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Author SHA1 Message Date
Spencer King 380d705b4e gnu: Add python-cotengra. 
* gnu/packages/python-science.scm (python-cotengra): New variable.

Merges guix/guix!8830

Change-Id: I414616ad579831498180578eb40682ac3c455df6
Signed-off-by: Cayetano Santos <csantosb@inventati.org>
 2026-05-29 07:58:20 +02:00
Nguyễn Gia Phong 13d24ec965 gnu: Remove snakemake-5. 
* gnu/packages/python-science.scm (snakemake-5): Delete variable.

Change-Id: I5ed4ed815a0271680ae7c7862a8acc2827b9aff9
 2026-05-29 12:00:51 +09:00
Nguyễn Gia Phong ab1cccf8d9 gnu: snakemake-6: Uninherit from snakemake-5. 
* gnu/packages/python-science.scm (snakemake-6):
  Do not inherit from snakemake-5.
  [home-page, synopsis, description, license]: Copy from snakemake-5.

Change-Id: I01aadb93d2acf13ba227cb113bd5ef7002194403
 2026-05-29 12:00:51 +09:00
luca 91c5e436f6 gnu: ninja: Move to build-tools. 
* gnu/packages/build-tools.scm (ninja, ninja/pinned, samurai)
  (samu-as-ninja-wrapper): Move to here...
* gnu/packages/ninja.scm (ninja, ninja/pinned, samurai)
  (samu-as-ninja-wrapper): ...from here.  New deprecated variables.
* guix/build-system/cmake.scm (default-ninja):
  Switch to loading from build-tools module.
* guix/build-system/meson.scm (default-ninja): Likewise.

Change-Id: Ia32fb258159cfcc9a0f1ef91c335c71c25a6d7ef
Closes: https://codeberg.org/guix/guix/issues/3595
Merges: https://codeberg.org/guix/guix/pulls/4329
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
 2026-05-27 16:55:34 +09:00
Sharlatan Hellseher d40667e9d9 gnu: packages/python-science: Sort python-[am] variables. 
* gnu/packages/python-science.scm (9python-dvc-data, python-dvc-objects,
python-einops, python-fbpca): Sort variables alphabetically.

Change-Id: I19e296bfcc2360e81ceaa81fd44688645113c1a4
 2026-05-25 23:57:00 +01:00
Spencer King 5b5ed99030 gnu: Add python-autoray. 
* gnu/packages/python-science.scm (python-autoray): New variable.

Merges: guix/guix!8810
Change-Id: I1393870b5e3881cb1e28154361b8c7f7853514eb
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-25 23:47:07 +01:00
Sharlatan Hellseher 9052cc623a gnu: python-pandas: Skip one test on 32bit systems. 
* gnu/packages/python-science.scm (python-pandas):
[arguments] <test-flags>: Skip one test on 32bit systems.

Change-Id: Ib7c46e4573358fa3088bdc4100b9ce112381d988
 2026-05-24 10:19:44 +01:00
Sharlatan Hellseher 48f38de73e gnu: snakemake-5: Fix build and tests. 
* gnu/packages/python-science.scm (snakemake-5):
[source] <snippet>: Delete versioneer.py script and relay on Guix's
custom package instead.
[arguments] <test-flags>: Skip the whole group of test_lint tests.
[native-inputs]: Remove python-wheel; add python-versioneer.

Change-Id: I4072fca930e2e148e1bc121f3ede5e2ad668fe14
 2026-05-24 10:19:40 +01:00
Sharlatan Hellseher 8422da898d gnu: snakemake-6: Fix build and tests. 
* gnu/packages/python-science.scm (snakemake-6):
[source] <snippet>: Delete versioneer.py script and relay on Guix's
custom package instead.
[arguments] <test-flags>: Skip the whole group of test_lint tests.
[native-inputs]: Remove python-wheel; add python-versioneer.

Change-Id: I7f9e9ec521f814ef7710c7b8036408fbf1eb2425
 2026-05-24 10:19:40 +01:00
Sharlatan Hellseher 2cf215ec54 gnu: python-plotly: Fix version setup. 
* gnu/packages/python-science.scm (python-plotly):
[source] <snippet>: Remove versioneer.py script to relay on Guix's
custom package.
[native-inputs]: Add python-versioneer.

