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2026-03-08gnu: python-scikit-image: Update to 0.26.0.Maxim Cournoyer
This fixes a test failure. * gnu/packages/python-science.scm (python-scikit-image): Update to 0.26.0. [#:test-flags]: Remove --pyargs (otherwise no test would run). Add upstream issue reference in comment. [#:phases]: Delete argument. [native-inputs]: Add python-pytest-pretty. Change-Id: I4ecf593faa74174d941f47f8569caa7badada1ee
2026-03-07gnu: python-cvxpy: Fix intermittent build failure.Danny Milosavljevic
* gnu/packages/python-science.scm (python-cvxpy)[arguments]<#:phases>{set-ci-environment}: New phase. Change-Id: I4e76b5e88c03f4b2c6915181231b700512d6f37a
2026-03-05gnu: Pin old pybind11 version.Gabriel Wicki
* gnu/packages/python-xyz.scm (pybind11): Move definition to (pybind11-2). (python-awkward-cpp, python-contourpy, python-hnswlib, python-dm-tree, python-matplotlib, python-pikepdf, python-optree, python-fusepy): Change reference to pybind11-2. * gnu/packages/astronomy.scm (aoflagger, python-galsim, python-pyclp), gnu/packages/bioinformatics.scm (python-metacells, python-strawc, python-coolbox, python-pyspoa, python-scvelo), gnu/packages/chemistry.scm (avogadrolibs), gnu/packages/computer-architecture.scm (gem5), gnu/packages/duckdb.scm (python-duckdb), gnu/packages/electronics.scm (nextpnr, prjtrellis), gnu/packages/engineering.scm (python-orocos-kinematics-dynamics), gnu/packages/geo.scm (ogs-serial), gnu/packages/graphics.scm (openshadinglanguage, openimageio), gnu/packages/image-processing.scm (opencolorio), gnu/packages/machine-learning.scm (python-fasttext, python-ml-dtypes, onnx, onnx-optimizer, onnxruntime, dlib, tensorflow-lite, tensorpipe, python-pytorch, python-torchvision, python-ctranslate2, python-hmmlearn, python-dlib), gnu/packages/maths.scm (python-accupy, python-ducc0), gnu/packages/networking.scm (libcamera), gnu/packages/opencl.scm (python-pyopencl), gnu/packages/package-management.scm (python-libmambapy), gnu/packages/physics.scm (python-brille, python-gofit), gnu/packages/python-check.scm (python-xdoctest), gnu/packages/python-science.scm (pyre, python-boost-histogram, python-cvxpy, python-iminuit, python-osqp, python-pyamg, python-qdldl, python-scikit-build-core, python-scipy, python-vaex-core, python-pyfma), gnu/packages/radio.scm (gnuradio, gr-osmosdr, gr-dsd, gr-iqbal, gr-satellites, limesuite-ng), gnu/packages/simulation.scm (fenics, python-dolfin-adjoint), gnu/packages/statistics.scm (python-diptest, python-george), gnu/packages/syndication.scm (syndication-domination): Change reference to pybind11-2. Change-Id: Ib6abc8580fc2b4c35172f251ff6ba7d80ced4b7b Signed-off-by: Gabriel Wicki <gabriel@erlikon.ch>
2026-03-01gnu: python-iminuit: Update to 2.32.0.Vinicius Monego
* gnu/packages/python-science.scm (python-iminuit): Update to 2.32.0. Change-Id: Ib60c59e34813ccc2e6276bff95d0804916863e71
2026-03-01gnu: python-decaylanguage: Update to 0.20.2.Vinicius Monego
* gnu/packages/python-science.scm (python-decaylanguage): Update to 0.20.2. Change-Id: I172a9d58f50d7deaaf270a8f39ecbbfc47e6d73e
2026-03-01gnu: python-particle: Update to 0.26.1.Vinicius Monego
* gnu/packages/python-science.scm (python-particle): Update to 0.26.1. Change-Id: I1fd567c879933d03019b65b5d55a2df491a7f850
2026-03-01gnu: python-hepunits: Update to 2.4.4.Vinicius Monego
* gnu/packages/python-science.scm (python-hepunits): Update to 2.4.4. [native-inputs]: Add python-pint. Change-Id: I9057457dde92ca2c6ce1684ec2df25be8301f304
2026-03-01gnu: python-vector: Update to 1.8.0.Vinicius Monego
* gnu/packages/python-science.scm (python-vector): Update to 1.8.0. Change-Id: Ib2c49a2701e222dd688b85d192d866c338cadbfa
2026-03-01gnu: python-hist: Update to 2.10.1.Vinicius Monego
