From a8a1c2eff71c55bf59ff57b836b705c1472f27b6 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Dec 2023 19:26:09 +0000 Subject: [PATCH 001/106] adding easyconfigs: pyiron-0.5.1-foss-2023a-Python-3.11.3.eb --- .../b/Biopython/Biopython-1.81-foss-2023a.eb | 45 +++++++++ .../b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb | 28 ++++++ .../b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb | 31 ++++++ .../coverage/coverage-7.2.3-GCCcore-12.3.0.eb | 33 +++++++ .../MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb | 57 +++++++++++ .../m/molmod/molmod-1.4.8-foss-2023a.eb | 37 ++++++++ .../n/nglview/nglview-3.0.8-foss-2023a.eb | 45 +++++++++ .../n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb | 36 +++++++ .../n/numexpr/numexpr-2.8.7-foss-2023a.eb | 23 +++++ .../p/PyTables/PyTables-3.8.0-foss-2023a.eb | 76 +++++++++++++++ .../p/phonopy/phonopy-2.20.0-gfbf-2023a.eb | 38 ++++++++ .../py-cpuinfo-9.0.0-GCCcore-12.3.0.eb | 39 ++++++++ .../pyiron-0.5.1-foss-2023a-Python-3.11.3.eb | 94 +++++++++++++++++++ .../q/QuickFF/QuickFF-2.2.7-foss-2023a.eb | 34 +++++++ .../t/TAMkin/TAMkin-1.2.6-foss-2023a.eb | 42 +++++++++ .../y/yaff/yaff-1.6.0-foss-2023a.eb | 58 ++++++++++++ 16 files changed, 716 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2023a.eb create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb create mode 100644 easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb create mode 100644 easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.8.7-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a-Python-3.11.3.eb create mode 100644 easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.7-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2023a.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2023a.eb new file mode 100644 index 00000000000..081bc0e46a7 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2023a.eb @@ -0,0 +1,45 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.81' + +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': '2023a'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +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' diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..60fb8a755d1 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.21.5' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['32e61961bbf81ffea6ff30e9d70fca36c86178afd3e3cfa13376adec8c687509'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..58f563af452 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.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) +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.8.0' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['be608cdf68deb02e0d3ee62e183942a0fe5d5d3185375b9b6566e2ae35a9bdbd'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f75075ae45e --- /dev/null +++ b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'coverage' +version = '7.2.3' + +homepage = 'https://coverage.readthedocs.io' +description = """ Coverage.py is a tool for measuring code coverage of Python programs. + It monitors your program, noting which parts of the code have been executed, + then analyzes the source to identify code that could have been executed but was not. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d298c2815fa4891edd9abe5ad6e6cb4207104c7dd9fd13aea3fdebf6f9b91259'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb new file mode 100644 index 00000000000..b2d9700e6ec --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb @@ -0,0 +1,57 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '2.6.1' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Biopython', '1.81'), + ('networkx', '3.1'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mrcfile', '1.4.3', { + 'checksums': ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5'], + }), + ('GridDataFormats', '1.0.1', { + 'modulename': 'gridData', + 'checksums': ['ad2c9ab7d672a6d8c426de7d083eee4f3e2b0bd59391675d30683c768ab83cc4'], + }), + ('gsd', '2.8.0', { + 'checksums': ['f2b031a26a7a5bee5f3940dc2f36c5a5b6670307b297c526adf2e26c1f5b46ae'], + }), + ('msgpack', '1.0.5', { + 'checksums': ['c075544284eadc5cddc70f4757331d99dcbc16b2bbd4849d15f8aae4cf36d31c'], + }), + ('mmtf-python', '1.1.3', { + 'modulename': 'mmtf', + 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + (name, version, { + 'modulename': 'MDAnalysis', + 'checksums': ['9cc69b94bddd026f26ffcaf5bdbed6d568c1c10e19a341d84f8d37a2a70222f2'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb new file mode 100644 index 00000000000..eb570fc1078 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.8-foss-2023a_fix-np-unicode.patch'] +checksums = [ + {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8-foss-2023a_fix-np-unicode.patch': + '85bd2e2981d2cdd8cfab5d1c2cf37432e2967ff82de603700383d7c31530327c'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; pytest -ra" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb b/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb new file mode 100644 index 00000000000..73b94940f74 --- /dev/null +++ b/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'nglview' +version = '3.0.8' + +homepage = 'https://github.com/arose/nglview' +description = "IPython widget to interactively view molecular structures and trajectories." + +toolchain = {'name': 'foss', 'version': '2023a'} + +local_gfbf_ver = '2023a' + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07', '', ('gfbf', local_gfbf_ver)), + ('JupyterLab', '4.0.5'), + ('nodejs', '18.17.1'), + ('MDAnalysis', '2.6.1'), # optional +] + +use_pip = True + +exts_list = [ + ('versioneer', '0.28', { + 'checksums': ['7175ca8e7bb4dd0e3c9779dd2745e5b4a6036304af3f5e50bd896f10196586d6'], + }), + (name, version, { + 'use_pip_extras': 'MDAnalysis', + 'checksums': ['f9e468cd813dac319cbeca6ae20ae099008ff3a06399f5d23d75582dde28623a'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/nglview'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..46f4f2d2669 --- /dev/null +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'nose3' +version = '1.3.8' + +homepage = 'https://nose.readthedocs.io/' +description = """Nose extends unittest to make testing easier.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('coverage', '7.2.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/nosetests'], + 'dirs': [], +} + +options = {'modulename': 'nose'} + +sanity_check_commands = ["nosetests --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.8.7-foss-2023a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.7-foss-2023a.eb new file mode 100644 index 00000000000..14d228ba563 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.7-foss-2023a.eb @@ -0,0 +1,23 @@ +name = 'numexpr' +version = '2.8.7' + +homepage = 'https://numexpr.readthedocs.io/en/latest/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['df5131349ec1e4b080a3e2df7abbb7bce20d023adff633d259e1ce1549a60ed1'] + +local_gfbf_ver = '2023a' + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07', '', ('gfbf', local_gfbf_ver)), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb new file mode 100644 index 00000000000..fd6d17abf9f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb @@ -0,0 +1,76 @@ +# http://www.pytables.org/usersguide/installation.html +# updated: Denis Kristak (INUITS) + +easyblock = 'PythonBundle' + +name = 'PyTables' +version = '3.8.0' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing, + processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and + disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions + such as relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +local_gfbf_ver = '2023a' + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('scikit-build', '0.17.6'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07', '', ('gfbf', local_gfbf_ver)), # provides numexpr + ('HDF5', '1.14.0'), + ('LZO', '2.10'), + ('Blosc', '1.21.5'), + ('Blosc2', '2.8.0'), + ('py-cpuinfo', '9.0.0'), +] + +use_pip = True + +exts_list = [ + ('blosc2', '2.0.0', { + 'patches': ['blosc2-2.0.0_use-Blosc2-dep.patch'], + 'checksums': [ + {'blosc2-2.0.0.tar.gz': 'f19b0b3674f6c825b490f00d8264b0c540c2cdc11ec7e81178d38b83c57790a1'}, + {'blosc2-2.0.0_use-Blosc2-dep.patch': '6a9443f378472ada3c8fe8a8a346fe16f22b01bab7d9e60c23b64b546178054b'}, + ], + }), + ('tables', version, { + 'patches': [ + 'PyTables-%(version)s_fix-libs.patch', + 'PyTables-%(version)s_fix-find-blosc2-library-path.patch', + ], + 'checksums': [ + {'tables-%(version)s.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'}, + {'PyTables-%(version)s_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'}, + {'PyTables-%(version)s_fix-find-blosc2-library-path.patch': + 'dcf6c3a16a138454296161e99cf6470620755d4c26303186a744f09a11e6013b'}, + ], + }), +] + +local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-gfbf-2023a.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-gfbf-2023a.eb new file mode 100644 index 00000000000..959805d4cce --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-gfbf-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '2.20.0' + +homepage = 'https://atztogo.github.io/phonopy/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://github.com/phonopy/phonopy/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1dd47cb6e5b427d5cb88ce0b810b91f05533f434d53d22ea69eb974d4eb0ab46'] + +local_foss_ver = '2023a' + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # for numpy + ('matplotlib', '3.7.2'), + ('PyYAML', '6.0'), + ('h5py', '3.9.0', '', ('foss', local_foss_ver)), + ('spglib-python', '2.1.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["phonopy --help"] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a4a0886152c --- /dev/null +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'py-cpuinfo' +version = '9.0.0' + +homepage = 'https://github.com/workhorsy/py-cpuinfo' +description = "py-cpuinfo gets CPU info with pure Python." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/cpuinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cpuinfo", + "python -m cpuinfo", +] + +options = {'modulename': 'cpuinfo'} + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a-Python-3.11.3.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a-Python-3.11.3.eb new file mode 100644 index 00000000000..5302218568b --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a-Python-3.11.3.eb @@ -0,0 +1,94 @@ +easyblock = 'PythonBundle' + +name = 'pyiron' +version = '0.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pyiron/pyiron' +description = "An integrated development environment (IDE) for computational materials science." + + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('h5py', '3.9.0'), + ('PyYAML', '6.0'), + ('phonopy', '2.20.0'), + ('spglib-python', '2.1.0'), + ('ASE', '3.22.1'), + ('numexpr', '2.8.7'), + ('PyTables', '3.8.0'), + ('nglview', '3.0.8'), + ('tqdm', '4.66.1'), + ('molmod', '1.4.8'), + ('scikit-learn', '1.3.1'), + ('yaff', '1.6.0'), + ('TAMkin', '1.2.6'), + ('QuickFF', '2.2.7'), +] + +check_ldshared = True +use_pip = True + +exts_list = [ + ('h5io', '0.1.2', { + 'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'], + }), + ('defusedxml', '0.6.0', { + 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], + }), + ('pysqa', '0.0.11', { + 'checksums': ['b1a1995ac8b83b86046cef8b72cda962c5fdbf480c6dbba906a467a5dd1d3c81'], + }), + ('paramiko', '3.3.1', { + 'checksums': ['6a3777a961ac86dbef375c5f5b8d50014a1a96d0fd7f054a43bc880134b0ff77'], + }), + ('pyiron_atomistics', '0.3.11', { + 'source_urls': ['https://github.com/pyiron/pyiron_atomistics/archive/refs/tags/'], + 'checksums': ['8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'], + }), + ('SQLAlchemy', '1.3.19', { + 'checksums': ['3bba2e9fbedb0511769780fe1d63007081008c5c2d7d715e91858c94dbaa260e'], + }), + ('dill', '0.3.2', { + 'source_tmpl': 'dill-%(version)s.zip', + 'checksums': ['6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e'], + }), + ('smmap', '3.0.4', { + 'checksums': ['9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24'], + }), + ('gitdb', '4.0.5', { + 'checksums': ['c9e1f2d0db7ddb9a704c2a0217be31214e91a4fe1dea1efad19ae42ba0c285c9'], + }), + ('GitPython', '3.1.8', { + 'modulename': 'git', + 'checksums': ['080bf8e2cf1a2b907634761c2eaefbe83b69930c94c66ad11b65a8252959f912'], + }), + ('colorama', '0.4.3', { + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), + ('pyfiglet', '0.8.post1', { + 'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'], + }), + ('mendeleev', '0.6.0', { + 'checksums': ['944d185e81f158e48dd394b011e6c14acb612c2ffbc3c32c4aa490cd5b4f65dd'], + }), + ('pyfileindex', '0.0.4', { + 'checksums': ['bbfbfc9372f810587917ab1a88bebb8de44d32a1210bbd436c5b88447d97dfd2'], + }), + ('seekpath', '2.0.1', { + 'checksums': ['188513ee187fbbace49066a29ecea9bbd351f23da3bea33d507d0f590856b082'], + }), + (name, version, { + 'modulename': False, + 'source_urls': ['https://github.com/pyiron/pyiron/archive/refs/tags/%(name)s-%(version)s.tar.gz'], + 'checksums': ['2e5e3f892b7e49a15443569870aa4ea049951b71fe2ad1ad7f4ac7551d475788'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.7-foss-2023a.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.7-foss-2023a.eb new file mode 100644 index 00000000000..5bf05e90cf8 --- /dev/null +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.7-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'QuickFF' +version = '2.2.7' + +homepage = 'https://molmod.github.io/QuickFF/' +description = """QuickFF is a Python package developed at the Center for +Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio +calculations.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/molmod/QuickFF/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a71922dd39869770b03809355f13bcabdbb8d50429f4d3574cf427ea762f4023'] + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('molmod', '1.4.8'), + ('yaff', '1.6.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb new file mode 100644 index 00000000000..3d4cbd10978 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['TAMkin-1.2.6_fix-python38.patch'] +checksums = [ + {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, + {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('molmod', '1.4.8'), + ('nose3', '1.3.8') +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb new file mode 100644 index 00000000000..f1a97e2256a --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb @@ -0,0 +1,58 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# +# Building this in interactive Slurm session will result in freeze during either +# runtest phase or sanity_check_commands phase (python -c 'import yaff') +# +# If you submit this as non-interactive Slurm job, it will build just fine. +# Possibly root cause: https://github.com/h5py/h5py/issues/917 +# +easyblock = 'PythonBundle' + +name = 'yaff' +version = '1.6.0' + +homepage = 'https://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('pkgconfig', '1.5.5', '-python')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('h5py', '3.9.0'), + ('molmod', '1.4.8'), + ('nose3', '1.3.8') +] + +use_pip = True +sanity_pip_check = True + +local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +local_runtest += "python setup.py build_ext -i; nosetests -v" + +exts_list = [ + (name, version, { + 'patches': [ + 'yaff-1.6.0-foss-2023a_fix-random-import.patch', + 'yaff-1.6.0-foss-2023a_fix-h5py.patch', + 'yaff-1.6.0-foss-2023a_fix-nose-dep.patch', + ], + 'runtest': "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v", + 'source_urls': ['https://github.com/molmod/yaff/releases/download/%(version)s'], + 'checksums': [ + {'yaff-1.6.0.tar.gz': 'a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'}, + {'yaff-1.6.0-foss-2023a_fix-random-import.patch': + 'a38afacbcbfbf16a80742ae8253852e725e656c9d684310894c806f689362840'}, + {'yaff-1.6.0-foss-2023a_fix-h5py.patch': + 'bd2a73f375910360fd5dd22b3ec006344527476e80dea549f4d82297257105f9'}, + {'yaff-1.6.0-foss-2023a_fix-nose-dep.patch': + '2314c487c4a847d7740d7dfc97052cf7efd764ced726d098def0a1aef0b498e0'}, + ], + }), +] + +moduleclass = 'chem' From 88bd336ef7be3a01de210b460a1c6496ce42bfc9 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Dec 2023 19:35:33 +0000 Subject: [PATCH 002/106] add patches --- .../yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch | 293 ++++++++++++++++++ .../yaff-1.6.0-foss-2023a_fix-nose-dep.patch | 13 + ...f-1.6.0-foss-2023a_fix-random-import.patch | 14 + 3 files changed, 320 insertions(+) create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch new file mode 100644 index 00000000000..13476202a1a --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch @@ -0,0 +1,293 @@ +Adds write mode to ensure h5 files are created as intended. + +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_rdf.py.orig 2023-12-11 16:49:03.170062363 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_rdf.py 2023-12-11 16:54:57.393259317 +0000 +@@ -54,7 +54,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File(__name__ + 'test_rdf1_online.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + 'test_rdf1_online.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + select = ff.system.get_indexes('O') + rdf0 = RDF(4.5*angstrom, 0.1*angstrom, f, select0=select) +@@ -85,7 +85,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File(__name__ + '.test_rdf2_online.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_rdf2_online.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + select0 = ff.system.get_indexes('O') + select1 = ff.system.get_indexes('H') +@@ -156,7 +156,7 @@ + fn_xyz = pkg_resources.resource_filename(__name__, '../../data/test/chloro_pos.xyz') + fn_vol = pkg_resources.resource_filename(__name__, '../../data/test/chloro_vol.txt') + system = System.from_file(fn_xyz, rvecs=np.diag([48.877]*3)) +- with h5.File(__name__ + '.test_rdf_from_file_variable_cell', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_rdf_from_file_variable_cell', mode='w', driver='core', backing_store=False) as f: + # Prepare in-memory HDF5 file + system.to_hdf5(f) + xyz_to_hdf5(f, fn_xyz) +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_spectrum.py.orig 2023-12-11 16:56:45.254710284 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_spectrum.py 2023-12-11 16:57:01.733626405 +0000 +@@ -58,7 +58,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File('yaff.analysis.test.test_spectrum.test_spectrum_online_%i.h5' % bsize, driver='core', backing_store=False) as f: ++ with h5.File('yaff.analysis.test.test_spectrum.test_spectrum_online_%i.h5' % bsize, mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + spectrum0 = Spectrum(f, bsize=bsize) + nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=[hdf5, spectrum0]) +@@ -95,7 +95,7 @@ + + + def test_spectrum_iter_indexes(): +- with h5.File('yaff.analysis.test.test_spectrum.test_spectrum_iter_indexes.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.analysis.test.test_spectrum.test_spectrum_iter_indexes.h5', mode='w', driver='core', backing_store=False) as f: + spectrum = Spectrum(f, bsize=10) + l = list(spectrum._iter_indexes(np.zeros((10, 5, 3), float))) + assert l == [(0, 0), (0, 1), (0, 2), (1, 0), (1, 1), (1, 2), (2, 0), (2, 1), +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_cp2k.py.orig 2023-12-11 16:58:37.780137513 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_cp2k.py 2023-12-11 16:58:51.184069284 +0000 +@@ -33,7 +33,7 @@ + + + def test_cp2k_ener_to_hdf5(): +- with h5.File(__name__ + '.test_xyz_to_hdf5.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_xyz_to_hdf5.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. The trajectory file has no system directory... + # Actual trajectory conversion, twice + for i in range(2): +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_dlpoly.py.orig 2023-12-11 17:01:09.540364868 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_dlpoly.py 2023-12-11 17:01:36.290228634 +0000 +@@ -33,7 +33,7 @@ + + + def test_dlpoly_history_uo(): +- with h5.File(__name__ + '.test_dlpoly_history_uo.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_dlpoly_history_uo.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. The trajectory file has no system directory... + # Actual trajectory conversion, twice + for i in range(2): +@@ -60,7 +60,7 @@ + + + def test_dlpoly_history_sam(): +- with h5.File(__name__ + '.test_dlpoly_history_sam.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_dlpoly_history_sam.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. The trajectory file has no system directory... + # Actual trajectory conversion, twice + for i in range(2): +@@ -84,7 +84,7 @@ + + def test_dlpoly_history_an(): + raise SkipTest('Fails, ask An why because dlpoly_history_sam does work') +- with h5.File(__name__ + '.test_dlpoly_history_an.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_dlpoly_history_an.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. The trajectory file has no system directory... + # Actual trajectory conversion, par1 + fn = pkg_resources.resource_filename(__name__, '../../data/test/dlpoly_HISTORY_an1') +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_gaussian.py.orig 2023-12-11 17:03:12.986736177 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_gaussian.py 2023-12-11 17:03:28.326658047 +0000 +@@ -85,7 +85,7 @@ + vel_unit = np.sqrt(amu)/second + fn_xyz = pkg_resources.resource_filename(__name__, '../../data/test/gaussian_sioh4_md.xyz') + fn_log = pkg_resources.resource_filename(__name__, '../../data/test/gaussian_sioh4_md.log') +- with h5.File('yaff.conversion.test.test_gaussian.test_to_hdf5.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.conversion.test.test_gaussian.test_to_hdf5.h5', mode='w', driver='core', backing_store=False) as f: + system = System.from_file(fn_xyz) + system.to_hdf5(f) + # Actual trajectory conversion, twice +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_xyz.py.orig 2023-12-11 17:04:41.964283021 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_xyz.py 2023-12-11 17:04:52.624228732 +0000 +@@ -34,7 +34,7 @@ + + + def test_xyz_to_hdf5(): +- with h5.File('yaff.conversion.test.test_xyz.test_xyz_to_hdf5.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.conversion.test.test_xyz.test_xyz_to_hdf5.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. Proper use is to initialize the system object from a + # different XYZ (or yet something else) with a single geometry. + fn_xyz = pkg_resources.resource_filename(__name__, '../../data/test/water_trajectory.xyz') +@@ -55,7 +55,7 @@ + + + def test_xyz_to_hdf5_alt(): +- with h5.File('yaff.conversion.test.test_xyz.test_xyz_to_hdf5_alt.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.conversion.test.test_xyz.test_xyz_to_hdf5_alt.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. Proper use is to initialize the system object from a + # different XYZ (or yet something else) with a single geometry. + fn_xyz = pkg_resources.resource_filename(__name__, '../../data/test/water_trajectory.xyz') +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/examples/001_tutorial_bks/nvt/analysis.py.orig 2023-12-11 17:16:05.373802516 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/examples/001_tutorial_bks/nvt/analysis.py 2023-12-11 17:16:27.458690041 +0000 +@@ -48,7 +48,7 @@ + p_unit = 1e9*pascal + + # Open the trajectory file for post-processing the MD simulation +-with h5.File('traj_%s.h5' % suffix) as f: ++with h5.File('traj_%s.h5' % suffix, mode='r+') as f: + # Get the isotropic pressure. This is the trace of the time-dependent virial + # stress divided by three. + press = np.array(f['trajectory/press'][nskip:]) + +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_verlet.py.orig 2023-12-11 17:37:15.223312935 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_verlet.py 2023-12-11 17:37:28.158245974 +0000 +@@ -77,7 +77,7 @@ + + + def test_hdf5(): +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + nve = VerletIntegrator(get_ff_water32(), 1.0*femtosecond, hooks=hdf5) + nve.run(15) +@@ -88,7 +88,7 @@ + + + def test_hdf5_start(): +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5_start.