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2024-05-05gnu: python-pandas-stubs: Update tests.Ricardo Wurmus
This is a follow-up to adding ORC support to pyarrow. * gnu/packages/python-science.scm (python-pandas-stubs)[arguments]: Disable more tests that are due to enabling ORC support to pyarrow. Change-Id: I8c3ca6afff8128792738251c85a1dba3dc3b0569
2024-05-05gnu: Add python-scikit-build-core.Ricardo Wurmus
* gnu/packages/python-science.scm (python-scikit-build-core): New variable. Change-Id: If234d19d720afe88f6893bdd36fcc4955a45c5d3
2024-05-05gnu: python-distributed: Update to 2024.4.2.Ricardo Wurmus
* gnu/packages/python-science.scm (python-distributed): Update to 2024.4.2. [propagated-inputs]: Add python-dask-expr. [arguments]: Adjust tests. Change-Id: I9d3b45d14ae052f3a5a5dec3587bc01d13e4b71f
2024-05-05gnu: Add python-dask-expr.Ricardo Wurmus
* gnu/packages/python-science.scm (python-dask-expr): New variable. Change-Id: I691593ab713fe865c771aa68b5521c4c10cc58f6
2024-05-05gnu: python-pandas-stub: Update to 2.1.1.230928.Ricardo Wurmus
This is a follow-up to commit ff2d0ecfca87450c82df8d74666261b1c19cbe66. * gnu/packages/python-science.scm (python-pandas-stub): Update to 2.1.1.230928. Change-Id: I2e8ce18bd25399b467a6ff2a6fb846f8bb969e4c
2024-05-05gnu: python-pandas-2: Fix version.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Write version string to "_version.py", not "_version_meson.py" to avoid reporting the version as "0+unknown". Change-Id: I1a18814e37c023102714326bc8bd505705234205
2024-05-05gnu: python-pyjanitor: Update to 0.27.0.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pyjanitor): Update to 0.27.0. [arguments]: Disable a few more tests; add phase 'pandas-compat. Change-Id: Ia8891971a687342166f30ded11f9e341a208d95e
2024-05-05gnu: python-xarray: Disable tests that are known to fail.Ricardo Wurmus
* gnu/packages/python-science.scm (python-xarray)[arguments]: Disable two tests. Change-Id: I70954173e0aca5a377cf19476e9390a97febadc7
2024-05-05gnu: python-pandas: Default to version 2.x.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pandas): Define as alias for python-pandas-2; rename existing definition to... (python-pandas-1): ...this new variable. Change-Id: If359e3b2d42c683d7d0152b1757bbc5a979c999b
2024-05-05gnu: python-scikit-opt: Add missing input.Ricardo Wurmus
* gnu/packages/python-science.scm (python-scikit-opt)[propagated-inputs]: Add python-pytorch. Change-Id: I037cc43bedeaebb05bf038c0bca72919f8c27c40
2024-05-05gnu: Add python-cvxpy.Marco Baggio
* gnu/packages/python-science.scm (python-cvxpy): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I440ab3768cbc4e78364dc31cf9484effd9670f49
2024-05-05gnu: Add python-ecos.Marco Baggio
* gnu/packages/python-science.scm (python-ecos): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I83d9b746f5f3563f417efc5d18911f2eb04f201c
2024-05-05gnu: Add python-osqp.Marco Baggio
* gnu/packages/python-science.scm (python-osqp): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: Id6f1665505469fd6543046636b82d0730b319df3
2024-05-05gnu: Add python-qdldl.Marco Baggio
* gnu/packages/python-science.scm (python-qdldl): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I523ecb2292c9b514b548e2130d0d43bb77317b00
2024-05-05gnu: Add python-scs.Marco Baggio
* gnu/packages/python-science.scm (python-scs): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I6c5ecdac4b558aab4b8ee396dff1dfc9cdec07f0
2024-05-05gnu: Add python-fastcluster.Marco Baggio
* gnu/packages/python-science.scm (python-fastcluster): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: Ifc5229a4d00f581eb358a1f41fc3479fd1c33c2e
2024-05-05gnu: Add python-clarabel.Ricardo Wurmus
* gnu/packages/python-science.scm (python-clarabel): New variable. Change-Id: I28459162460ca9bf9e9557122f611c677afadc27
2024-05-05gnu: Add python-xarray-schema.Ricardo Wurmus
* gnu/packages/python-science.scm (python-xarray-schema): New variable. Change-Id: I4ca650f2c2872698fc22392add169f44b9e2e035
2024-05-05gnu: python-xarray-datatree: Add missing input.Ricardo Wurmus
