From 6bb1bcb21ae67f04e106bd83301241b4c7e61630 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 14 Mar 2024 15:03:53 +0100 Subject: [PATCH 01/22] adding easyconfigs: Single-cell-python-bundle-2024.02-foss-2023a.eb --- ...e-cell-python-bundle-2024.02-foss-2023a.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb new file mode 100644 index 00000000000..fd51741e663 --- /dev/null +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'Single-cell-python-bundle' +version = '2024.02' + +homepage = 'xxx' +description = """Bundle for single-cell ???""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('PyTorch', '2.1.2'), + ('scanpy', '1.9.8'), + # scvi-tools TODO + # scArches TODO + # scib-metrics TODO + ('scib', '1.1.4'), + ('scVelo', '0.3.1'), # imports loompy + ('CellTypist', '1.6.2'), + # loompy in scVelo + ('epiScanpy', '0.4.0'), + ('CellRank', '2.0.2'), + ('scCODA', '0.1.9'), # imports rpy2 + # rpy2 in scCODA + ('infercnvpy', '4.0.3'), + ('pySCENIC', '0.12.1-20240311'), + ('Squidpy', '1.4.1'), + ('umap-learn', '0.5.5'), # bbknn dep + ('scikit-learn', '1.3.1'), # bbknn dep +] + +# DEPS to add: +# Anndata2ri +# Cassiopeia +# Sc_toolbox +# Altair +# Pertpy +# Tasccoda +# Liana-py +# Harmonypy +# Scirpy +# CellPhoneDB +# Decoupler +# contrastiveVI +# Schist + +exts_list = [ + ('pynndescent', '0.5.11'), + ('annoy', '1.17.3'), + ('bbknn', '1.6.0'), # requested +] + +moduleclass = 'bio' From 248a561ed299b36c26c53befaf23cf38441fcdb3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 15 Mar 2024 10:23:43 +0100 Subject: [PATCH 02/22] update1 bundle --- ...e-cell-python-bundle-2024.02-foss-2023a.eb | 55 +++++++++++++++---- 1 file changed, 43 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index fd51741e663..8629de7f8be 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -8,6 +8,8 @@ description = """Bundle for single-cell ???""" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [('poetry', '1.5.1')] + dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), @@ -20,23 +22,22 @@ dependencies = [ # scArches TODO # scib-metrics TODO ('scib', '1.1.4'), - ('scVelo', '0.3.1'), # imports loompy + # ('scVelo', '0.3.1'), # imports loompy ('CellTypist', '1.6.2'), # loompy in scVelo ('epiScanpy', '0.4.0'), - ('CellRank', '2.0.2'), + # ('CellRank', '2.0.2'), ('scCODA', '0.1.9'), # imports rpy2 # rpy2 in scCODA - ('infercnvpy', '4.0.3'), - ('pySCENIC', '0.12.1-20240311'), - ('Squidpy', '1.4.1'), - ('umap-learn', '0.5.5'), # bbknn dep - ('scikit-learn', '1.3.1'), # bbknn dep + ('infercnvpy', '0.4.3'), + # ('pySCENIC', '0.12.1-20240311'), + # ('Squidpy', '1.4.1'), + ('umap-learn', '0.5.5'), # bbknn + ('scikit-learn', '1.3.1'), # bbknn + ('Pillow', '10.0.0'), # cassiopeia ] # DEPS to add: -# Anndata2ri -# Cassiopeia # Sc_toolbox # Altair # Pertpy @@ -50,9 +51,39 @@ dependencies = [ # Schist exts_list = [ - ('pynndescent', '0.5.11'), - ('annoy', '1.17.3'), - ('bbknn', '1.6.0'), # requested + ('arrow', '0.17.0', { + 'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'], + }), + ('datapipelines', '1.0.7', { + 'checksums': ['752bc71a1e03a45d723fc4d9b56c641ed0b872ed1df73b08896ee34d93c56e8f'], + }), + ('merakicommons', '1.0.10', { + 'checksums': ['fc99ebe0cb85c4af0093a9454294adcb97c0792f8a8dd03898242ab2446aa77e'], + }), + ('flake8', '7.0.0', { + 'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('annoy', '1.17.3', { + 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], + }), + ('tzlocal', '5.2', { + 'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'], + }), + ('anndata2ri', '1.3.1', { + 'checksums': ['0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42'], + }), + ('bbknn', '1.6.0', { + 'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'], + }), + ('cassiopeia', '5.0.3', { + 'checksums': ['18adfc81f795f807ce6e6674da5c81c801d28ecf42f9ce94e23fc018b6840d63'], + }), + # ('sc_toolbox', '0.12.3', { + # 'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'], + # }), ] moduleclass = 'bio' From 6a42985e50fd8e880a6ebae42f245ca7ac2536f0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 19 Mar 2024 18:20:27 +0100 Subject: [PATCH 03/22] update bundle + add adjustText pycodestyle --- .../adjustText/adjustText-1.1.1-foss-2023a.eb | 27 +++++++ .../pycodestyle-2.11.1-foss-2023a.eb | 24 ++++++ ...e-cell-python-bundle-2024.02-foss-2023a.eb | 81 +++++++++++++++---- 3 files changed, 118 insertions(+), 14 deletions(-) create mode 100644 easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb b/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb new file mode 100644 index 00000000000..f109d19d3aa --- /dev/null +++ b/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'adjustText' +version = '1.1.1' + +homepage = 'https://github.com/Phlya/adjustText' +description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'adjustText', + 'checksums': ['e2c0975ef2c642478e60f4c03c5e9afbdeda7764336907ef69a9205bfa2d9896'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb new file mode 100644 index 00000000000..c704acc3b36 --- /dev/null +++ b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonBundle' + +name = 'pycodestyle' +version = '2.11.1' + +homepage = "https://pycodestyle.readthedocs.io" +description = """pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), +] + +exts_list = [ + (name, version, { + 'checksums': ['41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index 8629de7f8be..a3c7011d4ac 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -8,7 +8,7 @@ description = """Bundle for single-cell ???""" toolchain = {'name': 'foss', 'version': '2023a'} -builddependencies = [('poetry', '1.5.1')] +# builddependencies = [('poetry', '1.5.1')] dependencies = [ ('Python', '3.11.3'), @@ -22,7 +22,7 @@ dependencies = [ # scArches TODO # scib-metrics TODO ('scib', '1.1.4'), - # ('scVelo', '0.3.1'), # imports loompy + ('scVelo', '0.3.1'), # imports loompy ('CellTypist', '1.6.2'), # loompy in scVelo ('epiScanpy', '0.4.0'), @@ -32,13 +32,29 @@ dependencies = [ ('infercnvpy', '0.4.3'), # ('pySCENIC', '0.12.1-20240311'), # ('Squidpy', '1.4.1'), - ('umap-learn', '0.5.5'), # bbknn - ('scikit-learn', '1.3.1'), # bbknn + # deps for exts: ('Pillow', '10.0.0'), # cassiopeia + ('pycodestyle', '2.11.1'), # cassiopeia, created + ('umap-learn', '0.5.5'), # bbknn + ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox + ('PyYAML', '6.0'), # sc_toolbox + ('typing-extensions', '4.9.0'), # sc_toolbox + ('adjustText', '1.1.1'), ] # DEPS to add: -# Sc_toolbox +# Cassiopeia OK + # arrow, datapipelines,merakicommons, flake8, Pillow + # flake8: mccabe, pycodestyle (created for 2023a), pyflakes +# Bbknn OK + # umap-learn, scikit-learn, pynndescent, annoy, flit_core +# Anndata2ri OK + # rpy2, anndata, tzlocal +# Sc_toolbox - adjustText (created), rich, PyYAML, questionary, cookiecutter (in eb, not 2023b), matplotlib, scanpy, seaborn, scikit-learn, typing-extensions, pypi-latest + # OK cookiecutter - binaryornot, python-slugify + # OK questionary 2.0.1 has requirement prompt_toolkit<=3.0.36,>=2.0, but you have prompt-toolkit 3.0.39 -> 3.0.36 to exts_list + # OKpython-slugify 8.0.4 requires text-unidecode, which is not installed. + # questionary needs poetry-core? # Altair # Pertpy # Tasccoda @@ -51,6 +67,12 @@ dependencies = [ # Schist exts_list = [ + ('pyflakes', '3.2.0', { + 'checksums': ['1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f'], + }), + ('mccabe', '0.7.0', { + 'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'], + }), ('arrow', '0.17.0', { 'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'], }), @@ -63,27 +85,58 @@ exts_list = [ ('flake8', '7.0.0', { 'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'], }), - ('pynndescent', '0.5.11', { - 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + ('cassiopeia', '5.0.3', { + 'checksums': ['18adfc81f795f807ce6e6674da5c81c801d28ecf42f9ce94e23fc018b6840d63'], + }), + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], }), ('annoy', '1.17.3', { 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('bbknn', '1.6.0', { + 'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'], + }), ('tzlocal', '5.2', { 'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'], }), ('anndata2ri', '1.3.1', { 'checksums': ['0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42'], }), - ('bbknn', '1.6.0', { - 'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'], + ('pypi-latest', '0.1.2', { + 'checksums': ['b195654567e6abaac6acfec37638d8e000838f419bc6b129962a896eedc4ed4e'], }), - ('cassiopeia', '5.0.3', { - 'checksums': ['18adfc81f795f807ce6e6674da5c81c801d28ecf42f9ce94e23fc018b6840d63'], + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '8.0.4', { + 'modulename': 'slugify', + 'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'], + }), + ('prompt_toolkit', '3.0.36', { + 'checksums': ['3e163f254bef5a03b146397d7c1963bd3e2812f0964bb9a24e6ec761fd28db63'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('cookiecutter', '2.6.0', { + 'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'], + }), + ('questionary', '2.0.1', { + 'checksums': ['bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('sc_toolbox', '0.12.3', { + 'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'], }), - # ('sc_toolbox', '0.12.3', { - # 'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'], - # }), ] +use_pip = True +sanity_pip_check = True + moduleclass = 'bio' From 06537c9a9e4ab3b62f51d2a04b24eab77c1c67b3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 25 Mar 2024 11:07:06 +0100 Subject: [PATCH 04/22] tascCODA added, cassiopeia remove --- ...e-cell-python-bundle-2024.02-foss-2023a.eb | 139 +++++++++++++----- 1 file changed, 106 insertions(+), 33 deletions(-) diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index a3c7011d4ac..f7976233e97 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -4,7 +4,7 @@ name = 'Single-cell-python-bundle' version = '2024.02' homepage = 'xxx' -description = """Bundle for single-cell ???""" +description = """Bundle of softwares for single-cell research ???""" toolchain = {'name': 'foss', 'version': '2023a'} @@ -33,31 +33,56 @@ dependencies = [ # ('pySCENIC', '0.12.1-20240311'), # ('Squidpy', '1.4.1'), # deps for exts: - ('Pillow', '10.0.0'), # cassiopeia - ('pycodestyle', '2.11.1'), # cassiopeia, created + # ('Pillow', '10.0.0'), # cassiopeia + # ('pycodestyle', '2.11.1'), # cassiopeia, created ('umap-learn', '0.5.5'), # bbknn ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox ('PyYAML', '6.0'), # sc_toolbox ('typing-extensions', '4.9.0'), # sc_toolbox - ('adjustText', '1.1.1'), + ('adjustText', '1.1.1'), # sc_toolbox, created ] # DEPS to add: -# Cassiopeia OK +# Cassiopeia-lineage +# Cassiopeia NO! do it again for https://pypi.org/project/cassiopeia-lineage/ # arrow, datapipelines,merakicommons, flake8, Pillow # flake8: mccabe, pycodestyle (created for 2023a), pyflakes # Bbknn OK # umap-learn, scikit-learn, pynndescent, annoy, flit_core # Anndata2ri OK # rpy2, anndata, tzlocal -# Sc_toolbox - adjustText (created), rich, PyYAML, questionary, cookiecutter (in eb, not 2023b), matplotlib, scanpy, seaborn, scikit-learn, typing-extensions, pypi-latest - # OK cookiecutter - binaryornot, python-slugify +# Sc_toolbox OK + # adjustText (created), rich, PyYAML, questionary, cookiecutter (in eb, not 2023b), matplotlib, scanpy, seaborn, scikit-learn, typing-extensions, pypi-latest + # OK cookiecutter - binaryornot, python-slugify, arrow # OK questionary 2.0.1 has requirement prompt_toolkit<=3.0.36,>=2.0, but you have prompt-toolkit 3.0.39 -> 3.0.36 to exts_list - # OKpython-slugify 8.0.4 requires text-unidecode, which is not installed. - # questionary needs poetry-core? -# Altair -# Pertpy -# Tasccoda + # OK python-slugify 8.0.4 requires text-unidecode, which is not installed. + # questionary needs poetry-core? Seems NOT + # arrow 1.3.0 requires types-python-dateutil