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5_start.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f, start=2) + nve = VerletIntegrator(get_ff_water32(), 1.0*femtosecond, hooks=hdf5) + nve.run(5) +@@ -99,7 +99,7 @@ + + + def test_hdf5_step(): +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5_step.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5_step.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f, step=2) + nve = VerletIntegrator(get_ff_water32(), 1.0*femtosecond, hooks=hdf5) + nve.run(5) +@@ -113,7 +113,7 @@ + # This test does not write all possible outputs + sys = get_system_water() + ff = ForceField.generate(sys, pkg_resources.resource_filename(__name__, '../../data/test/parameters_water_bondharm.txt')) +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5_simple.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5_simple.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=hdf5) + nve.run(15) +@@ -138,7 +138,7 @@ + part_bias.add_term(bias1) + cv_tracker = CVStateItem([cv0,cv1]) + bias_tracker = BiasStateItem(part_bias) +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5_cvs.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5_cvs.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=hdf5, state=[cv_tracker, bias_tracker]) + nve.run(5) +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/common.py.orig 2023-12-11 17:47:09.632235821 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/common.py 2023-12-11 17:47:19.706183672 +0000 +@@ -40,7 +40,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File('%s/output.h5' % dn_tmp) as f: ++ with h5.File('%s/output.h5' % dn_tmp, mode='w') as f: + hdf5 = HDF5Writer(f) + nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=hdf5) + nve.run(5) +@@ -55,7 +55,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File('%s/output.h5' % dn_tmp) as f: ++ with h5.File('%s/output.h5' % dn_tmp, mode='w') as f: + hdf5 = HDF5Writer(f) + thermostat = LangevinThermostat(temp=300) + nvt = VerletIntegrator(ff, 1.0*femtosecond, hooks=[hdf5, thermostat]) +@@ -71,7 +71,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File('%s/output.h5' % dn_tmp) as f: ++ with h5.File('%s/output.h5' % dn_tmp, mode='w') as f: + hdf5 = HDF5Writer(f) + opt = CGOptimizer(FullCellDOF(ff), hooks=hdf5) + opt.run(5) +@@ -94,7 +94,7 @@ + # Dihedral angles are periodic, this has to be taken into account! + periodicities = np.array([2.0*np.pi,2.0*np.pi]) + # Run a test simulation +- with h5.File('%s/output.h5' % dn_tmp) as f: ++ with h5.File('%s/output.h5' % dn_tmp, mode='w') as f: + hdf5 = HDF5Writer(f) + mtd = MTDHook(ff, [cv0,cv1], sigmas, K, f=f, start=pace, step=pace, + periodicities=periodicities) +53c53 +< with h5.File('yaff.sampling.test.test_enhanced.test_mtd_alanine.h5', driver='core', backing_store=False) as f: +--- +> with h5.File('yaff.sampling.test.test_enhanced.test_mtd_alanine.h5', mode='w', driver='core', backing_store=False) as f: +140c140 +< driver='core', backing_store=False) as f0: +--- +> mode='w', driver='core', backing_store=False) as f0: +148c148 +< driver='core', backing_store=False) as f1: +--- +> mode='w', driver='core', backing_store=False) as f1: +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_diffusion.py.orig 2023-12-11 17:54:24.258996848 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_diffusion.py 2023-12-11 17:54:35.027941887 +0000 +@@ -53,7 +53,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File('yaff.analysis.test.test_diffusion.test_diff_online.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.analysis.test.test_diffusion.test_diff_online.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + select = ff.system.get_indexes('O') + diff0 = Diffusion(f, select=select) +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_enhanced.py.orig 2023-12-11 17:55:55.676530269 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_enhanced.py 2023-12-11 17:56:12.271445571 +0000 +@@ -50,7 +50,7 @@ + # Construct metadynamics as a Yaff hook + ff = get_alaninedipeptide_amber99ff() + cv = CVInternalCoordinate(ff.system, DihedAngle(4,6,8,14)) +- with h5.File('yaff.sampling.test.test_enhanced.test_mtd_alanine.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_enhanced.test_mtd_alanine.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + mtd = MTDHook(ff, cv, sigma, K, f = f, start=pace, step=pace, periodicities=2*np.pi) + nvt = VerletIntegrator(ff, 1.0*femtosecond, hooks=[mtd]) +@@ -137,7 +137,7 @@ + ff = get_alaninedipeptide_amber99ff() + cv = CVInternalCoordinate(ff.system, DihedAngle(4,6,8,14)) + with h5.File('yaff.sampling.test.test_enhanced.test_mtd_restart.h5', +- driver='core', backing_store=False) as f0: ++ mode='w', driver='core', backing_store=False) as f0: + hdf5 = HDF5Writer(f0) + mtd = MTDHook(ff, cv, sigma, K, f = f0, start=pace, step=pace, periodicities=2*np.pi) + nvt = VerletIntegrator(ff, 1.0*femtosecond, hooks=[mtd]) +@@ -145,7 +145,7 @@ + nvt.run(12) + ff = get_alaninedipeptide_amber99ff() + with h5.File('yaff.sampling.test.test_enhanced.test_mtd_restarted.h5', +- driver='core', backing_store=False) as f1: ++ mode='w', driver='core', backing_store=False) as f1: + mtd_restart = MTDHook(ff, cv, sigma, K, f=f1, start=pace, + step=pace, restart_file=f0, periodicities=2*np.pi) + nvt = VerletIntegrator(ff, 1.0*femtosecond, hooks=[mtd_restart]) +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_mc.py.orig 2023-12-11 17:57:03.929181919 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_mc.py 2023-12-11 17:57:38.412005932 +0000 +@@ -110,7 +110,7 @@ + fn_host = pkg_resources.resource_filename(__name__, '../../data/test/CAU_13.chk') + fn_pars = pkg_resources.resource_filename(__name__, '../../data/test/parameters_CAU-13_xylene.txt') + fn_guest = pkg_resources.resource_filename(__name__, '../../data/test/xylene.chk') +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5_start.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5_start.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = MCHDF5Writer(f) + gcmc = GCMC.from_files(fn_guest, fn_pars, host=fn_host, hooks=[hdf5]) + gcmc.set_external_conditions(200*kelvin, 1000*bar) +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_opt.py.orig 2023-12-11 18:10:36.504037548 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_opt.py 2023-12-11 18:10:48.346977460 +0000 +@@ -120,7 +120,7 @@ + + + def test_cg_hdf5(): +- with h5.File(__name__ + '.test_cg_hdf5.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_cg_hdf5.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + opt = CGOptimizer(CartesianDOF(get_ff_water32()), hooks=hdf5) + opt.run(15) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch new file mode 100644 index 00000000000..eae5fd3999f --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch @@ -0,0 +1,13 @@ +This patch replaces the dependency on nose with a dependency on nose3. + +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/setup.py.orig 2023-12-11 18:18:12.215725329 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/setup.py 2023-12-11 18:19:04.794458554 +0000 +@@ -90,7 +90,7 @@ + include_package_data=True, + zip_safe=False, + setup_requires=['numpy>=1.5', 'cython>=0.26'], +- install_requires=['numpy>=1.5', 'nose>=0.11', 'cython>=0.26', 'matplotlib>1.0.0', ++ install_requires=['numpy>=1.5', 'nose3', 'cython>=0.26', 'matplotlib>1.0.0', + 'h5py>=2.0.0', 'molmod>=1.4.1', 'scipy>=0.17.1'], + ext_modules=[ + Extension("yaff.pes.ext", diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch new file mode 100644 index 00000000000..787c1d31a84 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch @@ -0,0 +1,14 @@ +Replaces import of scipy.random with numpy.random. + +--- /dev/shm/yaff/1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/pca.py.orig 2023-12-11 16:29:17.807097965 +0000 ++++ /dev/shm/yaff/1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/pca.py 2023-12-11 16:29:46.094953909 +0000 +@@ -30,7 +30,7 @@ + import numpy as np + import scipy.linalg as spla + import matplotlib.pyplot as pt +-from scipy import random ++from numpy import random + + from molmod.units import * + from molmod.constants import boltzmann + From 25f279eb84eaa768ff80d2b0344bdcf10e0b4ce4 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Dec 2023 19:55:24 +0000 Subject: [PATCH 003/106] fix pytables config --- .../easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb index fd6d17abf9f..a0f4b362b19 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb @@ -53,9 +53,9 @@ exts_list = [ 'PyTables-%(version)s_fix-find-blosc2-library-path.patch', ], 'checksums': [ - {'tables-%(version)s.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'}, - {'PyTables-%(version)s_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'}, - {'PyTables-%(version)s_fix-find-blosc2-library-path.patch': + {'tables-3.8.0.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'}, + {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'}, + {'PyTables-3.8.0_fix-find-blosc2-library-path.patch': 'dcf6c3a16a138454296161e99cf6470620755d4c26303186a744f09a11e6013b'}, ], }), From 45d47e64997cd986d88b4147c95e94a6cfaf8c41 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Dec 2023 19:58:04 +0000 Subject: [PATCH 004/106] add molmod patcyh --- ...lmod-1.4.8-foss-2023a_fix-np-unicode.patch | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch new file mode 100644 index 00000000000..278ec6a95ad --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch @@ -0,0 +1,38 @@ +Fixes use of `np.unicode` instead of `np.unicode_`. + ++++ 1.4.8/foss-2023a/molmod-1.4.8/molmod/io/test/test_chk.py 2023-12-11 14:55:11.534543922 +0000 +--- 1.4.8/foss-2023a/molmod-1.4.8/molmod/io/test/test_chk.py.orig 2023-12-11 14:53:00.080194283 +0000 +@@ -62,7 +62,7 @@ + + + def test_strings_array_unicode(): ++ data = {'values': np.array(['foo', 'bar'], dtype=np.unicode_)} +- data = {'values': np.array(['foo', 'bar'], dtype=np.unicode)} + check_data_array('test_strings_array', data, np.dtype('U22')) + + +@@ -90,8 +90,8 @@ + + + def test_strings(): ++ check_data('test_strings_array', {'values': 'foo'}, (str, np.unicode_)) ++ check_data('test_strings_array', {'values': 'foo bar'}, (str, np.unicode_)) +- check_data('test_strings_array', {'values': 'foo'}, (str, np.unicode)) +- check_data('test_strings_array', {'values': 'foo bar'}, (str, np.unicode)) + + + def test_floats(): + +--- 1.4.8/foss-2023a/molmod-1.4.8/molmod/io/chk.py.orig 2023-12-11 15:11:10.785959605 +0000 ++++ 1.4.8/foss-2023a/molmod-1.4.8/molmod/io/chk.py 2023-12-11 15:12:24.978584525 +0000 +@@ -141,8 +141,8 @@ + if value.dtype.fields is not None: + raise TypeError('Arrays with fields are not supported.') + shape_str = ','.join(str(i) for i in value.shape) +- if issubclass(value.dtype.type, (str, np.unicode, np.bytes_)): +- value = value.astype(np.unicode) ++ if issubclass(value.dtype.type, (str, np.unicode_, np.bytes_)): ++ value = value.astype(np.unicode_) + for cell in value.flat: + if len(cell) >= 22: + raise ValueError('In case of string arrays, a string may contain at most 21 characters.') From 0d047bebc6f6e3b782bab3fd7f557479bdec1e2d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Wed, 13 Dec 2023 18:42:09 +0000 Subject: [PATCH 005/106] update to pyiron build --- .../p/Pint/Pint-0.22-GCCcore-12.3.0.eb | 28 +++++ .../p/pyiron/pyiron-0.5.1-foss-2023a.eb | 104 ++++++++++++++++++ ...-2023a_fix-pyiron-atomistics-version.patch | 53 +++++++++ ...1-foss-2023a_fix-pyiron-base-version.patch | 41 +++++++ .../typing-extensions-4.9.0-GCCcore-12.3.0.eb | 21 ++++ 5 files changed, 247 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch create mode 100644 easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..63340322e4e --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Pint' +version = '0.22' + +homepage = 'https://github.com/hgrecco/pint' +description = """Pint is a Python package to define, operate and +manipulate physical quantities: the product of a numerical value and a +unit of measurement. It allows arithmetic operations between them and +conversions from and to different units.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2d139f6abbcf3016cad7d3cec05707fe908ac4f99cf59aedfd6ee667b7a64433'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('typing-extensions', '4.9.0') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb new file mode 100644 index 00000000000..24e244b6524 --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -0,0 +1,104 @@ +easyblock = 'PythonBundle' + +name = 'pyiron' +version = '0.5.1' + +homepage = 'https://github.com/pyiron/pyiron' +description = "An integrated development environment (IDE) for computational materials science." + + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('h5py', '3.9.0'), + ('PyYAML', '6.0'), + ('phonopy', '2.20.0'), + ('spglib-python', '2.1.0'), + ('ASE', '3.22.1'), + ('numexpr', '2.8.7'), + ('PyTables', '3.8.0'), + ('nglview', '3.0.8'), + ('tqdm', '4.66.1'), + ('molmod', '1.4.8'), + ('scikit-learn', '1.3.1'), + ('yaff', '1.6.0'), + ('TAMkin', '1.2.6'), + ('QuickFF', '2.2.7'), + ('Pint', '0.22'), +] + +check_ldshared = True +use_pip = True + +exts_list = [ + ('h5io', '0.1.2', { + 'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'], + }), + ('defusedxml', '0.6.0', { + 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], + }), + ('pysqa', '0.0.11', { + 'checksums': ['b1a1995ac8b83b86046cef8b72cda962c5fdbf480c6dbba906a467a5dd1d3c81'], + }), + ('paramiko', '3.3.1', { + 'checksums': ['6a3777a961ac86dbef375c5f5b8d50014a1a96d0fd7f054a43bc880134b0ff77'], + }), + ('SQLAlchemy', '1.3.19', { + 'checksums': ['3bba2e9fbedb0511769780fe1d63007081008c5c2d7d715e91858c94dbaa260e'], + }), + ('dill', '0.3.2', { + 'source_tmpl': 'dill-%(version)s.zip', + 'checksums': ['6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e'], + }), + ('smmap', '3.0.4', { + 'checksums': ['9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24'], + }), + ('gitdb', '4.0.5', { + 'checksums': ['c9e1f2d0db7ddb9a704c2a0217be31214e91a4fe1dea1efad19ae42ba0c285c9'], + }), + ('GitPython', '3.1.8', { + 'modulename': 'git', + 'checksums': ['080bf8e2cf1a2b907634761c2eaefbe83b69930c94c66ad11b65a8252959f912'], + }), + ('colorama', '0.4.3', { + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), + ('pyfiglet', '0.8.post1', { + 'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'], + }), + ('mendeleev', '0.6.0', { + 'checksums': ['944d185e81f158e48dd394b011e6c14acb612c2ffbc3c32c4aa490cd5b4f65dd'], + }), + ('pyfileindex', '0.0.4', { + 'checksums': ['bbfbfc9372f810587917ab1a88bebb8de44d32a1210bbd436c5b88447d97dfd2'], + }), + ('seekpath', '2.0.1', { + 'checksums': ['188513ee187fbbace49066a29ecea9bbd351f23da3bea33d507d0f590856b082'], + }), + (name, version, { + 'modulename': False, + 'source_urls': ['https://github.com/pyiron/pyiron/archive/refs/tags/%(name)s-%(version)s.tar.gz'], + 'checksums': ['2e5e3f892b7e49a15443569870aa4ea049951b71fe2ad1ad7f4ac7551d475788'], + }), + ('pyiron_base', '0.6.12', { + 'patches': ['pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch'], + 'source_urls': ['https://github.com/pyiron/pyiron_base/archive/refs/tags/'], + 'checksums': ['7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'], + }), + ('atomistics', '0.1.15', { + 'patches': ['pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch'], + 'source_urls': ['https://github.com/pyiron/atomistics/archive/refs/tags/'], + }), + ('pyiron_atomistics', '0.3.11', { + 'patches': ['pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch'], + 'source_urls': ['https://github.com/pyiron/pyiron_atomistics/archive/refs/tags/'], + 'checksums': ['8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch new file mode 100644 index 00000000000..9a72f51055b --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -0,0 +1,53 @@ +Fix versioning related issue in pyiron atomistics. + +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig 2023-12-13 17:37:16.618007520 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml 2023-12-13 17:38:08.416737658 +0000 +@@ -43,7 +43,7 @@ + "spglib==2.1.0", + "structuretoolkit==0.0.15", + ] +-dynamic = ["version"] ++version = "0.3.11" + + [project.urls] + Homepage = "https://pyiron.org" +@@ -55,13 +55,3 @@ + + [tool.setuptools.package-data] + "*" = ["data/*.csv"] +- +-[tool.setuptools.dynamic] +-version = {attr = "pyiron_atomistics.__version__"} +- +-[tool.versioneer] +-VCS = "git" +-style = "pep440-pre" +-versionfile_source = "pyiron_atomistics/_version.py" +-parentdir_prefix = "pyiron_atomistics" +-tag_prefix = "pyiron_atomistics-" +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py 2023-12-13 17:41:48.007593887 +0000 +@@ -3,6 +3,6 @@ + import versioneer + + setup( +- version=versioneer.get_version(), +- cmdclass=versioneer.get_cmdclass(), +-) +\ ++ version="0.3.11", ++) ++ +--- 0.5.1/foss-2023a-Python-3.11.3/atomistics/atomistics-atomistics-0.1.15/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/atomistics/atomistics-atomistics-0.1.15/setup.py 2023-12-13 17:41:48.007593887 +0000 +@@ -3,6 +3,6 @@ + import versioneer + + setup( +- version=versioneer.get_version(), +- cmdclass=versioneer.get_cmdclass(), +-) +\ ++ version="0.3.11", ++) ++ diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch new file mode 100644 index 00000000000..8cdbfa8916b --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch @@ -0,0 +1,41 @@ +Fixes use of dynamic versioning in pyproject.toml and puts in a specific version instead. + +--- /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig 2023-12-13 15:51:48.895090935 +0000 ++++ /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml 2023-12-13 15:53:26.626579151 +0000 +@@ -40,7 +40,7 @@ + "tqdm==4.66.1", + "traitlets==5.14.0", + ] +-dynamic = ["version"] ++version = "0.6.12" + + [project.urls] + Homepage = "https://github.com/pyiron/pyiron_base" +@@ -53,12 +53,3 @@ + [tool.setuptools.packages.find] + include = ["pyiron_base*"] + +-[tool.setuptools.dynamic] +-version = {attr = "pyiron_base.__version__"} +- +-[tool.versioneer] +-VCS = "git" +-style = "pep440-pre" +-versionfile_source = "pyiron_base/_version.py" +-parentdir_prefix = "pyiron_base" +-tag_prefix = "pyiron_base-" + +--- /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 ++++ /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py 2023-12-13 17:18:56.504736380 +0000 +@@ -3,6 +3,6 @@ + import versioneer + + setup( +- version=versioneer.get_version(), +- cmdclass=versioneer.get_cmdclass(), +-) +\ No newline at end ++ version="0.6.12", ++) ++ + diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2078482b45a --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.9.0' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions – Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From ba6627ba4a24064d6e948711a9e13c8fbb3e627d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 15:18:14 +0100 Subject: [PATCH 006/106] Delete easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a-Python-3.11.3.eb deleted erroneous rfile --- .../pyiron-0.5.1-foss-2023a-Python-3.11.3.eb | 94 ------------------- 1 file changed, 94 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a-Python-3.11.3.eb diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a-Python-3.11.3.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a-Python-3.11.3.eb deleted file mode 100644 index 5302218568b..00000000000 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a-Python-3.11.3.eb +++ /dev/null @@ -1,94 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pyiron' -version = '0.5.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/pyiron/pyiron' -description = "An integrated development environment (IDE) for computational materials science." - - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('matplotlib', '3.7.2'), - ('h5py', '3.9.0'), - ('PyYAML', '6.0'), - ('phonopy', '2.20.0'), - ('spglib-python', '2.1.0'), - ('ASE', '3.22.1'), - ('numexpr', '2.8.7'), - ('PyTables', '3.8.0'), - ('nglview', '3.0.8'), - ('tqdm', '4.66.1'), - ('molmod', '1.4.8'), - ('scikit-learn', '1.3.1'), - ('yaff', '1.6.0'), - ('TAMkin', '1.2.6'), - ('QuickFF', '2.2.7'), -] - -check_ldshared = True -use_pip = True - -exts_list = [ - ('h5io', '0.1.2', { - 'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'], - }), - ('defusedxml', '0.6.0', { - 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], - }), - ('pysqa', '0.0.11', { - 'checksums': ['b1a1995ac8b83b86046cef8b72cda962c5fdbf480c6dbba906a467a5dd1d3c81'], - }), - ('paramiko', '3.3.1', { - 'checksums': ['6a3777a961ac86dbef375c5f5b8d50014a1a96d0fd7f054a43bc880134b0ff77'], - }), - ('pyiron_atomistics', '0.3.11', { - 'source_urls': ['https://github.com/pyiron/pyiron_atomistics/archive/refs/tags/'], - 'checksums': ['8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'], - }), - ('SQLAlchemy', '1.3.19', { - 'checksums': ['3bba2e9fbedb0511769780fe1d63007081008c5c2d7d715e91858c94dbaa260e'], - }), - ('dill', '0.3.2', { - 'source_tmpl': 'dill-%(version)s.zip', - 'checksums': ['6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e'], - }), - ('smmap', '3.0.4', { - 'checksums': ['9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24'], - }), - ('gitdb', '4.0.5', { - 'checksums': ['c9e1f2d0db7ddb9a704c2a0217be31214e91a4fe1dea1efad19ae42ba0c285c9'], - }), - ('GitPython', '3.1.8', { - 'modulename': 'git', - 'checksums': ['080bf8e2cf1a2b907634761c2eaefbe83b69930c94c66ad11b65a8252959f912'], - }), - ('colorama', '0.4.3', { - 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], - }), - ('pyfiglet', '0.8.post1', { - 'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'], - }), - ('mendeleev', '0.6.0', { - 'checksums': ['944d185e81f158e48dd394b011e6c14acb612c2ffbc3c32c4aa490cd5b4f65dd'], - }), - ('pyfileindex', '0.0.4', { - 'checksums': ['bbfbfc9372f810587917ab1a88bebb8de44d32a1210bbd436c5b88447d97dfd2'], - }), - ('seekpath', '2.0.1', { - 'checksums': ['188513ee187fbbace49066a29ecea9bbd351f23da3bea33d507d0f590856b082'], - }), - (name, version, { - 'modulename': False, - 'source_urls': ['https://github.com/pyiron/pyiron/archive/refs/tags/%(name)s-%(version)s.tar.gz'], - 'checksums': ['2e5e3f892b7e49a15443569870aa4ea049951b71fe2ad1ad7f4ac7551d475788'], - }), -] - -sanity_pip_check = True - -moduleclass = 'tools' From 4e0a5ec68620c1bed064f5647d25ccd91777c122 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 21 Dec 2023 14:59:42 +0000 Subject: [PATCH 007/106] fixed paths in patches --- ...oss-2023a_fix-pyiron-atomistics-version.patch | 16 ++++++++-------- ....5.1-foss-2023a_fix-pyiron-base-version.patch | 8 ++++---- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index 9a72f51055b..f420a6e7526 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -1,18 +1,18 @@ Fix versioning related issue in pyiron atomistics. ---- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig 2023-12-13 17:37:16.618007520 +0000 -+++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml 2023-12-13 17:38:08.416737658 +0000 +--- 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig 2023-12-13 17:37:16.618007520 +0000 ++++ 