adding easyconfigs: MONAI-1.4.0-foss-2023b.eb, PyAMG-5.2.1-gfbf-2023b…

….eb, zarr-2.18.3-foss-2023b.eb, ONNX-1.17.0-gfbf-2023b.eb, clearml-1.16.5-foss-2023b.eb, MLflow-2.18.0-gfbf-2023b.eb, scikit-image-0.24.0-foss-2023b.eb, openslide-python-1.4.1-GCCcore-13.2.0.eb, OpenSlide-4.0.0-GCCcore-13.2.0.eb, NiBabel-5.3.2-gfbf-2023b.eb, pydicom-3.0.1-GCCcore-13.2.0.eb, einops-0.8.0-GCCcore-13.2.0.eb
pavelToman · Nov 29, 2024 · e551f51 · e551f51
1 parent 58b09e4
commit e551f51
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diff --git a/easybuild/easyconfigs/c/clearml/clearml-1.16.5-foss-2023b.eb b/easybuild/easyconfigs/c/clearml/clearml-1.16.5-foss-2023b.eb
@@ -0,0 +1,52 @@
+easyblock = 'PythonBundle'
+
+name = 'clearml'
+version = '1.16.5'
+
+homepage = 'https://github.com/allegroai/clearml'
+description = """Auto-Magical CI/CD to streamline your AI workload. 
+Experiment Management, Data Management, Pipeline, Orchestration, Scheduling & Serving in one MLOps/LLMOps solution."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+    ('maturin', '1.3.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('PyYAML', '6.0.1'),
+    ('Pillow', '10.2.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('orderedmultidict', '1.0.1', {
+        'checksums': ['04070bbb5e87291cc9bfa51df413677faf2141c73c61d2a5f7b26bea3cd882ad'],
+    }),
+    ('rpds_py', '0.18.0', {
+        'modulename': 'rpds',
+        'checksums': ['42821446ee7a76f5d9f71f9e33a4fb2ffd724bb3e7f93386150b61a43115788d'],
+    }),
+    ('referencing', '0.35.1', {
+        'checksums': ['25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c'],
+    }),
+    ('PyJWT', '2.8.0', {
+        'modulename': 'jwt',
+        'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'],
+    }),
+    ('furl', '2.1.3', {
+        'checksums': ['5a6188fe2666c484a12159c18be97a1977a71d632ef5bb867ef15f54af39cc4e'],
+    }),
+    (name, version, {
+        'source_tmpl': 'clearml-1.16.5-py2.py3-none-any.whl',
+        'checksums': ['3caa00914e039cb2b62ca90795c3ca17077042ae1edcefc17bf13f695653480f'],
+    }),
+]
+
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/e/einops/einops-0.8.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/e/einops/einops-0.8.0-GCCcore-13.2.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'einops'
+version = '0.8.0'
+
+homepage = 'https://einops.rocks/'
+description = """
+Flexible and powerful tensor operations for readable and reliable code.
+Supports numpy, pytorch, tensorflow, jax, and others."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['63486517fed345712a8385c100cb279108d9d47e6ae59099b07657e983deae85']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('hatchling', '1.18.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/m/MLflow/MLflow-2.18.0-gfbf-2023b.eb b/easybuild/easyconfigs/m/MLflow/MLflow-2.18.0-gfbf-2023b.eb
@@ -0,0 +1,109 @@
+easyblock = 'PythonBundle'
+
+name = 'MLflow'
+version = '2.18.0'
+
+homepage = 'https://mlflow.org'
+description = """MLflow is a platform to streamline machine learning development, including tracking experiments,
+packaging code into reproducible runs, and sharing and deploying models."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('hatchling', '1.18.0'),
+    ('poetry', '1.6.1'),
+]
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('GitPython', '3.1.42'),
+    ('SciPy-bundle', '2023.11'),
+    ('matplotlib', '3.8.2'),
+    ('scikit-learn', '1.4.0'),
+    ('PyYAML', '6.0.1'),
+    ('SQLAlchemy', '2.0.29'),
+    ('protobuf-python', '4.25.3'),
+    ('Flask', '3.0.0'),
+    ('Arrow', '16.1.0'),
+    ('Markdown', '3.6'),
+    ('Deprecated', '1.2.14'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('pyasn1-modules', '0.4.1', {
