (UGent) +--- Build/makefile 2023-04-18 13:06:40.000000000 +0200 ++++ Build/makefile 2024-04-25 11:18:43.434666819 +0200 +@@ -231,9 +231,9 @@ + impi_intel_linux : setup $(obj_mpi) + $(FCOMPL) $(FFLAGS) -o $(obj) $(obj_mpi) $(LFLAGSMKL) + +-impi_intel_linux_openmp : FFLAGS = -m64 -fc=$(I_IFORT) -O2 -ipo -no-wrap-margin $(GITINFO) $(INTELMPI_COMPINFO) $(FFLAGSMKL_INTEL) -DUSE_IFPORT ++impi_intel_linux_openmp : FFLAGS = -m64 -fc=$(I_IFORT) -O2 -ipo -no-wrap-margin $(GITINFO) $(OPENMPI_COMPINFO) $(FFLAGSMKL_INTEL) -DUSE_IFPORT + impi_intel_linux_openmp : LFLAGSMKL = $(LFLAGSMKL_INTEL_OPENMP) +-impi_intel_linux_openmp : FCOMPL = mpiifort ++impi_intel_linux_openmp : FCOMPL = mpifort + impi_intel_linux_openmp : FOPENMPFLAGS = -qopenmp + impi_intel_linux_openmp : obj = fds_impi_intel_linux_openmp + impi_intel_linux_openmp : setup $(obj_mpi) diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iompi-2022b.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iompi-2022b.eb new file mode 100644 index 00000000000..7d7330b02f3 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iompi-2022b.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iompi', 'version': '2022b'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2022b.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2022b.eb new file mode 100755 index 00000000000..eeb317feb6a --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2022b.eb @@ -0,0 +1,19 @@ +easyblock = 'Toolchain' + +name = 'iomkl' +version = '2022b' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('OpenMPI', '4.1.4', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2022b.eb b/easybuild/easyconfigs/i/iompi/iompi-2022b.eb new file mode 100755 index 00000000000..ed2cf6f6a77 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2022b.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iompi' +version = '2022b' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('OpenMPI', '4.1.4', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..a3563b50808 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-intel-compilers-2022.2.1.eb @@ -0,0 +1,66 @@ +name = 'OpenMPI' +version = '4.1.4' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', + 'OpenMPI-4.1.4_intel_iso_c99.patch', +] +checksums = [ + {'openmpi-4.1.4.tar.bz2': '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d'}, + {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, + {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, + {'OpenMPI-4.1.4_intel_iso_c99.patch': 'b138ec15e43bbf83fb2c60884898135e952b66c7a0da9ec34a62a1a6ac53aec7'}, +] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('Perl', '5.36.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('hwloc', '2.8.0'), + ('libevent', '2.1.12'), + ('UCX', '1.13.1'), + ('libfabric', '1.16.1'), + ('PMIx', '4.2.2'), + ('UCC', '1.1.0'), +] + +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' + +# 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-4.1.4_intel_iso_c99.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_intel_iso_c99.patch new file mode 100644 index 00000000000..bc493ed963b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_intel_iso_c99.patch @@ -0,0 +1,19 @@ +# Compilation fails with: +#mtl_ofi_component.c:298:5: error: call to undeclared function 'mca_common_cuda_fini'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] +# mca_common_cuda_fini(); +# ^ +#1 error generated. +# Patch generated from OpenMPI version 4.1.5 +# April 25 2024 by B. Hajgato (UGent) +--- openmpi-4.1.4/ompi/mca/mtl/ofi/mtl_ofi_component.c 2022-05-26 16:32:35.000000000 +0200 ++++ openmpi-4.1.5/ompi/mca/mtl/ofi/mtl_ofi_component.c 2023-02-23 05:25:04.000000000 +0100 +@@ -294,9 +294,6 @@ + static int + ompi_mtl_ofi_component_close(void) + { +-#if OPAL_CUDA_SUPPORT +- mca_common_cuda_fini(); +-#endif + return opal_common_ofi_close(); + } + From c86e7423bb92d9a89d25db1f1a8997c466ed09d9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 25 Apr 2024 12:21:03 +0200 Subject: [PATCH 003/414] fix permissions --- easybuild/easyconfigs/i/iomkl/iomkl-2022b.eb | 0 easybuild/easyconfigs/i/iompi/iompi-2022b.eb | 0 2 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/i/iomkl/iomkl-2022b.eb mode change 100755 => 100644 easybuild/easyconfigs/i/iompi/iompi-2022b.eb diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2022b.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2022b.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/i/iompi/iompi-2022b.eb b/easybuild/easyconfigs/i/iompi/iompi-2022b.eb old mode 100755 new mode 100644 From 6884db5a48745bbd7ae9138db42c103ded06f387 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 16 Jun 2024 14:05:13 +0200 Subject: [PATCH 004/414] adding easyconfigs: gnuplot-6.0.1-GCCcore-13.2.0.eb --- .../g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..29e3f916718 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '6.0.1' + +homepage = 'http://gnuplot.sourceforge.net' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['e85a660c1a2a1808ff24f7e69981ffcbac66a45c9dcf711b65610b26ea71379a'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('cairo', '1.18.0'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('libgd', '2.3.3'), + ('Pango', '1.51.0'), + ('libcerf', '2.4'), + ('X11', '20231019'), + ('Qt6', '6.6.3'), + ('Lua', '5.4.6'), +] + +preconfigopts = 'autoreconf && ' + +# make sure that right Lua library is used (bypassing pkg-config) +preconfigopts += 'export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' + +configopts = '--with-qt=qt6 --without-latex --disable-wxwidgets' + +buildopts = 'LDFLAGS="$LDFLAGS -Wl,--copy-dt-needed-entries" ' +buildopts += 'LIBS="-lcerf -lcairo -lpangocairo-1.0"' + +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' From 4b2a6ca1d1dd19ab6fd28714addfa1de5aa335c6 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 18 Jun 2024 13:11:59 +0200 Subject: [PATCH 005/414] libcerf-2.4-GCCcore-13.2.0.eb --- .../l/libcerf/libcerf-2.4-GCCcore-13.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-2.4-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-2.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-2.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8f2bb266b13 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-2.4-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '2.4' + +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': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['080b30ae564c3dabe3b89264522adaf5647ec754021572bee54929697b276cdc'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('Perl', '5.38.0'), # required for pod2html +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From 7ab0505036df5d0f641f7809839cdd89df49e88c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 7 Aug 2024 12:58:47 +0200 Subject: [PATCH 006/414] adding easyconfigs: synthcity-0.2.10-foss-2022b.eb, DECAF-synthetic-data-0.1.6-foss-2022b.eb, PyTorch-Lightning-1.8.4-foss-2022b.eb, torchtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb, fastai-2.7.15-foss-2022b.eb, spaCy-3.7.4-foss-2022b.eb, Optuna-3.5.0-foss-2022b.eb, redis-py-5.0.1-GCCcore-12.2.0.eb, Redis-7.2.3-GCCcore-12.2.0.eb, lifelines-0.27.7-foss-2022b.eb, SHAP-0.43.0-foss-2022b.eb, XGBoost-1.7.2-foss-2022b.eb, imbalanced-learn-0.12.3-gfbf-2022b.eb, pycodestyle-2.11.1-foss-2022b.eb --- .../DECAF-synthetic-data-0.1.6-foss-2022b.eb | 42 +++ .../f/fastai/fastai-2.7.15-foss-2022b.eb | 42 +++ .../imbalanced-learn-0.12.3-gfbf-2022b.eb | 27 ++ .../lifelines/lifelines-0.27.7-foss-2022b.eb | 45 ++++ .../o/Optuna/Optuna-3.5.0-foss-2022b.eb | 50 ++++ .../PyTorch-Lightning-1.8.4-foss-2022b.eb | 121 +++++++++ .../pycodestyle-2.11.1-foss-2022b.eb | 22 ++ .../r/Redis/Redis-7.2.3-GCCcore-12.2.0.eb | 37 +++ .../redis-py/redis-py-5.0.1-GCCcore-12.2.0.eb | 33 +++ .../s/SHAP/SHAP-0.43.0-foss-2022b.eb | 37 +++ .../s/spaCy/spaCy-3.7.4-foss-2022b.eb | 81 ++++++ .../synthcity/synthcity-0.2.10-foss-2022b.eb | 239 ++++++++++++++++++ ...chtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb | 45 ++++ .../x/XGBoost/XGBoost-1.7.2-foss-2022b.eb | 29 +++ 14 files changed, 850 insertions(+) create mode 100644 easybuild/easyconfigs/d/DECAF-synthetic-data/DECAF-synthetic-data-0.1.6-foss-2022b.eb create mode 100644 easybuild/easyconfigs/f/fastai/fastai-2.7.15-foss-2022b.eb create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/l/lifelines/lifelines-0.27.7-foss-2022b.eb create mode 100644 easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2022b.eb create mode 100644 easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/d/DECAF-synthetic-data/DECAF-synthetic-data-0.1.6-foss-2022b.eb b/easybuild/easyconfigs/d/DECAF-synthetic-data/DECAF-synthetic-data-0.1.6-foss-2022b.eb new file mode 100644 index 00000000000..a46a26ae49d --- /dev/null +++ b/easybuild/easyconfigs/d/DECAF-synthetic-data/DECAF-synthetic-data-0.1.6-foss-2022b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'DECAF-synthetic-data' +version = '0.1.6' + +homepage = 'https://github.com/vanderschaarlab/DECAF' +description = """DEbiasing CAusal Fairness - +Generating Fair Synthetic Data Using Causally-Aware Generative Networks""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('PyTorch-Lightning', '1.8.4'), + ('PyTorch', '1.13.1'), + ('XGBoost', '1.7.2'), + ('scikit-learn', '1.2.1'), + ('torchtext', '0.14.1', '-PyTorch-1.13.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('networkx', '2.8.8', { + 'checksums': ['230d388117af870fce5647a3c52401fcf753e94720e6ea6b4197a5355648885e'], + }), + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + (name, version, { + 'modulename': 'decaf', + 'source_urls': ['https://github.com/vanderschaarlab/DECAF/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['8f34e99937d2ccc43bff97b310c371c450e27313c0801cdd36aa91664c8e3180'], + }), +] + +sanity_check_commands = ["python -c 'from decaf import DECAF, DataModule'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastai/fastai-2.7.15-foss-2022b.eb b/easybuild/easyconfigs/f/fastai/fastai-2.7.15-foss-2022b.eb new file mode 100644 index 00000000000..20e8dcdf96d --- /dev/null +++ b/easybuild/easyconfigs/f/fastai/fastai-2.7.15-foss-2022b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'fastai' +version = '2.7.15' + +homepage = 'https://www.fast.ai/' +description = """The fastai deep learning library.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +use_pip = True + +dependencies = [ + ('Python', '3.10.8'), + ('PyTorch', '1.13.1'), + ('matplotlib', '3.7.0'), + ('SciPy-bundle', '2023.02'), + ('PyYAML', '6.0'), + ('Pillow', '9.4.0'), + ('scikit-learn', '1.2.1'), + ('spaCy', '3.7.4'), + ('torchvision', '0.14.1'), +] + +exts_list = [ + ('fastdownload', '0.0.7', { + 'checksums': ['20507edb8e89406a1fbd7775e6e2a3d81a4dd633dd506b0e9cf0e1613e831d6a'], + }), + ('fastcore', '1.5.54', { + 'checksums': ['3f23dfadd77428be99558fdad66bf04c79a9c626e694c7404ede816ed8372987'], + }), + ('fastprogress', '1.0.3', { + 'checksums': ['7a17d2b438890f838c048eefce32c4ded47197ecc8ea042cecc33d3deb8022f5'], + }), + (name, version, { + 'checksums': ['f2cc20fd18cdf5ec738cc56d29d54de75887d48ad15f9d35cf50c38d3a856923'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2022b.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2022b.eb new file mode 100644 index 00000000000..10e219da604 --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'imbalanced-learn' +version = '0.12.3' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('scikit-learn', '1.2.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'imblearn', + 'checksums': ['5b00796a01419e9102bd425e27c319d58d1f6cf2dfa751e02ed7f4edf67c3c1b'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.27.7-foss-2022b.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.27.7-foss-2022b.eb new file mode 100644 index 00000000000..69b35bc787f --- /dev/null +++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.27.7-foss-2022b.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'lifelines' +version = '0.27.7' + +homepage = "https://lifelines.readthedocs.io/en/latest/" +description = """lifelines is a complete survival analysis library, written in pure Python.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('wrapt', '1.16.0', { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('interface_meta', '1.3.0', { + 'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'], + }), + ('autograd', '1.6.2', { + 'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'], + }), + ('autograd-gamma', '0.5.0', { + 'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'], + }), + ('formulaic', '1.0.1', { + 'checksums': ['64dd7992a7aa5bbceb1e40679d0f01fc6f0ba12b7d23d78094a88c2edc68fba1'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['44d60171f5abe85506b55cdf754b4ba769f61a5f8f18a9d05491009c6cee5803'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2022b.eb b/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2022b.eb new file mode 100644 index 00000000000..26185a5afe2 --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2022b.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '3.5.0' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2023.02'), + ('tqdm', '4.64.1'), + ('matplotlib', '3.7.0'), # optional + ('plotly.py', '5.13.1'), # optional + ('redis-py', '5.0.1'), # optional + ('scikit-learn', '1.2.1'), # optional + ('SQLAlchemy', '2.0.29'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cmaes', '0.10.0', { + 'checksums': ['48afc70df027114739872b50489ae6b32461c307b92d084a63c7090a9742faf9'], + }), + ('colorlog', '6.8.0', { + 'checksums': ['fbb6fdf9d5685f2517f388fb29bb27d54e8654dd31f58bc2a3b217e967a95ca6'], + }), + ('optuna', version, { + 'use_pip_extras': 'optional', + 'checksums': ['ca9e1ce16aa6c6a5af0e1cc1d0cbcd98eb1c75b6a2f06be6bd9c0c5ab0698724'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022b.eb new file mode 100644 index 00000000000..acec48e2187 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022b.eb @@ -0,0 +1,121 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.8.4' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + # dependencies from requirements/app/base.txt + ('aiohttp', '3.8.5'), + ('BeautifulSoup', '4.11.1'), + ('deepdiff', '6.7.1'), + # dependencies from requirements/pytorch/base.txt + ('PyTorch', '1.13.1'), + ('tqdm', '4.64.1'), + ('tensorboardX', '2.6.2.2'), +] + +use_pip = True + +# dependencies from requirements/app/base.txt and requirements/pytorch/base.txt +exts_list = [ + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.5.1', { + 'checksums': ['63a5c5ce3673d3d5fbbf23cd87e11ab84b6b451436f1b7f19ec54b6bc36ed7ca'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), + ('starlette', '0.19.1', { + 'checksums': ['c6d21096774ecb9639acad41b86b7706e52ba3bf1dc13ea4ed9ad593d47e24c7'], + }), + ('fastapi', '0.79.1', { + 'checksums': ['006862dec0f0f5683ac21fb0864af2ff12a931e7ba18920f28cc8eceed51896b'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + ('lightning_cloud', '0.5.12', { + 'checksums': ['5b0cf53ecfb512f9476eec3a7f425c0e174ca9d0e726673605d5e1e57074eb0c'], + }), + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('starsessions', '1.3.0', { + 'checksums': ['8d3b509d4e6d235655f7dd495fcf0afc1bd86da84de3a8d434e6f82137ebcde8'], + }), + ('fsspec', '2022.7.1', { + 'checksums': ['7f9fb19d811b027b97c4636c6073eb53bc4cbee2d3c4b33fa88b9f26906fd7d7'], + }), + ('croniter', '1.3.8', { + 'checksums': ['32a5ec04e97ec0837bcdf013767abd2e71cceeefd3c2e14c804098ce51ad6cd9'], + }), + ('traitlets', '5.2.0', { + 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('lightning-utilities', '0.4.2', { + 'checksums': ['dc6696ab180117f7e97b5488dac1d77765ab891022f7521a97a39e10d362bdb8'], + }), + ('blessed', '1.19.1', { + 'checksums': ['9a0d099695bf621d4680dd6c73f6ad547f6a3442fbdbe80c4b1daa1edbc492fc'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('readchar', '4.0.3', { + 'checksums': ['1d920d0e9ab76ec5d42192a68d15af2562663b5dfbf4a67cf9eba520e1ca57e6'], + }), + ('inquirer', '2.10.1', { + 'checksums': ['e9876258183e24f6e8c44136b04f6f2e18dd6684aee59b86a8057c50601a6523'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('botocore', '1.24.21', { + 'checksums': ['7e976cfd0a61601e74624ef8f5246b40a01f2cce73a011ef29cf80a6e371d0fa'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('aiobotocore', '2.3.4', { + 'checksums': ['6554ebea5764f66f4be544a4fcaa0953ee80e600dd7bd818ba4893d72bf12bfb'], + }), + ('s3fs', '2022.7.1', { + 'checksums': ['4883d682cb96b769fca568dbbcaa33ff457ac8077a03af221e6f253adac05771'], + }), + ('torchmetrics', '0.9.3', { + 'checksums': ['4ebfd2466021db26397636966ee1a195d3b340ba5d71bb258e764340dfc2476f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['c2771f966fc1b909cdfd1d603a87b8c84a3d5ff7aacf35b2c0260f697ec0c8be'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022b.eb b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022b.eb new file mode 100644 index 00000000000..562cc2adea8 --- /dev/null +++ b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022b.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'pycodestyle' +version = '2.11.1' + +homepage = "https://pycodestyle.readthedocs.io" +description = """pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f'] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..823ff30517e --- /dev/null +++ b/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Redis' +version = '7.2.3' + +homepage = 'https://redis.io' +description = """Redis is an open source (BSD licensed), in-memory data structure store, used as +a database, cache, and message broker. Redis provides data structures such as +strings, hashes, lists, sets, sorted sets with range queries, bitmaps, +hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, +Lua scripting, LRU eviction, transactions, and different levels of on-disk +persistence, and provides high availability via Redis Sentinel and automatic +partitioning with Redis Cluster.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://download.redis.io/releases'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3e2b196d6eb4ddb9e743088bfc2915ccbb42d40f5a8a3edd8cb69c716ec34be7'] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('binutils', '2.39'), +] + +skipsteps = ['configure'] + +installopts = 'PREFIX="%(installdir)s"' + +sanity_check_paths = { + 'files': ['bin/redis-cli', 'bin/redis-server'], + 'dirs': [], +} + +sanity_check_commands = [('redis-server', '--version')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..3c71c6c7190 --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'redis-py' +version = '5.0.1' + +homepage = 'https://github.com/redis/redis-py' +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] +dependencies = [ + ('Python', '3.10.8'), + ('typing-extensions', '4.9.0'), + ('Redis', '7.2.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['0a40afc824a5a3b465db4ba868a056a83779482f22d7d003c48fca230d9fe93a'], + }), +] + +moduleclass = "data" diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb new file mode 100644 index 00000000000..25053fc5fd3 --- /dev/null +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'SHAP' +version = '0.43.0' + +homepage = "https://github.com/shap/shap" +description = """SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any + machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley + values from game theory and their related extensions.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('scikit-learn', '1.2.1'), + ('tqdm', '4.64.1'), + ('numba', '0.58.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('slicer', '0.0.7', { + 'checksums': ['f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['1eabe01444a24e181ef6a7c9593b4d7c7143eefaeb1fa4d97bd5d9fdc96c4c1e'], + }), +] + +moduleclass = 'data' \ No newline at end of file diff --git a/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2022b.eb b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2022b.eb new file mode 100644 index 00000000000..825f9f573c3 --- /dev/null +++ b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2022b.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'spaCy' +version = '3.7.4' + +homepage = 'https://spacy.io/' +description = "Industrial-strength Natural Language Processing (NLP) in Python." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('tqdm', '4.64.1'), + ('pydantic', '2.5.3'), +] + +use_pip = True + +exts_list = [ + ('spacy-legacy', '3.0.12', { + 'checksums': ['b37d6e0c9b6e1d7ca1cf5bc7152ab64a4c4671f59c85adaf7a3fcb870357a774'], + }), + ('spacy-loggers', '1.0.5', { + 'checksums': ['d60b0bdbf915a60e516cc2e653baeff946f0cfc461b452d11a4d5458c6fe5f24'], + }), + ('cymem', '2.0.8', { + 'checksums': ['8fb09d222e21dcf1c7e907dc85cf74501d4cea6c4ed4ac6c9e016f98fb59cbbf'], + }), + ('murmurhash', '1.0.10', { + 'checksums': ['5282aab1317804c6ebd6dd7f69f15ba9075aee671c44a34be2bde0f1b11ef88a'], + }), + ('preshed', '3.0.9', { + 'checksums': ['721863c5244ffcd2651ad0928951a2c7c77b102f4e11a251ad85d37ee7621660'], + }), + ('blis', '0.7.11', { + 'checksums': ['cec6d48f75f7ac328ae1b6fbb372dde8c8a57c89559172277f66e01ff08d4d42'], + }), + ('confection', '0.1.4', { + 'checksums': ['e80f22fd008b5231a2e8852fac6de9e28f2276a04031d0536cff74fe4a990c8f'], + }), + ('thinc', '8.2.3', { + 'checksums': ['f5afc5222912a80bda8bdcec958362a2ba538d7027dc8db6154845d2859dca76'], + }), + ('ml_datasets', '0.2.0', { + 'checksums': ['3f9c8901f8d6be3dab5b23ec3a6c01e619a60d0184696b1030cde2e3086943f1'], + }), + ('wasabi', '1.1.2', { + 'checksums': ['1aaef3aceaa32edb9c91330d29d3936c0c39fdb965743549c173cb54b16c30b5'], + }), + ('srsly', '2.4.8', { + 'checksums': ['b24d95a65009c2447e0b49cda043ac53fecf4f09e358d87a57446458f91b8a91'], + }), + ('catalogue', '2.0.10', { + 'checksums': ['4f56daa940913d3f09d589c191c74e5a6d51762b3a9e37dd53b7437afd6cda15'], + }), + ('typer', '0.9.0', { + 'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'], + }), + ('smart-open', '6.4.0', { + 'source_tmpl': 'smart_open-%(version)s.tar.gz', + 'checksums': ['be3c92c246fbe80ebce8fbacb180494a481a77fcdcb7c1aadb2ea5b9c2bee8b9'], + }), + ('langcodes', '3.3.0', { + 'checksums': ['794d07d5a28781231ac335a1561b8442f8648ca07cd518310aeb45d6f0807ef6'], + }), + ('weasel', '0.3.4', { + 'checksums': ['eb16f92dc9f1a3ffa89c165e3a9acd28018ebb656e0da4da02c0d7d8ae3f6178'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['525f2ced2e40761562c8cace93ef6a1e6e8c483f27bd564bc1b15f608efbe85b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb new file mode 100644 index 00000000000..105a486ab07 --- /dev/null +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -0,0 +1,239 @@ +easyblock = 'PythonBundle' + +name = 'synthcity' +version = '0.2.10' + +local_pytorch_version = '1.13.1' + +homepage = 'https://github.com/vanderschaarlab/synthcity' +description = """A library for generating and evaluating synthetic tabular data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [('hypothesis', '6.68.2')] # for numpy 1.23.5 +dependencies = [ + ('Python', '3.10.8'), + ('lifelines', '0.27.7'), + ('SciPy-bundle', '2023.02'), + ('pydantic', '2.5.3'), + ('Redis', '7.2.3'), + ('scikit-learn', '1.2.1'), + ('SHAP', '0.43.0'), + ('PyTorch', local_pytorch_version), + ('XGBoost', '1.7.2'), + ('tqdm', '4.64.1'), + ('HF-Datasets', '2.14.4'), + ('Transformers', '4.30.2'), + ('fastai', '2.7.15'), + ('h5py', '3.8.0'), + ('Brotli-python', '1.0.9'), + ('statsmodels', '0.14.0'), + ('imbalanced-learn', '0.12.3'), + ('Optuna', '3.5.0'), + ('MONAI', '1.3.0'), + ('DECAF-synthetic-data', '0.1.6'), + ('PyTorch-Lightning', '1.8.4'), + # TESTS + ('JupyterNotebook', '7.0.3'), + ('python-igraph', '0.10.6'), + ('coverage', '7.2.3'), + ('py-cpuinfo', '9.0.0'), + ('pycodestyle', '2.11.1'), +] + +# unpin pydantic version restriction +local_preinstallopts = "sed -i 's/pydantic<2.0/pydantic/' %(builddir)s/%(name)s/%(name)s-%(version)s/setup.cfg && " + +# ignore the failing part of ddpm test - seems constraints are wrong +# https://github.com/vanderschaarlab/synthcity/blob/v0.2.10/tests/plugins/generic/test_ddpm.py#L114 +local_pretestopts = ( + "sed -i '138,144d' %(builddir)s/%(name)s/%(name)s-%(version)s/tests/plugins/generic/test_ddpm.py && " +) + +# fix invalid syntax of xgbse/setup.py +local_xgbse_preinstallopts = "sed -i -e '45,49d' -e 's/pandas>=1.0.\*/pandas>=1.0.0/' setup.py && " + +exts_list = [ + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pyflakes', '3.2.0', { + 'checksums': ['1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f'], + }), + ('mccabe', '0.7.0', { + 'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'], + }), + ('restructuredtext_lint', '1.4.0', { + 'checksums': ['1b235c0c922341ab6c530390892eb9e92f90b9b75046063e047cacfb0f050c45'], + }), + ('stevedore', '5.2.0', { + 'checksums': ['46b93ca40e1114cea93d738a6c1e365396981bb6bb78c27045b7587c9473544d'], + }), + ('nodeenv', '1.9.1', { + 'checksums': ['6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f'], + }), + ('identify', '2.6.0', { + 'checksums': ['cb171c685bdc31bcc4c1734698736a7d5b6c8bf2e0c15117f4d469c8640ae5cf'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('pytest-cov', '5.0.0', { + 'checksums': ['5837b58e9f6ebd335b0f8060eecce69b662415b16dc503883a02f45dfeb14857'], + }), + ('bandit', '1.7.9', { + 'checksums': ['7c395a436743018f7be0a4cbb0a4ea9b902b6d87264ddecf8cfdc73b4f78ff61'], + }), + ('black', '22.12.0', { + 'checksums': ['229351e5a18ca30f447bf724d007f890f97e13af070bb6ad4c0a441cd7596a2f'], + }), + ('black-nb', '0.7', { + 'checksums': ['8742a4f7c728302c91954325168d779f9444f8e3c31b19598ee8e98fc4bf4782'], + }), + ('darglint', '1.8.1', { + 'checksums': ['080d5106df149b199822e7ee7deb9c012b49891538f14a11be681044f0bb20da'], + }), + ('doc8', '1.1.1', { + 'checksums': ['d97a93e8f5a2efc4713a0804657dedad83745cca4cd1d88de9186f77f9776004'], + }), + ('flake8', '7.0.0', { + 'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'], + }), + ('isort', '5.13.2', { + 'checksums': ['48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109'], + }), + ('pytest-benchmark', '4.0.0', { + 'checksums': ['fb0785b83efe599a6a956361c0691ae1dbb5318018561af10f3e915caa0048d1'], + }), + ('pytest-xprocess', '1.0.2', { + 'modulename': 'xprocess', + 'checksums': ['15e270637586eabc56755ee5fcc81c48bdb46ba7ef7c0d5b1b64302d080cc60f'], + }), + ('pre_commit', '3.7.1', { + 'checksums': ['8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a'], + }), + ('typing_extensions', '4.9.0', { + 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], + }), + ('fflows', '0.0.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['18de7a7b98e3708ff2d5ae9f10fad625740230c4de6447906b7ca477667b78fb'], + }), + ('geomloss', '0.2.6', { + 'checksums': ['491c47085c5001b2cb6128ea541fd2d0a8808ae50e88a0798c7853c9d995faeb'], + }), + ('nflows', '0.14', { + 'checksums': ['6299844a62f9999fcdf2d95cb2d01c091a50136bd17826e303aba646b2d11b55'], + }), + ('opt_einsum', '3.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['2455e59e3947d3c275477df7f5205b30635e266fe6dc300e3d9f9646bfcea147'], + }), + ('opacus', '1.4.0', { + 'checksums': ['7a41d49c34af8e4308189bc8c2b22e65cf1edc0373477a02a43ccd957bac970d'], + }), + ('pgmpy', '0.1.25', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['7c4fb15e4c0fd0310160a6a77297d6db382bd18f6ff35fcd0458c3cbd42caf78'], + }), + ('feather-format', '0.4.1', { + 'modulename': 'feather', + 'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'], + }), + ('inflate64', '1.0.0', { + 'checksums': ['3278827b803cf006a1df251f3e13374c7d26db779e5a33329cc11789b804bc2d'], + }), + ('multivolumefile', '0.2.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['237f4353b60af1703087cf7725755a1f6fcaeeea48421e1896940cd1c920d678'], + }), + ('pybcj', '1.0.2', { + 'modulename': 'bcj', + 'checksums': ['c7f5bef7f47723c53420e377bc64d2553843bee8bcac5f0ad076ab1524780018'], + }), + ('pycryptodomex', '3.20.0', { + 'modulename': 'Crypto', + 'checksums': ['7a710b79baddd65b806402e14766c721aee8fb83381769c27920f26476276c1e'], + }), + ('pyppmd', '1.0.0', { + 'checksums': ['075c9bd297e3b0a87dd7aeabca7fee668218acbe69ecc1c6511064558de8840f'], + }), + ('pyzstd', '0.16.0', { + 'checksums': ['fd43a0ae38ae15223fb1057729001829c3336e90f4acf04cf12ebdec33346658'], + }), + ('texttable', '1.7.0', { + 'checksums': ['2d2068fb55115807d3ac77a4ca68fa48803e84ebb0ee2340f858107a36522638'], + }), + ('py7zr', '0.20.6', { + 'checksums': ['d036dee11fce69ad8d4fa86025ccfc4a3511ec27ee1c6b5bd8d6759313dbd077'], + }), + ('torchtuples', '0.2.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['186625230a149cc09f64116d51b203ffefe78160f5a0445adad195893663f55b'], + }), + ('pycox', '0.2.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['9ea3c64a4a650ccf6c96cf512712de330f2d75de32122d86995c7cd37ff105d1'], + }), + ('keopscore', '2.2.3', { + 'checksums': ['64d5dad1e8c806d7070cdc60e48fd5bbf006f2bf1afd39ad3fa5e9fb213517d2'], + }), + ('pykeops', '2.2.3', { + 'checksums': ['2e2cba1de5e05c35559957a14f41cb5165dc667cc51b3b2118d7e0027eb435a1'], + }), + ('pyts', '0.13.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['b49608267b686ea693dba31316ef2b22ad73ea29b27144696c347809ecd5ad62'], + }), + ('tsai', '0.3.9', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['0e6460e9ff075176c8af25ef90444ef2e287bc5fe5510e2a0f427e4d0b37ebc0'], + }), + ('accelerate', '0.31.0', { + 'checksums': ['b5199865b26106ccf9205acacbe8e4b3b428ad585e7c472d6a46f6fb75b6c176'], + }), + ('be_great', '0.0.7', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['824f10482581f5211d3a435d8b14adcc6c21b38d952f00b6a792fc7c089788b1'], + }), + ('xgbse', '0.2.3', { + 'preinstallopts': local_xgbse_preinstallopts, + 'source_urls': ['https://github.com/loft-br/xgboost-survival-embeddings/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['9e6b71539b2b533c00eddfe7681cdd541f393d9573594eca358d263b141c127d'], + }), + ('arfpy', '0.1.1', { + 'checksums': ['88170d5e72638b0dbfec28cfbdfee02e97bd6a06d5a636e960acd5d90d480707'], + }), + ('numpy', '1.23.5', { + 'patches': [ + 'numpy-1.20.3_fix-fortran-compiler-error.patch', + 'numpy-1.22.3_disable-broken-override-test.patch', + ], + 'checksums': [ + {'numpy-1.23.5.tar.gz': '1b1766d6f397c18153d40015ddfc79ddb715cabadc04d2d228d4e5a8bc4ded1a'}, + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + 'f12a49a754cb4c01a39691f8a7470bfa0e56c70139d78ca8b188f049010e7647'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '0d894fa9592ba9855397bc89fd4408bd911d49e6b6449d1693f87d2e5fcac486'}, + ], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/vanderschaarlab/synthcity/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'testinstall': True, + 'runtest': local_pretestopts + 'cd tests && pytest -vvvs -m "not slow" --durations=50', + 'checksums': ['122a8546cad35e3ac5c74cf81281252dec4dd3c7b1d7afe0f45ef785f89cc682'], + }), +] + +sanity_pip_check = True +use_pip = True + +sanity_check_commands = [ + "python -c 'from synthcity.plugins import Plugins'", + "python -c 'from decaf import DECAF, DataModule'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb new file mode 100644 index 00000000000..7903b8102f8 --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.14.1' +local_pytorch_version = '1.13.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'foss', 'version': '2022b'} + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +patches = ['torchtext-0.14.1_deps_fix.patch'] +checksums = [ + {'torchtext-0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, + {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'}, +] + +builddependencies = [ + ('RE2', '2023-03-01'), + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('SentencePiece', '0.1.99'), + ('tqdm', '4.64.1'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.2.1'), + ('utf8proc', '2.8.0'), +] + +download_dep_fail = True, +use_pip = True +sanity_pip_check = True, + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && " + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022b.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022b.eb new file mode 100644 index 00000000000..937201a36b5 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '1.7.2' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f1a749aedb9330afc48007cc78b8bbbbea35ce372f48a2735f9c71bbc7b8dcfb'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# use the parallel parameter from EB instead of total procs in the system +preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&" + +moduleclass = 'lib' From e1847a481007b496eb5344be4ba6449e432bb1a1 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 7 Aug 2024 13:09:59 +0200 Subject: [PATCH 007/414] Update synthcity-0.2.10-foss-2022b.eb try raw string --- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index 105a486ab07..bc1eeafab12 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -51,7 +51,7 @@ local_pretestopts = ( ) # fix invalid syntax of xgbse/setup.py -local_xgbse_preinstallopts = "sed -i -e '45,49d' -e 's/pandas>=1.0.\*/pandas>=1.0.0/' setup.py && " +local_xgbse_preinstallopts = r"sed -i -e '45,49d' -e 's/pandas>=1.0.\*/pandas>=1.0.0/' setup.py && " exts_list = [ ('cfgv', '3.4.0', { From 51357fa5cc27149e7f4ded01b61be58a2b3257b5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 7 Aug 2024 13:26:25 +0200 Subject: [PATCH 008/414] Update easyconfigs.py - PyTorch-Lightning exception for synthcity --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d228333cca6..231863a7c76 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -625,6 +625,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'NGSpeciesID-0.1.1.1-']), ('0.18.0;', ['medaka-1.6.0-', 'NGSpeciesID-0.1.2.1-', 'WhatsHap-1.4-']), ], + # PyTorch-Lightning-1.8.4 is requiered in synthcity-0.2.10 and DECAF-synthetic-data-0.1.6 + 'PyTorch-Lightning': [('1.8.4;', ['synthcity-0.2.10-', 'DECAF-synthetic-data-0.1.6-'])], # OPERA requires SAMtools 0.x 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], From eaf2389064b30227f13f2f2f55927db34ef92a2a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 7 Aug 2024 15:22:06 +0200 Subject: [PATCH 009/414] fix new line and comment indent --- easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb | 2 +- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb index 25053fc5fd3..cca163e6ee4 100644 --- a/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb @@ -34,4 +34,4 @@ exts_list = [ }), ] -moduleclass = 'data' \ No newline at end of file +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index bc1eeafab12..7ef97fcc743 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -10,7 +10,7 @@ description = """A library for generating and evaluating synthetic tabular data. toolchain = {'name': 'foss', 'version': '2022b'} -builddependencies = [('hypothesis', '6.68.2')] # for numpy 1.23.5 +builddependencies = [('hypothesis', '6.68.2')] # for numpy 1.23.5 dependencies = [ ('Python', '3.10.8'), ('lifelines', '0.27.7'), From 5e0f098c80e611b193c8d198768a1efb99bad7c6 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 7 Aug 2024 16:05:42 +0200 Subject: [PATCH 010/414] add HF-Datasets ec --- .../HF-Datasets-2.14.4-gfbf-2022b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.14.4-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.14.4-gfbf-2022b.eb b/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.14.4-gfbf-2022b.eb new file mode 100644 index 00000000000..e92ec85db93 --- /dev/null +++ b/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.14.4-gfbf-2022b.eb @@ -0,0 +1,44 @@ +easyblock = "PythonBundle" + +name = 'HF-Datasets' +version = '2.14.4' + +homepage = 'https://github.com/huggingface/datasets' +description = """ +The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient +data manipulation tools. +""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('aiohttp', '3.8.5'), + ('dill', '0.3.7'), + ('Arrow', '11.0.0'), + ('PyYAML', '6.0'), + ('tqdm', '4.64.1'), + ('python-xxhash', '3.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyarrow_hotfix', '0.6', { + 'checksums': ['79d3e030f7ff890d408a100ac16d6f00b14d44a502d7897cd9fc3e3a534e9945'], + }), + ('multiprocess', '0.70.15', { + 'checksums': ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'], + }), + ('huggingface-hub', '0.15.1', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['a61b7d1a7769fe10119e730277c72ab99d95c48d86a3d6da3e9f3d0f632a4081'], + }), + ('datasets', version, { + 'checksums': ['ef29c2b5841de488cd343cfc26ab979bff77efa4d2285af51f1ad7db5c46a83b'], + }), +] + +moduleclass = 'data' From 2a64e21cbba6f6090a6ef38ccef7bef367aa7810 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 13 Aug 2024 15:08:09 +0200 Subject: [PATCH 011/414] add alt_location for numpy patches --- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index 7ef97fcc743..7d53f08dd4e 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -207,8 +207,8 @@ exts_list = [ }), ('numpy', '1.23.5', { 'patches': [ - 'numpy-1.20.3_fix-fortran-compiler-error.patch', - 'numpy-1.22.3_disable-broken-override-test.patch', + {'name': 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'alt_location': 'Scipy-bundle'}, + {'name': 'numpy-1.22.3_disable-broken-override-test.patch', 'alt_location': 'Scipy-bundle'}, ], 'checksums': [ {'numpy-1.23.5.tar.gz': '1b1766d6f397c18153d40015ddfc79ddb715cabadc04d2d228d4e5a8bc4ded1a'}, From fb9f1822994a88d40b3a6be8c04d3ca078a591e3 Mon Sep 17 00:00:00 2001 From: thoffman Date: Sat, 17 Aug 2024 20:03:08 +0200 Subject: [PATCH 012/414] {bio}[foss/2023a] AlphaPulldown v2.0.0b4 Uni-Core v0.0.3 w/ CUDA v12.1.1 --- ...Pulldown-2.0.0b4-foss-2023a-CUDA-12.1.1.eb | 85 +++++++++++++++++++ ..._af2_biopython_IUPACData_as_SCOPData.patch | 27 ++++++ .../dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb | 57 +++++++++++++ .../OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb | 70 +++++++++++++++ .../Uni-Core-0.0.3-foss-2023a-CUDA-12.1.1.eb | 60 +++++++++++++ 5 files changed, 299 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch create mode 100644 easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..62c616bf500 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,85 @@ +# created by Denis Kristak (Inuits) +# update: Thomas Hoffmann, EMBL +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0b4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('OpenMM', '8.0.0', versionsuffix), + ('Kalign', '3.4.0'), + ('PyYAML', '6.0'), + ('jax', '0.4.25', versionsuffix), # also provides absl-py + ('Biopython', '1.83'), + ('h5py', '3.9.0'), + ('IPython', '8.14.0'), + ('JupyterLab', '4.0.5'), + ('matplotlib', '3.7.2'), + ('TensorFlow', '2.15.1', versionsuffix), + ('PyTorch', '2.1.2', versionsuffix), + ('tqdm', '4.66.1'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.1.0'), + ('HMMER', '3.4'), + ('HH-suite', '3.3.0'), + ('dm-haiku', '0.0.11', versionsuffix), + ('Uni-Core', '0.0.3', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + (name, version, { + 'patches': ['AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch'], + 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + 'sources': [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': '2.0.0b4', + 'recursive': True + } + }], + 'checksums': [ + None, + # AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch: + '0f8ff118bbab50b97a397a9e4de890155b77f868db9913ea3b496d422330bc18' + ], + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = ["run_multimer_jobs.py --help | grep 'A script to perform structure prediction'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch new file mode 100644 index 00000000000..f6a89591dcf --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch @@ -0,0 +1,27 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/08 +# allow to use BioPython >= 1.83 +diff -ru AlphaPulldown/alphafold/alphafold/data/mmcif_parsing.py AlphaPulldown-2.0.0b4_alphfold_SCOP.patch/alphafold/alphafold/data/mmcif_parsing.py +--- AlphaPulldown/alphafold/alphafold/data/mmcif_parsing.py 2024-08-17 15:34:23.000000000 +0200 ++++ AlphaPulldown-2.0.0b4_alphfold_SCOP.patch/alphafold/alphafold/data/mmcif_parsing.py 2024-08-17 15:44:47.460653530 +0200 +@@ -21,7 +21,7 @@ + + from absl import logging + from Bio import PDB +-from Bio.Data import SCOPData ++from Bio.Data import IUPACData as SCOPData + + # Type aliases: + ChainId = str +fix import of protein_letters_3to1 from Biopython +author: Kenneth Hoste (HPC-UGent) +--- AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py.orig 2024-06-05 09:30:16.114746286 +0200 ++++ AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py 2024-06-05 09:30:35.242665615 +0200 +@@ -4,7 +4,7 @@ + from alphafold.data.mmcif_parsing import parse + from alphafold.common.residue_constants import residue_atoms, atom_types + from Bio.PDB import NeighborSearch, PDBIO, MMCIFIO +-from Bio.PDB.Polypeptide import protein_letters_3to1 ++from Bio.Data.IUPACData import protein_letters_3to1 + from Bio import SeqIO + from colabfold.batch import convert_pdb_to_mmcif + from Bio.PDB import Structure, Model, Chain, Residue diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..a30f458a967 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,57 @@ +# update 0.9.11: Thomas Hoffmann (EMBL) +easyblock = 'PythonBundle' + +name = 'dm-haiku' +version = '0.0.11' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/deepmind/dm-haiku' +description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural +network library for TensorFlow.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), # required by jmp, also provides absl-py + ('PyYAML', '6.0'), + ('CUDA', '12.1.1', '', SYSTEM), + ('tensorstore', '0.1.53'), + ('protobuf-python', '4.24.0'), +] + +use_pip = True + +exts_list = [ + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('flax', '0.8.1', { + 'checksums': ['ce3d99e9b4c0d2e4d9fc28bc56cced8ba953adfd695aabd24f096b4c8a7e2f92'], + }), + ('optax', '0.1.9', { + 'checksums': ['731f43e8b404f50a5ef025b1261894d7d0300f7ad9cb688ea08f67b40822e94f'], + }), + ('orbax_checkpoint', '0.5.3', { + 'modulename': 'orbax', + 'checksums': ['1572904cbbfe8513927e0d80f80b730e0ef2f680332d3c2810d8443532938b45'], + }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('chex', '0.1.85', { + 'checksums': ['a27cfe87119d6e1fe24ccc1438a59195e6dc1d6e0e10099fcf618c3f64771faf'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + (name, version, { + 'modulename': 'haiku', + 'checksums': ['c420a90c6a76c1d941996698840089df0d352806312eaf7b737486f6c6a32ef2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..8cf271071e7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,70 @@ +# 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 +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch'] +checksums = [ + 'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e', # 8.0.0.tar.gz + '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd', # OpenMM-8.0.0_add_no_tree_vectorize.patch +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('SWIG', '4.1.1'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +# Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc, +# Otherwise they will use the wrong path: `/usr/local/cuda/bin/nvcc` +pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && ' +pretestopts += " CTEST_OUTPUT_ON_FAILURE=1" +# Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(CudaCompiler)" +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], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..24fb0a0d2e2 --- /dev/null +++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'Uni-Core' +version = '0.0.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/dptech-corp/Uni-Core' +description = "An efficient distributed PyTorch framework" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('maturin', '1.4.0', '-Rust-1.75.0') +] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), + ('jax', '0.4.25', versionsuffix), # provides absl-py + ('tensorboardX', '2.6.2.2'), + ('tqdm', '4.66.1'), + ('wandb', '0.16.1'), +] + +use_pip = True +local_preinstallopts = "sed -i " +# local_preinstallopts += "-e 's/DISABLE_CUDA_EXTENSION = False/DISABLE_CUDA_EXTENSION = True/g' " +local_preinstallopts += "-e 's/torch>=[0-9.]*/torch/g' setup.py && " + +exts_list = [ + ('lmdb', '1.5.1', { + 'checksums': ['717c255827d331e02f7242b44051aa06466c90f6d732ecb07b31edfb1e06c67a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('huggingface-hub', '0.24.5', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + ('tokenizers', '0.20.0', { + 'checksums': ['39d7acc43f564c274085cafcd1dae9d36f332456de1a31970296a6b8da4eac8d'], + }), + (name, version, { + 'modulename': 'unicore', + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 1e5d9a16cad81029ce63cedb46e14abbade2322f Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Sun, 18 Aug 2024 09:23:12 +0200 Subject: [PATCH 013/414] Add files via upload --- .../t/tensorstore-0.1.53-foss-2023a.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb b/easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb new file mode 100644 index 00000000000..0637b6107cb --- /dev/null +++ b/easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb @@ -0,0 +1,62 @@ +# Thomas Hoffmann, EMBL Heidlelberg, structures-it@embl.de, 2024/02 +easyblock = 'PythonBundle' + +name = 'tensorstore' +version = '0.1.53' + +homepage = 'https://github.com/google/tensorstore' +description = """TensorStore is an open-source C++ and Python software library designed for +storage and manipulation of large multi-dimensional arrays.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('NASM', '2.16.01'), + ('pybind11', '2.11.1'), + ('Bazel', '6.3.1'), + + + + ('PyYAML', '6.0'), + ('zlib', '1.2.13'), + ('LibTIFF', '4.5.0'), + ('snappy', '1.1.10'), + ('Brotli', '1.0.9'), + ('protobuf', '24.0'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.5'), + ('libwebp', '1.3.1'), + ('nlohmann_json', '3.11.2'), + ('Blosc', '1.21.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ml_dtypes', '0.3.2'), +] + +use_pip = True + + +local_ts_useebbazel = """sed -i 's/bazel_path =.*/""" +local_ts_useebbazel += """bazel_path = os.path.join(os.getenv("EBROOTBAZEL"),"bin", "bazel")/g'""" +local_ts_useebbazel += " bazelisk.py&& " # TODO: patch? +local_ts_version = """sed -i "s/use_scm_version=/version='%(version)s',&/g" setup.py&&""" +local_ts_bzl_exp = """export TENSORSTORE_BAZEL_STARTUP_OPTIONS='--output_user_root %(builddir)s/cache' &&""" +# inject CFLAGS: +local_ts_bzl_exp += """export TENSORSTORE_BAZEL_BUILD_OPTIONS="$(for i in $CFLAGS;do echo --copt=$i; done)" &&""" + + +local_ts_preinstall = local_ts_version + local_ts_useebbazel + local_ts_bzl_exp + +exts_list = [ + (name, version, { + 'installopts': '-v', + 'preinstallopts': local_ts_preinstall, + 'checksums': ['45ef74b2dc9f2cd5f766bc373ded91d681cd021cc69d16592df48abaeb81af56'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 641d19d0d5f697a5438733999484f8b187823e54 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Sun, 18 Aug 2024 09:24:07 +0200 Subject: [PATCH 014/414] Rename easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb to easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb --- .../t/{ => tensorstore}/tensorstore-0.1.53-foss-2023a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/t/{ => tensorstore}/tensorstore-0.1.53-foss-2023a.eb (100%) diff --git a/easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb b/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb similarity index 100% rename from easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb rename to easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb From 324d07c96588cce54592662ad90a2e95ddb271ec Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Mon, 19 Aug 2024 12:33:12 +0200 Subject: [PATCH 015/414] Update easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb - SciPy typo Co-authored-by: Kenneth Hoste --- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index 7d53f08dd4e..522830f8f40 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -207,8 +207,8 @@ exts_list = [ }), ('numpy', '1.23.5', { 'patches': [ - {'name': 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'alt_location': 'Scipy-bundle'}, - {'name': 'numpy-1.22.3_disable-broken-override-test.patch', 'alt_location': 'Scipy-bundle'}, + {'name': 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'alt_location': 'SciPy-bundle'}, + {'name': 'numpy-1.22.3_disable-broken-override-test.patch', 'alt_location': 'SciPy-bundle'}, ], 'checksums': [ {'numpy-1.23.5.tar.gz': '1b1766d6f397c18153d40015ddfc79ddb715cabadc04d2d228d4e5a8bc4ded1a'}, From f2f5962754e38c655d63c4358f071e8772052d25 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 19 Aug 2024 14:35:24 +0200 Subject: [PATCH 016/414] update patches checksums --- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index 522830f8f40..29a94b22448 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -213,9 +213,9 @@ exts_list = [ 'checksums': [ {'numpy-1.23.5.tar.gz': '1b1766d6f397c18153d40015ddfc79ddb715cabadc04d2d228d4e5a8bc4ded1a'}, {'numpy-1.20.3_fix-fortran-compiler-error.patch': - 'f12a49a754cb4c01a39691f8a7470bfa0e56c70139d78ca8b188f049010e7647'}, + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, {'numpy-1.22.3_disable-broken-override-test.patch': - '0d894fa9592ba9855397bc89fd4408bd911d49e6b6449d1693f87d2e5fcac486'}, + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, ], }), (name, version, { From 12443eae5a0c1b9826ccf8e0e8a09537aaf459d9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 30 Sep 2024 07:21:10 +0200 Subject: [PATCH 017/414] adding easyconfigs: FDS-6.9.1-foss-2023b.eb --- .../easyconfigs/f/FDS/FDS-6.9.1-foss-2023b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.9.1-foss-2023b.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.9.1-foss-2023b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.9.1-foss-2023b.eb new file mode 100644 index 00000000000..96e873161bd --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.9.1-foss-2023b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.9.1' + +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': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['FDS-%(version)s.tar.gz'] +checksums = ['e0fe22d1386dc06512489ddf190dbdbee4c9865856f4a7ca48aec8425b4c0867'] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +buildopts = 'ompi_gnu_linux &&' +buildopts += 'cd %(installdir)s/Build && ln -s fds_ompi_gnu_linux fds' + +modextrapaths = {'PATH': 'Build'} + +sanity_check_paths = { + 'files': ['Build/fds'], + 'dirs': [], +} + +sanity_check_commands = [ + "fds -v", +] + +moduleclass = 'phys' From 1d878256f85c4f1c9e12eb644627d8de57c96217 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 9 Jan 2024 10:33:22 +0100 Subject: [PATCH 018/414] adding easyconfigs: CubeLib-4.8.2-GCCcore-11.3.0.eb, CubeLib-4.8.2-GCCcore-12.3.0.eb, CubeWriter-4.8.2-GCCcore-11.3.0.eb, CubeWriter-4.8.2-GCCcore-12.3.0.eb, Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb, Score-P-8.4-gompi-2022a.eb, Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb, Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb, Score-P-8.4-gompi-2023a.eb --- .../c/CubeLib/CubeLib-4.8.2-GCCcore-11.3.0.eb | 50 ++++++++++++++++ .../c/CubeLib/CubeLib-4.8.2-GCCcore-12.3.0.eb | 51 +++++++++++++++++ .../CubeWriter-4.8.2-GCCcore-11.3.0.eb | 50 ++++++++++++++++ .../CubeWriter-4.8.2-GCCcore-12.3.0.eb | 51 +++++++++++++++++ .../Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb | 57 +++++++++++++++++++ .../s/Score-P/Score-P-8.4-gompi-2022a.eb | 54 ++++++++++++++++++ .../Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb | 57 +++++++++++++++++++ .../s/Score-P/Score-P-8.4-gompi-2022b.eb | 54 ++++++++++++++++++ .../Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb | 57 +++++++++++++++++++ .../s/Score-P/Score-P-8.4-gompi-2023a.eb | 54 ++++++++++++++++++ 10 files changed, 535 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5d28ebcf501 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-11.3.0.eb @@ -0,0 +1,50 @@ +# Copyright 2019 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# 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 = '4.8.2' + +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': '11.3.0'} +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d6fdef57b1bc9594f1450ba46cf08f431dd0d4ae595c47e2f3454e17e4ae74f4'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +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/CubeLib/CubeLib-4.8.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3039dd547d5 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +# Copyright 2019 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# 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 = '4.8.2' + +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': '12.3.0'} +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d6fdef57b1bc9594f1450ba46cf08f431dd0d4ae595c47e2f3454e17e4ae74f4'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +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-4.8.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..17faeb9292b --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-11.3.0.eb @@ -0,0 +1,50 @@ +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# 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 = '4.8.2' + +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': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['4f3bcf0622c2429b8972b5eb3f14d79ec89b8161e3c1cc5862ceda417d7975d2'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +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/CubeWriter/CubeWriter-4.8.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ccb04669874 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# 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 = '4.8.2' + +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': '12.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['4f3bcf0622c2429b8972b5eb3f14d79ec89b8161e3c1cc5862ceda417d7975d2'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +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/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..f195f0ceaeb --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb @@ -0,0 +1,57 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +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': 'gompi', 'version': '2022a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.2'), + # Hardware counter support (optional): + ('PAPI', '7.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_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/Score-P/Score-P-8.4-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb new file mode 100644 index 00000000000..1317ae392d9 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb @@ -0,0 +1,54 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' + +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': 'gompi', 'version': '2022a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.2'), + # Hardware counter support (optional): + ('PAPI', '7.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_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/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb new file mode 100644 index 00000000000..8b60baea472 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb @@ -0,0 +1,57 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +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': 'gompi', 'version': '2022b'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CUDA', '12.0.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', versionsuffix), + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_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/Score-P/Score-P-8.4-gompi-2022b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b.eb new file mode 100644 index 00000000000..e19b8fcc05b --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b.eb @@ -0,0 +1,54 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' + +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': 'gompi', 'version': '2022b'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_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/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..51caeb1df08 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb @@ -0,0 +1,57 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +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': 'gompi', 'version': '2023a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('UCX-CUDA', '1.14.1', versionsuffix), + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_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/Score-P/Score-P-8.4-gompi-2023a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb new file mode 100644 index 00000000000..2e47de3fd8b --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb @@ -0,0 +1,54 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' + +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': 'gompi', 'version': '2023a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_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' From ba5e7e811c6360806db878ca38d7951c105baec4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 2 Oct 2024 12:56:35 +0200 Subject: [PATCH 019/414] Use PAPI 7.1.0 --- .../p/PAPI/PAPI-7.1.0-GCCcore-11.3.0.eb | 54 +++++++++++++++++++ .../p/PAPI/PAPI-7.1.0-GCCcore-12.2.0.eb | 54 +++++++++++++++++++ .../p/PAPI/PAPI-7.1.0-GCCcore-12.3.0.eb | 53 ++++++++++++++++++ .../Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb | 2 +- .../s/Score-P/Score-P-8.4-gompi-2022a.eb | 2 +- .../Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb | 2 +- .../Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb | 2 +- .../s/Score-P/Score-P-8.4-gompi-2023a.eb | 2 +- 8 files changed, 166 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7ea6627c95d --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,54 @@ +## +# Author: Robert Mijakovic +# Updated: Alexander Grund +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.1.0' + +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': '11.3.0'} + +source_urls = ['https://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch'] +checksums = [ + '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f', + {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'} +] + +builddependencies = [ + ('binutils', '2.38'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +# There is also "fulltest" that is a superset of "test" but hangs on some processors +# indefinitely with a defunct `make` process. So use only "test". +runtest = 'test' + +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/PAPI/PAPI-7.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7cc95d73ce4 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,54 @@ +## +# Author: Robert Mijakovic +# Updated: Alexander Grund +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.1.0' + +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': '12.2.0'} + +source_urls = ['https://icl.utk.edu/projects/papi/downloads'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch'] +checksums = [ + '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f', + {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'} +] + +builddependencies = [ + ('binutils', '2.39'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +# There is also "fulltest" that is a superset of "test" but hangs on some processors +# indefinitely with a defunct `make` process. So use only "test". +runtest = 'test' + +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/PAPI/PAPI-7.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0577b800a8f --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,53 @@ +## +# Author: Robert Mijakovic +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.1.0' + +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': '12.3.0'} + +source_urls = ['https://icl.utk.edu/projects/papi/downloads'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch'] +checksums = [ + '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f', + {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'} +] + +builddependencies = [ + ('binutils', '2.40'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +# There is also "fulltest" that is a superset of "test" but hangs on some processors +# indefinitely with a defunct `make` process. So use only "test". +runtest = 'test' + +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/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb index f195f0ceaeb..3d015439b57 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb @@ -33,7 +33,7 @@ dependencies = [ ('OPARI2', '2.0.7'), ('OTF2', '3.0.2'), # Hardware counter support (optional): - ('PAPI', '7.0.0'), + ('PAPI', '7.1.0'), # PDT source-to-source instrumentation support (optional): ('PDT', '3.25.1'), ] diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb index 1317ae392d9..7f419b6cca2 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb @@ -30,7 +30,7 @@ dependencies = [ ('OPARI2', '2.0.7'), ('OTF2', '3.0.2'), # Hardware counter support (optional): - ('PAPI', '7.0.0'), + ('PAPI', '7.1.0'), # PDT source-to-source instrumentation support (optional): ('PDT', '3.25.1'), ] diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb index 8b60baea472..035733cf1a3 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb @@ -33,7 +33,7 @@ dependencies = [ ('OPARI2', '2.0.7'), ('OTF2', '3.0.3'), # Hardware counter support (optional): - ('PAPI', '7.0.1'), + ('PAPI', '7.1.0'), # PDT source-to-source instrumentation support (optional): ('PDT', '3.25.1'), ] diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb index 51caeb1df08..c3189274ea8 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb @@ -33,7 +33,7 @@ dependencies = [ ('OPARI2', '2.0.7'), ('OTF2', '3.0.3'), # Hardware counter support (optional): - ('PAPI', '7.0.1'), + ('PAPI', '7.1.0'), # PDT source-to-source instrumentation support (optional): ('PDT', '3.25.1'), ] diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb index 2e47de3fd8b..ecf8aa15fb7 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb @@ -30,7 +30,7 @@ dependencies = [ ('OPARI2', '2.0.7'), ('OTF2', '3.0.3'), # Hardware counter support (optional): - ('PAPI', '7.0.1'), + ('PAPI', '7.1.0'), # PDT source-to-source instrumentation support (optional): ('PDT', '3.25.1'), ] From 97ab7235d10276b6d902872461312681ec56fef9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 2 Oct 2024 13:50:10 +0200 Subject: [PATCH 020/414] Remove conflicting PAPI versions --- .../p/PAPI/PAPI-7.1.0-GCCcore-11.3.0.eb | 54 ------------------- .../p/PAPI/PAPI-7.1.0-GCCcore-12.2.0.eb | 54 ------------------- .../p/PAPI/PAPI-7.1.0-GCCcore-12.3.0.eb | 53 ------------------ .../Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb | 2 +- .../s/Score-P/Score-P-8.4-gompi-2022a.eb | 2 +- .../Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb | 2 +- .../Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb | 2 +- .../s/Score-P/Score-P-8.4-gompi-2023a.eb | 2 +- 8 files changed, 5 insertions(+), 166 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.2.0.eb delete mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-11.3.0.eb deleted file mode 100644 index 7ea6627c95d..00000000000 --- a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-11.3.0.eb +++ /dev/null @@ -1,54 +0,0 @@ -## -# Author: Robert Mijakovic -# Updated: Alexander Grund -## - -easyblock = 'ConfigureMake' - -name = 'PAPI' -version = '7.1.0' - -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': '11.3.0'} - -source_urls = ['https://icl.cs.utk.edu/projects/papi/downloads/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch'] -checksums = [ - '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f', - {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'} -] - -builddependencies = [ - ('binutils', '2.38'), -] - -start_dir = 'src' - -configopts = "--with-components=rapl " # for energy measurements - -# There is also "fulltest" that is a superset of "test" but hangs on some processors -# indefinitely with a defunct `make` process. So use only "test". -runtest = 'test' - -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/PAPI/PAPI-7.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.2.0.eb deleted file mode 100644 index 7cc95d73ce4..00000000000 --- a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.2.0.eb +++ /dev/null @@ -1,54 +0,0 @@ -## -# Author: Robert Mijakovic -# Updated: Alexander Grund -## - -easyblock = 'ConfigureMake' - -name = 'PAPI' -version = '7.1.0' - -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': '12.2.0'} - -source_urls = ['https://icl.utk.edu/projects/papi/downloads'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch'] -checksums = [ - '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f', - {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'} -] - -builddependencies = [ - ('binutils', '2.39'), -] - -start_dir = 'src' - -configopts = "--with-components=rapl " # for energy measurements - -# There is also "fulltest" that is a superset of "test" but hangs on some processors -# indefinitely with a defunct `make` process. So use only "test". -runtest = 'test' - -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/PAPI/PAPI-7.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.3.0.eb deleted file mode 100644 index 0577b800a8f..00000000000 --- a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,53 +0,0 @@ -## -# Author: Robert Mijakovic -## - -easyblock = 'ConfigureMake' - -name = 'PAPI' -version = '7.1.0' - -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': '12.3.0'} - -source_urls = ['https://icl.utk.edu/projects/papi/downloads'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch'] -checksums = [ - '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f', - {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'} -] - -builddependencies = [ - ('binutils', '2.40'), -] - -start_dir = 'src' - -configopts = "--with-components=rapl " # for energy measurements - -# There is also "fulltest" that is a superset of "test" but hangs on some processors -# indefinitely with a defunct `make` process. So use only "test". -runtest = 'test' - -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/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb index 3d015439b57..f195f0ceaeb 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb @@ -33,7 +33,7 @@ dependencies = [ ('OPARI2', '2.0.7'), ('OTF2', '3.0.2'), # Hardware counter support (optional): - ('PAPI', '7.1.0'), + ('PAPI', '7.0.0'), # PDT source-to-source instrumentation support (optional): ('PDT', '3.25.1'), ] diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb index 7f419b6cca2..1317ae392d9 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb @@ -30,7 +30,7 @@ dependencies = [ ('OPARI2', '2.0.7'), ('OTF2', '3.0.2'), # Hardware counter support (optional): - ('PAPI', '7.1.0'), + ('PAPI', '7.0.0'), # PDT source-to-source instrumentation support (optional): ('PDT', '3.25.1'), ] diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb index 035733cf1a3..8b60baea472 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb @@ -33,7 +33,7 @@ dependencies = [ ('OPARI2', '2.0.7'), ('OTF2', '3.0.3'), # Hardware counter support (optional): - ('PAPI', '7.1.0'), + ('PAPI', '7.0.1'), # PDT source-to-source instrumentation support (optional): ('PDT', '3.25.1'), ] diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb index c3189274ea8..51caeb1df08 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb @@ -33,7 +33,7 @@ dependencies = [ ('OPARI2', '2.0.7'), ('OTF2', '3.0.3'), # Hardware counter support (optional): - ('PAPI', '7.1.0'), + ('PAPI', '7.0.1'), # PDT source-to-source instrumentation support (optional): ('PDT', '3.25.1'), ] diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb index ecf8aa15fb7..2e47de3fd8b 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb @@ -30,7 +30,7 @@ dependencies = [ ('OPARI2', '2.0.7'), ('OTF2', '3.0.3'), # Hardware counter support (optional): - ('PAPI', '7.1.0'), + ('PAPI', '7.0.1'), # PDT source-to-source instrumentation support (optional): ('PDT', '3.25.1'), ] From 42cc68c89e75ad53f7ac7e7209237189c8fa7c56 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 9 Oct 2024 18:32:51 +0200 Subject: [PATCH 021/414] Add GDAL and deps --- .../Armadillo/Armadillo-14.0.3-foss-2024a.eb | 25 ++++++ .../a/arpack-ng/arpack-ng-3.9.1-foss-2024a.eb | 36 +++++++++ .../g/GDAL/GDAL-3.9.2-foss-2024a.eb | 81 +++++++++++++++++++ .../h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb | 57 +++++++++++++ 4 files changed, 199 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-14.0.3-foss-2024a.eb create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2024a.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-14.0.3-foss-2024a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-14.0.3-foss-2024a.eb new file mode 100644 index 00000000000..68036ea413e --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-14.0.3-foss-2024a.eb @@ -0,0 +1,25 @@ +name = 'Armadillo' +version = '14.0.3' + +homepage = 'https://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +source_urls = ['https://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ebd6215eeb01ee412fed078c8a9f7f87d4e1f6187ebcdc1bc09f46095a4f4003'] + +builddependencies = [ + ('CMake', '3.29.3'), +] +dependencies = [ + ('Boost', '1.85.0'), + ('HDF5', '1.14.5'), + ('arpack-ng', '3.9.1'), +] + + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2024a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2024a.eb new file mode 100644 index 00000000000..29d5a002190 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2024a.eb @@ -0,0 +1,36 @@ +# Author: Robert Mijakovic + +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.9.1' + +homepage = 'https://github.com/opencollab/arpack-ng' +description = "ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems." + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['f6641deb07fa69165b7815de9008af3ea47eb39b2bb97521fbf74c97aba6e844'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('Eigen', '3.4.0'), +] + +preconfigopts = "sh bootstrap && " +configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +github_account = 'opencollab' + +sanity_check_paths = { + 'files': ['lib64/libarpack.la', 'lib64/libarpack.so', 'lib64/libparpack.la', 'lib64/libparpack.so'], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb new file mode 100644 index 00000000000..3ee9842a103 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb @@ -0,0 +1,81 @@ +easyblock = 'CMakeMake' + +name = 'GDAL' +version = '3.9.2' + +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': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/OSGeo/gdal/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-3.6.2_fix-python-CC-CXX.patch'] +checksums = [ + {'gdal-3.9.2.tar.gz': 'c9767e79ca7245f704bfbcb47d771b2dc317d743536b78d648c3e92b95fbc21e'}, + {'GDAL-3.6.2_fix-python-CC-CXX.patch': '859b874b0c8ff7626a76d51f008bf05b7f89a35b325bdd1d126d2364154acc63'}, +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), + ('Bison', '3.8.2'), +] +dependencies = [ + ('Python', '3.12.3'), + ('netCDF', '4.9.2'), + ('expat', '2.6.2'), + ('GEOS', '3.13.0'), + ('SQLite', '3.45.3'), + ('libarchive', '3.7.4'), + ('libxml2', '2.12.7'), + ('libpng', '1.6.43'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('zlib', '1.3.1'), + ('cURL', '8.7.1'), + ('PCRE', '8.45'), + ('PROJ', '9.4.1'), + ('libgeotiff', '1.7.3'), + ('SciPy-bundle', '2024.05'), + ('HDF5', '1.14.5'), + ('HDF', '4.3.0'), + ('Armadillo', '14.0.3'), + ('CFITSIO', '4.4.1'), + ('zstd', '1.5.6'), + ('giflib', '5.2.2'), + ('json-c', '0.17'), + ('Xerces-C++', '3.2.5'), + ('PCRE2', '10.43'), + ('OpenEXR', '3.2.4'), + ('Brunsli', '0.1'), + ('Qhull', '2020.2'), + ('LERC', '4.0.0'), + ('OpenJPEG', '2.5.2'), + ('SWIG', '4.2.1'), +] + +# iterative build for both static and shared libraries +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF " +local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " + +configopts = [ + local_configopts_common + "-DBUILD_SHARED_LIBS=OFF", + local_configopts_common +] + + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.so'], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import osgeo.%(namelower)s'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5a83567541d --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,57 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.3.0' + +homepage = 'https://support.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': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/HDFGroup/hdf4/archive/refs/tags/'] +sources = ['%(namelower)s%(version)s.tar.gz'] +checksums = ['a6639a556650e6ea8632a17b8188a69de844bdff54ce121a1fd5b92c8dd06cb1'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('Szip', '2.1.1'), + ('zlib', '1.3.1'), + ('libtirpc', '1.3.5'), +] + +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 = [ + local_common_configopts, + # 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", +] + + +sanity_check_paths = { + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', 'lib/libmfhdf.so'], + 'dirs': ['include/%(namelower)s'], +} + +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + +modextrapaths = {'CPATH': 'include/%(namelower)s'} + +moduleclass = 'data' From 23468a0bea0dd365dfee97e4207b6271ba8e3e11 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 9 Oct 2024 18:38:06 +0200 Subject: [PATCH 022/414] Remove HDF4 --- .../h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb | 57 ------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb deleted file mode 100644 index 5a83567541d..00000000000 --- a/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb +++ /dev/null @@ -1,57 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'HDF' -version = '4.3.0' - -homepage = 'https://support.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': '13.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/HDFGroup/hdf4/archive/refs/tags/'] -sources = ['%(namelower)s%(version)s.tar.gz'] -checksums = ['a6639a556650e6ea8632a17b8188a69de844bdff54ce121a1fd5b92c8dd06cb1'] - -builddependencies = [ - ('binutils', '2.42'), - ('Bison', '3.8.2'), - ('flex', '2.6.4'), -] -dependencies = [ - ('libjpeg-turbo', '3.0.1'), - ('Szip', '2.1.1'), - ('zlib', '1.3.1'), - ('libtirpc', '1.3.5'), -] - -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 = [ - local_common_configopts, - # 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", -] - - -sanity_check_paths = { - 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', 'lib/libmfhdf.so'], - 'dirs': ['include/%(namelower)s'], -} - -sanity_check_commands = [ - "h4cc --help", - "ncdump -V", -] - -modextrapaths = {'CPATH': 'include/%(namelower)s'} - -moduleclass = 'data' From 3d24b89f59b087f6262c793340ee65cc59cea837 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 10 Oct 2024 15:17:30 +0200 Subject: [PATCH 023/414] Add Fiona for 2024a --- .../f/Fiona/Fiona-1.10.1-foss-2024a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb new file mode 100644 index 00000000000..3b27879b543 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.10.1' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('GDAL', '3.9.2'), + ('Shapely', '2.0.6'), # optional for 'calc' extras +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '4.0.0', { + 'checksums': ['542cb151461263216a4e37c3fd9afc425feeaf38aaa3025cd2a981fadb422235'], + }), + ('%(namelower)s', version, { + 'use_pip_extras': 'calc', + 'checksums': ['b00ae357669460c6491caba29c2022ff0acfcbde86a95361ea8ff5cd14a86b68'], + }), +] + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['fio --help'] + +moduleclass = 'data' From 72101f27c32b721656820eee211e9de2d97d8bfe Mon Sep 17 00:00:00 2001 From: thoffman Date: Mon, 14 Oct 2024 12:32:14 +0200 Subject: [PATCH 024/414] update 2.0.0b6 --- ...Pulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb | 108 ++++++++++++++++++ 1 file changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..db4efafa541 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,108 @@ +# created by Denis Kristak (Inuits) +# update: Thomas Hoffmann, EMBL +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0b6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('OpenMM', '8.0.0', versionsuffix), + ('Kalign', '3.4.0'), + ('PyYAML', '6.0'), + ('jax', '0.4.25', versionsuffix), # also provides absl-py + ('Biopython', '1.83'), + ('h5py', '3.9.0'), + ('IPython', '8.14.0'), + ('JupyterLab', '4.0.5'), + ('matplotlib', '3.7.2'), + # ('TensorFlow', '2.15.1', versionsuffix), + ('TensorFlow', '2.13.0', versionsuffix), # to be consistent with AF2 ? + ('PyTorch', '2.1.2', versionsuffix), + ('tqdm', '4.66.1'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.1.0'), + ('HMMER', '3.4'), + ('HH-suite', '3.3.0'), + ('dm-haiku', '0.0.12', versionsuffix), + ('Uni-Core', '0.0.3', versionsuffix), +] +local_commit = 'cc4b0af60518c078305bbe4c584691d1ed9ade31' +use_pip = True + +local_tests = [ + 'custom_db', + 'remove_clashes_low_plddt', + 'modelcif', + 'features_with_templates', + 'post_prediction', + # require pyrosetta, analysis aptainer image, and AlphaFold2 data: + # 'pdb_analyser', + # 'get_good_inter_pae', +] +local_testinstall_PATH = """ PATH=$(echo $PYTHONPATH|awk -F ':' '{print $1}')/../../../bin:$PATH """ +exts_list = [ + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('ihm', '1.3', { + 'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'], + }), + ('modelcif', '1.0', { + 'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'], + }), + ('looseversion', '1.1.2'), # for test only ? + ('mmtf-python', '1.1.3', {'modulename': 'mmtf'}), + ('biopandas', '0.5.1.dev0'), # for test only ? + (name, version, { + 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + 'sources': [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': version, + 'recursive': True + } + }], + 'testinstall': True, + 'runtest': '%s pytest -s %s ' % (local_testinstall_PATH, " ".join('test/test_%s.py' % x for x in local_tests)), + 'checksums': [ + None, + ], + }), +] + +fix_python_shebang_for = ['bin/*.py'] +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py', + 'lib/python%(pyshortver)s/site-packages/alphafold/common/stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = [ + "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'", + "create_individual_features.py --helpfull|grep 'Additional allowance for hydrogen bonding'", +] + +moduleclass = 'bio' From 6e3c92dbe99e77e355626c19002751c0e9887376 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 14 Oct 2024 12:32:49 +0200 Subject: [PATCH 025/414] Delete easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb --- .../dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb | 57 ------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb deleted file mode 100644 index a30f458a967..00000000000 --- a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CUDA-12.1.1.eb +++ /dev/null @@ -1,57 +0,0 @@ -# update 0.9.11: Thomas Hoffmann (EMBL) -easyblock = 'PythonBundle' - -name = 'dm-haiku' -version = '0.0.11' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://github.com/deepmind/dm-haiku' -description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural -network library for TensorFlow.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('jax', '0.4.25', versionsuffix), # required by jmp, also provides absl-py - ('PyYAML', '6.0'), - ('CUDA', '12.1.1', '', SYSTEM), - ('tensorstore', '0.1.53'), - ('protobuf-python', '4.24.0'), -] - -use_pip = True - -exts_list = [ - ('jmp', '0.0.4', { - 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], - }), - ('flax', '0.8.1', { - 'checksums': ['ce3d99e9b4c0d2e4d9fc28bc56cced8ba953adfd695aabd24f096b4c8a7e2f92'], - }), - ('optax', '0.1.9', { - 'checksums': ['731f43e8b404f50a5ef025b1261894d7d0300f7ad9cb688ea08f67b40822e94f'], - }), - ('orbax_checkpoint', '0.5.3', { - 'modulename': 'orbax', - 'checksums': ['1572904cbbfe8513927e0d80f80b730e0ef2f680332d3c2810d8443532938b45'], - }), - ('toolz', '0.12.1', { - 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], - }), - ('chex', '0.1.85', { - 'checksums': ['a27cfe87119d6e1fe24ccc1438a59195e6dc1d6e0e10099fcf618c3f64771faf'], - }), - ('nest_asyncio', '1.6.0', { - 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], - }), - (name, version, { - 'modulename': 'haiku', - 'checksums': ['c420a90c6a76c1d941996698840089df0d352806312eaf7b737486f6c6a32ef2'], - }), -] - -sanity_pip_check = True - -moduleclass = 'lib' From 190006958f5cffc94b7df9e31ab54eadaf6f908b Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 14 Oct 2024 12:33:07 +0200 Subject: [PATCH 026/414] Delete easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb --- .../OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb | 70 ------------------- 1 file changed, 70 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb deleted file mode 100644 index 8cf271071e7..00000000000 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb +++ /dev/null @@ -1,70 +0,0 @@ -# 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 -# Update to 7.5.1 -# J. Sassmannshausen / GSTT - -easyblock = 'CMakeMake' - -name = 'OpenMM' -version = '8.0.0' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://openmm.org' -description = "OpenMM is a toolkit for molecular simulation." - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'opt': True} - -source_urls = ['https://github.com/openmm/openmm/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch'] -checksums = [ - 'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e', # 8.0.0.tar.gz - '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd', # OpenMM-8.0.0_add_no_tree_vectorize.patch -] - -builddependencies = [ - ('CMake', '3.26.3'), - ('Doxygen', '1.9.7'), -] - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('SWIG', '4.1.1'), - ('CUDA', '12.1.1', '', SYSTEM), -] - -# Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc, -# Otherwise they will use the wrong path: `/usr/local/cuda/bin/nvcc` -pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && ' -pretestopts += " CTEST_OUTPUT_ON_FAILURE=1" -# Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set -local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(CudaCompiler)" -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], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - -sanity_check_commands = [ - "python -c 'import simtk.openmm'", - "python -m openmm.testInstallation", -] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - -moduleclass = 'bio' From d36e3edadffd484ea817f9270011e10af98e61ef Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 14 Oct 2024 12:33:23 +0200 Subject: [PATCH 027/414] Delete easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb --- .../tensorstore-0.1.53-foss-2023a.eb | 62 ------------------- 1 file changed, 62 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb b/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb deleted file mode 100644 index 0637b6107cb..00000000000 --- a/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb +++ /dev/null @@ -1,62 +0,0 @@ -# Thomas Hoffmann, EMBL Heidlelberg, structures-it@embl.de, 2024/02 -easyblock = 'PythonBundle' - -name = 'tensorstore' -version = '0.1.53' - -homepage = 'https://github.com/google/tensorstore' -description = """TensorStore is an open-source C++ and Python software library designed for -storage and manipulation of large multi-dimensional arrays.""" - -toolchain = {'name': 'foss', 'version': '2023a'} -builddependencies = [ - ('NASM', '2.16.01'), - ('pybind11', '2.11.1'), - ('Bazel', '6.3.1'), - - - - ('PyYAML', '6.0'), - ('zlib', '1.2.13'), - ('LibTIFF', '4.5.0'), - ('snappy', '1.1.10'), - ('Brotli', '1.0.9'), - ('protobuf', '24.0'), - ('bzip2', '1.0.8'), - ('zstd', '1.5.5'), - ('libwebp', '1.3.1'), - ('nlohmann_json', '3.11.2'), - ('Blosc', '1.21.5'), -] - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('ml_dtypes', '0.3.2'), -] - -use_pip = True - - -local_ts_useebbazel = """sed -i 's/bazel_path =.*/""" -local_ts_useebbazel += """bazel_path = os.path.join(os.getenv("EBROOTBAZEL"),"bin", "bazel")/g'""" -local_ts_useebbazel += " bazelisk.py&& " # TODO: patch? -local_ts_version = """sed -i "s/use_scm_version=/version='%(version)s',&/g" setup.py&&""" -local_ts_bzl_exp = """export TENSORSTORE_BAZEL_STARTUP_OPTIONS='--output_user_root %(builddir)s/cache' &&""" -# inject CFLAGS: -local_ts_bzl_exp += """export TENSORSTORE_BAZEL_BUILD_OPTIONS="$(for i in $CFLAGS;do echo --copt=$i; done)" &&""" - - -local_ts_preinstall = local_ts_version + local_ts_useebbazel + local_ts_bzl_exp - -exts_list = [ - (name, version, { - 'installopts': '-v', - 'preinstallopts': local_ts_preinstall, - 'checksums': ['45ef74b2dc9f2cd5f766bc373ded91d681cd021cc69d16592df48abaeb81af56'], - }), -] - -sanity_pip_check = True - -moduleclass = 'lib' From c9b0f98aaba547b2f1de126d0d76fc780958b979 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 14 Oct 2024 12:33:40 +0200 Subject: [PATCH 028/414] Delete easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2023a-CUDA-12.1.1.eb --- ...Pulldown-2.0.0b4-foss-2023a-CUDA-12.1.1.eb | 85 ------------------- 1 file changed, 85 deletions(-) delete mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2023a-CUDA-12.1.1.eb deleted file mode 100644 index 62c616bf500..00000000000 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2023a-CUDA-12.1.1.eb +++ /dev/null @@ -1,85 +0,0 @@ -# created by Denis Kristak (Inuits) -# update: Thomas Hoffmann, EMBL -easyblock = 'PythonBundle' - -name = 'AlphaPulldown' -version = '2.0.0b4' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://github.com/KosinskiLab/AlphaPulldown' -description = """AlphaPulldown is a Python package that streamlines protein-protein -interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('CUDA', '12.1.1', '', SYSTEM), - ('Python', '3.11.3'), - ('OpenMM', '8.0.0', versionsuffix), - ('Kalign', '3.4.0'), - ('PyYAML', '6.0'), - ('jax', '0.4.25', versionsuffix), # also provides absl-py - ('Biopython', '1.83'), - ('h5py', '3.9.0'), - ('IPython', '8.14.0'), - ('JupyterLab', '4.0.5'), - ('matplotlib', '3.7.2'), - ('TensorFlow', '2.15.1', versionsuffix), - ('PyTorch', '2.1.2', versionsuffix), - ('tqdm', '4.66.1'), - ('dm-tree', '0.1.8'), - ('py3Dmol', '2.1.0'), - ('HMMER', '3.4'), - ('HH-suite', '3.3.0'), - ('dm-haiku', '0.0.11', versionsuffix), - ('Uni-Core', '0.0.3', versionsuffix), -] - -use_pip = True - -exts_list = [ - ('contextlib2', '21.6.0', { - 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], - }), - ('ml-collections', '0.1.1', { - 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", - 'sources': ['ml_collections-%(version)s.tar.gz'], - 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], - }), - ('PDBFixer', '1.9', { - 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], - }), - (name, version, { - 'patches': ['AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch'], - 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", - 'sources': [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/KosinskiLab', - 'repo_name': 'AlphaPulldown', - 'tag': '2.0.0b4', - 'recursive': True - } - }], - 'checksums': [ - None, - # AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch: - '0f8ff118bbab50b97a397a9e4de890155b77f868db9913ea3b496d422330bc18' - ], - }), -] - -fix_python_shebang_for = ['bin/*.py'] - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], -} - -sanity_check_commands = ["run_multimer_jobs.py --help | grep 'A script to perform structure prediction'"] - -moduleclass = 'bio' From b6567471ce6c43cdebe369e7a58a68f3c883a62d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 14 Oct 2024 12:33:55 +0200 Subject: [PATCH 029/414] Delete easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch --- ..._af2_biopython_IUPACData_as_SCOPData.patch | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch deleted file mode 100644 index f6a89591dcf..00000000000 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4_af2_biopython_IUPACData_as_SCOPData.patch +++ /dev/null @@ -1,27 +0,0 @@ -# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/08 -# allow to use BioPython >= 1.83 -diff -ru AlphaPulldown/alphafold/alphafold/data/mmcif_parsing.py AlphaPulldown-2.0.0b4_alphfold_SCOP.patch/alphafold/alphafold/data/mmcif_parsing.py ---- AlphaPulldown/alphafold/alphafold/data/mmcif_parsing.py 2024-08-17 15:34:23.000000000 +0200 -+++ AlphaPulldown-2.0.0b4_alphfold_SCOP.patch/alphafold/alphafold/data/mmcif_parsing.py 2024-08-17 15:44:47.460653530 +0200 -@@ -21,7 +21,7 @@ - - from absl import logging - from Bio import PDB --from Bio.Data import SCOPData -+from Bio.Data import IUPACData as SCOPData - - # Type aliases: - ChainId = str -fix import of protein_letters_3to1 from Biopython -author: Kenneth Hoste (HPC-UGent) ---- AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py.orig 2024-06-05 09:30:16.114746286 +0200 -+++ AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py 2024-06-05 09:30:35.242665615 +0200 -@@ -4,7 +4,7 @@ - from alphafold.data.mmcif_parsing import parse - from alphafold.common.residue_constants import residue_atoms, atom_types - from Bio.PDB import NeighborSearch, PDBIO, MMCIFIO --from Bio.PDB.Polypeptide import protein_letters_3to1 -+from Bio.Data.IUPACData import protein_letters_3to1 - from Bio import SeqIO - from colabfold.batch import convert_pdb_to_mmcif - from Bio.PDB import Structure, Model, Chain, Residue From d96e84f16dcc216bdaafa70b17aef5e95dcd2663 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 14 Oct 2024 13:10:48 +0200 Subject: [PATCH 030/414] Update AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb update TensorFlow dependency from 2.13.0 to 2.15.2-CUDA --- .../AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb index db4efafa541..d1a950bddd4 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb @@ -24,8 +24,7 @@ dependencies = [ ('IPython', '8.14.0'), ('JupyterLab', '4.0.5'), ('matplotlib', '3.7.2'), - # ('TensorFlow', '2.15.1', versionsuffix), - ('TensorFlow', '2.13.0', versionsuffix), # to be consistent with AF2 ? + ('TensorFlow', '2.15.1', versionsuffix), ('PyTorch', '2.1.2', versionsuffix), ('tqdm', '4.66.1'), ('dm-tree', '0.1.8'), From cbc778dc189a024af0ba815a528cfeb5ef945532 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 14 Oct 2024 14:58:33 +0200 Subject: [PATCH 031/414] Update easyconfigs.py AlphaPulldown TF2.15.1 multivariant dependency --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d228333cca6..71f38c23ae6 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -655,6 +655,8 @@ def check_dep_vars(self, gen, dep, dep_vars): ('2.5.3;', ['medaka-1.5.0-']), # tensorflow-probability version to TF version ('2.8.4;', ['tensorflow-probability-0.16.0-']), + # AlphaPulldown + ('2.15.1', ['AlphaPulldown-2.0.0b6']), ], # smooth-topk uses a newer version of torchvision 'torchvision': [('0.11.3;', ['smooth-topk-1.0-20210817-'])], From 54d32148cc1ad082e414996050c83df23081e60d Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 15 Oct 2024 00:31:15 +0200 Subject: [PATCH 032/414] adding easyconfigs: Anaconda3-2024.06-1.eb --- .../a/Anaconda3/Anaconda3-2024.06-1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb new file mode 100644 index 00000000000..674a7cc8fd6 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb @@ -0,0 +1,33 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, +# 2019.10, 2020.2, 2020.11, 2022.05, +# 2022.10, 2024.2-1 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +# config upgrade to 2023.09 by Sarah Walters + +# no support for power architecture in 2024.02-1 on https://repo.anaconda.com/archive/, as off 13 Feb 2024 +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2024.06-1' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH) +sources = ['%%(name)s-%%(version)s-Linux-%s.sh' % local_arch] +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': '539bb43d9a52d758d0fdfa1b1b049920ec6f8c6d15ee9fe4a423355fe551a8f7', + '%(name)s-%(version)s-Linux-aarch64.sh': 'b4be0ad2052236882402902a31d32cd37635d3db194a42f977be0d68a8ff1a31', + } +] + +moduleclass = 'lang' From 1eaea1acdef5da61fef008a0b226fef43b1c5e9a Mon Sep 17 00:00:00 2001 From: thoffman Date: Tue, 15 Oct 2024 09:29:49 +0200 Subject: [PATCH 033/414] add missing checksums; use TF-CPU 2.13.0 --- ...Pulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb | 25 +++++++++++-------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb index d1a950bddd4..5f318543631 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb @@ -24,7 +24,8 @@ dependencies = [ ('IPython', '8.14.0'), ('JupyterLab', '4.0.5'), ('matplotlib', '3.7.2'), - ('TensorFlow', '2.15.1', versionsuffix), + # ('TensorFlow', '2.15.1', versionsuffix), + ('TensorFlow', '2.13.0'), # to be consistent with AF2 ? ('PyTorch', '2.1.2', versionsuffix), ('tqdm', '4.66.1'), ('dm-tree', '0.1.8'), @@ -68,25 +69,29 @@ exts_list = [ ('modelcif', '1.0', { 'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'], }), - ('looseversion', '1.1.2'), # for test only ? - ('mmtf-python', '1.1.3', {'modulename': 'mmtf'}), - ('biopandas', '0.5.1.dev0'), # for test only ? + ('looseversion', '1.1.2', { + 'checksums': ['94d80bdbd0b6d57c11b886147ba1601f7d1531571621b81933b34537cbe469ad'], + }), + ('mmtf-python', '1.1.3', { + 'modulename': 'mmtf', + 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], + }), + ('biopandas', '0.5.1.dev0', { + 'checksums': ['6dc9de631babf8221c1ac60230133717039e08911f15e8ac48498c787022de12'], + }), (name, version, { 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + 'runtest': '%s pytest -s %s ' % (local_testinstall_PATH, " ".join('test/test_%s.py' % x for x in local_tests)), 'sources': [{ 'filename': '%(name)s-%(version)s.tar.gz', 'git_config': { 'url': 'https://github.com/KosinskiLab', 'repo_name': 'AlphaPulldown', - 'tag': version, - 'recursive': True + 'tag': version, 'recursive': True } }], 'testinstall': True, - 'runtest': '%s pytest -s %s ' % (local_testinstall_PATH, " ".join('test/test_%s.py' % x for x in local_tests)), - 'checksums': [ - None, - ], + 'checksums': ['41b73bfe91719522713ed155a43cc7dda2474c954d723fe382d9676e41c6e241'], }), ] From 11bc9c065611f101e5b3e2b3421a416ad92836b0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 17 Oct 2024 13:59:32 +0200 Subject: [PATCH 034/414] adding easyconfigs: Spyder-6.0.1-gfbf-2023b.eb, Deprecated-1.2.14-gfbf-2023b.eb, PyQt-builder-1.16.4-GCCcore-13.2.0.eb, PyQt5-5.15.10-GCCcore-13.2.0.eb, Qtconsole-5.6.0-GCCcore-13.2.0.eb, QtPy-2.4.1-GCCcore-13.2.0.eb, Rtree-1.2.0-GCCcore-13.2.0.eb, wrapt-1.16.0-gfbf-2023b.eb --- .../Deprecated-1.2.14-gfbf-2023b.eb | 29 ++++ .../PyQt-builder-1.16.4-GCCcore-13.2.0.eb | 37 ++++ .../p/PyQt5/PyQt5-5.15.10-GCCcore-13.2.0.eb | 112 ++++++++++++ .../q/QtPy/QtPy-2.4.1-GCCcore-13.2.0.eb | 29 ++++ .../Qtconsole-5.6.0-GCCcore-13.2.0.eb | 32 ++++ .../r/Rtree/Rtree-1.2.0-GCCcore-13.2.0.eb | 28 +++ .../s/Spyder/Spyder-6.0.1-gfbf-2023b.eb | 162 ++++++++++++++++++ .../w/wrapt/wrapt-1.16.0-gfbf-2023b.eb | 27 +++ 8 files changed, 456 insertions(+) create mode 100644 easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.16.4-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/q/QtPy/QtPy-2.4.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.6.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/r/Rtree/Rtree-1.2.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb new file mode 100644 index 00000000000..a8c2c5730e3 --- /dev/null +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb @@ -0,0 +1,29 @@ +# author: Denis Kristak (INUITS) +# update: Pavel Tománek (INUITS) + +easyblock = 'PythonBundle' + +name = 'Deprecated' +version = '1.2.14' + +homepage = 'https://github.com/tantale/deprecated' +description = "If you need to mark a function or a method as deprecated, you can use the @deprecated decorator." + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('wrapt', '1.16.0'), +] + + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.16.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.16.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ce86a241e38 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.16.4-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/01 +easyblock = 'PythonBundle' + +name = 'PyQt-builder' +version = '1.16.4' + +homepage = 'https://github.com/Python-PyQt/PyQt-builder' +description = """PyQt-builder is the PEP 517 compliant build system for PyQt and projects that +extend PyQt. It extends the SIP build system and uses Qt's qmake to perform the +actual compilation and installation of extension modules. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.5'), + ('SIP', '6.8.3'), +] + + +exts_list = [ + ('pyqt_builder', version, { + 'modulename': 'pyqtbuild', + 'checksums': ['4515e41ae379be2e54f88a89ecf47cd6e4cac43e862c4abfde18389c2666afdf'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..30cbfa784ca --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-13.2.0.eb @@ -0,0 +1,112 @@ +easyblock = 'PythonBundle' + +name = 'PyQt5' +version = '5.15.10' + +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [ + ('binutils', '2.40'), + ('PyQt-builder', '1.16.4'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Qt5', '5.15.13'), +] +local_sipdir = '%(installdir)s/share/sip' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%s:$PYTHONPATH && " % local_pylibdir + + +local_sip_configopts_common = [ + "--no-make", + "--jobs %(parallel)s", + "--qmake-setting 'QMAKE_CXXFLAGS+=$$(CFLAGS)'", + "--qmake-setting 'QMAKE_CFLAGS+=$$(CFLAGS)'", + "--qmake-setting 'QMAKE_LFLAGS+=$$(LDFLAGS)'", + "--api-dir %(installdir)s/qsci", + "--scripts-dir %(installdir)s/bin", + "--target-dir %s" % local_pylibdir, +] + +local_pyqt5_configopts = [ + "--confirm-license", + "--no-designer-plugin", + "--no-qml-plugin", +] + local_sip_configopts_common + +local_pyqtwebengine_configopts = local_sip_configopts_common +default_easyblock = 'PythonPackage' + +components = [ + ('%s_sip' % name, '12.13.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'checksums': ['7f321daf84b9c9dbca61b80e1ef37bdaffc0e93312edae2cd7da25b953971d91'], + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'easyblock': 'ConfigureMake', + 'configure_cmd': 'sip-build', + 'start_dir': '%(name)s-%(version)s', + 'configure_without_installdir': True, + 'preconfigopts': local_setup_env, + 'configopts': ' '.join(local_pyqt5_configopts), + 'prebuildopts': local_setup_env + "cd build && ", + 'preinstallopts': "cd build && ", + 'checksums': ['d46b7804b1b10a4ff91753f8113e5b5580d2b4462f3226288e2d84497334898a'], + }), + ('PyQtWebEngine', '5.15.7', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'easyblock': 'ConfigureMake', + 'configure_cmd': 'sip-build', + 'start_dir': '%(name)s-%(version)s', + 'configure_without_installdir': True, + 'preconfigopts': local_setup_env, + 'configopts': ' '.join(local_pyqtwebengine_configopts), + 'prebuildopts': local_setup_env + "cd build && ", + 'preinstallopts': "cd build && ", + 'checksums': ['f121ac6e4a2f96ac289619bcfc37f64e68362f24a346553f5d6c42efa4228a4d'], + }) +] + +postinstallcmds = [ + 'mkdir %(installdir)s/share', + 'ln -s --relative %s/%%(name)s/bindings %s' % (local_pylibdir, local_sipdir) +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5']], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'qsci'], +} + +use_pip = True + +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'import %(name)s.QtCore'", + "python -c 'import %(name)s.QtWebEngineWidgets'", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", +] + +modextrapaths = { + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-2.4.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-2.4.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ef825aea14b --- /dev/null +++ b/easybuild/easyconfigs/q/QtPy/QtPy-2.4.1-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'QtPy' +version = '2.4.1' + +homepage = "https://github.com/spyder-ide/qtpy" +description = """QtPy is a small abstraction layer that lets you write applications using a single API call to + either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a5a15ffd519550a1361bdc56ffc07fda56a6af7292f17c7b395d4083af632987'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('PyQt5', '5.15.10'), + ('Python-bundle-PyPI', '2023.10'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.6.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..632269b4830 --- /dev/null +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.6.0-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Qtconsole' +version = '5.6.0' + +homepage = 'https://jupyter.org/' +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media +output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a +terminal, but provides a number of enhancements only possible in a GUI, such as +inline figures, proper multiline editing with syntax highlighting, graphical +calltips, and more.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4c82120a3b53a3d36e3f76e6a1a26ffddf4e1ce2359d56a19889c55e1d73a436'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('IPython', '8.17.2'), + ('QtPy', '2.4.1'), + ('Jupyter-bundle', '20240522'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/Rtree/Rtree-1.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/Rtree/Rtree-1.2.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b0d0844989f --- /dev/null +++ b/easybuild/easyconfigs/r/Rtree/Rtree-1.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Rtree' +version = '1.2.0' + +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': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f5145f7852bf7f95c126fb16bf1a4c2ca9300ae151b07f8a0f7083ea47912675'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('libspatialindex', '1.9.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb new file mode 100644 index 00000000000..7f85770bd79 --- /dev/null +++ b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb @@ -0,0 +1,162 @@ +easyblock = 'PythonBundle' + +name = 'Spyder' +version = '6.0.1' + +homepage = 'https://github.com/spyder-ide/spyder' +description = """Spyder is an interactive Python development environment providing MATLAB-like features in a simple + and light-weighted software.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('poetry', '1.6.1'), + ('maturin', '1.3.1'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('aiohttp', '3.9.5'), + ('IPython', '8.17.2'), + ('jedi', '0.19.1'), + ('jupyter-server', '2.14.0'), + ('Pylint', '3.2.5'), + ('PyZMQ', '25.1.2'), + ('PyQt5', '5.15.10'), + ('Qtconsole', '5.6.0'), + ('Rtree', '1.2.0'), + ('Deprecated', '1.2.14'), + ('tornado', '6.4'), +] + +use_pip = True + +# fix deleting of PYTHONPATH +local_preinstallopts = "sed -i '13,19d' spyder/app/start.py && " +local_preinstallopts += "sed -i '171,173d' spyder/plugins/ipythonconsole/utils/kernelspec.py && " + +exts_list = [ + ('asyncssh', '2.17.0', { + 'checksums': ['3b159c105aa388c1e2245c4faf483f540ada8cad99402281119100166e5edb3c'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '8.0.4', { + 'modulename': 'slugify', + 'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'], + }), + ('types-python-dateutil', '2.9.0.20241003', { + 'modulename': False, + 'checksums': ['58cb85449b2a56d6684e41aeefb4c4280631246a0da1a719bdbe6f3fb0317446'], + }), + ('arrow', '1.3.0', { + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), + ('cookiecutter', '2.6.0', { + 'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'], + }), + ('diff-match-patch', '20230430', { + 'checksums': ['953019cdb9c9d2c9e47b5b12bcff3cf4746fc4598eb406076fa1fc27e6a1f15c'], + }), + ('importlib_metadata', '8.4.0', { + 'checksums': ['9a547d3bc3608b025f93d403fdd1aae741c24fbb8314df4b155675742ce303c5'], + }), + ('numpydoc', '1.8.0', { + 'checksums': ['022390ab7464a44f8737f79f8b31ce1d3cfa4b4af79ccaa1aac5e8368db587fb'], + }), + ('pygithub', '2.4.0', { + 'modulename': 'github', + 'checksums': ['6601e22627e87bac192f1e2e39c6e6f69a43152cfb8f307cee575879320b3051'], + }), + ('pylint_venv', '3.0.3', { + 'checksums': ['df12a17fca39a94acc1c9a0f1dcf68141e90fe685569d78c046695c67c4e55fa'], + }), + ('pyls-spyder', '0.4.0', { + 'checksums': ['45a321c83f64267d82907492c55199fccabda45bc872dd23bf1efd08edac1b0b'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('black', '24.10.0', { + 'checksums': ['846ea64c97afe3bc677b761787993be4991810ecc7a4a937816dd6bddedc4875'], + }), + ('python-lsp-black', '2.0.0', { + 'modulename': False, + 'checksums': ['8286d2d310c566844b3c116b824ada6fccfa6ba228b1a09a0526b74c04e0805f'], + }), + ('docstring-to-markdown', '0.15', { + 'checksums': ['e146114d9c50c181b1d25505054a8d0f7a476837f0da2c19f07e06eaed52b73d'], + }), + ('python-lsp-jsonrpc', '1.1.2', { + 'modulename': False, + 'checksums': ['4688e453eef55cd952bff762c705cedefa12055c0aec17a06f595bcc002cc912'], + }), + ('python_lsp_server', '1.12.0', { + 'modulename': 'pylsp', + 'checksums': ['b6a336f128da03bd9bac1e61c3acca6e84242b8b31055a1ccf49d83df9dc053b'], + }), + ('pyuca', '1.2', { + 'checksums': ['8a382fe74627f08c0d18908c0713ca4a20aad5385f077579e56208beea2893b2'], + }), + ('pyxdg', '0.28', { + 'modulename': 'xdg', + 'checksums': ['3267bb3074e934df202af2ee0868575484108581e6f3cb006af1da35395e88b4'], + }), + ('QDarkStyle', '3.2.3', { + 'checksums': ['0c0b7f74a6e92121008992b369bab60468157db1c02cd30d64a5e9a3b402f1ae'], + }), + ('inflection', '0.5.1', { + 'checksums': ['1a29730d366e996aaacffb2f1f1cb9593dc38e2ddd30c91250c6dde09ea9b417'], + }), + ('qstylizer', '0.2.3', { + 'checksums': ['5f2f5eb2c65c6c45e950462b565fcaa5107a91d1cfc1a85b8e0d831d727ee8f6'], + }), + ('QtAwesome', '1.3.1', { + 'checksums': ['075b2c9ee01cbaf5e3a4bebed0e5529ee8605981355f21dea051b15c1b869e1b'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + ('spyder_kernels', '3.0.0', { + 'checksums': ['3d316ea04802ed1feb366405cca03df2349dc9e35ad8653538d2fe48c0e9417f'], + }), + ('superqt', '0.6.6', { + 'checksums': ['792e09165c8a788ee245bdb784e018f9077fb309253354d86793cdf1d092f99f'], + }), + ('textdistance', '4.6.3', { + 'checksums': ['d6dabc50b4ea832cdcf0e1e6021bd0c7fcd9ade155888d79bb6a3c31fce2dc6f'], + }), + ('three-merge', '0.1.1', { + 'checksums': ['60f6afe144595560d63ae32625351bcef3b94733b54eb97800a9feb0f3d9d970'], + }), + ('watchdog', '5.0.3', { + 'checksums': ['108f42a7f0345042a854d4d0ad0834b741d421330d5f575b81cb27b883500176'], + }), + ('jellyfish', '1.1.0', { + 'checksums': ['2a2eec494c81dc1eb23dfef543110dad1873538eccaffabea8520bdac8aecbc1'], + }), + ('platformdirs', '3.11.0', { + 'checksums': ['cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'preinstallopts': local_preinstallopts, + 'checksums': ['709782e88091588bbe614de6ebbde7b47544a4d6c225e199de5ad22b77d8b130'], + }), +] + +sanity_check_paths = { + 'files': ['bin/spyder'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["spyder --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb new file mode 100644 index 00000000000..40f123c00cb --- /dev/null +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'wrapt' +version = '1.16.0' + +homepage = 'https://pypi.org/project/wrapt/' +description = """The aim of the wrapt module is to provide a transparent object +proxy for Python, which can be used as the basis for the construction of +function wrappers and decorator functions.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), +] + +moduleclass = 'tools' From 4164dcb9de87e0309e22831e0a5e24140d0289a6 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 18 Oct 2024 11:38:58 +0200 Subject: [PATCH 035/414] fix SLURM NTASK in test step --- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index 29a94b22448..cd64d6ed49a 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -45,10 +45,13 @@ dependencies = [ local_preinstallopts = "sed -i 's/pydantic<2.0/pydantic/' %(builddir)s/%(name)s/%(name)s-%(version)s/setup.cfg && " # ignore the failing part of ddpm test - seems constraints are wrong -# https://github.com/vanderschaarlab/synthcity/blob/v0.2.10/tests/plugins/generic/test_ddpm.py#L114 +# see https://github.com/vanderschaarlab/synthcity/blob/v0.2.10/tests/plugins/generic/test_ddpm.py#L114 local_pretestopts = ( "sed -i '138,144d' %(builddir)s/%(name)s/%(name)s-%(version)s/tests/plugins/generic/test_ddpm.py && " ) +# solve problem with PyTorch-Lightning _validate_srun_variables method +# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21141#issuecomment-2318854045 +local_pretestopts += "export SLURM_NTASKS_PER_NODE=$SLURM_NTASKS && " # fix invalid syntax of xgbse/setup.py local_xgbse_preinstallopts = r"sed -i -e '45,49d' -e 's/pandas>=1.0.\*/pandas>=1.0.0/' setup.py && " From 10cf300e3501a8057f886e3237f909486d0c2297 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 21 Oct 2024 14:18:28 +0200 Subject: [PATCH 036/414] add ecs for deps and remove them from exts_list --- .../b/black/black-24.10.0-GCCcore-13.2.0.eb | 42 +++++++++++++++ .../cookiecutter-2.6.0-GCCcore-13.2.0.eb | 39 ++++++++++++++ .../numpydoc/numpydoc-1.8.0-GCCcore-13.2.0.eb | 29 +++++++++++ ...python-lsp-server-1.12.0-GCCcore-13.2.0.eb | 43 +++++++++++++++ .../python-slugify-8.0.4-GCCcore-13.2.0.eb | 27 ++++++++++ .../s/Spyder/Spyder-6.0.1-gfbf-2023b.eb | 52 ++----------------- .../text-unidecode-1.3-GCCcore-13.2.0.eb | 25 +++++++++ .../wurlitzer-3.1.1-GCCcore-13.2.0.eb | 26 ++++++++++ 8 files changed, 235 insertions(+), 48 deletions(-) create mode 100644 easybuild/easyconfigs/b/black/black-24.10.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/c/cookiecutter/cookiecutter-2.6.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/numpydoc/numpydoc-1.8.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-lsp-server/python-lsp-server-1.12.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/t/text-unidecode/text-unidecode-1.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/b/black/black-24.10.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/black/black-24.10.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a973a0c1cf3 --- /dev/null +++ b/easybuild/easyconfigs/b/black/black-24.10.0-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'black' +version = '24.10.0' + +homepage = 'https://black.readthedocs.io' +description = """Black is the uncompromising Python code formatter. +By using it, you agree to cede control over minutiae of hand-formatting. +In return, Black gives you speed, determinism, and freedom from pycodestyle nagging about formatting. +You will save time and mental energy for more important matters. + +Blackened code looks the same regardless of the project you're reading. +Formatting becomes transparent after a while and you can focus on the content instead. + +Black makes code review faster by producing the smallest diffs possible. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mypy-extensions', '1.0.0', { + 'source_tmpl': 'mypy_extensions-%(version)s.tar.gz', + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + (name, version, { + 'checksums': ['846ea64c97afe3bc677b761787993be4991810ecc7a4a937816dd6bddedc4875'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cookiecutter/cookiecutter-2.6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cookiecutter/cookiecutter-2.6.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..669b9407374 --- /dev/null +++ b/easybuild/easyconfigs/c/cookiecutter/cookiecutter-2.6.0-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'cookiecutter' +version = '2.6.0' + +homepage = 'https://github.com/cookiecutter/cookiecutter' +description = """A command-line utility that creates projects from project templates. +E.g. creating a Python package project from a Python package project template.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('PyYAML', '6.0.1'), + ('python-slugify', '8.0.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('types-python-dateutil', '2.9.0.20241003', { + 'modulename': False, + 'checksums': ['58cb85449b2a56d6684e41aeefb4c4280631246a0da1a719bdbe6f3fb0317446'], + }), + ('arrow', '1.3.0', { + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + (name, version, { + 'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpydoc/numpydoc-1.8.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/numpydoc/numpydoc-1.8.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..96254b855c2 --- /dev/null +++ b/easybuild/easyconfigs/n/numpydoc/numpydoc-1.8.0-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'numpydoc' +version = '1.8.0' + +homepage = 'https://numpydoc.readthedocs.io/' +description = """Sphinx extension to support docstrings in Numpy format + +This package provides the numpydoc Sphinx extension for handling docstrings formatted +according to the NumPy documentation format. +The extension also adds the code description directives np:function, np-c:function, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['022390ab7464a44f8737f79f8b31ce1d3cfa4b4af79ccaa1aac5e8368db587fb'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-lsp-server/python-lsp-server-1.12.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/python-lsp-server/python-lsp-server-1.12.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c0ad5338dfa --- /dev/null +++ b/easybuild/easyconfigs/p/python-lsp-server/python-lsp-server-1.12.0-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'python-lsp-server' +version = '1.12.0' + +homepage = 'https://github.com/spyder-ide/spyder' +description = """Python Language Server for the Language Server Protocol +A Python 3.8+ implementation of the Language Server Protocol. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.5'), + ('Pylint', '3.2.5'), + ('black', '24.10.0'), + ('jedi', '0.19.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('docstring-to-markdown', '0.15', { + 'checksums': ['e146114d9c50c181b1d25505054a8d0f7a476837f0da2c19f07e06eaed52b73d'], + }), + ('python-lsp-jsonrpc', '1.1.2', { + 'modulename': 'pylsp_jsonrpc', + 'checksums': ['4688e453eef55cd952bff762c705cedefa12055c0aec17a06f595bcc002cc912'], + }), + ('python-lsp-black', '2.0.0', { + 'modulename': 'pylsp_black', + 'checksums': ['8286d2d310c566844b3c116b824ada6fccfa6ba228b1a09a0526b74c04e0805f'], + }), + (name, version, { + 'modulename': 'pylsp', + 'source_tmpl': 'python_lsp_server-%(version)s.tar.gz', + 'checksums': ['b6a336f128da03bd9bac1e61c3acca6e84242b8b31055a1ccf49d83df9dc053b'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0320e308105 --- /dev/null +++ b/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'python-slugify' +version = '8.0.4' + +homepage = 'https://github.com/un33k/python-slugify' +description = """Best attempt to create slugs from unicode strings while keeping it DRY.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.5'), + ('text-unidecode', '1.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'slugify', + 'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb index 7f85770bd79..4cb1124e13f 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb @@ -27,6 +27,10 @@ dependencies = [ ('Rtree', '1.2.0'), ('Deprecated', '1.2.14'), ('tornado', '6.4'), + ('numpydoc', '1.8.0'), + ('cookiecutter', '2.6.0'), + ('wurlitzer', '3.1.1'), + ('python-lsp-server', '1.12.0'), ] use_pip = True @@ -39,35 +43,12 @@ exts_list = [ ('asyncssh', '2.17.0', { 'checksums': ['3b159c105aa388c1e2245c4faf483f540ada8cad99402281119100166e5edb3c'], }), - ('binaryornot', '0.4.4', { - 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], - }), - ('text-unidecode', '1.3', { - 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], - }), - ('python-slugify', '8.0.4', { - 'modulename': 'slugify', - 'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'], - }), - ('types-python-dateutil', '2.9.0.20241003', { - 'modulename': False, - 'checksums': ['58cb85449b2a56d6684e41aeefb4c4280631246a0da1a719bdbe6f3fb0317446'], - }), - ('arrow', '1.3.0', { - 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], - }), - ('cookiecutter', '2.6.0', { - 'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'], - }), ('diff-match-patch', '20230430', { 'checksums': ['953019cdb9c9d2c9e47b5b12bcff3cf4746fc4598eb406076fa1fc27e6a1f15c'], }), ('importlib_metadata', '8.4.0', { 'checksums': ['9a547d3bc3608b025f93d403fdd1aae741c24fbb8314df4b155675742ce303c5'], }), - ('numpydoc', '1.8.0', { - 'checksums': ['022390ab7464a44f8737f79f8b31ce1d3cfa4b4af79ccaa1aac5e8368db587fb'], - }), ('pygithub', '2.4.0', { 'modulename': 'github', 'checksums': ['6601e22627e87bac192f1e2e39c6e6f69a43152cfb8f307cee575879320b3051'], @@ -78,27 +59,6 @@ exts_list = [ ('pyls-spyder', '0.4.0', { 'checksums': ['45a321c83f64267d82907492c55199fccabda45bc872dd23bf1efd08edac1b0b'], }), - ('mypy_extensions', '1.0.0', { - 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], - }), - ('black', '24.10.0', { - 'checksums': ['846ea64c97afe3bc677b761787993be4991810ecc7a4a937816dd6bddedc4875'], - }), - ('python-lsp-black', '2.0.0', { - 'modulename': False, - 'checksums': ['8286d2d310c566844b3c116b824ada6fccfa6ba228b1a09a0526b74c04e0805f'], - }), - ('docstring-to-markdown', '0.15', { - 'checksums': ['e146114d9c50c181b1d25505054a8d0f7a476837f0da2c19f07e06eaed52b73d'], - }), - ('python-lsp-jsonrpc', '1.1.2', { - 'modulename': False, - 'checksums': ['4688e453eef55cd952bff762c705cedefa12055c0aec17a06f595bcc002cc912'], - }), - ('python_lsp_server', '1.12.0', { - 'modulename': 'pylsp', - 'checksums': ['b6a336f128da03bd9bac1e61c3acca6e84242b8b31055a1ccf49d83df9dc053b'], - }), ('pyuca', '1.2', { 'checksums': ['8a382fe74627f08c0d18908c0713ca4a20aad5385f077579e56208beea2893b2'], }), @@ -118,10 +78,6 @@ exts_list = [ ('QtAwesome', '1.3.1', { 'checksums': ['075b2c9ee01cbaf5e3a4bebed0e5529ee8605981355f21dea051b15c1b869e1b'], }), - ('wurlitzer', '3.1.1', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], - }), ('spyder_kernels', '3.0.0', { 'checksums': ['3d316ea04802ed1feb366405cca03df2349dc9e35ad8653538d2fe48c0e9417f'], }), diff --git a/easybuild/easyconfigs/t/text-unidecode/text-unidecode-1.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/text-unidecode/text-unidecode-1.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..669e440cb4d --- /dev/null +++ b/easybuild/easyconfigs/t/text-unidecode/text-unidecode-1.3-GCCcore-13.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonBundle' + +name = 'text-unidecode' +version = '1.3' + +homepage = 'https://github.com/kmike/text-unidecode' +description = """Text-unidecode is the most basic port of the Text::Unidecode Perl library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..489d841f2a0 --- /dev/null +++ b/easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'wurlitzer' +version = '3.1.1' + +homepage = 'https://github.com/minrk/wurlitzer' +description = """Capture C-level output in context managers + +For more details on why this is needed, please read this blog post: +https://eli.thegreenplace.net/2015/redirecting-all-kinds-of-stdout-in-python +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['bfb9144ab9f02487d802b9ff89dbd3fa382d08f73e12db8adc4c2fb00cd39bd9'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From 2b74dfa776abd8eb534c0c43bb971485653b19da Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 22 Oct 2024 11:44:05 +0200 Subject: [PATCH 037/414] update text-unicode EC to PythonPackage --- .../text-unidecode-1.3-GCCcore-13.2.0.eb | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/t/text-unidecode/text-unidecode-1.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/text-unidecode/text-unidecode-1.3-GCCcore-13.2.0.eb index 669e440cb4d..66af7e16ce8 100644 --- a/easybuild/easyconfigs/t/text-unidecode/text-unidecode-1.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/t/text-unidecode/text-unidecode-1.3-GCCcore-13.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'text-unidecode' version = '1.3' @@ -8,18 +8,14 @@ description = """Text-unidecode is the most basic port of the Text::Unidecode Pe toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +sources = [SOURCE_TAR_GZ] +checksums = ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'] + builddependencies = [('binutils', '2.40')] -dependencies = [ - ('Python', '3.11.5'), -] +dependencies = [('Python', '3.11.5')] use_pip = True +download_dep_fail = True sanity_pip_check = True -exts_list = [ - (name, version, { - 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], - }), -] - moduleclass = 'devel' From 8a99b68bfe123c9cf97f9ed7a7b9e117767cddfb Mon Sep 17 00:00:00 2001 From: tanmoy1989 Date: Tue, 29 Oct 2024 12:39:52 +0000 Subject: [PATCH 038/414] adding easyconfigs: orjson-3.10.10-GCCcore-13.2.0.eb --- .../o/orjson/orjson-3.10.10-GCCcore-13.