* gnu/packages/python-science.scm (python-hist): Update to 2.10.1. Change-Id: Ia78e515fc2b6bf113b4112a2da81260091fa0130
2026-03-01gnu: python-boost-histogram: Update to 1.7.1.Vinicius Monego
* gnu/packages/python-science.scm (python-boost-histogram): Update to 1.7.1. Change-Id: I6223fbc1ab0a19d2da7b3cc627e9927619c77937
2026-02-28gnu: Add python-quantities.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-quantities): New variable. Change-Id: I40a28c0943a37d2c298b3031f5b22c09cc37b487
2026-02-28gnu: python-unyt: Update to 3.1.0.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-unyt): Update to 3.1.0. [native-inputs]: Remove python-setuptools and python-setuptools-scm; add python-flit-core. Change-Id: I37d7844d15c7ae892834f870c30ac7f0009446f2
2026-02-21gnu: python-pyvista: Update to 0.46.5.Danny Milosavljevic
* gnu/packages/python-science.scm (python-pyvista): Update to 0.46.5. [arguments]<#:test-flags>: Ignore tests/core/test_dataobject_filters.py, tests/core/test_dataset_filters.py, and tests/plotting/test_plotter.py. Disable test_read_exodus, test_nek5000_reader, test_exodus_reader_ext, test_exodus_reader_core, test_exodus_blocks, test_download_dataset_texture, test_structured_grid_cast_to_explicit_structured_grid, test_pad_image_multi_component_with_scalar, test_pad_image_raises, test_points_to_cells_and_cells_to_points_dimensions, test_meshio[cow_ugrid], test_meshio[points_only], and test_max_positional_args_matches_pyproject. <#:phases>{patch-pyproject}: Generalize vtk version pattern. [native-inputs]: Add nss-certs-for-test, python-aiohttp, python-mypy, python-pandas, python-pytest-cases, python-pytest-mock, python-pytest-pyvista, which, and xorg-server-for-tests. Replace python-pytest with python-pytest-8. [propagated-inputs]: Add python-cmcrameri, python-cmocean, and python-colorcet. Replace vtk-9.3 with vtk-9.5. Change-Id: Ic5b9a7a46c5fee8682a9d0f47d791e2d07de5f64
2026-02-21gnu: Add python-pytest-pyvista.Danny Milosavljevic
* gnu/packages/python-science.scm (python-pytest-pyvista): New variable. Change-Id: I03233bf19ba66bf4f33cf92e60de24da8c661562
2026-02-21gnu: Add python-cmcrameri.Danny Milosavljevic
* gnu/packages/python-science.scm (python-cmcrameri): New variable. Change-Id: I6b41ceeb5774564734a0b7ce5ac6baf0b5d23670
2026-02-21gnu: python-euphonic: Move to (gnu packages physics).Danny Milosavljevic
* gnu/packages/python-science.scm (python-euphonic): Move from here… * gnu/packages/physics.scm (python-euphonic): …to here. Change-Id: Ica393a72f5c9b8875bef4b4186bc4a8571b83007
2026-02-21gnu: python-seekpath: Move to (gnu packages physics).Danny Milosavljevic
* gnu/packages/python-science.scm (python-seekpath): Move from here… * gnu/packages/physics.scm (python-seekpath): …to here. Change-Id: I67d060c3c5aeebe117b7d5cdeac0666a46e8f270
2026-02-21gnu: python-spglib: Move to (gnu packages physics).Danny Milosavljevic
* gnu/packages/python-science.scm (python-spglib): Move from here… * gnu/packages/physics.scm (python-spglib): …to here. Change-Id: I19a757ffbb7ba42065a35e1213b789dae93c645c
2026-02-21gnu: python-quasielasticbayes: Move to (gnu packages physics).Danny Milosavljevic
* gnu/packages/python-science.scm (python-quasielasticbayes): Move from here… * gnu/packages/physics.scm (python-quasielasticbayes): …to here. Change-Id: Ib3788df8af26a08ede247ddc243286e107db81c2
2026-02-21gnu: python-pystog: Move to (gnu packages physics).Danny Milosavljevic
* gnu/packages/python-science.scm (python-pystog): Move from here… * gnu/packages/physics.scm (python-pystog): …to here. Change-Id: Ic2051954eb1c126bde11b2d4545d14065cd8b16b
2026-02-21gnu: python-pycifrw: Move to (gnu packages physics).Danny Milosavljevic