+        'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz',
+        'checksums': ['c28e2dbf9c06ad61c71a075c7e0f9fd0f1b0bb2d2ad4377f240d33ac2ab60a7c'],
+    }),
+    ('rsa', '4.9', {
+        'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'],
+    }),
+    ('google-auth', '2.35.0', {
+        'modulename': 'google.auth',
+        'source_tmpl': 'google_auth-%(version)s.tar.gz',
+        'checksums': ['f4c64ed4e01e8e8b646ef34c018f8bf3338df0c8e37d8b3bba40e7f574a3278a'],
+    }),
+    ('sqlparse', '0.5.1', {
+        'checksums': ['bb6b4df465655ef332548e24f08e205afc81b9ab86cb1c45657a7ff173a3a00e'],
+    }),
+    ('opentelemetry_semantic_conventions', '0.48b0', {
+        'modulename': False,
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['a0de9f45c413a8669788a38569c7e0a11ce6ce97861a628cca785deecdc32a1f'],
+    }),
+    ('opentelemetry_sdk', '1.27.0', {
+        'modulename': 'opentelemetry.sdk',
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['365f5e32f920faf0fd9e14fdfd92c086e317eaa5f860edba9cdc17a380d9197d'],
+    }),
+    ('opentelemetry_api', '1.27.0', {
+        'modulename': 'opentelemetry',
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['953d5871815e7c30c81b56d910c707588000fff7a3ca1c73e6531911d53065e7'],
+    }),
+    ('databricks_sdk', '0.36.0', {
+        'modulename': 'databricks.sdk',
+        'checksums': ['d8c46348cbd3e0b56991a6b7a59d7a6e0437947f6387bef832e6fe092e2dd427'],
+    }),
+    ('cachetools', '5.5.0', {
+        'checksums': ['2cc24fb4cbe39633fb7badd9db9ca6295d766d9c2995f245725a46715d050f2a'],
+    }),
+    ('graphql-relay', '3.2.0', {
+        'checksums': ['1ff1c51298356e481a0be009ccdff249832ce53f30559c1338f22a0e0d17250c'],
+    }),
+    ('graphql_core', '3.2.5', {
+        'modulename': 'graphql',
+        'checksums': ['e671b90ed653c808715645e3998b7ab67d382d55467b7e2978549111bbabf8d5'],
+    }),
+    ('graphene', '3.4.1', {
+        'checksums': ['828a8d7b1bce450566a72cc8733716c20f3acfc659960de73dd38f46dc302040'],
+    }),
+    ('alembic', '1.14.0', {
+        'checksums': ['b00892b53b3642d0b8dbedba234dbf1924b69be83a9a769d5a624b01094e304b'],
+    }),
+    ('docker', '7.1.0', {
+        'checksums': ['ad8c70e6e3f8926cb8a92619b832b4ea5299e2831c14284663184e200546fa6c'],
+    }),
+    ('gunicorn', '23.0.0', {
+        'checksums': ['f014447a0101dc57e294f6c18ca6b40227a4c90e9bdb586042628030cba004ec'],
+    }),
+    ('mlflow_skinny', version, {
+        'modulename': False,
+        'checksums': ['87e83f56c362a520196b2f0292b24efdca7f8b2068a6a6941f2ec9feb9bfd914'],
+    }),
+    ('mlflow', version, {
+        'checksums': ['90f0d04b02e35c0f2fccc88e892e37b84871cb4f766acd3ef904c1c30be63ee3'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
+}
+
+sanity_check_commands = ['%(namelower)s --help']
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.4.0-foss-2023b.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.4.0-foss-2023b.eb
@@ -0,0 +1,107 @@
+easyblock = 'PythonBundle'
+
+name = 'MONAI'
+version = '1.4.0'
+
+homepage = 'https://monai.io/'
+description = """
+MONAI is a PyTorch-based, open-source framework for deep learning in healthcare
+imaging, part of PyTorch Ecosystem.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+github_account = 'Project-MONAI'
+
+local_pip_extras = "einops,fire,gdown,ignite,scipy,tqdm,itk,jsonschema,lmdb,nibabel,pydicom,ninja,h5py,optuna,pyamg,"
+local_pip_extras += "openslide,pandas,pillow,psutil,pyyaml,skimage,tensorboard,torchvision,huggingface_hub,"
+local_pip_extras += "transformers,mlflow,clearml,matplotlib,tensorboardX,tifffile,imagecodecs,onnx,zarr,lpips,pynrrd"
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('PyTorch', '2.1.2'),