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml 2023-12-13 17:38:08.416737658 +0000 @@ -43,7 +43,7 @@ "spglib==2.1.0", "structuretoolkit==0.0.15", ] -dynamic = ["version"] +version = "0.3.11" - + [project.urls] Homepage = "https://pyiron.org" @@ -55,13 +55,3 @@ - + [tool.setuptools.package-data] "*" = ["data/*.csv"] - @@ -25,8 +25,8 @@ Fix versioning related issue in pyiron atomistics. -versionfile_source = "pyiron_atomistics/_version.py" -parentdir_prefix = "pyiron_atomistics" -tag_prefix = "pyiron_atomistics-" ---- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 -+++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py 2023-12-13 17:41:48.007593887 +0000 +--- 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 ++++ 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py 2023-12-13 17:41:48.007593887 +0000 @@ -3,6 +3,6 @@ import versioneer @@ -38,8 +38,8 @@ Fix versioning related issue in pyiron atomistics. + version="0.3.11", +) + ---- 0.5.1/foss-2023a-Python-3.11.3/atomistics/atomistics-atomistics-0.1.15/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 -+++ 0.5.1/foss-2023a-Python-3.11.3/atomistics/atomistics-atomistics-0.1.15/setup.py 2023-12-13 17:41:48.007593887 +0000 +--- 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 ++++ 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/setup.py 2023-12-13 17:41:48.007593887 +0000 @@ -3,6 +3,6 @@ import versioneer diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch index 8cdbfa8916b..46225bc6616 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch @@ -1,7 +1,7 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version instead. ---- /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig 2023-12-13 15:51:48.895090935 +0000 -+++ /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml 2023-12-13 15:53:26.626579151 +0000 +--- /dev/shm/pyiron/0.5.1/foss-2023a/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig 2023-12-13 15:51:48.895090935 +0000 ++++ /dev/shm/pyiron/0.5.1/foss-2023a/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml 2023-12-13 15:53:26.626579151 +0000 @@ -40,7 +40,7 @@ "tqdm==4.66.1", "traitlets==5.14.0", @@ -25,8 +25,8 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version -parentdir_prefix = "pyiron_base" -tag_prefix = "pyiron_base-" ---- /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 -+++ /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py 2023-12-13 17:18:56.504736380 +0000 +--- /dev/shm/pyiron/0.5.1/foss-2023a/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 ++++ /dev/shm/pyiron/0.5.1/foss-2023a/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py 2023-12-13 17:18:56.504736380 +0000 @@ -3,6 +3,6 @@ import versioneer From f9fd2c1cef9c2150de93fd5b5ce029bc80665d66 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 21 Dec 2023 15:09:34 +0000 Subject: [PATCH 008/106] fixed paths in patches --- ....1-foss-2023a_fix-pyiron-atomistics-version.patch | 12 ++++++------ ...on-0.5.1-foss-2023a_fix-pyiron-base-version.patch | 8 ++++---- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index f420a6e7526..a4d4ada46fe 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -1,7 +1,7 @@ Fix versioning related issue in pyiron atomistics. ---- 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig 2023-12-13 17:37:16.618007520 +0000 -+++ 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml 2023-12-13 17:38:08.416737658 +0000 +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig 2023-12-13 17:37:16.618007520 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml 2023-12-13 17:38:08.416737658 +0000 @@ -43,7 +43,7 @@ "spglib==2.1.0", "structuretoolkit==0.0.15", @@ -25,8 +25,8 @@ Fix versioning related issue in pyiron atomistics. -versionfile_source = "pyiron_atomistics/_version.py" -parentdir_prefix = "pyiron_atomistics" -tag_prefix = "pyiron_atomistics-" ---- 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 -+++ 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py 2023-12-13 17:41:48.007593887 +0000 +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py 2023-12-13 17:41:48.007593887 +0000 @@ -3,6 +3,6 @@ import versioneer @@ -38,8 +38,8 @@ Fix versioning related issue in pyiron atomistics. + version="0.3.11", +) + ---- 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 -+++ 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/setup.py 2023-12-13 17:41:48.007593887 +0000 +--- 0.5.1/foss-2023a-Python-3.11.3/atomistics/atomistics-atomistics-0.1.15/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/atomistics/atomistics-atomistics-0.1.15/setup.py 2023-12-13 17:41:48.007593887 +0000 @@ -3,6 +3,6 @@ import versioneer diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch index 46225bc6616..8cdbfa8916b 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch @@ -1,7 +1,7 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version instead. ---- /dev/shm/pyiron/0.5.1/foss-2023a/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig 2023-12-13 15:51:48.895090935 +0000 -+++ /dev/shm/pyiron/0.5.1/foss-2023a/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml 2023-12-13 15:53:26.626579151 +0000 +--- /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig 2023-12-13 15:51:48.895090935 +0000 ++++ /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml 2023-12-13 15:53:26.626579151 +0000 @@ -40,7 +40,7 @@ "tqdm==4.66.1", "traitlets==5.14.0", @@ -25,8 +25,8 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version -parentdir_prefix = "pyiron_base" -tag_prefix = "pyiron_base-" ---- /dev/shm/pyiron/0.5.1/foss-2023a/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 -+++ /dev/shm/pyiron/0.5.1/foss-2023a/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py 2023-12-13 17:18:56.504736380 +0000 +--- /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 ++++ /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py 2023-12-13 17:18:56.504736380 +0000 @@ -3,6 +3,6 @@ import versioneer From 57a786e87f8014fa8a4f3df7eeee1a9c7a437b41 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 16:29:47 +0100 Subject: [PATCH 009/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- .../pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index a4d4ada46fe..e95f68f2c31 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -25,6 +25,7 @@ Fix versioning related issue in pyiron atomistics. -versionfile_source = "pyiron_atomistics/_version.py" -parentdir_prefix = "pyiron_atomistics" -tag_prefix = "pyiron_atomistics-" + --- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 +++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py 2023-12-13 17:41:48.007593887 +0000 @@ -3,6 +3,6 @@ From fbf2412a44d1851d4e167d89ec60aca42a55021a Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 17:07:16 +0100 Subject: [PATCH 010/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- ...n-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index e95f68f2c31..14b12f39ef3 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -17,14 +17,14 @@ Fix versioning related issue in pyiron atomistics. "*" = ["data/*.csv"] - -[tool.setuptools.dynamic] --version = {attr = "pyiron_atomistics.__version__"} +-version = {attr = "atomistics.__version__"} - -[tool.versioneer] -VCS = "git" -style = "pep440-pre" --versionfile_source = "pyiron_atomistics/_version.py" --parentdir_prefix = "pyiron_atomistics" --tag_prefix = "pyiron_atomistics-" +-versionfile_source = "atomistics/_version.py" +-parentdir_prefix = "atomistics" +-tag_prefix = "atomistics-" --- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 +++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py 2023-12-13 17:41:48.007593887 +0000 From af05aa2bdc30a0cfcd005a05e180008c01e3a3d5 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 17:14:13 +0100 Subject: [PATCH 011/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- ....1-foss-2023a_fix-pyiron-atomistics-version.patch | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index 14b12f39ef3..67fa0d67878 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -39,16 +39,4 @@ Fix versioning related issue in pyiron atomistics. + version="0.3.11", +) + ---- 0.5.1/foss-2023a-Python-3.11.3/atomistics/atomistics-atomistics-0.1.15/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 -+++ 0.5.1/foss-2023a-Python-3.11.3/atomistics/atomistics-atomistics-0.1.15/setup.py 2023-12-13 17:41:48.007593887 +0000 -@@ -3,6 +3,6 @@ - import versioneer - - setup( -- version=versioneer.get_version(), -- cmdclass=versioneer.get_cmdclass(), --) -\ -+ version="0.3.11", -+) + From 9e50f1615a99ff6f16696cdc4c812ca1f51cbbb3 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 17:24:09 +0100 Subject: [PATCH 012/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- ...-2023a_fix-pyiron-atomistics-version.patch | 23 +++++++++---------- 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index 67fa0d67878..8feeb22899e 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -1,21 +1,20 @@ Fix versioning related issue in pyiron atomistics. ---- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig 2023-12-13 17:37:16.618007520 +0000 -+++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml 2023-12-13 17:38:08.416737658 +0000 -@@ -43,7 +43,7 @@ - "spglib==2.1.0", - "structuretoolkit==0.0.15", +--- 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml.orig 2023-12-12 07:51:23.000000000 +0000 ++++ 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml 2023-12-21 16:23:25.950798734 +0000 +@@ -30,7 +30,7 @@ + "scipy==1.11.4", + "spglib==2.2.0", ] -dynamic = ["version"] +version = "0.3.11" - + [project.urls] - Homepage = "https://pyiron.org" -@@ -55,13 +55,3 @@ - - [tool.setuptools.package-data] - "*" = ["data/*.csv"] -- + Homepage = "https://github.com/pyiron/atomistics" +@@ -64,12 +64,3 @@ + [tool.setuptools.packages.find] + include = ["atomistics*"] + -[tool.setuptools.dynamic] -version = {attr = "atomistics.__version__"} - From 90775dc6ec6d7d1f89e6435dc9f70d4c3f33598f Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 17:40:56 +0100 Subject: [PATCH 013/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- ...-2023a_fix-pyiron-atomistics-version.patch | 27 ++++++++++--------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index 8feeb22899e..923f893db7a 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -1,29 +1,30 @@ Fix versioning related issue in pyiron atomistics. ---- 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml.orig 2023-12-12 07:51:23.000000000 +0000 -+++ 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml 2023-12-21 16:23:25.950798734 +0000 -@@ -30,7 +30,7 @@ - "scipy==1.11.4", - "spglib==2.2.0", +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig 2023-12-21 16:39:17.769971429 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml 2023-12-21 16:39:59.280760858 +0000 +@@ -43,7 +43,7 @@ + "spglib==2.1.0", + "structuretoolkit==0.0.15", ] -dynamic = ["version"] +version = "0.3.11" [project.urls] - Homepage = "https://github.com/pyiron/atomistics" -@@ -64,12 +64,3 @@ - [tool.setuptools.packages.find] - include = ["atomistics*"] + Homepage = "https://pyiron.org" +@@ -55,13 +55,3 @@ + [tool.setuptools.package-data] + "*" = ["data/*.csv"] +- -[tool.setuptools.dynamic] --version = {attr = "atomistics.__version__"} +-version = {attr = "pyiron_atomistics.__version__"} - -[tool.versioneer] -VCS = "git" -style = "pep440-pre" --versionfile_source = "atomistics/_version.py" --parentdir_prefix = "atomistics" --tag_prefix = "atomistics-" +-versionfile_source = "pyiron_atomistics/_version.py" +-parentdir_prefix = "pyiron_atomistics" +-tag_prefix = "pyiron_atomistics-" --- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 +++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py 2023-12-13 17:41:48.007593887 +0000 From fd675447952e17436d96e5ea5c4423cba1d7790a Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 17:52:27 +0100 Subject: [PATCH 014/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 24e244b6524..dc8497e1f71 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -89,7 +89,6 @@ exts_list = [ 'checksums': ['7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'], }), ('atomistics', '0.1.15', { - 'patches': ['pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch'], 'source_urls': ['https://github.com/pyiron/atomistics/archive/refs/tags/'], }), ('pyiron_atomistics', '0.3.11', { From 2ac96a23098d71ceadb7c896a892942e4a2cd36a Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 18:04:03 +0100 Subject: [PATCH 015/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index dc8497e1f71..e0a852a81be 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -96,6 +96,12 @@ exts_list = [ 'source_urls': ['https://github.com/pyiron/pyiron_atomistics/archive/refs/tags/'], 'checksums': ['8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'], }), + ('mp-api', '0.39.4', { + 'source_urls': ['https://github.com/materialsproject/api/archive/refs/tags/'] + }), + ('pylammpsmpi', '0.2.10', { + 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], + }), ] sanity_pip_check = True From 240162dbcd30a9643a52be5dfda0ac33dd1de43e Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 18:06:36 +0100 Subject: [PATCH 016/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index e0a852a81be..695d6d8cda3 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -102,6 +102,9 @@ exts_list = [ ('pylammpsmpi', '0.2.10', { 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], }), + ('bcrypt', '4.1.2', { + 'source_urls': ['https://github.com/pyca/bcrypt/archive/refs/tags/'] + }), ] sanity_pip_check = True From de89d51d08f934b48d39fbbec17622db127f283d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 18:09:42 +0100 Subject: [PATCH 017/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 695d6d8cda3..f19b62e5022 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -103,7 +103,7 @@ exts_list = [ 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], }), ('bcrypt', '4.1.2', { - 'source_urls': ['https://github.com/pyca/bcrypt/archive/refs/tags/'] + 'source_urls': ['https://github.com/pyca/bcrypt/archive/refs/tags/4.1.2.tar.gz'] }), ] From 30516e3e4bbbaa64a79f01af26acb043e996a0b3 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 18:11:35 +0100 Subject: [PATCH 018/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index f19b62e5022..2f3f158c7b2 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -97,7 +97,7 @@ exts_list = [ 'checksums': ['8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'], }), ('mp-api', '0.39.4', { - 'source_urls': ['https://github.com/materialsproject/api/archive/refs/tags/'] + 'source_urls': ['https://github.com/materialsproject/api/archive/refs/tags/v0.39.4.tar.gz'] }), ('pylammpsmpi', '0.2.10', { 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], From fab600725ab4d9a0845fb55af96c83090e66c884 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 18:18:08 +0100 Subject: [PATCH 019/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 2f3f158c7b2..e3d4881ce45 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -96,15 +96,11 @@ exts_list = [ 'source_urls': ['https://github.com/pyiron/pyiron_atomistics/archive/refs/tags/'], 'checksums': ['8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'], }), - ('mp-api', '0.39.4', { - 'source_urls': ['https://github.com/materialsproject/api/archive/refs/tags/v0.39.4.tar.gz'] - }), + ('mp-api', '0.39.4'), ('pylammpsmpi', '0.2.10', { 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], }), - ('bcrypt', '4.1.2', { - 'source_urls': ['https://github.com/pyca/bcrypt/archive/refs/tags/4.1.2.tar.gz'] - }), + ('bcrypt', '4.1.2'), ] sanity_pip_check = True From fa89079fb9f4dc2644f0bcf4df15bacb1f259056 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 18:32:39 +0100 Subject: [PATCH 020/106] Create pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch --- .../pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch new file mode 100644 index 00000000000..89afdd3dade --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch @@ -0,0 +1,12 @@ +--- 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/setup.py.orig 2023-12-21 17:27:54.405181324 +0000 ++++ 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/setup.py 2023-12-21 17:28:49.249903688 +0000 +@@ -1,8 +1,3 @@ + from setuptools import setup + +-import versioneer ++setup(version='0.2.10') + +-setup( +- version=versioneer.get_version(), +- cmdclass=versioneer.get_cmdclass(), +-) From 5bfa267359e2dcf3e77d5a541f9b84ac60bd88f0 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 18:34:00 +0100 Subject: [PATCH 021/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index e3d4881ce45..8a2b727cb82 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -98,6 +98,7 @@ exts_list = [ }), ('mp-api', '0.39.4'), ('pylammpsmpi', '0.2.10', { + 'patches': ['pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch'], 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], }), ('bcrypt', '4.1.2'), From d00212b4a4957e11a7de7b6b4ca7c92050b35c44 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 18:42:18 +0100 Subject: [PATCH 022/106] Update pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch --- .../pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch index 89afdd3dade..287d94bbc54 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch @@ -1,12 +1,15 @@ +Fix versioning issue. + --- 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/setup.py.orig 2023-12-21 17:27:54.405181324 +0000 -+++ 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/setup.py 2023-12-21 17:28:49.249903688 +0000 -@@ -1,8 +1,3 @@ ++++ 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/setup.py 2023-12-21 17:31:38.136048756 +0000 +@@ -1,8 +1,4 @@ from setuptools import setup -import versioneer +setup(version='0.2.10') - + -setup( - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), -) +\ Ingen nyrad vid filslut From 31a0dbc46e14867e7569092964f0545cee966f8f Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 18:59:43 +0100 Subject: [PATCH 023/106] Update pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch --- ...ron-0.5.1-foss-2023a_fix-pylammpsmpi.patch | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch index 287d94bbc54..4df677ebc66 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch @@ -13,3 +13,29 @@ Fix versioning issue. - cmdclass=versioneer.get_cmdclass(), -) \ Ingen nyrad vid filslut + +--- 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/pyproject.toml.orig 2023-12-21 17:57:36.066162000 +0000 ++++ 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/pyproject.toml 2023-12-21 17:58:37.373851635 +0000 +@@ -28,7 +28,7 @@ + "pympipool==0.7.9", + "numpy==1.26.2", + ] +-dynamic = ["version"] ++version = '0.2.10' + + [project.urls] + Homepage = "https://github.com/pyiron/pylammpsmpi" +@@ -43,13 +43,3 @@ + + [tool.setuptools.packages.find] + include = ["pylammpsmpi*"] +- +-[tool.setuptools.dynamic] +-version = {attr = "pylammpsmpi.__version__"} +- +-[tool.versioneer] +-VCS = "git" +-style = "pep440-pre" +-versionfile_source = "pylammpsmpi/_version.py" +-parentdir_prefix = "pylammpsmpi" +-tag_prefix = "pylammpsmpi-" From 998abb56323286d0acab40ef861fc3b8d8b6f588 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 19:13:03 +0100 Subject: [PATCH 024/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 8a2b727cb82..7672d3103eb 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -28,6 +28,7 @@ dependencies = [ ('TAMkin', '1.2.6'), ('QuickFF', '2.2.7'), ('Pint', '0.22'), + ('setuptools-rust', '1.6.0'), ] check_ldshared = True From 8eaf183e36771f2d2a14fd4abedbc81d6ead4ebe Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 19:21:52 +0100 Subject: [PATCH 025/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 7672d3103eb..3fe30996eeb 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -29,6 +29,7 @@ dependencies = [ ('QuickFF', '2.2.7'), ('Pint', '0.22'), ('setuptools-rust', '1.6.0'), + ('Rust', '1.70.0'), ] check_ldshared = True From d0c881236da560f59947885604e91bb37e022744 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 19:27:49 +0100 Subject: [PATCH 026/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 3fe30996eeb..961f091d36f 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -28,8 +28,7 @@ dependencies = [ ('TAMkin', '1.2.6'), ('QuickFF', '2.2.7'), ('Pint', '0.22'), - ('setuptools-rust', '1.6.0'), - ('Rust', '1.70.0'), + ('bcrypt', '4.0.1'), ] check_ldshared = True @@ -103,7 +102,6 @@ exts_list = [ 'patches': ['pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch'], 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], }), - ('bcrypt', '4.1.2'), ] sanity_pip_check = True From 2c751c070102d115047dbc591e2a85df0a9fd2a2 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 19:45:52 +0100 Subject: [PATCH 027/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 961f091d36f..d1f0308b91d 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -102,6 +102,12 @@ exts_list = [ 'patches': ['pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch'], 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], }), + ('emmet-core', '0.75.0'), + ('maggma', '0.6.0'), + ('monty', '2023.11.3'), + ('pymatgen', '2023.12.18'), + ('pympipool', '0.7.9'), + ('structuretoolkit', '0.0.15'), ] sanity_pip_check = True From 9b85120004d2664406ef621c7180cd152606470c Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 20:01:03 +0100 Subject: [PATCH 028/106] Create pyiron-0.5.1-foss-2023a_fix_emmet_readme.patch --- .../pyiron-0.5.1-foss-2023a_fix_emmet_readme.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix_emmet_readme.patch diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix_emmet_readme.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix_emmet_readme.patch new file mode 100644 index 00000000000..b5cf94ef1b2 --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix_emmet_readme.patch @@ -0,0 +1,13 @@ +Fixes attempt to open nonexistent README.md. + +--- /dev/shm/pyiron/0.5.1/foss-2023a/emmetcore/emmet-core-0.75.0/setup.py.orig 2023-12-21 18:58:49.428075405 +0000 ++++ /dev/shm/pyiron/0.5.1/foss-2023a/emmetcore/emmet-core-0.75.0/setup.py 2023-12-21 18:59:10.200024324 +0000 +@@ -7,8 +7,6 @@ + description="Core Emmet Library", + author="The Materials Project", + author_email="feedback@materialsproject.org", +- long_description=open("../README.md").read(), # noqa: SIM115 +- long_description_content_type="text/markdown", + url="https://github.com/materialsproject/emmet", + packages=find_namespace_packages(include=["emmet.*"]), + package_data={ From fbd1ac0bb2dd62372a381274f9c58e1cd9026ae6 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 20:01:23 +0100 Subject: [PATCH 029/106] Rename pyiron-0.5.1-foss-2023a_fix_emmet_readme.patch to pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch --- ...eadme.patch => pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/pyiron/{pyiron-0.5.1-foss-2023a_fix_emmet_readme.patch => pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch} (100%) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix_emmet_readme.