* gnu/packages/python-science.scm (python-pycifrw): Move from here… * gnu/packages/physics.scm (python-pycifrw): …to here. Change-Id: I5b0f5ccb148b555d898a4584da9eb6897ad3126e
2026-02-21gnu: python-brille: Move to (gnu packages physics).Danny Milosavljevic
* gnu/packages/python-science.scm (python-brille): Move from here… * gnu/packages/physics.scm (python-brille): …to here. * gnu/local.mk (GNU_SYSTEM_MODULES): Add reference to that file. * etc/teams.scm (science): Add reference to that file. Change-Id: I207940441fb4406fb034d5582ba9f5517544179b
2026-02-13gnu: python-vedo: Update to 2025.5.4.Andreas Enge
* gnu/packages/python-science.scm (python-vedo): Update to 2025.5.4. Change-Id: Ide16096a2bde0460c62e62b5aa260a5d557e7fc7
2026-02-13gnu: vtk: Update to 9.4.2 and add vtk-9.3.Andreas Enge
* gnu/packages/image-processing.scm (vtk): Update to 9.4.2. [origin]: Adapt snippet. (vtk-9.3): Add back the previous version. (opencv)[inputs], * gnu/packages/geo.scm (ogs-serial)[inputs], * gnu/packages/python-science.scm (python-pyvista)[inputs]: Replace vtk by vtk-9.3. Change-Id: I1a567bc30c7845fdd647db0f93cef2cafe1ced76
2026-02-12gnu: Add python-quasielasticbayes.Danny Milosavljevic
* gnu/packages/python-science.scm (python-quasielasticbayes): New variable. Change-Id: I4a80e53c2f4c058b8678b599d9a4a3d7752efedb
2026-02-12gnu: Add python-euphonic.Danny Milosavljevic
* gnu/packages/python-science.scm (python-euphonic): New variable. Change-Id: I10ce0b9193e5d342ead24b9e16daefd9d16d40eb
2026-02-12gnu: Add python-pycifrw.Danny Milosavljevic
* gnu/packages/python-science.scm (python-pycifrw): New variable. Change-Id: Iaee90ca32d519f1b621e6323e636bfcf231a61f1
2026-02-12gnu: Add python-pystog.Danny Milosavljevic
* gnu/packages/python-science.scm (python-pystog): New variable. Change-Id: I75eb64488c6a190aebee221bb7387dde2c0797c7
2026-02-12gnu: Add python-seekpath.Danny Milosavljevic
* gnu/packages/python-science.scm (python-seekpath): New variable. Change-Id: I8892e74d89112d8927c0a1d223962b9e86742f8b
2026-02-12gnu: Add python-spglib.Danny Milosavljevic
* gnu/packages/python-science.scm (python-spglib): New variable. Change-Id: I425a7906fe4d9eaa21e7597c6ace97650e58b53a
2026-02-12gnu: Add python-brille.Danny Milosavljevic
* gnu/packages/python-science.scm (python-brille): New variable. Change-Id: I39db7aff28c9d3d80c1cd404ee91fd1ec5fc89cd
2026-02-07gnu: python-scikit-surprise: Relocate phase 'set-home.Nicolas Graves
* gnu/packages/python-science.scm (python-scikit-surprise)[arguments] <#:phases>: Relocate phase 'set-home. Change-Id: Id6e5993e167f1f61865fcfe31caba0bce2d5263a Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: snakemake: Update to 8.30.0.Nicolas Graves
* gnu/packages/python-science.scm (snakemake): Update to 8.30.0. [arguments]<#:test-flags>: Refresh them. [native-inputs]: Remove python-wheel. Change-Id: I5b509cdf177224a71c313fed32f913cca85410d6 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: python-snakemake-interface-storage-plugins: Update to 3.6.0.Nicolas Graves
* gnu/packages/python-science.scm (python-snakemake-interface-storage-plugins): Update to 3.6.0. [arguments]<#:phases>: Add phase 'relax-requirements. Change-Id: I5e0028168d261ba12dbce846253ca4c8274710d7 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: pyre: Switch to pyproject.Nicolas Graves
* gnu/packages/python-science.scm (pyre): [arguments]<#:imported-modules, #:modules, #:phases>: Switch to pyproject-build-system. Change-Id: Iba843ba453ab2ed6958b546f27724d1cf3392f2c Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: python-plotly: Use python-pytest-8.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-plotly): [native-inputs]: Remove python-pytest; add python-pytest-8. Change-Id: I6ae645843e661c60c05e40823a6c0b0330144d35
