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Author SHA1 Message Date
Sharlatan Hellseher aeb265f1f9 gnu: maturin: Move to (gnu packages build-tools). 
Authors were parsed from git history with the following command:

    git log --all --grep="maturin:" \
    --pretty=format:";;; Copyright © %as %aN <%aE>"

* gnu/packages/rust-apps.scm (vtracer, uv)[native-inputs]: Replace
maturing with (@ (gnu packages build-tools) maturin).
(maturing): Deprecate variable and move from here ...
* gnu/packages/build-tools.scm: ... to here.

* gnu/packages/embedded.scm: Replace rust-apps with build-tools module.
* gnu/packages/python-crypto.scm: Likewise.
* gnu/packages/python-web.scm: Likewise.
* gnu/packages/time.scm: Likewise.

* gnu/packages/machine-learning.scm: Remove rust-apps module.
* gnu/packages/python-compression.scm: Likewise.
* gnu/packages/python-science.scm: Likewise.
* gnu/packages/python-xyz.scm: Likewise.

Signed-off-by: Maxim Cournoyer <maxim@guixotic.coop>
 2026-08-19 08:31:56 +09:00
Sharlatan Hellseher 24b061c3c0 gnu: python-adjusttext: Update to 1.4.0. 
* gnu/packages/python-science.scm (python-adjusttext): Update to 1.4.0.
[source]: Switch to git-fetch.
[native-inputs]: Remove python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-14 13:28:18 +01:00
Nguyễn Gia Phong e1d4a53286 gnu: python-pandas-stubs: Update to 3.0.3.260530. 
* gnu/packages/python-science.scm (python-pandas-stubs):
  Update to 3.0.3.260530.
  [arguments]<#:test-flags>: Deselect additional failing tests.
  [native-inputs]: Add python-pytz and python-tables.

Merges: guix/guix!10525
Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-14 13:28:11 +01:00
Sharlatan Hellseher d2bd37e9ed gnu: packages/python-science: Sort variables. 
* gnu/packages/python-science.scm: Sort all variables in alphabetical order.
Adjust module footer comment.
 2026-08-14 11:41:22 +01:00
Sharlatan Hellseher 3adaee52d9 gnu: python-flox: Update to 0.11.2-0.d2857f3. 
* gnu/packages/python-science.scm (python-flox): Update to
d2857f323a3f5b7c737b34e8cfc09492cc9ef2bf commit.
[arguments] <#:test-flags>: Rework ignored and skipped tests.
[propagated-inputs]: Add python-cachey, python-cftime, python-dask,
python-lxml, python-matplotlib, python-numba, python-numbagg,
python-sparse, python-xarray, and python-zarr.
[native-inputs]: Remove python-dask, python-numbagg, python-sparse, and
python-xarray.
[description]: Start from a new line, fix fill column indentation.
 2026-08-08 23:02:35 +01:00
Nicolas Graves cd835b47fb gnu: python-pytensor: Update to 3.2.4. 
* gnu/packages/python-science.scm (python-pytensor): Update to 3.2.4.

Merges: guix/guix!10394
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:34 +01:00
Nicolas Graves 95a19cf332 gnu: python-salib: Fix build. 
* gnu/packages/python-science.scm (python-salib)[arguments]
{phases}: Add phase fix-for-pandas-3.

Relates-to: guix/guix!10394
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:33 +01:00
Nicolas Graves 15273a3c14 gnu: python-pyts: Fix build. 
* gnu/packages/python-science.scm (python-pyts)[arguments]{phases}:
Add phase fix-scikit-learn-compat.

Merges: guix/guix!10413
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:33 +01:00
Nicolas Graves 19cb9b7257 gnu: python-numbagg: Ignore failing tests. 
* gnu/packages/python-science.scm (python-numbagg)[arguments]
{test-flags}: Ignore tests failing because of Pandas@3.0.  These are
edge cases, they probably don't affect other dependencies.

Relates-to: guix/guix!10413
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:32 +01:00
Nicolas Graves edca3954b6 gnu: python-formulaic: Fix tests. 
* gnu/packages/python-science.scm (python-fomulaic)[native-inputs]:
Add python-sympy.