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/orjson/orjson-3.10.10-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/o/orjson/orjson-3.10.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/orjson/orjson-3.10.10-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6063a217204 --- /dev/null +++ b/easybuild/easyconfigs/o/orjson/orjson-3.10.10-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'orjson' +version = '3.10.10' + +homepage = 'https://github.com/ijl/orjson' +description = """Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.5.0', '-Rust-1.76.0'), +] +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True + +exts_list = [ + ('ruff', '0.7.0', { + 'checksums': ['47a86360cf62d9cd53ebfb0b5eb0e882193fc191c6d717e8bef4462bc3b9ea2b'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('mypy', '1.13.0', { + 'checksums': ['0291a61b6fbf3e6673e3405cfcc0e7650bebc7939659fdca2702958038bd835e'], + }), + (name, version, { + 'checksums': ['37949383c4df7b4337ce82ee35b6d7471e55195efa7dcb45ab8226ceadb0fe3b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From fd45c7fa111f0374425e1b8d4891ee97c6bd8351 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 30 Oct 2024 12:39:10 +0100 Subject: [PATCH 039/414] adding easyconfigs: FDS-6.9.1-intel-2023a.eb --- .../f/FDS/FDS-6.9.1-intel-2023a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.9.1-intel-2023a.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.9.1-intel-2023a.eb b/easybuild/easyconfigs/f/FDS/FDS-6.9.1-intel-2023a.eb new file mode 100644 index 00000000000..cda862525f9 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.9.1-intel-2023a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.9.1' + +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': '2023a'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['e0fe22d1386dc06512489ddf190dbdbee4c9865856f4a7ca48aec8425b4c0867'] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +buildopts = 'impi_intel_linux_openmp &&' +buildopts += ' cd %(installdir)s/Build && ln -s fds_impi_intel_linux_openmp fds' + +modextrapaths = {'PATH': 'Build'} + +sanity_check_paths = { + 'files': ['Build/fds'], + 'dirs': [], +} + +sanity_check_commands = [ + "fds 2>&1 | grep 'MPI version'", +] + +moduleclass = 'phys' From 4cb831f5c59a3592c0c9c58701da13c68d22f36b Mon Sep 17 00:00:00 2001 From: software Date: Thu, 31 Oct 2024 17:00:01 +0000 Subject: [PATCH 040/414] adding easyconfigs: Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb, prokka-1.14.5-gompi-2023a.eb --- .../Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb | 28 +++++++++++ .../p/prokka/prokka-1.14.5-gompi-2023a.eb | 50 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..8c8af50568f --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.36.1'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb new file mode 100644 index 00000000000..05fe75468f6 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.14.1'), + ('Java', '11', '', SYSTEM), + ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20230722'), + ('tbl2asn', '20230713', '-linux64', SYSTEM), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' From 8dd4e0cac8db7fc34c0c57fac9b9ee60cf819b50 Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 1 Nov 2024 13:55:54 +0100 Subject: [PATCH 041/414] Update GEOS version in GDAL-3.9.2-foss-2024a.eb --- easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb index 3ee9842a103..85b6186916e 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb @@ -29,7 +29,7 @@ dependencies = [ ('Python', '3.12.3'), ('netCDF', '4.9.2'), ('expat', '2.6.2'), - ('GEOS', '3.13.0'), + ('GEOS', '3.12.2'), ('SQLite', '3.45.3'), ('libarchive', '3.7.4'), ('libxml2', '2.12.7'), From 829a7d4eaaca79d55a93bdf8d276f6031034ef17 Mon Sep 17 00:00:00 2001 From: Maxim Date: Sat, 2 Nov 2024 00:44:22 +0100 Subject: [PATCH 042/414] Update Fiona-1.10.1-foss-2024a.eb --- easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb index 3b27879b543..a46045749ab 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb @@ -12,6 +12,10 @@ packages such as pyproj, Rtree, and Shapely.""" toolchain = {'name': 'foss', 'version': '2024a'} +builddependencies = [ + ('Cython', '3.0.10'), +] + dependencies = [ ('Python', '3.12.3'), ('GDAL', '3.9.2'), From 4a19dc7ac11fc8291a1eebebde6b9b9412a97ab7 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 6 Nov 2024 18:48:43 +0100 Subject: [PATCH 043/414] adding easyconfigs: PDM-2.18.2-GCCcore-13.2.0.eb, tiktoken-0.7.0-GCCcore-13.2.0.eb, openai-python-1.39.0-foss-2023b.eb --- .../openai-python-1.39.0-foss-2023b.eb | 51 +++++++ .../p/PDM/PDM-2.18.2-GCCcore-13.2.0.eb | 57 ++++++++ .../tiktoken/tiktoken-0.7.0-GCCcore-13.2.0.eb | 136 ++++++++++++++++++ 3 files changed, 244 insertions(+) create mode 100644 easybuild/easyconfigs/o/openai-python/openai-python-1.39.0-foss-2023b.eb create mode 100644 easybuild/easyconfigs/p/PDM/PDM-2.18.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/o/openai-python/openai-python-1.39.0-foss-2023b.eb b/easybuild/easyconfigs/o/openai-python/openai-python-1.39.0-foss-2023b.eb new file mode 100644 index 00000000000..1928880bb43 --- /dev/null +++ b/easybuild/easyconfigs/o/openai-python/openai-python-1.39.0-foss-2023b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'openai-python' +version = '1.39.0' + +homepage = 'https://github.com/openai/openai-python' +description = """ +The OpenAI Python library provides convenient access to the OpenAI REST API from any +Python 3.7+ application. The library includes type definitions for all request params and +response fields, and offers both synchronous and asynchronous clients powered by httpx. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('pydantic', '2.7.4'), + ('typing-extensions', '4.10.0'), + ('tqdm', '4.66.2'), +] + +exts_list = [ + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('httpcore', '1.0.5', { + 'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61'], + }), + ('httpx', '0.27.0', { + 'checksums': ['a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5'], + }), + ('anyio', '4.4.0', { + 'checksums': ['5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94'], + }), + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('openai', version, { + 'checksums': ['0cea446082f50985f26809d704a97749cb366a1ba230ef432c684a9745b3f2d9'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PDM/PDM-2.18.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PDM/PDM-2.18.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8fa515508dd --- /dev/null +++ b/easybuild/easyconfigs/p/PDM/PDM-2.18.2-GCCcore-13.2.0.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'PDM' +version = '2.18.2' + +homepage = 'https://pdm-project.org' +description = "A modern Python package and dependency manager supporting the latest PEP standards." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.6.1'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('pdm_backend', '2.3.3', { + 'modulename': 'pdm.backend', + 'checksums': ['a8616f628ec84353d7a0ba86b228dcf01bab5debc9e4d1a29e5311a52425d594'], + }), + ('installer', '0.7.0', {'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631']}), + ('sniffio', '1.3.1', {'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc']}), + ('h11', '0.14.0', {'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d']}), + ('httpcore', '1.0.5', {'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61']}), + ('anyio', '4.4.0', {'checksums': ['5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94']}), + ('httpx', '0.27.2', {'checksums': ['f7c2be1d2f3c3c3160d441802406b206c2b76f5947b11115e6df10c6c65e66c2']}), + ('unearth', '0.17.2', {'checksums': ['0b8a2afd3476f1ab6155fc579501ac47fffe43547d88a70e5a5b76a7fe6caa2c']}), + ('installer', '0.7.0', {'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631']}), + ('truststore', '0.9.2', {'checksums': ['a1dee0d0575ff22d2875476343783a5d64575419974e228f3248772613c3d993']}), + ('resolvelib', '1.0.1', {'checksums': ['04ce76cbd63fded2078ce224785da6ecd42b9564b1390793f64ddecbe997b309']}), + ('python-dotenv', '1.0.1', { + 'modulename': 'dotenv', + 'checksums': ['e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca'], + }), + ('pyproject_hooks', '1.1.0', {'checksums': ['4b37730834edbd6bd37f26ece6b44802fb1c1ee2ece0e54ddff8bfc06db86965']}), + ('pbs-installer', '2024.9.9', { + 'source_tmpl': 'pbs_installer-%(version)s.tar.gz', + 'checksums': ['bed162d05ef71c53a0e5e5c6349bab1b07a3d0e5af1800d619a4414a1fda309a'], + }), + ('hishel', '0.0.30', {'checksums': ['656393ee77e9c39a0d6c527c74810e15d96e598dcb9b191f20a788608ceaca99']}), + ('findpython', '0.6.1', {'checksums': ['56e52b409a92bcbd495cf981c85acf137f3b3e51cc769b46eba219bb1ab7533c']}), + ('dep-logic', '0.4.6', { + 'source_tmpl': 'dep_logic-%(version)s.tar.gz', + 'checksums': ['673d45402e9f11c4e501b08ebaea1efaa5e9bc6f69410684a9e448f8f5b26d6a'], + }), + ('blinker', '1.8.2', {'checksums': ['8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83']}), + ('pdm', version, {'checksums': ['6d93a18d52edca056fafed7b262fe48ddc61984dabf73eb9365ad61a90caebb6']}), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8bb760b89cc --- /dev/null +++ b/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-13.2.0.eb @@ -0,0 +1,136 @@ +easyblock = 'CargoPythonPackage' + +name = 'tiktoken' +version = '0.7.0' +_rust_ver = '1.76.0' + +homepage = 'https://github.com/openai/tiktoken' +description = "tiktoken is a fast BPE tokeniser for use with OpenAI's models" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', _rust_ver), + ('maturin', '1.5.0', '-Rust-%s' % _rust_ver), + ('hypothesis', '6.90.0'), + ('setuptools-rust', '1.8.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), # regex (and pytest for tests) +] + +crates = [ + ('aho-corasick', '1.1.3'), + ('autocfg', '1.2.0'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bstr', '1.9.1'), + ('cfg-if', '1.0.0'), + ('fancy-regex', '0.11.0'), + ('heck', '0.4.1'), + ('indoc', '2.0.5'), + ('libc', '0.2.153'), + ('lock_api', '0.4.11'), + ('memchr', '2.7.2'), + ('memoffset', '0.9.1'), + ('once_cell', '1.19.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.9'), + ('portable-atomic', '1.6.0'), + ('proc-macro2', '1.0.79'), + ('pyo3', '0.20.3'), + ('pyo3-build-config', '0.20.3'), + ('pyo3-ffi', '0.20.3'), + ('pyo3-macros', '0.20.3'), + ('pyo3-macros-backend', '0.20.3'), + ('quote', '1.0.36'), + ('redox_syscall', '0.4.1'), + ('regex', '1.10.4'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.3'), + ('rustc-hash', '1.1.0'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.197'), + ('serde_derive', '1.0.197'), + ('smallvec', '1.13.2'), + ('syn', '2.0.58'), + ('target-lexicon', '0.12.14'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('windows-targets', '0.48.5'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_msvc', '0.48.5'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'tiktoken-0.7.0.tar.gz': '1077266e949c24e0291f6c350433c6f0971365ece2b173a23bc3b9f9defef6b6'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'autocfg-1.2.0.tar.gz': 'f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80'}, + {'bit-set-0.5.3.tar.gz': '0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1'}, + {'bit-vec-0.6.3.tar.gz': '349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'bstr-1.9.1.tar.gz': '05efc5cfd9110c8416e471df0e96702d58690178e206e61b7173706673c93706'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'fancy-regex-0.11.0.tar.gz': 'b95f7c0680e4142284cf8b22c14a476e87d61b004a3a0861872b32ef7ead40a2'}, + {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'}, + {'indoc-2.0.5.tar.gz': 'b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5'}, + {'libc-0.2.153.tar.gz': '9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd'}, + {'lock_api-0.4.11.tar.gz': '3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45'}, + {'memchr-2.7.2.tar.gz': '6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d'}, + {'memoffset-0.9.1.tar.gz': '488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a'}, + {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'}, + {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'}, + {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'}, + {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'}, + {'proc-macro2-1.0.79.tar.gz': 'e835ff2298f5721608eb1a980ecaee1aef2c132bf95ecc026a11b7bf3c01c02e'}, + {'pyo3-0.20.3.tar.gz': '53bdbb96d49157e65d45cc287af5f32ffadd5f4761438b527b055fb0d4bb8233'}, + {'pyo3-build-config-0.20.3.tar.gz': 'deaa5745de3f5231ce10517a1f5dd97d53e5a2fd77aa6b5842292085831d48d7'}, + {'pyo3-ffi-0.20.3.tar.gz': '62b42531d03e08d4ef1f6e85a2ed422eb678b8cd62b762e53891c05faf0d4afa'}, + {'pyo3-macros-0.20.3.tar.gz': '7305c720fa01b8055ec95e484a6eca7a83c841267f0dd5280f0c8b8551d2c158'}, + {'pyo3-macros-backend-0.20.3.tar.gz': '7c7e9b68bb9c3149c5b0cade5d07f953d6d125eb4337723c4ccdb665f1f96185'}, + {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'}, + {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'}, + {'regex-1.10.4.tar.gz': 'c117dbdfde9c8308975b6a18d71f3f385c89461f7b3fb054288ecf2a2058ba4c'}, + {'regex-automata-0.4.6.tar.gz': '86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea'}, + {'regex-syntax-0.8.3.tar.gz': 'adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56'}, + {'rustc-hash-1.1.0.tar.gz': '08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2'}, + {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'}, + {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'}, + {'serde_derive-1.0.197.tar.gz': '7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b'}, + {'smallvec-1.13.2.tar.gz': '3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67'}, + {'syn-2.0.58.tar.gz': '44cfb93f38070beee36b3fef7d4f5a16f27751d94b187b666a5cc5e9b0d30687'}, + {'target-lexicon-0.12.14.tar.gz': 'e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# https://github.com/openai/tiktoken/issues/194 +runtest = ( + 'ln -s $PWD/tests ../tests_%(name)s' + ' && cd ..' + ' && pytest tests_%(name)s/' +) +testinstall = True + +moduleclass = 'lib' From 0a4b966c7d8817e6c9a6966e200d783b4afbed74 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 7 Nov 2024 12:14:35 +0100 Subject: [PATCH 044/414] Update openai-python-1.39.0-foss-2023b.eb - update pydantic version --- .../o/openai-python/openai-python-1.39.0-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/openai-python/openai-python-1.39.0-foss-2023b.eb b/easybuild/easyconfigs/o/openai-python/openai-python-1.39.0-foss-2023b.eb index 1928880bb43..579cc0124f5 100644 --- a/easybuild/easyconfigs/o/openai-python/openai-python-1.39.0-foss-2023b.eb +++ b/easybuild/easyconfigs/o/openai-python/openai-python-1.39.0-foss-2023b.eb @@ -19,7 +19,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.5'), ('SciPy-bundle', '2023.11'), - ('pydantic', '2.7.4'), + ('pydantic', '2.6.4'), ('typing-extensions', '4.10.0'), ('tqdm', '4.66.2'), ] From 87fee9275e95b1216617f2cfd83bceaf8d936099 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 7 Nov 2024 14:33:13 +0100 Subject: [PATCH 045/414] adding easyconfigs: VEP-113.0-GCC-12.3.0.eb, Archive-Zip-1.68-GCCcore-12.3.0.eb, DBD-mysql-4.050-GCC-12.3.0.eb, Bio-DB-HTS-3.01-GCC-12.3.0.eb, Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb --- .../Archive-Zip-1.68-GCCcore-12.3.0.eb | 32 ++++++++++++++ .../Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb | 32 ++++++++++++++ .../Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb | 31 ++++++++++++++ .../d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb | 30 +++++++++++++ .../easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb | 42 +++++++++++++++++++ 5 files changed, 167 insertions(+) create mode 100644 easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2ecc296bdf1 --- /dev/null +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Archive-Zip' +version = '1.68' + +homepage = 'https://metacpan.org/pod/Archive::Zip' +description = "Provide an interface to ZIP archive files." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Perl', '5.36.1'), + ('UnZip', '6.0'), + ('Zip', '3.0'), +] + +options = {'modulename': 'Archive::Zip'} + +sanity_check_paths = { + 'files': ['bin/crc32'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb new file mode 100644 index 00000000000..1714b928bbc --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Bio-DB-HTS' +version = '3.01' + +homepage = 'https://metacpan.org/release/Bio-DB-HTS' +description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/'] +sources = ['Bio-DB-HTS-%(version)s.tar.gz'] +checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42'] + +builddependencies = [('pkgconf', '1.9.5')] + +dependencies = [ + ('Perl', '5.36.1'), + ('BioPerl', '1.7.8'), + ('HTSlib', '1.18'), +] + +preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB" + +options = {'modulename': 'Bio::DB::HTS'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d483a1964f4 --- /dev/null +++ b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'Compress-Raw-Zlib' +version = '2.213' + +homepage = 'https://metacpan.org/pod/Compress::Raw::Zlib' +description = "Low-Level Interface to zlib or zlib-ng compression library" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['56b21c99cb3a3a7f7876a74dd05daa3f41fc9143ddd4dc98f8e46710a106af45'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Perl', '5.36.1'), + ('zlib', '1.2.13'), +] + +options = {'modulename': 'Compress::Raw::Zlib'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/Compress/Raw/Zlib.pm'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb new file mode 100644 index 00000000000..eec33081a4c --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.050' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['4f48541ff15a0a7405f76adc10f81627c33996fbf56c95c26c094444c0928d78'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('MariaDB', '11.6.0'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql.pm' % ARCH], + 'dirs': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql' % ARCH], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..0419059c6ad --- /dev/null +++ b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb @@ -0,0 +1,42 @@ +name = 'VEP' +version = '113.0' + +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': '12.3.0'} + +source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5bb9aa8098d36c75076204693e13ef38b43c57dfce3d7d0169d119a5b4f87164'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Archive-Zip', '1.68'), + ('DBD-mysql', '4.050'), + ('BioPerl', '1.7.8'), + ('Bio-DB-HTS', '3.01'), + # VEP requires Compress::Raw::Zlib >= 2.103 + ('Compress-Raw-Zlib', '2.213'), +] + +# To select all species use 'all' (but this was broken as of 2024.02.01 and species need to explicitly listed +# with comma separation, see https://github.com/Ensembl/ensembl-vep/issues/1364#issuecomment-1753080504) +species = 'cyprinus_carpio_carpio' + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", "") + +exts_list = [ + ('Bio::EnsEMBL::XS', '2.3.2', { + 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], + }), +] + +moduleclass = 'bio' From 0126a76f0db22ce3b168c4696e3b8d6468a849b4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 8 Nov 2024 10:08:36 +0100 Subject: [PATCH 046/414] Update and rename AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb to AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb update 2.0.0 --- ...2.1.1.eb => AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/a/AlphaPulldown/{AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb => AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb} (97%) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb similarity index 97% rename from easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb rename to easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb index 5f318543631..22ad35947c8 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'AlphaPulldown' -version = '2.0.0b6' +version = '2.0.0' versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://github.com/KosinskiLab/AlphaPulldown' @@ -91,7 +91,7 @@ exts_list = [ } }], 'testinstall': True, - 'checksums': ['41b73bfe91719522713ed155a43cc7dda2474c954d723fe382d9676e41c6e241'], + 'checksums': ['e338195987e003f3caadb06bda0ca56dece87e358738143ea72662f9ad69b1d4], }), ] From b3c9399681b4c762a84e0f7569f9066645c147f8 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 8 Nov 2024 10:34:36 +0100 Subject: [PATCH 047/414] Update AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb add ext. immutabledict; fix tensorflow-cpu requirement --- .../AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb index 22ad35947c8..4c54a12c72f 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb @@ -12,6 +12,10 @@ interaction screens and high-throughput modelling of higher-order oligomers usin toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('poetry', '1.5.1'), +] + dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), ('Python', '3.11.3'), @@ -79,8 +83,11 @@ exts_list = [ ('biopandas', '0.5.1.dev0', { 'checksums': ['6dc9de631babf8221c1ac60230133717039e08911f15e8ac48498c787022de12'], }), + ('immutabledict', '4.1.0', { + 'checksums': ['93d100ccd2cd09a1fd3f136b9328c6e59529ba341de8bb499437f6819159fe8a'], + }), (name, version, { - 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + 'preinstallopts': "sed -i 's/[>=]=.*//g;s/tensorflow-cpu/tensorflow/g' setup.cfg && ", 'runtest': '%s pytest -s %s ' % (local_testinstall_PATH, " ".join('test/test_%s.py' % x for x in local_tests)), 'sources': [{ 'filename': '%(name)s-%(version)s.tar.gz', From 95d423750af93bf8544ea42ff42f253bad66f818 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 8 Nov 2024 12:19:21 +0100 Subject: [PATCH 048/414] Update AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb fix typo --- .../AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb index 4c54a12c72f..cdcc434dc64 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb @@ -98,7 +98,7 @@ exts_list = [ } }], 'testinstall': True, - 'checksums': ['e338195987e003f3caadb06bda0ca56dece87e358738143ea72662f9ad69b1d4], + 'checksums': ['e338195987e003f3caadb06bda0ca56dece87e358738143ea72662f9ad69b1d4'], }), ] From d4a3b7ee2d0bb20441d0091395b98434c02e0800 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 8 Nov 2024 12:32:01 +0100 Subject: [PATCH 049/414] adding easyconfigs: BEDOPS-2.4.41-foss-2023b.eb --- .../b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb new file mode 100644 index 00000000000..d6a87743c86 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# updated: Denis Kristak (INUITS) +# Update: Petr Král (INUITS) + +easyblock = 'MakeCp' + +name = 'BEDOPS' +version = '2.4.41' + +homepage = 'http://%(namelower)s.readthedocs.io/en/latest/index.html' +description = """BEDOPS is an open-source command-line toolkit that performs highly efficient and + scalable Boolean and other set operations, statistical calculations, archiving, conversion and + other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for + distributing whole-genome analyses across a computational cluster.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3b868c820d59dd38372417efc31e9be3fbdca8cf0a6b39f13fb2b822607d6194'] + +# else build of jansson library fails with: 'configure: error: C compiler cannot create executables' +prebuildopts = 'unset LIBS && ' +# builds all variants and copies executables to bin directory +buildopts = ' all && make install' +# actually used variant is linked to via symlinks +keepsymlinks = True + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % x for x in ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch'] + ], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' From c5dc54e0c67c7d972fab446c49204c1909fd11df Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 8 Nov 2024 12:44:02 +0100 Subject: [PATCH 050/414] adding easyconfigs: iodata-1.0.0a5-foss-2023a.eb --- .../i/iodata/iodata-1.0.0a5-foss-2023a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/i/iodata/iodata-1.0.0a5-foss-2023a.eb diff --git a/easybuild/easyconfigs/i/iodata/iodata-1.0.0a5-foss-2023a.eb b/easybuild/easyconfigs/i/iodata/iodata-1.0.0a5-foss-2023a.eb new file mode 100644 index 00000000000..701c6f2a898 --- /dev/null +++ b/easybuild/easyconfigs/i/iodata/iodata-1.0.0a5-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'iodata' +version = '1.0.0a5' + +homepage = 'https://github.com/theochem/iodata' +description = """Python library for reading, writing, and converting computational chemistry file formats and + generating input files.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/theochem/iodata/releases/download/v%(version)s/'] +sources = ['qc_iodata-%(version)s-py3-none-any.whl'] +checksums = ['90e11e34df77498e187ac876bf4822799850996f1d880e8a298fa0fc5fd27001'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/iodata-convert'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["iodata-convert --help"] + +sanity_pip_check = True + +moduleclass = 'chem' From b3e2307b89af89a837df89507ff780fc16c1c92d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Mon, 26 Aug 2024 11:42:16 +0200 Subject: [PATCH 051/414] [GCCcore/13.2.0] CubeGUI 4.8.2 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d1d3b98fad6 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.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 +# Authors:: Jan André Reuter +# 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 = '4.8.2' + +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': '13.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1df8fcaea95323e7eaf0cc010784a41243532c2123a27ce93cb7e3241557ff76'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Qt6', '6.6.3'), + ('CubeLib', '4.8.2'), +] + +configopts = [ + '--with-qt=$EBROOTQT6/bin ', +] + +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' From 2c15712255780bed1f0accc3caf3367aab1a7268 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Tue, 6 Aug 2024 14:31:10 +0200 Subject: [PATCH 052/414] Scalasca 2.6.1 for 2023b, patch to fix configure after OpenMP MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../s/Scalasca/Scalasca-2.6.1-gompi-2022a.eb | 13 +++- .../s/Scalasca/Scalasca-2.6.1-gompi-2023b.eb | 61 +++++++++++++++++++ .../Scalasca-2.6.1_nowarn_omp_pragmas.patch | 39 ++++++++++++ 3 files changed, 111 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1_nowarn_omp_pragmas.patch diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2022a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2022a.eb index 0169c602509..772ee3e531e 100644 --- a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2022a.eb @@ -1,9 +1,10 @@ ## # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer # Robert Mijakovic +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -28,7 +29,15 @@ toolchain = {'name': 'gompi', 'version': '2022a'} source_urls = ['https://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['a0dbc3de82a6c0fe598de9e340513cff2882c199410a632d3a7f073ba921c7e7'] +patches = [ + 'Scalasca-2.6.1_nowarn_omp_pragmas.patch', +] +checksums = [ + 'a0dbc3de82a6c0fe598de9e340513cff2882c199410a632d3a7f073ba921c7e7', + # scalasca-2.6.1.tar.gz + '6f1df13cd8683e4867b8e4b321c5f89e94430d1281f29f8eb084762a050f9e90', + # Scalasca-2.6.1_nowarn_omp_pragmas.patch +] builddependencies = [ ('CubeWriter', '4.8'), diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2023b.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2023b.eb new file mode 100644 index 00000000000..cd07bfe7ada --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2023b.eb @@ -0,0 +1,61 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Robert Mijakovic +# Jan Andre Reuter +# 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 = 'Scalasca' +version = '2.6.1' + +homepage = 'https://www.scalasca.org/' +description = """ + Scalasca is a software tool that supports the performance optimization of + parallel programs by measuring and analyzing their runtime behavior. The + analysis identifies potential performance bottlenecks -- in particular + those concerning communication and synchronization -- and offers guidance + in exploring their causes. +""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'Scalasca-2.6.1_nowarn_omp_pragmas.patch', +] +checksums = [ + 'a0dbc3de82a6c0fe598de9e340513cff2882c199410a632d3a7f073ba921c7e7', + # scalasca-2.6.1.tar.gz + '6f1df13cd8683e4867b8e4b321c5f89e94430d1281f29f8eb084762a050f9e90', + # Scalasca-2.6.1_nowarn_omp_pragmas.patch +] + +builddependencies = [ + ('CubeWriter', '4.8.2'), +] + +dependencies = [ + ('CubeGUI', '4.8.2'), + ('CubeLib', '4.8.2'), + ('OTF2', '3.0.3'), + ('Score-P', '8.4'), +] + +sanity_check_paths = { + 'files': ['bin/scalasca', 'lib/libpearl.replay.a'], + 'dirs': [], +} + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scalasca/patterns'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1_nowarn_omp_pragmas.patch b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1_nowarn_omp_pragmas.patch new file mode 100644 index 00000000000..e3ec91cea86 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1_nowarn_omp_pragmas.patch @@ -0,0 +1,39 @@ +This patch fixes a missing $ in configure, which causes following checks to +fail if they produce any output to stdout or stderr. + +diff -Nrup scalasca-2.6.1.orig/build-config/m4/scalasca_nowarn_omp_pragmas.m4 scalasca-2.6.1/build-config/m4/scalasca_nowarn_omp_pragmas.m4 +--- scalasca-2.6.1.orig/build-config/m4/scalasca_nowarn_omp_pragmas.m4 2022-12-14 11:55:38.810618928 +0100 ++++ scalasca-2.6.1/build-config/m4/scalasca_nowarn_omp_pragmas.m4 2023-09-27 09:47:31.155201804 +0200 +@@ -62,7 +62,7 @@ AS_CASE([$_scalasca_nowarn_omp_pragmas], + AC_SUBST([NOWARN_OMP_PRAGMAS_]_AC_LANG_PREFIX[FLAGS]) + + dnl Reset environment +-ac_[]_AC_LANG_ABBREV[]_werror_flag=_scalasca_save_[]_AC_LANG_ABBREV[]_werror_flag ++ac_[]_AC_LANG_ABBREV[]_werror_flag=$_scalasca_save_[]_AC_LANG_ABBREV[]_werror_flag + ]) + + +diff -Nrup scalasca-2.6.1.orig/build-backend/configure scalasca-2.6.1/build-backend/configure +--- scalasca-2.6.1.orig/build-backend/configure 2022-12-14 11:56:16.350709778 +0100 ++++ scalasca-2.6.1/build-backend/configure 2023-09-27 09:49:35.847822426 +0200 +@@ -21128,7 +21128,7 @@ case $_scalasca_nowarn_omp_pragmas in #( + esac + + +-ac_cxx_werror_flag=_scalasca_save_cxx_werror_flag ++ac_cxx_werror_flag=$_scalasca_save_cxx_werror_flag + + if test "x${ac_cv_prog_cxx_openmp}" != "xunsupported" \ + && test "x${enable_openmp}" != "xno"; then +diff -Nrup scalasca-2.6.1.orig/build-mpi/configure scalasca-2.6.1/build-mpi/configure +--- scalasca-2.6.1.orig/build-mpi/configure 2022-12-14 11:56:33.574751469 +0100 ++++ scalasca-2.6.1/build-mpi/configure 2023-09-27 09:49:06.135678364 +0200 +@@ -21878,7 +21878,7 @@ case $_scalasca_nowarn_omp_pragmas in #( + esac + + +-ac_cxx_werror_flag=_scalasca_save_cxx_werror_flag ++ac_cxx_werror_flag=$_scalasca_save_cxx_werror_flag + + if test "x${ac_cv_prog_cxx_openmp}" != "xunsupported" \ + && test "x${enable_openmp}" != "xno"; then \ No newline at end of file From 36774fd40df2efe3559c61d316d1bd18a771e3e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Sat, 9 Nov 2024 13:29:53 +0100 Subject: [PATCH 053/414] Fix download path for CubeGUI MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb index d1d3b98fad6..5c79272ea54 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb @@ -29,7 +29,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] sources = [SOURCELOWER_TAR_GZ] checksums = ['1df8fcaea95323e7eaf0cc010784a41243532c2123a27ce93cb7e3241557ff76'] From 5af46b45fa679ea124a9825a711b6274d8fd04cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Sat, 9 Nov 2024 14:07:34 +0100 Subject: [PATCH 054/414] Fix CubeGUI 4.8.2 checksum MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb index 5c79272ea54..0a3759b0e90 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.2.0.eb @@ -31,7 +31,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['1df8fcaea95323e7eaf0cc010784a41243532c2123a27ce93cb7e3241557ff76'] +checksums = ['bf2e02002bb2e5c4f61832ce37b62a440675c6453463014b33b2474aac78f86d'] builddependencies = [('binutils', '2.40')] From ea768d41304eaa141accb70e1a2f005f6013bec2 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 10:57:28 +0000 Subject: [PATCH 055/414] adding easyconfigs: Optuna-4.0.0-foss-2024a.eb --- .../o/Optuna/Optuna-4.0.0-foss-2024a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb new file mode 100644 index 00000000000..9eb3aab5255 --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '4.0.0' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), + ('SciPy-bundle', '2024.05'), + ('tqdm', '4.66.5'), + ('matplotlib', '3.9.2'), # optional + ('plotly.py', '5.24.1'), # optional + ('redis-py', '5.1.1'), # optional + ('scikit-learn', '1.5.2'), # optional + ('SQLAlchemy', '2.0.36'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cmaes', '0.11.1', { + 'checksums': ['cf71fa3679814723be771f2c9edd85f465b1bc1e409e1ad6d8a9e481efcd5160'], + }), + ('colorlog', '6.9.0', { + 'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'], + }), + ('optuna', version, { + 'use_pip_extras': 'optional', + 'checksums': ['844949f09e2a7353ab414e9cfd783cf0a647a65fc32a7236212ed6a37fe08973'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' From 44f88b234b5e4091190c66a67ecb8cf0ef0aa167 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 11:28:30 +0000 Subject: [PATCH 056/414] templated optuna python package name --- easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb index 9eb3aab5255..f85fda01479 100644 --- a/easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb +++ b/easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb @@ -35,7 +35,7 @@ exts_list = [ ('colorlog', '6.9.0', { 'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'], }), - ('optuna', version, { + ('%(namelower)s', version, { 'use_pip_extras': 'optional', 'checksums': ['844949f09e2a7353ab414e9cfd783cf0a647a65fc32a7236212ed6a37fe08973'], }), From 434b40708b906027402548b90491be5a8833fedb Mon Sep 17 00:00:00 2001 From: software Date: Mon, 11 Nov 2024 17:09:18 +0000 Subject: [PATCH 057/414] adding easyconfigs: HOMER-5.1-foss-2023a-R-4.3.2.eb --- .../h/HOMER/HOMER-5.1-foss-2023a-R-4.3.2.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/h/HOMER/HOMER-5.1-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-5.1-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/h/HOMER/HOMER-5.1-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..554852bed54 --- /dev/null +++ b/easybuild/easyconfigs/h/HOMER/HOMER-5.1-foss-2023a-R-4.3.2.eb @@ -0,0 +1,49 @@ +easyblock = 'Binary' + +name = 'HOMER' +version = '5.1' +versionsuffix = '-R-%(rver)s' + +homepage = "http://homer.ucsd.edu/homer/" +description = """HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and + next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written + in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding + 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, + RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['http://homer.ucsd.edu/homer'] +sources = ['configureHomer.pl'] +checksums = ['ccdaa3004a0e0df0882634671d4a1acc88364761e0e6c7ea329ebbf1eb729537'] + +builddependencies = [ + ('wget', '1.24.5'), + ('Zip', '3.0'), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Perl', '5.36.1'), + ('R', '4.3.2'), + ('SAMtools', '1.18'), + ('R-bundle-Bioconductor', '3.18', versionsuffix) +] + +postinstallcmds = ["cd %(installdir)s && perl ./configureHomer.pl -install homer -version v%(version)s"] + +sanity_check_paths = { + 'files': [ + 'bin/homer', + 'bin/getGenomeTilingPeaks', + 'config.txt', + 'DoughnutDocumentation.pdf', + 'data/accession/homologene.data', + 'motifs/hnf1b.motif', + ], + 'dirs': ['bin', 'data', 'motifs', 'update'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' From bb1d9aba6ee31b0ce3427b7bd506f8cd0a66ae4a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 12 Nov 2024 11:38:45 +0100 Subject: [PATCH 058/414] adding easyconfigs: Kraken2-2.1.3-gompi-2023a.eb --- .../k/Kraken2/Kraken2-2.1.3-gompi-2023a.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3-gompi-2023a.eb diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3-gompi-2023a.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3-gompi-2023a.eb new file mode 100644 index 00000000000..f4733d380e3 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3-gompi-2023a.eb @@ -0,0 +1,68 @@ +easyblock = 'PackedBinary' + +name = 'Kraken2' +version = '2.1.3' + +homepage = 'https://github.com/DerrickWood/kraken2/wiki' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# part is compiled with $CXX, the rest is in Perl +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-2.1.3_fix_installation_for_easybuild.patch', +] +checksums = [ + {'v2.1.3.tar.gz': '5269fa14adfb02e38c2da2e605e909a432d76c680d73e2e0e80e27ccd04d7c69'}, + {'Kraken2-2.1.3_fix_installation_for_easybuild.patch': + 'd2faecff258133033cb81d5ac70d1a7ff1b4323091411aa835a13de83f2cc174'}, +] + +dependencies = [ + ('Perl', '5.36.1'), + ('BLAST+', '2.14.1'), + ('wget', '1.24.5'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken2.sh %(installdir)s/bin' + +# Kraken2 databases can be downloaded from https://benlangmead.github.io/aws-indexes/k2 +# or built as described in https://github.com/DerrickWood/kraken2/wiki/Manual#kraken-2-databases +# The following commands will build and install the standard databases (100GB) in local_db_path +# local_db_path = '%(installdir)s/db' +# postinstallcmds = [ +# 'mkdir %s' % local_db_path, +# 'cd %%(installdir)s/bin && ./kraken2-build --standard --threads %%(parallel)s --db %s' % local_db_path, +# ] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + '16S_gg_installation.sh', '16S_rdp_installation.sh', '16S_silva_installation.sh', 'add_to_library.sh', + 'build_db', 'build_gg_taxonomy.pl', 'build_kraken2_db.sh', 'build_rdp_taxonomy.pl', 'build_silva_taxonomy.pl', + 'classify', 'clean_db.sh', 'cp_into_tempfile.pl', 'download_genomic_library.sh', 'download_taxonomy.sh', + 'dump_table', 'estimate_capacity', 'kraken2', 'kraken2-build', 'kraken2-inspect', 'kraken2lib.pm', + 'lookup_accession_numbers.pl', 'make_seqid2taxid_map.pl', 'mask_low_complexity.sh', 'rsync_from_ncbi.pl', + 'scan_fasta_file.pl']], + 'dirs': [], +} + +sanity_check_commands = [ + 'kraken2 --help', + 'kraken2-build --help', + 'kraken2-inspect --help', + 'build_db -h', + 'classify -h', +] + +moduleclass = 'bio' From af777fb7271ab65385d7d9f81f922b2da449ee71 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 12 Nov 2024 12:58:02 +0100 Subject: [PATCH 059/414] add patch file --- ...2.1.3_fix_installation_for_easybuild.patch | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3_fix_installation_for_easybuild.patch diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3_fix_installation_for_easybuild.patch b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3_fix_installation_for_easybuild.patch new file mode 100644 index 00000000000..7dbe6fb40db --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.3_fix_installation_for_easybuild.patch @@ -0,0 +1,30 @@ +Fix install script and src/Makefile for EasyBuild. + +Åke Sandgren, 2021-04-30 +Update: Petr Král (INUITS) +diff -u install_kraken2.sh.orig install_kraken2.sh +--- install_kraken2.sh.orig 2023-06-07 02:25:37.000000000 +0200 ++++ install_kraken2.sh 2024-11-12 11:34:20.122193572 +0100 +@@ -23,7 +23,9 @@ + + # Perl cmd used to canonicalize dirname - "readlink -f" doesn't work + # on OS X. +-export KRAKEN2_DIR=$(perl -MCwd=abs_path -le 'print abs_path(shift)' "$1") ++# export KRAKEN2_DIR=$(perl -MCwd=abs_path -le 'print abs_path(shift)' "$1") ++ ++export KRAKEN2_DIR=$1 + + mkdir -p "$KRAKEN2_DIR" + make -C src install +diff -u src/Makefile.orig src/Makefile +--- src/Makefile.orig 2023-06-07 02:25:37.000000000 +0200 ++++ src/Makefile 2024-11-12 10:13:26.330138787 +0100 +@@ -1,6 +1,6 @@ +-CXX = g++ ++CXX ?= g++ + KRAKEN2_SKIP_FOPENMP ?= -fopenmp +-CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O3 ++CXXFLAGS ?= $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O3 + CXXFLAGS += -DLINEAR_PROBING + + .PHONY: all clean install From ad68aed19d08584348591051ff92bc95eb29fe91 Mon Sep 17 00:00:00 2001 From: software Date: Tue, 12 Nov 2024 18:03:24 +0000 Subject: [PATCH 060/414] adding easyconfigs: fsm-lite-1.0-GCCcore-12.3.0.eb, sdsl-lite-2.0.3-GCCcore-12.3.0.eb --- .../f/fsm-lite/fsm-lite-1.0-GCCcore-12.3.0.eb | 36 +++++++++++++++++++ .../sdsl-lite-2.0.3-GCCcore-12.3.0.eb | 31 ++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4343ab3d95a --- /dev/null +++ b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = "MakeCp" + +name = 'fsm-lite' +version = '1.0' + +homepage = "https://github.com/nvalimak/fsm-lite" +description = """A singe-core implemetation of frequency-based substring mining.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/nvalimak/%(name)s/archive/'] +sources = ['v%(version)s-stable.tar.gz'] +checksums = ['f781a9fbab5265bd09b3b5b7e1cba904582ec201c3d30baed36e28a03de3ac61'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('sdsl-lite', '2.0.3'), +] + +prebuildopts = "sed -i '1s/.*/SDSL_INSTALL_PREFIX=${EBROOTSDSLMINLITE}/' Makefile && make depend &&" + +files_to_copy = [(['fsm-lite'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fsm-lite'], + 'dirs': [], +} + +sanity_check_commands = ["fsm-lite --help 2>&1 | grep usage"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8a00e44e265 --- /dev/null +++ b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = "CMakeMake" + +name = 'sdsl-lite' +version = '2.0.3' + +homepage = "https://github.com/simongog/sdsl-lite" +description = """The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing + succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct + data structures can represent an object (such as a bitvector or a tree) in space close to the information-theoretic + lower bound of the object while supporting operations of the original object efficiently. The theoretical time + complexity of an operation performed on the classical data structure and the equivalent succinct data structure + are (most of the time) identical.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/simongog/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['08ece40ce44041906bfa425af81a20a8071d187285f674debd8816c2e3113c2f'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['lib/libdivsufsort64.a', 'lib/libdivsufsort.a', 'lib/libsdsl.a', 'include/divsufsort64.h'], + 'dirs': ['include/sdsl'], +} + +moduleclass = 'tools' From 3de2b43ed247d694c9b11718990d7fc9bd192b3e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 13 Nov 2024 13:37:48 +0100 Subject: [PATCH 061/414] adding easyconfigs: sdsl-lite-2.1.1-foss-2023a.eb, libdivsufsort-2.0.1-foss-2023a.eb --- .../libdivsufsort-2.0.1-foss-2023a.eb | 36 +++++++++++++++++ .../s/sdsl-lite/sdsl-lite-2.1.1-foss-2023a.eb | 40 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.1.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2023a.eb b/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2023a.eb new file mode 100644 index 00000000000..2ad493ff64d --- /dev/null +++ b/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2023a.eb @@ -0,0 +1,36 @@ +# Author: Iñaki Mtz de Ilarduya +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update: Petr Král (INUITS) + +easyblock = 'CMakeMake' + +name = 'libdivsufsort' +version = '2.0.1' + +homepage = 'https://github.com/y-256/libdivsufsort' +description = """libdivsufsort is a software library that implements a lightweight suffix + array construction algorithm.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/y-256/libdivsufsort/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9164cb6044dcb6e430555721e3318d5a8f38871c2da9fd9256665746a69351e0'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +unpack_options = '--strip-components=1' + +# For `divsufsort64.h` to be available. +# See https://github.com/y-256/libdivsufsort/blob/2.0.1/include/CMakeLists.txt#L161 +configopts = '-DBUILD_DIVSUFSORT64=ON' + +sanity_check_paths = { + 'files': ['lib/libdivsufsort.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.1.1-foss-2023a.eb b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.1.1-foss-2023a.eb new file mode 100644 index 00000000000..46cba5e14f0 --- /dev/null +++ b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.1.1-foss-2023a.eb @@ -0,0 +1,40 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +# Update: Petr Král (INUITS) +easyblock = "CMakeMake" + +name = 'sdsl-lite' +version = '2.1.1' + +homepage = "https://github.com/simongog/sdsl-lite" +description = """The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing + succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct + data structures can represent an object (such as a bitvector or a tree) in space close to the information-theoretic + lower bound of the object while supporting operations of the original object efficiently. The theoretical time + complexity of an operation performed on the classical data structure and the equivalent succinct data structure + are (most of the time) identical.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/simongog/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e36591338c390184760dbdddbb653d972d9c1986c8819f462e7e73ddd28b992b'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), + ('googletest', '1.13.0'), +] + +dependencies = [ + ('libdivsufsort', '2.0.1'), +] + +# Use our `googletest` and `libdivsufsort`. +preconfigopts = "sed -i '/external/d' %(builddir)s/%(name)s-%(version)s/CMakeLists.txt && " + +sanity_check_paths = { + 'files': ['lib/libsdsl.a'], + 'dirs': ['include/sdsl'], +} + +moduleclass = 'tools' From ef500b61aca09f78e420abbe4873c2023da92621 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 14 Nov 2024 16:23:26 +0100 Subject: [PATCH 062/414] adding easyconfigs: kaggle-1.6.17-foss-2023b.eb --- .../k/kaggle/kaggle-1.6.17-foss-2023b.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/k/kaggle/kaggle-1.6.17-foss-2023b.eb diff --git a/easybuild/easyconfigs/k/kaggle/kaggle-1.6.17-foss-2023b.eb b/easybuild/easyconfigs/k/kaggle/kaggle-1.6.17-foss-2023b.eb new file mode 100644 index 00000000000..b36fb397280 --- /dev/null +++ b/easybuild/easyconfigs/k/kaggle/kaggle-1.6.17-foss-2023b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'kaggle' +version = '1.6.17' + +homepage = "https://github.com/Kaggle/kaggle-api" +description = """Official API for https://www.kaggle.com, + accessible using a command line tool implemented in Python 3.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('tqdm', '4.66.2'), + # for certifi, python-dateutil, requests, six, urllib3 and webencodings + ('Python-bundle-PyPI', '2023.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bleach', '6.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e'], + }), + ('text_unidecode', '1.3', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['1311f10e8b895935241623731c2ba64f4c455287888b18189350b67134a822e8'], + }), + ('python_slugify', '8.0.4', { + 'modulename': 'slugify', + 'source_tmpl': SOURCE_WHL, + 'checksums': ['276540b79961052b66b7d116620b36518847f52d5fd9e3a70164fc8c50faa6b8'], + }), + (name, version, { + # `import kaggle` fails for missing API token (`kaggle.json`) + # see `api.authenticate()` in `kaggle/__init__.py` + 'modulename': False, + 'checksums': ['439a7dea1d5039f320fd6ad5ec21b688dcfa70d405cb42095b81f41edc401b81'], + }), +] + +moduleclass = 'tools' From 9d95ef80b00cd075027b2df90404979c5d4add06 Mon Sep 17 00:00:00 2001 From: crivella Date: Mon, 18 Nov 2024 14:18:52 +0100 Subject: [PATCH 063/414] Added QE 7.4 EC file and patch for d3q --- .../QuantumESPRESSO-7.4.0-d3q.patch | 30 ++++ .../QuantumESPRESSO-7.4.0-foss-2024a.eb | 163 ++++++++++++++++++ 2 files changed, 193 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-d3q.patch create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-d3q.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-d3q.patch new file mode 100644 index 00000000000..d2a91a510b6 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-d3q.patch @@ -0,0 +1,30 @@ +Fix line length greather than 132 characters. +Also fix the use of ZGEMM3M, which is not available in the FlexiBLAS library. +See https://github.com/anharmonic/d3q/issues/22 +--- a/d3q/thermal2/PROGRAM_r2q.f90 ++++ b/d3q/thermal2/PROGRAM_r2q.f90 +@@ -744,7 +744,8 @@ PROGRAM r2q + + + WRITE(*,'(2x,a,f12.8)') "Note: q-point and path length in units of 2pi/alat, conversion to bohr^-1: ", S%tpiba +- WRITE(*,'(2x,2(a,f12.8))') "Note: phonons are in cm^-1, conversion to Rydberg: ", 1.d+5/RY_TO_CMM1,"E-5 to THz:", RY_TO_THZ/RY_TO_CMM1 ++ WRITE(*,'(2x,2(a,f12.8))') "Note: phonons are in cm^-1, conversion to Rydberg: ", & ++ 1.d+5/RY_TO_CMM1,"E-5 to THz:", RY_TO_THZ/RY_TO_CMM1 + + IF( input%calculation=="dos") THEN + CALL PH_DOS(input,S,fc2) +diff --git a/thermal2/functions.f90 b/thermal2/functions.f90 +index 90d8a90..9e9adb2 100644 +--- a/d3q/thermal2/functions.f90 ++++ b/d3q/thermal2/functions.f90 +@@ -465,8 +465,8 @@ end subroutine quicksort_idx + ! + !rotate_d2 = MATMUL(TRANSPOSE(CONJG(U)), MATMUL(D,U)) + ! +- CALL ZGEMM3M('N', 'N', nat3, nat3, nat3, alpha, D, nat3, U, nat3, beta, A, nat3) +- CALL ZGEMM3M('C', 'N', nat3, nat3, nat3, alpha, U, nat3, A, nat3, beta, rotate_d2, nat3) ++ CALL ZGEMM('N', 'N', nat3, nat3, nat3, alpha, D, nat3, U, nat3, beta, A, nat3) ++ CALL ZGEMM('C', 'N', nat3, nat3, nat3, alpha, U, nat3, A, nat3, beta, rotate_d2, nat3) + ! + END FUNCTION + ! diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-foss-2024a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-foss-2024a.eb new file mode 100644 index 00000000000..bf8ced82f9a --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-foss-2024a.eb @@ -0,0 +1,163 @@ +name = 'QuantumESPRESSO' +version = '7.4' + +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': '2024a'} + +toolchainopts = { + "usempi": True, + "openmp": True, +} + +# Check hashes inside external/submodule_commit_hash_records when making file for new version +local_lapack_hash = "12d825396fcef1e0a1b27be9f119f9e554621e55" +local_mbd_hash = "89a3cc199c0a200c9f0f688c3229ef6b9a8d63bd" +local_devxlib_hash = "a6b89ef77b1ceda48e967921f1f5488d2df9226d" +local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40" +# Different from the one at tag qe-7.4, see https://github.com/anharmonic/d3q/issues/22 +local_d3q_hash = "808acbaf012468f42147d8d6af452ec64b9e5ab0" +# Different from the one at tag qe-7.4 +local_qe_gipaw_hash = "9b2ae1a46cae045cc04ef02c1072f2e1e74873b2" +local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70" +local_w90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1" + + +sources = [ + { + "filename": "q-e-qe-%(version)s.tar.gz", + "extract_cmd": "mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_", + "source_urls": ["https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s"], + }, + { + "filename": "lapack-%s.tar.gz" % local_lapack_hash, + "git_config": { + "url": "https://github.com/Reference-LAPACK", + "repo_name": "lapack", + "commit": local_lapack_hash, + }, + }, + { + "filename": "mbd-%s.tar.gz" % local_mbd_hash, + "git_config": { + "url": "https://github.com/libmbd", + "repo_name": "libmbd", + "commit": local_mbd_hash, + 'clone_into': 'mbd', + }, + }, + { + "filename": "devxlib-%s.tar.gz" % local_devxlib_hash, + "git_config": { + "url": "https://gitlab.com/max-centre/components", + "repo_name": "devicexlib", + "commit": local_devxlib_hash, + 'clone_into': 'devxlib', + }, + }, + { + "filename": "d3q-%s.tar.gz" % local_d3q_hash, + "git_config": { + "url": "https://github.com/anharmonic", + "repo_name": "d3q", + "commit": local_d3q_hash, + }, + }, + { + "filename": "fox-%s.tar.gz" % local_fox_hash, + "git_config": { + "url": "https://github.com/pietrodelugas", + "repo_name": "fox", + "commit": local_fox_hash, + }, + }, + { + "filename": "qe-gipaw-%s.tar.gz" % local_qe_gipaw_hash, + "git_config": { + "url": "https://github.com/dceresoli", + "repo_name": "qe-gipaw", + "commit": local_qe_gipaw_hash, + }, + }, + { + "filename": "pw2qmcpack-%s.tar.gz" % local_qmcpack_hash, + "git_config": { + "url": "https://github.com/QMCPACK", + "repo_name": "pw2qmcpack", + "commit": local_qmcpack_hash, + }, + }, + { + "filename": "wannier90-%s.tar.gz" % local_w90_hash, + "git_config": { + "url": "https://github.com/wannier-developers", + "repo_name": "wannier90", + "commit": local_w90_hash, + }, + }, +] +patches = [ + { + 'name': 'QuantumESPRESSO-7.4.0-d3q.patch', + 'sourcepath': '../' # Needed as patches are normally applied to the first `finalpath` directory + }, +] +# Holding off checksum checks untill 5.0.x +# https://github.com/easybuilders/easybuild-framework/pull/4248 +# checksums = [ +# {'q-e-qe-7.4.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'}, +# {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'}, +# {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'}, +# {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'}, +# {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'}, +# {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'}, +# {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'}, +# {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'}, +# {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'}, +# ] +checksums = [ + None, + None, None, None, None, None, None, None, None +] + +builddependencies = [ + ('M4', '1.4.19'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('HDF5', '1.14.5'), + ('ELPA', '2024.05.001'), + ('libxc', '6.2.2'), +] + +# Disabled because of +# https://gitlab.com/QEF/q-e/-/issues/667 +# https://github.com/anharmonic/d3q/issues/15 +build_shared_libs = False +with_scalapack = True +with_fox = True +with_gipaw = True +with_d3q = True +with_qmcpack = True + +moduleclass = "chem" + +test_suite_threshold = ( + 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665 +) +test_suite_max_failed = ( + 5 # Allow for some flaky tests (failed due to strict thresholds) +) +test_suite_allow_failures = [ + "test_qe_xclib_", # 7.3.1: https://gitlab.com/QEF/q-e/-/issues/640 + # "--hp_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + # "--ph_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + # "--epw_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + # "--tddfpt_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) +] From 507b1ae9d92c633f75f1abcf54fb319eb9bc7548 Mon Sep 17 00:00:00 2001 From: crivella Date: Mon, 18 Nov 2024 14:33:13 +0100 Subject: [PATCH 064/414] Updated test-suite data --- .../QuantumESPRESSO-7.4.0-foss-2024a.eb | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-foss-2024a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-foss-2024a.eb index bf8ced82f9a..4c846fcaa9e 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-foss-2024a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-foss-2024a.eb @@ -149,15 +149,9 @@ with_qmcpack = True moduleclass = "chem" test_suite_threshold = ( - 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665 + 0.98 ) test_suite_max_failed = ( 5 # Allow for some flaky tests (failed due to strict thresholds) ) -test_suite_allow_failures = [ - "test_qe_xclib_", # 7.3.1: https://gitlab.com/QEF/q-e/-/issues/640 - # "--hp_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) - # "--ph_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) - # "--epw_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) - # "--tddfpt_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) -] +test_suite_allow_failures = [] From cb3639f6e181e6baf231c9e9155463cac049d300 Mon Sep 17 00:00:00 2001 From: crivella Date: Mon, 18 Nov 2024 15:03:27 +0100 Subject: [PATCH 065/414] Fixed names --- ...umESPRESSO-7.4.0-d3q.patch => QuantumESPRESSO-7.4-d3q.patch} | 0 ...SO-7.4.0-foss-2024a.eb => QuantumESPRESSO-7.4-foss-2024a.eb} | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/q/QuantumESPRESSO/{QuantumESPRESSO-7.4.0-d3q.patch => QuantumESPRESSO-7.4-d3q.patch} (100%) rename easybuild/easyconfigs/q/QuantumESPRESSO/{QuantumESPRESSO-7.4.0-foss-2024a.eb => QuantumESPRESSO-7.4-foss-2024a.eb} (99%) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-d3q.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-d3q.patch similarity index 100% rename from easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-d3q.patch rename to easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-d3q.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-foss-2024a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb similarity index 99% rename from easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-foss-2024a.eb rename to easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb index 4c846fcaa9e..c998a464a39 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4.0-foss-2024a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb @@ -103,7 +103,7 @@ sources = [ ] patches = [ { - 'name': 'QuantumESPRESSO-7.4.0-d3q.patch', + 'name': 'QuantumESPRESSO-7.4-d3q.patch', 'sourcepath': '../' # Needed as patches are normally applied to the first `finalpath` directory }, ] From 1b20d6213750892c45ff16b5e515dda355df636e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 18 Nov 2024 15:33:16 +0100 Subject: [PATCH 066/414] adding easyconfigs: bin2cell-0.3.2-foss-2023a.eb, fastparquet-2024.11.0-gfbf-2023a.eb, stardist-0.8.5-foss-2023a.eb --- .../b/bin2cell/bin2cell-0.3.2-foss-2023a.eb | 37 +++++ .../fastparquet-2024.11.0-gfbf-2023a.eb | 146 ++++++++++++++++++ .../s/stardist/stardist-0.8.5-foss-2023a.eb | 37 +++++ 3 files changed, 220 insertions(+) create mode 100644 easybuild/easyconfigs/b/bin2cell/bin2cell-0.3.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/s/stardist/stardist-0.8.5-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/bin2cell/bin2cell-0.3.2-foss-2023a.eb b/easybuild/easyconfigs/b/bin2cell/bin2cell-0.3.2-foss-2023a.eb new file mode 100644 index 00000000000..85e6f82cb90 --- /dev/null +++ b/easybuild/easyconfigs/b/bin2cell/bin2cell-0.3.2-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'bin2cell' +version = '0.3.2' + +homepage = 'https://github.com/Teichlab/bin2cell' +description = """Bin2cell proposes 2um bin to cell groupings based on segmentation, +which can be done on the morphology image and/or a visualisation of the gene expression.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scanpy', '1.9.8'), + ('OpenCV', '4.8.1', '-contrib'), + ('stardist', '0.8.5'), + ('fastparquet', '2024.11.0'), +] + +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + (name, version, { + # opencv-python is installed via OpenCV, python module name is 'cv2' + 'preinstallopts': "sed -i '/opencv-python/d' pyproject.toml &&", + 'checksums': ['6529a8260b75c8c0237938f4ea389dfe055aea0909a31315f8fec32d44b2c531'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['python -c "import cv2"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb new file mode 100644 index 00000000000..0aa5903ee6e --- /dev/null +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb @@ -0,0 +1,146 @@ +easyblock = 'CargoPythonBundle' + +name = 'fastparquet' +version = '2024.11.0' + +homepage = "https://fastparquet.readthedocs.io/" +description = """fastparquet is a python implementation of the parquet format, aiming to integrate +into python-based big data work-flows. It is used implicitly by the projects +Dask, Pandas and intake-parquet.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('maturin', '1.4.0', '-Rust-1.75.0'), + ('Autotools', '20220317'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('NASM', '2.16.01'), +] + +crates = [ + ('adler2', '2.0.0'), + ('alloc-no-stdlib', '2.0.4'), + ('alloc-stdlib', '0.2.2'), + ('atty', '0.2.14'), + ('autocfg', '1.4.0'), + ('bitflags', '1.3.2'), + ('bitflags', '2.6.0'), + ('blosc2-rs', '0.3.1+2.15.1'), + ('blosc2-sys', '0.3.1+2.15.1'), + ('brotli', '7.0.0'), + ('brotli-decompressor', '4.0.1'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cbindgen', '0.24.5'), + ('cc', '1.1.30'), + ('cfg-if', '1.0.0'), + ('clap', '3.2.25'), + ('clap_lex', '0.2.4'), + ('cmake', '0.1.51'), + ('copy_dir', '0.1.3'), + ('crc32fast', '1.4.2'), + ('errno', '0.3.9'), + ('fastrand', '2.1.1'), + ('flate2', '1.0.34'), + ('hashbrown', '0.12.3'), + ('heck', '0.4.1'), + ('heck', '0.5.0'), + ('hermit-abi', '0.1.19'), + ('indexmap', '1.9.3'), + ('indoc', '2.0.5'), + ('isal-rs', '0.5.3+496255c'), + ('isal-sys', '0.5.3+496255c'), + ('itoa', '1.0.11'), + ('jobserver', '0.1.32'), + ('libc', '0.2.159'), + ('libcramjam', '0.6.0'), + ('libdeflate-sys', '1.19.3'), + ('libdeflater', '1.19.3'), + ('linux-raw-sys', '0.4.14'), + ('lock_api', '0.4.12'), + ('log', '0.4.22'), + ('lz4', '1.28.0'), + ('lz4-sys', '1.11.1+lz4-1.10.0'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.4'), + ('memoffset', '0.9.1'), + ('miniz_oxide', '0.8.0'), + ('once_cell', '1.20.2'), + ('os_str_bytes', '6.6.1'), + ('parking_lot', '0.12.3'), + ('parking_lot_core', '0.9.10'), + ('pkg-config', '0.3.31'), + ('portable-atomic', '1.9.0'), + ('proc-macro2', '1.0.87'), + ('pyo3', '0.22.5'), + ('pyo3-build-config', '0.22.5'), + ('pyo3-ffi', '0.22.5'), + ('pyo3-macros', '0.22.5'), + ('pyo3-macros-backend', '0.22.5'), + ('python3-dll-a', '0.2.10'), + ('quote', '1.0.37'), + ('redox_syscall', '0.5.7'), + ('rustix', '0.38.37'), + ('ryu', '1.0.18'), + ('same-file', '1.0.6'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.210'), + ('serde_derive', '1.0.210'), + ('serde_json', '1.0.128'), + ('shlex', '1.3.0'), + ('smallvec', '1.13.2'), + ('snap', '1.1.1'), + ('strsim', '0.10.0'), + ('syn', '1.0.109'), + ('syn', '2.0.79'), + ('target-lexicon', '0.12.16'), + ('tempfile', '3.13.0'), + ('termcolor', '1.4.1'), + ('textwrap', '0.16.1'), + ('toml', '0.5.11'), + ('unicode-ident', '1.0.13'), + ('unindent', '0.2.3'), + ('walkdir', '2.5.0'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.9'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-sys', '0.59.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('xz2', '0.1.7'), + ('zstd', '0.13.2'), + ('zstd-safe', '7.2.1'), + ('zstd-sys', '2.0.13+zstd.1.5.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('thrift', '0.21.0', { + 'checksums': ['5e6f7c50f936ebfa23e924229afc95eb219f8c8e5a83202dd4a391244803e402'], + }), + ('cramjam', '2.9.0', { + 'checksums': ['f103e648aa3ebe9b8e2c1a3a92719288d8f3f41007c319ad298cdce2d0c28641'], + }), + (name, version, { + 'checksums': ['e3b1fc73fd3e1b70b0de254bae7feb890436cb67e99458b88cb9bd3cc44db419'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/stardist/stardist-0.8.5-foss-2023a.eb b/easybuild/easyconfigs/s/stardist/stardist-0.8.5-foss-2023a.eb new file mode 100644 index 00000000000..de10882b67d --- /dev/null +++ b/easybuild/easyconfigs/s/stardist/stardist-0.8.5-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'stardist' +version = '0.8.5' + +homepage = 'https://github.com/stardist/stardist' +description = "Object Detection with Star-convex Shapes." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['260a31df86ca711e5e98cb91597c6cb9a10dcd1dc3c6b826d41b7c73c9646a1e'] + +dependencies = [ + ('Python', '3.11.3'), + ('TensorFlow', '2.13.0'), + ('numba', '0.58.1'), + ('scikit-image', '0.22.0'), + ('imageio', '2.33.1'), + ('CSBDeep', '0.7.4'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/stardist-predict2d', 'bin/stardist-predict3d'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "stardist-predict2d --help", + "stardist-predict3d --help", +] + +moduleclass = 'vis' From b4e457d355e68c1d07fa3888179cbc3c2b3a46de Mon Sep 17 00:00:00 2001 From: crivella Date: Mon, 18 Nov 2024 15:33:50 +0100 Subject: [PATCH 067/414] Added extra None checksum --- .../q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb index c998a464a39..6caaf6e98cf 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb @@ -121,7 +121,7 @@ patches = [ # {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'}, # ] checksums = [ - None, + None, None, None, None, None, None, None, None, None, None ] From b22f9840a7aacca926d8c0101189d974bc7393a4 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 18 Nov 2024 16:35:50 +0100 Subject: [PATCH 068/414] add checksums to fastparquet ec --- .../fastparquet-2024.11.0-gfbf-2023a.eb | 106 ++++++++++++++++++ 1 file changed, 106 insertions(+) diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb index 0aa5903ee6e..74a3177e8c3 100644 --- a/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb @@ -143,4 +143,110 @@ exts_list = [ }), ] +checksums = [ + {'fastparquet-2024.11.0.tar.gz': 'e3b1fc73fd3e1b70b0de254bae7feb890436cb67e99458b88cb9bd3cc44db419'}, + {'adler2-2.0.0.tar.gz': '512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627'}, + {'alloc-no-stdlib-2.0.4.tar.gz': 'cc7bb162ec39d46ab1ca8c77bf72e890535becd1751bb45f64c597edb4c8c6b3'}, + {'alloc-stdlib-0.2.2.tar.gz': '94fb8275041c72129eb51b7d0322c29b8387a0386127718b096429201a5d6ece'}, + {'atty-0.2.14.tar.gz': 'd9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8'}, + {'autocfg-1.4.0.tar.gz': 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'89132cd0bf050864e1d38dc3bbc07a0eb8e7530af26344d3d2bbbef83499f590'}, + {'target-lexicon-0.12.16.tar.gz': '61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1'}, + {'tempfile-3.13.0.tar.gz': 'f0f2c9fc62d0beef6951ccffd757e241266a2c833136efbe35af6cd2567dca5b'}, + {'termcolor-1.4.1.tar.gz': '06794f8f6c5c898b3275aebefa6b8a1cb24cd2c6c79397ab15774837a0bc5755'}, + {'textwrap-0.16.1.tar.gz': '23d434d3f8967a09480fb04132ebe0a3e088c173e6d0ee7897abbdf4eab0f8b9'}, + {'toml-0.5.11.tar.gz': 'f4f7f0dd8d50a853a531c426359045b1998f04219d88799810762cd4ad314234'}, + {'unicode-ident-1.0.13.tar.gz': 'e91b56cd4cadaeb79bbf1a5645f6b4f8dc5bde8834ad5894a8db35fda9efa1fe'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'walkdir-2.5.0.tar.gz': '29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.9.tar.gz': 'cf221c93e13a30d793f7645a0e7762c55d169dbb0a49671918a2319d289b10bb'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-sys-0.59.0.tar.gz': '1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, + {'zstd-0.13.2.tar.gz': 'fcf2b778a664581e31e389454a7072dab1647606d44f7feea22cd5abb9c9f3f9'}, + {'zstd-safe-7.2.1.tar.gz': '54a3ab4db68cea366acc5c897c7b4d4d1b8994a9cd6e6f841f8964566a419059'}, + {'zstd-sys-2.0.13+zstd.1.5.6.tar.gz': '38ff0f21cfee8f97d94cef41359e0c89aa6113028ab0291aa8ca0038995a95aa'}, +] + moduleclass = 'tools' From a2aa723613e290a5d9270f17f3a2e47482096edb Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 18 Nov 2024 17:04:59 +0100 Subject: [PATCH 069/414] fix fastparquet checksums --- .../f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb index 74a3177e8c3..6724da1d7f8 100644 --- a/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb @@ -144,7 +144,6 @@ exts_list = [ ] checksums = [ - {'fastparquet-2024.11.0.tar.gz': 'e3b1fc73fd3e1b70b0de254bae7feb890436cb67e99458b88cb9bd3cc44db419'}, {'adler2-2.0.0.tar.gz': '512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627'}, {'alloc-no-stdlib-2.0.4.tar.gz': 'cc7bb162ec39d46ab1ca8c77bf72e890535becd1751bb45f64c597edb4c8c6b3'}, {'alloc-stdlib-0.2.2.tar.gz': '94fb8275041c72129eb51b7d0322c29b8387a0386127718b096429201a5d6ece'}, From 90344be33544fcfee777ec6f3079de7eaaa05237 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 18 Nov 2024 17:31:26 +0100 Subject: [PATCH 070/414] Fix confliction platformdirs dependency in Pylint-3.2.5-GCCcore-13.2.0 The PyLint EasyConfig installs a different version of the `platformdirs` package than available in e.g. Python-bundle-PyPI which leads to conflicts later on. Depend on that to pull in the right version --- .../p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb index c919c6c4dd4..49cfa894154 100644 --- a/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb @@ -18,20 +18,13 @@ builddependencies = [ dependencies = [ ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('dill', '0.3.8'), ] use_pip = True exts_list = [ - ('dill', '0.3.8', { - 'checksums': ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'], - }), - ('platformdirs', '4.2.2', { - 'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'], - }), - ('tomlkit', '0.12.5', { - 'checksums': ['eef34fba39834d4d6b73c9ba7f3e4d1c417a4e56f89a7e96e090dd0d24b8fb3c'], - }), ('astroid', '3.2.2', { 'checksums': ['8ead48e31b92b2e217b6c9733a21afafe479d52d6e164dd25fb1a770c7c3cf94'], }), From 93086f0e497760d779900754e708c572399315fd Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:01:20 +0100 Subject: [PATCH 071/414] Update easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb Co-authored-by: Alexander Grund --- .../p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb index 0320e308105..20ba54c49e8 100644 --- a/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'python-slugify' version = '8.0.4' From c6276cd4cd3c46ccc418ca18cf8db6446a2d6a54 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:01:42 +0100 Subject: [PATCH 072/414] Update easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb Co-authored-by: Alexander Grund --- .../python-slugify-8.0.4-GCCcore-13.2.0.eb | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb index 20ba54c49e8..4df717643a6 100644 --- a/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb @@ -14,14 +14,10 @@ dependencies = [ ('text-unidecode', '1.3'), ] +options = {'modulename': 'slugify'} + use_pip = True +download_dep_fail = True sanity_pip_check = True -exts_list = [ - (name, version, { - 'modulename': 'slugify', - 'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'], - }), -] - moduleclass = 'devel' From 887c0fb19e7c91e609b86a53b10a5eae6cca53dd Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:01:56 +0100 Subject: [PATCH 073/414] Update easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb Co-authored-by: Alexander Grund --- .../p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb index 4df717643a6..2b70a5d64e0 100644 --- a/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/python-slugify/python-slugify-8.0.4-GCCcore-13.2.0.eb @@ -8,6 +8,9 @@ description = """Best attempt to create slugs from unicode strings while keeping toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +sources = [SOURCE_TAR_GZ] +checksums = ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'] + builddependencies = [('binutils', '2.40')] dependencies = [ ('Python', '3.11.5'), From 9fd5f732eb5fedead2626b7875b6f166f9763abc Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:02:14 +0100 Subject: [PATCH 074/414] Update easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb index 40f123c00cb..56d2e7cb7c3 100644 --- a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'wrapt' version = '1.16.0' From 10cab0f794f3a950e2df09c3c703fb51e3d6acba Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:02:39 +0100 Subject: [PATCH 075/414] Update easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb index 56d2e7cb7c3..11794955bb2 100644 --- a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb @@ -10,10 +10,8 @@ function wrappers and decorator functions.""" toolchain = {'name': 'gfbf', 'version': '2023b'} -dependencies = [ - ('Python', '3.11.5'), - ('SciPy-bundle', '2023.11'), -] +dependencies = [('Python', '3.11.5')] +builddependencies = [('binutils', '2.40')] use_pip = True sanity_pip_check = True From 00bb6c24e29e3786d520e9e5f04965887dd57112 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:02:52 +0100 Subject: [PATCH 076/414] Update easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb index 11794955bb2..291caf556ec 100644 --- a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb @@ -8,7 +8,7 @@ description = """The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions.""" -toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} dependencies = [('Python', '3.11.5')] builddependencies = [('binutils', '2.40')] From e226b318b7935f6a327451940bc6d80d6a284b58 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:03:07 +0100 Subject: [PATCH 077/414] Update easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb index 291caf556ec..5c3a87666be 100644 --- a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb @@ -10,6 +10,9 @@ function wrappers and decorator functions.""" toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +sources = [SOURCE_TAR_GZ] +checksums = ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'] + dependencies = [('Python', '3.11.5')] builddependencies = [('binutils', '2.40')] From 6a734abf28a7cafc05cf623742620171ac1eeaf9 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:03:24 +0100 Subject: [PATCH 078/414] Update easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb index 5c3a87666be..8e5cb585bdb 100644 --- a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb @@ -17,12 +17,7 @@ dependencies = [('Python', '3.11.5')] builddependencies = [('binutils', '2.40')] use_pip = True +download_dep_fail = True sanity_pip_check = True -exts_list = [ - (name, version, { - 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], - }), -] - moduleclass = 'tools' From 2798bc47ccf7bd810e2882ad77f0ccff87ad9dbe Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:03:35 +0100 Subject: [PATCH 079/414] Update easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb Co-authored-by: Alexander Grund --- .../easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb index a8c2c5730e3..f686536e813 100644 --- a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb @@ -1,7 +1,7 @@ # author: Denis Kristak (INUITS) # update: Pavel Tománek (INUITS) -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'Deprecated' version = '1.2.14' From 571348290f444e5a04a0db6f8a4a50198040db50 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:03:53 +0100 Subject: [PATCH 080/414] Update easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb Co-authored-by: Alexander Grund --- .../easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb index f686536e813..e414503cc01 100644 --- a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb @@ -9,7 +9,7 @@ version = '1.2.14' homepage = 'https://github.com/tantale/deprecated' description = "If you need to mark a function or a method as deprecated, you can use the @deprecated decorator." -toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} dependencies = [ ('Python', '3.11.5'), From e09142b67e290e9ceb894818af107fe811e977a4 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:04:05 +0100 Subject: [PATCH 081/414] Update easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb Co-authored-by: Alexander Grund --- .../easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb index e414503cc01..d69639ab678 100644 --- a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb @@ -11,6 +11,9 @@ description = "If you need to mark a function or a method as deprecated, you can toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +sources = [SOURCE_TAR_GZ] +checksums = ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'] + dependencies = [ ('Python', '3.11.5'), ('wrapt', '1.16.0'), From cb0ff0afe26cede910a619d72ab9a9ccd54ec751 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:20:32 +0100 Subject: [PATCH 082/414] Update easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb Co-authored-by: Alexander Grund --- .../easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb index d69639ab678..588609a8198 100644 --- a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.11.5'), ('wrapt', '1.16.0'), ] - +builddependencies = [('binutils', '2.40')] use_pip = True sanity_pip_check = True From 4307c709896eeb056bafed5a51aca5545b4a111d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:20:45 +0100 Subject: [PATCH 083/414] Update easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb Co-authored-by: Alexander Grund --- .../d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb index 588609a8198..c80cc41c6da 100644 --- a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb @@ -23,10 +23,8 @@ builddependencies = [('binutils', '2.40')] use_pip = True sanity_pip_check = True -exts_list = [ - (name, version, { - 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], - }), -] +use_pip = True +download_dep_fail = True +sanity_pip_check = True moduleclass = 'tools' From 79ef0c11475dc5cca0dba13a6cfdd741c5f41cd3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:20:57 +0100 Subject: [PATCH 084/414] Update easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb index 4cb1124e13f..991db22bd57 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/spyder-ide/spyder' description = """Spyder is an interactive Python development environment providing MATLAB-like features in a simple and light-weighted software.""" -toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} builddependencies = [ ('poetry', '1.6.1'), From 1bf24c895b5b69ed29ca4f732e42d941f1494ee0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:21:08 +0100 Subject: [PATCH 085/414] Update easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb index 991db22bd57..52e22b303e3 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb @@ -10,6 +10,7 @@ description = """Spyder is an interactive Python development environment providi toolchain = {'name': 'GCCcore', 'version': '13.2.0'} builddependencies = [ + ('binutils', '2.40'), ('poetry', '1.6.1'), ('maturin', '1.3.1'), ] From 78e21b89d1a86131ae4c2dc0728af464459f9aac Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:21:25 +0100 Subject: [PATCH 086/414] Update easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb index 52e22b303e3..4b709d246a3 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb @@ -19,7 +19,6 @@ dependencies = [ ('Python-bundle-PyPI', '2023.10'), ('aiohttp', '3.9.5'), ('IPython', '8.17.2'), - ('jedi', '0.19.1'), ('jupyter-server', '2.14.0'), ('Pylint', '3.2.5'), ('PyZMQ', '25.1.2'), From b3e3a5a6e56aecb8de93fff3b22b222ff2d6ee48 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:22:26 +0100 Subject: [PATCH 087/414] Update easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb index 4b709d246a3..e2dec4c82b0 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb @@ -46,9 +46,6 @@ exts_list = [ ('diff-match-patch', '20230430', { 'checksums': ['953019cdb9c9d2c9e47b5b12bcff3cf4746fc4598eb406076fa1fc27e6a1f15c'], }), - ('importlib_metadata', '8.4.0', { - 'checksums': ['9a547d3bc3608b025f93d403fdd1aae741c24fbb8314df4b155675742ce303c5'], - }), ('pygithub', '2.4.0', { 'modulename': 'github', 'checksums': ['6601e22627e87bac192f1e2e39c6e6f69a43152cfb8f307cee575879320b3051'], From 67f95396222a42f1eed11dd9bf7c90e2b5db319f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:22:34 +0100 Subject: [PATCH 088/414] Update easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb index e2dec4c82b0..f4b3c256afb 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb @@ -46,7 +46,8 @@ exts_list = [ ('diff-match-patch', '20230430', { 'checksums': ['953019cdb9c9d2c9e47b5b12bcff3cf4746fc4598eb406076fa1fc27e6a1f15c'], }), - ('pygithub', '2.4.0', { + ('PyGithub', '2.4.0', { + 'source_tmpl': SOURCELOWER_TAR_GZ, 'modulename': 'github', 'checksums': ['6601e22627e87bac192f1e2e39c6e6f69a43152cfb8f307cee575879320b3051'], }), From f28a80c3907d8b1a644b0ad4fb889cc192b31809 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:23:01 +0100 Subject: [PATCH 089/414] Update easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb index f4b3c256afb..08412a34e9d 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb @@ -94,9 +94,6 @@ exts_list = [ ('jellyfish', '1.1.0', { 'checksums': ['2a2eec494c81dc1eb23dfef543110dad1873538eccaffabea8520bdac8aecbc1'], }), - ('platformdirs', '3.11.0', { - 'checksums': ['cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3'], - }), (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', 'preinstallopts': local_preinstallopts, From 10ab09c81b7ec8818ee08655b32feafba9647083 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:23:31 +0100 Subject: [PATCH 090/414] Update easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb index 08412a34e9d..779cc908ec0 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb @@ -101,10 +101,8 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': ['bin/spyder'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} +enhance_sanity_check = True +sanity_check_paths = {'files': ['bin/spyder']} sanity_check_commands = ["spyder --help"] From 4726b781d911a616b7fbd6a72014b0780da1ff63 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 21 Nov 2024 10:17:47 +0100 Subject: [PATCH 091/414] correct versions of deps --- .../d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb | 84 +++++++++++++++++++ .../git-annex-10.20240531-GCCcore-13.2.0.eb | 49 +++++++++++ .../l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb | 33 ++++++++ 3 files changed, 166 insertions(+) create mode 100644 easybuild/easyconfigs/d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/git-annex/git-annex-10.20240531-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a215ceeed07 --- /dev/null +++ b/easybuild/easyconfigs/d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'datalad' +version = "1.1.0" + +homepage = 'https://www.datalad.org/' +description = "DataLad is a free and open source distributed data management system that keeps track of your data, \ +creates structure, ensures reproducibility, supports collaboration, \ +and integrates with widely used data infrastructure." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), + ('poetry', '1.6.1') +] + +dependencies = [ + ('git-annex', '10.20240531'), + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('tqdm', '4.66.2'), + ('PLY', '3.11'), + ('scikit-build', '0.17.6'), +] + +use_pip = True + +exts_list = [ + ('humanize', '4.9.0', { + 'checksums': ['582a265c931c683a7e9b8ed9559089dea7edcf6cc95be39a3cbc2c5d5ac2bcfa'], + }), + ('fasteners', '0.19', { + 'checksums': ['b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c'], + }), + ('patool', '2.3.0', { + 'modulename': 'patoolib', + 'checksums': ['498e294fd8c7d50889d65019d431c6867bf3fb1fec5ea2d39d1d39d1215002f8'], + }), + ('annexremote', '1.6.5', { + 'checksums': ['ad0ccdd84a8771ad58922d172ee68b225ece77bf464abe4d24ff91a4896a423e'], + }), + ('looseversion', '1.3.0', { + 'checksums': ['ebde65f3f6bb9531a81016c6fef3eb95a61181adc47b7f949e9c0ea47911669e'], + }), + ('botocore', '1.34.121', { + 'checksums': ['1a8f94b917c47dfd84a0b531ab607dc53570efb0d073d8686600f2d2be985323'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.10.2', { + 'checksums': ['0711534e9356d3cc692fdde846b4a1e4b0cb6519971860796e6bc4c7aea00ef6'], + }), + ('boto3', '1.34.121', { + 'checksums': ['ec89f3e0b0dc959c418df29e14d3748c0b05ab7acf7c0b90c839e9f340a659fa'], + }), + ('python_gitlab', '4.5.0', { + 'modulename': 'gitlab', + 'checksums': ['0a106174949819912b9abb4232e39059f83f613177fdb1787097eb84481c64b2'], + }), + ('iso8601', '2.1.0', { + 'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'], + }), + (name, version, { + 'checksums': ['3403232696ae0e6cbcec56d7cccfac1be8b5d98f66f235e4751dd44fd9f5e8eb'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/datalad'], + 'dirs': [], +} + +sanity_check_commands = [ + "datalad --help", + "datalad --version", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240531-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240531-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8ff1261cea3 --- /dev/null +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240531-GCCcore-13.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'MakeCp' + +name = 'git-annex' +version = '10.20240531' + +homepage = 'https://git-annex.branchable.com' +description = """git-annex allows managing large files with git, without storing the file contents in git. It can sync, +backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the +power and distributed nature of git to bear on your large files with git-annex.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40') +] + +dependencies = [ + ('GHC', '9.10.1', '-x86_64', SYSTEM), + ('Stack', '3.1.1', '-x86_64', SYSTEM), + ('git', '2.42.0'), + ('libnsl', '2.0.1'), +] + +sources = [{ + 'git_config': {'url': 'git://git-annex.branchable.com', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'clone_into': '%(name)s-%(version)s', + }, + 'filename': '%(name)s-%(version)s.tar.gz', +}] + +checksums = [None] + +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " +buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" + +files_to_copy = [ + (['git-annex', 'git-annex-shell'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/git-annex', 'bin/git-annex-shell'], + 'dirs': [], +} + +sanity_check_commands = ['git-annex version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d71707d2105 --- /dev/null +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libnsl' +version = '2.0.1' + +homepage = 'https://github.com/thkukuk/libnsl' +description = """The libnsl package contains the public client interface for NIS(YP).""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5c9e470b232a7acd3433491ac5221b4832f0c71318618dc6aa04dd05ffcd8fd9'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('libtirpc', '1.3.4'), +] + +# Provide a symlink for libnsl.so.1, which used to be part of glibc. +# This new version of libnsl should be backwards compatible. +postinstallcmds = ['ln -s libnsl.so %(installdir)s/lib/libnsl.so.1'] + +sanity_check_paths = { + 'files': ['include/rpcsvc/yp.h', 'lib/libnsl.a', + 'lib/libnsl.%s' % SHLIB_EXT, 'lib/libnsl.%s.1' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' From f65c8b2f5dee1caf6bdf3f9a0482c640e34fcab0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 21 Nov 2024 17:49:10 +0100 Subject: [PATCH 092/414] adding easyconfigs: juliaup-1.17.9-GCCcore-12.3.0.eb --- .../juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb | 558 ++++++++++++++++++ 1 file changed, 558 insertions(+) create mode 100644 easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c7a3fcb714e --- /dev/null +++ b/easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb @@ -0,0 +1,558 @@ +easyblock = 'Cargo' + +name = 'juliaup' +version = '1.17.9' + +homepage = 'https://github.com/JuliaLang/juliaup/' +description = """This repository contains a cross-platform installer for the Julia programming language.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [] +checksums = [ + {'juliaup-1.17.9.tar.gz': '623e65f93377b21096e2fec84c7474ed940d10956ca5d51dbaf04e3b428e0261'}, + {'addr2line-0.24.2.tar.gz': 'dfbe277e56a376000877090da837660b4427aad530e3028d44e0bffe4f89a1c1'}, + {'adler2-2.0.0.tar.gz': '512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'android-tzdata-0.1.1.tar.gz': 'e999941b234f3131b00bc13c22d06e8c5ff726d1b6318ac7eb276997bbb4fef0'}, + {'android_system_properties-0.1.5.tar.gz': '819e7219dbd41043ac279b19830f2efc897156490d7fd6ea916720117ee66311'}, + {'anstream-0.6.15.tar.gz': '64e15c1ab1f89faffbf04a634d5e1962e9074f2741eef6d97f3c4e322426d526'}, + {'anstyle-1.0.8.tar.gz': '1bec1de6f59aedf83baf9ff929c98f2ad654b97c9510f4e70cf6f661d49fd5b1'}, + {'anstyle-parse-0.2.5.tar.gz': 'eb47de1e80c2b463c735db5b217a0ddc39d612e7ac9e2e96a5aed1f57616c1cb'}, + {'anstyle-query-1.1.1.tar.gz': '6d36fc52c7f6c869915e99412912f22093507da8d9e942ceaf66fe4b7c14422a'}, + {'anstyle-wincon-3.0.4.tar.gz': '5bf74e1b6e971609db8ca7a9ce79fd5768ab6ae46441c572e46cf596f59e57f8'}, + {'anyhow-1.0.90.tar.gz': '37bf3594c4c988a53154954629820791dde498571819ae4ca50ca811e060cc95'}, + {'assert_cmd-2.0.16.tar.gz': 'dc1835b7f27878de8525dc71410b5a31cdcc5f230aed5ba5df968e09c201b23d'}, + {'assert_fs-1.1.2.tar.gz': '7efdb1fdb47602827a342857666feb372712cbc64b414172bd6b167a02927674'}, + {'autocfg-1.4.0.tar.gz': 'ace50bade8e6234aa140d9a2f552bbee1db4d353f69b8217bc503490fc1a9f26'}, + {'backtrace-0.3.74.tar.gz': '8d82cb332cdfaed17ae235a638438ac4d4839913cc2af585c3c6746e8f8bee1a'}, + {'base64-0.22.1.tar.gz': '72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6'}, + {'bitflags-2.6.0.tar.gz': 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'1.0.23'), + ('serde', '1.0.210'), + ('serde_derive', '1.0.210'), + ('serde_json', '1.0.131'), + ('serde_spanned', '0.6.8'), + ('serde_urlencoded', '0.7.1'), + ('shell-words', '1.1.0'), + ('shellexpand', '3.1.0'), + ('shlex', '1.3.0'), + ('slab', '0.4.9'), + ('smallvec', '1.13.2'), + ('socket2', '0.5.7'), + ('spin', '0.9.8'), + ('strsim', '0.11.1'), + ('subtle', '2.6.1'), + ('syn', '1.0.109'), + ('syn', '2.0.79'), + ('sync_wrapper', '1.0.1'), + ('tar', '0.4.42'), + ('tempfile', '3.13.0'), + ('termcolor', '1.4.1'), + ('termtree', '0.4.1'), + ('thiserror', '1.0.64'), + ('thiserror-impl', '1.0.64'), + ('tinyvec', '1.8.0'), + ('tinyvec_macros', '0.1.1'), + ('tokio', '1.40.0'), + ('tokio-native-tls', '0.3.1'), + ('tokio-rustls', '0.26.0'), + ('tokio-socks', '0.5.2'), + ('toml', '0.5.11'), + ('toml', '0.8.19'), + ('toml_datetime', '0.6.8'), + ('toml_edit', '0.22.22'), + ('tower-service', '0.3.3'), + ('tracing', '0.1.40'), + ('tracing-core', '0.1.32'), + ('try-lock', '0.2.5'), + ('unicode-bidi', '0.3.17'), + ('unicode-ident', '1.0.13'), + ('unicode-normalization', '0.1.24'), + ('unicode-width', '0.1.14'), + ('untrusted', '0.9.0'), + ('url', '2.5.2'), + ('utf8parse', '0.2.2'), + ('uuid', '1.11.0'), + ('vcpkg', '0.2.15'), + ('wait-timeout', '0.2.0'), + ('walkdir', '2.5.0'), + ('want', '0.3.1'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.95'), + ('wasm-bindgen-backend', '0.2.95'), + ('wasm-bindgen-futures', '0.4.45'), + ('wasm-bindgen-macro', '0.2.95'), + ('wasm-bindgen-macro-support', '0.2.95'), + ('wasm-bindgen-shared', '0.2.95'), + ('web-sys', '0.3.72'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.9'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows', '0.58.0'), + ('windows-core', '0.52.0'), + ('windows-core', '0.58.0'), + ('windows-implement', '0.58.0'), + ('windows-interface', '0.58.0'), + ('windows-registry', '0.2.0'), + ('windows-result', '0.2.0'), + ('windows-strings', '0.1.0'), + ('windows-sys', '0.48.0'), + ('windows-sys', '0.52.0'), + ('windows-sys', '0.59.0'), + ('windows-targets', '0.48.5'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.48.5'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.48.5'), + ('windows_x86_64_msvc', '0.52.6'), + ('winres', '0.1.12'), + ('xattr', '1.3.1'), + ('zerocopy', '0.7.35'), + ('zerocopy-derive', '0.7.35'), + ('zeroize', '1.8.1'), +] + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = [f"{name} --help"] + +moduleclass = 'lang' From 89fc7b47010a9d5622cd67e84da1485e6dac8a9d Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 22 Nov 2024 10:27:29 +0100 Subject: [PATCH 093/414] adding easyconfigs: HyperQueue-0.20.0.eb --- .../h/HyperQueue/HyperQueue-0.20.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.20.0.eb diff --git a/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.20.0.eb b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.20.0.eb new file mode 100644 index 00000000000..c71c91f554b --- /dev/null +++ b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.20.0.eb @@ -0,0 +1,29 @@ +easyblock = 'BinariesTarball' + +name = 'HyperQueue' +version = '0.20.0' + +homepage = 'https://it4innovations.github.io/hyperqueue/stable/' +description = """ +HyperQueue is a tool designed to simplify execution of large workflows (task graphs) on HPC clusters. +It allows you to execute a large number of tasks in a simple way, without having to manually submit jobs +into batch schedulers like Slurm or PBS. + +You just specify what you want to compute – HyperQueue will automatically ask for computational resources and +dynamically load-balance tasks across all allocated nodes and cores. +HyperQueue can also work without Slurm/PBS as a general task executor. +""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/It4innovations/hyperqueue/releases/download/v%(version)s/'] + +sources = ['hq-v%(version)s-linux-x64.tar.gz'] +checksums = ['1b05177c9dd562a7ce1480796da2e8db169f963608719d398f21899d4f79f934'] + +sanity_check_paths = { + 'files': ['bin/hq'], + 'dirs': [], +} + +moduleclass = 'tools' From bb21b43533b60a8b5d22b293a94b297597f0f5f6 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 22 Nov 2024 13:07:07 +0100 Subject: [PATCH 094/414] adding easyconfigs: vLLM-0.4.0-foss-2023a-CUDA-12.1.1.eb, xformers-0.0.23.post1-foss-2023a-CUDA-12.1.1.eb --- .../vLLM/vLLM-0.4.0-foss-2023a-CUDA-12.1.1.eb | 97 +++++++++++++++++++ ...ers-0.0.23.post1-foss-2023a-CUDA-12.1.1.eb | 40 ++++++++ 2 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/v/vLLM/vLLM-0.4.0-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/x/xformers/xformers-0.0.23.post1-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/v/vLLM/vLLM-0.4.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/v/vLLM/vLLM-0.4.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..90663d6e83b --- /dev/null +++ b/easybuild/easyconfigs/v/vLLM/vLLM-0.4.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,97 @@ +easyblock = 'PythonBundle' + +name = 'vLLM' +version = '0.4.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/vllm-project/vllm' +description = """A high-throughput and memory-efficient inference and serving engine for LLMs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('maturin', '1.1.0'), + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('SentencePiece', '0.2.0'), + ('py-cpuinfo', '9.0.0'), + ('Transformers', '4.39.3'), + ('pydantic', '2.5.3'), + ('tiktoken', '0.6.0'), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('Triton', '2.1.0', versionsuffix), + ('Ray-project', '2.9.1'), + ('numba', '0.58.1'), + ('xformers', '0.0.23.post1', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '4.3.0', { + 'checksums': ['f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6'], + }), + ('starlette', '0.36.3', { + 'checksums': ['90a671733cfb35771d8cc605e0b679d23b992f8dcfad48cc60b38cb29aeb7080'], + }), + ('fastapi', '0.110.0', { + 'checksums': ['266775f0dcc95af9d3ef39bad55cff525329a931d5fd51930aadd4f428bf7ff3'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('uvicorn', '0.30.0', { + 'checksums': ['f678dec4fa3a39706bbf49b9ec5fc40049d42418716cea52b53f07828a60aa37'], + }), + ('prometheus_client', '0.21.0', { + 'checksums': ['96c83c606b71ff2b0a433c98889d275f51ffec6c5e267de37c7a2b5c9aa9233e'], + }), + ('pynvml', '11.5.0', { + 'checksums': ['d027b21b95b1088b9fc278117f9f61b7c67f8e33a787e9f83f735f0f71ac32d0'], + }), + ('diskcache', '5.6.3', { + 'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'], + }), + ('interegular', '0.3.3', { + 'checksums': ['d9b697b21b34884711399ba0f0376914b81899ce670032486d0d048344a76600'], + }), + ('lark', '1.2.2', { + 'checksums': ['ca807d0162cd16cef15a8feecb862d7319e7a09bdb13aef927968e45040fed80'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('rpds_py', '0.18.0', { + 'modulename': 'rpds', + 'checksums': ['42821446ee7a76f5d9f71f9e33a4fb2ffd724bb3e7f93386150b61a43115788d'], + }), + ('referencing', '0.35.1', { + 'checksums': ['25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c'], + }), + ('outlines', '0.0.34', { + 'checksums': ['594e7204c770b47a62eb5c2ba7d25ea0ab2e16882b5f04556712a0228d3d3309'], + }), + (name, version, { + # delete cmake and ninja deps to let pip check pass + 'preinstallopts': "sed -i -e '/cmake>=3.21/d' -e '/ninja/d' requirements.txt && ", + 'source_urls': ['https://github.com/vllm-project/vllm/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['95e5fa8f6ac63f11b4c7122e01c0892beae91f754a64a7e525bc06c3b49feac7'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from vllm import LLM, SamplingParams'"] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/x/xformers/xformers-0.0.23.post1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/x/xformers/xformers-0.0.23.post1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..46ddc7138f7 --- /dev/null +++ b/easybuild/easyconfigs/x/xformers/xformers-0.0.23.post1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'xformers' +version = '0.0.23.post1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/facebookresearch/xformers' +description = """Flexible Transformers, defined by interoperable and optimized building blocks.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b443b158bd7b5275b485d2c6aee94ebc2152878fd784e379b1c8bcb1d67f3b81'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('flash-attention', '2.6.3', versionsuffix), + ('CUTLASS', '3.4.0', versionsuffix), + ('Triton', '2.1.0', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +preinstallopts = 'export XFORMERS_MORE_DETAILS=1 && ' +preinstallopts += 'export XFORMERS_DISABLE_FLASH_ATTN=1 && ' +preinstallopts += 'export TORCH_CUDA_ARCH_LIST="5.2;6.0;7.0;7.5;8.0;8.6;9.0" && ' +preinstallopts += 'export MAX_JOBS=3 && ' + +sanity_pip_check = True + +moduleclass = 'ai' From 28410b6206f4ec95ac66d1e4b392c83948a5fe7e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 22 Nov 2024 14:51:22 +0100 Subject: [PATCH 095/414] Update easyconfigs.py - add exception for tiktoken version --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4b1c4dd770e..916196f9440 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -658,6 +658,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # tensorflow-probability version to TF version ('2.8.4;', ['tensorflow-probability-0.16.0-']), ], + # vLLM has pinned dependency tiktoken == 0.6.0 + 'tiktoken': [('0.6.0;', ['vLLM-0.4.0-'])], # smooth-topk uses a newer version of torchvision 'torchvision': [('0.11.3;', ['smooth-topk-1.0-20210817-'])], # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 From 9d4ee61a7c78a1231eb72fe0463fb5f33d66a4f7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 24 Nov 2024 16:01:22 +0000 Subject: [PATCH 096/414] adding easyconfigs: GDAL-3.10.0-foss-2024a.eb --- .../g/GDAL/GDAL-3.10.0-foss-2024a.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb new file mode 100644 index 00000000000..7d854ed7422 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb @@ -0,0 +1,79 @@ +easyblock = 'CMakeMake' + +name = 'GDAL' +version = '3.10.0' + +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': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/%(namelower)s/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['%(name)s-3.6.2_fix-python-CC-CXX.patch'] +checksums = [ + {'gdal-3.10.0.tar.xz': 'af821a3bcf68cf085724c21c9b53605fd451d83af3c8854d8bf194638eb734a8'}, + {'GDAL-3.6.2_fix-python-CC-CXX.patch': '859b874b0c8ff7626a76d51f008bf05b7f89a35b325bdd1d126d2364154acc63'}, +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), + ('Bison', '3.8.2'), +] +dependencies = [ + ('Python', '3.12.3'), + ('netCDF', '4.9.2'), + ('expat', '2.6.2'), + ('GEOS', '3.12.2'), + ('SQLite', '3.45.3'), + ('libarchive', '3.7.4'), + ('libxml2', '2.12.7'), + ('libpng', '1.6.43'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('zlib', '1.3.1'), + ('cURL', '8.7.1'), + ('PCRE', '8.45'), + ('PROJ', '9.4.1'), + ('libgeotiff', '1.7.3'), + ('SciPy-bundle', '2024.05'), + ('HDF5', '1.14.5'), + ('HDF', '4.3.0'), + ('Armadillo', '14.0.3'), + ('CFITSIO', '4.4.1'), + ('zstd', '1.5.6'), + ('giflib', '5.2.2'), + ('json-c', '0.17'), + ('Xerces-C++', '3.2.5'), + ('PCRE2', '10.43'), + ('OpenEXR', '3.2.4'), + ('Brunsli', '0.1'), + ('Qhull', '2020.2'), + ('LERC', '4.0.0'), + ('OpenJPEG', '2.5.2'), + ('SWIG', '4.2.1'), +] + +# iterative build for both static and shared libraries +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF " +local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " + +configopts = [ + local_configopts_common + "-DBUILD_SHARED_LIBS=OFF", + local_configopts_common +] + + +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.%(namelower)s'"] + +moduleclass = 'data' From d78ea49de16edc71c71d359f2ef0efb877581b17 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 24 Nov 2024 16:03:01 +0000 Subject: [PATCH 097/414] EB4 --- easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb index 7d854ed7422..7b452e77df4 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb @@ -76,4 +76,6 @@ sanity_check_paths = { sanity_check_commands = ["python -c 'import osgeo.%(namelower)s'"] +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'data' From 8780b0c75ff4d579e50fe048f3f74df1cd180a1d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 24 Nov 2024 16:14:05 +0000 Subject: [PATCH 098/414] adding easyconfigs: R-4.4.2-gfbf-2024a.eb, R-bundle-CRAN-2024.11-foss-2024a.eb --- .../R-bundle-CRAN-2024.11-foss-2024a.eb | 3508 +++++++++++++++++ .../easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb | 368 ++ 2 files changed, 3876 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.11-foss-2024a.eb create mode 100644 easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.11-foss-2024a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.11-foss-2024a.eb new file mode 100644 index 00000000000..7c36a151d4a --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.11-foss-2024a.eb @@ -0,0 +1,3508 @@ +easyblock = 'Bundle' + +name = 'R-bundle-CRAN' +version = '2024.11' + +homepage = 'https://www.r-project.org/' +description = "Bundle of R packages from CRAN" + +toolchain = {'name': 'foss', 'version': '2024a'} + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('Xvfb', '21.1.14'), + ('Autotools', '20231222'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('R', '4.4.2'), + ('libxml2', '2.12.7'), # for XML + ('GMP', '6.3.0'), # for igraph + ('NLopt', '2.7.1'), # for nlopt + ('FFTW', '3.3.10'), # for fftw + ('libsndfile', '1.2.2'), # for seewave + ('ICU', '75.1'), # for rJava & gdsfmt + ('HDF5', '1.14.5'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.8'), # for RcppGSL + ('ImageMagick', '7.1.1-38'), + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '20.13.1'), # for V8 (required by rstan) + ('GDAL', '3.10.0'), # for sf + ('MPFR', '4.2.1'), # for Rmpfr + ('PostgreSQL', '16.4'), # for RPostgreSQL +] + +# 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" + +exts_defaultclass = 'RPackage' + +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', +} + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors +# cfr. https://github.com/vdorie/dbarts/issues/66 +if ARCH == 'aarch64': + local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"' + local_dbarts_preinstallopts += ' src/misc/Makefile && ' +else: + local_dbarts_preinstallopts = '' + +# !! order of packages is important !! +# packages updated on 24 November 2024 +exts_list = [ + ('abind', '1.4-8', { + 'checksums': ['264a051b523ceae1795a0879e7768949ea55c586ac8db0adf1f5ebeddd2623e1'], + }), + ('magic', '1.6-1', { + 'checksums': ['ca79ec7ae92b736cb128556c081abf547f49956c326e053a76579889cbcb7976'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.22', { + 'checksums': ['2a64dc46d6764f890704c186d0af0c3ead335e8604320bfe71a70872a14e745f'], + }), + ('linprog', '0.9-4', { + 'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'], + }), + ('geometry', '0.5.0', { + 'checksums': ['b5f7554d6304e7bd0cda730e743b54634296391c1051663889980ebd7aaf9e61'], + }), + ('bit', '4.5.0', { + 'checksums': ['89ddc5e38c2d61718d117a0288828ab61dee93269ca61c609d3e173a85e7cbed'], + }), + ('filehash', '2.4-6', { + 'checksums': ['558b446ba354c6fa88f694e8d6d068f999d1e7b626164eb2aeacccbb0dee81b1'], + }), + ('ff', '4.5.0', { + 'checksums': ['2aed9052a93ca81af4c8cc7defce0f7aa0206b442b4795b6219f6e56b341188e'], + }), + ('bnlearn', '5.0.1', { + 'checksums': ['2452bd9523dbb4d6a44553cd67096523ba4d18800deef7b376e694d7c60af99e'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-42', { + 'checksums': ['a17f452a94fc3964c939c5b147ad6d4f326a0990493519d376d6700cf733a134'], + }), + ('fdrtool', '1.2.18', { + 'checksums': ['649966996bfaa71932eddfb8ab371187377d8b0212548305dd7b18664ae6baef'], + }), + ('formatR', '1.14', { + 'checksums': ['4ebaab2c3f8527871655246b62abd060bc75dae1cec7f962ca4752b8080f474c'], + }), + ('gtools', '3.9.5', { + 'checksums': ['dee9b6c1152db1a5dc427d074b32bbbb738708683f17a95e0e95e4d79fdf174b'], + }), + ('gdata', '3.0.1', { + 'checksums': ['db3a96dd2ba3c0ef6fc6b5176eba7b4d3eaa06b96fba3d8d0b13450c66763862'], + }), + ('GSA', '1.03.3', { + 'checksums': ['5459786190f40339addc45e7bb58c6a983548aa8feac7277ea7ec0662c5a282c'], + }), + ('infotheo', '1.2.0.1', { + 'checksums': ['c0fb8ec97ad3a49f231c4c993b5eee70c6a61c8c30dc4a46197867e4763a29d4'], + }), + ('lars', '1.3', { + 'checksums': ['c69e6a8da6a3344c0915dd1fd4c78fec5cdf50c62cf6297476e9bb7dc10b549d'], + }), + ('lazy', '1.2-18', { + 'checksums': ['99441bcae2dfbf450eee91f3ec969d416c225f671ac54459c50536916890f00a'], + }), + ('kernlab', '0.9-33', { + 'checksums': ['70c0787d6d3762c89bb68218fbee19e861fcb5d4c05b787a9692055d95dd3061'], + }), + ('markdown', '1.13', { + 'checksums': ['385421c674cf5bf2ba04d1df7c16bb5d857bec03755a36321999ac37f5b3cfd9'], + }), + ('mlbench', '2.1-5', { + 'checksums': ['4dbfd652adda7c0caf544d3a6cd23a2ee97c22faefe4d15b8a6782061cc9e76f'], + }), + ('NLP', '0.3-2', { + 'checksums': ['c59e8bc6485336bc076e7c37129814fa8ef558ce711fa493510206e6a9254225'], + }), + ('mclust', '6.1.1', { + 'checksums': ['ddd7018e5e6ea7f92c7fc9872b391491b7e91c2cd89ef1dcaf4408afb5116775'], + }), + ('RANN', '2.6.2', { + 'checksums': ['6ef7d5b555ab6b051da86896aeb4d18e8174b22dbe2fc1543888d3b88d9b9772'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('MASS', '7.3-61', { + 'checksums': ['3144c8bf579dd7b7c47c259728c27f53f53e294e7ed307da434dfd144e800a90'], + }), + ('lattice', '0.22-6', { + 'checksums': ['4b377211e472ece7872b9d6759f9b9c660b09594500462eb6146312a1d4d00f7'], + }), + ('nlme', '3.1-166', { + 'checksums': 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('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.6', { + 'checksums': ['efccaa309a150d11c6b402b912e618ea041f25cca3101f32cd821a6f41684e35'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.2-1', { + 'checksums': ['68b4215a9dfff65880a3ba6f7febe4929b197611344932b79af05d91dc584558'], + }), + ('hdf5r', '1.3.11', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['9795d667bc72acfabece1e3ece1aa4e60e8194cb4eb8b46985efccd19a55a8c4'], + }), + ('DTRreg', '2.2', { + 'checksums': ['9c8954d5c342af85611d13dab5be64c4a7a5904644a6e04ff21d5494559e2fc7'], + }), + ('pulsar', '0.3.11', { + 'checksums': ['ee82ef25b2be4bbac713c34bca85d8ea1fa0e32eb8c800dad7256e145fc79393'], + }), + ('bayesm', '3.1-6', { + 'checksums': ['17d72b9cdc090845f98e7a04640380d0baef8bc23d1487c8f64dc192fdb93cb5'], + }), + ('gsl', '2.1-8', { + 'checksums': ['f33609bf485abd190e65ff5d0fdab438b759294c47b921d983d89d6f053a2d95'], + }), + ('energy', '1.7-12', { + 'checksums': ['ac2224befa4c6ab62f99816ff670b1ee35288cabb7db362257e9af21c87e6f72'], + }), + ('compositions', '2.0-8', { + 'checksums': ['c5063488f456992b5821458b3237322addffd3451ae91f9474707886971ef290'], + }), + ('clustree', '0.5.1', { + 'checksums': ['b5f2496e596e3fd140ace69c4837085e13f3abb850f5eb57d496380691fdd117'], + }), + ('tweedie', '2.3.5', { + 'checksums': ['983c745fee5a780d46e8dd04c2eb1c10cb2e222d3679654f0d6934d3db7b1c3e'], + }), + ('RcppGSL', '0.3.13', { + 'checksums': ['fe5e73bc119c6424e1a40b6fea17417a7bba93e81dbe9b7cf86dde9b8e8d93e7'], + }), + ('mvabund', '4.2.1', { + 'checksums': ['ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06'], + }), + ('fishMod', '0.29.2', { + 'checksums': ['6cd0feedebbaa68f841a4e5ee82cc7f2a048c30e5632184921acb06824a72f5a'], + }), + ('alabama', '2023.1.0', { + 'checksums': ['925f67c72d9cdb677105377777bd09e9b56a61573bea7e3f69e0a49595c7bf1c'], + }), + ('gllvm', '1.4.3', { + 'checksums': ['63b77040e9cf2694882d1d80a3bc3030b3a348819ea38e6728417e4c5de07ecc'], + }), + ('grpreg', '3.5.0', { + 'checksums': ['160b321aee0bb911cc9cdf50f1a9b3884ecfab2b77e200aef38b18df0f98840c'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('lpSolveAPI', '5.5.2.0-17.12', { + 'checksums': ['4f00a9d27055ddf3e2a4b0a529b720861b9f916f2ceb1fe0b71e4c52da5b70ef'], + }), + ('ergm', '4.7.5', { + 'checksums': ['f4f768df44f9594f74faf82cdcfcb4d6eeeafffb9785e3687586234c6a612c96'], + }), + ('networkLite', '1.0.5', { + 'checksums': ['aaab55d4f8f0b330fe7c1ecbab3c44746c52c2fda99c53c6b46042bb8775718b'], + }), + ('networkDynamic', '0.11.5', { + 'checksums': ['a33ff40ca8d7f923915219793eb6b5acfa9a2c888e3dacc031210f414bf2a5c0'], + }), + ('ergm.multi', '0.2.1.1', { + 'checksums': ['b661d8ccc2d7fa1959bcb93db15cb448bd39d21d192aa62fe0cdad4c9ea15e88'], + }), + ('tergm', '4.2.1', { + 'checksums': ['8a1cc04350e6d46bf510558ca47fe51a3b81d26214ecfc2d73ba35d3600e60d7'], + }), + ('ergm.count', '4.1.2', { + 'checksums': ['9bce70b64a2f60b242603b771370b40d7f7aeed37ed426670131fd966c13b020'], + }), + ('tsna', '0.3.5', { + 'checksums': ['4ee2f773d573f0f4bd93131156fdccf01d7f1a3f725eff3e885021098c6bff65'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-8', { + 'checksums': ['6a06440d4b58e8a7f122747d92046ff40da4bb58a20bf642228a648a0c826ea7'], + }), + ('MCMCpack', '1.7-1', { + 'checksums': ['3b0b46746324197c38826cde06729f031311c3520d9d42815b7b356d29b58529'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.3', { + 'checksums': ['62b4e24e82e702537c907522e73b3f7381a6aa274e97ac7d1ab01d513d61c41b'], + }), + ('asnipe', '1.1.17', { + 'checksums': ['e7b4010fa1adf27534420db2971dae3c63190920a4323c86fd586842e22d9b07'], + }), + ('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': [ + {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, + {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch': + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'}, + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.44.0.3', { + 'checksums': ['61a85f6c2f15e8e96839f8a4fd3a45eaa6bca90517bb20a4dd36e951d6fd0c82'], + }), + ('mlegp', '3.1.9', { + 'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.5', { + 'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'], + }), + ('bartMachineJARs', '1.2.1', { + 'checksums': ['9f7a20acf4aec249e16f83d81f5ec796aa718deb1b8bc24393fc0421eb8ce1c0'], + }), + ('bartMachine', '1.3.4.1', { + 'checksums': ['3b0a5250f5425a8efe460adcb58ea1342f1d845ae3a8db29dbf4806653884b89'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.11', { + 'checksums': ['c63a6453783865b7c69c580a09a769e99390dd8b2e0f63e48fbfc86da3bee4b7'], + }), + ('GUTS', '1.2.5', { + 'checksums': ['9d983a566daa07d3e0036fe7011efe94f29e31a611493ba16bd316b61730a7b7'], + }), + ('GenSA', '1.1.14.1', { + 'checksums': ['2fdd54cbd670c9eaba304547d8c44fc51578cb317adb9788a0fc82f58ace377f'], + }), + ('parsedate', '1.3.1', { + 'checksums': ['1fc31ab9813b61680abf4f4c2705b8f484d56d1d3ef256df84b342b628b6d1b1'], + }), + ('circular', '0.5-1', { + 'checksums': ['fb59fc9119d777fbc77fe054db83abce84c470ac3269c2aa42b5f5df7683f3d9'], + }), + ('cobs', '1.3-8', { + 'checksums': ['2c2049c7cb868a2e4e1a530fe7218fac56e6157ef64ad57b91c5bb457dbc9821'], + }), + ('resample', '0.6', { + 'checksums': ['1b958009b18c92a47971847c782af76952ea4e85d5f1e3e1e70fa35c67b95265'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-10', { + 'checksums': ['bd89a8fe939f3becd71a9dab30fe27fa43c96572d8309d2c1a70633117d4cb33'], + }), + ('Rserve', '1.8-13', { + 'checksums': ['7e5d312fca8029d746f60e7d9e701129561942f97dfc33b036b123f159d69a4c'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '8.0.0', { + 'checksums': ['38e75b1ebc8b2d1c54b3373a42529b819c7b4773fd4932f57bc9701d1e3e3dc7'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '2.0.1.1', { + 'checksums': ['8c2448f176ed94201affb8a9c42a5d0f56f26e88131ff2c1f4a9d14c5a0d87f6'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.20', { + 'checksums': ['72c4af5d872fe2689444d74d5722e732d7a4b896aca73aad0b3f200268570204'], + }), + ('BMA', '3.18.19', { + 'checksums': ['09ead6ec3dc0bcc1de4d47b18b705fd2a7637cd888eec220cbc5b175e8ca8d42'], + }), + ('BCEE', '1.3.2', { + 'checksums': ['f0e0a6a4eb11213073aa2f0cd6c76d87e8b3965124d8ca509538eb3c128533a0'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-66', { + 'checksums': ['aa86dd58c05635eb394c9ede0dd15a4f24af4815f299451bbc7895c0f737c2fb'], + }), + ('bdsmatrix', '1.3-7', { + 'checksums': ['c3505e5ac06d5e01b3a6bad94177f8375cd9867bb0146cc9c63d92424ecb7922'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.22.3', { + 'checksums': ['fd094f0ea1a163ad1bd290e789ad827a76075d82ae5ce8a8e53a7095a7479383'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.6', { + 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], + }), + ('rda', '1.2-1', { + 'checksums': ['37038a9131c9133519f5e64fa1a86dbe28b21f519cf6528503234648a139ae9a'], + }), + ('sampling', '2.10', { + 'checksums': ['fdec976ec0abfb5c690049d76f89ebcb8ab3650e2eb28a5b54c3984d17372775'], + }), + ('lda', '1.5.2', { + 'checksums': ['95d354786e002352a973052df993b9d3acfc9f9598a053afb95ac27c7e150fd4'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.2', { + 'checksums': ['3354b22752f0aa0c0d9c8c12b38810202b6380f2587e539be11d9a358412fe6a'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '4.3', { + 'checksums': ['f755808fcb618582acb862729b20e267d9c2214f22e6e7a0c8d29073d8faa7b8'], + }), + ('bbmle', '1.0.25.1', { + 'checksums': ['d92a0cf819fe4c08b8eb17f5e03275c8accde7f3b54f990cbba5ab926575b60b'], + }), + ('emdbook', '1.3.13', { + 'checksums': ['26044b7ea1b42304b4dfde48afa94dd487acf979da4db2bf670ba41222083c19'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.51.6', { + 'checksums': ['61bd0d19d045b50c6764f3a7c95ce1e734af9e5f964449825d002afe02109489'], + }), + ('tictoc', '1.2.1', { + 'checksums': ['8fcdb7c9a1e4b4817bcab654effd64dea6ec749a7901d4060d5b5c625fc88833'], + }), + ('ISOcodes', '2024.02.12', { + 'checksums': ['02cb7b918034085dffcba0d329a2bc52514873f898a3a716560ebf17b57ae2e6'], + }), + ('stopwords', '2.3', { + 'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'], + }), + ('janeaustenr', '1.0.0', { + 'checksums': ['b4c32ee1395ee4a8efe714c535c0fe578b0dbf5f3bb85b41fa5cc87569b8e8aa'], + }), + ('SnowballC', '0.7.1', { + 'checksums': ['753cf13f3206751662c03b1cf39bce9e680024f6d9f8503b836a83797181c034'], + }), + ('tokenizers', '0.3.0', { + 'checksums': ['24571e4642a1a2d9f4f4c7a363b514eece74788d59c09012a5190ee718a91c29'], + }), + ('hunspell', '3.0.5', { + 'checksums': ['bcceadda94f5c87ffe1c8695f9d4cc561c2618b4ac7432aa56b833567d90fc3a'], + }), + ('topicmodels', '0.2-17', { + 'checksums': ['3867e15ff5d318307695c1aa196b8fe405ee4cbd4f7574e298d78ef778d5168d'], + }), + ('tidytext', '0.4.2', { + 'checksums': ['0cf4180c2ab9fdb158337a7bfb6ba32f15fb61aae28abce425deaa5933ed2d54'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.3-3', { + 'checksums': ['f612289f8da9894aaaee843125c2d491390bbcb527a7d8462f4398137df8f485'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.3', { + 'checksums': ['6b3910dc48495439cd01828f8999823864a6712f73560ee3e6c903065c67d1e4'], + }), + ('entropy', '1.3.1', { + 'checksums': ['6f5a89f5ce0e90cbed1695b81259326c976e7a8f538157e223ee5f63b54412b8'], + }), + ('kedd', '1.0.4', { + 'checksums': 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('testit', '0.13', { + 'checksums': ['90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-4', { + 'checksums': ['d4b3d65a33cae454d3ab13343bceabfb3f6b8004ac64ae7bd86dee92a1cd2055'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-6', { + 'checksums': ['9ab2c58290be25dbe00e5edc32406f92cc1663745ea5f12224c33a32678f392c'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.21', { + 'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'], + }), + ('dbarts', '0.9-28', { + 'preinstallopts': local_dbarts_preinstallopts, + 'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.2.0', { + 'checksums': ['26fcfbc79810f23a28389a5ce5519e6ddc2470c5e924ba8cf4dd19a1b0fd9f83'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-10', { + 'checksums': ['f6fcd9012f2fa777127c86ba520d8dc834f4ea746a6e29623edd072479191c75'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('minty', '0.0.4', { + 'checksums': ['96222703655deb365dc4199ff54daa17e7030949e4d921d6e9c039861ef60742'], + }), + ('readODS', '2.3.1', { + 'checksums': ['95ee571fc22ec3fb5db1de973f9eabdf4f73577972d3fe3283b5012614bbaf22'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '3.0.0', { + 'checksums': ['0413ec3d44b3251549a254b4afd76f520aaacd5374b463a5813e23e1fa8cd248'], + }), + ('outliers', '0.15', { + 'checksums': ['cc31d7f2faefd2c3a27f8ce78c7e67d3b321dcd6690292fad2468125e5e635fb'], + }), + ('gWidgets2', '1.0-9', { + 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], + }), + ('gWidgets2tcltk', '1.0-8', { + # 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, + 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + }), + ('mgsub', '1.7.3', { + 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], + }), + ('ie2misc', '0.9.1', { + 'checksums': ['f1db0c66c8fa05e99c4059c1799abc3eb7effd7113baf03f38d26853ac05c425'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-5', { + 'checksums': ['b68954f53082561f0242682611bf3373e0bf30d8ac2256d82474edc5f992f4dd'], + }), + ('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', '0.0-4', { + 'checksums': ['2f820474ed20e06f65b284962c87cd1e85220a11cc7fcde09716f0eee5821387'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '3.3', { + 'checksums': ['fbd0d09ba1a28265f3c6c5043ebcded1f33c89fb46766374e79eae141cfa3342'], + }), + ('lmom', '3.2', { + 'checksums': ['da3c7bedb0f1b70423f0deba03cb936632d615fa509791ce998a8fedd1c7ad98'], + }), + ('gld', '2.6.6', { + 'checksums': ['ea23e9781207b5d47ed04e4d5758d9652cab5d1eedcf9fbc9c2ee4d3babffdc4'], + }), + ('DescTools', '0.99.58', { + 'checksums': ['62907753c4d3efe4ef6990f0e381dcac24c00956531f3d52b337896cf827e8b4'], + }), + ('orthopolynom', '1.0-6.1', { + 'checksums': ['ec4a6ed266532f2f6d37a4ca6bd1b74c1df28a8c2caeab60e5d6af15bdbfe2c5'], + }), + ('gaussquad', '1.0-3', { + 'checksums': ['a3337ce52bc53435cb4565a38bf48b72b384be397d2e86bb66f62973004dc810'], + }), + ('nlsem', '0.8-1', { + 'checksums': ['0674ec2a1ae7e50b08ee1b156674c2f2100258b14d6a9068f7dd6ad1ee128377'], + }), + ('tableone', '0.13.2', { + 'checksums': ['b1cf15579abd4240e24435d2d9aad255c839d2a0293e28cb2eef0c808c4727af'], + }), + ('jstable', '1.3.6', { + 'checksums': ['dbc7b6bba9c845948c7546910ff0f8d9b73549ed9f4fc4cd3890752df201c48d'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.3', { + 'checksums': ['208e9b48a11cf56ce142731c204f3d2bcb5b68719f84309a36362cd925414265'], + }), + ('sensemakr', '0.1.6', { + 'checksums': ['bf27b92781f4746cdc7b2401d592c674baf0b05286573a936a2b24ccf3ad9be4'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-8', { + 'checksums': ['19a5acd430a5b24e4ef72624ef065d0395b7fbedfeee4d09e3eb5e86c142dc82'], + }), + ('blavaan', '0.5-6', { + 'checksums': ['1e1f3c9debdc14b39a9ae98ef4269457cac19b9015aa6f7b0196a865d4d37b51'], + }), + ('mathjaxr', '1.6-0', { + 'checksums': ['ecc47607111b788d84789459af7f4f9102719f98640b7a23bd5a4eb1a6d3c179'], + }), + ('metadat', '1.2-0', { + 'checksums': ['f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8'], + }), + ('metafor', '4.6-0', { + 'checksums': ['07344cc3bd87b8bd25ef998e9a6ce322ae8e448ef5af06ec3e79631724e18666'], + }), + ('RNifti', '1.7.0', { + 'checksums': ['e58cf73a0f5fbf5d6a2c845bfdeea193eb5262c73d0f329beae17d68f40e18e8'], + }), + ('oro.nifti', '0.11.4', { + 'checksums': ['efe4f5d2c2e37ff6c3e9250f54ef775e4d452c1334f781f22f219ed53148b606'], + }), + ('fmri', '1.9.12.1', { + 'checksums': ['4497b5a29d936552e1d2c07e2ea71d3b446f2e35dc8a21527bbc289a06b3db3b'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.6', { + 'checksums': ['4f28ae62748654cb6f90e1ffa17b05bb8b89eb6a20262d9c5d39cb862f71dc91'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2024.2-1', { + 'checksums': ['e3b21b08b7db3c2c06543a21718e1c18a2b2d2ddf4c92f0e44841d10f55d5c40'], + }), + ('Rvmmin', '2018-4.17.1', { + 'checksums': ['55000ac4ff57d42f172c46c7d6b0a603da3b65866d6440d6b32bac4d2b81814e'], + }), + ('Rcgmin', '2022-4.30', { + 'checksums': ['2684b8e7fb970da2afbc00e482031cf4447416249d04c4c1740400ad112fb911'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '4.0.1', { + 'checksums': ['e648bb8d364847448ef54e953d9c089c4aedb638aed9e2394723b0e85157c864'], + }), + ('miceadds', '3.17-44', { + 'checksums': ['6ef69dd1ac3b547a1450ca54c719c5d1f983a585207cb09ae3ad6b42a8cc2165'], + }), + ('visdat', '0.6.0', { + 'checksums': ['104acdbb9d41167b861ab24de0e1e1e14f61c1b476bac112fcbc6e47c157e598'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('norm', '1.0-11.1', { + 'checksums': ['c2ffe6c30fc203337bde49ef630a740141604d8e648c558e58c20116c47963bc'], + }), + ('naniar', '1.1.0', { + 'checksums': ['a94c46c3a78893bd935a0a51adb6a523915afb35427a56ce650b1e1ab28c6f44'], + }), + ('stringdist', '0.9.12', { + 'checksums': ['e1843452ff4184b8d3bc5168732c0c65d3fce11f0df9fcf92173a22ef92e66c4'], + }), + ('image.binarization', '0.1.3', { + 'checksums': ['ecc844bdd9bf15b88ce1e1afc8321c177bdc8ec32618c22102b1e8b02b36e00e'], + }), + ('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', '0.6.11', { + 'checksums': ['373cfb1e79174b568dac254fab02d99bf79b830218bf18f0cc592af6fef853d6'], + }), + ('truncnorm', '1.0-9', { + 'checksums': ['5156acc4d63243bf95326d6285b0ba3cdf710697d67c233a12ae56f3d87ec708'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.9.5', { + 'checksums': ['7392bd644efe82f96da0df470a962de398f1d0162273cba1ff31c2ecd7f17a53'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('admisc', '0.36', { + 'checksums': ['8fda4804c1674b9df545bf232ea05a214be9d102d21a6fd067d91ea757e86f6a'], + }), + ('polycor', '0.8-1', { + 'checksums': ['f05f53e0b5c992de0e5b4c6b2e998148cf83310358821e1bba180d81face0509'], + }), + ('multipol', '1.0-9', { + 'checksums': ['4ec305565c214872705f7d5ea4928c8761750663d664a77f1676d81a1ca0c632'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('rngWELL', '0.10-10', { + 'checksums': ['844499ce38622955a1d428a0ef62abe192bb2151a928c5bd933f34c062fd576f'], + }), + ('randtoolbox', '2.0.5', { + 'checksums': ['ab6eb953feb928e205a1d21dd577bef2b71d2108a61c4ce5e3879d7b53fed61f'], + }), + ('qrng', '0.0-10', { + 'checksums': ['51ee4eb9bf66fd125db8e5ed750edbc09e41a220994d06c3111f2ae73bcd8648'], + }), + ('spacefillr', '0.3.3', { + 'checksums': ['6cdaeaa7f617d5a94e90f0d6c32e16be8e86702d41e1ea7d08891452fdb9f021'], + }), + ('TruncatedNormal', '2.3', { + 'checksums': ['efb77996e2d263cc239d74658ce6cfb89822b7143b16fd5d0598ccc36ca08064'], + }), + ('cSEM', '0.5.0', { + 'checksums': ['25ae115520aab7d916da9ded1f87b8519c4e15101c4adef2284c51eb03d81728'], + }), + ('cubelyr', '1.0.2', { + 'checksums': ['18b10f1fe561305a1e115a438460264b88b301b3e8c086b931500a798be39b94'], + }), + ('furrr', '0.3.1', { + 'checksums': ['0d91735e2e9be759b1ab148d115c2c7429b79740514778828e5dab631dc0e48b'], + }), + ('broom.mixed', '0.2.9.6', { + 'checksums': ['f06bfd7ddec2db64ef53cfb02bcb2c0dc90ec3c27e41236c2930820a79e3988c'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.4.0', { + 'checksums': ['b53fb9b27a9d2e0e4f9da46e787c317118ace9e45e659d128af2ed8ca9176bc5'], + }), + ('twang', '2.6.1', { + 'checksums': ['0bb87dcd8f9b0628d96c50b565e9aa6222dfeb446165e12f52e4ee9b2e4e9179'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), + ('PCAmatchR', '0.3.3', { + 'checksums': ['5dc9d8bb4c0020b5e51a53a4fa71afa9adc6b907ea618b231f5cfc2877a49779'], + }), + ('origami', '1.0.7', { + 'checksums': ['b44034541ac358e0686682684c40e9a1de8d78c7913e56e4d3dbe41a2a55c62c'], + }), + ('hal9001', '0.4.6', { + 'checksums': ['1123288b603f97de98b42178ab5b4809536f64d7884a46b829795245eacd08dd'], + }), + ('cobalt', '4.5.5', { + 'checksums': ['076c1956e1a24d3ded5ac6227bf05cb294e103dc0d02d825e65b72d2c5f62ec0'], + }), + ('CBPS', '0.23', { + 'checksums': ['ed8fe09b642db459a516bdeb03a49e718a7d5ad915cbf82400029508efe9b32d'], + }), + ('SBdecomp', '1.2', { + 'checksums': ['0be4e1c9e8bed87fd1712e62346a97148a1a295ff56981e832921cc390006e5c'], + }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], 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['c5a8248708e4803b28cd33189963eb5dd1624df10ecf90f4c8ef7895cc022c0b'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['abind', 'base64', 'calibrate'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb b/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb new file mode 100644 index 00000000000..f6f0344f84b --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb @@ -0,0 +1,368 @@ +name = 'R' +version = '4.4.2' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['1578cd603e8d866b58743e49d8bf99c569e81079b6a60cf33cdf7bdffeb817ec'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('Autotools', '20231222'), +] +dependencies = [ + ('X11', '2024060'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('cairo', '1.18.0'), + ('libreadline', '8.2'), + ('ncurses', '6.5'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.5'), + ('zlib', '1.3.1'), + ('SQLite', '3.45.3'), + ('PCRE2', '10.43'), + ('libpng', '1.6.43'), # for plotting in R + ('libjpeg-turbo', '3.0.1'), # for plottting in R + ('LibTIFF', '4.6.0'), + ('Java', '11', '', SYSTEM), + ('libgit2', '1.8.1'), + ('OpenSSL', '1.1', '', SYSTEM), + ('cURL', '8.7.1'), + ('Tk', '8.6.14'), # for tcltk + ('HarfBuzz', '9.0.0'), # for textshaping + ('FriBidi', '1.0.15'), # for textshaping + +] + +# 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" + +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 24 November 2024 +exts_list = [ + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('rlang', '1.1.4', { + 'checksums': ['f2d74527508bf3287102470beb27de0d234c3cbba399c28d3312f2c83c64a6e1'], + }), + ('Rcpp', '1.0.13-1', { + 'checksums': ['1d1fc623d27082b5749f9584a9204de410134b6412a192157a3e42e2ba43969a'], + }), + ('R6', '2.5.1', { + 'checksums': 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('devtools', '2.4.5', { + 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], + }), +] + +moduleclass = 'lang' From c8ae1eb8fae5c6421878833f846cae34dedf793f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 24 Nov 2024 16:15:25 +0000 Subject: [PATCH 099/414] adding easyconfigs: R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb, arrow-R-17.0.0-foss-2024a-R-4.4.2.eb --- .../arrow-R-17.0.0-foss-2024a-R-4.4.2.eb | 35 + ...le-Bioconductor-3.20-foss-2024a-R-4.4.2.eb | 1373 +++++++++++++++++ 2 files changed, 1408 insertions(+) create mode 100644 easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0-foss-2024a-R-4.4.2.