+    ('einops', '0.8.0'),
+    ('BeautifulSoup', '4.12.2'),
+    ('tqdm', '4.66.2'),
+    ('ITK', '5.4.0'),
+    ('pydicom', '3.0.1'),
+    ('NiBabel', '5.3.2'),
+    ('openslide-python', '1.4.1'),
+    ('Pillow-SIMD', '10.4.0'),
+    ('PyYAML', '6.0.1'),
+    ('scikit-image', '0.24.0'),
+    ('tensorboard', '2.18.0'),
+    ('torchvision', '0.17.0'),
+    ('Transformers', '4.44.0'),
+    ('MLflow', '2.18.0'),
+    ('matplotlib', '3.8.2'),
+    ('clearml', '1.16.5'),
+    ('tensorboardX', '2.6.2.2'),
+    ('imagecodecs', '2024.6.1'),
+    ('h5py', '3.11.0'),
+    ('Optuna', '3.6.1'),
+    ('ONNX', '1.17.0'),
+    ('zarr', '2.18.3'),
+    ('PyAMG', '5.2.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('nptyping', '2.5.0', {
+        'checksums': ['e3d35b53af967e6fb407c3016ff9abae954d3a0568f7cc13a461084224e8e20a'],
+    }),
+    ('pynrrd', '1.0.0', {
+        'modulename': 'nrrd',
+        'checksums': ['4eb4caba03fbca1b832114515e748336cb67bce70c7f3ae36bfa2e135fc990d2'],
+    }),
+    ('lpips', '0.1.4', {
+        'checksums': ['3846331df6c69688aec3d300a5eeef6c529435bc8460bd58201c3d62e56188fa'],
+    }),
+    ('typeguard', '4.1.2', {
+        'checksums': ['3be187945f9ef5a9f6d7a926dfe54babb7dfd807085ce05f9a5e8735f2487990'],
+    }),
+    ('huggingface-hub', '0.26.2', {
+        'sources': ['huggingface_hub-%(version)s.tar.gz'],
+        'checksums': ['b100d853465d965733964d123939ba287da60a547087783ddff8a323f340332b'],
+    }),
+    ('lmdb', '1.5.1', {
+        'checksums': ['717c255827d331e02f7242b44051aa06466c90f6d732ecb07b31edfb1e06c67a'],
+    }),
+    ('pytorch-ignite', '0.4.11', {
+        'modulename': 'ignite',
+        'patches': ['PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch'],
+        'checksums': [
+            {'pytorch-ignite-0.4.11.tar.gz': 'ee31096a58679417097ef7f3f27d88bec40b789ac5e13cd9ed08bc89ca8ce2e2'},
+            {'PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch':
+             'd45c0da30c01f7ce47b7be49a6d5d6eb9529c94a0b9de89260d4b07d9d2359e0'},
+        ],
+    }),
+    ('gdown', '5.2.0', {
+        'checksums': ['2145165062d85520a3cd98b356c9ed522c5e7984d408535409fd46f94defc787'],
+    }),
+    ('termcolor', '2.5.0', {
+        'checksums': ['998d8d27da6d48442e8e1f016119076b690d962507531df4890fcd2db2ef8a6f'],
+    }),
+    ('fire', '0.7.0', {
+        'checksums': ['961550f07936eaf65ad1dc8360f2b2bf8408fad46abbfa4d2a3794f8d2a95cdf'],
+    }),
+    (name, version, {
+        'preinstallopts': 'BUILD_MONAI=1',
+        'use_pip_extras': local_pip_extras,
+        'checksums': ['3ed592c7a760f5c3084021da5585cd1ba5e52a969b85a62e1f15495cb71ae26e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"]
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-5.3.2-gfbf-2023b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.3.2-gfbf-2023b.eb
@@ -0,0 +1,48 @@
+easyblock = 'PythonBundle'
+
+name = 'NiBabel'
+version = '5.3.2'
+
+homepage = 'https://nipy.github.io/nibabel'
+description = """NiBabel provides read/write access to some common medical and neuroimaging file formats,
+ including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT
+ as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and
+ annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Pillow', '10.2.0'),
+    ('pydicom', '3.0.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('bz2file', '0.98', {
+        'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'],
+    }),
+    ('nibabel', version, {
+        'checksums': ['0bdca6503b1c784b446c745a4542367de7756cfba0d72143b91f9ffb78be569b'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "nib-diff --help",
+    "parrec2nii --help",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'