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2026-01-25gnu: python-pygenometracks: Update to 3.9.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.9. [source]: Switch to git-fetch. [arguments] <tests?, test-flags>: Enable them. <phases>: Remove 'remove-invalid-syntax; adjust 'relax-requirements. [propagated-inputs]: Add python-bx-python, python-pybedtools, and python-pyfaidx. [native-inputs]: Remove python-wheel; add python-setuptools. Change-Id: I364255a3e4d072535a871340588cdff0f30b83ff Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-hicmatrix: Update to 17.2.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 17.2. [arguments] <test-flags>: Skip one test. <phases>: Remove 'find-blosc2. [inputs]: Remove c-blosc2. [native-inputs]: Remove python-wheel. Change-Id: I45972befc224d9c85858d1c1ac9be885f63cdf01 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: pigx-scrnaseq: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): [inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I3bd24084626d2c1720c899a2bae6e9be4ab99c09 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-sbpy: Skip one doc test.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-sbpy) [arguments] <test-flags>: Skip one test. Change-Id: Ie3c929d9367f596561f67e34f7bebf9024641654 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: scvelo: Update to 0.3.3.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (scvelo): Update to 0.3.3. [source]: Switch to git-fetch. [arguments] <test-flags>: Run all tests in "tests/core" <phases>: Remove 'matplotlib-compatibility; add 'set-version. Change-Id: Iea4f9e9b7d385033b1131644c0145a5fdc3a7db7 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-hic2cool: Fix tests.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-hic2cool) [arguments] <test-backend, test-flags>: Use custom. Change-Id: I1bfacc5b91a31e3bcd9434589d1d9e1a7b4d4076 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-hdf5storage: Use pythno-numpy@1.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-hdf5storage): [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-wheel. Change-Id: I1d2e3d4d5b654e4025aa16f4d1aa9230c10a3e0a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-dcor: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/statistics.scm (python-dcor): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: Ida842dda2adea1e6a2085ae219b7e95988c14f85 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: coda: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/maths.scm (coda): [native-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I1419ec3eb9cb4f25b1078908e305c99ec8bd59c4 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: dolphin-emu: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/emulators.scm (dolphin-emu)[native-inputs]: Remove python-numpy, add python-numpy-1. Change-Id: I1693aa1af04d8c2abca4781b81143cb9a22275d8 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-statannotations.Sharlatan Hellseher
* gnu/packages/statistics.scm (python-statannotations): New variable. Change-Id: Ib8a51d7b63c9be9af2addf193c8241569c793569 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-scikit-surprise: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-surprise): [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-wheel. Change-Id: I4ae8d087b602a04ff94ad1ef72c6ef0589938054 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-spisea: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-spisea): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: Iab368ddefd7e73021e1377292afa9bfbd4ccba4d Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pysynphot: Update to 2.0.0-1.a5e76c3.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-pysynphot): Update to a5e76c398f5b03192fa54659f81e7e1a929d9f7c commit. [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-wheel. Change-Id: Ic2f211ff766291665fdc40df7d06884d22093f0b Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-paramz Move to machinve-learning.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-paramz): Move from here ... * gnu/packages/machine-learning.scm: ... to here. Change-Id: I128d863626a9b70bf31c37e200d40ad6ccd48ad2 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-gpy: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/machine-learning.scm (python-gpy): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: Ie8740ce69188726c58b9a6ee753bdd3ac6b214a8 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-paramz: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-paramz): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: Ibc355d9a6e1ab635f63c21fe5e068a0ddfcc906a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: rdkit: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/chemistry.scm (rdkit)[propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: Iab529bb547832bd56040cf4ea1cc414b14c37dd2 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: boost-numpy: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/boost.scm (boost-numpy)[native-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I4ee9b625c69951099929873f2f7bbd7a7d0f6e29 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-scikit-learn-1.6: Skip 3 more tests.Sharlatan Hellseher
