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2026-01-25gnu: python-graphtools: Update to 2.1.0.Sharlatan Hellseher
* gnu/packages/graph.scm (python-graphtools): Update to 2.1.0. [arguments]<phases>: Remove 'patch-tets; use default 'check; add 'fix-pytest-config. [native-inputs]: Remove util-linux, python-pynose, and python-nose2; add python-pytest and python-setuptools. Change-Id: If5561d5c4de1a9c78e7d4baa7011bd0ad622c4ef Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pygsp: Update to 0.6.0.Sharlatan Hellseher
* gnu/packages/graph.scm (python-pygsp): Update to 0.6.0. [source] <pypi-uri>: Fix name. [arguments] <test-flags>: Rework skipped tests. <phases>: Remove 'disable-doctets. [propagated-inputs]: Remove python-scikit-image. [native-inputs]: Remove python-coverage, python-coveralls, and python-flake8; add python-matplotlib, python-pyunlocbox, python-scikit-image, and python-setuptools. Change-Id: Ic2ef43e47967897e2d7df7e628a8d02ff7684360 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-pyunlocbox.Sharlatan Hellseher
* gnu/packages/graph.scm (python-pyunlocbox): New variable. Change-Id: I0281d2e1cfa4ad61a64e168f2c70344afd96ad3a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-verde: Update to 1.8.1.Sharlatan Hellseher
* gnu/packages/geo.scm (python-verde): Update to 1.8.1. [arguments] <test-flag>: Skip one more test. [propagated-inputs]: Add python-pykdtree and python-numba. [native-inputs]: Remove python-wheel; add python-matplotlib and python-pytest-mpl. Change-Id: Iaeefd5f40cb553fd0c76556663279f75aa7917ad Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-metacells: Simplify.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-metacells): [arguments] <phases>: Merge 'set-numba-cache-dir and 'build-extension into 'pre-check and just remove local source to prevent rebuilding expansions for tests, it saves some compute time with the same output. [native-inputs]: Add pybind11. Change-Id: I95e6706813cc5d3167593440c714c5091303cb00 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-crosshair: Update to 0.0.101.Sharlatan Hellseher
* gnu/packages/python-check.scm (python-crosshair): Update to 0.0.101. [arguments] <test-flags>: Rework skipped tests, pass more. <phases>: Remove 'fix-dependencies; add 'relax-requirements. [native-inputs]: Remove python-wheel. [propagated-inputs]: Add python-pygls. Change-Id: I5b9c84d165c09ce62d364dbbd2da7108dc2eda1c Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-pygls.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-pygls): New variable. Change-Id: Ifb4bf0277f87fec87161f57ec09b8916ee5de077 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-lsprotocol.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-lsprotocol): New variable. Change-Id: Id12df328f4c8f51f9c45914fba8f4991857f7596 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-fastcluster: Update to 1.3.0.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-fastcluster): Update to 1.3.0. [arguments]: Drop all. [native-inputs]: Remove python-wheel; add python-pytest. Change-Id: Ib57e7067d7eff527f5d84f297d668cc0c7997a9c Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-cvxpy: Update to 1.7.5.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-cvxpy): Update to 1.7.5. [arguments] <test-flags>: Skip some tests. [propagated-inputs]: Remove pybind11; add python-cvxopt. [native-inputs]: Remove python-wheel; add pybind11. Change-Id: I83974c14d6422284c1f31fe8922cd9e7bc5a9253 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-scs: Update to 3.2.10.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scs): Update to 3.2.10. [source]: Do not pull git submodules. [phases]{substitute-git-submodules}: New phase. [inputs]: Add lapack. [native-inputs]: Add pythoncapi-compat and scs. Change-Id: I44778c1969f074c80ca4ddf8350b6db5c2db136a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add scs.Sharlatan Hellseher
* gnu/packages/maths.scm (scs): New variable. Change-Id: Iea504b64a1da5cb4d446fe6461bbf4b2a47f4139 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-osqp: Update to 1.0.5.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-osqp): Update to 1.0.5. [arguments] <test-flags>: Rework skipped tests. [phases]{relax-requirements}: Remove phase. {fix-osqp-source-location}: New phase. [propagated-inputs]: Remove python-qdldl; add python-jinja2, python-joblib, and python-setuptools. [native-inputs]: Remove python-setuptools and python-wheel; add osqp, pybind11, python-pytorch, python-scikit-build-core, and qdldl. Change-Id: Ic6180f814a215d5bd772e4134f7ca291f1120081 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add osqp.Sharlatan Hellseher