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch similarity index 100% rename from easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix_emmet_readme.patch rename to easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch From 4fb4e1d6a3145aaeace506200f7cac5d96aeb88e Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 20:02:12 +0100 Subject: [PATCH 030/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index d1f0308b91d..67720b6ec9b 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -102,7 +102,9 @@ exts_list = [ 'patches': ['pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch'], 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], }), - ('emmet-core', '0.75.0'), + ('emmet-core', '0.75.0', { + 'patches': ['pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch'], + }), ('maggma', '0.6.0'), ('monty', '2023.11.3'), ('pymatgen', '2023.12.18'), From 629cbe27cdeac12ce3fa03f501c70187812090fa Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 20:36:13 +0100 Subject: [PATCH 031/106] Update pyiron-0.5.1-foss-2023a.eb --- .../p/pyiron/pyiron-0.5.1-foss-2023a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 67720b6ec9b..c9e06c44aaa 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -29,6 +29,10 @@ dependencies = [ ('QuickFF', '2.2.7'), ('Pint', '0.22'), ('bcrypt', '4.0.1'), + ('ruamel.yaml', '0.17.32'), + ('plotly.py', '5.16.0'), + ('Flask', '2.3.3'), + ('boto3', '1.28.70'), ] check_ldshared = True @@ -110,6 +114,23 @@ exts_list = [ ('pymatgen', '2023.12.18'), ('pympipool', '0.7.9'), ('structuretoolkit', '0.0.15'), + ('uncertainties', '3.1.7'), + ('sympy', '1.12'), + ('pydantic', '2.5.2'), + ('palettable', '3.1.1'), + ('pydantic_core', '2.14.5'), + ('pybtex', '0.24.0'), + ('h11', '0.14.0'), + ('mongogrant', '0.3.3'), + ('mongomock', '4.1.2'), + ('pymongo', '4.6.1'), + ('pydash', '7.0.6'), + ('uvicorn', '0.25.0'), + ('starlette', '0.28.0'), + ('orjson', '3.9.10'), + ('dnspython', '2.4.2'), + ('fastapi', '0.105.0'), + ('aioitertools', '0.11.0'), ] sanity_pip_check = True From 0e4fdab10a10f7c2a5e4ff31be82538b66263d99 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 21:01:21 +0100 Subject: [PATCH 032/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index c9e06c44aaa..aa3482cdb6a 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -33,6 +33,7 @@ dependencies = [ ('plotly.py', '5.16.0'), ('Flask', '2.3.3'), ('boto3', '1.28.70'), + ('sympy', '1.12'), ] check_ldshared = True From 5cd693ca8c243a255e1aa39cc426d9f5022ff8b2 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 21:02:24 +0100 Subject: [PATCH 033/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index aa3482cdb6a..901e059ddcb 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -116,7 +116,6 @@ exts_list = [ ('pympipool', '0.7.9'), ('structuretoolkit', '0.0.15'), ('uncertainties', '3.1.7'), - ('sympy', '1.12'), ('pydantic', '2.5.2'), ('palettable', '3.1.1'), ('pydantic_core', '2.14.5'), From 53f0edc454657afc856ebc938c010c86a3b6bd69 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 8 Jan 2024 00:53:43 +0100 Subject: [PATCH 034/106] Update Pint-0.22-GCCcore-12.3.0.eb --- easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb index 63340322e4e..fb5a9be76b2 100644 --- a/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = [SOURCE_TAR_GZ] checksums = ['2d139f6abbcf3016cad7d3cec05707fe908ac4f99cf59aedfd6ee667b7a64433'] +patches = [('Pint-0.22-GCCcore-12.3.0_fix-version.patch', 3)] builddependencies = [('binutils', '2.40')] From 7445a7a2fab3dc7f76287e045cade3399bf52413 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 8 Jan 2024 00:55:32 +0100 Subject: [PATCH 035/106] Create Pint-0.22-GCCcore-12.3.0_fix-version.patch --- .../p/Pint-0.22-GCCcore-12.3.0_fix-version.patch | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pint-0.22-GCCcore-12.3.0_fix-version.patch diff --git a/easybuild/easyconfigs/p/Pint-0.22-GCCcore-12.3.0_fix-version.patch b/easybuild/easyconfigs/p/Pint-0.22-GCCcore-12.3.0_fix-version.patch new file mode 100644 index 00000000000..763bcfeca9f --- /dev/null +++ b/easybuild/easyconfigs/p/Pint-0.22-GCCcore-12.3.0_fix-version.patch @@ -0,0 +1,7 @@ +--- 0.22/GCCcore-12.3.0/Pint-0.22/setup.py.orig 2023-12-13 18:45:35.241637807 +0000 ++++ 0.22/GCCcore-12.3.0/Pint-0.22/setup.py 2023-12-13 18:49:29.304418276 +0000 +@@ -0,0 +1,4 @@ ++from setuptools import setup ++ ++ ++setup(version='0.22') From 6cd4e0a41b4a890973ffd46cdf4544c7a632124f Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 8 Jan 2024 03:25:12 +0100 Subject: [PATCH 036/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 901e059ddcb..840e73132af 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -34,6 +34,7 @@ dependencies = [ ('Flask', '2.3.3'), ('boto3', '1.28.70'), ('sympy', '1.12'), + ('maturin', '1.1.0'), ] check_ldshared = True From 158eca7b8a197ed61a75a6ef90c32c40d6bd66af Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 8 Jan 2024 03:44:00 +0100 Subject: [PATCH 037/106] Create pydantic-1.10.4-GCCcore-12.3.0.eb --- .../pydantic-1.10.4-GCCcore-12.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..652608e8127 --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'pydantic' +version = '1.10.4' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + (name, version, { + 'checksums': ['b9a3859f24eb4e097502a3be1fb4b2abb79b6103dd9e2e0edb70613a4459a648'], + }), +] + +moduleclass = 'devel' From 3cb72c8df029f34bb460cbfe20e31e2b1c78d4f0 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 8 Jan 2024 03:44:57 +0100 Subject: [PATCH 038/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 840e73132af..70b3b70af3e 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -34,7 +34,7 @@ dependencies = [ ('Flask', '2.3.3'), ('boto3', '1.28.70'), ('sympy', '1.12'), - ('maturin', '1.1.0'), + ('pydantic', '1.10.4'), ] check_ldshared = True @@ -117,9 +117,7 @@ exts_list = [ ('pympipool', '0.7.9'), ('structuretoolkit', '0.0.15'), ('uncertainties', '3.1.7'), - ('pydantic', '2.5.2'), ('palettable', '3.1.1'), - ('pydantic_core', '2.14.5'), ('pybtex', '0.24.0'), ('h11', '0.14.0'), ('mongogrant', '0.3.3'), From a9efc0f243a56556930042d87b83b49d4c69c1c2 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 8 Jan 2024 23:39:03 +0100 Subject: [PATCH 039/106] Update pyiron-0.5.1-foss-2023a.eb --- .../p/pyiron/pyiron-0.5.1-foss-2023a.eb | 114 ++++++++++++++---- 1 file changed, 91 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 70b3b70af3e..7d887dc1d4b 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -34,13 +34,16 @@ dependencies = [ ('Flask', '2.3.3'), ('boto3', '1.28.70'), ('sympy', '1.12'), - ('pydantic', '1.10.4'), + ('pydantic', '2.1.1'), + ('maturin', '1.1.0'), + ('poetry', '1.5.1'), ] check_ldshared = True use_pip = True exts_list = [ + ('sshtunnel', '0.4.0'), ('h5io', '0.1.2', { 'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'], }), @@ -93,43 +96,108 @@ exts_list = [ ('pyiron_base', '0.6.12', { 'patches': ['pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch'], 'source_urls': ['https://github.com/pyiron/pyiron_base/archive/refs/tags/'], - 'checksums': ['7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'], + 'checksums': [ + {'pyiron_base-0.6.12.tar.gz': '7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'}, + {'pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch': + '761fb6123c16fa1a785c5c6425626522bd019613b1cb3ba0912b52538a8c682d'}, + ], }), ('atomistics', '0.1.15', { 'source_urls': ['https://github.com/pyiron/atomistics/archive/refs/tags/'], + 'checksums': ['e9c505cace0cbeb9ea5ed33799f332f5cc95230a05ba14b646475cff1bdecaee'], }), ('pyiron_atomistics', '0.3.11', { 'patches': ['pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch'], 'source_urls': ['https://github.com/pyiron/pyiron_atomistics/archive/refs/tags/'], - 'checksums': ['8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'], + 'checksums': [ + {'pyiron_atomistics-0.3.11.tar.gz': '8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'}, + {'pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch': + '30d5dcf024520ac687fb6bcbd3a8d3c8155e1a386ce4ff67557b1f1c73189995'}, + ], + }), + ('mp-api', '0.39.4', { + 'checksums': ['692abefd6adec36eb4fa193f914e08167ed33a5a3a9714ec3c15606839649f32'], }), - ('mp-api', '0.39.4'), ('pylammpsmpi', '0.2.10', { 'patches': ['pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch'], 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], + 'checksums': [ + {'pylammpsmpi-0.2.10.tar.gz': 'bd5af29a935dacbee743c3cc0bcc799e24e7c2483801f56cb9092a79f016f2ed'}, + {'pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch': + 'f509db8ae6776ec01bcb97cb50ec20b74319ed82432fa3bede0ef7132c841fef'}, + ], }), ('emmet-core', '0.75.0', { 'patches': ['pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch'], + 'checksums': [ + {'emmet-core-0.75.0.tar.gz': '2d4b20d542e56c97009d05d03f5595be9395ac27c2fe9809d617f28596c40640'}, + {'pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch': + '4cfe7ab122f37ff4a5f1ba52f69d84ab43fc2abfafd6efe71c401319d1258e1c'}, + ], + }), + ('maggma', '0.60.2', { + 'checksums': ['12e8da1f80505f39432b972cbe47fb378cd9aa51fab968877a2d3b2588c96c69'], + }), + ('monty', '2023.11.3', { + 'checksums': ['d961c14b0b20901c7603aa00d275e62dee8333fbdaf1179f5d862c6fb3f3c52f'], + }), + ('pymatgen', '2023.12.18', { + 'checksums': ['56c0041fe5431ac1b8f8c0c17d06091c4d61082c3a99924f3940d73ebb6656eb'], + }), + ('pympipool', '0.7.9', { + 'checksums': ['5698181bc5dc9a69595fd00ff6a8ba651b77734ccf00df79ae3aea8aaf32790a'], + }), + ('structuretoolkit', '0.0.15', { + 'checksums': ['1a258a072055d0c20e9d56156afd4481cfc94c2612c1b908de4b274b423cc6e6'], + }), + ('uncertainties', '3.1.7', { + 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], + }), + ('palettable', '3.1.1', { + 'checksums': ['0685b223a236bb7e2a900ef7a855ccf9a4027361c8acf400f3b350ea51870f80'], + }), + ('pybtex', '0.24.0', { + 'checksums': ['818eae35b61733e5c007c3fcd2cfb75ed1bc8b4173c1f70b56cc4c0802d34755'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('mongogrant', '0.3.3', { + 'checksums': ['ad494b8638adfa840cdd5568af44448dd43771b58102550cf7c61402b1620ab4'], + }), + ('mongomock', '4.1.2', { + 'checksums': ['f06cd62afb8ae3ef63ba31349abd220a657ef0dd4f0243a29587c5213f931b7d'], + }), + ('pymongo', '4.6.1', { + 'checksums': ['31dab1f3e1d0cdd57e8df01b645f52d43cc1b653ed3afd535d2891f4fc4f9712'], + }), + ('pydash', '7.0.6', { + 'checksums': ['7d9df7e9f36f2bbb08316b609480e7c6468185473a21bdd8e65dda7915565a26'], + }), + ('uvicorn', '0.25.0', { + 'checksums': ['6dddbad1d7ee0f5140aba5ec138ddc9612c5109399903828b4874c9937f009c2'], + }), + ('starlette', '0.27.0', { + 'checksums': ['6a6b0d042acb8d469a01eba54e9cda6cbd24ac602c4cd016723117d6a7e73b75'], + }), + ('orjson', '3.9.10', { + 'checksums': ['9ebbdbd6a046c304b1845e96fbcc5559cd296b4dfd3ad2509e33c4d9ce07d6a1'], + }), + ('dnspython', '2.4.2', { + 'checksums': ['8dcfae8c7460a2f84b4072e26f1c9f4101ca20c071649cb7c34e8b6a93d58984'], + }), + ('fastapi', '0.105.0', { + 'checksums': ['4d12838819aa52af244580675825e750ad67c9df4614f557a769606af902cf22'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('latexcodec', '2.0.1', { + 'checksums': ['2aa2551c373261cefe2ad3a8953a6d6533e68238d180eb4bb91d7964adb3fe9a'], + }), + ('sentinels', '1.0.0', { + 'checksums': ['7be0704d7fe1925e397e92d18669ace2f619c92b5d4eb21a89f31e026f9ff4b1'], }), - ('maggma', '0.6.0'), - ('monty', '2023.11.3'), - ('pymatgen', '2023.12.18'), - ('pympipool', '0.7.9'), - ('structuretoolkit', '0.0.15'), - ('uncertainties', '3.1.7'), - ('palettable', '3.1.1'), - ('pybtex', '0.24.0'), - ('h11', '0.14.0'), - ('mongogrant', '0.3.3'), - ('mongomock', '4.1.2'), - ('pymongo', '4.6.1'), - ('pydash', '7.0.6'), - ('uvicorn', '0.25.0'), - ('starlette', '0.28.0'), - ('orjson', '3.9.10'), - ('dnspython', '2.4.2'), - ('fastapi', '0.105.0'), - ('aioitertools', '0.11.0'), ] sanity_pip_check = True From c97cd583d048099f6650d29e4b7ec851a6454fbb Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 8 Jan 2024 23:43:42 +0100 Subject: [PATCH 040/106] Update and rename pydantic-1.10.4-GCCcore-12.3.0.eb to pydantic-2.1.1-GCCcore-12.3.0.eb --- .../pydantic-1.10.4-GCCcore-12.3.0.eb | 29 ----------- .../pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb | 48 +++++++++++++++++++ 2 files changed, 48 insertions(+), 29 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-12.3.0.eb deleted file mode 100644 index 652608e8127..00000000000 --- a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-12.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pydantic' -version = '1.10.4' - -homepage = 'https://github.com/samuelcolvin/pydantic' -description = """Data validation and settings management using Python type hinting.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [('binutils', '2.40')] - -dependencies = [ - ('Python', '3.11.3'), -] - -sanity_pip_check = True -use_pip = True - -exts_list = [ - ('typing_extensions', '4.4.0', { - 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], - }), - (name, version, { - 'checksums': ['b9a3859f24eb4e097502a3be1fb4b2abb79b6103dd9e2e0edb70613a4459a648'], - }), -] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5cb85f6a578 --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'pydantic' +version = '2.1.1' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('hatchling', '1.18.0'), + ('maturin', '1.1.0') +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('typing_extensions', '4.9.0', { + 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], + }), + ('python-dotenv', '1.0.0', { + 'modulename': 'dotenv', + 'checksums': ['a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba'], + }), + (name, version, { + 'sources': {'source_urls': ['https://github.com/pydantic/%(name)s/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, + 'checksums': ['ae48a2ffe679ae003bb52b511ecfe85bed70f4b8a955c76e0957dd29c003cdbf'], + }), + ('pydantic-settings', '2.0.1', { + 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, + 'checksums': ['bf8e327234e4ffab3642e72e677c1b176d358bab551090a1b1cea6f462cd9a1e'], + }), + ('pydantic-core', '2.4.0', { + 'sources': {'source_urls': ['https://github.com/pydantic/%(name)s/archive/refs/tags/'], 'filename': 'v%(version)s.tar.gz'}, + 'checksums': ['94b4ef19df7e0ea5e9f32590afc3673dab0d9855ed786d3dc95513124d842874'], + }), + ('annotated-types', '0.6.0', { + 'sources': {'source_urls': ['https://github.com/%(name)s/%(name)s/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, + 'checksums': ['0b99aba34b87840d7578705968d87fe6265c1a1604bcf9ccc11902b1d8d39ad8'], + }), +] + +moduleclass = 'devel' From fa1216606a6777530b668f9015ca1015bf58fecd Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Tue, 9 Jan 2024 13:32:17 +0100 Subject: [PATCH 041/106] Update pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch --- .../pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch index 4df677ebc66..c306bf08da9 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch @@ -1,4 +1,4 @@ -Fix versioning issue. +Fix versioning issue and relax requirements. --- 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/setup.py.orig 2023-12-21 17:27:54.405181324 +0000 +++ 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/setup.py 2023-12-21 17:31:38.136048756 +0000 @@ -16,9 +16,15 @@ Fix versioning issue. --- 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/pyproject.toml.orig 2023-12-21 17:57:36.066162000 +0000 +++ 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/pyproject.toml 2023-12-21 17:58:37.373851635 +0000 -@@ -28,7 +28,7 @@ +@@ -24,11 +24,11 @@ + "Programming Language :: Python :: 3.11", + ] + dependencies = [ +- "mpi4py==3.1.5", ++ "mpi4py>=3.1.4", "pympipool==0.7.9", - "numpy==1.26.2", +- "numpy==1.26.2", ++ "numpy>=1.25.1", ] -dynamic = ["version"] +version = '0.2.10' From c77d886087bf6924526c31d43ed5be6b7b31d780 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Tue, 9 Jan 2024 13:41:16 +0100 Subject: [PATCH 042/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- ...-2023a_fix-pyiron-atomistics-version.patch | 34 +++++++++++++++++-- 1 file changed, 32 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index 923f893db7a..9891b611865 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -1,8 +1,38 @@ -Fix versioning related issue in pyiron atomistics. +Fix versioning related issue and requirements in pyiron atomistics. --- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig 2023-12-21 16:39:17.769971429 +0000 +++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml 2023-12-21 16:39:59.280760858 +0000 -@@ -43,7 +43,7 @@ +@@ -26,24 +26,24 @@ + dependencies = [ + "ase==3.22.1", +- "atomistics==0.1.12", +- "defusedxml==0.7.1", +- "h5py==3.10.0", +- "matplotlib==3.8.2", +- "mendeleev==0.14.0", +- "mp-api==0.39.1", +- "numpy==1.26.2", +- "pandas==2.1.3", +- "phonopy==2.21.0", ++ "atomistics>=0.1.12", ++ "defusedxm>=0.6.0", ++ "h5py>=3.9.0", ++ "matplotlib>=3.7.2", ++ "mendeleev>=0.6.0", ++ "mp-api>=0.39.1", ++ "numpy>=1.25.1", ++ "pandas>=2.0.3", ++ "phonopy>=2.20.0", + "pint==0.22", + "pyiron_base==0.6.12", +- "pylammpsmpi==0.2.9", +- "scipy==1.11.4", +- "scikit-learn==1.3.2", +- "seekpath==2.1.0", ++ "pylammpsmpi>=0.2.9", ++ "scipy>=1.11.1", ++ "scikit-learn>=1.3.1", ++ "seekpath>=2.01" "spglib==2.1.0", "structuretoolkit==0.0.15", ] From b6fd61773a8f903f14e5c08b1c66579f96514d0f Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Tue, 9 Jan 2024 13:46:07 +0100 Subject: [PATCH 043/106] Create pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch --- ...oss-2023a_fix-atomistics-requirements.patch | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch new file mode 100644 index 00000000000..0a3f2a238ac --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch @@ -0,0 +1,18 @@ +Relax requirements of `atomistics`. + +/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml.orig 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml +--- 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml.orig 2024-01-09 12:42:59.508409527 +0000 ++++ 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml2024-01-09 12:43:44.589293464 +0000 +@@ -26,9 +26,9 @@ + ] + dependencies = [ + "ase==3.22.1", +- "numpy==1.26.2", +- "scipy==1.11.4", +- "spglib==2.2.0", ++ "numpy>=1.25.1", ++ "scipy>=1.11.1", ++ "spglib>=2.1.0", + ] + dynamic = ["version"] + From e2aa5482bc7897ab1827c8641eaa8740bc3697d2 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Tue, 9 Jan 2024 14:11:56 +0100 Subject: [PATCH 044/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 7d887dc1d4b..decd2b0ecf0 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -104,7 +104,12 @@ exts_list = [ }), ('atomistics', '0.1.15', { 'source_urls': ['https://github.com/pyiron/atomistics/archive/refs/tags/'], - 'checksums': ['e9c505cace0cbeb9ea5ed33799f332f5cc95230a05ba14b646475cff1bdecaee'], + 'patches': ['pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch'] + 'checksums': [ + {'atomistics-0.1.15.tar.gz': 'e9c505cace0cbeb9ea5ed33799f332f5cc95230a05ba14b646475cff1bdecaee'}, + {'pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch': + '0e3c86605d2b5d7bc16ec9342a246bd44617e7b1cbfab708b7085f70ee65cb08'} + ], }), ('pyiron_atomistics', '0.3.11', { 'patches': ['pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch'], From 6114ea364f80b52cfced656123778a0b2d8dd610 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Tue, 9 Jan 2024 14:14:04 +0100 Subject: [PATCH 045/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch --- ...1-foss-2023a_fix-pyiron-base-version.patch | 31 +++++++++++++++++-- 1 file changed, 28 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch index 8cdbfa8916b..c66e3c2804a 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch @@ -2,9 +2,34 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version --- /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig 2023-12-13 15:51:48.895090935 +0000 +++ /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml 2023-12-13 15:53:26.626579151 +0000 -@@ -40,7 +40,7 @@ - "tqdm==4.66.1", - "traitlets==5.14.0", +@@ -28,19 +28,19 @@ +- "dill==0.3.7", +- "gitpython==3.1.40", +- "h5io==0.1.9", +- "h5py==3.10.0", ++ "dill>=0.3.2", ++ "gitpython>=3.1.8", ++ "h5io>=0.12", ++ "h5py>=3.9.0", + "jinja2==3.1.2", +- "numpy==1.26.2", +- "pandas==2.1.3", ++ "numpy>=1.25.1", ++ "pandas>=2.0.3", + "pint==0.22", + "psutil==5.9.5", +- "pyfileindex==0.0.18", +- "pysqa==0.1.7", +- "sqlalchemy==2.0.23", +- "tables==3.9.2", +- "tqdm==4.66.1", +- "traitlets==5.14.0" ++ "pyfileindex>=0.0.4", ++ "pysqa>=0.1.7", ++ "sqlalchemy>=2.0.23", ++ "tables>=3.8.0", ++ "tqdm>=4.66.1", ++ "traitlets>=5.9.0", ] -dynamic = ["version"] +version = "0.6.12" From 3cb8e56813b4656cee9efc4d944c315a655b7fab Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Tue, 9 Jan 2024 14:14:26 +0100 Subject: [PATCH 046/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index decd2b0ecf0..2e5dcde22eb 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -104,7 +104,7 @@ exts_list = [ }), ('atomistics', '0.1.15', { 'source_urls': ['https://github.com/pyiron/atomistics/archive/refs/tags/'], - 'patches': ['pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch'] + 'patches': ['pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch'], 'checksums': [ {'atomistics-0.1.15.tar.gz': 'e9c505cace0cbeb9ea5ed33799f332f5cc95230a05ba14b646475cff1bdecaee'}, {'pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch': From 3c7f4de8d5c0182ead1524659ef0012392a0585f Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Tue, 9 Jan 2024 14:16:42 +0100 Subject: [PATCH 047/106] Update pyiron-0.5.1-foss-2023a.eb --- .../p/pyiron/pyiron-0.5.1-foss-2023a.eb | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 2e5dcde22eb..b8a58dcacda 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -43,7 +43,9 @@ check_ldshared = True use_pip = True exts_list = [ - ('sshtunnel', '0.4.0'), + ('sshtunnel', '0.4.0', { + 'checksums': ['e7cb0ea774db81bf91844db22de72a40aae8f7b0f9bb9ba0f666d474ef6bf9fc'], + }), ('h5io', '0.1.2', { 'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'], }), @@ -99,16 +101,16 @@ exts_list = [ 'checksums': [ {'pyiron_base-0.6.12.tar.gz': '7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch': - '761fb6123c16fa1a785c5c6425626522bd019613b1cb3ba0912b52538a8c682d'}, + '085166e2795ae18ec22fb3cb0e0b720f65e97c69c1e374e4aff3b4230546898b'}, ], }), ('atomistics', '0.1.15', { - 'source_urls': ['https://github.com/pyiron/atomistics/archive/refs/tags/'], 'patches': ['pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch'], + 'source_urls': ['https://github.com/pyiron/atomistics/archive/refs/tags/'], 'checksums': [ {'atomistics-0.1.15.tar.gz': 'e9c505cace0cbeb9ea5ed33799f332f5cc95230a05ba14b646475cff1bdecaee'}, {'pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch': - '0e3c86605d2b5d7bc16ec9342a246bd44617e7b1cbfab708b7085f70ee65cb08'} + 'cb7c859ac82d924b9642ffdc03033212f63f1221c9e5c8165281cc5008661bfc'}, ], }), ('pyiron_atomistics', '0.3.11', { @@ -117,7 +119,7 @@ exts_list = [ 'checksums': [ {'pyiron_atomistics-0.3.11.tar.gz': '8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch': - '30d5dcf024520ac687fb6bcbd3a8d3c8155e1a386ce4ff67557b1f1c73189995'}, + 'c4efd2685c714a5cbae32899fd5b3152db633c0d0d889022a95c8cd580d88ba9'}, ], }), ('mp-api', '0.39.4', { @@ -129,7 +131,7 @@ exts_list = [ 'checksums': [ {'pylammpsmpi-0.2.10.tar.gz': 'bd5af29a935dacbee743c3cc0bcc799e24e7c2483801f56cb9092a79f016f2ed'}, {'pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch': - 'f509db8ae6776ec01bcb97cb50ec20b74319ed82432fa3bede0ef7132c841fef'}, + 'd7cacf8eb73cb43e47526bfa3f98157073c01cd88918f191f87d7e75ab4c7c30'}, ], }), ('emmet-core', '0.75.0', { From 4351abcd9cc5d7f3ae8d7e828dff2a0f87223483 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 11 Jan 2024 15:38:15 +0100 Subject: [PATCH 048/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch --- ...1-foss-2023a_fix-pyiron-base-version.patch | 40 +++++++++++-------- 1 file changed, 23 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch index c66e3c2804a..5bcb556a62b 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch @@ -1,35 +1,41 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version instead. ---- /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig 2023-12-13 