Change-Id: I08e600e7708a8024d296b356296b471d5e7e4dd2
 2026-05-24 10:19:38 +01:00
Nicolas Graves 27c3c72525 gnu: python-polars: Disable tests temporarily. 
Rationale: We could already do that, but polars is outdated, costly to
compile, python-team is already blocking the queue for more that a
week, and it'll be easier to write after delete-all-but has made it
into guix.  It seems more convenient to postpone that for a couple of
weeks than fix it now.

* gnu/packages/python-science.scm (python-polars)[arguments]
<#:tests?>: Disable them.

Change-Id: I3bb722021cb5f99f70515c598c84ce8de5afeb20
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:19:33 +01:00
Nicolas Graves e0d2ba79c3 gnu: python-upsetplot: Fix build with Python@3.12. 
* gnu/packages/python-science.scm (python-upsetplot)[native-inputs]:
Add python-setuptools, remove python-wheel.

Change-Id: If86859969fd02c77cb5f0fe173c8c52ad6094a24
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:19:31 +01:00
Nicolas Graves 048989a3ad gnu: python-orsopy: Fix tests-flags. 
This is a follow-up to an overlook in commit
a15d374d5f.

* gnu/packages/python-science.scm (python-orsopy)[arguments]
<#:test-flags>: Fix them.

Change-Id: Ib22f61de8930fe99fc95ce51e894535d26084310
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:19:31 +01:00
Nicolas Graves a7e7fa3f3a gnu: python-polars-runtime-32: Disable tests. 
* gnu/packages/python-science.scm (python-polars-runtime-32)
[arguments]<#:tests?>: Disable them.  They were not running until now
anyway, and there are no python tests in this package.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:19:29 +01:00
Nicolas Graves 23bcb26db1 gnu: python-cmcrameri: Fix tests on Python@3.12. 
* gnu/packages/python-science.scm (python-cmcrameri):
[source]: Switch to git-fetch.
[native-inputs]: Add python-pytest.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:15:00 +01:00
Sharlatan Hellseher c52e7d38b5 gnu: python-opt-einsum: Update to 3.4.0. 
* gnu/packages/python-science.scm (python-opt-einsum): Update to 3.4.0.
[source]: Switch to git-fetch.
[propagated-inputs]: Add python-dask and python-sparse.
[native-inputs]: Remove python-setuptools and python-wheel; add
python-hatch-fancy-pypi-readme, python-hatch-vcs, and
python-hatchling.

Change-Id: I9aea1e93908bc06374e0ea9577e3b46492b64e40
 2026-05-24 10:14:50 +01:00
Sharlatan Hellseher 74110f0896 gnu: python-ndindex: Fix tests. 
* gnu/packages/python-science.scm (python-ndindex):
[arguments] <test-flags>: Run tests in parallel, proper ignore and
deselect coverage markers warnings.
[native-inputs]: Add python-pytest-xdist.

Change-Id: Icf34370cfd0fa37cf34bf1f7efc08b8efb95f700
 2026-05-24 10:14:50 +01:00
Sharlatan Hellseher d230047fda gnu: python-scikit-build-core: Update to 0.12.2. 
* gnu/packages/python-science.scm (python-scikit-build-core): Update to 0.12.2.
[source]: Switch to git-source.
[arguments] <tests?, test-flags>: Enable the most portion of tests.
[propagated-inputs]: Remove python-importlib-metadata,
python-importlib-resources, python-tomli, and python-typing-extensions;
add cmake-minimal.
[native-inputs]: Remove pybind11-2, python-fastjsonschema,
python-hatch-fancy-pypi-readme, python-numpy, python-pytest-subprocess,
python-rich, python-setuptools, python-setuptools-scm, and python-wheel.

Change-Id: Ib62523b96c069358838135923b39bf617797c2e0
 2026-05-24 10:14:50 +01:00
Nicolas Graves eaa713dc46 gnu: packages: Drop python-pytest-runner native-inputs. 
This commit was generated using https://codeberg.org/guix/guix/pulls/5862:

   guix style -S remove-native-inputs --parameter=python-pytest-runner

and adding back python-pytest if necessary.