* gnu/packages/maths.scm (osqp): New variable. Change-Id: If2eded2af7fa7060e793867f1128210e3b8f2ed1 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add qdldl.Sharlatan Hellseher
* gnu/packages/maths.scm (qdldl): New variable. Change-Id: Ic43b3a4e6af342748367e93f22f37efea4b923f6 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Remove python-eventio-1.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-eventio-1): Delete variable. Fixes: guix/guix#5305 Change-Id: If753c3b722e748aafb52329e9fe8bab338617437 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: tangos: Update to 1.11.0.Sharlatan Hellseher
* gnu/packages/astronomy.scm (tangos): Update to 1.11.0. Change-Id: Iab7d48ccd5c29ad5ae4d37ebcad575af19ff2510 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-chaospy: Update to 4.3.21.Sharlatan Hellseher
* gnu/packages/statistics.scm (python-chaospy): Update to 4.3.21. [propagated-inputs]: Remove python-importlib-metadata. [native-inputs]: Remove python-wheel. Change-Id: I686c7fbaea1cf2e238c4a9eb3f1800489122b1c8 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-numpoly: Update to 1.3.4.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-numpoly): Update to 1.3.4. [arguments] <test-flags>: Skip one test. [native-inputs]: Remove python-wheel; add python-cython. Change-Id: I62142fd288ccfbc6506ed44d054b25af801a6b16 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pyudev: Update to 0.24.4.Hugo Buddelmeijer
* gnu/packages/admin.scm (python-pyudev): Update to 0.24.4. [source]: Switch to git-fetch for tests. [build-system]: Switch to pyproject-build-system. [arguments]: Use gexps. <#:tests?>: Enable tests. <#:test-flags>: Disable tests that need /sys/devices. <#:phases>: Update 'patch-ctypes-udev phase. [propagated-inputs]: Remove python-six. [native-inputs]: Remove python-docutils, python-hypothesis, python-mock, and python-sphinx; add python-setuptools. Change-Id: I70834b09e280ef52c621b2a98455a8b7897f4367 Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-plotly: Update to 5.24.1.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-plotly): Update to 5.24.1. [arguments] <test-flags>: Rework skipped tests. [propagated-inputs]: Remove python-ipython, python-pandas, python-pillow, python-requests, python-retrying, python-scikit-image, python-statsmodels, and python-vaex-core; add python-packaging. [native-inputs]: Add python-geopandas, python-ipykernel, python-ipython-minimal, python-matplotlib, python-numpy-1, python-orjson, python-pandas, python-pillow, python-psutil, python-pyshp, python-pytz, python-requests, python-retrying, python-scikit-image, python-scipy, python-shapely, python-statsmodels, python-tenacity, and python-vaex-core. Change-Id: Ib9c80494d708627f4c0b30a18b4ddf53a33484ce Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-array-api-strict.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-array-api-strict): New variable. Change-Id: Iab9649b967da898521316481ac466342afff2631 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-ipywidgets: Update to 8.1.4.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-ipywidgets): Update to 8.1.4. [build-system]: Switch pyproject-build-system. [native-inputs]: Remove python-pytest-cov and python-setuptools-67; add python-setuptools. Change-Id: I09799c7cbcc5c59a04a792411977974c95d1688e Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-jupyterlab-widgets: Update to 3.0.12.Sharlatan Hellseher
* gnu/packages/jupyter.scm (python-jupyterlab-widgets): Update to 3.0.12. Change-Id: I934b1f4d3a9458821fbdcffb96ec663c7d315131 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-vaex-core: Update to 4.19.0.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-vaex-core): Update to 4.19.0. [inputs]: Remove pybind11. [propagated-inputs]: Remove python-click, python-progressbar2, python-pydantic-settings, and python-requests; add python-diskcache, python-fsspec, python-graphviz, python-h5py, python-httpx, python-psutil, and python-s3fs. [native-inputs]: Remove python-pytest and python-wheel; add pybind11. Change-Id: Id9f65420d6be54e27ba850528c3fc3599696f320 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: htseq: Update to 2.0.9.