Sharlatan Hellseher
45146d392d
gnu: python-fenics-ffc: Use python-numpy@1.
...
* gnu/packages/simulation.scm (python-fenics-ffc):
[propagated-inputs]: Add python-numpy-1.
Change-Id: I57a991c70947babc1734660c1d6723789ef77466
2026-01-21 22:56:58 +01:00
Sharlatan Hellseher
c34ab1ebd5
gnu: python-fenics-ufl-2019: Use python-numpy@1.
...
* gnu/packages/simulation.scm (python-fenics-ufl-2019):
[inputs]: Remove python-numpy.
[propagated-inputs]: Add python-numpy-1
Change-Id: I3171b24924f08a6210504ee03b3726a18609b186
2026-01-21 22:56:58 +01:00
Sharlatan Hellseher
47dfedfdc4
gnu: python-episcanpy: Use python-numpy@1.
...
* 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
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
a9773c491b
gnu: python-utilities-awetzel: Remove relax-requirements phase.
...
* gnu/packages/astronomy.scm (python-utilities-awetzel):
[phases]{relax-requirements}: Remove phase.
Change-Id: I00ac6703449056eefd27e3b0ceb60499c5a9fdcb
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
210f141bb8
gnu: python-specreduce: Remove relax-requirements phase.
...
* gnu/packages/astronomy.scm (python-specreduce):
[phases]{relax-requirements}: Remove phase.
Change-Id: Ibf28ad731ffcffda538b6ab0499774be36b666ea
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
f6e47165dd
gnu: python-sncosmo: Adjust phases.
...
* 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
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
ae2ad97fa3
gnu: python-sep: Remove relax-requirements phase.
...
* gnu/packages/astronomy.scm (python-sep):
[phases]{relax-requirements}: Remove phase.
[native-inputs]: Remove python-wheel.
Change-Id: Ifb16d132624f1fb3c9b578e6644fda5ee524745b
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
ca9a0b38f2
gnu: python-gizmo-analysis: Remove relax-requirements phase.
...
* gnu/packages/astronomy.scm (python-gizmo-analysis):
[phases]{relax-requirements}: Remove phase.
Change-Id: Id35c2554efe5dcdf84fd0bcbc947e3017e345646
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
2ac335b3a3
gnu: python-drizzlepac: Update to 3.10.0-0.e01563c.
...
* 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
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
244a578be3
gnu: Add python-stregion.
...
* gnu/packages/astronomy.scm (python-stregion): New variable.
Change-Id: Ic3854a54498e628ead422eba5b223773c700c98b
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
89cef8768a
gnu: python-drep: Update to 3.6.2-0.7b4b8fb.
...
* 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
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
b84be773d5
gnu: python-mygene: Switch to pyproject.
...
* 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
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
92c7352529
gnu: python-funsor: Update to 0.4.6.
...
* 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
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
a00320576e
gnu: python-deeptools: Update to 3.5.6.
...
* 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
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
6f4ed682c7
gnu: python-deepdish: Use python-numpy@1.
...
* gnu/packages/python-science.scm (python-deepdish):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.
Change-Id: I8c4e2bd6538411df0f33d05b80fe178690fcc4d8
2026-01-21 22:56:57 +01:00
Sharlatan Hellseher
f4b424bd3a
gnu: python-tdda: Skip one more test.
...
* gnu/packages/python-science.scm (python-tdda):
[arguments] <test-flags>: Skip one more test.
[native-inputs]: Remove python-wheel.
Change-Id: I1bcb5223627945d580d64e911cd73cf2da06287a
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
a335ce1224
gnu: piglit: Use python-numpy@1.
...
* gnu/packages/gl.scm (piglit):
[inputs]: Remove python-numpy; add python-numpy-1.
Change-Id: I9d8975ebaff57e56fe293b7f2c6f5c86aa181115
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
e60090e7f6
gnu: cnvkit: Update to 0.9.12-0.52f367b.
...
* gnu/packages/bioinformatics.scm (cnvkit): Update to
52f367bd0edbf55cabaaa2fbcf68c8742dc97b4c commit.