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0-foss-2024a-R-4.4.2.eb new file mode 100644 index 00000000000..958db3419fa --- /dev/null +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0-foss-2024a-R-4.4.2.eb @@ -0,0 +1,35 @@ +easyblock = 'RPackage' + +name = 'arrow-R' +version = '17.0.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/arrow' +description = "R interface to the Apache Arrow C++ library" + +toolchain = {'name': 'foss', 'version': '2024a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/arrow', # 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 = ['arrow_%(version)s.tar.gz'] +checksums = ['6e3ee6c07d8a53e74a04e13e828e88defac41c97f80bea4b26c08dbf307fca82'] + +dependencies = [ + ('R', '4.4.2'), + ('R-bundle-CRAN', '2024.11'), + ('Arrow', '17.0.0'), # arrow-R x.y.z[.N] only works with Arrow x.y.z +] + +preinstallopts = "export LIBARROW_BINARY=true && " + +sanity_check_paths = { + 'files': [], + 'dirs': ['arrow'], +} + +options = {'modulename': 'arrow'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb new file mode 100644 index 00000000000..8f9120fa33a --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb @@ -0,0 +1,1373 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.20' +versionsuffix = '-R-%(rver)s' + +local_biocver = '3.20' + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +builddependencies = [('pkgconf', '2.2.0')] + +dependencies = [ + ('R', '4.4.2'), + ('Boost', '1.85.0'), # for mzR + ('GSL', '2.8'), # for flowClust + ('arrow-R', '17.0.0', versionsuffix), # required by RcisTarget +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.20/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.20/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.20/data/experiment/src/contrib/', + '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'], +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on 24 June 2024 +exts_list = [ + ('BiocGenerics', '0.52.0', { + 'checksums': ['14f56a8d34dc2c005a8f07711cef22321eba92bfc5548853e8fcec03565e7fd9'], + }), + ('Biobase', '2.66.0', { + 'checksums': ['330cde8cac09e362d689725a547a0c35218a16dd31a8f9d2e0baf54b08ddb3d9'], + }), + ('S4Vectors', '0.44.0', { + 'checksums': ['34aa8f96c07506fd3157d6b9af8bf2796a24fbf4265105b556d10b12b3252c72'], + }), + ('IRanges', '2.40.0', { + 'checksums': ['1e5cdc62893ff35f701b43fb5a7b01f94152139d202bd1522dd7e53c3baa74d7'], + }), + ('GenomeInfoDbData', '1.2.13', { + 'checksums': ['51a33c432e65261ef81a7c2039b17cbdf7a0b417376fdb7ada4d618566f7074e'], + }), + ('UCSC.utils', '1.2.0', { + 'checksums': ['c45c98fa6391dcfb13b58196dfcc26c10a670a44721839cb526ad7f03956de92'], + }), + ('GenomeInfoDb', '1.42.0', { + 'checksums': ['6a05e22a783fbac5dabd0d8482a27d64c1e7ab00cec56c88867e6c6c5ca7141c'], + }), + ('zlibbioc', '1.52.0', { + 'checksums': ['dfb69c584fda322ae8b9faed8e011b7f604dfd76f65acdc461a7c8ddca3be15b'], + }), + ('XVector', '0.46.0', { + 'checksums': ['ce261b3fda9a7ca809bdd2b92a8550de7ec9a3fd6153dc5358e12453d5d6f636'], + }), + ('Biostrings', '2.74.0', { + 'checksums': ['74b3ea7dcc18d0676557364d93c2b48c76eb36e4e18553724df466326eada0fc'], + }), + ('KEGGREST', '1.46.0', { + 'checksums': ['0ed4e2247f04de5f15b5c9743f7ccb3f8ed2408fbe3eecffd5344f43a8355ea6'], + }), + ('AnnotationDbi', '1.68.0', { + 'checksums': ['ee6edacc616943e278b1ffc78bb0a44b06c3ad8ee1cf83c033d4e27b7a5df88d'], + }), + ('GenomicRanges', '1.58.0', { + 'checksums': ['10c8c13bacc3cf36fa70bc0f58916b97da36381811dac361a062a2f58a958cc5'], + }), + ('BiocParallel', '1.40.0', { + 'checksums': ['3f6c7a0bf2fbad3712c9f5879bccaeb472d46977c6f472f8387c2976fbb176ab'], + }), + ('Rhtslib', '3.2.0', { + 'checksums': ['f5ef39119bbe9005b563719a879b6a341274f68fbb77e75ed946635c2b0c3225'], + }), + ('Rsamtools', '2.22.0', { + 'checksums': ['25dbdcdb5a53b01014600c59f1bba5593a2e2f57ab6cb0c76660b88aaf0e1073'], + }), + ('MatrixGenerics', '1.18.0', { + 'checksums': ['b359c661e7e614495d04e82291de646ed62ded0a16389581d816e7c1f1694c8c'], + }), + ('S4Arrays', '1.6.0', { + 'checksums': ['b08d3d4ea418160f9987564d329f1d23b6a04df7c0a6a5110f1655ca130e4e3a'], + }), + ('SparseArray', '1.6.0', { + 'checksums': ['07444f36cebd7dd2d905cbd0c3c493a88540ef9e96eec57762e370926e72a52d'], + }), + ('DelayedArray', '0.32.0', { + 'checksums': ['feeb4c6250d509556bd6c059ea0892b7d8ddc981d501b54304c2850e99fcab89'], + }), + ('SummarizedExperiment', '1.36.0', { + 'checksums': ['0585846f5f5f4fc316a6a10648054bcd92a09b225fb4bb00a0e965768a6dd3cd'], + }), + ('GenomicAlignments', '1.42.0', { + 'checksums': ['deb84da29edd12ae7de90d93c163d2360fe809a69337cc984ef3a1052ee78af9'], + }), + ('pwalign', '1.2.0', { + 'checksums': ['6bfc0cda03c245b95554c1dd64534574849caae2082b7c4b7fe94b8d1eec01c4'], + }), + ('ShortRead', '1.64.0', { + 'checksums': ['c8a1e60472ffd8bb7dbfec6676a8bbcf894f3c3c25f21f0fc4bc6e663220137f'], + }), + ('graph', '1.84.0', { + 'checksums': ['970bec2341a1c492f5d1cfb41659d9ffaf257a43bff50715fcd0d7cbd6b2073b'], + }), + ('affyio', '1.76.0', { + 'checksums': ['91154048012c076e6c467a12e686438e0d61f5faca3c90bda000ea2860cc5a05'], + }), + ('preprocessCore', '1.68.0', { + 'installopts': "--configure-args='--disable-threading'", + 'checksums': ['50d9b6c2c1e4758dd19cc11470951d7e0d60f5ba315701835bc13dc9cbf3fb62'], + }), + ('BiocManager', '1.30.25', { + 'checksums': ['83ef8b57dcc7350fe1e8c62590a60d3ad3e1f9c8660930c946b20340a4a81e15'], + }), + ('affy', '1.84.0', { + 'checksums': ['c39cd36c731cb82ce2ee61e151206ecc902b5d736edbb23f3db5dca8f16247f4'], + }), + ('GO.db', '3.20.0', { + 'checksums': ['ff968e338624697f33cc318de6af34d684c88ed019107aeebb071f6564e110dc'], + }), + ('limma', '3.62.1', { + 'checksums': ['ee9404341828621fb2a9e24dddc66ed4099531f61b08175f9175d942a122e408'], + }), + ('RBGL', '1.82.0', { + 'checksums': ['88d3dee84338329016d0ccd18fb1c332b543cdccded2914dfe946fa9df3c5e13'], + }), + ('org.Hs.eg.db', '3.20.0', { + 'checksums': ['8c36c3cde805cae99f1d391cf00aec8983f6d0b4fabd75e71aa8ef3f5d6ed3bf'], + }), + ('AnnotationForge', '1.48.0', { + 'checksums': ['f782a66fdbf5e7503b798aa06e2184f158d5ec73988d477225890f82a71c7ad4'], + }), + ('annaffy', '1.78.0', { + 'checksums': ['f305f903a4465ffd50f8c574c06e000a5e472e02f389273b8abf7701b98ffa6a'], + }), + ('gcrma', '2.78.0', { + 'checksums': ['4abf83b3bc232052191275b771c287e43d3fa10be8bf7fe32dfe9b5aab3d696c'], + }), + ('oligoClasses', '1.68.0', { + 'checksums': ['673d65ec706940c6ac5f5b238aa224ef5720986090701bd59766771f665eec07'], + }), + ('edgeR', '4.4.0', { + 'checksums': ['6712e35f54b79b960fbe7452594124f3242371199efd8ebb0b0a168b809ed140'], + }), + ('PFAM.db', '3.20.0', { + 'checksums': ['86abbacc940ae76447c0accbb6c09bfbb9e44f1923e0662c385ab07dd66e7045'], + }), + ('perm', '1.0-0.4', { + 'checksums': ['561e01793a9032b6a3676a7819fe24175eeb9e96a5314bd78b9c48d46e627be9'], + }), + ('baySeq', '2.40.0', { + 'checksums': ['f54f35781e8fb82718166dd5c6cd486793fbf14b6dce03b43bd54ddc9f4a176e'], + }), + ('qvalue', '2.38.0', { + 'checksums': ['210e0ac56fddaa6b6f5014d0c459677f163f9acf10abf6b098b62790a3533161'], + }), + ('impute', '1.80.0', { + 'checksums': ['ff145193a2bb3fbb4f6873213b7c53fdc2bb55ee6d11ea9414a2b0c44a4688a7'], + }), + ('shinyFiles', '0.9.3', { + 'checksums': ['4a72e165ee8a6e8256988f27286a2cfc4d7a42e2a902f4f2a728b1c237c07286'], + }), + ('samr', '3.0', { + 'checksums': ['25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506'], + }), + ('DEGseq', '1.60.0', { + 'checksums': ['90f3d5e2fd866fef031e6a4c429d6196dfc02230f4533f13455a1d193bf9773e'], + }), + ('hgu133plus2.db', '3.13.0', { + 'checksums': ['ddde58e777a8341536a664c7d4be874a2f395f8aaa019c1f738462a8ce74cc44'], + }), + ('illuminaio', '0.48.0', { + 'checksums': ['ba7a6db66ab0a69924d5d98a7236d75b74a0387b38297378072b127a8c55fbb3'], + }), + ('BiocIO', '1.16.0', { + 'checksums': ['99868a2f80ab71ff28fceef592bffe7552fbb0338e2d027c5dbc174e218d1ab7'], + }), + ('restfulr', '0.0.15', { + 'checksums': ['40ff8f1fb2987af2223e1a855bb1680c5ce2143fbce7ebc42f1edb291f80e692'], + }), + ('rtracklayer', '1.66.0', { + 'checksums': ['6f35a3465ecd67f1b9e4904a064ea533b7ec6d2509d467e9520336a87a0e093e'], + }), + ('filelock', '1.0.3', { + 'checksums': ['2dcd0ec453f5ec4d96f69b0c472569d57d3c5f9956a82a48492ee02f12071137'], + }), + ('BiocFileCache', '2.14.0', { + 'checksums': ['6c0a463f7ef65e482b98ba02793fb9ae98b476997c916c94cd917a9e132a4022'], + }), + ('biomaRt', '2.62.0', { + 'checksums': ['e9243d81c38aab9f91b3228e6817573a95cf64e13a70604c7a522771e416b09b'], + }), + ('GenomicFeatures', '1.58.0', { + 'checksums': ['2526d42ee489d7bfccf147b441050bb56c312be351a45650b24dc0e62a34ac47'], + }), + ('bumphunter', '1.48.0', { + 'checksums': ['a40472da917c50687e6185e0b078ce43f1acbab5303173b9a3de327afaecb3a0'], + }), + ('multtest', '2.62.0', { + 'checksums': ['d3cd6e5c4ed4b19ae633b6be05bec771bc7a1d773622c59354a587335605fa01'], + }), + ('scrime', '1.3.5', { + 'checksums': ['5d97d3e57d8eb30709340fe572746029fd139456d7a955421c4e3aa75d825578'], + }), + ('siggenes', '1.80.0', { + 'checksums': ['07e78f47532d57978157d390eb3e5e756b766ee7f89f72c376fc49fa2af13e35'], + }), + ('DynDoc', '1.84.0', { + 'checksums': ['b528ea448d4e1dac3d766ed417a62c0921997815025ac85dbeb8959bd2d7e25f'], + }), + ('NOISeq', '2.50.0', { + 'checksums': ['fe3b645a683b731d2d80a458b327ec458eb75813fbae6efba18a9d8cf986280d'], + }), + ('Rgraphviz', '2.50.0', { + 'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'], + 'checksums': [ + {'Rgraphviz_2.50.0.tar.gz': '3730011326fd04992e07c249074c962a985e7a3ce79993c23201b79e11ba924a'}, + {'Rgraphviz-2.28.0_fno-tree-vectorize.patch': + '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9'}, + ], + }), + ('RNASeqPower', '1.46.0', { + 'checksums': ['ab2dd42efe57bcddca34b9f7ed8d92c3bcb349348b9ee566edf66a37ff812025'], + }), + ('annotate', '1.84.0', { + 'checksums': ['fed0e3e8cc818091d7847ce34f920d5bdb1b69648ed01816a8bb7dae6061ecd4'], + }), + ('GSEABase', '1.68.0', { + 'checksums': ['367d0d9b7a61d33a781365ccce6ea81d6127eac9738b35687fc97fd1af3ca37d'], + }), + ('genefilter', '1.88.0', { + 'checksums': ['cd7fa6d046adbefd344a25c9ee0139713a7ef16647340628ea01145ade89b5b0'], + }), + ('Category', '2.72.0', { + 'checksums': ['62f2b2da396ff5eb7d67edd60830045587bebc9c0bca3371c302709da6cbc568'], + }), + ('GOstats', '2.72.0', { + 'checksums': ['f22f944c3db01357362b22edd07f0a0a39866e49eb13d917c80c3d28767de27f'], + }), + ('BSgenome', '1.74.0', { + 'checksums': ['510657a451b1b2b983bcf1b8cfa9d43a9ad15753e66bed1d134e257eb3f86c29'], + }), + ('VariantAnnotation', '1.52.0', { + 'checksums': ['7579f8820ec4d7974c06a74bc7d031c111367de79685479296225ba27f73f329'], + }), + ('interactiveDisplayBase', '1.44.0', { + 'checksums': ['2174ab1ac206e1d503f58c2b62598583f1a62a609fbda5939ab6660580dd69f0'], + }), + ('BiocVersion', '3.20.0', { + 'checksums': ['9de14e40e3f085da92bc9f375ee6e1a81b8676b43882a45a3abf84faf94db6c7'], + }), + ('AnnotationHub', '3.14.0', { + 'checksums': ['362279548b64dc2d075e66ed4aab14e1e996552927847708907b5e350d931cd0'], + }), + ('AnnotationFilter', '1.30.0', { + 'checksums': ['b6b8c84c44a1e1d4f72508606faf3e8e966ee0d5076a91d9cab1a4de3a73eea8'], + }), + ('ProtGenerics', '1.38.0', { + 'checksums': ['b3d2a1d36cbdae5736dffdf7df4749beb0b63149d5fae5318c51f5083ecee75d'], + }), + ('ensembldb', '2.30.0', { + 'checksums': ['0a78d89df51c694a09986461023ca90e9849e8c85098085ec0ece7f83da4f0dc'], + }), + ('biovizBase', '1.54.0', { + 'checksums': ['e6fb8ba6cfab2e5c75036e2ccbf17f1a1fdb8949c183e4aaf221a1a4e680903c'], + }), + ('txdbmaker', '1.2.0', { + 'checksums': ['9748c0a666d318a62e2bc4f8a0c952afb4db2005299065414f4b047eb3a70c4c'], + }), + ('OrganismDbi', '1.48.0', { + 'checksums': ['3d6fe5d5643d1132ebff21a583ee64e657d6734c4f04a757dc7e08cbfadd7cf5'], + }), + ('ggbio', '1.54.0', { + 'checksums': ['f0079f581d92a3430113a9063180a264b7b5f9ccf3ea555f716ddb2c8c5032dd'], + }), + ('geneplotter', '1.84.0', { + 'checksums': ['476dc1c27d76dd57983705fcb73c6f36f7873fc6a9a6f84b35d9e023143778fb'], + }), + ('DESeq2', '1.46.0', { + 'checksums': ['abf33acf09ac80bf82b546ac9e46e980e951e1cf7a04df2dea49b78cd0c00c58'], + }), + ('ReportingTools', '2.46.0', { + 'checksums': ['f4b4a02435c62fb62f05a172544140269e28f427bca75b56637152022c4be4f0'], + }), + ('Glimma', '2.16.0', { + 'checksums': ['ea4c82d89074f72c9320076c8d24bf75c22a45701337791da4ebc7b3169a0f4b'], + }), + ('affycoretools', '1.78.0', { + 'checksums': ['2e1301a50c2bae6527a5cbbe23676bf35490d0b860e55285c438eb6b24b7caf7'], + }), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', { + 'checksums': ['063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9'], + }), + ('Homo.sapiens', '1.3.1', { + 'checksums': ['014809fc6ef6410be8dc1094c9cb083719f20d999065ae4bf388855be0913b94'], + }), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.3', { + 'checksums': ['5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a'], + }), + ('AgiMicroRna', '2.56.0', { + 'checksums': ['b1982b7377c60ce1ec983ff15133af7de03ba92612803352277823adfe0d3df0'], + }), + ('geneLenDataBase', '1.42.0', { + 'checksums': ['f731cfa1ff83a38dbee104778377f1b206121144e500ba05ddba1c9e0ada43ec'], + }), + ('goseq', '1.58.0', { + 'checksums': ['855c83001d0b2de1fb3e85dc6289471dabbaa5267e6e902bd86bffbd09515edd'], + }), + ('KEGGgraph', '1.66.0', { + 'checksums': ['45f00c398d0875f23926e1cfec4a562a831a069f0cf0c2bbe67e35736e41b323'], + }), + ('GEOquery', '2.74.0', { + 'checksums': ['d4fe4e43496726eda6f64ec17b0af2228925639fbd16cb562acdbe4f3b439153'], + }), + ('gsignal', '0.3-7', { + 'checksums': ['43430b138a58237a4e416cf85069b08054c41e1cb150c37cd0ca86bec6fe13b2'], + }), + ('mixOmics', '6.30.0', { + 'checksums': ['ae460d85ea22913a392a168e0cc7d5ad3e2bcf536ac469aa3ea2afc7a0e45c2e'], + }), + ('Rhdf5lib', '1.28.0', { + 'patches': ['Rhdf5lib-1.20.0_fix_hardcoded_path_to_mv.patch'], + 'checksums': [ + {'Rhdf5lib_1.28.0.tar.gz': '394d2ec56065066075d6f1299550dd39a9510064b8a030a038ec2b42c8c13051'}, + {'Rhdf5lib-1.20.0_fix_hardcoded_path_to_mv.patch': + 'fd35fd20166aa67cf5fbc194861d9196a2220fd40057b0524722ecc3de4774e8'}, + ], + }), + ('rhdf5filters', '1.18.0', { + 'checksums': ['6a277d569fb2929cd5e8515dde2849eeb6b82cfc86c8267caefc018157e1c8cd'], + }), + ('rhdf5', '2.50.0', { + 'checksums': ['6b5c82b4d0ffc9712bdf4cee27ededfc5409e2eec2b6a91b70c1c72f52295f62'], + }), + ('HDF5Array', '1.34.0', { + 'checksums': ['2072bcba0a5cf788c32f56e77d9b52d51a2b19ba49ac7328d1cc16a76da579ca'], + }), + ('sparseMatrixStats', '1.18.0', { + 'checksums': ['e5e090a99995246b0e93e14c11de01694e57cccec277820ae82bd0ebf915b73e'], + }), + ('DelayedMatrixStats', '1.28.0', { + 'checksums': ['a3a1929ada54b3f00f78af0edc1cc3159b8dbeb4e56d0b2c8126a3215b5dd907'], + }), + ('minfi', '1.52.1', { + 'checksums': ['b3a13303880db264c12dce391c8ab3c5a9036cbfe15fc444e23383aad9926a8d'], + }), + ('FDb.InfiniumMethylation.hg19', '2.2.0', { + 'checksums': ['605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f'], + }), + ('methylumi', '2.52.0', { + 'checksums': ['a49c1af3b900c37c2480c2372579905425dc97c82f15484eae66cadd70408c96'], + }), + ('lumi', '2.58.0', { + 'checksums': ['2b7237ed13f9b6c76b69f1214c96adcc7281430de0150428e6f7feb4d7e47591'], + }), + ('widgetTools', '1.84.0', { + 'checksums': ['ab5b0af8dcec3298e7146d2d596e4753848d574fe63954e41eb031cab9ed2856'], + }), + ('tkWidgets', '1.84.0', { + 'checksums': ['725184828cb79ab1c84237413b02b8707bb62db1bff010a9e9e19907c9e68368'], + }), + ('Mfuzz', '2.66.0', { + 'checksums': 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['d5e142305d596615bc2c170fe78487641e6ccf68420e3896589dbe9a9b934bbc'], + }), + ('flowFP', '1.64.0', { + 'checksums': ['6eab954f7e5672a28db2ab89c89f40e39f4947390a0a2127fd8bdbd114412181'], + }), + ('simona', '1.4.0', { + 'checksums': ['fdb7b9055efc287f0520aad4354c2860fd049fb7ef3fca826bf71ec88c62138f'], + }), + ('simplifyEnrichment', '2.0.0', { + 'checksums': ['e9b21015131db9d26fdf7bd7e6d3a61fdeec4b844b39ecb591a641abcb289c13'], + }), + ('RPMG', '2.2-7', { + 'checksums': ['c413de3c126bc377fe31a948887d27f404a9637c57fe0e07b087d5509cb99f11'], + }), + ('Rwave', '2.6-5', { + 'checksums': ['6c9ef75bb376f2e3f5c5dcd3b3fdca7d86797ce809da34f444632657189be2e4'], + }), + ('RSEIS', '4.2-4', { + 'checksums': ['7a9b04135eaf6a6e6a2bcea75db5a4ee36888f1d1a1a2c2d3b07889a4dd0cfaa'], + }), + ('splancs', '2.01-45', { + 'checksums': ['8bccf1d61d7feaab52da07a9c95aa66bcd3986a6b214f13b232c1e2bea4b76d3'], + }), + ('MBA', '0.1-2', { + 'checksums': ['a5b5a1b47fa7bea3c2ca54a447ac3d55ceff7fa894fc2caca462928a79f24e92'], + 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['40d0f1305afa29dfc4e38d19904d7323515c624eee138e8aefca0e15b8548d82'], + }), + ('slingshot', '2.14.0', { + 'checksums': ['6cc4f546b2deedef2d3fc67e70f6e24f31d7294da3df1b43cda90f3504833065'], + }), + ('TreeSummarizedExperiment', '2.14.0', { + 'checksums': ['9f407b74e724dfd6eb1c05d1f2655b81c1dd2112d38350fa13bb101e965ceda0'], + }), + ('decontam', '1.26.0', { + 'checksums': ['7f76ff0904c73c0c7739d8bb0d913f0c0ffd7e0a9a8d32834dd6cfa61aa8cc46'], + }), + ('DECIPHER', '3.2.0', { + 'checksums': ['f5e34ad45bc5f254b57c4a40d35f944b9e6c40119c7b4b137d1704c83aaddba1'], + }), + ('rbiom', '1.0.3', { + 'checksums': ['8f7d1c380148022ea677066fd57757a967eff1ac36cfb82b827f913b7450d58e'], + }), + ('mia', '1.14.0', { + 'checksums': ['ed6685eeaa49a510b6f286e1703e5611fb1af38c4c08b29deeb51ba3536bc7e1'], + }), + ('ANCOMBC', '2.8.0', { + 'checksums': ['2c49cb3060bb9c6779e84965257c3f3087f8a773a915e4766ca74496bb3f7f31'], + }), + ('decoupleR', '2.12.0', { + 'checksums': ['2792f18f05043ee05d26b1962ccc5dca9ec4d1956a748b090daf434a4caff954'], + }), + ('UCell', '2.10.1', { + 'checksums': ['0c544d25c64b6b942f36df5aa2537cf452ee31278bce98aeded360dbbd6bdd85'], + }), + ('intervals', '0.15.5', { + 'checksums': ['11907be2c47ee4f6359055113dc0dab9ba2c35fbc743c2d52fd1ba1006c7ce5c'], + }), + ('oompaBase', '3.2.9', { + 'checksums': ['14ca2b8e713a6a7ce13758f7f5c183dbc4fdfedc4f1244ca31bbdadf8a16bcb2'], + }), + ('oompaData', '3.1.4', { + 'checksums': ['06252409a94f9eaf4ef723becd24d17e1ef7b495aada44853f4661d942292d3d'], + }), + ('TailRank', '3.2.2', { + 'checksums': ['21ed95ea47d21155f08ae2ad7bca9547f89f492000bc1defe1cc5ec172739d09'], + }), + ('RnBeads', '2.24.0', { + 'checksums': ['497ea1e1c4ebdc5f0c0f64f69ea9be2ac04e0a3da0b0c5d24f4a7b1a9eabd300'], + }), + ('RnBeads.hg19', '1.38.0', { + 'checksums': ['95359f1982cf81d42639307dc8dc2e84b0a0d8dda4f4cd33cee250bfed707a43'], + }), + ('RnBeads.hg38', '1.38.0', { + 'checksums': ['17af910379438ab495c440d830468626179c72a509f943d7da36479d039cf6f2'], + }), + ('RnBeads.mm9', '1.38.0', { + 'checksums': ['0758e772629793a879ba0dccca91651986ac6a0ca26208598fa4ba8cbfc1ce68'], + }), + ('RnBeads.mm10', '2.14.0', { + 'checksums': ['58d7d36040eef7b8950f6c8d64098def970fd085b05023b7305a6a3a271562f9'], + }), + ('RnBeads.rn5', '1.38.0', { + 'checksums': ['f74b03a48ceda1385cebc64e7bb10e93b9d8f7adc6b855487f0e5070b8946b8b'], + }), + ('log4r', '0.4.4', { + 'checksums': ['ff1f2d2552f492d66680e36776ecb515479483da5e09f260f1ada661776ce732'], + }), + ('MSstatsConvert', '1.16.0', { + 'checksums': ['a8785b97fbe275ae8518c47eb99c58f0fc571d15f85237eb1402149b27b9815e'], + }), + ('MSstats', '4.14.0', { + 'checksums': ['90e9500c2c92ca72eaa954a8dc5399e217e623c63adbe5dfa09aa7539fe80ffe'], + }), + ('MSstatsTMT', '2.14.1', { + 'checksums': ['b5da9ac80d06ea47751515ef605873b936bbc7c0d3ea5a9761baaacc75b8d8ea'], + }), + ('factoextra', '1.0.7', { + 'checksums': ['624ff01c74933352aca55966f8a052b1ccc878f52c2c307e47f88e0665db94aa'], + }), + ('babelgene', '22.9', { + 'checksums': ['ce6601dcb78352516d3b0355042c52a20e154b39d3b27b93ff52150a59c885e2'], + }), + ('msigdbr', '7.5.1', { + 'checksums': ['dc30487bdf3594425ae9faec1ca0d7d0cd7278f4f177689133f92880e74acaca'], + }), + ('escape', '2.2.1', { + 'checksums': ['15303bc49b2309a8d48e1b0965e2770eb7a699453fabc476727d0ef501cae420'], + }), + ('plyranges', '1.26.0', { + 'checksums': ['7df12c4aee8b045ff5ff905b15d813a7edb8c34500806a391044ed48f0b9262a'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' From 81d5a54e58b0e80c5bf711ff487cbe9d612d59a8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 24 Nov 2024 16:44:24 +0000 Subject: [PATCH 100/414] typo in X11 version --- easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb b/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb index f6f0344f84b..e8bba353a0c 100644 --- a/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb +++ b/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('Autotools', '20231222'), ] dependencies = [ - ('X11', '2024060'), + ('X11', '20240607'), ('Mesa', '24.1.3'), ('libGLU', '9.0.3'), ('cairo', '1.18.0'), From 21b3719704e10bfc7a3500f287bf89d21f93885b Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 24 Nov 2024 17:51:15 +0000 Subject: [PATCH 101/414] extension date --- .../R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb index 8f9120fa33a..c723a53abc1 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb @@ -44,7 +44,7 @@ exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_s # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! -# packages updated on 24 June 2024 +# packages updated on 24 November 2024 exts_list = [ ('BiocGenerics', '0.52.0', { 'checksums': ['14f56a8d34dc2c005a8f07711cef22321eba92bfc5548853e8fcec03565e7fd9'], From 6d5afcebdde3c92b36bf082ead5709d4e0e3dd74 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 24 Nov 2024 17:57:34 +0000 Subject: [PATCH 102/414] consistent OpenSSL version --- easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb b/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb index e8bba353a0c..1f9e2348866 100644 --- a/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb +++ b/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb @@ -32,7 +32,7 @@ dependencies = [ ('LibTIFF', '4.6.0'), ('Java', '11', '', SYSTEM), ('libgit2', '1.8.1'), - ('OpenSSL', '1.1', '', SYSTEM), + ('OpenSSL', '3', '', SYSTEM), ('cURL', '8.7.1'), ('Tk', '8.6.14'), # for tcltk ('HarfBuzz', '9.0.0'), # for textshaping From 4605ac32fca8368dd7cab346e524cac84c93be86 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 25 Nov 2024 09:20:23 +0000 Subject: [PATCH 103/414] remove arrow from extensions --- .../R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb index c723a53abc1..201f5c211d8 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb @@ -1091,9 +1091,6 @@ exts_list = [ ('AUCell', '1.28.0', { 'checksums': ['00e1c45c8f861bf0cfdf977e64f944c767f831ed7406682d7ddcbbeab159bdd8'], }), - ('arrow', '17.0.0.1', { - 'checksums': ['0214dbf5d958968172a6f67abbae916d33933625cf41dc22e89ab77a29cde75e'], - }), ('RcisTarget', '1.26.0', { 'checksums': ['bc0750a2ada9bb808b16efd17aae8a9ea56d93b340af960e7ddd8c38eeb0ef45'], }), From 5915a55c9204bb2fab7b8cb3f38ca97e4100eea2 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 25 Nov 2024 13:55:25 +0000 Subject: [PATCH 104/414] use arrow-R 17.0.0.1 --- .../a/arrow-R/arrow-R-17.0.0-foss-2024a-R-4.4.2.eb | 9 ++++++--- .../R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb | 2 +- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0-foss-2024a-R-4.4.2.eb index 958db3419fa..5001d9e13e2 100644 --- a/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0-foss-2024a-R-4.4.2.eb +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0-foss-2024a-R-4.4.2.eb @@ -1,7 +1,7 @@ easyblock = 'RPackage' name = 'arrow-R' -version = '17.0.0' +version = '17.0.0.1' versionsuffix = '-R-%(rver)s' homepage = 'https://cran.r-project.org/web/packages/arrow' @@ -15,7 +15,10 @@ source_urls = [ 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ] sources = ['arrow_%(version)s.tar.gz'] -checksums = ['6e3ee6c07d8a53e74a04e13e828e88defac41c97f80bea4b26c08dbf307fca82'] + +builddependencies = [ + ('pkgconf', '2.2.0'), +] dependencies = [ ('R', '4.4.2'), @@ -23,7 +26,7 @@ dependencies = [ ('Arrow', '17.0.0'), # arrow-R x.y.z[.N] only works with Arrow x.y.z ] -preinstallopts = "export LIBARROW_BINARY=true && " +preinstallopts = "export LIBARROW_BUILD=false && " sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb index 201f5c211d8..19364b2127d 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb @@ -18,7 +18,7 @@ dependencies = [ ('R', '4.4.2'), ('Boost', '1.85.0'), # for mzR ('GSL', '2.8'), # for flowClust - ('arrow-R', '17.0.0', versionsuffix), # required by RcisTarget + ('arrow-R', '17.0.0.1', versionsuffix), # required by RcisTarget ] exts_default_options = { From d695622e7d4d2fc42c2a65a6fa9c7f05059733fd Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 25 Nov 2024 13:56:11 +0000 Subject: [PATCH 105/414] rename file --- ...ss-2024a-R-4.4.2.eb => arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/arrow-R/{arrow-R-17.0.0-foss-2024a-R-4.4.2.eb => arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb} (100%) diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb similarity index 100% rename from easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0-foss-2024a-R-4.4.2.eb rename to easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb From 9292217395d326834be2fe5a482ed269d589748f Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Wed, 27 Nov 2024 11:29:09 +0100 Subject: [PATCH 106/414] Add easyconfig Paraver-4.11.4-GCC-13.2.0.eb --- .../p/Paraver/Paraver-4.11.4-GCC-13.2.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-13.2.0.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-13.2.0.eb new file mode 100644 index 00000000000..b0a8b4bac7b --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-13.2.0.eb @@ -0,0 +1,21 @@ +name = 'Paraver' +version = '4.11.4' + +homepage = 'https://tools.bsc.es/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://ftp.tools.bsc.es/wxparaver/'] +sources = ['wxparaver-%(version)s-src.tar.bz2'] +checksums = ['8f65fbeacaef003b544ecc0244a4ed9a99e9521cdd027889106fbce0b052fd8d'] + +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('wxWidgets', '3.2.2.1'), +] + +moduleclass = 'perf' From 2d928ae77a419812290edbecce05e220dd9cb981 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Wed, 27 Nov 2024 11:42:08 +0100 Subject: [PATCH 107/414] Upgrade Boost and wxWidgets versions in Paraver-4.11.4-GCC-13.2.0.eb --- .../p/Paraver/Paraver-4.11.4-GCC-13.2.0.eb | 4 +- .../w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb | 71 +++++++++++++++++++ 2 files changed, 73 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-13.2.0.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-13.2.0.eb index b0a8b4bac7b..49f5d0511e8 100644 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-13.2.0.eb @@ -14,8 +14,8 @@ checksums = ['8f65fbeacaef003b544ecc0244a4ed9a99e9521cdd027889106fbce0b052fd8d'] dependencies = [ ('zlib', '1.2.13'), - ('Boost', '1.82.0'), - ('wxWidgets', '3.2.2.1'), + ('Boost', '1.83.0'), + ('wxWidgets', '3.2.6'), ] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb new file mode 100644 index 00000000000..4b0a8553970 --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb @@ -0,0 +1,71 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.2.6' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'wxWidgets' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_BZ2] +checksums = ['939e5b77ddc5b6092d1d7d29491fe67010a2433cf9b9c0d841ee4d04acb9dce7'] + +builddependencies = [ + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('libjpeg-turbo', '3.0.1'), + ('XZ', '5.4.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.6.0'), + ('expat', '2.6.2'), + ('GTK3', '3.24.42'), + ('X11', '20240607'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('SDL2', '2.30.6'), + ('cairo', '1.18.0'), + ('GST-plugins-base', '1.24.8'), + ('GLib', '2.80.4'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From bc813db67ba0fff2487c1899c6a91d622e10614d Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Wed, 27 Nov 2024 11:52:01 +0100 Subject: [PATCH 108/414] Downgrade GTK3, Mesa, and SDL2 versions and add easyconfig GST-plugins-base/1.24.8-GCC-13.2.0 --- .../GST-plugins-base-1.24.8-GCC-13.2.0.eb | 43 +++++++++++++++++++ .../w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb | 6 +-- 2 files changed, 46 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb new file mode 100644 index 00000000000..8c1fc32bc84 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-base' +version = '1.24.8' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['10fb31743750ccd498d3933e8aaecda563ebc65596a6ab875b47ee936e4b9599'] + +builddependencies = [ + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('GObject-Introspection', '1.80.1'), + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('GLib', '2.80.4'), + ('GStreamer', '1.24.8'), + ('Gdk-Pixbuf', '2.42.11'), + ('X11', '20240607'), + ('Mesa', '24.1.3'), + ('Graphene', '1.10.8'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb index 4b0a8553970..4c5a5bec723 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb @@ -33,11 +33,11 @@ dependencies = [ ('jbigkit', '2.1'), ('LibTIFF', '4.6.0'), ('expat', '2.6.2'), - ('GTK3', '3.24.42'), + ('GTK3', '3.24.39'), ('X11', '20240607'), - ('Mesa', '24.1.3'), + ('Mesa', '23.1.9'), ('libGLU', '9.0.3'), - ('SDL2', '2.30.6'), + ('SDL2', '2.28.5'), ('cairo', '1.18.0'), ('GST-plugins-base', '1.24.8'), ('GLib', '2.80.4'), From e781285b86aac809ac01977f3f6ac5f9d5f9f584 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Wed, 27 Nov 2024 12:12:07 +0100 Subject: [PATCH 109/414] Adjust dependency versions in GST-plugins-base-1.24.8-GCC-13.2.0.eb --- .../GST-plugins-base-1.24.8-GCC-13.2.0.eb | 4 +- .../GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb | 47 +++++++++++++++++++ 2 files changed, 49 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb index 8c1fc32bc84..1e884931863 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb @@ -28,9 +28,9 @@ dependencies = [ ('zlib', '1.3.1'), ('GLib', '2.80.4'), ('GStreamer', '1.24.8'), - ('Gdk-Pixbuf', '2.42.11'), + ('Gdk-Pixbuf', '2.42.10'), ('X11', '20240607'), - ('Mesa', '24.1.3'), + ('Mesa', '23.1.9'), ('Graphene', '1.10.8'), ] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb new file mode 100644 index 00000000000..de209870bcd --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MesonNinja' + +name = 'GStreamer' +version = '1.24.8' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://%(namelower)s.freedesktop.org/src/%(namelower)s'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['%(name)s-1.24_fix_bad_suid.patch'] +checksums = ['b807dbf36c5d2b3ce1c604133ed0c737350f9523ce4d8d644a1177c5f9d6ded3', # gstreamer-1.24.8.tar.xz + 'e40c8b195cc9d44f2d9b92e57608e097ef8dac6fa761c5610fcb836f88610cb1', # %(name)s-1.24_fix_bad_suid.patch + ] + +builddependencies = [ + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('Perl', '5.38.2'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.80.1'), + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('Python', '3.12.3'), + ('zlib', '1.3.1'), + ('GMP', '6.3.0'), + ('GSL', '2.8'), + ('GLib', '2.80.4'), + ('libunwind', '1.8.1'), + ('elfutils', '0.191'), +] + + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +moduleclass = 'vis' From 4214bf6a7cdde20cb84a83d9580b39b59f7cc20d Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Wed, 27 Nov 2024 12:18:38 +0100 Subject: [PATCH 110/414] Adjust dependeny versions in GStreamer-1.24.8-GCC-13.2.0.eb --- .../g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb index de209870bcd..b2ce916817e 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb @@ -21,7 +21,7 @@ checksums = ['b807dbf36c5d2b3ce1c604133ed0c737350f9523ce4d8d644a1177c5f9d6ded3', builddependencies = [ ('Meson', '1.4.0'), ('Ninja', '1.12.1'), - ('Perl', '5.38.2'), + ('Perl', '5.38.0'), ('Bison', '3.8.2'), ('flex', '2.6.4'), ('GObject-Introspection', '1.80.1'), @@ -32,10 +32,10 @@ dependencies = [ ('Python', '3.12.3'), ('zlib', '1.3.1'), ('GMP', '6.3.0'), - ('GSL', '2.8'), + ('GSL', '2.7'), ('GLib', '2.80.4'), - ('libunwind', '1.8.1'), - ('elfutils', '0.191'), + ('libunwind', '1.6.2'), + ('elfutils', '0.190'), ] From 0e206ce38bee94365717b9ff22b6581400c05550 Mon Sep 17 00:00:00 2001 From: software Date: Wed, 27 Nov 2024 14:14:50 +0000 Subject: [PATCH 111/414] adding easyconfigs: Monocle3-1.3.1-foss-2023a-R-4.3.2.eb --- .../Monocle3-1.3.1-foss-2023a-R-4.3.2.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..4c6da7d43e0 --- /dev/null +++ b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2023a-R-4.3.2.eb @@ -0,0 +1,79 @@ +easyblock = 'Bundle' + +name = 'Monocle3' +version = '1.3.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cole-trapnell-lab.github.io/monocle3/' +description = """ An analysis toolkit for single-cell RNA-seq. """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('pkgconf', '1.9.5')] # for textshaping + +dependencies = [ + ('R', '4.3.2'), + ('Python', '3.11.3'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), + ('GDAL', '3.7.1'), + ('HarfBuzz', '5.3.1'), # for textshaping + ('FriBidi', '1.0.12'), # for textshaping +] + +github_account = 'cole-trapnell-lab' +exts_defaultclass = 'RPackage' +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', +} + +exts_list = [ + ('grr', '0.9.5', { + 'checksums': ['292606de2983ac5840c90d3e0977441b482c9e73c1674b662f8b4fb8f3632b2b'], + }), + ('Matrix.utils', '0.9.8', { + 'checksums': ['ebc59d3ef751775515586ff1f2396e429a1e9d91a10099d804134fcf74c0ae28'], + }), + ('pbmcapply', '1.5.1', { + 'checksums': ['7ffc2854a384962f0dd523aa9ef33ce8fc290997206b71b840a49049d87112dd'], + }), + ('furrr', '0.3.1', { + 'checksums': ['0d91735e2e9be759b1ab148d115c2c7429b79740514778828e5dab631dc0e48b'], + }), + ('RhpcBLASctl', '0.21-247.1', { + 'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'], + }), + ('spdep', '1.2-7', { + 'checksums': ['9dac594825bf2d0aa31e845bfec05d8ce206327840fe455391741dbbdf9c9eea'], + }), + ('biglm', '0.9-2.1', { + 'checksums': ['6dcf3c9e7c3f56cdaac94cc0c427f606880467e1e753fe7ea45c10bc44eec947'], + }), + ('speedglm', '0.3-5', { + 'checksums': ['f8663677c10ff324c5639402060ddd2b1a1e917445cb0f8f84e146b85e82bb4b'], + }), + ('leidenbase', '0.1.9', { + 'source_urls': ['https://github.com/%(github_account)s/leidenbase/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'leidenbase-%(version)s.tar.gz'}], + 'checksums': ['dd893b13b04d4b943243e7ac8d2ef1850b60d0437b2e4d36a9cff57cd4953f54'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_urls': ['https://github.com/%(github_account)s/monocle3/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'Monocle3-%(version)s.tar.gz'}], + 'checksums': ['30e86d5323ea22b302614813ecf102f26774b42710589671a1f1d51ef9ad183d'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['leidenbase', '%(namelower)s'], +} + +moduleclass = 'bio' From b209d38d563f4675e1e56806ac8678fdbb804fca Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Wed, 27 Nov 2024 17:41:02 +0100 Subject: [PATCH 112/414] Upgrade GLib version in Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb --- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb index ac99b2584dd..df1d93a6b9c 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb @@ -26,7 +26,7 @@ builddependencies = [ ] dependencies = [ - ('GLib', '2.78.1'), + ('GLib', '2.80.4'), ('libjpeg-turbo', '3.0.1'), ('libpng', '1.6.40'), ('LibTIFF', '4.6.0'), From 598ac0469057895a5deeb90bdd1f88726fcca980 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Wed, 27 Nov 2024 17:49:58 +0100 Subject: [PATCH 113/414] Upgrade GLib version in Graphene-1.10.8-GCCcore-13.2.0.eb --- .../easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb index b8b16bdc898..ca9d870a5cd 100644 --- a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('GObject-Introspection', '1.78.1'), ('binutils', '2.40'), ] -dependencies = [('GLib', '2.78.1')] +dependencies = [('GLib', '2.80.4')] configopts = "-Dgobject_types=true -Dintrospection=enabled" From 63fbf75c0a16a38bfebaec49810de78b8b93387e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Nov 2024 14:12:09 +0100 Subject: [PATCH 114/414] fix Score-P configure when install paths contains 'yes/no' --- .../Score-P/Score-P-8.0_fix-path-check.patch | 98 +++++++++++++++++++ .../Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb | 6 +- .../s/Score-P/Score-P-8.4-gompi-2022a.eb | 6 +- .../Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb | 6 +- .../s/Score-P/Score-P-8.4-gompi-2022b.eb | 6 +- .../Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb | 6 +- .../s/Score-P/Score-P-8.4-gompi-2023a.eb | 6 +- 7 files changed, 128 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-path-check.patch diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-path-check.patch b/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-path-check.patch new file mode 100644 index 00000000000..93ede893a82 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-path-check.patch @@ -0,0 +1,98 @@ +In various places paths passed via the commandline are validated that they are not "yes" or "no". +However, that check was too broad, checking for any matching substring in the given path. +This could fail if some folder included "yes" or "no". +Make the check more strict to ensure that we do only abort when "yes" or "no" is actually passed. + +Author: Alexander Grund (TU Dresden) +Ported to upstream patch from build-config/common/m4/afs_external_lib.m4 to the generated configure files. + +diff -ur scorep-8.0-orig/build-backend/configure scorep-8.0/build-backend/configure +--- scorep-8.0-orig/build-backend/configure 2024-11-28 13:53:42.539876288 +0100 ++++ scorep-8.0/build-backend/configure 2024-11-28 13:58:04.917444170 +0100 +@@ -37776,7 +37776,7 @@ + esac ;; #( + set2set3) : + case ${with_libbfd_lib}${with_libbfd_include} in #( +- *yes*|*no*) : ++ yes,*|no,*|*,yes|*,no) : + as_fn_error $? "Both, --with-libbfd-lib and --with-libbfd-include require a ." "$LINENO" 5 ;; #( + *) : + +@@ -46006,7 +46006,7 @@ + esac ;; #( + set2set3) : + case ${with_libunwind_lib}${with_libunwind_include} in #( +- *yes*|*no*) : ++ yes,*|no,*|*,yes|*,no) : + as_fn_error $? "Both, --with-libunwind-lib and --with-libunwind-include require a ." "$LINENO" 5 ;; #( + *) : + +@@ -56137,7 +56137,7 @@ + esac ;; #( + set2set3) : + case ${with_liblustreapi_lib}${with_liblustreapi_include} in #( +- *yes*|*no*) : ++ yes,*|no,*|*,yes|*,no) : + as_fn_error $? "Both, --with-liblustreapi-lib and --with-liblustreapi-include require a ." "$LINENO" 5 ;; #( + *) : + +diff -ur scorep-8.0-orig/build-mpi/configure scorep-8.0/build-mpi/configure +--- scorep-8.0-orig/build-mpi/configure 2024-11-28 13:53:42.542876249 +0100 ++++ scorep-8.0/build-mpi/configure 2024-11-28 13:57:20.805021198 +0100 +@@ -35736,7 +35736,7 @@ + esac ;; #( + set2set3) : + case ${with_libbfd_lib}${with_libbfd_include} in #( +- *yes*|*no*) : ++ yes,*|no,*|*,yes|*,no) : + as_fn_error $? "Both, --with-libbfd-lib and --with-libbfd-include require a ." "$LINENO" 5 ;; #( + *) : + +@@ -44343,7 +44343,7 @@ + esac ;; #( + set2set3) : + case ${with_libunwind_lib}${with_libunwind_include} in #( +- *yes*|*no*) : ++ yes,*|no,*|*,yes|*,no) : + as_fn_error $? "Both, --with-libunwind-lib and --with-libunwind-include require a ." "$LINENO" 5 ;; #( + *) : + +@@ -53306,7 +53306,7 @@ + esac ;; #( + set2set3) : + case ${with_liblustreapi_lib}${with_liblustreapi_include} in #( +- *yes*|*no*) : ++ yes,*|no,*|*,yes|*,no) : + as_fn_error $? "Both, --with-liblustreapi-lib and --with-liblustreapi-include require a ." "$LINENO" 5 ;; #( + *) : + +diff -ur scorep-8.0-orig/build-shmem/configure scorep-8.0/build-shmem/configure +--- scorep-8.0-orig/build-shmem/configure 2024-11-28 13:53:42.541876262 +0100 ++++ scorep-8.0/build-shmem/configure 2024-11-28 13:57:42.765733935 +0100 +@@ -35545,7 +35545,7 @@ + esac ;; #( + set2set3) : + case ${with_libbfd_lib}${with_libbfd_include} in #( +- *yes*|*no*) : ++ yes,*|no,*|*,yes|*,no) : + as_fn_error $? "Both, --with-libbfd-lib and --with-libbfd-include require a ." "$LINENO" 5 ;; #( + *) : + +@@ -43965,7 +43965,7 @@ + esac ;; #( + set2set3) : + case ${with_libunwind_lib}${with_libunwind_include} in #( +- *yes*|*no*) : ++ yes,*|no,*|*,yes|*,no) : + as_fn_error $? "Both, --with-libunwind-lib and --with-libunwind-include require a ." "$LINENO" 5 ;; #( + *) : + +@@ -52914,7 +52914,7 @@ + esac ;; #( + set2set3) : + case ${with_liblustreapi_lib}${with_liblustreapi_include} in #( +- *yes*|*no*) : ++ yes,*|no,*|*,yes|*,no) : + as_fn_error $? "Both, --with-liblustreapi-lib and --with-liblustreapi-include require a ." "$LINENO" 5 ;; #( + *) : + diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb index f195f0ceaeb..96bbe1238fb 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'gompi', 'version': '2022a'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] +patches = ['Score-P-8.0_fix-path-check.patch'] +checksums = [ + {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, + {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, +] dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb index 1317ae392d9..af1e313b5d8 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb @@ -21,7 +21,11 @@ toolchain = {'name': 'gompi', 'version': '2022a'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] +patches = ['Score-P-8.0_fix-path-check.patch'] +checksums = [ + {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, + {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, +] dependencies = [ ('CubeLib', '4.8.2'), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb index 8b60baea472..b178c316bd9 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'gompi', 'version': '2022b'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] +patches = ['Score-P-8.0_fix-path-check.patch'] +checksums = [ + {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, + {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, +] dependencies = [ ('CUDA', '12.0.0', '', SYSTEM), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b.eb index e19b8fcc05b..11e45db406c 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b.eb @@ -21,7 +21,11 @@ toolchain = {'name': 'gompi', 'version': '2022b'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] +patches = ['Score-P-8.0_fix-path-check.patch'] +checksums = [ + {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, + {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, +] dependencies = [ ('CubeLib', '4.8.2'), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb index 51caeb1df08..68b77c135df 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'gompi', 'version': '2023a'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] +patches = ['Score-P-8.0_fix-path-check.patch'] +checksums = [ + {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, + {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, +] dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb index 2e47de3fd8b..e1f17d258fa 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb @@ -21,7 +21,11 @@ toolchain = {'name': 'gompi', 'version': '2023a'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] +patches = ['Score-P-8.0_fix-path-check.patch'] +checksums = [ + {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, + {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, +] dependencies = [ ('CubeLib', '4.8.2'), From 8a8983aa6c7c35e3b9cf73773605831e526201d2 Mon Sep 17 00:00:00 2001 From: software Date: Thu, 28 Nov 2024 14:51:51 +0000 Subject: [PATCH 115/414] adding easyconfigs: Tombo-1.5.1-foss-2023a.eb --- .../t/Tombo/Tombo-1.5.1-foss-2023a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2023a.eb b/easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2023a.eb new file mode 100644 index 00000000000..b4191a47cf0 --- /dev/null +++ b/easybuild/easyconfigs/t/Tombo/Tombo-1.5.1-foss-2023a.eb @@ -0,0 +1,50 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'Tombo' +version = '1.5.1' + +homepage = 'https://github.com/nanoporetech/tombo' +description = """Tombo is a suite of tools primarily for the identification of modified nucleotides + from raw nanopore sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('h5py', '3.9.0'), + ('tqdm', '4.66.1'), + ('rpy2', '3.5.15'), +] + +use_pip = True + +exts_list = [ + ('pyfaidx', '0.5.8', { + 'checksums': ['58f0ff57a875af7e69a12cf1e7086efa4976919ac4dcebbc5f3def6fd4881d0d'], + }), + ('mappy', '2.28', { + 'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'], + }), + ('ont-tombo', version, { + 'modulename': 'tombo', + 'patches': ['Tombo-%(version)s_rpy2-v3.patch'], + 'use_pip_extras': 'full', + 'checksums': [ + {'ont-tombo-1.5.1.tar.gz': 'f5ae8f4c5fc1ab212306ff14ae93fbd1c1034421148ff2e728f169f69a824380'}, + {'Tombo-1.5.1_rpy2-v3.patch': '0d9e5e96aa741b70acbbddbf0d403f55878bdb956def57f1332a4b0d7582a8ff'}, + ], + }), +] + +sanity_pip_check = True + +sanity_check_commands = [ + "tombo --help", + "tombo --version", +] + +moduleclass = 'bio' From dac02272f7587d2d115239d7e73b0f8de85acec7 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 28 Nov 2024 16:27:28 +0100 Subject: [PATCH 116/414] Graphviz-12.2.0-GCCcore-13.3.0.eb --- .../Graphviz-12.2.0-GCCcore-13.3.0.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5b1a57e3dfa --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,97 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '12.2.0' +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': '13.3.0'} + +source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = [ + {'graphviz-12.2.0.tar.gz': '0063e501fa4642b55f4daf82820b2778bfb7dafa651a862ae5c9810efb8e2311'}, +] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('SWIG', '4.2.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('Java', '21.0.2', '', SYSTEM), + ('Python', '3.12.3'), + ('FriBidi', '1.0.15'), + ('Gdk-Pixbuf', '2.42.11'), + ('Ghostscript', '10.03.1'), + ('GTS', '0.7.6'), + ('libgd', '2.3.3'), + ('Pango', '1.54.0'), + ('Perl', '5.38.2'), + ('Qt5', '5.15.15'), + ('Tcl', '8.6.14'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('libjpeg-turbo', '3.0.1'), + ('expat', '2.6.2'), +] + +preconfigopts = './autogen.sh NOCONFIG && ' + +_copts = [ + '--enable-python%s=yes' % local_pyver_major, + '--enable-guile=no --enable-lua=no --enable-ocaml=no', + '--enable-r=no --enable-ruby=no --enable-php=no', + # Use ltdl from libtool in EB + '--enable-ltdl --without-included-ltdl --disable-ltdl-install', + '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib', + # Override the hardcoded paths to Java libraries + '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux', + '--with-javalibdir=$JAVA_HOME/lib', + '--with-expatincludedir=$EBROOTEXPAT/include --with-expatlibdir=$EBROOTEXPAT/lib', + '--with-zincludedir=$EBROOTZLIB/include --with-zlibdir=$EBROOTZLIB/lib', +] + +configopts = ' '.join(_copts) + +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', 'edgepaint', 'gc', 'gml2gv', 'graphml2gv', 'gv2gml', + 'gvcolor', 'gvedit', 'gvgen', 'gvmap', 'gvmap.sh', 'gvpack', 'gvpr', 'gxl2gv', + 'neato', 'mm2gv', 'nop', 'prune', 'sccmap', 'tred', 'unflatten', + 'vimdot']] + + ['lib/%s.%s' % (x, SHLIB_EXT) for x in ['libcdt', 'libcgraph', 'libgvc', 'libgvpr', + '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' From 5a90567f43915fe118dc318a3b010715bb6d1e95 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 28 Nov 2024 16:59:09 +0100 Subject: [PATCH 117/414] adding easyconfigs: imagecodecs-2024.6.1-foss-2023b.eb, CharLS-2.4.2-GCCcore-13.2.0.eb, jxrlib-1.1-GCCcore-13.2.0.eb, libyuv-20241125-GCCcore-13.2.0.eb, libavif-1.1.1-GCCcore-13.2.0.eb, libde265-1.0.15-GCCcore-13.2.0.eb, libheif-1.19.5-GCCcore-13.2.0.eb, LibLZF-3.6-GCCcore-13.2.0.eb, Zopfli-1.0.3-GCCcore-13.2.0.eb, zfp-1.0.1-GCCcore-13.2.0.eb, bitshuffle-0.5.2-foss-2023b.eb --- .../bitshuffle/bitshuffle-0.5.2-foss-2023b.eb | 30 +++++++ .../c/CharLS/CharLS-2.4.2-GCCcore-13.2.0.eb | 30 +++++++ .../imagecodecs-2024.6.1-foss-2023b.eb | 78 +++++++++++++++++++ .../j/jxrlib/jxrlib-1.1-GCCcore-13.2.0.eb | 39 ++++++++++ .../l/LibLZF/LibLZF-3.6-GCCcore-13.2.0.eb | 31 ++++++++ .../l/libavif/libavif-1.1.1-GCCcore-13.2.0.eb | 36 +++++++++ .../libde265-1.0.15-GCCcore-13.2.0.eb | 34 ++++++++ .../libheif/libheif-1.19.5-GCCcore-13.2.0.eb | 43 ++++++++++ .../libyuv/libyuv-20241125-GCCcore-13.2.0.eb | 29 +++++++ .../z/Zopfli/Zopfli-1.0.3-GCCcore-13.2.0.eb | 37 +++++++++ .../z/zfp/zfp-1.0.1-GCCcore-13.2.0.eb | 40 ++++++++++ 11 files changed, 427 insertions(+) create mode 100644 easybuild/easyconfigs/b/bitshuffle/bitshuffle-0.5.2-foss-2023b.eb create mode 100644 easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/i/imagecodecs/imagecodecs-2024.6.1-foss-2023b.eb create mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libavif/libavif-1.1.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libheif/libheif-1.19.5-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libyuv/libyuv-20241125-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/b/bitshuffle/bitshuffle-0.5.2-foss-2023b.eb b/easybuild/easyconfigs/b/bitshuffle/bitshuffle-0.5.2-foss-2023b.eb new file mode 100644 index 00000000000..f56e5fa8903 --- /dev/null +++ b/easybuild/easyconfigs/b/bitshuffle/bitshuffle-0.5.2-foss-2023b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'bitshuffle' +version = '0.5.2' + +homepage = 'https://github.com/kiyo-masui/bitshuffle' +description = """ +Filter for improving compression of typed binary data. +Bitshuffle is an algorithm that rearranges typed, binary data for improving compression, as +well as a python/C package that implements this algorithm within the Numpy framework. +The library can be used along side HDF5 to compress and decompress datasets and is integrated +through the dynamically loaded filters framework. Bitshuffle is HDF5 filter number 32008. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dc0e3fb7bdbf42be1009cc3028744180600d625a75b31833a24aa32aeaf83d8d'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('h5py', '3.11.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3c8d212818c --- /dev/null +++ b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CharLS' +version = '2.4.2' + +homepage = 'https://github.com/team-charls/charls' +description = """CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image +compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 +compression ratios.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/team-charls/charls/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d1c2c35664976f1e43fec7764d72755e6a50a80f38eca70fcc7553cad4fe19d9'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libcharls.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2024.6.1-foss-2023b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2024.6.1-foss-2023b.eb new file mode 100644 index 00000000000..72d46164bfb --- /dev/null +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2024.6.1-foss-2023b.eb @@ -0,0 +1,78 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL), Denis Kristak (Inuits), Cintia Willemyns (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'imagecodecs' +version = '2024.6.1' + +homepage = 'https://github.com/cgohlke/imagecodecs' +description = """Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, +compression, and decompression functions for use in the tifffile, czifile, zarr, and other +scientific image input/output modules.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +local_openjpeg_maj_min = '2.5' +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Python-bundle-PyPI', '2023.10'), + ('Cython', '3.0.10'), + ('matplotlib', '3.8.2'), + ('Brotli', '1.1.0'), + ('Blosc', '1.21.5'), + ('Blosc2', '2.13.2'), + ('Brunsli', '0.1'), + ('bzip2', '1.0.8'), + ('CFITSIO', '4.3.1'), + ('CharLS', '2.4.2'), + ('giflib', '5.2.1'), + ('jxrlib', '1.1'), + ('LittleCMS', '2.15'), + ('LERC', '4.0.0'), + ('libaec', '1.0.6'), + ('libavif', '1.1.1'), + ('libdeflate', '1.19'), + ('libheif', '1.19.5'), + ('libjpeg-turbo', '3.0.1'), + ('libjxl', '0.8.2'), + ('LibLZF', '3.6'), + ('libpng', '1.6.40'), + ('LibTIFF', '4.6.0'), + ('libwebp', '1.3.2'), + ('lz4', '1.9.4'), + ('OpenJPEG', local_openjpeg_maj_min + '.0'), + ('snappy', '1.1.10'), + ('zlib-ng', '2.2.2'), + ('Zopfli', '1.0.3'), + ('zfp', '1.0.1'), + ('zstd', '1.5.5'), + ('HDF5', '1.14.3'), + ('h5py', '3.11.0'), + ('bitshuffle', '0.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('colorlog', '6.9.0', { + 'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'], + }), + (name, version, { + 'buildopts': '--global-option="build_ext" --global-option="--lite"', + 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", + 'patches': ['imagecodecs-2024.1.1_fix-aec-version.patch'], + 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.5/:$CPATH && ", + 'source_urls': ['https://github.com/cgohlke/imagecodecs/releases/download/v%(version)s/'], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': [ + {'imagecodecs-2024.6.1.tar.gz': '0f3e94b7f51e2f78287b7ffae82cd850b1007639148894538274fa50bd179886'}, + {'imagecodecs-2024.1.1_fix-aec-version.patch': + '7feb0a5fe37893d1a186f85c8f6cdb940704605ee2da5ea8e5d555ec5bfa01aa'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a57082eb758 --- /dev/null +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +# Update: Thomas Hoffmann (EMBL) +## + +easyblock = 'CMakeMake' + +name = 'jxrlib' +version = '1.1' + +homepage = 'https://github.com/4creators/jxrlib' +description = """Open source implementation of jpegxr""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] +sources = ['%(name)s_%(version)s.orig.tar.gz'] +patches = [('jxrlib-%(version)s_cmake.patch', 1)] +checksums = [ + {'jxrlib_1.1.orig.tar.gz': 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303'}, + {'jxrlib-1.1_cmake.patch': 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] + +modextrapaths = {'CPATH': 'include/jxrlib'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..029c67711ac --- /dev/null +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL), Denis Kristak +easyblock = 'ConfigureMake' + +name = 'LibLZF' +version = '3.6' + +homepage = 'http://oldhome.schmorp.de/marc/liblzf.html' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] +sources = ['liblzf-%(version)s.tar.gz'] +checksums = ['9c5de01f7b9ccae40c3f619d26a7abec9986c06c36d260c179cedd04b89fb46a'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_commands = ['lzf -h'] + +sanity_check_paths = { + 'files': ['bin/lzf', 'lib/liblzf.a'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libavif/libavif-1.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libavif/libavif-1.1.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..38463d8530a --- /dev/null +++ b/easybuild/easyconfigs/l/libavif/libavif-1.1.1-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak (Inuits) +# Update: Thomas Hoffmann (EMBL), Denis Kristak (Inuits) +easyblock = 'CMakeMake' + +name = 'libavif' +version = '1.1.1' + +homepage = 'https://github.com/AOMediaCodec/libavif' +description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format, +as described here: https://aomediacodec.github.io/av1-avif/ +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['914662e16245e062ed73f90112fbb4548241300843a7772d8d441bb6859de45b'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), + ('NASM', '2.16.01'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('Rust', '1.76.0'), + ('pkgconf', '2.0.3'), + ('libyuv', '20241125'), +] + +sanity_check_paths = { + 'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d9cd9ccc66f --- /dev/null +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libde265' +version = '1.0.15' + +homepage = 'https://github.com/strukturag/libde265' +description = "libde265 is an open source implementation of the h.265 video codec" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['00251986c29d34d3af7117ed05874950c875dd9292d016be29d3b3762666511d'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +configopts = "-DENABLE_DECODER=ON -DENABLE_ENCODER=ON" + +sanity_check_paths = { + 'files': ['bin/dec265', 'bin/enc265', 'lib/libde265.%s' % SHLIB_EXT, 'lib/pkgconfig/libde265.pc'], + 'dirs': ['include/libde265', 'lib/cmake/libde265'], +} + +sanity_check_commands = [ + "dec265 --help", + "enc265 --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.19.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.19.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6bf423096b7 --- /dev/null +++ b/easybuild/easyconfigs/l/libheif/libheif-1.19.5-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libheif' +version = '1.19.5' + +homepage = 'https://github.com/strukturag/libheif' +description = "libheif is an HEIF and AVIF file format decoder and encoder" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d3cf0a76076115a070f9bc87cf5259b333a1f05806500045338798486d0afbaf'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('libpng', '1.6.40'), + ('libjpeg-turbo', '3.0.1'), + ('libde265', '1.0.15'), + ('x265', '3.5'), + ('Gdk-Pixbuf', '2.42.10'), +] + +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +sanity_check_paths = { + 'files': ['bin/heif-info', 'lib/libheif.a', 'lib/libheif.%s' % SHLIB_EXT, 'lib/pkgconfig/libheif.pc'], + 'dirs': ['include/libheif'], +} + +sanity_check_commands = ["heif-info --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libyuv/libyuv-20241125-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libyuv/libyuv-20241125-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6d388b8ffc2 --- /dev/null +++ b/easybuild/easyconfigs/l/libyuv/libyuv-20241125-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'libyuv' +version = '20241125' +local_commit = '9a97521' + +homepage = 'https://github.com/lemenkov/libyuv' +description = """libyuv is an open source project that includes YUV scaling and conversion functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/lemenkov/libyuv/archive/'] +sources = [{ + "download_filename": "%s.tar.gz" % local_commit, + "filename": SOURCE_TAR_GZ, +}] +checksums = ['25e48eb78c41383e391b68ed017e82e42ded0ae2667fb399f7b2442582ae2af2'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/yuvconvert', f'lib/{name}.so', f'lib/{name}.a', f'include/{name}.h'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..29b3e948dfa --- /dev/null +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits) +easyblock = 'CMakeMake' + +name = 'Zopfli' +version = '1.0.3' + +homepage = 'https://github.com/google/zopfli' +description = """Zopfli Compression Algorithm is a compression library programmed in C to perform +very good, but slow, deflate or zlib compression.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF', +] + +sanity_check_paths = { + 'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["zopfli --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ed80aaa5316 --- /dev/null +++ b/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'MakeCp' + +name = 'zfp' +version = '1.0.1' + +homepage = 'https://github.com/LLNL/zfp' +description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. +zfp provides compressed-array classes that support high throughput read and write random access to individual array +elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications +that read and write large data sets to and from disk.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/zfp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['4984db6a55bc919831966dd17ba5e47ca7ac58668f4fd278ebd98cd2200da66f'] + +builddependencies = [ + ('binutils', '2.40'), +] + +prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && " +buildopts = 'ZFP_WITH_OPENMP=1' + +runtest = 'test' + +files_to_copy = ['bin', 'include', 'lib'] + +sanity_check_paths = { + 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], + 'dirs': ['include/zfp'], +} + +sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] + +moduleclass = 'lib' From 40df7e0095e8a7289393ca80053952c5d0cd5cd5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 28 Nov 2024 18:15:12 +0100 Subject: [PATCH 118/414] adding easyconfigs: ITK-5.4.0-foss-2023b.eb, CastXML-0.6.10-GCCcore-13.2.0.eb, SWIG-4.3.0-GCCcore-13.2.0.eb --- .../CastXML/CastXML-0.6.10-GCCcore-13.2.0.eb | 34 +++++++ .../easyconfigs/i/ITK/ITK-5.4.0-foss-2023b.eb | 90 +++++++++++++++++++ .../s/SWIG/SWIG-4.3.0-GCCcore-13.2.0.eb | 27 ++++++ 3 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/c/CastXML/CastXML-0.6.10-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.4.0-foss-2023b.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-4.3.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/CastXML/CastXML-0.6.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CastXML/CastXML-0.6.10-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7ddff2c0183 --- /dev/null +++ b/easybuild/easyconfigs/c/CastXML/CastXML-0.6.10-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'CastXML' +version = '0.6.10' + +homepage = 'https://github.com/CastXML/CastXML' +description = """CastXML is a C-family abstract syntax tree XML output tool.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'CastXML' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d8498b39b4cf3d57671254056013de177f47fc7a2683f1a53049ab854d85ad55'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('Clang', '17.0.6'), + ('ncurses', '6.4'), + ('zlib', '1.2.13'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/castxml'], + 'dirs': ['share/castxml'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.4.0-foss-2023b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.4.0-foss-2023b.eb new file mode 100644 index 00000000000..d916fd1ddd9 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.4.0-foss-2023b.eb @@ -0,0 +1,90 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak (INUITS), Pavel Tománek (INUITS) + +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.4.0' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'ITK-5.3.0_add-vtk-include-dir.patch', +] +checksums = [ + {'v5.4.0.tar.gz': 'd71a36fc0aee2c9257fe128f7657feb1e671461bd48561b620619f290c71795e'}, + {'ITK-5.3.0_add-vtk-include-dir.patch': 'df7e834a024db5d1a1459d898bd43a044351e29759ab0bf69ce03d64da95b3f7'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Bison', '3.8.2'), + ('Eigen', '3.4.0'), + ('SWIG', '4.3.0'), + ('Perl', '5.38.0'), + ('git', '2.42.0'), +] +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('double-conversion', '3.3.0'), + ('expat', '2.5.0'), + ('HDF5', '1.14.3'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('LibTIFF', '4.6.0'), + ('VTK', '9.3.0'), + ('zlib', '1.2.13'), + ('CastXML', '0.6.10'), +] + +# Features +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +# Enable Python bindings +configopts += '-DITK_WRAP_PYTHON:BOOL=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' +configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig -DSWIG_DIR=$EBROOTSWIG ' +configopts += '-DPY_SITE_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +# Dependencies from EB +local_sys_deps = [ + 'CASTXML', + 'DOUBLECONVERSION', + 'EIGEN', + 'EXPAT', + 'FFTW', + 'HDF5', + 'JPEG', + 'PNG', + 'SWIG', + 'TIFF', + 'ZLIB' +] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] +configopts += ' '.join(local_sys_cmake) + +prebuildopts = 'LC_ALL=C ' + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (lname, SHLIB_EXT) for lname in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = ["python -c 'import itk'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.3.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.3.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d91aa92ae70 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.3.0-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +name = 'SWIG' +version = '4.3.0' + +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': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f7203ef796f61af986c70c05816236cbd0d31b7aa9631e5ab53020ab7804aa9e'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('PCRE2', '10.42'), +] + +configopts = '--without-alllang --with-boost=no' + +moduleclass = 'devel' From e318ac968cac108e0fc84cff9c01263edc81f98c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 28 Nov 2024 18:45:02 +0100 Subject: [PATCH 119/414] adding easyconfigs: GeoDict-2024.SP5-gmpich-2024.06.eb --- .../GeoDict-2024.SP5-gmpich-2024.06.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP5-gmpich-2024.06.eb diff --git a/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP5-gmpich-2024.06.eb b/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP5-gmpich-2024.06.eb new file mode 100644 index 00000000000..4c9110b8af2 --- /dev/null +++ b/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP5-gmpich-2024.06.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'GeoDict' +version = '2024.SP5' + +homepage = 'https://www.math2market.com/geodict-software/geodict-applications.html' +description = """ +The innovative and easy-to-use material simulator GeoDict is the most complete software +solution for multi-scale 3D image processing, modeling of materials, visualization, material +property characterization, simulation-based material development, and optimization of +processes. +""" + +toolchain = {'name': 'gmpich', 'version': '2024.06'} + +source_urls = [ + 'https://www.gddownload.de/Releases' +] +sources = [ + '%(name)s2024-3-4-Linux-x86_64-ServicePack5.tar.gz', + '%(name)s2024-3-4-Linux-x86_64-ServicePack5-Tools.tar.gz' +] +checksums = [ + {'GeoDict2024-3-4-Linux-x86_64-ServicePack5.tar.gz': + '049401063d892eac65696d7d1ed8d4b915c9a81bb13e325cc0657c60ce8aeb28'}, + {'GeoDict2024-3-4-Linux-x86_64-ServicePack5-Tools.tar.gz': + '1b50fb840e8e78c225c748d73eaca60faedd822de33f20c716b1e98b15492eac'}, +] + +dependencies = [ + ('X11', '20230603'), +] + +modextrapaths = {'PATH': '.'} + +sanity_check_paths = { + 'files': ['geodict2024'], + 'dirs': ['Python', 'Tools'], +} + +moduleclass = 'geo' From db3d1762cc3287464f4a86e72ca1e2e8ae54ec07 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 29 Nov 2024 08:29:16 +0100 Subject: [PATCH 120/414] Revert "fix Score-P configure when install paths contains 'yes/no'" This reverts commit 63fbf75c0a16a38bfebaec49810de78b8b93387e. --- .../Score-P/Score-P-8.0_fix-path-check.patch | 98 ------------------- .../Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb | 6 +- .../s/Score-P/Score-P-8.4-gompi-2022a.eb | 6 +- .../Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb | 6 +- .../s/Score-P/Score-P-8.4-gompi-2022b.eb | 6 +- .../Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb | 6 +- .../s/Score-P/Score-P-8.4-gompi-2023a.eb | 6 +- 7 files changed, 6 insertions(+), 128 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-path-check.patch diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-path-check.patch b/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-path-check.patch deleted file mode 100644 index 93ede893a82..00000000000 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-path-check.patch +++ /dev/null @@ -1,98 +0,0 @@ -In various places paths passed via the commandline are validated that they are not "yes" or "no". -However, that check was too broad, checking for any matching substring in the given path. -This could fail if some folder included "yes" or "no". -Make the check more strict to ensure that we do only abort when "yes" or "no" is actually passed. - -Author: Alexander Grund (TU Dresden) -Ported to upstream patch from build-config/common/m4/afs_external_lib.m4 to the generated configure files. - -diff -ur scorep-8.0-orig/build-backend/configure scorep-8.0/build-backend/configure ---- scorep-8.0-orig/build-backend/configure 2024-11-28 13:53:42.539876288 +0100 -+++ scorep-8.0/build-backend/configure 2024-11-28 13:58:04.917444170 +0100 -@@ -37776,7 +37776,7 @@ - esac ;; #( - set2set3) : - case ${with_libbfd_lib}${with_libbfd_include} in #( -- *yes*|*no*) : -+ yes,*|no,*|*,yes|*,no) : - as_fn_error $? "Both, --with-libbfd-lib and --with-libbfd-include require a ." "$LINENO" 5 ;; #( - *) : - -@@ -46006,7 +46006,7 @@ - esac ;; #( - set2set3) : - case ${with_libunwind_lib}${with_libunwind_include} in #( -- *yes*|*no*) : -+ yes,*|no,*|*,yes|*,no) : - as_fn_error $? "Both, --with-libunwind-lib and --with-libunwind-include require a ." "$LINENO" 5 ;; #( - *) : - -@@ -56137,7 +56137,7 @@ - esac ;; #( - set2set3) : - case ${with_liblustreapi_lib}${with_liblustreapi_include} in #( -- *yes*|*no*) : -+ yes,*|no,*|*,yes|*,no) : - as_fn_error $? "Both, --with-liblustreapi-lib and --with-liblustreapi-include require a ." "$LINENO" 5 ;; #( - *) : - -diff -ur scorep-8.0-orig/build-mpi/configure scorep-8.0/build-mpi/configure ---- scorep-8.0-orig/build-mpi/configure 2024-11-28 13:53:42.542876249 +0100 -+++ scorep-8.0/build-mpi/configure 2024-11-28 13:57:20.805021198 +0100 -@@ -35736,7 +35736,7 @@ - esac ;; #( - set2set3) : - case ${with_libbfd_lib}${with_libbfd_include} in #( -- *yes*|*no*) : -+ yes,*|no,*|*,yes|*,no) : - as_fn_error $? "Both, --with-libbfd-lib and --with-libbfd-include require a ." "$LINENO" 5 ;; #( - *) : - -@@ -44343,7 +44343,7 @@ - esac ;; #( - set2set3) : - case ${with_libunwind_lib}${with_libunwind_include} in #( -- *yes*|*no*) : -+ yes,*|no,*|*,yes|*,no) : - as_fn_error $? "Both, --with-libunwind-lib and --with-libunwind-include require a ." "$LINENO" 5 ;; #( - *) : - -@@ -53306,7 +53306,7 @@ - esac ;; #( - set2set3) : - case ${with_liblustreapi_lib}${with_liblustreapi_include} in #( -- *yes*|*no*) : -+ yes,*|no,*|*,yes|*,no) : - as_fn_error $? "Both, --with-liblustreapi-lib and --with-liblustreapi-include require a ." "$LINENO" 5 ;; #( - *) : - -diff -ur scorep-8.0-orig/build-shmem/configure scorep-8.0/build-shmem/configure ---- scorep-8.0-orig/build-shmem/configure 2024-11-28 13:53:42.541876262 +0100 -+++ scorep-8.0/build-shmem/configure 2024-11-28 13:57:42.765733935 +0100 -@@ -35545,7 +35545,7 @@ - esac ;; #( - set2set3) : - case ${with_libbfd_lib}${with_libbfd_include} in #( -- *yes*|*no*) : -+ yes,*|no,*|*,yes|*,no) : - as_fn_error $? "Both, --with-libbfd-lib and --with-libbfd-include require a ." "$LINENO" 5 ;; #( - *) : - -@@ -43965,7 +43965,7 @@ - esac ;; #( - set2set3) : - case ${with_libunwind_lib}${with_libunwind_include} in #( -- *yes*|*no*) : -+ yes,*|no,*|*,yes|*,no) : - as_fn_error $? "Both, --with-libunwind-lib and --with-libunwind-include require a ." "$LINENO" 5 ;; #( - *) : - -@@ -52914,7 +52914,7 @@ - esac ;; #( - set2set3) : - case ${with_liblustreapi_lib}${with_liblustreapi_include} in #( -- *yes*|*no*) : -+ yes,*|no,*|*,yes|*,no) : - as_fn_error $? "Both, --with-liblustreapi-lib and --with-liblustreapi-include require a ." "$LINENO" 5 ;; #( - *) : - diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb index 96bbe1238fb..f195f0ceaeb 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a-CUDA-11.7.0.eb @@ -22,11 +22,7 @@ toolchain = {'name': 'gompi', 'version': '2022a'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -patches = ['Score-P-8.0_fix-path-check.patch'] -checksums = [ - {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, - {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, -] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb index af1e313b5d8..1317ae392d9 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022a.eb @@ -21,11 +21,7 @@ toolchain = {'name': 'gompi', 'version': '2022a'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -patches = ['Score-P-8.0_fix-path-check.patch'] -checksums = [ - {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, - {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, -] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] dependencies = [ ('CubeLib', '4.8.2'), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb index b178c316bd9..8b60baea472 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b-CUDA-12.0.0.eb @@ -22,11 +22,7 @@ toolchain = {'name': 'gompi', 'version': '2022b'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -patches = ['Score-P-8.0_fix-path-check.patch'] -checksums = [ - {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, - {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, -] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] dependencies = [ ('CUDA', '12.0.0', '', SYSTEM), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b.eb index 11e45db406c..e19b8fcc05b 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2022b.eb @@ -21,11 +21,7 @@ toolchain = {'name': 'gompi', 'version': '2022b'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -patches = ['Score-P-8.0_fix-path-check.patch'] -checksums = [ - {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, - {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, -] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] dependencies = [ ('CubeLib', '4.8.2'), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb index 68b77c135df..51caeb1df08 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a-CUDA-12.1.1.eb @@ -22,11 +22,7 @@ toolchain = {'name': 'gompi', 'version': '2023a'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -patches = ['Score-P-8.0_fix-path-check.patch'] -checksums = [ - {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, - {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, -] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb index e1f17d258fa..2e47de3fd8b 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023a.eb @@ -21,11 +21,7 @@ toolchain = {'name': 'gompi', 'version': '2023a'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -patches = ['Score-P-8.0_fix-path-check.patch'] -checksums = [ - {'scorep-8.4.tar.gz': '7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'}, - {'Score-P-8.0_fix-path-check.patch': '6502490954eaf4bbcf9bbdbebc290dc2c666a68dd1b0bd579f1450e489901998'}, -] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] dependencies = [ ('CubeLib', '4.8.2'), From 1254d24e6a01cca6e0addf6601010b70c929f58a Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 29 Nov 2024 09:53:17 +0100 Subject: [PATCH 121/414] WPS 4.6.0 WRF 4.6.1 --- .../w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb | 38 +++++ ...S-4.6.0_netCDF-Fortran_separate_path.patch | 51 ++++++ .../w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb | 44 +++++ ...F-4.6.1_netCDF-Fortran_separate_path.patch | 156 ++++++++++++++++++ 4 files changed, 289 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.6.0_netCDF-Fortran_separate_path.patch create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb new file mode 100644 index 00000000000..45612b84fa5 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb @@ -0,0 +1,38 @@ +name = 'WPS' +version = '4.6.0' + +homepage = 'https://www.mmm.ucar.edu/models/wrf' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WPS-%(version)s_netCDF-Fortran_separate_path.patch', +] +checksums = [ + 'ca7bbfc6c28a107c6eb00ded70e693f5c9a3926ecde7656f49e306c9eb9a309b', # v4.6.1.tar.gz + 'ed49d5af4e6c80d9ddd9954b968c514cf888c3b35dce64744d1ac1eaa38b7042', # WPS-4.4_netCDF-Fortran_separate_path.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +builddependencies = [ + ('Perl', '5.38.2'), +] + +dependencies = [ + ('WRF', '4.6.1', versionsuffix), + ('JasPer', '4.2.4'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..098eed8d7fe --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_netCDF-Fortran_separate_path.patch @@ -0,0 +1,51 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since 2013; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain +# updated for WPS v4.6.0 by Stefan Wolfsheimer (SURF) + + +diff -Nru WPS-4.6.0.orig/arch/preamble WPS-4.6.0/arch/preamble +--- WPS-4.6.0.orig/arch/preamble 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/arch/preamble 2024-11-29 09:25:27.634254674 +0100 +@@ -39,13 +39,14 @@ + -I$(WRF_DIR)/external/io_grib1 \ + -I$(WRF_DIR)/external/io_int \ + -I$(WRF_DIR)/inc \ +- -I$(NETCDF)/include ++ -I$(NETCDF)/include \ ++ -I$(NETCDFF_DIR)/include + + WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ + -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ + -L$(WRF_DIR)/external/io_int -lwrfio_int \ + -L$(WRF_DIR)/external/io_netcdf -lwrfio_nf \ +- -L$(NETCDF)/lib CONFIGURE_NETCDFF_LIB -lnetcdf ++ -L$(NETCDF)/lib -L$(NETCDFF_DIR)/lib -lnetcdff -lnetcdf + + #### Architecture specific settings #### + +diff -Nru WPS-4.6.0.orig/configure WPS-4.6.0/configure +--- WPS-4.6.0.orig/configure 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/configure 2024-11-29 09:17:10.196985634 +0100 +@@ -161,7 +161,7 @@ + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available + NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then ++ if [ -f "$NETCDFF_DIR/lib/libnetcdff.a" ] ; then + NETCDFF="-lnetcdff" + fi + else +@@ -429,9 +429,9 @@ + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` + FORMAT_FREE=`grep ^FORMAT_FREE configure.wps | cut -d"=" -f2-` + FFLAGS=`printf "%s" "${FFLAGS}" | sed -e "s/\\$(FORMAT_FREE)/${FORMAT_FREE}/g"` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF_DIR/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -L${NETCDFF_DIR}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + ./fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb new file mode 100644 index 00000000000..64e92c7f014 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb @@ -0,0 +1,44 @@ +name = 'WRF' +version = '4.6.1' +buildtype = 'dmpar' +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.mmm.ucar.edu/models/wrf' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +github_account = 'wrf-model' +source_urls = [GITHUB_RELEASE] +sources = ['v%(version)s.tar.gz'] +patches = ['WRF-4.6.1_netCDF-Fortran_separate_path.patch'] + +checksums = [ + {'v4.6.1.tar.gz': 'b8ec11b240a3cf1274b2bd609700191c6ec84628e4c991d3ab562ce9dc50b5f2'}, + {'WRF-4.6.1_netCDF-Fortran_separate_path.patch': + '0fcc55df295910fe507a3938b420a9a211e6e2ce82de8ded347b54135994e716'}, +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20231222'), + ('tcsh', '6.24.13'), + ('time', '1.9'), + ('Perl', '5.38.2'), +] + +dependencies = [ + ('JasPer', '4.2.4'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), +] + +runtest = True + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..b2f654ab876 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch @@ -0,0 +1,156 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since WRF3.5; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain +# +# updated for WPS v4.4 by Maxim Masterov (SURF) +# updated for WRF v4.5.1 by Stefan Wolfsheimer (SURF) +# updated for WRF v4.6.1 by Stefan Wolfsheimer (SURF) + + +diff -Nru WRFV4.6.1.orig/arch/Config.pl WRFV4.6.1/arch/Config.pl +--- WRFV4.6.1.orig/arch/Config.pl 2024-10-16 23:05:18.000000000 +0200 ++++ WRFV4.6.1/arch/Config.pl 2024-11-28 15:38:43.864070000 +0100 +@@ -11,6 +11,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; + $sw_pnetcdf_path = "" ; + $sw_netcdfpar_path = "" ; + $sw_adios2_path = "" ; +@@ -70,6 +71,10 @@ + { + $sw_netcdf_path = substr( $ARGV[0], 8 ) ; + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 16 ) eq "netcdf4_dep_lib=" ) + { + $sw_netcdf4_dep_lib = substr( $ARGV[0], 17 ) ; +@@ -626,6 +631,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_NETCDFPAR_PATH/$sw_netcdfpar_path/g ; + $_ =~ s/CONFIGURE_ADIOS2_PATH/$sw_adios2_path/g ; +@@ -695,7 +701,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdff_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +@@ -1083,7 +1089,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdff_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +diff -Nru WRFV4.6.1.orig/arch/postamble WRFV4.6.1/arch/postamble +--- WRFV4.6.1.orig/arch/postamble 2024-10-16 23:05:18.000000000 +0200 ++++ WRFV4.6.1/arch/postamble 2024-11-28 15:38:38.086016000 +0100 +@@ -55,7 +55,8 @@ + -I$(WRF_SRC_ROOT_DIR)/wrftladj \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ + -I$(NETCDFPATH)/include \ +- CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC ++ -I$(NETCDFFPATH)/include \ ++ CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC + REGISTRY = Registry + CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE + +@@ -64,6 +65,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + RTTOVPATH = CONFIGURE_RTTOV_PATH +@@ -96,7 +98,7 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" NETCDF4_DEP_LIB="$(NETCDF4_DEP_LIB)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + +diff -Nru WRFV4.6.1.orig/configure WRFV4.6.1/configure +--- WRFV4.6.1.orig/configure 2024-11-28 15:36:44.834084000 +0100 ++++ WRFV4.6.1/configure 2024-11-28 15:51:45.766140000 +0100 +@@ -242,10 +242,13 @@ + USENETCDFF="" + USENETCDF="" + if [ -n "$NETCDF" ] ; then +- echo "Will use NETCDF in dir: $NETCDF" ++ echo "Will use NETCDF in dir: $NETCDF" ++ echo "Will use NETCDFF in dir: $NETCDFF" + # Oh UNIDATA, why make it so hard ... + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then + USENETCDFF="-lnetcdff" ++ elif [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib/libnetcdff.dll.a" ] ; then ++ USENETCDFF="-lnetcdff" + else + USENETCDFF=" " + fi +@@ -265,7 +268,6 @@ + echo ' ' + exit 6 + fi +- + # If the user asked for classic netcdf, acquiesce to the request. + + if [ ! -f "$NETCDF/bin/nf-config" ] ; then +@@ -538,7 +540,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -adios2=$ADIOS2 -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -adios2=$ADIOS2 -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -netcdf4_dep_lib="$NETCDF4_DEP_LIB" +@@ -620,14 +622,14 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo + echo "Error : Not found $NETCDF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +diff -Nru WRFV4.6.1.orig/external/io_netcdf/makefile WRFV4.6.1/external/io_netcdf/makefile +--- WRFV4.6.1.orig/external/io_netcdf/makefile 2024-10-16 23:05:19.000000000 +0200 ++++ WRFV4.6.1/external/io_netcdf/makefile 2024-11-28 16:38:31.349880802 +0100 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share ++FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include -I../ioapi_share + LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar From 420e7e805f11787e63923515cd08cc57b7a3e37e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 29 Nov 2024 10:23:43 +0100 Subject: [PATCH 122/414] added JasPer patch --- .../w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb | 2 + .../w/WPS/WPS-4.6.0_fix_jasper_decode.patch | 122 ++++++++++++++++++ 2 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb index 45612b84fa5..ddf1835f790 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb @@ -13,10 +13,12 @@ source_urls = ['https://github.com/wrf-model/WPS/archive/'] sources = ['v%(version)s.tar.gz'] patches = [ 'WPS-%(version)s_netCDF-Fortran_separate_path.patch', + 'WPS-4.6.0_fix_jasper_decode.patch', ] checksums = [ 'ca7bbfc6c28a107c6eb00ded70e693f5c9a3926ecde7656f49e306c9eb9a309b', # v4.6.1.tar.gz 'ed49d5af4e6c80d9ddd9954b968c514cf888c3b35dce64744d1ac1eaa38b7042', # WPS-4.4_netCDF-Fortran_separate_path.patch + '60bc9feae34a5939cc749582554712c0370606b06c6cd49235260137475c7c8e', # WPS-4.6.0_fix_jasper_decode.patch ] buildtype = "dmpar" diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch new file mode 100644 index 00000000000..7d1f3c49e28 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch @@ -0,0 +1,122 @@ +# Using correct JasPer functions +# ============================== +# WPS uses depreceated version of JasPer interface. +# See https://github.com/wrf-model/WPS/issues/207 +# @author Stefan Wolfsheimer (SURF) + + +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/base/jas_init.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/base/jas_init.c +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/base/jas_init.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/base/jas_init.c 2024-11-29 10:17:24.964788000 +0100 +@@ -123,8 +123,8 @@ + jas_image_addfmt(fmtid, "jp2", "jp2", + "JPEG-2000 JP2 File Format Syntax (ISO/IEC 15444-1)", &fmtops); + ++fmtid; +- fmtops.decode = jpc_decode; +- fmtops.encode = jpc_encode; ++ fmtops.decode = jas_image_decode; ++ fmtops.encode = jas_image_encode; + fmtops.validate = jpc_validate; + jas_image_addfmt(fmtid, "jpc", "jpc", + "JPEG-2000 Code Stream Syntax (ISO/IEC 15444-1)", &fmtops); +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h WPS-4.6.0/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h 2024-11-29 10:17:24.977624441 +0100 +@@ -557,8 +557,8 @@ + + #if !defined(EXCLUDE_JPC_SUPPORT) + /* Format-dependent operations for JPEG-2000 code stream support. */ +-jas_image_t *jpc_decode(jas_stream_t *in, const char *optstr); +-int jpc_encode(jas_image_t *image, jas_stream_t *out, const char *optstr); ++jas_image_t *jas_image_decode(jas_stream_t *in, const char *optstr); ++int jas_image_encode(jas_image_t *image, jas_stream_t *out, const char *optstr); + int jpc_validate(jas_stream_t *in); + #endif + +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c 2024-11-29 10:17:24.990192019 +0100 +@@ -215,7 +215,7 @@ + goto error; + } + +- if (!(dec->image = jpc_decode(in, optstr))) { ++ if (!(dec->image = jas_image_decode(in, optstr))) { + jas_eprintf("error: cannot decode code stream\n"); + goto error; + } +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c 2024-11-29 10:17:25.002777520 +0100 +@@ -346,7 +346,7 @@ + sprintf(buf, "%s\n_jp2overhead=%lu\n", (optstr ? optstr : ""), + (unsigned long) overhead); + +- if (jpc_encode(image, out, buf)) { ++ if (jas_image_encode(image, out, buf)) { + goto error; + } + +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c 2024-11-29 10:17:25.015484538 +0100 +@@ -235,7 +235,7 @@ + * The main entry point for the JPEG-2000 decoder. + \******************************************************************************/ + +-jas_image_t *jpc_decode(jas_stream_t *in, const char *optstr) ++jas_image_t *jas_image_decode(jas_stream_t *in, const char *optstr) + { + jpc_dec_importopts_t *opts; + jpc_dec_t *dec; +@@ -244,7 +244,7 @@ + dec = 0; + opts = 0; + +- JAS_DBGLOG(100, ("jpc_decode(%p, \"%s\")\n", in, optstr)); ++ JAS_DBGLOG(100, ("jas_image_decode(%p, \"%s\")\n", in, optstr)); + + if (!(opts = jpc_dec_opts_create(optstr))) { + goto error; +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c 2024-11-29 10:17:25.028597372 +0100 +@@ -277,7 +277,7 @@ + * The main encoder entry point. + \******************************************************************************/ + +-int jpc_encode(jas_image_t *image, jas_stream_t *out, const char *optstr) ++int jas_image_encode(jas_image_t *image, jas_stream_t *out, const char *optstr) + { + jpc_enc_t *enc; + jpc_enc_cp_t *cp; +diff -Nru WPS-4.6.0.orig/ungrib/src/ngl/g2/dec_jpeg2000.c WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c +--- WPS-4.6.0.orig/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-11-29 10:17:25.041671000 +0100 +@@ -80,9 +80,9 @@ + /* + * Decode JPEG200 codestream into jas_image_t structure. + */ +- image=jpc_decode(jpcstream,opts); ++ image=jas_image_decode(jpcstream,opts); + if ( image == 0 ) { +- printf(" jpc_decode return = %d \n",ier); ++ printf(" jas_image_decode return = %d \n",ier); + return -3; + } + +diff -Nru WPS-4.6.0.orig/ungrib/src/ngl/g2/enc_jpeg2000.c WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c +--- WPS-4.6.0.orig/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-11-29 10:17:25.054123000 +0100 +@@ -178,9 +178,9 @@ + /* + * Encode image. + */ +- ier=jpc_encode(&image,jpcstream,opts); ++ ier=jas_image_encode(&image,jpcstream,opts); + if ( ier != 0 ) { +- printf(" jpc_encode return = %d \n",ier); ++ printf(" jas_image_encode return = %d \n",ier); + return -3; + } + /* From c28eafd236ff55e96a2794cfd7592878041aeb3e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 29 Nov 2024 11:10:30 +0100 Subject: [PATCH 123/414] fix patch --- .../w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb | 3 +- .../w/WPS/WPS-4.6.0_fix_jasper_decode.patch | 105 ++---------------- 2 files changed, 9 insertions(+), 99 deletions(-) diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb index ddf1835f790..389aac870e5 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb @@ -15,10 +15,11 @@ patches = [ 'WPS-%(version)s_netCDF-Fortran_separate_path.patch', 'WPS-4.6.0_fix_jasper_decode.patch', ] + checksums = [ 'ca7bbfc6c28a107c6eb00ded70e693f5c9a3926ecde7656f49e306c9eb9a309b', # v4.6.1.tar.gz 'ed49d5af4e6c80d9ddd9954b968c514cf888c3b35dce64744d1ac1eaa38b7042', # WPS-4.4_netCDF-Fortran_separate_path.patch - '60bc9feae34a5939cc749582554712c0370606b06c6cd49235260137475c7c8e', # WPS-4.6.0_fix_jasper_decode.patch + 'f4ea3c77c42c3474d582e311b8bd0d80c67243f45922e85ee3ff52df61d6c77e', # WPS-4.6.0_fix_jasper_decode.patch ] buildtype = "dmpar" diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch index 7d1f3c49e28..4f6d416931f 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch @@ -5,118 +5,27 @@ # @author Stefan Wolfsheimer (SURF) -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/base/jas_init.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/base/jas_init.c ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/base/jas_init.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/base/jas_init.c 2024-11-29 10:17:24.964788000 +0100 -@@ -123,8 +123,8 @@ - jas_image_addfmt(fmtid, "jp2", "jp2", - "JPEG-2000 JP2 File Format Syntax (ISO/IEC 15444-1)", &fmtops); - ++fmtid; -- fmtops.decode = jpc_decode; -- fmtops.encode = jpc_encode; -+ fmtops.decode = jas_image_decode; -+ fmtops.encode = jas_image_encode; - fmtops.validate = jpc_validate; - jas_image_addfmt(fmtid, "jpc", "jpc", - "JPEG-2000 Code Stream Syntax (ISO/IEC 15444-1)", &fmtops); -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h WPS-4.6.0/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h 2024-11-29 10:17:24.977624441 +0100 -@@ -557,8 +557,8 @@ - - #if !defined(EXCLUDE_JPC_SUPPORT) - /* Format-dependent operations for JPEG-2000 code stream support. */ --jas_image_t *jpc_decode(jas_stream_t *in, const char *optstr); --int jpc_encode(jas_image_t *image, jas_stream_t *out, const char *optstr); -+jas_image_t *jas_image_decode(jas_stream_t *in, const char *optstr); -+int jas_image_encode(jas_image_t *image, jas_stream_t *out, const char *optstr); - int jpc_validate(jas_stream_t *in); - #endif - -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c 2024-11-29 10:17:24.990192019 +0100 -@@ -215,7 +215,7 @@ - goto error; - } - -- if (!(dec->image = jpc_decode(in, optstr))) { -+ if (!(dec->image = jas_image_decode(in, optstr))) { - jas_eprintf("error: cannot decode code stream\n"); - goto error; - } -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c 2024-11-29 10:17:25.002777520 +0100 -@@ -346,7 +346,7 @@ - sprintf(buf, "%s\n_jp2overhead=%lu\n", (optstr ? optstr : ""), - (unsigned long) overhead); - -- if (jpc_encode(image, out, buf)) { -+ if (jas_image_encode(image, out, buf)) { - goto error; - } - -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c 2024-11-29 10:17:25.015484538 +0100 -@@ -235,7 +235,7 @@ - * The main entry point for the JPEG-2000 decoder. - \******************************************************************************/ - --jas_image_t *jpc_decode(jas_stream_t *in, const char *optstr) -+jas_image_t *jas_image_decode(jas_stream_t *in, const char *optstr) - { - jpc_dec_importopts_t *opts; - jpc_dec_t *dec; -@@ -244,7 +244,7 @@ - dec = 0; - opts = 0; - -- JAS_DBGLOG(100, ("jpc_decode(%p, \"%s\")\n", in, optstr)); -+ JAS_DBGLOG(100, ("jas_image_decode(%p, \"%s\")\n", in, optstr)); - - if (!(opts = jpc_dec_opts_create(optstr))) { - goto error; -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c 2024-11-29 10:17:25.028597372 +0100 -@@ -277,7 +277,7 @@ - * The main encoder entry point. - \******************************************************************************/ - --int jpc_encode(jas_image_t *image, jas_stream_t *out, const char *optstr) -+int jas_image_encode(jas_image_t *image, jas_stream_t *out, const char *optstr) - { - jpc_enc_t *enc; - jpc_enc_cp_t *cp; diff -Nru WPS-4.6.0.orig/ungrib/src/ngl/g2/dec_jpeg2000.c WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c --- WPS-4.6.0.orig/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-11-29 10:17:25.041671000 +0100 -@@ -80,9 +80,9 @@ ++++ WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-11-29 10:58:34.322941000 +0100 +@@ -80,7 +80,7 @@ /* * Decode JPEG200 codestream into jas_image_t structure. */ - image=jpc_decode(jpcstream,opts); -+ image=jas_image_decode(jpcstream,opts); ++ image=jas_image_decode(jpcstream,jas_image_getfmt(jpcstream),opts); if ( image == 0 ) { -- printf(" jpc_decode return = %d \n",ier); -+ printf(" jas_image_decode return = %d \n",ier); + printf(" jpc_decode return = %d \n",ier); return -3; - } - diff -Nru WPS-4.6.0.orig/ungrib/src/ngl/g2/enc_jpeg2000.c WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c --- WPS-4.6.0.orig/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-11-29 10:17:25.054123000 +0100 -@@ -178,9 +178,9 @@ ++++ WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-11-29 10:58:40.467583000 +0100 +@@ -178,7 +178,7 @@ /* * Encode image. */ - ier=jpc_encode(&image,jpcstream,opts); + ier=jas_image_encode(&image,jpcstream,opts); if ( ier != 0 ) { -- printf(" jpc_encode return = %d \n",ier); -+ printf(" jas_image_encode return = %d \n",ier); + printf(" jpc_encode return = %d \n",ier); return -3; - } - /* From 7be979a1b0dded744d7f6c0143ab473c549a9304 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Fri, 29 Nov 2024 11:53:03 +0100 Subject: [PATCH 124/414] Fix missing dependencies in wxWidgets-3.2.6-GCC-13.2.0.eb --- .../w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb index 4c5a5bec723..1805d927dbb 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.2.0.eb @@ -20,27 +20,27 @@ sources = [SOURCE_TAR_BZ2] checksums = ['939e5b77ddc5b6092d1d7d29491fe67010a2433cf9b9c0d841ee4d04acb9dce7'] builddependencies = [ - ('gettext', '0.22.5'), - ('pkgconf', '2.2.0'), - ('Python', '3.12.3'), + ('gettext', '0.22'), + ('pkgconf', '2.0.3'), + ('Python', '3.11.5'), ] dependencies = [ - ('libpng', '1.6.43'), - ('zlib', '1.3.1'), + ('libpng', '1.6.40'), + ('zlib', '1.2.13'), ('libjpeg-turbo', '3.0.1'), - ('XZ', '5.4.5'), + ('XZ', '5.4.4'), ('jbigkit', '2.1'), ('LibTIFF', '4.6.0'), - ('expat', '2.6.2'), + ('expat', '2.5.0'), ('GTK3', '3.24.39'), - ('X11', '20240607'), + ('X11', '20231019'), ('Mesa', '23.1.9'), ('libGLU', '9.0.3'), ('SDL2', '2.28.5'), ('cairo', '1.18.0'), ('GST-plugins-base', '1.24.8'), - ('GLib', '2.80.4'), + ('GLib', '2.78.1'), ] local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' From eace94becd7bec4ad58b3dfd489cfab6004e807c Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Fri, 29 Nov 2024 11:59:22 +0100 Subject: [PATCH 125/414] Fix missing dependencies in GST-plugins-base-1.24.8-GCC-13.2.0.eb --- .../GST-plugins-base-1.24.8-GCC-13.2.0.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb index 1e884931863..014fbdb6aba 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.2.0.eb @@ -16,20 +16,20 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['10fb31743750ccd498d3933e8aaecda563ebc65596a6ab875b47ee936e4b9599'] builddependencies = [ - ('Meson', '1.4.0'), - ('Ninja', '1.12.1'), - ('GObject-Introspection', '1.80.1'), - ('gettext', '0.22.5'), - ('pkgconf', '2.2.0'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.78.1'), + ('gettext', '0.22'), + ('pkgconf', '2.0.3'), ('Bison', '3.8.2'), ] dependencies = [ - ('zlib', '1.3.1'), - ('GLib', '2.80.4'), + ('zlib', '1.2.13'), + ('GLib', '2.78.1'), ('GStreamer', '1.24.8'), ('Gdk-Pixbuf', '2.42.10'), - ('X11', '20240607'), + ('X11', '20231019'), ('Mesa', '23.1.9'), ('Graphene', '1.10.8'), ] From a1116f0ff62d7fe93267f534df2ed62ccc276c33 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Fri, 29 Nov 2024 12:04:34 +0100 Subject: [PATCH 126/414] Fix Glib dependency --- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb index df1d93a6b9c..ac99b2584dd 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb @@ -26,7 +26,7 @@ builddependencies = [ ] dependencies = [ - ('GLib', '2.80.4'), + ('GLib', '2.78.1'), ('libjpeg-turbo', '3.0.1'), ('libpng', '1.6.40'), ('LibTIFF', '4.6.0'), From a4ddc8a65781a5a6ceab1a6ea34b0307ba72f6d7 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Fri, 29 Nov 2024 12:08:09 +0100 Subject: [PATCH 127/414] Fix Glib dependeny in Graphene-1.10.8-GCCcore-13.2.0.eb --- .../easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb index ca9d870a5cd..b8b16bdc898 100644 --- a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('GObject-Introspection', '1.78.1'), ('binutils', '2.40'), ] -dependencies = [('GLib', '2.80.4')] +dependencies = [('GLib', '2.78.1')] configopts = "-Dgobject_types=true -Dintrospection=enabled" From f4fc8ba4871a68eb6b709124c46665fde006363a Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Fri, 29 Nov 2024 12:35:28 +0100 Subject: [PATCH 128/414] Fix dependencies in GStreamer-1.24.8-GCC-13.2.0.eb --- .../g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb index b2ce916817e..ba08e2547cf 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb @@ -19,14 +19,14 @@ checksums = ['b807dbf36c5d2b3ce1c604133ed0c737350f9523ce4d8d644a1177c5f9d6ded3', ] builddependencies = [ - ('Meson', '1.4.0'), - ('Ninja', '1.12.1'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), ('Perl', '5.38.0'), ('Bison', '3.8.2'), ('flex', '2.6.4'), - ('GObject-Introspection', '1.80.1'), - ('gettext', '0.22.5'), - ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.78.1'), + ('gettext', '0.22'), + ('pkgconf', '2.0.3'), ] dependencies = [ ('Python', '3.12.3'), From c54bdfdc68d8b2a4e16fc65b8298e5dc267d55a8 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Fri, 29 Nov 2024 14:04:30 +0100 Subject: [PATCH 129/414] Fix dependencies in GStreamer-1.24.8-GCC-13.2.0.eb --- .../easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb index ba08e2547cf..4b2634beaaa 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.2.0.eb @@ -29,11 +29,11 @@ builddependencies = [ ('pkgconf', '2.0.3'), ] dependencies = [ - ('Python', '3.12.3'), - ('zlib', '1.3.1'), + ('Python', '3.11.5'), + ('zlib', '1.2.13'), ('GMP', '6.3.0'), ('GSL', '2.7'), - ('GLib', '2.80.4'), + ('GLib', '2.78.1'), ('libunwind', '1.6.2'), ('elfutils', '0.190'), ] From c93ea274deb422edba24c52fe0653f967e919e5b Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 29 Nov 2024 15:55:55 +0100 Subject: [PATCH 130/414] adding easyconfigs: Molden-7.3-GCCcore-13.3.0.eb --- .../m/Molden/Molden-7.3-GCCcore-13.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8a246a42a5c --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'MakeCp' + +name = 'Molden' +version = '7.3' + +homepage = 'https://www.theochem.ru.nl/molden/' +description = """Molden is a package for displaying Molecular Density from the + Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical + packages Mopac/Ampac""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.science.ru.nl/Molden/'] +sources = ['%(namelower)s%(version)s.tar.gz'] +patches = [ + 'Molden-7.3_fix_makefile_for_easybuild.patch', + 'Molden-7.3_fix_arg_handling.patch', +] +checksums = [ + {'molden7.3.tar.gz': '870f4fa6635229791bb09bbbd07f51456b2c90101d73564dc47ed7769b8c07a1'}, + {'Molden-7.3_fix_makefile_for_easybuild.patch': 'b97d794cf92978d151d70485250367eebf719885c6a909ca3404a800903e3f7a'}, + {'Molden-7.3_fix_arg_handling.patch': 'e7d0654a7c7a0b069ff4a904d3334ea19f6b0147003bc460745db8b8d5f931cf'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('makedepend', '1.0.9'), +] + +dependencies = [ + ('X11', '20240607'), + ('libglvnd', '1.7.0'), + ('libGLU', '9.0.3'), +] + +buildopts = 'CC="$CC" FC="$F90" FFLAGS="$FFLAGS -fallow-argument-mismatch" all' + +parallel = 1 + +files_to_copy = [(['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']], 'bin'), + 'CopyRight', 'README', 'REGISTER'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']] + ['README', 'REGISTER'], + 'dirs': [], +} + +sanity_check_commands = ["molden -h"] + +moduleclass = 'chem' From cb6eaf9a41fad482043c34b3f20a42291fdf90ce Mon Sep 17 00:00:00 2001 From: software Date: Fri, 29 Nov 2024 15:53:55 +0000 Subject: [PATCH 131/414] adding easyconfigs: mlst-2.23.0-foss-2023a.eb --- .../m/mlst/mlst-2.23.0-foss-2023a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/mlst/mlst-2.23.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/m/mlst/mlst-2.23.0-foss-2023a.eb b/easybuild/easyconfigs/m/mlst/mlst-2.23.0-foss-2023a.eb new file mode 100644 index 00000000000..7962db95bf6 --- /dev/null +++ b/easybuild/easyconfigs/m/mlst/mlst-2.23.0-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'mlst' +version = '2.23.0' + +homepage = "https://github.com/tseemann/mlst" +description = "Scan contig files against PubMLST typing schemes" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/tseemann/mlst/archive/refs/tags/'] +sources = ['v2.23.0.tar.gz'] +checksums = ['35bdbde309ba25293c3cce417d82e79594b9f78365133062923dc3d629bd8846'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('any2fasta', '0.4.2'), + ('BLAST+', '2.14.1'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['scripts', 'db'], +} + +sanity_check_commands = [ + "mlst --help", +] + +moduleclass = 'bio' From e420a130cff12a566afbd2a5818d431d2eb68c64 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 29 Nov 2024 17:27:00 +0100 Subject: [PATCH 132/414] removed patch --- .../w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb | 9 +- ...F-4.6.1_netCDF-Fortran_separate_path.patch | 156 ------------------ 2 files changed, 6 insertions(+), 159 deletions(-) delete mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb index 64e92c7f014..26865bf2a0e 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb @@ -14,12 +14,13 @@ toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 github_account = 'wrf-model' source_urls = [GITHUB_RELEASE] sources = ['v%(version)s.tar.gz'] -patches = ['WRF-4.6.1_netCDF-Fortran_separate_path.patch'] + +# patches = ['WRF-4.6.1_netCDF-Fortran_separate_path.patch'] checksums = [ {'v4.6.1.tar.gz': 'b8ec11b240a3cf1274b2bd609700191c6ec84628e4c991d3ab562ce9dc50b5f2'}, - {'WRF-4.6.1_netCDF-Fortran_separate_path.patch': - '0fcc55df295910fe507a3938b420a9a211e6e2ce82de8ded347b54135994e716'}, +# {'WRF-4.6.1_netCDF-Fortran_separate_path.patch': +# '0fcc55df295910fe507a3938b420a9a211e6e2ce82de8ded347b54135994e716'}, ] # csh is used by WRF install scripts @@ -36,6 +37,8 @@ dependencies = [ ('netCDF-Fortran', '4.6.1'), ] +preconfigopts = "export NETCDF=$EBROOTNETCDFMINFORTRAN && export NETCDF_C=$EBROOTNETCDF &&" + runtest = True # limit parallel build to 20 diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch deleted file mode 100644 index b2f654ab876..00000000000 --- a/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch +++ /dev/null @@ -1,156 +0,0 @@ -# Allow netCDF library with separate directories for C and Fortran -# ============================================================================ -# This patch has been around in EasyBuild since WRF3.5; it was committed by -# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain -# -# updated for WPS v4.4 by Maxim Masterov (SURF) -# updated for WRF v4.5.1 by Stefan Wolfsheimer (SURF) -# updated for WRF v4.6.1 by Stefan Wolfsheimer (SURF) - - -diff -Nru WRFV4.6.1.orig/arch/Config.pl WRFV4.6.1/arch/Config.pl ---- WRFV4.6.1.orig/arch/Config.pl 2024-10-16 23:05:18.000000000 +0200 -+++ WRFV4.6.1/arch/Config.pl 2024-11-28 15:38:43.864070000 +0100 -@@ -11,6 +11,7 @@ - select((select(STDOUT), $|=1)[0]); - $sw_perl_path = perl ; - $sw_netcdf_path = "" ; -+$sw_netcdff_path = "" ; - $sw_pnetcdf_path = "" ; - $sw_netcdfpar_path = "" ; - $sw_adios2_path = "" ; -@@ -70,6 +71,10 @@ - { - $sw_netcdf_path = substr( $ARGV[0], 8 ) ; - } -+ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) -+ { -+ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; -+ } - if ( substr( $ARGV[0], 1, 16 ) eq "netcdf4_dep_lib=" ) - { - $sw_netcdf4_dep_lib = substr( $ARGV[0], 17 ) ; -@@ -626,6 +631,7 @@ - { - $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; - $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; -+ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; - $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; - $_ =~ s/CONFIGURE_NETCDFPAR_PATH/$sw_netcdfpar_path/g ; - $_ =~ s/CONFIGURE_ADIOS2_PATH/$sw_adios2_path/g ; -@@ -695,7 +701,7 @@ - } elsif ( $sw_os eq "Interix" ) { - $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; - } else { -- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; -+ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdff_path/lib $sw_usenetcdff $sw_usenetcdf : ; - } - } - else -@@ -1083,7 +1089,7 @@ - } elsif ( $sw_os eq "Interix" ) { - $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; - } else { -- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; -+ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdff_path/lib $sw_usenetcdff $sw_usenetcdf : ; - } - } - else -diff -Nru WRFV4.6.1.orig/arch/postamble WRFV4.6.1/arch/postamble ---- WRFV4.6.1.orig/arch/postamble 2024-10-16 23:05:18.000000000 +0200 -+++ WRFV4.6.1/arch/postamble 2024-11-28 15:38:38.086016000 +0100 -@@ -55,7 +55,8 @@ - -I$(WRF_SRC_ROOT_DIR)/wrftladj \ - -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ - -I$(NETCDFPATH)/include \ -- CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC -+ -I$(NETCDFFPATH)/include \ -+ CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC - REGISTRY = Registry - CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE - -@@ -64,6 +65,7 @@ - ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS - CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE - NETCDFPATH = CONFIGURE_NETCDF_PATH -+NETCDFFPATH = CONFIGURE_NETCDFF_PATH - HDF5PATH = CONFIGURE_HDF5_PATH - WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH - RTTOVPATH = CONFIGURE_RTTOV_PATH -@@ -96,7 +98,7 @@ - - wrfio_nf : - ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ -- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ -+ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ - CC="$(SCC)" CFLAGS="$(CFLAGS)" NETCDF4_DEP_LIB="$(NETCDF4_DEP_LIB)" \ - FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) - -diff -Nru WRFV4.6.1.orig/configure WRFV4.6.1/configure ---- WRFV4.6.1.orig/configure 2024-11-28 15:36:44.834084000 +0100 -+++ WRFV4.6.1/configure 2024-11-28 15:51:45.766140000 +0100 -@@ -242,10 +242,13 @@ - USENETCDFF="" - USENETCDF="" - if [ -n "$NETCDF" ] ; then -- echo "Will use NETCDF in dir: $NETCDF" -+ echo "Will use NETCDF in dir: $NETCDF" -+ echo "Will use NETCDFF in dir: $NETCDFF" - # Oh UNIDATA, why make it so hard ... - if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then - USENETCDFF="-lnetcdff" -+ elif [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib/libnetcdff.dll.a" ] ; then -+ USENETCDFF="-lnetcdff" - else - USENETCDFF=" " - fi -@@ -265,7 +268,6 @@ - echo ' ' - exit 6 - fi -- - # If the user asked for classic netcdf, acquiesce to the request. - - if [ ! -f "$NETCDF/bin/nf-config" ] ; then -@@ -538,7 +540,7 @@ - srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` - if [ -n "$srch" ] ; then - $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ -- -netcdf=$NETCDF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -adios2=$ADIOS2 -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ -+ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -adios2=$ADIOS2 -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ - -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ - -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ - -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -netcdf4_dep_lib="$NETCDF4_DEP_LIB" -@@ -620,14 +622,14 @@ - echo "If you wish to change the default options, edit the file:" - echo " arch/configure.defaults" - --if test -n "$NETCDF" ; then -- if [ ! -f $NETCDF/include/netcdf.inc ] ; then -+if test -n "$NETCDFF" ; then -+ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then - echo - echo "Error : Not found $NETCDF/include/netcdf.inc" - echo " Please check this installation of NetCDF and re-run this configure script" - exit -1 - fi -- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null -+ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null - configure_aaaa=$? ; export configure_aaaa - if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then - echo "NetCDF users note:" -diff -Nru WRFV4.6.1.orig/external/io_netcdf/makefile WRFV4.6.1/external/io_netcdf/makefile ---- WRFV4.6.1.orig/external/io_netcdf/makefile 2024-10-16 23:05:19.000000000 +0200 -+++ WRFV4.6.1/external/io_netcdf/makefile 2024-11-28 16:38:31.349880802 +0100 -@@ -3,9 +3,9 @@ - OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o - OBJS = $(OBJSL) - CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code --FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share -+FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include -I../ioapi_share - LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf --LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) -+LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) - CPP1 = $(CPP) -P $(TRADFLAG) - M4 = m4 -Uinclude -Uindex -Ulen - AR = ar From dc96e2dfa9a3b8faeea2081e3decbb71d9110cfe Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 29 Nov 2024 17:31:54 +0100 Subject: [PATCH 133/414] removed commented lines --- easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb index 26865bf2a0e..82904273536 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb @@ -15,12 +15,10 @@ github_account = 'wrf-model' source_urls = [GITHUB_RELEASE] sources = ['v%(version)s.tar.gz'] -# patches = ['WRF-4.6.1_netCDF-Fortran_separate_path.patch'] +# WRF-4.5.1_netCDF-Fortran_separate_path.patch no longer required for version 4.5.2 checksums = [ {'v4.6.1.tar.gz': 'b8ec11b240a3cf1274b2bd609700191c6ec84628e4c991d3ab562ce9dc50b5f2'}, -# {'WRF-4.6.1_netCDF-Fortran_separate_path.patch': -# '0fcc55df295910fe507a3938b420a9a211e6e2ce82de8ded347b54135994e716'}, ] # csh is used by WRF install scripts From 370fb36e79ead6a3fc289e9343477e0d8cfff939 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 29 Nov 2024 18:30:31 +0100 Subject: [PATCH 134/414] adding easyconfigs: WebKitGTK+-2.41.4-foss-2023a.eb, Perl-5.36.1-GCCcore-12.3.0-minimal.eb, unifdef-2.12-GCCcore-12.3.0.eb, wpebackend-fdo-1.15.90-GCCcore-12.3.0.eb, pugixml-1.14-GCCcore-12.3.0.eb, Waylandpp-1.0.0-GCCcore-12.3.0.eb, libwpe-1.16.0-GCCcore-12.3.0.eb --- .../l/libwpe/libwpe-1.16.0-GCCcore-12.3.0.eb | 43 +++++++++ .../Perl-5.36.1-GCCcore-12.3.0-minimal.eb | 31 +++++++ .../p/pugixml/pugixml-1.14-GCCcore-12.3.0.eb | 37 ++++++++ .../u/unifdef/unifdef-2.12-GCCcore-12.3.0.eb | 34 +++++++ .../Waylandpp-1.0.0-GCCcore-12.3.0.eb | 52 +++++++++++ .../WebKitGTK+-2.41.4-foss-2023a.eb | 89 +++++++++++++++++++ .../wpebackend-fdo-1.15.90-GCCcore-12.3.0.eb | 41 +++++++++ 7 files changed, 327 insertions(+) create mode 100644 easybuild/easyconfigs/l/libwpe/libwpe-1.16.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb create mode 100644 easybuild/easyconfigs/p/pugixml/pugixml-1.14-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/u/unifdef/unifdef-2.12-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb create mode 100644 easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.15.90-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libwpe/libwpe-1.16.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libwpe/libwpe-1.16.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1b821100762 --- /dev/null +++ b/easybuild/easyconfigs/l/libwpe/libwpe-1.16.0-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# update 1.14.1 THEMBL +easyblock = 'CMakeMake' + +name = 'libwpe' +version = '1.16.0' + +homepage = 'https://webkit.org/wpe' +description = """WPE is the reference WebKit port for embedded and +low-consumption computer devices. It has been designed from the +ground-up with performance, small footprint, accelerated content +rendering, and simplicity of deployment in mind, bringing the +excellence of the WebKit engine to countless platforms and target devices.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://wpewebkit.org/releases'] +sources = ['%(name)s-%(version)s.tar.xz'] +patches = ['%(name)s-1.13.3_include-string-before-poison.patch'] +checksums = [ + {'libwpe-1.16.0.tar.xz': 'c7f3a3c6b3d006790d486dc7cceda2b6d2e329de07f33bc47dfc53f00f334b2a'}, + {'libwpe-1.13.3_include-string-before-poison.patch': + '2d21ed6b2dafa758126cda162e450ab2b3a3c0b622e375ff443523ba32fc5812'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('CMake', '3.26.3'), + ('Meson', '1.1.1'), +] + +dependencies = [ + ('glew', '2.2.0', '-egl'), +] + +sanity_check_paths = { + 'files': ['lib/libwpe-1.0.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb new file mode 100644 index 00000000000..e2918eba70a --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb @@ -0,0 +1,31 @@ +name = 'Perl' +version = '5.36.1' +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': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.36.1.tar.gz': '68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.14-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.14-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..edfa9577d6e --- /dev/null +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.14-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'pugixml' +version = '1.14' + +homepage = 'https://pugixml.org/' +description = "pugixml is a light-weight C++ XML processing library" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/zeux/pugixml/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['610f98375424b5614754a6f34a491adbddaaec074e9044577d965160ec103d2e'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = " ".join([ + "-DBUILD_SHARED_LIBS=ON", + "-DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON", +]) + +sanity_check_paths = { + 'files': [ + 'include/pugiconfig.hpp', + 'include/pugixml.hpp', + 'lib/libpugixml.a', + 'lib/libpugixml.%s' % SHLIB_EXT, + 'lib/pkgconfig/pugixml.pc' + ], + 'dirs': ['lib/cmake/pugixml'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/u/unifdef/unifdef-2.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/unifdef/unifdef-2.12-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4f5d0a500cd --- /dev/null +++ b/easybuild/easyconfigs/u/unifdef/unifdef-2.12-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/07 +easyblock = 'ConfigureMake' + +name = 'unifdef' +version = '2.12' + +homepage = 'https://github.com/fanf2/unifdef' +description = """unifdef - selectively remove C preprocessor conditionals +The unifdef utility selectively processes conditional C preprocessor +and the additional text that they delimit, while otherwise leaving the +file alone.