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2025-12-30gnu: Remove python-climin.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-climin): Delete variable. Fixes: guix/guix#4556 Change-Id: I8e26118c854a6ece21a5d8946a30812b626dc52e
2025-12-30gnu: Add python-osfclient.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-osfclient): New variable. Change-Id: I236ee7e8f56758fbd75b8b83f67161f37d812e6e
2025-12-27gnu: python-pylems: Update to v0.6.9.Aaron Covrig
* gnu/packages/python-science.scm (python-pylems): Update to v0.6.9. [source]: Switch to git-fetch. [build-system]: Switch to pyproject-build-system. [arguments]: Execute project tests. [native-inputs]: Add python-pytest and python-setuptools. [propagated-inputs]: Add python-matplotlib. [description]: Update with acronym. Closes guix/guix#5024 Change-Id: Id3e454e5ae6f4ca49fad29cd4e0238aeb75e7653 Signed-off-by: Cayetano Santos <csantosb@inventati.org>
2025-12-27gnu: python-pytensor: Simplify package.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pytensor): [arguments] <test-flags>: Let pytest discover tests. [phases]{pre-check}: Replace re-build extensions by deleting local source. [propagated-inputs]: Remove python-typing-extensions. [native-inputs]: Remove python-wheel. Change-Id: I42f97a93e1704856d29691f99414d4f2497723b9
2025-12-27python-pytensor: Skip more tests.Ghislain Vaillant
* gnu/packages/python-science.scm (python-pytensor) [arguments]<#:test-flags>: Ignore more failing tests. Change-Id: I542ba0025bf43ebef08b2ab67c19e618b3b32621 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-12-27gnu: python-tspex: Update to 0.6.3-0.d393ff4.Hugo Buddelmeijer
* gnu/packages/python-science.scm (python-tspex): Update to d393ff497b7c14d673e792bd6c84ddd734be1239 commit. [source]: Switch to git-fetch for tests. [build-system]: Switch to pyproject-build-system. [arguments]<#:phases>: Add 'remove-coverage and 'fix-seaborn phases. [propagated-inputs]: Add python-seaborn. [native-inputs]: Add python-pytest and python-setuptools. Change-Id: I367198165d5d78e1f1e04708272136711e5b22b5 Reviewed-by: Nicolas Graves <ngraves@ngraves.fr> Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-12-27gnu: python-pynrrd: Update to 1.1.3.Hugo Buddelmeijer
* gnu/packages/python-science.scm (python-pynrrd): Update to 1.1.3. [build-system]: Switch to pyproject-build-system. [propagated-inputs]: Remove python-nptyping and python-typing-extensions. [native-inputs]: Add python-pytest and python-setuptools. Change-Id: Id98a3424f35fc791324010deae357f89e2d93362 Reviewed-by: Nicolas Graves <ngraves@ngraves.fr> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-12-27gnu: python-simplespectral: Switch to pyproject-build-system.Hugo Buddelmeijer
* gnu/packages/python-science.scm (python-simplespectral): Switch to pyproject-build-system. [build-system]: Switch to pyproject-build-system. [arguments]<#:tests>: Set to #f, as there are no tests. [native-inputs]: Add python-setuptools. Change-Id: Ifabd9561978fec3a7380d8cdb7641732baad01d8 Reviewed-by: Nicolas Graves <ngraves@ngraves.fr> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-12-18Update Nguyễn Gia Phong's new email address.Nguyễn Gia Phong
* .mailmap: New entry. Change-Id: I839ba6c7be463c5b59c7e68247ae5e46d2ceeeaf Reviewed-by: Maxim Cournoyer <maxim@guixotic.coop> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-12-17gnu: python-numpy-groupies: Update to 0.11.3.Hugo Buddelmeijer
* gnu/packages/python-science.scm (python-numpy-groupies): Update to 0.11.3. [build-system]: Switch to pyproject-build-system. [propagated-inputs]: Add python-numpy. [native-inputs]: Remove python-pytest-runner and python-numpy; add python-pandas, python-setuptools, and python-setuptools-scm. Change-Id: Iffe9007c357ac5f299a07cfb1d3fcd20da862c81 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-12-17gnu: python-msgpack-numpy: Switch to pyproject-build-system.Hugo Buddelmeijer
