{bio}[foss/2023a] scArches v0.6.1, scib-metrics v0.5.1, scvi-tools v1.1.2, ...

easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb

@@ -0,0 +1,112 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Updated by: Alex Domingo (Vrije Universiteit Brussel), Pavel Tománek (INUITS)
+# Update v0.4.25 based on: https://github.com/easybuilders/easybuild-easyconfigs/pull/20119
+
+easyblock = 'PythonBundle'
+
+name = 'jax'
+version = '0.4.25'
+
+homepage = 'https://jax.readthedocs.io/'
+description = """Composable transformations of Python+NumPy programs:
+differentiate, vectorize, JIT to GPU/TPU, and more"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('Bazel', '6.3.1'),
+    ('pytest-xdist', '3.3.1'),
+    # git 2.x required to fetch repository 'io_bazel_rules_docker'
+    ('git', '2.41.0', '-nodocs'),
+    ('matplotlib', '3.7.2'),
+    ('poetry', '1.5.1'),
+    ('pybind11', '2.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('zlib', '1.2.13'),
+    ('flatbuffers-python', '23.5.26'),
+    ('ml_dtypes', '0.3.2'),
+]
+
+use_pip = True
+
+local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
+local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
+
+local_extract_cmd = 'cp %s %(builddir)s/archives'
+
+local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" '
+local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
+local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
+
+default_easyblock = 'PythonPackage'
+default_component_specs = {
+    'sources': [SOURCE_TAR_GZ],
+    'source_urls': [PYPI_SOURCE],
+    'start_dir': '%(name)s-%(version)s',
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'download_dep_fail': True,
+}
+
+components = [
+    ('absl-py', '2.1.0', {
+        'options': {'modulename': 'absl'},
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('jaxlib', version, {
+        'sources': [
+            '%(name)s-v%(version)s.tar.gz',
+            {
+                'download_filename': '%s.tar.gz' % local_xla_commit,
+                'filename': 'xla-%s.tar.gz' % local_xla_commit,
+                'extract_cmd': local_extract_cmd,
+            },
+            {
+                'download_filename': '%s.tar.gz' % local_tfrt_commit,
+                'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit,
+                'extract_cmd': local_extract_cmd,
+            },
+        ],
+        'source_urls': [
+            'https://github.com/google/jax/archive/',
+            'https://github.com/tensorflow/runtime/archive',
+            'https://github.com/openxla/xla/archive'
+        ],
+        'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'],
+        'checksums': [
+            {'jaxlib-v0.4.25.tar.gz':
+             'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'},
+            {'xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4.tar.gz':
+             '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'},
+            {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz':
+             'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
+            {'jax-0.4.25_fix-pybind11-systemlib.patch':
+             'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'},
+        ],
+        'start_dir': 'jax-jaxlib-v%(version)s',
+        # Avoid warning (treated as error) in upb/table.c
+        'buildopts': local_repo_opt + ' --bazel_options="--copt=-Wno-maybe-uninitialized"'
+    }),
+]
+
+exts_list = [
+    (name, version, {
+        'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'],
+        'source_tmpl': '%(name)s-v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/google/jax/archive/'],
+        'checksums': [
+            {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'},
+            {'jax-0.4.25_fix_env_test_no_log_spam.patch':
+             'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'},
+        ],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch

@@ -0,0 +1,38 @@
+Add missing value for System Pybind11 Bazel config
+
+Author: Alexander Grund (TU Dresden)
+
+diff --git a/third_party/xla/fix-pybind11-systemlib.patch b/third_party/xla/fix-pybind11-systemlib.patch
+new file mode 100644
+index 000000000..68bd2063d
+--- /dev/null
++++ b/third_party/xla/fix-pybind11-systemlib.patch
+@@ -0,0 +1,13 @@
++--- xla-orig/third_party/tsl/third_party/systemlibs/pybind11.BUILD
+++++ xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4/third_party/tsl/third_party/systemlibs/pybind11.BUILD
++@@ -6,3 +6,10 @@
++         "@tsl//third_party/python_runtime:headers",
++     ],
++ )
+++
+++# Needed by pybind11_bazel.
+++config_setting(
+++    name = "osx",
+++    constraint_values = ["@platforms//os:osx"],
+++)
+++
+diff --git a/third_party/xla/workspace.bzl b/third_party/xla/workspace.bzl
+index ebc8d9838..125e1c173 100644
+--- a/third_party/xla/workspace.bzl
++++ b/third_party/xla/workspace.bzl
+@@ -29,6 +29,9 @@ def repo():
+         sha256 = XLA_SHA256,
+         strip_prefix = "xla-{commit}".format(commit = XLA_COMMIT),
+         urls = tf_mirror_urls("https://github.com/openxla/xla/archive/{commit}.tar.gz".format(commit = XLA_COMMIT)),
++        patch_file = [
++            "//third_party/xla:fix-pybind11-systemlib.patch",
++        ],
+     )
+
+     # For development, one often wants to make changes to the TF repository as well
+

easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch

@@ -0,0 +1,18 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/03
+# avoid overriding LD_LIBRARY_PATH, which would lead to test error: error while loading shared libraries: libpython3.11.so.1.0: cannot open shared object file: No such file or directory'
+diff -ru jax-jax-v0.4.25/tests/logging_test.py jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py
+--- jax-jax-v0.4.25/tests/logging_test.py	2024-02-24 19:25:17.000000000 +0100
++++ jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py	2024-03-15 12:00:34.133022613 +0100
+@@ -72,8 +72,11 @@
+     python = sys.executable
+     assert "python" in python
+     # Make sure C++ logging is at default level for the test process.
++    import os
++    tmp_env=os.environ.copy()
++    tmp_env['TF_CPP_MIN_LOG_LEVEL']='1'
+     proc = subprocess.run([python, "-c", program], capture_output=True,
+-                          env={"TF_CPP_MIN_LOG_LEVEL": "1"})
++                          env=tmp_env)
+
+     lines = proc.stdout.split(b"\n")
+     lines.extend(proc.stderr.split(b"\n"))

easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb

@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'ml-collections'
+version = '0.1.1'
+
+homepage = 'https://github.com/google/ml_collections'
+description = """
+ML Collections is a library of Python Collections designed for ML use cases.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyYAML', '6.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('absl-py', '2.1.0', {
+        'modulename': 'absl',
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', version, {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'

easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb

@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'Optax'
+version = '0.2.2'
+
+homepage = 'https://github.com/deepmind/optax'
+description = """Optax is a gradient processing and optimization library for JAX."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('jax', '0.4.25'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('toolz', '0.12.1', {
+        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
+    }),
+    ('flit_core', '3.9.0', {
+        'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'],
+    }),
+    ('absl-py', '2.1.0', {
+        'modulename': 'absl',
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('chex', '0.1.86', {
+        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
+    }),
+    ('optax', version, {
+        'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = ["python -c 'from optax import GradientTransformation'"]
+
+moduleclass = 'lib'

easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb

@@ -0,0 +1,52 @@
+easyblock = 'PythonBundle'
+
+name = 'scArches'
+version = '0.6.1'
+
+homepage = 'https://github.com/theislab/scarches'
+description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell
+ data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('matplotlib', '3.7.2'),
+    ('anndata', '0.10.5.post1'),
+    ('h5py', '3.9.0'),
+    ('leidenalg', '0.10.2'),
+    ('scanpy', '1.9.8'),
+    ('scikit-learn', '1.3.1'),
+    ('scvi-tools', '1.1.2'),
+    ('PyTorch', '2.1.2'),
+    ('tqdm', '4.66.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('gdown', '5.1.0', {
+        'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'],
+    }),
+    ('muon', '0.1.6', {
+        'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'],
+    }),
+    ('newick', '1.9.0', {
+        'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'],
+    }),
+    ('scHPL', '1.0.5', {
+        'modulename': 'scHPL',
+        # unpin pandas and newick versions to be compatible with foss/2023a versions
+        'preinstallopts': "sed -i 's/~=/>=/g' setup.py && sed -i 's/pandas>=1.1.2,<2/pandas/g' setup.py && ",
+        'checksums': ['3eb62b2e65b1faba04b7bcb86f7bf6967a6301866a605551211b8f14fd27eced'],
+    }),
+    (name, version, {
+        'checksums': ['187463c25781d5c5586c129ad137d96327a9f8604d530a696d5f568a9225d77c'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb

@@ -0,0 +1,54 @@
+easyblock = 'PythonBundle'
+
+name = 'scib-metrics'
+version = '0.5.1'
+
+homepage = 'https://scib-metrics.readthedocs.io'
+description = "Accelerated and Python-only metrics for benchmarking single-cell integration outputs"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+    ('poetry', '1.5.1'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('anndata', '0.10.5.post1'),
+    ('jax', '0.4.25'),
+    ('scikit-learn', '1.3.1'),
+    ('scanpy', '1.9.8'),
+    ('python-igraph', '0.11.4'),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
+    ('umap-learn', '0.5.5'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('toolz', '0.12.1', {
+        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
+    }),
+    ('plottable', '0.1.5', {
+        'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'],
+    }),
+    ('pynndescent', '0.5.11', {
+        'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'],
+    }),
+    ('rich', '13.7.1', {
+        'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'],
+    }),
+    ('chex', '0.1.86', {
+        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
+    }),
+    (name, version, {
+        'sources': ['scib_metrics-%(version)s.tar.gz'],
+        'checksums': ['74d10251acf1c11402b994faf063e55317881d7950fb78f6cef011d232a1e266'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'