Relates-to: guix/guix!10354
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:31 +01:00
Nicolas Graves bba7c079e6 gnu: python-pyjanitor: Update to 0.32.23. 
* gnu/packages/python-science.scm (python-pyjanitor): Update to 0.32.23.
[arguments]{test-flags}: Ignore flaky test.
[propagated-inputs]: Add python-janitor-rs.

Merges: guix/guix!10392
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:31 +01:00
Nicolas Graves e529df4655 gnu: Add python-janitor-rs. 
* gnu/packages/python-science.scm (python-janitor-rs): New variable.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Add janitor-rs
entry.

Relates-to: guix/guix!10392
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:30 +01:00
Nicolas Graves 6ccb309f39 gnu: python-numba-stats: Update to 1.12.0. 
* gnu/packages/python-science.scm (python-numba-stats): Update to 1.12.0.
[source]: Switch to git-fetch.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-08-08 23:02:29 +01:00
Nicolas Graves 1b5efea90a gnu: python-plotnine: Ignore failing tests. 
* gnu/packages/python-science.scm (python-plotnine)[arguments]
{test-flags}: Refresh them, ignore test_geom* and test_stat* more
robustly.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-08-08 23:02:28 +01:00
Nicolas Graves 71a35a1ad8 gnu: python-pingouin: Update to 0.6.1. 
* gnu/packages/python-science.scm (python-pingouin): Update to 0.6.1.
[arguments]{test-flags}: Refresh them.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-08-08 23:02:28 +01:00
Nicolas Graves 277abc66cf gnu: python-pandarallel: Fix build. 
* gnu/packages/patches/python-pandarallel-fix-df-applymap.patch: Add
patch.
* gnu/packages/patches/python-pandarallel-fix-parallel_apply.patch:
Likewise.
* gnu/local.mk (dist_patch_DATA): Record patches.
* gnu/packages/python-science.scm (python-pandarallel)
[source]{patches}: Record them.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-08-08 23:02:28 +01:00
Hugo Buddelmeijer 6794e79176 gnu: python-plotnine: Update to 0.15.7. 
* gnu/packages/python-science.scm (python-plotnine): Update to 0.15.7.

Relates-to: guix/guix!10013
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:26 +01:00
Hugo Buddelmeijer 13af20dcba gnu: python-numdifftools: Fix build. 
Only dependency, python-pynt-pulsar builds fine, so these tests cannot
be too important.

* gnu/packages/python-science.scm (python-numdifftools): Fix build.
[arguments]<#:test-flags>: Skip two failing tests.

Relates-to: guix/guix!9909
 2026-08-08 23:02:25 +01:00
Hugo Buddelmeijer 15b27fa9b7 gnu: python-pandera: Reduce threads even more. 
* gnu/packages/python-science.scm (python-pandera): Reduce threads.
[arguments]<#:test-flags>: Reduce numprocesses to 2.

Relates-to: guix/guix!9909
 2026-08-08 23:02:25 +01:00
Hugo Buddelmeijer 333e0cfebf gnu: python-decaylanguage: Update to 1.0.0. 
* gnu/packages/python-science.scm (python-decaylanguage): Update to 1.0.0.
[native-inputs]: Add python-pytest-benchmark.

Relates-to: guix/guix!9885
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:23 +01:00
Hugo Buddelmeijer 975037164b gnu: python-particle: Update to 1.0.0. 
* gnu/packages/python-science.scm (python-particle): Update to 1.0.0.
[propagated-inputs]: Remove python-typing-extensions.

Relates-to: guix/guix!9885
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:23 +01:00
Hugo Buddelmeijer 82c0091495 gnu: python-tdda: Update to 3.2.03. 
* gnu/packages/python-science.scm (python-tdda): Update to 3.2.03.
[arguments]<#:test-flags>: Update deselected tests; add comments.
[native-inputs]: Add tzdata-for-tests.

Relates-to: guix/guix!9885
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:23 +01:00
Hugo Buddelmeijer b80ce11cad gnu: python-upsetplot: Update to 0.9.0-1.e9603da. 
* gnu/packages/python-science.scm (python-upsetplot): Update to 0.9.0-1.e9603da.
[source]: Switch to git-fetch and to maintained fork.