* gnu/packages/machine-learning.scm (python-scikit-learn-1.6)[arguments] <test-flags>: Skip 3 more tests. Change-Id: I1c7e2eb7c18ddc5479cf45b84a6cf07d374842fe Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-vector: Update to 1.7.0.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-vector): Update to 1.7.0. [propagated-inputs]: Add python-awkward, python-numba, and python-sympy. [native-inputs]: Remove python-awkward and python-sympy; add python-notebook, python-optree, and python-papermill. Change-Id: I760c26d69b5a5e4530e80d8e57af65db2fdf319f Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-papermill: Reduce closure size; skip 2 tests.Sharlatan Hellseher
The most of the native inputs were there to tests ignored tests, they are removed now to reduce closure size. * gnu/packages/jupyter.scm (python-papermill): [arguments] <test-flags>: Skip 2 failing tests. [native-inputs]: Remove python-boto3, python-botocore, python-ipython, python-ipywidgets, python-moto, and python-requests. Change-Id: I4c07a024a9514a44b5819196754e44ee86d47883 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-glue-qt: Relax requirements for ipython version.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-glue-qt): [phases]{relax-requirements}: New phase. Change-Id: I25ede5ae073ff7e5d568e99b29b15a95008a696f Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Remove python-xarray-datatree.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-xarray-datatree): Delete variable. Fixes: guix/guix#5348 Change-Id: I7150cbe534f900286fb575f5883d9fe0980aa975 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-multiscale-spatial-image: Update to 2.0.3.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-multiscale-spatial-image): Update to 2.0.3. [propagated-inputs]: Remove quasiquote and ((unquote insight-toolkit) "python"); add python-dask, python-numpy, python-dateutil, python-spatial-image, python-xarray, python-xarray-dataclass, and python-zarr. [native-inputs]: Remove python-fsspec, python-ipfsspec, python-jsonschema, python-nbmake, python-pooch, python-pytest, python-pytest-mypy, python-urllib3, and python-zarr. Change-Id: I22f93379f92da785f851c17d149745ea9124a999 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-xarray-dataclass.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-xarray-dataclass): New variable. Change-Id: Id4293a97741704c434b6847b7b1ede8d35dd1edd Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-fenics-ffc: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/simulation.scm (python-fenics-ffc): [propagated-inputs]: Add python-numpy-1. Change-Id: I57a991c70947babc1734660c1d6723789ef77466 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-fenics-ufl-2019: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/simulation.scm (python-fenics-ufl-2019): [inputs]: Remove python-numpy. [propagated-inputs]: Add python-numpy-1 Change-Id: I3171b24924f08a6210504ee03b3726a18609b186 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-episcanpy: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-episcanpy): [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-pytest and python-wheel; add python-setuptools. Change-Id: I896e2e9c44383d71ad4cea3ca7e4f445999f5842 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-utilities-awetzel: Remove relax-requirements phase.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-utilities-awetzel): [phases]{relax-requirements}: Remove phase. Change-Id: I00ac6703449056eefd27e3b0ceb60499c5a9fdcb Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-specreduce: Remove relax-requirements phase.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-specreduce): [phases]{relax-requirements}: Remove phase. Change-Id: Ibf28ad731ffcffda538b6ab0499774be36b666ea Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-sncosmo: Adjust phases.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-sncosmo): [phases]{relax-requirements, prepare-test-environment}: Remove phases. {pre-check}: New phase, do not re-build extension just remove local source to reduce compute time. [native-inputs]: Remove python-wheel; add python-iminuit and python-pytest-xdist. Change-Id: I3b8642b1a55a1563640b1a5306614f2cb9ec5c2a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-sep: Remove relax-requirements phase.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-sep): [phases]{relax-requirements}: Remove phase. [native-inputs]: Remove python-wheel. Change-Id: Ifb16d132624f1fb3c9b578e6644fda5ee524745b Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-gizmo-analysis: Remove relax-requirements phase.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-gizmo-analysis): [phases]{relax-requirements}: Remove phase. Change-Id: Id35c2554efe5dcdf84fd0bcbc947e3017e345646 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-drizzlepac: Update to 3.10.0-0.e01563c.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-drizzlepac): Update to e01563c48206f02f4cd4c525732764b9b827b3c4 commit. [source]: Switch to git-fetch. [phases]{set-version}: New phase. [propagated-inputs]: Remove python-markupsafe, python-pypdf2, python-regions, and python-tables; add python-pypdf and python-stregion. [native-inputs]: Remove python-astropy and python-wheel; add python-markupsafe. Change-Id: I623f369b763d741405a6f25ed455466d009cb3d5 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-stregion.