OK exts +# Altair OK + # altair 5.2.0 requires toolz OK exts +# Pertpy NO - needs scvi-tools + # pertpy 0.6.0 requires decoupler, which is not installed. -> Do decoupler first + # pertpy 0.6.0 requires ipywidgets, which is not installed. + # pertpy 0.6.0 requires muon, which is not installed. + # pertpy 0.6.0 requires numpyro, which is not installed. + # pertpy 0.6.0 requires ott-jax, which is not installed. + # pertpy 0.6.0 requires plotnine, which is not installed. + # pertpy 0.6.0 requires scvi-tools, which is not installed. + # pertpy 0.6.0 requires sparsecca, which is not installed. + # pertpy 0.6.0 requires toytree OK exts + # ('pertpy', '0.6.0', { + # 'checksums': ['0f9ed443a74a07ab8cd0fb6d2d06275df30ec836c161124b83c9505b7cab182b'], + # }), +# tascCODA OK + # tasccoda 0.1.3 requires tensorflow-probability OK in scCoda -> delete TF-prob. from setup.py as in scCoda + # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes + # tasccoda 0.1.3 requires toytree OK exts + # toytree 2.0.5 requires toyplot OK exts + # toyplot 1.0.3 requires arrow OK exts + # toyplot 1.0.3 requires custom-inherit OK exts + # toyplot 1.0.3 requires multipledispatch OK exts + # toyplot 1.0.3 requires pypng OK exts + # toyplot 1.0.3 requires reportlab OK exts # Liana-py # Harmonypy # Scirpy @@ -66,28 +91,18 @@ dependencies = [ # contrastiveVI # Schist +# cassiopeia-lineage Error: +# gcc -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errn +# O2 -ftree-vectorize -march=native -fno-math-errno -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-12.3.0/include -I/apps/gent/RHEL8/cas +# ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include/flexiblas -fPIC -I/sc +# t/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Python/3.11.3-GCCcore-12.3.0/include/python3.11 -c cassiopeia/TreeSolver/lineage_ +# lver_utils.c -o build/temp.linux-x86_64-cpython-311/cassiopeia/TreeSolver/lineage_solver/solver_utils.o +# cassiopeia/TreeSolver/lineage_solver/solver_utils.c:208:12: fatal error: longintrepr.h: No such file or directory +# 208 | #include "longintrepr.h" +# | ^~~~~~~~~~~~~~~ +# compilation terminated. + exts_list = [ - ('pyflakes', '3.2.0', { - 'checksums': ['1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f'], - }), - ('mccabe', '0.7.0', { - 'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'], - }), - ('arrow', '0.17.0', { - 'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'], - }), - ('datapipelines', '1.0.7', { - 'checksums': ['752bc71a1e03a45d723fc4d9b56c641ed0b872ed1df73b08896ee34d93c56e8f'], - }), - ('merakicommons', '1.0.10', { - 'checksums': ['fc99ebe0cb85c4af0093a9454294adcb97c0792f8a8dd03898242ab2446aa77e'], - }), - ('flake8', '7.0.0', { - 'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'], - }), - ('cassiopeia', '5.0.3', { - 'checksums': ['18adfc81f795f807ce6e6674da5c81c801d28ecf42f9ce94e23fc018b6840d63'], - }), ('flit_core', '3.9.0', { 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], }), @@ -122,6 +137,13 @@ exts_list = [ ('binaryornot', '0.4.4', { 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], }), + ('types-python-dateutil', '2.9.0.20240316', { + 'modulename': False, + 'checksums': ['5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202'], + }), + ('arrow', '1.3.0', { + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), ('cookiecutter', '2.6.0', { 'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'], }), @@ -134,8 +156,59 @@ exts_list = [ ('sc_toolbox', '0.12.3', { 'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'], }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('altair', '5.2.0', { + 'checksums': ['2ad7f0c8010ebbc46319cc30febfb8e59ccf84969a201541c207bc3a4fa6cf81'], + }), + ('custom_inherit', '2.4.1', { + 'checksums': ['7052eb337bcce83551815264391cc4efc2bf70b295a3c52aba64f1ab57c3a8a2'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('pypng', '0.20220715.0', { + 'modulename': 'png', + 'checksums': ['739c433ba96f078315de54c0db975aee537cbc3e1d0ae4ed9aab0ca1e427e2c1'], + }), + ('reportlab', '4.1.0', { + 'checksums': ['3a99faf412691159c068b3ff01c15307ce2fd2cf6b860199434874e002040a84'], + }), + ('toyplot', '1.0.3', { + 'checksums': ['7b7b2bc5784fd75e5c695300bffc80d568c83bebef543bb54e6e6c2229912edd'], + }), + ('toytree', '2.0.5', { + 'checksums': ['7be04ca310067e0e9737449700d6ab1b68b4379b64e2d22f2f7697a70030ceb0'], + }), + ('tascCODA', '0.1.3', { + 'preinstallopts': "sed -i '28d' setup.py && ", + 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], + }), + # ('cassiopeia-lineage', '1.0.4', { + # 'checksums': ['c341f6f4f0e4cb422c657387336f001a9e5d4eaff8fe0b40a00508b307de27aa'], + # }), ] + # ('pyflakes', '3.2.0', { + # 'checksums': ['1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f'], + # }), + # ('mccabe', '0.7.0', { + # 'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'], + # }), + # ('arrow', '0.17.0', { + # 'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'], + # }), + # ('datapipelines', '1.0.7', { + # 'checksums': ['752bc71a1e03a45d723fc4d9b56c641ed0b872ed1df73b08896ee34d93c56e8f'], + # }), + # ('merakicommons', '1.0.10', { + # 'checksums': ['fc99ebe0cb85c4af0093a9454294adcb97c0792f8a8dd03898242ab2446aa77e'], + # }), + # ('flake8', '7.0.0', { + # 'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'], + # }), + use_pip = True sanity_pip_check = True From f988b1d6072749c2ca5708abbbe333ff3b03ce59 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 8 Apr 2024 11:03:20 +0200 Subject: [PATCH 05/22] cassiopeia added, homepage, description --- ...e-cell-python-bundle-2024.02-foss-2023a.eb | 46 +++---------------- 1 file changed, 6 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index f7976233e97..9f0a5b02b36 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -3,8 +3,8 @@ easyblock = 'PythonBundle' name = 'Single-cell-python-bundle' version = '2024.02' -homepage = 'xxx' -description = """Bundle of softwares for single-cell research ???""" +homepage = (None) +description = """Bundle of tools for single-cell sequence analysis.""" toolchain = {'name': 'foss', 'version': '2023a'} @@ -26,15 +26,14 @@ dependencies = [ ('CellTypist', '1.6.2'), # loompy in scVelo ('epiScanpy', '0.4.0'), - # ('CellRank', '2.0.2'), ('scCODA', '0.1.9'), # imports rpy2 # rpy2 in scCODA ('infercnvpy', '0.4.3'), - # ('pySCENIC', '0.12.1-20240311'), + ('pySCENIC', '0.12.1-20240311'), + # ('CellRank', '2.0.2'), # ('Squidpy', '1.4.1'), + # ('Cassiopeia', '2.0.0'), # deps for exts: - # ('Pillow', '10.0.0'), # cassiopeia - # ('pycodestyle', '2.11.1'), # cassiopeia, created ('umap-learn', '0.5.5'), # bbknn ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox ('PyYAML', '6.0'), # sc_toolbox @@ -43,7 +42,7 @@ dependencies = [ ] # DEPS to add: -# Cassiopeia-lineage +# Cassiopeia-lineage OK deps # Cassiopeia NO! do it again for https://pypi.org/project/cassiopeia-lineage/ # arrow, datapipelines,merakicommons, flake8, Pillow # flake8: mccabe, pycodestyle (created for 2023a), pyflakes @@ -90,17 +89,6 @@ dependencies = [ # Decoupler # contrastiveVI # Schist - -# cassiopeia-lineage Error: -# gcc -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errn -# O2 -ftree-vectorize -march=native -fno-math-errno -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-12.3.0/include -I/apps/gent/RHEL8/cas -# ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include/flexiblas -fPIC -I/sc -# t/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Python/3.11.3-GCCcore-12.3.0/include/python3.11 -c cassiopeia/TreeSolver/lineage_ -# lver_utils.c -o build/temp.linux-x86_64-cpython-311/cassiopeia/TreeSolver/lineage_solver/solver_utils.o -# cassiopeia/TreeSolver/lineage_solver/solver_utils.c:208:12: fatal error: longintrepr.h: No such file or directory -# 208 | #include "longintrepr.h" -# | ^~~~~~~~~~~~~~~ -# compilation terminated. exts_list = [ ('flit_core', '3.9.0', { @@ -185,29 +173,7 @@ exts_list = [ 'preinstallopts': "sed -i '28d' setup.py && ", 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], }), - # ('cassiopeia-lineage', '1.0.4', { - # 'checksums': ['c341f6f4f0e4cb422c657387336f001a9e5d4eaff8fe0b40a00508b307de27aa'], - # }), ] - - # ('pyflakes', '3.2.0', { - # 'checksums': ['1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f'], - # }), - # ('mccabe', '0.7.0', { - # 'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'], - # }), - # ('arrow', '0.17.0', { - # 'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'], - # }), - # ('datapipelines', '1.0.7', { - # 'checksums': ['752bc71a1e03a45d723fc4d9b56c641ed0b872ed1df73b08896ee34d93c56e8f'], - # }), - # ('merakicommons', '1.0.10', { - # 'checksums': ['fc99ebe0cb85c4af0093a9454294adcb97c0792f8a8dd03898242ab2446aa77e'], - # }), - # ('flake8', '7.0.0', { - # 'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'], - # }), use_pip = True sanity_pip_check = True From 4ea706341c818df7e7d1a6429762520e9a552a1e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 24 Apr 2024 16:22:13 +0200 Subject: [PATCH 06/22] add another dependencies --- .../Single-cell-python-bundle-2024.02-foss-2023a.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index 9f0a5b02b36..637f3767f2b 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -30,9 +30,9 @@ dependencies = [ # rpy2 in scCODA ('infercnvpy', '0.4.3'), ('pySCENIC', '0.12.1-20240311'), - # ('CellRank', '2.0.2'), - # ('Squidpy', '1.4.1'), - # ('Cassiopeia', '2.0.0'), + ('CellRank', '2.0.2'), + ('Squidpy', '1.4.1'), + ('Cassiopeia', '2.0.0'), # deps for exts: ('umap-learn', '0.5.5'), # bbknn ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox @@ -89,7 +89,7 @@ dependencies = [ # Decoupler # contrastiveVI # Schist - + exts_list = [ ('flit_core', '3.9.0', { 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], @@ -174,7 +174,7 @@ exts_list = [ 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], }), ] - + use_pip = True sanity_pip_check = True From 90be71a02be9a6ab1e7b606261ebafcdef08c80c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 6 May 2024 10:57:07 +0200 Subject: [PATCH 07/22] poetry as a builddep --- .../Single-cell-python-bundle-2024.02-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index 637f3767f2b..eb1ab72f5f4 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -8,7 +8,7 @@ description = """Bundle of tools for single-cell sequence analysis.""" toolchain = {'name': 'foss', 'version': '2023a'} -# builddependencies = [('poetry', '1.5.1')] +builddependencies = [('poetry', '1.5.1')] dependencies = [ ('Python', '3.11.3'), From 9b4d4824914b770e58427ebc7e571e002a5c08ad Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 6 May 2024 13:11:54 +0200 Subject: [PATCH 08/22] delete comments to let tests pass --- ...e-cell-python-bundle-2024.02-foss-2023a.eb | 49 ------------------- 1 file changed, 49 deletions(-) diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index eb1ab72f5f4..d99406dc627 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -41,55 +41,6 @@ dependencies = [ ('adjustText', '1.1.1'), # sc_toolbox, created ] -# DEPS to add: -# Cassiopeia-lineage OK deps -# Cassiopeia NO! do it again for https://pypi.org/project/cassiopeia-lineage/ - # arrow, datapipelines,merakicommons, flake8, Pillow - # flake8: mccabe, pycodestyle (created for 2023a), pyflakes -# Bbknn OK - # umap-learn, scikit-learn, pynndescent, annoy, flit_core -# Anndata2ri OK - # rpy2, anndata, tzlocal -# Sc_toolbox OK - # adjustText (created), rich, PyYAML, questionary, cookiecutter (in eb, not 2023b), matplotlib, scanpy, seaborn, scikit-learn, typing-extensions, pypi-latest - # OK cookiecutter - binaryornot, python-slugify, arrow - # OK questionary 2.0.1 has requirement prompt_toolkit<=3.0.36,>=2.0, but you have prompt-toolkit 3.0.39 -> 3.0.36 to exts_list - # OK python-slugify 8.0.4 requires text-unidecode, which is not installed. - # questionary needs poetry-core? Seems NOT - # arrow 1.3.0 