[native-inputs]: Remove python-wheel.
Change-Id: I1d26ac113414b0d6428678b61acefa058d0af6f7
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
16ccbfc2fe
gnu: python-pyfaidx: Update to 0.9.0.3.
...
* 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
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
a3637e0170
gnu: python-pomegranate: Move to machine-learning.
...
* gnu/packages/python-xyz.scm (python-pomegranate): Move from here ...
* gnu/packages/machine-learning.scm: ... to here.
Change-Id: I1ef53f52439c0cae22e96ec381ecff3e2f616d71
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
4e62565c96
gnu: python-pomegranate: Update to 1.1.0.
...
* 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
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
27d5334f0c
gnu: Add python-apricot-select.
...
* gnu/packages/machine-learning.scm (python-apricot-select): New variable.
Change-Id: Ib4e7b76e4025870e73a52d67277f8bc302740d01
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
a013420837
gnu: python-presto: Improve package, fix tests.
...
* gnu/packages/bioinformatics.scm (python-presto): Refresh package style.
[arguments] <test-flags>: Skip 3 tests.
[native-inputs]: Remove python-wheel.
Change-Id: I5992e127fd653aa04711647cf0a458586029b3d4
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
a1899bf5d0
gnu: python-brian2: Update to 2.10.1.
...
* 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
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
9d0c0fbef5
gnu: macs-3: Update to 3.0.3.
...
* gnu/packages/bioinformatics.scm (macs-3): Update to 3.0.3.
[arguments, properties]: Drop all.
[native-inputs]: Remove python-wheel.
Change-Id: Ida52036ce3305d1db67f27f98cbc0d48c1f9650a
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
00d46432d2
gnu: python-cellbender: Update to 0.3.2.
...
* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.3.2.
[arguments] <phases>: Add 'relax-requirements.
[propagated-inputs]: Remove python-scikit-learn, python-sphinx,
python-sphinx-argparse, python-sphinx-autodoc-typehints,
python-sphinx-rtd-theme, and python-sphinxcontrib-programoutput; add
python-loompy, python-lxml-html-clean, python-nbconvert,
python-notebook, python-psutil, and python-pytorch.
[native-inputs]: Add python-setuptools.
Change-Id: I79473da4ca33b648fd9bd19f21dc91edb4a12cc3
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
3004634006
gnu: python-captum: Update to 0.8.0-0.4fade3a.
...
* gnu/packages/machine-learning.scm (python-captum): Update to
4fade3af8dc398c1f96b193c969565aad23aedf5 commit.
[propagated-inputs]: Add python-openai.
Change-Id: Ic51de929ac28f565244b7aec93b9b2be7211fb02
2026-01-21 22:56:56 +01:00
Sharlatan Hellseher
76ee5c0a5c
gnu: mageck: Use python-numpy@1.
...
* gnu/packages/bioinformatics.scm (mageck):
[inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel; add python-setuptools.
Change-Id: If26cf31016b769b01d502c33b97c5579873337b6
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
4113323a93
gnu: idr: Fix build.
...
* gnu/packages/bioinformatics.scm (idr):
[propagated-inputs]: Use python-numpy-1.
[native-inputs]: Use python-cython-0.
Change-Id: Ic1fabb53311a74db3872f50c2f67f8e1310be204
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
edb9b9ec88
gnu: python-cnmf: Update to 1.7.0.
...
* gnu/packages/bioinformatics.scm (python-cnmf): Update to 1.7.0.
[arguments] <tests?, test-flags>: Enable them.
[native-inputs]: Remove python-wheel; add python-pytest.
Change-Id: I927b10045e563cc81bcb077f3af9ba3312869280
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
a3f40acb87
gnu: python-cooltools: Update to 0.7.1.
...
* gnu/packages/bioinformatics.scm (python-cooltools): Update to 0.7.1.
[arguments] <phases>: Add 'fix-pytest-config.
[native-inputs]: Add python-setuptools.