Relates-to: guix/guix!9885
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:22 +01:00
Sharlatan Hellseher e771dfeecc gnu: python-cvxpy: Update to 1.7.5. 
* gnu/packages/python-science.scm (python-cvxpy): Update to 1.7.5.
[source]: Switch to git-fetch.
[arguments] <#:test-flags>: Skip one more test.
[propagated-inputs]: Add python-cylp.
[native-inputs]: Replace pybind11-2 with pybind11.
 2026-08-08 23:02:21 +01:00
Sharlatan Hellseher 24d11767e6 gnu: python-pint: Update to 0.25.3. 
* gnu/packages/python-science.scm (python-pint): Update to 0.25.3.
[native-inputs]: Remove python-setuptools, python-setuptools-scm, and python-wheel;
add python-hatch-vcs and python-hatchling.
 2026-08-08 23:02:18 +01:00
Sharlatan Hellseher 46db5b9a0b gnu: python-anndata: Update to 0.13.0rc3. 
* gnu/packages/python-science.scm (python-anndata): Update to 0.13.0rc3.
[arguments] <test-flags> Simplify skipped tests by utilizing "not gpu"
marker to ignore all tests requiring CUDA.
[propagated-inputs]: Add python-scverse-misc and python-typing-extensions.
[native-inputs]: Add python-jsonschema.
 2026-08-08 23:02:17 +01:00
Sharlatan Hellseher a53eaa3647 gnu: python-vaex-core: Relax requirements for Pandas. 
* gnu/packages/python-science.scm (python-vaex-core):
[phases]{relax-requirements}: Drop higher bar for Pandas.
[native-inputs]: Remove pybind11-2; add pybind11.
 2026-08-08 23:02:16 +01:00
Sharlatan Hellseher ebd837c151 gnu: python-pandera: Update to 0.31.1. 
* gnu/packages/python-science.scm (python-pandera): Update to 0.31.1.
[arguments] <test-flags>: Disable tests for Modin, enable for Polars;
simplify skipped tests.
[inputs]: Remove python-modin; add python-polars.
[native-inputs]: Add python-black, python-mypy-for-tests, python-pytz,
python-sphinx, and tzdata-for-tests.

Change-Id: Ie750a3795d87fec54386c35aec6f569c7798f55f
 2026-08-08 23:02:15 +01:00
Sharlatan Hellseher ca58a4c8f3 gnu: python-narwhals: Fix tests. 
* gnu/packages/python-science.scm (python-narwhals):
[propagated-inputs]: Remove python-modin.
[native-inputs]: Add tzdata-for-tests.

Change-Id: I78ce19bc5cabb511b2bf77b765dd6bdfccd88ea5
 2026-08-08 23:02:15 +01:00
Sharlatan Hellseher 35263062ef gnu: python-modin: Use python-pandas-2 
* gnu/packages/python-science.scm (python-modin):
[propagated-inputs]: Remove python-pandas; add python-pandas-2.

Relates-to: guix/guix#9336
Change-Id: I2ae9ee81e46b778f9444f3b07067bd44dd49f2bb
 2026-08-08 23:02:15 +01:00
Sharlatan Hellseher c7418834af gnu: python-dask-image: Update to 2026.5.0. 
* gnu/packages/python-science.scm (python-dask-image): Update to 2026.5.0.
[source]: Switch to git-source.
[arguments]: Drop all.

Change-Id: Iff8d1ddd63509f87ba8e0e57b24875d00e64544e
 2026-08-08 23:02:14 +01:00
Sharlatan Hellseher 212b01cdaf gnu: python-pythran: Unvendor xsimd. 
* gnu/packages/python-science.scm (python-pythran):
[phases]{unvendor-xsimd}: New phase.

Change-Id: I2b8a86d15720d0573099792d74e2c37bc414f850
 2026-08-08 23:02:14 +01:00
Hugo Buddelmeijer 74f2f72dd6 gnu: python-pythran: Update to 0.18.1-0.1159b80. 
* gnu/packages/python-science.scm (python-pythran): Update to
1159b80a09ece110a369729507ba5d0bc8e895b2 commit.