* gnu/packages/geo.scm (python-pyshp)
* gnu/packages/backup.scm (vorta)
[native-inptus]: Remove python-pytest-runner, add python-pytest.

* gnu/packages/backup.scm (duplicity)
* gnu/packages/linux.scm (python-spython)
* gnu/packages/bioinformatics.scm (python-cwl-utils)
* gnu/packages/databases.scm (python-pyarrow, datasette)
* gnu/packages/fontutils.scm (python-cu2qu)
* gnu/packages/gnome.scm (terminator)
* gnu/packages/music.scm (stargate)
* gnu/packages/python-science.scm (python-upsetplot)
* gnu/packages/python-web.scm (python-falcon, python-cssselect2)
* gnu/packages/python-xyz.scm (python-docrep, python-cairocffi,
  python-entrypoint2)
* gnu/packages/task-management.scm (todoman)
* gnu/packages/video.scm (yle-dl)
* gnu/packages/vpn.scm (sshuttle)
[native-inptus]: Remove python-pytest-runner.

Relates-to: https://codeberg.org/guix/guix/issues/7474
Change-Id: Ia79595309ba8965c4374e7c24a1ef4c3e36fe1ea
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:48 +01:00
Nicolas Graves 803e96bf55 guix: build-system: Set pypi-uri in pyproject, drop python module. 
After this commit, when both modules are imported:

- if pyproject is imported before, the warning is 'pypi-uri' is
deprecated, use '(@ (guix build-system pyproject) pypi-uri)' instead

- if python is imported before, the warning is `pypi-uri' imported from
both (guix build-system python) and (guix build-system pyproject)

This seems convenient enough to warn for deprecation in the short term,
while avoiding any breaking changes.

* guix/build-system/pyproject.scm (pypi-uri): Move the procedure from
(guix build-system python) here.

* guix/build-system/python (pypi-uri): Drop definition, import it
from (guix build-system pyproject) and deprecate it.

* gnu/packages/openldap.scm: Reorder modules to get the right warning.

* gnu/packages/pypy.scm: Likewise.

* gnu/packages/*.scm : Drop module (guix build-system python).

* tests/import/pypi.scm: Likewise.

Merges: https://codeberg.org/guix/guix/pulls/7448
Change-Id: Ib42f53bc545052eb7918a25afe9db6d5fc2cb834
Reviewed-by: Nguyễn Gia Phong <cnx@loang.net>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:45 +01:00
Sharlatan Hellseher f61830339c gnu: python-pandas: Fix build. 
* gnu/packages/python-science.scm (python-pandas):
[phases]{version-set-by-guix}: Remove phases.
{patch-generate-version}: New phase.

Change-Id: Iee36356021f5bab3656ee39f3600af8b9d297a05
 2026-05-24 10:14:45 +01:00
Hugo Buddelmeijer c68918cba7 gnu: python-scikit-image: Fix build with python-pillow 12.1.1. 
Followup to 017903d435f987c50c085bf415a07a551684412b.

* gnu/packages/python-science.scm (python-scikit-image): Fix build.
[source]: Add patch.
* gnu/packages/patchen/python-scikit-image-fix-python-pillow.patch: Add.
* gnu/local.mk (dist_patch_DATA): Register patch.

Merges: https://codeberg.org/guix/guix/pulls/7261
Change-Id: I7eee2e1f397f1f1ce0757f588da921687296ad41
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:43 +01:00
Nicolas Graves 30b8a50880 gnu: python-orsopy: Switch to pyproject. 
* gnu/packages/python-science.scm (python-orsopy):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:test-flags>: Set them.
<#:phases>: Drop them accordingly.
[native-inputs]: Add python-setuptools.

Change-Id: Ic7116a6d6a23eea4b8e15c557b2967fd9d0d48af
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:43 +01:00
Nicolas Graves fb51dc5c5c gnu: packages: Remove python-pytest-cov native-inputs. 
Obtained with
./pre-inst-env guix style -S remove-native-inputs -t python-pytest-cov
on top of https://codeberg.org/guix/guix/pulls/5862

For this reason, I don't think it's relevant to generate a GNU Style
Changelog.

