summaryrefslogtreecommitdiff
path: root/gnu/packages/python-science.scm
AgeCommit message (Collapse)Author
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
2026-02-07build-system/pyproject: Remove uneeded use of pyproject-guile-json.Nicolas Graves
* gnu/packages/bioinformatics.scm (python-bed-reader, python-gseapy) * gnu/packages/chemistry.scm (gemmi, ringdecomposerlib, rdkit) * gnu/packages/cinnamon.scm (libxapp) * gnu/packages/cups.scm (hplip) * gnu/packages/djvu.scm (ocrodjvu) * gnu/packages/finance.scm (electron-cash) * gnu/packages/gnome.scm (terminator) * gnu/packages/image-processing.scm (insight-toolkit) * gnu/packages/machine-learning.scm (onnxruntime, tensorflow-lite, koboldcpp, python-tokenizers) * gnu/packages/maths.scm (gmsh, z3, fp16) * gnu/packages/music.scm (quodlibet) * gnu/packages/photo.scm (lensfun) * gnu/packages/python-science.scm (python-clarabel) * gnu/packages/python-xyz.scm (python-orjson, python-libcst, python-rpds-py, python-streamtracer, python-tiktoken) * gnu/packages/rpm.scm (createrepo-c) * gnu/packages/rust-apps.scm (maturin) * gnu/packages/sugar.scm (sugar, sugar-datastore) * gnu/packages/version-control.scm (mercurial, hg-commitsigs) * gnu/packages/vpn.scm (python-proton-vpn-local-agent) [arguments]<#:phases>: Remove uneeded use of pyproject-guile-json extension. * gnu/packages/python-xyz.scm (python-streamtracer)[arguments] <#:phases>: Also rewrite 'check phase replacement. Change-Id: I779c354120ada3d94f07a127b9ec5011e73254c2 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-01-30gnu: Add python-cmasher.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-cmasher): New variable. Change-Id: I74c8ad6f9170b34b8c4fd1760c2ca3ba90d2a1f5
2026-01-25gnu: python-pyjanitor: Update to 0.32.5.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pyjanitor): Update to 0.32.5. [arguments] <test-flags>: Rework ignored/skipped tests. [propagated-inputs]: Remove python-requests. [native-inputs]: Add python-openpyxl and python-requests. [synopsys]: pandas->Pandas. Change-Id: I12f3f1f6ab84d63882325103e8c729d44656c97c Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pandas-flavor: Update to 0.8.1.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pandas-flavor): Update to 0.8.1. [phases]{fix-pytest-config}: New phase. [propagated-inputs]: Remove python-lazy-loader and python-packaging. [native-inputs]: Add python-setuptools and python-setuptools-scm. Change-Id: I1f1325350f77ed61146f32da5bdc81aad1daec27 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-scikit-misc: Don't propagate python-numpydoc.Sören Tempel
* gnu/packages/python-science.scm (python-scikit-misc) [propagated-inputs]: Remove python-numpydoc. [native-inputs]: Add python-numpydoc. Change-Id: I9f3d3550789dd2943f496d90f59a063ac7df5e97 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pynetdicom: Don't propagate python-numpydoc.Sören Tempel
* gnu/packages/python-science.scm (python-pynetdicom) [propagated-inputs]: Remove python-numpydoc. [native-inputs]: Add python-numpydoc. Change-Id: Ib0bc20a289972af1d346f38213413c6930218ef0 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-ruffus: Switch to pyproject.Nicolas Graves
* gnu/packages/python-science.scm (python-ruffus): [build-system]: Switch to pyproject-build-system. [arguments]<#:phases>: Improve style. Improve 'check phase. [native-inputs]: Add python-setuptools. Change-Id: If6607ce5db313c97d5aaff062ac8bfa4b55d5dee Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-geosketch: Update to 1.3.Nicolas Graves
* gnu/packages/python-science.scm (python-geosketch): Update to 1.3. [source]: Switch to git-fetch. [build-system]: Switch to pyproject-build-system. [arguments]<#:tests>: Ignore them. [native-inputs]: Add python-setuptools. Change-Id: Ib86bb1a690585d925f3cd7ba801e89e04273d8e1 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pyvista: Ignore failing test.Nicolas Graves
* gnu/packages/python-science.scm (python-pyvista)[arguments] <#:test-flags>: Ignore failing test. Change-Id: I0dba730e92c7fd7e9d7d6273bba3b5e7646278c2 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pyts: Update to 0.13.0-0.4f3d97b.Nicolas Graves
