From 96ab214452b8d8c9f38a43b323803eafbe70d6f4 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 23 Feb 2024 15:38:54 +0100 Subject: [PATCH 1/3] adding easyconfigs: scanpy-1.9.8-foss-2023a.eb, anndata-0.10.5.post1-foss-2023a.eb --- .../anndata-0.10.5.post1-foss-2023a.eb | 44 +++++++++ .../s/scanpy/scanpy-1.9.8-foss-2023a.eb | 92 +++++++++++++++++++ 2 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb b/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb new file mode 100644 index 000000000000..b49190c6e5a2 --- /dev/null +++ b/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'anndata' +version = '0.10.5.post1' + +homepage = 'https://github.com/scverse/anndata' +description = """anndata is a Python package for handling annotated data matrices in memory and on disk, + positioned between pandas and xarray""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('h5py', '3.9.0'), + ('hatchling', '1.18.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('array_api_compat', '1.4.1', { + 'checksums': ['053103b7c0ba73626bff7380abf27a29dc80de144394137bc7455b7eba23d8c0'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + (name, version, { + 'checksums': ['9a17c6eda9fc40759b3f5f81742f5d18c1a0a1acdf02f13e1646700ec082c155'], + }), +] + +sanity_check_paths = { + 'files': ['bin/natsort'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["natsort --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb new file mode 100644 index 000000000000..38f1324a6d0e --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb @@ -0,0 +1,92 @@ +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.9.8' + +homepage = 'https://scanpy.readthedocs.io/en/stable/' +description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('h5py', '3.9.0'), + ('tqdm', '4.66.1'), + ('scikit-learn', '1.3.1'), + ('statsmodels', '0.14.1'), + ('networkx', '3.1'), + ('numba', '0.58.1'), + ('umap-learn', '0.5.5'), + ('hatchling', '1.18.0'), + ('anndata', '0.10.5.post1'), + # ('leidenalg', '0.9.1'), +] + +# "anndata>=0.8", OK +# "numpy>=1.23", OK - scipy bundle +# "matplotlib>=3.6", OK +# "pandas >=1.5", OK - scipy bundle +# "scipy>=1.8", OK - scipy bundle +# "seaborn>=0.13", OK +# "h5py>=3.1", OK +# "tqdm", OK +# "scikit-learn>=0.24", OK +# "statsmodels>=0.13", OK +# "patsy", OK - statsmodels +# "networkx>=2.7", OK +# "natsort", OK - exts +# "joblib", OK - exts +# "numba>=0.56", OK +# "umap-learn>=0.5,!=0.5.0", OK +# "pynndescent>=0.5", OK - umap-learn +# "packaging>=21.3", OK - exts +# "session-info", OK - exts +# "legacy-api-wrap>=1.4", OK - exts +# "get-annotations; python_version < '3.10'", OK/ only need for python < 3.10 + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('stdlib_list', '0.10.0', { + 'checksums': ['6519c50d645513ed287657bfe856d527f277331540691ddeaf77b25459964a14'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('joblib', '1.3.2', { + 'checksums': ['92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1'], + }), + ('session-info', '1.0.0', { + 'sources': ['session_info-%(version)s.tar.gz'], + 'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'], + }), + ('legacy_api_wrap', '1.4', { + 'checksums': ['92dfa274cedb26d6e6f70fac85c856fbdcc05058066656d76a665fb4bf11b785'], + }), + (name, version, { + 'checksums': ['2ab1790d2b82eadb0cf8d487f468beac7a8f6a3a8fd7112d1ae989f8c52a4353'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "natsort --help", +] + +moduleclass = 'bio' From d296f8c657671170a5501db06179d1162a3befa5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 23 Feb 2024 15:42:16 +0100 Subject: [PATCH 2/3] clean dep comments --- .../s/scanpy/scanpy-1.9.8-foss-2023a.eb | 23 ------------------- 1 file changed, 23 deletions(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb index 38f1324a6d0e..ae5530e1e0db 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb @@ -27,30 +27,7 @@ dependencies = [ ('umap-learn', '0.5.5'), ('hatchling', '1.18.0'), ('anndata', '0.10.5.post1'), - # ('leidenalg', '0.9.1'), ] - -# "anndata>=0.8", OK -# "numpy>=1.23", OK - scipy bundle -# "matplotlib>=3.6", OK -# "pandas >=1.5", OK - scipy bundle -# "scipy>=1.8", OK - scipy bundle -# "seaborn>=0.13", OK -# "h5py>=3.1", OK -# "tqdm", OK -# "scikit-learn>=0.24", OK -# "statsmodels>=0.13", OK -# "patsy", OK - statsmodels -# "networkx>=2.7", OK -# "natsort", OK - exts -# "joblib", OK - exts -# "numba>=0.56", OK -# "umap-learn>=0.5,!=0.5.0", OK -# "pynndescent>=0.5", OK - umap-learn -# "packaging>=21.3", OK - exts -# "session-info", OK - exts -# "legacy-api-wrap>=1.4", OK - exts -# "get-annotations; python_version < '3.10'", OK/ only need for python < 3.10 use_pip = True sanity_pip_check = True From a5f2dd5a3c5a0c4e3fed54b439d2ed0d82b7bc34 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 23 Feb 2024 15:58:19 +0100 Subject: [PATCH 3/3] fix whitespaces --- easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb index ae5530e1e0db..dc34504eeee2 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb @@ -28,7 +28,7 @@ dependencies = [ ('hatchling', '1.18.0'), ('anndata', '0.10.5.post1'), ] - + use_pip = True sanity_pip_check = True