* gnu/packages/python-science.scm (python-msgpack-numpy): Switch to pyproject-build-system. [build-system]: Switch to pyproject-build-system. [arguments]<#:test-backend>: Select unittest. [native-inputs]: Add python-setuptools. Change-Id: I47958f2fe83411cefd91b664197a5b08e33205b4 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-12-03gnu: python-traittypes: Replace python-nose by python-pynose.Nicolas Graves
* gnu/packages/python-science.scm (python-traittypes)[native-inputs]: Replace python-nose by python-pynose. Remove python-wheel. Change-Id: Ia90b2d1311026af1bfee295cc5db3c0cac392932 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-12-03Update Giacomo's email address.Giacomo Leidi
The change was automated via: git grep -l goodoldpaul@autistici.org | xargs sed -i 's/goodoldpaul@autistici.org/therewasa@fishinthecalculator.me/g' * .mailmap: New entry. Change-Id: I1629388334695d221647afe6a14faf61af5fe0d6 Signed-off-by: Maxim Cournoyer <maxim@guixotic.coop>
2025-11-30gnu: python-unyt: Update to 3.0.4.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-unyt): Update to 3.0.4. [arguments]: Drop all. [propagated-inputs]: Remove python-h5py and python-matplotlib; add python-packaging. [native-inputs]: Remove python-pint and python-wheel. Change-Id: I3759ce1befbb804d1c2508df042c19082f9a7833
2025-11-30gnu: Add python-nestcheck.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-nestcheck): New variable. Change-Id: Ieb2d6942e0f8f802853f821bc13c3b86aee74a6f
2025-11-30gnu: Add python-fgivenx.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-fgivenx): New variable. Change-Id: I2f3d49e5340b803616618628439df6889c86fc61
2025-11-20gnu: python-pynetdicom: Reduce closure size.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pynetdicom): [propagated-inputs]: Remove python-mypy. [native-inputs]: Remove python-codespell, python-coverage, python-pytest-cov, pythonb-pytest-xdist, python-sphinx, and python-sphinx-rtd-theme. Change-Id: Ie0fc078cec3473e061ebc4dc87de59ca309a6194
2025-11-20gnu: python-clarabel: Extend with (pyproject-guile-json).Nicolas Graves
* gnu/packages/python-xyz.scm (python-clarabel)[arguments] <#:phases>: Extend with (pyproject-guile-json). Change-Id: I258bc867cc4269779ccf886601a00323b8f80083 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-11-11gnu: python-duckdb: Move to duckdb.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-duckdb): Move from here ... * gnu/packages/duckdb.scm: ... to here. * gnu/packages/python-science.scm: Add (gnu packages duckdb). Change-Id: Ic8551cdd64f718e62a12576fbc1a38bf861d1644
2025-11-04gnu: packages/python-science: Remove package-management module.Sharlatan Hellseher
* gnu/packages/python-science.scm: Remove unused (gnu packages package-management) module. Change-Id: I6760dab3d684077f0d121c6d2591e4430205035d
2025-10-30gnu: Add python-iminuit.Vinicius Monego
* gnu/packages/python-science.scm (python-iminuit): New variable. Change-Id: I65da990dda737fd744e22d83007c736a92a8ec0a Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-10-30gnu: Add python-numba-stats.Vinicius Monego
* gnu/packages/python-science.scm (python-numba-stats): New variable. Change-Id: Iff8181ec1c9341081c09afcaf4fbdc2d57b1ccec Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-10-30gnu: Add python-jacobi.Vinicius Monego
* gnu/packages/python-science.scm (python-jacobi): New variable. Change-Id: I1db0a588789c0cb6c79d298f97b71ee7958eab39 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-10-28gnu: pyzo: Move to python-science.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (pyzo): Move from here ... * gnu/packages/python-science.scm: ... to here. Change-Id: I8b50396d0d863e1bda5d7686ae2826a3bfe544dd
2025-10-24gnu: python-cython-3: Mark as deprecated.Sharlatan Hellseher