Relates-to: guix/guix!9327.
Change-Id: I408e718acc942dc514e8874ac161ac226f107f2f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-08-08 23:02:14 +01:00
Sharlatan Hellseher 3a56140051 gnu: Add python-dask-gateway. 
* gnu/packages/python-science.scm (python-dask-gateway): New variable.

Change-Id: I1b466e0d41d8d09c3b12829011b4e92acd0782e9
 2026-08-08 23:02:14 +01:00
Sharlatan Hellseher 36c4ad11c8 gnu: python-distributed: Update to 2026.3.0. 
* gnu/packages/python-science.scm (python-distributed): Update to 2026.3.0.

Change-Id: I7f1f371f147b2deb576d2777fc77a77284db6834
 2026-08-08 23:02:14 +01:00
Sharlatan Hellseher 54155fde54 gnu: python-dask: Update to 2026.3.0. 
* gnu/packages/python-science.scm (python-dask): Update to 2026.3.0.
[arguments] <test-flags>: Skip 4 tests from the same test group - "Test
that cpu_count() respects the taskset command line tool"; the test was
introduced after 2025.11.0 version.
[propagated-inputs]: Remove python-importlib-metadata.
[native-inputs]: Remove python-pytest-asyncio.
[home-page]: Use official URL as seen on GitHub package.

Change-Id: Ibc77dad531b2c71a37713b14a261696c86cfbd62
 2026-08-08 23:02:13 +01:00
Sharlatan Hellseher 3610aef02f gnu: python-formulaic: Update to 1.2.2. 
* gnu/packages/python-science.scm (python-formulaic): Update to 1.2.2.
[source]: Switch to git-fetch.
[propagated-inputs]: Remove python-astor and python-cached-property; add
python-narwhals.

Change-Id: I0f0c7319a8d0e9289ce5682760236571d150f53f
 2026-08-08 23:02:12 +01:00
Sharlatan Hellseher 10f3e5f05a gnu: python-xarray: Update to 2026.04.0. 
* gnu/packages/python-science.scm (python-xarray): Update to 2026.04.0.
[source]: Switch to git-fetch.
[arguments] <test-flags>: Run tests in parallel, skip problematic tests.
[propagated-inputs]: Add python-bottleneck, python-numba,
and python-scipy-minimal.
[native-inputs]: Add python-pytz, python-pytest-xdist, and
tzdata-for-tests.

Change-Id: Iada5e0b3302ee1d7b7adbcbc4ba974fb602bc1fe
 2026-08-08 23:02:10 +01:00
Sharlatan Hellseher 57c99a5956 gnu: python-numbagg: Adjust inputs and skip benchmark tests. 
* gnu/packages/python-science.scm (python-numbagg):
[arguments] <test-flags>: Do not run benchmark tests.
[native-inputs]: Remove python-pandas; add python-pandas-minimal.
[description]: Start from a new line.

Change-Id: If90f279be3c950adbe1eca172a8171bd72bbb1df
 2026-08-08 23:02:10 +01:00
Sharlatan Hellseher 60e013aa0e gnu: python-bottleneck: Update to 1.6.0. 
* gnu/packages/python-science.scm (python-bottleneck): Update to 1.6.0.
[source]: Switch to git-fetch.
[arguments] <test-flags>: Run tests from compiled and installed package.
<phases>: Remove 'rebuild-ext; add 'remove-local-source.
[native-inputs]: Remove python-wheel; add python-versioneer.

Change-Id: Iddba3402326d63542a4aae5cbe43bbf562ed141c
 2026-08-08 23:02:08 +01:00
Sharlatan Hellseher 3d405b0a3f gnu: python-scikit-build-core: Enable all tests, propagate pybind11. 
* gnu/packages/python-science.scm (python-scikit-build-core):
[arguments] <test-flags>: Enable all tests; provide marker skipping
isolated and network tests.
[propagated-inputs]: Add pybind11.
[native-inputs]: Remove python-cattrs; add python-cattrs-minimal and
python-pytest-subprocess.

