Merge pull request easybuilders#25022 from pavelToman/20260108150318_new_pr_scvi-tools141

{ai,bio}[foss/2024a] scvi-tools v1.4.1, captum v0.8.0 w/ CUDA 12.6.0

Author: boegel

easybuild/easyconfigs/c/captum/captum-0.8.0-foss-2024a-CUDA-12.6.0.eb

@@ -0,0 +1,33 @@
+easyblock = 'PythonBundle'
+
+name = 'captum'
+version = '0.8.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://captum.ai/'
+description = """
+Captum is a model interpretability and understanding library for PyTorch.
+Captum means comprehension in Latin and contains general purpose
+implementations of integrated gradients, saliency maps, smoothgrad, vargrad and
+others for PyTorch models. It has quick integration for models built with
+domain-specific libraries such as torchvision, torchtext, and others.
+"""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+dependencies = [
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('Python', '3.12.3'),
+    ('PyTorch', '2.7.1', versionsuffix),
+    ('matplotlib', '3.9.2'),
+    ('tqdm', '4.66.5'),
+    ('scikit-learn', '1.5.2'),
+]
+
+exts_list = [
+    (name, version, {
+        'checksums': ['73f2e5a07ffe6ac6647a6f12cd2f67f0d8f717329f150ddf08ef73cba0858d26'],
+    }),
+]
+
+moduleclass = 'ai'

easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.4.1-foss-2024a-CUDA-12.6.0.eb

@@ -0,0 +1,79 @@
+easyblock = 'PythonBundle'
+
+name = 'scvi-tools'
+version = '1.4.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/scverse/scvi-tools'
+description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and
+analysis of single-cell omics data, built on top of PyTorch and AnnData."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [
+    ('hatchling', '1.27.0'),
+    ('coverage', '7.9.2'),
+    ('captum', '0.8.0', versionsuffix),
+]
+dependencies = [
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('PyTorch', '2.7.1', versionsuffix),
+    ('PyTorch-Lightning', '2.5.6', versionsuffix),
+    ('Lightning', '2.5.6', versionsuffix),
+    ('anndata', '0.11.4'),
+    ('matplotlib', '3.9.2'),
+    ('scikit-learn', '1.5.2'),
+    ('tqdm', '4.66.5'),
+    ('h5py', '3.12.1'),
+    ('pyro-ppl', '1.9.1', versionsuffix),
+    ('ml-collections', '1.1.0'),
+    ('numba', '0.60.0'),
+    ('scanpy', '1.10.4'),
+    ('tensorboard', '2.18.0'),
+    ('xarray', '2024.11.0'),
+]
+
+# avoid srun problem
+# https://github.com/easybuilders/easybuild-easyconfigs/pull/25021#issuecomment-3744728157
+local_test_command = 'export SLURM_NTASKS_PER_NODE=$SLURM_NTASKS && '
+local_test_command += 'pytest -vs tests '
+# skip tests required optional dependencies
+local_test_command += (
+    '--ignore=tests/external/mrvi_jax '
+    '--ignore=tests/external/tangram '
+    '--ignore=tests/model/test_jaxscvi.py '
+    '--ignore=tests/hub '
+    '--ignore=tests/criticism '
+    '--ignore=tests/external/cytovi '
+    '--deselect=tests/data/test_anndata.py::test_anntorchdataset_dask '
+    '--deselect tests/model/test_multivi.py::test_multivi_mudata_rna_atac '
+)
+
+exts_list = [
+    ('packaging', '25.0', {
+        'checksums': ['d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f'],
+    }),
+    ('pytest_pretty', '1.3.0', {
+        'checksums': ['97e9921be40f003e40ae78db078d4a0c1ea42bf73418097b5077970c2cc43bf3'],
+    }),
+    ('mudata', '0.3.2', {
+        'checksums': ['c9b24f2429f369512f38e48599e341e7684abcf769df277e473700d4f1212740'],
+    }),
+    ('sparse', '0.17.0', {
+        'checksums': ['6b1ad51a810c5be40b6f95e28513ec810fe1c785923bd83b2e4839a751df4bf7'],
+    }),
+    ('docrep', '0.3.2', {
+        'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'],
+    }),
+    (name, version, {
+        'modulename': 'scvi',
+        'runtest': local_test_command,
+        'sources': ['scvi_tools-%(version)s.tar.gz'],
+        'testinstall': True,
+        'checksums': ['ee75eaac665618b9ee6fa466f6353ef68eb33cd3d7e2c77069e743471ca2103a'],
+    }),
+]
+
+moduleclass = 'bio'