From f54b4e2ac86a28ca1a52d38221ad3355f81aa1f8 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 13 Jun 2024 12:08:46 +0200 Subject: [PATCH 1/4] adding easyconfigs: scArches-0.6.1-foss-2023a.eb, scib-metrics-0.5.1-foss-2023a.eb, scvi-tools-1.1.2-foss-2023a.eb, Optax-0.2.2-foss-2023a.eb, ml-collections-0.1.1-foss-2023a.eb, jax-0.4.25-foss-2023a.eb and patches: jax-0.4.25_fix-pybind11-systemlib.patch, jax-0.4.25_fix_env_test_no_log_spam.patch --- .../j/jax/jax-0.4.25-foss-2023a.eb | 112 ++++++++++++++++++ .../jax-0.4.25_fix-pybind11-systemlib.patch | 38 ++++++ .../jax-0.4.25_fix_env_test_no_log_spam.patch | 18 +++ .../ml-collections-0.1.1-foss-2023a.eb | 37 ++++++ .../o/Optax/Optax-0.2.2-foss-2023a.eb | 42 +++++++ .../s/scArches/scArches-0.6.1-foss-2023a.eb | 87 ++++++++++++++ .../scib-metrics-0.5.1-foss-2023a.eb | 54 +++++++++ .../scvi-tools/scvi-tools-1.1.2-foss-2023a.eb | 68 +++++++++++ 8 files changed, 456 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb create mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch create mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch create mode 100644 easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb new file mode 100644 index 00000000000..64a723ffe37 --- /dev/null +++ b/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' diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch new file mode 100644 index 00000000000..c404ee6917f --- /dev/null +++ b/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 + diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch new file mode 100644 index 00000000000..ad919608437 --- /dev/null +++ b/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")) diff --git a/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb b/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb new file mode 100644 index 00000000000..79034a7433d --- /dev/null +++ b/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' diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb new file mode 100644 index 00000000000..be05f009e9e --- /dev/null +++ b/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' diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb new file mode 100644 index 00000000000..c703d0beede --- /dev/null +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb @@ -0,0 +1,87 @@ +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'), + ('IPython', '8.14.0'), + ('pkgconfig', '1.5.5', '-python'), + ('PyZMQ', '25.1.1'), + ('tornado', '6.3.2'), +] + +use_pip = True + +exts_list = [ + ('sphinx_basic_ng', '1.0.0b2', { + 'checksums': ['9ec55a47c90c8c002b5960c57492ec3021f5193cb26cebc2dc4ea226848651c9'], + }), + ('nodeenv', '1.9.0', { + 'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'], + }), + ('sphinx-theme-builder', '0.2.0b2', { + 'checksums': ['e9cd98c2bb35bf414fe721469a043cdcc10f0808d1ffcf606acb4a6282a6f288'], + }), + ('furo', '2024.1.29', { + 'checksums': ['4d6b2fe3f10a6e36eb9cc24c1e7beb38d7a23fc7b3c382867503b7fcac8a1e02'], + }), + ('numpydoc', '1.6.0', { + 'checksums': ['ae7a5380f0a06373c3afe16ccd15bd79bc6b07f2704cbc6f1e7ecc94b4f5fc0d'], + }), + ('jupyter_core', '5.7.2', { + 'checksums': ['aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'], + }), + ('jupyter_client', '8.6.1', { + 'checksums': ['e842515e2bab8e19186d89fdfea7abd15e39dd581f94e399f00e2af5a1652d3f'], + }), + ('debugpy', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['28acbe2241222b87e255260c76741e1fbf04fdc3b6d094fcf57b6c6f75ce1242'], + }), + ('comm', '0.2.2', { + 'checksums': ['3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e'], + }), + ('ipykernel', '6.29.3', { + 'checksums': ['e14c250d1f9ea3989490225cc1a542781b095a18a19447fcf2b5eaf7d0ac5bd2'], + }), + ('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' diff --git a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb new file mode 100644 index 00000000000..68ef32b71ad --- /dev/null +++ b/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' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb new file mode 100644 index 00000000000..f79f5895f45 --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb @@ -0,0 +1,68 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '1.1.2' + +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': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('jax', '0.4.25'), + ('h5py', '3.9.0'), + ('PyTorch-Lightning', '2.2.1'), + ('pyro-ppl', '1.9.0'), + ('ml-collections', '0.1.1'), + ('Optax', '0.2.2'), +] + +use_pip = True + +exts_list = [ + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('numpyro', '0.15.0', { + 'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.15', { + 'modulename': 'orbax.checkpoint', + 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], + }), + ('tensorstore', '0.1.60', { + 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('lightning', '2.1.4', { + 'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'], + }), + (name, version, { + 'modulename': 'scvi', + 'sources': ['scvi_tools-%(version)s.tar.gz'], + 'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 6fd64492be78702677369e143bad52fc466f4b9e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 14 Jun 2024 11:55:24 +0200 Subject: [PATCH 2/4] add builddep for pyproject_metadata --- easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb index c703d0beede..f72ebf96042 100644 --- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb @@ -9,6 +9,7 @@ description = """Single-cell architecture surgery (scArches) is a package for re toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [('scikit-build-core', '0.5.0')] dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), From deb66d06567e8624bbb9e8c6eb747e15a6bb832a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 18 Jun 2024 15:39:26 +0200 Subject: [PATCH 3/4] add pyproject-metadata to exts --- .../easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb index f72ebf96042..ef28b4b84b0 100644 --- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb @@ -9,7 +9,6 @@ description = """Single-cell architecture surgery (scArches) is a package for re toolchain = {'name': 'foss', 'version': '2023a'} -builddependencies = [('scikit-build-core', '0.5.0')] dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), @@ -32,6 +31,10 @@ dependencies = [ use_pip = True exts_list = [ + ('pyproject-metadata', '0.8.0', { + 'sources': ['pyproject_metadata-%(version)s.tar.gz'], + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), ('sphinx_basic_ng', '1.0.0b2', { 'checksums': ['9ec55a47c90c8c002b5960c57492ec3021f5193cb26cebc2dc4ea226848651c9'], }), From db19c291e9da02d8b16ca7065b4a59f8e7e9ab3f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 19 Jun 2024 14:47:57 +0200 Subject: [PATCH 4/4] update scArches deps --- .../s/scArches/scArches-0.6.1-foss-2023a.eb | 39 ------------------- 1 file changed, 39 deletions(-) diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb index ef28b4b84b0..bdcb1ab880c 100644 --- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb @@ -22,50 +22,11 @@ dependencies = [ ('scvi-tools', '1.1.2'), ('PyTorch', '2.1.2'), ('tqdm', '4.66.1'), - ('IPython', '8.14.0'), - ('pkgconfig', '1.5.5', '-python'), - ('PyZMQ', '25.1.1'), - ('tornado', '6.3.2'), ] use_pip = True exts_list = [ - ('pyproject-metadata', '0.8.0', { - 'sources': ['pyproject_metadata-%(version)s.tar.gz'], - 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], - }), - ('sphinx_basic_ng', '1.0.0b2', { - 'checksums': ['9ec55a47c90c8c002b5960c57492ec3021f5193cb26cebc2dc4ea226848651c9'], - }), - ('nodeenv', '1.9.0', { - 'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'], - }), - ('sphinx-theme-builder', '0.2.0b2', { - 'checksums': ['e9cd98c2bb35bf414fe721469a043cdcc10f0808d1ffcf606acb4a6282a6f288'], - }), - ('furo', '2024.1.29', { - 'checksums': ['4d6b2fe3f10a6e36eb9cc24c1e7beb38d7a23fc7b3c382867503b7fcac8a1e02'], - }), - ('numpydoc', '1.6.0', { - 'checksums': ['ae7a5380f0a06373c3afe16ccd15bd79bc6b07f2704cbc6f1e7ecc94b4f5fc0d'], - }), - ('jupyter_core', '5.7.2', { - 'checksums': ['aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'], - }), - ('jupyter_client', '8.6.1', { - 'checksums': ['e842515e2bab8e19186d89fdfea7abd15e39dd581f94e399f00e2af5a1652d3f'], - }), - ('debugpy', '1.8.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - 'checksums': ['28acbe2241222b87e255260c76741e1fbf04fdc3b6d094fcf57b6c6f75ce1242'], - }), - ('comm', '0.2.2', { - 'checksums': ['3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e'], - }), - ('ipykernel', '6.29.3', { - 'checksums': ['e14c250d1f9ea3989490225cc1a542781b095a18a19447fcf2b5eaf7d0ac5bd2'], - }), ('gdown', '5.1.0', { 'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'], }),