This is a followup to 941b6ff1c11be3ba73e4e67bc661bd0eed3e9d58 commit. Replace all python-cython-3 occurrences with python-cython. * gnu/packages/python-xyz.scm (python-cython-3): Deprecate variable. * gnu/packages/algebra.scm (python-fpylll, python-flint)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/astronomy.scm (python-astropy, python-astroscrappy, python-halotools, python-healpy, python-libstempo, python-lofar-h5plot, python-losoto, python-photutils, python-pyxsim, python-regions, python-reproject, python-sncosmo, python-sndata, python-stcal, python-yt)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/bioinformatics.scm (macs-3, python-pyrodigal): [native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/build-tools.scm (meson-python)[propagated-inputs]: Remove python-cython-3; add python-cython. [native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/databases.scm: (python-adbc-driver-manager, python-psycopg, python-pyarrow)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/finance.scm (python-ta-lib)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/game-development.scm (python-pygame-ce)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/geo.scm (python-pyogrio, python-cf-units)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/machine-learning.scm: (python-scikit-learn, python-opentsne)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/maths.scm: (python-cylp, python-petsc4py, python-primecountpy, python-slepc4py)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/python-check.scm (python-line-profiler)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/python-compression.scm (python-blosc2)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/python-graphics.scm (python-vispy)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/python-science.scm: (python-pykdtree, python-qutip, python-scikit-misc, python-scikit-surprise, python-pandas-2, python-vaex-core)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/python-web.scm: (python-aiohttp, python-falcon, python-yarl, python-uvloop)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/python-xyz.scm: (python-logbook, python-netcdf4, python-pyyaml, python-propcache, python-pywavelets, python-symengine, python-cysignals, python-pyemd, python-rbfly)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/sagemath.scm: (python-cypari2, python-pplpy, sage) [native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/sphinx.scm (python-sphinx)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/statistics.scm: (python-statsmodels, python-pyreadstat): [native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/tor.scm (onionshare-cli)[native-inputs]: Remove python-cython-3; add python-cython. * gnu/packages/xorg.scm (xpra)[native-inputs]: Remove python-cython-3; add python-cython. Change-Id: I38038d2ab18e6a7b549070083d6e4c5beb8b0293
2025-10-23gnu: python-pyvistaqt: Fix tests.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pyvistaqt)[native-inputs]: Add python-pyqt-6. Change-Id: I9c1d29224109a97db47f4ce27d7ba9a98f650625
2025-10-23gnu: python-pyqtgraph: Reduce closure size, don't propagate Qt5/Qt6.Sharlatan Hellseher
Don't propagate Qt5/Qt6 and let the user of the package to select which one is required. From project's documentation: When pyqtgraph is first imported, if the environment variable PYQTGRAPH_QT_LIB is not set, it automatically determines which library to use by making the following checks: - If PyQt6 is already imported, use that - Else, if PySide6 is already imported, use that - Else, if PyQt5 is already imported, use that - Else, if PySide2 is already imported, use that - Else, attempt to import PyQt6, PySide6, PyQt5, PySide2, in that order. See: <https://pyqtgraph.readthedocs.io/en/pyqtgraph-0.13.7/getting_started/how_to_use.html#pyqt-and-pyside>. * gnu/packages/python-science.scm (python-pyqtgraph)[arguments] <test-flags>: Run unit tests only, skip one more failing test, run in a single thread. [inputs]: Remove qtbase-5. [propagated-inputs]: Remove python-pyqt. [native-inputs]: Remove python-pytest-cov, python-pytest-xdist, and python-wheel; add python-pyqt-6 and python-pytest-qt. Change-Id: Icb272c5215215b96faad8420e1781a5e61ab838d