Change-Id: I58fe10452d7eaf2e8bb4dc88dfac5b4a5ee46165
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:39 +01:00
Nicolas Graves aab86e7acf gnu: python-pingouin: Drop phase 'fix-pytest-config. 
* gnu/packages/python-science.scm (python-pingouin)[arguments]
<#:phases>: Drop phase 'fix-pytest-config.

Change-Id: Ieadcbabed58f87ae3e5a4d54e158bfa6d8b322a2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:37 +01:00
Nicolas Graves ebab4423a8 gnu: python-tspex: Drop phase 'fix-pytest-config. 
* gnu/packages/python-science.scm (python-tspex)[arguments]
<#:phases>: Drop phase 'fix-pytest-config.

Change-Id: I41624e1f8dd044e25408b445b28759d8d52d62e4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:37 +01:00
Nicolas Graves df4bccfb55 gnu: python-scikit-misc: Drop phase 'fix-pytest-config. 
* gnu/packages/python-science.scm (python-scikit-misc)[arguments]
<#:phases>: Drop phase 'fix-pytest-config.

Change-Id: Ic828d3d3d645b8e87c6ad50ed08008a9a6987372
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:36 +01:00
Nicolas Graves 3dec13b1e6 gnu: python-numdifftools: Drop phase 'fix-pytest-config. 
* gnu/packages/python-science.scm (python-numdifftools)[arguments]
<#:phases>: Drop phase 'fix-pytest-config.

Change-Id: Ib0cd60fd668cccab7cbb16d5e4b1bdb9fd7f96aa
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:36 +01:00
Nicolas Graves 168f830b5a gnu: python-pandas-flavor: Improve python-pytest-cov removal. 
* gnu/packages/python-science.scm (python-pandas-flavor)[arguments]:
Drop them.

Change-Id: I3c83750eeb95b755c6160fc10b0d34cb8fd9a465
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:35 +01:00
Nicolas Graves 6c462b3c5a gnu: python-distributed: Drop phase 'fix-pytest-config. 
* gnu/packages/python-science.scm (python-distributed)[arguments]
<#:phases>: Drop phase 'fix-pytest-config.

Change-Id: Id5312389fdca9f9a456163d649084ef69e1d6a33
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:35 +01:00
Nicolas Graves d0d1272e44 gnu: python-dask: Drop phase 'fix-pytest-config. 
* gnu/packages/python-science.scm (python-dask)[arguments]<#:phases>:
 Drop phase 'fix-pytest-config.

Change-Id: I6eea2cf2b1685b0fdb61afb6c55cda2605056ff1
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:35 +01:00
Nicolas Graves 30b3cbc90f build-system/pyproject: Stop hiding options. 
* gnu/packages/python-crypto.scm (python-keyring)
[arguments]<#:test-flags>: Remove arguments hiding coverage options.

* gnu/packages/python-web.scm (python-asgi-lifespan,
python-openapi-schema-validator, python-openapi-spec-validator,
python-openapi-core)[arguments]<#:test-flags>: Remove arguments hiding
coverage options.
(python-openapi-schema-validator, python-openapi-spec-validator)
[arguments]<#:phases>: Remove 'remove-coverage-pytest-options phase.
(python-cssselect2)[arguments]: Remove uneeded field.
(python-quart)[arguments]: Remove uneeded field.
(python-jsonpickle)[arguments]<#:test-flags>: Remove uneeded
test-flags.