15:51:48.895090935 +0000 -+++ /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml 2023-12-13 15:53:26.626579151 +0000 -@@ -28,19 +28,19 @@ +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig 2023-12-13 15:51:48.895090935 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml 2023-12-13 15:53:26.626579151 +0000 +@@ -24,23 +24,23 @@ + "Programming Language :: Python :: 3.11", + ] + dependencies = [ - "dill==0.3.7", - "gitpython==3.1.40", - "h5io==0.1.9", - "h5py==3.10.0", -+ "dill>=0.3.2", -+ "gitpython>=3.1.8", -+ "h5io>=0.12", -+ "h5py>=3.9.0", - "jinja2==3.1.2", +- "jinja2==3.1.2", - "numpy==1.26.2", - "pandas==2.1.3", -+ "numpy>=1.25.1", -+ "pandas>=2.0.3", - "pint==0.22", - "psutil==5.9.5", +- "pint==0.22", +- "psutil==5.9.5", - "pyfileindex==0.0.18", - "pysqa==0.1.7", - "sqlalchemy==2.0.23", - "tables==3.9.2", - "tqdm==4.66.1", -- "traitlets==5.14.0" -+ "pyfileindex>=0.0.4", +- "traitlets==5.14.0", ++ "dill>=0.3.2", ++ "gitpython>=3.1.8", ++ "h5io>=0.1.2", ++ "h5py>=3.9.0", ++ "jinja2>=3.1.2", ++ "numpy>=1.25.1", ++ "pandas>=2.0.3", ++ "pint>=0.22", ++ "psutil>=5.9.5", ++ "pyfileindex>=0.0.18", + "pysqa>=0.1.7", + "sqlalchemy>=2.0.23", + "tables>=3.8.0", + "tqdm>=4.66.1", -+ "traitlets>=5.9.0", ++ "traitlet>=5.9.0", ] -dynamic = ["version"] +version = "0.6.12" @@ -50,8 +56,8 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version -parentdir_prefix = "pyiron_base" -tag_prefix = "pyiron_base-" ---- /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 -+++ /dev/shm/pyiron/0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py 2023-12-13 17:18:56.504736380 +0000 +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py 2023-12-13 17:18:56.504736380 +0000 @@ -3,6 +3,6 @@ import versioneer From acff09de8faad41698345be9b7976bc642283394 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 11 Jan 2024 15:39:16 +0100 Subject: [PATCH 049/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index b8a58dcacda..3320c1d2974 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -101,7 +101,7 @@ exts_list = [ 'checksums': [ {'pyiron_base-0.6.12.tar.gz': '7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch': - '085166e2795ae18ec22fb3cb0e0b720f65e97c69c1e374e4aff3b4230546898b'}, + '9668e4d5b607e60f7950ef9c386a79611cf9382266ec345d7aa589ee28210e1f'}, ], }), ('atomistics', '0.1.15', { From 0ce612f5cf20e7b41202a96eb4e79298040371ac Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 11 Jan 2024 15:42:06 +0100 Subject: [PATCH 050/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 3320c1d2974..a03bda2c971 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -101,7 +101,7 @@ exts_list = [ 'checksums': [ {'pyiron_base-0.6.12.tar.gz': '7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch': - '9668e4d5b607e60f7950ef9c386a79611cf9382266ec345d7aa589ee28210e1f'}, + 'f7fe1bda2672894a42b20df268f27f77cc4bd65f7540752b4b46d4ceb2eaef5c'}, ], }), ('atomistics', '0.1.15', { From e13715bf057f37e16fcc7e7ff8be2f80dc0c139d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 15 Jan 2024 13:35:05 +0100 Subject: [PATCH 051/106] Update yaff-1.6.0-foss-2023a.eb style errro --- easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb index f1a97e2256a..4bc49223ce2 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb @@ -41,7 +41,9 @@ exts_list = [ 'yaff-1.6.0-foss-2023a_fix-h5py.patch', 'yaff-1.6.0-foss-2023a_fix-nose-dep.patch', ], - 'runtest': "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v", + 'runtest': ("export MATPLOTLIBRC=$PWD; " + "echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " + "python setup.py build_ext -i; nosetests -v"), 'source_urls': ['https://github.com/molmod/yaff/releases/download/%(version)s'], 'checksums': [ {'yaff-1.6.0.tar.gz': 'a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'}, From 15b5849c54f7980af5883eae5c7d52282155a323 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 15 Jan 2024 13:40:10 +0100 Subject: [PATCH 052/106] Update pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch --- .../p/pyiron/pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch index b5cf94ef1b2..2ed9d7c4983 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch @@ -1,7 +1,7 @@ Fixes attempt to open nonexistent README.md. ---- /dev/shm/pyiron/0.5.1/foss-2023a/emmetcore/emmet-core-0.75.0/setup.py.orig 2023-12-21 18:58:49.428075405 +0000 -+++ /dev/shm/pyiron/0.5.1/foss-2023a/emmetcore/emmet-core-0.75.0/setup.py 2023-12-21 18:59:10.200024324 +0000 +--- 0.5.1/foss-2023a/emmetcore/emmet-core-0.75.0/setup.py.orig 2023-12-21 18:58:49.428075405 +0000 ++++ 0.5.1/foss-2023a/emmetcore/emmet-core-0.75.0/setup.py 2023-12-21 18:59:10.200024324 +0000 @@ -7,8 +7,6 @@ description="Core Emmet Library", author="The Materials Project", From 963138f7d0d9030cea55351541bb7513b0c51b9a Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 15 Jan 2024 13:40:34 +0100 Subject: [PATCH 053/106] Update pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch --- .../pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch index 0a3f2a238ac..8046feee46d 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch @@ -1,6 +1,5 @@ Relax requirements of `atomistics`. -/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml.orig 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml --- 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml.orig 2024-01-09 12:42:59.508409527 +0000 +++ 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml2024-01-09 12:43:44.589293464 +0000 @@ -26,9 +26,9 @@ From 3752ef5f8ea0debec49fe720aad921f42b600114 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 15 Jan 2024 13:42:37 +0100 Subject: [PATCH 054/106] Update pyiron-0.5.1-foss-2023a.eb update checksums --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index a03bda2c971..61fbee16b51 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -110,7 +110,7 @@ exts_list = [ 'checksums': [ {'atomistics-0.1.15.tar.gz': 'e9c505cace0cbeb9ea5ed33799f332f5cc95230a05ba14b646475cff1bdecaee'}, {'pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch': - 'cb7c859ac82d924b9642ffdc03033212f63f1221c9e5c8165281cc5008661bfc'}, + '748f2e720c07e9dbe3eb04c6b1e89aa021b99671f6212c5c958ffa5d9cd286ed'}, ], }), ('pyiron_atomistics', '0.3.11', { @@ -139,7 +139,7 @@ exts_list = [ 'checksums': [ {'emmet-core-0.75.0.tar.gz': '2d4b20d542e56c97009d05d03f5595be9395ac27c2fe9809d617f28596c40640'}, {'pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch': - '4cfe7ab122f37ff4a5f1ba52f69d84ab43fc2abfafd6efe71c401319d1258e1c'}, + 'd299f388044fdcff32fc246b0215ae4b656bc20d9d3c759d545cbe3167df08b8'}, ], }), ('maggma', '0.60.2', { From 58eaea993fd1881c431a0696e83f14dbbdf1e0d3 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 15 Jan 2024 15:11:10 +0100 Subject: [PATCH 055/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- ...yiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index 9891b611865..5c99390a01b 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -15,7 +15,7 @@ Fix versioning related issue and requirements in pyiron atomistics. - "pandas==2.1.3", - "phonopy==2.21.0", + "atomistics>=0.1.12", -+ "defusedxm>=0.6.0", ++ "defusedxml>=0.6.0", + "h5py>=3.9.0", + "matplotlib>=3.7.2", + "mendeleev>=0.6.0", @@ -32,7 +32,7 @@ Fix versioning related issue and requirements in pyiron atomistics. + "pylammpsmpi>=0.2.9", + "scipy>=1.11.1", + "scikit-learn>=1.3.1", -+ "seekpath>=2.01" ++ "seekpath>=2.0.1", "spglib==2.1.0", "structuretoolkit==0.0.15", ] From 3447f23a68c5c1925c2945003ffcdff988e9f829 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 15 Jan 2024 15:15:14 +0100 Subject: [PATCH 056/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- ...-2023a_fix-pyiron-atomistics-version.patch | 87 +++++++++---------- 1 file changed, 43 insertions(+), 44 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index 5c99390a01b..299f079890b 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -1,63 +1,63 @@ -Fix versioning related issue and requirements in pyiron atomistics. +Fixes use of dynamic versioning in pyproject.toml and puts in a specific version instead. ---- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig 2023-12-21 16:39:17.769971429 +0000 -+++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml 2023-12-21 16:39:59.280760858 +0000 -@@ -26,24 +26,24 @@ +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig 2023-12-13 15:51:48.895090935 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml 2023-12-13 15:53:26.626579151 +0000 +@@ -24,23 +24,23 @@ + "Programming Language :: Python :: 3.11", + ] dependencies = [ - "ase==3.22.1", -- "atomistics==0.1.12", -- "defusedxml==0.7.1", +- "dill==0.3.7", +- "gitpython==3.1.40", +- "h5io==0.1.9", - "h5py==3.10.0", -- "matplotlib==3.8.2", -- "mendeleev==0.14.0", -- "mp-api==0.39.1", +- "jinja2==3.1.2", - "numpy==1.26.2", - "pandas==2.1.3", -- "phonopy==2.21.0", -+ "atomistics>=0.1.12", -+ "defusedxml>=0.6.0", +- "pint==0.22", +- "psutil==5.9.5", +- "pyfileindex==0.0.18", +- "pysqa==0.1.7", +- "sqlalchemy==2.0.23", +- "tables==3.9.2", +- "tqdm==4.66.1", +- "traitlets==5.14.0", ++ "dill>=0.3.2", ++ "gitpython>=3.1.8", ++ "h5io>=0.1.2", + "h5py>=3.9.0", -+ "matplotlib>=3.7.2", -+ "mendeleev>=0.6.0", -+ "mp-api>=0.39.1", ++ "jinja2>=3.1.2", + "numpy>=1.25.1", + "pandas>=2.0.3", -+ "phonopy>=2.20.0", - "pint==0.22", - "pyiron_base==0.6.12", -- "pylammpsmpi==0.2.9", -- "scipy==1.11.4", -- "scikit-learn==1.3.2", -- "seekpath==2.1.0", -+ "pylammpsmpi>=0.2.9", -+ "scipy>=1.11.1", -+ "scikit-learn>=1.3.1", -+ "seekpath>=2.0.1", - "spglib==2.1.0", - "structuretoolkit==0.0.15", ++ "pint>=0.22", ++ "psutil>=5.9.5", ++ "pyfileindex>=0.0.18", ++ "pysqa>=0.1.7", ++ "sqlalchemy>=2.0.23", ++ "tables>=3.8.0", ++ "tqdm>=4.66.1", ++ "traitlets>=5.9.0", ] -dynamic = ["version"] -+version = "0.3.11" ++version = "0.6.12" [project.urls] - Homepage = "https://pyiron.org" -@@ -55,13 +55,3 @@ + Homepage = "https://github.com/pyiron/pyiron_base" +@@ -53,12 +53,3 @@ + [tool.setuptools.packages.find] + include = ["pyiron_base*"] - [tool.setuptools.package-data] - "*" = ["data/*.csv"] -- -[tool.setuptools.dynamic] --version = {attr = "pyiron_atomistics.__version__"} +-version = {attr = "pyiron_base.__version__"} - -[tool.versioneer] -VCS = "git" -style = "pep440-pre" --versionfile_source = "pyiron_atomistics/_version.py" --parentdir_prefix = "pyiron_atomistics" --tag_prefix = "pyiron_atomistics-" +-versionfile_source = "pyiron_base/_version.py" +-parentdir_prefix = "pyiron_base" +-tag_prefix = "pyiron_base-" ---- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig 2023-12-13 17:41:20.162738914 +0000 -+++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py 2023-12-13 17:41:48.007593887 +0000 +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py 2023-12-13 17:18:56.504736380 +0000 @@ -3,6 +3,6 @@ import versioneer @@ -65,8 +65,7 @@ Fix versioning related issue and requirements in pyiron atomistics. - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), -) -\ -+ version="0.3.11", +\ No newline at end ++ version="0.6.12", +) + -+ From 1412653410afc3f4c487aed09b94146d4e79ec0c Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 15 Jan 2024 15:16:30 +0100 Subject: [PATCH 057/106] Update pyiron-0.5.1-foss-2023a.eb --- .../p/pyiron/pyiron-0.5.1-foss-2023a.eb | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 61fbee16b51..73d0e97845e 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -43,6 +43,9 @@ check_ldshared = True use_pip = True exts_list = [ + ('jsonschema', '4.18.0', { + 'checksums': ['8caf5b57a990a98e9b39832ef3cb35c176fe331414252b6e1b26fd5866f891a4'], + }), ('sshtunnel', '0.4.0', { 'checksums': ['e7cb0ea774db81bf91844db22de72a40aae8f7b0f9bb9ba0f666d474ef6bf9fc'], }), @@ -52,14 +55,14 @@ exts_list = [ ('defusedxml', '0.6.0', { 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], }), - ('pysqa', '0.0.11', { - 'checksums': ['b1a1995ac8b83b86046cef8b72cda962c5fdbf480c6dbba906a467a5dd1d3c81'], + ('pysqa', '0.1.7', { + 'checksums': ['fdc37e0178649750e7386b4e9b8287693ee2d47559723c11b9ad42afcfc55900'], }), ('paramiko', '3.3.1', { 'checksums': ['6a3777a961ac86dbef375c5f5b8d50014a1a96d0fd7f054a43bc880134b0ff77'], }), - ('SQLAlchemy', '1.3.19', { - 'checksums': ['3bba2e9fbedb0511769780fe1d63007081008c5c2d7d715e91858c94dbaa260e'], + ('SQLAlchemy', '2.0.3', { + 'checksums': ['c2b924f6d0162ed1c0d8f47db1e56498702b1c3c953ad84f0eefbf5b4e53bb05'], }), ('dill', '0.3.2', { 'source_tmpl': 'dill-%(version)s.zip', @@ -84,8 +87,8 @@ exts_list = [ ('mendeleev', '0.6.0', { 'checksums': ['944d185e81f158e48dd394b011e6c14acb612c2ffbc3c32c4aa490cd5b4f65dd'], }), - ('pyfileindex', '0.0.4', { - 'checksums': ['bbfbfc9372f810587917ab1a88bebb8de44d32a1210bbd436c5b88447d97dfd2'], + ('pyfileindex', '0.0.18', { + 'checksums': ['6d5acf2500f568667aa5273ae57692c2b62facbcaae7c0bbbf21ba3bdd904961'], }), ('seekpath', '2.0.1', { 'checksums': ['188513ee187fbbace49066a29ecea9bbd351f23da3bea33d507d0f590856b082'], @@ -101,7 +104,7 @@ exts_list = [ 'checksums': [ {'pyiron_base-0.6.12.tar.gz': '7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch': - 'f7fe1bda2672894a42b20df268f27f77cc4bd65f7540752b4b46d4ceb2eaef5c'}, + 'a6390dcd366e17361fb71f26c6d3b75835526bdf773d9ef535c02836fe551b31'}, ], }), ('atomistics', '0.1.15', { @@ -119,7 +122,7 @@ exts_list = [ 'checksums': [ {'pyiron_atomistics-0.3.11.tar.gz': '8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch': - 'c4efd2685c714a5cbae32899fd5b3152db633c0d0d889022a95c8cd580d88ba9'}, + '6d608199f430bf6d6de159943cec76157ecbf345deb35398510bf12f64b3ec7e'}, ], }), ('mp-api', '0.39.4', { From 6fbe709aa657ce6845b5d52b87ddaac73146524e Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 15 Jan 2024 15:41:19 +0100 Subject: [PATCH 058/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 73d0e97845e..73097d8340a 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -43,6 +43,9 @@ check_ldshared = True use_pip = True exts_list = [ + ('greenlet', '2.0.2', { + 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], + }), ('jsonschema', '4.18.0', { 'checksums': ['8caf5b57a990a98e9b39832ef3cb35c176fe331414252b6e1b26fd5866f891a4'], }), @@ -61,8 +64,8 @@ exts_list = [ ('paramiko', '3.3.1', { 'checksums': ['6a3777a961ac86dbef375c5f5b8d50014a1a96d0fd7f054a43bc880134b0ff77'], }), - ('SQLAlchemy', '2.0.3', { - 'checksums': ['c2b924f6d0162ed1c0d8f47db1e56498702b1c3c953ad84f0eefbf5b4e53bb05'], + ('SQLAlchemy', '2.0.23', { + 'checksums': ['c1bda93cbbe4aa2aa0aa8655c5aeda505cd219ff3e8da91d1d329e143e4aff69'], }), ('dill', '0.3.2', { 'source_tmpl': 'dill-%(version)s.zip', From 91d88a63f9e7369fe003a045ebc598849d4eb94b Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 15 Jan 2024 15:42:56 +0100 Subject: [PATCH 059/106] Update pydantic-2.1.1-GCCcore-12.3.0.eb --- .../easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb index 5cb85f6a578..39e0670651b 100644 --- a/easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb @@ -31,9 +31,8 @@ exts_list = [ 'sources': {'source_urls': ['https://github.com/pydantic/%(name)s/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, 'checksums': ['ae48a2ffe679ae003bb52b511ecfe85bed70f4b8a955c76e0957dd29c003cdbf'], }), - ('pydantic-settings', '2.0.1', { + ('pydantic-settings', '2.0.3', { 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, - 'checksums': ['bf8e327234e4ffab3642e72e677c1b176d358bab551090a1b1cea6f462cd9a1e'], }), ('pydantic-core', '2.4.0', { 'sources': {'source_urls': ['https://github.com/pydantic/%(name)s/archive/refs/tags/'], 'filename': 'v%(version)s.tar.gz'}, From f217900d8c0f62afd46e5bd936215592a1b65411 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 15 Jan 2024 17:30:02 +0100 Subject: [PATCH 060/106] Update pyiron-0.5.1-foss-2023a.eb --- .../p/pyiron/pyiron-0.5.1-foss-2023a.eb | 24 ++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 73097d8340a..ce03c06ed0e 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -34,7 +34,6 @@ dependencies = [ ('Flask', '2.3.3'), ('boto3', '1.28.70'), ('sympy', '1.12'), - ('pydantic', '2.1.1'), ('maturin', '1.1.0'), ('poetry', '1.5.1'), ] @@ -43,9 +42,31 @@ check_ldshared = True use_pip = True exts_list = [ + ('pydantic_core', '2.14.6', { + 'source_tmpl': '%(name)s-%(version)s-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'checksums': ['b2602177668f89b38b9f84b7b3435d0a72511ddef45dc14446811759b82235a1'], + }), + ('pydantic', '2.5.3', { + 'checksums': ['b3ef57c62535b0941697cce638c08900d87fcb67e29cfa99e8a68f747f393f7a'], + }), ('greenlet', '2.0.2', { 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], }), + ('typing_extensions', '4.9.0', { + 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], + }), + ('python-dotenv', '1.0.0', { + 'modulename': 'dotenv', + 'checksums': ['a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba'], + }), + ('pydantic-settings', '2.1.0', { + 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, + 'checksums': ['be83f7a7da10a0686a00da1b9e62856072bbcfb7d6a420ea3c78c66b145fcd93'], + }), + ('annotated-types', '0.6.0', { + 'sources': {'source_urls': ['https://github.com/%(name)s/%(name)s/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, + 'checksums': ['0b99aba34b87840d7578705968d87fe6265c1a1604bcf9ccc11902b1d8d39ad8'], + }), ('jsonschema', '4.18.0', { 'checksums': ['8caf5b57a990a98e9b39832ef3cb35c176fe331414252b6e1b26fd5866f891a4'], }), @@ -141,6 +162,7 @@ exts_list = [ ], }), ('emmet-core', '0.75.0', { + 'modulename': 'emmet', 'patches': ['pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch'], 'checksums': [ {'emmet-core-0.75.0.tar.gz': '2d4b20d542e56c97009d05d03f5595be9395ac27c2fe9809d617f28596c40640'}, From 000fcfe90d963a10c475ef9156cf206be99be8cd Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 15 Jan 2024 17:56:17 +0100 Subject: [PATCH 061/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index ce03c06ed0e..7acfbeff8be 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -219,6 +219,7 @@ exts_list = [ 'checksums': ['9ebbdbd6a046c304b1845e96fbcc5559cd296b4dfd3ad2509e33c4d9ce07d6a1'], }), ('dnspython', '2.4.2', { + 'modulename': False, 'checksums': ['8dcfae8c7460a2f84b4072e26f1c9f4101ca20c071649cb7c34e8b6a93d58984'], }), ('fastapi', '0.105.0', { From 95de3c7ec68757ec81437a52da69ef223796f1ab Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 10:43:40 +0100 Subject: [PATCH 062/106] Delete easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb --- .../pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb deleted file mode 100644 index 39e0670651b..00000000000 --- a/easybuild/easyconfigs/p/pydantic/pydantic-2.1.1-GCCcore-12.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pydantic' -version = '2.1.1' - -homepage = 'https://github.com/samuelcolvin/pydantic' -description = """Data validation and settings management using Python type hinting.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [('binutils', '2.40')] - -dependencies = [ - ('Python', '3.11.3'), - ('hatchling', '1.18.0'), - ('maturin', '1.1.0') -] - -sanity_pip_check = True -use_pip = True - -exts_list = [ - ('typing_extensions', '4.9.0', { - 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], - }), - ('python-dotenv', '1.0.0', { - 'modulename': 'dotenv', - 'checksums': ['a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba'], - }), - (name, version, { - 'sources': {'source_urls': ['https://github.com/pydantic/%(name)s/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, - 'checksums': ['ae48a2ffe679ae003bb52b511ecfe85bed70f4b8a955c76e0957dd29c003cdbf'], - }), - ('pydantic-settings', '2.0.3', { - 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, - }), - ('pydantic-core', '2.4.0', { - 'sources': {'source_urls': ['https://github.com/pydantic/%(name)s/archive/refs/tags/'], 'filename': 'v%(version)s.tar.gz'}, - 'checksums': ['94b4ef19df7e0ea5e9f32590afc3673dab0d9855ed786d3dc95513124d842874'], - }), - ('annotated-types', '0.6.0', { - 'sources': {'source_urls': ['https://github.com/%(name)s/%(name)s/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, - 'checksums': ['0b99aba34b87840d7578705968d87fe6265c1a1604bcf9ccc11902b1d8d39ad8'], - }), -] - -moduleclass = 'devel' From 239f4cbe355cf8010021655df11a61bcbaaa7dc8 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 10:49:14 +0100 Subject: [PATCH 063/106] Update pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch --- .../pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch index 8046feee46d..5b47f86d759 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch @@ -1,7 +1,7 @@ Relax requirements of `atomistics`. --- 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml.orig 2024-01-09 12:42:59.508409527 +0000 -+++ 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml2024-01-09 12:43:44.589293464 +0000 ++++ 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml 2024-01-09 12:43:44.589293464 +0000 @@ -26,9 +26,9 @@ ] dependencies = [ From 056161749f60dc04c4287522924feb30ef6fdb03 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 11:29:02 +0100 Subject: [PATCH 064/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- ...-2023a_fix-pyiron-atomistics-version.patch | 83 +++++++++---------- 1 file changed, 41 insertions(+), 42 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index 299f079890b..40ac0f4360e 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -1,63 +1,62 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version instead. ---- 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig 2023-12-13 15:51:48.895090935 +0000 -+++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml 2023-12-13 15:53:26.626579151 +0000 -@@ -24,23 +24,23 @@ - "Programming Language :: Python :: 3.11", - ] +--- 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig 2024-01-22 10:12:31.768251943 +0000 ++++ 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml 2024-01-22 10:26:21.997455595 +0000 +@@ -26,24 +26,24 @@ dependencies = [ -- "dill==0.3.7", -- "gitpython==3.1.40", -- "h5io==0.1.9", + "ase==3.22.1", + "atomistics==0.1.12", +- "defusedxml==0.7.1", - "h5py==3.10.0", -- "jinja2==3.1.2", +- "matplotlib==3.8.2", +- "mendeleev==0.14.0", +- "mp-api==0.39.1", - "numpy==1.26.2", - "pandas==2.1.3", -- "pint==0.22", -- "psutil==5.9.5", -- "pyfileindex==0.0.18", -- "pysqa==0.1.7", -- "sqlalchemy==2.0.23", -- "tables==3.9.2", -- "tqdm==4.66.1", -- "traitlets==5.14.0", -+ "dill>=0.3.2", -+ "gitpython>=3.1.8", -+ "h5io>=0.1.2", -+ "h5py>=3.9.0", -+ "jinja2>=3.1.2", +- "phonopy==2.21.0", ++ "defusedxml>=0.6.0", ++ "h5py>=3.9.8", ++ "matplotlib>=3.7.2", ++ "mendeleev>=0.14.0", ++ "mp-api>=0.39.1", + "numpy>=1.25.1", + "pandas>=2.0.3", -+ "pint>=0.22", -+ "psutil>=5.9.5", -+ "pyfileindex>=0.0.18", -+ "pysqa>=0.1.7", -+ "sqlalchemy>=2.0.23", -+ "tables>=3.8.0", -+ "tqdm>=4.66.1", -+ "traitlets>=5.9.0", ++ "phonopy>=2.20.0", + "pint==0.22", + "pyiron_base==0.6.12", + "pylammpsmpi==0.2.9", +- "scipy==1.11.4", +- "scikit-learn==1.3.2", +- "seekpath==2.1.0", +- "spglib==2.1.0", ++ "scipy>=1.11.1", ++ "scikit-learn>=1.3.1", ++ "seekpath>=2.1.0", ++ "spglib>=2.1.0", + "structuretoolkit==0.0.15", ] -dynamic = ["version"] -+version = "0.6.12" ++version = '0.3.11' [project.urls] - Homepage = "https://github.com/pyiron/pyiron_base" -@@ -53,12 +53,3 @@ - [tool.setuptools.packages.find] - include = ["pyiron_base*"] + Homepage = "https://pyiron.org" +@@ -55,13 +55,3 @@ + [tool.setuptools.package-data] + "*" = ["data/*.csv"] +- -[tool.setuptools.dynamic] --version = {attr = "pyiron_base.__version__"} +-version = {attr = "pyiron_atomistics.