2025-10-21gnu: Add python-dvc-data.Janneke Nieuwenhuizen
* gnu/packages/python-science.scm (python-dvc-data): New variable. Change-Id: I4479129a1842d2133acec6f7aeb1d4a95e9e6162
2025-10-21gnu: Add python-dvc-objects.Janneke Nieuwenhuizen
* gnu/packages/python-science.scm (python-dvc-objects): New variable. Change-Id: Ibd4247ab12b161392de7d351195646f7215610bd
2025-10-21gnu: Add python-snakemake-executor-plugin-slurm.Janneke Nieuwenhuizen
* gnu/packages/python-science.scm (python-snakemake-executor-plugin-slurm): New variable. Change-Id: I7ca462dc224dc6947130fa9842f26c25cd7349a4
2025-10-21gnu: Add python-snakemake-executor-plugin-slurm-jobstep.Janneke Nieuwenhuizen
* gnu/packages/python-science.scm (python-snakemake-executor-plugin-slurm-jobstep): New variable. Change-Id: I477b8a30ae6642fa0e8d6e49a828ab0d3aa589b4
2025-10-21gnu: python-scikit-misc: Remove development inputs.Hartmut Goebel
* gnu/packages/python-science.scm (python-scikit-misc): [arguments][phases][fix-pytest-config]: New phase. [propagated-inputs]: Remove python-twine. [native-inputs]: Remove python-pytest-cov. Change-Id: I4f52ff2819775d65fd205f6222c8fba854161580
2025-10-19gnu: Add python-efficient-apriori.Hartmut Goebel
* gnu/packages/python-science.scm (python-efficient-apriori): New variable. Change-Id: I30ee0c1f3f825a8c4573abfe598a63ca5594b5a0
2025-10-18gnu: snakemake-6: Fix tests.Sharlatan Hellseher
* gnu/packages/python-science.scm (snakemake-6)[arguments]<test-flags>: Ignore test file requiring not available optional package. Change-Id: Ic43e84284502d7d57e95de2e68eecb25eafae8ac
2025-10-16gnu: python-anndata: Add test dependency python-filelock.Alexis Simon
It was found this build issue while building dependents of python-zarr. * gnu/packages/python-science.scm (python-anndata): [native-inputs]: Add python-filelock; missing for tests. Change-Id: Ia83b631bc321f43e7a51fa558753f6189530bd76 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-10-15gnu: python-dask-image: Fix tests.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-dask-image)[arguments] <test-flags>: Rework skipped tests and enable more tests. [propagated-inputs]: Remove python-tifffile; add python-tifffile-for-dask-image. [description]: Remove new line in the end. * gnu/packages/python-xyz.scm (python-tifffile-for-dask-image): New variable. Change-Id: I8539569aab1134d049ec8e8c0041191ce61e2eb7
2025-10-15gnu: Add python-scikit-image-next.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-image-next): New variable. Change-Id: Ie8f576ff3d6b4e92a34565b130c00697e985ac6b
2025-10-14gnu: python-imagehash: Update to 4.3.2.Hugo Buddelmeijer
* gnu/packages/python-science.scm (python-imagehash): Update to 4.3.2. [arguments] <#:phases>: Add 'remove-six phase. Change-Id: I201164afd8c327db4f9f652967c7ea30dfd84a8c Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-10-08gnu: Add python-pyvistaqt.Ghislain Vaillant
* gnu/packages/python-science.scm (python-pyvistaqt): New variable. Change-Id: I0f843fb4e7bf160e0f8625824c172d11b2405fab Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-10-08gnu: python-pyvista: Improve package style.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pyvista): Use G-Expressions, fix indentation, remove necessary comments. [arguments] <test-flags>: Utilize Pytest option to ignore and skip tests instead modifying test files. [phases]{fix-failing-tests}: Keep file modifications which can't be skipped with Pytest options. Change-Id: I51cbf14a9572bd096d409fa6b4b7b9c8bef5eea1
