Merge branch 'as-pytorch-geometric-2023' into '2023'

Pytorch-geometric 2023

See merge request software-team/easybuild!1545

Golden_Repo/h/HDF5/HDF5-1.12.2-gompi-2022a.eb

@@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'usempi': True}
 
 source_urls = [
     'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
+
+
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14']
 

Golden_Repo/h/h5py/h5py-3.7.0-foss-2022a.eb

+easyblock = 'PythonPackage'
+
+name = 'h5py'
+version = '3.7.0'
+
+homepage = 'https://www.h5py.org/'
+description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
+ version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
+ amounts of data."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'usempi': True}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['3fcf37884383c5da64846ab510190720027dca0768def34dd8dcb659dbe5cbf3']
+
+builddependencies = [('pkgconfig', '1.5.5', '-python')]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05', '', ('gcccoremkl', '11.3.0-2022.1.0')),
+    ('HDF5', '1.12.2'),
+    ('mpi4py', '3.1.4'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0
+# without this environment variable, pip will fetch the minimum numpy version h5py supports during install,
+# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency.
+preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 '
+
+moduleclass = 'data'

Golden_Repo/i/imageio/imageio-2.22.2-foss-2022a.eb

+easyblock = 'PythonPackage'
+
+name = 'imageio'
+version = '2.22.2'
+
+homepage = 'https://imageio.github.io'
+description = """Imageio is a Python library that provides an easy interface to read and write a wide range of
+ image data, including animated images, video, volumetric data, and scientific formats."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['db7010cd10712518819a4187baf61b05988361ea20c23e829918727b27acb977']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05', '', ('gcccoremkl', '11.3.0-2022.1.0')),
+    ('Pillow-SIMD', '9.2.0'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'vis'

Golden_Repo/m/mpi4py/mpi4py-3.1.4-gompi-2022a.eb

+easyblock = 'PythonPackage'
+
+name = 'mpi4py'
+version = '3.1.4'
+
+homepage = 'https://bitbucket.org/mpi4py/mpi4py'
+description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
+ the Python programming language, allowing any Python program to exploit multiple processors.
+"""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+
+source_urls = ['https://github.com/%(name)s/%(name)s/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['0ac7cc1fbd1d026b519c4f439ffc15d8776e5615c262dd233a418d73539c352b']
+
+dependencies = [('Python', '3.10.4')]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'],
+}
+
+moduleclass = 'lib'

Golden_Repo/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.1-CUDA-11.7.eb

+easyblock = 'PythonBundle'
+
+name = 'PyTorch-Geometric'
+version = '2.1.0'
+local_pytorchver = '1.12.0'
+versionsuffix = '-PyTorch-%s-CUDA-%%(cudaver)s' % local_pytorchver
+
+homepage = 'https://github.com/rusty1s/pytorch_geometric'
+description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('CUDA', '11.7', '', SYSTEM),
+    ('PyTorch', local_pytorchver, '-CUDA-%(cudaver)s'),
+    ('scikit-learn', '1.1.2'),
+    ('scikit-image', '0.19.3'),
+    ('numba', '0.56.4', '-CUDA-%(cudaver)s'),
+    ('h5py', '3.7.0'),
+    ('tqdm', '4.64.0'),
+    ('RDFlib', '6.2.0'),
+    ('ASE', '3.22.1'),
+    ('YACS', '0.1.8'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('googledrivedownloader', '0.4', {
+        'modulename': 'google_drive_downloader',
+        'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'],
+    }),
+    ('plyfile', '0.7.4', {
+        'checksums': ['9e9a18d22a3158fcd74df38761d43a7facc6df75126f2ab9f4e9a5d4d2188652'],
+    }),
+    ('torch_scatter', version, {
+        'checksums': ['3a7124c2a033552febbdc72407f7d4d8cb6dce465720e84ab831512e81c1d208'],
+    }),
+    ('torch_sparse', '0.6.15', {
+        'checksums': ['3a741ae8a7cc19247a44de549fa4d593c4257b5f741e1eb5110b712a14209dd9'],
+    }),
+    ('torch_cluster', '1.6.0', {
+        'checksums': ['249c1bd8c33a887b22bf569a59d0868545804032123594dd8c76ba1885859c39'],
+    }),
+    ('torch_spline_conv', '1.2.1', {
+        'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'],
+    }),
+    ('python-louvain', '0.16', {
+        'modulename': 'community.community_louvain',
+        'checksums': ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'],
+    }),
+    ('torch_geometric', version, {
+        'checksums': ['72653deca925885e4d613eb5c72268bb9710325d9c717516922499fbe1197079'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

Golden_Repo/r/RDFlib/RDFlib-6.2.0-GCCcore-11.3.0.eb

+easyblock = 'PythonBundle'
+
+name = 'RDFlib'
+version = '6.2.0'
+
+homepage = 'https://github.com/RDFLib/rdflib'
+description = """RDFLib is a Python library for working with RDF, a simple yet powerful language
+ for representing information."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [('Python', '3.10.4')]
+
+use_pip = True
+
+exts_list = [
+    ('isodate', '0.6.1', {
+        'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'],
+    }),
+    ('rdflib', version, {
+        'checksums': ['62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

Golden_Repo/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb

+easyblock = 'PythonBundle'
+
+name = 'scikit-image'
+version = '0.19.3'
+
+homepage = 'https://scikit-image.org/'
+description = "scikit-image is a collection of algorithms for image processing."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('matplotlib', '3.5.2', '', ('gcccoremkl', '11.3.0-2022.1.0')),
+    ('Pillow-SIMD', '9.2.0'),
+    ('networkx', '2.8.4', '', ('gcccoremkl', '11.3.0-2022.1.0')),
+    ('dask', '2022.10.2', '', ('gcccoremkl', '11.3.0-2022.1.0')),
+    ('imageio', '2.22.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('PyWavelets', '1.4.1', {
+        'modulename': 'pywt',
+        'checksums': ['6437af3ddf083118c26d8f97ab43b0724b956c9f958e9ea788659f6a2834ba93'],
+    }),
+    ('imread', '0.7.4', {
+        'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'],
+    }),
+    ('pooch', '1.6.0', {
+        'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'],
+    }),
+    ('tifffile', '2022.10.10', {
+        'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'],
+    }),
+    (name, version, {
+        'modulename': 'skimage',
+        'checksums': ['24b5367de1762da6ee126dd8f30cc4e7efda474e0d7d70685433f0e3aa2ec450'],
+    }),
+]
+
+moduleclass = 'vis'

Golden_Repo/s/scikit-learn/scikit-learn-1.1.2-foss-2022a.eb

+easyblock = 'PythonBundle'
+
+name = 'scikit-learn'
+version = '1.1.2'
+
+homepage = 'https://scikit-learn.org/stable/index.html'
+description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world,
+building upon numpy, scipy, and matplotlib. As a machine-learning module,
+it provides versatile tools for data mining and analysis in any field of science and engineering.
+It strives to be simple and efficient, accessible to everybody, and reusable in various contexts."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05', '', ('gcccoremkl', '11.3.0-2022.1.0')),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'modulename': 'sklearn',
+        'checksums': ['7c22d1305b16f08d57751a4ea36071e2215efb4c09cb79183faa4e8e82a3dbf8'],
+    }),
+    ('sklearn', '0.0', {
+        'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'],
+    }),
+]
+
+moduleclass = 'data'