* gnu/packages/python-science.scm (python-xarray-datatree)[native-inputs]: Add python-setuptools-scm. Change-Id: I86a7280ba687385edb15f30dae1a20e3811a0beb
2024-04-30gnu: Add python-supersmoother.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-supersmoother): New variable. Change-Id: I8fb43d746757014e3b773c07458b777b893adb4a
2024-04-22gnu: python-xarray-dataclasses: Add missing test input.Ricardo Wurmus
* gnu/packages/python-science.scm (python-xarray-dataclasses)[native-inputs]: Add python-pytest. Change-Id: I137d49380d772f11f75837aa9a915ced85cfc1a2
2024-04-22gnu: python-pandas-2: Skip expensive tests.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Set PANDAS_CI variable. Change-Id: I7c400ff260b3c833be1a55a30de021a81a5cbacb
2024-04-22gnu: Add python-pandas-2.Nicolas Graves
* gnu/packages/python-science.scm (python-pandas-2): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I7f0510f9021d4eac3c981e5e58f73dc3ec7efd2f
2024-04-22gnu: Add python-xarray-datatree.Ricardo Wurmus
* gnu/packages/python-science.scm (python-xarray-datatree): New variable. Change-Id: I403f241b6daae8b5c835f4517a1dceca0393f8e6
2024-04-22gnu: Add python-xarray-dataclasses.Ricardo Wurmus
* gnu/packages/python-science.scm (python-xarray-dataclasses): New variable. Change-Id: I55f258e36ea70a2efb142bd652a81d70771a457c
2024-03-31gnu: Add python-pods.Maxim Cournoyer
* gnu/packages/python-science.scm (python-pods): New variable. Change-Id: I9044baaa750ee9cb7411e41dcee1df17b57741db
2024-03-29gnu: python-distributed: Disable parallel tests.Sharlatan Hellseher
As seen in <https://ci.guix.gnu.org/build/3708961/log/raw>, parallel tests introduced package build regression. * gnu/packages/python-science.scm (python-distributed) [arguments] <#:test-flags>: Disable parallel tests. [native-inputs]: Remove python-pytest-xdist. Change-Id: I3a04098604fa03ab91ceb228dd70c34c3d84db78
2024-03-29gnu: python-distributed: Speed up tests.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-distributed) [arguments] <#:test-flags>: Add option to run tests in parallel. Disable 3 more flaky tests. [native-inputs]: Add python-pytest-xdist. Sort alphabetically. Change-Id: I588c1a1dc82e3208cc1eeeefbdc58fb080775ac0
2024-03-28gnu: python-upsetplot: Update to 0.9.0.nafkhamdc
* gnu/packages/python-science.scm (python-upsetplot): Update to 0.9.0. [source]: Remove obsolete snippet. [arguments]: Remove custom check phase. [build-system]: Use pyproject-build-system. Change-Id: I68bcd6840577a12594e491e9fd5e114f9261f6c7 Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2024-02-10gnu: Add python-scikit-opt.TimotheeMathieu
* gnu/packages/python-science.scm (python-scikit-opt): New variable. Change-Id: I47d6b35d9658a37a242b4db61d293fa7efd33802 Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-02-06gnu: python-traittypes: Simplify package.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-traittypes) [build-system]: Swap to pyproject-build-system. [arguments]: Move excluded tests to <#:test-flags>. Use standard 'check phase. Change-Id: I4cab0c94036a7e5f0851edf2833dfac2f675d2a0
2024-02-06gnu: python-pynrrd: Update to 1.0.0.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pynrrd): Update to 1.0.0. [arguments]: Keep 'ensure-no-mtimes-pre-1980 phase as it's building with it successfully. [propagated-inputs]: Add python-nptyping and python-typing-extensions. Change-Id: Ic4dcd0825e71d3eb4acd39694bee9e22e8485f9f
2024-02-06gnu: python-pynrrd: Improve description.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pynrrd) [description]: Add definition of NRRD. Change-Id: I0335df0eb4be600d81799da64374ddfb49b06720
2024-02-06gnu: Add python-pynrrd.Antero Mejr
* gnu/packages/python-science.scm (python-pynrrd): New variable. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-02-01gnu: Add python-pandarallel.Wiktor Żelazny
* gnu/packages/python-science.scm (python-pandarallel): New variable. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-30gnu: python-scipy: Enable building on more architectures.Efraim Flashner
* gnu/packages/python-science.scm (python-scipy)[propagated-inputs]: Only include python-jupytext on systems where it is supported. Change-Id: Ic085094e4e3977e4c0698e8c03de09ee8e70f144