Change-Id: I1a5c03cc626c1401f1a6b34f7af13d2a259e74a3
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
78773bf10d
gnu: python-magic-impute: Update to 3.0.0.
...
* gnu/packages/bioinformatics.scm (python-magic-impute): Update to 3.0.0.
[arguments] <tests?, test-flags>: Enable them.
[native-inputs]: Add python-pytest and python-setuptools.
[propagated-inputs]: Add python-scprep.
Change-Id: I4e1567fc6b5b32ee77f13d801042ea321f33dfa8
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
dc44a54df7
gnu: Add python-scprep.
...
* gnu/packages/bioinformatics.scm (python-scprep): New variable.
Change-Id: I61674e690bf798c17e84806b606673f84bd07636
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
ed6d94d437
gnu: python-fcsparser: Use python-numpy@1.
...
* gnu/packages/bioinformatics.scm (python-fcsparser):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
Change-Id: I2a069293821b769aa981c15ccbc5c96cde5a497a
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
60e80c439c
gnu: python-graphtools: Update to 2.1.0.
...
* 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
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
510480a7ec
gnu: python-pygsp: Update to 0.6.0.
...
* 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
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
7856fceb31
gnu: Add python-pyunlocbox.
...
* gnu/packages/graph.scm (python-pyunlocbox): New variable.
Change-Id: I0281d2e1cfa4ad61a64e168f2c70344afd96ad3a
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
a3520cea9b
gnu: python-verde: Update to 1.8.1.
...
* 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
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
d2f3f13873
gnu: python-metacells: Simplify.
...
* 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
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
4b138ea01c
gnu: python-crosshair: Update to 0.0.101.
...
* 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
2026-01-21 22:56:55 +01:00
Sharlatan Hellseher
aaf435818d
gnu: Add python-pygls.
...
* gnu/packages/python-xyz.scm (python-pygls): New variable.
Change-Id: Ifb4bf0277f87fec87161f57ec09b8916ee5de077
2026-01-21 22:56:54 +01:00
Sharlatan Hellseher
17cf15aa25
gnu: Add python-lsprotocol.
...
* gnu/packages/python-xyz.scm (python-lsprotocol): New variable.
Change-Id: Id12df328f4c8f51f9c45914fba8f4991857f7596
2026-01-21 22:56:54 +01:00
Sharlatan Hellseher
8bf66eb934
gnu: python-fastcluster: Update to 1.3.0.
...
* 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
2026-01-21 22:56:54 +01:00
Sharlatan Hellseher
e9a5236f62
gnu: python-cvxpy: Update to 1.7.5.
...
* 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
2026-01-21 22:56:54 +01:00
Sharlatan Hellseher
6d81eb8f6a
gnu: python-scs: Update to 3.2.10.
...
* 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
2026-01-21 22:56:54 +01:00
Sharlatan Hellseher
6695a1ecba
gnu: Add scs.
...
* gnu/packages/maths.scm (scs): New variable.
Change-Id: Iea504b64a1da5cb4d446fe6461bbf4b2a47f4139
2026-01-21 22:56:54 +01:00
Sharlatan Hellseher
ef4cae7468
gnu: python-osqp: Update to 1.0.5.
...
* 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
2026-01-21 22:56:54 +01:00
Sharlatan Hellseher
c4c88fd251
gnu: Add osqp.
...
* gnu/packages/maths.scm (osqp): New variable.
Change-Id: If2eded2af7fa7060e793867f1128210e3b8f2ed1
2026-01-21 22:56:54 +01:00
Sharlatan Hellseher
896118913a
gnu: Add qdldl.
...
* gnu/packages/maths.scm (qdldl): New variable.
Change-Id: Ic43b3a4e6af342748367e93f22f37efea4b923f6
2026-01-21 22:56:54 +01:00
Sharlatan Hellseher
8e7249553f
gnu: Remove python-eventio-1.
...
* gnu/packages/astronomy.scm (python-eventio-1): Delete variable.
Fixes : guix/guix#5305
Change-Id: If753c3b722e748aafb52329e9fe8bab338617437
2026-01-21 22:56:54 +01:00