* gnu/packages/python-xyz.scm (python-cattrs)
[arguments]<#:phases>: Remove arguments hiding coverage options.
(python-blessed)[arguments]: Remove uneeded field.

python-pytest-cov remove option

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:33 +01:00
Nicolas Graves 684b10f1db build-system/pyproject: Remove python-pytest-cov native-input. 
* gnu/packages/astronomy.scm (python-wiimatch)
* gnu/packages/audio.scm (python-resampy, python-librosa)
* gnu/packages/backup.scm (borgmatic)
* gnu/packages/bioinformatics.scm (python-bed-reader, python-pysnptool)
(python-pairtools):
* gnu/packages/check.scm (python-pytest-nunit, python-pytest-perf)
* gnu/packages/dav.scm (vdirsyncer, radicale)
* gnu/packages/django.scm (python-django-redis)
* gnu/packages/engineering.scm (python-scikit-rf)
* gnu/packages/fediverse.scm (python-mastodon-py)
* gnu/packages/fontutils.scm (psautohint)
* gnu/packages/geo.scm (python-pyogrio)
* gnu/packages/graphviz.scm (python-uqbar)
* gnu/packages/jupyter.scm (python-jupyterlab-server python-nbclient,
python-jupyterlite-core, python-ipydatawidgets)
* gnu/packages/machine-learning.scm
(python-pymanopt, python-tensorly, python-torchmetrics)
* gnu/packages/maths.scm (python-libensemble)
* gnu/packages/music.scm (stargate)
* gnu/packages/python-check.scm (python-atpublic, python-vcrpy)
* gnu/packages/python-compression.scm (python-zipstream-ng)
* gnu/packages/python-science.scm (python-plotnine,
python-pandaparallel, python-pyts, python-pingouin)
* gnu/packages/python-web.scm (python-devpi-process, python-cheroot,
python-jsonpickle, python-flask-babel, python-url-normalize,
python-elasticsearch, python-hupper, python-simple-websocket,
python-apiron, python-huggingface-hub, python-aiosignal, python-ovh,
python-cbor2, python-zeep, hypercorn, python-warcio, python-aioftp,
python-oauthlib, python-tinycss2, python-cssselect2, python-httpcore,
python-wsgiprox, python-venusian, gunicorn)
* gnu/packages/python-xyz.scm (python-janus, python-affine,
python-contourpy, python-echo, python-rasterio, python-rich-tables,
python-babel, python-pymarshal, python-portalocker, python-expandvars,
python-mizani, python-cligj, autokey,
python-robotframework-pythonlibcore, python-lsp-jsonrpc,
python-numpydoc, python-pillow, python-manimpango, python-cairocffi,
python-pubmed-parser, python-sentry-sdk, python-prettytable,
python-sniffio, python-ipywidgets, python-pyproject-api,
python-pymemcache, python-async-lru, python-numcodecs, python-mwclient,
python-cmd2, python-pyan3, python-platformdirs, python-multipart,
python-shtab, python-scooby)
* gnu/packages/rdf.scm (python-rdflib-6)
* gnu/packages/simulation.scm (python-fenics-dijitso)
* gnu/packages/sphinx.scm (python-sphinx-design)
* gnu/packages/statistics.scm (python-patsy, python-rchitect)
* gnu/packages/task-management.scm (todoman)
* gnu/packages/vpn.scm (sshuttle)
* gnu/packages/web.scm (anonip, python-tibanna)
[native-inputs]: Remove python-pytest-cov.

Change-Id: I32f027794e90333c27fdff5871180779f603846c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:33 +01:00
Nguyễn Gia Phong a550ba8906 gnu: Remove phase done by set-version in pyproject-build-system. 
* gnu/packages/astronomy.scm (python-kanon)[arguments]<#:phases>:
  Remove 'relax-requirements and 'set-version.
* gnu/packages/machine-learning.scm
  (python-botorch)[arguments]<#:phases>: Remove 'pretend-version.
* gnu/packages/openstack.scm
  (python-os-testr, python-requestsexceptions)[arguments]<#:phases>:
  Remove 'set-version.
* gnu/packages/package-management.scm
  (python-conda-libmamba-solver)[arguments]<#:phases>:
  Remove 'set-version.
* gnu/packages/patchutils.scm (pwclient)[arguments]<#:phases>:
  Remove 'set-PBR_VERSION.
* gnu/packages/python-check.scm
  (python-aioresponses)[arguments]<#:phases>: Remove 'set-pbr-version.
* gnu/packages/python-science.scm
  (python-modin, python-plotly, python-pytensor)[arguments]<#:phases>:
  Remove 'versioneer.
  (snakemake-5, snakemake-6, snakemake-7)[arguments]<#:phases>:
  Remove 'patch-version.
* gnu/packages/python-web.scm (python-alpaca-py)[arguments]<#:phases>:
  Remove 'set-version.
* gnu/packages/python-xyz.scm
  (python-logical-unification)[arguments]<#:phases>:
  Remove 'versioneer.
  (python-debugpy, python-strenum)[arguments]<#:phases>:
  Remove 'fix-version.
  (python-qstylizer)[arguments]<#:phases>: Remove 'set-pbr-version.
  (python-retry)[arguments]<#:phases>: Remove 'set-version.
* gnu/packages/statistics.scm (python-pymc)[arguments]<#:phases>:
  Remove 'versioneer.