requires types-python-dateutil OK exts -# Altair OK - # altair 5.2.0 requires toolz OK exts -# Pertpy NO - needs scvi-tools - # pertpy 0.6.0 requires decoupler, which is not installed. -> Do decoupler first - # pertpy 0.6.0 requires ipywidgets, which is not installed. - # pertpy 0.6.0 requires muon, which is not installed. - # pertpy 0.6.0 requires numpyro, which is not installed. - # pertpy 0.6.0 requires ott-jax, which is not installed. - # pertpy 0.6.0 requires plotnine, which is not installed. - # pertpy 0.6.0 requires scvi-tools, which is not installed. - # pertpy 0.6.0 requires sparsecca, which is not installed. - # pertpy 0.6.0 requires toytree OK exts - # ('pertpy', '0.6.0', { - # 'checksums': ['0f9ed443a74a07ab8cd0fb6d2d06275df30ec836c161124b83c9505b7cab182b'], - # }), -# tascCODA OK - # tasccoda 0.1.3 requires tensorflow-probability OK in scCoda -> delete TF-prob. from setup.py as in scCoda - # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes - # tasccoda 0.1.3 requires toytree OK exts - # toytree 2.0.5 requires toyplot OK exts - # toyplot 1.0.3 requires arrow OK exts - # toyplot 1.0.3 requires custom-inherit OK exts - # toyplot 1.0.3 requires multipledispatch OK exts - # toyplot 1.0.3 requires pypng OK exts - # toyplot 1.0.3 requires reportlab OK exts -# Liana-py -# Harmonypy -# Scirpy -# CellPhoneDB -# Decoupler -# contrastiveVI -# Schist - exts_list = [ ('flit_core', '3.9.0', { 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], From 97b22a899b4adcb9aa0860b79f383e124d45cf41 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 9 May 2024 15:15:20 +0200 Subject: [PATCH 09/22] update comment for tascCODA deletion in setup.py --- .../Single-cell-python-bundle-2024.02-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index d99406dc627..28a63c085a6 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -121,6 +121,7 @@ exts_list = [ 'checksums': ['7be04ca310067e0e9737449700d6ab1b68b4379b64e2d22f2f7697a70030ceb0'], }), ('tascCODA', '0.1.3', { + # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes 'preinstallopts': "sed -i '28d' setup.py && ", 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], }), From 9e61515095a6388a3aad6ac4329e906f44823cc3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 28 May 2024 17:24:15 +0200 Subject: [PATCH 10/22] add harmonypy, cellphonedb, decoupler --- ...e-cell-python-bundle-2024.02-foss-2023a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index 28a63c085a6..d554e9fddca 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -125,6 +125,35 @@ exts_list = [ 'preinstallopts': "sed -i '28d' setup.py && ", 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], }), + ('harmonypy', '0.0.9', { + 'checksums': ['85bfdd4e6ec6e0fa8816a276639358d3598a40d60ba9f7a5d9dada8706be8c4d'], + }), + ('fbpca', '1.0', { + 'checksums': ['150677642479663f317fdbb5e06dab3f98721cf7031bb4a84113d7a631c472d1'], + }), + ('geosketch', '1.2', { + 'checksums': ['bbfe97366b91c5927b6076d5a6738d9cfbe094efb5ac1117aab7a30b6081cc4e'], + }), + ('python_circos', '0.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'modulename': 'pycircos', + 'checksums': ['410eaffc4eb2933cd688897356813da23310f5e2f14a8bceb003e9b96faa715b'], + }), + ('mizani', '0.9.3', { + 'checksums': ['fb61339e9e4711850e902ca286b1ae75255f483823d891aa0515b426d56c606d'], + }), + ('plotnine', '0.12.4', { + 'checksums': ['adc41a672503594445a8fa19872799253bd0784cdbd5a1cc16657a1dd20ba905'], + }), + ('ktplotspy', '0.2.3', { + 'checksums': ['9a1e3646217e6e99f59ab2258dfd76120cf1f50880c9cb2f9005de397c00f0a9'], + }), + ('cellphonedb', '5.0.0', { + 'checksums': ['1c96173d8527f1655216d265fc50a28ea3360d70486afa5050e3f5565fa3a8cd'], + }), + ('decoupler', '1.6.0', { + 'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'], + }), ] use_pip = True From 4d3a007527f87c7f4c08be9a81d67b71b80a75d0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 30 May 2024 14:18:18 +0200 Subject: [PATCH 11/22] add scirpy, liana, muon, mudata --- ...e-cell-python-bundle-2024.02-foss-2023a.eb | 54 ++++++++++++++++++- 1 file changed, 53 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index d554e9fddca..0fa2bcb2cf6 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -8,7 +8,11 @@ description = """Bundle of tools for single-cell sequence analysis.""" toolchain = {'name': 'foss', 'version': '2023a'} -builddependencies = [('poetry', '1.5.1')] +builddependencies = [ + ('poetry', '1.5.1'), + ('CMake', '3.26.3'), + ('hatchling', '1.18.0'), +] dependencies = [ ('Python', '3.11.3'), @@ -39,6 +43,7 @@ dependencies = [ ('PyYAML', '6.0'), # sc_toolbox ('typing-extensions', '4.9.0'), # sc_toolbox ('adjustText', '1.1.1'), # sc_toolbox, created + ('python-parasail', '1.3.4'), # scirpy ] exts_list = [ @@ -154,6 +159,53 @@ exts_list = [ ('decoupler', '1.6.0', { 'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'], }), + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('nodeenv', '1.9.0', { + 'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'], + }), + ('identify', '2.5.36', { + 'checksums': ['e5e00f54165f9047fbebeb4a560f9acfb8af4c88232be60a488e9b68d122745d'], + }), + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pre_commit', '3.7.1', { + 'checksums': ['8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('liana', '1.2.0', { + 'checksums': ['be899c69bfcbf3d0f8b61c04c35f225ac6b11fe1ea80e6ed4bdc0e6212cb2379'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('scikit_build_core', '0.9.3', { + 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], + }), + ('awkward-cpp', '33', { + 'checksums': ['550adebccd329d18d02e95226d0b89698188fd33e44f07450942c692881927d8'], + }), + ('awkward', '2.6.4', { + 'checksums': ['ee0cb27c64150f368749983dda499c108848c64dc830912480eb37b78c04300f'], + }), + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('airr', '1.5.0', { + 'checksums': ['febc0a881bf46b1a9c29ac6a7089dd733ff9120d114585e75dede26403f68d42'], + }), + ('scirpy', '0.17.0', { + 