Change-Id: I17a828caa838e3217e43beb1d635487b13a9c497
 2026-08-08 23:02:07 +01:00
Sharlatan Hellseher ad93ee9ed8 gnu: Add python-scikit-build-core-bootstrap. 
* gnu/packages/python-science.scm (python-scikit-build-core-bootstrap): New variable.

Change-Id: I6a75a70762ace5554c0d66cb1e92a36853fec557
 2026-08-08 23:02:07 +01:00
Sharlatan Hellseher 4e93d946bb gnu: python-scipy: Update to 1.17.1. 
* gnu/packages/python-science.scm (python-scipy): Update to 1.17.1.
[arguments] <test-flags>: Rework skipped tests, run more.
[inputs]: Remove boost-1.88 and pybind11-2; add boost and pybind11.
[native-inputs]: Remove python-click, python-doit, python-numpydoc,
python-pycodestyle, python-pydevtool, python-rich-click, and
python-typing-extensions.

Change-Id: Ib7aa47ec497c1f15c7309387313e52a029f4919d
 2026-08-08 23:02:06 +01:00
Sharlatan Hellseher 313fda1006 gnu: Add python-pandas-2. 
* gnu/packages/python-science.scm (python-pandas-2): New variable.

Change-Id: If844ed26e830ea10cb7dd9d81cb2f7184945a522
 2026-08-08 23:02:05 +01:00
Sharlatan Hellseher a82556a59d gnu: python-pandas: Update to 3.0.3. 
This update includes releases since 2.3.3 (2025-09-29):
- 3.0.3 (2026-05-11):
  <https://pandas.pydata.org/docs/whatsnew/v3.0.3.html>
- 3.0.2 (2026-03-30):
  <https://pandas.pydata.org/docs/whatsnew/v3.0.2.html>
- 3.0.1 (2026-02-17):
  <https://pandas.pydata.org/docs/whatsnew/v3.0.1.html>
- 3.0.0 (2026-01-21):
  <https://pandas.pydata.org/docs/whatsnew/v3.0.0.html>

* gnu/packages/python-science.scm (python-pandas): Update to 3.0.3.
[source] <patches>: Drop all.
[arguments] <test-flags>: Run more tests and provide extra options.
<phases>: Fix custom 'check phase.
[propagated-inputs]: Remove python-pytz and python-tzdata; add
python-bottleneck, python-lxml, python-numba, and python-numexpr.
[native-inputs]: Remove python-lxml and python-pytest-asyncio; add
python-hypothesis, python-pytest-localserver, and python-pytz.

Fixes: guix/guix#9244
Change-Id: I59a51ef1ba264905fc5fee44e894f1963cbd866d
 2026-08-08 23:02:05 +01:00
Sharlatan Hellseher f83b0f2019 gnu: python-pandas: Skip some tests. 
* gnu/packages/python-science.scm (python-pandas):
[arguments] <test-flags>: Skip some tests, regression introduced by the
recent NumPy 2.4.6 (2026-05-18) and Cython 3.2.5 (2026-05-23).

Change-Id: I55971318fd081faa67532fa209e1bfe22859a0d6
 2026-08-08 23:02:05 +01:00
Sharlatan Hellseher 6a22f163a6 gnu: Remove python-anndata-0.11. 
* gnu/packages/python-science.scm (python-anndata-0.11): Delete variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
Merges: guix/guix#9985
 2026-08-01 11:35:46 +02:00
Sharlatan Hellseher d2699a2f82 gnu: Remove python-pyfma. 
* gnu/packages/python-science.scm (python-pyfma): Delete variable.

Relates-to: guix/guix#6610
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-08-01 11:35:45 +02:00
Sharlatan Hellseher 371f6e9535 gnu: Remove python-deepdish. 
* gnu/packages/python-science.scm (python-deepdish): Delete variable.

Relates-to: guix/guix#6610
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-08-01 11:35:43 +02:00
Sharlatan Hellseher a2d943dc53 gnu: Add python-scikit-base. 
* gnu/packages/python-science.scm (python-scikit-base): New variable.
 2026-07-21 22:59:41 +01:00