Change-Id: I7b4557c576730e47575305f4f03bfe2523412c6c
Reviewed-by: Nicolas Graves <ngraves@ngraves.fr>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-24 10:14:30 +01:00
Cayetano Santos 06ec87bd52 gnu: python-tdda: Update to 3.0.02. 
* gnu/packages/python-science.scm (python-tdda): Update to 3.0.02.
[source]: Switch to git-fetch.
[arguments]: Update #:test-flags.
[propagated-inputs]: Add python-chardet, python-numpy, python-pandas,
python-polars, python-pyarrow, python-pyyaml, python-regex,
python-requests, python-rich, python-tomli, and python-tomli-w.
[native-inputs]: Remove python-numpy, python-chardet, python-pandas,
python-pyarrow, and python-rich.
[home-page]: Update.

Change-Id: Iebc7b720019d99be859c5ec51361a30357aae012
 2026-05-23 10:02:20 +02:00
Reza Housseini 4ca739f886 gnu: Add python-openpmd-api. 
* gnu/packages/python-xyz.scm (python-openpmd-api): New variable.

Change-Id: Ibe42302342ec4a8fd551d417959a7d045ba13f05
Relates-to: guix/guix!8352
Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl>
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-05-17 00:52:59 +01:00
Nicolas Graves 5ee0ece891 gnu: python-fast-histogram: Update to 0.14-0.92ed204. 
* gnu/packages/python-science.scm (python-fast-histogram): Update to 0.14-0.92ed204.
[source]: Switch to git-fetch.
[arguments]: Ignore failing test.

Change-Id: I78510869691e0b198a65b62f9bcad614198a20e2
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-04-23 22:47:11 +02:00
Efraim Flashner 30442f49a5 gnu: Fix some spelling errors. 
* gnu/packages/ocaml.scm, gnu/packages/orange.scm,
gnu/packages/package-management.scm, gnu/packages/password-utils.scm,
gnu/packages/pdf.scm, gnu/packages/perl6.scm, gnu/packages/php.scm,
gnu/packages/power.scm, gnu/packages/prometheus.scm,
gnu/packages/protobuf.scm, gnu/packages/python-check.scm,
gnu/packages/python-compression.scm, gnu/packages/python-crypto.scm,
gnu/packages/python-science.scm, gnu/packages/python-web.scm,
gnu/packages/python-xyz.scm, gnu/packages/qt.scm,
gnu/packages/racket.scm, gnu/packages/radio.scm, gnu/packages/rdf.scm,
gnu/packages/rocm.scm, gnu/packages/rpc.scm, gnu/packages/ruby-xyz.scm,
gnu/packages/rust-apps.scm, gnu/packages/rust-crates.scm,
gnu/packages/rust.scm, gnu/packages/telephony.scm,
gnu/packages/terminals.scm: Fix some spelling errors.

Change-Id: Iac58897304e471f42ecfbaa3a750ff10ee734ca6
 2026-04-19 11:42:53 +03:00
Vinicius Monego 346f9a93ef gnu: Add python-flox. 
* gnu/packages/python-science.scm (python-flox): New variable.

Change-Id: I661c37869a28e65bd707ef09a909278d5412ae9a
 2026-03-30 20:59:38 -03:00
Vinicius Monego 7eb217dc99 gnu: Add python-numbagg. 
* gnu/packages/python-science.scm (python-numbagg): New variable.