__version__"} - -[tool.versioneer] -VCS = "git" -style = "pep440-pre" --versionfile_source = "pyiron_base/_version.py" --parentdir_prefix = "pyiron_base" --tag_prefix = "pyiron_base-" +-versionfile_source = "pyiron_atomistics/_version.py" +-parentdir_prefix = "pyiron_atomistics" +-tag_prefix = "pyiron_atomistics-" ---- 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 -+++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py 2023-12-13 17:18:56.504736380 +0000 +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.111/setup.py 2023-12-13 17:18:56.504736380 +0000 @@ -3,6 +3,6 @@ import versioneer @@ -66,6 +65,6 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version - cmdclass=versioneer.get_cmdclass(), -) \ No newline at end -+ version="0.6.12", ++ version="0.3.11", +) + From 4ecdbfc5ce5c53651133cfbd8d27d95f2ca416fe Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 11:30:10 +0100 Subject: [PATCH 065/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 7acfbeff8be..d5377be5e17 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -114,7 +114,7 @@ exts_list = [ ('pyfileindex', '0.0.18', { 'checksums': ['6d5acf2500f568667aa5273ae57692c2b62facbcaae7c0bbbf21ba3bdd904961'], }), - ('seekpath', '2.0.1', { + ('seekpath', '2.1.0', { 'checksums': ['188513ee187fbbace49066a29ecea9bbd351f23da3bea33d507d0f590856b082'], }), (name, version, { From f46619e6adcf1e9f04f18efd0419cf1405df5e3c Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 11:32:17 +0100 Subject: [PATCH 066/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index d5377be5e17..d5a7aa673a2 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -115,7 +115,7 @@ exts_list = [ 'checksums': ['6d5acf2500f568667aa5273ae57692c2b62facbcaae7c0bbbf21ba3bdd904961'], }), ('seekpath', '2.1.0', { - 'checksums': ['188513ee187fbbace49066a29ecea9bbd351f23da3bea33d507d0f590856b082'], + 'checksums': ['31cec579628262e6d4a4c3693fefa70d6ccae1ceeef7c9d10ea3cd48988452c4'], }), (name, version, { 'modulename': False, @@ -128,7 +128,7 @@ exts_list = [ 'checksums': [ {'pyiron_base-0.6.12.tar.gz': '7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch': - 'a6390dcd366e17361fb71f26c6d3b75835526bdf773d9ef535c02836fe551b31'}, + 'f7fe1bda2672894a42b20df268f27f77cc4bd65f7540752b4b46d4ceb2eaef5c'}, ], }), ('atomistics', '0.1.15', { @@ -137,7 +137,7 @@ exts_list = [ 'checksums': [ {'atomistics-0.1.15.tar.gz': 'e9c505cace0cbeb9ea5ed33799f332f5cc95230a05ba14b646475cff1bdecaee'}, {'pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch': - '748f2e720c07e9dbe3eb04c6b1e89aa021b99671f6212c5c958ffa5d9cd286ed'}, + 'deaa57c27be147efc7e4926f6795bfa421280a299fc96de8c0bae342e4770d6c'}, ], }), ('pyiron_atomistics', '0.3.11', { @@ -146,7 +146,7 @@ exts_list = [ 'checksums': [ {'pyiron_atomistics-0.3.11.tar.gz': '8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch': - '6d608199f430bf6d6de159943cec76157ecbf345deb35398510bf12f64b3ec7e'}, + 'df83534e5df96ccbb432001f1a40b9f0bf5403bb477fd94016a193dfd3c6321d'}, ], }), ('mp-api', '0.39.4', { From 28f63cf6fed0aa12308d4be4242d17efcb44fcfe Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 11:40:07 +0100 Subject: [PATCH 067/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch --- .../pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch index 5bcb556a62b..9efc42afbb9 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch @@ -35,7 +35,7 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version + "sqlalchemy>=2.0.23", + "tables>=3.8.0", + "tqdm>=4.66.1", -+ "traitlet>=5.9.0", ++ "traitlets>=5.9.0", ] -dynamic = ["version"] +version = "0.6.12" From ed18d5a0449e72e248689e1f62b12ae2b16c1f0e Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 11:42:17 +0100 Subject: [PATCH 068/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- ...n-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index 40ac0f4360e..402bd476a10 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -5,7 +5,7 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version @@ -26,24 +26,24 @@ dependencies = [ "ase==3.22.1", - "atomistics==0.1.12", +- "atomistics==0.1.12", - "defusedxml==0.7.1", - "h5py==3.10.0", - "matplotlib==3.8.2", @@ -14,8 +14,9 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version - "numpy==1.26.2", - "pandas==2.1.3", - "phonopy==2.21.0", ++ "atomistics>=0.1.12", + "defusedxml>=0.6.0", -+ "h5py>=3.9.8", ++ "h5py>=3.9.0", + "matplotlib>=3.7.2", + "mendeleev>=0.14.0", + "mp-api>=0.39.1", @@ -24,7 +25,8 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version + "phonopy>=2.20.0", "pint==0.22", "pyiron_base==0.6.12", - "pylammpsmpi==0.2.9", +- "pylammpsmpi==0.2.9", ++ "pylammpsmpi>=0.2.9", - "scipy==1.11.4", - "scikit-learn==1.3.2", - "seekpath==2.1.0", From 059c9824bb4a5db529ecc6d26c1faece76219f46 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 11:42:47 +0100 Subject: [PATCH 069/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index d5a7aa673a2..776305fa4ba 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -108,7 +108,7 @@ exts_list = [ ('pyfiglet', '0.8.post1', { 'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'], }), - ('mendeleev', '0.6.0', { + ('mendeleev', '0.14.0', { 'checksums': ['944d185e81f158e48dd394b011e6c14acb612c2ffbc3c32c4aa490cd5b4f65dd'], }), ('pyfileindex', '0.0.18', { From e939dd862bad26fec85c2ea303ccfdf20baf58df Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 11:44:35 +0100 Subject: [PATCH 070/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 776305fa4ba..2d644fe7b57 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -109,7 +109,7 @@ exts_list = [ 'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'], }), ('mendeleev', '0.14.0', { - 'checksums': ['944d185e81f158e48dd394b011e6c14acb612c2ffbc3c32c4aa490cd5b4f65dd'], + 'checksums': ['1a89ccf05c708aebe627c5eb19ff5c6379585a2f9e588e1dcf9b03182fe61f3c'], }), ('pyfileindex', '0.0.18', { 'checksums': ['6d5acf2500f568667aa5273ae57692c2b62facbcaae7c0bbbf21ba3bdd904961'], @@ -128,7 +128,7 @@ exts_list = [ 'checksums': [ {'pyiron_base-0.6.12.tar.gz': '7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch': - 'f7fe1bda2672894a42b20df268f27f77cc4bd65f7540752b4b46d4ceb2eaef5c'}, + 'a6390dcd366e17361fb71f26c6d3b75835526bdf773d9ef535c02836fe551b31'}, ], }), ('atomistics', '0.1.15', { @@ -146,7 +146,7 @@ exts_list = [ 'checksums': [ {'pyiron_atomistics-0.3.11.tar.gz': '8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch': - 'df83534e5df96ccbb432001f1a40b9f0bf5403bb477fd94016a193dfd3c6321d'}, + 'e7059f005eef599668022f1796acb5ac4cb82bcef6abe732bb15ec6dc44e86a2'}, ], }), ('mp-api', '0.39.4', { From b7fedfa67bdd6ccbea4c89c73540835a2ebc33ff Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 12:15:16 +0100 Subject: [PATCH 071/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 2d644fe7b57..3ca8cc2dd2f 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -102,8 +102,8 @@ exts_list = [ 'modulename': 'git', 'checksums': ['080bf8e2cf1a2b907634761c2eaefbe83b69930c94c66ad11b65a8252959f912'], }), - ('colorama', '0.4.3', { - 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + ('colorama', '0.4.4', { + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], }), ('pyfiglet', '0.8.post1', { 'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'], From efd0fac77b958895599bcb24b3228ab246b706bc Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:00:17 +0100 Subject: [PATCH 072/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 3ca8cc2dd2f..2311e800cb6 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -60,11 +60,15 @@ exts_list = [ 'checksums': ['a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba'], }), ('pydantic-settings', '2.1.0', { - 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, + 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz'}, 'checksums': ['be83f7a7da10a0686a00da1b9e62856072bbcfb7d6a420ea3c78c66b145fcd93'], }), ('annotated-types', '0.6.0', { - 'sources': {'source_urls': ['https://github.com/%(name)s/%(name)s/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, + 'sources': {'source_urls': ['https://github.com/%(name)s/%(name)s/archive/refs/tags/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz'}, 'checksums': ['0b99aba34b87840d7578705968d87fe6265c1a1604bcf9ccc11902b1d8d39ad8'], }), ('jsonschema', '4.18.0', { From e961d0a9ed842f92ba55666f6c476fbb564ba145 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:06:25 +0100 Subject: [PATCH 073/106] Update Pint-0.22-GCCcore-12.3.0.eb --- easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb index fb5a9be76b2..0702d78f0f4 100644 --- a/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb @@ -12,8 +12,11 @@ conversions from and to different units.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = [SOURCE_TAR_GZ] -checksums = ['2d139f6abbcf3016cad7d3cec05707fe908ac4f99cf59aedfd6ee667b7a64433'] patches = [('Pint-0.22-GCCcore-12.3.0_fix-version.patch', 3)] +checksums = [ + {'Pint-0.22.tar.gz': '2d139f6abbcf3016cad7d3cec05707fe908ac4f99cf59aedfd6ee667b7a64433'}, + {'Pint-0.22-GCCcore-12.3.0_fix-version.patch': '6a01aca1d0a6a9b91499787e39497d7ca44befcbb21b82fd9a1036d7b6c84a58'}, +] builddependencies = [('binutils', '2.40')] From 1d9811bf6bd2f067bd4bf41d686ed72e3e8dbb57 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:08:12 +0100 Subject: [PATCH 074/106] Update typing-extensions-4.9.0-GCCcore-12.3.0.eb --- .../typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb index 2078482b45a..44a057a01fd 100644 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb @@ -9,6 +9,7 @@ description = 'Typing Extensions – Backported and Experimental Type Hints for toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'] builddependencies = [('binutils', '2.40')] From 20f3075f50a34d4528281643c5f4f88f4324fa3a Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:11:10 +0100 Subject: [PATCH 075/106] Create Pint-0.22-GCCcore-12.3.0_fix-version.patch --- .../p/Pint/Pint-0.22-GCCcore-12.3.0_fix-version.patch | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0_fix-version.patch diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0_fix-version.patch b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0_fix-version.patch new file mode 100644 index 00000000000..763bcfeca9f --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0_fix-version.patch @@ -0,0 +1,7 @@ +--- 0.22/GCCcore-12.3.0/Pint-0.22/setup.py.orig 2023-12-13 18:45:35.241637807 +0000 ++++ 0.22/GCCcore-12.3.0/Pint-0.22/setup.py 2023-12-13 18:49:29.304418276 +0000 +@@ -0,0 +1,4 @@ ++from setuptools import setup ++ ++ ++setup(version='0.22') From 258ae16c70082e01800d6faa37a336ead02d959b Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:11:44 +0100 Subject: [PATCH 076/106] Delete easybuild/easyconfigs/p/Pint-0.22-GCCcore-12.3.0_fix-version.patch --- .../p/Pint-0.22-GCCcore-12.3.0_fix-version.patch | 7 ------- 1 file changed, 7 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Pint-0.22-GCCcore-12.3.0_fix-version.patch diff --git a/easybuild/easyconfigs/p/Pint-0.22-GCCcore-12.3.0_fix-version.patch b/easybuild/easyconfigs/p/Pint-0.22-GCCcore-12.3.0_fix-version.patch deleted file mode 100644 index 763bcfeca9f..00000000000 --- a/easybuild/easyconfigs/p/Pint-0.22-GCCcore-12.3.0_fix-version.patch +++ /dev/null @@ -1,7 +0,0 @@ ---- 0.22/GCCcore-12.3.0/Pint-0.22/setup.py.orig 2023-12-13 18:45:35.241637807 +0000 -+++ 0.22/GCCcore-12.3.0/Pint-0.22/setup.py 2023-12-13 18:49:29.304418276 +0000 -@@ -0,0 +1,4 @@ -+from setuptools import setup -+ -+ -+setup(version='0.22') From 50820bf64e1a9738b065b44f74a55654f3940bab Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:31:23 +0100 Subject: [PATCH 077/106] Delete easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb --- .../p/Pint/Pint-0.22-GCCcore-12.3.0.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb deleted file mode 100644 index 0702d78f0f4..00000000000 --- a/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pint' -version = '0.22' - -homepage = 'https://github.com/hgrecco/pint' -description = """Pint is a Python package to define, operate and -manipulate physical quantities: the product of a numerical value and a -unit of measurement. It allows arithmetic operations between them and -conversions from and to different units.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -sources = [SOURCE_TAR_GZ] -patches = [('Pint-0.22-GCCcore-12.3.0_fix-version.patch', 3)] -checksums = [ - {'Pint-0.22.tar.gz': '2d139f6abbcf3016cad7d3cec05707fe908ac4f99cf59aedfd6ee667b7a64433'}, - {'Pint-0.22-GCCcore-12.3.0_fix-version.patch': '6a01aca1d0a6a9b91499787e39497d7ca44befcbb21b82fd9a1036d7b6c84a58'}, -] - -builddependencies = [('binutils', '2.40')] - -dependencies = [ - ('Python', '3.11.3'), - ('typing-extensions', '4.9.0') -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -moduleclass = 'numlib' From a41c651623cb8bb3c9e8928753fa01c2873f756e Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:31:35 +0100 Subject: [PATCH 078/106] Delete easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0_fix-version.patch --- .../p/Pint/Pint-0.22-GCCcore-12.3.0_fix-version.patch | 7 ------- 1 file changed, 7 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0_fix-version.patch diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0_fix-version.patch b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0_fix-version.patch deleted file mode 100644 index 763bcfeca9f..00000000000 --- a/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-12.3.0_fix-version.patch +++ /dev/null @@ -1,7 +0,0 @@ ---- 0.22/GCCcore-12.3.0/Pint-0.22/setup.py.orig 2023-12-13 18:45:35.241637807 +0000 -+++ 0.22/GCCcore-12.3.0/Pint-0.22/setup.py 2023-12-13 18:49:29.304418276 +0000 -@@ -0,0 +1,4 @@ -+from setuptools import setup -+ -+ -+setup(version='0.22') From ae881430a13aa3c0d06f7e65e007b20e233c9066 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:31:56 +0100 Subject: [PATCH 079/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 2311e800cb6..01ef3789d01 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -27,7 +27,7 @@ dependencies = [ ('yaff', '1.6.0'), ('TAMkin', '1.2.6'), ('QuickFF', '2.2.7'), - ('Pint', '0.22'), + ('Pint', '0.23'), ('bcrypt', '4.0.1'), ('ruamel.yaml', '0.17.32'), ('plotly.py', '5.16.0'), From 84c315fc3b63d3f0a46cc38c52561420bc226cf6 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:32:34 +0100 Subject: [PATCH 080/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- ...pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index 402bd476a10..c0854e34c37 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -23,7 +23,8 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version + "numpy>=1.25.1", + "pandas>=2.0.3", + "phonopy>=2.20.0", - "pint==0.22", +- "pint==0.22", ++ "pint>=0.22", "pyiron_base==0.6.12", - "pylammpsmpi==0.2.9", + "pylammpsmpi>=0.2.9", From eba4b27f893c5ba1520aa52377b6859f2a41fa96 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:35:07 +0100 Subject: [PATCH 081/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 01ef3789d01..d771af25f92 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -27,7 +27,6 @@ dependencies = [ ('yaff', '1.6.0'), ('TAMkin', '1.2.6'), ('QuickFF', '2.2.7'), - ('Pint', '0.23'), ('bcrypt', '4.0.1'), ('ruamel.yaml', '0.17.32'), ('plotly.py', '5.16.0'), @@ -42,6 +41,7 @@ check_ldshared = True use_pip = True exts_list = [ + ('pint', '0.23'), ('pydantic_core', '2.14.6', { 'source_tmpl': '%(name)s-%(version)s-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', 'checksums': ['b2602177668f89b38b9f84b7b3435d0a72511ddef45dc14446811759b82235a1'], From d66786f03d113939e3f6bf06fd409afd11636c78 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:41:12 +0100 Subject: [PATCH 082/106] Update pyiron-0.5.1-foss-2023a.eb --- .../p/pyiron/pyiron-0.5.1-foss-2023a.eb | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index d771af25f92..c1e9e5fdcb7 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -41,7 +41,10 @@ check_ldshared = True use_pip = True exts_list = [ - ('pint', '0.23'), + ('pint', '0.23', { + 'source_tmpl': 'Pint-%(version)s.tar.gz', + 'checksums': ['e1509b91606dbc52527c600a4ef74ffac12fff70688aff20e9072409346ec9b4'], + }), ('pydantic_core', '2.14.6', { 'source_tmpl': '%(name)s-%(version)s-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', 'checksums': ['b2602177668f89b38b9f84b7b3435d0a72511ddef45dc14446811759b82235a1'], @@ -61,14 +64,14 @@ exts_list = [ }), ('pydantic-settings', '2.1.0', { 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], - 'download_filename': 'v%(version)s.tar.gz', - 'filename': '%(name)s-%(version)s.tar.gz'}, + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz'}, 'checksums': ['be83f7a7da10a0686a00da1b9e62856072bbcfb7d6a420ea3c78c66b145fcd93'], }), ('annotated-types', '0.6.0', { 'sources': {'source_urls': ['https://github.com/%(name)s/%(name)s/archive/refs/tags/'], - 'download_filename': 'v%(version)s.tar.gz', - 'filename': '%(name)s-%(version)s.tar.gz'}, + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz'}, 'checksums': ['0b99aba34b87840d7578705968d87fe6265c1a1604bcf9ccc11902b1d8d39ad8'], }), ('jsonschema', '4.18.0', { @@ -150,7 +153,7 @@ exts_list = [ 'checksums': [ {'pyiron_atomistics-0.3.11.tar.gz': '8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch': - 'e7059f005eef599668022f1796acb5ac4cb82bcef6abe732bb15ec6dc44e86a2'}, + '17375bfadfe22d575d92bab92e4318a2a1a475efefc3739d4a461b9efeea39be'}, ], }), ('mp-api', '0.39.4', { From 5cdd5875183f23c50c73271d40b2cf5e0d8d8734 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 15:19:17 +0100 Subject: [PATCH 083/106] Update pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch --- ...yiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch index c0854e34c37..46ab8c36467 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch @@ -23,8 +23,8 @@ Fixes use of dynamic versioning in pyproject.toml and puts in a specific version + "numpy>=1.25.1", + "pandas>=2.0.3", + "phonopy>=2.20.0", -- "pint==0.22", -+ "pint>=0.22", +- "pint==0.22", ++ "pint>=0.22", "pyiron_base==0.6.12", - "pylammpsmpi==0.2.9", + "pylammpsmpi>=0.2.9", From 8c317da76231fe0b444de9b738d3f91b8942b692 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 15:19:56 +0100 Subject: [PATCH 084/106] Update pyiron-0.5.1-foss-2023a.eb --- .../easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index c1e9e5fdcb7..c11b7870d3d 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -63,15 +63,11 @@ exts_list = [ 'checksums': ['a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba'], }), ('pydantic-settings', '2.1.0', { - 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], - 'download_filename': 'v%(version)s.tar.gz', - 'filename': '%(name)s-%(version)s.tar.gz'}, + 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, 'checksums': ['be83f7a7da10a0686a00da1b9e62856072bbcfb7d6a420ea3c78c66b145fcd93'], }), ('annotated-types', '0.6.0', { - 'sources': {'source_urls': ['https://github.com/%(name)s/%(name)s/archive/refs/tags/'], - 'download_filename': 'v%(version)s.tar.gz', - 'filename': '%(name)s-%(version)s.tar.gz'}, + 'sources': {'source_urls': ['https://github.com/%(name)s/%(name)s/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, 'checksums': ['0b99aba34b87840d7578705968d87fe6265c1a1604bcf9ccc11902b1d8d39ad8'], }), ('jsonschema', '4.18.0', { @@ -153,7 +149,7 @@ exts_list = [ 'checksums': [ {'pyiron_atomistics-0.3.11.tar.gz': '8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'}, {'pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch': - '17375bfadfe22d575d92bab92e4318a2a1a475efefc3739d4a461b9efeea39be'}, + '5c9b987cb63508f482bff696e252987e10df9b8ee8e860491583c8e547d4568c'}, ], }), ('mp-api', '0.39.4', { From 02e7a99122d2fea26a2f6581d32290f1cb79a7a7 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 22 Jan 2024 15:34:26 +0100 Subject: [PATCH 085/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index c11b7870d3d..36c7b676185 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -63,11 +63,15 @@ exts_list = [ 'checksums': ['a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba'], }), ('pydantic-settings', '2.1.0', { - 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, + 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz'}, 'checksums': ['be83f7a7da10a0686a00da1b9e62856072bbcfb7d6a420ea3c78c66b145fcd93'], }), ('annotated-types', '0.6.0', { - 'sources': {'source_urls': ['https://github.com/%(name)s/%(name)s/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}, + 'sources': {'source_urls': ['https://github.com/%(name)s/%(name)s/archive/refs/tags/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz'}, 'checksums': ['0b99aba34b87840d7578705968d87fe6265c1a1604bcf9ccc11902b1d8d39ad8'], }), ('jsonschema', '4.18.0', { From d5130a44076919fc201d36e29a47562c68efda7c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 23 Jan 2024 10:58:35 +0100 Subject: [PATCH 086/106] Remove toolchain suffix from patch files --- .../m/molmod/molmod-1.4.8-foss-2023a.eb | 4 ++-- ...atch => molmod-1.4.8_fix-np-unicode.patch} | 0 .../p/pyiron/pyiron-0.5.1-foss-2023a.eb | 20 +++++++++---------- ...n-0.5.1_fix-atomistics-requirements.patch} | 0 ...ch => pyiron-0.5.1_fix-emmet-readme.patch} | 0 ...0.5.1_fix-pyiron-atomistics-version.patch} | 0 ...yiron-0.5.1_fix-pyiron-base-version.patch} | 0 ...tch => pyiron-0.5.1_fix-pylammpsmpi.patch} | 0 .../y/yaff/yaff-1.6.0-foss-2023a.eb | 12 +++++------ ...x-h5py.patch => yaff-1.6.0_fix-h5py.patch} | 0 ...ep.patch => yaff-1.6.0_fix-nose-dep.patch} | 0 ...tch => yaff-1.6.0_fix-random-import.patch} | 0 12 files changed, 18 insertions(+), 18 deletions(-) rename easybuild/easyconfigs/m/molmod/{molmod-1.4.8-foss-2023a_fix-np-unicode.patch => molmod-1.4.8_fix-np-unicode.patch} (100%) rename easybuild/easyconfigs/p/pyiron/{pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch => pyiron-0.5.1_fix-atomistics-requirements.patch} (100%) rename easybuild/easyconfigs/p/pyiron/{pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch => pyiron-0.5.1_fix-emmet-readme.patch} (100%) rename easybuild/easyconfigs/p/pyiron/{pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch => pyiron-0.5.1_fix-pyiron-atomistics-version.patch} (100%) rename easybuild/easyconfigs/p/pyiron/{pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch => pyiron-0.5.1_fix-pyiron-base-version.patch} (100%) rename easybuild/easyconfigs/p/pyiron/{pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch => pyiron-0.5.1_fix-pylammpsmpi.patch} (100%) rename easybuild/easyconfigs/y/yaff/{yaff-1.6.0-foss-2023a_fix-h5py.patch => yaff-1.6.0_fix-h5py.patch} (100%) rename easybuild/easyconfigs/y/yaff/{yaff-1.6.0-foss-2023a_fix-nose-dep.patch => yaff-1.6.0_fix-nose-dep.patch} (100%) rename easybuild/easyconfigs/y/yaff/{yaff-1.6.0-foss-2023a_fix-random-import.patch => yaff-1.6.0_fix-random-import.patch} (100%) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb index eb570fc1078..6d091b4f23b 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb @@ -10,10 +10,10 @@ toolchain = {'name': 'foss', 'version': '2023a'} source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -patches = ['molmod-1.4.8-foss-2023a_fix-np-unicode.patch'] +patches = ['molmod-1.4.8_fix-np-unicode.patch'] checksums = [ {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, - {'molmod-1.4.8-foss-2023a_fix-np-unicode.patch': + {'molmod-1.4.8_fix-np-unicode.patch': '85bd2e2981d2cdd8cfab5d1c2cf37432e2967ff82de603700383d7c31530327c'}, ] diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch b/easybuild/easyconfigs/m/molmod/molmod-1.4.8_fix-np-unicode.patch similarity index 100% rename from easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch rename to easybuild/easyconfigs/m/molmod/molmod-1.4.8_fix-np-unicode.patch diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 36c7b676185..20b07b632d4 