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'fanf2' +source_urls = [GITHUB_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['030369db9ff917acfae7fa4e90bcc1dff8a8dc534d82d1c72c12ef698d2f20e4'] + +preconfigopts = 'echo V=\\"%(name)s-%(version)s\\" > version.sh &&' +preconfigopts += 'echo D=\\"2020-02-14 0:00:00 +0000\\" >> version.sh&&' +configure_cmd = 'sed -i "s/HOME/PREF/g" Makefile #' +preinstallopts = 'export PREF=%(installdir)s &&' + +dependencies = [('binutils', '2.40')] + +sanity_check_commands = ['%(name)s -h'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'share/man'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e661a73e704 --- /dev/null +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,52 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'Waylandpp' +version = '1.0.0' + +homepage = 'https://github.com/NilsBrause/waylandpp' +description = """Wayland is an object oriented display protocol, which +features request and events. Requests can be seen as method calls on +certain objects, whereas events can be seen as signals of an object. +This makes the Wayland protocol a perfect candidate for a C++ binding. + +The goal of this library is to create such a C++ binding for Wayland +using the most modern C++ technology currently available, providing +an easy to use C++ API to Wayland.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/NilsBrause/waylandpp/archive'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + 'b20b45917382c6b87e9380130c9a1a1c563da2f498de5830df12fbce326dd9f5', # 1.0.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkg-config', '0.29.2'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('pugixml', '1.14'), + ('Wayland', '1.22.0'), + ('freeglut', '3.4.0'), +] + +sanity_check_paths = { + 'files': ['bin/wayland-scanner++', 'lib//libwayland-client-extra++.%s' % SHLIB_EXT, + 'lib/libwayland-client++.%s' % SHLIB_EXT, + 'lib/libwayland-client-unstable++.%s' % SHLIB_EXT, + 'lib/libwayland-cursor++.%s' % SHLIB_EXT, + 'lib/libwayland-egl++.%s' % SHLIB_EXT, + 'lib/libwayland-server-extra++.%s' % SHLIB_EXT, + 'lib/libwayland-server++.%s' % SHLIB_EXT, + 'lib/libwayland-server-unstable++.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb new file mode 100644 index 00000000000..0f6b697bc48 --- /dev/null +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb @@ -0,0 +1,89 @@ +# Updated from WebKitGTK+-2.27.4-GCC-8.3.0.eb with more modules added +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: THEMBL + +easyblock = 'CMakeMake' + +name = 'WebKitGTK+' +version = '2.41.4' + +homepage = 'https://webkitgtk.org/' +description = """WebKitGTK+ is a full-featured port of the WebKit +rendering engine, suitable for projects requiring any kind of web +integration, from hybrid HTML/CSS applications to full-fledged web +browsers. It offers WebKit's full functionality and is useful in a wide +range of systems from desktop computers to embedded systems like phones, +tablets, and televisions.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://webkitgtk.org/releases'] +sources = ['webkitgtk-%(version)s.tar.xz'] +checksums = ['ad792d4acd4e8536cc0a652fd0303bfef93a7f8718d2b3d72db83e25f52777af'] + +osdependencies = [ + # Would be better to use the system package due to security reasons + # But we need at least libgcrypt 1.7.0 and Ubuntu 16.04 and RH 7.5 + # are both using a too old version. + # Update: Libcrypt 1.9.3 from EasyBuild added (J.S) + # ('libgcrypt-dev', 'libgcrypt20-dev', 'libgcrypt-devel'), + # libsecret is not actually needed since USE_LIBSECRET option is disabled + # ('libsecret-1-dev', 'libsecret-devel'), +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('Perl', '5.36.1', '-minimal'), + ('GObject-Introspection', '1.76.1'), + ('pkg-config', '0.29.2'), + ('ccache', '4.9'), + ('unifdef', '2.12'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('gperf', '3.1'), + ('cairo', '1.17.8'), + ('GTK3', '3.24.37'), + ('LibSoup', '3.6.1'), + ('ATK', '2.38.0'), + ('libgcrypt', '1.10.3'), + ('wpebackend-fdo', '1.15.90'), + ('libxslt', '1.1.38'), + ('libtasn1', '4.19.0'), + ('GStreamer', '1.22.5'), + ('OpenJPEG', '2.5.0'), + ('Ruby', '3.3.0'), + ('GSL', '2.7'), + ('glew', '2.2.0', '-egl'), + ('enchant-2', '2.6.5'), + ('LittleCMS', '2.15'), + ('GST-plugins-base', '1.22.5'), + ('libwebp', '1.3.1'), + ('libavif', '1.0.4'), +] + + +# The build takes around 2.5 hours on 24 cores on AMD Rome! +# So be patient! + +# Instead of using a patch file, we are disabling problematic builds in the command line. +# At least this way, if something is not needed it can be turned off, without looking into +# a patch file. +configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON -DPORT=GTK -DCMAKE_FIND_USE_PACKAGE_REGISTRY=FALSE " +configopts += "-DENABLE_GAMEPAD=OFF -DUSE_LIBSECRET=OFF -DUSE_LIBHYPHEN=OFF " +configopts += "-DUSE_WOFF2=OFF -DENABLE_JOURNALD_LOG=OFF -DENABLE_BUBBLEWRAP_SANDBOX=OFF " +configopts += "-DENABLE_INTROSPECTION=OFF -DUSE_LIBNOTIFY=OFF " +configopts += "-DUSE_GSTREAMER_TRANSCODER=OFF " + +prebuildopts = "export CCACHE_DIR=%(builddir)s/ccache && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/WebKitWebDriver', 'lib/libwebkit2gtk-4.1.%s' % SHLIB_EXT, + 'lib/libjavascriptcoregtk-4.1.%s' % SHLIB_EXT], + 'dirs': ['include/webkitgtk-4.1/webkit2', 'libexec/webkit2gtk-4.1'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.15.90-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.15.90-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..aad4f18049c --- /dev/null +++ b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.15.90-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# update 1.14.1 THEMBL +easyblock = 'MesonNinja' + +name = 'wpebackend-fdo' +version = '1.15.90' + +homepage = 'https://wpewebkit.org/' +description = """WPE WebKit allows embedders to create simple and performant +systems based on Web platform technologies. It is a WebKit port designed with +flexibility and hardware acceleration in mind, leveraging common 3D graphics +APIs for best performance.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://wpewebkit.org/releases'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['4ac5be554560ed48b13a0745fc779d7f6663904f35f510a6c50e34cb96999083'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('pugixml', '1.14'), + ('Waylandpp', '1.0.0'), + ('libepoxy', '1.5.10'), + ('glib-networking', '2.72.1'), + ('libwpe', '1.16.0'), +] + +sanity_check_paths = { + 'files': ['lib/libWPEBackend-fdo-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From c54e425b4b3af490ac5eba0494090a3297e2e5fc Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 29 Nov 2024 18:51:31 +0100 Subject: [PATCH 135/414] adding easyconfigs: LibSoup-3.6.1-GCC-12.3.0.eb, pkg-config-0.29.2-GCCcore-12.3.0.eb, libpsl-0.21.5-GCCcore-12.3.0.eb, glib-networking-2.72.1-GCCcore-12.3.0.eb, GConf-3.2.6-GCCcore-12.3.0.eb, dbus-glib-0.112-GCCcore-12.3.0.eb --- .../dbus-glib-0.112-GCCcore-12.3.0.eb | 37 ++++++++++++ .../g/GConf/GConf-3.2.6-GCCcore-12.3.0.eb | 59 +++++++++++++++++++ .../glib-networking-2.72.1-GCCcore-12.3.0.eb | 36 +++++++++++ .../l/LibSoup/LibSoup-3.6.1-GCC-12.3.0.eb | 45 ++++++++++++++ .../l/libpsl/libpsl-0.21.5-GCCcore-12.3.0.eb | 32 ++++++++++ .../pkg-config-0.29.2-GCCcore-12.3.0.eb | 36 +++++++++++ 6 files changed, 245 insertions(+) create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/LibSoup/LibSoup-3.6.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpsl/libpsl-0.21.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7755c976098 --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.112' + +homepage = 'https://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] +checksums = ['7d550dccdfcd286e33895501829ed971eeb65c614e73aadb4a08aeef719b143a'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Python', '3.11.3'), # Python is needed for building against GLib. +] + +dependencies = [ + ('GLib', '2.77.1'), + ('DBus', '1.15.4'), + ('expat', '2.5.0'), +] + +sanity_check_commands = [ + 'dbus-binding-tool --version', + 'dbus-binding-tool --help', +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..6a65661ebd9 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-12.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +# The homeage is no longer reachable! +# homepage = 'https://developer.gnome.org/gconf/' +# The project was depricated with the move to Gnome-3 +# Possible alternative, although 6 years old: +homepage = 'https://gitlab.gnome.org/iainl/gconf' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +patches = [ + '%(name)s-%(version)s_call-dbus_g_thread_init.patch', + '%(name)s-%(version)s_fix_wrong_return_value.patch', + '%(name)s-%(version)s_gconf-path-max-hurd.patch', + '%(name)s-%(version)s_readd_gconf_engine_key_is_writable.patch', +] +checksums = [ + {'GConf-3.2.6.tar.xz': '1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'}, + {'GConf-3.2.6_call-dbus_g_thread_init.patch': 'ed55bff5bc239115ae27b8520a923ae0d5cab6cb15ca9921a8c23b939306489f'}, + {'GConf-3.2.6_fix_wrong_return_value.patch': 'f8f7745c3648953098eb56af0f64adc69d8c0b0e78c8db351746a2b4c58e8bb4'}, + {'GConf-3.2.6_gconf-path-max-hurd.patch': 'ee5524c3cb985088bbe4884531ddc48ba22d2fced2a34865304c77e194a55bde'}, + {'GConf-3.2.6_readd_gconf_engine_key_is_writable.patch': + 'b95dfc2f0474d9162fc686f26cd4d3da5c9b01a9c609dc0a4f2b2bd901d497f3'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('GObject-Introspection', '1.76.1'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('dbus-glib', '0.112'), + ('libxml2', '2.11.4'), + ('GTK3', '3.24.37'), + ('intltool', '0.51.0'), +] + +configopts = '--disable-orbit ' + +local_check_filelist = ['bin/gconf%s' % x for x in ['-merge-tree', 'tool-2']] +local_check_filelist += ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] +local_check_filelist += ['lib/libgconf-2.%s' % x for x in ['a', 'so']] + +sanity_check_paths = { + 'files': local_check_filelist, + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1b89b9c31d2 --- /dev/null +++ b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MesonNinja' + +name = 'glib-networking' +version = '2.72.1' + +homepage = 'https://gitlab.gnome.org/GNOME/glib-networking' +description = "Network extensions for GLib" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/glib-networking/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['675a654ae55d381490c5d76b84e088f684125415fbd2d46f74dfa5522c4a1268'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('GnuTLS', '3.7.8'), + ('libidn2', '2.3.7'), +] + +sanity_check_paths = { + 'files': ['lib/gio/modules/libgiognutls.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'GIO_EXTRA_MODULES': 'lib/gio/modules'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-3.6.1-GCC-12.3.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.6.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..a5a488ffb36 --- /dev/null +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.6.1-GCC-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MesonNinja' + +name = 'LibSoup' +version = '3.6.1' + +homepage = 'https://wiki.gnome.org/Projects/libsoup' +description = """libsoup is an HTTP client/server library for GNOME. It +uses GObjects and the glib main loop, to integrate well with GNOME +applications, and also has a synchronous API, for use in threaded +applications.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'cstd': 'gnu11'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ceb1f1aa2bdd73b2cd8159d3998c96c55ef097ef15e4b4f36029209fa18af838'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.76.1'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('libxml2', '2.11.4'), + ('SQLite', '3.42.0'), + ('GLib', '2.77.1'), + ('libpsl', '0.21.5'), + ('cURL', '8.0.1'), + ('GnuTLS', '3.7.8'), + ('nghttp2', '1.58.0'), + ('glib-networking', '2.72.1'), + ('Brotli', '1.0.9'), +] + +sanity_check_paths = { + 'files': ['lib/libsoup-3.0.%s' % SHLIB_EXT], + 'dirs': ['include/libsoup-3.0/libsoup/', 'lib/pkgconfig'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..cce4f27173d --- /dev/null +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.5-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libpsl' +version = '0.21.5' + +homepage = 'https://rockdaboot.github.io/libpsl' +description = "C library for the Public Suffix List" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/rockdaboot/libpsl/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1dcc9ceae8b128f3c0b3f654decd0e1e891afc6ff81098f227ef260449dae208'] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('libidn2', '2.3.7'), + ('libunistring', '1.1'), +] + +sanity_check_commands = [('psl --version')] + +sanity_check_paths = { + 'files': ['bin/psl', 'lib/libpsl.a'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..aaef19ca7c3 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +# pkgconf should be used in preference to pkg-config +# This is included for use only in software that fails to build when using pkgconf +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [('binutils', '2.40')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' From ff147e2a6ddc4daded12ad6c4398f74250bfb398 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 1 Dec 2024 18:35:54 +0100 Subject: [PATCH 136/414] add tblite for DFTB+ --- easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb index c862fcea552..bb993fb6e99 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -58,7 +58,8 @@ dependencies = [ # Prefer dependencies from EB than bundled sources configopts = '-DHYBRID_CONFIG_METHODS="Find;Submodule;Fetch" ' -configopts += '-DWITH_MPI=1 -DWITH_OMP=1 -DWITH_SDFTD3=1 -DWITH_ELSI=1 -DWITH_MBD=1 -DWITH_UNIT_TESTS=1 ' +configopts += '-DWITH_MPI=1 -DWITH_OMP=1 ' +configopts += '-DWITH_SDFTD3=1 -DWITH_ELSI=1 -DWITH_MBD=1 -DWITH_UNIT_TESTS=1 -DWITH_TBLITE=1 ' configopts += '-DBUILD_SHARED_LIBS=1 -DWITH_API=1 -DWITH_PYTHON=0 ' # Python bindings installed as extension configopts += '-DSCALAPACK_LIBRARY="$LIBSCALAPACK" ' From 1c8e8ac7e5ce4a1444e38b1b7e29007f7e46f534 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 2 Dec 2024 10:33:53 +0100 Subject: [PATCH 137/414] add SimBu to R-bundle-Bioconductor --- .../R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb index 7d2ebad2d77..b0327bb008c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb @@ -1361,6 +1361,9 @@ exts_list = [ ('ChIPseeker', '1.38.0', { 'checksums': ['a0d4710fccda620b750f933916acac6d12999a077e1c17632d8823848a2fa82f'], }), + ('SimBu', '1.4.3', { + 'checksums': ['c32c0b5cf71b7b8e13b52739e34993c1e7df8bf9d40fc9d3d5e1df4048468bfe'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} @@ -1370,4 +1373,4 @@ sanity_check_paths = { 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], } -moduleclass = 'bio' +moduleclass = 'bio' \ No newline at end of file From e9a36171c68414f933ab1afa03b32422491f0f96 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Mon, 2 Dec 2024 12:38:12 +0100 Subject: [PATCH 138/414] Update R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb - end newline --- .../R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb index b0327bb008c..40ffdbcb3a4 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb @@ -1373,4 +1373,4 @@ sanity_check_paths = { 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 0e7a21eef6fe43ce3683158cf5893d1e1f5760c7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 2 Dec 2024 14:01:25 +0100 Subject: [PATCH 139/414] Fix Boost 1.85 build on PPC --- .../b/Boost/Boost-1.85.0-GCC-13.3.0.eb | 6 +- .../Boost/Boost-1.85.0_fix-ppc-charconv.patch | 1160 +++++++++++++++++ 2 files changed, 1165 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.85.0_fix-ppc-charconv.patch diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb index 10518dc36a3..d1a8434d8e4 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb @@ -12,7 +12,11 @@ toolchainopts = {'pic': True} source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['be0d91732d5b0cc6fbb275c7939974457e79b54d6f07ce2e3dfdd68bef883b0b'] +patches = ['Boost-1.85.0_fix-ppc-charconv.patch'] +checksums = [ + 'be0d91732d5b0cc6fbb275c7939974457e79b54d6f07ce2e3dfdd68bef883b0b', + {'Boost-1.85.0_fix-ppc-charconv.patch': 'bb392cc087fe4951e2c427731020b541c3258ec75f113524303dfb44624f98bc'}, +] dependencies = [ ('bzip2', '1.0.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.85.0_fix-ppc-charconv.patch b/easybuild/easyconfigs/b/Boost/Boost-1.85.0_fix-ppc-charconv.patch new file mode 100644 index 00000000000..d82089cf5cc --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.85.0_fix-ppc-charconv.patch @@ -0,0 +1,1160 @@ +Avoid compile errors on ppc64le like +> libs/charconv/build/../src/from_chars.cpp: In function 'boost::charconv::from_chars_result boost::charconv::from_chars_erange(const char*, const char*, __ieee128&, chars_format)': +> libs/charconv/build/../src/from_chars.cpp:120:48: error: 'compute_float128' is not a member of 'boost::charconv::detail'; did you mean 'compute_float32'? +> 120 | auto return_val = boost::charconv::detail::compute_float128(exponent, significand, sign, success); +> | ^~~~~~~~~~~~~~~~ +> | compute_float32 +> libs/charconv/build/../src/from_chars.cpp: In function 'boost::charconv::from_chars_result boost::charconv::from_chars_erange(const char*, const char*, long double&, chars_format)': +> libs/charconv/build/../src/from_chars.cpp:258:48: error: 'compute_float80' is not a member of 'boost::charconv::detail'; did you mean 'compute_float64'? +> 258 | auto return_val = boost::charconv::detail::compute_float80(exponent, significand, sign, success); +> | ^~~~~~~~~~~~~~~ +> | compute_float64 + +Combined https://github.com/boostorg/charconv/pull/177, https://github.com/boostorg/charconv/pull/183, https://github.com/boostorg/charconv/pull/222 +Author: Matt Borland + +Patch-file Author: Alexander Grund (TU Dresden) + +diff --git a/libs/charconv/CMakeLists.txt b/libs/charconv/CMakeLists.txt +index 8120419..b5f468e 100644 +--- a/libs/charconv/CMakeLists.txt ++++ b/libs/charconv/CMakeLists.txt +@@ -22,24 +22,20 @@ target_include_directories(boost_charconv PUBLIC include) + include(CheckCXXSourceCompiles) + check_cxx_source_compiles(config/has_float128.cpp QUADMATH_FOUND) + ++target_link_libraries(boost_charconv ++ PUBLIC ++ Boost::config ++ Boost::assert ++ Boost::core ++) ++ + if(NOT QUADMATH_FOUND) + message(STATUS "Boost.Charconv: quadmath support OFF") + target_compile_definitions(boost_charconv PUBLIC BOOST_CHARCONV_NO_QUADMATH) +- target_link_libraries(boost_charconv +- PUBLIC +- Boost::config +- Boost::assert +- Boost::core +- ) + else() + message(STATUS "Boost.Charconv: quadmath support ON") +- target_link_libraries(boost_charconv +- PUBLIC +- Boost::config +- Boost::assert +- Boost::core +- quadmath +- ) ++ target_compile_definitions(boost_charconv PUBLIC BOOST_CHARCONV_HAS_QUADMATH) ++ target_link_libraries(boost_charconv PUBLIC quadmath) + endif() + + target_compile_features(boost_charconv PUBLIC cxx_std_11) +diff --git a/libs/charconv/build/Jamfile b/libs/charconv/build/Jamfile +index 09802d5..695f1b2 100644 +--- a/libs/charconv/build/Jamfile ++++ b/libs/charconv/build/Jamfile +@@ -21,7 +21,7 @@ lib boost_charconv + BOOST_CHARCONV_SOURCE=1 + + [ requires cxx11_variadic_templates cxx11_decltype ] +- [ check-target-builds ../config//has_float128 "GCC libquadmath and __float128 support" : "quadmath" ] ++ [ check-target-builds ../config//has_float128 "GCC libquadmath and __float128 support" : "quadmath" BOOST_CHARCONV_HAS_QUADMATH ] + + # default-build + : +diff --git a/libs/charconv/doc/charconv/build.adoc b/libs/charconv/doc/charconv/build.adoc +index db17732..f7da7fa 100644 +--- a/libs/charconv/doc/charconv/build.adoc ++++ b/libs/charconv/doc/charconv/build.adoc +@@ -68,6 +68,13 @@ For example, using a `conanfile.txt`: + boost_charconv/1.0.0 + ---- + ++== `__float128` and `std::float128_t` Support ++ ++If using B2 or CMake the build system will automatically define `BOOST_CHARCONV_HAS_QUADMATH` and link against it if the build system can successfully run a small test case. ++If you are using another build system and you want support for these types you will have to define `BOOST_CHARCONV_HAS_QUADMATH`, and link against https://gcc.gnu.org/onlinedocs/libquadmath/[libquadmath]. ++ ++IMPORTANT: libquadmath is only available on supported platforms (e.g. Linux with x86, x86_64, PPC64, and IA64). ++ + == Dependencies + +-This library depends on: Boost.Assert, Boost.Config, Boost.Core, and https://gcc.gnu.org/onlinedocs/libquadmath/[libquadmath] on supported platforms (e.g. Linux with x86, x86_64, PPC64, and IA64). ++This library depends on: Boost.Assert, Boost.Config, Boost.Core, and optionally libquadmath (see above). +diff --git a/boost/charconv/detail/compute_float80.hpp b/boost/charconv/detail/compute_float80.hpp +index c12a4f5..ad1e514 100644 +--- a/boost/charconv/detail/compute_float80.hpp ++++ b/boost/charconv/detail/compute_float80.hpp +@@ -37,19 +37,6 @@ static constexpr long double powers_of_ten_ld[] = { + 1e49L, 1e50L, 1e51L, 1e52L, 1e53L, 1e54L, 1e55L + }; + +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 +-static constexpr __float128 powers_of_tenq[] = { +- 1e0Q, 1e1Q, 1e2Q, 1e3Q, 1e4Q, 1e5Q, 1e6Q, +- 1e7Q, 1e8Q, 1e9Q, 1e10Q, 1e11Q, 1e12Q, 1e13Q, +- 1e14Q, 1e15Q, 1e16Q, 1e17Q, 1e18Q, 1e19Q, 1e20Q, +- 1e21Q, 1e22Q, 1e23Q, 1e24Q, 1e25Q, 1e26Q, 1e27Q, +- 1e28Q, 1e29Q, 1e30Q, 1e31Q, 1e32Q, 1e33Q, 1e34Q, +- 1e35Q, 1e36Q, 1e37Q, 1e38Q, 1e39Q, 1e40Q, 1e41Q, +- 1e42Q, 1e43Q, 1e44Q, 1e45Q, 1e46Q, 1e47Q, 1e48Q, +- 1e49Q, 1e50Q, 1e51Q, 1e52Q, 1e53Q, 1e54Q, 1e55Q +-}; +-#endif +- + template + inline ResultType fast_path(std::int64_t q, Unsigned_Integer w, bool negative, ArrayPtr table) noexcept + { +@@ -78,42 +65,6 @@ inline ResultType fast_path(std::int64_t q, Unsigned_Integer w, bool negative, A + return ld; + } + +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 +-template +-inline __float128 compute_float128(std::int64_t q, Unsigned_Integer w, bool negative, std::errc& success) noexcept +-{ +- // GLIBC uses 2^-16444 but MPFR uses 2^-16445 as the smallest subnormal value for 80 bit +- // 39 is the max number of digits in an uint128_t +- static constexpr auto smallest_power = -4951 - 39; +- static constexpr auto largest_power = 4932; +- +- if (-55 <= q && q <= 48 && w <= static_cast(1) << 113) +- { +- success = std::errc(); +- return fast_path<__float128>(q, w, negative, powers_of_tenq); +- } +- +- if (w == 0) +- { +- success = std::errc(); +- return negative ? -0.0Q : 0.0Q; +- } +- else if (q > largest_power) +- { +- success = std::errc::result_out_of_range; +- return negative ? -HUGE_VALQ : HUGE_VALQ; +- } +- else if (q < smallest_power) +- { +- success = std::errc::result_out_of_range; +- return negative ? -0.0Q : 0.0Q; +- } +- +- success = std::errc::not_supported; +- return 0; +-} +-#endif +- + template + inline ResultType compute_float80(std::int64_t q, Unsigned_Integer w, bool negative, std::errc& success) noexcept + { +diff --git a/boost/charconv/detail/config.hpp b/boost/charconv/detail/config.hpp +index 714d4a8..e0e2500 100644 +--- a/boost/charconv/detail/config.hpp ++++ b/boost/charconv/detail/config.hpp +@@ -27,11 +27,6 @@ + # define BOOST_CHARCONV_UINT128_MAX (2 * static_cast(BOOST_CHARCONV_INT128_MAX) + 1) + #endif + +-#if defined(BOOST_HAS_FLOAT128) && !defined(__STRICT_ANSI__) && !defined(BOOST_CHARCONV_NO_QUADMATH) +-# define BOOST_CHARCONV_HAS_FLOAT128 +-# include +-#endif +- + #ifndef BOOST_NO_CXX14_CONSTEXPR + # define BOOST_CHARCONV_CXX14_CONSTEXPR BOOST_CXX14_CONSTEXPR + # define BOOST_CHARCONV_CXX14_CONSTEXPR_NO_INLINE BOOST_CXX14_CONSTEXPR +diff --git a/boost/charconv/detail/emulated128.hpp b/boost/charconv/detail/emulated128.hpp +index 5e12930..e77133d 100644 +--- a/boost/charconv/detail/emulated128.hpp ++++ b/boost/charconv/detail/emulated128.hpp +@@ -136,10 +136,6 @@ struct uint128 + explicit constexpr operator boost::uint128_type() const noexcept { return (static_cast(high) << 64) + low; } + #endif + +- #ifdef BOOST_CHARCONV_HAS_FLOAT128 +- explicit operator __float128() const noexcept { return ldexpq(static_cast<__float128>(high), 64) + static_cast<__float128>(low); } +- #endif +- + FLOAT_CONVERSION_OPERATOR(float) // NOLINT + FLOAT_CONVERSION_OPERATOR(double) // NOLINT + FLOAT_CONVERSION_OPERATOR(long double) // NOLINT +diff --git a/boost/charconv/detail/fallback_routines.hpp b/boost/charconv/detail/fallback_routines.hpp +index d2349c7..681aef5 100644 +--- a/boost/charconv/detail/fallback_routines.hpp ++++ b/boost/charconv/detail/fallback_routines.hpp +@@ -21,13 +21,6 @@ namespace boost { + namespace charconv { + namespace detail { + +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 +-inline int print_val(char* first, std::size_t size, char* format, __float128 value) noexcept +-{ +- return quadmath_snprintf(first, size, format, value); +-} +-#endif +- + template + inline int print_val(char* first, std::size_t size, char* format, T value) noexcept + { +@@ -73,19 +66,11 @@ to_chars_result to_chars_printf_impl(char* first, char* last, T value, chars_for + } + + // Add the type identifier +- #ifdef BOOST_CHARCONV_HAS_FLOAT128 +- BOOST_CHARCONV_IF_CONSTEXPR (std::is_same::value || std::is_same::value) +- { +- format[pos] = std::is_same::value ? 'Q' : 'L'; +- ++pos; +- } +- #else + BOOST_CHARCONV_IF_CONSTEXPR (std::is_same::value) + { + format[pos] = 'L'; + ++pos; + } +- #endif + + // Add the format character + switch (fmt) +@@ -205,18 +190,7 @@ from_chars_result from_chars_strtod_impl(const char* first, const char* last, T& + r = {last, std::errc::result_out_of_range}; + } + } +- #ifdef BOOST_CHARCONV_HAS_FLOAT128 +- else +- { +- return_value = strtoflt128(buffer, &str_end); +- +- if (return_value == HUGE_VALQ) +- { +- r = {last, std::errc::result_out_of_range}; +- } +- } +- #endif +- ++ + // Since this is a fallback routine we are safe to check for 0 + if (return_value == 0 && str_end == last) + { +diff --git a/boost/charconv/detail/generate_nan.hpp b/boost/charconv/detail/generate_nan.hpp +deleted file mode 100644 +index e527ade..0000000 +--- a/boost/charconv/detail/generate_nan.hpp ++++ /dev/null +@@ -1,56 +0,0 @@ +-// Copyright 2024 Matt Borland +-// Distributed under the Boost Software License, Version 1.0. +-// https://www.boost.org/LICENSE_1_0.txt +- +-#ifndef BOOST_GENERATE_NAN_HPP +-#define BOOST_GENERATE_NAN_HPP +- +-#include +-#include +- +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 +- +-namespace boost { +-namespace charconv { +-namespace detail { +- +-struct words +-{ +-#if BOOST_CHARCONV_ENDIAN_LITTLE_BYTE +- std::uint64_t lo; +- std::uint64_t hi; +-#else +- std::uint64_t hi; +- std::uint64_t lo; +-#endif +-}; +- +-inline __float128 nans BOOST_PREVENT_MACRO_SUBSTITUTION () noexcept +-{ +- words bits; +- bits.hi = UINT64_C(0x7FFF400000000000); +- bits.lo = UINT64_C(0); +- +- __float128 return_val; +- std::memcpy(&return_val, &bits, sizeof(__float128)); +- return return_val; +-} +- +-inline __float128 nanq BOOST_PREVENT_MACRO_SUBSTITUTION () noexcept +-{ +- words bits; +- bits.hi = UINT64_C(0x7FFF800000000000); +- bits.lo = UINT64_C(0); +- +- __float128 return_val; +- std::memcpy(&return_val, &bits, sizeof(__float128)); +- return return_val; +-} +- +-} //namespace detail +-} //namespace charconv +-} //namespace boost +- +-#endif +- +-#endif //BOOST_GENERATE_NAN_HPP +diff --git a/boost/charconv/detail/issignaling.hpp b/boost/charconv/detail/issignaling.hpp +index 5ff8a5d..865460e 100644 +--- a/boost/charconv/detail/issignaling.hpp ++++ b/boost/charconv/detail/issignaling.hpp +@@ -15,7 +15,7 @@ namespace boost { namespace charconv { namespace detail { + template + inline bool issignaling BOOST_PREVENT_MACRO_SUBSTITUTION (T x) noexcept; + +-#if BOOST_CHARCONV_LDBL_BITS == 128 || defined(BOOST_CHARCONV_HAS_FLOAT128) ++#if BOOST_CHARCONV_LDBL_BITS == 128 + + struct words128 + { +diff --git a/boost/charconv/detail/ryu/ryu_generic_128.hpp b/boost/charconv/detail/ryu/ryu_generic_128.hpp +index ad69202..9a04ef2 100644 +--- a/boost/charconv/detail/ryu/ryu_generic_128.hpp ++++ b/boost/charconv/detail/ryu/ryu_generic_128.hpp +@@ -662,7 +662,7 @@ static inline struct floating_decimal_128 long_double_to_fd128(long double d) no + return generic_binary_to_decimal(bits, 64, 15, true); + } + +-#else ++#elif BOOST_CHARCONV_LDBL_BITS == 128 + + static inline struct floating_decimal_128 long_double_to_fd128(long double d) noexcept + { +@@ -682,42 +682,6 @@ static inline struct floating_decimal_128 long_double_to_fd128(long double d) no + + #endif + +-#ifdef BOOST_HAS_FLOAT128 +- +-static inline struct floating_decimal_128 float128_to_fd128(__float128 d) noexcept +-{ +- #ifdef BOOST_CHARCONV_HAS_INT128 +- unsigned_128_type bits = 0; +- std::memcpy(&bits, &d, sizeof(__float128)); +- #else +- trivial_uint128 trivial_bits; +- std::memcpy(&trivial_bits, &d, sizeof(__float128)); +- unsigned_128_type bits {trivial_bits}; +- #endif +- +- return generic_binary_to_decimal(bits, 112, 15, false); +-} +- +-#endif +- +-#ifdef BOOST_CHARCONV_HAS_STDFLOAT128 +- +-static inline struct floating_decimal_128 stdfloat128_to_fd128(std::float128_t d) noexcept +-{ +- #ifdef BOOST_CHARCONV_HAS_INT128 +- unsigned_128_type bits = 0; +- std::memcpy(&bits, &d, sizeof(std::float128_t)); +- #else +- trivial_uint128 trivial_bits; +- std::memcpy(&trivial_bits, &d, sizeof(std::float128_t)); +- unsigned_128_type bits {trivial_bits}; +- #endif +- +- return generic_binary_to_decimal(bits, 112, 15, false); +-} +- +-#endif +- + }}}} // Namespaces + + #endif //BOOST_RYU_GENERIC_128_HPP +diff --git a/boost/charconv/from_chars.hpp b/boost/charconv/from_chars.hpp +index 459d4c8..50f911a 100644 +--- a/boost/charconv/from_chars.hpp ++++ b/boost/charconv/from_chars.hpp +@@ -141,7 +141,7 @@ BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const char* last, double& value, chars_format fmt = chars_format::general) noexcept; + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const char* last, long double& value, chars_format fmt = chars_format::general) noexcept; + +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 ++#ifdef BOOST_CHARCONV_HAS_QUADMATH + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const char* last, __float128& value, chars_format fmt = chars_format::general) noexcept; + #endif + +@@ -155,7 +155,7 @@ BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const + #ifdef BOOST_CHARCONV_HAS_FLOAT64 + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const char* last, std::float64_t& value, chars_format fmt = chars_format::general) noexcept; + #endif +-#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_FLOAT128) ++#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_QUADMATH) + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const char* last, std::float128_t& value, chars_format fmt = chars_format::general) noexcept; + #endif + #ifdef BOOST_CHARCONV_HAS_BRAINFLOAT16 +diff --git a/boost/charconv/limits.hpp b/boost/charconv/limits.hpp +index beac057..f62809f 100644 +--- a/boost/charconv/limits.hpp ++++ b/boost/charconv/limits.hpp +@@ -72,7 +72,7 @@ template struct limits + std::numeric_limits::max_digits10 + 3 + 2 + detail::exp_digits( std::numeric_limits::max_exponent10 ); // as above + }; + +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 ++#if defined(BOOST_CHARCONV_HAS_QUADMATH) + + template <> struct limits<__float128> + { +diff --git a/boost/charconv/to_chars.hpp b/boost/charconv/to_chars.hpp +index 3946e46..53f0c56 100644 +--- a/boost/charconv/to_chars.hpp ++++ b/boost/charconv/to_chars.hpp +@@ -91,7 +91,7 @@ BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, double val + BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, long double value, + chars_format fmt, int precision) noexcept; + +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 ++#ifdef BOOST_CHARCONV_HAS_QUADMATH + BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, __float128 value, + chars_format fmt = chars_format::general) noexcept; + +@@ -120,7 +120,7 @@ BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, std::float + BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, std::float64_t value, + chars_format fmt, int precision) noexcept; + #endif +-#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_FLOAT128) ++#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_QUADMATH) + BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, std::float128_t value, + chars_format fmt = chars_format::general) noexcept; + +diff --git a/libs/charconv/src/from_chars.cpp b/libs/charconv/src/from_chars.cpp +index 4fe8829..ec8d741 100644 +--- a/libs/charconv/src/from_chars.cpp ++++ b/libs/charconv/src/from_chars.cpp +@@ -11,11 +11,11 @@ + # define NO_WARN_MBCS_MFC_DEPRECATION + #endif + ++#include "float128_impl.hpp" + #include "from_chars_float_impl.hpp" + #include + #include + #include +-#include + #include + #include + #include +@@ -50,7 +50,7 @@ boost::charconv::from_chars_result boost::charconv::from_chars_erange(const char + return boost::charconv::detail::from_chars_float_impl(first, last, value, fmt); + } + +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 ++#ifdef BOOST_CHARCONV_HAS_QUADMATH + boost::charconv::from_chars_result boost::charconv::from_chars_erange(const char* first, const char* last, __float128& value, boost::charconv::chars_format fmt) noexcept + { + bool sign {}; +@@ -271,7 +271,7 @@ boost::charconv::from_chars_result boost::charconv::from_chars_erange(const char + return r; + } + +-#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_FLOAT128) ++#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_QUADMATH) + boost::charconv::from_chars_result boost::charconv::from_chars_erange(const char* first, const char* last, std::float128_t& value, boost::charconv::chars_format fmt) noexcept + { + static_assert(sizeof(__float128) == sizeof(std::float128_t)); +@@ -304,7 +304,7 @@ boost::charconv::from_chars_result boost::charconv::from_chars_erange(boost::cor + return boost::charconv::from_chars_erange(sv.data(), sv.data() + sv.size(), value, fmt); + } + +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 ++#ifdef BOOST_CHARCONV_HAS_QUADMATH + boost::charconv::from_chars_result boost::charconv::from_chars_erange(boost::core::string_view sv, __float128& value, boost::charconv::chars_format fmt) noexcept + { + return boost::charconv::from_chars_erange(sv.data(), sv.data() + sv.size(), value, fmt); +@@ -330,7 +330,7 @@ boost::charconv::from_chars_result boost::charconv::from_chars_erange(boost::cor + return boost::charconv::from_chars_erange(sv.data(), sv.data() + sv.size(), value, fmt); + } + #endif +-#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_FLOAT128) ++#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_QUADMATH) + boost::charconv::from_chars_result boost::charconv::from_chars_erange(boost::core::string_view sv, std::float128_t& value, boost::charconv::chars_format fmt) noexcept + { + return boost::charconv::from_chars_erange(sv.data(), sv.data() + sv.size(), value, fmt); +@@ -377,7 +377,7 @@ boost::charconv::from_chars_result boost::charconv::from_chars(const char* first + return from_chars_strict_impl(first, last, value, fmt); + } + +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 ++#ifdef BOOST_CHARCONV_HAS_QUADMATH + boost::charconv::from_chars_result boost::charconv::from_chars(const char* first, const char* last, __float128& value, boost::charconv::chars_format fmt) noexcept + { + return from_chars_strict_impl(first, last, value, fmt); +@@ -405,7 +405,7 @@ boost::charconv::from_chars_result boost::charconv::from_chars(const char* first + } + #endif + +-#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_FLOAT128) ++#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_QUADMATH) + boost::charconv::from_chars_result boost::charconv::from_chars(const char* first, const char* last, std::float128_t& value, boost::charconv::chars_format fmt) noexcept + { + return from_chars_strict_impl(first, last, value, fmt); +@@ -434,7 +434,7 @@ boost::charconv::from_chars_result boost::charconv::from_chars(boost::core::stri + return from_chars_strict_impl(sv.data(), sv.data() + sv.size(), value, fmt); + } + +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 ++#ifdef BOOST_CHARCONV_HAS_QUADMATH + boost::charconv::from_chars_result boost::charconv::from_chars(boost::core::string_view sv, __float128& value, boost::charconv::chars_format fmt) noexcept + { + return from_chars_strict_impl(sv.data(), sv.data() + sv.size(), value, fmt); +@@ -462,7 +462,7 @@ boost::charconv::from_chars_result boost::charconv::from_chars(boost::core::stri + } + #endif + +-#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_FLOAT128) ++#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_QUADMATH) + boost::charconv::from_chars_result boost::charconv::from_chars(boost::core::string_view sv, std::float128_t& value, boost::charconv::chars_format fmt) noexcept + { + return from_chars_strict_impl(sv.data(), sv.data() + sv.size(), value, fmt); +diff --git a/libs/charconv/src/to_chars.cpp b/libs/charconv/src/to_chars.cpp +index 0293126..38ccf19 100644 +--- a/libs/charconv/src/to_chars.cpp ++++ b/libs/charconv/src/to_chars.cpp +@@ -4,6 +4,7 @@ + // Distributed under the Boost Software License, Version 1.0. + // https://www.boost.org/LICENSE_1_0.txt + ++#include "float128_impl.hpp" + #include "to_chars_float_impl.hpp" + #include + #include +@@ -660,7 +661,7 @@ boost::charconv::to_chars_result boost::charconv::to_chars( char* first, char* l + + #endif + +-#ifdef BOOST_CHARCONV_HAS_FLOAT128 ++#ifdef BOOST_CHARCONV_HAS_QUADMATH + + boost::charconv::to_chars_result boost::charconv::to_chars(char* first, char* last, __float128 value, boost::charconv::chars_format fmt) noexcept + { +@@ -747,7 +748,7 @@ boost::charconv::to_chars_result boost::charconv::to_chars(char* first, char* la + } + #endif + +-#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_FLOAT128) ++#if defined(BOOST_CHARCONV_HAS_STDFLOAT128) && defined(BOOST_CHARCONV_HAS_QUADMATH) + + boost::charconv::to_chars_result boost::charconv::to_chars(char* first, char* last, std::float128_t value, + boost::charconv::chars_format fmt) noexcept +diff --git a/libs/charconv/src/to_chars_float_impl.hpp b/libs/charconv/src/to_chars_float_impl.hpp +index 3db4567..2ae90bf 100644 +--- a/libs/charconv/src/to_chars_float_impl.hpp ++++ b/libs/charconv/src/to_chars_float_impl.hpp +@@ -7,6 +7,7 @@ + #ifndef BOOST_CHARCONV_DETAIL_TO_CHARS_FLOAT_IMPL_HPP + #define BOOST_CHARCONV_DETAIL_TO_CHARS_FLOAT_IMPL_HPP + ++#include "float128_impl.hpp" + #include + #include + #include +@@ -38,7 +39,7 @@ + #include + #endif + +-#if (BOOST_CHARCONV_LDBL_BITS == 80 || BOOST_CHARCONV_LDBL_BITS == 128) || defined(BOOST_CHARCONV_HAS_FLOAT128) ++#if (BOOST_CHARCONV_LDBL_BITS == 80 || BOOST_CHARCONV_LDBL_BITS == 128) + # include + # include + #endif +@@ -274,13 +274,17 @@ to_chars_result to_chars_hex(char* first, char* last, Real value, int precision) + typename std::conditional::value, ieee754_binary32, + typename std::conditional::value, ieee754_binary64, + #ifdef BOOST_CHARCONV_HAS_FLOAT128 +- typename std::conditional::value || BOOST_CHARCONV_LDBL_BITS == 128, ieee754_binary128, ieee754_binary80>::type +- #elif BOOST_CHARCONV_LDBL_BITS == 128 +- ieee754_binary128 +- #elif BOOST_CHARCONV_LDBL_BITS == 80 +- ieee754_binary80 +- #else +- ieee754_binary64 ++ typename std::conditional::value, ieee754_binary128, ++ #endif ++ #if BOOST_CHARCONV_LDBL_BITS == 128 ++ ieee754_binary128 ++ #elif BOOST_CHARCONV_LDBL_BITS == 80 ++ ieee754_binary80 ++ #else ++ ieee754_binary64 ++ #endif ++ #ifdef BOOST_CHARCONV_HAS_FLOAT128 ++ >::type + #endif + >::type>::type + #ifdef BOOST_CHARCONV_HAS_FLOAT16 + +diff --git a/libs/charconv/src/float128_impl.hpp b/libs/charconv/src/float128_impl.hpp +new file mode 100644 +index 0000000..e6b2261 +--- /dev/null ++++ b/libs/charconv/src/float128_impl.hpp +@@ -0,0 +1,359 @@ ++// Copyright 2024 Matt Borland ++// Distributed under the Boost Software License, Version 1.0. ++// https://www.boost.org/LICENSE_1_0.txt ++ ++#ifndef BOOST_CHARCONV_FLOAT128_IMPL_HPP ++#define BOOST_CHARCONV_FLOAT128_IMPL_HPP ++ ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++ ++// Only add in float128 support if the build system says it can ++#ifdef BOOST_CHARCONV_HAS_QUADMATH ++ ++#include ++ ++#define BOOST_CHARCONV_HAS_FLOAT128 ++ ++namespace boost { ++namespace charconv { ++ ++namespace detail { ++ ++// -------------------------------------------------------------------------------------------------------------------- ++// Ryu ++// -------------------------------------------------------------------------------------------------------------------- ++ ++ ++namespace ryu { ++ ++inline struct floating_decimal_128 float128_to_fd128(__float128 d) noexcept ++{ ++#ifdef BOOST_CHARCONV_HAS_INT128 ++ unsigned_128_type bits = 0; ++ std::memcpy(&bits, &d, sizeof(__float128)); ++#else ++ trivial_uint128 trivial_bits; ++ std::memcpy(&trivial_bits, &d, sizeof(__float128)); ++ unsigned_128_type bits {trivial_bits}; ++#endif ++ ++ return generic_binary_to_decimal(bits, 112, 15, false); ++} ++ ++# ifdef BOOST_CHARCONV_HAS_STDFLOAT128 ++ ++inline struct floating_decimal_128 stdfloat128_to_fd128(std::float128_t d) noexcept ++{ ++#ifdef BOOST_CHARCONV_HAS_INT128 ++ unsigned_128_type bits = 0; ++ std::memcpy(&bits, &d, sizeof(std::float128_t)); ++#else ++ trivial_uint128 trivial_bits; ++ std::memcpy(&trivial_bits, &d, sizeof(std::float128_t)); ++ unsigned_128_type bits {trivial_bits}; ++#endif ++ ++ return generic_binary_to_decimal(bits, 112, 15, false); ++} ++ ++# endif ++ ++} // namespace ryu ++ ++// -------------------------------------------------------------------------------------------------------------------- ++// fast_float ++// -------------------------------------------------------------------------------------------------------------------- ++ ++static constexpr __float128 powers_of_tenq[] = { ++ 1e0Q, 1e1Q, 1e2Q, 1e3Q, 1e4Q, 1e5Q, 1e6Q, ++ 1e7Q, 1e8Q, 1e9Q, 1e10Q, 1e11Q, 1e12Q, 1e13Q, ++ 1e14Q, 1e15Q, 1e16Q, 1e17Q, 1e18Q, 1e19Q, 1e20Q, ++ 1e21Q, 1e22Q, 1e23Q, 1e24Q, 1e25Q, 1e26Q, 1e27Q, ++ 1e28Q, 1e29Q, 1e30Q, 1e31Q, 1e32Q, 1e33Q, 1e34Q, ++ 1e35Q, 1e36Q, 1e37Q, 1e38Q, 1e39Q, 1e40Q, 1e41Q, ++ 1e42Q, 1e43Q, 1e44Q, 1e45Q, 1e46Q, 1e47Q, 1e48Q, ++ 1e49Q, 1e50Q, 1e51Q, 1e52Q, 1e53Q, 1e54Q, 1e55Q ++}; ++ ++template ++inline __float128 to_float128(Unsigned_Integer w) noexcept ++{ ++ return static_cast<__float128>(w); ++} ++ ++template <> ++inline __float128 to_float128(uint128 w) noexcept ++{ ++ return ldexp(static_cast<__float128>(w.high), 64) + static_cast<__float128>(w.low); ++} ++ ++template ++inline __float128 fast_path_float128(std::int64_t q, Unsigned_Integer w, bool negative, ArrayPtr table) noexcept ++{ ++ // The general idea is as follows. ++ // if 0 <= s <= 2^64 and if 10^0 <= p <= 10^27 ++ // Both s and p can be represented exactly ++ // because of this s*p and s/p will produce ++ // correctly rounded values ++ ++ auto ld = to_float128(w); ++ ++ if (q < 0) ++ { ++ ld /= table[-q]; ++ } ++ else ++ { ++ ld *= table[q]; ++ } ++ ++ if (negative) ++ { ++ ld = -ld; ++ } ++ ++ return ld; ++} ++ ++template ++inline __float128 compute_float128(std::int64_t q, Unsigned_Integer w, bool negative, std::errc& success) noexcept ++{ ++ // GLIBC uses 2^-16444 but MPFR uses 2^-16445 as the smallest subnormal value for 80 bit ++ // 39 is the max number of digits in an uint128_t ++ static constexpr auto smallest_power = -4951 - 39; ++ static constexpr auto largest_power = 4932; ++ ++ if (-55 <= q && q <= 48 && w <= static_cast(1) << 113) ++ { ++ success = std::errc(); ++ return fast_path_float128(q, w, negative, powers_of_tenq); ++ } ++ ++ if (w == 0) ++ { ++ success = std::errc(); ++ return negative ? -0.0Q : 0.0Q; ++ } ++ else if (q > largest_power) ++ { ++ success = std::errc::result_out_of_range; ++ return negative ? -HUGE_VALQ : HUGE_VALQ; ++ } ++ else if (q < smallest_power) ++ { ++ success = std::errc::result_out_of_range; ++ return negative ? -0.0Q : 0.0Q; ++ } ++ ++ success = std::errc::not_supported; ++ return 0; ++} ++ ++// -------------------------------------------------------------------------------------------------------------------- ++// fallback printf ++// -------------------------------------------------------------------------------------------------------------------- ++ ++template <> ++inline to_chars_result to_chars_printf_impl<__float128>(char* first, char* last, __float128 value, chars_format fmt, int precision) ++{ ++ // v % + . + num_digits(INT_MAX) + specifier + null terminator ++ // 1 + 1 + 10 + 1 + 1 ++ char format[14] {}; ++ std::memcpy(format, "%", 1); // NOLINT : No null terminator is purposeful ++ std::size_t pos = 1; ++ ++ // precision of -1 is unspecified ++ if (precision != -1 && fmt != chars_format::fixed) ++ { ++ format[pos] = '.'; ++ ++pos; ++ const auto unsigned_precision = static_cast(precision); ++ if (unsigned_precision < 10) ++ { ++ boost::charconv::detail::print_1_digit(unsigned_precision, format + pos); ++ ++pos; ++ } ++ else if (unsigned_precision < 100) ++ { ++ boost::charconv::detail::print_2_digits(unsigned_precision, format + pos); ++ pos += 2; ++ } ++ else ++ { ++ boost::charconv::detail::to_chars_int(format + pos, format + sizeof(format), precision); ++ pos = std::strlen(format); ++ } ++ } ++ else if (fmt == chars_format::fixed) ++ { ++ // Force 0 decimal places ++ std::memcpy(format + pos, ".0", 2); // NOLINT : No null terminator is purposeful ++ pos += 2; ++ } ++ ++ // Add the type identifier ++ format[pos] = 'Q'; ++ ++pos; ++ ++ // Add the format character ++ switch (fmt) ++ { ++ case boost::charconv::chars_format::general: ++ format[pos] = 'g'; ++ break; ++ ++ case boost::charconv::chars_format::scientific: ++ format[pos] = 'e'; ++ break; ++ ++ case boost::charconv::chars_format::fixed: ++ format[pos] = 'f'; ++ break; ++ ++ case boost::charconv::chars_format::hex: ++ format[pos] = 'a'; ++ break; ++ } ++ ++ const auto rv = quadmath_snprintf(first, static_cast(last - first), format, value); ++ ++ if (rv <= 0) ++ { ++ return {last, static_cast(errno)}; ++ } ++ ++ return {first + rv, std::errc()}; ++} ++ ++// -------------------------------------------------------------------------------------------------------------------- ++// fallback strtod ++// -------------------------------------------------------------------------------------------------------------------- ++ ++template <> ++inline from_chars_result from_chars_strtod_impl<__float128>(const char* first, const char* last, __float128& value, char* buffer) noexcept ++{ ++ // For strto(f/d) ++ // Floating point value corresponding to the contents of str on success. ++ // If the converted value falls out of range of corresponding return type, range error occurs and HUGE_VAL, HUGE_VALF or HUGE_VALL is returned. ++ // If no conversion can be performed, 0 is returned and *str_end is set to str. ++ ++ std::memcpy(buffer, first, static_cast(last - first)); ++ buffer[last - first] = '\0'; ++ convert_string_locale(buffer); ++ ++ char* str_end; ++ __float128 return_value {}; ++ from_chars_result r {nullptr, std::errc()}; ++ ++ return_value = strtoflt128(buffer, &str_end); ++ ++ if (return_value == HUGE_VALQ) ++ { ++ r = {last, std::errc::result_out_of_range}; ++ } ++ ++ // Since this is a fallback routine we are safe to check for 0 ++ if (return_value == 0 && str_end == last) ++ { ++ r = {first, std::errc::result_out_of_range}; ++ } ++ ++ if (r) ++ { ++ value = return_value; ++ r = {first + (str_end - buffer), std::errc()}; ++ } ++ ++ return r; ++} ++ ++template <> ++inline from_chars_result from_chars_strtod<__float128>(const char* first, const char* last, __float128& value) noexcept ++{ ++ if (last - first < 1024) ++ { ++ char buffer[1024]; ++ return from_chars_strtod_impl(first, last, value, buffer); ++ } ++ ++ // If the string to be parsed does not fit into the 1024 byte static buffer than we have to allocate a buffer. ++ // malloc is used here because it does not throw on allocation failure. ++ ++ char* buffer = static_cast(std::malloc(static_cast(last - first + 1))); ++ if (buffer == nullptr) ++ { ++ return {first, std::errc::not_enough_memory}; ++ } ++ ++ auto r = from_chars_strtod_impl(first, last, value, buffer); ++ std::free(buffer); ++ ++ return r; ++} ++ ++// -------------------------------------------------------------------------------------------------------------------- ++// nans ++// -------------------------------------------------------------------------------------------------------------------- ++ ++struct words ++{ ++#if BOOST_CHARCONV_ENDIAN_LITTLE_BYTE ++ std::uint64_t lo; ++ std::uint64_t hi; ++#else ++ std::uint64_t hi; ++ std::uint64_t lo; ++#endif ++}; ++ ++inline __float128 nans BOOST_PREVENT_MACRO_SUBSTITUTION () noexcept ++{ ++ words bits; ++ bits.hi = UINT64_C(0x7FFF400000000000); ++ bits.lo = UINT64_C(0); ++ ++ __float128 return_val; ++ std::memcpy(&return_val, &bits, sizeof(__float128)); ++ return return_val; ++} ++ ++inline __float128 nanq BOOST_PREVENT_MACRO_SUBSTITUTION () noexcept ++{ ++ words bits; ++ bits.hi = UINT64_C(0x7FFF800000000000); ++ bits.lo = UINT64_C(0); ++ ++ __float128 return_val; ++ std::memcpy(&return_val, &bits, sizeof(__float128)); ++ return return_val; ++} ++ ++template <> ++inline bool issignaling<__float128> BOOST_PREVENT_MACRO_SUBSTITUTION (__float128 x) noexcept ++{ ++ words bits; ++ std::memcpy(&bits, &x, sizeof(__float128)); ++ ++ std::uint64_t hi_word = bits.hi; ++ std::uint64_t lo_word = bits.lo; ++ ++ hi_word ^= UINT64_C(0x0000800000000000); ++ hi_word |= (lo_word | -lo_word) >> 63; ++ return ((hi_word & INT64_MAX) > UINT64_C(0x7FFF800000000000)); ++} ++ ++} //namespace detail ++} //namespace charconv ++} //namespace boost ++ ++#endif //BOOST_CHARCONV_HAS_FLOAT128 ++ ++#endif //BOOST_CHARCONV_FLOAT128_IMPL_HPP +diff --git a/boost/charconv/detail/bit_layouts.hpp b/boost/charconv/detail/bit_layouts.hpp +index 498b5bb8..c163ce06 100644 +--- a/boost/charconv/detail/bit_layouts.hpp ++++ b/boost/charconv/detail/bit_layouts.hpp +@@ -126,7 +126,8 @@ struct IEEEl2bits + #define BOOST_CHARCONV_LDBL_BITS 64 + + #else // Unsupported long double representation +-# define BOOST_MATH_UNSUPPORTED_LONG_DOUBLE ++# define BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE ++# define BOOST_CHARCONV_LDBL_BITS -1 + #endif + + struct IEEEbinary128 +diff --git a/boost/charconv/from_chars.hpp b/boost/charconv/from_chars.hpp +index 50f911ae..10e4cb4a 100644 +--- a/boost/charconv/from_chars.hpp ++++ b/boost/charconv/from_chars.hpp +@@ -139,7 +139,10 @@ BOOST_CHARCONV_GCC5_CONSTEXPR from_chars_result from_chars(boost::core::string_v + + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const char* last, float& value, chars_format fmt = chars_format::general) noexcept; + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const char* last, double& value, chars_format fmt = chars_format::general) noexcept; ++ ++#ifndef BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const char* last, long double& value, chars_format fmt = chars_format::general) noexcept; ++#endif + + #ifdef BOOST_CHARCONV_HAS_QUADMATH + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const char* last, __float128& value, chars_format fmt = chars_format::general) noexcept; +@@ -164,7 +167,10 @@ BOOST_CHARCONV_DECL from_chars_result from_chars_erange(const char* first, const + + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(boost::core::string_view sv, float& value, chars_format fmt = chars_format::general) noexcept; + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(boost::core::string_view sv, double& value, chars_format fmt = chars_format::general) noexcept; ++ ++#ifndef BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(boost::core::string_view sv, long double& value, chars_format fmt = chars_format::general) noexcept; ++#endif + + #ifdef BOOST_CHARCONV_HAS_FLOAT128 + BOOST_CHARCONV_DECL from_chars_result from_chars_erange(boost::core::string_view sv, __float128& value, chars_format fmt = chars_format::general) noexcept; +@@ -193,7 +199,10 @@ BOOST_CHARCONV_DECL from_chars_result from_chars_erange(boost::core::string_view + + BOOST_CHARCONV_DECL from_chars_result from_chars(const char* first, const char* last, float& value, chars_format fmt = chars_format::general) noexcept; + BOOST_CHARCONV_DECL from_chars_result from_chars(const char* first, const char* last, double& value, chars_format fmt = chars_format::general) noexcept; ++ ++#ifndef BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE + BOOST_CHARCONV_DECL from_chars_result from_chars(const char* first, const char* last, long double& value, chars_format fmt = chars_format::general) noexcept; ++#endif + + #ifdef BOOST_CHARCONV_HAS_FLOAT128 + BOOST_CHARCONV_DECL from_chars_result from_chars(const char* first, const char* last, __float128& value, chars_format fmt = chars_format::general) noexcept; +@@ -216,7 +225,10 @@ BOOST_CHARCONV_DECL from_chars_result from_chars(const char* first, const char* + + BOOST_CHARCONV_DECL from_chars_result from_chars(boost::core::string_view sv, float& value, chars_format fmt = chars_format::general) noexcept; + BOOST_CHARCONV_DECL from_chars_result from_chars(boost::core::string_view sv, double& value, chars_format fmt = chars_format::general) noexcept; ++ ++#ifndef BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE + BOOST_CHARCONV_DECL from_chars_result from_chars(boost::core::string_view sv, long double& value, chars_format fmt = chars_format::general) noexcept; ++#endif + + #ifdef BOOST_CHARCONV_HAS_FLOAT128 + BOOST_CHARCONV_DECL from_chars_result from_chars(boost::core::string_view sv, __float128& value, chars_format fmt = chars_format::general) noexcept; +diff --git a/boost/charconv/to_chars.hpp b/boost/charconv/to_chars.hpp +index 53f0c56e..7192fda5 100644 +--- a/boost/charconv/to_chars.hpp ++++ b/boost/charconv/to_chars.hpp +@@ -81,15 +81,21 @@ BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, float valu + chars_format fmt = chars_format::general) noexcept; + BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, double value, + chars_format fmt = chars_format::general) noexcept; ++ ++#ifndef BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE + BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, long double value, + chars_format fmt = chars_format::general) noexcept; ++#endif + + BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, float value, + chars_format fmt, int precision) noexcept; + BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, double value, + chars_format fmt, int precision) noexcept; ++ ++#ifndef BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE + BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, long double value, + chars_format fmt, int precision) noexcept; ++#endif + + #ifdef BOOST_CHARCONV_HAS_QUADMATH + BOOST_CHARCONV_DECL to_chars_result to_chars(char* first, char* last, __float128 value, +diff --git a/libs/charconv/src/from_chars.cpp b/libs/charconv/src/from_chars.cpp +index bbfaff29..2c01e73c 100644 +--- a/libs/charconv/src/from_chars.cpp ++++ b/libs/charconv/src/from_chars.cpp +@@ -229,7 +229,7 @@ boost::charconv::from_chars_result boost::charconv::from_chars_erange(const char + return r; + } + +-#else ++#elif !defined(BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE) + + boost::charconv::from_chars_result boost::charconv::from_chars_erange(const char* first, const char* last, long double& value, boost::charconv::chars_format fmt) noexcept + { +@@ -323,10 +323,12 @@ boost::charconv::from_chars_result boost::charconv::from_chars_erange(boost::cor + return boost::charconv::from_chars_erange(sv.data(), sv.data() + sv.size(), value, fmt); + } + ++#ifndef BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE + boost::charconv::from_chars_result boost::charconv::from_chars_erange(boost::core::string_view sv, long double& value, boost::charconv::chars_format fmt) noexcept + { + return boost::charconv::from_chars_erange(sv.data(), sv.data() + sv.size(), value, fmt); + } ++#endif + + #ifdef BOOST_CHARCONV_HAS_QUADMATH + boost::charconv::from_chars_result boost::charconv::from_chars_erange(boost::core::string_view sv, __float128& value, boost::charconv::chars_format fmt) noexcept +@@ -396,10 +398,12 @@ boost::charconv::from_chars_result boost::charconv::from_chars(const char* first + return from_chars_strict_impl(first, last, value, fmt); + } + ++#ifndef BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE + boost::charconv::from_chars_result boost::charconv::from_chars(const char* first, const char* last, long double& value, boost::charconv::chars_format fmt) noexcept + { + return from_chars_strict_impl(first, last, value, fmt); + } ++#endif + + #ifdef BOOST_CHARCONV_HAS_QUADMATH + boost::charconv::from_chars_result boost::charconv::from_chars(const char* first, const char* last, __float128& value, boost::charconv::chars_format fmt) noexcept +@@ -453,10 +457,12 @@ boost::charconv::from_chars_result boost::charconv::from_chars(boost::core::stri + return from_chars_strict_impl(sv.data(), sv.data() + sv.size(), value, fmt); + } + ++#ifndef BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE + boost::charconv::from_chars_result boost::charconv::from_chars(boost::core::string_view sv, long double& value, boost::charconv::chars_format fmt) noexcept + { + return from_chars_strict_impl(sv.data(), sv.data() + sv.size(), value, fmt); + } ++#endif + + #ifdef BOOST_CHARCONV_HAS_QUADMATH + boost::charconv::from_chars_result boost::charconv::from_chars(boost::core::string_view sv, __float128& value, boost::charconv::chars_format fmt) noexcept +diff --git a/libs/charconv/src/to_chars.cpp b/libs/charconv/src/to_chars.cpp +index 06be7e46..035a44a5 100644 +--- a/libs/charconv/src/to_chars.cpp ++++ b/libs/charconv/src/to_chars.cpp +@@ -602,7 +602,7 @@ boost::charconv::to_chars_result boost::charconv::to_chars(char* first, char* la + return boost::charconv::detail::to_chars_float_impl(first, last, static_cast(value), fmt, precision); + } + +-#elif (BOOST_CHARCONV_LDBL_BITS == 80 || BOOST_CHARCONV_LDBL_BITS == 128) ++#elif !defined(BOOST_CHARCONV_UNSUPPORTED_LONG_DOUBLE) + + boost::charconv::to_chars_result boost::charconv::to_chars(char* first, char* last, long double value, + boost::charconv::chars_format fmt) noexcept +@@ -621,44 +621,6 @@ boost::charconv::to_chars_result boost::charconv::to_chars(char* first, char* la + return boost::charconv::detail::to_chars_float_impl(first, last, value, fmt, precision); + } + +-#else +- +-boost::charconv::to_chars_result boost::charconv::to_chars( char* first, char* last, long double value, +- boost::charconv::chars_format fmt, int precision) noexcept +-{ +- if (std::isnan(value)) +- { +- bool is_negative = false; +- if (std::signbit(value)) +- { +- is_negative = true; +- *first++ = '-'; +- } +- +- if (issignaling(value)) +- { +- std::memcpy(first, "nan(snan)", 9); +- return { first + 9 + static_cast(is_negative), std::errc() }; +- } +- else +- { +- if (is_negative) +- { +- std::memcpy(first, "nan(ind)", 8); +- return { first + 9, std::errc() }; +- } +- else +- { +- std::memcpy(first, "nan", 3); +- return { first + 3, std::errc() }; +- } +- } +- } +- +- // Fallback to printf +- return boost::charconv::detail::to_chars_printf_impl(first, last, value, fmt, precision); +-} +- + #endif + + #ifdef BOOST_CHARCONV_HAS_QUADMATH From 00d346f497a58e26c54c100c4c564263649295a8 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Mon, 2 Dec 2024 14:52:13 +0100 Subject: [PATCH 140/414] added skip install data hook patch --- .../easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb index 5b1a57e3dfa..9466e971528 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb @@ -14,10 +14,12 @@ description = """Graphviz is open source graph visualization software. Graph vis toolchain = {'name': 'GCCcore', 'version': '13.3.0'} source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] +patches = ['%(name)s-8.1.0_skip-install-data-hook.patch'] sources = [SOURCELOWER_TAR_GZ] checksums = [ {'graphviz-12.2.0.tar.gz': '0063e501fa4642b55f4daf82820b2778bfb7dafa651a862ae5c9810efb8e2311'}, + {'Graphviz-8.1.0_skip-install-data-hook.patch': '834666f1b5a8eff35f30899419e322739d71a2936408b27c8ffb4423a99a38e1'}, ] builddependencies = [ From f84dbf454771752441479037feccb3daf376f837 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 2 Dec 2024 16:19:47 +0100 Subject: [PATCH 141/414] Add easyconfig Cbc-2.10.11-foss-2023b.eb --- .../c/Cbc/Cbc-2.10.11-foss-2023b.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb new file mode 100644 index 00000000000..a1427ddab2f --- /dev/null +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb @@ -0,0 +1,63 @@ +easyblock = "ConfigureMake" + +name = 'Cbc' +version = '2.10.11' + +homepage = "https://github.com/coin-or/Cbc" +description = """Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming +solver written in C++. It can be used as a callable library or using a +stand-alone executable.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/Cbc/archive/refs/tags/releases'] +sources = ['%(version)s.tar.gz'] +checksums = ['1fb591dd88336fdaf096b8e42e46111e41671a5eb85d4ee36e45baff1678bd33'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.7'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.6.1', '-metis'), + ('CoinUtils', '2.11.10'), + ('Osi', '0.108.9'), + ('Clp', '1.17.9'), + ('Cgl', '0.60.8'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +# Use BLAS/LAPACK from toolchain +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +# Use METIS AND MUMPS from EB +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +# Disable GLPK, dependencies have to be built with it as well +configopts += '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' +# Use Cgl from EB +configopts += '--with-cgl-lib="-lCgl" ' +configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" From 92eef65869f4a92bffc754116f67f076ea981dc0 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 2 Dec 2024 16:31:50 +0100 Subject: [PATCH 142/414] Add easyconfig CoinUtils-2.11.10-GCC-13.2.0.eb --- .../c/Cbc/Cbc-2.10.11-foss-2023b.eb | 2 +- .../CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb | 36 +++++++++++++++++++ 2 files changed, 37 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb index a1427ddab2f..2fcdba53e06 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb @@ -17,7 +17,7 @@ checksums = ['1fb591dd88336fdaf096b8e42e46111e41671a5eb85d4ee36e45baff1678bd33'] builddependencies = [ ('Autotools', '20220317'), - ('Doxygen', '1.9.7'), + ('Doxygen', '1.9.8'), ('pkgconf', '1.9.5'), ] diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb new file mode 100644 index 00000000000..fd2c5b6a9f8 --- /dev/null +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CoinUtils' +version = '2.11.10' + +homepage = "https://github.com/coin-or/CoinUtils" +description = """CoinUtils (Coin-OR Utilities) is an open-source collection of classes and +functions that are generally useful to more than one COIN-OR project.""" + +source_urls = ['https://github.com/coin-or/CoinUtils/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['80c7c215262df8d6bd2ba171617c5df844445871e9891ec6372df12ccbe5bcfd'] + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.7'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['lib/libCoinUtils.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" From a46799ecd19f8f516cb935aa076d8523ff00f9dd Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 2 Dec 2024 16:33:53 +0100 Subject: [PATCH 143/414] Add easyconfig Osi-0.108.9-GCC-13.2.0.eb --- .../o/Osi/Osi-0.108.9-GCC-13.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb new file mode 100644 index 00000000000..f7d1fdd77ad --- /dev/null +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Osi' +version = '0.108.9' + +homepage = "https://github.com/coin-or/Osi" +description = """Osi (Open Solver Interface) provides an abstract base class to a generic linear +programming (LP) solver, along with derived classes for specific solvers. Many +applications may be able to use the Osi to insulate themselves from a specific +LP solver. That is, programs written to the OSI standard may be linked to any +solver with an OSI interface and should produce correct results. The OSI has +been significantly extended compared to its first incarnation. Currently, the +OSI supports linear programming solvers and has rudimentary support for integer +programming.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/coin-or/Osi/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8b09802960d7d4fd9579b3e4320bfb36e7f8dca5e5094bf1f5edf1b7003f5562'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.7'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('CoinUtils', '2.11.10'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +# Disable GLPK because Osi requires GLPK<=4.48 +configopts = '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + +sanity_check_paths = { + 'files': ['lib/libOsi.%s' % SHLIB_EXT, 'lib/libOsiCommonTests.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" From c10313ab569034d4178f3de612665c824048f371 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 2 Dec 2024 16:35:43 +0100 Subject: [PATCH 144/414] Add easyconfig Clp-1.17.9-foss-2023b.eb --- .../c/Clp/Clp-1.17.9-foss-2023b.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb new file mode 100644 index 00000000000..11835580e1b --- /dev/null +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'Clp' +version = '1.17.9' + +homepage = "https://github.com/coin-or/Clp" +description = """Clp (Coin-or linear programming) is an open-source linear programming solver. +It is primarily meant to be used as a callable library, but a basic, +stand-alone executable version is also available.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/Clp/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b02109be54e2c9c6babc9480c242b2c3c7499368cfca8c0430f74782a694a49f'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.7'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.6.1', '-metis'), + ('CoinUtils', '2.11.10'), + ('Osi', '0.108.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +# Use BLAS/LAPACK from toolchain +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' + +# Use METIS AND MUMPS from EB +# --with-metis-lib is ignored +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh ' +configopts += '-lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' + +# Disable GLPK because Clp requires headers from its sources +configopts += '--without-glpk ' + +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' + +# Use Osi from EB +configopts += '--with-osi-lib="-lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Clp', 'ClpSolver', 'OsiClp']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" From 40c0430dbe71f768de10a160c863c0b2547f5327 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 2 Dec 2024 16:37:38 +0100 Subject: [PATCH 145/414] Add easyconfig Cgl-0.60.8-foss-2023b.eb --- .../c/Cgl/Cgl-0.60.8-foss-2023b.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb new file mode 100644 index 00000000000..7efb1695844 --- /dev/null +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb @@ -0,0 +1,50 @@ +easyblock = "ConfigureMake" + +name = 'Cgl' +version = '0.60.8' + +homepage = "https://github.com/coin-or/Cgl" +description = """The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that +can be used with other COIN-OR packages that make use of cuts, such as, among +others, the linear solver Clp or the mixed integer linear programming solvers +Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or +communicate with a solver. It does not directly call a solver.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/Cgl/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1482ba38afb783d124df8d5392337f79fdd507716e9f1fb6b98fc090acd1ad96'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.7'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('CoinUtils', '2.11.10'), + ('Osi', '0.108.9'), + ('Clp', '1.17.9'), +] + +# Use CoinUtils from EB +configopts = '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['lib/libCgl.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" From 3d93dd60b6c501d4337530fb6f56ed0f3d3fa395 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 2 Dec 2024 16:40:52 +0100 Subject: [PATCH 146/414] Upgrade Doxygen version in Cgl-0.60.8-foss-2023b.eb --- easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb index 7efb1695844..e003856df24 100644 --- a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb @@ -19,7 +19,7 @@ checksums = ['1482ba38afb783d124df8d5392337f79fdd507716e9f1fb6b98fc090acd1ad96'] builddependencies = [ ('Autotools', '20220317'), - ('Doxygen', '1.9.7'), + ('Doxygen', '1.9.8'), ('pkgconf', '1.9.5'), ] From 706e89e28293b00ca6429593cfe24983cb462331 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 2 Dec 2024 16:42:14 +0100 Subject: [PATCH 147/414] Upgrade pkgconf in Cgl-0.60.8-foss-2023b.eb --- easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb index e003856df24..275169c6992 100644 --- a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023b.eb @@ -20,7 +20,7 @@ checksums = ['1482ba38afb783d124df8d5392337f79fdd507716e9f1fb6b98fc090acd1ad96'] builddependencies = [ ('Autotools', '20220317'), ('Doxygen', '1.9.8'), - ('pkgconf', '1.9.5'), + ('pkgconf', '2.0.3'), ] dependencies = [ From d7e3e158296dff8dff0e075df43de1540ae7767c Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 2 Dec 2024 16:43:29 +0100 Subject: [PATCH 148/414] Upgrade Doxygen version in Clp-1.17.9-foss-2023b.eb --- easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb index 11835580e1b..8f96ff7547e 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb @@ -17,7 +17,7 @@ checksums = ['b02109be54e2c9c6babc9480c242b2c3c7499368cfca8c0430f74782a694a49f'] builddependencies = [ ('Autotools', '20220317'), - ('Doxygen', '1.9.7'), + ('Doxygen', '1.9.8'), ('pkgconf', '1.9.5'), ] From ee9b6521bddc6f4997630346adbc7c5603a3e7e1 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 2 Dec 2024 16:50:54 +0100 Subject: [PATCH 149/414] Upgrade Doxygen version in Osi-0.108.9-GCC-13.2.0.eb --- easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb index f7d1fdd77ad..7f3c753ed40 100644 --- a/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb @@ -21,7 +21,7 @@ checksums = ['8b09802960d7d4fd9579b3e4320bfb36e7f8dca5e5094bf1f5edf1b7003f5562'] builddependencies = [ ('Autotools', '20220317'), - ('Doxygen', '1.9.7'), + ('Doxygen', '1.9.8'), ('pkgconf', '1.9.5'), ] From 0c4a86e0ea16502467cbf096854330356a9fdcfa Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 2 Dec 2024 16:52:25 +0100 Subject: [PATCH 150/414] Upgrade pkgconf dependency in Osi-0.108.9-GCC-13.2.0.eb --- easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb index 7f3c753ed40..81f021f837c 100644 --- a/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb @@ -22,7 +22,7 @@ checksums = ['8b09802960d7d4fd9579b3e4320bfb36e7f8dca5e5094bf1f5edf1b7003f5562'] builddependencies = [ ('Autotools', '20220317'), ('Doxygen', '1.9.8'), - ('pkgconf', '1.9.5'), + ('pkgconf', '2.0.3'), ] dependencies = [ From f14f7244117166d4c655eec8fee9afe4d3ac7b65 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 2 Dec 2024 17:02:49 +0100 Subject: [PATCH 151/414] Upgrade Doxygen and pkgconf dependencies in CoinUtils-2.11.10-GCC-13.2.0.eb --- .../easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb index fd2c5b6a9f8..8d9e9c2a4f7 100644 --- a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb @@ -16,8 +16,8 @@ toolchain = {'name': 'GCC', 'version': '13.2.0'} builddependencies = [ ('Autotools', '20220317'), - ('Doxygen', '1.9.7'), - ('pkgconf', '1.9.5'), + ('Doxygen', '1.9.8'), + ('pkgconf', '2.0.3'), ] dependencies = [ From fe257410f8ab59670b5ee8ad0488adea246f20ed Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 2 Dec 2024 19:48:07 +0000 Subject: [PATCH 152/414] adding easyconfigs: VEP-113.3-GCC-13.3.0.eb --- .../easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb b/easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb new file mode 100644 index 00000000000..1996303d91d --- /dev/null +++ b/easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb @@ -0,0 +1,44 @@ +name = 'VEP' +version = '113.3' + +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': '13.3.0'} + +source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ee68013eb035e17129e8f69977f525ebdd8321e73b3164a7bda6e103e2d10beb'] + +dependencies = [ + ('Perl', '5.38.2'), + ('Archive-Zip', '1.68'), + ('DBD-mysql', '4.051'), + ('BioPerl', '1.7.8'), + ('Bio-DB-HTS', '3.01'), + # VEP requires Compress::Raw::Zlib >= 2.103 + ('Compress-Raw-Zlib', '2.213'), +] + +# To select all species use 'all' (but this was broken as of 2024.02.01 and species need to explicitly listed +# with comma separation, see https://github.com/Ensembl/ensembl-vep/issues/1364#issuecomment-1753080504) +species = 'cyprinus_carpio_carpio' + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", "") + +exts_list = [ + ('Bio::EnsEMBL::XS', '2.3.2', { + 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], + }), +] + +sanity_check_commands = ['vep --help'] + +moduleclass = 'bio' From 0d566e293293a1cdca989a0f47b74de8a90df6fc Mon Sep 17 00:00:00 2001 From: crivella Date: Tue, 3 Dec 2024 10:24:59 +0100 Subject: [PATCH 153/414] Added checksums for QE and patch --- .../QuantumESPRESSO-7.4-foss-2024a.eb | 20 +++++-------------- 1 file changed, 5 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb index 6caaf6e98cf..f017367700b 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb @@ -107,22 +107,12 @@ patches = [ 'sourcepath': '../' # Needed as patches are normally applied to the first `finalpath` directory }, ] -# Holding off checksum checks untill 5.0.x -# https://github.com/easybuilders/easybuild-framework/pull/4248 -# checksums = [ -# {'q-e-qe-7.4.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'}, -# {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'}, -# {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'}, -# {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'}, -# {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'}, -# {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'}, -# {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'}, -# {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'}, -# {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'}, -# ] +# Holding off git clone checksum checks untill 5.0.x +# See https://github.com/easybuilders/easybuild-framework/pull/4248 checksums = [ - None, None, - None, None, None, None, None, None, None, None + 'b15dcfe25f4fbf15ccd34c1194021e90996393478226e601d876f7dea481d104', + None, None, None, None, None, None, None, None, + '1f1686365fbf0cc56f634e072a92b3d336fe454348e514d0b4136d447f0d4923' ] builddependencies = [ From 8dcf4b13119211642750dab85fc5c513aede7107 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Tue, 3 Dec 2024 10:12:46 +0000 Subject: [PATCH 154/414] adding easyconfigs: dm-control-1.0.18-foss-2023a.eb and patches: labmaze-1.0.6_use-bazel-v6.patch --- .../dm-control-1.0.18-foss-2023a.eb | 53 +++++++++++++++++++ .../labmaze-1.0.6_use-bazel-v6.patch | 35 ++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/d/dm-control/dm-control-1.0.18-foss-2023a.eb create mode 100644 easybuild/easyconfigs/d/dm-control/labmaze-1.0.6_use-bazel-v6.patch diff --git a/easybuild/easyconfigs/d/dm-control/dm-control-1.0.18-foss-2023a.eb b/easybuild/easyconfigs/d/dm-control/dm-control-1.0.18-foss-2023a.eb new file mode 100644 index 00000000000..35e3e548fe8 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-control/dm-control-1.0.18-foss-2023a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'dm-control' +version = '1.0.18' + +homepage = 'https://github.com/deepmind/tree' +description = """ +DeepMind's software stack for physics-based simulation and Reinforcement Learning environments, using MuJoCo physics. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('Bazel', '6.3.1'), # labmaze +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('lxml', '4.9.2'), + ('dm-tree', '0.1.8'), + ('python-mujoco', '3.1.4'), + ('PyOpenGL', '3.1.7'), + ('h5py', '3.9.0'), # extras [h5py] + ('protobuf-python', '4.24.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('dm-env', '1.6', { + 'checksums': ['a436eb1c654c39e0c986a516cee218bea7140b510fceff63f97eb4fcff3d93de'], + }), + ('labmaze', '1.0.6', { + 'patches': ['labmaze-1.0.6_use-bazel-v6.patch'], + 'checksums': [ + {'labmaze-1.0.6.tar.gz': '2e8de7094042a77d6972f1965cf5c9e8f971f1b34d225752f343190a825ebe73'}, + {'labmaze-1.0.6_use-bazel-v6.patch': '7aea4376952f493d2c2da101ff408577b1f91ae7a957083659497b6926ee226e'}, + ], + }), + (name, version, { + 'sources': ['dm_control-%(version)s.tar.gz'], + 'use_pip_extras': 'h5py', + 'checksums': ['9dc825a7719e0386364417746dd85e5fe0a235f2597a0b13323407b273a3633e'], + }), +] + +sanity_pip_check = True + +options = {'modulename': 'tree'} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/d/dm-control/labmaze-1.0.6_use-bazel-v6.patch b/easybuild/easyconfigs/d/dm-control/labmaze-1.0.6_use-bazel-v6.patch new file mode 100644 index 00000000000..b8ac319cc40 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-control/labmaze-1.0.6_use-bazel-v6.patch @@ -0,0 +1,35 @@ +From 0db42e859462a3b04c14a0155253b0ca4b9b64c9 Mon Sep 17 00:00:00 2001 +From: Viktor Rehnberg +Date: Tue, 3 Dec 2024 09:54:22 +0000 +Subject: [PATCH] Migrate to Bazel v6 + +--- + bazel/BUILD | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/bazel/BUILD b/bazel/BUILD +index 05458d5..7075c8f 100644 +--- a/bazel/BUILD ++++ b/bazel/BUILD +@@ -24,15 +24,15 @@ licenses(["notice"]) + + config_setting( + name = "linux", +- constraint_values = ["@bazel_tools//platforms:linux"], ++ constraint_values = ["@platforms//os:linux"], + ) + + config_setting( + name = "apple", +- constraint_values = ["@bazel_tools//platforms:osx"], ++ constraint_values = ["@platforms//os:osx"], + ) + + config_setting( + name = "windows", +- constraint_values = ["@bazel_tools//platforms:windows"], ++ constraint_values = ["@platforms//os:windows"], + ) +-- +2.39.3 + From 1518f0593f992f0803ea261956335c29934f9e13 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 3 Dec 2024 12:12:08 +0100 Subject: [PATCH 155/414] adding easyconfigs: Fiji-2.14.0-Java-11.eb --- .../easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb new file mode 100644 index 00000000000..3a474015f21 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb @@ -0,0 +1,49 @@ +easyblock = 'PackedBinary' + +name = 'Fiji' +version = '2.14.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://fiji.sc/' +description = """Fiji is an image processing package—a 'batteries-included' distribution of + ImageJ, bundling a lot of plugins which facilitate scientific image analysis. +This release is based on ImageJ-2.1.0 and Fiji-2.1.1""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s'] +sources = ['%(namelower)s-%(version)s-nojre.zip'] +checksums = ['1dcf6efd7a2c99b70ab921bea3b9e7c74ef99acf35b9857199de7f9c424187db'] + +dependencies = [('Java', '11', '', SYSTEM)] + +postinstallcmds = [ + # Remove binaries for other platforms + 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}', + # Enable any update site (edit existing site with same parameters to enable it) + # Full list at https://imagej.github.io/list-of-update-sites/ + '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless' + ' --update edit-update-site "ImageScience" https://sites.imagej.net/ImageScience/', + '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless' + ' --update edit-update-site "3D ImageJ Suite" https://sites.imagej.net/Tboudier/', + '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless' + ' --update edit-update-site "ilastik" https://sites.imagej.net/Ilastik/', + # Add a new update site + # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' + # ' https://site.url/NewName/', + # Update the installation + '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless --update update', +] + +sanity_check_paths = { + 'files': ['ImageJ-linux64'], + 'dirs': [], +} + +modloadmsg = """ +Additional plugins can be installed in your $HOME/.plugins folder or requested to user support +Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless` +More information at https://imagej.net/Headless +""" + +moduleclass = 'vis' From 0bdc75d8bb9b0d4c5c426547ca0ddfd532870d75 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 3 Dec 2024 12:21:52 +0100 Subject: [PATCH 156/414] adding easyconfigs: BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb --- .../BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb | 91 +++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..c8ea0187e5a --- /dev/null +++ b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,91 @@ +easyblock = 'Tarball' + +name = 'BindCraft' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/martinpacesa/BindCraft' +description = """Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. + Select your target and let the script do the rest of the work and finish once you have enough designs to order!""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7'] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Seaborn', '0.13.2'), + ('tqdm', '4.66.1'), + ('OpenMM', '8.0.0', versionsuffix), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('PyRosetta', '4.release-387'), + ('jax', '0.4.25', versionsuffix), + ('dm-haiku', '0.0.12', versionsuffix), + ('dm-tree', '0.1.8'), + ('ml-collections', '0.1.1'), + ('Optax', '0.2.2', versionsuffix), + ('py3Dmol', '2.1.0'), + ('JupyterLab', '4.0.5'), + ('hatchling', '1.18.0'), + ('Flax', '0.8.4', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + # older version compatible with `jupyterlab-4.0.5` + ('notebook', '7.0.8', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['7f421b3fd46a17d91830e724b94e8e9ae922af152ebfd48b1e13ae4a07d8193c'], + }), + ('jupyter', '1.1.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['7a59533c22af65439b24bbe60373a4e95af8f16ac65a6c00820ad378e3f7cc83'], + }), + ('immutabledict', '4.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d728b2c2410d698d95e6200237feb50a695584d20289ad3379a439aa3d90baba'], + }), + ('colabdesign', '1.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8f556fb575d2bbef79fa1789698d55221f2cc51df38f2cc054f38cb6ecc08e27'], + }), +] + +fix_python_shebang_for = ['bindcraft.py'] + +postinstallcmds = ['chmod a+x %(installdir)s/bindcraft.py'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': ['', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': ['bindcraft.py'], + 'dirs': [], +} + +sanity_check_commands = ["bindcraft.py --help"] + +moduleclass = 'bio' From 49c1d81dfb1cbe9f131403b2f49b1800d2ec0adb Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 3 Dec 2024 12:32:24 +0100 Subject: [PATCH 157/414] dependency: Qt5 -> Qt6 --- .../easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb index 9466e971528..2ad5b88af1c 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-12.2.0-GCCcore-13.3.0.eb @@ -41,7 +41,7 @@ dependencies = [ ('libgd', '2.3.3'), ('Pango', '1.54.0'), ('Perl', '5.38.2'), - ('Qt5', '5.15.15'), + ('Qt6', '6.7.2'), ('Tcl', '8.6.14'), ('zlib', '1.3.1'), ('bzip2', '1.0.8'), From 4bb2db7bd8c83cb5fdf04700b5a1fd209b494cf5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 3 Dec 2024 13:19:39 +0100 Subject: [PATCH 158/414] adding easyconfigs: llama-cpp-python-0.3.2-gfbf-2023a.eb, llama-cpp-python-0.3.2-gfbf-2023a-CUDA-12.1.1.eb --- ...cpp-python-0.3.2-gfbf-2023a-CUDA-12.1.1.eb | 46 +++++++++++++++++++ .../llama-cpp-python-0.3.2-gfbf-2023a.eb | 44 ++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/l/llama-cpp-python/llama-cpp-python-0.3.2-gfbf-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/l/llama-cpp-python/llama-cpp-python-0.3.2-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/l/llama-cpp-python/llama-cpp-python-0.3.2-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/l/llama-cpp-python/llama-cpp-python-0.3.2-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..b2772ea22c5 --- /dev/null +++ b/easybuild/easyconfigs/l/llama-cpp-python/llama-cpp-python-0.3.2-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'llama-cpp-python' +version = '0.3.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://github.com/abetlen/llama-cpp-python/" +description = """The main goal of llama.cpp is to enable LLM inference with minimal setup and state-of-the-art +performance on a wide range of hardware - locally and in the cloud. Simple Python bindings.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('diskcache', '5.6.3', { + 'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'], + }), + ('huggingface-hub', '0.26.3', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['90e1fe62ffc26757a073aaad618422b899ccf9447c2bba8c902a90bef5b42e1d'], + }), + (name, version, { + 'modulename': 'llama_cpp', + 'preinstallopts': 'export CMAKE_ARGS="-DGGML_CUDA=on" && ', + 'source_tmpl': 'llama_cpp_python-%(version)s.tar.gz', + 'checksums': ['8fbf246a55a999f45015ed0d48f91b4ae04ae959827fac1cd6ac6ec65aed2e2f'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/llama-cpp-python/llama-cpp-python-0.3.2-gfbf-2023a.eb b/easybuild/easyconfigs/l/llama-cpp-python/llama-cpp-python-0.3.2-gfbf-2023a.eb new file mode 100644 index 00000000000..578011ea5c3 --- /dev/null +++ b/easybuild/easyconfigs/l/llama-cpp-python/llama-cpp-python-0.3.2-gfbf-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'llama-cpp-python' +version = '0.3.2' + +homepage = "https://github.com/abetlen/llama-cpp-python/" +description = """The main goal of llama.cpp is to enable LLM inference with minimal setup and state-of-the-art +performance on a wide range of hardware - locally and in the cloud. Simple Python bindings.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('diskcache', '5.6.3', { + 'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'], + }), + ('huggingface-hub', '0.26.3', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['90e1fe62ffc26757a073aaad618422b899ccf9447c2bba8c902a90bef5b42e1d'], + }), + (name, version, { + 'modulename': 'llama_cpp', + 'source_tmpl': 'llama_cpp_python-%(version)s.tar.gz', + 'preinstallopts': 'export CMAKE_ARGS="-DGGML_BLAS=ON -DGGML_BLAS_VENDOR=FlexiBLAS" && ', + 'checksums': ['8fbf246a55a999f45015ed0d48f91b4ae04ae959827fac1cd6ac6ec65aed2e2f'], + }), +] + +moduleclass = 'tools' From 65424b645abb47de445780849e685d7accac1145 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 3 Dec 2024 13:11:08 +0000 Subject: [PATCH 159/414] minor suggestions applied --- .../o/Optuna/Optuna-4.1.0-foss-2024a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb new file mode 100644 index 00000000000..7fd4f38dd54 --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '4.1.0' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), + ('SciPy-bundle', '2024.05'), + ('tqdm', '4.66.5'), + ('SQLAlchemy', '2.0.36'), + ('matplotlib', '3.9.2'), # optional + ('plotly.py', '5.24.1'), # optional + ('redis-py', '5.1.1'), # optional + ('scikit-learn', '1.5.2'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cmaes', '0.11.1', { # optional + 'checksums': ['cf71fa3679814723be771f2c9edd85f465b1bc1e409e1ad6d8a9e481efcd5160'], + }), + ('colorlog', '6.9.0', { + 'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'], + }), + ('%(namelower)s', version, { + 'use_pip_extras': 'optional', + 'checksums': ['844949f09e2a7353ab414e9cfd783cf0a647a65fc32a7236212ed6a37fe08973'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' From cf12fe4cff35319914a1042092113f559f9456e2 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Tue, 3 Dec 2024 14:12:06 +0100 Subject: [PATCH 160/414] Delete easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb --- .../o/Optuna/Optuna-4.0.0-foss-2024a.eb | 50 ------------------- 1 file changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb deleted file mode 100644 index f85fda01479..00000000000 --- a/easybuild/easyconfigs/o/Optuna/Optuna-4.0.0-foss-2024a.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Optuna' -version = '4.0.0' - -homepage = "https://optuna.org/" -description = """Optuna is an automatic hyperparameter optimization software framework, -particularly designed for machine learning. It features an imperative, -define-by-run style user API. Thanks to our define-by-run API, the code written -with Optuna enjoys high modularity, and the user of Optuna can dynamically -construct the search spaces for the hyperparameters.""" - - -toolchain = {'name': 'foss', 'version': '2024a'} - -dependencies = [ - ('Python', '3.12.3'), - ('PyYAML', '6.0.2'), - ('SciPy-bundle', '2024.05'), - ('tqdm', '4.66.5'), - ('matplotlib', '3.9.2'), # optional - ('plotly.py', '5.24.1'), # optional - ('redis-py', '5.1.1'), # optional - ('scikit-learn', '1.5.2'), # optional - ('SQLAlchemy', '2.0.36'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('cmaes', '0.11.1', { - 'checksums': ['cf71fa3679814723be771f2c9edd85f465b1bc1e409e1ad6d8a9e481efcd5160'], - }), - ('colorlog', '6.9.0', { - 'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'], - }), - ('%(namelower)s', version, { - 'use_pip_extras': 'optional', - 'checksums': ['844949f09e2a7353ab414e9cfd783cf0a647a65fc32a7236212ed6a37fe08973'], - }), -] - -sanity_check_paths = { - 'files': ['bin/optuna'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} -sanity_check_commands = [('optuna', '--help')] - -moduleclass = 'tools' From bcf1b4a7e8f7bcc35883bbe73d803f4d7eaea317 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 3 Dec 2024 13:17:54 +0000 Subject: [PATCH 161/414] fix hashes --- easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb index 7fd4f38dd54..283ec0fa9dc 100644 --- a/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb +++ b/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb @@ -29,15 +29,15 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('cmaes', '0.11.1', { # optional + ('cmaes', '0.11.1', { 'checksums': ['cf71fa3679814723be771f2c9edd85f465b1bc1e409e1ad6d8a9e481efcd5160'], }), ('colorlog', '6.9.0', { 'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'], }), - ('%(namelower)s', version, { + ('optuna', version, { 'use_pip_extras': 'optional', - 'checksums': ['844949f09e2a7353ab414e9cfd783cf0a647a65fc32a7236212ed6a37fe08973'], + 'checksums': ['b364e87a2038f9946c5e2770c130597538aac528b4a82c1cab5267f337ea7679'], }), ] From 806691f0b20469fb4f2d83fb4e3731bc3f26defe Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Tue, 3 Dec 2024 14:22:52 +0100 Subject: [PATCH 162/414] Update Optuna-4.1.0-foss-2024a.eb add optional back, got eaten by inject checksums --- easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb index 283ec0fa9dc..2a324cfcc5a 100644 --- a/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb +++ b/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb @@ -29,6 +29,7 @@ use_pip = True sanity_pip_check = True exts_list = [ + # optional ('cmaes', '0.11.1', { 'checksums': ['cf71fa3679814723be771f2c9edd85f465b1bc1e409e1ad6d8a9e481efcd5160'], }), From 17174c2e66a17bc50c16a439831fc4b999d2f985 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 3 Dec 2024 14:36:56 +0100 Subject: [PATCH 163/414] adding easyconfigs: GPAW-setups-24.11.0.eb --- .../g/GPAW-setups/GPAW-setups-24.11.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.11.0.eb diff --git a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.11.0.eb b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.11.0.eb new file mode 100644 index 00000000000..7edbb913770 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.11.0.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'GPAW-setups' +version = '24.11.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """PAW setups for the GPAW Density Functional Theory package. +Users can install setups manually using 'gpaw install-data' or use setups from this package. +The versions of GPAW and GPAW-setups can be intermixed. + +Compared to version 0.9.20000, version 24.1.0 contains an new improved Cr setup with 14 electrons, +which can be manually selected. Otherwise no changes are made, so no results will change. + +Version 21.11.0 contains setups for the Lanthanides. +""" + +toolchain = SYSTEM +source_urls = ['https://wiki.fysik.dtu.dk/gpaw-files/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['964c81cc28f7f91a4686d3d3182c4ebda30efb09d3f96b7f95eae3146499c110'] + +modextrapaths = {'GPAW_SETUP_PATH': ''} + +moduleclass = 'chem' + +sanity_check_paths = { + 'files': ['H.LDA.gz'], + 'dirs': [] +} From 111f4ea06df36cc89d65f43008cc9c7e3e7e0148 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Tue, 3 Dec 2024 16:12:43 +0100 Subject: [PATCH 164/414] some small fixes --- easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb index 2a324cfcc5a..cbc97bccf09 100644 --- a/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb +++ b/easybuild/easyconfigs/o/Optuna/Optuna-4.1.0-foss-2024a.eb @@ -29,15 +29,13 @@ use_pip = True sanity_pip_check = True exts_list = [ - # optional - ('cmaes', '0.11.1', { + ('cmaes', '0.11.1', { # optional 'checksums': ['cf71fa3679814723be771f2c9edd85f465b1bc1e409e1ad6d8a9e481efcd5160'], }), ('colorlog', '6.9.0', { 'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'], }), - ('optuna', version, { - 'use_pip_extras': 'optional', + ('%(namelower)s', version, { 'checksums': ['b364e87a2038f9946c5e2770c130597538aac528b4a82c1cab5267f337ea7679'], }), ] From 6944c324c8b975174fd70a44401db05c65d15088 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 3 Dec 2024 17:39:38 +0100 Subject: [PATCH 165/414] adding easyconfigs: CubeGUI-4.8.2-GCCcore-13.3.0.eb --- .../c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.3.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fc23873bc4a --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.3.0.eb @@ -0,0 +1,52 @@ +## +# 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 = '4.8.2' + +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': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bf2e02002bb2e5c4f61832ce37b62a440675c6453463014b33b2474aac78f86d'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Qt6', '6.7.2'), + ('CubeLib', '4.8.2'), +] + +configopts = [ + '--with-qt=$EBROOTQT6/bin ', +] + +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' From 992ee1ec33ce0a5254bdb0a5201c3a37b4c1f1e1 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 3 Dec 2024 18:12:07 +0100 Subject: [PATCH 166/414] adding easyconfigs: ncview-2.1.11-gompi-2024a.eb --- .../n/ncview/ncview-2.1.11-gompi-2024a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.11-gompi-2024a.eb diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.11-gompi-2024a.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.11-gompi-2024a.eb new file mode 100644 index 00000000000..7b0da0b8865 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.11-gompi-2024a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.11' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://cirrus.ucsd.edu/~pierce/ncview/'] +sources = [SOURCE_TAR_GZ] +checksums = ['597cfddf9c2d7993e9b0b86bca1b73839567ee9116ee33f6d750a449b5033d91'] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(nc-config --cc) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('UDUNITS', '2.2.28'), + ('X11', '20240607'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' From 0928b17aa44cde2c06508872997491824e279a01 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 4 Dec 2024 10:29:58 +0100 Subject: [PATCH 167/414] adding easyconfigs: Rust-1.83.0-GCCcore-13.3.0.eb --- .../r/Rust/Rust-1.83.0-GCCcore-13.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.83.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.83.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.83.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f614946f548 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.83.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +name = 'Rust' +version = '1.83.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.83.0-src.tar.gz': '722d773bd4eab2d828d7dd35b59f0b017ddf9a97ee2b46c1b7f7fac5c8841c6e'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Python', '3.12.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +moduleclass = 'lang' From 06ed664ab8a827da84f9444468c1139d0e553759 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Wed, 4 Dec 2024 12:00:14 +0100 Subject: [PATCH 168/414] Fix pkgconf dependency in Cbc-2.10.11-foss-2023b.eb --- easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb index 2fcdba53e06..39ee2bbd8f2 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023b.eb @@ -18,7 +18,7 @@ checksums = ['1fb591dd88336fdaf096b8e42e46111e41671a5eb85d4ee36e45baff1678bd33'] builddependencies = [ ('Autotools', '20220317'), ('Doxygen', '1.9.8'), - ('pkgconf', '1.9.5'), + ('pkgconf', '2.0.3'), ] dependencies = [ From 84b57f9e53d0d81c1ff875dfc730024784f5fe32 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Wed, 4 Dec 2024 12:01:36 +0100 Subject: [PATCH 169/414] Fix pkgconf dependency in Clp-1.17.9-foss-2023b.eb --- easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb index 8f96ff7547e..115ff64223e 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb @@ -18,7 +18,7 @@ checksums = ['b02109be54e2c9c6babc9480c242b2c3c7499368cfca8c0430f74782a694a49f'] builddependencies = [ ('Autotools', '20220317'), ('Doxygen', '1.9.8'), - ('pkgconf', '1.9.5'), + ('pkgconf', '2.0.3'), ] dependencies = [ From 8308e83ed0fbe2f4f57864e0fad005e4a6ff5120 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 4 Dec 2024 13:29:27 +0100 Subject: [PATCH 170/414] highlight mandatory arguments in load message --- easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb index 3a474015f21..6e3f4cddaeb 100644 --- a/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb +++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb @@ -44,6 +44,9 @@ modloadmsg = """ Additional plugins can be installed in your $HOME/.plugins folder or requested to user support Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless` More information at https://imagej.net/Headless +Also for Fiji 2.14.0 the arguments `--default-gc --java-home "$EBROOTJAVA/lib/server/"` +should always be used when running `ImageJ-linux64` commands to avoid errors like: +`Could not load Java library` and `Unrecognized option: -Xincgc`. """ moduleclass = 'vis' From 7a20e579785aa6e09d2617e082cdcb4db83452f0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 5 Dec 2024 11:08:36 +0100 Subject: [PATCH 171/414] adding easyconfigs: OPEN-SURFEX-8.1.0-GCCcore-12.3.0.eb --- .../OPEN-SURFEX-8.1.0-GCCcore-12.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/o/OPEN-SURFEX/OPEN-SURFEX-8.1.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/o/OPEN-SURFEX/OPEN-SURFEX-8.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OPEN-SURFEX/OPEN-SURFEX-8.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..86382c4106b --- /dev/null +++ b/easybuild/easyconfigs/o/OPEN-SURFEX/OPEN-SURFEX-8.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'OPEN-SURFEX' +version = '8.1.0' +local_commit = '70d2395' + +homepage = 'https://github.com/joewkr/open-SURFEX' +description = """ +SURFEX (SURFace EXternalisée) is a modelling platform that parametrizes land and water surfaces. +SURFEX is being developed by Météo-France and Open-SURFEX is a freely available SURFEX version +released under terms of CECILL-C Licence. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/joewkr/open-SURFEX/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['44341eee2ae952a21cc0055533c1ea7b3ef27fc88b716b46f88ca339a7bfebe1'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +build_cmd = 'cmake --build .' +install_cmd = 'cmake --build . --target install' + +sanity_check_paths = { + 'files': ['bin/PGD', 'bin/PREP', 'bin/OFFLINE'], + 'dirs': ['lib'], +} + +modextrapaths = { + 'PATH': 'lib/surfex/bin', + 'CPATH': 'lib/surfex/include', + 'LD_LIBRARY_PATH': 'lib/surfex/lib', +} + +moduleclass = 'geo' From 3c676cd7fbd0c60e659cc2237b4ead340d38c76f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 5 Dec 2024 16:02:55 +0100 Subject: [PATCH 172/414] adding easyconfigs: OpenNMT-py-3.5.1-foss-2023a-CUDA-12.1.1.eb --- ...OpenNMT-py-3.5.1-foss-2023a-CUDA-12.1.1.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenNMT-py/OpenNMT-py-3.5.1-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/o/OpenNMT-py/OpenNMT-py-3.5.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/OpenNMT-py/OpenNMT-py-3.5.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..b90d39736d6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenNMT-py/OpenNMT-py-3.5.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,74 @@ +easyblock = 'PythonBundle' + +name = 'OpenNMT-py' +version = '3.5.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://opennmt.net' +description = "OpenNMT is an open source ecosystem for neural machine translation and neural sequence learning" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('PyYAML', '6.0'), + ('PyTorch', '2.1.2', versionsuffix), + ('Flask', '2.3.3'), + ('tensorboard', '2.15.1'), + ('spaCy', '3.7.4'), + ('Safetensors', '0.4.3'), + ('bitsandbytes', '0.43.3', versionsuffix), + ('Gradio', '4.19.0'), + ('lxml', '4.9.2'), + ('flash-attention', '2.6.3', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('portalocker', '3.0.0', { + 'checksums': ['21f535de2e7a82c94c130c054adb5c7421d480d5619d61073996e2f89bcb879b'], + }), + ('subword_nmt', '0.3.8', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['d22526b557752f35ac15e8ea384ea7773e50a51d966b8752d023d16cb87eac36'], + }), + ('fasttext-wheel', '0.9.2', { + 'modulename': 'fasttext', + 'checksums': ['056e088318ef0e0cc690c4cb18637320eaa3cdb986b62d67bb50d6a7a82e4051'], + }), + ('pyahocorasick', '2.1.0', { + 'modulename': 'ahocorasick', + 'checksums': ['4df4845c1149e9fa4aa33f0f0aa35f5a42957a43a3d6e447c9b44e679e2672ea'], + }), + ('pyonmttok', '1.37.1', { + 'source_tmpl': '%(name)s-%(version)s-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'checksums': ['3ec8f8eedb82c059cff10cc9ac74747e2b61e607cdf7744a2e1c7d0bb2d170c9'], + }), + ('ConfigArgParse', '1.7', { + 'checksums': ['e7067471884de5478c58a511e529f0f9bd1c66bfef1dea90935438d6c23306d1'], + }), + ('ctranslate2', '4.5.0', { + 'source_tmpl': '%(name)s-%(version)s-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'checksums': ['89db5b18dfc7f7bf84cafaf7cc36e885aafcaeac936977eefd3e4768fd7b2879'], + }), + ('sacrebleu', '2.4.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['a976fd6998d8ced267a722120ec7fc47083c8e9745d8808ccee6424464a0aa31'], + }), + ('waitress', '3.0.2', { + 'checksums': ['682aaaf2af0c44ada4abfb70ded36393f0e307f4ab9456a215ce0020baefc31f'], + }), + (name, version, { + 'modulename': 'onmt', + 'checksums': ['8af6693ff0be0623683a5a9773b8d55b377fc14073f4897b6e6de3d482d338b2'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["onmt_train --help"] + +moduleclass = 'ai' From fa952a590c2137dec3256c023e45bc9cbec40e19 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 5 Dec 2024 16:47:50 +0100 Subject: [PATCH 173/414] adding easyconfigs: Hydra-1.3.2-foss-2023a-with-plugins.eb --- .../Hydra-1.3.2-foss-2023a-with-plugins.eb | 100 ++++++++++++++++++ 1 file changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-foss-2023a-with-plugins.eb diff --git a/easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-foss-2023a-with-plugins.eb b/easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-foss-2023a-with-plugins.eb new file mode 100644 index 00000000000..0267d417c80 --- /dev/null +++ b/easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-foss-2023a-with-plugins.eb @@ -0,0 +1,100 @@ +easyblock = 'PythonBundle' + +name = 'Hydra' +version = '1.3.2' +versionsuffix = '-with-plugins' + +homepage = "https://hydra.cc/" +description = """ +Hydra is an open-source Python framework that simplifies the development of +research and other complex applications. The key feature is the ability to +dynamically create a hierarchical configuration by composition and override it +through config files and the command line. The name Hydra comes from its +ability to run multiple similar jobs - much like a Hydra with multiple heads. +""" + +github_account = 'facebookresearch' + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('binutils', '2.40'), + ('Java', '17', '', SYSTEM), # needed by ANTLR runtime + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), # needed by omegaconf + ('tqdm', '4.66.1'), + ('SciPy-bundle', '2023.07'), + ('Greenlet', '3.0.2'), + ('SQLAlchemy', '2.0.25'), + ('Mako', '1.2.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('alembic', '1.12.1', { + 'checksums': ['bca5877e9678b454706347bc10b97cb7d67f300320fa5c3a94423e8266e2823f'], + }), + ('autopage', '0.5.2', { + 'checksums': ['826996d74c5aa9f4b6916195547312ac6384bac3810b8517063f293248257b72'], + }), + ('cliff', '4.3.0', { + 'checksums': ['fc5b6ebc8fb815332770b2485ee36c09753937c37cce4f3227cdd4e10b33eacc'], + }), + ('cmd2', '2.4.3', { + 'checksums': ['71873c11f72bd19e2b1db578214716f0d4f7c8fa250093c601265a9a717dee52'], + }), + ('cmaes', '0.10.0', { + 'checksums': ['48afc70df027114739872b50489ae6b32461c307b92d084a63c7090a9742faf9'], + }), + ('colorlog', '6.7.0', { + 'checksums': ['bd94bd21c1e13fac7bd3153f4bc3a7dc0eb0974b8bc2fdf1a989e474f6e582e5'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('prettytable', '3.9.0', { + 'checksums': ['f4ed94803c23073a90620b201965e5dc0bccf1760b7a7eaf3158cab8aaffdf34'], + }), + ('stevedore', '5.1.0', { + 'checksums': ['a54534acf9b89bc7ed264807013b505bf07f74dbe4bcfa37d32bd063870b087c'], + }), + ('optuna', '2.10.1', { + 'checksums': ['8a12009b57757c1070b3bff2261c24824d6430c22926dd1e2ace33b3deff555f'], + }), + ('antlr4-python3-runtime', '4.9', { + 'modulename': 'antlr4', + 'checksums': ['02d9afb720c13c52b336234286966cdf5aff704f230a513e635adb0d94de97ae'], + }), + ('omegaconf', '2.3.0', { + 'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'], + }), + ('read_version', '0.3.2', { + 'checksums': ['3f2d30852bce9174b244f7f29aaebf4e79904c6ed51a19716325015ff306ce3f'], + }), + ('hydra-optuna-sweeper', '1.2.0', { + 'modulename': False, + 'checksums': ['f20b56dfdc4db9f84f3b502c8e60a5269967197c4df4c28653cf17f71b2136ce'], + }), + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('submitit', '1.5.0', { + 'checksums': ['2766868e71656b1e278a42f33bced74faebf2c525dba74f4cc43be8cbef6c588'], + }), + ('hydra-submitit-launcher', '1.2.0', { + 'modulename': False, + 'checksums': ['e14c8eb46d020fac60ba25f82bcc368dc55851d2683dc95c88631ffcf15e4a34'], + }), + ('hydra-core', version, { + 'modulename': 'hydra', + 'checksums': ['8a878ed67216997c3e9d88a8e72e7b4767e81af37afb4ea3334b269a4390a824'], + }), +] + +moduleclass = 'data' From 4dfeea37a4cc38caa08ab4b85e3e4e86d8b2f1c5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 5 Dec 2024 18:20:32 +0100 Subject: [PATCH 174/414] adding easyconfigs: Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb, ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb --- .../Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb | 61 ++++++++++++++++++ ...ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb | 62 +++++++++++++++++++ 2 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..83cbc16113e --- /dev/null +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'Bonito' +version = '0.8.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/bonito' +description = "Convolution Basecaller for Oxford Nanopore Reads" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyTorch', '2.1.2', versionsuffix), + ('edlib', '1.3.9'), + ('ont-fast5-api', '4.1.2'), + ('ont-remora', '3.3.0', versionsuffix), + ('python-parasail', '1.3.4'), + ('pod5-file-format', '0.3.10'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('fast-ctc-decode', '0.3.6', { + 'source_tmpl': 'fast_ctc_decode-0.3.6-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl', + 'unpack_sources': False, + 'checksums': ['f49994a475866edf0e61f0d9e1b41185c035ba559b8c2aa68f83342d2c80ee6b'], + }), + ('mappy', '2.28', { + 'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'], + }), + ('ont_koi', '0.4.4', { + 'source_tmpl': 'ont_koi-0.4.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'modulename': 'koi', + 'checksums': ['e5d7c93b26363a3d4e3778f972d1f149447adbde91925e8876a97e7a63774e28'], + }), + ('ont-bonito', version, { + 'modulename': 'bonito', + 'checksums': ['26df86ee233bf020b549177e1e2aaa7ad7d99cf0927d79ab3fa31c1670d09ba6'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bonito'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "bonito --help", + "bonito download --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3fcee4f2eb2 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'ont-remora' +version = '3.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/remora' +description = """Methylation/modified base calling separated from basecalling. Remora primarily +provides an API to call modified bases for basecaller programs such as Bonito. +Remora also provides the tools to prepare datasets, train modified base models +and run simple inference.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ONNX-Runtime', '1.19.2', versionsuffix), + ('PyTorch', '2.1.2', versionsuffix), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('python-parasail', '1.3.4'), + ('polars', '0.20.2'), + ('Pysam', '0.22.0'), + ('pod5-file-format', '0.3.10'), + ('statsmodels', '0.14.1'), +] + +use_pip = True + +exts_list = [ + ('thop', '0.1.1.post2209072238', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['01473c225231927d2ad718351f78ebf7cffe6af3bed464c4f1ba1ef0f7cdda27'], + }), + ('mizani', '0.9.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ac5d49b913de88dc2fb28d82141e9777b97407a6971a158f758093ad5bb820a1'], + }), + ('plotnine', '0.12.4', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['12748f346f107c33f3e0658ac46fbb052205ae7e97ffaf52be68310e5d29f799'], + }), + (name, version, { + 'modulename': 'remora', + 'checksums': ['3c899e7333ae33ebec31c8a59650ab4d553e8a62c0abf7b03899e2ee9a0bc88a'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/remora'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('remora', '--help'), +] + +moduleclass = 'bio' From 643a24bd61caa62093a41fddb121d1a45c69597b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 6 Dec 2024 10:03:12 +0100 Subject: [PATCH 175/414] gnuplot/6.0.1-GCCcore-13.2.0: fix underfined reference to symbol libiconv_open --- .../easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb index 29e3f916718..ebe86fdb902 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb @@ -8,7 +8,7 @@ description = """Portable interactive, function plotting utility""" toolchain = {'name': 'GCCcore', 'version': '13.2.0'} -source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +source_urls = [('https://sourceforge.net/projects/%(name)s/files/%(name)s/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] checksums = ['e85a660c1a2a1808ff24f7e69981ffcbac66a45c9dcf711b65610b26ea71379a'] @@ -36,6 +36,9 @@ preconfigopts = 'autoreconf && ' # make sure that right Lua library is used (bypassing pkg-config) preconfigopts += 'export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' +# fix undefined reference to symbol 'libiconv_open' +preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' + configopts = '--with-qt=qt6 --without-latex --disable-wxwidgets' buildopts = 'LDFLAGS="$LDFLAGS -Wl,--copy-dt-needed-entries" ' From 037dac99d44c7a1bd3cd2d64b8eba08d021eef4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2024 10:36:21 +0100 Subject: [PATCH 176/414] add missing cutadapt dependency for decona 1.4-20240731 --- easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb b/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb index 3e1eb388a12..9fb32627c23 100644 --- a/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb +++ b/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb @@ -22,6 +22,7 @@ dependencies = [ ('Racon', '1.5.0'), ('medaka', '1.11.3'), ('BLAST+', '2.14.1'), + ('cutadapt', '4.9'), ] fix_python_shebang_for = ['decona'] From fbf6b1fa701af243bb0799063e999dd4301bfa4d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 6 Dec 2024 11:00:47 +0100 Subject: [PATCH 177/414] gnuplot/6.0.1-GCCcore-13.2.0: avoid duplicate config/build LDFLAGS --- .../easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb index ebe86fdb902..d3f29dbab9a 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb @@ -37,12 +37,11 @@ preconfigopts = 'autoreconf && ' preconfigopts += 'export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' # fix undefined reference to symbol 'libiconv_open' -preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' +preconfigopts += 'export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' configopts = '--with-qt=qt6 --without-latex --disable-wxwidgets' -buildopts = 'LDFLAGS="$LDFLAGS -Wl,--copy-dt-needed-entries" ' -buildopts += 'LIBS="-lcerf -lcairo -lpangocairo-1.0"' +buildopts = 'LIBS="-lcerf -lcairo -lpangocairo-1.0"' sanity_check_paths = { 'files': ['bin/gnuplot'], From 9426737ca0e628ed3d5e045a3002635766c29a81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2024 11:09:59 +0100 Subject: [PATCH 178/414] add missing (optional) pyabpoa dependency as extension to medaka 1.11.3 --- easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2022a.eb | 3 +++ easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2022a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2022a.eb index 85c733711d1..1be61af126b 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2022a.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2022a.eb @@ -57,6 +57,9 @@ exts_list = [ ('wurlitzer', '3.0.3', { 'checksums': ['224f5fe70618be3872c05dfddc8c457191ec1870654596279fcc1edadebe3e5b'], }), + ('pyabpoa', '1.5.3', { + 'checksums': ['94714bb5c6be9f5ca35b66a5c63490237ebff2498ff93b82a842a9512b0bbc08'], + }), (name, version, { 'checksums': ['940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9'], # remove TensorFlow version requirement which is too strict diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb index dffdad4341f..b38484c3cd8 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb @@ -57,6 +57,9 @@ exts_list = [ ('wurlitzer', '3.0.3', { 'checksums': ['224f5fe70618be3872c05dfddc8c457191ec1870654596279fcc1edadebe3e5b'], }), + ('pyabpoa', '1.5.3', { + 'checksums': ['94714bb5c6be9f5ca35b66a5c63490237ebff2498ff93b82a842a9512b0bbc08'], + }), (name, version, { 'checksums': ['940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9'], # Some requirements are too strict. From fb2a2676dfa0ec1b6ae5d6c000b80decd8befffc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 6 Dec 2024 11:11:40 +0100 Subject: [PATCH 179/414] gnuplot/6.0.1-GCCcore-13.2.0: remove unnecessary buildopts --- easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb index d3f29dbab9a..13e699ab12e 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.2.0.eb @@ -41,8 +41,6 @@ preconfigopts += 'export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' configopts = '--with-qt=qt6 --without-latex --disable-wxwidgets' -buildopts = 'LIBS="-lcerf -lcairo -lpangocairo-1.0"' - sanity_check_paths = { 'files': ['bin/gnuplot'], 'dirs': [] From 797d762de9d71a982f3e7ab121aba56c8b51c6bd Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 6 Dec 2024 11:35:10 +0100 Subject: [PATCH 180/414] Delete easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb --- .../g/GDAL/GDAL-3.9.2-foss-2024a.eb | 81 ------------------- 1 file changed, 81 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb deleted file mode 100644 index 85b6186916e..00000000000 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb +++ /dev/null @@ -1,81 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'GDAL' -version = '3.9.2' - -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': '2024a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/OSGeo/gdal/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-3.6.2_fix-python-CC-CXX.patch'] -checksums = [ - {'gdal-3.9.2.tar.gz': 'c9767e79ca7245f704bfbcb47d771b2dc317d743536b78d648c3e92b95fbc21e'}, - {'GDAL-3.6.2_fix-python-CC-CXX.patch': '859b874b0c8ff7626a76d51f008bf05b7f89a35b325bdd1d126d2364154acc63'}, -] - -builddependencies = [ - ('CMake', '3.29.3'), - ('pkgconf', '2.2.0'), - ('Bison', '3.8.2'), -] -dependencies = [ - ('Python', '3.12.3'), - ('netCDF', '4.9.2'), - ('expat', '2.6.2'), - ('GEOS', '3.12.2'), - ('SQLite', '3.45.3'), - ('libarchive', '3.7.4'), - ('libxml2', '2.12.7'), - ('libpng', '1.6.43'), - ('libjpeg-turbo', '3.0.1'), - ('LibTIFF', '4.6.0'), - ('zlib', '1.3.1'), - ('cURL', '8.7.1'), - ('PCRE', '8.45'), - ('PROJ', '9.4.1'), - ('libgeotiff', '1.7.3'), - ('SciPy-bundle', '2024.05'), - ('HDF5', '1.14.5'), - ('HDF', '4.3.0'), - ('Armadillo', '14.0.3'), - ('CFITSIO', '4.4.1'), - ('zstd', '1.5.6'), - ('giflib', '5.2.2'), - ('json-c', '0.17'), - ('Xerces-C++', '3.2.5'), - ('PCRE2', '10.43'), - ('OpenEXR', '3.2.4'), - ('Brunsli', '0.1'), - ('Qhull', '2020.2'), - ('LERC', '4.0.0'), - ('OpenJPEG', '2.5.2'), - ('SWIG', '4.2.1'), -] - -# iterative build for both static and shared libraries -local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF " -local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " - -configopts = [ - local_configopts_common + "-DBUILD_SHARED_LIBS=OFF", - local_configopts_common -] - - -sanity_check_paths = { - 'files': ['lib/libgdal.a', 'lib/libgdal.so'], - 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["python -c 'import osgeo.%(namelower)s'"] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -moduleclass = 'data' From f770977972c8f35bc38d89319df97196ca4a4919 Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 6 Dec 2024 11:41:12 +0100 Subject: [PATCH 181/414] Update Fiona-1.10.1-foss-2024a.eb --- easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb index a46045749ab..06bc9936c30 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.10.1-foss-2024a.eb @@ -18,7 +18,7 @@ builddependencies = [ dependencies = [ ('Python', '3.12.3'), - ('GDAL', '3.9.2'), + ('GDAL', '3.10.0'), ('Shapely', '2.0.6'), # optional for 'calc' extras ] From 250ae54bb87d35a9228c8d689a966ec3b6251299 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Fri, 6 Dec 2024 13:06:09 +0100 Subject: [PATCH 182/414] adding easyconfigs: Gurobi-12.0.0-GCCcore-13.2.0.eb --- .../g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..48f991538d9 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,64 @@ +name = 'Gurobi' +version = '12.0.0' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +local_archs = {'aarch64': 'armlinux64', 'x86_64': 'linux64'} +sources = ['gurobi%%(version)s_%s.tar.gz' % local_archs[ARCH]] +patches = ['Gurobi-11.0.0_use-eb-python-gurobi-shell.patch'] +checksums = [ + {'gurobi12.0.0_linux64.tar.gz': 'a2bdc9c1d6bf8eb4e551a184af1ce8d7b0435ea8e7d19a017cc7d53fd5efda12', + 'gurobi12.0.0_armlinux64.tar.gz': '8e1202cbf0866a16fa78c3e4be0fa32888ec912f8ddf333c29561d057964ef86'}, + {'Gurobi-11.0.0_use-eb-python-gurobi-shell.patch': + '566473a3ba4e35b0e74595368f9f4133fc4a3c97cca84154c4b938645786e663'}, +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('gurobipy', version, { + 'sources': ['gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_%(arch)s.whl'], + 'checksums': [{ + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_aarch64.whl': + 'fc3892e3d88d0f8a01da75f12f74023d398ef599a9e1add66ed76313733e30fb', + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl': + 'a08fb42a5e7cb02cdb993c1381c8b8c5a3baeedcadd56e7288d8458a57b81442', + }], + }), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license is mandatory for installation +# use EB_GUROBI_LICENSE_FILE environment variable, or +# uncomment and modify the following variable: +# license_file = '/path/to/my-license-file' +license_file = HOME + '/licenses/%(name)s.lic' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' From d918d5394dadfd9d3217e4c84fac1966a681bb1a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 6 Dec 2024 13:37:45 +0100 Subject: [PATCH 183/414] adding easyconfigs: Wengan-0.2-GCCcore-12.3.0.eb --- .../w/Wengan/Wengan-0.2-GCCcore-12.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wengan/Wengan-0.