2026-02-07gnu: python-meson-python: Rename to python-meson.Sharlatan Hellseher
This change adjusts the package name to follow Guix naming convention for Python packages, see: <https://codeberg.org/guix/guix/issues/5917#issuecomment-10168830>. * gnu/packages/python-xyz.scm (python-meson): New variable. (python-meson-python): Deprecate variable. * gnu/packages/algebra.scm (python-flint): * gnu/packages/astronomy.scm (python-pixell) * gnu/packages/finance.scm (beancount) * gnu/packages/game-development.scm (python-pygame-ce) * gnu/packages/machine-learning.scm (python-scikit-learn) * gnu/packages/python-science.scm (python-pandas, python-scikit-image, python-scikit-misc, python-scipy, python-scs) * gnu/packages/python-xyz.scm (python-contourpy, python-cysignals, python-dbus-python, python-matplotlib, python-numpy, python-numpy-1, python-pywavelets, python-siphash24) [native-inputs]: Remove python-meson-python; add python-meson. Fixes: guix/guix#5917 Change-Id: I0a9d53a164e542831fb5c3292ba71583f30d3b74
2026-02-07gnu: python-scikit-misc: Adjust inputs.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-misc): [propagated-inputs]: Remove meson-python and python-spin. [native-inputs]: Remove pkg-config, python-cython, python-numpy, python-numpydoc, and python-wheel; add python-spin. Change-Id: If2a9f9f3a003d2edc960ca5382d66fba604defef
2026-02-07gnu: python-scs: Adjust native inputs.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scs)[native-inputs]: Remove meson-python; add python-meson-python. Change-Id: I903af2c7c8a06cd616c39feb37ba7b42ba30bc0e
2026-02-07gnu: python-scikit-image: Adjust native inputs.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-image): [native-inputs]: Remove meson-python and python-cython; add python-meson-python. Change-Id: Ic273fd889d108ed896d753702a5ef977ade3a5f9
2026-02-07gnu: python-scipy: Adjust inputs and native inputs.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scipy): [phases]{relax-requirements}: Remove phase. [inputs]: Remove boost; add boost-1.88. [native-inputs]: Remove meson-python and python-cython; add python-meson-python. Change-Id: Ic9534456c52f0a93086ad9275c2e4ca2f93661a9
2026-02-07gnu: python-pandas: Adjust native inputs.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pandas)[native-inputs]: Remove meson and meson-python; add python-meson-python. Change-Id: I5f947f9a81e6931261ad16a3648fc1350d50c7f9
2026-02-07gnu: python-numpoly: Update to 1.3.9.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-numpoly): Update to 1.3.9. [source] <commit>: Upstream tagging style by removing "v" from the tag. [phases]{set-version}: New phase. [arguments] <test-flags>: Run all tests. Change-Id: I601ed70b8f4e65782b6bbe98ea7ddc7f91a0b60b
2026-02-07gnu: python-tornado: Update to 6.4.2.Sharlatan Hellseher
* gnu/packages/python-web.scm (python-tornado): Absorb definition of python-tornado-6. (python-tornado-5): New variable, inherit from python-tornado. (python-tornado-6): Deprecate variable. * gnu/packages/jupyter.scm (python-jupyterlite-core) * gnu/packages/jupyter.scm (python-pytest-jupyter) * gnu/packages/jupyter.scm (python-voila) * gnu/packages/python-xyz.scm (python-pypugjs) * gnu/packages/python-xyz.scm (python-tenacity): [native-inputs]: Remove python-tornado-6; add python-tornado. * gnu/packages/machine-learning.scm (kaldi-gstreamer-server): [inputs]: Remove python-tornado-6; add python-tornado. * gnu/packages/bioinformatics.scm (python-bulkvis) * gnu/packages/jupyter.scm (python-ipykernel) * gnu/packages/jupyter.scm (python-jupyter-client) * gnu/packages/jupyter.scm (python-jupyter-client-7) * gnu/packages/jupyter.scm (python-jupyter-server) * gnu/packages/jupyter.scm (python-nbclassic) * gnu/packages/jupyter.scm (python-nbdime) * gnu/packages/jupyter.scm (python-notebook) * gnu/packages/jupyter.scm (python-terminado) * gnu/packages/python-check.scm (python-pytest-tornasync) * gnu/packages/python-science.scm (python-distributed) * gnu/packages/python-xyz.scm (python-bokeh) * gnu/packages/python-xyz.scm (python-ipyparallel-bootstrap) * gnu/packages/python-xyz.scm (python-nbconvert) [propagated-inputs]: Remove python-tornado-6; add python-tornado. Change-Id: I437d73a0711c88e329666b6bc853f6332c277098