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-stregion): New variable. Change-Id: Ic3854a54498e628ead422eba5b223773c700c98b Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-drep: Update to 3.6.2-0.7b4b8fb.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-drep): Update to 7b4b8fbf9dfdfef61caf949f1aa1d4fc3be61d5a commit. [source]: Switch to git-fetch providing tests. [arguments] <test-flags>: Skip some tests requiring not available optional packages. [build-system]: Switch to pyproject-build-system. [propagated-inputs]: Remove python-pytest; add python-networkx. [native-inputs]: Add mash, python-pytest, and python-setuptools. Change-Id: I5e22f7c142e267592b2ed74cf1c1d37a02472992 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-mygene: Switch to pyproject.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-mygene): [source]: Switch to git-fetch. [build-system]: Switch to pyproject-build-system. [native-inputs]: Add python-setuptools. Change-Id: Ieb062c8dc8f8e2a8cede4b5d1bb816ec9d9d10db Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-funsor: Update to 0.4.6.Sharlatan Hellseher
* gnu/packages/machine-learning.scm (python-funsor): Update to 0.4.6. [source]: Switch to git-fetch providing a fresh version. [arguments] <test-flags>: Run tests in parallel, supported upstream; skip more problematic tests. [propagated-inputs]: Remove python-numpy; add python-numpy-1, python-pyro-ppl, and python-pytorch. [native-inputs]: Add python-pytest-xdist. Change-Id: I6a82951485324e465c93aec07b4f98ef632ebae3 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-deeptools: Update to 3.5.6.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-deeptools): Update to 3.5.6. [arguments] <test-flags>: Skip one test. <phases>: Remove 'fix-test. [native-inputs]: Remove python-wheel. Change-Id: I233b272ee06ab6c290c11a6875961de0fe52b8e8 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-deepdish: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-deepdish): [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-wheel. Change-Id: I8c4e2bd6538411df0f33d05b80fe178690fcc4d8 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-tdda: Skip one more test.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-tdda): [arguments] <test-flags>: Skip one more test. [native-inputs]: Remove python-wheel. Change-Id: I1bcb5223627945d580d64e911cd73cf2da06287a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: piglit: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/gl.scm (piglit): [inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I9d8975ebaff57e56fe293b7f2c6f5c86aa181115 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: cnvkit: Update to 0.9.12-0.52f367b.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (cnvkit): Update to 52f367bd0edbf55cabaaa2fbcf68c8742dc97b4c commit. [native-inputs]: Remove python-wheel. Change-Id: I1d26ac113414b0d6428678b61acefa058d0af6f7 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pyfaidx: Update to 0.9.0.3.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.9.0.3. [arguments] <tests?>: Disable for now. <phases>: Remove 'fix-version; add 'set-version. [propagated-inputs]: Remove python-setuptools; add python-packaging. [native-inputs]: Remove libc-utf8-locales-for-target; add python-biopython, python-fsspec, python-numpy, python-pytest, python-setuptools, and python-setuptools-scm. Change-Id: I49e95f8e1b19a181d4d1b2e344cf1a00b055eefd Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pomegranate: Move to machine-learning.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-pomegranate): Move from here ... * gnu/packages/machine-learning.scm: ... to here. Change-Id: I1ef53f52439c0cae22e96ec381ecff3e2f616d71 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pomegranate: Update to 1.1.0.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-pomegranate): Update to 1.1.0. [source]: Switch to git-fetch providing tests. [arguments] <tests?, test-flags>: Enable them. [propagated-inputs]: Remove python-joblib and python-pyyaml; add python-apricot-select, python-scikit-learn, and python-pytorch. [native-inputs]: Remove python-pandas and python-wheel; add python-pytest. Change-Id: Idf53aff2124c98fd7dc1172a31028a57347d2a4b Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-apricot-select.Sharlatan Hellseher
* gnu/packages/machine-learning.scm (python-apricot-select): New variable. Change-Id: Ib4e7b76e4025870e73a52d67277f8bc302740d01 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-presto: Improve package, fix tests.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-presto): Refresh package style. [arguments] <test-flags>: Skip 3 tests. [native-inputs]: Remove python-wheel. Change-Id: I5992e127fd653aa04711647cf0a458586029b3d4 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-brian2: Update to 2.10.1.Sharlatan Hellseher
* gnu/packages/machine-learning.scm (python-brian2): Update to 2.10.1. [arguments] <test-flags>: Run portion of tests. <phases>: Use default 'check; add 'relax-requirements. [propagated-inputs]: Remove python-py-cpuinfo; add python-packaging. [native-inputs]: Remove python-wheel; add python-pytest-timeout and python-setuptools-scm. Fixes: guix/guix#2568 Change-Id: Iad4d1bc211069fccbec7eb9b0082bf2ea73c8e41 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
generated by cgit v1.3 (git 2.53.0) at 2026-08-09 23:09:07 +0000