2024-01-29gnu: Add python-pyjanitor.Troy Figiel
* gnu/packages/python-science.scm (python-pyjanitor): New variable. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-29gnu: Add python-unyt.Troy Figiel
* gnu/packages/python-science.scm (python-unyt): New variable. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-28gnu: python-pyamg: Regenerate bundled files.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pyamg) [source]: Delete auto-generated files. [arguments] <#:phases>: Add 'amg-core-bind-them phase to re-generate *_bind.cpp files deleted in snippet. [native-inputs]: Add python-cppheaderparser and python-pyyaml. [description]: Improve style, omit implementation details. Change-Id: I6f68914cd912e6f4592e51c21b129847e73be847
2024-01-28gnu: python-trimesh: Enable tests.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-trimesh): Enable tests and apply new package style. [source]: Use git checkout which has working test suit. [arguments] <#:test-flags>: Disable tests requiring optional Python modules. [propagated-inputs]: Add python-chardet, python-colorlog python-httpx python-jsonschema python-lxml python-networkx python-pillow python-requests python-rtree python-scipy python-setuptools python-shapely python-sympy and python-xxhash. Change-Id: I1aa363053c2d736bc44b8f9071c637256cc2d952
2024-01-28gnu: python-trimesh: Update to 4.0.10.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-trimesh): Update to 4.0.10. [build-system]: Swap to pyproject-build-system. Change-Id: I757b4c27db9969d42021434883a057debbbc83fd
2024-01-24gnu: python-xarray-einstats: Update to 0.7.0.Vinicius Monego
* gnu/packages/python-science.scm (python-xarray-einstats): Update to 0.7.0. Change-Id: Iddd1fca8c37f05a928d20b90f9f95814f31435b2
2024-01-24gnu: python-pyts: Update to 0.13.0.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pyts): Update to 0.13.0. [build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase; enable all tests. [propagated-inputs]: Remove python-matplotlib. Change-Id: Iafcc047d8bb14e1eef514fd92aa53f8fda38eab0
2024-01-23gnu: python-pydicom: Update to 2.4.4.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pydicom): Update to 2.4.4. Change-Id: I996115fb3bdf0bd61d2b2dcdb2500b31ce104597
2024-01-23gnu: python-pydicom: Simplify package style.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pydicom)[build-system]: Swap to pyproject-build-system. [description]: Simplify wording, indent. Change-Id: I7ef413ea2da6cbb83eb33424c559f7ac5ed549cb
2024-01-23gnu: python-pynetdicom: Simplify package style.Sharlatan Hellseher
* gnu/package/python-science.scm (python-pynetdicom)[build-system]: Swap to pyproject-build-system. [description]: Simplify wording, indent. Change-Id: If4e80d06edb0080685d0695f30abc2f9db669f45
2024-01-23gnu: Add python-pynetdicom.Antero Mejr
* gnu/packages/python-science.scm (python-pynetdicom): New variable. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-23gnu: python-scipy: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/python-science.scm (python-scipy): Update to 1.12.0. [propagated-inputs]: Add python-jupytext, python-mpmath, python-mypy, python-numpydoc, python-pydata-sphinx-theme, python-pydevtool, python-rich-click, python-sphinx, python-threadpoolctl, and python-typing-extensions; remove python-pyparsing. [native-inputs]: Add python-hypothesis, python-pycodestyle, python-pytest-cov, and python-pytest-xdist; remove python-threadpoolctl. Change-Id: I81a4831e3d94c58416f7d35ec47de90370b88210
2024-01-22gnu: python-tdda: Remove relax-requirements phase.Troy Figiel
* gnu/packages/python-science.scm (python-tdda)[arguments]<#:phases>: Remove relax-requirements phase. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-21gnu: python-scikit-fem: Update to 9.0.1.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-fem): Update to 9.0.1. [arguments]<#:test-flags>: Drop it to activate all tests. [native-inputs]: Add python-autograd, python-pyamg, and python-shapely. Change-Id: Ic4706196026bd5756b4db8230b15efacdca7d463
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