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/w/Wengan/Wengan-0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/Wengan/Wengan-0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ae08781f875 --- /dev/null +++ b/easybuild/easyconfigs/w/Wengan/Wengan-0.2-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'Binary' + +name = 'Wengan' +version = '0.2' + +homepage = 'https://github.com/adigenova/wengan/' +description = 'An accurate and ultra-fast genome assembler.' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/adigenova/wengan/releases/download/v%(version)s/'] +sources = [{'download_filename': '%(namelower)s-v%(version)s-bin-Linux.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['754848566611c599c62886455cc88451a56c99e7102d71f28c283b6b851d2b27'] + +dependencies = [ + ('Perl', '5.36.1'), +] + +extract_sources = True + +# create 'wengan' script and make it executable +postinstallcmds = [ + 'cd %(installdir)s/bin && touch wengan && ' + 'echo "#!/bin/bash" >> wengan && ' + 'echo "export LC_ALL=C" >> wengan && ' + r'echo "exec perl \$EBROOTWENGAN/wengan.pl \$*" >> wengan && ' + 'chmod +x %(installdir)s/bin/wengan' +] + +sanity_check_paths = { + 'files': ['wengan.pl', 'bin/wengan'], + 'dirs': ['bin'], +} +sanity_check_commands = [ + 'wengan 2>&1 | grep "Usage"' +] + +modloadmsg = r"Run 'wengan' instead of 'perl ${WG}' to run Wengan." + +moduleclass = 'bio' From dc6cd3565c32962cfee17abda284f8187e12c3e9 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 6 Dec 2024 14:15:08 +0100 Subject: [PATCH 184/414] Update easyconfigs.py --- test/easyconfigs/easyconfigs.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index adc1ab93062..4b1c4dd770e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -657,8 +657,6 @@ def check_dep_vars(self, gen, dep, dep_vars): ('2.5.3;', ['medaka-1.5.0-']), # tensorflow-probability version to TF version ('2.8.4;', ['tensorflow-probability-0.16.0-']), - # AlphaPulldown - ('2.15.1', ['AlphaPulldown-2.0.0b6']), ], # smooth-topk uses a newer version of torchvision 'torchvision': [('0.11.3;', ['smooth-topk-1.0-20210817-'])], From 3ed0dcfa64500b42a34c4194bf97fc7a0ae5bc04 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 6 Dec 2024 15:19:28 +0000 Subject: [PATCH 185/414] giflib/5.2.1 --- easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb index 7b452e77df4..c84c253b59e 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.10.0-foss-2024a.eb @@ -47,7 +47,7 @@ dependencies = [ ('Armadillo', '14.0.3'), ('CFITSIO', '4.4.1'), ('zstd', '1.5.6'), - ('giflib', '5.2.2'), + ('giflib', '5.2.1'), ('json-c', '0.17'), ('Xerces-C++', '3.2.5'), ('PCRE2', '10.43'), From 4956d8e9b2ac51cd16f53cb5dc0116c39867b0ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 7 Dec 2024 00:48:47 +0000 Subject: [PATCH 186/414] adding easyconfigs: buildenv-default-foss-2023b-CUDA-12.4.0.eb, buildenv-default-foss-2024a-CUDA-12.6.0.eb, buildenv-default-foss-2024a.eb, buildenv-default-intel-2024a.eb --- ...buildenv-default-foss-2023b-CUDA-12.4.0.eb | 20 +++++++++++++++++++ ...buildenv-default-foss-2024a-CUDA-12.6.0.eb | 20 +++++++++++++++++++ .../b/buildenv/buildenv-default-foss-2024a.eb | 13 ++++++++++++ .../buildenv/buildenv-default-intel-2024a.eb | 13 ++++++++++++ 4 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023b-CUDA-12.4.0.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2024a-CUDA-12.6.0.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2024a.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2024a.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023b-CUDA-12.4.0.eb new file mode 100644 index 00000000000..2a58e5fbb42 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023b-CUDA-12.4.0.eb @@ -0,0 +1,20 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', versionsuffix), + ('UCC-CUDA', '1.2.0', versionsuffix), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2024a-CUDA-12.6.0.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2024a-CUDA-12.6.0.eb new file mode 100644 index 00000000000..a43fd7490d8 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2024a-CUDA-12.6.0.eb @@ -0,0 +1,20 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2024a'} + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('UCX-CUDA', '1.16.0', versionsuffix), + ('UCC-CUDA', '1.3.0', versionsuffix), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2024a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2024a.eb new file mode 100644 index 00000000000..d5909cd1320 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2024a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2024a'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2024a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2024a.eb new file mode 100644 index 00000000000..ed6366787d8 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2024a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2024a'} + +moduleclass = 'devel' From 238ea2b24be29afcfee1aebdaaf941af33496c7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Dec 2024 17:15:00 +0100 Subject: [PATCH 187/414] add sanity check command for HyperQueue v0.20.0 --- easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.20.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.20.0.eb b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.20.0.eb index c71c91f554b..3db9b775db1 100644 --- a/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.20.0.eb +++ b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.20.0.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["hq --help"] + moduleclass = 'tools' From 001e979be9758ea951db81fcb78a80542c20055d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 7 Dec 2024 16:15:02 +0000 Subject: [PATCH 188/414] adding easyconfigs: Autoconf-2.72-GCCcore-14.2.0.eb, Automake-1.17-GCCcore-14.2.0.eb, Autotools-20240712-GCCcore-14.2.0.eb, expat-2.6.4-GCCcore-14.2.0.eb, groff-1.23.0-GCCcore-14.2.0.eb, libreadline-8.2-GCCcore-14.2.0.eb, libtool-2.5.4-GCCcore-14.2.0.eb, Perl-5.40.0-GCCcore-14.2.0.eb, Perl-bundle-CPAN-5.40.0-GCCcore-14.2.0.eb --- .../Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb | 48 + .../Automake/Automake-1.17-GCCcore-14.2.0.eb | 39 + .../Autotools-20240712-GCCcore-14.2.0.eb | 24 + .../e/expat/expat-2.6.4-GCCcore-14.2.0.eb | 31 + .../g/groff/groff-1.23.0-GCCcore-14.2.0.eb | 26 + .../libreadline-8.2-GCCcore-14.2.0.eb | 41 + .../l/libtool/libtool-2.5.4-GCCcore-14.2.0.eb | 32 + .../Perl-bundle-CPAN-5.40.0-GCCcore-14.2.0.eb | 2155 +++++++++++++++++ .../p/Perl/Perl-5.40.0-GCCcore-14.2.0.eb | 86 + 9 files changed, 2482 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20240712-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.6.4-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.5.4-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.40.0-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.40.0-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..fe4b4d3a0de --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.72' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('M4', '1.4.19'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.40.0'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +sanity_check_commands = [ + "autoconf --help", + "autom4te --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..79c73627108 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.17' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Autoconf', '2.72'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.40.0'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ['bin/aclocal', 'bin/automake'], + 'dirs': [] +} + +sanity_check_commands = [ + "aclocal --help", + "automake --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20240712-GCCcore-14.2.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20240712-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..cd7cab79455 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20240712-GCCcore-14.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20240712' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +dependencies = [ + ('Autoconf', '2.72'), # 20240712 + ('Automake', '1.17'), # 20211003 + ('libtool', '2.5.4'), # 20220317 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/expat/expat-2.6.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.6.4-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..e4ced852952 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.6.4-GCCcore-14.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.6.4' + +homepage = 'https://libexpat.github.io' + +description = """Expat is an XML parser library written in C. It is a stream-oriented parser +in which an application registers handlers for things the parser might find +in the XML document (like start tags).""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_TAR_BZ2] +checksums = ['8dc480b796163d4436e6f1352e71800a774f73dbae213f1860b60607d2a83ada'] + +builddependencies = [('binutils', '2.42')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..3f1c7189bb7 --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-14.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.23.0' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['6b9757f592b7518b4902eb6af7e54570bdccba37a871fddb2d30ae3863511c13'] + +builddependencies = [ + ('binutils', '2.42'), + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..e36045456fb --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-14.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.2' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['3feb7171f16a84ee82ca18a36d7b9be109a52c04f492a053331d7d1095007c35'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('ncurses', '6.5'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.5.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.5.4-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..dfe44f36c0f --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.5.4-GCCcore-14.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.5.4' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.40.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.40.0-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..7e287c21239 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.40.0-GCCcore-14.2.0.eb @@ -0,0 +1,2155 @@ +easyblock = 'PerlBundle' + +name = 'Perl-bundle-CPAN' +version = '5.40.0' + +homepage = 'https://www.perl.org/' +description = """A set of common packages from CPAN""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('groff', '1.23.0'), +] + +dependencies = [ + ('Perl', version), + ('zlib', '1.3.1'), # for Net::SSLeay + ('expat', '2.6.4'), # for XML::Parser + ('ncurses', '6.5'), # for Term::ReadLine::Gnu + ('libreadline', '8.2'), # for Term::ReadLine::Gnu + ('OpenSSL', '3', '', SYSTEM), # required for Net::SSLeay +] + +# !! order of extensions is important !! +# extensions updated on 2024-07-08 +exts_list = [ + ('Config::General', '2.65', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['4d6d5754be3a9f30906836f0cc10e554c8832e14e7a1341efb15b05d706fc58f'], + }), + ('HTTP::Date', '6.06', { + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['7b685191c6acc3e773d1fc02c95ee1f9fae94f77783175f5e78c181cc92d2b52'], + }), + ('File::Listing', '6.16', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['189b3a13fc0a1ba412b9d9ec5901e9e5e444cc746b9f0156d4399370d33655c6'], + }), + ('ExtUtils::Config', '0.010', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['82e7e4e90cbe380e152f5de6e3e403746982d502dd30197a123652e46610c66d'], + }), + ('ExtUtils::InstallPaths', '0.014', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae65d20cc3c7e14b3cd790915c84510f82dfb37a4c9b88aa74b2e843af417d01'], + }), + ('ExtUtils::Helpers', '0.028', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['c8574875cce073e7dc5345a7b06d502e52044d68894f9160203fcaab379514fe'], + }), + ('Test::Harness', '3.50', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['79b6acdc444f1924cd4c2e9ed868bdc6e09580021aca8ff078ede2ffef8a6f54'], + }), + ('CPAN::Meta::Requirements', '2.143', { + 'source_tmpl': 'CPAN-Meta-Requirements-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['6ec7e4697bb5a8cea0ee3c8bd5d4b20ce086168a8084778d6e7a4c37356fdf8b'], + }), + ('CPAN::Requirements::Dynamic', '0.001', { + 'source_tmpl': 'CPAN-Requirements-Dynamic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['4b590e712b9aca680c3631855ee16a50b84fa0227c362e13b237a75a01489ef5'], + }), + ('Module::Build::Tiny', '0.051', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['74fdce35e8cd4d787bc2d4fc1d43a291b7bbced4e94dc5fc592bd81ca93a98e9'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2024080801', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['0677afaec8e1300cefe246b4d809e75cdf55e2cc0f77c486d13073b69ab4fbdd'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '6.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['2743f1cb59c2cac21bf14f0f71beab5ced75a589394a1fd8ac09ecc71599299e'], + }), + ('Try::Tiny', '0.32', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ef2d6cab0bad18e3ab1c4e6125cc5f695c7e459899f512451c8fa3ef83fa7fc0'], + }), + ('Test::Fatal', '0.017', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['37dfffdafb84b762efe96b02fb2aa41f37026c73e6b83590db76229697f3c4a6'], + }), + ('Test::Warnings', '0.033', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b9c375719f2c61c5f97aa5ee6cf4c901a972347c415969379b0b51f67c48bbcb'], + }), + ('Class::Inspector', '1.36', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['cc295d23a472687c24489d58226ead23b9fdc2588e522f0b5f0747741700694e'], + }), + ('File::ShareDir::Install', '0.14', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'], + }), + ('File::ShareDir', '1.118', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], + }), + ('IPC::System::Simple', '1.30', { + 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], + }), + ('Importer', '0.026', { + 'source_tmpl': 'Importer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], + }), + ('Term::Table', '0.023', { + 'source_tmpl': 'Term-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['e45042face1801d99c0bead6ca5f363a34e0e055f4fe6b0ccb208de481072bd3'], + }), + ('Scope::Guard', '0.21', { + 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], + 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], + }), + ('Sub::Info', '0.002', { + 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], + }), + ('Test2::Require::Module', '1.302204', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['03749d1027a7817ca7f11e420ef72951f20a849ea65af2eb595f34df47d1226e'], + }), + ('Test2::Plugin::NoWarnings', '0.10', { + 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c97cb1122cc6e3e4a079059da71e12f65760bfb0671d19d25a7ec7c5f1f240fb'], + }), + ('Class::Tiny', '1.008', { + 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], + }), + ('Path::Tiny', '0.146', { + 'source_tmpl': 'Path-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['861ef09bca68254e9ab24337bb6ec9d58593a792e9d68a27ee6bec2150f06741'], + }), + ('Test::Deep', '1.204', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['b6591f6ccdd853c7efc9ff3c5756370403211cffe46047f082b1cd1611a84e5f'], + }), + ('Test::File', '1.993', { + 'source_tmpl': 'Test-File-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['ef2ffe1aaec7b42d874ad411ec647547b9b9bc2f5fb93e49e3399488456afc7a'], + }), + ('Test::Needs', '0.002010', { + 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['923ffdc78fcba96609753e4bae26b0ba0186893de4a63cd5236e012c7c90e208'], + }), + ('Test::Requires', '0.11', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': ['4b88de549597eecddf7c3c38a4d0204a16f59ad804577b671896ac04e24e040f'], + }), + ('File::Copy::Recursive', '0.45', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['d3971cf78a8345e38042b208bb7b39cb695080386af629f4a04ffd6549df1157'], + }), + ('Test::File::ShareDir::Dist', '1.001002', { + 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], + }), + ('CPAN::Meta::Check', '0.018', { + 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['f619d2df5ea0fd91c8cf83eb54acccb5e43d9e6ec1a3f727b3d0ac15d0cf378a'], + }), + ('Sub::Exporter::Progressive', '0.001013', { + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + 'checksums': ['d535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056'], + }), + ('Module::Runtime', '0.016', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + 'checksums': ['68302ec646833547d410be28e09676db75006f4aa58a11f3bdb44ffe99f0f024'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], + }), + ('B::Hooks::EndOfScope', '0.28', { + 'source_tmpl': 'B-Hooks-EndOfScope-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['edac77a17fc36620c8324cc194ce1fad2f02e9fcbe72d08ad0b2c47f0c7fd8ef'], + }), + ('Package::Stash', '0.40', { + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['5a9722c6d9cb29ee133e5f7b08a5362762a0b5633ff5170642a5b0686e95e066'], + }), + ('namespace::clean', '0.27', { + 'source_tmpl': 'namespace-clean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + 'checksums': ['8a10a83c3e183dc78f9e7b7aa4d09b47c11fb4e7d3a33b9a12912fd22e31af9d'], + }), + ('Sub::Identify', '0.14', { + 'source_tmpl': 'Sub-Identify-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RG/RGARCIA'], + 'checksums': ['068d272086514dd1e842b6a40b1bedbafee63900e5b08890ef6700039defad6f'], + }), + ('namespace::autoclean', '0.31', { + 'source_tmpl': 'namespace-autoclean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['d3b32c82e1d2caa9d58b8c8075965240e6cab66ab9350bd6f6bea4ca07e938d6'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': ['ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad'], + }), + ('Exporter::Tiny', '1.006002', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': ['6f295e2cbffb1dbc15bdb9dadc341671c1e0cd2bdf2d312b17526273c322638d'], + }), + ('Type::Tiny', '2.006000', { + 'source_tmpl': 'Type-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': ['4c685ebbba5145dc02944c305e8e82759811032a55e6da270a751b63b76500ea'], + }), + ('Class::Data::Inheritable', '0.10', { + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSHERER'], + 'checksums': ['aa1ae68a611357b7bfd9a2f64907cc196ddd6d047cae64ef9d0ad099d98ae54a'], + }), + ('Devel::StackTrace', '2.05', { + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['63cb6196e986a7e578c4d28b3c780e7194835bfc78b68eeb8f00599d4444888c'], + }), + ('Exception::Class', '1.45', { + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['5482a77ef027ca1f9f39e1f48c558356e954936fc8fbbdee6c811c512701b249'], + }), + ('Role::Tiny', '2.002004', { + 'source_tmpl': 'Role-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['d7bdee9e138a4f83aa52d0a981625644bda87ff16642dfa845dcb44d9a242b45'], + }), + ('MRO::Compat', '0.15', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['0d4535f88e43babd84ab604866215fc4d04398bd4db7b21852d4a31b1c15ef61'], + }), + ('Sub::Quote', '2.006008', { + 'source_tmpl': 'Sub-Quote-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['94bebd500af55762e83ea2f2bc594d87af828072370c7110c60c238a800d15b2'], + }), + ('Specio', '0.48', { + 'source_tmpl': 'Specio-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['0c85793580f1274ef08173079131d101f77b22accea7afa8255202f0811682b2'], + }), + ('Test::Without::Module', '0.23', { + 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['8289e1cd7f57017a816ab4127e29ecd7a754ae7cd5c037c41b3b3bf849c21d21'], + }), + ('Params::ValidationCompiler', '0.31', { + 'source_tmpl': 'Params-ValidationCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['7b6497173f1b6adb29f5d51d8cf9ec36d2f1219412b4b2410e9d77a901e84a6d'], + }), + ('DateTime::Locale', '1.44', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['12a584a4a43c46114cd41ab6981be3609588604a906463fe4f844bb88a31c2de'], + }), + ('Class::Singleton', '1.6', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['27ba13f0d9512929166bbd8c9ef95d90d630fc80f0c9a1b7458891055e9282a4'], + }), + ('DateTime::TimeZone', '2.63', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['79ac1c34fb2129b1ad88e0c7090166b98f2a7fd658358f2e1ae7e9bac963cc0f'], + }), + ('Module::Build', '0.4234', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['66aeac6127418be5e471ead3744648c766bd01482825c5b66652675f2bc86a8f'], + }), + ('Params::Validate', '1.31', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['1bf2518ef2c4869f91590e219f545c8ef12ed53cf313e0eb5704adf7f1b2961e'], + }), + ('List::MoreUtils::XS', '0.430', { + 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], + }), + ('List::MoreUtils', '0.430', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['63b1f7842cd42d9b538d1e34e0330de5ff1559e4c2737342506418276f646527'], + }), + ('DateTime', '1.65', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['0bfda7ff0253fb3d88cf4bdb5a14afb8cea24d147975d5bdf3c88b40e7ab140e'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['83293737e803b43112830443fb5208ec5208a2e6ea512ed54ef8e4dd2b880827'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['7e6f16cc33eb1f29ff25bee51d513f4b8a84947bbfa18edb2d3cc40a2d64cafe'], + }), + ('Params::Util', '1.102', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['499bb1b482db24fda277a51525596ad092c2bd51dd508fa8fec2e9f849097402'], + }), + ('File::Find::Rule::Perl', '1.16', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ae1886050d9ca21223c073e2870abdc80dc30e3f55289a11c37da3820a8321ff'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + 'checksums': ['4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e'], + }), + ('Git', '0.42', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + 'checksums': ['9469a9f398f3a2bf2b0500566ee41d3ff6fae460412a137185767a1cc4783a6d'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['452995beeabf0e923e65fdc627a725dbb12c9e10c00d8018c16d10ba62757f1e'], + }), + ('Tree::DAG_Node', '1.32', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['22d9de3d6e6f4afd89e6d825c664f9482878bd49e29cb81342a707af40542d3d'], + }), + ('Template', '3.102', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['d161c89dee9b213a7c55709ea782e2dd5923dbd1215b9576612889e6e74a2e06'], + }), + ('DBI', '1.645', { + 'pretestopts': 'LC_ALL=C ', # Test fails if run in localized environments + 'source_tmpl': 'DBI-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['e38b7a5efee129decda12383cf894963da971ffac303f54cc1b93e40e3cf9921'], + }), + ('DBD::SQLite', '1.76', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['0a33a7a935be63371071dbe600cfaefa67cd971b67580a917bbf6ebaf723c584'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': ['11a815fc45fdf0efabb1822ab77faad8b9eea162572c5f0940c8ed7d56e6b8b8'], + }), + ('Archive::Extract', '0.88', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['cffcf135cd0622287d3b02154f7d6716495449fcaed03966621948e25ea5f742'], + }), + ('DBIx::Simple', '1.37', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + 'checksums': ['46d311aa2ce08907401c56119658426dbb044c5a40de73d9a7b79bf50390cae3'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + 'checksums': ['f7dbebf65261ed0e5abd0f57052b64d665a1a830bab4c8bbc220f235bd39caf5'], + }), + ('Test::Simple', '1.302204', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['03749d1027a7817ca7f11e420ef72951f20a849ea65af2eb595f34df47d1226e'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + 'checksums': ['a3dc1526f3dde72d3c64ea00007b86ce608cdcd93567cf6e6e42dc10fdc4511d'], + }), + ('IO::Stringy', '2.113', { + 'source_tmpl': 'IO-Stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['51220fcaf9f66a639b69d251d7b0757bf4202f4f9debd45bdd341a6aca62fe4e'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1'], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0'], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': ['47e995859f8dd0413aa3f22d350c4a62da652e854267aa0586ae544ae2bae5ef'], + }), + ('XML::SAX', '1.02', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['4506c387043aa6a77b455f00f57409f3720aa7e553495ab2535263b4ed1ea12a'], + }), + ('Test::LeakTrace', '0.17', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': ['777d64d2938f5ea586300eef97ef03eacb43d4c1853c9c3b1091eb3311467970'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['156b13f07764f766d8b45a43728f2439af81a3512625438deab783b7883eb533'], + }), + ('Text::Aligner', '0.16', { + 'source_tmpl': 'Text-Aligner-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['5c857dbce586f57fa3d7c4ebd320023ab3b2963b2049428ae01bd3bc4f215725'], + }), + ('Text::Table', '1.135', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['fca3c16e83127f7c44dde3d3f7e3c73ea50d109a1054445de8082fea794ca5d2'], + }), + ('MIME::Types', '2.26', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['bc738483cb4cdb47d61e85fe9304fa929aa9ab927e3171ec2ba2ab1cd7cefdff'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + 'checksums': ['7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77'], + }), + ('Capture::Tiny', '0.48', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['6c23113e87bad393308c90a207013e505f659274736638d8c79bac9c67cc3e19'], + }), + ('File::Copy::Recursive::Reduced', '0.008', { + 'source_tmpl': 'File-Copy-Recursive-Reduced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['462bd66bf55e74b78f29ebdc9626af622d4f0115b5191b03167e82164db98f5a'], + }), + ('Module::Build::XSUtil', '0.19', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + 'checksums': ['9063b3c346edeb422807ffe49ffb23038c4f900d4a77b845ce4b53d97bf29400'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + 'checksums': ['0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117'], + }), + ('Number::Format', '1.76', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0e0060eb363635a885706c6a26f5fcaafeae759f7b2acae49dda70e195dd44d6'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + 'checksums': ['0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843'], + }), + ('HTML::Tagset', '3.24', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['eb89e145a608ed1f8f141a57472ee5f69e67592a432dcd2e8b1dbb445f2b230b'], + }), + ('URI', '5.31', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['b9c4d58b2614b8611ae03a95a6d60ed996f4b311ef3cd5a937b92f1825ecc564'], + }), + ('B::COW', '0.007', { + 'source_tmpl': 'B-COW-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['1290daf227e8b09889a31cf182e29106f1cf9f1a4e9bf7752f9de92ed1158b44'], + }), + ('Clone', '0.47', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['4c2c0cb9a483efbf970cb1a75b2ca75b0e18cb84bcb5c09624f86e26b09c211d'], + }), + ('IO::HTML', '1.004', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + 'checksums': ['c87b2df59463bbf2c39596773dfb5c03bde0f7e1051af339f963f58c1cbd8bf5'], + }), + ('LWP::MediaTypes', '6.04', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['8f1bca12dab16a1c2a7c03a49c5e58cce41a6fec9519f0aadfba8dad997919d9'], + }), + ('HTTP::Message', '7.00', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['5afa95eb6ed1c632e81656201a2738e2c1bc6cbfae2f6d82728e2bb0b519c1dc'], + }), + ('HTML::Parser', '3.83', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['7278ce9791256132b26a71a5719451844704bb9674b58302c3486df43584f8c0'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + 'checksums': ['c36fd2b68d48c2e17417bf2873c78820f3ae02460fdf5976b8eeab887d59e16c'], + }), + ('XML::Parser', '2.47', { + 'source_tmpl': 'XML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['ad4aae643ec784f489b956abe952432871a622d4e2b5c619e8855accbfc4d1d8'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + 'checksums': ['4571059b7b5d48b7ce52b01389e95d798bf5cf2020523c153ff27b498153c9cb'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['8816f34e9a38e849a10df756030dccf9fe061a196c11ac3faafd7113c929b964'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': ['85e2f805bfc81cd738c294316b27a515397036f397a0ff1c6c8d754c38530306'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + 'checksums': ['8b481ceedbf0ae4a83effb80581550008bfdd3885ef01145e3733c7097c00a08'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': ['fabb0b8c97e67c9b34b6cc18ed66f6c5e01c55b257dcf007555e0b027d4caf56'], + }), + ('Parse::RecDescent', '1.967015', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + 'checksums': ['1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37'], + }), + ('GO', '0.04', { + 'runtest': False, # Problem with indirect dependency DBD::Pg + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + 'checksums': ['8eb73d591ad767e7cf26def40cffd84833875f1ad51e456960b9ed73dc23641b'], + }), + ('Class::Trigger', '0.15', { + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['b7a878d44dea67d64df2ca18020d9d868a95596debd16f1a264874209332b07f'], + }), + ('Class::Accessor', '0.51', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['bf12a3e5de5a2c6e8a447b364f4f5a050bf74624c56e315022ae7992ff2f411c'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['94ce27a546cd57cb52e080a8f2533a7cc2350028388582485bd1039a37871f9c'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': ['541354fe361c56850cb11261f6ca089a14573fa764792447444ff736ae626206'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['c4661b00afb7e53c97ac36e13f34dde43c1a93540a2f4ff97e6182b0c731e4e7'], + }), + ('File::Slurper', '0.014', { + 'source_tmpl': 'File-Slurper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['d5a36487339888c3cd758e648160ee1d70eb4153cacbaff57846dbcefb344b0c'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['1b50fba9bbdde3ead192beeba0eaddd0c614e3afb1743fa6fff805f57c56f7f4'], + }), + ('Math::Round', '0.08', { + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['7b4d2775ad3b859a5fd61f7f3fc5cfba42b1a10df086d2ed15a0ae712c8fd402'], + }), + ('Algorithm::Diff', '1.201', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0022da5982645d9ef0207f3eb9ef63e70e9713ed2340ed7b3850779b0d842a7d'], + }), + ('Text::Diff', '1.45', { + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['bd697dd62aaf26d118e9f0a0813429deb1c544e4501559879b61fcbdfe99fe46'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'], + }), + ('Net::SSLeay', '1.94', { + 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", + 'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'], + 'checksums': ['9d7be8a56d1bedda05c425306cc504ba134307e0c09bda4a788c98744ebcd95d'], + }), + ('IO::Socket::SSL', '2.089', { + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + 'checksums': ['f683112c1642967e9149f51ad553eccd017833b2f22eb23a9055609d2e3a14d1'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['dce28e3932762c2ff92aa52d90405c06e898e81cb7b164ccae8966ae77f1dcab'], + }), + ('Meta::Builder', '0.004', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['acb499aa7206eb9db21eb85357a74521bfe3bdae4a6416d50a7c75b939cf56fe'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['4bd70d6ca76f6f6ba7e4c618d4ac93b8593a58f1233ccbe18b10f5f204f1d4e4'], + }), + ('Mouse', 'v2.5.11', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SK/SKAJI'], + 'checksums': ['e2a0d0930190c21a444b960793aa2e369ef28a1dd0b8f34829795f86a1915956'], + }), + ('Test::Version', '2.09', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['9ce1dd2897a5f30e1b7f8966ec66f57d8d8f280f605f28c7ca221fa79aca38e0'], + }), + ('Class::Method::Modifiers', '2.15', { + 'source_tmpl': 'Class-Method-Modifiers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['65cd85bfe475d066e9186f7a8cc636070985b30b0ebb1cde8681cf062c2e15fc'], + }), + ('Moo', '2.005005', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['fb5a2952649faed07373f220b78004a9c6aba387739133740c1770e9b1f4b108'], + }), + ('Data::Dumper::Concise', '2.023', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['a6c22f113caf31137590def1b7028a7e718eface3228272d0672c25e035d5853'], + }), + ('DBIx::Admin::CreateTable', '2.11', { + 'source_tmpl': 'DBIx-Admin-CreateTable-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['07b1427fbc15455657ca57217749004162a50c04abb243022a5b479e4b2a5912'], + }), + ('Config::Tiny', '2.30', { + 'source_tmpl': 'Config-Tiny-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['b2f7345619b3b8e636dd39ea010731c9dc2bfb8f022bcbd86ae6ad17866e110d'], + }), + ('File::Slurp', '9999.32', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['4c3c21992a9d42be3a79dd74a3c83d27d38057269d65509a2f555ea0fb2bc5b0'], + }), + ('DBIx::Admin::DSNManager', '2.02', { + 'source_tmpl': 'DBIx-Admin-DSNManager-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['c25511f42328ccb606a0cd78413a74181c87fb37a382d38aa3fad106b540adcb'], + }), + ('Lingua::EN::PluralToSingular', '0.21', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + 'checksums': ['f8a8b7de28c25c96190d7f48c90b5ad9b9bf517f3835c77641f0e8fa546c0d1d'], + }), + ('Test::Warn', '0.37', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + 'checksums': ['98ca32e7f2f5ea89b8bfb9a0609977f3d153e242e2e51705126cb954f1a06b57'], + }), + ('Test::Differences', '0.71', { + 'runtest': False, # Cryptic test failing + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': ['cac16a56cd843b0809e5b49199d60d75a8dbad7ca9a08380dbf3f5cc3aaa38d9'], + }), + ('Test::Most', '0.38', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + 'checksums': ['089eb894f7bace4c37c6334e0e290eb20338ee10223af0c82cbe7281c78382df'], + }), + ('Const::Fast', '0.014', { + 'source_tmpl': 'Const-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['f805953a08c57846a16a4d85d7b766398afaf7c36c1465fcb1dea09e5fa394db'], + }), + ('Ref::Util', '0.204', { + 'source_tmpl': 'Ref-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARC'], + 'checksums': ['415fa73dbacf44f3d5d79c14888cc994562720ab468e6f71f91cd1f769f105e1'], + }), + ('Class::XSAccessor', '1.19', { + 'source_tmpl': 'Class-XSAccessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['99c56b395f1239af19901f2feeb125d9ecb4e351a0d80daa9529211a4700a6f2'], + }), + ('Hash::Objectify', '0.008', { + 'source_tmpl': 'Hash-Objectify-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['236d5829cdebf3ba648d34e1295cd9099a20506d8d0284668e617e0058cebeed'], + }), + ('Const::Exporter', 'v1.2.3', { + 'source_tmpl': 'Const-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRWO'], + 'checksums': ['53e59b4764aebcf79bbed533ab5a6107339fe516b7f2f607b1bae8dd9dcf7015'], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c'], + }), + ('List::SomeUtils', '0.59', { + 'source_tmpl': 'List-SomeUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['fab30372e4c67bf5a46062da38d1d0c8756279feada866eb439fa29571a2dc7b'], + }), + ('List::UtilsBy', '0.12', { + 'source_tmpl': 'List-UtilsBy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['fff1281fd469fe982b1a58044becfd970f313bff3a26e1c7b2b3f4c0a5ed71e0'], + }), + ('List::AllUtils', '0.19', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['30a8146ab21a7787b8c56d5829cf9a7f2b15276d3b3fca07336ac38d3002ffbc'], + }), + ('Unicode::EastAsianWidth', '12.0', { + 'source_tmpl': 'Unicode-EastAsianWidth-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AU/AUDREYT'], + 'checksums': ['2a5bfd926c4fe5f77e6137da2c31ac2545282ae5fec6e9af0fdd403555a90ff4'], + }), + ('String::TtyLength', '0.03', { + 'source_tmpl': 'String-TtyLength-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['4fedaf72028511d80eb6afba523993e9aaa245d7af558345d5d4ed46e2e82ce1'], + }), + ('Text::Table::Manifold', '1.03', { + 'source_tmpl': 'Text-Table-Manifold-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['e680713169557b0768952fa6932f25576a61dccfb96bd9036dcf6fcefb35e09e'], + }), + ('DBIx::Admin::TableInfo', '3.04', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['b9625992683b97378bea0947773f50e3c9f81974048b84f4c3422cae7e6082f4'], + }), + ('Net::HTTP', '6.23', { + 'runtest': False, # Fragile tests + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['0d65c09dd6c8589b2ae1118174d3c1a61703b6ecfc14a3442a8c74af65e0c94e'], + }), + ('Clone::Choose', '0.010', { + 'source_tmpl': 'Clone-Choose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'], + 'checksums': ['5623481f58cee8edb96cd202aad0df5622d427e5f748b253851dfd62e5123632'], + }), + ('Hash::Merge', '0.302', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'], + 'checksums': ['ae0522f76539608b61dde14670e79677e0f391036832f70a21f31adde2538644'], + }), + ('SQL::Abstract', '2.000001', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSTROUT'], + 'checksums': ['35a642662c349420d44be6e0ef7d8765ea743eb12ad14399aa3a232bb94e6e9a'], + }), + ('HTML::Form', '6.12', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['2ced87d0878afa007d22c41927f0e8da63844608f20881f645f364dc32cdce6f'], + }), + ('IPC::Run', '20231003.0', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eb25bbdf5913d291797ef1bfe998f15130b455d3ed02aacde6856f0b25e4fe57'], + }), + ('File::Remove', '1.61', { + 'source_tmpl': 'File-Remove-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['fd857f585908fc503461b9e48b3c8594e6535766bc14beb17c90ba58d5dc4975'], + }), + ('YAML::Tiny', '1.74', { + 'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['7b38ca9f5d3ce24230a6b8bdc1f47f5b2db348e7f7f9666c26f5955636e33d6c'], + }), + ('Module::Install', '1.21', { + 'source_tmpl': 'Module-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['fbf91007f30565f3920e106055fd0d4287981d5e7dad8b35323ce4b733f15a7b'], + }), + ('Test::ClassAPI', '1.07', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['30e9dbfc5e0cc2ee14eae8f3465a908a710daecbd0a3ebdb2888fc4504fa18aa'], + }), + ('HTTP::Tiny', '0.090', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['faaf60b3f9baf4b8f703632aba223648aaa58b0107e64ca515ed00247978d83e'], + }), + ('Sub::Install', '0.929', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['80b1e281d8cd3b2b31dac711f5c8a1657a87cd80bbe69af3924bcbeb4e5db077'], + }), + ('Package::DeprecationManager', '0.18', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['b68d3f0ced55b7615fddbb6029b89f92a34fe0dd8c6fd6bceffc157d56834fe8'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['68c1dac2187421f0eb7abf71452a06f190181b8fc4b28ededf5b90296fb943cc'], + }), + ('Date::Language', '2.33', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['c0b69c4b039de6f501b0d9f13ec58c86b040c1f7e9b27ef249651c143d605eb2'], + }), + ('version', '0.9933', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['dc07d9388ca3d3f67146312904bcdb35fe416bb30056158f80df3281a94fae58'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'checksums': ['865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': ['ea844b9686c94d666d9d444321d764490b2cde2f985c4165b4c2c77665caedc4'], + }), + ('Sub::Name', '0.27', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ecf36fba1c47ca93e1daa394968ed39c4186867459d9cd173c421e2b972043e8'], + }), + ('Time::Piece', '1.3401', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + 'checksums': ['4b55b7bb0eab45cf239a54dfead277dfa06121a43e63b3fce0853aecfdb04c27'], + }), + ('Digest::HMAC', '1.05', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARODLAND'], + 'checksums': ['215cb59cba610745cfb2d4b3f8ef756d590e57e3ad7986a992e87c4969fcdc7a'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016'], + }), + ('Email::Date::Format', '1.008', { + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['432b7c83ff88749af128003f5257c573aec1a463418db90ed22843cbbc258b4f'], + }), + ('MIME::Lite', '3.033', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['78a279f1d2e242551c347ef97a13fc675766602cb84c2a80c569400f4f368bab'], + }), + ('Crypt::Rijndael', '1.16', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['6540085e3804b82a6f0752c1122cf78cadd221990136dd6fd4c097d056c84d40'], + }), + ('B::Lint', '1.20', { + 'runtest': False, + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['dc49408964fd8b7963859c92e013f0b9f92f74be5a7c2a78e3996279827c10b3'], + }), + ('Canary::Stability', '2013', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a5c91c62cf95fcb868f60eab5c832908f6905221013fea2bce3ff57046d7b6ea'], + }), + ('AnyEvent', '7.17', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['50beea689c098fe4aaeb83806c40b9fe7f946d5769acf99f849f099091a4b985'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['76cb824a27b6b4e560409fcf6fd5b3bfbbd38b72f1f3d37ed0b54bd9c0baeade'], + }), + ('Data::UUID', '1.227', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GT/GTERMARS'], + 'checksums': ['95bda7276265f57bc48ffdeddec5ef28cd6f765e3a183757fa5f09f0ce6b98ac'], + }), + ('Test::Pod', '1.52', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['60a8dbcc60168bf1daa5cc2350236df9343e9878f4ab9830970a5dde6fe8e5fc'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['1177027025ecb09ee64d9f9f255615c04db5e14f7536c344af632032eb887b0f'], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7b29c45add19d3d5084b751f7ba89a8e40479a446ce21cfd9cc741e558332a00'], + }), + ('XML::Tiny', '2.07', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': ['ce39fcb53e0fe9f1cbcd86ddf152e1db48566266b70ec0769ef364eeabdd8941'], + }), + ('HTML::Tree', '5.07', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['f0374db84731c204b86c1d5b90975fef0d30a86bd9def919343e554e31a9dbbf'], + }), + ('Devel::GlobalDestruction', '0.14', { + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['34b8a5f29991311468fe6913cadaba75fd5d2b0b3ee3bb41fe5b53efab9154ab'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['46b502e7a288d559429891eeb5d979461dd3ecc6a5c491ead85d165b6e03a51e'], + }), + ('IO::Tty', '1.20', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['b15309fc85623893289cb9b2b88dfa9ed1e69156b75f29938553a45be6d730af'], + }), + ('Expect', '1.38', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], + 'checksums': ['7b1048335f327958903867cea079dc072ea07f4eafae1b40c2e6f25db21686c0'], + }), + ('Term::UI', '0.50', { + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['60bfdd6d4c158b88d370133fc65b20485a36a45b12d906000b81c78ca524163d'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + 'checksums': ['14c37bc1cbb3f3cdc7d6c13e0f27a859f14cdcfd5ea54a0467a88bc259b0b741'], + }), + ('XML::Filter::BufferText', '1.01', { + 'source_tmpl': 'XML-Filter-BufferText-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RB/RBERJON'], + 'checksums': ['8fd2126d3beec554df852919f4739e689202cbba6a17506e9b66ea165841a75c'], + }), + ('XML::SAX::Writer', '0.57', { + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': ['3d61d07ef43b0126f5b4de4f415a256fa859fa88dc4fdabaad70b7be7c682cf0'], + }), + ('Statistics::Descriptive', '3.0801', { + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['047b70a63fdcaa916168e0ff2d58e155e0ebbc68ed4ccbd73a7213dca3028f65'], + }), + ('Data::OptList', '0.114', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9fd1093b917a21fb79ae1607db53d113b4e0ad8fe0ae776cb077a7e50044fdf3'], + }), + ('Class::Load', '0.25', { + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['2a48fa779b5297e56156380e8b32637c6c58decb4f4a7f3c7350523e11275f8f'], + }), + ('HTTP::Daemon', '6.16', { + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['b38d092725e6fa4e0c4dc2a47e157070491bafa0dbe16c78a358e806aa7e173d'], + }), + ('Test::RequiresInternet', '0.05', { + 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN'], + 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], + }), + ('HTTP::Cookies', '6.11', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['8c9a541a4a39f6c0c7e3d0b700b05dfdb830bd490a1b1942a7dedd1b50d9a8c8'], + }), + ('HTTP::CookieJar', '0.014', { + 'source_tmpl': 'HTTP-CookieJar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['7094ea5c91f536d263b85e83ab4e9a963e11c4408ce08ecae553fa9c0cc47e73'], + }), + ('LWP::Simple', '6.77', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['94a907d6b3ea8d966ef43deffd4fa31f5500142b4c00489bfd403860a5f060e4'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['319601feec17fae344988a5ee91cfc6a0bcfe742af77dba254724c3268b2a60f'], + }), + ('Package::Stash::XS', '0.30', { + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['26bad65c1959c57379b3e139dc776fbec5f702906617ef27cdc293ddf1239231'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': 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['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + 'checksums': ['84d6318279d77844923e4de4275fe4345cd08b225edd7f9ed6a16f87a91aca39'], + }), + ('Devel::CheckLib', '1.16', { + 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], + 'checksums': ['869d38c258e646dcef676609f0dd7ca90f085f56cf6fd7001b019a5d5b831fca'], + }), + ('SVG', '2.87', { + 'source_tmpl': 'SVG-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['b3fa58c1c59942b4ebef003da97c3e01e531480ca29e8efbe327ff0589c0bd3c'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JETTERO'], + 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], + }), + ('Log::Log4perl', '1.57', { + 'source_tmpl': 'Log-Log4perl-%(version)s.tar.gz', + 'source_urls': 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['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['2290d61bf5c39882fc3311da9ce1c7f42dbdf825ae169e552c59fe4598b36f4a'], + }), + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), + ('Heap', '0.80', { + 'source_tmpl': 'Heap-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM'], + 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], + }), + ('Graph', '0.9732', { + 'source_tmpl': 'Graph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['eafc9e519a04ac0a61a3eb34b6e18709411e5abde4bf1d9019c2e371aedf6c50'], + }), + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + ('Parse::Yapp', '1.21', { + 'source_tmpl': 'Parse-Yapp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WB/WBRASWELL'], + 'checksums': ['3810e998308fba2e0f4f26043035032b027ce51ce5c8a52a8b8e340ca65f13e5'], + }), + ('Graph::ReadWrite', '2.10', { + 'source_tmpl': 'Graph-ReadWrite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['516c1ea9facb995dbc38d1735d58974b2399862567e731b729c8d0bc2ee5a14b'], + }), + ('PerlIO::utf8_strict', '0.010', { + 'source_tmpl': 'PerlIO-utf8_strict-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['bcd2848b72df290b5e984fae8b1a6ca96f6d072003cf222389a8c9e8e1c570cd'], + }), + ('Digest::MD5::File', '0.08', { + 'source_tmpl': 'Digest-MD5-File-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['adb43a54e32627b4f7e57c9640e6eb06d0bb79d8ea54cd0bd79ed35688fb1218'], + }), + ('String::RewritePrefix', '0.009', { + 'source_tmpl': 'String-RewritePrefix-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['44918bec96a54af8ca37ca897e436709ec284a07b28516ef3cce4666869646d5'], + }), + ('Getopt::Long::Descriptive', '0.115', { + 'source_tmpl': 'Getopt-Long-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['ea1185a9465cf0790e81827f13c860f18e40ab817ad03b9659a9f28ae1ec5411'], + }), + ('IO::TieCombine', '1.005', { + 'source_tmpl': 'IO-TieCombine-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['402d4db8300b3d271632f4995e0ade329d89280a7e47f2badf8b38af6e5569af'], + }), + ('App::Cmd', '0.336', { + 'source_tmpl': 'App-Cmd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['df966b57d59abb196e00304885e5bf117ca958182ae3f4eedf17218ea2838e81'], + }), + ('Carp::Clan', '6.08', { + 'source_tmpl': 'Carp-Clan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c75f92e34422cc5a65ab05d155842b701452434e9aefb649d6e2289c47ef6708'], + }), + ('Sub::Exporter::ForMethods', '0.100055', { + 'source_tmpl': 'Sub-Exporter-ForMethods-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['791f4203ba7c0f7d8380bc01bec20215f7c8bc70d7ed03e552eee44541abe94e'], + }), + ('MooseX::Types', '0.50', { + 'source_tmpl': 'MooseX-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['9cd87b3492cbf0be9d2df9317b2adf9fc30663770e69906654bea3f41b17cb08'], + }), + ('Variable::Magic', '0.64', { + 'pretestopts': 'LC_ALL=C ', # Test fails if run in localized environments + 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT'], + 'checksums': ['9f7853249c9ea3b4df92fb6b790c03a60680fc029f44c8bf9894dccf019516bd'], + }), + ('MooseX::Types::Perl', '0.101344', { + 'source_tmpl': 'MooseX-Types-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['87644354f74fa65235cb2bfca44277930a7eabe51acc5f81fb631530a8355e24'], + }), + ('Log::Dispatch', '2.71', { + 'source_tmpl': 'Log-Dispatch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['9d60d9648c35ce2754731eb4deb7f05809ece1bd633b74d74795aed9ec732570'], + }), + ('JSON::MaybeXS', '1.004008', { + 'source_tmpl': 'JSON-MaybeXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['cd3937afa78831f80a2ad5abab6c51b9e82fca4c31e5856ea208d598db5dc867'], + }), + ('String::Flogger', '1.101246', { + 'source_tmpl': 'String-Flogger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['15f8491e07818bb3cfa9f6bd3aabf6430ba9b4e309f18114358be3d81bff3a0f'], + }), + ('Log::Dispatch::Array', '1.005', { + 'source_tmpl': 'Log-Dispatch-Array-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['311640b7a967f8dd7c9bb41a227073565636d70df4fcc1d44fed8a8223b347ca'], + }), + ('Sub::Exporter::GlobExporter', '0.006', { + 'source_tmpl': 'Sub-Exporter-GlobExporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['de743f08026701c2a6a222a8b41c4cdc254b1a4afe7ef98987cd3aba4ce52696'], + }), + ('Log::Dispatchouli', '3.008', { + 'source_tmpl': 'Log-Dispatchouli-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7318665b7bcec3cad8dfda1ffe7f026a2d564c721ad31843e3d6e8f5a5ad22ef'], + }), + ('Test::FailWarnings', '0.008', { + 'source_tmpl': 'Test-FailWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['da34ef9029f6849d6026201d49127d054ee6ac4b979c82210315f5721964a96f'], + }), + ('Data::Section', '0.200008', { + 'source_tmpl': 'Data-Section-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['83acc7a55d3dd7ed36e9d78d350af3138c69cfa178a44765822712ff433b990e'], + }), + ('Test::CheckDeps', '0.010', { + 'source_tmpl': 'Test-CheckDeps-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['66fccca6c6f330e7ecc898bd6a51846e2145b3e02d78c4997ba6b7de23b551ee'], + }), + ('Software::License', '0.104006', { + 'runtest': False, # This test just suddenly started to fail + 'source_tmpl': 'Software-License-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['65c8ee1c2da2a4de10139863df668fa6b3b3e24a39d69a7cca39f284fb6b9c0f'], + }), + ('MooseX::SetOnce', '0.203', { + 'source_tmpl': 'MooseX-SetOnce-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['3cd2f3664e438382cf844b679350a2e428b760927e2cf18fccdc468a7bc3066f'], + }), + ('Term::Encoding', '0.03', { + 'source_tmpl': 'Term-Encoding-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['95ba9687d735d25a3cbe64508d7894f009c7fa2a1726c3e786e9e21da2251d0b'], + }), + ('Throwable', '1.001', { + 'source_tmpl': 'Throwable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['d0cb5e9d7d06d70f2cc56eecf857a83a45eaca43850dcdda91d3feb4ddde4c51'], + }), + ('Role::Identifiable::HasIdent', '0.009', { + 'source_tmpl': 'Role-Identifiable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5a735e9f7177f9ebae047eb7bae29b7ec29ec020ae37637aea5350d30c087b76'], + }), + ('MooseX::Role::Parameterized', '1.11', { + 'source_tmpl': 'MooseX-Role-Parameterized-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['1cfe766c5d7f0ecab57f733dcca430a2a2acd6b995757141b940ade3692bec9e'], + }), + ('MooseX::OneArgNew', '0.007', { + 'source_tmpl': 'MooseX-OneArgNew-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['84282435f1169cf09d7513fa9387e2091791635cf35a078b500b829aeea06138'], + }), + ('MooseX::LazyRequire', '0.11', { + 'source_tmpl': 'MooseX-LazyRequire-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ef620c1e019daf9cf3f23a943d25a94c91e93ab312bcd63be2e9740ec0b94288'], + }), + ('String::Formatter', '1.235', { + 'source_tmpl': 'String-Formatter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['08236a913b911ce652cf08598e7c07d2df3f369fc47bf401a485a504a1660783'], + }), + ('String::Errf', '0.009', { + 'source_tmpl': 'String-Errf-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['e1fedbf9b4fd64b64ea81038ddb76a4c6cd85f5db15bc21f10656a298349dc1f'], + }), + ('Role::HasMessage', '0.007', { + 'source_tmpl': 'Role-HasMessage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5e267a4d7620b368481204c88ea2044b8b2a58ff8b05577f2717b2754c0414ce'], + }), + ('Config::MVP', '2.200013', { + 'source_tmpl': 'Config-MVP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['018d161623ee3a67f860d9e680e22e61b79eae6018f0e7c3b525fc934f5b7d45'], + }), + ('Mixin::Linewise::Readers', '0.111', { + 'source_tmpl': 'Mixin-Linewise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['d28e88516ce9b5295c31631dcccdc0fc8f2ab7d8a5cc876bb1b20131087b01db'], + }), + ('Config::INI', '0.029', { + 'source_tmpl': 'Config-INI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0bbe797a730210644a907d90cd4aa2b23ad580cb27bd39393bfc6a7ef9fdfdea'], + }), + ('String::Truncate', '1.100603', { + 'source_tmpl': 'String-Truncate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['ab45602cce2dd9515edfbb2e6e5cde19cdd5498d61a23afd8c46c1f11f8eec62'], + }), + ('Pod::Eventual', '0.094003', { + 'source_tmpl': 'Pod-Eventual-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7f060cc34d11656ce069db061e3d60edc0cabc8f89a4a2dc7eaae95dac856d2d'], + }), + ('Pod::Elemental', '0.103006', { + 'source_tmpl': 'Pod-Elemental-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['750c3a79d8e1824758a6ef7d2dd077dcddca503542b8c34eccd5acbb779dc423'], + }), + ('Test::Object', '0.08', { + 'source_tmpl': 'Test-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['65278964147837313f4108e55b59676e8a364d6edf01b3dc198aee894ab1d0bb'], + }), + ('Hook::LexWrap', '0.26', { + 'source_tmpl': 'Hook-LexWrap-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b60bdc5f98f94f9294b06adef82b1d996da192d5f183f9f434b610fd1137ec2d'], + }), + ('Test::SubCalls', '1.10', { + 'source_tmpl': 'Test-SubCalls-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['cbc1e9b35a05e71febc13e5ef547a31c8249899bb6011dbdc9d9ff366ddab6c2'], + }), + ('PPI', '1.279', { + 'source_tmpl': 'PPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MITHALDU'], + 'checksums': ['f69f4cc2c56d6e92183b80b1dd7337957623c509377ad5578edf1a3b467efa5a'], + }), + ('Config::MVP::Reader::INI', '2.101465', { + 'source_tmpl': 'Config-MVP-Reader-INI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['13c7aa27c1df98cd33ada399e59ff38fabfa9d65513e42af02f72c2d3f636247'], + }), + ('Pod::Weaver', '4.020', { + 'source_tmpl': 'Pod-Weaver-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['655fcf261206c1adbc3038981790b116c31508485135c648093b99b3b3de09d2'], + }), + ('CPAN::Uploader', '0.103018', { + 'source_tmpl': 'CPAN-Uploader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['c4ffe4ede9db79b396e3bfc5e7cdf0e2e9821e1f1e087f523bcfa74c9fc9e248'], + }), + ('Devel::FindPerl', '0.016', { + 'source_tmpl': 'Devel-FindPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['43a2bf2f787a3f1b881179063162b2aa3e7cb044f6e5e76ec6466ae90a861138'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), + ('Perl::PrereqScanner', '1.100', { + 'source_tmpl': 'Perl-PrereqScanner-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['01181d38a2e7aff838d262122563c50636ba4b3652ee5d1d4f8ef5ba3f5b186b'], + }), + ('Dist::Zilla', '6.032', { + 'source_tmpl': 'Dist-Zilla-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5c771a1dc2daab5afae0fd59e5046111970f73bf3eaec9df70d8e07346f8165e'], + }), + ('XML::RegExp', '0.04', { + 'source_tmpl': 'XML-RegExp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'], + 'checksums': ['df1990096036085c8e2d45904fe180f82bfed40f1a7e05243f334ea10090fc54'], + }), + ('XML::DOM', '1.46', { + 'source_tmpl': 'XML-DOM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'], + 'checksums': ['8ba24b0b459b01d6c5e5b0408829c7d5dfe47ff79b3548c813759048099b175e'], + }), + ('Data::Dump', '1.25', { + 'source_tmpl': 'Data-Dump-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': ['a4aa6e0ddbf39d5ad49bddfe0f89d9da864e3bc00f627125d1bc580472f53fbd'], + }), + ('File::Next', '1.18', { + 'source_tmpl': 'File-Next-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['f900cb39505eb6e168a9ca51a10b73f1bbde1914b923a09ecd72d9c02e6ec2ef'], + }), + ('App::cpanminus', '1.7048', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['59b60907ab9fa4f72ca2004fbe6054911439ae9a906890b4d842a87b25f20f3c'], + }), + ('Parallel::ForkManager', '2.03', { + 'source_tmpl': 'Parallel-ForkManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Y/YA/YANICK'], + 'checksums': ['c0e0bead458224b9ac5bb32ed2b1fa088963b565521c1bb1a6a3566d522c2e35'], + }), + ('Object::InsideOut', '4.05', { + 'source_tmpl': 'Object-InsideOut-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], + }), + ('Logger::Simple', '2.0', { + 'source_tmpl': 'Logger-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TS/TSTANLEY'], + 'checksums': ['2e63fd3508775b5902132ba1bfb03b42bee468dfaf35dfe42e1909ff6d291b2d'], + }), + ('Scalar::Util::Numeric', '0.40', { + 'source_tmpl': 'Scalar-Util-Numeric-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], + 'checksums': ['d7501b6d410703db5b1c1942fbfc41af8964a35525d7f766058acf5ca2cc4440'], + }), + ('Spiffy', '0.46', { + 'source_tmpl': 'Spiffy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['8f58620a8420255c49b6c43c5ff5802bd25e4f09240c51e5bf2b022833d41da3'], + }), + ('Test::Base', '0.89', { + 'source_tmpl': 'Test-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['2794a1aaaeb1d3a287dd2c7286258663796562f7db9ccc6b424bc4f1de8ad014'], + }), + ('Test::YAML', '1.07', { + 'source_tmpl': 'Test-YAML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TINITA'], + 'checksums': ['1f300d034f46298cb92960912cc04bac33fb27f05b8852d8f051e110b9cd995f'], + }), + ('YAML', '1.31', { + 'source_tmpl': 'YAML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['a0ce30381657dce8e694df9a09e95d818d13beb03698fd2cf79d0c8d564a9b8e'], + }), + ('Object::InsideOut', '4.05', { + 'source_tmpl': 'Object-InsideOut-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], + }), + ('Term::ReadLine::Gnu', '1.46', { + 'modulename': 'Term::ReadLine', + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", + 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], + 'checksums': ['b13832132e50366c34feac12ce82837c0a9db34ca530ae5d27db97cf9c964c7b'], + }), + ('ExtUtils::MakeMaker', '7.70', { + 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['f108bd46420d2f00d242825f865b0f68851084924924f92261d684c49e3e7a74'], + }), + ('Scalar::Util', '1.68', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['23317e4346fe8747f0167eccd1881d6369aa71023f014cd6f846988843295906'], + }), + ('Module::CoreList', '5.20241120', { + 'source_tmpl': 'Module-CoreList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['ece8351079ef8577dae8681ff6fa351850b06d2afba50a306bfb29921668abd9'], + }), + ('Module::Metadata', '1.000038', { + 'source_tmpl': 'Module-Metadata-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b599d8770a9a9fa0a8ae3cd0ed395a9cf71b4eb53aed82989a6bece33485a9cd'], + }), + ('Params::Check', '0.38', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Params-Check-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['f0c9d33876c36b1bca1475276d26d2efaf449b256d7cc8118fae012e89a26290'], + }), + ('Locale::Maketext::Simple', '0.21', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Locale-Maketext-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], + 'checksums': ['b009ff51f4fb108d19961a523e99b4373ccf958d37ca35bf1583215908dca9a9'], + }), + ('Perl::OSType', '1.010', { + 'source_tmpl': 'Perl-OSType-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['e7ed4994b5d547cb23aadb84dc6044c5eb085d5a67a6c5624f42542edd3403b2'], + }), + ('IPC::Cmd', '1.04', { + 'source_tmpl': 'IPC-Cmd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['d110a0f60e35c65721454200f0d2f0f8965529a2add9649d1fa6f4f9eccb6430'], + }), + ('Pod::Escapes', '1.07', { + 'source_tmpl': 'Pod-Escapes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], + }), + ('if', '0.0608', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'modulename': False, + 'source_tmpl': 'if-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], + }), + ('Test', '1.26', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Test-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], + 'checksums': ['f7701bd28e05e7f82fe9a181bbab38f53fa6aeae48d2a810da74d1b981d4f392'], + }), + ('ExtUtils::Constant', '0.25', { + 'runtest': False, # Somehow has syntax errors in tests + 'source_tmpl': 'ExtUtils-Constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['6933d0e963b62281ef7561068e6aecac8c4ac2b476b2bba09ab0b90fbac9d757'], + }), + ('ExtUtils::CBuilder', '0.280236', { + 'source_tmpl': 'ExtUtils-CBuilder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AM/AMBS'], + 'checksums': ['abc21827eb8a513171bf7fdecefce9945132cb76db945036518291f607b1491f'], + }), + ('Carp::Heavy', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('Pod::Simple', '3.45', { + 'source_tmpl': 'Pod-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KH/KHW'], + 'checksums': ['8483bb95cd3e4307d66def092a3779f843af772482bfdc024e3e00d0c4db0cfa'], + }), + ('Socket', '2.038', { + 'source_tmpl': 'Socket-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['563d11731ff44307fa2779a6958fd2d2f6643fbd9a3174cbf350228b159681f8'], + }), + ('Time::Local', '1.35', { + 'source_tmpl': 'Time-Local-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['1d136b71bd041cbe6f66c43180ee79e675b72ad5a3596abd6a44d211072ada29'], + }), + ('Storable', '3.25', { + 'source_tmpl': 'Storable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['e1e96b24a076792fde52154789fe4b76034b9ad39c8a1a819ead77d50d5f1817'], + }), + ('ExtUtils::ParseXS', '3.51', { + 'source_tmpl': 'ExtUtils-ParseXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['82431a57425d78682acefb3a2cc9287683d091c8d034b825c584d9805bed6535'], + }), + ('Pod::Man', 'v6.0.2', { + 'source_tmpl': 'podlators-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRA'], + 'checksums': ['2992125eab7d2b1c5a2b15a26ad7955f7d989eba6c831abdcaf2000e86a91337'], + }), + ('Mozilla::CA', '20240924', { + 'source_tmpl': 'Mozilla-CA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LW/LWP'], + 'checksums': ['c4b1412bbc37dff8cf29af6f92cb47defbe90eebcbc29e407a98638f7a31bcd0'], + }), + ('LWP::Protocol::https', '6.14', { + 'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['59cdeabf26950d4f1bef70f096b0d77c5b1c5a7b5ad1b66d71b681ba279cbb2a'], + }), + ('Module::Load', '0.36', { + 'source_tmpl': 'Module-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['d825020ac00b220e89f9524e24d838f9438b072fcae8c91938e4026677bef6e0'], + }), + ('Module::Load::Conditional', '0.74', { + 'source_tmpl': 'Module-Load-Conditional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['54c354a9393820f1ebc2a095da084ea0392dcbccb0cb38a187a71831cc60a730'], + }), + ('parent', '0.243', { + 'source_tmpl': 'parent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['47b3e7af5c59bf88073bb8095b91c53fb8e35f915dc159370f6c11479c279b02'], + }), + ('Net::Domain', '3.15', { + 'source_tmpl': 'libnet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['a71f4db580e1a767d6936faa5baf38f1fa617824342da078b561283e86f8f4a2'], + }), + ('Encode', '3.21', { + 'source_tmpl': 'Encode-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], + 'checksums': ['eacf71c5eb49e0e590de797f1982d7fb95d8481e4d13c3ce79eb32ef9373b3db'], + }), + ('Cwd', '3.75', { + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'runtest': False, # Single failure about a tainted PATH + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': [ + {'PathTools-3.75.tar.gz': 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'}, + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], + }), + ('MIME::Base64', '3.16', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['77f73d6f7aeb8d33be08b0d8c2617f9b6c77fb7fc45422d507ca8bafe4246017'], + }), + ('ExtUtils::CppGuess', '0.27', { + 'runtest': False, # Poorly written test + 'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['b2c7b581901054a32dfcea12536fda8626457ed0bfbc02600bd354bde7e2a9b4'], + }), + ('XSLoader', '0.24', { + 'source_tmpl': 'XSLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'], + 'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], + }), + ('AutoLoader', '5.74', { + 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], + 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], + }), + ('MCE::Mutex', '1.900', { + 'runtest': False, # Single failing subtest + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], + 'checksums': ['f83132da7a993a4700464cdbf1665bab8ec8ec120beb86e607cd983d207fc935'], + }), + ('Text::CSV_XS', '1.57', { + 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['54dd63feb59e80d2ec596ac6bd8f8f80eb2042099fb68e35f3b47901c768621f'], + }), + ('DBD::CSV', '0.60', { + 'source_tmpl': 'DBD-CSV-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['018b83a30f799979bc8c3c3044c8b1c8001cdf60bdc3e746848818195254b4e7'], + }), + ('Array::Transpose', '0.06', { + 'source_tmpl': 'Array-Transpose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'], + 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], + }), + ('Config::Simple', '4.58', { + 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], + 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], + }), + ('Business::ISBN::Data', '20241205.001', { + 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BR/BRIANDFOY'], + 'checksums': ['582db1dae54c135f0a64357b366fb4690121a4279a11636998f596918328e496'], + }), + ('Business::ISBN', '3.009', { + 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BR/BRIANDFOY'], + 'checksums': ['d2ec1970454af1b2c099dd34caa7a348ca6fd323bb7ddbfad55389bd7f96789b'], + }), + ('common::sense', '3.75', { + 'source_tmpl': 'common-sense-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], + }), + ('Compress::Raw::Zlib', '2.213', { + 'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['56b21c99cb3a3a7f7876a74dd05daa3f41fc9143ddd4dc98f8e46710a106af45'], + }), + ('Compress::Raw::Bzip2', '2.213', { + 'source_tmpl': 'Compress-Raw-Bzip2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['8d75d3d366c9101ca18061b00d438d3da39478c06159147dea3c666770577c7b'], + }), + ('IO::Compress::Zip', '2.213', { + 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['ae4d01ae574e4568c5f2fb0573e74631e2720b71ad3bc5a3ffe9480f1cb9a851'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('JSON::XS', '4.03', { + 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], + }), + ('Authen::NTLM', '1.09', { + 'source_tmpl': 'NTLM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'], + 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('XML::SAX::Expat', '0.51', { + 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN'], + 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], + }), + ('Inline', '0.86', { + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], + }), + ('Test::Sys::Info', '0.23', { + # test fails on systems without /etc/fstab - so comment it out + 'preconfigopts': "sed -i 's/ok( my %fs/# ok( my %fs/' lib/Test/Sys/Info/Driver.pm && ", + 'source_tmpl': 'Test-Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['30c5f2c4cfee8e1ae6d9fb6291f79addbff5739ba4efa5b1e034520f18fbc95a'], + }), + ('Sys::Info::Base', '0.7807', { + 'source_tmpl': 'Sys-Info-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['132362b0046e8dc4f12e1560903623a88a8871d09bf1c29d93d48d3f4a582acb'], + }), + ('Sys::Info::Driver::Unknown::Device::CPU', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('Sys::Info::Driver::Linux::Device::CPU', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Sys::Info', '0.7811', { + 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'], + }), + ('CGI', '4.66', { + 'source_tmpl': 'CGI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': ['4697437688a193e3f02556e1d223015590c1f2800b40becf83dc12d5cc5ed8e1'], + }), + ('HTML::Template', '2.97', { + 'source_tmpl': 'HTML-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR'], + 'checksums': ['6547af61f3aa85793f8616190938d677d7995fb3b720c16258040bc935e2129f'], + }), + ('MIME::Charset', 'v1.013.1', { + 'source_tmpl': 'MIME-Charset-1.013.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'], + 'checksums': ['1bb7a6e0c0d251f23d6e60bf84c9adefc5b74eec58475bfee4d39107e60870f0'], + }), + ('Unicode::LineBreak', '2019.001', { + 'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'], + 'checksums': ['486762e4cacddcc77b13989f979a029f84630b8175e7fef17989e157d4b6318a'], + }), + ('String::Print', '0.94', { + 'source_tmpl': 'String-Print-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'], + }), + ('Log::Report::Optional', '1.07', { + 'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], + }), + ('Log::Report', '1.39', { + 'source_tmpl': 'Log-Report-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['79ac19f474ca4c078e5b66073478d37a83ef6a02b6689e4a59a9fcc838976f2b'], + }), + ('Sys::Info::Driver::Unknown', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Sys::Info::Driver::Linux', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), + ('Devel::Size', '0.84', { + 'source_tmpl': 'Devel-Size-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['db2e4d65f688dbf59273b5e82101ac3f1a66f665afb0594dce168b8650a4d0e4'], + }), + ('Math::Utils', '1.14', { + 'source_tmpl': 'Math-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE'], + 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.40.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.40.0-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..43ab8107099 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.40.0-GCCcore-14.2.0.eb @@ -0,0 +1,86 @@ +name = 'Perl' +version = '5.40.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +Includes a small selection of extra CPAN packages for core functionality. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c740348f357396327a9795d3e8323bafd0fe8a5c7835fc1cbaba0cc8dfe7161f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('zlib', '1.3.1'), +] + +# !! order of extensions is important !! +# extensions updated on 2024-06-11 +# includes all dependencies for Autotools +exts_list = [ + ('threads', '2.21', { + 'source_tmpl': 'threads-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['28394c98a2bcae6f20ffb8a3d965a1c194b764c650169e2050ee38dbaa10f110'], + }), + ('constant', '1.33', { + 'source_tmpl': 'constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], + }), + ('Getopt::Long', '2.58', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + 'checksums': ['1305ed46ea21f794304e97aa3dcd3a38519059785e9db7415daf2c218506c569'], + }), + ('File::Path', '2.18', { + 'source_tmpl': 'File-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN/'], + 'checksums': ['980f0a17edb353df46e9cd7b357f9f5929cde0f80c45fd7a06cf7e0e8bd6addd'], + }), + ('File::Spec', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('IO::File', '1.55', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'], + 'checksums': ['0443afebb9a48f29611e9b17a017f430b51167a498fa4646c07f8dce03b6b95f'], + }), + ('Thread::Queue', '3.13', { + 'source_tmpl': 'Thread-Queue-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['6ba3dacddd2fbb66822b4aa1d11a0a5273cd04c825cb3ff31c20d7037cbfdce8'], + }), + ('Carp', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('Exporter', '5.78', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['bd17e99219aa2fb6a8acb3d11deffcb588708c70fc29f346e20ea7f71d3a48f0'], + }), + ('Text::ParseWords', '3.31', { + 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], + 'checksums': ['2ae555ba084d75b2b8feeeb8d1a00911276815ada86bccb1452236964d5a2fc7'], + }), + ('Data::Dumper', '2.183', { + 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], + 'checksums': ['e42736890b7dae1b37818d9c5efa1f1fdc52dec04f446a33a4819bf1d4ab5ad3'], + }), +] + +moduleclass = 'lang' From 0a7c8cecae0da86d04f05892bd1a8e977af702b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Dec 2024 17:16:32 +0100 Subject: [PATCH 189/414] remove empty 'sources' list in juliaup easyconfig --- easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb index c7a3fcb714e..91e51f8555c 100644 --- a/easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb @@ -8,7 +8,6 @@ description = """This repository contains a cross-platform installer for the Jul toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -sources = [] checksums = [ {'juliaup-1.17.9.tar.gz': '623e65f93377b21096e2fec84c7474ed940d10956ca5d51dbaf04e3b428e0261'}, {'addr2line-0.24.2.tar.gz': 'dfbe277e56a376000877090da837660b4427aad530e3028d44e0bffe4f89a1c1'}, From 1a260b0c046842727e1b4e70e3b12ae6cd25302e Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 7 Dec 2024 17:33:20 +0000 Subject: [PATCH 190/414] checksums --- .../easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb | 2 +- easybuild/easyconfigs/l/libtool/libtool-2.5.4-GCCcore-14.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb index 79c73627108..3ce264f9c90 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '14.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] +checksums = ['397767d4db3018dd4440825b60c64258b636eaf6bf99ac8b0897f06c89310acd'] builddependencies = [ ('binutils', '2.42'), diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.5.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.5.4-GCCcore-14.2.0.eb index dfe44f36c0f..b44f9ef2f77 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.5.4-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.5.4-GCCcore-14.2.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '14.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] +checksums = ['da8ebb2ce4dcf46b90098daf962cffa68f4b4f62ea60f798d0ef12929ede6adf'] builddependencies = [ ('binutils', '2.42'), From 0bd94feaa58e235933fb1762cd5e4b3dcb485284 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 8 Dec 2024 12:04:15 +0000 Subject: [PATCH 191/414] Drop extensions already included in Perl dist --- .../p/Perl/Perl-5.40.0-GCCcore-14.2.0.eb | 37 +------------------ 1 file changed, 1 insertion(+), 36 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.40.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.40.0-GCCcore-14.2.0.eb index 43ab8107099..505064f36f4 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.40.0-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.40.0-GCCcore-14.2.0.eb @@ -23,19 +23,9 @@ dependencies = [ ] # !! order of extensions is important !! -# extensions updated on 2024-06-11 +# extensions updated on 2024-12-08 # includes all dependencies for Autotools exts_list = [ - ('threads', '2.21', { - 'source_tmpl': 'threads-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], - 'checksums': ['28394c98a2bcae6f20ffb8a3d965a1c194b764c650169e2050ee38dbaa10f110'], - }), - ('constant', '1.33', { - 'source_tmpl': 'constant-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], - }), ('Getopt::Long', '2.58', { 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], @@ -51,36 +41,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], }), - ('IO::File', '1.55', { - 'source_tmpl': 'IO-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'], - 'checksums': ['0443afebb9a48f29611e9b17a017f430b51167a498fa4646c07f8dce03b6b95f'], - }), - ('Thread::Queue', '3.13', { - 'source_tmpl': 'Thread-Queue-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], - 'checksums': ['6ba3dacddd2fbb66822b4aa1d11a0a5273cd04c825cb3ff31c20d7037cbfdce8'], - }), - ('Carp', '1.50', { - 'source_tmpl': 'Carp-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], - }), - ('Exporter', '5.78', { - 'source_tmpl': 'Exporter-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], - 'checksums': ['bd17e99219aa2fb6a8acb3d11deffcb588708c70fc29f346e20ea7f71d3a48f0'], - }), ('Text::ParseWords', '3.31', { 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], 'checksums': ['2ae555ba084d75b2b8feeeb8d1a00911276815ada86bccb1452236964d5a2fc7'], }), - ('Data::Dumper', '2.183', { - 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], - 'checksums': ['e42736890b7dae1b37818d9c5efa1f1fdc52dec04f446a33a4819bf1d4ab5ad3'], - }), ] moduleclass = 'lang' From ee413cf2b37abe669e07249848df419e01b3661b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 8 Dec 2024 14:48:25 +0000 Subject: [PATCH 192/414] Fix automake --- .../Automake/Automake-1.17-GCCcore-14.2.0.eb | 6 +++++- .../Automake-1.17_perl_env_space.patch | 19 +++++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.17_perl_env_space.patch diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb index 3ce264f9c90..289fab45a9c 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '14.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['397767d4db3018dd4440825b60c64258b636eaf6bf99ac8b0897f06c89310acd'] +patches = ['Automake-%(version)s_perl_env_space.patch'] +checksums = [ + {'automake-1.17.tar.gz': '397767d4db3018dd4440825b60c64258b636eaf6bf99ac8b0897f06c89310acd'}, + {'Automake-1.17_perl_env_space.patch': 'a416eeb854df009f0cdec0484282a3cf7ff6b2637a59e1188932d946625196ab'}, +] builddependencies = [ ('binutils', '2.42'), diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.17_perl_env_space.patch b/easybuild/easyconfigs/a/Automake/Automake-1.17_perl_env_space.patch new file mode 100644 index 00000000000..45b96bee3e1 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.17_perl_env_space.patch @@ -0,0 +1,19 @@ +Removes the incorrect assumption that the shebang must not have spaces, +since we correctly use "/usr/bin/env perl" + +author: micketeer@gmail.com + +--- configure.orig 2024-12-08 14:41:01.243852603 +0000 ++++ configure 2024-12-08 14:41:51.837762787 +0000 +@@ -3513,11 +3513,6 @@ + '') + as_fn_error $? "perl not found" "$LINENO" 5 + ;; +- *' '* | *' '*) +- as_fn_error $? "The path to your Perl contains spaces or tabs. +-This would cause build failures later or unusable programs. +-Please use a path without spaces and try again." "$LINENO" 5 +- ;; + esac + + # Save details about the selected perl interpreter in config.log. From 9debfc554bfb590d8727506d4a5c6ca04c08da64 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 9 Dec 2024 10:24:14 +0100 Subject: [PATCH 193/414] Update AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb move Jupyterlab dependency to end of list --- .../AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb index cdcc434dc64..d654f63ae5f 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb @@ -26,7 +26,6 @@ dependencies = [ ('Biopython', '1.83'), ('h5py', '3.9.0'), ('IPython', '8.14.0'), - ('JupyterLab', '4.0.5'), ('matplotlib', '3.7.2'), # ('TensorFlow', '2.15.1', versionsuffix), ('TensorFlow', '2.13.0'), # to be consistent with AF2 ? @@ -38,6 +37,7 @@ dependencies = [ ('HH-suite', '3.3.0'), ('dm-haiku', '0.0.12', versionsuffix), ('Uni-Core', '0.0.3', versionsuffix), + ('JupyterLab', '4.0.5'), ] local_commit = 'cc4b0af60518c078305bbe4c584691d1ed9ade31' use_pip = True From 2935eb6d2910ae9c52100c01c61d064573073add Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 9 Dec 2024 11:00:10 +0100 Subject: [PATCH 194/414] fix failing test --- .../easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb index 91e51f8555c..2d3ee84f6e1 100644 --- a/easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/juliaup/juliaup-1.17.9-GCCcore-12.3.0.eb @@ -547,6 +547,8 @@ builddependencies = [ ('Rust', '1.75.0'), ] +pretestopts = "sed -i 's/1.11.1/1.11/' tests/command_initial_setup_from_launcher_test.rs && " + sanity_check_paths = { 'files': ['bin/%(name)s'], 'dirs': [], From 3151a274b5b8610f6b320273c5727ca7cabaf314 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 9 Dec 2024 15:54:37 +0100 Subject: [PATCH 195/414] adding easyconfigs: L_RNA_scaffolder-20190530-GCC-13.2.0.eb --- .../b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb | 58 +++++++++++++++++++ .../d/DB/DB-18.1.40-GCCcore-13.2.0.eb | 33 +++++++++++ .../d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb | 31 ++++++++++ .../L_RNA_scaffolder-20190530-GCC-13.2.0.eb | 38 ++++++++++++ 4 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..73cecdb978c --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb @@ -0,0 +1,58 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center +# Thomas Eylenbosch - Gluo NV + +easyblock = 'Bundle' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.38.0'), + ('Perl-bundle-CPAN', '5.38.0'), + ('XML-LibXML', '2.0210'), + ('DB_File', '1.859'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..40a6ad43ecc --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('OpenSSL', '3', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7e40f6d223f --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.859' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['5674e0d2cd0b060c4d1253670ea022c64d842a55257f9eb8edb19c0f53e2565c'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Perl', '5.38.0'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-13.2.0.eb b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-13.2.0.eb new file mode 100644 index 00000000000..3655f3168bb --- /dev/null +++ b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'L_RNA_scaffolder' +local_commit = '98f19e3' +version = '20190530' + +homepage = 'https://github.com/CAFS-bioinformatics/L_RNA_scaffolder' +description = "L_RNA_scaffolder is a genome scaffolding tool with long trancriptome reads" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/CAFS-bioinformatics/L_RNA_scaffolder/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['ef4c5bf3511e9947bdb33201bdcaf1ff779ca315a2139f73bb549fb6bfc05f5a'] + +dependencies = [ + ('BioPerl', '1.7.8'), +] + +fix_perl_shebang_for = ['*.pl'] + +# make sure exec permissions are set for all binaries and scripts (everything except README.md and easybuild subdir) +postinstallcmds = ["ls -d %(installdir)s/* | egrep -v '/README.md|/easybuild$' | xargs chmod a+x"] + +sanity_check_paths = { + 'files': ['calculate-lc', 'calculate-pid', 'convert', 'convert_linker', 'count_connection_frequency', + 'delete_block', 'delete_linker', 'delete_same_fragment', 'filter_scaffold.pl', + 'find_end_node', 'find_reliable_connection', 'find_start_node', 'form_block', + 'form_path.pl', 'generate_scaffold.pl', 'generate_unscaffold.pl', 'L_RNA_scaffolder.sh', 'link_block', + 'order', 'overlap', 'route.pl', 'search_guider', 'select_nodes'], + 'dirs': [], +} + +sanity_check_commands = ["L_RNA_scaffolder.sh -? | grep '^Usage: sh L_RNA_scaffolder.sh'"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From e26bc12c9da9007c763d73726a20c795b331b701 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 9 Dec 2024 16:16:24 +0100 Subject: [PATCH 196/414] adding easyconfigs: purge_dups-1.2.6-foss-2023b.eb --- .../purge_dups/purge_dups-1.2.6-foss-2023b.eb | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb diff --git a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb new file mode 100644 index 00000000000..6848c4131d1 --- /dev/null +++ b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb @@ -0,0 +1,85 @@ +easyblock = 'PythonBundle' + +name = 'purge_dups' +version = '1.2.6' + +homepage = 'https://github.com/dfguan/purge_dups' +description = "purge haplotigs and overlaps in an assembly based on read depth" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('pybind11', '2.11.1'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('Python', '3.11.5'), + ('matplotlib', '3.8.2'), + ('minimap2', '2.28'), +] + +use_pip = True + +default_easyblock = 'MakeCp' + +components = [ + (name, version, { + 'source_urls': ['https://github.com/dfguan/purge_dups/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['75b20df834d28410858ccd4e2d65b6c70849f3cbe5fc05959f38bfc2d041c704'], + 'start_dir': 'purge_dups-%(version)s', + 'prebuildopts': "cd src && ", + 'buildopts': 'CC="$CC" CFLAGS="$CFLAGS"', + 'files_to_copy': ['bin', 'scripts'], + }), + ('KMC', '20190629', { + 'source_urls': ['https://github.com/dfguan/KMC/archive'], + 'sources': [{'download_filename': 'c05a5f9.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [{ + 'name': 'KMC_use_EB_pybind11_and_libs.patch', + 'sourcepath': 'KMC-c05a5f9fd94683248ebe04484a60f86792cf328f', + }], + 'checksums': [ + '7251941f4b1913bfdd68759d9292b419d95fe7c63815056e15ecb097a12a0bc4', + '2f54971aae26787777d0e4b638a9682bd4bc22cbf3fda170c7baf4c610808ac9', + ], + 'prebuildopts': 'cd KMC-* && ', + 'buildopts': 'CC="$CXX"', + 'files_to_copy': [(['KMC-*/bin/*kmc*'], 'bin'), 'KMC-*/spectra.py'], + }), +] + +exts_list = [ + ('runner', '20191220', { + 'preinstallopts': "sed -i 's/0.0.0/%(version)s/g' setup.py && ", + 'sources': [{ + 'git_config': { + 'url': 'https://github.com/dfguan/', + 'repo_name': 'runner', + 'commit': '73a4d11', + }, + 'filename': 'runner-%(version)s.tar.gz', + }], + 'checksums': [None], + }), +] + +sanity_check_paths = { + 'files': ['bin/kmc', 'bin/purge_dups'], + 'dirs': ['scripts'], +} + +sanity_check_commands = [ + "purge_dups -h 2>&1 | grep 'Program: purge_dups'", + "kmc --help", + "run_purge_dups.py -h", + "hist_plot.py -h", +] + +sanity_pip_check = True + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From 7b618299a721907a13fe315099a5343b8676b8ed Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 9 Dec 2024 16:19:15 +0100 Subject: [PATCH 197/414] purge_dups: Add KMC patch to use EB pybind11 and libs --- .../KMC_use_EB_pybind11_and_libs.patch | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/purge_dups/KMC_use_EB_pybind11_and_libs.patch diff --git a/easybuild/easyconfigs/p/purge_dups/KMC_use_EB_pybind11_and_libs.patch b/easybuild/easyconfigs/p/purge_dups/KMC_use_EB_pybind11_and_libs.patch new file mode 100644 index 00000000000..465979ce64b --- /dev/null +++ b/easybuild/easyconfigs/p/purge_dups/KMC_use_EB_pybind11_and_libs.patch @@ -0,0 +1,39 @@ +Use pybind11 from EasyBuild install +Required to use Python != 3.10 +Also use zlib and bzip2 from EB install + +Åke Sandgren, 2024-12-09 +diff --git a/makefile b/makefile +index 09f4de3..918dcae 100644 +--- a/makefile ++++ b/makefile +@@ -36,9 +36,7 @@ $(KMC_MAIN_DIR)/raduls_sse41.o \ + $(KMC_MAIN_DIR)/raduls_avx2.o \ + $(KMC_MAIN_DIR)/raduls_avx.o + +-KMC_LIBS = \ +-$(KMC_MAIN_DIR)/libs/libz.a \ +-$(KMC_MAIN_DIR)/libs/libbz2.a ++KMC_LIBS = -lz -lbz2 + + KMC_DUMP_OBJS = \ + $(KMC_DUMP_DIR)/nc_utils.o \ +@@ -64,9 +62,7 @@ $(KMC_TOOLS_DIR)/fastq_reader.o \ + $(KMC_TOOLS_DIR)/fastq_writer.o \ + $(KMC_TOOLS_DIR)/percent_progress.o + +-KMC_TOOLS_LIBS = \ +-$(KMC_TOOLS_DIR)/libs/libz.a \ +-$(KMC_TOOLS_DIR)/libs/libbz2.a ++KMC_TOOLS_LIBS = -lz -lbz2 + + $(KMC_OBJS) $(KMC_DUMP_OBJS) $(KMC_API_OBJS): %.o: %.cpp + $(CC) $(CFLAGS) -c $< -o $@ +@@ -102,7 +98,6 @@ py_kmc_api: $(PY_KMC_API_OBJS) $(PY_KMC_API_OBJS) + -mkdir -p $(KMC_BIN_DIR) + $(CC) -fPIC -Wall -shared -std=c++11 -O3 $(PY_KMC_API_DIR)/py_kmc_api.cpp $(PY_KMC_API_OBJS) \ + -I $(KMC_API_DIR) \ +- -I $(PY_KMC_API_DIR)/libs/pybind11/include \ + -I `python3 -c "import sysconfig;print(sysconfig.get_paths()['include'])"` \ + -o $(KMC_BIN_DIR)/$@`python3-config --extension-suffix` + From 344cf1f67fc5f7bea9da2ff73c173fb4b08495dc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 9 Dec 2024 16:32:41 +0100 Subject: [PATCH 198/414] DB: downlevel OpenSSL to match other usages in this toolchain version. --- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb index 40a6ad43ecc..a15e88f596d 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.40')] -dependencies = [('OpenSSL', '3', '', SYSTEM)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', From 0ddf49cda2e87a7160b3910efac82042b19ca8e8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 9 Dec 2024 16:43:53 +0100 Subject: [PATCH 199/414] adding easyconfigs: KMC-3.2.4-GCC-13.2.0.eb and patches: KMC-3.2.4_use_EB_pybind11_and_libs.patch --- .../easyconfigs/k/KMC/KMC-3.2.4-GCC-13.2.0.eb | 51 +++++++++++++++++ .../KMC-3.2.4_use_EB_pybind11_and_libs.patch | 57 +++++++++++++++++++ 2 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/k/KMC/KMC-3.2.4-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/k/KMC/KMC-3.2.4_use_EB_pybind11_and_libs.patch diff --git a/easybuild/easyconfigs/k/KMC/KMC-3.2.4-GCC-13.2.0.eb b/easybuild/easyconfigs/k/KMC/KMC-3.2.4-GCC-13.2.0.eb new file mode 100644 index 00000000000..954078ee206 --- /dev/null +++ b/easybuild/easyconfigs/k/KMC/KMC-3.2.4-GCC-13.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' + +name = 'KMC' +version = '3.2.4' + +homepage = 'http://sun.aei.polsl.pl/kmc' +description = "KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/refresh-bio/KMC/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['KMC-3.2.4_use_EB_pybind11_and_libs.patch'] +checksums = [ + {'v3.2.4.tar.gz': 'dde49d9a3c9b30dd9e231650265f6de335e180e5a642503677ebbcad8e85504c'}, + {'KMC-3.2.4_use_EB_pybind11_and_libs.patch': 'b8cba49891a6243381b8b4efec099c4907499863b3f89c2c7c6348103e9c86ef'}, +] + +builddependencies = [ + ('pybind11', '2.11.1'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('Python', '3.11.5'), +] + +# Makefile does static linking with libc.a, libpthread.a, libm.a +osdependencies = [('glibc-static', 'libc6-dev')] + +prebuildopts = """sed -i 's@^#include.*zlib.h.*@#include @' ./kmc_core/fastq_reader.h && """ +prebuildopts += """sed -i 's@^#include.*zlib.h.*@#include @' ./kmc_tools/fastq_reader.h && """ + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/kmc', 'bin/kmc_dump'], + 'dirs': [], +} + +sanity_check_commands = [ + "kmc", + "kmc_dump", + "python -c 'import py_kmc_api'", +] + +# Python bindings are also located in bin/ +modextrapaths = {'PYTHONPATH': ['bin']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/KMC/KMC-3.2.4_use_EB_pybind11_and_libs.patch b/easybuild/easyconfigs/k/KMC/KMC-3.2.4_use_EB_pybind11_and_libs.patch new file mode 100644 index 00000000000..0b00174e146 --- /dev/null +++ b/easybuild/easyconfigs/k/KMC/KMC-3.2.4_use_EB_pybind11_and_libs.patch @@ -0,0 +1,57 @@ +Use pybind11 from EasyBuild install +Required to use Python != 3.10 +Also use zlib from EB install + +Åke Sandgren, 2024-12-09 +diff --git a/Makefile b/Makefile +index d5b9f21..e81661c 100644 +--- a/Makefile ++++ b/Makefile +@@ -115,7 +115,7 @@ else + endif + endif + +-LIB_ZLIB=3rd_party/cloudflare/libz.a ++LIB_ZLIB=-lz + LIB_KMC_CORE = $(OUT_BIN_DIR)/libkmc_core.a + + +@@ -144,8 +144,6 @@ $(KMC_TOOLS_DIR)/fastq_writer.o \ + $(KMC_TOOLS_DIR)/percent_progress.o \ + $(KMC_TOOLS_DIR)/kff_info_reader.o + +-$(LIB_ZLIB): +- cd 3rd_party/cloudflare; ./configure; make libz.a + + $(KMC_CLI_OBJS) $(KMC_CORE_OBJS) $(KMC_DUMP_OBJS) $(KMC_API_OBJS) $(KFF_OBJS) $(KMC_TOOLS_OBJS): %.o: %.cpp + $(CC) $(CFLAGS) -I 3rd_party/cloudflare -c $< -o $@ +@@ -169,17 +167,17 @@ $(LIB_KMC_CORE): $(KMC_CORE_OBJS) $(RADULS_OBJS) $(KMC_API_OBJS) $(KFF_OBJS) + -mkdir -p $(OUT_BIN_DIR) + ar rcs $@ $^ + +-kmc: $(KMC_CLI_OBJS) $(LIB_KMC_CORE) $(LIB_ZLIB) ++kmc: $(KMC_CLI_OBJS) $(LIB_KMC_CORE) + -mkdir -p $(OUT_BIN_DIR) +- $(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^ ++ $(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^ $(LIB_ZLIB) + + kmc_dump: $(KMC_DUMP_OBJS) $(KMC_API_OBJS) + -mkdir -p $(OUT_BIN_DIR) + $(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^ + +-kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS) $(KFF_OBJS) $(LIB_ZLIB) ++kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS) $(KFF_OBJS) + -mkdir -p $(OUT_BIN_DIR) +- $(CC) $(CLINK) -I 3rd_party/cloudflare -o $(OUT_BIN_DIR)/$@ $^ ++ $(CC) $(CLINK) -I 3rd_party/cloudflare -o $(OUT_BIN_DIR)/$@ $^ $(LIB_ZLIB) + + $(PY_KMC_API_DIR)/%.o: $(KMC_API_DIR)/%.cpp + $(CC) -c -fPIC -Wall -O3 $(CPU_FLAGS) -std=c++14 $^ -o $@ +@@ -188,7 +186,6 @@ py_kmc_api: $(PY_KMC_API_OBJS) $(PY_KMC_API_OBJS) + -mkdir -p $(OUT_BIN_DIR) + $(CC) $(PY_KMC_API_CFLAGS) $(PY_KMC_API_DIR)/py_kmc_api.cpp $(PY_KMC_API_OBJS) \ + -I $(KMC_API_DIR) \ +- -I $(PY_KMC_API_DIR)/libs/pybind11/include \ + -I `python3 -c "import sysconfig;print(sysconfig.get_paths()['include'])"` \ + -o $(OUT_BIN_DIR)/$@`python3-config --extension-suffix` + From de97043c4bb8192c0a2c550dec29f682c82cc2c7 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 9 Dec 2024 16:48:48 +0100 Subject: [PATCH 200/414] add more packeges to R-bundle-CRAN --- .../r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb | 6 ++++++ .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb | 3 +++ 2 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb index 972a8488f6a..3625c697b99 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb @@ -3430,6 +3430,12 @@ exts_list = [ ('missMDA', '1.19', { 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], }), + ('gcmr', '1.0.3', { + 'checksums': ['75773d5119179f186467d33608e9ce1c030d0755dfd6ff196546884078e89754'], + }), + ('frbs', '3.2-0', { + 'checksums': ['48505d415e3687afcb837e162b63b74173b3cd5df5f96140240e441c86343b2e'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index 09e8f65ae06..7fbf2167f2e 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -3469,6 +3469,9 @@ exts_list = [ ('gsDesign', '3.6.4', { 'checksums': ['b96075650a5bcbb9ebab78b7094d51f451d086b7c97a3a427635b52fece176d2'], }), + ('frbs', '3.2-0', { + 'checksums': ['48505d415e3687afcb837e162b63b74173b3cd5df5f96140240e441c86343b2e'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From e4464eb86af34d9321cc406413e4629ad81f6328 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 9 Dec 2024 16:54:20 +0000 Subject: [PATCH 201/414] Add MIME::Base32 and add patches for XML::Bare and Crypt:DES --- ...rl_des_expand_key-and-perl_des_crypt.patch | 23 +++++++ .../Perl-bundle-CPAN-5.40.0-GCCcore-14.2.0.eb | 19 +++++- .../Perl-bundle-CPAN/XML-Bare-0.53_c99.patch | 61 +++++++++++++++++++ 3 files changed, 101 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/Perl-bundle-CPAN/Crypt-DES-2.07_expose-perl_des_expand_key-and-perl_des_crypt.patch create mode 100644 easybuild/easyconfigs/p/Perl-bundle-CPAN/XML-Bare-0.53_c99.patch diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Crypt-DES-2.07_expose-perl_des_expand_key-and-perl_des_crypt.patch b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Crypt-DES-2.07_expose-perl_des_expand_key-and-perl_des_crypt.patch new file mode 100644 index 00000000000..fef8544d3eb --- /dev/null +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Crypt-DES-2.07_expose-perl_des_expand_key-and-perl_des_crypt.patch @@ -0,0 +1,23 @@ +From 51fda02d223f516c4948606c050bfc732b95f481 Mon Sep 17 00:00:00 2001 +From: Brian Fraser +Date: Thu, 24 Sep 2020 15:00:20 +0200 +Subject: [PATCH] _des.h: expose perl_des_expand_key() and perl_des_crypt() to + prevent implicit delaration errors/warnings + +--- + _des.h | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/_des.h b/_des.h +index ec56b27..b636cda 100644 +--- a/_des.h ++++ b/_des.h +@@ -4,4 +4,6 @@ typedef unsigned long des_ks[32]; + + void _des_crypt( des_cblock in, des_cblock out, des_ks key, int encrypt ); + void _des_expand_key( des_user_key userKey, des_ks key ); ++void perl_des_expand_key(des_user_key userKey, des_ks ks); ++void perl_des_crypt( des_cblock input, des_cblock output, des_ks ks, int encrypt ); + +-- +2.24.3 (Apple Git-128) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.40.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.40.0-GCCcore-14.2.0.eb index 7e287c21239..b76649ae62e 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.40.0-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.40.0-GCCcore-14.2.0.eb @@ -542,6 +542,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], 'checksums': ['eb89e145a608ed1f8f141a57472ee5f69e67592a432dcd2e8b1dbb445f2b230b'], }), + ('MIME::Base32', '1.303', { + 'source_tmpl': 'MIME-Base32-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['ab21fa99130e33a0aff6cdb596f647e5e565d207d634ba2ef06bdbef50424e99'], + }), ('URI', '5.31', { 'source_tmpl': 'URI-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], @@ -924,7 +929,12 @@ exts_list = [ ('XML::Bare', '0.53', { 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], - 'checksums': ['865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd'], + 'patches': ['XML-Bare-0.53_c99.patch'], + 'checksums': [ + {'XML-Bare-0.53.tar.gz': '865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd'}, + {'XML-Bare-0.53_c99.patch': + 'ce62ce2fb65b495193a969df987facb280669dfe5c5013441f1e7fc59614a713'}, + ], }), ('Dist::CheckConflicts', '0.11', { 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', @@ -1130,7 +1140,12 @@ exts_list = [ ('Crypt::DES', '2.07', { 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], - 'checksums': ['2db1ebb5837b4cb20051c0ee5b733b4453e3137df0a92306034c867621edd7e7'], + 'patches': ['Crypt-DES-2.07_expose-perl_des_expand_key-and-perl_des_crypt.patch'], + 'checksums': [ + {'Crypt-DES-2.07.tar.gz': '2db1ebb5837b4cb20051c0ee5b733b4453e3137df0a92306034c867621edd7e7'}, + {'Crypt-DES-2.07_expose-perl_des_expand_key-and-perl_des_crypt.patch': + '1c8346121049b8dffd06a34d98b0e0484db2b0f2ab66655531009b53b42b03a1'}, + ], }), ('XML::XPath', '1.48', { 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/XML-Bare-0.53_c99.patch b/easybuild/easyconfigs/p/Perl-bundle-CPAN/XML-Bare-0.53_c99.patch new file mode 100644 index 00000000000..d572537aec8 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/XML-Bare-0.53_c99.patch @@ -0,0 +1,61 @@ +From +* https://rt.cpan.org/Public/Bug/Display.html?id=145653 +* https://rt.cpan.org/Public/Bug/Display.html?id=151041 + +diff --git a/parser.c b/parser.c +index 4d770e0efba0e336..26fbd4127fa64753 100644 +--- a/parser.c ++++ b/parser.c +@@ -1,8 +1,6 @@ + #include "parser.h" +-#include +-#ifdef DARWIN +- #include "stdlib.h" +-#endif ++#include ++#include + #ifdef NOSTRING + void memset(char *s, int c, int n) { + char *se = s + n; + +diff --git a/parser.c b/parser.c +index 26fbd4127fa64753..e6cea50335b28eb5 100644 +--- a/parser.c ++++ b/parser.c +@@ -417,7 +417,7 @@ int parserc_parse( struct parserc *self, char *xmlin ) { + case 0: last_state = ST_att_name; goto done; + case '/': // self closing !! /> is assumed !! + curatt = nodec_addattr( curnode, attname, attname_len ); +- if( !att_has_val ) { curatt->value = -1; curatt->vallen = 0; } ++ if( !att_has_val ) { curatt->value = (char *) -1; curatt->vallen = 0; } + attname_len = 0; + + curnode->z = cpos+1-xmlin; +@@ -436,7 +436,7 @@ int parserc_parse( struct parserc *self, char *xmlin ) { + goto att_space; + case '>': + curatt = nodec_addattr( curnode, attname, attname_len ); +- if( !att_has_val ) { curatt->value = -1; curatt->vallen = 0; } ++ if( !att_has_val ) { curatt->value = (char *) -1; curatt->vallen = 0; } + attname_len = 0; + cpos++; + goto val_1; +@@ -832,7 +832,7 @@ int parserc_parse_unsafely( struct parserc *self, char *xmlin ) { + switch( let ) { + case '/': // self closing !! /> is assumed !! + curatt = nodec_addattr( curnode, attname, attname_len ); +- if( !att_has_val ) { curatt->value = -1; curatt->vallen = 0; } ++ if( !att_has_val ) { curatt->value = (char *) -1; curatt->vallen = 0; } + attname_len = 0; + + curnode = curnode->parent; +@@ -850,7 +850,7 @@ int parserc_parse_unsafely( struct parserc *self, char *xmlin ) { + goto u_att_space; + case '>': + curatt = nodec_addattr( curnode, attname, attname_len ); +- if( !att_has_val ) { curatt->value = -1; curatt->vallen = 0; } ++ if( !att_has_val ) { curatt->value = (char *) -1; curatt->vallen = 0; } + attname_len = 0; + cpos++; + goto u_val_1; + From c4353b4bbfe324328e24d72252c28357d0b2444c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 9 Dec 2024 21:43:29 +0100 Subject: [PATCH 202/414] adding easyconfigs: SPEI-0.6.0-gfbf-2023a.eb --- .../s/SPEI/SPEI-0.6.0-gfbf-2023a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPEI/SPEI-0.6.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/s/SPEI/SPEI-0.6.0-gfbf-2023a.eb b/easybuild/easyconfigs/s/SPEI/SPEI-0.6.0-gfbf-2023a.eb new file mode 100644 index 00000000000..5e4d9526329 --- /dev/null +++ b/easybuild/easyconfigs/s/SPEI/SPEI-0.6.0-gfbf-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'SPEI' +version = '0.6.0' + +homepage = 'https://github.com/martinvonk/spei' +description = """ +A simple Python package to calculate drought indices for time series such as the SPI, SPEI and SGI. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('spei', version, { + 'checksums': ['a21933a65c6d7639881671a82b9eb79ee34cd5b52ca7b2a73a55d3988aa93f5c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 55fb0eeffb4cdd6312925a79cae6cf97bc9aeca3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 10 Dec 2024 11:05:08 +0100 Subject: [PATCH 203/414] adding easyconfigs: dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb --- .../dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..8432e8fcefe --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,104 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.8.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = [ + '%(name)s-0.8.0_dont_install_external_libraries.patch', +] +checksums = [ + None, + '28942b7057af00c574a5e70d33a58b4036fd09ae0b041f45b67581c8dda832b1', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('patchelf', '0.18.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), + ('HTSlib', '1.18'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && " + +# disable treating warnings like errors by stripping out -Werror +# cfr. https://github.com/nanoporetech/dorado/issues/779 +preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " + +_copts = [ + "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA", + "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc", + '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL', + "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib", + # add -pthread flag (in addition to -lpthread) to avoid linking error: + # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' + '-DCMAKE_C_FLAGS="$CFLAGS -pthread"', +] + +configopts = ' '.join(_copts) + ' ' + +# disable CMake fiddling with RPATH when EasyBuild is configured to use RPATH linking +configopts += "$(if %(rpath_enabled)s; then " +configopts += "echo '-DCMAKE_SKIP_INSTALL_RPATH=YES -DCMAKE_SKIP_RPATH=YES'; fi) " + +# CUDA libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); +# by default, CMake sets RUNPATH to '$ORIGIN' rather than RPATH (but that's disabled above) +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " for lib in $(ls %(installdir)s/lib/lib{cu,nv}*.so*); do " + " echo setting RPATH in $lib;" + " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" + " done;" + "fi", +] + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' From 66f6a43486cd3d13b23b6bf1317568726b734777 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 10 Dec 2024 14:05:09 +0100 Subject: [PATCH 204/414] adding easyconfigs: EMMAX-20120210-GCCcore-13.2.0-intel-binary.eb --- ...AX-20120210-GCCcore-13.2.0-intel-binary.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/e/EMMAX/EMMAX-20120210-GCCcore-13.2.0-intel-binary.eb diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20120210-GCCcore-13.2.0-intel-binary.eb b/easybuild/easyconfigs/e/EMMAX/EMMAX-20120210-GCCcore-13.2.0-intel-binary.eb new file mode 100644 index 00000000000..9d7150c71b2 --- /dev/null +++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20120210-GCCcore-13.2.0-intel-binary.eb @@ -0,0 +1,39 @@ +easyblock = 'Binary' + +name = 'EMMAX' + +version = '20120210' +versionsuffix = '-intel-binary' + +homepage = 'https://csg.sph.umich.edu/kang/emmax' +description = """EMMAX is a statistical test for large scale human or model organism + association mapping accounting for the sample structure""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://csg.sph.umich.edu//kang/emmax/download/'] +sources = [ + { + 'download_filename': f'{name.lower()}{versionsuffix}-{version}.tar.gz', + 'filename': f'{name}-{version}{versionsuffix}.tar.gz' + } +] +checksums = ['e2a582851ba1be908757d4ef436e98ad76664a0c55e00d13e55fa35fe2ba54dd'] + +dependencies = [ + ('zlib', '1.2.13'), +] + +extract_sources = True + +sanity_check_paths = { + 'files': ['emmax-intel64', 'emmax-kin-intel64'], + 'dirs': [], +} + +sanity_check_commands = [ + "emmax-intel64 2>&1 | grep '^Usage: emmax'", + "emmax-kin-intel64 2>&1 | grep '^Usage: emmax_kin'", +] + +moduleclass = 'bio' From 5b7c849c65c6d973579d7720172c8ea5cef412d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Dec 2024 14:30:08 +0100 Subject: [PATCH 205/414] use proper release of MATES v0.1.5 --- .../m/MATES/MATES-0.1.5-foss-2023b.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATES/MATES-0.1.5-foss-2023b.eb diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.5-foss-2023b.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-foss-2023b.eb new file mode 100644 index 00000000000..d142586c26f --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-foss-2023b.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'MATES' +version = '0.1.5' + +homepage = 'https://github.com/mcgilldinglab/MATES' +description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data." + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('matplotlib', '3.8.2'), + ('anndata', '0.11.1'), + ('pybedtools', '0.10.0'), + ('PyTorch', '2.1.2'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.2'), + ('SAMtools', '1.19.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + (name, version, { + 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['be0170d83bf1d039c9de278791e2ad5a61476581c59c245f53ba087b3a5a3407'], + # unpin exact versions of dependencies + 'preinstallopts': """sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && """, + 'modulename': 'MATES', + }), +] + +sanity_check_commands = [ + "python -c 'from MATES import bam_processor, data_processor, MATES_model'", + "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'", +] + +moduleclass = 'bio' From 7d19ea2bfbbd8d0a6c812a223544a25e6c4ff621 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 10 Dec 2024 15:52:09 +0100 Subject: [PATCH 206/414] add TorchRL to PyTorch-bundle v2.1.2 --- .../PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb | 10 ++++++++++ .../PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb | 10 ++++++++++ 2 files changed, 20 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb index d7e1c6cc2e0..985e8ad0158 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -179,6 +179,16 @@ exts_list = [ ), 'testinstall': True, }), + ('tensordict', '0.3.0', { + 'source_urls': ['https://github.com/pytorch/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f0d95e8f055c3f82838fdbeb03c6a907f8786c1046791db7e39cdcd9cb8f1889'], + }), + ('torchrl', '0.3.1', { + 'source_urls': ['https://github.com/pytorch/rl/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['882ed50cfd868c6b730834f2d7136a3039767061f075ba3cf194acf07e0be742'], + }), ] sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb index 4c8d8ef847a..50a7708dfa0 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb @@ -176,6 +176,16 @@ exts_list = [ ), 'testinstall': True, }), + ('tensordict', '0.3.0', { + 'source_urls': ['https://github.com/pytorch/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f0d95e8f055c3f82838fdbeb03c6a907f8786c1046791db7e39cdcd9cb8f1889'], + }), + ('torchrl', '0.3.1', { + 'source_urls': ['https://github.com/pytorch/rl/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['882ed50cfd868c6b730834f2d7136a3039767061f075ba3cf194acf07e0be742'], + }), ] sanity_pip_check = True From c2a978b99477f0961899a912d99373fa364d5207 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Dec 2024 17:12:30 +0100 Subject: [PATCH 207/414] add custom sanity check command for VEP --- easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb index 0419059c6ad..fc4166c3cd1 100644 --- a/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/v/VEP/VEP-113.0-GCC-12.3.0.eb @@ -39,4 +39,6 @@ exts_list = [ }), ] +sanity_check_commands = ['vep --help'] + moduleclass = 'bio' From da96c0a1b169793af667df008abbcecba92722bc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Dec 2024 23:36:49 +0000 Subject: [PATCH 208/414] Set PKG_CONFIG variable to pkgconf --- .../i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb | 1 - .../i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb | 1 - .../i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb | 1 - .../i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb | 1 - .../i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb | 1 - .../i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb | 1 - easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-10.3.0.eb | 2 ++ easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb | 2 ++ easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb | 2 ++ easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb | 2 ++ easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb | 2 ++ easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb | 2 ++ easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb | 2 ++ easybuild/easyconfigs/p/pkgconf/pkgconf-2.0.3-GCCcore-13.2.0.eb | 2 ++ easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0-GCCcore-13.3.0.eb | 2 ++ easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0.eb | 2 ++ easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb | 2 ++ easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb | 2 ++ 18 files changed, 24 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb index 6a78cb9c5a9..8edbf91b842 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb @@ -30,7 +30,6 @@ builddependencies = [ ('pkgconf', '1.8.0'), ] -preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb index 7d03b87d1d8..bc63a2d88d1 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb @@ -30,7 +30,6 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb index e758d987dfa..ee6ed5c39bd 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb @@ -30,7 +30,6 @@ builddependencies = [ ('pkgconf', '1.9.3'), ] -preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb index 4fe1068022b..ebe2bb56629 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb @@ -29,7 +29,6 @@ dependencies = [ ('FriBidi', '1.0.12'), ] -preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb index 2ccdcb32a55..eaa7378dd71 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb @@ -29,7 +29,6 @@ dependencies = [ ('FriBidi', '1.0.13'), ] -preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb index 776471b14b2..27142117380 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb @@ -33,7 +33,6 @@ dependencies = [ ('FriBidi', '1.0.15'), ] -preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-10.3.0.eb index fa7cf70d46b..6c763def290 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-10.3.0.eb @@ -28,4 +28,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb index 0d6dab08f33..acd1f2251ec 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb @@ -28,4 +28,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb index cffdf67d1da..3e82ba18c42 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb @@ -28,4 +28,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb index 710f2739928..1c340a27259 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb @@ -30,4 +30,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb index 2d47decfa86..05cf64168ab 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb @@ -28,4 +28,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb index c80ab34d708..3f7c00ed2d2 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb @@ -28,4 +28,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb index 1896354cb61..87bf0c0e104 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb @@ -28,4 +28,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.0.3-GCCcore-13.2.0.eb index a9a638fa1ef..5a81ceda025 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.0.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.0.3-GCCcore-13.2.0.eb @@ -28,4 +28,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0-GCCcore-13.3.0.eb index aaaecf30a9a..8294511f61a 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0-GCCcore-13.3.0.eb @@ -28,4 +28,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0.eb index 3440e388cc3..5c877cef741 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0.eb @@ -30,4 +30,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb index de13aa5fb33..76421187079 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb @@ -28,4 +28,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb index c90cecda0a1..b06a5414e80 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb @@ -30,4 +30,6 @@ sanity_check_commands = [ "pkgconf --help", ] +modextravars = {'PKG_CONFIG': '%(installdir)s/bin/pkgconf'} + moduleclass = 'devel' From 025064238a3410dc051322d07ef046700e04b694 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2024 08:07:52 +0100 Subject: [PATCH 209/414] fix name of easyconfigs that are using GCCcore/13.2.0 toolchain + fix sanity check for Spyder v6.0.1 --- ...14-gfbf-2023b.eb => Deprecated-1.2.14-GCCcore-13.2.0.eb} | 0 ...r-6.0.1-gfbf-2023b.eb => Spyder-6.0.1-GCCcore-13.2.0.eb} | 6 ++++-- ...-1.16.0-gfbf-2023b.eb => wrapt-1.16.0-GCCcore-13.2.0.eb} | 0 3 files changed, 4 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/d/Deprecated/{Deprecated-1.2.14-gfbf-2023b.eb => Deprecated-1.2.14-GCCcore-13.2.0.eb} (100%) rename easybuild/easyconfigs/s/Spyder/{Spyder-6.0.1-gfbf-2023b.eb => Spyder-6.0.1-GCCcore-13.2.0.eb} (97%) rename easybuild/easyconfigs/w/wrapt/{wrapt-1.16.0-gfbf-2023b.eb => wrapt-1.16.0-GCCcore-13.2.0.eb} (100%) diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-GCCcore-13.2.0.eb similarity index 100% rename from easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-gfbf-2023b.eb rename to easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-GCCcore-13.2.0.eb similarity index 97% rename from easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb rename to easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-GCCcore-13.2.0.eb index 779cc908ec0..08412a34e9d 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-6.0.1-GCCcore-13.2.0.eb @@ -101,8 +101,10 @@ exts_list = [ }), ] -enhance_sanity_check = True -sanity_check_paths = {'files': ['bin/spyder']} +sanity_check_paths = { + 'files': ['bin/spyder'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} sanity_check_commands = ["spyder --help"] diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-GCCcore-13.2.0.eb similarity index 100% rename from easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2023b.eb rename to easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-GCCcore-13.2.0.eb From ce02d1c6b87fc675205a1fccce441651613b5c47 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 11 Dec 2024 12:02:17 +0100 Subject: [PATCH 210/414] add wayland-utils to Wayland-1.23.0-GCCcore-13.3.0.eb --- .../easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb index b774886e5cb..e34af4bbf3e 100644 --- a/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb @@ -50,6 +50,12 @@ components = [ 'sources': [SOURCE_TAR_XZ], 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH " }), + ('wayland-utils', '1.2.0', { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/wayland-utils/-/releases/%(version)s/downloads'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['d9278c22554586881802540751bcc42569262bf80cd9ac9b0fd12ff4bd09a9e4'], + 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH " + }), ] _libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']] From c617fe0361a58c242138ea34279a5b9d5c084c31 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 11 Dec 2024 17:49:13 +0000 Subject: [PATCH 211/414] adding easyconfigs: rDock-24.03.192-GCCcore-13.3.0.eb --- .../r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..de31be18ec5 --- /dev/null +++ b/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'rDock' +version = '24.03.192' + +homepage = 'https://rdock.github.io/' +description = """ +rDock is a fast and versatile Open Source docking program that can be used to dock small +molecules against proteins and nucleic acids. It is designed for High Throughput Virtual +Screening (HTVS) campaigns and Binding Mode prediction studies. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/CBDD/rDock/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4cb4267831a30010d2bca7daf13f74ab113df2c19a140859e9878a02038f551b'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('tcsh', '6.24.13'), + ('popt', '1.19'), +] + +configure_without_installdir = True +configure_cmd = ' ' + +preinstallopts = 'export PREFIX=%(installdir)s && ' + +runtest = 'test' + +postinstallcmds = ['sed -i "s|/bin/csh -f|/usr/bin/env tcsh -f|" %(installdir)s/bin/make_grid.csh'] + +sanity_check_paths = { + 'files': ['bin/rbhtfinder', 'bin/sdreport', 'bin/run_rbdock.pl', 'lib/libRbt.so'], + 'dirs': ['include'], +} + +moduleclass = 'bio' From d646c40063ce0f8340e5c4c18d1c36af761ff878 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 12 Dec 2024 11:48:40 +0100 Subject: [PATCH 212/414] Update easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-GCCcore-13.2.0.eb Co-authored-by: Alexander Grund --- .../d/Deprecated/Deprecated-1.2.14-GCCcore-13.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-GCCcore-13.2.0.eb index c80cc41c6da..247c6ed45e4 100644 --- a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-GCCcore-13.2.0.eb @@ -20,9 +20,6 @@ dependencies = [ ] builddependencies = [('binutils', '2.40')] -use_pip = True -sanity_pip_check = True - use_pip = True download_dep_fail = True sanity_pip_check = True From 1f000967386c35f69a585efed6a9ab4b77f07836 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 12 Dec 2024 12:36:41 +0100 Subject: [PATCH 213/414] Fix for using rpath wrapper with LASTZ-1.04.22 --- .../l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb | 6 +- ...STZ-1.04.22_fix-rpath-wrapper-compat.patch | 76 +++++++++++++++++++ 2 files changed, 81 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22_fix-rpath-wrapper-compat.patch diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb index bd9b31a13ac..8981bdfd0bd 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb @@ -13,7 +13,11 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = [GITHUB_LOWER_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['4c829603ba4aed7ddf64255b528cd88850e4557382fca29580d3576c25c5054a'] +patches = ['LASTZ-1.04.22_fix-rpath-wrapper-compat.patch'] +checksums = [ + {'1.04.22.tar.gz': '4c829603ba4aed7ddf64255b528cd88850e4557382fca29580d3576c25c5054a'}, + {'LASTZ-1.04.22_fix-rpath-wrapper-compat.patch': '565c87e47755d22e44ddb8e60a36f3a65ba69d9f4e1967ba6521a58aefa30f46'}, +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22_fix-rpath-wrapper-compat.patch b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22_fix-rpath-wrapper-compat.patch new file mode 100644 index 00000000000..34c2b6e99e3 --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22_fix-rpath-wrapper-compat.patch @@ -0,0 +1,76 @@ +Avoid requiring score type define to be escaped +This ensures that it works even when our rpath-wrapper removes the quotes passed as `-Dscore_type=\'I\'` +This avoids +> #error ***** undecipherable score type definition ***** + +See https://github.com/lastz/lastz/pull/64 + +Author: Alexander Grund (TU Dresden) + +diff --git a/src/Makefile b/src/Makefile +index 1908774..cd7a55a 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -91,10 +91,10 @@ incFiles = lastz.h infer_scores.h \ + utilities.h dna_utilities.h sequences.h capsule.h + + %.o: %.c version.mak ${incFiles} +- ${CC} -c ${CFLAGS} -Dscore_type=\'I\' $< -o $@ ++ ${CC} -c ${CFLAGS} -Dscore_type=I $< -o $@ + + %_D.o: %.c version.mak ${incFiles} +- ${CC} -c ${CFLAGS} -Dscore_type=\'D\' $< -o $@ ++ ${CC} -c ${CFLAGS} -Dscore_type=D $< -o $@ + + %_32.o: %.c version.mak ${incFiles} + ${CC} -c ${CFLAGS} ${flagsFor32} $< -o $@ +diff --git a/src/Makefile.warnings b/src/Makefile.warnings +index 50109a6..dec9189 100644 +--- a/src/Makefile.warnings ++++ b/src/Makefile.warnings +@@ -91,10 +91,10 @@ incFiles = lastz.h infer_scores.h \ + utilities.h dna_utilities.h sequences.h capsule.h + + %.o: %.c version.mak ${incFiles} +- ${CC} -c ${CFLAGS} -Dscore_type=\'I\' $< -o $@ ++ ${CC} -c ${CFLAGS} -Dscore_type=I $< -o $@ + + %_D.o: %.c version.mak ${incFiles} +- ${CC} -c ${CFLAGS} -Dscore_type=\'D\' $< -o $@ ++ ${CC} -c ${CFLAGS} -Dscore_type=D $< -o $@ + + %_32.o: %.c version.mak ${incFiles} + ${CC} -c ${CFLAGS} ${flagsFor32} $< -o $@ +diff --git a/src/dna_utilities.h b/src/dna_utilities.h +index f3a0ce2..ed4ef23 100644 +--- a/src/dna_utilities.h ++++ b/src/dna_utilities.h +@@ -35,9 +35,7 @@ global int dna_utilities_dbgShowQToBest; + // score values-- + // Scores used for sequence comparisons are normally signed 32-bit integers, + // but the programmer can override this at compile time by defining score_type +-// as one of 'F', 'D', or 'I'. Note that some effort must be taken to get +-// the apostrophes into the definition from the compiler command line, such as +-// -Dscore_type=\'F\' . ++// as one of 'F', 'D', or 'I'. E.g.: -Dscore_type=F + // + //---------- + // +@@ -66,7 +64,16 @@ global int dna_utilities_dbgShowQToBest; + //---------- + + #if defined(score_type) +-#define scoreType score_type ++// Convert the score_type define to one of the valid character constants ++#define LASTZ_CONCAT(a, b) a ## b ++ ++#define LASTZ_SCORE_TYPE_I 'I' ++#define LASTZ_SCORE_TYPE_F 'F' ++#define LASTZ_SCORE_TYPE_D 'D' ++// Indirection required to expand the macro argument ++#define LASTZ_MAKE_SCORE_TYPE(c) LASTZ_CONCAT(LASTZ_SCORE_TYPE_, c) ++#define scoreType LASTZ_MAKE_SCORE_TYPE(score_type) ++ + #else + #define scoreType 'I' + #endif From 4ace84e8357fede977d264eb138d85c6cf64c63d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 12 Dec 2024 13:34:59 +0100 Subject: [PATCH 214/414] Fix line length --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb index 8981bdfd0bd..06a1cef8c6e 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb @@ -16,7 +16,8 @@ sources = ['%(version)s.tar.gz'] patches = ['LASTZ-1.04.22_fix-rpath-wrapper-compat.patch'] checksums = [ {'1.04.22.tar.gz': '4c829603ba4aed7ddf64255b528cd88850e4557382fca29580d3576c25c5054a'}, - {'LASTZ-1.04.22_fix-rpath-wrapper-compat.patch': '565c87e47755d22e44ddb8e60a36f3a65ba69d9f4e1967ba6521a58aefa30f46'}, + {'LASTZ-1.04.22_fix-rpath-wrapper-compat.patch': + '565c87e47755d22e44ddb8e60a36f3a65ba69d9f4e1967ba6521a58aefa30f46'}, ] skipsteps = ['configure'] From 9884b710c0455b055d9841545a33a860baf59c26 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 12 Dec 2024 14:51:21 +0100 Subject: [PATCH 215/414] adding easyconfigs: MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb, IDBA-UD-1.1.3-GCCcore-12.3.0.eb --- .../i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb | 51 +++++++++++++++++ ...toFinder-1.4.2-foss-2023a-Python-2.7.18.eb | 55 +++++++++++++++++++ 2 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..83d24a82eec --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +# 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 +# Updated: Pavel Grochal (INUITS) +# License: GPLv2 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in prebuildopts + +# modified by Tom Strempel +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.3' + +homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads +Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. +IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth +contigs are removed iteratively with cutoff threshold from low to high to reduce the errors +in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled +locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD +can iterate k value of de Bruijn graph to a very large value with less gaps and less branches +to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] +sources = ['idba-%(version)s.tar.gz'] +checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] + +builddependencies = [('binutils', '2.40')] + +prebuildopts = './configure && ' + +# we delete every .o and Makefile file which is left in bin folder +buildopts = ' && rm -fr bin/*.o bin/Makefile*' + +files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] + +pretestopts = "cd test && " +runtest = "check" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..b0262f35599 --- /dev/null +++ b/easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,55 @@ +easyblock = 'Tarball' + +name = 'MitoFinder' +version = '1.