'checksums': ['f61653a4f7387562ec89b00fbfd7cab762c0bf3320f21ccfc47df80a13cc5d41'], + }), + # ('schist', '0.8.3', { + # 'source_tmpl': 'v%(version)s.tar.gz', + # 'source_urls': ['https://github.com/dawe/schist/archive/'], + # 'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'], + # }), ] use_pip = True From 99804a10b0644ad1d986b0b65f8845bea8753b35 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 3 Jun 2024 11:31:11 +0200 Subject: [PATCH 12/22] add schist to bundle --- .../c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb | 39 ++++++++++++ .../graph-tool/graph-tool-2.59-foss-2023a.eb | 61 +++++++++++++++++++ ...e-cell-python-bundle-2024.02-foss-2023a.eb | 11 ++-- 3 files changed, 106 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..2ca14e07c7c --- /dev/null +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +# Updated to MesonNinja as the autogen.sh complained. +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MesonNinja' + +name = 'cairomm' +version = '1.16.2' + +homepage = 'http://cairographics.org' +description = "The Cairomm package provides a C++ interface to Cairo." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['6a63bf98a97dda2b0f55e34d1b5f3fb909ef8b70f9b8d382cb1ff3978e7dc13f'] + +builddependencies = [ + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('Doxygen', '1.9.7'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('cairo', '1.17.8'), + ('libsigc++', '3.6.0'), + ('mm-common', '1.0.6'), + ('Boost', '1.82.0'), +] + +runtest = 'ninja test' + +sanity_check_paths = { + 'files': ['lib/libcairomm-1.16.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb new file mode 100644 index 00000000000..2ca6027a864 --- /dev/null +++ b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb @@ -0,0 +1,61 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: Pavel Tománek (Inuits) + +easyblock = 'ConfigureMake' + +name = 'graph-tool' +version = '2.59' + +homepage = 'https://graph-tool.skewed.de/' +description = """Graph-tool is an efficient Python module for manipulation and + statistical analysis of graphs (a.k.a. networks). Contrary to + most other python modules with similar functionality, the core + data structures and algorithms are implemented in C++, making + extensive use of template metaprogramming, based heavily on + the Boost Graph Library. This confers it a level of + performance that is comparable (both in memory usage and + computation time) to that of a pure C/C++ library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'cstd': 'c++17', 'openmp': True} + +source_urls = ['https://downloads.skewed.de/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['cde479c0a7254b72f6e795d03b0273b0a7d81611a6a3364ba649c2c85c99acae'] + +builddependencies = [ + ('gawk', '5.3.0'), + ('pkgconf', '1.9.5'), + ('expat', '2.5.0'), + ('CGAL', '5.6'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Boost.Python', '1.83.0'), + ('sparsehash', '2.0.4'), + ('matplotlib', '3.7.2'), + ('PyCairo', '1.25.0'), + ('cairomm', '1.16.2'), + ('PyGObject', '3.46.0'), + ('GTK3', '3.24.37'), +] + +configopts = '--enable-openmp --with-cgal=$EBROOTCGAL --with-boost=$EBROOTBOOST ' +configopts += '--with-boost-python=boost_python311 ' +configopts += '--with-python-module-path=%(installdir)s/lib/python%(pyshortver)s/site-packages ' + + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/graph_tool/all.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/graph_tool/include', 'share'], +} + +sanity_check_commands = [ + "python -c 'from graph_tool.all import Graph, BlockState'", + "python -c 'import graph_tool.inference'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index 0fa2bcb2cf6..bb7237e35f1 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -44,6 +44,7 @@ dependencies = [ ('typing-extensions', '4.9.0'), # sc_toolbox ('adjustText', '1.1.1'), # sc_toolbox, created ('python-parasail', '1.3.4'), # scirpy + ('graph-tool', '2.59'), # schist ] exts_list = [ @@ -201,11 +202,11 @@ exts_list = [ ('scirpy', '0.17.0', { 'checksums': ['f61653a4f7387562ec89b00fbfd7cab762c0bf3320f21ccfc47df80a13cc5d41'], }), - # ('schist', '0.8.3', { - # 'source_tmpl': 'v%(version)s.tar.gz', - # 'source_urls': ['https://github.com/dawe/schist/archive/'], - # 'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'], - # }), + ('schist', '0.8.3', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/dawe/schist/archive/'], + 'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'], + }), ] use_pip = True From 8a00362056ceb096c785c8de4706befe6b11bb34 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 3 Jun 2024 12:12:46 +0200 Subject: [PATCH 13/22] add gawk for schist --- .../g/gawk/gawk-5.3.0-GCC-12.3.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..8c63821d169 --- /dev/null +++ b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gawk' +version = '5.3.0' + +homepage = 'https://www.gnu.org/software/gawk' +description = """The awk utility interprets a special-purpose programming language that makes it possible to handle +simple data-reformatting jobs with just a few lines of code.