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (htseq): Update to 2.0.9. [propagated-inputs]: Remove python-matplotlib. [native-inputs]: Remove python-wheel; add python-matplotlib. Change-Id: I026cd0ecf01418b4c112b8d0f2f6c0ab709c38d7 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-coolbox: Update to 0.3.9.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-coolbox): Update to 0.3.9. [source]: Switch to git-fetch. [build-system]: Switch to pyproject-build-system. [arguments] <tests?, test-flags>: Enable them. <phases>: Delete 'sanity-check. [inputs]: Remove pybind11. [propagated-inputs]: Remove python-pybbi, python-pytest, and python-termcolor. [native-inputs]: Add pybind11, python-pytest, python-pypairix, python-pybbi, python-setuptools, and samtools. Change-Id: I356fa043a18e7901e50b15f2815f84178cf4e969 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-cooler: Update to 0.10.4.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.10.4. [arguments] <phases>: Add 'fix-pytest-config. [propagated-inputs]: Remove python-pypairix; add python-ipywidgets, python-matplotlib, and python-psutil. [native-inputs]: Remove python-coverage, python-isort, and python-pytest-cov. Change-Id: I61157064630416c599f05639ddcd21c6ace8cefb Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-circe: Update to 0.3.9.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-circe): Update to 0.3.9. [source] <uri>: Use direct URL string. [arguments] <tests?, test-flags>: Enable them. [inputs]: Add python-numpy-1. [propagated-inputs]: Remove python-numpy; add python-attrs. [native-inputs]: Add python-pytest. [home-page]: Move above synopsis. Change-Id: Ia4e7a18c3225b1134b71ba33c369429bc4c01305 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-scanpy: Update to 1.11.5.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.11.5. [arguments] <test-flags>: Rework skipped tests. <phases>: Remove 'patch-version-check and 'add-anndata-source. [propagated-inputs]: Remove python-pytoml, python-sinfo, and python-tables; add python-numpy, python-pynndescent, and python-typing-extensions. [native-inputs]: Remove (package-source python-anndata), python-flaky, python-flit, python-leidenalg, python-pytest-nunit, and python-scanorama; add python-dependency-groups, python-pytest-randomly, and python-pytest-rerunfailures. Change-Id: I7a9a18434ddf3cca4d34a7909cce22ef86ffa054 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-statsmodels: Update to 0.14.5.Sharlatan Hellseher
* gnu/packages/statistics.scm (python-statsmodels): Update to 0.14.5. Change-Id: I071c163f68f0171d16c1fe9be85783c4d00bfca3 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-biopython: Update to 1.86.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.86, use G-Expressions. [arguments] <phases>: Remove 'numpy-compatibility. [native-inputs]: Remove python-wheel. Change-Id: I060455d474934b6b09c5adbbdec213b89496d9a5 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-fbpca: Fix tests.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-fbpca)[arguments] <test-flags>: Skip one test. Change-Id: I98ea94a1986e465ad41e6d0099ad4a1f45506c8e Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pandera: Update to 0.27.1.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pandera): Update to 0.27.1. [arguments] <test-flags>: Rework skipped tests. Change-Id: I7a21aa0e343cdf726e9d2c677bfccb0041dac39a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: pyscenic: Add missing python-diptest.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (pyscenic): [propagated-inputs]: Add python-diptest. Change-Id: I4871895c22e08bcdc442b7edc99c07fd796bc245 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-diptest.Sharlatan Hellseher
* gnu/packages/statistics.scm (python-diptest): New variable. Change-Id: I7104617dfb182b85494febe2a483c7681cdb5929 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-scikit-bio: Update to 0.7.1.post1.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.7.1.post1. [arguments] <test-backend, test-flags>: Use 'custom, run all tests. <phases>: Remove 'build-extensions; use default 'check; add 'remove-local-source. [propagated-inputs]: Remove python-hdmedians; add python-array-api-compat, python-patsy, and python-statsmodels. [native-inputs]: Remove python-coverage; add python-cython and python-setuptools. Change-Id: I460ba8dd7362f5d4bbf16a5923403ecbf5fc2026 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: endgame-singularity: Update to 1.1.Sharlatan Hellseher