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/RemiAllio/MitoFinder' +description = """MitoFinder is a pipeline to assemble mitochondrial genomes and +annotate mitochondrial genes from trimmed read sequencing data""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/RemiAllio/MitoFinder/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2d6d3925fb014777df97f272134143cc518944ae05d000a44ada2862d46ec95a'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Python', '2.7.18'), + ('IDBA-UD', '1.1.3'), + ('Infernal', '1.1.5'), + ('tRNAscan-SE', '2.0.12'), + ('Automake', '1.16.5'), +] + +postinstallcmds = [ + # avoid run install.sh + link EB modules + "rm -rf %(installdir)s/idba/bin && cd %(installdir)s/idba && ln -s $EBROOTIDBAMINUD/bin && " + "cd %(installdir)s/metaspades/bin && ln -s spades.py metaspades.py && " + "cd %(installdir)s/trnascanSE && mkdir -p infernal-1.1.3/exec && cd infernal-1.1.3/exec && " + "ln -s $EBROOTINFERNAL/bin && ln -s $EBROOTINFERNAL/share && " + "cd %(installdir)s/trnascanSE && mkdir -p automake-1.13.4/exec && cd automake-1.13.4/exec && " + "ln -s $EBROOTAUTOMAKE/bin && ln -s $EBROOTAUTOMAKE/share && " + "cd %(installdir)s/trnascanSE && mkdir -p tRNAscan-SE-2.0/exec && cd tRNAscan-SE-2.0/exec && " + "ln -s $EBROOTTRNASCANMINSE/bin && ln -s $EBROOTTRNASCANMINSE/lib && ln -s $EBROOTTRNASCANMINSE/include && " + "cd %(installdir)s/mitfi && mkdir -p infernal-1.0.2/exec && cd infernal-1.0.2/exec && " + "ln -s $EBROOTINFERNAL/bin && ln -s $EBROOTINFERNAL/share && " + "cd %(installdir)s/mitfi/infernal-1.0.2 && ln -s $EBROOTINFERNAL/bin src && " + 'cd %(installdir)s && touch install.sh.ok && ' + # fix mitofinder - https://github.com/RemiAllio/MitoFinder/issues/26 + "sed -i 's/os.devnull, \'wb\')/os.devnull, \'wb\'), shell=True/g' mitofinder" +] + +fix_python_shebang_for = ['mitofinder', '*.py'] + +sanity_check_paths = { + 'files': ['mitofinder'], + 'dirs': ['idba', 'megahit', 'metaspades', 'mitfi', 'trnascanSE'], +} + +sanity_check_commands = ['mitofinder -h'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From a8cae9bcaf1150ae78d991eefd83bc57061ea8fb Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 12 Dec 2024 16:28:29 +0000 Subject: [PATCH 216/414] update homepage for DFTB+ --- easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb | 4 +--- easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb | 6 +----- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb index 5711e31168d..dd4cc9c4f69 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'DFTB+' version = '21.1' -homepage = 'https://www.dftb-plus.info' +homepage = 'https://www.dftbplus.org/' description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB @@ -77,6 +77,4 @@ sanity_check_paths = { sanity_check_commands = [("python -c 'import dptools'")] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb index c862fcea552..bc04511e7da 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'DFTB+' version = '24.1' -homepage = 'https://www.dftb-plus.info' +homepage = 'https://www.dftbplus.org/' description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB @@ -66,8 +66,6 @@ runtest = 'test' exts_defaultclass = 'PythonPackage' exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, 'runtest': False, } exts_list = [ @@ -88,6 +86,4 @@ sanity_check_paths = { sanity_check_commands = ["python -c 'import dptools'"] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - moduleclass = 'phys' From abaf168d58121d617a07dda15ad7b6d6528a235f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 12 Dec 2024 16:45:08 +0000 Subject: [PATCH 217/414] use EB4 as a starting point --- easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb | 2 ++ easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb | 4 ++++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb index dd4cc9c4f69..567ceb13c55 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb @@ -77,4 +77,6 @@ sanity_check_paths = { sanity_check_commands = [("python -c 'import dptools'")] +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb index bc04511e7da..1d2538ed7d2 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -66,6 +66,8 @@ runtest = 'test' exts_defaultclass = 'PythonPackage' exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, 'runtest': False, } exts_list = [ @@ -86,4 +88,6 @@ sanity_check_paths = { sanity_check_commands = ["python -c 'import dptools'"] +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'phys' From f76acd623e037ac2ff597eaf1910c30bf8770b57 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 13 Dec 2024 10:01:19 +0100 Subject: [PATCH 218/414] Update AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb --- .../AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb index d654f63ae5f..e1dd253f812 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb @@ -98,7 +98,9 @@ exts_list = [ } }], 'testinstall': True, - 'checksums': ['e338195987e003f3caadb06bda0ca56dece87e358738143ea72662f9ad69b1d4'], + # This needs to be [None], at least until EB v5 is out + # 'checksums': ['e338195987e003f3caadb06bda0ca56dece87e358738143ea72662f9ad69b1d4'], + 'checksums': [None], }), ] From 6f1d40b10da15dd192af6e003f09c5649b9aa834 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 13 Dec 2024 12:02:00 +0100 Subject: [PATCH 219/414] adding easyconfigs: COMSOL-6.3.0.290.eb --- .../easyconfigs/c/COMSOL/COMSOL-6.3.0.290.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/COMSOL/COMSOL-6.3.0.290.eb diff --git a/easybuild/easyconfigs/c/COMSOL/COMSOL-6.3.0.290.eb b/easybuild/easyconfigs/c/COMSOL/COMSOL-6.3.0.290.eb new file mode 100644 index 00000000000..9d20fcbcb8e --- /dev/null +++ b/easybuild/easyconfigs/c/COMSOL/COMSOL-6.3.0.290.eb @@ -0,0 +1,24 @@ +name = 'COMSOL' +version = '6.3.0.290' + +homepage = 'https://www.comsol.com' +description = """ +COMSOL Multiphysics is a general-purpose software platform, based on +advanced numerical methods, for modeling and simulating physics-based +problems. +""" + +toolchain = SYSTEM + +# Note: sources from COMSOL are often named poorly. You can view the exact version in the "ver" file inside the iso: +# 7z x COMSOL-*.iso ver; cat ver +sources = ['COMSOL-%(version)s.iso'] +checksums = ['0b27e68052c9a6c209b50ba22a07667c0d57b86ba5a4daf2282413a63a375c22'] + +download_instructions = 'Obtain from comsol.com' + +osdependencies = [('p7zip-plugins', 'p7zip-full'), 'csh'] # for extracting iso-files + +# license_file = 'license.dat' # or EB_COMSOL_LICENSE_FILE or LMCOMSOL_LICENSE_FILE or LM_LICENSE_FILE + +moduleclass = 'phys' From 7f76a9e587464f08df63d482abd8354d63251387 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 13 Dec 2024 14:10:56 +0100 Subject: [PATCH 220/414] adding easyconfigs: HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb --- .../HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb diff --git a/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb new file mode 100644 index 00000000000..5d397feb581 --- /dev/null +++ b/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'HeFFTe' +version = '2.4.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://icl.utk.edu/fft' +description = "Highly Efficient FFT for Exascale (HeFFTe) library" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://github.com/icl-utk-edu/heffte/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['de2cf26df5d61baac7841525db3f393cb007f79612ac7534fd4757f154ba3e6c'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', versionsuffix), +] + +build_shared_libs = True + +configopts = "-DHeffte_ENABLE_FFTW=ON -DFFTW_ROOT=$EBROOTFFTW -DHeffte_ENABLE_MKL=OFF " +configopts += "-DHeffte_ENABLE_CUDA=ON -DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DHeffte_ENABLE_GPU_AWARE_MPI=ON" + +# allow oversubscription of MPI ranks to cores, tests are hardcoded to use up to 12 MPI ranks +pretestopts = "export OMPI_MCA_rmaps_base_oversubscribe=true && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libheffte.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/cmake/Heffte', 'share/heffte/examples'], +} + +moduleclass = 'lib' From c13d720d30eca83a616583b8ff19d00f519d2696 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 13 Dec 2024 15:59:09 +0100 Subject: [PATCH 221/414] Update easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb index 5d397feb581..b0d179ed27c 100644 --- a/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb +++ b/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b-CUDA-12.4.0.eb @@ -25,7 +25,7 @@ dependencies = [ build_shared_libs = True configopts = "-DHeffte_ENABLE_FFTW=ON -DFFTW_ROOT=$EBROOTFFTW -DHeffte_ENABLE_MKL=OFF " -configopts += "-DHeffte_ENABLE_CUDA=ON -DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DHeffte_ENABLE_GPU_AWARE_MPI=ON" +configopts += "-DHeffte_ENABLE_CUDA=ON -DCUDAToolkit_ROOT=$EBROOTCUDA -DHeffte_ENABLE_GPU_AWARE_MPI=ON" # allow oversubscription of MPI ranks to cores, tests are hardcoded to use up to 12 MPI ranks pretestopts = "export OMPI_MCA_rmaps_base_oversubscribe=true && " From b37be0cb021aafaff34d44afd7b3be7136acf3fc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 13 Dec 2024 16:40:30 +0100 Subject: [PATCH 222/414] adding easyconfigs: ABRicate-1.0.0-gompi-2023b.eb, BLAST+-2.16.0-gompi-2023b.eb, BWA-0.7.18-GCCcore-13.2.0.eb, prokka-1.14.5-gompi-2023b.eb, SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb, VCFtools-0.1.16-GCC-13.2.0.eb --- .../a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb | 41 +++++++++++ .../any2fasta-0.4.2-GCCcore-13.2.0.eb | 35 ++++++++++ .../b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb | 58 ++++++++++++++++ .../b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb | 52 ++++++++++++++ .../Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb | 28 ++++++++ .../p/prokka/prokka-1.14.5-gompi-2023b.eb | 50 ++++++++++++++ .../SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb | 37 ++++++++++ .../tbl2asn-20230713-GCCcore-13.2.0.eb | 69 +++++++++++++++++++ .../v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb | 36 ++++++++++ 9 files changed, 406 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb new file mode 100644 index 00000000000..3e980962ec8 --- /dev/null +++ b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'ABRicate' +version = '1.0.0' + +homepage = 'https://github.com/tseemann/abricate' +description = "Mass screening of contigs for antimicrobial and virulence genes" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +# https://github.com/tseemann/abricate +github_account = 'tseemann' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9'] + +dependencies = [ + ('Perl', '5.38.0'), + ('any2fasta', '0.4.2'), + ('BioPerl', '1.7.8'), + ('BLAST+', '2.16.0'), +] + +postinstallcmds = ['%(installdir)s/bin/abricate --setupdb'] + +sanity_check_paths = { + 'files': ['bin/abricate', 'bin/abricate-get_db'], + 'dirs': ['db'], +} + +sanity_check_commands = [ + "abricate --help", + "abricate --list", +] + +modloadmsg = "abricate databases are located in $EBROOTABRICATE/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..91034a25be8 --- /dev/null +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# Updated by: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'any2fasta' +version = '0.4.2' + +homepage = 'https://github.com/tseemann/any2fasta' +description = "Convert various sequence formats to FASTA" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +# https://github.com/tseemann/any2fasta +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] + +dependencies = [('Perl', '5.38.0')] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['any2fasta'], + 'dirs': [], +} + +sanity_check_commands = [ + 'any2fasta -h', + 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb new file mode 100644 index 00000000000..d43cb118efd --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb @@ -0,0 +1,58 @@ +# # +# 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 = '2.16.0' + +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': '2023b'} +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 = ['17c93cf009721023e5aecf5753f9c6a255d157561638b91b3ad7276fd6950c2b'] + +builddependencies = [('cpio', '2.15')] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.5'), + ('PCRE', '8.45'), + ('Boost', '1.83.0'), + ('GMP', '6.3.0'), + ('libpng', '1.6.40'), + ('libjpeg-turbo', '3.0.1'), + ('LMDB', '0.9.31'), + ('SQLite', '3.43.1'), +] + +# remove line that prepends system paths to $PATH from configure script +preconfigopts = r'sed -i "s|^PATH=\(.*\)$|#PATH=\1 |" %(start_dir)s/src/build-system/configure && ' + +configopts = "--with-z=$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/BWA/BWA-0.7.18-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d65b73e57e9 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb @@ -0,0 +1,52 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# 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 +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +# +# 0.7.18 +# Erica Bianco (HPCNow!) +## + +name = 'BWA' +version = '0.7.18' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('zlib', '1.2.13'), + ('Perl', '5.38.0'), +] + +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb new file mode 100644 index 00000000000..b26850e9d30 --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.38.0'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb new file mode 100644 index 00000000000..bd7648a5418 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.16.0'), + ('Java', '11', '', SYSTEM), + ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20240322'), + ('tbl2asn', '20230713'), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb new file mode 100644 index 00000000000..5baecf1ad17 --- /dev/null +++ b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'SKESA' +version = '2.4.0' +versionsuffix = '_saute.1.3.0_2' + +homepage = 'https://github.com/ncbi/SKESA' +description = "SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs." + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/ncbi/SKESA/archive/'] +sources = ['skesa.%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['dc5ad60f963afb09d3f2a3bab8917e657bd93364f0deca6e6844ede44968e979'] + +dependencies = [ + ('Boost', '1.83.0'), + ('SRA-Toolkit', '3.1.1'), + ('ncbi-vdb', '3.1.1'), +] + +prebuildopts = "touch %(builddir)s/ngs.done && " + +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS" ' +buildopts += "NGS_DIR=%(builddir)s BOOST_PATH=$EBROOTBOOST NGS_PATH=$EBROOTSRAMINTOOLKIT VDB_PATH=$EBROOTNCBIMINVDB" + +files_to_copy = [(['skesa'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/skesa'], + 'dirs': [], +} + +sanity_check_commands = ["skesa --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3571e61aac4 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb @@ -0,0 +1,69 @@ +# 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 +# revised by Ariel Lozano + +easyblock = 'Bundle' + +name = 'tbl2asn' +version = '20230713' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('patchelf', '0.18.0'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +# libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); + +default_easyblock = 'CmdCp' + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. + +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.linux64.gz', + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), +] + +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;" + "fi", + "chmod +x %(installdir)s/bin/tbl2asn", +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['tbl2asn --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb new file mode 100644 index 00000000000..3a4edc7bc1c --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = 'https://vcftools.github.io' +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = '%(namelower)s' +source_urls = [GITHUB_LOWER_RELEASE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +builddependencies = [ + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('Perl', '5.38.0'), + ('HTSlib', '1.19.1'), +] + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/vcf-sort', 'bin/vcf-stats'], + 'dirs': [], +} + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +moduleclass = 'bio' From 5069cd341c0646adeeef560437d3a97b36f0c771 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 13 Dec 2024 16:43:29 +0100 Subject: [PATCH 223/414] adding easyconfigs: Mashtree-1.4.6-GCC-13.2.0.eb, Mash-2.3-GCC-13.2.0.eb and patches: Mash-2.3_fix_missing_cstdint.patch --- .../easyconfigs/m/Mash/Mash-2.3-GCC-13.2.0.eb | 50 +++++++++++++++ .../m/Mash/Mash-2.3_fix_missing_cstdint.patch | 14 +++++ .../m/Mashtree/Mashtree-1.4.6-GCC-13.2.0.eb | 61 +++++++++++++++++++ 3 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mash/Mash-2.3_fix_missing_cstdint.patch create mode 100644 easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.6-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-13.2.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-13.2.0.eb new file mode 100644 index 00000000000..e2b387eaecb --- /dev/null +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-13.2.0.eb @@ -0,0 +1,50 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v2.2 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'Mash' +version = '2.3' + +homepage = 'http://mash.readthedocs.org' +description = "Fast genome and metagenome distance estimation using MinHash" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/marbl/Mash/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Mash-2.2_fix-hardcoding.patch', + 'Mash-2.1_disable-memcpy-wrap.patch', + 'Mash-2.3_fix-GCC-11.patch', + 'Mash-2.3_fix_missing_cstdint.patch', +] +checksums = [ + {'v2.3.tar.gz': 'f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1'}, + {'Mash-2.2_fix-hardcoding.patch': '0c7315af727a06f408ab3ca69da0860fc671aa870b448a41a509b1e6d7027db5'}, + {'Mash-2.1_disable-memcpy-wrap.patch': '40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e'}, + {'Mash-2.3_fix-GCC-11.patch': '47a55459d4e8c57949648e0f33f3ffc3529563db0efe60f495fdec046f48d94e'}, + {'Mash-2.3_fix_missing_cstdint.patch': 'cd760fe1f5703ed5e4a859e0ebdc088d02fef23ce85e99e916de7c8721d1ebeb'}, +] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [ + ('zlib', '1.2.13'), + ('GSL', '2.7'), + ('CapnProto', '1.0.1.1'), +] + +preconfigopts = "./bootstrap.sh && " +configopts = "--with-capnp=$EBROOTCAPNPROTO --with-gsl=$EBROOTGSL" + +sanity_check_paths = { + 'files': ['bin/mash', 'lib/libmash.a'], + 'dirs': ['include/mash'], +} + +sanity_check_commands = ['mash --version'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3_fix_missing_cstdint.patch b/easybuild/easyconfigs/m/Mash/Mash-2.3_fix_missing_cstdint.patch new file mode 100644 index 00000000000..8a83ae49613 --- /dev/null +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3_fix_missing_cstdint.patch @@ -0,0 +1,14 @@ +Add missing include of cstdint + +Åke Sandgren, 2024-12-13 +diff -ru Mash-2.3.orig/src/mash/Command.cpp Mash-2.3/src/mash/Command.cpp +--- Mash-2.3.orig/src/mash/Command.cpp 2021-02-27 00:13:33.000000000 +0100 ++++ Mash-2.3/src/mash/Command.cpp 2024-12-13 08:08:30.586895593 +0100 +@@ -8,6 +8,7 @@ + #include + #include + #include ++#include + + #include "Command.h" + #include "version.h" diff --git a/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.6-GCC-13.2.0.eb b/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.6-GCC-13.2.0.eb new file mode 100644 index 00000000000..6806c56e037 --- /dev/null +++ b/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.6-GCC-13.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'Bundle' + +name = 'Mashtree' +version = '1.4.6' + +homepage = 'https://github.com/lskatz/mashtree' +description = "Create a tree using Mash distances." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +builddependencies = [ + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Perl', '5.38.0'), + ('BioPerl', '1.7.8'), + ('Mash', '2.3'), + ('QuickTree', '2.5'), +] + +# this is a bundle of Perl modules +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('Class::Interface', '1.01', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SINISTER/'], + 'sources': ['Class-Interface-1.01.tar.gz'], + 'checksums': ['9fba15cda745ad37f451a0b9e698da3dfc12c2e8589016416a1e3ad77e444b7b'], + }), + ('Bio::Sketch', '0.3', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LS/LSKATZ/'], + 'sources': ['Bio-Sketch-0.3.tar.gz'], + 'checksums': ['7ac38552c80ae38e0c72ba3cfa4ecf667aca8b4080616415027bcba1420c8ae2'], + }), + ('Bio::Sketch::Mash', '0.9', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LS/LSKATZ/'], + 'sources': ['Bio-Sketch-Mash-0.9.tar.gz'], + 'checksums': ['ea15858bc75674e22bb26d570d5f94c1b4eb5476bbc7bbabdf07359ebd041280'], + }), + (name, version, { + 'source_urls': ['https://github.com/lskatz/mashtree/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['1bd427aba025886d9df99c95f685e06dc2226bca080a64a9cb9d341b5a3d6dac'], + }), +] + +sanity_check_paths = { + 'files': ['bin/mashtree'], + 'dirs': [] +} + +modextrapaths = {'PERL5LIB': [ + 'lib/perl5/site_perl/%(perlver)s', + 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi', +]} + +sanity_check_commands = ["mashtree -h"] + +moduleclass = 'bio' From 2078bb0d2d612a014791d4a258ba0f0834b86293 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 13 Dec 2024 16:44:49 +0100 Subject: [PATCH 224/414] adding easyconfigs: Parsnp-2.1.1-foss-2023b.eb and patches: Parsnp-2.1.1_fix_configure_search_for_libMUSCLE.patch --- .../p/Parsnp/Parsnp-2.1.1-foss-2023b.eb | 81 +++++++++++++++++++ ...1_fix_configure_search_for_libMUSCLE.patch | 27 +++++++ 2 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1-foss-2023b.eb create mode 100644 easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1_fix_configure_search_for_libMUSCLE.patch diff --git a/easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1-foss-2023b.eb b/easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1-foss-2023b.eb new file mode 100644 index 00000000000..2117add9996 --- /dev/null +++ b/easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1-foss-2023b.eb @@ -0,0 +1,81 @@ +easyblock = 'ConfigureMake' + +name = 'Parsnp' +version = '2.1.1' + +homepage = 'https://harvest.readthedocs.io/en/latest/content/parsnp.html' +description = """Parsnp was designed to align the core genome of +hundreds to thousands of bacterial genomes within a few minutes to few +hours. Input can be both draft assemblies and finished genomes, and +output includes variant (SNP) calls, core genome phylogeny and +multi-alignments. Parsnp leverages contextual information provided by +multi-alignments surrounding SNP sites for filtration/cleaning, in +addition to existing tools for recombination detection/filtration and +phylogenetic reconstruction.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True} + +github_account = 'marbl' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Parsnp-2.1.1_fix_configure_search_for_libMUSCLE.patch', +] +checksums = [ + {'v2.1.1.tar.gz': '7887ee4030dad6f30a4b735f1ee463024204030adbdcb0fa96562e6e8664474e'}, + {'Parsnp-2.1.1_fix_configure_search_for_libMUSCLE.patch': + '7b601c442ed4f64b53195b9adefafbb0d9639296513e22961a8e0de672dbb3fb'}, +] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('tqdm', '4.66.2'), + ('Biopython', '1.84'), +] + +preconfigopts = ' && '.join([ + 'cd muscle', + './autogen.sh', + './configure --prefix=%(installdir)s', + 'make install', + 'cd ..', + './autogen.sh', + '', +]) + +configopts = '--with-libmuscle=%(installdir)s' + +preinstallopts = ' && '.join([ + 'cd muscle', + 'make install', + 'cd ..', + '', +]) + +postinstallcmds = [ + 'cp parsnp %(installdir)s/bin', + 'cp template.ini %(installdir)s', + 'mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages', + 'cp partition.py extend.py logger.py %(installdir)s/lib/python%(pyshortver)s/site-packages', +] + +sanity_check_paths = { + 'files': ['bin/parsnp_core', 'bin/parsnp', 'template.ini'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextravars = { + 'PARSNPDIR': '', +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1_fix_configure_search_for_libMUSCLE.patch b/easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1_fix_configure_search_for_libMUSCLE.patch new file mode 100644 index 00000000000..eba4332c436 --- /dev/null +++ b/easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1_fix_configure_search_for_libMUSCLE.patch @@ -0,0 +1,27 @@ +Fix search for libMUSCLE's include files and install target + +Åke Sandgren, 2024-12-13 +diff -ru parsnp-2.1.1.orig/configure.ac parsnp-2.1.1/configure.ac +--- parsnp-2.1.1.orig/configure.ac 2024-11-21 00:54:04.000000000 +0100 ++++ parsnp-2.1.1/configure.ac 2024-12-13 12:33:40.964024323 +0100 +@@ -11,7 +11,7 @@ + + AC_LANG(C++) + +-CPPFLAGS="-I$with_libmuscle" ++CPPFLAGS="-I$with_libmuscle/include" + AC_CHECK_HEADER(libMUSCLE/muscle.h, [result=1], [result=0]) + + if test $result == 0 +diff -ru parsnp-2.1.1.orig/src/Makefile.am parsnp-2.1.1/src/Makefile.am +--- parsnp-2.1.1.orig/src/Makefile.am 2024-11-21 00:54:04.000000000 +0100 ++++ parsnp-2.1.1/src/Makefile.am 2024-12-13 12:55:02.385984661 +0100 +@@ -2,6 +2,6 @@ + parsnp_core_LDFLAGS = -fopenmp -lstdc++ -lpthread -std=gnu++0x -Wl,-rpath,$(libmuscle)/lib -L$(libmuscle)/lib -L${CONDA_PREFIX}/lib -lMUSCLE-3.7 + bin_PROGRAMS = parsnp_core + parsnp_core_SOURCES = MuscleInterface.cpp MuscleInterface.h parsnp.cpp parsnp.hh LCB.cpp LCB.hh LCR.cpp LCR.hh TMum.cpp TMum.hh Converter.cpp Converter.hh ./ext/iniFile.cpp ./ext/iniFile.h +-bindir = $(top_srcdir)/bin +-libdir = $(top_srcdir)/lib ++#bindir = $(top_srcdir)/bin ++#libdir = $(top_srcdir)/lib + From 63cb7a1deb0f75d7341d8c428b0c3c78c5840376 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 13 Dec 2024 16:47:11 +0000 Subject: [PATCH 225/414] Sanity check commands added --- .../easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb index de31be18ec5..44ae4090d0a 100644 --- a/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb @@ -40,4 +40,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + 'rbdock --help', + 'rbcavity --help', +] + moduleclass = 'bio' From b1801793bce304e8d68442df57ee26684dc6b866 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 13 Dec 2024 20:29:55 +0100 Subject: [PATCH 226/414] add QuickTree-2.5-GCC-13.2.0.eb, dep for Mashtree. Forgot to do --new-pr -r originally --- .../q/QuickTree/QuickTree-2.5-GCC-13.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuickTree/QuickTree-2.5-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/q/QuickTree/QuickTree-2.5-GCC-13.2.0.eb b/easybuild/easyconfigs/q/QuickTree/QuickTree-2.5-GCC-13.2.0.eb new file mode 100644 index 00000000000..05579588a7a --- /dev/null +++ b/easybuild/easyconfigs/q/QuickTree/QuickTree-2.5-GCC-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'QuickTree' +version = '2.5' + +homepage = 'https://github.com/khowe/quicktree' +description = """QuickTree is an efficient implementation of the +Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing +phylogenies from huge alignments in time less than the age of the +universe.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/khowe/quicktree/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['731aa845ce3f1f0645bd0df2b54df75f78fce065d6a3ddc47fedf4bdcb11c248'] + +files_to_copy = [ + (["quicktree"], "bin/"), + 'README.md', + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/quicktree', 'README.md'], + 'dirs': [] +} + +sanity_check_commands = ["quicktree -h"] + +moduleclass = 'bio' From a3157a4696dd15609a92dd8df5bbf621df547c9a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 13 Dec 2024 20:30:41 +0100 Subject: [PATCH 227/414] adding easyconfigs: hifiasm-0.23.0-GCCcore-13.2.0.eb --- .../hifiasm/hifiasm-0.23.0-GCCcore-13.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/h/hifiasm/hifiasm-0.23.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/h/hifiasm/hifiasm-0.23.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.23.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6d9b52352a5 --- /dev/null +++ b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.23.0-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +# Author: Jasper Grimm (UoY) +# Update: Sebastien Moretti (SIB), Denis Kristak (Inuits) + +easyblock = 'MakeCp' + +name = 'hifiasm' +version = '0.23.0' + +homepage = 'https://github.com/chhylp123/hifiasm' +description = """Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.""" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'opt': True} + +github_account = 'chhylp123' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['52b4b615c2d2938b3b10cca4890c7857750f4a5ee54d5eb78c49dc638c9f14e0'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +buildopts = 'CC="$CC" CXX="$CXX" CXXFLAGS="$CXXFLAGS" CPPFLAGS="$CPPFLAGS"' + +files_to_copy = [ + ([name], 'bin'), + (['*.h'], 'include/hifiasm'), + 'LICENSE', 'README.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} +sanity_check_commands = ["%(name)s -h"] + +moduleclass = 'bio' From 9a8105fb588ce65d08d01ad6dbfb45e1f33fdb13 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2024 17:32:44 +0100 Subject: [PATCH 228/414] adding easyconfigs: Whisper-20240930-foss-2023a-CUDA-12.1.1.eb --- ...Whisper-20240930-foss-2023a-CUDA-12.1.1.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/w/Whisper/Whisper-20240930-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/w/Whisper/Whisper-20240930-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/w/Whisper/Whisper-20240930-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3cb03e7142a --- /dev/null +++ b/easybuild/easyconfigs/w/Whisper/Whisper-20240930-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'Whisper' +version = '20240930' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/openai/whisper' +description = "Whisper is a general-purpose speech recognition model" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('numba', '0.58.1'), + ('PyTorch', '2.1.2', versionsuffix), + ('tiktoken', '0.7.0'), + ('Triton', '2.1.0', versionsuffix), + ('FFmpeg', '6.0'), +] + +use_pip = True + +exts_list = [ + ('openai-whisper', version, { + 'modulename': 'whisper', + 'checksums': ['b7178e9c1615576807a300024f4daa6353f7e1a815dac5e38c33f1ef055dd2d2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/whisper'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["whisper --help"] + +sanity_pip_check = True + +moduleclass = 'ai' From 9c32130d827bbd16b59516311ceb9de8dfc9b669 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 16 Dec 2024 09:18:41 +0100 Subject: [PATCH 229/414] purge_dups: Rename KMC patch to better show where it belongs --- ....patch => KMC-dfguan-c05a5f9_use_EB_pybind11_and_libs.patch} | 0 .../easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/purge_dups/{KMC_use_EB_pybind11_and_libs.patch => KMC-dfguan-c05a5f9_use_EB_pybind11_and_libs.patch} (100%) diff --git a/easybuild/easyconfigs/p/purge_dups/KMC_use_EB_pybind11_and_libs.patch b/easybuild/easyconfigs/p/purge_dups/KMC-dfguan-c05a5f9_use_EB_pybind11_and_libs.patch similarity index 100% rename from easybuild/easyconfigs/p/purge_dups/KMC_use_EB_pybind11_and_libs.patch rename to easybuild/easyconfigs/p/purge_dups/KMC-dfguan-c05a5f9_use_EB_pybind11_and_libs.patch diff --git a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb index 6848c4131d1..a407a2ec4b4 100644 --- a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb +++ b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb @@ -38,7 +38,7 @@ components = [ 'source_urls': ['https://github.com/dfguan/KMC/archive'], 'sources': [{'download_filename': 'c05a5f9.tar.gz', 'filename': SOURCE_TAR_GZ}], 'patches': [{ - 'name': 'KMC_use_EB_pybind11_and_libs.patch', + 'name': 'KMC-dfguan-c05a5f9_use_EB_pybind11_and_libs.patch', 'sourcepath': 'KMC-c05a5f9fd94683248ebe04484a60f86792cf328f', }], 'checksums': [ From 8defa58ac9cf12d1e2a4d419eb4169cb6a9ebdde Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 16 Dec 2024 12:50:19 +0100 Subject: [PATCH 230/414] add gcmr either to 2023b-CRAN-bundle --- .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index 7fbf2167f2e..43ac06c0cc7 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -3469,6 +3469,9 @@ exts_list = [ ('gsDesign', '3.6.4', { 'checksums': ['b96075650a5bcbb9ebab78b7094d51f451d086b7c97a3a427635b52fece176d2'], }), + ('gcmr', '1.0.3', { + 'checksums': ['75773d5119179f186467d33608e9ce1c030d0755dfd6ff196546884078e89754'], + }), ('frbs', '3.2-0', { 'checksums': ['48505d415e3687afcb837e162b63b74173b3cd5df5f96140240e441c86343b2e'], }), From fe34f6009e9148edeaba4bee0bb0c5773657a32f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 16 Dec 2024 12:59:19 +0100 Subject: [PATCH 231/414] adding easyconfigs: scNanoGPS-1.1-foss-2023a.eb, LIQA-1.3.4-foss-2023a.eb, lifelines-0.28.0-gfbf-2023a.eb, annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb, BCFtools-1.21-GCC-12.3.0.eb, tabix-0.2.6-GCCcore-12.3.0.eb --- ...var-20200607-GCCcore-12.3.0-Perl-5.36.1.eb | 37 +++++++++ .../b/BCFtools/BCFtools-1.21-GCC-12.3.0.eb | 38 ++++++++++ .../l/LIQA/LIQA-1.3.4-foss-2023a.eb | 33 ++++++++ .../lifelines/lifelines-0.28.0-gfbf-2023a.eb | 43 +++++++++++ .../s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb | 76 +++++++++++++++++++ .../t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb | 47 ++++++++++++ 6 files changed, 274 insertions(+) create mode 100644 easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/LIQA/LIQA-1.3.4-foss-2023a.eb create mode 100644 easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb new file mode 100644 index 00000000000..19fd3f0a7be --- /dev/null +++ b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen /NHS/GSTT: toolchain updated to GCCcore-11.2 + +easyblock = 'Tarball' + +name = 'annovar' +version = '20200607' # version reported by `annotate_variation.pl -h` +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://annovar.openbioinformatics.org/en/latest/' +description = """ANNOVAR is an efficient software tool to utilize update-to-date information +to functionally annotate genetic variants detected from diverse genomes (including human +genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +# Registration required for download +# http://www.openbioinformatics.org/annovar/annovar_download_form.php +# rename after download to %(name)s-%(version)s.tar.gz +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] + +dependencies = [('Perl', '5.36.1'),] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl", + "variants_reduction.pl", "table_annovar.pl"], + 'dirs': ["example", "humandb"], +} + +sanity_check_commands = [ + "annotate_variation.pl --help 2>&1 | grep 'Version: $Date: %s-%s-%s'" % (version[:4], version[4:6], version[6:]), + 'retrieve_seq_from_fasta.pl --help 2>&1 | grep "reformat sequences at specific genomic positions"', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-12.3.0.eb new file mode 100644 index 00000000000..f6fd731b03b --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.21' + +homepage = 'https://github.com/samtools/bcftools/' +description = """BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) +and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, +both uncompressed and BGZF-compressed.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/samtools/bcftools/releases/download/%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['528a4cc1d3555368db75a700b22a3c95da893fd1827f6d304716dfd45ea4e282'] + +builddependencies = [ + ('Autotools', '20220317'), +] +dependencies = [ + ('HTSlib', '1.18'), + ('GSL', '2.7'), + ('Perl', '5.36.1'), +] + +preconfigopts = 'autoheader && autoconf && ' +configopts = '--enable-libgsl --enable-perl-filters ' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/bcftools'], + 'dirs': ['libexec', 'share'], +} + +modextravars = {'BCFTOOLS_PLUGINS': '%(installdir)s/libexec/%(namelower)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LIQA/LIQA-1.3.4-foss-2023a.eb b/easybuild/easyconfigs/l/LIQA/LIQA-1.3.4-foss-2023a.eb new file mode 100644 index 00000000000..42f1c68574f --- /dev/null +++ b/easybuild/easyconfigs/l/LIQA/LIQA-1.3.4-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'LIQA' +version = '1.3.4' + +homepage = "https://pypi.org/project/liqa/" +description = """LIQA (Long-read Isoform Quantification and Analysis) is an Expectation-Maximization +based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) +events using long-read RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pysam', '0.22.0'), + ('lifelines', '0.28.0'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': '%(namelower)s_src'} + +sanity_check_commands = ['liqa -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb new file mode 100644 index 00000000000..15c494664b2 --- /dev/null +++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'lifelines' +version = '0.28.0' + +homepage = "https://lifelines.readthedocs.io/en/latest/" +description = """Lifelines is a complete survival analysis library, written in pure Python.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('wrapt', '1.15.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('interface_meta', '1.3.0', { + 'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'], + }), + ('autograd', '1.6.2', { + 'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'], + }), + ('autograd-gamma', '0.5.0', { + 'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'], + }), + ('formulaic', '1.0.1', { + 'checksums': ['64dd7992a7aa5bbceb1e40679d0f01fc6f0ba12b7d23d78094a88c2edc68fba1'], + }), + (name, version, { + 'checksums': ['eecf726453fd409c94fef8a521f8e593bcd09337f920fe885131f01cfe58b25e'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb b/easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb new file mode 100644 index 00000000000..66ea0238f26 --- /dev/null +++ b/easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb @@ -0,0 +1,76 @@ +easyblock = 'Tarball' + +name = 'scNanoGPS' +version = '1.1' + +homepage = 'https://github.com/gaolabtools/scNanoGPS/' +description = "Single cell Nanopore sequencing data for Genotype and Phenotype." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/gaolabtools/scNanoGPS/archive/refs/tags/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['60cce1c771283b6d7a3639aa5744acfd6162306d95dd419ad3c265461fdda218'] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('matplotlib', '3.7.2'), + ('Pysam', '0.22.0'), + ('Seaborn', '0.13.2'), + ('Perl', '5.36.1'), + ('minimap2', '2.26'), + ('SAMtools', '1.18'), + ('tabix', '0.2.6'), + ('spoa', '4.1.0'), + ('Subread', '2.0.6'), + ('Longshot', '1.0.0'), + ('BCFtools', '1.21'), + ('gffread', '0.12.7'), + ('LIQA', '1.3.4'), + # Optional - load 'annovar/20200607-GCCcore-12.3.0-Perl-5.36.1' to make 'reporter_SNV.py' work +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('Distance', '0.1.3', { + 'checksums': ['60807584f5b6003f5c521aa73f39f51f631de3be5cccc5a1d67166fcbf0d4551'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'liqa -h', + "python other_utils/read_length_profiler.py -h", + "python scanner.py -h", + "python assigner.py -h", + "python curator.py -h ", + "python reporter_expression.py -h", + "python reporter_isoform.py -h", + "python reporter_SNV.py -h", + "python reporter_summary.py -h" +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +modloadmsg = """ +If you like to use script 'reporter_SNV.py' you need to load annovar module as: +'ml annovar/20200607-GCCcore-12.3.0-Perl-5.36.1' +Source files of annovar (latest) are available after registration on: +http://www.openbioinformatics.org/annovar/annovar_download_form.php +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c27a6c1f603 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb @@ -0,0 +1,47 @@ +# 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 +# Author: Jens Timmerman, Ghent University +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# updated to newer toolchain + +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'https://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] +checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + (["libtabix.a"], "lib64"), + (["*.h"], "include"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py", "lib/libtabix.a"], + 'dirs': ["include"], +} + +moduleclass = 'bio' From 1887eddcbbc213d382da0221e3be4c2f02865ddd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 16 Dec 2024 13:26:29 +0100 Subject: [PATCH 232/414] make hatchling only a build dependency --- .../b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb index c8ea0187e5a..6cc5d76a73d 100644 --- a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -14,6 +14,10 @@ source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/'] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7'] +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), ('Python', '3.11.3'), @@ -32,7 +36,6 @@ dependencies = [ ('Optax', '0.2.2', versionsuffix), ('py3Dmol', '2.1.0'), ('JupyterLab', '4.0.5'), - ('hatchling', '1.18.0'), ('Flax', '0.8.4', versionsuffix), ] From c8b1ab5064d88b3a600aa37c94e19a0589f1396a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Mon, 16 Dec 2024 13:54:56 +0100 Subject: [PATCH 233/414] Update annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb - fix comma --- .../a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb index 19fd3f0a7be..55490da3de7 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] -dependencies = [('Perl', '5.36.1'),] +dependencies = [('Perl', '5.36.1')] modextrapaths = {'PATH': ''} From 13a9af40983417cc6a90675ad6682cb9975f6998 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 16 Dec 2024 15:47:25 +0100 Subject: [PATCH 234/414] update BCFtools dependency --- .../b/BCFtools/BCFtools-1.21-GCC-12.3.0.eb | 38 ------------------- .../s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb | 2 +- 2 files changed, 1 insertion(+), 39 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-12.3.0.eb deleted file mode 100644 index f6fd731b03b..00000000000 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-12.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'BCFtools' -version = '1.21' - -homepage = 'https://github.com/samtools/bcftools/' -description = """BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) -and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, -both uncompressed and BGZF-compressed.""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -source_urls = ['https://github.com/samtools/bcftools/releases/download/%(version)s/'] -sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['528a4cc1d3555368db75a700b22a3c95da893fd1827f6d304716dfd45ea4e282'] - -builddependencies = [ - ('Autotools', '20220317'), -] -dependencies = [ - ('HTSlib', '1.18'), - ('GSL', '2.7'), - ('Perl', '5.36.1'), -] - -preconfigopts = 'autoheader && autoconf && ' -configopts = '--enable-libgsl --enable-perl-filters ' - -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/bcftools'], - 'dirs': ['libexec', 'share'], -} - -modextravars = {'BCFTOOLS_PLUGINS': '%(installdir)s/libexec/%(namelower)s'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb b/easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb index 66ea0238f26..07c83a5af44 100644 --- a/easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb @@ -27,7 +27,7 @@ dependencies = [ ('spoa', '4.1.0'), ('Subread', '2.0.6'), ('Longshot', '1.0.0'), - ('BCFtools', '1.21'), + ('BCFtools', '1.18'), ('gffread', '0.12.7'), ('LIQA', '1.3.4'), # Optional - load 'annovar/20200607-GCCcore-12.3.0-Perl-5.36.1' to make 'reporter_SNV.py' work From 46c83d99a5b2dc47bcc6c36ae8de8adefa580695 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 16 Dec 2024 16:28:23 +0100 Subject: [PATCH 235/414] adding easyconfigs: SMV-6.9.5-GCCcore-12.3.0.eb --- .../s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b164481d03e --- /dev/null +++ b/easybuild/easyconfigs/s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'SMV' # SmokeView +version = '6.9.5' + +homepage = 'https://github.com/firemodels/smv' +description = """Smokeview is a visualization program that displays output of FDS and CFAST simulations.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/firemodels/smv/archive/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6c6203f6d6cd83c3525c7447ce4201c8df373d18d0c992d607ad232a77590ef7'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), +] +dependencies = [ + ('libgd', '2.3.3'), + ('freeglut', '3.4.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('json-c', '0.16'), + ('Doxygen', '1.9.7'), + ('glew', '2.2.0', '-osmesa'), +] + +configopts = '-DVERIFICATION_TESTS=ON' + +sanity_check_commands = [ + 'smokediff -h', + 'smokezip -h', + 'smvq -h', + 'smokeview -h 2>&1 | grep "Visualize"', +] + +sanity_check_paths = { + 'files': ['bin/smokeview', 'bin/smokediff', 'bin/smokezip', 'bin/smvq'], + 'dirs': [], +} + +moduleclass = 'vis' From 6524c754e5fbe39c4d45f11c76ad191520955d61 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 16 Dec 2024 18:42:15 +0100 Subject: [PATCH 236/414] adding easyconfigs: chewBBACA-3.3.10-foss-2023a.eb --- .../chewBBACA/chewBBACA-3.3.10-foss-2023a.eb | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb new file mode 100644 index 00000000000..09f05c43286 --- /dev/null +++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'chewBBACA' +version = '3.3.10' + +homepage = 'https://github.com/B-UMMI/chewBBACA' +description = """ +chewBBACA is a software suite for the creation and evaluation of core genome and +whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results. +The "BBACA" stands for "BSR-Based Allele Calling Algorithm". +BSR stands for BLAST Score Ratio as proposed by Rasko DA et al. +The "chew" part adds extra coolness to the name and could be thought of as +"Comprehensive and Highly Efficient Workflow".""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('scikit-build-core', '0.9.3'), + ('poetry', '1.5.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('Biopython', '1.83'), + ('plotly.py', '5.16.0'), + ('Cython', '3.0.7'), + ('BLAST+', '2.14.1'), + ('MAFFT', '7.520', '-with-extensions'), + ('FastTree', '2.1.11'), + ('archspec', '0.2.1'), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = ( + "sed -i " + "-e 's/numpy~=1.24.3/numpy>=1.24.3/g' " + "-e 's/scipy~=1.10.1/scipy>=1.10.1/g' " + 'pyproject.toml && ' +) + +exts_list = [ + ('pyrodigal', '3.6.3', { + 'checksums': ['3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', '7.1.1', { + 'checksums': ['164de86bd3564558802ca983d84f6616a4a1a420c7a17a8152f5016076b2913e'], + }), + ('SPARQLWrapper', '2.0.0', { + 'modulename': 'SPARQLWrapper', + 'checksums': ['3fed3ebcc77617a4a74d2644b86fd88e0f32e7f7003ac7b2b334c026201731f1'], + }), + (name, version, { + 'modulename': 'CHEWBBACA', + 'sources': [SOURCELOWER_TAR_GZ], + 'preinstallopts': local_preinstallopts, + 'testinstall': True, + 'runtest': "python setup.py test", + 'checksums': ['f22cc90a3ac55c203669fc3d6647aabd4f939999c44ddd9d4d44881f7304cb0e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/chewBBACA.py', 'bin/chewie'], + 'dirs': [], +} + +sanity_check_commands = [ + 'chewBBACA.py --help', + 'chewie --help', +] + +moduleclass = 'bio' From 74b52caa8baa395aa31e0061c0a11d23422b5578 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 17 Dec 2024 07:56:50 +0100 Subject: [PATCH 237/414] Parsnp: Add required and optional dependencies --- .../f/FastANI/FastANI-1.34-GCC-13.2.0.eb | 45 +++++++ .../harvest-tools-1.3-GCCcore-13.2.0.eb | 60 ++++++++++ ...3_adapt_to_newer-gcc_protobuf_and_EB.patch | 113 ++++++++++++++++++ .../p/Parsnp/Parsnp-2.1.1-foss-2023b.eb | 7 ++ .../PhiPack/PhiPack-2016.06.14-GCC-13.2.0.eb | 39 ++++++ .../r/RAxML/RAxML-8.2.13-gompi-2023b-avx2.eb | 39 ++++++ 6 files changed, 303 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.34-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/h/harvest-tools/harvest-tools-1.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/h/harvest-tools/harvest-tools-1.3_adapt_to_newer-gcc_protobuf_and_EB.patch create mode 100644 easybuild/easyconfigs/p/PhiPack/PhiPack-2016.06.14-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023b-avx2.eb diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.34-GCC-13.2.0.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.34-GCC-13.2.0.eb new file mode 100644 index 00000000000..73ffad70a87 --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.34-GCC-13.2.0.eb @@ -0,0 +1,45 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'ConfigureMake' + +name = 'FastANI' +version = '1.34' + +homepage = "https://github.com/ParBLiSS/FastANI" +description = """FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean + nucleotide identity of orthologous gene pairs shared between two microbial + genomes. FastANI supports pairwise comparison of both complete and draft + genome assemblies.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] +sources = ['v%(version)s.zip'] +patches = ['FastANI-1.2-memcpy.patch'] +checksums = [ + {'v1.34.zip': 'cb15540634c725cb46dded7becaff38b27a7f709c0a8589db986674effcc6180'}, + {'FastANI-1.2-memcpy.patch': 'eebcf0b64c31ee360ca79136f644157064ac69747ed13cff70f5c9932c6bb0d5'}, +] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [ + ('GSL', '2.7'), + ('zlib', '1.2.13'), +] + +preconfigopts = 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/fastANI'], + 'dirs': [] +} + +sanity_check_commands = ["fastANI --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/harvest-tools/harvest-tools-1.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/harvest-tools/harvest-tools-1.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..fad02bd2552 --- /dev/null +++ b/easybuild/easyconfigs/h/harvest-tools/harvest-tools-1.3-GCCcore-13.2.0.eb @@ -0,0 +1,60 @@ +easyblock = 'ConfigureMake' + +name = 'harvest-tools' +version = '1.3' + +homepage = 'https://harvest.readthedocs.io/en/latest/content/harvest-tools.html' +description = """HarvestTools is a utility for creating and interfacing +with Gingr files, which are efficient archives that the Harvest Suite +uses to store reference-compressed multi-alignments, phylogenetic trees, +filtered variants and annotations. Though designed for use with Parsnp +and Gingr, HarvestTools can also be used for generic conversion between +standard bioinformatics file formats.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'marbl' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'harvest-tools-1.3_adapt_to_newer-gcc_protobuf_and_EB.patch', +] +checksums = [ + {'v1.3.tar.gz': 'ffbcf0a115c74507695fd6cee4a9d5ba27a700db36b32d226521ef8dd3309264'}, + {'harvest-tools-1.3_adapt_to_newer-gcc_protobuf_and_EB.patch': + '9d04d6c942d42a8147f43f8f086f436d284925f3a3acdd9620df84d4041dff61'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('protobuf', '25.3'), + ('CapnProto', '1.0.1.1'), +] + +preconfigopts = 'autoconf && ' + +configopts = ' '.join([ + '--with-protobuf=$EBROOTPROTOBUF', + '--with-capnp=$EBROOTCAPNPROTO', +]) + +postinstallcmds = [ + 'ln -s harvesttools %(installdir)s/bin/harvest', +] + +sanity_check_paths = { + 'files': ['bin/harvesttools', 'lib/libharvest.%s' % SHLIB_EXT], + 'dirs': ['include/harvest'], +} + +sanity_check_commands = [ + 'harvest -h', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/harvest-tools/harvest-tools-1.3_adapt_to_newer-gcc_protobuf_and_EB.patch b/easybuild/easyconfigs/h/harvest-tools/harvest-tools-1.3_adapt_to_newer-gcc_protobuf_and_EB.patch new file mode 100644 index 00000000000..a8fa6e16f8d --- /dev/null +++ b/easybuild/easyconfigs/h/harvest-tools/harvest-tools-1.3_adapt_to_newer-gcc_protobuf_and_EB.patch @@ -0,0 +1,113 @@ +commit 845bb6e29bc12cf5f989c0c64fb98002cb57b343 +Author: Ake Sandgren +Date: Mon Dec 16 18:10:22 2024 +0100 + + Adapt to newer compiler/protobuf and EasyBuild + And actually install the binary, library and include files + +diff --git a/Makefile.in b/Makefile.in +index fdb2ce0..434ba0a 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -1,4 +1,4 @@ +-CXXFLAGS += -std=c++11 -Isrc -I@protobuf@/include -I@capnp@/include ++CXXFLAGS += -Isrc + + UNAME_S=$(shell uname -s) + +@@ -23,10 +23,13 @@ SOURCES=\ + + OBJECTS=$(SOURCES:.cpp=.o) src/harvest/pb/harvest.pb.o src/harvest/capnp/harvest.capnp.o + +-all : harvesttools libharvest.a ++all : harvesttools libharvest.a libharvest.so + +-harvesttools : libharvest.a src/harvest/memcpyWrap.o +- $(CXX) $(CXXFLAGS) $(CPPFLAGS) -o harvesttools src/harvest/memcpyWrap.o libharvest.a @protobuf@/lib/libprotobuf.a @capnp@/lib/libcapnp.a @capnp@/lib/libkj.a -lstdc++ -lz -lm -lpthread ++harvesttools : libharvest.so src/harvest/memcpyWrap.o ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -o harvesttools src/harvest/memcpyWrap.o -L. -lharvest -lprotobuf -lcapnp -lkj -lstdc++ -lz -lm -lpthread ++ ++libharvest.so : $(OBJECTS) ++ g++ -shared -o libharvest.so $(OBJECTS) + + libharvest.a : $(OBJECTS) + ar -cr libharvest.a $(OBJECTS) +@@ -52,27 +55,28 @@ src/harvest/pb/harvest.pb.cc src/harvest/pb/harvest.pb.h : src/harvest/pb/harves + src/harvest/capnp/harvest.capnp.c++ src/harvest/capnp/harvest.capnp.h : src/harvest/capnp/harvest.capnp + cd src/harvest/capnp;export PATH=@capnp@/bin/:${PATH};capnp compile -I @capnp@/include -oc++ harvest.capnp + +-install : libharvest.a +- mkdir -p @prefix@/bin/ +- mkdir -p @prefix@/lib/ +- mkdir -p @prefix@/include/ +- mkdir -p @prefix@/include/harvest +- mkdir -p @prefix@/include/harvest/capnp +- mkdir -p @prefix@/include/harvest/pb +- ln -sf `pwd`/harvesttools @prefix@/bin/ +- ln -sf `pwd`/libharvest.a @prefix@/lib/ +- ln -sf `pwd`/src/harvest/exceptions.h @prefix@/include/harvest/ +- ln -sf `pwd`/src/harvest/HarvestIO.h @prefix@/include/harvest/ +- ln -sf `pwd`/src/harvest/capnp/harvest.capnp.h @prefix@/include/harvest/capnp/ +- ln -sf `pwd`/src/harvest/pb/harvest.pb.h @prefix@/include/harvest/pb/ +- ln -sf `pwd`/src/harvest/ReferenceList.h @prefix@/include/harvest/ +- ln -sf `pwd`/src/harvest/AnnotationList.h @prefix@/include/harvest/ +- ln -sf `pwd`/src/harvest/parse.h @prefix@/include/harvest/ +- ln -sf `pwd`/src/harvest/PhylogenyTree.h @prefix@/include/harvest/ +- ln -sf `pwd`/src/harvest/PhylogenyTreeNode.h @prefix@/include/harvest/ +- ln -sf `pwd`/src/harvest/TrackList.h @prefix@/include/harvest/ +- ln -sf `pwd`/src/harvest/LcbList.h @prefix@/include/harvest/ +- ln -sf `pwd`/src/harvest/VariantList.h @prefix@/include/harvest/ ++install : all ++ install -d @prefix@/bin/ ++ install -d @prefix@/lib/ ++ install -d @prefix@/include/ ++ install -d @prefix@/include/harvest ++ install -d @prefix@/include/harvest/capnp ++ install -d @prefix@/include/harvest/pb ++ install harvesttools @prefix@/bin/ ++ install libharvest.a @prefix@/lib/ ++ install libharvest.so @prefix@/lib/ ++ install src/harvest/exceptions.h @prefix@/include/harvest/ ++ install src/harvest/HarvestIO.h @prefix@/include/harvest/ ++ install src/harvest/capnp/harvest.capnp.h @prefix@/include/harvest/capnp/ ++ install src/harvest/pb/harvest.pb.h @prefix@/include/harvest/pb/ ++ install src/harvest/ReferenceList.h @prefix@/include/harvest/ ++ install src/harvest/AnnotationList.h @prefix@/include/harvest/ ++ install src/harvest/parse.h @prefix@/include/harvest/ ++ install src/harvest/PhylogenyTree.h @prefix@/include/harvest/ ++ install src/harvest/PhylogenyTreeNode.h @prefix@/include/harvest/ ++ install src/harvest/TrackList.h @prefix@/include/harvest/ ++ install src/harvest/LcbList.h @prefix@/include/harvest/ ++ install src/harvest/VariantList.h @prefix@/include/harvest/ + + clean : + -rm harvesttools +diff --git a/configure.ac b/configure.ac +index fc8e61d..5e2fc22 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -29,8 +29,6 @@ then + AC_MSG_ERROR([Cap'n Proto compiler (capnp) not found.]) + fi + +-CPPFLAGS="-I$with_protobuf/include -I$with_capnp/include -std=c++11" +- + AC_CHECK_HEADER(google/protobuf/stubs/common.h, [result=1], [result=0]) + + if test $result == 0 +diff --git a/src/harvest/HarvestIO.cpp b/src/harvest/HarvestIO.cpp +index c165dce..c1dbb7a 100755 +--- a/src/harvest/HarvestIO.cpp ++++ b/src/harvest/HarvestIO.cpp +@@ -208,7 +208,11 @@ bool HarvestIO::loadHarvestProtocolBuffer(const char * file) + GzipInputStream gz(&raw_input); + CodedInputStream coded_input(&gz); + ++#if GOOGLE_PROTOBUF_VERSION >= 3002000 ++ coded_input.SetTotalBytesLimit(INT_MAX); ++#else + coded_input.SetTotalBytesLimit(INT_MAX, INT_MAX); ++#endif + + if ( ! harvest.ParseFromCodedStream(&coded_input) ) + { diff --git a/easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1-foss-2023b.eb b/easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1-foss-2023b.eb index 2117add9996..fe8537ddca9 100644 --- a/easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1-foss-2023b.eb +++ b/easybuild/easyconfigs/p/Parsnp/Parsnp-2.1.1-foss-2023b.eb @@ -37,6 +37,13 @@ dependencies = [ ('SciPy-bundle', '2023.11'), ('tqdm', '4.66.2'), ('Biopython', '1.84'), + ('FastTree', '2.1.11'), + ('harvest-tools', '1.3'), + ('RAxML', '8.2.13', '-avx2'), + ('pyspoa', '0.2.1'), + ('Mash', '2.3'), + ('FastANI', '1.34'), + ('PhiPack', '2016.06.14'), ] preconfigopts = ' && '.join([ diff --git a/easybuild/easyconfigs/p/PhiPack/PhiPack-2016.06.14-GCC-13.2.0.eb b/easybuild/easyconfigs/p/PhiPack/PhiPack-2016.06.14-GCC-13.2.0.eb new file mode 100644 index 00000000000..b4320c8b0b6 --- /dev/null +++ b/easybuild/easyconfigs/p/PhiPack/PhiPack-2016.06.14-GCC-13.2.0.eb @@ -0,0 +1,39 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = "MakeCp" + +name = "PhiPack" +# No version is specified by default, copyright is 2005 latest update 2016 +# find -type f -printf '%T+ %p\n' | sort -r | head -n 1 +# 2016-06-14+06:18:29.0000000000 ./PhiPack/src/fasta.c +# latest edit time of file in the archive +version = "2016.06.14" + +homepage = "http://www.maths.otago.ac.nz/~dbryant/software.html" +description = """The PhiPack software package implements (in C) a few tests for +recombination and can produce refined incompatibility matrices as well.""" + +docurls = ["http://www.maths.otago.ac.nz/~dbryant/software/phimanual.pdf"] +software_license = "LicenseGPLv3" +software_license_urls = ['https://www.gnu.org/licenses/lgpl-3.0.en.html'] + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['http://www.maths.otago.ac.nz/~dbryant/software/'] +sources = [{'download_filename': 'PhiPack.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['af43326e021f1f2e590be2cba3caa44a0963f237386e63209ccc26b5bfb02db9'] + +start_dir = 'src/' +buildopts = 'CXX="$CC" CXXFLAGS="$CFLAGS"' + +files_to_copy = [(['Phi', 'Profile', 'ppma_2_bmp/ppma_2_bmp'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Phi', 'bin/Profile', 'bin/ppma_2_bmp'], + 'dirs': [], +} + +sanity_check_commands = ["Phi -f %(builddir)s/%(name)s/noro.fasta"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023b-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023b-avx2.eb new file mode 100644 index 00000000000..35faf662fe2 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023b-avx2.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.13' +versionsuffix = '-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['28e500793324bd7d330b396ef27ea49c9186fa5e1edb3d5439036dc6c33e6067'] + +buildopts = '-f Makefile.AVX2.gcc CC="$CC" && rm *.o && ' +buildopts += 'make -j %(parallel)s -f Makefile.AVX2.PTHREADS.gcc CC="$CC" && rm *.o && ' +buildopts += 'make -j %(parallel)s -f Makefile.AVX2.HYBRID.gcc CC="$CC"' + +files_to_copy = [ + (["raxmlHPC-AVX2", "raxmlHPC-PTHREADS-AVX2", "raxmlHPC-HYBRID-AVX2"], "bin"), + "usefulScripts", "README.md", "manual", +] + +postinstallcmds = [ + "ln -s raxmlHPC-AVX2 %(installdir)s/bin/raxmlHPC", + "ln -s raxmlHPC-PTHREADS-AVX2 %(installdir)s/bin/raxmlHPC-PTHREADS", + "ln -s raxmlHPC-HYBRID-AVX2 %(installdir)s/bin/raxmlHPC-HYBRID", +] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC%s' % x for x in ['', '-PTHREADS', '-HYBRID']], + 'dirs': [], +} + +sanity_check_commands = ["raxmlHPC -%s" % x for x in ['h', 'v']] + +moduleclass = 'bio' From 0e8239afb5922bfd20cc2b109cf5680aa04996c8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 17 Dec 2024 08:53:39 +0100 Subject: [PATCH 238/414] move `hatchling` from deps to build deps for `BindCraft` --- .../easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb index 49345e486d8..fd6186d58ec 100644 --- a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb @@ -13,6 +13,10 @@ source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/'] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7'] +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), @@ -30,7 +34,6 @@ dependencies = [ ('Optax', '0.2.2'), ('py3Dmol', '2.1.0'), ('JupyterLab', '4.0.5'), - ('hatchling', '1.18.0'), ('Flax', '0.8.4'), ] From c186c60810e155a2097ccd0f88208eb89924a407 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 17 Dec 2024 11:02:21 +0100 Subject: [PATCH 239/414] Update chewBBACA-3.3.10-foss-2023a.eb - update Cython version --- .../easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb index 09f05c43286..64194b1357a 100644 --- a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb +++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb @@ -24,7 +24,7 @@ dependencies = [ ('Python-bundle-PyPI', '2023.06'), ('Biopython', '1.83'), ('plotly.py', '5.16.0'), - ('Cython', '3.0.7'), + ('Cython', '3.0.8'), ('BLAST+', '2.14.1'), ('MAFFT', '7.520', '-with-extensions'), ('FastTree', '2.1.11'), From a3d73f02f85adcfa41c5705613fbd9ef5ca3ce22 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 17 Dec 2024 15:20:26 +0100 Subject: [PATCH 240/414] adding easyconfigs: IGV-2.19.1-Java-17.eb --- .../easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb b/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb new file mode 100644 index 00000000000..9a2bc1d7398 --- /dev/null +++ b/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'Tarball' + +name = 'IGV' +version = '2.19.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/software/igv/' +description = """This package contains command line utilities for + preprocessing, computing feature count density (coverage), sorting, and + indexing data files.""" + +toolchain = SYSTEM + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s'] +sources = ['%(name)s_%(version)s.zip'] +checksums = ['e7d7803cab4e12e84f5359a3d73915a45acc6d676151ca18e91fb2d39432b568'] + +dependencies = [('Java', '17', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 57a3430380df7d2c9fbb41b1fccd241defbc234b Mon Sep 17 00:00:00 2001 From: Mody-SHARK Date: Tue, 17 Dec 2024 16:17:20 +0100 Subject: [PATCH 241/414] Added SlurmViewer-1.0.2 --- .../SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5e76a90026f --- /dev/null +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,61 @@ +# # +# Authors: +# - Patrick de Koning +# - Prerak Mody +# # +easyblock = 'PythonBundle' + +name = 'SlurmViewer' +version = '1.0.2' + +homepage = 'https://gitlab.com/lkeb/slurm_viewer' +description = """One-stop command to view the status of a Slurm cluster, including nodes, jobs and resource utilization""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), + ('poetry', '1.6.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('pydantic', '2.7.4'), +] + +use_pip = True + +exts_list = [ + ('plotext', '5.2.8', { + 'checksums': ['319a287baabeb8576a711995f973a2eba631c887aa6b0f33ab016f12c50ffebe'], + }), + ('textual', '0.85.2', { + 'checksums': ['2a416995c49d5381a81d0a6fd23925cb0e3f14b4f239ed05f35fa3c981bb1df2'], + }), + ('textual-plotext', '0.2.1', { + 'source_tmpl': 'textual_plotext-%(version)s.tar.gz', + 'checksums': ['bc6f2d75d8e20dda6321f8254dc3decda8f41f60e6e70a3ddd83b652b890c081'], + }), + ('asyncssh', '2.18.0', { + 'checksums': ['1a322161c01f60b9719dc8f39f80db71e61f3f5e04abbc3420ce503126d87123'], + }), + ('slurm-viewer', version, { + 'source_tmpl': 'slurm_viewer-%(version)s-py3-none-any.whl', + 'checksums': ['00baa6a9b26b36592e361486d58df3d68a8df970dfc66ebc2ba7cdd67994bfe0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/slurm-viewer'], + 'dirs': ['lib'] +} + +sanity_pip_check = True + +modloadmsg = """Slurm Viewer uses a configuration file. +This is made by default (from v1.0.2) in the ~/.config/slurm-viewer/ directory., +YOu can also point to a settings file by setting the environment variable $SLURM_VIEW_CONFIG.""" + +moduleclass = 'tools' From 8688a026a812f5d75c4d3b147a1ce317eae6049a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 17 Dec 2024 19:08:28 +0000 Subject: [PATCH 242/414] fix conflict of multiple tbl2asn --- .../p/prokka/prokka-1.14.5-gompi-2023a.eb | 2 +- .../t/tbl2asn/tbl2asn-20230713-linux64.eb | 56 ------------------- 2 files changed, 1 insertion(+), 57 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb index 05fe75468f6..2e84effbc53 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb @@ -25,7 +25,7 @@ dependencies = [ ('Java', '11', '', SYSTEM), ('Bio-SearchIO-hmmer', '1.7.3'), ('parallel', '20230722'), - ('tbl2asn', '20230713', '-linux64', SYSTEM), + ('tbl2asn', '20230713'), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb deleted file mode 100644 index 71b750650ba..00000000000 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb +++ /dev/null @@ -1,56 +0,0 @@ -# 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 -# revised by Ariel Lozano - -easyblock = 'Bundle' - -name = 'tbl2asn' -version = '20230713' -versionsuffix = '-linux64' - -homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' -description = """Tbl2asn is a command-line program that automates the creation of - sequence records for submission to GenBank""" - -toolchain = SYSTEM -builddependencies = [ - ('binutils', '2.35'), -] - -default_easyblock = 'CmdCp' - -# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, -# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 -# checksums. - -components = [ - ('libidn', '1.34', { - 'easyblock': 'ConfigureMake', - 'source_urls': [GNU_SOURCE], - 'sources': [SOURCELOWER_TAR_GZ], - 'start_dir': '%(namelower)s-%(version)s', - 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], - }), - (name, version, { - 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % - (version[:4] + '-' + version[4:6] + '-' + version[6:])], - 'sources': [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:], - 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], - 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], - 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], - 'files_to_copy': [(['tbl2asn'], 'bin')], - }), -] - -postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] - -sanity_check_paths = { - 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -sanity_check_commands = ['tbl2asn --help'] - -moduleclass = 'bio' From ac210a3ccbf8373d4396673dcec48b86363590c6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 17 Dec 2024 19:39:54 +0000 Subject: [PATCH 243/414] restore tbl2asn-20230713-linux64.eb as it is still needed for prokka-1.14.5-gompi-2022b.eb --- .../t/tbl2asn/tbl2asn-20230713-linux64.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb new file mode 100644 index 00000000000..71b750650ba --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb @@ -0,0 +1,56 @@ +# 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 +# revised by Ariel Lozano + +easyblock = 'Bundle' + +name = 'tbl2asn' +version = '20230713' +versionsuffix = '-linux64' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = SYSTEM +builddependencies = [ + ('binutils', '2.35'), +] + +default_easyblock = 'CmdCp' + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. + +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:], + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), +] + +postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] + +sanity_check_paths = { + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['tbl2asn --help'] + +moduleclass = 'bio' From 8d6a293820589ad38236e4d71c319235a94986cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Dec 2024 13:37:52 +0100 Subject: [PATCH 244/414] {tools}[system] EasyBuild v5.0.0beta1 (WIP) --- .../e/EasyBuild/EasyBuild-5.0.0beta1.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.0.0beta1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.0.0beta1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.0.0beta1.eb new file mode 100644 index 00000000000..ed54b7bbacd --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.0.0beta1.eb @@ -0,0 +1,35 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '5.0.0beta1' + +homepage = 'https://easybuild.io' +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 = SYSTEM + +source_urls = [ + 'https://github.com/easybuilders/easybuild-framework/archive/', + 'https://github.com/easybuilders/easybuild-easyblocks/archive/', + 'https://github.com/easybuilders/easybuild-easyconfigs/archive/', +] +sources = [ + 'easybuild-framework-v%(version)s.tar.gz', + 'easybuild-easyblocks-v%(version)s.tar.gz', + 'easybuild-easyconfigs-v%(version)s.tar.gz', +] + +# 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' From 80c6d45ea2b7ecccf848edeeae4fde69920e7777 Mon Sep 17 00:00:00 2001 From: pmod <2803936+prerakmody@users.noreply.github.com> Date: Wed, 18 Dec 2024 14:11:18 +0100 Subject: [PATCH 245/414] Update spelling error on easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb Co-authored-by: ocaisa --- .../s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb index 5e76a90026f..f38a500a82d 100644 --- a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -56,6 +56,6 @@ sanity_pip_check = True modloadmsg = """Slurm Viewer uses a configuration file. This is made by default (from v1.0.2) in the ~/.config/slurm-viewer/ directory., -YOu can also point to a settings file by setting the environment variable $SLURM_VIEW_CONFIG.""" +You can also point to a settings file by setting the environment variable $SLURM_VIEW_CONFIG.""" moduleclass = 'tools' From a9cb1adbec2fd707750fed3276003fb144b0351d Mon Sep 17 00:00:00 2001 From: pmod <2803936+prerakmody@users.noreply.github.com> Date: Wed, 18 Dec 2024 14:12:03 +0100 Subject: [PATCH 246/414] Update punctuation error on easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb Co-authored-by: ocaisa --- .../s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb index f38a500a82d..bce5884983c 100644 --- a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -55,7 +55,7 @@ sanity_check_paths = { sanity_pip_check = True modloadmsg = """Slurm Viewer uses a configuration file. -This is made by default (from v1.0.2) in the ~/.config/slurm-viewer/ directory., +This is made by default (from v1.0.2) in the ~/.config/slurm-viewer/ directory. You can also point to a settings file by setting the environment variable $SLURM_VIEW_CONFIG.""" moduleclass = 'tools' From 6250a2ef043ec494c5a452077c2d0b62bad19bfb Mon Sep 17 00:00:00 2001 From: pmod <2803936+prerakmody@users.noreply.github.com> Date: Wed, 18 Dec 2024 14:17:15 +0100 Subject: [PATCH 247/414] Update "pydantic to 2.9.1" in easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb index bce5884983c..56f76b2ae69 100644 --- a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.5'), ('Python-bundle-PyPI', '2023.10'), - ('pydantic', '2.7.4'), + ('pydantic', '2.9.1'), ] use_pip = True From ed209175a6d6a31b8e958cb573844232246d25e7 Mon Sep 17 00:00:00 2001 From: pmod <2803936+prerakmody@users.noreply.github.com> Date: Wed, 18 Dec 2024 14:32:49 +0100 Subject: [PATCH 248/414] Update "bintuls==2.4.2" in easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb index 56f76b2ae69..902f15704ea 100644 --- a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -14,7 +14,7 @@ description = """One-stop command to view the status of a Slurm cluster, includi toolchain = {'name': 'GCCcore', 'version': '13.3.0'} builddependencies = [ - ('binutils', '2.40'), + ('binutils', '2.42'), ('hatchling', '1.18.0'), ('poetry', '1.6.1'), ] From 4df5e390aceebd68063c21764444c65fbc725372 Mon Sep 17 00:00:00 2001 From: pmod <2803936+prerakmody@users.noreply.github.com> Date: Wed, 18 Dec 2024 14:33:11 +0100 Subject: [PATCH 249/414] Update "hatchling==1.24.2" in easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb index 902f15704ea..feaa51a7f8f 100644 --- a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} builddependencies = [ ('binutils', '2.42'), - ('hatchling', '1.18.0'), + ('hatchling', '1.24.2), ('poetry', '1.6.1'), ] From 2c88a1ed59479940f1206999324370ab397d194f Mon Sep 17 00:00:00 2001 From: pmod <2803936+prerakmody@users.noreply.github.com> Date: Wed, 18 Dec 2024 14:33:32 +0100 Subject: [PATCH 250/414] Update "poetry==1.8.3" in easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb index feaa51a7f8f..cbd3de6cffe 100644 --- a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} builddependencies = [ ('binutils', '2.42'), ('hatchling', '1.24.2), - ('poetry', '1.6.1'), + ('poetry', '1.8.3'), ] dependencies = [ From 236d0be51d4c765b0cc96ffbf95711e191532ef2 Mon Sep 17 00:00:00 2001 From: pmod <2803936+prerakmody@users.noreply.github.com> Date: Wed, 18 Dec 2024 14:34:00 +0100 Subject: [PATCH 251/414] Update "python==3.12.3" in easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb index cbd3de6cffe..fd3425dea82 100644 --- a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('Python', '3.11.5'), + ('Python', '3.12.3'), ('Python-bundle-PyPI', '2023.10'), ('pydantic', '2.9.1'), ] From c724668ff638ca526d748efa0a45440b5ba858c2 Mon Sep 17 00:00:00 2001 From: pmod <2803936+prerakmody@users.noreply.github.com> Date: Wed, 18 Dec 2024 14:35:47 +0100 Subject: [PATCH 252/414] Update "Python-bundle-PyPi==2024.06" in easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb index fd3425dea82..0f82803b808 100644 --- a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('Python', '3.12.3'), - ('Python-bundle-PyPI', '2023.10'), + ('Python-bundle-PyPI', '2024.06), ('pydantic', '2.9.1'), ] From 4aa063e64098001f8c66a7b455ef3d64fd700a27 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 18 Dec 2024 13:45:09 +0000 Subject: [PATCH 253/414] add rsvg dep to DjVuLibre --- .../easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb index 355a9996fbc..f4b0e614fd7 100644 --- a/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb @@ -25,6 +25,7 @@ builddependencies = [ dependencies = [ ('libjpeg-turbo', '2.1.5.1'), ('LibTIFF', '4.5.0'), + ('librsvg', '2.58.0'), ] _bins = ['bin/%s' % x for x in ['any2djvu', 'bzz', 'c44', 'cjb2', 'cpaldjvu', 'csepdjvu', 'ddjvu', 'djvm', 'djvmcvt', From b7b40a3b44acc839c0e945487fa5841b0a56c892 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 18 Dec 2024 13:49:21 +0000 Subject: [PATCH 254/414] add Doxygen build dep to libheif --- easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb | 1 + easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb | 1 + easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb | 1 + easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb index bb5cb6bf57c..7850c1ed564 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb @@ -14,6 +14,7 @@ checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] builddependencies = [ ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb index cf871e99182..31a01b9b103 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb @@ -14,6 +14,7 @@ checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] builddependencies = [ ('CMake', '3.22.1'), + ('Doxygen', '1.9.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb index 9d966d5571b..9eb3548d709 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb @@ -16,6 +16,7 @@ checksums = ['7f97e4205c0bd9f9b8560536c8bd2e841d1c9a6d610401eb3eb87ed9cdfe78ea'] builddependencies = [ ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb index ee355100089..77784e13457 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb @@ -16,6 +16,7 @@ checksums = ['8390baf4913eda0a183e132cec62b875fb2ef507ced5ddddc98dfd2f17780aee'] builddependencies = [ ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), ] dependencies = [ From 3a7d593be38b6948b3d703ea58f47d11060bf2ce Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 18 Dec 2024 15:12:13 +0000 Subject: [PATCH 255/414] edit libheif and libde265 to GCCcore --- ....11-GCC-11.3.0.eb => libde265-1.0.11-GCCcore-11.3.0.eb} | 3 ++- ....15-GCC-12.3.0.eb => libde265-1.0.15-GCCcore-12.3.0.eb} | 3 ++- ....0.8-GCC-11.2.0.eb => libde265-1.0.8-GCCcore-10.3.0.eb} | 7 +++++-- ....0.8-GCC-10.3.0.eb => libde265-1.0.8-GCCcore-11.2.0.eb} | 7 +++++-- ...12.0-GCC-10.3.0.eb => libheif-1.12.0-GCCcore-10.3.0.eb} | 3 ++- ...12.0-GCC-11.2.0.eb => libheif-1.12.0-GCCcore-11.2.0.eb} | 3 ++- ...16.2-GCC-11.3.0.eb => libheif-1.16.2-GCCcore-11.3.0.eb} | 3 ++- ...17.6-GCC-12.3.0.eb => libheif-1.17.6-GCCcore-12.3.0.eb} | 3 ++- 8 files changed, 22 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/l/libde265/{libde265-1.0.11-GCC-11.3.0.eb => libde265-1.0.11-GCCcore-11.3.0.eb} (91%) rename easybuild/easyconfigs/l/libde265/{libde265-1.0.15-GCC-12.3.0.eb => libde265-1.0.15-GCCcore-12.3.0.eb} (91%) rename easybuild/easyconfigs/l/libde265/{libde265-1.0.8-GCC-11.2.0.eb => libde265-1.0.8-GCCcore-10.3.0.eb} (83%) rename easybuild/easyconfigs/l/libde265/{libde265-1.0.8-GCC-10.3.0.eb => libde265-1.0.8-GCCcore-11.2.0.eb} (83%) rename easybuild/easyconfigs/l/libheif/{libheif-1.12.0-GCC-10.3.0.eb => libheif-1.12.0-GCCcore-10.3.0.eb} (92%) rename easybuild/easyconfigs/l/libheif/{libheif-1.12.0-GCC-11.2.0.eb => libheif-1.12.0-GCCcore-11.2.0.eb} (92%) rename easybuild/easyconfigs/l/libheif/{libheif-1.16.2-GCC-11.3.0.eb => libheif-1.16.2-GCCcore-11.3.0.eb} (93%) rename easybuild/easyconfigs/l/libheif/{libheif-1.17.6-GCC-12.3.0.eb => libheif-1.17.6-GCCcore-12.3.0.eb} (93%) diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCCcore-11.3.0.eb similarity index 91% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCCcore-11.3.0.eb index 7640cb6a545..b7fbebbccca 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCCcore-11.3.0.eb @@ -8,13 +8,14 @@ version = '1.0.11' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['2f8f12cabbdb15e53532b7c1eb964d4e15d444db1be802505e6ac97a25035bab'] builddependencies = [ + ('binutils', '2.38'), ('CMake', '3.23.1'), ] diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-12.3.0.eb similarity index 91% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-12.3.0.eb index 9d6371e84ba..7d6d8ec7ec1 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-12.3.0.eb @@ -8,13 +8,14 @@ version = '1.0.15' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['00251986c29d34d3af7117ed05874950c875dd9292d016be29d3b3762666511d'] builddependencies = [ + ('binutils', '2.40'), ('CMake', '3.26.3'), ] diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-10.3.0.eb similarity index 83% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-10.3.0.eb index 38d6c4a7d6e..3cf9fb88dc9 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-10.3.0.eb @@ -6,13 +6,16 @@ version = '1.0.8' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['24c791dd334fa521762320ff54f0febfd3c09fc978880a8c5fbc40a88f21d905'] -builddependencies = [('CMake', '3.22.1')] +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] sanity_check_paths = { 'files': ['bin/dec265', 'bin/enc265', 'lib/liblibde265.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-11.2.0.eb similarity index 83% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-11.2.0.eb index 647d345e73e..e2065d805b0 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-11.2.0.eb @@ -6,13 +6,16 @@ version = '1.0.8' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['24c791dd334fa521762320ff54f0febfd3c09fc978880a8c5fbc40a88f21d905'] -builddependencies = [('CMake', '3.20.1')] +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] sanity_check_paths = { 'files': ['bin/dec265', 'bin/enc265', 'lib/liblibde265.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-10.3.0.eb similarity index 92% rename from easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-10.3.0.eb index 7850c1ed564..93f14603ac1 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-10.3.0.eb @@ -6,13 +6,14 @@ version = '1.12.0' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] builddependencies = [ + ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('Doxygen', '1.9.1'), ] diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-11.2.0.eb similarity index 92% rename from easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-11.2.0.eb index 31a01b9b103..164821bc84e 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-11.2.0.eb @@ -6,13 +6,14 @@ version = '1.12.0' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] builddependencies = [ + ('binutils', '2.37'), ('CMake', '3.22.1'), ('Doxygen', '1.9.1'), ] diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb similarity index 93% rename from easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb index 9eb3548d709..c2051457429 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb @@ -8,13 +8,14 @@ version = '1.16.2' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['7f97e4205c0bd9f9b8560536c8bd2e841d1c9a6d610401eb3eb87ed9cdfe78ea'] builddependencies = [ + ('binutils', '2.3'), ('CMake', '3.23.1'), ('Doxygen', '1.9.4'), ] diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCCcore-12.3.0.eb similarity index 93% rename from easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCCcore-12.3.0.eb index 77784e13457..9ca2db177a2 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCCcore-12.3.0.eb @@ -8,13 +8,14 @@ version = '1.17.6' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['8390baf4913eda0a183e132cec62b875fb2ef507ced5ddddc98dfd2f17780aee'] builddependencies = [ + ('binutils', '2.40'), ('CMake', '3.26.3'), ('Doxygen', '1.9.7'), ] From 6b820831e8c5819ebef60196ff56f6a174c3cd4a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Wed, 18 Dec 2024 15:53:21 +0000 Subject: [PATCH 256/414] Revert "{bio}[GCCcore/13.3.0] rDock v24.03.192" --- .../r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb | 48 ------------------- 1 file changed, 48 deletions(-) delete mode 100644 easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb deleted file mode 100644 index 44ae4090d0a..00000000000 --- a/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -# Author: J. Sassmannshausen (Imperial College London/UK) - -easyblock = 'ConfigureMake' - -name = 'rDock' -version = '24.03.192' - -homepage = 'https://rdock.github.io/' -description = """ -rDock is a fast and versatile Open Source docking program that can be used to dock small -molecules against proteins and nucleic acids. It is designed for High Throughput Virtual -Screening (HTVS) campaigns and Binding Mode prediction studies. -""" - -toolchain = {'name': 'GCCcore', 'version': '13.3.0'} - -source_urls = ['https://github.com/CBDD/rDock/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['4cb4267831a30010d2bca7daf13f74ab113df2c19a140859e9878a02038f551b'] - -builddependencies = [ - ('binutils', '2.42'), -] -dependencies = [ - ('tcsh', '6.24.13'), - ('popt', '1.19'), -] - -configure_without_installdir = True -configure_cmd = ' ' - -preinstallopts = 'export PREFIX=%(installdir)s && ' - -runtest = 'test' - -postinstallcmds = ['sed -i "s|/bin/csh -f|/usr/bin/env tcsh -f|" %(installdir)s/bin/make_grid.csh'] - -sanity_check_paths = { - 'files': ['bin/rbhtfinder', 'bin/sdreport', 'bin/run_rbdock.pl', 'lib/libRbt.so'], - 'dirs': ['include'], -} - -sanity_check_commands = [ - 'rbdock --help', - 'rbcavity --help', -] - -moduleclass = 'bio' From 3b353aad832c5d74742b2ddd617a0818261fabb9 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 18 Dec 2024 15:55:05 +0000 Subject: [PATCH 257/414] Missing directories added --- .../r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ac6f496471c --- /dev/null +++ b/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'rDock' +version = '24.03.192' + +homepage = 'https://rdock.github.io/' +description = """ +rDock is a fast and versatile Open Source docking program that can be used to dock small +molecules against proteins and nucleic acids. It is designed for High Throughput Virtual +Screening (HTVS) campaigns and Binding Mode prediction studies. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/CBDD/rDock/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4cb4267831a30010d2bca7daf13f74ab113df2c19a140859e9878a02038f551b'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('tcsh', '6.24.13'), + ('popt', '1.19'), +] + +configure_without_installdir = True +configure_cmd = ' ' + +preinstallopts = 'export PREFIX=%(installdir)s && ' + +runtest = 'test' + +postinstallcmds = [ + 'sed -i "s|/bin/csh -f|/usr/bin/env tcsh|" %(installdir)s/bin/make_grid.csh ; ', + 'cp -ra %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s ; ', + 'sed -i "s|/bin/csh -f|/usr/bin/env tcsh|" %(installdir)s/scripts/make_grid.csh ; ', + 'cp -ra %(builddir)s/%(name)s-%(version)s/data %(installdir)s ; ', +] + +sanity_check_paths = { + 'files': ['bin/rbhtfinder', 'bin/sdreport', 'bin/run_rbdock.pl', 'lib/libRbt.so'], + 'dirs': ['include', 'scripts', 'data'], +} + +sanity_check_commands = [ + 'rbdock --help', + 'rbcavity --help', +] + +moduleclass = 'bio' From 3a247203f82ed994ee575cbc63b146a685b3a8a9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 18 Dec 2024 16:01:19 +0000 Subject: [PATCH 258/414] fix type --- .../easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb index c2051457429..c0a02db1292 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] checksums = ['7f97e4205c0bd9f9b8560536c8bd2e841d1c9a6d610401eb3eb87ed9cdfe78ea'] builddependencies = [ - ('binutils', '2.3'), + ('binutils', '2.38'), ('CMake', '3.23.1'), ('Doxygen', '1.9.4'), ] From 892e94bc13619683dc608b0075bbf6c205d8c8f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 18 Dec 2024 20:00:42 +0100 Subject: [PATCH 259/414] Update easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb --- easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb index 48f991538d9..b677adb6a37 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb @@ -55,7 +55,6 @@ postinstallcmds = ['rm %(installdir)s/bin/python*'] # use EB_GUROBI_LICENSE_FILE environment variable, or # uncomment and modify the following variable: # license_file = '/path/to/my-license-file' -license_file = HOME + '/licenses/%(name)s.lic' modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' From b51e7f1ae7aa196bb293060902fb0df66c33f1a9 Mon Sep 17 00:00:00 2001 From: Mody-SHARK Date: Wed, 18 Dec 2024 23:17:58 +0100 Subject: [PATCH 260/414] Added missing commas --- .../s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb index 0f82803b808..ec74287d759 100644 --- a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} builddependencies = [ ('binutils', '2.42'), - ('hatchling', '1.24.2), + ('hatchling', '1.24.2'), ('poetry', '1.8.3'), ] From ab507e4ac5d84178a58f025bbd5996f517ac8dfb Mon Sep 17 00:00:00 2001 From: Mody-SHARK Date: Wed, 18 Dec 2024 23:22:43 +0100 Subject: [PATCH 261/414] Added missing commas --- .../s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb index ec74287d759..97f475d94c4 100644 --- a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('Python', '3.12.3'), - ('Python-bundle-PyPI', '2024.06), + ('Python-bundle-PyPI', '2024.06'), ('pydantic', '2.9.1'), ] From b44b43be71460bb3156a667a5788859e483d3985 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 19 Dec 2024 10:08:46 +0100 Subject: [PATCH 262/414] adding easyconfigs: freeglut-3.6.0-GCCcore-13.3.0.eb --- .../freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..41676a0155c --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.6.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('X11', '20240607'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.so" -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" -DX11_Xext_LIB="$EBROOTX11/lib/libXext.so" -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.so" -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.so" -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.so', 'lib64/libglut.so')], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' From 759b9d69cffe5b7e6e243c4be64875c0b50ef468 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 19 Dec 2024 10:25:20 +0100 Subject: [PATCH 263/414] added checksum --- .../easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb index 41676a0155c..68489093554 100644 --- a/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['9c3d4d6516fbfa0280edc93c77698fb7303e443c1aaaf37d269e3288a6c3ea52'] builddependencies = [ ('binutils', '2.42'), From e88f0698c084700aa06a122d3e687d52e8a6fcae Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Thu, 19 Dec 2024 10:37:55 +0100 Subject: [PATCH 264/414] Update easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Jan André Reuter --- easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.3.0.eb index fc23873bc4a..4d3e6ac0849 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8.2-GCCcore-13.3.0.eb @@ -28,7 +28,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] sources = [SOURCELOWER_TAR_GZ] checksums = ['bf2e02002bb2e5c4f61832ce37b62a440675c6453463014b33b2474aac78f86d'] From 082e64f32e91d6a4cc2c65f6eea5e52f67a6fc48 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 19 Dec 2024 13:21:44 +0000 Subject: [PATCH 265/414] Fix checksums for Safetensors-0.4.4-gfbf-2023b.eb --- .../Safetensors-0.4.4-gfbf-2023b.eb | 114 ++++++++++++++++++ 1 file changed, 114 insertions(+) diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb index 50ead1b54c1..ddaa26cbca6 100644 --- a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb @@ -139,6 +139,120 @@ crates = [ ('zerocopy-derive', '0.7.35'), ] +checksums = [ + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'anes-0.1.6.tar.gz': '4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299'}, + {'anstyle-1.0.8.tar.gz': '1bec1de6f59aedf83baf9ff929c98f2ad654b97c9510f4e70cf6f661d49fd5b1'}, + {'autocfg-1.3.0.tar.gz': '0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0'}, + {'bit-set-0.5.3.tar.gz': '0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1'}, + {'bit-vec-0.6.3.tar.gz': '349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb'}, + {'bitflags-2.6.0.tar.gz': 'b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de'}, + {'bumpalo-3.16.0.tar.gz': '79296716171880943b8470b5f8d03aa55eb2e645a4874bdbb28adb49162e012c'}, + {'byteorder-1.5.0.tar.gz': '1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b'}, + {'cast-0.3.0.tar.gz': '37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'ciborium-0.2.2.tar.gz': '42e69ffd6f0917f5c029256a24d0161db17cea3997d185db0d35926308770f0e'}, + {'ciborium-io-0.2.2.tar.gz': '05afea1e0a06c9be33d539b876f1ce3692f4afea2cb41f740e7743225ed1c757'}, + {'ciborium-ll-0.2.2.tar.gz': '57663b653d948a338bfb3eeba9bb2fd5fcfaecb9e199e87e1eda4d9e8b240fd9'}, + {'clap-4.5.16.tar.gz': 'ed6719fffa43d0d87e5fd8caeab59be1554fb028cd30edc88fc4369b17971019'}, + {'clap_builder-4.5.15.tar.gz': 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{'rand_xorshift-0.3.0.tar.gz': 'd25bf25ec5ae4a3f1b92f929810509a2f53d7dca2f50b794ff57e3face536c8f'}, + {'rayon-1.10.0.tar.gz': 'b418a60154510ca1a002a752ca9714984e21e4241e804d32555251faf8b78ffa'}, + {'rayon-core-1.12.1.tar.gz': '1465873a3dfdaa8ae7cb14b4383657caab0b3e8a0aa9ae8e04b044854c8dfce2'}, + {'regex-1.10.6.tar.gz': '4219d74c6b67a3654a9fbebc4b419e22126d13d2f3c4a07ee0cb61ff79a79619'}, + {'regex-automata-0.4.7.tar.gz': '38caf58cc5ef2fed281f89292ef23f6365465ed9a41b7a7754eb4e26496c92df'}, + {'regex-syntax-0.8.4.tar.gz': '7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b'}, + {'rustix-0.38.34.tar.gz': '70dc5ec042f7a43c4a73241207cecc9873a06d45debb38b329f8541d85c2730f'}, + {'rusty-fork-0.3.0.tar.gz': 'cb3dcc6e454c328bb824492db107ab7c0ae8fcffe4ad210136ef014458c1bc4f'}, + {'ryu-1.0.18.tar.gz': 'f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f'}, + {'same-file-1.0.6.tar.gz': '93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502'}, + {'serde-1.0.204.tar.gz': 'bc76f558e0cbb2a839d37354c575f1dc3fdc6546b5be373ba43d95f231bf7c12'}, + {'serde-1.0.208.tar.gz': 'cff085d2cb684faa248efb494c39b68e522822ac0de72ccf08109abde717cfb2'}, + {'serde_derive-1.0.204.tar.gz': 'e0cd7e117be63d3c3678776753929474f3b04a43a080c744d6b0ae2a8c28e222'}, + {'serde_derive-1.0.208.tar.gz': '24008e81ff7613ed8e5ba0cfaf24e2c2f1e5b8a0495711e44fcd4882fca62bcf'}, + {'serde_json-1.0.122.tar.gz': '784b6203951c57ff748476b126ccb5e8e2959a5c19e5c617ab1956be3dbc68da'}, + {'serde_json-1.0.125.tar.gz': '83c8e735a073ccf5be70aa8066aa984eaf2fa000db6c8d0100ae605b366d31ed'}, + {'syn-2.0.72.tar.gz': 'dc4b9b9bf2add8093d3f2c0204471e951b2285580335de42f9d2534f3ae7a8af'}, + {'syn-2.0.75.tar.gz': 'f6af063034fc1935ede7be0122941bafa9bacb949334d090b77ca98b5817c7d9'}, + {'target-lexicon-0.12.16.tar.gz': '61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1'}, + {'tempfile-3.12.0.tar.gz': '04cbcdd0c794ebb0d4cf35e88edd2f7d2c4c3e9a5a6dab322839b321c6a87a64'}, + {'tinytemplate-1.2.1.tar.gz': 'be4d6b5f19ff7664e8c98d03e2139cb510db9b0a60b55f8e8709b689d939b6bc'}, + {'unarray-0.1.4.tar.gz': 'eaea85b334db583fe3274d12b4cd1880032beab409c0d774be044d4480ab9a94'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'wait-timeout-0.2.0.tar.gz': '9f200f5b12eb75f8c1ed65abd4b2db8a6e1b138a20de009dacee265a2498f3f6'}, + {'walkdir-2.5.0.tar.gz': '29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'wasm-bindgen-0.2.93.tar.gz': 'a82edfc16a6c469f5f44dc7b571814045d60404b55a0ee849f9bcfa2e63dd9b5'}, + {'wasm-bindgen-backend-0.2.93.tar.gz': '9de396da306523044d3302746f1208fa71d7532227f15e347e2d93e4145dd77b'}, + {'wasm-bindgen-macro-0.2.93.tar.gz': '585c4c91a46b072c92e908d99cb1dcdf95c5218eeb6f3bf1efa991ee7a68cccf'}, + {'wasm-bindgen-macro-support-0.2.93.tar.gz': 'afc340c74d9005395cf9dd098506f7f44e38f2b4a21c6aaacf9a105ea5e1e836'}, + {'wasm-bindgen-shared-0.2.93.tar.gz': 'c62a0a307cb4a311d3a07867860911ca130c3494e8c2719593806c08bc5d0484'}, + {'web-sys-0.3.70.tar.gz': '26fdeaafd9bd129f65e7c031593c24d62186301e0c72c8978fa1678be7d532c0'}, + {'winapi-util-0.1.9.tar.gz': 'cf221c93e13a30d793f7645a0e7762c55d169dbb0a49671918a2319d289b10bb'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-sys-0.59.0.tar.gz': '1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, +] use_pip = True From a35ec39bdd702b3b4c61f7c0650d32cd9cf1b807 Mon Sep 17 00:00:00 2001 From: pmod <2803936+prerakmody@users.noreply.github.com> Date: Thu, 19 Dec 2024 15:07:43 +0100 Subject: [PATCH 266/414] Update "description content" in easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb index 97f475d94c4..9474793b5b8 100644 --- a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.2-GCCcore-13.3.0.eb @@ -9,7 +9,8 @@ name = 'SlurmViewer' version = '1.0.2' homepage = 'https://gitlab.com/lkeb/slurm_viewer' -description = """One-stop command to view the status of a Slurm cluster, including nodes, jobs and resource utilization""" +description = """One-stop command to view the status of a Slurm cluster, +including nodes, jobs and resource utilization.""" toolchain = {'name': 'GCCcore', 'version': '13.3.0'} From 61ac5cc4a383cad1d4655ba26e840a2e409e6eb5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Dec 2024 15:09:23 +0100 Subject: [PATCH 267/414] adding easyconfigs: FastK-1.1.0-foss-2023a.eb --- .../f/FastK/FastK-1.1.0-foss-2023a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..2bced6f8312 --- /dev/null +++ b/easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'FastK' +version = '1.1.0' + +homepage = 'https://github.com/thegenemyers/FASTK' +description = """FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets + such as those produced with an Illumina instrument or a PacBio run in HiFi mode. For example it is about 2 times + faster than KMC3 when counting 40-mers in a 50X HiFi data set. Its relative speedup decreases with increasing error + rate or increasing values of k, but regardless is a general program that works for any DNA sequence data set + and choice of k. It is further designed to handle data sets of arbitrarily large size, e.g. a 100X data + set of a 32GB Axolotl genome (3.2Tbp) can be performed on a machine with just 12GB of memory provided it + has ~6.5TB of disk space available.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/thegenemyers/FASTK/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['28a2de98ede77d4b4476596851f92413a9d99a1d3341afc6682d5333ac797f07'] + +dependencies = [ + ('cURL', '8.0.1'), +] + +skipsteps = ['configure'] + +prebuildopts = 'cd %(builddir)s/FASTK-%(version)s/HTSLIB/ && make CC="$CC" CFLAGS="$CFLAGS" && cd - && ' +prebuildopts += 'cd %(builddir)s/FASTK-%(version)s/LIBDEFLATE/ && make CC="$CC" CFLAGS="$CFLAGS" && cd - && ' + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -fno-strict-aliasing" ' + +preinstallopts = "mkdir -p %(installdir)s/bin && " +installopts = "DEST_DIR=%(installdir)s/bin" + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["command -v %(name)s"] + +moduleclass = 'bio' From 96d90e92d50345e74c6c9f1a621d68960612caa7 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 19 Dec 2024 14:30:14 +0000 Subject: [PATCH 268/414] use Java/17 --- easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb b/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb index 1f9e2348866..b0294d69ae3 100644 --- a/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb +++ b/easybuild/easyconfigs/r/R/R-4.4.2-gfbf-2024a.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.43'), # for plotting in R ('libjpeg-turbo', '3.0.1'), # for plottting in R ('LibTIFF', '4.6.0'), - ('Java', '11', '', SYSTEM), + ('Java', '17', '', SYSTEM), ('libgit2', '1.8.1'), ('OpenSSL', '3', '', SYSTEM), ('cURL', '8.7.1'), From 70b92492a6d186510eae785ae4e0a34d16055966 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 19 Dec 2024 14:40:25 +0000 Subject: [PATCH 269/414] add ANTLR using Java/17 and switch NCO-5.2.9-foss-2024a.eb to use it --- .../ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb | 36 +++++++++++++++++++ .../easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb | 4 +-- 2 files changed, 38 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb new file mode 100644 index 00000000000..e614536bfb5 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Java', '17', '', SYSTEM)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +sanity_check_commands = ["antlr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb index cf83d365785..b0a8726462e 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb @@ -4,7 +4,7 @@ name = 'NCO' version = '5.2.9' homepage = "https://github.com/nco/nco" -description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.""" toolchain = {'name': 'foss', 'version': '2024a'} @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('UDUNITS', '2.2.28'), ('expat', '2.6.2'), - ('ANTLR', '2.7.7', '-Java-21.0.2'), + ('ANTLR', '2.7.7', '-Java-17'), ('libdap', '3.21.0-131'), ('GSL', '2.8'), ('netCDF', '4.9.2'), From 57708900f71e4de2b8e997efff1abbfef4891c8f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 19 Dec 2024 14:42:26 +0000 Subject: [PATCH 270/414] remove ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb --- .../ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb deleted file mode 100644 index 333a0374279..00000000000 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ANTLR' -version = '2.7.7' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://www.antlr2.org/' -description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) - is a language tool that provides a framework for constructing recognizers, - compilers, and translators from grammatical descriptions containing - Java, C#, C++, or Python actions.""" - -toolchain = {'name': 'GCCcore', 'version': '13.3.0'} - -source_urls = ['https://www.antlr2.org/download/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_includes.patch'] -checksums = [ - '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz - 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch -] - -builddependencies = [('binutils', '2.42')] - -dependencies = [('Java', '21.0.2', '', SYSTEM)] - -configopts = '--disable-examples --disable-csharp --disable-python' - -sanity_check_paths = { - 'files': ['bin/antlr', 'bin/antlr-config'], - 'dirs': ['include'], -} - -sanity_check_commands = ["antlr --help"] - -moduleclass = 'tools' From dc9ca979e8c07743f8b6e5e3b96324d5395e531f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 19 Dec 2024 14:51:21 +0000 Subject: [PATCH 271/414] sync in updates to R-bundle-CRAN-2024.06-foss-2023b.eb --- .../r/R-bundle-CRAN/R-bundle-CRAN-2024.11-foss-2024a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.11-foss-2024a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.11-foss-2024a.eb index 7c36a151d4a..7ca98e9d621 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.11-foss-2024a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.11-foss-2024a.eb @@ -3496,6 +3496,12 @@ exts_list = [ ('gsDesign', '3.6.5', { 'checksums': ['c5a8248708e4803b28cd33189963eb5dd1624df10ecf90f4c8ef7895cc022c0b'], }), + ('gcmr', '1.0.3', { + 'checksums': ['75773d5119179f186467d33608e9ce1c030d0755dfd6ff196546884078e89754'], + }), + ('frbs', '3.2-0', { + 'checksums': ['48505d415e3687afcb837e162b63b74173b3cd5df5f96140240e441c86343b2e'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 17d5f02ab9eef333258c106505fe288b7747f554 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Dec 2024 17:00:09 +0100 Subject: [PATCH 272/414] add missing dependency --- easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb index 2bced6f8312..507cab1640f 100644 --- a/easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb @@ -20,6 +20,7 @@ checksums = ['28a2de98ede77d4b4476596851f92413a9d99a1d3341afc6682d5333ac797f07'] dependencies = [ ('cURL', '8.0.1'), + ('bzip2', '1.0.8'), ] skipsteps = ['configure'] From 84d36652d40763746fb654a509204faad5305233 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 20 Dec 2024 08:45:09 +0000 Subject: [PATCH 273/414] restore MSstatsPTM and MSstatsLiP --- .../R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb index 19364b2127d..dee51ada1a5 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb @@ -1343,9 +1343,15 @@ exts_list = [ ('MSstatsTMT', '2.14.1', { 'checksums': ['b5da9ac80d06ea47751515ef605873b936bbc7c0d3ea5a9761baaacc75b8d8ea'], }), + ('MSstatsPTM', '2.8.1', { + 'checksums': ['874baf624574cfe05cf286f0a202de4a314742a3429d14d883e5dac4b91bcaba'], + }), ('factoextra', '1.0.7', { 'checksums': ['624ff01c74933352aca55966f8a052b1ccc878f52c2c307e47f88e0665db94aa'], }), + ('MSstatsLiP', '1.12.0', { + 'checksums': ['ea383205608fad8cab28adae560675e26f2031ff131fbbdd07acc127a4a5e2e8'], + }), ('babelgene', '22.9', { 'checksums': ['ce6601dcb78352516d3b0355042c52a20e154b39d3b27b93ff52150a59c885e2'], }), From bae6385eebde02a64c3d9526b899b386d81667d7 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 20 Dec 2024 09:14:56 +0000 Subject: [PATCH 274/414] checksums --- .../easyconfigs/a/arrow-R/arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb index 5001d9e13e2..a17fa67fc1b 100644 --- a/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb @@ -15,6 +15,7 @@ source_urls = [ 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ] sources = ['arrow_%(version)s.tar.gz'] +checksums = ['0214dbf5d958968172a6f67abbae916d33933625cf41dc22e89ab77a29cde75e'] builddependencies = [ ('pkgconf', '2.2.0'), From 30164a674bf46df9532e1b9b91edfb6a791568f5 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 20 Dec 2024 13:47:27 +0100 Subject: [PATCH 275/414] adding easyconfigs: hatch-1.9.7-GCCcore-12.3.0.eb --- .../h/hatch/hatch-1.9.7-GCCcore-12.3.0.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/h/hatch/hatch-1.9.7-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/h/hatch/hatch-1.9.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hatch/hatch-1.9.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9df7323c889 --- /dev/null +++ b/easybuild/easyconfigs/h/hatch/hatch-1.9.7-GCCcore-12.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'hatch' +version = '1.9.7' + +homepage = 'https://github.com/joshua-auchincloss/hatch-cython' +description = "cython hooks for hatch" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('hatchling', '1.18.0'), + ('zstd', '1.5.5'), +] + +use_pip = True + +exts_list = [ + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('httpcore', '1.0.5', { + 'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61'], + }), + ('anyio', '4.4.0', { + 'checksums': ['5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94'], + }), + ('httpx', '0.27.2', { + 'checksums': ['f7c2be1d2f3c3c3160d441802406b206c2b76f5947b11115e6df10c6c65e66c2'], + }), + ('hyperlink', '21.0.0', { + 'checksums': ['427af957daa58bc909471c6c40f74c5450fa123dd093fc53efd2e91d2705a56b'], + }), + ('userpath', '1.9.2', { + 'checksums': ['6c52288dab069257cc831846d15d48133522455d4677ee69a9781f11dbefd815'], + }), + ('zstandard', '0.23.0', { + 'checksums': ['b2d8c62d08e7255f68f7a740bae85b3c9b8e5466baa9cbf7f57f1cde0ac6bc09'], + }), + (name, version, { + 'checksums': ['19a7b82179f94f2adddbad76aa7e65ab90cad55ab103d53827637935c9e6624c'], + }), + ('hatch-cython', '0.5.1', { + 'source_tmpl': 'hatch_cython-%(version)s.tar.gz', + 'checksums': ['d01135e092544069c3e61f6dc36748ee369beacb893a5c43b9593a533f839703'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 84a3aece02c8cd5f4cd94541cd6838b404f1d6d3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 20 Dec 2024 14:05:58 +0100 Subject: [PATCH 276/414] fix homepage and descr --- easybuild/easyconfigs/h/hatch/hatch-1.9.7-GCCcore-12.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hatch/hatch-1.9.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hatch/hatch-1.9.7-GCCcore-12.3.0.eb index 9df7323c889..82c797c9631 100644 --- a/easybuild/easyconfigs/h/hatch/hatch-1.9.7-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/hatch/hatch-1.9.7-GCCcore-12.3.0.eb @@ -3,8 +3,8 @@ easyblock = 'PythonBundle' name = 'hatch' version = '1.9.7' -homepage = 'https://github.com/joshua-auchincloss/hatch-cython' -description = "cython hooks for hatch" +homepage = 'https://hatch.pypa.io' +description = "Hatch is a modern, extensible Python project manager." toolchain = {'name': 'GCCcore', 'version': '12.3.0'} From 68fdba82e430f6080e0f3f9ef3dbb98cb345c1e4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Juli=C3=A1n=20Morillo?= Date: Fri, 20 Dec 2024 15:42:16 +0100 Subject: [PATCH 277/414] Add easyconfig FreeImage-3.18.0-GCCcore-13.2.0.eb --- .../FreeImage-3.18.0-GCCcore-13.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0b82c899e93 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FreeImage' +version = '3.18.0' + +homepage = 'http://freeimage.sourceforge.net' +description = """FreeImage is an Open Source library project for developers who would like to support popular graphics +image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to +use, fast, multithreading safe.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'cstd': 'c++14'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s3180.zip'] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip + '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # %(name)s-%(version)s-fix-makefile.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +skipsteps = ['configure'] + +buildopts = ['', '-f Makefile.fip'] + +installopts = [ + "INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib", + "-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib", +] + +_incs = ['include/FreeImage%s.h' % x for x in ['', 'Plus']] +_libs = ['lib/libfreeimage%s.%s' % (x, y) for x in ['', 'plus'] for y in ['a', SHLIB_EXT]] + +sanity_check_paths = { + 'files': _incs + _libs, + 'dirs': [], +} + +moduleclass = 'vis' From a2f7558f93986bd3e18d1f9c1aacdeab63125cab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Dec 2024 16:19:45 +0000 Subject: [PATCH 278/414] adding easyconfigs: OSU-Micro-Benchmarks-7.5-gompi-2024a-CUDA-12.6.0.eb --- ...-Benchmarks-7.5-gompi-2024a-CUDA-12.6.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2024a-CUDA-12.6.0.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2024a-CUDA-12.6.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2024a-CUDA-12.6.0.eb new file mode 100644 index 00000000000..1d7dcac27de --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2024a-CUDA-12.6.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1cf84ac5419456202757a757c5f9a4f5c6ecd05c65783c7976421cfd6020b3b3'] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('NCCL', '2.22.3', versionsuffix), + ('UCX-CUDA', '1.16.0', versionsuffix), + ('UCC-CUDA', '1.3.0', versionsuffix), +] + +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA --enable-ncclomb --with-nccl=$EBROOTNCCL' + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] + [ + 'libexec/osu-micro-benchmarks/xccl/%s' % x for x in ['collective', 'pt2pt'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 0fb89ced2c5f47625deea4a6e2d9e0725c459d12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2024 22:59:05 +0100 Subject: [PATCH 279/414] add test to check easyconfig that would be picked by 'eb --install-latest-eb-release' --- test/easyconfigs/easyconfigs.py | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4b1c4dd770e..921871be93f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1011,6 +1011,30 @@ def test_easyconfig_locations(self): if not dirpath.endswith('/easybuild/easyconfigs'): self.fail("There should be no easyconfig files in %s, found %s" % (dirpath, easyconfig_files)) + def test_easybuild_easyconfigs_latest_release(self): + """ + Check which easyconfig file would be picked up by 'eb --install-latest-eb-release' + """ + # this mimics the logic used in the find_easybuild_easyconfig used by EasyBuild framework + # to obtain an easyconfig file when --install-latest-eb-release is used + topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) + easybuild_dir = os.path.join(topdir, 'easybuild', 'easyconfigs', 'e', 'EasyBuild') + ecs = os.listdir(easybuild_dir) + + file_versions = [] + for ec in ecs: + txt = read_file(os.path.join(easybuild_dir, ec)) + for line in txt.split('\n'): + if re.search(r'^version\s*=', line): + scope = {} + exec(line, scope) + version = scope['version'] + file_versions.append((LooseVersion(version), ec)) + + most_recent = sorted(file_versions)[-1] + self.assertEqual(most_recent[0], LooseVersion('4.9.4')) + self.assertEqual(most_recent[1], 'EasyBuild-4.9.4.eb') + def test_easyconfig_name_clashes(self): """Make sure there is not a name clash when all names are lowercase""" topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) From 49011fa63910e3061a472c965345d8c7320f00ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2024 23:33:11 +0100 Subject: [PATCH 280/414] use '0.5.0.0beta1' as version for EasyBuild v5.0.0beta1, to avoid 'eb --install-latest-eb-release' picking up on EasyBuild v5.0.0beta1 --- .../e/EasyBuild/EasyBuild-0.5.0.0beta1.eb | 59 +++++++++++++++++++ .../e/EasyBuild/EasyBuild-5.0.0beta1.eb | 35 ----------- 2 files changed, 59 insertions(+), 35 deletions(-) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-0.5.0.0beta1.eb delete mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.0.0beta1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-0.5.0.0beta1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-0.5.0.0beta1.eb new file mode 100644 index 00000000000..434df6f94dc --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-0.5.0.0beta1.eb @@ -0,0 +1,59 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '0.5.0.0beta1' + +homepage = 'https://easybuild.io' +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 = SYSTEM + +sources = [ + { + 'filename': 'easybuild-framework-v%s.tar.gz' % version[2:], + 'git_config': { + 'url': 'https://github.com/easybuilders', + 'repo_name': 'easybuild-framework', + 'tag': 'easybuild-framework-v%s' % version[2:], + 'keep_git_dir': True, + }, + }, + { + 'filename': 'easybuild-easyblocks-v%s.tar.gz' % version[2:], + 'git_config': { + 'url': 'https://github.com/easybuilders', + 'repo_name': 'easybuild-easyblocks', + 'tag': 'easybuild-easyblocks-v%s' % version[2:], + 'keep_git_dir': True, + }, + }, + { + 'filename': 'easybuild-easyconfigs-v%s.tar.gz' % version[2:], + 'git_config': { + 'url': 'https://github.com/easybuilders', + 'repo_name': 'easybuild-easyconfigs', + 'tag': 'easybuild-easyconfigs-v%s' % version[2:], + 'keep_git_dir': True, + }, + }, +] +checksums = [ + None, + None, + None, +] + +# 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/EasyBuild/EasyBuild-5.0.0beta1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.0.0beta1.eb deleted file mode 100644 index ed54b7bbacd..00000000000 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.0.0beta1.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'EB_EasyBuildMeta' - -name = 'EasyBuild' -version = '5.0.0beta1' - -homepage = 'https://easybuild.io' -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 = SYSTEM - -source_urls = [ - 'https://github.com/easybuilders/easybuild-framework/archive/', - 'https://github.com/easybuilders/easybuild-easyblocks/archive/', - 'https://github.com/easybuilders/easybuild-easyconfigs/archive/', -] -sources = [ - 'easybuild-framework-v%(version)s.tar.gz', - 'easybuild-easyblocks-v%(version)s.tar.gz', - 'easybuild-easyconfigs-v%(version)s.tar.gz', -] - -# 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' From 0972271846402260767b4bda00b7fd166393bfab Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 24 Dec 2024 12:22:24 +0000 Subject: [PATCH 281/414] scripts directory removed, RBT_ROOT path set --- .../easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb index ac6f496471c..e575ee048ee 100644 --- a/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/r/rDock/rDock-24.03.192-GCCcore-13.3.0.eb @@ -35,14 +35,16 @@ runtest = 'test' postinstallcmds = [ 'sed -i "s|/bin/csh -f|/usr/bin/env tcsh|" %(installdir)s/bin/make_grid.csh ; ', - 'cp -ra %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s ; ', - 'sed -i "s|/bin/csh -f|/usr/bin/env tcsh|" %(installdir)s/scripts/make_grid.csh ; ', 'cp -ra %(builddir)s/%(name)s-%(version)s/data %(installdir)s ; ', ] +modextrapaths = { + 'RBT_ROOT': '', +} + sanity_check_paths = { 'files': ['bin/rbhtfinder', 'bin/sdreport', 'bin/run_rbdock.pl', 'lib/libRbt.so'], - 'dirs': ['include', 'scripts', 'data'], + 'dirs': ['include', 'data'], } sanity_check_commands = [ From f1495774b7d21e336bcc5eede9cabdcb93d07ec3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 30 Dec 2024 17:11:25 +0000 Subject: [PATCH 282/414] adding easyconfigs: libxml2-2.13.5-GCCcore-14.2.0.eb, xorg-macros-1.20.2-GCCcore-14.2.0.eb, numactl-2.0.19-GCCcore-14.2.0.eb, libpciaccess-0.18.1-GCCcore-14.2.0.eb, hwloc-2.11.2-GCCcore-14.2.0.eb, libevent-2.1.12-GCCcore-14.2.0.eb --- .../h/hwloc/hwloc-2.11.2-GCCcore-14.2.0.eb | 44 +++++++++++++++++++ .../libevent-2.1.12-GCCcore-14.2.0.eb | 38 ++++++++++++++++ .../libpciaccess-0.18.1-GCCcore-14.2.0.eb | 26 +++++++++++ .../libxml2/libxml2-2.13.5-GCCcore-14.2.0.eb | 27 ++++++++++++ .../numactl/numactl-2.0.19-GCCcore-14.2.0.eb | 34 ++++++++++++++ .../xorg-macros-1.20.2-GCCcore-14.2.0.eb | 27 ++++++++++++ 6 files changed, 196 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.11.2-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.13.5-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.19-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.2-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.11.2-GCCcore-14.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.11.2-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..51a244a1d9d --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.11.2-GCCcore-14.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.11.2' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['866ac8ef07b350a6a2ba0c6826c37d78e8994dcbcd443bdd2b436350de19d540'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('numactl', '2.0.19'), + ('libxml2', '2.13.5'), + ('libpciaccess', '0.18.1'), +] + +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..624f42a212b --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-14.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.3.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..d2b310fdc16 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.18.1' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bf6985a77d2ecb00e2c79da3edfb26b909178ffca3f2e9d14ed0620259ab733b'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20240712'), + ('xorg-macros', '1.20.2'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.13.5-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.13.5-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..e91415cf605 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.13.5-GCCcore-14.2.0.