Change-Id: I49856891cdbfc3f85c0753d5d3ea344c58ac4565
 2026-03-30 20:59:38 -03:00
Efraim Flashner 2f4e0e7026 gnu: python-polars-runtime-32: Fix build. 
* gnu/packages/python-science.scm (python-polars-runtime-32)[arguments]:
In the prepare-cargo-build-system phase, add prepare-rust-crates phase
from cargo-build-system.

Change-Id: Ibec2f8b9299d7510a9258c73e8dc64a6b8e184d3
 2026-03-30 19:28:35 +03:00
Vinicius Monego ee567ba7b9 gnu: python-sparse: Update to 0.18.0. 
* gnu/packages/python-science.scm (python-sparse): Update to 0.18.0.
[native-inputs]: Remove python-wheel.

Change-Id: I524ff3eef96f73c6dc12efb3b60288d122dc4d8b
 2026-03-29 11:18:33 -03:00
Ludovic Courtès 2a50c9598b gnu: Reference the inherited ‘arguments’ value. 
This commit was made by running this command:

  sed -e's/substitute-keyword-arguments (package-arguments [a-zA-Z0-9-]\+)/substitute-keyword-arguments arguments/g' -i gnu/packages/*.scm

… and then:

  1. reverting changes from ‘gnu/packages/rust.scm’ and
     ‘gnu/packages/java.scm’ since they would incur derivation changes and/or
     breakage;
  2. reverting the change for ‘gcc-final’ in ‘gnu/packages/commencement.scm’;
  3. reverting the change for ‘onnx-optimizer’, ‘openquest’, and ‘certbot’,
     which use ‘substitute-keyword-arguments’ for arguments that are not
     inherited (and thus ‘arguments’ would be unbound);
  4. reverting the change for ‘insight-toolkit-legacy’ and ‘wine64-staging’
     which make bogus assumptions about inherited arguments.

Change-Id: I122a7cf517b6b63cae38944b5d33ade4b1f5a89c
 2026-03-20 13:27:15 +01:00
Alexis Simon 2676117710 gnu: Add python-polars. 
* gnu/packages/python-science.scm (python-polars-runtime-32,
python-polars): New variables.
* gnu/packages/rust-crates.scm: Add python-polars-runtime-32.
* gnu/packages/rust-sources.scm: Add rust-tikv-jemallocator-for-polars.

Change-Id: Ib36d95a0102da990512002b29f0a55732922040b
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2026-03-10 12:46:17 +02:00
Maxim Cournoyer e819590cdf gnu: python-scikit-image: Update to 0.26.0. 
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
 2026-03-08 09:49:45 +09:00
Danny Milosavljevic f674270c07 gnu: python-cvxpy: Fix intermittent build failure. 
* gnu/packages/python-science.scm (python-cvxpy)[arguments]<#:phases>{set-ci-environment}:
New phase.

Change-Id: I4e76b5e88c03f4b2c6915181231b700512d6f37a
 2026-03-07 03:09:48 +01:00
Gabriel Wicki f86ff1db98 gnu: Pin old pybind11 version. 
* 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>
 2026-03-05 15:53:36 +01:00
Vinicius Monego 78e801ab9c gnu: python-iminuit: Update to 2.32.0. 
* gnu/packages/python-science.scm (python-iminuit): Update to 2.32.0.

Change-Id: Ib60c59e34813ccc2e6276bff95d0804916863e71
 2026-03-01 23:38:56 -03:00
Vinicius Monego e479e7a8cb gnu: python-decaylanguage: Update to 0.20.2. 
* gnu/packages/python-science.scm (python-decaylanguage): Update to
0.20.2.

Change-Id: I172a9d58f50d7deaaf270a8f39ecbbfc47e6d73e
 2026-03-01 23:38:56 -03:00
Vinicius Monego d46f3e7fc2 gnu: python-particle: Update to 0.26.1. 
* gnu/packages/python-science.scm (python-particle): Update to 0.26.1.

Change-Id: I1fd567c879933d03019b65b5d55a2df491a7f850
 2026-03-01 23:38:56 -03:00