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -130,29 +130,29 @@ exts_list = [ 'checksums': ['2e5e3f892b7e49a15443569870aa4ea049951b71fe2ad1ad7f4ac7551d475788'], }), ('pyiron_base', '0.6.12', { - 'patches': ['pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch'], + 'patches': ['pyiron-0.5.1_fix-pyiron-base-version.patch'], 'source_urls': ['https://github.com/pyiron/pyiron_base/archive/refs/tags/'], 'checksums': [ {'pyiron_base-0.6.12.tar.gz': '7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'}, - {'pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch': + {'pyiron-0.5.1_fix-pyiron-base-version.patch': 'a6390dcd366e17361fb71f26c6d3b75835526bdf773d9ef535c02836fe551b31'}, ], }), ('atomistics', '0.1.15', { - 'patches': ['pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch'], + 'patches': ['pyiron-0.5.1_fix-atomistics-requirements.patch'], 'source_urls': ['https://github.com/pyiron/atomistics/archive/refs/tags/'], 'checksums': [ {'atomistics-0.1.15.tar.gz': 'e9c505cace0cbeb9ea5ed33799f332f5cc95230a05ba14b646475cff1bdecaee'}, - {'pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch': + {'pyiron-0.5.1_fix-atomistics-requirements.patch': 'deaa57c27be147efc7e4926f6795bfa421280a299fc96de8c0bae342e4770d6c'}, ], }), ('pyiron_atomistics', '0.3.11', { - 'patches': ['pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch'], + 'patches': ['pyiron-0.5.1_fix-pyiron-atomistics-version.patch'], 'source_urls': ['https://github.com/pyiron/pyiron_atomistics/archive/refs/tags/'], 'checksums': [ {'pyiron_atomistics-0.3.11.tar.gz': '8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'}, - {'pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch': + {'pyiron-0.5.1_fix-pyiron-atomistics-version.patch': '5c9b987cb63508f482bff696e252987e10df9b8ee8e860491583c8e547d4568c'}, ], }), @@ -160,20 +160,20 @@ exts_list = [ 'checksums': ['692abefd6adec36eb4fa193f914e08167ed33a5a3a9714ec3c15606839649f32'], }), ('pylammpsmpi', '0.2.10', { - 'patches': ['pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch'], + 'patches': ['pyiron-0.5.1_fix-pylammpsmpi.patch'], 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], 'checksums': [ {'pylammpsmpi-0.2.10.tar.gz': 'bd5af29a935dacbee743c3cc0bcc799e24e7c2483801f56cb9092a79f016f2ed'}, - {'pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch': + {'pyiron-0.5.1_fix-pylammpsmpi.patch': 'd7cacf8eb73cb43e47526bfa3f98157073c01cd88918f191f87d7e75ab4c7c30'}, ], }), ('emmet-core', '0.75.0', { 'modulename': 'emmet', - 'patches': ['pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch'], + 'patches': ['pyiron-0.5.1_fix-emmet-readme.patch'], 'checksums': [ {'emmet-core-0.75.0.tar.gz': '2d4b20d542e56c97009d05d03f5595be9395ac27c2fe9809d617f28596c40640'}, - {'pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch': + {'pyiron-0.5.1_fix-emmet-readme.patch': 'd299f388044fdcff32fc246b0215ae4b656bc20d9d3c759d545cbe3167df08b8'}, ], }), diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-atomistics-requirements.patch similarity index 100% rename from easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-atomistics-requirements.patch rename to easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-atomistics-requirements.patch diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-emmet-readme.patch similarity index 100% rename from easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-emmet-readme.patch rename to easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-emmet-readme.patch diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-atomistics-version.patch similarity index 100% rename from easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-atomistics-version.patch rename to easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-atomistics-version.patch diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-base-version.patch similarity index 100% rename from easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pyiron-base-version.patch rename to easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-base-version.patch diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pylammpsmpi.patch similarity index 100% rename from easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a_fix-pylammpsmpi.patch rename to easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pylammpsmpi.patch diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb index 4bc49223ce2..743974c697c 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb @@ -37,9 +37,9 @@ local_runtest += "python setup.py build_ext -i; nosetests -v" exts_list = [ (name, version, { 'patches': [ - 'yaff-1.6.0-foss-2023a_fix-random-import.patch', - 'yaff-1.6.0-foss-2023a_fix-h5py.patch', - 'yaff-1.6.0-foss-2023a_fix-nose-dep.patch', + 'yaff-1.6.0_fix-random-import.patch', + 'yaff-1.6.0_fix-h5py.patch', + 'yaff-1.6.0_fix-nose-dep.patch', ], 'runtest': ("export MATPLOTLIBRC=$PWD; " "echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " @@ -47,11 +47,11 @@ exts_list = [ 'source_urls': ['https://github.com/molmod/yaff/releases/download/%(version)s'], 'checksums': [ {'yaff-1.6.0.tar.gz': 'a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'}, - {'yaff-1.6.0-foss-2023a_fix-random-import.patch': + {'yaff-1.6.0_fix-random-import.patch': 'a38afacbcbfbf16a80742ae8253852e725e656c9d684310894c806f689362840'}, - {'yaff-1.6.0-foss-2023a_fix-h5py.patch': + {'yaff-1.6.0_fix-h5py.patch': 'bd2a73f375910360fd5dd22b3ec006344527476e80dea549f4d82297257105f9'}, - {'yaff-1.6.0-foss-2023a_fix-nose-dep.patch': + {'yaff-1.6.0_fix-nose-dep.patch': '2314c487c4a847d7740d7dfc97052cf7efd764ced726d098def0a1aef0b498e0'}, ], }), diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-h5py.patch similarity index 100% rename from easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch rename to easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-h5py.patch diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-nose-dep.patch similarity index 100% rename from easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch rename to easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-nose-dep.patch diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-random-import.patch similarity index 100% rename from easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch rename to easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-random-import.patch From a9c2c1e38751b9f4152561ad01dd0d4869b9f343 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 23 Jan 2024 12:28:10 +0100 Subject: [PATCH 087/106] Fix toolchains Remove already existing numexpr (in SciPy-bundle) and phonopy (foss variant) Remove explicit toolchain specifications for dependencies --- .../n/nglview/nglview-3.0.8-foss-2023a.eb | 4 +- .../n/numexpr/numexpr-2.8.7-foss-2023a.eb | 23 ----------- .../p/PyTables/PyTables-3.8.0-foss-2023a.eb | 2 +- .../p/phonopy/phonopy-2.20.0-gfbf-2023a.eb | 38 ------------------- .../p/pyiron/pyiron-0.5.1-foss-2023a.eb | 1 - 5 files changed, 2 insertions(+), 66 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.8.7-foss-2023a.eb delete mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb b/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb index 73b94940f74..a0fd0895046 100644 --- a/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb +++ b/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb @@ -8,11 +8,9 @@ description = "IPython widget to interactively view molecular structures and tra toolchain = {'name': 'foss', 'version': '2023a'} -local_gfbf_ver = '2023a' - dependencies = [ ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07', '', ('gfbf', local_gfbf_ver)), + ('SciPy-bundle', '2023.07'), ('JupyterLab', '4.0.5'), ('nodejs', '18.17.1'), ('MDAnalysis', '2.6.1'), # optional diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.8.7-foss-2023a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.7-foss-2023a.eb deleted file mode 100644 index 14d228ba563..00000000000 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.8.7-foss-2023a.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'numexpr' -version = '2.8.7' - -homepage = 'https://numexpr.readthedocs.io/en/latest/' -description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. - It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into - code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a - compiler at runtime.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['df5131349ec1e4b080a3e2df7abbb7bce20d023adff633d259e1ce1549a60ed1'] - -local_gfbf_ver = '2023a' - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07', '', ('gfbf', local_gfbf_ver)), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb index a0f4b362b19..3804e6016ca 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb @@ -29,7 +29,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07', '', ('gfbf', local_gfbf_ver)), # provides numexpr + ('SciPy-bundle', '2023.07'), # provides numexpr ('HDF5', '1.14.0'), ('LZO', '2.10'), ('Blosc', '1.21.5'), diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-gfbf-2023a.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-gfbf-2023a.eb deleted file mode 100644 index 959805d4cce..00000000000 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-gfbf-2023a.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'phonopy' -version = '2.20.0' - -homepage = 'https://atztogo.github.io/phonopy/' -description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" - -toolchain = {'name': 'gfbf', 'version': '2023a'} - -source_urls = ['https://github.com/phonopy/phonopy/archive/refs/tags/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['1dd47cb6e5b427d5cb88ce0b810b91f05533f434d53d22ea69eb974d4eb0ab46'] - -local_foss_ver = '2023a' - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), # for numpy - ('matplotlib', '3.7.2'), - ('PyYAML', '6.0'), - ('h5py', '3.9.0', '', ('foss', local_foss_ver)), - ('spglib-python', '2.1.0'), -] - -download_dep_fail = True -use_pip = True - -sanity_check_paths = { - 'files': ['bin/phonopy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["phonopy --help"] - -sanity_pip_check = True - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 20b07b632d4..b60efd6141d 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -18,7 +18,6 @@ dependencies = [ ('phonopy', '2.20.0'), ('spglib-python', '2.1.0'), ('ASE', '3.22.1'), - ('numexpr', '2.8.7'), ('PyTables', '3.8.0'), ('nglview', '3.0.8'), ('tqdm', '4.66.1'), From 3158cece4f0bcc01b1f39aab34f28de371410484 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 24 Jan 2024 11:07:44 +0100 Subject: [PATCH 088/106] Remove explicit C++ standard from Blosc/Blosc2 Not required for newer GCC versions and can cause trouble --- easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb index 60fb8a755d1..8ec9141c86c 100644 --- a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb @@ -8,7 +8,7 @@ homepage = 'https://www.blosc.org/' description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} +toolchainopts = {'pic': True} source_urls = ['https://github.com/Blosc/c-blosc/archive/'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb index 58f563af452..9cebfb5a167 100644 --- a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb @@ -11,7 +11,7 @@ homepage = 'https://www.blosc.org/' description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} +toolchainopts = {'pic': True} source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] sources = ['v%(version)s.tar.gz'] From ea209e99b26e8fca59dbcb7157a3e7f571194366 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 24 Jan 2024 11:10:28 +0100 Subject: [PATCH 089/106] Convert some ECs to PythonPackage and improve formatting --- .../coverage/coverage-7.2.3-GCCcore-12.3.0.eb | 9 +-- .../n/nglview/nglview-3.0.8-foss-2023a.eb | 19 +++--- .../n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb | 4 +- .../py-cpuinfo-9.0.0-GCCcore-12.3.0.eb | 9 +-- .../y/yaff/yaff-1.6.0-foss-2023a.eb | 58 ++++++++----------- 5 files changed, 36 insertions(+), 63 deletions(-) diff --git a/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb index f75075ae45e..66cdb2b6ec4 100644 --- a/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb @@ -13,13 +13,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = [SOURCE_TAR_GZ] checksums = ['d298c2815fa4891edd9abe5ad6e6cb4207104c7dd9fd13aea3fdebf6f9b91259'] -builddependencies = [ - ('binutils', '2.40'), -] - -dependencies = [ - ('Python', '3.11.3'), -] +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.3')] use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb b/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb index a0fd0895046..b96adf11bdc 100644 --- a/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb +++ b/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'nglview' version = '3.0.8' @@ -16,20 +16,15 @@ dependencies = [ ('MDAnalysis', '2.6.1'), # optional ] -use_pip = True - -exts_list = [ - ('versioneer', '0.28', { - 'checksums': ['7175ca8e7bb4dd0e3c9779dd2745e5b4a6036304af3f5e50bd896f10196586d6'], - }), - (name, version, { - 'use_pip_extras': 'MDAnalysis', - 'checksums': ['f9e468cd813dac319cbeca6ae20ae099008ff3a06399f5d23d75582dde28623a'], - }), -] +sources = [SOURCE_TAR_GZ] +checksums = ['f9e468cd813dac319cbeca6ae20ae099008ff3a06399f5d23d75582dde28623a'] +use_pip = True +download_dep_fail = True sanity_pip_check = True +use_pip_extras = 'MDAnalysis' + sanity_check_paths = { 'files': ['bin/nglview'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb index 46f4f2d2669..bc5d8e11586 100644 --- a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb @@ -11,9 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = [SOURCE_TAR_GZ] checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'] -builddependencies = [ - ('binutils', '2.40'), -] +builddependencies = [('binutils', '2.40')] dependencies = [ ('Python', '3.11.3'), diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb index a4a0886152c..43afd372fa5 100644 --- a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb @@ -11,13 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = [SOURCE_TAR_GZ] checksums = ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'] -builddependencies = [ - ('binutils', '2.40'), -] - -dependencies = [ - ('Python', '3.11.3'), -] +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.3')] download_dep_fail = True use_pip = True diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb index 743974c697c..47eba698998 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb @@ -1,14 +1,7 @@ # Updated from previous config # Author: Pavel Grochal (INUITS) # License: GPLv2 -# -# Building this in interactive Slurm session will result in freeze during either -# runtest phase or sanity_check_commands phase (python -c 'import yaff') -# -# If you submit this as non-interactive Slurm job, it will build just fine. -# Possibly root cause: https://github.com/h5py/h5py/issues/917 -# -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'yaff' version = '1.6.0' @@ -19,7 +12,6 @@ description = """Yaff stands for 'Yet another force field'. It is a pythonic for toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [('pkgconfig', '1.5.5', '-python')] - dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), @@ -28,33 +20,31 @@ dependencies = [ ('nose3', '1.3.8') ] +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'yaff-1.6.0_fix-random-import.patch', + 'yaff-1.6.0_fix-h5py.patch', + 'yaff-1.6.0_fix-nose-dep.patch', +] +checksums = [ + {'yaff-1.6.0.tar.gz': 'a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'}, + {'yaff-1.6.0_fix-random-import.patch': + 'a38afacbcbfbf16a80742ae8253852e725e656c9d684310894c806f689362840'}, + {'yaff-1.6.0_fix-h5py.patch': + 'bd2a73f375910360fd5dd22b3ec006344527476e80dea549f4d82297257105f9'}, + {'yaff-1.6.0_fix-nose-dep.patch': + '2314c487c4a847d7740d7dfc97052cf7efd764ced726d098def0a1aef0b498e0'}, +] + use_pip = True +download_dep_fail = True sanity_pip_check = True -local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " -local_runtest += "python setup.py build_ext -i; nosetests -v" - -exts_list = [ - (name, version, { - 'patches': [ - 'yaff-1.6.0_fix-random-import.patch', - 'yaff-1.6.0_fix-h5py.patch', - 'yaff-1.6.0_fix-nose-dep.patch', - ], - 'runtest': ("export MATPLOTLIBRC=$PWD; " - "echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " - "python setup.py build_ext -i; nosetests -v"), - 'source_urls': ['https://github.com/molmod/yaff/releases/download/%(version)s'], - 'checksums': [ - {'yaff-1.6.0.tar.gz': 'a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'}, - {'yaff-1.6.0_fix-random-import.patch': - 'a38afacbcbfbf16a80742ae8253852e725e656c9d684310894c806f689362840'}, - {'yaff-1.6.0_fix-h5py.patch': - 'bd2a73f375910360fd5dd22b3ec006344527476e80dea549f4d82297257105f9'}, - {'yaff-1.6.0_fix-nose-dep.patch': - '2314c487c4a847d7740d7dfc97052cf7efd764ced726d098def0a1aef0b498e0'}, - ], - }), -] +runtest = ' '.join([ + "export MATPLOTLIBRC=$PWD;", + "echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;", + "python setup.py build_ext -i; nosetests -v", +]) moduleclass = 'chem' From c6d1c61d531bdc51cbe5ce86180454b3d232054e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 24 Jan 2024 11:11:59 +0100 Subject: [PATCH 090/106] Move some PythonPackages into own ECs and use existing ones Reduce number of additional packages installed in pyiron --- .../g/Greenlet/Greenlet-2.0.2-foss-2023a.eb | 27 ++++ .../pydantic/pydantic-2.5.3-GCCcore-12.3.0.eb | 122 +++++++++++++++ .../p/pyiron/pyiron-0.5.1-foss-2023a.eb | 139 +----------------- .../emmet-core-0.75.0-fix-readme.patch} | 0 .../pymatgen-2023.12.18-foss-2023a.eb | 138 +++++++++++++++++ .../uncertainties-3.1.7-foss-2023a.eb | 24 +++ 6 files changed, 317 insertions(+), 133 deletions(-) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.3.0.eb rename easybuild/easyconfigs/p/{pyiron/pyiron-0.5.1_fix-emmet-readme.patch => pymatgen/emmet-core-0.75.0-fix-readme.patch} (100%) create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-2023.12.18-foss-2023a.eb create mode 100644 easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2023a.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2023a.eb new file mode 100644 index 00000000000..29d04a9e7b5 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Greenlet' +version = '2.0.2' + +homepage = 'https://github.com/python-greenlet/greenlet' + +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [('Python', '3.11.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..23955f5d21d --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.3.0.eb @@ -0,0 +1,122 @@ +easyblock = 'CargoPythonBundle' + +name = 'pydantic' +version = '2.5.3' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), + ('maturin', '1.4.0', '-Rust-1.75.0'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('typing-extensions', '4.9.0'), +] + +use_pip = True +sanity_pip_check = True + +crates = [ + ('ahash', '0.8.6'), + ('aho-corasick', '1.0.2'), + ('autocfg', '1.1.0'), + ('base64', '0.21.5'), + ('bitflags', '1.3.2'), + ('cc', '1.0.79'), + ('cfg-if', '1.0.0'), + ('enum_dispatch', '0.3.12'), + ('equivalent', '1.0.1'), + ('form_urlencoded', '1.2.0'), + ('getrandom', '0.2.10'), + ('hashbrown', '0.14.0'), + ('heck', '0.4.1'), + ('idna', '0.4.0'), + ('indexmap', '2.0.0'), + ('indoc', '2.0.4'), + ('itoa', '1.0.8'), + ('jiter', '0.0.4'), + ('lexical-core', '0.8.5'), + ('lexical-parse-float', '0.8.5'), + ('lexical-parse-integer', '0.8.6'), + ('lexical-util', '0.8.5'), + ('lexical-write-float', '0.8.5'), + ('lexical-write-integer', '0.8.5'), + ('libc', '0.2.147'), + ('lock_api', '0.4.10'), + ('memchr', '2.6.3'), + ('memoffset', '0.9.0'), + ('num-bigint', '0.4.4'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.16'), + ('once_cell', '1.18.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('percent-encoding', '2.3.0'), + ('proc-macro2', '1.0.69'), + ('pyo3', '0.20.0'), + ('pyo3-build-config', '0.20.0'), + ('pyo3-ffi', '0.20.0'), + ('pyo3-macros', '0.20.0'), + ('pyo3-macros-backend', '0.20.0'), + ('python3-dll-a', '0.2.9'), + ('quote', '1.0.29'), + ('redox_syscall', '0.3.5'), + ('regex', '1.10.2'), + ('regex-automata', '0.4.3'), + ('regex-syntax', '0.8.2'), + ('rustversion', '1.0.13'), + ('ryu', '1.0.14'), + ('scopeguard', '1.1.0'), + ('serde', '1.0.190'), + ('serde_derive', '1.0.190'), + ('serde_json', '1.0.108'), + ('smallvec', '1.11.1'), + ('speedate', '0.13.0'), + ('static_assertions', '1.1.0'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.3'), + ('syn', '2.0.38'), + ('target-lexicon', '0.12.9'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('unicode-bidi', '0.3.13'), + ('unicode-ident', '1.0.10'), + ('unicode-normalization', '0.1.22'), + ('unindent', '0.2.3'), + ('url', '2.4.1'), + ('uuid', '1.5.0'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('windows-targets', '0.48.1'), + ('windows_aarch64_gnullvm', '0.48.0'), + ('windows_aarch64_msvc', '0.48.0'), + ('windows_i686_gnu', '0.48.0'), + ('windows_i686_msvc', '0.48.0'), + ('windows_x86_64_gnu', '0.48.0'), + ('windows_x86_64_gnullvm', '0.48.0'), + ('windows_x86_64_msvc', '0.48.0'), + ('zerocopy', '0.7.20'), + ('zerocopy-derive', '0.7.20'), +] + +exts_list = [ + ('annotated_types', '0.6.0', { + 'checksums': ['563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d'], + }), + ('pydantic_core', '2.14.6', { + 'checksums': ['1fd0c1d395372843fba13a51c28e3bb9d59bd7aebfeb17358ffaaa1e4dbbe948'], + }), + (name, version, { + 'preinstallopts': "sed -i '/Framework :: Pydantic/d' pyproject.toml && ", + 'checksums': ['b3ef57c62535b0941697cce638c08900d87fcb67e29cfa99e8a68f747f393f7a'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index b60efd6141d..132fa8d3080 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -9,14 +9,15 @@ description = "An integrated development environment (IDE) for computational mat toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [('poetry', '1.5.1')] dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), ('matplotlib', '3.7.2'), ('h5py', '3.9.0'), ('PyYAML', '6.0'), ('phonopy', '2.20.0'), - ('spglib-python', '2.1.0'), ('ASE', '3.22.1'), ('PyTables', '3.8.0'), ('nglview', '3.0.8'), @@ -26,14 +27,12 @@ dependencies = [ ('yaff', '1.6.0'), ('TAMkin', '1.2.6'), ('QuickFF', '2.2.7'), - ('bcrypt', '4.0.1'), - ('ruamel.yaml', '0.17.32'), ('plotly.py', '5.16.0'), - ('Flask', '2.3.3'), - ('boto3', '1.28.70'), + ('GitPython', '3.1.40'), + ('Greenlet', '2.0.2'), + ('dill', '0.3.7'), ('sympy', '1.12'), - ('maturin', '1.1.0'), - ('poetry', '1.5.1'), + ('pymatgen', '2023.12.18'), ] check_ldshared = True @@ -44,41 +43,6 @@ exts_list = [ 'source_tmpl': 'Pint-%(version)s.tar.gz', 'checksums': ['e1509b91606dbc52527c600a4ef74ffac12fff70688aff20e9072409346ec9b4'], }), - ('pydantic_core', '2.14.6', { - 'source_tmpl': '%(name)s-%(version)s-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', - 'checksums': ['b2602177668f89b38b9f84b7b3435d0a72511ddef45dc14446811759b82235a1'], - }), - ('pydantic', '2.5.3', { - 'checksums': ['b3ef57c62535b0941697cce638c08900d87fcb67e29cfa99e8a68f747f393f7a'], - }), - ('greenlet', '2.0.2', { - 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], - }), - ('typing_extensions', '4.9.0', { - 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], - }), - ('python-dotenv', '1.0.0', { - 'modulename': 'dotenv', - 'checksums': ['a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba'], - }), - ('pydantic-settings', '2.1.0', { - 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], - 'download_filename': 'v%(version)s.tar.gz', - 'filename': '%(name)s-%(version)s.tar.gz'}, - 'checksums': ['be83f7a7da10a0686a00da1b9e62856072bbcfb7d6a420ea3c78c66b145fcd93'], - }), - ('annotated-types', '0.6.0', { - 