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.13.5' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['74fc163217a3964257d3be39af943e08861263c4231f9ef5b496b6f6d4c7b2b6'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('XZ', '5.6.3'), + ('zlib', '1.3.1'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.19-GCCcore-14.2.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.19-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..eb30503f38d --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.19-GCCcore-14.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.19' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8b84ffdebfa0d730fb2fc71bb7ec96bb2d38bf76fb67246fde416a68e04125e4'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20240712'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.2-GCCcore-14.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.2-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..17638beb58f --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.2-GCCcore-14.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.20.2' + +homepage = 'https://gitlab.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['beac7e00e5996bd0c9d9bd8cf62704583b22dbe8613bd768626b95fcac955744'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20240712'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From 7686f7241087b3be704e3804f021f8517885f571 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 30 Dec 2024 17:18:15 +0000 Subject: [PATCH 283/414] Source is now XZ --- .../l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb index d2b310fdc16..95f0bc392fb 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb @@ -9,8 +9,8 @@ description = """Generic PCI access library.""" toolchain = {'name': 'GCCcore', 'version': '14.2.0'} source_urls = ['https://www.x.org/releases/individual/lib/'] -sources = [SOURCE_TAR_GZ] -checksums = ['bf6985a77d2ecb00e2c79da3edfb26b909178ffca3f2e9d14ed0620259ab733b'] +sources = [SOURCE_TAR_XZ] +checksums = ['4af43444b38adb5545d0ed1c2ce46d9608cc47b31c2387fc5181656765a6fa76'] builddependencies = [ ('binutils', '2.42'), From e8d6898312ece099ba7bae3ffe2c0d259840eb1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Jan 2025 11:35:03 +0100 Subject: [PATCH 284/414] update copyright lines for 2025 --- setup.py | 2 +- test/__init__.py | 2 +- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/styletests.py | 2 +- test/easyconfigs/suite.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/setup.py b/setup.py index 15cbcf7470d..0a09e705557 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ ## -# Copyright 2012-2024 Ghent University +# Copyright 2012-2025 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/__init__.py b/test/__init__.py index 8ab7c0ed706..c084153bcca 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -1,5 +1,5 @@ ## -# Copyright 2009-2024 Ghent University +# Copyright 2009-2025 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index ff7efe1ecda..1cdea56bf93 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1,5 +1,5 @@ ## -# Copyright 2013-2024 Ghent University +# Copyright 2013-2025 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index 8c695514aba..2a868c79518 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -1,5 +1,5 @@ ## -# Copyright 2016-2024 Ghent University +# Copyright 2016-2025 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 4218fcaa7b2..82bae80f1ac 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -1,6 +1,6 @@ #!/usr/bin/python ## -# Copyright 2012-2024 Ghent University +# Copyright 2012-2025 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), From 8dec7d8e00b3488aacd08719496e79f29ea7f7fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Jan 2025 10:48:07 +0000 Subject: [PATCH 285/414] adding easyconfigs: SQLite-3.47.2-GCCcore-14.2.0.eb, libffi-3.4.5-GCCcore-14.2.0.eb, bzip2-1.0.8-GCCcore-14.2.0.eb, Tcl-8.6.16-GCCcore-14.2.0.eb, UnZip-6.0-GCCcore-14.2.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-14.2.0.eb | 27 +++++++++ .../l/libffi/libffi-3.4.5-GCCcore-14.2.0.eb | 29 +++++++++ .../s/SQLite/SQLite-3.47.2-GCCcore-14.2.0.eb | 39 ++++++++++++ .../t/Tcl/Tcl-8.6.16-GCCcore-14.2.0.eb | 41 +++++++++++++ .../u/UnZip/UnZip-6.0-GCCcore-14.2.0.eb | 59 +++++++++++++++++++ 5 files changed, 195 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.5-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.47.2-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.16-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-14.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..9634dec3932 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-14.2.0.eb @@ -0,0 +1,27 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.42'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.5-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.5-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..8f542a95ff0 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.5-GCCcore-14.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.5' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96fff4e589e3b239d888d9aa44b3ff30693c2ba1617f953925a70ddebcc102b2'] + +builddependencies = [ + ('binutils', '2.42'), +] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.47.2-GCCcore-14.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.47.2-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..672ce23bc0d --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.47.2-GCCcore-14.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.47.2' +local_filename_version = '3470200' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2024/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['f1b2ee412c28d7472bc95ba996368d6f0cdcf00362affdadb27ed286c179540b'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('libreadline', '8.2'), + ('Tcl', '8.6.16'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.16-GCCcore-14.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.16-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..c73860a71ef --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.16-GCCcore-14.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.16' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['91cb8fa61771c63c262efb553059b7c7ad6757afa5857af6265e4b0bdc2a14a5'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('zlib', '1.3.1'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..89a5fdc16d1 --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-14.2.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT' + '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD', + '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT'] + +buildopts = ' '.join([ + "-f unix/Makefile", + 'CC="$CC"', + 'D_USE_BZ2=-DUSE_BZIP2', + 'L_BZ2=-lbz2', + 'LF2="$LDFLAGS"', + 'CF="%s"' % ' '.join(local_cf), + 'unzips', +]) + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From 3fc2dae1ca3ce5376e56f795a386d8400f326e6b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Jan 2025 11:13:00 +0000 Subject: [PATCH 286/414] adding easyconfigs: Python-3.13.1-GCCcore-14.2.0.eb --- .../p/Python/Python-3.13.1-GCCcore-14.2.0.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..35d9df3be0f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb @@ -0,0 +1,71 @@ +name = 'Python' +version = '3.13.1' + +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': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +patches = ['Python-3.12.3_avoid-tkinter-build.patch'] +checksums = [ + {'Python-3.13.1.tgz': '1513925a9f255ef0793dbf2f78bb4533c9f184bdd0ad19763fd7f47a400a7c55'}, + {'Python-3.12.3_avoid-tkinter-build.patch': '34fa44ca67fc08d41c58db2e289317f12f32777a352a982dca2e63459fc089e3'}, +] + +builddependencies = [ + ('UnZip', '6.0'), + ('pkgconf', '2.3.0'), +] + +dependencies = [ + ('binutils', '2.42'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.3.1'), + ('libreadline', '8.2'), + ('ncurses', '6.5'), + ('SQLite', '3.47.2'), + ('XZ', '5.6.3'), + ('libffi', '3.4.5'), + ('OpenSSL', '3', '', SYSTEM), +] + +install_pip = True + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} + +# order is important! +# package versions updated 2025-01-02 +exts_list = [ + ('flit_core', '3.10.1', { + 'checksums': ['66e5b87874a0d6e39691f0e22f09306736b633548670ad3c09ec9db03c5662f7'], + }), + ('wheel', '0.45.1', { + 'checksums': ['661e1abd9198507b1409a20c02106d9670b2576e916d58f520316666abca6729'], + }), + ('tomli', '2.2.1', { + 'checksums': ['cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff'], + }), + ('packaging', '24.2', { + 'checksums': ['c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f'], + }), + ('typing_extensions', '4.12.2', { + 'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'], + }), + ('setuptools', '75.6.0', { + 'checksums': ['8199222558df7c86216af4f84c30e9b34a61d8ba19366cc914424cdbd28252f6'], + }), + ('setuptools_scm', '8.1.0', { + 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], + }), + ('pip', '24.3.1', { + 'checksums': ['ebcb60557f2aefabc2e0f918751cd24ea0d56d8ec5445fe1807f1d2109660b99'], + }), +] + +moduleclass = 'lang' From c95c94b8ee386b93fe5a665953414ef978a25d56 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Jan 2025 13:43:28 +0100 Subject: [PATCH 287/414] Update easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb index 35d9df3be0f..1161c01a346 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb @@ -37,6 +37,7 @@ install_pip = True exts_default_options = { 'source_urls': [PYPI_SOURCE], + 'use_pip': True, } # order is important! From 3b32e1a0037c75df4a543be913a602116911848a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Jan 2025 13:34:59 +0000 Subject: [PATCH 288/414] Include disabled GIL variant --- easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb index 1161c01a346..a809bc5b847 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb @@ -40,6 +40,8 @@ exts_default_options = { 'use_pip': True, } +configopts = '--disable-gil' # builds separate experimental python3.13t binary without GIL + # order is important! # package versions updated 2025-01-02 exts_list = [ From 7c579d629836b18b5cbebc245cc52a29c437a8ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Jan 2025 13:38:35 +0000 Subject: [PATCH 289/414] adding easyconfigs: Meson-1.6.1-GCCcore-14.2.0.eb, Ninja-1.12.1-GCCcore-14.2.0.eb --- .../m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb | 32 +++++++++++++++++++ .../n/Ninja/Ninja-1.12.1-GCCcore-14.2.0.eb | 31 ++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.12.1-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..e0bd051624e --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '1.6.1' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8fd6630c25c27f1489a8a0392b311a60481a3c161aa699b330e25935b750138d'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.13.1'), # includes required 'wheel' package + ('Ninja', '1.12.1'), +] + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["meson --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.12.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.12.1-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..d40f9dee68b --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.12.1-GCCcore-14.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.12.1' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['821bdff48a3f683bc4bb3b6f0b5fe7b2d647cf65d52aeb63328c91a6c6df285a'] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.13.1'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +sanity_check_commands = ["ninja --version"] + +moduleclass = 'tools' From 6597493dd2e8a5ac35e72e73ee99cfce8782198c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 2 Jan 2025 14:42:56 +0100 Subject: [PATCH 290/414] adding easyconfigs: dotNET-SDK-8.0.302-linux-x64.eb, MaxQuant-2.6.7.0.eb --- .../dotNET-SDK-8.0.302-linux-x64.eb | 36 ++++++++++++++++++ .../m/MaxQuant/MaxQuant-2.6.7.0.eb | 38 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-8.0.302-linux-x64.eb create mode 100644 easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb diff --git a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-8.0.302-linux-x64.eb b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-8.0.302-linux-x64.eb new file mode 100644 index 00000000000..40f20366f73 --- /dev/null +++ b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-8.0.302-linux-x64.eb @@ -0,0 +1,36 @@ +## +# Authors:: Robert Qiao +# Robert Mijakovic +# +# License:: MIT +# Notes:: requires glibc v2.14 or higher +## +easyblock = 'Tarball' + +name = 'dotNET-SDK' +version = '8.0.302' +versionsuffix = '-linux-x64' + +homepage = 'https://www.microsoft.com/net/' +description = """.NET is a free, cross-platform, open source developer platform for building many different types + of applications.""" + +toolchain = SYSTEM +source_urls = ['https://download.visualstudio.microsoft.com/download/pr/' + + 'dd6ee0c0-6287-4fca-85d0-1023fc52444b/874148c23613c594fc8f711fc0330298'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['8c84340e7bbbe478463debb9230e18d5b1a94583c2ebc04eb28a39a232b37f55'] + +sanity_check_paths = { + 'files': ['dotnet'], + 'dirs': ['shared/Microsoft.NETCore.App', 'shared/Microsoft.AspNetCore.App'], +} + +sanity_check_commands = ["dotnet --help"] + +modextrapaths = { + 'PATH': [''], + 'DOTNET_ROOT': [''], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb new file mode 100644 index 00000000000..e61dcf3aa8b --- /dev/null +++ b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'MaxQuant' +version = '2.6.7.0' + +homepage = 'https://maxquant.org/maxquant' +description = """MaxQuant is a quantitative proteomics software package designed for analyzing large + mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling + techniques as well as label-free quantification are supported.""" + +toolchain = SYSTEM + +# requires registration at https://www.maxquant.org/download_asset/maxquant/latest +sources = ['%(name)s_v%(version)s.zip'] +checksums = ['f210706f31704151a6e532da107278621badb92ebbcfcf9f19c2a7d111b2e275'] + +dependencies = [('dotNET-SDK', '8.0.302', '-linux-x64')] + +sanity_check_paths = { + 'files': ['bin/%(name)sCmd.exe', 'bin/%(name)sGui.exe'], + 'dirs': [], +} + +sanity_check_commands = [ + ("dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.dll --version 2>&1 | grep -q 2.6.7.0", ''), + ("dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.dll --help 2>&1 | grep -q USAGE", '')] + +modaliases = { + 'maxquantcmd': 'dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.dll', + 'maxquantgui': 'dotnet $EBROOTMAXQUANT/bin/%(name)sGui.dll', +} + +modloadmsg = """ +To run MaxQuant in command-line mode: maxquantcmd + in GUI mode: maxquantgui +""" + +moduleclass = 'bio' From 2566f8c8347ae25b181fa4a4ac2cb8a2c44e6e0f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Jan 2025 14:21:32 +0000 Subject: [PATCH 291/414] Revert nogil --- easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb index a809bc5b847..1161c01a346 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb @@ -40,8 +40,6 @@ exts_default_options = { 'use_pip': True, } -configopts = '--disable-gil' # builds separate experimental python3.13t binary without GIL - # order is important! # package versions updated 2025-01-02 exts_list = [ From 69b6710574ef8a9516c9160efb6fdaf0dfa02e66 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 2 Jan 2025 15:07:46 +0000 Subject: [PATCH 292/414] EB4 options --- easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb index e0bd051624e..6d3db9286ff 100644 --- a/easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb @@ -20,6 +20,10 @@ dependencies = [ ('Ninja', '1.12.1'), ] +download_dep_fail = True +use_pip = True +sanity_pip_check = True + options = {'modulename': 'mesonbuild'} sanity_check_paths = { From fe14b193f0ca5ed138d3a55580acaf4c943705f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 2 Jan 2025 16:08:29 +0100 Subject: [PATCH 293/414] switch to dotNET-Core --- .../d/dotNET-Core/dotNET-Core-8.0.302.eb | 56 +++++++++++++++++++ .../dotNET-SDK-8.0.302-linux-x64.eb | 36 ------------ .../m/MaxQuant/MaxQuant-2.6.7.0.eb | 2 +- 3 files changed, 57 insertions(+), 37 deletions(-) create mode 100644 easybuild/easyconfigs/d/dotNET-Core/dotNET-Core-8.0.302.eb delete mode 100644 easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-8.0.302-linux-x64.eb diff --git a/easybuild/easyconfigs/d/dotNET-Core/dotNET-Core-8.0.302.eb b/easybuild/easyconfigs/d/dotNET-Core/dotNET-Core-8.0.302.eb new file mode 100644 index 00000000000..1b6fc7b0b30 --- /dev/null +++ b/easybuild/easyconfigs/d/dotNET-Core/dotNET-Core-8.0.302.eb @@ -0,0 +1,56 @@ +easyblock = "Tarball" + +name = "dotNET-Core" +version = "8.0.302" # uses the SDK version string, runtime is 8.0.6 + +homepage = "https://www.microsoft.com/net/" +description = """.NET is a free, cross-platform, open source developer platform for building many different types of +applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, +gaming, and IoT. + +Contains the SDK and the Runtime. +""" + +toolchain = SYSTEM + +local_variant = {'aarch64': 'linux-x64', 'x86_64': 'linux-x64', 'arm64': 'osx-x86'}.get(ARCH) +source_urls = [ + 'https://download.visualstudio.microsoft.com/download/pr/' + 'dd6ee0c0-6287-4fca-85d0-1023fc52444b/874148c23613c594fc8f711fc0330298', # x86_64 + 'https://download.visualstudio.microsoft.com/download/pr/' + '9d5ec61f-58b3-412f-a4b7-be8c295b4877/fcd77a3d07f2c2054b86154634402527', # arm64 + 'https://download.visualstudio.microsoft.com/download/pr/' + 'ccc923ed-10de-4131-9c65-2a73f51185cb/3c04869af60dc562d81a673b2fb95515', # osx arm64 +] +sources = ["dotnet-sdk-%%(version)s-%s.tar.gz" % local_variant] +checksums = [{ + 'dotnet-sdk-8.0.302-linux-x64.tar.gz': '8c84340e7bbbe478463debb9230e18d5b1a94583c2ebc04eb28a39a232b37f55', + 'dotnet-sdk-8.0.302-linux-arm64.tar.gz': '8cc5b1216e0ef019199bbe5907cbe24d6110a6fd4c836c6892349a4532184337', + 'dotnet-sdk-8.0.302-osx-arm64.tar.gz': '0a786792c6ff41a7cf3c5d43bc2bbffe4a96a9c9df709cb816111ff670d33eb9', +}] + +sanity_check_paths = { + "files": ["dotnet", "LICENSE.txt"], + "dirs": [ + "shared/Microsoft.NETCore.App/", + "shared/Microsoft.AspNetCore.App/", + "sdk", + ], +} + +sanity_check_commands = ['dotnet --help'] + +modextrapaths = {"PATH": ""} + +# We are not sending usage stats to Microsoft...hopefully. +# The .NET Core tools collect usage data in order to help us improve your experience. The data is anonymous. +# It is collected by Microsoft and shared with the community. +# You can opt-out of telemetry by setting the DOTNET_CLI_TELEMETRY_OPTOUT environment variable to '1' or 'true' using +# your favorite shell. +# Read more about .NET Core CLI Tools telemetry: https://aka.ms/dotnet-cli-telemetry +modextravars = { + "DOTNET_ROOT": "%(installdir)s", + "DOTNET_CLI_TELEMETRY_OPTOUT": "1", +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-8.0.302-linux-x64.eb b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-8.0.302-linux-x64.eb deleted file mode 100644 index 40f20366f73..00000000000 --- a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-8.0.302-linux-x64.eb +++ /dev/null @@ -1,36 +0,0 @@ -## -# Authors:: Robert Qiao -# Robert Mijakovic -# -# License:: MIT -# Notes:: requires glibc v2.14 or higher -## -easyblock = 'Tarball' - -name = 'dotNET-SDK' -version = '8.0.302' -versionsuffix = '-linux-x64' - -homepage = 'https://www.microsoft.com/net/' -description = """.NET is a free, cross-platform, open source developer platform for building many different types - of applications.""" - -toolchain = SYSTEM -source_urls = ['https://download.visualstudio.microsoft.com/download/pr/' + - 'dd6ee0c0-6287-4fca-85d0-1023fc52444b/874148c23613c594fc8f711fc0330298'] -sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['8c84340e7bbbe478463debb9230e18d5b1a94583c2ebc04eb28a39a232b37f55'] - -sanity_check_paths = { - 'files': ['dotnet'], - 'dirs': ['shared/Microsoft.NETCore.App', 'shared/Microsoft.AspNetCore.App'], -} - -sanity_check_commands = ["dotnet --help"] - -modextrapaths = { - 'PATH': [''], - 'DOTNET_ROOT': [''], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb index e61dcf3aa8b..7bb7c12e5f7 100644 --- a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb +++ b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb @@ -14,7 +14,7 @@ toolchain = SYSTEM sources = ['%(name)s_v%(version)s.zip'] checksums = ['f210706f31704151a6e532da107278621badb92ebbcfcf9f19c2a7d111b2e275'] -dependencies = [('dotNET-SDK', '8.0.302', '-linux-x64')] +dependencies = [('dotNET-Core', '8.0.302')] sanity_check_paths = { 'files': ['bin/%(name)sCmd.exe', 'bin/%(name)sGui.exe'], From 56c02cae09b776349698c2d9cd24b1fc0f9244cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 2 Jan 2025 16:10:12 +0100 Subject: [PATCH 294/414] use version variable in sanity check --- easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb index 7bb7c12e5f7..990ca4b8af9 100644 --- a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb +++ b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb @@ -22,7 +22,7 @@ sanity_check_paths = { } sanity_check_commands = [ - ("dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.dll --version 2>&1 | grep -q 2.6.7.0", ''), + ("dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.dll --version 2>&1 | grep -q %(version)s", ''), ("dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.dll --help 2>&1 | grep -q USAGE", '')] modaliases = { From 121bfb07e6ae3413af1c60b87d37a9178aae7b36 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 2 Jan 2025 15:12:08 +0000 Subject: [PATCH 295/414] checksum --- easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb index 6d3db9286ff..687848535ee 100644 --- a/easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/m/Meson/Meson-1.6.1-GCCcore-14.2.0.eb @@ -9,7 +9,7 @@ description = "Meson is a cross-platform build system designed to be both as fas toolchain = {'name': 'GCCcore', 'version': '14.2.0'} sources = [SOURCELOWER_TAR_GZ] -checksums = ['8fd6630c25c27f1489a8a0392b311a60481a3c161aa699b330e25935b750138d'] +checksums = ['1eca49eb6c26d58bbee67fd3337d8ef557c0804e30a6d16bfdf269db997464de'] builddependencies = [ ('binutils', '2.42'), From 38a4959100856c66f318ca13a06f5a39fe5a5d33 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Jan 2025 15:48:52 +0000 Subject: [PATCH 296/414] Use mesonninja in libpciaccess --- .../l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb index 95f0bc392fb..972a2b83379 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MesonNinja' name = 'libpciaccess' version = '0.18.1' @@ -14,12 +14,13 @@ checksums = ['4af43444b38adb5545d0ed1c2ce46d9608cc47b31c2387fc5181656765a6fa76'] builddependencies = [ ('binutils', '2.42'), - ('Autotools', '20240712'), ('xorg-macros', '1.20.2'), + ('Meson', '1.6.1'), + ('Ninja', '1.12.1'), ] sanity_check_paths = { - 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'files': ['include/pciaccess.h', 'lib/libpciaccess.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } From 0e76dcef5e70152b06e6f8d413a07ed37719a293 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Jan 2025 17:03:54 +0000 Subject: [PATCH 297/414] Use already merged libxml2 --- .../h/hwloc/hwloc-2.11.2-GCCcore-14.2.0.eb | 2 +- .../libxml2/libxml2-2.13.5-GCCcore-14.2.0.eb | 27 ------------------- 2 files changed, 1 insertion(+), 28 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.13.5-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.11.2-GCCcore-14.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.11.2-GCCcore-14.2.0.eb index 51a244a1d9d..8fc25208616 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.11.2-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.11.2-GCCcore-14.2.0.eb @@ -28,7 +28,7 @@ builddependencies = [ dependencies = [ ('numactl', '2.0.19'), - ('libxml2', '2.13.5'), + ('libxml2', '2.13.4'), ('libpciaccess', '0.18.1'), ] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.13.5-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.13.5-GCCcore-14.2.0.eb deleted file mode 100644 index e91415cf605..00000000000 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.13.5-GCCcore-14.2.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'libxml2' -version = '2.13.5' - -homepage = 'http://xmlsoft.org/' - -description = """ - Libxml2 is the XML C parser and toolchain developed for the Gnome project - (but usable outside of the Gnome platform). -""" - -toolchain = {'name': 'GCCcore', 'version': '14.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] -sources = [SOURCE_TAR_XZ] -checksums = ['74fc163217a3964257d3be39af943e08861263c4231f9ef5b496b6f6d4c7b2b6'] - -builddependencies = [ - ('binutils', '2.42'), -] - -dependencies = [ - ('XZ', '5.6.3'), - ('zlib', '1.3.1'), -] - -moduleclass = 'lib' From 811c08863307133fe74ce214b22075665dc36672 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Jan 2025 17:45:54 +0000 Subject: [PATCH 298/414] adding easyconfigs: GMP-6.3.0-GCCcore-14.2.0.eb, cURL-8.11.1-GCCcore-14.2.0.eb, libarchive-3.7.7-GCCcore-14.2.0.eb, CMake-3.31.3-GCCcore-14.2.0.eb, Z3-4.13.4-GCCcore-14.2.0.eb --- .../c/CMake/CMake-3.31.3-GCCcore-14.2.0.eb | 30 ++++++++++++ .../c/cURL/cURL-8.11.1-GCCcore-14.2.0.eb | 43 +++++++++++++++++ .../g/GMP/GMP-6.3.0-GCCcore-14.2.0.eb | 40 ++++++++++++++++ .../libarchive-3.7.7-GCCcore-14.2.0.eb | 33 +++++++++++++ .../z/Z3/Z3-4.13.4-GCCcore-14.2.0.eb | 46 +++++++++++++++++++ 5 files changed, 192 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.31.3-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-8.11.1-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.7.7-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.13.4-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.31.3-GCCcore-14.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.31.3-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..85d409561a1 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.31.3-GCCcore-14.2.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.31.3' + +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 = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fac45bc6d410b49b3113ab866074888d6c9e9dc81a141874446eb239ac38cb87'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('cURL', '8.11.1'), + ('libarchive', '3.7.7'), + ('OpenSSL', '3', '', SYSTEM), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-8.11.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-8.11.1-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..f723318f3a1 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-8.11.1-GCCcore-14.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '8.11.1' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a889ac9dbba3644271bd9d1302b5c22a088893719b72be3487bc3d401e5c4e80'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..99aa882e75c --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-14.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.3.0' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'] + +builddependencies = [ + ('Autotools', '20240712'), + ('binutils', '2.42'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +# copy libgmp.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, e) for x in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.7.7-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.7.7-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..c7a0cf103f0 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.7.7-GCCcore-14.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.7.7' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4cc540a3e9a1eebdefa1045d2e4184831100667e6d7d5b315bb1cbc951f8ddff'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('XZ', '5.6.3'), + ('OpenSSL', '3', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.13.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.13.4-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..a42ca9017d9 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.13.4-GCCcore-14.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.13.4' + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3-solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +builddependencies = [ + ('CMake', '3.31.3'), + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.13.1'), + ('GMP', '6.3.0'), +] + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py && """ +_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py && """ + +exts_list = [ + ('z3_solver', version + '.0', { + 'modulename': 'z3', + 'checksums': ['66944689398d19f831f94524e95e99961d998afa27cfef1918a5a441029ea73f'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +local_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + 'ln -s %s/include "%%(installdir)s/include"' % local_z3_site_path, + 'cd "%%(installdir)s"; for lib in %s/lib/*; do ln -s ../$lib lib/$(basename $lib); done' % local_z3_site_path +] + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.' + SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 01ec5b75df0d2e1f0666a259e0f1a1313cf64424 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Jan 2025 18:13:08 +0000 Subject: [PATCH 299/414] Add bunch of cURL deps --- .../c/cURL/cURL-8.11.1-GCCcore-14.2.0.eb | 2 ++ .../libiconv/libiconv-1.18-GCCcore-14.2.0.eb | 23 ++++++++++++ .../l/libidn2/libidn2-2.3.7-GCCcore-14.2.0.eb | 27 ++++++++++++++ .../l/libpsl/libpsl-0.21.5-GCCcore-14.2.0.eb | 32 +++++++++++++++++ .../libunistring-1.3-GCCcore-14.2.0.eb | 35 +++++++++++++++++++ 5 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.18-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/l/libidn2/libidn2-2.3.7-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpsl/libpsl-0.21.5-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.3-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-8.11.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-8.11.1-GCCcore-14.2.0.eb index f723318f3a1..3255b4e3113 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-8.11.1-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-8.11.1-GCCcore-14.2.0.eb @@ -23,10 +23,12 @@ checksums = ['a889ac9dbba3644271bd9d1302b5c22a088893719b72be3487bc3d401e5c4e80'] builddependencies = [ ('binutils', '2.42'), + ('pkgconf', '2.3.0'), ] dependencies = [ ('zlib', '1.3.1'), + ('libpsl', '0.21.5'), ('OpenSSL', '3', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.18-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.18-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..2cb9ee7b456 --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.18-GCCcore-14.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.18' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3b08f5f4f9b4eb82f151a7040bfd6fe6c6fb922efe4b1659c66ea933276965e8'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.7-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.7-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..ff72132f5ee --- /dev/null +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.7-GCCcore-14.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libidn2' +version = '2.3.7' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = "Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46." + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libidn/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4c21a791b610b9519b9d0e12b8097bf2f359b12f8dd92647611a929e6bfd7d64'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +sanity_check_paths = { + 'files': ['bin/idn2', 'lib/%s.%s' % (name, SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['idn2 --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.5-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.5-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..0e079f84f8e --- /dev/null +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.5-GCCcore-14.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libpsl' +version = '0.21.5' + +homepage = 'https://rockdaboot.github.io/libpsl' +description = "C library for the Public Suffix List" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://github.com/rockdaboot/libpsl/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1dcc9ceae8b128f3c0b3f654decd0e1e891afc6ff81098f227ef260449dae208'] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.13.1'), +] + +dependencies = [ + ('libidn2', '2.3.7'), + ('libunistring', '1.3'), +] + +sanity_check_commands = [('psl --version')] + +sanity_check_paths = { + 'files': ['bin/psl', 'lib/libpsl.a'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.3-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.3-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..2f81c97f028 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.3-GCCcore-14.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.3' + +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': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['f245786c831d25150f3dfb4317cda1acc5e3f79a5da4ad073ddca58886569527'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('libiconv', '1.18'), +] + +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' From d5e5149011213634d6b9bc0fa1bff49c6bf5412c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 3 Jan 2025 07:37:44 +0100 Subject: [PATCH 300/414] update dotNET-Core wrapper and use it --- easybuild/easyconfigs/d/dotNET-Core/dotNET-Core-8.0.eb | 2 +- easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/dotNET-Core/dotNET-Core-8.0.eb b/easybuild/easyconfigs/d/dotNET-Core/dotNET-Core-8.0.eb index e96d2cda876..e41e056f33d 100644 --- a/easybuild/easyconfigs/d/dotNET-Core/dotNET-Core-8.0.eb +++ b/easybuild/easyconfigs/d/dotNET-Core/dotNET-Core-8.0.eb @@ -13,6 +13,6 @@ Contains the SDK and the Runtime. toolchain = SYSTEM -dependencies = [('dotNET-Core', '%(version)s.203')] +dependencies = [('dotNET-Core', '%(version)s.302')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb index 990ca4b8af9..6bfd20c804e 100644 --- a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb +++ b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.6.7.0.eb @@ -14,7 +14,7 @@ toolchain = SYSTEM sources = ['%(name)s_v%(version)s.zip'] checksums = ['f210706f31704151a6e532da107278621badb92ebbcfcf9f19c2a7d111b2e275'] -dependencies = [('dotNET-Core', '8.0.302')] +dependencies = [('dotNET-Core', '8.0')] sanity_check_paths = { 'files': ['bin/%(name)sCmd.exe', 'bin/%(name)sGui.exe'], From d585d081f597b6e4201f4b214749067e575cbed8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 3 Jan 2025 09:07:45 +0000 Subject: [PATCH 301/414] sync with new PRs --- .../R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb index dee51ada1a5..f60f2fc4fa8 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.20-foss-2024a-R-4.4.2.eb @@ -1364,6 +1364,18 @@ exts_list = [ ('plyranges', '1.26.0', { 'checksums': ['7df12c4aee8b045ff5ff905b15d813a7edb8c34500806a391044ed48f0b9262a'], }), + ('seqPattern', '1.38.0', { + 'checksums': ['f5ab6b839ce9ae65b0239890e742fafe7e81712f8588453918f14c4f1da6ba05'], + }), + ('genomation', '1.38.0', { + 'checksums': ['88f844c364ce6aa560dd4cb3fdd3feb768792869f20d50786fd08c54109f7c9f'], + }), + ('ChIPseeker', '1.42.0', { + 'checksums': ['b0aba9eb505ce8034f2b69e5c274247bb49fa86f9ff4b6296317b0a4de552550'], + }), + ('SimBu', '1.8.0', { + 'checksums': ['38257ab4b3dcd30d9a4f50704ef0619175706a5c05e1c5772e018ace40621ecc'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 6183734fc4beacdf0d36e57b09c5e223feadda70 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 3 Jan 2025 11:30:46 +0100 Subject: [PATCH 302/414] adding easyconfigs: gpustat-1.1.1-GCCcore-12.3.0.eb --- .../g/gpustat/gpustat-1.1.1-GCCcore-12.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/gpustat/gpustat-1.1.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-1.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gpustat/gpustat-1.1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f2a799a260d --- /dev/null +++ b/easybuild/easyconfigs/g/gpustat/gpustat-1.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'gpustat' +version = '1.1.1' + +homepage = 'https://github.com/wookayin/gpustat' +description = "A simple command-line utility for querying and monitoring GPU status" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +# This software works directly against the nvidia drivers and doesn't require CUDA. +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True + +exts_list = [ + ('blessed', '1.20.0', { + 'checksums': ['2cdd67f8746e048f00df47a2880f4d6acbcdb399031b604e34ba8f71d5787680'], + }), + ('nvidia-ml-py', '12.560.30', { + 'modulename': 'pynvml', + 'checksums': ['f0254dc7400647680a072ee02509bfd46102b60bdfeca321576d4d4817e7fe97'], + }), + (name, version, { + 'checksums': ['c18d3ed5518fc16300c42d694debc70aebb3be55cae91f1db64d63b5fa8af9d8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gpustat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gpustat --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From 68eace5ca3b69b78c3fa686bba490fc19485777a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Jan 2025 12:23:41 +0000 Subject: [PATCH 303/414] Use 4.9 options for pythonpackage --- easybuild/easyconfigs/z/Z3/Z3-4.13.4-GCCcore-14.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.13.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.13.4-GCCcore-14.2.0.eb index a42ca9017d9..60a4b16d6f3 100644 --- a/easybuild/easyconfigs/z/Z3/Z3-4.13.4-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/z/Z3/Z3-4.13.4-GCCcore-14.2.0.eb @@ -20,6 +20,9 @@ dependencies = [ ('GMP', '6.3.0'), ] +use_pip = True + + _fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py && """ _enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py && """ @@ -38,6 +41,8 @@ postinstallcmds = [ 'cd "%%(installdir)s"; for lib in %s/lib/*; do ln -s ../$lib lib/$(basename $lib); done' % local_z3_site_path ] +sanity_pip_check = True + sanity_check_paths = { 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.' + SHLIB_EXT], 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], From 7fa53d01175104afa365ffc0161879304f9f79fe Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 3 Jan 2025 16:27:19 +0100 Subject: [PATCH 304/414] remove pkg-config dep from glib-networking-2.72.1 --- .../g/glib-networking/glib-networking-2.72.1-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-12.3.0.eb index 1b89b9c31d2..1a24b265083 100644 --- a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-12.3.0.eb @@ -17,7 +17,6 @@ builddependencies = [ ('Meson', '1.1.1'), ('Ninja', '1.11.1'), ('pkgconf', '1.9.5'), - ('pkg-config', '0.29.2'), ] dependencies = [ From 17c9e874d86e012c6752a1298476573f36f82933 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 3 Jan 2025 16:45:51 +0100 Subject: [PATCH 305/414] adding easyconfigs: Biopython-1.84-foss-2024a.eb --- .../b/Biopython/Biopython-1.84-foss-2024a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2024a.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2024a.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2024a.eb new file mode 100644 index 00000000000..260b432d76e --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2024a.eb @@ -0,0 +1,46 @@ +# Updated from previous easyconfig +# Author: Robert Mijakovic +# Update: Pavel Tománek (INUITS) + +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.84' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2024a'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4'] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From bbe4e609d2b9d1cae8fb9ea11de89cbeaf6d3cc5 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 3 Jan 2025 18:32:43 +0100 Subject: [PATCH 306/414] adding easyconfigs: pydot-3.0.3-GCCcore-13.3.0.eb, XlsxWriter-3.2.0-GCCcore-13.3.0.eb, openpyxl-3.1.5-GCCcore-13.3.0.eb, GOATOOLS-1.4.12-foss-2024a.eb --- .../g/GOATOOLS/GOATOOLS-1.4.12-foss-2024a.eb | 72 +++++++++++++++++++ .../openpyxl/openpyxl-3.1.5-GCCcore-13.3.0.eb | 35 +++++++++ .../p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb | 28 ++++++++ .../XlsxWriter-3.2.0-GCCcore-13.3.0.eb | 34 +++++++++ 4 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.12-foss-2024a.eb create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.2.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.12-foss-2024a.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.12-foss-2024a.eb new file mode 100644 index 00000000000..ba3ae7b8125 --- /dev/null +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.12-foss-2024a.eb @@ -0,0 +1,72 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Pavel Tománek (Inuits) + +easyblock = 'PythonPackage' + +name = 'GOATOOLS' +version = '1.4.12' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2024a'} + +sources = [{ + 'git_config': { + 'url': 'https://github.com/tanghaibao', + 'repo_name': 'goatools', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [('cURL', '8.7.1')] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('XlsxWriter', '3.2.0'), + ('statsmodels', '0.14.4'), + ('pydot', '3.0.3'), + ('openpyxl', '3.1.5'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('ftpretty', '0.4.0', { + 'checksums': ['61233b9212f2cceec96ee2c972738fa31cae7248e92d0874c99c04ee739bb5a9'], + }), +] + +download_dep_fail = True +use_pip = True + +postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "mkdir -p %(builddir)s", + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9242d1fedf5 --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.5-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.1.5' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('lxml', '5.3.0'), + ('Pillow', '10.4.0'), +] + +use_pip = True + +exts_list = [ + ('et_xmlfile', '2.0.0', { + 'checksums': ['dab3f4764309081ce75662649be815c4c9081e88f0837825f90fd28317d4da54'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['cf0e3cf56142039133628b5acffe8ef0c12bc902d2aadd3e0fe5878dc08d1050'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e304bbecc1a --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +# updated: Denis Kristak, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'pydot' +version = '3.0.3' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +exts_list = [ + (name, version, { + 'checksums': ['5e009d97b2fff92b7a88f09ec1fd5b163f07f3b10469c927d362471d6faa0d50'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8c54c8caada --- /dev/null +++ b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'XlsxWriter' +version = '3.2.0' + +homepage = 'https://xlsxwriter.readthedocs.io/' +description = "A Python module for creating Excel XLSX files" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9977d0c661a72866a61f9f7a809e25ebbb0fb7036baa3b9fe74afcfca6b3cb8c'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/vba_extract.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['vba_extract.py --help'] + +sanity_pip_check = True + +moduleclass = 'tools' From 4902117c3a66835b208f0d0cb535fc1a4d79061b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Jan 2025 19:23:07 +0100 Subject: [PATCH 307/414] Apply suggestions from code review Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb index 972a2b83379..91e939f7d1b 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-14.2.0.eb @@ -19,8 +19,10 @@ builddependencies = [ ('Ninja', '1.12.1'), ] +configopts = "--default-library=both" # static and shared library + sanity_check_paths = { - 'files': ['include/pciaccess.h', 'lib/libpciaccess.%s' % SHLIB_EXT], + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a', 'lib/libpciaccess.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } From 88ef8db91f4843ba95bf7eb8c2400c86b8325ecd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Jan 2025 19:03:53 +0000 Subject: [PATCH 308/414] adding easyconfigs: gzip-1.13-GCCcore-14.2.0.eb, lz4-1.10.0-GCCcore-14.2.0.eb, zstd-1.5.6-GCCcore-14.2.0.eb, ICU-76.1-GCCcore-14.2.0.eb --- .../g/gzip/gzip-1.13-GCCcore-14.2.0.eb | 24 +++++++++++ .../i/ICU/ICU-76.1-GCCcore-14.2.0.eb | 29 +++++++++++++ .../l/lz4/lz4-1.10.0-GCCcore-14.2.0.eb | 30 ++++++++++++++ .../z/zstd/zstd-1.5.6-GCCcore-14.2.0.eb | 41 +++++++++++++++++++ 4 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/i/ICU/ICU-76.1-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.10.0-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.5.6-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-14.2.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..464afb53abb --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-14.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.13' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['20fc818aeebae87cdbf209d35141ad9d3cf312b35a5e6be61bfcfbf9eddd212a'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ICU/ICU-76.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-76.1-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..093119bed3c --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-76.1-GCCcore-14.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '76.1' + +homepage = 'https://icu.unicode.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': '14.2.0'} +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 = ['cb968df3e4d2e87e8b11c49a5d01c787bd13b9545280fc6642f826527618caef'] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.13.1'), +] + +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/l/lz4/lz4-1.10.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.10.0-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..4e42b4248bc --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.10.0-GCCcore-14.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.10.0' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['537512904744b35e232912055ccf8ec66d768639ff3abe5788d90d792ec5f48b'] + +builddependencies = [('binutils', '2.42')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.6-GCCcore-14.2.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.6-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..f80a68ab8ec --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.6-GCCcore-14.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.5.6' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['30f35f71c1203369dc979ecde0400ffea93c27391bfd2ac5a9715d2173d92ff7'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('gzip', '1.13'), + ('XZ', '5.6.3'), + ('lz4', '1.10.0'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From ab46e9a1b32f6d9ebdd6b5b096e1b10e091c1f7f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Jan 2025 19:06:27 +0000 Subject: [PATCH 309/414] Add patchelf --- .../patchelf-0.18.0-GCCcore-14.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..91b430e2eb9 --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-14.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.18.0' + +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': '14.2.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['patchelf-0.18.0_fix-alignment.patch'] +checksums = [ + {'0.18.0.tar.gz': '1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'}, + {'patchelf-0.18.0_fix-alignment.patch': '87936627643b2212e8261b0f3d5905f12d0fc91f73503e12124f93ff972e0a03'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20240712'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +sanity_check_commands = ["patchelf --help"] + +moduleclass = 'tools' From 4a1490d4ce326c526198de6e0bad3502a3f9d975 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Jan 2025 19:13:00 +0000 Subject: [PATCH 310/414] Fix checksum --- easybuild/easyconfigs/i/ICU/ICU-76.1-GCCcore-14.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ICU/ICU-76.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-76.1-GCCcore-14.2.0.eb index 093119bed3c..9cbd0b74016 100644 --- a/easybuild/easyconfigs/i/ICU/ICU-76.1-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/i/ICU/ICU-76.1-GCCcore-14.2.0.eb @@ -12,7 +12,7 @@ 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 = ['cb968df3e4d2e87e8b11c49a5d01c787bd13b9545280fc6642f826527618caef'] +checksums = ['dfacb46bfe4747410472ce3e1144bf28a102feeaa4e3875bac9b4c6cf30f4f3e'] builddependencies = [ ('binutils', '2.42'), From e5a5fed72802735a09805f93f306f884f9cf8fdc Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 4 Jan 2025 18:08:12 +0100 Subject: [PATCH 311/414] adding easyconfigs: ASE-3.24.0-gfbf-2023a.eb --- .../a/ASE/ASE-3.24.0-gfbf-2023a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2023a.eb new file mode 100644 index 00000000000..90aa48cd8d9 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.24.0' + +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': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Flask', '2.3.3'), + ('matplotlib', '3.7.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.1.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.14.0', { + 'checksums': ['2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0'], + }), + ('ase', version, { + 'checksums': ['9acc93d6daaf48cd27b844c56f8bf49428b9db0542faa3cc30d9d5b8e1842195'], + }), + ('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' From 057cc6007ee2840fe5b21d08fa13646ca148500b Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sun, 5 Jan 2025 00:07:17 +0100 Subject: [PATCH 312/414] adding easyconfigs: ASE-3.24.0-gfbf-2024a.eb --- .../a/ASE/ASE-3.24.0-gfbf-2024a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2024a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2024a.eb new file mode 100644 index 00000000000..e52fa3d949e --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2024a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.24.0' + +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': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('Flask', '3.0.3'), + ('matplotlib', '3.9.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.5.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.14.0', { + 'checksums': ['2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0'], + }), + ('ase', version, { + 'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'], + }), + ('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' From d65158e15e60a356e3118815e0b21733bed3a941 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 6 Jan 2025 10:37:37 +0100 Subject: [PATCH 313/414] Forgot to update a checksum. --- easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2024a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2024a.eb index e52fa3d949e..bb32c583471 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2024a.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.24.0-gfbf-2024a.eb @@ -30,7 +30,7 @@ exts_list = [ 'checksums': ['2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0'], }), ('ase', version, { - 'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'], + 'checksums': ['9acc93d6daaf48cd27b844c56f8bf49428b9db0542faa3cc30d9d5b8e1842195'], }), ('ase-ext', '20.9.0', { 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], From 0c64e41d6b1d0ed2d8cea57e81a7098d5d533834 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 6 Jan 2025 11:08:57 +0100 Subject: [PATCH 314/414] update Java version --- .../easyconfigs/i/IGV/IGV-2.19.1-Java-21.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-21.eb diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-21.eb b/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-21.eb new file mode 100644 index 00000000000..2a905f69a78 --- /dev/null +++ b/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-21.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'Tarball' + +name = 'IGV' +version = '2.19.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/software/igv/' +description = """This package contains command line utilities for + preprocessing, computing feature count density (coverage), sorting, and + indexing data files.""" + +toolchain = SYSTEM + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s'] +sources = ['%(name)s_%(version)s.zip'] +checksums = ['e7d7803cab4e12e84f5359a3d73915a45acc6d676151ca18e91fb2d39432b568'] + +dependencies = [('Java', '21', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 03ffc9abec0095018c0e0098966d39be4e2c1d81 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Mon, 6 Jan 2025 11:13:03 +0100 Subject: [PATCH 315/414] Delete easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb --- .../easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb b/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb deleted file mode 100644 index 9a2bc1d7398..00000000000 --- a/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb +++ /dev/null @@ -1,34 +0,0 @@ -# EasyBuild easyconfig -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# Modified by Adam Huffman -# Big Data Institute, University of Oxford - -easyblock = 'Tarball' - -name = 'IGV' -version = '2.19.1' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://www.broadinstitute.org/software/igv/' -description = """This package contains command line utilities for - preprocessing, computing feature count density (coverage), sorting, and - indexing data files.""" - -toolchain = SYSTEM - -source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s'] -sources = ['%(name)s_%(version)s.zip'] -checksums = ['e7d7803cab4e12e84f5359a3d73915a45acc6d676151ca18e91fb2d39432b568'] - -dependencies = [('Java', '17', '', SYSTEM)] - -sanity_check_paths = { - 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], - 'dirs': [], -} - -modextrapaths = {'PATH': ''} - -moduleclass = 'bio' From 51a12b74139b6a5e9d0ea9dbbe73e1cff5553a86 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 6 Jan 2025 12:12:05 +0100 Subject: [PATCH 316/414] use `GCC` toolchain --- .../{FastK-1.1.0-foss-2023a.eb => FastK-1.1.0-GCC-12.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/f/FastK/{FastK-1.1.0-foss-2023a.eb => FastK-1.1.0-GCC-12.3.0.eb} (97%) diff --git a/easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/f/FastK/FastK-1.1.0-GCC-12.3.0.eb similarity index 97% rename from easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb rename to easybuild/easyconfigs/f/FastK/FastK-1.1.0-GCC-12.3.0.eb index 507cab1640f..79114014136 100644 --- a/easybuild/easyconfigs/f/FastK/FastK-1.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/f/FastK/FastK-1.1.0-GCC-12.3.0.eb @@ -12,7 +12,7 @@ description = """FastK is a k‑mer counter that is optimized for processing hig set of a 32GB Axolotl genome (3.2Tbp) can be performed on a machine with just 12GB of memory provided it has ~6.5TB of disk space available.""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/thegenemyers/FASTK/archive/'] sources = ['v%(version)s.tar.gz'] From 90788e55876c85d943632f1a57ef487e49a263cf Mon Sep 17 00:00:00 2001 From: software Date: Mon, 6 Jan 2025 11:21:04 +0000 Subject: [PATCH 317/414] adding easyconfigs: BEDOPS-2.4.41-foss-2023a.eb --- .../b/BEDOPS/BEDOPS-2.4.41-foss-2023a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023a.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023a.eb new file mode 100644 index 00000000000..0162f62c877 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023a.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# updated: Denis Kristak (INUITS) +# Update: Petr Král (INUITS) + +easyblock = 'MakeCp' + +name = 'BEDOPS' +version = '2.4.41' + +homepage = 'http://%(namelower)s.readthedocs.io/en/latest/index.html' +description = """BEDOPS is an open-source command-line toolkit that performs highly efficient and + scalable Boolean and other set operations, statistical calculations, archiving, conversion and + other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for + distributing whole-genome analyses across a computational cluster.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3b868c820d59dd38372417efc31e9be3fbdca8cf0a6b39f13fb2b822607d6194'] + +# else build of jansson library fails with: 'configure: error: C compiler cannot create executables' +prebuildopts = 'unset LIBS && ' +# builds all variants and copies executables to bin directory +buildopts = ' all && make install' +# actually used variant is linked to via symlinks +keepsymlinks = True + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % x for x in ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch'] + ], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' From 82ebfa46c571e93838ee3c65a1256b3588e09bf5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 6 Jan 2025 12:45:28 +0100 Subject: [PATCH 318/414] add missing dependency --- easybuild/easyconfigs/f/FastK/FastK-1.1.0-GCC-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FastK/FastK-1.1.0-GCC-12.3.0.eb b/easybuild/easyconfigs/f/FastK/FastK-1.1.0-GCC-12.3.0.eb index 79114014136..784fdd460d8 100644 --- a/easybuild/easyconfigs/f/FastK/FastK-1.1.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/f/FastK/FastK-1.1.0-GCC-12.3.0.eb @@ -21,6 +21,7 @@ checksums = ['28a2de98ede77d4b4476596851f92413a9d99a1d3341afc6682d5333ac797f07'] dependencies = [ ('cURL', '8.0.1'), ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), ] skipsteps = ['configure'] From 45afab8720e334a71f49bacff8958e5e69d13899 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 6 Jan 2025 13:50:38 +0100 Subject: [PATCH 319/414] adding easyconfigs: bwa-mem2-2.2.1-GCC-11.2.0.eb and patches: bwa-mem2-2.2.1_fix_rdtsc_definition.patch --- .../b/bwa-mem2/bwa-mem2-2.2.1-GCC-11.2.0.eb | 42 +++++++++++++++++++ .../bwa-mem2-2.2.1_fix_rdtsc_definition.patch | 14 +++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_fix_rdtsc_definition.patch diff --git a/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..46e3165b997 --- /dev/null +++ b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-GCC-11.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'bwa-mem2' +version = '2.2.1' + +homepage = 'https://github.com/bwa-mem2/bwa-mem2' +description = """ +The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It +produces alignment identical to bwa and is ~1.3-3.1x faster depending on the +use-case, dataset and the running machine.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'bwa-mem2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'bwa-mem2-%(version)s_use_external_deps.patch', + 'bwa-mem2-%(version)s_common_avx512_flags.patch', + 'bwa-mem2-%(version)s_fix_rdtsc_definition.patch', +] +checksums = [ + {'v2.2.1.tar.gz': '36ddd28ce7020d5a036ddeffa00e692296fd40c80380671bd4ea5757bd28841b'}, + {'bwa-mem2-2.2.1_use_external_deps.patch': '0a9d7f7b3289029e19cf7dbab1778448097b9e0f92fa41a74a8cf81c9e114967'}, + {'bwa-mem2-2.2.1_common_avx512_flags.patch': '1a784bca167c6e3576a83c11715cbf6f8dced09d46021c0d283f7a1b185d6569'}, + {'bwa-mem2-2.2.1_fix_rdtsc_definition.patch': '06e9ccfcd394d9b54cb3052951aa896b3b8b5963b787038fea5df269103e33ed'}, +] + +dependencies = [('safestringlib', '20240228')] + +build_cmd_targets = 'multi' + +files_to_copy = [(['%(name)s*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s version'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_fix_rdtsc_definition.patch b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_fix_rdtsc_definition.patch new file mode 100644 index 00000000000..34ced9a0c9e --- /dev/null +++ b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_fix_rdtsc_definition.patch @@ -0,0 +1,14 @@ +__rdtsc is already defined in GCC 11 +see https://github.com/bwa-mem2/bwa-mem2/pull/205 +author: Paul Jähne +--- src/utils.h.orig 2024-08-29 13:39:59.324480171 +0200 ++++ src/utils.h 2024-08-29 13:40:39.392029793 +0200 +@@ -48,7 +48,7 @@ + + #define xassert(cond, msg) if ((cond) == 0) _err_fatal_simple_core(__func__, msg) + +-#if defined(__GNUC__) && !defined(__clang__) ++#if defined(__GNUC__) && __GNUC__ < 11 && !defined(__clang__) + #if defined(__i386__) + static inline unsigned long long __rdtsc(void) + { From e118cf27e15333b397a2487c0094bc29fe272df9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 6 Jan 2025 14:32:29 +0100 Subject: [PATCH 320/414] add missing dependency --- .../safestringlib-20240228-GCC-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/safestringlib/safestringlib-20240228-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/safestringlib/safestringlib-20240228-GCC-11.2.0.eb b/easybuild/easyconfigs/s/safestringlib/safestringlib-20240228-GCC-11.2.0.eb new file mode 100644 index 00000000000..58cb7850edd --- /dev/null +++ b/easybuild/easyconfigs/s/safestringlib/safestringlib-20240228-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'safestringlib' +version = '20240228' +_commit = 'b006356' + +homepage = 'https://github.com/intel/safestringlib' +description = """ +The Secure Development Lifecycle (SDL) recommends banning certain C Library +functions because they directly contribute to security vulnerabilities such as +buffer overflows. However routines for the manipulation of strings and memory +buffers are common in software and firmware, and are essential to accomplish +certain programming tasks. Safer replacements for these functions that avoid or +prevent serious security vulnerabilities (e.g. buffer overflows, string format +attacks, conversion overflows/underflows, etc.) are available in the SafeString +Library.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'intel' +sources = [{ + 'source_urls': [GITHUB_SOURCE], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['ea8e8952d7ade32a19df18af3a645ea54af924ff63a9b1a0b60e0e51be396d31'] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +postinstallcmds = ['cp libsafestring_static.a %(installdir)s/lib/'] + +sanity_check_paths = { + 'files': ['lib/libsafestring_shared.%s' % SHLIB_EXT, 'lib/libsafestring_static.a'], + 'dirs': ['include', 'share/safestring/cmake'], +} + +moduleclass = 'lib' From e771e4e17f35319c1db4af2e63b39348118680b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jan 2025 14:43:37 +0100 Subject: [PATCH 321/414] adding easyconfigs: XGBoost-2.1.3-gfbf-2023a.eb --- .../x/XGBoost/XGBoost-2.1.3-gfbf-2023a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.3-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.3-gfbf-2023a.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.3-gfbf-2023a.eb new file mode 100644 index 00000000000..374d45fbe28 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.3-gfbf-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '2.1.3' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7699ec4226156887d3afc665c63ab87469db9d46e361c702ba9fccd22535730c'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'ai' From 5f5270a980217632c139f0d7f1ae54bf7c3df7d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jan 2025 15:03:05 +0100 Subject: [PATCH 322/414] adding easyconfigs: XGBoost-2.1.3-gfbf-2023a-CUDA-12.1.1.eb --- .../XGBoost-2.1.3-gfbf-2023a-CUDA-12.1.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.3-gfbf-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.3-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.3-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..5abde61526c --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.3-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '2.1.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7699ec4226156887d3afc665c63ab87469db9d46e361c702ba9fccd22535730c'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +installopts = "--config-settings use_cuda=True --config-settings use_nccl=True" + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'ai' From 5213633ed339a468dd302fdb96bc23a87ff6d9f0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 6 Jan 2025 14:59:44 +0000 Subject: [PATCH 323/414] adding easyconfigs: ABINIT-10.2.5-intel-2023a.eb --- .../a/ABINIT/ABINIT-10.2.5-intel-2023a.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-10.2.5-intel-2023a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-10.2.5-intel-2023a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-10.2.5-intel-2023a.eb new file mode 100644 index 00000000000..4f1c9c56131 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-10.2.5-intel-2023a.eb @@ -0,0 +1,67 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '10.2.5' + +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': 'intel', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +source_urls = ['https://forge.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4f72fa457056617e6ed94db21264507eda66cc50224c7ed96b990d6b82de9ac1'] + +builddependencies = [ + ('Python', '3.11.3'), +] +dependencies = [ + ('libxc', '6.2.2'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('HDF5', '1.14.0'), + ('Wannier90', '3.1.0'), +] + +# Ensure MPI with intel wrappers. +configopts = '--with-mpi="yes" ' +configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# Enable OpenMP +configopts += '--enable-openmp="yes" ' + +# BLAS/Lapack from MKL +configopts += '--with-linalg-flavor=mkl ' + +# FFTW from MKL +configopts += '--with-fft-flavor=dfti ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# Enable double precision for GW calculations +configopts += '--enable-gw-dpc ' + +# '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' From 4599794b8ed629edc9e2971104b8fef0dd69060b Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 6 Jan 2025 17:35:54 +0100 Subject: [PATCH 324/414] Use Perl instead of Perl-minimal for WebKitGTK+ --- .../Perl-5.36.1-GCCcore-12.3.0-minimal.eb | 31 ------------------- .../WebKitGTK+-2.41.4-foss-2023a.eb | 2 +- 2 files changed, 1 insertion(+), 32 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb deleted file mode 100644 index e2918eba70a..00000000000 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'Perl' -version = '5.36.1' -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': '12.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] -checksums = [ - {'perl-5.36.1.tar.gz': '68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'}, - {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': - '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, -] - -builddependencies = [ - ('binutils', '2.40'), -] - -dependencies = [ - ('zlib', '1.2.13'), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb index 0f6b697bc48..71a73ed1dfc 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb @@ -34,7 +34,7 @@ osdependencies = [ builddependencies = [ ('CMake', '3.26.3'), ('Python', '3.11.3'), - ('Perl', '5.36.1', '-minimal'), + ('Perl', '5.36.1'), ('GObject-Introspection', '1.76.1'), ('pkg-config', '0.29.2'), ('ccache', '4.9'), From 53a59ab0b8ab673705ffb52c27dacdb49600a026 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 6 Jan 2025 21:04:51 +0000 Subject: [PATCH 325/414] update action/cache --- .github/workflows/unit_tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 82cf7cacef9..4d12efe8f2a 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -28,7 +28,7 @@ jobs: - name: Cache source files in /tmp/sources id: cache-sources - uses: actions/cache@v2 + uses: actions/cache@v4 with: path: /tmp/sources key: eb-sourcepath From 2bcfc6ed5b2aa63fb8ff5dbef588bf08b9f9dcb5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 7 Jan 2025 15:01:16 +0100 Subject: [PATCH 326/414] adding easyconfigs: ImageJ-1.54m-Java-11.eb --- .../i/ImageJ/ImageJ-1.54m-Java-11.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageJ/ImageJ-1.54m-Java-11.eb diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.54m-Java-11.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.54m-Java-11.eb new file mode 100644 index 00000000000..e8f6dedd7a6 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.54m-Java-11.eb @@ -0,0 +1,44 @@ +easyblock = 'PackedBinary' + +name = 'ImageJ' +version = '1.54m' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://imagej.nih.gov/ij' +description = "Image Processing and Analysis in Java" + +toolchain = SYSTEM + +source_urls = [ + 'https://imagej.net/ij/download/src/', + 'https://github.com/landinig/IJ-Morphology/raw/953503d/', # use git hash not main +] +sources = [ + 'ij%(version_major)s%(version_minor)s-src.zip', + # datestamp is determined by most recent file in zipball + {'download_filename': 'morphology.zip', 'filename': 'morphology-20210426.zip'}, +] +checksums = [ + {'ij154m-src.zip': '7fa33145b087bf3326b5ca6c2964dadea616011b9ec7dfe7773ccacc53408bce'}, + {'morphology-20210426.zip': '157f4b55759bf58458acfe073eff9af2e6bb305add2c8658f03f0ce579b3d578'}, +] + +builddependencies = [ + ('ant', '1.10.14', '-Java-%(javaver)s'), +] + +dependencies = [ + ('Java', '11'), +] + +install_cmd = "cd source && ant build && cp ij.jar %(installdir)s && " +install_cmd += "mkdir -p %(installdir)s/plugins && cp -a %(builddir)s/Morphology/* %(installdir)s/plugins/" + +sanity_check_paths = { + 'files': ['ij.jar'], + 'dirs': ['plugins'], +} + +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -ijpath $EBROOTIMAGEJ'\n" + +moduleclass = 'tools' From e86711ad37fc59b1a0479faa401521243294627b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jan 2025 10:44:53 +0100 Subject: [PATCH 327/414] simplify preinstallopts for chewBBACA --- .../easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb index 64194b1357a..c54b04f0134 100644 --- a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb +++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb @@ -34,12 +34,7 @@ dependencies = [ use_pip = True sanity_pip_check = True -local_preinstallopts = ( - "sed -i " - "-e 's/numpy~=1.24.3/numpy>=1.24.3/g' " - "-e 's/scipy~=1.10.1/scipy>=1.10.1/g' " - 'pyproject.toml && ' -) +local_preinstallopts = "sed -i -e 's/numpy~=/numpy>=/g' -e 's/scipy~=/scipy>=/g' pyproject.toml && " exts_list = [ ('pyrodigal', '3.6.3', { From 9d4ef451d63281469e96da83b24de80a2d6d2bf9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jan 2025 10:48:31 +0100 Subject: [PATCH 328/414] don't enable separate_build_dir in CastXML easyconfig, since it's enabled by default now by CMakeMake easyblock --- .../easyconfigs/c/CastXML/CastXML-0.6.10-GCCcore-13.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CastXML/CastXML-0.6.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CastXML/CastXML-0.6.10-GCCcore-13.2.0.eb index 7ddff2c0183..7bed29081ae 100644 --- a/easybuild/easyconfigs/c/CastXML/CastXML-0.6.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/c/CastXML/CastXML-0.6.10-GCCcore-13.2.0.eb @@ -24,8 +24,6 @@ dependencies = [ ('zlib', '1.2.13'), ] -separate_build_dir = True - sanity_check_paths = { 'files': ['bin/castxml'], 'dirs': ['share/castxml'], From 29a6c95280b6f12a50108c8c9371afe888a4e86e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jan 2025 11:00:11 +0100 Subject: [PATCH 329/414] don't use %(namelower)s template in LIQA easyconfig, just use 'liqa' --- easybuild/easyconfigs/l/LIQA/LIQA-1.3.4-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LIQA/LIQA-1.3.4-foss-2023a.eb b/easybuild/easyconfigs/l/LIQA/LIQA-1.3.4-foss-2023a.eb index 42f1c68574f..d1f5b0b3ca1 100644 --- a/easybuild/easyconfigs/l/LIQA/LIQA-1.3.4-foss-2023a.eb +++ b/easybuild/easyconfigs/l/LIQA/LIQA-1.3.4-foss-2023a.eb @@ -26,7 +26,7 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -options = {'modulename': '%(namelower)s_src'} +options = {'modulename': 'liqa_src'} sanity_check_commands = ['liqa -h'] From 2eb6589c5e3695a2ee1f59e2da1e6765cea627fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jan 2025 11:00:43 +0100 Subject: [PATCH 330/414] include annovar as dependency for scNanoGPS --- .../easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb b/easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb index 07c83a5af44..8340873a1f4 100644 --- a/easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb @@ -30,7 +30,7 @@ dependencies = [ ('BCFtools', '1.18'), ('gffread', '0.12.7'), ('LIQA', '1.3.4'), - # Optional - load 'annovar/20200607-GCCcore-12.3.0-Perl-5.36.1' to make 'reporter_SNV.py' work + ('annovar', '20200607'), ] exts_defaultclass = 'PythonPackage' @@ -66,11 +66,4 @@ sanity_check_commands = [ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} -modloadmsg = """ -If you like to use script 'reporter_SNV.py' you need to load annovar module as: -'ml annovar/20200607-GCCcore-12.3.0-Perl-5.36.1' -Source files of annovar (latest) are available after registration on: -http://www.openbioinformatics.org/annovar/annovar_download_form.php -""" - moduleclass = 'bio' From 8214b0718f866ac1290855b5232bc463d8da2115 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jan 2025 11:01:51 +0100 Subject: [PATCH 331/414] add download instructions to annovar easyconfig --- .../annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb index 55490da3de7..c6131befefd 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb @@ -13,9 +13,11 @@ genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -# Registration required for download -# http://www.openbioinformatics.org/annovar/annovar_download_form.php -# rename after download to %(name)s-%(version)s.tar.gz +download_instructions = """ +Registration required for download +via http://www.openbioinformatics.org/annovar/annovar_download_form.php +rename after download to '%(name)s-%(version)s.tar.gz' +""" sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] From 6bc401b8a43215a953ff2098eab331ae8a790387 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jan 2025 11:31:46 +0100 Subject: [PATCH 332/414] drop Perl versionsuffix for annovar with GCCcore/12.3.0 --- ...-12.3.0-Perl-5.36.1.eb => annovar-20200607-GCCcore-12.3.0.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/a/annovar/{annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb => annovar-20200607-GCCcore-12.3.0.eb} (97%) diff --git a/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0.eb similarity index 97% rename from easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb rename to easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0.eb index c6131befefd..9c027b42f62 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0.eb @@ -4,7 +4,6 @@ easyblock = 'Tarball' name = 'annovar' version = '20200607' # version reported by `annotate_variation.pl -h` -versionsuffix = '-Perl-%(perlver)s' homepage = 'http://annovar.openbioinformatics.org/en/latest/' description = """ANNOVAR is an efficient software tool to utilize update-to-date information From be8390ea95a435020e543329267f13b952b8d204 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 8 Jan 2025 14:30:51 +0100 Subject: [PATCH 333/414] adding easyconfigs: WIEN2k-24.1-intel-2023a.eb, DFT-D3-3.2.0-intel-2023a.eb, FFTW.MPI-3.3.10-iimpi-2023a.eb, FFTW-3.3.10-intel-compilers-2023.1.0.eb --- .../d/DFT-D3/DFT-D3-3.2.0-intel-2023a.eb | 34 ++++++++ .../f/FFTW.MPI/FFTW.MPI-3.3.10-iimpi-2023a.eb | 19 +++++ .../FFTW-3.3.10-intel-compilers-2023.1.0.eb | 26 ++++++ .../w/WIEN2k/WIEN2k-24.1-intel-2023a.eb | 81 +++++++++++++++++++ 4 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2023a.eb create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-iimpi-2023a.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-intel-compilers-2023.1.0.eb create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-24.1-intel-2023a.eb diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2023a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2023a.eb new file mode 100644 index 00000000000..eac91b100f3 --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'DFT-D3' +version = '3.2.0' + +homepage = 'https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3' +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical + quantum chemical methods.""" + +toolchain = {'name': 'intel', 'version': '2023a'} + +source_urls = ['https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3'] +sources = [{'download_filename': 'dftd3.tgz', 'filename': SOURCELOWER_TGZ}] +checksums = ['d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59'] + +# Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version +# numbering. Also, the authors are prone (alas) to stealth upgrades, so that two +# tarballs with the same version number can have different checksums. For this +# reason, it is suggested to manually download and rename the tarball. The +# checksum may also need updating from time to time. +# Checksum last updated: 20 September 2018 +# Date tarball was reported to have been modified: 14 June 2016 +prebuildopts = "sed -i 's/OSTYPE=LINUXL/OSTYPE=LINUXI/' Makefile && " + +files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/dftd3'], + 'dirs': [], +} + +sanity_check_commands = ['dftd3'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-iimpi-2023a.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-iimpi-2023a.eb new file mode 100644 index 00000000000..edd9aa01195 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-iimpi-2023a.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +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': 'iimpi', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-intel-compilers-2023.1.0.eb new file mode 100644 index 00000000000..79fb090b48c --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-intel-compilers-2023.1.0.eb @@ -0,0 +1,26 @@ +name = 'FFTW' +version = '3.3.10' + +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-compilers', 'version': '2023.1.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +# 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/w/WIEN2k/WIEN2k-24.1-intel-2023a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-24.1-intel-2023a.eb new file mode 100644 index 00000000000..5805e428637 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-24.1-intel-2023a.eb @@ -0,0 +1,81 @@ +name = 'WIEN2k' +version = '24.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2023a'} + +sources = ['%(name)s_%(version)s.tar'] +patches = [ + 'WIEN2k-23.2_fix_libxc_for_lapw0_mpi.patch', + 'WIEN2k-23.2_fix_system_stderr_redirection.patch', +] +checksums = [ + {'WIEN2k_24.1.tar': '15ccceea0fe64c2bb94b3e7252c36537c04c8fd7c0ae46367e837cedb5402713'}, + {'WIEN2k-23.2_fix_libxc_for_lapw0_mpi.patch': '1cc480a4824d9185ad5918dfc68c47bcb7826114626c8133d573be901bbdca84'}, + {'WIEN2k-23.2_fix_system_stderr_redirection.patch': + 'eb3f987b1f839b9f10c315d3f7a57e181e46bc98bec3a18e5b9942689b75fcc7'}, +] + +download_instructions = """ +WIEN2k can be ordered at http://susi.theochem.tuwien.ac.at/index.html. +""" + +dependencies = [ + ('Python', '3.11.3'), + ('Perl', '5.36.1'), + ('DFT-D3', '3.2.0'), + ('ELPA', '2023.05.001'), + ('FFTW.MPI', '3.3.10'), + ('libxc', '6.2.2'), +] + +osdependencies = [ + ('glibc-devel', 'libc6-dev'), # required for libpthread. + ('tcsh') +] + +# remote = 'pbsssh' +# If using a Slurm batch system it is highly recommended to use +# 'srun -n_NP_ _EXEC_' for wien_mpirun +wien_mpirun = 'mpirun -np _NP_ _EXEC_' +use_remote = False +mpi_remote = False +wien_granularity = True +taskset = 'no' + +# Change as needed, these are the defaults +# nmatmax = 19000 +# nume = 6000 + +fix_perl_shebang_for = [ + 'iniel_pressure_in2reader.pl_lapw', + 'iniel_pressure_reader.pl_lapw', + 'setrmt_lapw', + 'elast_setup_input.pl_lapw', + 'bashtime2csh.pl_lapw', +] + +# skip running of serial/parallel benchmark, because links to download test_case.tar.gz and mpi-benchmark.tar.gz +# from http://www.wien2k.at/reg_user/benchmark/ that are used by WIEN2k easyblock are broken... +runtest = False + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 100', [r'^:DIS.*0.1', r'^:ENE.*-1248.1']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.0', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*133.*total forces', + ]), +] + +moduleclass = 'chem' From 2b660d6eb5901725d15918f01fd80f88208c2be8 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 8 Jan 2025 16:38:07 +0100 Subject: [PATCH 334/414] adding easyconfigs: CTranslate2-4.5.0-foss-2023a-CUDA-12.6.0.eb, cpu_features-0.9.0-GCCcore-12.3.0.eb and patches: CTranslate2-4.5.0_fix-tests.patch, CTranslate2-4.5.0_fix-third-party.patch, CTranslate2-4.5.0_replace-cxxopts.patch --- ...Translate2-4.5.0-foss-2023a-CUDA-12.6.0.eb | 88 +++++++++++++++++++ .../CTranslate2-4.5.0_fix-tests.patch | 21 +++++ .../CTranslate2-4.5.0_fix-third-party.patch | 40 +++++++++ .../CTranslate2-4.5.0_replace-cxxopts.patch | 22 +++++ .../cpu_features-0.9.0-GCCcore-12.3.0.eb | 32 +++++++ 5 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0-foss-2023a-CUDA-12.6.0.eb create mode 100644 easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-tests.patch create mode 100644 easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-third-party.patch create mode 100644 easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_replace-cxxopts.patch create mode 100644 easybuild/easyconfigs/c/cpu_features/cpu_features-0.9.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0-foss-2023a-CUDA-12.6.0.eb b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0-foss-2023a-CUDA-12.6.0.eb new file mode 100644 index 00000000000..cc4c047888e --- /dev/null +++ b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0-foss-2023a-CUDA-12.6.0.eb @@ -0,0 +1,88 @@ +easyblock = 'CMakeMake' + +name = 'CTranslate2' +version = '4.5.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://opennmt.net/CTranslate2/' +description = "Fast inference engine for Transformer models." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/OpenNMT/CTranslate2/archive/'] +sources = [{ + "download_filename": "v%(version)s.tar.gz", + "filename": SOURCE_TAR_GZ, +}] +patches = [ + 'CTranslate2-4.5.0_fix-third-party.patch', + 'CTranslate2-4.5.0_fix-tests.patch', + 'CTranslate2-4.5.0_replace-cxxopts.patch', +] +checksums = [ + {'CTranslate2-4.5.0.tar.gz': 'f3040c7c3da5dde022fdc16906c279f3f936c6e79f3df8f998c908bb01a77cfe'}, + {'CTranslate2-4.5.0_fix-third-party.patch': '627b995f28d9beb764a9d491933d66d6bbaa26ab2a8f430c7d7e7f41c0ed4e4e'}, + {'CTranslate2-4.5.0_fix-tests.patch': '73123eafe612538354be5aa96c750199e1a219a5316800848c3894c1cc6ca2ad'}, + {'CTranslate2-4.5.0_replace-cxxopts.patch': 'e378969c2968e2fd57863956a4d2f267731a49d1b890dcc45593d6a310531271'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pybind11', '2.11.1'), + ('cxxopts', '3.0.0', '', SYSTEM), + ('spdlog', '1.11.0'), + ('cpu_features', '0.9.0'), +] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('googletest', '1.13.0'), + ('PyYAML', '6.0'), + ('cuDNN', '9.5.0.50', versionsuffix, SYSTEM), +] + +# make sure that CTranslate2 libraries are linked to FlexiBLAS, not OpenBLAS +preconfigopts = "export CMAKE_INCLUDE_PATH=$EBROOTFLEXIBLAS/include/flexiblas:${CMAKE_INCLUDE_PATH} && " +preconfigopts += "sed -i 's/openblas/flexiblas/g' %(start_dir)s/CMakeLists.txt && " + +configopts = '-DOPENMP_RUNTIME=COMP -DWITH_CUDA=ON -DWITH_MKL=OFF ' +configopts += '-DOPENBLAS_INCLUDE_DIR="$EBROOTFLEXIBLAS/include" -DWITH_OPENBLAS=ON ' +configopts += '-DWITH_CUDNN=ON ' +configopts += '-DENABLE_CPU_DISPATCH=OFF ' + +prebuildopts = 'export CT2_VERBOSE=3 && ' + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'installopts': '', + 'runtest': False, +} + +exts_list = [ + ('ctranslate2', version, { + 'sources': ['CTranslate2-%(version)s.tar.gz'], + 'start_dir': 'python', + 'checksums': ['f3040c7c3da5dde022fdc16906c279f3f936c6e79f3df8f998c908bb01a77cfe'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ct2-translator', 'lib/libctranslate2.%s' % SHLIB_EXT], + 'dirs': ['include/ctranslate2', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "ct2-translator --help", + "python -c 'import ctranslate2'", + "python -m pip check", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-tests.patch b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-tests.patch new file mode 100644 index 00000000000..e559871807f --- /dev/null +++ b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-tests.patch @@ -0,0 +1,21 @@ +Author: Pavel Tománek (pavelToman) +Fix compilation of tests + replace third_party GTest by one from EB. +--- tests/CMakeLists.txt.orig 2025-01-03 16:35:23.243495904 +0100 ++++ tests/CMakeLists.txt 2025-01-03 17:34:04.044755825 +0100 +@@ -2,7 +2,7 @@ + + option(BUILD_GMOCK "" OFF) + option(INSTALL_GTEST "" OFF) +-add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/../third_party/googletest ${CMAKE_CURRENT_BINARY_DIR}/googletest) ++find_package(GTest) + + add_executable(ctranslate2_test + batching_test.cc +@@ -21,6 +21,7 @@ + target_link_libraries(ctranslate2_test + ${PROJECT_NAME} + gtest_main ++ gtest + ) + + add_executable(benchmark_ops diff --git a/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-third-party.patch b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-third-party.patch new file mode 100644 index 00000000000..27d254e9d1d --- /dev/null +++ b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-third-party.patch @@ -0,0 +1,40 @@ +--- CMakeLists.txt.orig 2025-01-03 16:15:51.023557000 +0100 ++++ CMakeLists.txt 2025-01-08 15:50:57.345502000 +0100 +@@ -95,7 +95,7 @@ + endif() + + find_package(Threads) +-add_subdirectory(third_party/spdlog EXCLUDE_FROM_ALL) ++find_package(spdlog) + + set(PRIVATE_INCLUDE_DIRECTORIES + ${CMAKE_CURRENT_SOURCE_DIR}/src +@@ -246,7 +246,7 @@ + set(BUILD_SHARED_LIBS_SAVED "${BUILD_SHARED_LIBS}") + set(BUILD_SHARED_LIBS OFF) + set(BUILD_TESTING OFF) +- add_subdirectory(third_party/cpu_features EXCLUDE_FROM_ALL) ++ find_package(CpuFeatures) + set(BUILD_SHARED_LIBS "${BUILD_SHARED_LIBS_SAVED}") + list(APPEND LIBRARIES cpu_features) + endif() +@@ -498,19 +498,6 @@ + message(STATUS "NVCC host compiler: ${CUDA_HOST_COMPILER}") + message(STATUS "NVCC compilation flags: ${CUDA_NVCC_FLAGS}") + +- # We should ensure that the Thrust include directories appear before +- # -I/usr/local/cuda/include for both GCC and NVCC, so that the headers +- # are coming from the submodule and not the system. +- set(THRUST_INCLUDE_DIRS +- ${CMAKE_CURRENT_SOURCE_DIR}/third_party/thrust/dependencies/cub +- ${CMAKE_CURRENT_SOURCE_DIR}/third_party/thrust +- ) +- cuda_include_directories(${THRUST_INCLUDE_DIRS}) +- list(APPEND PRIVATE_INCLUDE_DIRECTORIES ${THRUST_INCLUDE_DIRS}) +- +- set(CUTLASS_INCLUDE_DIRS +- ${CMAKE_CURRENT_SOURCE_DIR}/third_party/cutlass/include +- ) + cuda_include_directories(${CUTLASS_INCLUDE_DIRS}) + list(APPEND PRIVATE_INCLUDE_DIRECTORIES ${CUTLASS_INCLUDE_DIRS}) + diff --git a/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_replace-cxxopts.patch b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_replace-cxxopts.patch new file mode 100644 index 00000000000..f690e3b157b --- /dev/null +++ b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_replace-cxxopts.patch @@ -0,0 +1,22 @@ +Author: Pavel Tománek (pavelToman) +Replace recursively downloaded third party cxxopts with cxxopts from EB. +--- cli/CMakeLists.txt.orig 2025-01-03 16:47:35.863270652 +0100 ++++ cli/CMakeLists.txt 2025-01-03 16:52:02.988342754 +0100 +@@ -1,15 +1,9 @@ +-if (NOT IS_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/../third_party/cxxopts/include") +- message(FATAL_ERROR "The client dependency repository (cxxopts) is missing! " +- "You probably didn't clone the project with --recursive. You can include it " +- "by calling \"git submodule update --init --recursive\"") +-endif() +- + add_executable(translator + translator.cc + ) + target_include_directories(translator +- PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../third_party/cxxopts/include +- ) ++ PRIVATE "$ENV{EBROOTCXXOPTS}/include" ++) + target_link_libraries(translator + PRIVATE ${PROJECT_NAME} + ) diff --git a/easybuild/easyconfigs/c/cpu_features/cpu_features-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cpu_features/cpu_features-0.9.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b2314ca5b78 --- /dev/null +++ b/easybuild/easyconfigs/c/cpu_features/cpu_features-0.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak, update: Pavel Tománek +easyblock = 'CMakeMake' + +name = 'cpu_features' +version = '0.9.0' + +homepage = 'https://github.com/google/cpu_features' +description = """A cross-platform C library to retrieve CPU features (such as available instructions) at runtime.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/cpu_features/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bdb3484de8297c49b59955c3b22dba834401bc2df984ef5cfc17acbe69c5018e'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +modextrapaths = {'CPATH': 'include/cpu_features'} + +sanity_check_paths = { + 'files': ['bin/list_cpu_features', 'lib/libcpu_features.a'], + 'dirs': ['include/cpu_features/'] +} + +sanity_check_commands = ['list_cpu_features'] + +moduleclass = 'tools' From 90b7f987c0143c8e6709c8ec0e88db888a92100b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 8 Jan 2025 17:02:19 +0100 Subject: [PATCH 335/414] adding easyconfigs: whisper-ctranslate2-0.5.2-foss-2023a-CUDA-12.6.0.eb, ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.6.0.eb, PortAudio-19.7.0-foss-2023a.eb, PyAV-11.0.0-GCCcore-12.3.0.eb --- ...X-Runtime-1.19.2-foss-2023a-CUDA-12.6.0.eb | 64 +++++++++++++++++++ .../PortAudio/PortAudio-19.7.0-foss-2023a.eb | 51 +++++++++++++++ .../p/PyAV/PyAV-11.0.0-GCCcore-12.3.0.eb | 32 ++++++++++ ...translate2-0.5.2-foss-2023a-CUDA-12.6.0.eb | 54 ++++++++++++++++ 4 files changed, 201 insertions(+) create mode 100644 easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.6.0.eb create mode 100644 easybuild/easyconfigs/p/PortAudio/PortAudio-19.7.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/PyAV/PyAV-11.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/w/whisper-ctranslate2/whisper-ctranslate2-0.5.2-foss-2023a-CUDA-12.6.0.eb diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.6.0.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.6.0.eb new file mode 100644 index 00000000000..68436eedc6c --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.6.0.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'ONNX-Runtime' +version = '1.19.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://onnxruntime.ai' +description = """ONNX Runtime inference can enable faster customer experiences and lower costs, +supporting models from deep learning frameworks such as PyTorch and +TensorFlow/Keras as well as classical machine learning libraries such as +scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different +hardware, drivers, and operating systems, and provides optimal performance by +leveraging hardware accelerators where applicable alongside graph optimizations +and transforms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('Python', '3.11.3'), + ('ONNX', '1.15.0'), + ('flatbuffers-python', '23.5.26'), + ('sympy', '1.12'), +] + +use_pip = True + +local_whl_tmpl = 'onnxruntime_gpu-%%(version)s-cp311-cp311-manylinux_2_27_%s.manylinux_2_28_%s.whl' + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + (name, version, { + 'modulename': 'onnxruntime', + 'source_urls': ['http://pypi.python.org/packages/source/o/onnxruntime-gpu'], + 'sources': ['onnxruntime_gpu-%(version)s-cp311-cp311-manylinux_2_27_%(arch)s.manylinux_2_28_%(arch)s.whl'], + 'checksums': ['562fc7c755393eaad9751e56149339dd201ffbfdb3ef5f43ff21d0619ba9045f'], + }), +] + +# Due to its name 'onnxruntime-gpu', this package does not fullfil requirements on 'onnxruntime' although it provides +# the 'onnxruntime' python module. Fix this dependency issue in pip by creating a stub 'onnxruntime' dist-info folder +_py_sitepkgs = '%(installdir)s/lib/python%(pyshortver)s/site-packages' +postinstallcmds = [ + "cp -r %s/onnxruntime{_gpu,}-%%(version)s.dist-info" % _py_sitepkgs, + "sed -i 's/onnxruntime.gpu/onnxruntime/g' %s/onnxruntime-%%(version)s.dist-info/{METADATA,RECORD}" % _py_sitepkgs, +] + +sanity_pip_check = True + +_py_sitepkgs_dirs = ['onnxruntime', 'onnxruntime-%(version)s.dist-info', 'onnxruntime_gpu-%(version)s.dist-info'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%%(pyshortver)s/site-packages/%s' % x for x in _py_sitepkgs_dirs], +} + +options = {'modulename': 'onnxruntime'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PortAudio/PortAudio-19.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/PortAudio/PortAudio-19.7.0-foss-2023a.eb new file mode 100644 index 00000000000..001f977a015 --- /dev/null +++ b/easybuild/easyconfigs/p/PortAudio/PortAudio-19.7.0-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'PortAudio' +version = '19.7.0' + +homepage = 'https://www.portaudio.com/' +description = """PortAudio is a free, cross-platform, open-source, audio I/O library. + It lets you write simple audio programs in 'C' or C++ that will compile and run on many platforms including Windows, + Macintosh OS X, and Unix (OSS/ALSA). It is intended to promote the exchange of audio software between + developers on different platforms. Many applications use PortAudio for Audio I/O.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ["https://github.com/PortAudio/portaudio/archive"] +sources = ["v%(version)s.tar.gz"] +checksums = ['5af29ba58bbdbb7bbcefaaecc77ec8fc413f0db6f4c4e286c40c3e1b83174fa0'] + +dependencies = [ + ('Python', '3.11.3'), + ('alsa-lib', '1.2.9'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'installopts': '', +} + +exts_list = [ + ('PyAudio', '0.2.14', { + 'checksums': ['78dfff3879b4994d1f4fc6485646a57755c6ee3c19647a491f790a0895bd2f87'], + }), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ["include/portaudio.h", "lib/libportaudio.a", "lib/libportaudio.so"], + 'dirs': ['include', 'lib', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'python -c "import pyaudio; pyaudio.get_portaudio_version_text()"' +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyAV/PyAV-11.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyAV/PyAV-11.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..05acd2727d2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyAV/PyAV-11.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'PyAV' +version = '11.0.0' + +homepage = 'https://pyav.org' +description = """PyAV is a Pythonic binding for FFmpeg. We aim to provide all of the power and +control of the underlying library, but manage the gritty details as much as possible.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Cython', '3.0.7'), + ('FFmpeg', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('av', version, { + 'installopts': '--no-binary av', + 'checksums': ['48223f000a252070f8e700ff634bb7fb3aa1b7bc7e450373029fbdd6f369ac31'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/whisper-ctranslate2/whisper-ctranslate2-0.5.2-foss-2023a-CUDA-12.6.0.eb b/easybuild/easyconfigs/w/whisper-ctranslate2/whisper-ctranslate2-0.5.2-foss-2023a-CUDA-12.6.0.eb new file mode 100644 index 00000000000..4a697095abc --- /dev/null +++ b/easybuild/easyconfigs/w/whisper-ctranslate2/whisper-ctranslate2-0.5.2-foss-2023a-CUDA-12.6.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'whisper-ctranslate2' +version = '0.5.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/Softcatala/whisper-ctranslate2/' +description = "Whisper command line client compatible with original OpenAI client based on CTranslate2." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('tokenizers', '0.15.2'), + ('CTranslate2', '4.5.0', versionsuffix), + ('PyAV', '11.0.0'), + ('ONNX-Runtime', '1.19.2', versionsuffix), + ('cffi', '1.15.1'), + ('PortAudio', '19.7.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('huggingface-hub', '0.26.5', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['1008bd18f60bfb65e8dbc0a97249beeeaa8c99d3c2fa649354df9fa5a13ed83b'], + }), + ('sounddevice', '0.5.1', { + 'checksums': ['09ca991daeda8ce4be9ac91e15a9a81c8f81efa6b695a348c9171ea0c16cb041'], + }), + ('faster-whisper', '1.1.1', { + 'checksums': ['50d27571970c1be0c2b2680a2593d5d12f9f5d2f10484f242a1afbe7cb946604'], + }), + (name, version, { + 'modulename': False, + 'source_urls': ['https://github.com/Softcatala/whisper-ctranslate2/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['8a7c7b232086b8bfa7022f3a3b3f95c8c5175c33663cf8d3fd840539f2be9a49'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'ai' From 729bc81d1d7aafa7f7167e73293c66de66a48c8b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 8 Jan 2025 17:09:46 +0100 Subject: [PATCH 336/414] add description to the patch --- .../c/CTranslate2/CTranslate2-4.5.0-foss-2023a-CUDA-12.6.0.eb | 2 +- .../c/CTranslate2/CTranslate2-4.5.0_fix-third-party.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0-foss-2023a-CUDA-12.6.0.eb b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0-foss-2023a-CUDA-12.6.0.eb index cc4c047888e..1a4d2608ad7 100644 --- a/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0-foss-2023a-CUDA-12.6.0.eb +++ b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0-foss-2023a-CUDA-12.6.0.eb @@ -21,7 +21,7 @@ patches = [ ] checksums = [ {'CTranslate2-4.5.0.tar.gz': 'f3040c7c3da5dde022fdc16906c279f3f936c6e79f3df8f998c908bb01a77cfe'}, - {'CTranslate2-4.5.0_fix-third-party.patch': '627b995f28d9beb764a9d491933d66d6bbaa26ab2a8f430c7d7e7f41c0ed4e4e'}, + {'CTranslate2-4.5.0_fix-third-party.patch': '45ab6d19954010dc5d515498a0827f0b13992d88b9691ab73ab27fee1114e3e3'}, {'CTranslate2-4.5.0_fix-tests.patch': '73123eafe612538354be5aa96c750199e1a219a5316800848c3894c1cc6ca2ad'}, {'CTranslate2-4.5.0_replace-cxxopts.patch': 'e378969c2968e2fd57863956a4d2f267731a49d1b890dcc45593d6a310531271'}, ] diff --git a/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-third-party.patch b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-third-party.patch index 27d254e9d1d..5d6e310e216 100644 --- a/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-third-party.patch +++ b/easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-third-party.patch @@ -1,3 +1,5 @@ +Author: Pavel Tománek (pavelToman) +Replace recursively downloaded third party sw with programs from EB. --- CMakeLists.txt.orig 2025-01-03 16:15:51.023557000 +0100 +++ CMakeLists.txt 2025-01-08 15:50:57.345502000 +0100 @@ -95,7 +95,7 @@ From 1f7162564227513e47b5ab6b52f164c0ab8e1d8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jan 2025 12:57:20 +0100 Subject: [PATCH 337/414] don't use single quotes in download_instructions in annovar easyconfig, to avoid tripping pattern matching that suggests to use SOURCE_TAR_GZ instead --- .../easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0.eb index 9c027b42f62..c3bf8224357 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} download_instructions = """ Registration required for download via http://www.openbioinformatics.org/annovar/annovar_download_form.php -rename after download to '%(name)s-%(version)s.tar.gz' +rename after download to %(name)s-%(version)s.tar.gz """ sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] From a51357d888a0c731dba1ed339564865398df2b68 Mon Sep 17 00:00:00 2001 From: andped Date: Thu, 9 Jan 2025 13:45:18 +0100 Subject: [PATCH 338/414] adding easyconfigs: snakemake-8.27.0-foss-2024a.eb --- .../snakemake/snakemake-8.27.0-foss-2024a.eb | 153 ++++++++++++++++++ 1 file changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb new file mode 100644 index 00000000000..9e09a6ceb82 --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -0,0 +1,153 @@ +easyblock = 'PythonBundle' + +name = 'snakemake' +version = '8.27.0' + +homepage = 'https://snakemake.readthedocs.io' +description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." + +toolchain = {'name': 'foss', 'version': '2024a'} + +builddependencies = [ + ('poetry', '1.8.3'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('GitPython', '3.1.43'), + ('IPython', '8.14.0'), + ('PyYAML', '6.0.2'), + ('wrapt', '1.15.0'), + ('PuLP', '2.8.0'), + ('Cython', '3.0.10', '', {'name': 'GCCcore', 'version': '13.3.0'}), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('plac', '1.4.3', { + 'checksums': ['d4cb3387b2113a28aebd509433d0264a4e5d9bb7c1a86db4fbd0a8f11af74eb3'], + }), + ('dpath', '2.2.0', { + 'checksums': ['34f7e630dc55ea3f219e555726f5da4b4b25f2200319c8e6902c394258dd6a3e'], + }), + ('yte', '1.5.5', { + 'checksums': ['2c49831859f3216f313a17688900690872e05f8fbe77cb5d151bdb896357d57e'], + }), + ('toposort', '1.10', { + 'checksums': ['bfbb479c53d0a696ea7402601f4e693c97b0367837c8898bc6471adfca37a6bd'], + }), + ('throttler', '1.2.2', { + 'checksums': ['d54db406d98e1b54d18a9ba2b31ab9f093ac64a0a59d730c1cf7bb1cdfc94a58'], + }), + ('stopit', '1.1.2', { + 'checksums': ['f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d'], + }), + ('ConfigArgParse', '1.7', { + 'checksums': ['e7067471884de5478c58a511e529f0f9bd1c66bfef1dea90935438d6c23306d1'], + }), + ('argparse-dataclass', '2.0.0', { + 'modulename': 'argparse_dataclass', + 'source_tmpl': 'argparse_dataclass-%(version)s.tar.gz', + 'checksums': ['09ab641c914a2f12882337b9c3e5086196dbf2ee6bf0ef67895c74002cc9297f'], + }), + ('snakemake-interface-common', '1.17.4', { + 'modulename': 'snakemake_interface_common', + 'source_tmpl': 'snakemake_interface_common-%(version)s.tar.gz', + 'checksums': ['c2142e1b93cbc18c2cf41d15968ba8688f60b077c8284e5de057cccfc215d4d3'], + }), + ('reretry', '0.11.8', { + 'checksums': ['f2791fcebe512ea2f1d153a2874778523a8064860b591cd90afc21a8bed432e3'], + }), + ('snakemake-interface-storage-plugins', '3.3.0', { + 'modulename': 'snakemake_interface_storage_plugins', + 'source_tmpl': 'snakemake_interface_storage_plugins-%(version)s.tar.gz', + 'checksums': ['203d8f794dfb37d568ad01a6c375fa8beac36df8e488c0f9b9f75984769c362a'], + }), + ('snakemake-interface-report-plugins', '1.1.0', { + 'modulename': 'snakemake_interface_report_plugins', + 'source_tmpl': 'snakemake_interface_report_plugins-%(version)s.tar.gz', + 'checksums': ['b1ee444b2fca51225cf8a102f8e56633791d01433cd00cf07a1d9713a12313a5'], + }), + ('snakemake-interface-executor-plugins', '9.3.3', { + 'modulename': 'snakemake_interface_executor_plugins', + 'source_tmpl': 'snakemake_interface_executor_plugins-%(version)s.tar.gz', + 'checksums': ['11e59af04bf00e9aaee7f0b99f9358910becfccdad7b18a455d37601f6d8d2ea'], + }), + ('smart-open', '7.1.0', { + 'sources': ['smart_open-%(version)s.tar.gz'], + 'checksums': ['a4f09f84f0f6d3637c6543aca7b5487438877a21360e7368ccf1f704789752ba'], + }), + ('jupyter-core', '5.7.2', { + 'modulename': 'jupyter_core', + 'source_tmpl': 'jupyter_core-%(version)s.tar.gz', + 'checksums': ['aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'], + }), + ('fastjsonschema', '2.19.1', { + 'checksums': ['e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d'], + }), + ('nbformat', '5.10.4', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b'], + }), + ('Jinja2', '3.1.4', { + 'sources': ['jinja2-%(version)s.tar.gz'], + 'checksums': ['4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369'], + }), + ('immutables', '0.21', { + 'checksums': ['b55ffaf0449790242feb4c56ab799ea7af92801a0a43f9e2f4f8af2ab24dfc4a'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('connection-pool', '0.0.3', { + 'sources': ['connection_pool-%(version)s.tar.gz'], + 'checksums': ['bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc'], + }), + ('conda-inject', '1.3.2', { + 'sources': ['conda_inject-%(version)s.tar.gz'], + 'checksums': ['0b8cde8c47998c118d8ff285a04977a3abcf734caf579c520fca469df1cd0aac'], + }), + (name, version, { + 'checksums': ['7bee7e4f255fd75738b6840c3453c9b5a4f33c628705c38a5a462db008f0334d'], + }), + ('snakemake-executor-plugin-slurm-jobstep', '0.2.1', { + 'modulename': 'snakemake_executor_plugin_slurm_jobstep', + 'source_tmpl': 'snakemake_executor_plugin_slurm_jobstep-%(version)s.tar.gz', + 'checksums': ['58894d52b5998a34fa6f60ec511ff0bfde4a9ec96714bcaa3cd2f46cf8a33859'], + }), + ('snakemake-executor-plugin-flux', '0.1.1', { + 'modulename': 'snakemake_executor_plugin_flux', + 'source_tmpl': 'snakemake_executor_plugin_flux-%(version)s.tar.gz', + 'checksums': ['26655bd1cf5d7db5dfcfdfbd006c1db35968c0ad1772e0b010e64e6f71b00163'], + }), + ('snakemake-executor-plugin-slurm', '0.12.0', { + 'modulename': 'snakemake_executor_plugin_slurm', + 'source_tmpl': 'snakemake_executor_plugin_slurm-%(version)s.tar.gz', + 'checksums': ['7069590060e914afcd608c75aee8ccf1128f662dda3e258a84f3c83302232763'], + }), + ('snakemake-executor-plugin-cluster-sync', '0.1.4', { + 'modulename': 'snakemake_executor_plugin_cluster_sync', + 'source_tmpl': 'snakemake_executor_plugin_cluster_sync-%(version)s.tar.gz', + 'checksums': ['6a6dcb2110d4c2ee74f9a48ea68e0fd7ddd2800672ebef00a01faa4affa835ad'], + }), + ('snakemake-executor-plugin-cluster-generic', '1.0.9', { + 'modulename': 'snakemake_executor_plugin_cluster_generic', + 'source_tmpl': 'snakemake_executor_plugin_cluster_generic-%(version)s.tar.gz', + 'checksums': ['ad0dc2d8bde7d4f336364bebe11a3b2209653c481ce8fbb0ae8bec81016a9a14'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'tools' From b811390d672eb702ad4da32961c1a1c9abc1e6f0 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Thu, 9 Jan 2025 18:48:48 +0100 Subject: [PATCH 339/414] Update easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb Co-authored-by: Alexander Grund --- .../easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb index 9e09a6ceb82..f9e497ff4fb 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -95,10 +95,6 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b'], }), - ('Jinja2', '3.1.4', { - 'sources': ['jinja2-%(version)s.tar.gz'], - 'checksums': ['4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369'], - }), ('immutables', '0.21', { 'checksums': ['b55ffaf0449790242feb4c56ab799ea7af92801a0a43f9e2f4f8af2ab24dfc4a'], }), From 2d924d2f97e5ad6144b5eaf40f525d76d5ba6178 Mon Sep 17 00:00:00 2001 From: andped Date: Thu, 9 Jan 2025 18:59:18 +0100 Subject: [PATCH 340/414] Removing redundant Cython from dependencies to builddependencies --- .../easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb index f9e497ff4fb..bbe5c31b3c0 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2024a'} builddependencies = [ ('poetry', '1.8.3'), + ('Cython', '3.0.10'), ] dependencies = [ ('Python', '3.12.3'), @@ -20,7 +21,6 @@ dependencies = [ ('PyYAML', '6.0.2'), ('wrapt', '1.15.0'), ('PuLP', '2.8.0'), - ('Cython', '3.0.10', '', {'name': 'GCCcore', 'version': '13.3.0'}), ] sanity_pip_check = True From 71ef70e871643ae282b33d1bea10e33206f8550d Mon Sep 17 00:00:00 2001 From: andped Date: Thu, 9 Jan 2025 19:44:51 +0100 Subject: [PATCH 341/414] Upgrading dependency IPython to v8.28.0 --- .../easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb index bbe5c31b3c0..b8c95d78033 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python-bundle-PyPI', '2024.06'), ('SciPy-bundle', '2024.05'), ('GitPython', '3.1.43'), - ('IPython', '8.14.0'), + ('IPython', '8.28.0'), ('PyYAML', '6.0.2'), ('wrapt', '1.15.0'), ('PuLP', '2.8.0'), From adb3420fe2e1b92d5dbc34fb0490f7548b12d8e7 Mon Sep 17 00:00:00 2001 From: andped Date: Thu, 9 Jan 2025 21:04:10 +0100 Subject: [PATCH 342/414] Upgrading dependency wrapt to v1.16.0 --- .../easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb index b8c95d78033..ee1af057ebf 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -19,7 +19,7 @@ dependencies = [ ('GitPython', '3.1.43'), ('IPython', '8.28.0'), ('PyYAML', '6.0.2'), - ('wrapt', '1.15.0'), + ('wrapt', '1.16.0'), ('PuLP', '2.8.0'), ] From aec7e7ef845fabc3e4454092c01d6c6dd06b19bb Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 09:17:00 +0100 Subject: [PATCH 343/414] Adding new easyconfig PuLP-2.8.0-foss-2024a.eb --- .../p/PuLP/PuLP-2.8.0-foss-2024a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2024a.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2024a.eb new file mode 100644 index 00000000000..8fa2ac3a40d --- /dev/null +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2024a.eb @@ -0,0 +1,35 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# Updated: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'PuLP' +version = '2.8.0' + +homepage = 'https://github.com/coin-or/pulp' +description = """ +PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and +call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to +solve linear problems. +""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4903bf96110bbab8ed2c68533f90565ebb76aa367d9e4df38e51bf727927c125'] + +dependencies = [ + ('Python', '3.12.3'), + ('GLPK', '5.0'), + ('Cbc', '2.10.12'), + # Gurobi requires a seperate license + # ('Gurobi', '9.5.0'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From dda7ff95d77d6ac17f16ed9f0ad235dcb09e0bc9 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 11:26:51 +0100 Subject: [PATCH 344/414] Adding new easyconfig Cbc-2.10.12-foss-2024a.eb --- .../c/Cbc/Cbc-2.10.12-foss-2024a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb new file mode 100644 index 00000000000..f205cbb1a3a --- /dev/null +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Cbc' +version = '2.10.12' + +homepage = 'https://github.com/coin-or/Cbc' +description = """Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming +solver written in C++. It can be used as a callable library or using a +stand-alone executable.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases'] +sources = ['%(version)s.tar.gz'] +checksums = ['9ed71e4b61668462fc3794c102e26b4bb01a047efbbbcbd69ae7bde1f04f46a8'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Doxygen', '1.11.0'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.6.1', '-metis'), + ('CoinUtils', '2.11.10'), + ('Osi', '0.108.9'), + ('Clp', '1.17.9'), + ('Cgl', '0.60.8'), + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + +# Use BLAS/LAPACK from toolchain +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" --with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" --without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data --with-clp-lib="-lOsiClp -lClpSolver -lClp" --with-clp-datadir=$EBROOTCLP/share/coin/Data --with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data --with-cgl-lib="-lCgl" --with-cgl-datadir=$EBROOTCGL/share/coin/Data ' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'lib/libCbc.so', 'lib/libCbcSolver.so', 'lib/libOsiCbc.so'], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = 'math' From 0fbc9cb62f3a1081d861a12053f3aac49ea7c06d Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 11:41:48 +0100 Subject: [PATCH 345/414] Adding new easyconfig SCOTCH-7.0.6-gompi-2024a.eb --- .../s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb new file mode 100644 index 00000000000..57b94076913 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb @@ -0,0 +1,25 @@ +name = 'SCOTCH' +version = '7.0.6' + +homepage = 'https://www.labri.fr/perso/pelegrin/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': '2024a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/%(namelower)s/%(namelower)s/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['b44acd0d2f53de4b578fa3a88944cccc45c4d2961cd8cefa9b9a1d5431de8e2b'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] +dependencies = [ + ('zlib', '1.3.1'), +] + +threadedmpi = False + +moduleclass = 'math' From 247786930e47b38e4fbb942a326bc6ad43c9134b Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 13:43:22 +0100 Subject: [PATCH 346/414] Updating Cbc-2.10.12-foss-2024a.eb --- easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb index f205cbb1a3a..8433f8b8bfb 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb @@ -22,7 +22,7 @@ builddependencies = [ ] dependencies = [ ('METIS', '5.1.0'), - ('MUMPS', '5.6.1', '-metis'), + ('MUMPS', '5.7.2', '-metis'), ('CoinUtils', '2.11.10'), ('Osi', '0.108.9'), ('Clp', '1.17.9'), From 4fd5997ab3361dd558d28f1fdf9338a595c80db5 Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Fri, 10 Jan 2025 13:44:05 +0100 Subject: [PATCH 347/414] Update easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb Co-authored-by: Sam Moors --- .../easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb index 68489093554..dc2e127e693 100644 --- a/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb @@ -26,7 +26,7 @@ configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.so" -DX11_X11_INCLUDE_PATH= sanity_check_paths = { - 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.so', 'lib64/libglut.so')], + 'files': ['lib/libglut.a', 'lib/libglut.%s' % SHLIB_EXT], 'dirs': ['include/GL'], } From fa3348c12a923e170c9e41c48cf6bc84b3c6bd18 Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Fri, 10 Jan 2025 13:44:22 +0100 Subject: [PATCH 348/414] Update easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb Co-authored-by: Sam Moors --- .../f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb index dc2e127e693..fd7092a2e2e 100644 --- a/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.6.0-GCCcore-13.3.0.eb @@ -22,7 +22,15 @@ dependencies = [ ('libGLU', '9.0.3'), ] -configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.so" -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" -DX11_Xext_LIB="$EBROOTX11/lib/libXext.so" -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.so" -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.so" -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts = ' '.join([ + '-DX11_X11_LIB="$EBROOTX11/lib/libX11.so"', + '-DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11"', + '-DX11_Xext_LIB="$EBROOTX11/lib/libXext.so"', + '-DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.so"', + '-DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/"', + '-DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.so"', + '-DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/"', +]) sanity_check_paths = { From e8b3603c7d83954b0f9f0839837cb8f23fa69533 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 13:49:41 +0100 Subject: [PATCH 349/414] Updating MUMPS-5.7.2-foss-2024a-metis.eb --- .../m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb new file mode 100644 index 00000000000..11d0f00df20 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb @@ -0,0 +1,27 @@ +name = 'MUMPS' +version = '5.7.2' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps-solver.org/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['1362d377ce7422fc886c55212b4a4d2c381918b5ca4478f682a22d0627a8fbf8'] + +dependencies = [ + ('SCOTCH', '7.0.6'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' From 2721934aef163035e6bf5f39247fe9f90cbee299 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Fri, 10 Jan 2025 17:32:28 +0100 Subject: [PATCH 350/414] Update easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb Co-authored-by: ocaisa --- easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb index 8433f8b8bfb..fa5a192bb78 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb @@ -32,7 +32,14 @@ dependencies = [ ] # Use BLAS/LAPACK from toolchain -configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" --with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" --without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data --with-clp-lib="-lOsiClp -lClpSolver -lClp" --with-clp-datadir=$EBROOTCLP/share/coin/Data --with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data --with-cgl-lib="-lCgl" --with-cgl-datadir=$EBROOTCGL/share/coin/Data ' +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" ' +configopts += ' --with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +configopts += ' --without-glpk --with-coinutils-lib="-lCoinUtils" ' +configopts += ' --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +configopts += ' --with-clp-lib="-lOsiClp -lClpSolver -lClp" --with-clp-datadir=$EBROOTCLP/share/coin/Data ' +configopts += ' --with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += ' --with-osi-datadir=$EBROOTOSI/share/coin/Data --with-cgl-lib="-lCgl" ' +configopts += ' --with-cgl-datadir=$EBROOTCGL/share/coin/Data ' sanity_check_paths = { From ecc83757119afba919ff1d94ac4b0af20fe55a88 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 17:57:20 +0100 Subject: [PATCH 351/414] Adding new easyconfig CoinUtils-2.11.12-GCC-13.3.0.eb --- .../CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb new file mode 100644 index 00000000000..1ba1a8733c8 --- /dev/null +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CoinUtils' +version = '2.11.12' + +homepage = 'https://github.com/coin-or/CoinUtils' +description = """CoinUtils (Coin-OR Utilities) is an open-source collection of classes and +functions that are generally useful to more than one COIN-OR project.""" + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['eef1785d78639b228ae2de26b334129fe6a7d399c4ac6f8fc5bb9054ba00de64'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Doxygen', '1.11.0'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + + +sanity_check_paths = { + 'files': ['lib/libCoinUtils.so'], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = 'math' \ No newline at end of file From 05cefe1019ef5c99b3ee85dad580919f5c07fdad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jan 2025 17:58:43 +0100 Subject: [PATCH 352/414] adding easyconfigs: elfx86exts-0.6.2-GCC-12.3.0.eb --- .../elfx86exts/elfx86exts-0.6.2-GCC-12.3.0.eb | 175 ++++++++++++++++++ 1 file changed, 175 insertions(+) create mode 100644 easybuild/easyconfigs/e/elfx86exts/elfx86exts-0.6.2-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/e/elfx86exts/elfx86exts-0.6.2-GCC-12.3.0.eb b/easybuild/easyconfigs/e/elfx86exts/elfx86exts-0.6.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..802fa23fb73 --- /dev/null +++ b/easybuild/easyconfigs/e/elfx86exts/elfx86exts-0.6.2-GCC-12.3.0.eb @@ -0,0 +1,175 @@ +easyblock = 'Cargo' + +name = 'elfx86exts' +version = '0.6.2' + +homepage = 'https://github.com/pkgw/elfx86exts' +description = "Decode binaries and print out which instruction set extensions they use." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/pkgw/elfx86exts/archive/'] +sources = [{'download_filename': '%(name)s@%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = [ + {'elfx86exts-0.6.2.tar.gz': '55e2ee8c6481e46749b622910597a01e86207250d57e4430b7ce31a22b982e1a'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'anstream-0.6.4.tar.gz': '2ab91ebe16eb252986481c5b62f6098f3b698a45e34b5b98200cf20dd2484a44'}, + {'anstyle-1.0.4.tar.gz': '7079075b41f533b8c61d2a4d073c4676e1f8b249ff94a393b0595db304e0dd87'}, + {'anstyle-parse-0.2.2.tar.gz': '317b9a89c1868f5ea6ff1d9539a69f45dffc21ce321ac1fd1160dfa48c8e2140'}, + {'anstyle-query-1.0.0.tar.gz': '5ca11d4be1bab0c8bc8734a9aa7bf4ee8316d462a08c6ac5052f888fef5b494b'}, + {'anstyle-wincon-3.0.1.tar.gz': 'f0699d10d2f4d628a98ee7b57b289abbc98ff3bad977cb3152709d4bf2330628'}, + {'assert_cmd-2.0.12.tar.gz': '88903cb14723e4d4003335bb7f8a14f27691649105346a0f0957466c096adfe6'}, + {'bstr-1.7.0.tar.gz': 'c79ad7fb2dd38f3dabd76b09c6a5a20c038fc0213ef1e9afd30eb777f120f019'}, + {'byteorder-1.5.0.tar.gz': '1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b'}, + {'capstone-0.11.0.tar.gz': '1097e608594dad3bad608295567f757742b883606fe150faf7a9740b849730d8'}, + {'capstone-sys-0.15.0.tar.gz': '2e7f651d5ec4c2a2e6c508f2c8032655003cd728ec85663e9796616990e25b5a'}, + {'cc-1.0.83.tar.gz': 'f1174fb0b6ec23863f8b971027804a42614e347eafb0a95bf0b12cdae21fc4d0'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'clap-4.4.6.tar.gz': 'd04704f56c2cde07f43e8e2c154b43f216dc5c92fc98ada720177362f953b956'}, + {'clap_builder-4.4.6.tar.gz': '0e231faeaca65ebd1ea3c737966bf858971cd38c3849107aa3ea7de90a804e45'}, + {'clap_derive-4.4.2.tar.gz': '0862016ff20d69b84ef8247369fabf5c008a7417002411897d40ee1f4532b873'}, + {'clap_lex-0.5.1.tar.gz': 'cd7cc57abe963c6d3b9d8be5b06ba7c8957a930305ca90304f24ef040aa6f961'}, + {'colorchoice-1.0.0.tar.gz': 'acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7'}, + {'crc32fast-1.3.2.tar.gz': 'b540bd8bc810d3885c6ea91e2018302f68baba2129ab3e88f32389ee9370880d'}, + {'difflib-0.4.0.tar.gz': '6184e33543162437515c2e2b48714794e37845ec9851711914eec9d308f6ebe8'}, + {'doc-comment-0.3.3.tar.gz': 'fea41bba32d969b513997752735605054bc0dfa92b4c56bf1189f2e174be7a10'}, + {'either-1.9.0.tar.gz': 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'10ac1c5050e43014d16b2f94d0d2ce79e65ffdd8b38d8048f9c8f6a8a6da62ac'}, + {'twox-hash-1.6.3.tar.gz': '97fee6b57c6a41524a810daee9286c02d7752c4253064d0b05472833a438f675'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'utf8parse-0.2.1.tar.gz': '711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a'}, + {'wait-timeout-0.2.0.tar.gz': '9f200f5b12eb75f8c1ed65abd4b2db8a6e1b138a20de009dacee265a2498f3f6'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.48.0.tar.gz': '677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, +] + +crates = [ + ('adler', '1.0.2'), + ('anstream', '0.6.4'), + ('anstyle', '1.0.4'), + ('anstyle-parse', '0.2.2'), + ('anstyle-query', '1.0.0'), + ('anstyle-wincon', '3.0.1'), + ('assert_cmd', '2.0.12'), + ('bstr', '1.7.0'), + ('byteorder', '1.5.0'), + ('capstone', '0.11.0'), + ('capstone-sys', '0.15.0'), + ('cc', '1.0.83'), + ('cfg-if', '1.0.0'), + ('clap', '4.4.6'), + ('clap_builder', '4.4.6'), + ('clap_derive', '4.4.2'), + ('clap_lex', '0.5.1'), + ('colorchoice', '1.0.0'), + ('crc32fast', '1.3.2'), + ('difflib', '0.4.0'), + ('doc-comment', '0.3.3'), + ('either', '1.9.0'), + ('escargot', '0.5.8'), + ('flate2', '1.0.27'), + ('heck', '0.4.1'), + ('itertools', '0.11.0'), + ('itoa', '1.0.9'), + ('libc', '0.2.149'), + ('log', '0.4.20'), + ('memchr', '2.6.4'), + ('memmap', '0.7.0'), + ('miniz_oxide', '0.7.1'), + ('object', '0.32.1'), + ('once_cell', '1.18.0'), + ('predicates', '3.0.4'), + ('predicates-core', '1.0.6'), + ('predicates-tree', '1.0.9'), + ('proc-macro2', '1.0.69'), + ('quote', '1.0.33'), + ('regex-automata', '0.4.1'), + ('ruzstd', '0.4.0'), + ('ryu', '1.0.15'), + ('serde', '1.0.188'), + ('serde_derive', '1.0.188'), + ('serde_json', '1.0.107'), + ('static_assertions', '1.1.0'), + ('strsim', '0.10.0'), + ('syn', '1.0.109'), + ('syn', '2.0.38'), + ('termtree', '0.4.1'), + ('thiserror-core', '1.0.38'), + ('thiserror-core-impl', '1.0.38'), + ('twox-hash', '1.6.3'), + ('unicode-ident', '1.0.12'), + ('utf8parse', '0.2.1'), + ('wait-timeout', '0.2.0'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.48.0'), + ('windows-targets', '0.48.5'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_msvc', '0.48.5'), +] + +builddependencies = [ + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'bio' From bc5541e2afb2e754c43b273fbb01fefd4d98f2c9 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 18:13:13 +0100 Subject: [PATCH 353/414] Adding new easyconfig Osi-0.108.11-GCC-13.3.0.eb --- .../o/Osi/Osi-0.108.11-GCC-13.