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['378f8864ec21cfceaa048f7e1869ac9b4597b449087caf1eb55e440d30273336'] + +sanity_check_paths = { + 'files': ['bin/gawk'], + 'dirs': [], +} + +sanity_check_commands = ["gawk --help"] + +moduleclass = 'tools' From b913d9c13bc5341d7d6e26231dce569fd0043cb8 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 5 Jun 2024 14:35:50 +0200 Subject: [PATCH 14/22] add scvi-tools, scArches, scib-metrics, pertpy --- .../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 +++++++ ...e-cell-python-bundle-2024.02-foss-2023a.eb | 39 +++++- .../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 +++++++++++ 9 files changed, 492 insertions(+), 3 deletions(-) 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..d1e5fc1aabd --- /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/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index bb7237e35f1..8a4cee8cfcf 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -22,9 +22,6 @@ dependencies = [ ('Seaborn', '0.13.2'), ('PyTorch', '2.1.2'), ('scanpy', '1.9.8'), - # scvi-tools TODO - # scArches TODO - # scib-metrics TODO ('scib', '1.1.4'), ('scVelo', '0.3.1'), # imports loompy ('CellTypist', '1.6.2'), @@ -37,6 +34,9 @@ dependencies = [ ('CellRank', '2.0.2'), ('Squidpy', '1.4.1'), ('Cassiopeia', '2.0.0'), + ('scvi-tools', '1.1.2'), # imports jax + ('scArches', '0.6.1'), + ('scib-metrics', '0.5.1'), # deps for exts: ('umap-learn', '0.5.5'), # bbknn ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox @@ -45,6 +45,8 @@ dependencies = [ ('adjustText', '1.1.1'), # sc_toolbox, created ('python-parasail', '1.3.4'), # scirpy ('graph-tool', '2.59'), # schist + ('Pyomo', '6.7.3'), # pertpy + ('mpmath', '1.3.0'), # blitzgsea ] exts_list = [ @@ -207,6 +209,37 @@ exts_list = [ 'source_urls': ['https://github.com/dawe/schist/archive/'], 'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'], }), + ('typeguard', '2.13.3', { + 'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'], + }), + ('jaxtyping', '0.2.29', { + 'checksums': ['e1cd916ed0196e40402b0638449e7d051571562b2cd68d8b94961a383faeb409'], + }), + ('equinox', '0.11.4', { + 'checksums': ['0033d9731083f402a855b12a0777a80aa8507651f7aa86d9f0f9503bcddfd320'], + }), + ('lineax', '0.0.4', { + 'checksums': ['e68f1eba2f352122fdce9adc0556684f31eb8364b1a00acee484dd6e44a34e5e'], + }), + ('jaxopt', '0.8.3', { + 'checksums': ['4b06dfa6f915a4f3291699606245af6069371a48dc5c92d4c507840d62990646'], + }), + ('ott_jax', '0.4.6', { + 'modulename': 'ott', + 'checksums': ['bc91f8d512cdb344439f5584712d76cd0650b6716b6686d53b828cc67abdbcba'], + }), + ('sparsecca', '0.3.1', { + 'checksums': ['be1526baebac5ce6efbc7190fd62a1cec13288c493f5d427024f66ca6afaec13'], + }), + ('PubChemPy', '1.0.4', { + 'checksums': ['24e9dc2fc90ab153b2764bf805e510b1410700884faf0510a9e7cf0d61d8ed0e'], + }), + ('blitzgsea', '1.3.42', { + 'checksums': ['dcc997b5d29d190d8632474f3bb57b5ead7fb1370b478c7f824b42782325a1ca'], + }), + ('pertpy', '0.7.0', { + 'checksums': ['273723b5b70f3cb714bb36d3234462014b72e133111eeaf08aa47153c9df14aa'], + }), ] use_pip = True 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 6a51ca70bb1bf16596a34c8847e2805abc0da29c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 5 Jun 2024 14:44:19 +0200 Subject: [PATCH 15/22] add pyomo, the dep of pertpy --- .../p/Pyomo/Pyomo-6.7.3-foss-2023a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb new file mode 100644 index 00000000000..64ee6de4f2b --- /dev/null +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'Pyomo' +version = '6.7.3' + +homepage = 'https://www.pyomo.org/' +description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization + capabilities for formulating and analyzing optimization models. """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('mpi4py', '3.1.4'), + ('PLY', '3.11'), +] + +exts_list = [ + ('PyUtilib', '6.0.0', { + 'preinstallopts': """sed -i "s/'nose',//g" setup.py && """, + 'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'], + }), + (name, version, { + 'checksums': ['b7f0441c405af4f42f38527ae38826a5c0a4984dd7bea1fe07172789d8594770'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['pyomo -h'] + +moduleclass = 'math' From b427446d0374a26411df3086cd309f649bf4e87c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 6 Jun 2024 11:38:14 +0200 Subject: [PATCH 16/22] fix jax --- easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 index d1e5fc1aabd..9cbbc9b1579 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb @@ -1,7 +1,7 @@ # 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 +# Update v0.4.25 based on: https://github.com/easybuilders/easybuild-easyconfigs/pull/20119 easyblock = 'PythonBundle' From be9f9a0d15a9d24dc43b513871469fa095d2d70c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 10 Jun 2024 13:31:19 +0200 Subject: [PATCH 17/22] move pycodestyle and adjustText to separate PR --- .../adjustText/adjustText-1.1.1-foss-2023a.eb | 27 ------------------- .../pycodestyle-2.11.1-foss-2023a.eb | 24 ----------------- 2 files changed, 51 deletions(-) delete mode 100644 easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb delete mode 100644 easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb b/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb deleted file mode 100644 index f109d19d3aa..00000000000 --- a/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'adjustText' -version = '1.1.1' - -homepage = 'https://github.com/Phlya/adjustText' -description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps." - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('matplotlib', '3.7.2'), - ('SciPy-bundle', '2023.07'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - (name, version, { - 'modulename': 'adjustText', - 'checksums': ['e2c0975ef2c642478e60f4c03c5e9afbdeda7764336907ef69a9205bfa2d9896'], - }), -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb deleted file mode 100644 index c704acc3b36..00000000000 --- a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pycodestyle' -version = '2.11.1' - -homepage = "https://pycodestyle.readthedocs.io" -description = """pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), -] - -exts_list = [ - (name, version, { - 'checksums': ['41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f'], - }), -] - -use_pip = True -sanity_pip_check = True - -moduleclass = 'lib' From 835da852a205e1fe99052ff3589a819781e5621f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 13 Jun 2024 11:59:06 +0200 Subject: [PATCH 18/22] try update --- easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 index 9cbbc9b1579..64a723ffe37 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb @@ -1,6 +1,6 @@ # 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) +# 