2025-10-06gnu: Add python-anndata-0.11.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-anndata-0.11): New variable. Change-Id: I49d804d4434dfde618cfe7da76cae1d8db9444af
2025-09-30gnu: python-scipy: Fix build on i686-linux.Dariqq
* gnu/packages/patches/python-scipy-i686.patch: Add patch. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python-science.scm (python-scipy): Add phase to apply the patch. Fixes guix/guix#2989 Change-Id: I6c5d807bd2ed23fca6e94b28cb6927c154bde0e8 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-09-28gnu: python-aplus: Update to 0.11.1-0.1ab8ebe.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-aplus): Update to 0.11.1-0.1ab8ebe. [source]: Switch to git-fetch and build from the latest commit. [build-system]: Switch to pyproject-build-system. [arguments] <tests?>: Disable them as depending on Nose test runner. [native-inputs]: Add python-setuptools. Change-Id: I34bf72f8d0103122dfcf399e6823eaca2db1d69d
2025-09-28gnu: python-fbpca: Switch to pyproject.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-fbpca): [build-system]: Switch to pyproject-build-system. [native-inputs]: Add python-pytest, and python-setuptools. Change-Id: Ib02a92066f6c06b1de73fb5e5c4888544db7b9f8
2025-09-28gnu: python-pyjanitor: Fix build.Hugo Buddelmeijer
* gnu/packages/python-science.scm (python-pyjanitor): Fix build. [propagated-inputs]: Add python-requests. [native-inputs]: Remove python-wheel. [arguments] <#:test-flags>: Disable failing test. Change-Id: I74b40149a3b87f0e748d79be2aae9978fa18de52 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-09-25gnu: python-scikit-fem: Update to 11.0.0.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-fem): Update to 11.0.0. [propagated-inputs]: Add python-matplotlib. [native-inputs]: Remove python-wheel. Change-Id: I52ac1f1125f7d5849b8a90f5db74aeabc08fd6ef
2025-09-25gnu: python-plotly: Fix tests.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-plotly) [native-inputs]: Remove python-wheel; add python-nbformat. Change-Id: I257a9b06343b37e95428bfa46f4b5547b7adb876
2025-09-25gnu: python-scipy: Reduce closure size.Hugo Buddelmeijer
As documentation was not built at all, this change removes everything requiring for to reduce the closue size. * gnu/packages/python-science.scm (python-scipy): Adjust inputs [arguments] <phases>: Remove 'install-doc. [propagated-inputs]: Keep only python-numpy. [native-inpusts]: Remove python-hypothesis, and python-pytest-cov; add python-mpmath, python-numpydoc, python-pythran, python-rich-click, python-threadpoolctl, and python-typing-extensions. Fixes: guix/guix#2944. Change-Id: I97e4914c3d705b47b276d3f88dc938f26b0d27a5 Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-09-25gnu: python-scikit-opt: Fix tests.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-opt)[native-inputs]: Add python-pytest. Change-Id: I55b2659c9b897ed170c12c9407d9828f469393c6
2025-09-25gnu: python-pandera: Update to 0.26.1.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pandera): Update to 0.26.1. [source]: Switch to url-fetch, PyPI archive provides tests and build successfully while git version missed a lot of sub module after install. [arguments] <test-flags>: Rework skipped tests and ignored test files. [inputs]: Add python-dask, python-distributed, python-geopandas, python-hypothesis, python-modin, python-numpy, python-pandas, python-scipy, and python-shapely. [propagated-inputs]: Remove python-hypothesis-next, python-modin, python-multimethod, python-numpy, python-pandas, python-pandas-stubs, python-scipy, and python-wrapt; add python-typing-extensions. [native-inputs]: Remove python-dask, python-fastapi, python-geopandas, python-pyarrow, python-sphinx, and python-wheel; add python-joblib and python-setuptools-scm. Change-Id: I376f11e39c47875a5a70ee5f7d4653dd77403e28
generated by cgit v1.3 (git 2.53.0) at 2026-05-30 15:03:01 +0000