'sources': {'source_urls': ['https://github.com/%(name)s/%(name)s/archive/refs/tags/'], - 'download_filename': 'v%(version)s.tar.gz', - 'filename': '%(name)s-%(version)s.tar.gz'}, - 'checksums': ['0b99aba34b87840d7578705968d87fe6265c1a1604bcf9ccc11902b1d8d39ad8'], - }), - ('jsonschema', '4.18.0', { - 'checksums': ['8caf5b57a990a98e9b39832ef3cb35c176fe331414252b6e1b26fd5866f891a4'], - }), - ('sshtunnel', '0.4.0', { - 'checksums': ['e7cb0ea774db81bf91844db22de72a40aae8f7b0f9bb9ba0f666d474ef6bf9fc'], - }), ('h5io', '0.1.2', { 'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'], }), @@ -88,29 +52,9 @@ exts_list = [ ('pysqa', '0.1.7', { 'checksums': ['fdc37e0178649750e7386b4e9b8287693ee2d47559723c11b9ad42afcfc55900'], }), - ('paramiko', '3.3.1', { - 'checksums': ['6a3777a961ac86dbef375c5f5b8d50014a1a96d0fd7f054a43bc880134b0ff77'], - }), ('SQLAlchemy', '2.0.23', { 'checksums': ['c1bda93cbbe4aa2aa0aa8655c5aeda505cd219ff3e8da91d1d329e143e4aff69'], }), - ('dill', '0.3.2', { - 'source_tmpl': 'dill-%(version)s.zip', - 'checksums': ['6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e'], - }), - ('smmap', '3.0.4', { - 'checksums': ['9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24'], - }), - ('gitdb', '4.0.5', { - 'checksums': ['c9e1f2d0db7ddb9a704c2a0217be31214e91a4fe1dea1efad19ae42ba0c285c9'], - }), - ('GitPython', '3.1.8', { - 'modulename': 'git', - 'checksums': ['080bf8e2cf1a2b907634761c2eaefbe83b69930c94c66ad11b65a8252959f912'], - }), - ('colorama', '0.4.4', { - 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], - }), ('pyfiglet', '0.8.post1', { 'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'], }), @@ -125,7 +69,6 @@ exts_list = [ }), (name, version, { 'modulename': False, - 'source_urls': ['https://github.com/pyiron/pyiron/archive/refs/tags/%(name)s-%(version)s.tar.gz'], 'checksums': ['2e5e3f892b7e49a15443569870aa4ea049951b71fe2ad1ad7f4ac7551d475788'], }), ('pyiron_base', '0.6.12', { @@ -155,9 +98,6 @@ exts_list = [ '5c9b987cb63508f482bff696e252987e10df9b8ee8e860491583c8e547d4568c'}, ], }), - ('mp-api', '0.39.4', { - 'checksums': ['692abefd6adec36eb4fa193f914e08167ed33a5a3a9714ec3c15606839649f32'], - }), ('pylammpsmpi', '0.2.10', { 'patches': ['pyiron-0.5.1_fix-pylammpsmpi.patch'], 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], @@ -167,79 +107,12 @@ exts_list = [ 'd7cacf8eb73cb43e47526bfa3f98157073c01cd88918f191f87d7e75ab4c7c30'}, ], }), - ('emmet-core', '0.75.0', { - 'modulename': 'emmet', - 'patches': ['pyiron-0.5.1_fix-emmet-readme.patch'], - 'checksums': [ - {'emmet-core-0.75.0.tar.gz': '2d4b20d542e56c97009d05d03f5595be9395ac27c2fe9809d617f28596c40640'}, - {'pyiron-0.5.1_fix-emmet-readme.patch': - 'd299f388044fdcff32fc246b0215ae4b656bc20d9d3c759d545cbe3167df08b8'}, - ], - }), - ('maggma', '0.60.2', { - 'checksums': ['12e8da1f80505f39432b972cbe47fb378cd9aa51fab968877a2d3b2588c96c69'], - }), - ('monty', '2023.11.3', { - 'checksums': ['d961c14b0b20901c7603aa00d275e62dee8333fbdaf1179f5d862c6fb3f3c52f'], - }), - ('pymatgen', '2023.12.18', { - 'checksums': ['56c0041fe5431ac1b8f8c0c17d06091c4d61082c3a99924f3940d73ebb6656eb'], - }), ('pympipool', '0.7.9', { 'checksums': ['5698181bc5dc9a69595fd00ff6a8ba651b77734ccf00df79ae3aea8aaf32790a'], }), ('structuretoolkit', '0.0.15', { 'checksums': ['1a258a072055d0c20e9d56156afd4481cfc94c2612c1b908de4b274b423cc6e6'], }), - ('uncertainties', '3.1.7', { - 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], - }), - ('palettable', '3.1.1', { - 'checksums': ['0685b223a236bb7e2a900ef7a855ccf9a4027361c8acf400f3b350ea51870f80'], - }), - ('pybtex', '0.24.0', { - 'checksums': ['818eae35b61733e5c007c3fcd2cfb75ed1bc8b4173c1f70b56cc4c0802d34755'], - }), - ('h11', '0.14.0', { - 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], - }), - ('mongogrant', '0.3.3', { - 'checksums': ['ad494b8638adfa840cdd5568af44448dd43771b58102550cf7c61402b1620ab4'], - }), - ('mongomock', '4.1.2', { - 'checksums': ['f06cd62afb8ae3ef63ba31349abd220a657ef0dd4f0243a29587c5213f931b7d'], - }), - ('pymongo', '4.6.1', { - 'checksums': ['31dab1f3e1d0cdd57e8df01b645f52d43cc1b653ed3afd535d2891f4fc4f9712'], - }), - ('pydash', '7.0.6', { - 'checksums': ['7d9df7e9f36f2bbb08316b609480e7c6468185473a21bdd8e65dda7915565a26'], - }), - ('uvicorn', '0.25.0', { - 'checksums': ['6dddbad1d7ee0f5140aba5ec138ddc9612c5109399903828b4874c9937f009c2'], - }), - ('starlette', '0.27.0', { - 'checksums': ['6a6b0d042acb8d469a01eba54e9cda6cbd24ac602c4cd016723117d6a7e73b75'], - }), - ('orjson', '3.9.10', { - 'checksums': ['9ebbdbd6a046c304b1845e96fbcc5559cd296b4dfd3ad2509e33c4d9ce07d6a1'], - }), - ('dnspython', '2.4.2', { - 'modulename': False, - 'checksums': ['8dcfae8c7460a2f84b4072e26f1c9f4101ca20c071649cb7c34e8b6a93d58984'], - }), - ('fastapi', '0.105.0', { - 'checksums': ['4d12838819aa52af244580675825e750ad67c9df4614f557a769606af902cf22'], - }), - ('aioitertools', '0.11.0', { - 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], - }), - ('latexcodec', '2.0.1', { - 'checksums': ['2aa2551c373261cefe2ad3a8953a6d6533e68238d180eb4bb91d7964adb3fe9a'], - }), - ('sentinels', '1.0.0', { - 'checksums': ['7be0704d7fe1925e397e92d18669ace2f619c92b5d4eb21a89f31e026f9ff4b1'], - }), ] sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-emmet-readme.patch b/easybuild/easyconfigs/p/pymatgen/emmet-core-0.75.0-fix-readme.patch similarity index 100% rename from easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-emmet-readme.patch rename to easybuild/easyconfigs/p/pymatgen/emmet-core-0.75.0-fix-readme.patch diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.12.18-foss-2023a.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.12.18-foss-2023a.eb new file mode 100644 index 00000000000..5432a146d04 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.12.18-foss-2023a.eb @@ -0,0 +1,138 @@ +easyblock = 'PythonBundle' + +name = 'pymatgen' +version = '2023.12.18' + +homepage = 'https://pymatgen.org/' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('hypothesis', '6.82.0'), # required for tests + ('maturin', '1.1.0'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), + ('PyZMQ', '25.1.1'), + ('bcrypt', '4.0.1'), + ('boto3', '1.28.70'), + ('Flask', '2.3.3'), + ('matplotlib', '3.7.2'), + ('networkx', '3.1'), + ('paramiko', '3.2.0'), + ('plotly.py', '5.16.0'), + ('pydantic', '2.5.3'), + ('ruamel.yaml', '0.17.32'), + ('spglib-python', '2.1.0'), + ('sympy', '1.12'), + ('tqdm', '4.66.1'), + ('uncertainties', '3.1.7'), +] + +use_pip = True + +exts_list = [ + ('palettable', '3.3.0', { + 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], + }), + ('latexcodec', '2.0.1', { + 'checksums': ['2aa2551c373261cefe2ad3a8953a6d6533e68238d180eb4bb91d7964adb3fe9a'], + }), + ('pybtex', '0.24.0', { + 'checksums': ['818eae35b61733e5c007c3fcd2cfb75ed1bc8b4173c1f70b56cc4c0802d34755'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('uvicorn', '0.25.0', { + 'checksums': ['6dddbad1d7ee0f5140aba5ec138ddc9612c5109399903828b4874c9937f009c2'], + }), + ('sshtunnel', '0.4.0', { + 'checksums': ['e7cb0ea774db81bf91844db22de72a40aae8f7b0f9bb9ba0f666d474ef6bf9fc'], + }), + ('dnspython', '2.4.2', { + 'modulename': False, + 'checksums': ['8dcfae8c7460a2f84b4072e26f1c9f4101ca20c071649cb7c34e8b6a93d58984'], + }), + ('pymongo', '4.6.1', { + 'checksums': ['31dab1f3e1d0cdd57e8df01b645f52d43cc1b653ed3afd535d2891f4fc4f9712'], + }), + ('pydash', '7.0.6', { + 'checksums': ['7d9df7e9f36f2bbb08316b609480e7c6468185473a21bdd8e65dda7915565a26'], + }), + ('python-dotenv', '1.0.0', { + 'modulename': 'dotenv', + 'checksums': ['a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba'], + }), + ('pydantic-settings', '2.1.0', { + 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ}, + 'checksums': ['be83f7a7da10a0686a00da1b9e62856072bbcfb7d6a420ea3c78c66b145fcd93'], + }), + ('emmet-core', '0.75.0', { + 'modulename': 'emmet', + 'patches': ['emmet-core-0.75.0-fix-readme.patch'], + 'checksums': [ + {'emmet-core-0.75.0.tar.gz': '2d4b20d542e56c97009d05d03f5595be9395ac27c2fe9809d617f28596c40640'}, + {'emmet-core-0.75.0-fix-readme.patch': + 'd299f388044fdcff32fc246b0215ae4b656bc20d9d3c759d545cbe3167df08b8'}, + ], + }), + ('orjson', '3.9.10', { + 'checksums': ['9ebbdbd6a046c304b1845e96fbcc5559cd296b4dfd3ad2509e33c4d9ce07d6a1'], + }), + ('monty', '2023.11.3', { + 'checksums': ['d961c14b0b20901c7603aa00d275e62dee8333fbdaf1179f5d862c6fb3f3c52f'], + }), + ('sentinels', '1.0.0', { + 'checksums': ['7be0704d7fe1925e397e92d18669ace2f619c92b5d4eb21a89f31e026f9ff4b1'], + }), + ('mongomock', '4.1.2', { + 'checksums': ['f06cd62afb8ae3ef63ba31349abd220a657ef0dd4f0243a29587c5213f931b7d'], + }), + ('mongogrant', '0.3.3', { + 'checksums': ['ad494b8638adfa840cdd5568af44448dd43771b58102550cf7c61402b1620ab4'], + }), + ('sniffio', '1.3.0', { # Same version as in jupyter-server + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.7.1', { # Same version as in jupyter-server + 'checksums': ['44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780'], + }), + ('starlette', '0.27.0', { + 'checksums': ['6a6b0d042acb8d469a01eba54e9cda6cbd24ac602c4cd016723117d6a7e73b75'], + }), + ('fastapi', '0.105.0', { + 'checksums': ['4d12838819aa52af244580675825e750ad67c9df4614f557a769606af902cf22'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('maggma', '0.60.2', { + 'checksums': ['12e8da1f80505f39432b972cbe47fb378cd9aa51fab968877a2d3b2588c96c69'], + }), + ('mp-api', '0.39.4', { + 'checksums': ['692abefd6adec36eb4fa193f914e08167ed33a5a3a9714ec3c15606839649f32'], + }), + (name, version, { + 'checksums': ['56c0041fe5431ac1b8f8c0c17d06091c4d61082c3a99924f3940d73ebb6656eb'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pmg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pmg --help"] + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2023a.eb b/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2023a.eb new file mode 100644 index 00000000000..2b643d74ce6 --- /dev/null +++ b/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2023a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'uncertainties' +version = '3.1.7' + +homepage = 'http://uncertainties-python-package.readthedocs.io' +description = """Transparent calculations with uncertainties on the quantities involved (aka error propagation); + fast calculation of derivatives""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' From 13dc28dee2f0b61d8d1c3899fd3eaceb7e26d809 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 23 Apr 2024 14:45:59 +0200 Subject: [PATCH 091/106] Update easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb index 3d4cbd10978..08b8a8ddb8f 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb @@ -12,10 +12,14 @@ toolchain = {'name': 'foss', 'version': '2023a'} source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -patches = ['TAMkin-1.2.6_fix-python38.patch'] +patches = [ + 'TAMkin-1.2.6_fix-python38.patch', + 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', +] checksums = [ {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, + {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, ] dependencies = [ From b63f81bc8022ee8a4a5056dc358511e24db6cfb5 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 23 Apr 2024 14:51:26 +0200 Subject: [PATCH 092/106] Update PyTables-3.8.0-foss-2023a.eb --- .../easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb index c55635bd696..aa0f5688a79 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb @@ -47,13 +47,13 @@ exts_list = [ }), ('tables', version, { 'patches': [ - 'PyTables-%(version)s_fix-libs.patch', - 'PyTables-%(version)s_fix-find-blosc2-library-path.patch', + 'PyTables-3.8.0_fix-libs.patch', + 'PyTables-3.8.0_fix-find-blosc2-library-path.patch', ], 'checksums': [ {'tables-%(version)s.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'}, - {'PyTables-%(version)s_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'}, - {'PyTables-%(version)s_fix-find-blosc2-library-path.patch': + {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'}, + {'PyTables-3.8.0_fix-find-blosc2-library-path.patch': 'dcf6c3a16a138454296161e99cf6470620755d4c26303186a744f09a11e6013b'}, ], }), From db1f2895631b913ef6e162e9a46bb395fe63caf0 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 10 Jun 2024 10:54:54 +0200 Subject: [PATCH 093/106] Update MDAnalysis-2.6.1-foss-2023a.eb --- .../easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb index b2d9700e6ec..70d65c39a78 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('matplotlib', '3.7.2'), - ('Biopython', '1.81'), + ('Biopython', '1.83'), ('networkx', '3.1'), ('tqdm', '4.66.1'), ] From 3b5dee519a20eefca335579a73854cca5c02c79d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 10 Jun 2024 11:04:34 +0200 Subject: [PATCH 094/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 132fa8d3080..f8d165074ea 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -29,7 +29,7 @@ dependencies = [ ('QuickFF', '2.2.7'), ('plotly.py', '5.16.0'), ('GitPython', '3.1.40'), - ('Greenlet', '2.0.2'), + ('Greenlet', '3.0.2'), ('dill', '0.3.7'), ('sympy', '1.12'), ('pymatgen', '2023.12.18'), From d6eb1ae225a60cffc9995e0e94171dd65a7c7137 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 10 Jun 2024 11:06:07 +0200 Subject: [PATCH 095/106] Delete easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2023a.eb --- .../b/Biopython/Biopython-1.81-foss-2023a.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2023a.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2023a.eb deleted file mode 100644 index 081bc0e46a7..00000000000 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2023a.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'PythonPackage' - -name = 'Biopython' -version = '1.81' - -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': '2023a'} - -source_urls = ['https://biopython.org/DIST'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0'] - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), -] - -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 8458dcfc586a5c1f123fbb1f51ee2d9bab60c28d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 10 Jun 2024 11:34:52 +0200 Subject: [PATCH 096/106] Update PyTables-3.8.0-foss-2023a.eb --- easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb index aa0f5688a79..71c5a28ec59 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2023a.eb @@ -47,11 +47,11 @@ exts_list = [ }), ('tables', version, { 'patches': [ - 'PyTables-3.8.0_fix-libs.patch', + 'PyTables-%(version)s_fix-libs.patch', 'PyTables-3.8.0_fix-find-blosc2-library-path.patch', ], 'checksums': [ - {'tables-%(version)s.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'}, + {'tables-3.8.0.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'}, {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'}, {'PyTables-3.8.0_fix-find-blosc2-library-path.patch': 'dcf6c3a16a138454296161e99cf6470620755d4c26303186a744f09a11e6013b'}, From e1adbd5fe70ec7c41daab2dd936a620763a3da44 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 10 Jun 2024 11:35:52 +0200 Subject: [PATCH 097/106] Update pyiron-0.5.1-foss-2023a.eb moved Pint to deps --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index f8d165074ea..a72a5a05f2d 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -33,16 +33,13 @@ dependencies = [ ('dill', '0.3.7'), ('sympy', '1.12'), ('pymatgen', '2023.12.18'), + ('Pint', '0.23') ] check_ldshared = True use_pip = True exts_list = [ - ('pint', '0.23', { - 'source_tmpl': 'Pint-%(version)s.tar.gz', - 'checksums': ['e1509b91606dbc52527c600a4ef74ffac12fff70688aff20e9072409346ec9b4'], - }), ('h5io', '0.1.2', { 'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'], }), From 45e7f441030c1fe4b029d555920b02ec26f5d9ce Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 10 Jun 2024 11:39:16 +0200 Subject: [PATCH 098/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index a72a5a05f2d..cd40acaf347 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -29,11 +29,11 @@ dependencies = [ ('QuickFF', '2.2.7'), ('plotly.py', '5.16.0'), ('GitPython', '3.1.40'), - ('Greenlet', '3.0.2'), ('dill', '0.3.7'), ('sympy', '1.12'), ('pymatgen', '2023.12.18'), - ('Pint', '0.23') + ('Pint', '0.23'), + ('SQLAlchemy', '2.0.25') ] check_ldshared = True @@ -49,9 +49,6 @@ exts_list = [ ('pysqa', '0.1.7', { 'checksums': ['fdc37e0178649750e7386b4e9b8287693ee2d47559723c11b9ad42afcfc55900'], }), - ('SQLAlchemy', '2.0.23', { - 'checksums': ['c1bda93cbbe4aa2aa0aa8655c5aeda505cd219ff3e8da91d1d329e143e4aff69'], - }), ('pyfiglet', '0.8.post1', { 'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'], }), From 5a8c4f66a50ef019b32c143af289a52ecbbf78b8 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 10 Jun 2024 11:44:38 +0200 Subject: [PATCH 099/106] Update pyiron-0.5.1-foss-2023a.eb checksum fix --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index cd40acaf347..a64e050dad3 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -96,7 +96,7 @@ exts_list = [ 'patches': ['pyiron-0.5.1_fix-pylammpsmpi.patch'], 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], 'checksums': [ - {'pylammpsmpi-0.2.10.tar.gz': 'bd5af29a935dacbee743c3cc0bcc799e24e7c2483801f56cb9092a79f016f2ed'}, + {'pylammpsmpi-0.2.10.tar.gz': '0e74b7ccfdb5550308ac3462cd02d1fd30d99472552271d17da0b00ba754281c'}, {'pyiron-0.5.1_fix-pylammpsmpi.patch': 'd7cacf8eb73cb43e47526bfa3f98157073c01cd88918f191f87d7e75ab4c7c30'}, ], From 644a18a35b0e0049eec4f16204dfe3cc6e7a6b4d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 10 Jun 2024 12:29:46 +0200 Subject: [PATCH 100/106] Delete easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb --- .../MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb | 57 ------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb deleted file mode 100644 index 70d65c39a78..00000000000 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.6.1-foss-2023a.eb +++ /dev/null @@ -1,57 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'PythonBundle' - -name = 'MDAnalysis' -version = '2.6.1' - -homepage = 'https://www.mdanalysis.org/' -description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) -simulations in many popular formats.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('matplotlib', '3.7.2'), - ('Biopython', '1.83'), - ('networkx', '3.1'), - ('tqdm', '4.66.1'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('mrcfile', '1.4.3', { - 'checksums': ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5'], - }), - ('GridDataFormats', '1.0.1', { - 'modulename': 'gridData', - 'checksums': ['ad2c9ab7d672a6d8c426de7d083eee4f3e2b0bd59391675d30683c768ab83cc4'], - }), - ('gsd', '2.8.0', { - 'checksums': ['f2b031a26a7a5bee5f3940dc2f36c5a5b6670307b297c526adf2e26c1f5b46ae'], - }), - ('msgpack', '1.0.5', { - 'checksums': ['c075544284eadc5cddc70f4757331d99dcbc16b2bbd4849d15f8aae4cf36d31c'], - }), - ('mmtf-python', '1.1.3', { - 'modulename': 'mmtf', - 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], - }), - ('funcsigs', '1.0.2', { - 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], - }), - ('fasteners', '0.18', { - 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], - }), - (name, version, { - 'modulename': 'MDAnalysis', - 'checksums': ['9cc69b94bddd026f26ffcaf5bdbed6d568c1c10e19a341d84f8d37a2a70222f2'], - }), -] - -moduleclass = 'bio' From de072e25725b83b169c72c98f9b9c9c252fae10c Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 10 Jun 2024 12:30:17 +0200 Subject: [PATCH 101/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index a64e050dad3..db51bc7847e 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -20,7 +20,7 @@ dependencies = [ ('phonopy', '2.20.0'), ('ASE', '3.22.1'), ('PyTables', '3.8.0'), - ('nglview', '3.0.8'), + ('nglview', '3.1.2'), ('tqdm', '4.66.1'), ('molmod', '1.4.8'), ('scikit-learn', '1.3.1'), From 00183327a05591a913cc92c374b19255abf3e0d2 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 10 Jun 2024 12:30:29 +0200 Subject: [PATCH 102/106] Delete easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb --- .../n/nglview/nglview-3.0.8-foss-2023a.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb b/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb deleted file mode 100644 index b96adf11bdc..00000000000 --- a/easybuild/easyconfigs/n/nglview/nglview-3.0.8-foss-2023a.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'nglview' -version = '3.0.8' - -homepage = 'https://github.com/arose/nglview' -description = "IPython widget to interactively view molecular structures and trajectories." - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('JupyterLab', '4.0.5'), - ('nodejs', '18.17.1'), - ('MDAnalysis', '2.6.1'), # optional -] - -sources = [SOURCE_TAR_GZ] -checksums = ['f9e468cd813dac319cbeca6ae20ae099008ff3a06399f5d23d75582dde28623a'] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -use_pip_extras = 'MDAnalysis' - -sanity_check_paths = { - 'files': ['bin/nglview'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = { - 'JUPYTER_PATH': 'share/jupyter', - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', -} - -moduleclass = 'chem' From 5c88b27faa0a9730c1fe432dd3dee9433c262f36 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 10 Jun 2024 12:55:10 +0200 Subject: [PATCH 103/106] Update TAMkin-1.2.6-foss-2023a.eb --- easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb index 08b8a8ddb8f..b3b40928643 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb @@ -26,7 +26,7 @@ dependencies = [ ('Python', '3.11.3'), ('matplotlib', '3.7.2'), ('molmod', '1.4.8'), - ('nose3', '1.3.8') + ('nose3', '1.3.8'), ] download_dep_fail = True From 611453f9e71e81895c05b7baf0fa625403556bc8 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 10 Jun 2024 13:03:07 +0200 Subject: [PATCH 104/106] Update easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index db51bc7847e..48cbc1fc346 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -33,7 +33,7 @@ dependencies = [ ('sympy', '1.12'), ('pymatgen', '2023.12.18'), ('Pint', '0.23'), - ('SQLAlchemy', '2.0.25') + ('SQLAlchemy', '2.0.25'), ] check_ldshared = True From 27bd9835fcf6c4e677d17180d985e4a9aaf1033c Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 10 Jun 2024 13:14:05 +0200 Subject: [PATCH 105/106] Update easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 48cbc1fc346..092094034b2 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -96,7 +96,7 @@ exts_list = [ 'patches': ['pyiron-0.5.1_fix-pylammpsmpi.patch'], 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], 'checksums': [ - {'pylammpsmpi-0.2.10.tar.gz': '0e74b7ccfdb5550308ac3462cd02d1fd30d99472552271d17da0b00ba754281c'}, + {%(name)s-%(version)s.tar.gz': 'bd5af29a935dacbee743c3cc0bcc799e24e7c2483801f56cb9092a79f016f2ed'}, {'pyiron-0.5.1_fix-pylammpsmpi.patch': 'd7cacf8eb73cb43e47526bfa3f98157073c01cd88918f191f87d7e75ab4c7c30'}, ], From e00ee944498a1bdb43104fe8678589f1b04f3fa6 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 10 Jun 2024 13:16:54 +0200 Subject: [PATCH 106/106] Update pyiron-0.5.1-foss-2023a.eb --- easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb index 092094034b2..79469b4b140 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -96,7 +96,7 @@ exts_list = [ 'patches': ['pyiron-0.5.1_fix-pylammpsmpi.patch'], 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], 'checksums': [ - {%(name)s-%(version)s.tar.gz': 'bd5af29a935dacbee743c3cc0bcc799e24e7c2483801f56cb9092a79f016f2ed'}, + {'%(name)s-%(version)s.tar.gz': 'bd5af29a935dacbee743c3cc0bcc799e24e7c2483801f56cb9092a79f016f2ed'}, {'pyiron-0.5.1_fix-pylammpsmpi.patch': 'd7cacf8eb73cb43e47526bfa3f98157073c01cd88918f191f87d7e75ab4c7c30'}, ],