* gnu/packages/python-science.scm (python-pyts): Update to 0.13.0-0.4f3d97b. [source]: Switch to git-fetch. [native-inputs]: Remove python-wheel. [description]: Improve it. Change-Id: I64947107888826ad3db8cf1e2e4d3790c6a3e070 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-qutip: Update to 5.2.2.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-qutip): Update to 5.2.2. [arguments] <test-flags>: Rework skipped/ignored tests. <phases>: Use default 'check; add 'remove-local-source. [propagated-inputs]: Add python-cvxopt, python-cvxpy, python-mpi4py, python-mpmath, and python-tqdm. [native-inputs]: Remove python-numpy, python-packaging, python-scipy, and python-wheel; add python-pytest-rerunfailures. Change-Id: I1ee08658e6a7c6ef2c6b42b9d121113dedad04f7 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pytensor: Update to 2.36.3.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pytensor): Update to 2.36.3. [arguments] <test-flags>: Add option to skip/disable benchmark tests and rework skipped tests. [native-inputs]: Add python-pytest-benchmark and python-pytest-xdist. Change-Id: I9c3c42c21091524741ccef55e4698b59e818512d Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pingouin: Fix tests.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pingouin): [arguments] <test-flags>: Rework skipped tests. <phases>: Add 'relax-requirements. [native-inputs]: Remove python-pytest-cov; add python-setuptools. Change-Id: If45e91fabbd479819731041c09dd6e1e561774d6 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-scikit-survival: Fix indentation.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-survival): Fix indentation. Change-Id: Iff0ab38a0b484938613df08ffb0fbd83da489289 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-scikit-survival: Update to 0.26.0.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-survival): Update to 0.26.0. [native-inputs]: Add python-pytest-xdist. Change-Id: If92ba627c894cb65976b7687062e738656b06e96 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Remove python-dask-expr.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-dask/bootstrap) (python-dask-expr): Delete variables. Fixes: guix/guix#4766 Change-Id: I8243329353fe41b0ffff35fd4383a9a09047cd52 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Remove python-statannot.Sharlatan Hellseher
A message from upstream: "This repository is not maintained anymore. I recommend using the forked package trevismd/statannotations, which has a cleaner API and further extends the functionalities of statannot." * gnu/packages/python-science.scm (python-statannot): Delete variable. Fixes: guix/guix#5355 Change-Id: Ib3347ff2077f62d4e97c0f9dc437b419d260c4b5 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pandas-stubs: Update to 2.3.3.251219.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pandas-stubs): Update to 2.3.3.251219. [arguments]: Drop all but 2 skipped tests. [propagated-inputs]: Add python-numpy. [native-inputs]: Remove python-tables, which, xclip, xorg-server-for-tests, and xsel; add python-beautifulsoup4, python-fsspec, python-html5lib, python-jinja2, python-loguru, python-mypy, python-numexpr, python-openpyxl, python-typing-extensions, python-xlrd, python-xlsxwriter, and tzdata-for-tests. Change-Id: I7b7b85c1ce9b1e575069a79321db4ff515372942 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-narwhals: Update to 2.15.0.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-narwhals): Update to 2.15.0. [propagated-inputs]: Add python-duckdb, python-packaging, and python-rich. [native-inputs]: Remove python-duckdb. Change-Id: I0af82e4cbe2b3c2b3ae3803b77cde5f6c921a1a6 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-narwhals-minimal.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-narwhals-minimal): New variable. Change-Id: I972010ea88c649d41227c51256b739a022a350df Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-libneuroml: Update to 0.6.7.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-libneuroml): Update to 0.6.7. [native-inputs]: Remove python-wheel. Change-Id: I7ef49953a922116bd2c1aeb12ea548d0dd8afb18 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pyfma: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pyfma): [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-wheel. Change-Id: I8236576e39b7e6f8b981126cbf67fc55f35db83c Signed-off-by: Rutherther <rutherther@ditigal.xyz>
generated by cgit v1.3 (git 2.53.0) at 2026-05-28 19:37:18 +0000