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' From 40383aa8aedfc26894b6a5536c73ba174de40ff7 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 13 Jun 2024 12:04:12 +0200 Subject: [PATCH 19/22] move jax dependent ecs to separate PR --- .../c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb | 2 +- .../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 ----------- 9 files changed, 1 insertion(+), 457 deletions(-) delete mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb delete mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch delete mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch delete mode 100644 easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb delete mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb delete mode 100644 easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb delete mode 100644 easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb delete mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb index 2ca14e07c7c..286c56e1bbb 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb @@ -1,5 +1,5 @@ # Updated to MesonNinja as the autogen.sh complained. -# Author: J. Sassmannshausen (Imperial College London/UK) +# Author: J. Sassmannshausen (Imperial College London) easyblock = 'MesonNinja' 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 deleted file mode 100644 index 64a723ffe37..00000000000 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb +++ /dev/null @@ -1,112 +0,0 @@ -# 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 deleted file mode 100644 index c404ee6917f..00000000000 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch +++ /dev/null @@ -1,38 +0,0 @@ -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 deleted file mode 100644 index ad919608437..00000000000 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch +++ /dev/null @@ -1,18 +0,0 @@ -# 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 deleted file mode 100644 index 79034a7433d..00000000000 --- a/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb +++ /dev/null @@ -1,37 +0,0 @@ -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 deleted file mode 100644 index be05f009e9e..00000000000 --- a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb +++ /dev/null @@ -1,42 +0,0 @@ -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 deleted file mode 100644 index c703d0beede..00000000000 --- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb +++ /dev/null @@ -1,87 +0,0 @@ -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 deleted file mode 100644 index 68ef32b71ad..00000000000 --- a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb +++ /dev/null @@ -1,54 +0,0 @@ -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 deleted file mode 100644 index f79f5895f45..00000000000 --- a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb +++ /dev/null @@ -1,68 +0,0 @@ -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 8082288b0043fb1273db4741fea3155ca0367ca8 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 14 Jun 2024 11:44:50 +0200 Subject: [PATCH 20/22] Update graph-tool-2.59-foss-2023a.eb boost-python version --- .../easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb index 2ca6027a864..ac416bcee76 100644 --- a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb +++ b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), - ('Boost.Python', '1.83.0'), + ('Boost.Python', '1.82.0'), ('sparsehash', '2.0.4'), ('matplotlib', '3.7.2'), ('PyCairo', '1.25.0'), From 347c72d543533a9cba970b3146f37382bcc826f7 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 26 Jun 2024 14:22:53 +0200 Subject: [PATCH 21/22] update graph-tools deps + fix preinstallopts of tascCODA --- .../easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb | 1 + .../Single-cell-python-bundle-2024.02-foss-2023a.eb | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb index ac416bcee76..307e764d139 100644 --- a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb +++ b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb @@ -28,6 +28,7 @@ builddependencies = [ ('pkgconf', '1.9.5'), ('expat', '2.5.0'), ('CGAL', '5.6'), + ('GMP', '6.2.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index 8a4cee8cfcf..e43e7a78e0c 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -130,7 +130,7 @@ exts_list = [ }), ('tascCODA', '0.1.3', { # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes - 'preinstallopts': "sed -i '28d' setup.py && ", + 'preinstallopts': "sed -i '/tensorflow-probability>=0.16/d' setup.py && ", 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], }), ('harmonypy', '0.0.9', { From 16954b2ecbc35f8432bf19ca77821608f0cc89c3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 26 Jun 2024 16:02:12 +0200 Subject: [PATCH 22/22] update adjustText version --- .../Single-cell-python-bundle-2024.02-foss-2023a.eb | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb index e43e7a78e0c..c0f6cb45631 100644 --- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -23,26 +23,24 @@ dependencies = [ ('PyTorch', '2.1.2'), ('scanpy', '1.9.8'), ('scib', '1.1.4'), - ('scVelo', '0.3.1'), # imports loompy + ('scVelo', '0.3.1'), ('CellTypist', '1.6.2'), - # loompy in scVelo ('epiScanpy', '0.4.0'), - ('scCODA', '0.1.9'), # imports rpy2 - # rpy2 in scCODA + ('scCODA', '0.1.9'), ('infercnvpy', '0.4.3'), ('pySCENIC', '0.12.1-20240311'), ('CellRank', '2.0.2'), ('Squidpy', '1.4.1'), ('Cassiopeia', '2.0.0'), - ('scvi-tools', '1.1.2'), # imports jax + ('scvi-tools', '1.1.2'), ('scArches', '0.6.1'), ('scib-metrics', '0.5.1'), - # deps for exts: + # deps of exts: ('umap-learn', '0.5.5'), # bbknn ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox ('PyYAML', '6.0'), # sc_toolbox ('typing-extensions', '4.9.0'), # sc_toolbox - ('adjustText', '1.1.1'), # sc_toolbox, created + ('adjustText', '0.7.3'), # sc_toolbox ('python-parasail', '1.3.4'), # scirpy ('graph-tool', '2.59'), # schist ('Pyomo', '6.7.3'), # pertpy