2026-02-07gnu: python-scikit-build-core: Drop python-exceptiongroup input.Nicolas Graves
* gnu/packages/python-science.scm (python-scikit-build-core) [propagated-inputs]: Drop python-exceptiongroup. Change-Id: Id6e5491f3bab5bfbe4719f5313ff21d72e44d232 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: Drop setting SETUPTOOLS_SCM_PRETEND_VERSION in some packages.Nicolas Graves
* gnu/packages/astronomy.scm (python-asdf-compression) (python-asdf-fits-schemas, python-cdflib, python-sunkit-spex): * gnu/packages/bioinformatics.scm (python-whatshap, python-mudata) (python-pyfaidx, python-ctxcore, scvelo): * gnu/packages/bootloaders.scm (dtc): * gnu/packages/check.scm (python-pytest-xdist, python-pytest-forked): * gnu/packages/databases.scm (python-fastparquet): * gnu/packages/disk.scm (greaseweazle-host-tools): * gnu/packages/docker.scm (python-docker): * gnu/packages/finance.scm (python-ledgerblue): * gnu/packages/fontutils.scm (python-compreffor) (python-defcon-bootstrap, nototools): * gnu/packages/games.scm (sc-controller): * gnu/packages/machine-learning.scm (python-botorch): * gnu/packages/music.scm (python-pylast): * gnu/packages/package-management.scm (conda): * gnu/packages/python-build.scm (python-exceptiongroup): * gnu/packages/python-science.scm (python-dask-image) (python-distributed, python-osqp): * gnu/packages/python-web.scm (python-branca, python-smart-open): * gnu/packages/python-xyz.scm (python-conda-content-trust) (python-menuinst, python-isort, python-pyclibrary) (python-pyclipper, python-csb43-0.10, python-orgparse) (python-deepmerge, python-scooby, python-uuid6): * gnu/packages/radio.scm (nanovna-saver): * gnu/packages/sphinx.scm (python-sphinx-autodoc-typehints): [arguments]: Remove phases setting SETUPTOOLS_SCM_PRETEND_VERSION. * gnu/packages/python-xyz.scm (python-bagit) [arguments]: Refactor manual 'check phase into #:test-flags. Change-Id: I0713d6603f982a7f956d02fc3b85a384f4dd6ce4 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: Remove python-pip native-input from some packages.Nicolas Graves
Remove python-pip from [native-inputs] in the following packages as not required for build/tests/install: * gnu/packages/python-science.scm: (python-scikit-build-core) * gnu/packages/python-xyz.scm: (python-pypandoc) * gnu/packages/shells.scm: (xonsh) Change-Id: I26579cf868b1e56d075b5c8d8ef7914feee44bcb Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: Remove python-coveralls native-input from some packages.Nicolas Graves
Remove python-coveralls from [native-inputs] in the following packages as not required for build/tests/install: * gnu/packages/python-science.scm (python-trimesh) * gnu/packages/python-xyz.scm (python-affine) Change-Id: Ia2beeec4ebc4e651f0a079efb644afa8026d53de Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07gnu: Remove python-scikit-image-next.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-image-next): Delete variable. Change-Id: Ieecd9370c75ba24ea1740615fc950d9b1ffcb216
2026-02-07gnu: Remove python-pandas-2.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pandas-2): Delete variable. Change-Id: Ia08c92f284f3bdb5849967376d5cfc38c61c7703
generated by cgit v1.3 (git 2.53.0) at 2026-05-27 21:07:57 +0000