* gnu/packages/games.scm (endgame-singularity): Update to 1.1. Change-Id: I8ff76a4e11ab949ad9576f14f74164dd567c6347 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-biom-format: Update to 2.1.17.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.17. [source] <snippet>: Remove redundant logic. [arguments] <test-flags>: Only skip some doctest requiring Nose test runner. <phases>: Remove 'use-cython, 'build-extensions, and 'pandas-compatibility; add 'remove-local-source. [propagated-inputs]: Remove python-flake8 and python-future. [native-inputs]: Remove python-pytest-cov and python-wheel; add python-setuptools. Change-Id: Ib497f771e5de40b07df4964ebcddf6c40c15fc85 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-anndata-minimal.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-anndata-minimal): New variable. Change-Id: I9503ac08d0fa630d748574bb121690144a80bfea Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-anndata: Update to 0.12.7.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-anndata): Update to 0.12.7. [arguments] <test-flags>: Skip CUDA dependent tests. [phases]{set-version}: Remove setting zip timestamp logic. [propagated-inputs]: Remove python-importlib-metadata, python-scikit-learn, and python-setuptools; add python-numpy. [native-inputs]: Add hdf5, python-openpyxl, python-pyarrow, python-pytest-randomly, and python-scikit-learn. Change-Id: I8e68cf85d435a13db995ea966ed5ff9edac3d672 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-awkward: Update to 2.8.5.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-awkward): Update to 2.8.5. [arguments] <test-flags>: Skip CUDA tests only. [propagated-inputs]: Remove python-typing-extensions. [home-page]: Refresh it as seen in project's README. Change-Id: I5cebada2be766618633b0d082c88ae3d15490e9f Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-awkward-cpp: Update to 47.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-awkward-cpp): Update to 47. [arguments]: Drop all. [home-page]: Refresh it as seen in project's README. Change-Id: I27be188fc95447a17c10b09f653bb28325367998 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: crossmap: Update to 0.7.3.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.7.3. [source] <snippet>: Adjust it for a new location of egg info directory. Change-Id: Ic826c4c42c2386dc9d1b301667be1dbb5d2db3eb Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pynbody: Use python-ipython-minimal for tests.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-pynbody)[native-inputs]: Remove python-ipython; add python-ipython-minimal. Change-Id: I2a87ff21b94cff7b3b3b2eb5c150b362fadede60 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pycollada: Update to 0.9.2.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-pycollada): Update to 0.9.2. [native-inputs]: Remove python-wheel. Change-Id: I3cc70c7eeda9e4c54a0457ba430e4c6cbe1697f3 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-notebook: Fix build.Sharlatan Hellseher
* gnu/packages/jupyter.scm (python-notebook)[arguments] <test-flags>: Skip one test. [propagated-inputs]: Swap python-jupyter-client@8 with python-jupyter-client@7. Change-Id: I37b420120395924c524f1936723e2a2c6228761d Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-jupyter-client-7.Sharlatan Hellseher
* gnu/packages/jupyter.scm (python-jupyter-client-7): New variable. Change-Id: I6164464161b0725d97c8eaf6ac1b46b03b1f13e3 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-jupyter-console: Move to jupyter.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-jupyter-console): Move from here ... * gnu/packages/jupyter.scm: ... to here. Change-Id: I687d44df58fab4d62a3eac92f2dab1eebdc89921 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-jupyter-console: Update to 6.6.3.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-jupyter-console): Update to 6.6.3. [arguments] <test-flags>: Skip one test. <phases>: Add 'pre-check. [propagated-inputs]: Add python-ipython, python-jupyter-core, python-pyzmq, and python-traitlets. [native-inputs]: Remove python-setuptools; add python-flaky and python-hatchling. Change-Id: Ia7d12b313cfcc890a5173813b92d97872ece742b Signed-off-by: Rutherther <rutherther@ditigal.xyz>
generated by cgit v1.3 (git 2.53.0) at 2026-08-04 03:19:23 +0000