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb new file mode 100644 index 00000000000..c1f3359f5ff --- /dev/null +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'Osi' +version = '0.108.11' + +homepage = 'https://github.com/coin-or/Osi' +description = """Osi (Open Solver Interface) provides an abstract base class to a generic linear +programming (LP) solver, along with derived classes for specific solvers. Many +applications may be able to use the Osi to insulate themselves from a specific +LP solver. That is, programs written to the OSI standard may be linked to any +solver with an OSI interface and should produce correct results. The OSI has +been significantly extended compared to its first incarnation. Currently, the +OSI supports linear programming solvers and has rudimentary support for integer +programming.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1063b6a057e80222e2ede3ef0c73c0c54697e0fee1d913e2bef530310c13a670'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Doxygen', '1.11.0'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('CoinUtils', '2.11.12'), + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + +# Disable GLPK because Osi requires GLPK<=4.48 +configopts = '--without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + + +sanity_check_paths = { + 'files': ['lib/libOsi.so', 'lib/libOsiCommonTests.so'], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = 'math' \ No newline at end of file From df145eb6e5517071d34e332c09cfbbb8719c53bb Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 18:37:11 +0100 Subject: [PATCH 354/414] Adding new easyconfig Clp-1.17.10-foss-2024a.eb --- .../c/Clp/Clp-1.17.10-foss-2024a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb new file mode 100644 index 00000000000..1b57ea3358e --- /dev/null +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'Clp' +version = '1.17.10' + +homepage = 'https://github.com/coin-or/Clp' +description = """Clp (Coin-or linear programming) is an open-source linear programming solver. +It is primarily meant to be used as a callable library, but a basic, +stand-alone executable version is also available.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['0d79ece896cdaa4a3855c37f1c28e6c26285f74d45f635046ca0b6d68a509885'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Doxygen', '1.11.0'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.7.2', '-metis'), + ('CoinUtils', '2.11.12'), + ('Osi', '0.108.11'), + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + +# Use BLAS/LAPACK from toolchain +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" --with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" --without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data --with-osi-lib="-lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data ' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'lib/libClp.so', 'lib/libClpSolver.so', 'lib/libOsiClp.so'], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = 'math' \ No newline at end of file From a7a56222be0674fff543bc46b3798d6faeffa560 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 19:17:44 +0100 Subject: [PATCH 355/414] Breaking up line for configopts in Clp-1.17.10-foss-2024a.eb --- easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb index 1b57ea3358e..9c00b4cba8e 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb @@ -30,7 +30,13 @@ dependencies = [ ] # Use BLAS/LAPACK from toolchain -configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" --with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" --without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data --with-osi-lib="-lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data ' +configopts = '--with-blas="$LIBBLAS" ' +configopts += '--with-lapack="$LIBLAPACK" ' +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' +configopts += '--without-glpk --with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +configopts += '--with-osi-lib="-lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data ' sanity_check_paths = { From 749530f69d184b2aba236eef98cd633b5508f331 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 10 Jan 2025 20:08:54 +0100 Subject: [PATCH 356/414] Update PyAV-11.0.0-GCCcore-12.3.0.eb - update Cython version --- easybuild/easyconfigs/p/PyAV/PyAV-11.0.0-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyAV/PyAV-11.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyAV/PyAV-11.0.0-GCCcore-12.3.0.eb index 05acd2727d2..bbc351e4c52 100644 --- a/easybuild/easyconfigs/p/PyAV/PyAV-11.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyAV/PyAV-11.0.0-GCCcore-12.3.0.eb @@ -15,7 +15,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), - ('Cython', '3.0.7'), + ('Cython', '3.0.8'), ('FFmpeg', '6.0'), ] From 5a3effccae249c25bc55ee990eb1d19da1e9d265 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 20:48:27 +0100 Subject: [PATCH 357/414] Updating some dependencies in Cbc-2.10.12-foss-2024a.eb --- easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb index fa5a192bb78..85661243b14 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb @@ -23,9 +23,9 @@ builddependencies = [ dependencies = [ ('METIS', '5.1.0'), ('MUMPS', '5.7.2', '-metis'), - ('CoinUtils', '2.11.10'), - ('Osi', '0.108.9'), - ('Clp', '1.17.9'), + ('CoinUtils', '2.11.12'), + ('Osi', '0.108.11'), + ('Clp', '1.17.10'), ('Cgl', '0.60.8'), ('bzip2', '1.0.8'), ('zlib', '1.3.1'), From 0ccb63780a3a2f562387247ecb375d8ae57ecd21 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 21:45:17 +0100 Subject: [PATCH 358/414] Adding easyconfig for Cgl-0.60.8-foss-2024a.eb --- .../c/Cgl/Cgl-0.60.8-foss-2024a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb new file mode 100644 index 00000000000..fa9f1a86c37 --- /dev/null +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Cgl' +version = '0.60.8' + +homepage = 'https://github.com/coin-or/Cgl' +description = """The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that +can be used with other COIN-OR packages that make use of cuts, such as, among +others, the linear solver Clp or the mixed integer linear programming solvers +Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or +communicate with a solver. It does not directly call a solver.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1482ba38afb783d124df8d5392337f79fdd507716e9f1fb6b98fc090acd1ad96'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Doxygen', '1.11.0'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('CoinUtils', '2.11.12'), + ('Osi', '0.108.11'), + ('Clp', '1.17.10'), +] + +# Use CoinUtils from EB +configopts = '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + + +sanity_check_paths = { + 'files': ['lib/libCgl.so'], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = 'math' From d3bf2e76bb62e9a2c60b9ebfaa3dd96327038d68 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 23:01:25 +0100 Subject: [PATCH 359/414] Reducing line length in Clp-1.17.10-foss-2024a.eb and Osi-0.108.11-GCC-13.3.0.eb --- easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb | 3 ++- easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb index 9c00b4cba8e..7631106f719 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb @@ -33,7 +33,8 @@ dependencies = [ configopts = '--with-blas="$LIBBLAS" ' configopts += '--with-lapack="$LIBLAPACK" ' configopts += '--with-metis-lib="-lmetis" ' -configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord ' +configopts += '-lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' configopts += '--without-glpk --with-coinutils-lib="-lCoinUtils" ' configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' configopts += '--with-osi-lib="-lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data ' diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb index c1f3359f5ff..5158800b817 100644 --- a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb @@ -31,7 +31,8 @@ dependencies = [ ] # Disable GLPK because Osi requires GLPK<=4.48 -configopts = '--without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +configopts = '--without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' sanity_check_paths = { From aea95f1efb05fb0df911ccc2dcd1db52e2aac4b9 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 10 Jan 2025 23:09:04 +0100 Subject: [PATCH 360/414] Update CoinUtils-2.11.12-GCC-13.3.0.eb --- .../easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb index 1ba1a8733c8..44817e45d52 100644 --- a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb @@ -33,4 +33,4 @@ sanity_check_paths = { # other coin-or projects expect instead of modextrapaths = {'CPATH': 'include/coin'} -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' From 926af35e1befe891297da8a548736921d7233d05 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 10 Jan 2025 23:11:03 +0100 Subject: [PATCH 361/414] Update Clp-1.17.10-foss-2024a.eb --- easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb index 7631106f719..79e1bb66dc3 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb @@ -48,4 +48,4 @@ sanity_check_paths = { # other coin-or projects expect instead of modextrapaths = {'CPATH': 'include/coin'} -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' From 2b3e4b2b3fda303c96be7e6b7167c0b99fc62ea1 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 10 Jan 2025 23:12:13 +0100 Subject: [PATCH 362/414] Update Osi-0.108.11-GCC-13.3.0.eb --- easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb index 5158800b817..3c1bdfbc9f4 100644 --- a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb @@ -43,4 +43,4 @@ sanity_check_paths = { # other coin-or projects expect instead of modextrapaths = {'CPATH': 'include/coin'} -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' From 31478e5c9869de3add74d0a02dd5df01ea65b21e Mon Sep 17 00:00:00 2001 From: ocaisa Date: Sat, 11 Jan 2025 11:46:02 +0100 Subject: [PATCH 363/414] Update easybuild/easyconfigs/e/elfx86exts/elfx86exts-0.6.2-GCC-12.3.0.eb --- .../easyconfigs/e/elfx86exts/elfx86exts-0.6.2-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/elfx86exts/elfx86exts-0.6.2-GCC-12.3.0.eb b/easybuild/easyconfigs/e/elfx86exts/elfx86exts-0.6.2-GCC-12.3.0.eb index 802fa23fb73..5419dd89ce9 100644 --- a/easybuild/easyconfigs/e/elfx86exts/elfx86exts-0.6.2-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/e/elfx86exts/elfx86exts-0.6.2-GCC-12.3.0.eb @@ -172,4 +172,4 @@ sanity_check_paths = { sanity_check_commands = ["%(name)s --help"] -moduleclass = 'bio' +moduleclass = 'tools' From c0b48d745ae2df72b1c1806281fce9dc6ffa0c9c Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 13 Jan 2025 15:03:17 +0100 Subject: [PATCH 364/414] Some style updates --- .../c/Cbc/Cbc-2.10.12-foss-2024a.eb | 31 ++++++++++++------- .../c/Cgl/Cgl-0.60.8-foss-2024a.eb | 6 ++-- .../c/Clp/Clp-1.17.10-foss-2024a.eb | 22 +++++++++---- .../o/Osi/Osi-0.108.11-GCC-13.3.0.eb | 9 +++--- .../snakemake/snakemake-8.27.0-foss-2024a.eb | 6 ++-- 5 files changed, 48 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb index 85661243b14..3fe2a0752e1 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb @@ -32,19 +32,28 @@ dependencies = [ ] # Use BLAS/LAPACK from toolchain -configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" ' -configopts += ' --with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' -configopts += ' --without-glpk --with-coinutils-lib="-lCoinUtils" ' -configopts += ' --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' -configopts += ' --with-clp-lib="-lOsiClp -lClpSolver -lClp" --with-clp-datadir=$EBROOTCLP/share/coin/Data ' -configopts += ' --with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' -configopts += ' --with-osi-datadir=$EBROOTOSI/share/coin/Data --with-cgl-lib="-lCgl" ' -configopts += ' --with-cgl-datadir=$EBROOTCGL/share/coin/Data ' - +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +# Use METIS AND MUMPS from EB +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +# Disable GLPK, dependencies have to be built with it as well +configopts += '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' +# Use Cgl from EB +configopts += '--with-cgl-lib="-lCgl" ' +configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'lib/libCbc.so', 'lib/libCbcSolver.so', 'lib/libOsiCbc.so'], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], + 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } # other coin-or projects expect instead of diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb index fa9f1a86c37..27b950093ca 100644 --- a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb @@ -31,15 +31,17 @@ dependencies = [ # Use CoinUtils from EB configopts = '--with-coinutils-lib="-lCoinUtils" ' configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +# Use Clp from EB configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' sanity_check_paths = { - 'files': ['lib/libCgl.so'], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], + 'files': ['lib/libCgl.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } # other coin-or projects expect instead of diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb index 79e1bb66dc3..1ca1d91bfec 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb @@ -32,17 +32,27 @@ dependencies = [ # Use BLAS/LAPACK from toolchain configopts = '--with-blas="$LIBBLAS" ' configopts += '--with-lapack="$LIBLAPACK" ' + +# Use METIS AND MUMPS from EB +# --with-metis-lib is ignored configopts += '--with-metis-lib="-lmetis" ' -configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord ' -configopts += '-lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' -configopts += '--without-glpk --with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh ' +configopts += '-lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' + +# Disable GLPK because Clp requires headers from its sources +configopts += '--without-glpk ' + +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' -configopts += '--with-osi-lib="-lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data ' +# Use Osi from EB +configopts += '--with-osi-lib="-lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'lib/libClp.so', 'lib/libClpSolver.so', 'lib/libOsiClp.so'], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Clp', 'ClpSolver', 'OsiClp']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } # other coin-or projects expect instead of diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb index 3c1bdfbc9f4..9462fa85bc9 100644 --- a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb @@ -31,13 +31,14 @@ dependencies = [ ] # Disable GLPK because Osi requires GLPK<=4.48 -configopts = '--without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' +configopts = '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' - sanity_check_paths = { - 'files': ['lib/libOsi.so', 'lib/libOsiCommonTests.so'], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], + 'files': ['lib/libOsi.%s' % SHLIB_EXT, 'lib/libOsiCommonTests.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } # other coin-or projects expect instead of diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb index ee1af057ebf..2c6a8120453 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -140,10 +140,10 @@ exts_list = [ ] sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], + 'files': ['bin/snakemake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], } -sanity_check_commands = ['%(name)s --help'] +sanity_check_commands = ['snakemake --help'] moduleclass = 'tools' From f99725bbd910faff71ace487cd7f520022c04921 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 13 Jan 2025 15:12:32 +0100 Subject: [PATCH 365/414] Final tweaks --- .../easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb | 5 ++--- easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb | 1 + 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb index 44817e45d52..8d58c97eb49 100644 --- a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb @@ -24,10 +24,9 @@ dependencies = [ ('zlib', '1.3.1'), ] - sanity_check_paths = { - 'files': ['lib/libCoinUtils.so'], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], + 'files': ['lib/libCoinUtils.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } # other coin-or projects expect instead of diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb index 57b94076913..27002098227 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb @@ -16,6 +16,7 @@ builddependencies = [ ('Bison', '3.8.2'), ('flex', '2.6.4'), ] + dependencies = [ ('zlib', '1.3.1'), ] From 1c4407fa062b48fa8379d2b9e78f985385d1bac9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 13 Jan 2025 15:24:56 +0100 Subject: [PATCH 366/414] fix test case --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-24.1-intel-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-24.1-intel-2023a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-24.1-intel-2023a.eb index 5805e428637..18fa1333158 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-24.1-intel-2023a.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-24.1-intel-2023a.eb @@ -74,7 +74,7 @@ tests = [ [ r'^:ENE.*-4018.0', r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', - r'^:FGL002.*133.*total forces', + r'^:FGL002.*total forces', ]), ] From f859e9c16f8da54f6db21174667b348dbc438359 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Jan 2025 17:30:28 +0000 Subject: [PATCH 367/414] adding easyconfigs: trimesh-4.5.3-gfbf-2024a.eb --- .../t/trimesh/trimesh-4.5.3-gfbf-2024a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/trimesh/trimesh-4.5.3-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-4.5.3-gfbf-2024a.eb b/easybuild/easyconfigs/t/trimesh/trimesh-4.5.3-gfbf-2024a.eb new file mode 100644 index 00000000000..94d8d985bc1 --- /dev/null +++ b/easybuild/easyconfigs/t/trimesh/trimesh-4.5.3-gfbf-2024a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'trimesh' +version = '4.5.3' + +homepage = 'https://trimsh.org/' +description = """Trimesh is a Python (2.7- 3.3+) library for loading and using triangular meshes with an emphasis on +watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy +manipulation and analysis, in the style of the excellent Polygon object in the Shapely library.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b1af60399f64f4715d744c5195754068bfeb98981b92feb0c15d016c99379f87'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), # numpy required +] + +moduleclass = 'lib' From c34db039005fde3e3c4f719aaa4f4d1388351749 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jan 2025 21:15:28 +0100 Subject: [PATCH 368/414] add seqPattern, genomation, ChIPseeker, SimBu extensions to R-bundle-Bioconductor v3.19 --- .../R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb index f426b6ffbc5..31a8d34d40c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb @@ -1350,6 +1350,18 @@ exts_list = [ ('plyranges', '1.24.0', { 'checksums': ['a8505d774d0cf9c1488205343abd1817dd5d016082597bb173d002d496a10566'], }), + ('seqPattern', '1.36.0', { + 'checksums': ['069625ed7b2ccdaeba935378da8bb5546303fff586c700e99320a21f346c6047'], + }), + ('genomation', '1.36.0', { + 'checksums': ['440600e76f82572d52e1e3b3036bb1713aebe3ed4b4341f448f81c35a721dead'], + }), + ('ChIPseeker', '1.40.0', { + 'checksums': ['2e48e504702eb6bd6cc14c8e5f12e9836d7b1e4af4dc1be44644be7da6b43302'], + }), + ('SimBu', '1.6.0', { + 'checksums': ['eb9eb8e5308ac3125db47bfa5f9f40aa9a51b1d3dd129e1e6891282a47305ed5'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 6e5bf91b7691d3eb397156233b6ce214ded9e173 Mon Sep 17 00:00:00 2001 From: thoffman Date: Tue, 14 Jan 2025 10:39:07 +0100 Subject: [PATCH 369/414] adding easyconfigs: pybind11_abseil-202402.0-GCC-13.3.0.eb and patches: pybind11_abseil-202402.0_cmake.patch --- .../pybind11_abseil-202402.0-GCC-13.3.0.eb | 52 ++++++++++++++++ .../pybind11_abseil-202402.0_cmake.patch | 61 +++++++++++++++++++ 2 files changed, 113 insertions(+) create mode 100644 easybuild/easyconfigs/p/pybind11_abseil/pybind11_abseil-202402.0-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/pybind11_abseil/pybind11_abseil-202402.0_cmake.patch diff --git a/easybuild/easyconfigs/p/pybind11_abseil/pybind11_abseil-202402.0-GCC-13.3.0.eb b/easybuild/easyconfigs/p/pybind11_abseil/pybind11_abseil-202402.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..47994c32727 --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11_abseil/pybind11_abseil-202402.0-GCC-13.3.0.eb @@ -0,0 +1,52 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2025/01 +easyblock = 'CMakePythonPackage' + +name = 'pybind11_abseil' +version = '202402.0' + +homepage = 'https://github.com/pybind/pybind11_abseil' +description = """Pybind11 bindings for the Abseil C++ Common Libraries""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + # disable FetchContent for abseil-cpp and pybind11, use find_package for abseil-cpp and pybind11, + # install header, and create cmake package config: + 'pybind11_abseil-202402.0_cmake.patch' +] +checksums = [ + {'v202402.0.tar.gz': '1496b112e86416e2dcf288569a3e7b64f3537f0b18132224f492266e9ff76c44'}, + {'pybind11_abseil-202402.0_cmake.patch': '06ac281d0bad44a72479dcaa6be51a5062d1503b35c849e1c825926da0823f2f'}, +] + +github_account = 'pybind' + +builddependencies = [ + ('CMake', '3.29.3'), + ('pybind11', '2.12.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Abseil', '20240722.0'), +] + +_confopts = [ + '-DCMAKE_INSTALL_PYDIR="%(installdir)s/lib/python%(pyshortver)s/site-packages"', + '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python', + '-DFETCHCONTENT_FULLY_DISCONNECTED=ON', +] + +configopts = ' '.join(_confopts) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/cmake/pybind11_abseil', 'include/pybind11_abseil'], +} + +sanity_check_commands = [ + "python -c 'from pybind11_abseil import status'" +] +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pybind11_abseil/pybind11_abseil-202402.0_cmake.patch b/easybuild/easyconfigs/p/pybind11_abseil/pybind11_abseil-202402.0_cmake.patch new file mode 100644 index 00000000000..93de1921e9d --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11_abseil/pybind11_abseil-202402.0_cmake.patch @@ -0,0 +1,61 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2025/01 +# - disable FetchContent for abseil-cpp and pybind11 +# - use find_package for abseil-cpp and pybind11 +# - install header +# - create cmake package config +diff -ruN pybind11_abseil-202402.0/CMakeLists.txt pybind11_abseil-202402.0_cmake/CMakeLists.txt +--- pybind11_abseil-202402.0/CMakeLists.txt 2024-02-16 18:39:49.000000000 +0100 ++++ pybind11_abseil-202402.0_cmake/CMakeLists.txt 2025-01-14 09:47:44.015942965 +0100 +@@ -26,8 +26,13 @@ + pybind11 + URL https://github.com/pybind/pybind11/archive/refs/heads/master.tar.gz) + +-FetchContent_MakeAvailable(abseil-cpp pybind11) +- ++#FetchContent_MakeAvailable(abseil-cpp pybind11) ++find_package( ++ Python3 ++ COMPONENTS Interpreter Development ++ REQUIRED) ++find_package(absl CONFIG REQUIRED) ++find_package(pybind11 CONFIG REQUIRED) + set(TOP_LEVEL_DIR ${CMAKE_CURRENT_LIST_DIR}) + include_directories(${TOP_LEVEL_DIR} ${pybind11_INCLUDE_DIRS}) + +diff -ruN pybind11_abseil-202402.0/pybind11_abseil/CMakeLists.txt pybind11_abseil-202402.0_cmake/pybind11_abseil/CMakeLists.txt +--- pybind11_abseil-202402.0/pybind11_abseil/CMakeLists.txt 2024-02-16 18:39:49.000000000 +0100 ++++ pybind11_abseil-202402.0_cmake/pybind11_abseil/CMakeLists.txt 2025-01-14 10:22:00.018008505 +0100 +@@ -21,6 +21,26 @@ + absl::optional + absl::span) + ++install(TARGETS absl_casters ++ EXPORT absl_casters-targets ++ LIBRARY DESTINATION lib ++ ARCHIVE DESTINATION lib ++) ++set(Headers ++ absl_casters.h ++) ++install(FILES ${Headers} DESTINATION include/pybind11_abseil/) ++ ++install(EXPORT absl_casters-targets ++ NAMESPACE pybind11_abseil:: ++ DESTINATION lib/cmake/pybind11_abseil) ++include(CMakePackageConfigHelpers) ++configure_package_config_file( ++ "pybind11_abseilConfig.cmake.in" "${CMAKE_CURRENT_BINARY_DIR}/pybind11_abseilConfig.cmake" ++ INSTALL_DESTINATION "lib/cmake/pybind11_abseil" ++) ++install(FILES "${CMAKE_CURRENT_BINARY_DIR}/pybind11_abseilConfig.cmake" DESTINATION "lib/cmake/pybind11_abseil") ++ + # ok_status_singleton_lib ====================================================== + + add_library(ok_status_singleton_lib STATIC ok_status_singleton_lib.cc) +diff -ruN pybind11_abseil-202402.0/pybind11_abseil/pybind11_abseilConfig.cmake.in pybind11_abseil-202402.0_cmake/pybind11_abseil/pybind11_abseilConfig.cmake.in +--- pybind11_abseil-202402.0/pybind11_abseil/pybind11_abseilConfig.cmake.in 1970-01-01 01:00:00.000000000 +0100 ++++ pybind11_abseil-202402.0_cmake/pybind11_abseil/pybind11_abseilConfig.cmake.in 2025-01-14 09:54:09.337489273 +0100 +@@ -0,0 +1,3 @@ ++@PACKAGE_INIT@ ++ ++include("${CMAKE_CURRENT_LIST_DIR}/absl_casters-targets.cmake") From dba028f1f339579329e429fc0e49be1d71f24069 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 14 Jan 2025 10:51:28 +0100 Subject: [PATCH 370/414] adding easyconfigs: bayesian-optimization-2.0.3-foss-2024a.eb --- .../bayesian-optimization-2.0.3-foss-2024a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-2.0.3-foss-2024a.eb diff --git a/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-2.0.3-foss-2024a.eb b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-2.0.3-foss-2024a.eb new file mode 100644 index 00000000000..607c640ed1e --- /dev/null +++ b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-2.0.3-foss-2024a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'bayesian-optimization' +version = '2.0.3' + +homepage = 'https://bayesian-optimization.github.io/BayesianOptimization/index.html' +description = "Pure Python implementation of bayesian global optimization with gaussian processes." + +toolchain = {'name': 'foss', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('scikit-learn', '1.5.2'), + ('SciPy-bundle', '2024.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('colorama', '0.4.6', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6'], + }), + ('bayesian_optimization', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'modulename': 'bayes_opt', + 'checksums': ['73d08237c46a1787c17333aeaae3e41c5fab8e58a68d979645b70e72ba22b63d'], + }), +] + +sanity_check_commands = ["python -c 'from bayes_opt import BayesianOptimization'"] + +moduleclass = 'math' From f52b946e5a254bd9e579274df8236d2bbc5fe64a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jan 2025 16:16:58 +0100 Subject: [PATCH 371/414] add symlinks for emmax and emmax-kin commands in easyconfig for EMMAX 20120210 --- .../EMMAX-20120210-GCCcore-13.2.0-intel-binary.eb | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20120210-GCCcore-13.2.0-intel-binary.eb b/easybuild/easyconfigs/e/EMMAX/EMMAX-20120210-GCCcore-13.2.0-intel-binary.eb index 9d7150c71b2..854f3f04718 100644 --- a/easybuild/easyconfigs/e/EMMAX/EMMAX-20120210-GCCcore-13.2.0-intel-binary.eb +++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20120210-GCCcore-13.2.0-intel-binary.eb @@ -26,14 +26,19 @@ dependencies = [ extract_sources = True +postinstallcmds = [ + "cd %(installdir)s && ln -s emmax-intel64 emmax", + "cd %(installdir)s && ln -s emmax-kin-intel64 emmax-kin", +] + sanity_check_paths = { - 'files': ['emmax-intel64', 'emmax-kin-intel64'], + 'files': ['emmax', 'emmax-kin'], 'dirs': [], } sanity_check_commands = [ - "emmax-intel64 2>&1 | grep '^Usage: emmax'", - "emmax-kin-intel64 2>&1 | grep '^Usage: emmax_kin'", + "emmax 2>&1 | grep '^Usage: emmax'", + "emmax-kin 2>&1 | grep '^Usage: emmax_kin'", ] moduleclass = 'bio' From eaa080948f1eebd028319e6e06d79ab72ad4dd6a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jan 2025 16:51:34 +0100 Subject: [PATCH 372/414] minor cleanup in sanity_check_paths for libyuv --- .../easyconfigs/l/libyuv/libyuv-20241125-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libyuv/libyuv-20241125-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libyuv/libyuv-20241125-GCCcore-13.2.0.eb index 6d388b8ffc2..f8c2453b70b 100644 --- a/easybuild/easyconfigs/l/libyuv/libyuv-20241125-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libyuv/libyuv-20241125-GCCcore-13.2.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['bin/yuvconvert', f'lib/{name}.so', f'lib/{name}.a', f'include/{name}.h'], + 'files': ['bin/yuvconvert', 'include/libyuv.h', 'lib/libyuv.a', 'lib/libyuv.%s' % SHLIB_EXT], 'dirs': [], } From f852a86cfd1a59a36ccafd1258e9dd9a034747e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jan 2025 21:05:56 +0100 Subject: [PATCH 373/414] remove unused local_whl_tmpl from easyconfig for ONNX-Runtime 1.19.2 --- .../ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.6.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.6.0.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.6.0.eb index 68436eedc6c..530ec58cd71 100644 --- a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.6.0.eb +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.6.0.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True -local_whl_tmpl = 'onnxruntime_gpu-%%(version)s-cp311-cp311-manylinux_2_27_%s.manylinux_2_28_%s.whl' - exts_list = [ ('humanfriendly', '10.0', { 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], From e29210626f076e3a207f1abf3759ea124e28f8b2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 15 Jan 2025 08:03:14 +0100 Subject: [PATCH 374/414] boost source url has changed to archives.boost.io --- easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb | 2 +- easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb | 2 +- easybuild/easyconfigs/b/Boost/Boost-1.83.0-GCC-13.2.0.eb | 2 +- easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb index 1ffc4b4cfac..78733bcc457 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb @@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries toolchain = {'name': 'GCC', 'version': '12.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +source_urls = ['https://archives.boost.io/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] checksums = ['205666dea9f6a7cfed87c7a6dfbeb52a2c1b9de55712c9c1a87735d7181452b6'] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb index b47082e09df..29770bd1c53 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb @@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries toolchain = {'name': 'GCC', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +source_urls = ['https://archives.boost.io/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] checksums = ['66a469b6e608a51f8347236f4912e27dc5c60c60d7d53ae9bfe4683316c6f04c'] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.83.0-GCC-13.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.83.0-GCC-13.2.0.eb index feafb10645f..3dc2c888a5c 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.83.0-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.83.0-GCC-13.2.0.eb @@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries toolchain = {'name': 'GCC', 'version': '13.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +source_urls = ['https://archives.boost.io/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628'] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb index d1a8434d8e4..a1507a88361 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb @@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries toolchain = {'name': 'GCC', 'version': '13.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +source_urls = ['https://archives.boost.io/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] patches = ['Boost-1.85.0_fix-ppc-charconv.patch'] checksums = [ From b2e8026e57a2dff7744c2ba0318e9bac0cc67fbc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 15 Jan 2025 14:02:23 +0100 Subject: [PATCH 375/414] adding easyconfigs: pmx-20241209-foss-2023b.eb --- .../p/pmx/pmx-20241209-foss-2023b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/pmx/pmx-20241209-foss-2023b.eb diff --git a/easybuild/easyconfigs/p/pmx/pmx-20241209-foss-2023b.eb b/easybuild/easyconfigs/p/pmx/pmx-20241209-foss-2023b.eb new file mode 100644 index 00000000000..2d7d95cf933 --- /dev/null +++ b/easybuild/easyconfigs/p/pmx/pmx-20241209-foss-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'pmx' +version = '20241209' +local_commit = '09b57c6' # develop branch + +homepage = 'https://degrootlab.github.io/pmx/' +description = "Toolkit for free-energy calculation setup/analysis and biomolecular structure handling." + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('matplotlib', '3.8.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/deGrootLab/pmx/archive/'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['b76d64a54fd05cb859d5bb4799f0929c9af3f789a2277d699a08962fbe6c4075'], + }), +] + +sanity_check_commands = [ + "python -c 'from pmx.gmx import set_gmxlib; set_gmxlib()'", + 'pmx --help', + 'echo "no" | pmx gmxlib', +] + +moduleclass = 'bio' From e423444b4355f16fff5659f389652a62e4d60722 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 15 Jan 2025 17:13:37 +0100 Subject: [PATCH 376/414] adding easyconfigs: Pillow-SIMD-10.4.0-GCCcore-13.2.0.eb, tensorboard-2.18.0-gfbf-2023b.eb, torchvision-0.17.0-foss-2023b.eb and patches: torchvision-0.17.0_fix-build-with-FFmpeg6.patch, torchvision-0.17.0_quantized_tol.patch --- .../Pillow-SIMD-10.4.0-GCCcore-13.2.0.eb | 48 +++++++++++++++ .../tensorboard-2.18.0-gfbf-2023b.eb | 59 +++++++++++++++++++ .../torchvision-0.17.0-foss-2023b.eb | 36 +++++++++++ ...vision-0.17.0_fix-build-with-FFmpeg6.patch | 36 +++++++++++ .../torchvision-0.17.0_quantized_tol.patch | 15 +++++ 5 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/t/tensorboard/tensorboard-2.18.0-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.17.0-foss-2023b.eb create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.17.0_fix-build-with-FFmpeg6.patch create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.17.0_quantized_tol.patch diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0abd176f2f2 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '10.4.0' + +homepage = 'https://github.com/uploadcare/pillow-simd' +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': '13.2.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8c7c3c0fc2952ff11b9a8c60365e098ee5334427dd5688c3584e77c25a7e1b3f'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('zlib', '1.2.13'), + ('LibTIFF', '4.6.0'), + ('freetype', '2.13.2'), + ('libwebp', '1.3.2'), + ('OpenJPEG', '2.5.0'), + ('LittleCMS', '2.15'), +] + +use_pip = True +download_dep_fail = True + +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.18.0-gfbf-2023b.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.18.0-gfbf-2023b.eb new file mode 100644 index 00000000000..d4e1338f463 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.18.0-gfbf-2023b.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'tensorboard' +version = '2.18.0' + +homepage = 'https://github.com/tensorflow/tensorboard' +description = """TensorBoard is a suite of web applications for inspecting and +understanding your TensorFlow runs and graphs.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('poetry', '1.6.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('protobuf-python', '4.25.3'), + ('grpcio', '1.67.1'), + ('Markdown', '3.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('cachetools', '5.5.0', { + 'checksums': ['2cc24fb4cbe39633fb7badd9db9ca6295d766d9c2995f245725a46715d050f2a'], + }), + ('pyasn1_modules', '0.4.1', { + 'checksums': ['c28e2dbf9c06ad61c71a075c7e0f9fd0f1b0bb2d2ad4377f240d33ac2ab60a7c'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('google_auth', '2.35.0', { + 'modulename': 'google.auth', + 'checksums': ['f4c64ed4e01e8e8b646ef34c018f8bf3338df0c8e37d8b3bba40e7f574a3278a'], + }), + ('tensorboard_data_server', '0.7.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], + }), + ('Werkzeug', '3.1.0', { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['6f2a0d38f25ba5a75c36c45b4ae350c7a23b57e3b974e9eb2d6851f2c648c00d'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['107ca4821745f73e2aefa02c50ff70a9b694f39f790b11e6f682f7d326745eab'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.17.0-foss-2023b.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.17.0-foss-2023b.eb new file mode 100644 index 00000000000..7579a357707 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.17.0-foss-2023b.eb @@ -0,0 +1,36 @@ +name = 'torchvision' +version = '0.17.0' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fix-build-with-FFmpeg6.patch', + '%(name)s-%(version)s_quantized_tol.patch' +] +checksums = [ + {'v0.17.0.tar.gz': '55e395d5c7d9bf7658c82ac633cac2224aa168e1bfe8bb5b2b2a296c792a3500'}, + {'torchvision-0.17.0_fix-build-with-FFmpeg6.patch': + '64404865a489c0348f79684419831ebd71ece7c7326a80184785578a368047b5'}, + {'torchvision-0.17.0_quantized_tol.patch': '991b959f7d5e0fd418a163fa3ad828a2b60a64d0ce894cf579847138b13b62af'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('FFmpeg', '6.0'), + ('Pillow-SIMD', '10.4.0'), + ('PyTorch', '2.1.2'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.17.0_fix-build-with-FFmpeg6.patch b/easybuild/easyconfigs/t/torchvision/torchvision-0.17.0_fix-build-with-FFmpeg6.patch new file mode 100644 index 00000000000..03fe3502ba1 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.17.0_fix-build-with-FFmpeg6.patch @@ -0,0 +1,36 @@ +From 86620bd84b872b76db0acafec167949dca03a29e Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Zolt=C3=A1n=20B=C3=B6sz=C3=B6rm=C3=A9nyi?= + +Date: Tue, 7 Nov 2023 10:43:11 +0100 +Subject: [PATCH] Fix build with ffmpeg 6.0 +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +Signed-off-by: Zoltán Böszörményi +--- + torchvision/csrc/io/decoder/stream.cpp | 11 ++--------- + 1 file changed, 2 insertions(+), 9 deletions(-) + +diff --git a/torchvision/csrc/io/decoder/stream.cpp b/torchvision/csrc/io/decoder/stream.cpp +index 0d625ef211c..8c914050587 100644 +--- a/torchvision/csrc/io/decoder/stream.cpp ++++ b/torchvision/csrc/io/decoder/stream.cpp +@@ -63,15 +63,8 @@ int Stream::openCodec(std::vector* metadata, int num_threads) { + codecCtx_->thread_count = num_threads; + } else { + // otherwise set sensible defaults +- // with the special case for the different MPEG4 codecs +- // that don't have threading context functions +- if (codecCtx_->codec->capabilities & AV_CODEC_CAP_INTRA_ONLY) { +- codecCtx_->thread_type = FF_THREAD_FRAME; +- codecCtx_->thread_count = 2; +- } else { +- codecCtx_->thread_count = 8; +- codecCtx_->thread_type = FF_THREAD_SLICE; +- } ++ codecCtx_->thread_count = 8; ++ codecCtx_->thread_type = FF_THREAD_SLICE; + } + + int ret; \ No newline at end of file diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.17.0_quantized_tol.patch b/easybuild/easyconfigs/t/torchvision/torchvision-0.17.0_quantized_tol.patch new file mode 100644 index 00000000000..040e82cd81f --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.17.0_quantized_tol.patch @@ -0,0 +1,15 @@ +Increase the toleances for quantized model that failed tests +The absolute error just barely exceed the default 0.02, but given the small numbers +the relative tolerance is high, thus the relative high tolerance of 0.5 +author: micketeer@gmail.com +--- test/test_models.py.orig 2024-03-21 10:54:03.467723691 +0000 ++++ test/test_models.py 2024-03-21 10:53:49.857749169 +0000 +@@ -987,7 +987,7 @@ + out = model(x) + + if model_name not in quantized_flaky_models: +- _assert_expected(out.cpu(), model_name + "_quantized", prec=2e-2) ++ _assert_expected(out.cpu(), model_name + "_quantized", prec=5e-1) + assert out.shape[-1] == 5 + _check_jit_scriptable(model, (x,), unwrapper=script_model_unwrapper.get(model_name, None), eager_out=out) + _check_fx_compatible(model, x, eager_out=out) \ No newline at end of file From 7ccf5fd2445573175f1e9a9f856ce1dffe41045b Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Wed, 15 Jan 2025 17:47:02 +0100 Subject: [PATCH 377/414] Add FreeImage-3.18-fix-makefile-riscv.patch --- .../FreeImage-3.18-fix-makefile-riscv.patch | 14 ++++++++++++++ .../f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb | 5 ++++- 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18-fix-makefile-riscv.patch diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18-fix-makefile-riscv.patch b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18-fix-makefile-riscv.patch new file mode 100644 index 00000000000..09e020c2416 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18-fix-makefile-riscv.patch @@ -0,0 +1,14 @@ +--- Makefile.gnu.orig 2025-01-15 17:26:47.616603010 +0100 ++++ Makefile.gnu 2025-01-15 17:28:09.158140964 +0100 +@@ -33,6 +33,11 @@ + CXXFLAGS += -fPIC + endif + ++ifeq ($(shell sh -c 'uname -m 2>/dev/null || echo not'),riscv64) ++ CFLAGS += -fPIC ++ CXXFLAGS += -fPIC ++endif ++ + TARGET = freeimage + STATICLIB = lib$(TARGET).a + SHAREDLIB = lib$(TARGET)-$(VER_MAJOR).$(VER_MINOR).so diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb index 0b82c899e93..75b11cbee2d 100644 --- a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb @@ -13,10 +13,13 @@ toolchainopts = {'cstd': 'c++14'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s3180.zip'] -patches = ['%(name)s-%(version)s-fix-makefile.patch'] +patches = ['%(name)s-%(version)s-fix-makefile.patch', + '%(name)s-%(version)s-fix-makefile-riscv.patch', +] checksums = [ 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # %(name)s-%(version)s-fix-makefile.patch + '1abd7f85c5bb8e1de456592459a017396115e2f74bb17bc67a548ee59935c09e', # %(name)s-%(version)s-fix-makefile-riscv.patch ] builddependencies = [('binutils', '2.40')] From bf20a362e2f2833fd265dcf6053f4b28a96e8ef7 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Wed, 15 Jan 2025 17:55:08 +0100 Subject: [PATCH 378/414] Fixed patch name --- ...file-riscv.patch => FreeImage-3.18.0-fix-makefile-riscv.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/f/FreeImage/{FreeImage-3.18-fix-makefile-riscv.patch => FreeImage-3.18.0-fix-makefile-riscv.patch} (100%) diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18-fix-makefile-riscv.patch b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch similarity index 100% rename from easybuild/easyconfigs/f/FreeImage/FreeImage-3.18-fix-makefile-riscv.patch rename to easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch From f94410f4319c00c3ec532c47749445d400a60f8b Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Thu, 16 Jan 2025 13:06:29 +0100 Subject: [PATCH 379/414] Fix patched Makefile and fix formatting issues in easyconfig --- .../f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb | 6 ++++-- .../f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch | 6 +++--- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb index 75b11cbee2d..d6925de5002 100644 --- a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb @@ -13,13 +13,15 @@ toolchainopts = {'cstd': 'c++14'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s3180.zip'] -patches = ['%(name)s-%(version)s-fix-makefile.patch', +patches = [ + '%(name)s-%(version)s-fix-makefile.patch', '%(name)s-%(version)s-fix-makefile-riscv.patch', ] + checksums = [ 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # %(name)s-%(version)s-fix-makefile.patch - '1abd7f85c5bb8e1de456592459a017396115e2f74bb17bc67a548ee59935c09e', # %(name)s-%(version)s-fix-makefile-riscv.patch + '1abd7f85c5bb8e1de456592459a017396115e2f74bb17bc67a548ee59935c09e', # %(name)s-%(version)s-fix-makefile-riscv.patch ] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch index 09e020c2416..2f39e695b30 100644 --- a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch @@ -1,5 +1,5 @@ ---- Makefile.gnu.orig 2025-01-15 17:26:47.616603010 +0100 -+++ Makefile.gnu 2025-01-15 17:28:09.158140964 +0100 +--- Makefile.fip.orig 2025-01-16 12:58:29.624119756 +0100 ++++ Makefile.fip 2025-01-16 13:00:01.016862229 +0100 @@ -33,6 +33,11 @@ CXXFLAGS += -fPIC endif @@ -9,6 +9,6 @@ + CXXFLAGS += -fPIC +endif + - TARGET = freeimage + TARGET = freeimageplus STATICLIB = lib$(TARGET).a SHAREDLIB = lib$(TARGET)-$(VER_MAJOR).$(VER_MINOR).so From 916436f169ceb01a98d8e0032bf9a8e89f63bcc2 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Thu, 16 Jan 2025 13:08:50 +0100 Subject: [PATCH 380/414] Fix patch checksum --- .../easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb index d6925de5002..0e2cd920f55 100644 --- a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # %(name)s-%(version)s-fix-makefile.patch - '1abd7f85c5bb8e1de456592459a017396115e2f74bb17bc67a548ee59935c09e', # %(name)s-%(version)s-fix-makefile-riscv.patch + '9f6e468b178a814029213b5ae651ddd01edc3a4781a290eb21e05638a3854509', # %(name)s-%(version)s-fix-makefile-riscv.patch ] builddependencies = [('binutils', '2.40')] From 28e256b5739b3e16c6e8ae2b25314641c50c7e18 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Thu, 16 Jan 2025 13:19:40 +0100 Subject: [PATCH 381/414] Add new needed patch for RISC-V --- .../f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb | 2 ++ .../FreeImage-3.18.0-fix-makefile-gnu.patch | 14 ++++++++++++++ 2 files changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-gnu.patch diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb index 0e2cd920f55..5fd3393c89e 100644 --- a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb @@ -16,12 +16,14 @@ sources = ['%(name)s3180.zip'] patches = [ '%(name)s-%(version)s-fix-makefile.patch', '%(name)s-%(version)s-fix-makefile-riscv.patch', + '%(name)s-%(version)s-fix-makefile-gnu.patch', ] checksums = [ 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # %(name)s-%(version)s-fix-makefile.patch '9f6e468b178a814029213b5ae651ddd01edc3a4781a290eb21e05638a3854509', # %(name)s-%(version)s-fix-makefile-riscv.patch + '1abd7f85c5bb8e1de456592459a017396115e2f74bb17bc67a548ee59935c09e', # %(name)s-%(version)s-fix-makefile-gnu.patch ] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-gnu.patch b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-gnu.patch new file mode 100644 index 00000000000..09e020c2416 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-gnu.patch @@ -0,0 +1,14 @@ +--- Makefile.gnu.orig 2025-01-15 17:26:47.616603010 +0100 ++++ Makefile.gnu 2025-01-15 17:28:09.158140964 +0100 +@@ -33,6 +33,11 @@ + CXXFLAGS += -fPIC + endif + ++ifeq ($(shell sh -c 'uname -m 2>/dev/null || echo not'),riscv64) ++ CFLAGS += -fPIC ++ CXXFLAGS += -fPIC ++endif ++ + TARGET = freeimage + STATICLIB = lib$(TARGET).a + SHAREDLIB = lib$(TARGET)-$(VER_MAJOR).$(VER_MINOR).so From 8f45102e415bce476e4bca502969e3dc039770f1 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Thu, 16 Jan 2025 14:47:42 +0100 Subject: [PATCH 382/414] Add description to the patches and adjust checksums --- .../f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb | 4 ++-- .../f/FreeImage/FreeImage-3.18.0-fix-makefile-gnu.patch | 1 + .../f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch | 1 + 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb index 5fd3393c89e..47979b9dac8 100644 --- a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-13.2.0.eb @@ -22,8 +22,8 @@ patches = [ checksums = [ 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # %(name)s-%(version)s-fix-makefile.patch - '9f6e468b178a814029213b5ae651ddd01edc3a4781a290eb21e05638a3854509', # %(name)s-%(version)s-fix-makefile-riscv.patch - '1abd7f85c5bb8e1de456592459a017396115e2f74bb17bc67a548ee59935c09e', # %(name)s-%(version)s-fix-makefile-gnu.patch + 'e845d53bfd829d771638b9952d3632010c7f19c88d761a786754453827bd7e9b', # %(name)s-%(version)s-fix-makefile-riscv.patch + 'b636012988e1b88609fbd2c130e2b4e6fa8c488cb07578e0353baf8e5aa52413', # %(name)s-%(version)s-fix-makefile-gnu.patch ] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-gnu.patch b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-gnu.patch index 09e020c2416..2ea87d4930f 100644 --- a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-gnu.patch +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-gnu.patch @@ -1,3 +1,4 @@ +# -fPIC flag is also needed for RISC-V builds --- Makefile.gnu.orig 2025-01-15 17:26:47.616603010 +0100 +++ Makefile.gnu 2025-01-15 17:28:09.158140964 +0100 @@ -33,6 +33,11 @@ diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch index 2f39e695b30..ac10020e319 100644 --- a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile-riscv.patch @@ -1,3 +1,4 @@ +# -fPIC flag is also needed for RISC-V builds --- Makefile.fip.orig 2025-01-16 12:58:29.624119756 +0100 +++ Makefile.fip 2025-01-16 13:00:01.016862229 +0100 @@ -33,6 +33,11 @@ From 4f397785c24e8a2126c6f2a389444f3a4db3f348 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 16 Jan 2025 14:48:11 +0000 Subject: [PATCH 383/414] update homepage and source_urls for libxsmm --- easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb | 4 ++-- .../l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb | 4 ++-- easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-GCC-10.3.0.eb | 4 ++-- .../l/libxsmm/libxsmm-1.16.2-intel-compilers-2021.2.0.eb | 4 ++-- easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb | 4 ++-- easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb | 4 ++-- easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.2.0.eb | 4 ++-- easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.3.0.eb | 4 ++-- 8 files changed, 16 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb index cc99b62c391..0d233d0fee6 100644 --- a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxsmm' version = '1.16.1' -homepage = 'https://github.com/hfp/libxsmm' +homepage = 'https://github.com/libxsmm/libxsmm' description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['https://github.com/hfp/libxsmm/archive/'] +source_urls = ['https://github.com/libxsmm/libxsmm/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['93dc7a3ec40401988729ddb2c6ea2294911261f7e6cd979cf061b5c3691d729d'] diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb index fba1cdf4790..4d9093e4d28 100644 --- a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxsmm' version = '1.16.1' -homepage = 'https://github.com/hfp/libxsmm' +homepage = 'https://github.com/libxsmm/libxsmm' description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).""" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://github.com/hfp/libxsmm/archive/'] +source_urls = ['https://github.com/libxsmm/libxsmm/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['93dc7a3ec40401988729ddb2c6ea2294911261f7e6cd979cf061b5c3691d729d'] diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-GCC-10.3.0.eb index 41104ec8354..a0e190a7177 100644 --- a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-GCC-10.3.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxsmm' version = '1.16.2' -homepage = 'https://github.com/hfp/libxsmm' +homepage = 'https://github.com/libxsmm/libxsmm' description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).""" toolchain = {'name': 'GCC', 'version': '10.3.0'} -source_urls = ['https://github.com/hfp/libxsmm/archive/'] +source_urls = ['https://github.com/libxsmm/libxsmm/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['bdc7554b56b9e0a380fc9c7b4f4394b41be863344858bc633bc9c25835c4c64e'] diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-intel-compilers-2021.2.0.eb index 86f5f13c7e4..8f958e9ca32 100644 --- a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-intel-compilers-2021.2.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxsmm' version = '1.16.2' -homepage = 'https://github.com/hfp/libxsmm' +homepage = 'https://github.com/libxsmm/libxsmm' description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).""" toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} -source_urls = ['https://github.com/hfp/libxsmm/archive/'] +source_urls = ['https://github.com/libxsmm/libxsmm/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['bdc7554b56b9e0a380fc9c7b4f4394b41be863344858bc633bc9c25835c4c64e'] diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb index d459d902f56..45044f6d90d 100644 --- a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxsmm' version = '1.17' -homepage = 'https://github.com/hfp/libxsmm' +homepage = 'https://github.com/libxsmm/libxsmm' description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).""" toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ['https://github.com/hfp/libxsmm/archive/'] +source_urls = ['https://github.com/libxsmm/libxsmm/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92'] diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb index 9fbbdba6329..53051f7f899 100644 --- a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxsmm' version = '1.17' -homepage = 'https://github.com/hfp/libxsmm' +homepage = 'https://github.com/libxsmm/libxsmm' description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).""" toolchain = {'name': 'GCC', 'version': '11.3.0'} -source_urls = ['https://github.com/hfp/libxsmm/archive/'] +source_urls = ['https://github.com/libxsmm/libxsmm/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92'] diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.2.0.eb index bd19b03924f..fc42848f68c 100644 --- a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.2.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxsmm' version = '1.17' -homepage = 'https://github.com/hfp/libxsmm' +homepage = 'https://github.com/libxsmm/libxsmm' description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).""" toolchain = {'name': 'GCC', 'version': '12.2.0'} -source_urls = ['https://github.com/hfp/libxsmm/archive/'] +source_urls = ['https://github.com/libxsmm/libxsmm/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92'] diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.3.0.eb index b20b327f489..4fb17fd7e2d 100644 --- a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.3.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxsmm' version = '1.17' -homepage = 'https://github.com/hfp/libxsmm' +homepage = 'https://github.com/libxsmm/libxsmm' description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).""" toolchain = {'name': 'GCC', 'version': '12.3.0'} -source_urls = ['https://github.com/hfp/libxsmm/archive/'] +source_urls = ['https://github.com/libxsmm/libxsmm/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92'] From f35230c5b71897432562964d8c731f70bd007485 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 16 Jan 2025 15:54:24 +0100 Subject: [PATCH 384/414] adding easyconfigs: HNOCA-tools-0.1.1-foss-2023a.eb --- .../HNOCA-tools-0.1.1-foss-2023a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/h/HNOCA-tools/HNOCA-tools-0.1.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/h/HNOCA-tools/HNOCA-tools-0.1.1-foss-2023a.eb b/easybuild/easyconfigs/h/HNOCA-tools/HNOCA-tools-0.1.1-foss-2023a.eb new file mode 100644 index 00000000000..f59319c9cf3 --- /dev/null +++ b/easybuild/easyconfigs/h/HNOCA-tools/HNOCA-tools-0.1.1-foss-2023a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'HNOCA-tools' +version = '0.1.1' + +homepage = 'https://github.com/devsystemslab/HNOCA-tools/' +description = "Toolbox of the Human Neural Organoid Cell Atlas." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('scanpy', '1.9.8'), + ('scvi-tools', '1.1.2'), + ('statsmodels', '0.14.1'), + ('matplotlib', '3.7.2'), + ('scArches', '0.6.1'), + ('numba', '0.58.1'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cloudpickle', '3.1.0', { + 'checksums': ['81a929b6e3c7335c863c771d673d105f02efdb89dfaba0c90495d1c64796601b'], + }), + ('joblib', '1.4.2', { + 'checksums': ['2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e'], + }), + ('decoupler', '1.6.0', { + 'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'], + }), + ('hnoca', version, { + 'preinstallopts': "sed -i 's/>=.*//g' requirements.txt && ", + 'source_urls': ['https://github.com/devsystemslab/HNOCA-tools//archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['5a433a9e5f59c449bdfa35a831fbfada329793e7c22e8f40c120ad57e2b213c0'], + }), +] + +sanity_check_commands = [ + 'python -c "import hnoca.snapseed"', + 'python -c "from hnoca.snapseed.utils import read_yaml"', + 'python -c "import hnoca.map"', + 'python -c "import hnoca.stats"', +] + +moduleclass = 'ai' From 09d717fb285e704c5424b281f1df6f82422a937f Mon Sep 17 00:00:00 2001 From: thoffman Date: Thu, 16 Jan 2025 16:23:48 +0100 Subject: [PATCH 385/414] adding easyconfigs: pybind11-2.13.6-GCC-13.3.0.eb --- .../p/pybind11/pybind11-2.13.6-GCC-13.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.13.6-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.13.6-GCC-13.3.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.13.6-GCC-13.3.0.eb new file mode 100644 index 00000000000..2e698fa2bb7 --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.13.6-GCC-13.3.0.eb @@ -0,0 +1,33 @@ +name = 'pybind11' +version = '2.13.6' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'pybind11-2.10.3_require-catch.patch', +] +checksums = [ + {'v2.13.6.tar.gz': 'e08cb87f4773da97fa7b5f035de8763abc656d87d5773e62f6da0587d1f0ec20'}, + {'pybind11-2.10.3_require-catch.patch': '4a27ba3ef1d5c535d120d6178a6e876ae678e4899a07500aab37908357b0b60b'}, +] + +builddependencies = [ + ('CMake', '3.29.3'), + # Test dependencies + ('Eigen', '3.4.0'), + ('Catch2', '2.13.10'), + ('Python-bundle-PyPI', '2024.06'), # to provide pytest +] + +dependencies = [ + ('Boost', '1.85.0'), + ('Python', '3.12.3'), +] + +moduleclass = 'lib' From 73034e453cc9d97bf653a215143e24854e15ee00 Mon Sep 17 00:00:00 2001 From: thoffman Date: Thu, 16 Jan 2025 16:26:31 +0100 Subject: [PATCH 386/414] adding easyconfigs: Catch2-3.8.0-GCCcore-13.3.0.eb --- .../c/Catch2/Catch2-3.8.0-GCCcore-13.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/Catch2/Catch2-3.8.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/c/Catch2/Catch2-3.8.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Catch2/Catch2-3.8.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..530eea1bbdf --- /dev/null +++ b/easybuild/easyconfigs/c/Catch2/Catch2-3.8.0-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'Catch2' +version = '3.8.0' + +homepage = 'https://github.com/catchorg/Catch2' +description = """A modern, C++-native, header-only, + test framework for unit-tests, TDD and BDD + - using C++11, C++14, C++17 and later +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/catchorg/Catch2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1ab2de20460d4641553addfdfe6acd4109d871d5531f8f519a52ea4926303087'] + +builddependencies = [ + ('binutils', '2.42'), # to make CMake compiler health check pass on old systems + ('CMake', '3.29.3'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['include/catch2/catch_all.hpp'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' From 9758acdc3e7eff3783375c8f6323f63911042e01 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 16 Jan 2025 16:28:14 +0100 Subject: [PATCH 387/414] add gpu version --- ...NOCA-tools-0.1.1-foss-2023a-CUDA-12.1.1.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/h/HNOCA-tools/HNOCA-tools-0.1.1-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/h/HNOCA-tools/HNOCA-tools-0.1.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/h/HNOCA-tools/HNOCA-tools-0.1.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..f58b9b821f4 --- /dev/null +++ b/easybuild/easyconfigs/h/HNOCA-tools/HNOCA-tools-0.1.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'HNOCA-tools' +version = '0.1.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/devsystemslab/HNOCA-tools/' +description = "Toolbox of the Human Neural Organoid Cell Atlas." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('scanpy', '1.9.8'), + ('scvi-tools', '1.1.2', versionsuffix), + ('statsmodels', '0.14.1'), + ('matplotlib', '3.7.2'), + ('scArches', '0.6.1', versionsuffix), + ('numba', '0.58.1'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cloudpickle', '3.1.0', { + 'checksums': ['81a929b6e3c7335c863c771d673d105f02efdb89dfaba0c90495d1c64796601b'], + }), + ('joblib', '1.4.2', { + 'checksums': ['2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e'], + }), + ('decoupler', '1.6.0', { + 'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'], + }), + ('hnoca', version, { + 'preinstallopts': "sed -i 's/>=.*//g' requirements.txt && ", + 'source_urls': ['https://github.com/devsystemslab/HNOCA-tools//archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['5a433a9e5f59c449bdfa35a831fbfada329793e7c22e8f40c120ad57e2b213c0'], + }), +] + +sanity_check_commands = [ + 'python -c "import hnoca.snapseed"', + 'python -c "from hnoca.snapseed.utils import read_yaml"', + 'python -c "import hnoca.map"', + 'python -c "import hnoca.stats"', +] + +moduleclass = 'ai' From d7d83826479be97c932e20f474e4df6a3caa6da2 Mon Sep 17 00:00:00 2001 From: thoffman Date: Thu, 16 Jan 2025 17:03:20 +0100 Subject: [PATCH 388/414] move pybind11 dependency to builddependencies --- .../s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb index 5584d888f30..b15452f6bb5 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb @@ -18,12 +18,12 @@ builddependencies = [ ('Ninja', '1.12.1'), ('pkgconf', '2.2.0'), # required by scipy ('Cython', '3.0.10'), # required by numpy and scipy + ('pybind11', '2.12.0'), # required by scipy ] dependencies = [ ('Python', '3.12.3'), ('Python-bundle-PyPI', '2024.06'), - ('pybind11', '2.12.0'), # required by scipy ] use_pip = True From 5848b7b74dc706f12b4b48706d2ba9009f06b976 Mon Sep 17 00:00:00 2001 From: thoffman Date: Thu, 16 Jan 2025 17:36:10 +0100 Subject: [PATCH 389/414] adding easyconfigs: HMMER-3.4-gompi-2024a.eb --- .../h/HMMER/HMMER-3.4-gompi-2024a.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb new file mode 100644 index 00000000000..f58d56361a1 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb @@ -0,0 +1,63 @@ +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.4' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3'] + +builddependencies = [ + ('Python', '3.12.3'), + ('Perl', '5.38.2'), +] + +# replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files +preconfigopts = "grep '/usr/bin/perl' . | cut -f1 -d: | xargs echo sed -i 's@/usr/bin/perl@/usr/bin/env perl@g' && " + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From f69fc111fed9c789fdfcf697465c3403681c18e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Fri, 17 Jan 2025 11:20:06 +0100 Subject: [PATCH 390/414] Improve handling for 'llc' flags appearing e.g. with NVHPC on aarch64 systems, causing application builds to abort when Fortran to C linking is used --- .../Autoconf/Autoconf-2.71-GCCcore-10.3.0.eb | 8 +++-- .../Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb | 6 +++- .../Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb | 6 +++- .../Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb | 6 +++- .../Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb | 6 +++- .../Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb | 6 +++- .../Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb | 6 +++- .../Autoconf-2.71-Port-better-to-NVHPC.patch | 29 +++++++++++++++++++ .../easyconfigs/a/Autoconf/Autoconf-2.71.eb | 8 +++-- .../Autoconf/Autoconf-2.72-GCCcore-13.3.0.eb | 6 +++- .../Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb | 6 +++- 11 files changed, 81 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-Port-better-to-NVHPC.patch diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-10.3.0.eb index c143a960e31..a513d76b34b 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-10.3.0.eb @@ -16,8 +16,12 @@ description = """Autoconf is an extensible package of M4 macros that produce she toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['f14c83cfebcc9427f2c3cea7258bd90df972d92eb26752da4ddad81c87a0faa4'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch'] +checksums = [ + '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz + '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch +] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb index 4a0acd7948a..9fac32ccf7f 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] +patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch'] +checksums = [ + '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz + '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch +] builddependencies = [ ('binutils', '2.37'), diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb index 84cfa189e05..8221b498cc8 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] +patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch'] +checksums = [ + '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz + '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch +] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb index 4e315d3a24c..7a58f051f70 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] +patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch'] +checksums = [ + '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz + '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch +] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb index 0b47b6d9a77..4213b397874 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] +patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch'] +checksums = [ + '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz + '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb index de56240d150..fae5c0c568b 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] +patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch'] +checksums = [ + '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz + '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb index 82a7f9766df..411b9e3a5c1 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] +patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch'] +checksums = [ + '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz + '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-Port-better-to-NVHPC.patch b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-Port-better-to-NVHPC.patch new file mode 100644 index 00000000000..3db644d18a3 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-Port-better-to-NVHPC.patch @@ -0,0 +1,29 @@ +From 632282145ba1d617f480cde74eef938826fef4d5 Mon Sep 17 00:00:00 2001 +From: Paul Eggert +Date: Thu, 16 Jan 2025 11:24:12 -0800 +Subject: Port better to NVHPC + +See . +* lib/autoconf/fortran.m4 (_AC_FC_LIBRARY_LDFLAGS): +Ignore -l options with embedded '='. +--- + lib/autoconf/fortran.m4 | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/lib/autoconf/fortran.m4 b/lib/autoconf/fortran.m4 +index 0fc7545d..4c39607c 100644 +--- a/lib/autoconf/fortran.m4 ++++ b/lib/autoconf/fortran.m4 +@@ -664,7 +664,7 @@ while test $[@%:@] != 1; do + ;; + # Ignore these flags. + -lang* | -lcrt*.o | -lc | -lgcc* | -lSystem | -libmil | -little \ +- |-LANG:=* | -LIST:* | -LNO:* | -link) ++ | -[[lLR]]*=* | -LIST:* | -LNO:* | -link) + ;; + -lkernel32) + # Ignore this library only on Windows-like systems. +-- +cgit v1.2.3-70-g09d2 + + diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71.eb index cb75bfdc12e..56641a83cc9 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71.eb @@ -16,8 +16,12 @@ description = """Autoconf is an extensible package of M4 macros that produce she toolchain = SYSTEM source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['f14c83cfebcc9427f2c3cea7258bd90df972d92eb26752da4ddad81c87a0faa4'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch'] +checksums = [ + '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz + '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch +] dependencies = [('M4', '1.4.18')] diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-13.3.0.eb index 8cbff6d13b2..0db4d794b42 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-13.3.0.eb @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e'] +patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch'] +checksums = [ + 'afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e', # autoconf-2.72.tar.gz + '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch +] builddependencies = [ ('binutils', '2.42'), diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb index fe4b4d3a0de..c4d097ab3d9 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '14.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e'] +patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch'] +checksums = [ + 'afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e', # autoconf-2.72.tar.gz + '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch +] builddependencies = [ ('binutils', '2.42'), From 5039661bb997482492dfdda54d249928ec4f27ec Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 17 Jan 2025 13:09:13 +0100 Subject: [PATCH 391/414] Update HMMER-3.4-gompi-2024a.eb @jpecar Can you please check the header I added? --- .../easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb index f58d56361a1..5e40c904940 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb @@ -1,3 +1,19 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# Updated by: Filip Kružík (INUITS) +# Jure Pečar (EMBL) +# 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 = 'HMMER' From bfb59c8fd28b4f38f270a4d92120af594358e876 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 17 Jan 2025 14:52:09 +0100 Subject: [PATCH 392/414] adding easyconfigs: cython-cmake-0.2.0-GCCcore-13.2.0.eb --- .../cython-cmake-0.2.0-GCCcore-13.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/cython-cmake/cython-cmake-0.2.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/cython-cmake/cython-cmake-0.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cython-cmake/cython-cmake-0.2.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..bc40ac3d1e9 --- /dev/null +++ b/easybuild/easyconfigs/c/cython-cmake/cython-cmake-0.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'cython-cmake' +version = '0.2.0' + +homepage = 'https://github.com/scikit-build/cython-cmake' +description = """ +Custom CMake rules to generate the source code +for a Python extension module using cython +""" +docurls = ['https://github.com/scikit-build/cython-cmake'] + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('flit', '3.9.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'sources': ['cython_cmake-%(version)s.tar.gz'], + 'checksums': ['f58e0006e8a7fe158c7b147f6469496945ec66ce11610e2f3a518c5d2598f738'], + }), +] + +moduleclass = 'devel' From 6ec0107ebb5dc8dd2c3b5a3a3b69d4da08681945 Mon Sep 17 00:00:00 2001 From: u0090231 Date: Fri, 17 Jan 2025 16:16:55 +0100 Subject: [PATCH 393/414] adding new Pandoc/3.6.2 --- .../easyconfigs/p/Pandoc/Pandoc-3.6.2.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pandoc/Pandoc-3.6.2.eb diff --git a/easybuild/easyconfigs/p/Pandoc/Pandoc-3.6.2.eb b/easybuild/easyconfigs/p/Pandoc/Pandoc-3.6.2.eb new file mode 100644 index 00000000000..7756e8e56c6 --- /dev/null +++ b/easybuild/easyconfigs/p/Pandoc/Pandoc-3.6.2.eb @@ -0,0 +1,32 @@ +# 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 +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'Tarball' + +name = 'Pandoc' +version = '3.6.2' + +homepage = 'https://pandoc.org' +description = "If you need to convert files from one markup format into another, pandoc is your swiss-army knife" + +toolchain = SYSTEM + +_archs = {'x86_64': 'amd64', 'aarch64': 'arm64'} + +source_urls = ['https://github.com/jgm/pandoc/releases/download/%(version)s/'] +sources = ['%%(namelower)s-%%(version)s-linux-%s.tar.gz' % _archs[ARCH]] +checksums = ['f11b3f21549f23e3d5b99dfacb96560c04c2f76027edb787c4d6551849acf54a'] + +sanity_check_paths = { + 'files': ['bin/pandoc'], + 'dirs': ['share'], +} + +sanity_check_commands = ['pandoc --help'] + +moduleclass = 'tools' From 9f2bd74c2605e58e8649da4a9e9e113a37534662 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 17 Jan 2025 16:37:33 +0100 Subject: [PATCH 394/414] adding easyconfigs: Beast-2.7.7-GCC-12.3.0-CUDA-12.1.1.eb, Beast-2.7.7-GCC-12.3.0.eb, beagle-lib-4.0.1-GCC-12.3.0.eb --- .../Beast-2.7.7-GCC-12.3.0-CUDA-12.1.1.eb | 40 +++++++++++++++++++ .../b/Beast/Beast-2.7.7-GCC-12.3.0.eb | 38 ++++++++++++++++++ .../beagle-lib/beagle-lib-4.0.1-GCC-12.3.0.eb | 33 +++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 00000000000..2070677b247 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,40 @@ +easyblock = 'Tarball' + +name = 'Beast' +version = '2.7.7' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://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': '12.3.0'} + +_archs = {'x86_64': 'x86', 'aarch64': 'aarch64'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%%(version)s.Linux.%s.tgz' % _archs[ARCH]] +checksums = [{ + 'BEAST.v2.7.7.Linux.x86.tgz': 'a866f3e5da4ef890a042f01849e32322aa0a8e16e3e1cb2c59f823de2611781a', + 'BEAST.v2.7.7.Linux.aarch64.tgz': 'aa14e4a950fe2d9f3db24102a4e7365d8d42f79da1d9b1cdcf3016e927d18b9e', +}] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Java', '11', '', SYSTEM), + ('beagle-lib', '4.0.1', versionsuffix), # optional but recommended by developers + ('GTK3', '3.24.37'), # optional for GUI tools +] + +sanity_check_paths = { + 'files': ['bin/beast'], + 'dirs': [] +} + +sanity_check_commands = ["beast -help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0.eb new file mode 100644 index 00000000000..140ba2418ac --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'Beast' +version = '2.7.7' + +homepage = 'https://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': '12.3.0'} + +_archs = {'x86_64': 'x86', 'aarch64': 'aarch64'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%%(version)s.Linux.%s.tgz' % _archs[ARCH]] +checksums = [{ + 'BEAST.v2.7.7.Linux.x86.tgz': 'a866f3e5da4ef890a042f01849e32322aa0a8e16e3e1cb2c59f823de2611781a', + 'BEAST.v2.7.7.Linux.aarch64.tgz': 'aa14e4a950fe2d9f3db24102a4e7365d8d42f79da1d9b1cdcf3016e927d18b9e', +}] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('beagle-lib', '4.0.1'), # optional but recommended by developers + ('GTK3', '3.24.37'), # optional for GUI tools +] + +sanity_check_paths = { + 'files': ['bin/beast'], + 'dirs': [] +} + +sanity_check_commands = ["beast -help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..a0732fa9521 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'beagle-lib' +version = '4.0.1' + +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': '12.3.0'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9d258cd9bedd86d7c28b91587acd1132f4e01d4f095c657ad4dc93bd83d4f120'] + +dependencies = [ + ('Java', '11', '', SYSTEM), +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +configopts = '-DBUILD_CUDA=OFF ' + +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' From d3f1c4b0048ceebbe610ef80cd29d48d0dcf73e1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 17 Jan 2025 16:49:08 +0100 Subject: [PATCH 395/414] adding easyconfigs: Biotite-0.41.0-foss-2022a.eb --- .../b/Biotite/Biotite-0.41.0-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-foss-2022a.eb b/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-foss-2022a.eb new file mode 100644 index 00000000000..96c629366e5 --- /dev/null +++ b/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'Biotite' +version = '0.41.0' + +homepage = 'https://www.biotite-python.org/' +description = """Biotite is your Swiss army knife for bioinformatics. Whether you want to +identify homologous sequence regions in a protein family or you would like to +find disulfide bonds in a protein structure: Biotite has the right tool for +you. This package bundles popular tasks in computational molecular biology into +a uniform Python library.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), +] + +use_pip = True + +exts_list = [ + ('biotite', version, { + 'checksums': ['a5fddb4d738291772735cf04dfa8b642e0bdd6b4c2c0c71e2db727c0a66bd106'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From fe3efa8f4dde6c36f355e7a9ef947e558da27447 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 20 Jan 2025 10:57:03 +0100 Subject: [PATCH 396/414] add grpcio --- .../g/grpcio/grpcio-1.67.1-GCCcore-13.2.0.eb | 52 +++++++++++++++++++ .../g/grpcio/grpcio-1.67.1_use-ebroot.patch | 52 +++++++++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/g/grpcio/grpcio-1.67.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/grpcio/grpcio-1.67.1_use-ebroot.patch diff --git a/easybuild/easyconfigs/g/grpcio/grpcio-1.67.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/grpcio/grpcio-1.67.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..dd33a6a7525 --- /dev/null +++ b/easybuild/easyconfigs/g/grpcio/grpcio-1.67.1-GCCcore-13.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'grpcio' +version = '1.67.1' + +homepage = 'https://grpc.io/' +description = """gRPC is a modern, open source, high-performance remote procedure call (RPC) +framework that can run anywhere. gRPC enables client and server applications to +communicate transparently, and simplifies the building of connected systems.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('binutils', '2.40'), + ('OpenSSL', '1.1', '', SYSTEM), + ('RE2', '2024-03-01'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('protobuf-python', '4.25.3'), + ('Abseil', '20240116.1'), +] + +exts_list = [ + (name, version, { + 'modulename': 'grpc', + 'preinstallopts': ( + # patch hardcoded /usr paths to prefix them with alternate sysroot path (if defined) + "sed -i 's@/usr@%(sysroot)s/usr@g' setup.py && " + "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && " + # Required to avoid building with non-default C++ standard but keep other flags, + # see https://github.com/grpc/grpc/issues/34256 + 'export GRPC_PYTHON_CFLAGS="-fvisibility=hidden -fno-wrapv -fno-exceptions" &&' + "GRPC_PYTHON_BUILD_SYSTEM_OPENSSL=True " + "GRPC_PYTHON_BUILD_SYSTEM_ZLIB=True " + "GRPC_PYTHON_BUILD_SYSTEM_RE2=True " + "GRPC_PYTHON_BUILD_SYSTEM_ABSL=True " + ), + 'patches': ['grpcio-1.67.1_use-ebroot.patch'], + 'checksums': [ + {'grpcio-1.67.1.tar.gz': '3dc2ed4cabea4dc14d5e708c2b426205956077cc5de419b4d4079315017e9732'}, + {'grpcio-1.67.1_use-ebroot.patch': '8606002b8689d9ffde1c7aa097f0fd430430b42f2230ea427b73525de69c568b'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/grpcio/grpcio-1.67.1_use-ebroot.patch b/easybuild/easyconfigs/g/grpcio/grpcio-1.67.1_use-ebroot.patch new file mode 100644 index 00000000000..df7cfd69433 --- /dev/null +++ b/easybuild/easyconfigs/g/grpcio/grpcio-1.67.1_use-ebroot.patch @@ -0,0 +1,52 @@ +Author: yqshao (Yunqi Shao), Update: Pavel Tománek (Inuits) +Update setup.py to use dependencies from EB +--- setup.py.orig 2024-11-04 12:15:44.508837000 +0100 ++++ setup.py 2024-11-04 12:20:12.717679000 +0100 +@@ -298,29 +298,33 @@ + CORE_C_FILES = filter(lambda x: "third_party/cares" not in x, CORE_C_FILES) + + if BUILD_WITH_SYSTEM_OPENSSL: ++ EBROOTOPENSSL = os.environ.get('EBROOTOPENSSL') + CORE_C_FILES = filter( + lambda x: "third_party/boringssl" not in x, CORE_C_FILES + ) + CORE_C_FILES = filter(lambda x: "src/boringssl" not in x, CORE_C_FILES) +- SSL_INCLUDE = (os.path.join("/usr", "include", "openssl"),) ++ SSL_INCLUDE = (os.path.join(EBROOTOPENSSL, "include", "openssl"),) + + if BUILD_WITH_SYSTEM_ZLIB: ++ EBROOTZLIB = os.environ.get('EBROOTZLIB') + CORE_C_FILES = filter(lambda x: "third_party/zlib" not in x, CORE_C_FILES) +- ZLIB_INCLUDE = (os.path.join("/usr", "include"),) ++ ZLIB_INCLUDE = (os.path.join(EBROOTZLIB, "include"),) + + if BUILD_WITH_SYSTEM_CARES: + CORE_C_FILES = filter(lambda x: "third_party/cares" not in x, CORE_C_FILES) + CARES_INCLUDE = (os.path.join("/usr", "include"),) + + if BUILD_WITH_SYSTEM_RE2: ++ EBROOTRE2 = os.environ.get('EBROOTRE2') + CORE_C_FILES = filter(lambda x: "third_party/re2" not in x, CORE_C_FILES) +- RE2_INCLUDE = (os.path.join("/usr", "include", "re2"),) ++ RE2_INCLUDE = (os.path.join(EBROOTRE2, "include", "re2"),) + + if BUILD_WITH_SYSTEM_ABSL: ++ EBROOTABSEIL = os.environ.get('EBROOTABSEIL') + CORE_C_FILES = filter( + lambda x: "third_party/abseil-cpp" not in x, CORE_C_FILES + ) +- ABSL_INCLUDE = (os.path.join("/usr", "include"),) ++ ABSL_INCLUDE = (os.path.join(EBROOTABSEIL, "include"),) + + EXTENSION_INCLUDE_DIRECTORIES = ( + (PYTHON_STEM,) +@@ -363,8 +367,7 @@ + EXTENSION_LIBRARIES += ("re2",) + if BUILD_WITH_SYSTEM_ABSL: + EXTENSION_LIBRARIES += tuple( +- lib.stem[3:] +- for lib in sorted(pathlib.Path("/usr").glob("lib*/libabsl_*.so")) ++ lib.stem[3:] for lib in pathlib.Path(EBROOTABSEIL).glob("lib*/libabsl_*.so") + ) + + DEFINE_MACROS = (("_WIN32_WINNT", 0x600),) From e6289fb1c0982f7b7311039b7f4038756a950a5c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Mon, 20 Jan 2025 12:47:21 +0100 Subject: [PATCH 397/414] fix setuptools issue by sticking to a single version --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb index f4319b13ae5..594791e43c7 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb @@ -32,6 +32,10 @@ exts_list = [ 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " # use PyYAML 6.0.1 to solve Cython 3 incompatibility issues "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && " + # use the same setuptools version n the requirements.txt of the docs + # to prevent jsonschema from installating the latest setuptools as well + "echo \"setuptools==59.6.0; python_version == '3.6'\" >> docs/requirements.txt && " + "echo \"setuptools==67.8.0; python_version >= '3.7'\" >> docs/requirements.txt && " "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', From fc82a41ac470a230d737cdf4bcdf9a1f10f003f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Jan 2025 13:28:08 +0100 Subject: [PATCH 398/414] adding easyconfigs: dorado-0.9.0-foss-2023a-CUDA-12.1.1.eb --- .../dorado-0.9.0-foss-2023a-CUDA-12.1.1.eb | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.9.0-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.9.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.9.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..21ff2208059 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.9.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,104 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.9.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = [ + '%(name)s-0.8.0_dont_install_external_libraries.patch', +] +checksums = [ + None, + '28942b7057af00c574a5e70d33a58b4036fd09ae0b041f45b67581c8dda832b1', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('patchelf', '0.18.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), + ('HTSlib', '1.18'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && " + +# disable treating warnings like errors by stripping out -Werror +# cfr. https://github.com/nanoporetech/dorado/issues/779 +preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " + +_copts = [ + "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA", + "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc", + '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL', + "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib", + # add -pthread flag (in addition to -lpthread) to avoid linking error: + # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' + '-DCMAKE_C_FLAGS="$CFLAGS -pthread"', +] + +configopts = ' '.join(_copts) + ' ' + +# disable CMake fiddling with RPATH when EasyBuild is configured to use RPATH linking +configopts += "$(if %(rpath_enabled)s; then " +configopts += "echo '-DCMAKE_SKIP_INSTALL_RPATH=YES -DCMAKE_SKIP_RPATH=YES'; fi) " + +# CUDA libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); +# by default, CMake sets RUNPATH to '$ORIGIN' rather than RPATH (but that's disabled above) +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " for lib in $(ls %(installdir)s/lib/lib{cu,nv}*.so*); do " + " echo setting RPATH in $lib;" + " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" + " done;" + "fi", +] + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' From a47b12ad82f1a57e647f1ff1df8ea445a1eb5688 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 20 Jan 2025 16:15:47 +0100 Subject: [PATCH 399/414] adding easyconfigs: OpenFOAM-8-foss-2023a.eb and patches: OpenFOAM-8_fix-OSHA1stream.patch --- .../o/OpenFOAM/OpenFOAM-8-foss-2023a.eb | 41 ++++ .../OpenFOAM/OpenFOAM-8_fix-OSHA1stream.patch | 227 ++++++++++++++++++ 2 files changed, 268 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2023a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8_fix-OSHA1stream.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2023a.eb new file mode 100644 index 00000000000..c6685bf0fb3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2023a.eb @@ -0,0 +1,41 @@ +name = 'OpenFOAM' +version = '8' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = [ + 'OpenFOAM-%(version)s-cleanup.patch', + 'OpenFOAM-%(version)s_fix-OSHA1stream.patch', +] +checksums = [ + {'version-8.tar.gz': '94ba11cbaaa12fbb5b356e01758df403ac8832d69da309a5d79f76f42eb008fc'}, + {'OpenFOAM-8-cleanup.patch': 'e3fac8049611ee109f07eb5b0ed4b1526782a21b3f12435e03529d56c8483b9f'}, + {'OpenFOAM-8_fix-OSHA1stream.patch': '09a361d5c19fe7e602025d42838af36474ed2902445001d2bf5cf744862240fb'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] +dependencies = [ + ('libreadline', '8.2'), + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('CGAL', '5.6'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8_fix-OSHA1stream.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8_fix-OSHA1stream.patch new file mode 100644 index 00000000000..06b6c14b15b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8_fix-OSHA1stream.patch @@ -0,0 +1,227 @@ +From b0c15bebd37142f3902901ed5e9a60e33ed456eb Mon Sep 17 00:00:00 2001 +From: Henry Weller +Date: Wed, 6 Jul 2022 21:12:23 +0100 +Subject: [PATCH] OSHA1stream: Updated to C++11 + +According to the C++11 standard the xsputn might call an overload function which +must be provided for correct operation and is required by gcc-12.1 but not +earlier releases. + +See + +https://cplusplus.com/reference/streambuf/streambuf/xsputn/ + + Its default behavior in streambuf is to retrieve n characters, as if calling + sputc for each, stopping if any call would return EOF. Except it is + unspecified whether member overflow is called or whether other means are + used in case of overflows. + +https://cplusplus.com/reference/streambuf/streambuf/overflow/ + + int overflow (int c = EOF); + + Put character on overflow + + Virtual function called by other member functions to put a character + into the controlled output sequence without changing the current + position. + + It is called by public member functions such as sputc to write a + character when there are no writing positions available at the put + pointer (pptr). + + Its default behavior in streambuf is to always return EOF (indicating + failure), but derived classes can override this behavior to attempt to + write the character directly and/or to alter pptr and other internal + pointers so that more storage is provided, potentially writing unwritten + characters to the controlled output sequence. Both filebuf and stringbuf + override this virtual member function. + + Parameters c + Character to be put. + + If this is the end-of-file value (EOF), no character is put, but the + other effects of calling this function are attempted. + + Return Value + In case of success, the character put is returned, converted to a value + of type int_type using member traits_type::to_int_type. + + Otherwise, it returns the end-of-file value (EOF) either if called with + this value as argument c or to signal a failure (some implementations + may throw an exception instead). + +Resolves bug-report https://bugs.openfoam.org/view.php?id=3856 +--- + .../db/IOstreams/hashes/OSHA1stream.H | 74 +++++++++++-------- + 1 file changed, 45 insertions(+), 29 deletions(-) + +diff --git a/src/OpenFOAM/db/IOstreams/hashes/OSHA1stream.H b/src/OpenFOAM/db/IOstreams/hashes/OSHA1stream.H +index f10f86b3a5..f7466d49fd 100644 +--- a/src/OpenFOAM/db/IOstreams/hashes/OSHA1stream.H ++++ b/src/OpenFOAM/db/IOstreams/hashes/OSHA1stream.H +@@ -2,7 +2,7 @@ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org +- \\ / A nd | Copyright (C) 2011-2019 OpenFOAM Foundation ++ \\ / A nd | Copyright (C) 2011-2022 OpenFOAM Foundation + \\/ M anipulation | + ------------------------------------------------------------------------------- + License +@@ -25,7 +25,7 @@ Class + Foam::OSHA1stream + + Description +- An output stream for calculating SHA1 digests. ++ A Foam::OSstream for calculating SHA-1 digests + + SourceFiles + OSHA1stream.C +@@ -43,24 +43,19 @@ SourceFiles + namespace Foam + { + +-class osha1stream; +-class OSHA1stream; +- + /*---------------------------------------------------------------------------*\ + Class sha1streambuf Declaration + \*---------------------------------------------------------------------------*/ + +-//- A streambuf class for calculating SHA1 digests + class sha1streambuf + : + public std::streambuf + { + // Private Data + +- //- This does all the work and has its own buffering +- SHA1 sha1_; ++ //- The SHA-1 class which processes the strings ++ SHA1 sha1_; + +- friend class osha1stream; + + public: + +@@ -70,16 +65,39 @@ public: + sha1streambuf() + {} + ++ + // Member Functions + +- // Write ++ //- Return the SHA-1 ++ SHA1& sha1() ++ { ++ return sha1_; ++ } + +- //- Process unbuffered +- virtual std::streamsize xsputn(const char* str, std::streamsize n) ++ //- Writes characters from the array pointed to by s ++ // into the controlled output sequence, until either n characters ++ // have been written or the end of the output sequence is reached ++ virtual std::streamsize xsputn(const char* s, std::streamsize n) + { +- sha1_.append(str, n); ++ sha1_.append(s, n); + return n; + } ++ ++ //- Writes c to the current position of the put pointer (pptr), ++ // and advances that pointer one position forward. ++ // If c is EOF, no characters are written and the put pointer ++ // (pptr) is not advanced. ++ // Maybe used by xsputn (C++11). ++ virtual int overflow(int c = EOF) ++ { ++ if (c != EOF) ++ { ++ const char cc = c; ++ sha1_.append(&cc, 1); ++ } ++ ++ return c; ++ } + }; + + +@@ -87,7 +105,6 @@ public: + Class osha1stream Declaration + \*---------------------------------------------------------------------------*/ + +-//- A basic output stream for calculating SHA1 digests + class osha1stream + : + virtual public std::ios, +@@ -95,7 +112,9 @@ class osha1stream + { + // Private Data + +- sha1streambuf sbuf_; ++ // SHA-1 stream buffer ++ sha1streambuf sbuf_; ++ + + public: + +@@ -107,22 +126,20 @@ public: + std::ostream(&sbuf_) + {} + +- // Member Functions + +- // Access ++ // Member Functions + +- //- This hides both signatures of std::basic_ios::rdbuf() +- sha1streambuf* rdbuf() ++ //- Return the SHA-1 ++ SHA1& sha1() + { +- return &sbuf_; ++ return sbuf_.sha1(); + } + +- //- Full access to the sha1 +- SHA1& sha1() ++ //- Return the stream buffer ++ sha1streambuf* rdbuf() + { +- return sbuf_.sha1_; ++ return &sbuf_; + } +- + }; + + +@@ -130,7 +147,6 @@ public: + Class OSHA1stream Declaration + \*---------------------------------------------------------------------------*/ + +-//- The output stream for calculating SHA1 digests + class OSHA1stream + : + public OSstream +@@ -169,14 +185,14 @@ public: + + // Member Functions + +- //- Full access to the sha1 +- Foam::SHA1& sha1() ++ //- Return the SHA-1 ++ SHA1& sha1() + { + return dynamic_cast(stdStream()).sha1(); + } + +- //- Return SHA1::Digest for the data processed until now +- Foam::SHA1Digest digest() ++ //- Return the SHA-1 digest for the data processed until now ++ SHA1Digest digest() + { + return sha1().digest(); + } \ No newline at end of file From 9f84c4aaa8021c2f4577ce2fc3be69ba1153f320 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 21 Jan 2025 10:58:17 +0100 Subject: [PATCH 400/414] {phys}[iomkl/2023a] FDS 6.9.1 --- .../f/FDS/FDS-6.9.1-iomkl-2023a.eb | 43 +++++++++++++++++++ .../f/FDS/FDS-6.9.1_intel_ompi.patch | 23 ++++++++++ .../imkl-FFTW-2023.1.0-iompi-2023a.eb | 11 +++++ easybuild/easyconfigs/i/iomkl/iomkl-2023a.eb | 19 ++++++++ easybuild/easyconfigs/i/iompi/iompi-2023a.eb | 18 ++++++++ 5 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.9.1-iomkl-2023a.eb create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.9.1_intel_ompi.patch create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iompi-2023a.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-2023a.eb create mode 100644 easybuild/easyconfigs/i/iompi/iompi-2023a.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.9.1-iomkl-2023a.eb b/easybuild/easyconfigs/f/FDS/FDS-6.9.1-iomkl-2023a.eb new file mode 100644 index 00000000000..12639f0e030 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.9.1-iomkl-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.9.1' + +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': 'iomkl', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['FDS-%(version)s.tar.gz'] +patches = ['FDS-%(version)s_intel_ompi.patch'] +checksums = [ + {'FDS-6.9.1.tar.gz': 'e0fe22d1386dc06512489ddf190dbdbee4c9865856f4a7ca48aec8425b4c0867'}, + {'FDS-6.9.1_intel_ompi.patch': '719137600e35025dce7dfcb88472e113143c571321bea01ceebfdbb6bc3c3fbb'}, +] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +buildopts = 'impi_intel_linux_openmp &&' +buildopts += 'cd %(installdir)s/Build && ln -s fds_impi_intel_linux_openmp fds' + +modextrapaths = {'PATH': 'Build'} + +sanity_check_paths = { + 'files': ['Build/fds'], + 'dirs': [], +} + +sanity_check_commands = [ + "fds 2>&1 | grep 'MPI version'", +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.9.1_intel_ompi.patch b/easybuild/easyconfigs/f/FDS/FDS-6.9.1_intel_ompi.patch new file mode 100644 index 00000000000..e442a389e19 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.9.1_intel_ompi.patch @@ -0,0 +1,23 @@ +# Pacth for OpenMPI with iomkl toolchain +# January 21 2025 by B. Hajgato (UGent) +--- Build/makefile.orig 2024-04-07 23:05:06.000000000 +0200 ++++ Build/makefile 2025-01-21 10:17:43.969175149 +0100 +@@ -74,7 +74,7 @@ + # Use cluster_sparse_solver with intelmpi blacs + FFLAGSMKL_INTEL = -DWITH_MKL -I"${MKLROOT}/include" + LFLAGSMKL_INTEL = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_sequential.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a -Wl,--end-group -lpthread -lm -ldl +- LFLAGSMKL_INTEL_OPENMP = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a -Wl,--end-group -liomp5 -lpthread -lm -ldl ++ LFLAGSMKL_INTEL_OPENMP = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_blacs_openmpi_lp64.a -Wl,--end-group -liomp5 -lpthread -lm -ldl + endif + ifneq ("$(wildcard ${MKLROOT}/lib/intel64/libmkl_blacs_openmpi_lp64.a)","") + # Use cluster_sparse_solver with openmpi blacs +@@ -216,7 +216,7 @@ + +-impi_intel_linux_openmp : FFLAGS = -m64 -fc=$(I_IFORT) -O2 -ipo -no-wrap-margin $(GITINFO) $(FFLAGSMKL_INTEL) -DUSE_IFPORT ++impi_intel_linux_openmp : FFLAGS = -m64 -O2 -ipo -no-wrap-margin $(GITINFO) $(FFLAGSMKL_INTEL) -DUSE_IFPORT + impi_intel_linux_openmp : LFLAGSMKL = $(LFLAGSMKL_INTEL_OPENMP) +-impi_intel_linux_openmp : FCOMPL = mpiifort ++impi_intel_linux_openmp : FCOMPL = mpifort + impi_intel_linux_openmp : FOPENMPFLAGS = -qopenmp + impi_intel_linux_openmp : obj = fds_impi_intel_linux_openmp + impi_intel_linux_openmp : setup $(obj_mpi) diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iompi-2023a.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iompi-2023a.eb new file mode 100644 index 00000000000..5b172e7d509 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iompi-2023a.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2023.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iompi', 'version': '2023a'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2023a.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2023a.eb new file mode 100644 index 00000000000..1f0a8248791 --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2023a.eb @@ -0,0 +1,19 @@ +easyblock = 'Toolchain' + +name = 'iomkl' +version = '2023a' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2023.1.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('OpenMPI', '4.1.5', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2023a.eb b/easybuild/easyconfigs/i/iompi/iompi-2023a.eb new file mode 100644 index 00000000000..643dbd10d39 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2023a.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iompi' +version = '2023a' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2023.1.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('OpenMPI', '4.1.5', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' From 647bf75b7722d8f27202585e1e4d9781dd54a84e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 21 Jan 2025 15:38:57 +0100 Subject: [PATCH 401/414] adding easyconfigs: NEURON-8.2.6-foss-2023a.eb --- .../n/NEURON/NEURON-8.2.6-foss-2023a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/n/NEURON/NEURON-8.2.6-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NEURON/NEURON-8.2.6-foss-2023a.eb b/easybuild/easyconfigs/n/NEURON/NEURON-8.2.6-foss-2023a.eb new file mode 100644 index 00000000000..902146ceca1 --- /dev/null +++ b/easybuild/easyconfigs/n/NEURON/NEURON-8.2.6-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'NEURON' +version = '8.2.6' + +homepage = 'https://www.neuron.yale.edu/neuron' +description = """Empirically-based simulations of neurons and networks of neurons.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/neuronsimulator/nrn/releases/download/%(version)s/'] +sources = ['nrn-full-src-package-%(version)s.tar.gz'] +checksums = ['eba1b379ae272aa2196263f6c5795f58e5dbf62c0899e82b0bb7c33dfb9c6afe'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +# turn off gui +configopts = '-DNRN_ENABLE_INTERVIEWS=OFF' + +sanity_check_paths = { + 'files': ['bin/nrnpyenv.sh', 'bin/nrniv', 'lib/libnrniv.so'], + 'dirs': ['lib/python/%(namelower)s'], +} + +sanity_check_commands = [ + 'export PYTHONPATH=%(installdir)s/lib/python:$PYTHONPATH && ' + "python -c 'import neuron; neuron.test()'" +] + +modextrapaths = {'PYTHONPATH': 'lib/python'} + +moduleclass = 'bio' From 0456535cbd948d839ad4c086994cbeabd6991548 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Jan 2025 18:38:47 +0100 Subject: [PATCH 402/414] use same sanity check command for FDS 6.9.1 as in existing easyconfigs --- easybuild/easyconfigs/f/FDS/FDS-6.9.1-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.9.1-foss-2023b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.9.1-foss-2023b.eb index 96e873161bd..25222e3bd50 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.9.1-foss-2023b.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.9.1-foss-2023b.eb @@ -33,7 +33,7 @@ sanity_check_paths = { } sanity_check_commands = [ - "fds -v", + "fds 2>&1 | grep 'MPI version'", ] moduleclass = 'phys' From 3fd2d30d4ca3e56d62d4bf3279ac94e1cc2a8892 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Wed, 22 Jan 2025 11:06:11 +0100 Subject: [PATCH 403/414] adding easyconfigs: libtree-3.1.1.eb --- .../easyconfigs/l/libtree/libtree-3.1.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtree/libtree-3.1.1.eb diff --git a/easybuild/easyconfigs/l/libtree/libtree-3.1.1.eb b/easybuild/easyconfigs/l/libtree/libtree-3.1.1.eb new file mode 100644 index 00000000000..649be0fa3f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libtree/libtree-3.1.1.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'libtree' +version = '3.1.1' + +homepage = 'https://github.com/haampie/libtree' +description = """libtree is a tool that turns ldd into a tree, explains why + shared libraries are found and why not and optionally deploys executables and + dependencies into a single directory""" + +toolchain = SYSTEM + +github_account = 'haampie' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6148436f54296945d22420254dd78e1829d60124bb2f5b9881320a6550f73f5c'] + +buildopts = "LDFLAGS='-static'" + +runtest = 'check' + +files_to_copy = [(['libtree'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/libtree"], + 'dirs': [], +} + +sanity_check_commands = [ + "libtree --help", + "libtree -v -p %(installdir)s/bin/libtree", +] + +moduleclass = 'tools' From d5fefe80c825db2c6f42f905f3e76c7857294544 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 22 Jan 2025 13:00:48 +0100 Subject: [PATCH 404/414] adding easyconfigs: wrf-python-1.3.4.1-20241111-foss-2024a.eb, basemap-1.4.1-foss-2024a.eb, Cartopy-0.24.1-foss-2024a.eb --- .../b/basemap/basemap-1.4.1-foss-2024a.eb | 59 +++++++++++++++++++ .../c/Cartopy/Cartopy-0.24.1-foss-2024a.eb | 51 ++++++++++++++++ .../wrf-python-1.3.4.1-20241111-foss-2024a.eb | 47 +++++++++++++++ 3 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/b/basemap/basemap-1.4.1-foss-2024a.eb create mode 100644 easybuild/easyconfigs/c/Cartopy/Cartopy-0.24.1-foss-2024a.eb create mode 100644 easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-20241111-foss-2024a.eb diff --git a/easybuild/easyconfigs/b/basemap/basemap-1.4.1-foss-2024a.eb b/easybuild/easyconfigs/b/basemap/basemap-1.4.1-foss-2024a.eb new file mode 100644 index 00000000000..f98b8a14269 --- /dev/null +++ b/easybuild/easyconfigs/b/basemap/basemap-1.4.1-foss-2024a.eb @@ -0,0 +1,59 @@ +# The newer version require also the installation of basemap-data. +# Conveniently, the tarball contains that too, so that is the one +# being used here. +# Based on basemap-1.2.2-foss-2020a-Python-3.8.2.eb +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'basemap' +version = '1.4.1' + +homepage = 'https://matplotlib.org/basemap/' +description = """The matplotlib basemap toolkit is a library for plotting +2D data on maps in Python""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +builddependencies = [ + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('matplotlib', '3.9.2'), + ('GEOS', '3.12.2'), + ('Pillow', '10.4.0'), + ('pyproj', '3.7.0'), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = "cd packages/%(name)s && " +# remote strict upper limit for required Python packages for recent Python versions +local_preinstallopts += "sed -i 's/< [0-9.]*; python_version >=/; python_version >=/g' requirements.txt && " +local_preinstallopts += "GEOS_DIR=$EBROOTGEOS" + +exts_list = [ + ('pyshp', '2.3.1', { + 'modulename': 'shapefile', + 'checksums': ['4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1'], + }), + ('basemap_data', version, { + 'modulename': 'mpl_toolkits.basemap_data', + 'preinstallopts': "cd packages/%(name)s && GEOS_DIR=$EBROOTGEOS", + 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['730b1e2ff5eb31c73680bd8ebabc6b11adfc587cfa6832c528a8a82822e5a490'], + }), + (name, version, { + 'modulename': 'mpl_toolkits.basemap', + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['730b1e2ff5eb31c73680bd8ebabc6b11adfc587cfa6832c528a8a82822e5a490'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.24.1-foss-2024a.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.24.1-foss-2024a.eb new file mode 100644 index 00000000000..7fdc81a29b7 --- /dev/null +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.24.1-foss-2024a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'Cartopy' +version = '0.24.1' + +homepage = 'https://scitools.org.uk/cartopy/docs/latest/' +description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('Fiona', '1.10.1'), + ('GDAL', '3.10.0'), + ('GEOS', '3.12.2'), + ('matplotlib', '3.9.2'), + ('pyproj', '3.7.0'), + ('SciPy-bundle', '2024.05'), + ('Shapely', '2.0.6'), + ('lxml', '5.3.0'), + ('Pillow', '10.4.0'), + ('PROJ', '9.4.1'), + ('PyYAML', '6.0.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('OWSLib', '0.32.0', { + 'checksums': ['7513860d3102ae8d4dc5efd8652ff3c61eca3a8cb220d6c8601121357cd2b01a'], + }), + ('pyepsg', '0.4.0', { + 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], + }), + ('pykdtree', '1.3.13', { + 'checksums': ['3accf852e946653e399c3d4dbbe119dbc6d3f72cfd2d5a95cabf0bf0c7f924fe'], + }), + ('pyshp', '2.3.1', { + 'modulename': 'shapefile', + 'checksums': ['4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1'], + }), + (name, version, { + 'preinstallopts': """sed -i 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """, + 'sources': ['cartopy-%(version)s.tar.gz'], + 'checksums': ['01c910d5634c69a7efdec46e0a17d473d2328767f001d4dc0b5c4b48e585c8bd'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-20241111-foss-2024a.eb b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-20241111-foss-2024a.eb new file mode 100644 index 00000000000..886d4eb8d81 --- /dev/null +++ b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-20241111-foss-2024a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'wrf-python' +version = '1.3.4.1-20241111' +local_commit = '5711683' + +homepage = 'https://wrf-python.readthedocs.io' +description = """A collection of diagnostic and interpolation routines for use with output from + the Weather Research and Forecasting (WRF-ARW) Model.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('CMake', '3.29.3'), + ('scikit-build-core', '0.10.6'), +] +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('netcdf4-python', '1.7.1.post2'), + ('xarray', '2024.11.0'), + ('matplotlib', '3.9.2'), + ('Cartopy', '0.24.1'), + ('basemap', '1.4.1'), + ('wrapt', '1.16.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'wrf', + # download latest commit with new build system - old one is not compatible with python 3.12 + # see https://github.com/NCAR/wrf-python/issues/217 and https://github.com/NCAR/wrf-python/pull/242 + 'source_urls': ['https://github.com/NCAR/wrf-python/archive/'], + 'sources': [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit, + }], + 'checksums': ['b501097ae8fbf121420371b1dc8911a8900968e4d63726a454886f855db618a5'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From c29445358e43a57f3990a9ea61c6c1c6010a28fa Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 22 Jan 2025 14:24:33 +0100 Subject: [PATCH 405/414] update Cartopy ec- cython --- easybuild/easyconfigs/c/Cartopy/Cartopy-0.24.1-foss-2024a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.24.1-foss-2024a.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.24.1-foss-2024a.eb index 7fdc81a29b7..cc42b4579ce 100644 --- a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.24.1-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.24.1-foss-2024a.eb @@ -8,6 +8,9 @@ description = """Cartopy is a Python package designed to make drawing maps for d toolchain = {'name': 'foss', 'version': '2024a'} +builddependencies = [ + ('Cython', '3.0.10'), +] dependencies = [ ('Python', '3.12.3'), ('Python-bundle-PyPI', '2024.06'), @@ -42,7 +45,7 @@ exts_list = [ 'checksums': ['4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1'], }), (name, version, { - 'preinstallopts': """sed -i 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """, + 'preinstallopts': r"sed -i 's/dynamic = \[\"version\"\]/version = \"%(version)s\"/g' pyproject.toml && ", 'sources': ['cartopy-%(version)s.tar.gz'], 'checksums': ['01c910d5634c69a7efdec46e0a17d473d2328767f001d4dc0b5c4b48e585c8bd'], }), From b2f04605a30050d0a344d6e5bbfad2df1d203f45 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 22 Jan 2025 18:03:17 +0100 Subject: [PATCH 406/414] added YaHS-1.2.2-foss-2024a.eb --- .../easyconfigs/y/YaHS-1.2.2-foss-2024a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/y/YaHS-1.2.2-foss-2024a.eb diff --git a/easybuild/easyconfigs/y/YaHS-1.2.2-foss-2024a.eb b/easybuild/easyconfigs/y/YaHS-1.2.2-foss-2024a.eb new file mode 100644 index 00000000000..1ca8263fc4d --- /dev/null +++ b/easybuild/easyconfigs/y/YaHS-1.2.2-foss-2024a.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = "YaHS" +version = "1.2.2" + +homepage = 'https://github.com/c-zhou/yahs' +description = "Yet another Hi-C scaffolding tool" + +toolchain = {'name': 'foss', 'version': '2024a'} + +source_urls = ['https://github.com/c-zhou/yahs/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9ee37f72ee9f62015fe92029d0fa97eec90963ddf15a2f4b760b45ee2e0014aa'] + +files_to_copy = [(["yahs", "juicer", "agp_to_fasta"], "bin"), "LICENSE", "README.md" ] + +sanity_check_paths = { + 'files': ["bin/yahs", "bin/juicer", "bin/agp_to_fasta"], + 'dirs': [], +} + +moduleclass = 'bio' From 3ab1f85816225f0530b826c8fb714e0ce847001b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Jan 2025 20:05:12 +0100 Subject: [PATCH 407/414] stick to osmesa variant of glew + prefer pkgconf over pkg-config as build dependency --- .../easyconfigs/l/libwpe/libwpe-1.16.0-GCCcore-12.3.0.eb | 2 +- .../easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-12.3.0.eb | 2 +- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb | 4 ++-- .../w/wpebackend-fdo/wpebackend-fdo-1.15.90-GCCcore-12.3.0.eb | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libwpe/libwpe-1.16.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libwpe/libwpe-1.16.0-GCCcore-12.3.0.eb index 1b821100762..7b67b5f70e8 100644 --- a/easybuild/easyconfigs/l/libwpe/libwpe-1.16.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libwpe/libwpe-1.16.0-GCCcore-12.3.0.eb @@ -32,7 +32,7 @@ builddependencies = [ ] dependencies = [ - ('glew', '2.2.0', '-egl'), + ('glew', '2.2.0', '-osmesa'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-12.3.0.eb index e661a73e704..a89b71a9110 100644 --- a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-12.3.0.eb @@ -27,7 +27,7 @@ checksums = [ builddependencies = [ ('binutils', '2.40'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.9.5'), ('CMake', '3.26.3'), ] diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb index 71a73ed1dfc..6ff71077409 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.41.4-foss-2023a.eb @@ -36,7 +36,7 @@ builddependencies = [ ('Python', '3.11.3'), ('Perl', '5.36.1'), ('GObject-Introspection', '1.76.1'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.9.5'), ('ccache', '4.9'), ('unifdef', '2.12'), ] @@ -56,7 +56,7 @@ dependencies = [ ('OpenJPEG', '2.5.0'), ('Ruby', '3.3.0'), ('GSL', '2.7'), - ('glew', '2.2.0', '-egl'), + ('glew', '2.2.0', '-osmesa'), ('enchant-2', '2.6.5'), ('LittleCMS', '2.15'), ('GST-plugins-base', '1.22.5'), diff --git a/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.15.90-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.15.90-GCCcore-12.3.0.eb index aad4f18049c..15dfe355e1a 100644 --- a/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.15.90-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.15.90-GCCcore-12.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('binutils', '2.40'), ('Meson', '1.1.1'), ('Ninja', '1.11.1'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.9.5'), ] dependencies = [ From 5afd2fbca243a845cc56d658e2dd1a44f463bbaa Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 22 Jan 2025 20:18:47 +0100 Subject: [PATCH 408/414] move YaSH easyconfig to right subdirectory --- easybuild/easyconfigs/y/{ => YaHS}/YaHS-1.2.2-foss-2024a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/y/{ => YaHS}/YaHS-1.2.2-foss-2024a.eb (100%) diff --git a/easybuild/easyconfigs/y/YaHS-1.2.2-foss-2024a.eb b/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb similarity index 100% rename from easybuild/easyconfigs/y/YaHS-1.2.2-foss-2024a.eb rename to easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb From 64c9b81ccf237e5a67af2ed86fc81b357d5d55a2 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Wed, 22 Jan 2025 21:49:05 +0100 Subject: [PATCH 409/414] Update YaHS-1.2.2-foss-2024a.eb style fix. remove space --- easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb b/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb index 1ca8263fc4d..e5c1989ee9c 100644 --- a/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb +++ b/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/c-zhou/yahs/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['9ee37f72ee9f62015fe92029d0fa97eec90963ddf15a2f4b760b45ee2e0014aa'] -files_to_copy = [(["yahs", "juicer", "agp_to_fasta"], "bin"), "LICENSE", "README.md" ] +files_to_copy = [(["yahs", "juicer", "agp_to_fasta"], "bin"), "LICENSE", "README.md"] sanity_check_paths = { 'files': ["bin/yahs", "bin/juicer", "bin/agp_to_fasta"], From b7f4dbaf7a9e0bb0ddc19d408ca5a1fa921cfcfa Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 23 Jan 2025 09:09:01 +0100 Subject: [PATCH 410/414] remove old easybuild url from easyconfig --- easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb b/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb index 1ca8263fc4d..254228afec3 100644 --- a/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb +++ b/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://easybuild.io/ # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics From 7ad37b1a210dd99589df2fec79ad1ccba91abb86 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Thu, 23 Jan 2025 11:11:11 +0100 Subject: [PATCH 411/414] libtree 3.1.1: fix build on aarch64 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../easyconfigs/l/libtree/libtree-3.1.1.eb | 6 ++- .../libtree-3.1.1_fix_32_bit_test.patch | 51 +++++++++++++++++++ 2 files changed, 56 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libtree/libtree-3.1.1_fix_32_bit_test.patch diff --git a/easybuild/easyconfigs/l/libtree/libtree-3.1.1.eb b/easybuild/easyconfigs/l/libtree/libtree-3.1.1.eb index 649be0fa3f5..3a45628af09 100644 --- a/easybuild/easyconfigs/l/libtree/libtree-3.1.1.eb +++ b/easybuild/easyconfigs/l/libtree/libtree-3.1.1.eb @@ -13,7 +13,11 @@ toolchain = SYSTEM github_account = 'haampie' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['6148436f54296945d22420254dd78e1829d60124bb2f5b9881320a6550f73f5c'] +patches = ['libtree-3.1.1_fix_32_bit_test.patch'] +checksums = [ + '6148436f54296945d22420254dd78e1829d60124bb2f5b9881320a6550f73f5c', # v3.1.1.tar.gz, + '489bf7c8f4b0d8e7c8023b3695096f7a6e13748c7036dd7d46deeb6189184251', # libtree-3.1.1_fix_32_bit_test.patch +] buildopts = "LDFLAGS='-static'" diff --git a/easybuild/easyconfigs/l/libtree/libtree-3.1.1_fix_32_bit_test.patch b/easybuild/easyconfigs/l/libtree/libtree-3.1.1_fix_32_bit_test.patch new file mode 100644 index 00000000000..516de64c149 --- /dev/null +++ b/easybuild/easyconfigs/l/libtree/libtree-3.1.1_fix_32_bit_test.patch @@ -0,0 +1,51 @@ +From 061d3ec62707a526a83482e57d202a66f9d776cd Mon Sep 17 00:00:00 2001 +From: Ismael Luceno +Date: Tue, 23 Aug 2022 19:34:39 +0200 +Subject: [PATCH] Test the -m32 and -m64 compiler flags before use + +Fixes: https://github.com/haampie/libtree/issues/78 +Signed-off-by: Ismael Luceno +--- + tests/05_32_bits/Makefile | 20 +++++++++++++++----- + 1 file changed, 15 insertions(+), 5 deletions(-) + +diff --git a/tests/05_32_bits/Makefile b/tests/05_32_bits/Makefile +index 2c0bece..5628f42 100644 +--- a/tests/05_32_bits/Makefile ++++ b/tests/05_32_bits/Makefile +@@ -3,7 +3,7 @@ + + LD_LIBRARY_PATH= + +-.PHONY: clean ++.PHONY: clean check + + all: check + +@@ -21,11 +21,21 @@ exe64: lib64/libx.so + exe32: lib32/libx.so + echo 'extern int a(); int _start(){return a();}' | $(CC) -m32 "-Wl,-rpath,$(CURDIR)/lib64" "-Wl,-rpath,$(CURDIR)/lib32" -o $@ -nostdlib -x c - -Llib32 -lx + +-check: exe32 exe64 +- ../../libtree exe32 +- ../../libtree exe64 +- + clean: + rm -rf lib32 lib64 exe* + + CURDIR ?= $(.CURDIR) ++ ++test-flag = 2>/dev/null ${CC} -E /dev/null ++test-end = && echo y || echo n ++support-m32 != ${test-flag} -m32 ${test-end} ++support-m64 != ${test-flag} -m64 ${test-end} ++ ++check${support-m32:y=}:: exe32 ++ ../../libtree exe32 ++ ++check${support-m64:y=}:: exe64 ++ ../../libtree exe64 ++ ++check${support-m32:n=} check${support-m64:n=}:: ++ @echo WARNING: test skipped at ${CURDIR} + From d61f494765ae33771384594c21fa8411a2cea408 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 23 Jan 2025 13:05:27 +0000 Subject: [PATCH 412/414] adding easyconfigs: matlab-proxy-0.23.4-GCCcore-13.2.0.eb --- .../matlab-proxy-0.23.4-GCCcore-13.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.23.4-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.23.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.23.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..00648bcb04d --- /dev/null +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.23.4-GCCcore-13.2.0.eb @@ -0,0 +1,49 @@ +easyblock = "PythonBundle" + +name = 'matlab-proxy' +version = '0.23.4' + +homepage = 'https://github.com/mathworks/matlab-proxy' +description = "A Python package which enables you to launch MATLAB and access it from a web browser." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('nodejs', '20.9.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('aiohttp', '3.9.5'), + ('Xvfb', '21.1.9'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('aiohttp-session', '2.12.0', { + 'checksums': ['0ccd11a7c77cb9e5a61f4daacdc9170d561112f9cfaf9e9a2d9867c0587d1950'], + }), + ('watchdog', '6.0.0', { + 'checksums': ['9ddf7c82fda3ae8e24decda1338ede66e1c99883db93711d8fb941eaa2d8c282'], + }), + (name, version, { + 'patches': ['%(name)s-0.18.1_use_lic_from_eb_installed_matlab.patch'], + 'checksums': [ + {'matlab-proxy-0.23.4.tar.gz': 'd9a0106d6831142477090863fbeaea27ff678f60daddacbd8f38c436109a67bf'}, + {'matlab-proxy-0.18.1_use_lic_from_eb_installed_matlab.patch': + 'a6b994d8b511bd00f86f232c9d9cf230883090b575383a42c06857f26ea08210'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/matlab-proxy-app'], + 'dirs': ['lib64/python%(pyshortver)s/site-packages'] +} + +modloadmsg = 'matlab-proxy requires MATLAB to be loaded separately and BEFORE this module (2020b or later)' + +moduleclass = 'math' From 98e14df81182569f304717e9938e77b57b307a03 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 23 Jan 2025 15:55:30 +0100 Subject: [PATCH 413/414] add sanity_check_command yahs easyconfig --- easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb b/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb index e5761fac3ba..04a01e18c48 100644 --- a/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb +++ b/easybuild/easyconfigs/y/YaHS/YaHS-1.2.2-foss-2024a.eb @@ -24,4 +24,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['yahs --help'] + moduleclass = 'bio' From b7a7339fe9551a8e6fb96d6d6d9899f144211010 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 23 Jan 2025 19:57:53 +0100 Subject: [PATCH 414/414] remove download_dep_fail --- .../c/cython-cmake/cython-cmake-0.2.0-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cython-cmake/cython-cmake-0.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cython-cmake/cython-cmake-0.2.0-GCCcore-13.2.0.eb index bc40ac3d1e9..16eb66f327e 100644 --- a/easybuild/easyconfigs/c/cython-cmake/cython-cmake-0.2.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/c/cython-cmake/cython-cmake-0.2.0-GCCcore-13.2.0.eb @@ -22,7 +22,6 @@ dependencies = [ ('flit', '3.9.0'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True