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e074256fb83bb2bbf55da462a4c10119188045ca
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148377 Commits

Author SHA1 Message Date
Andreas Enge
e074256fb8 gnu: ruby-puma: Update to 6.6.1. 
* gnu/packages/ruby-xyz.scm (ruby-puma): Update to 6.6.1.

Change-Id: I73d24797a77c9b5c6f3b81e92ef89ab2a943dc4c
 2025-08-08 15:12:20 +02:00
gemmaro
79ca67bf0f gnu: ruby-nio4r: Update to 2.7.4. 
* gnu/packages/ruby-xyz.scm (ruby-nio4r): Update to 2.7.4.
[source]: Switch to git-fetch.
[arguments]<#:test-target>: Add.
<#:phases>: Remove remove-unnecessary-dependencies and check.
Add delete-certificate to delete certificate fields from gemspec file.

Change-Id: Iaf9efd43a81da0238a07effd811e21edf4b1c12a
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-08-08 15:01:18 +02:00
Cayetano Santos
dd6f0eb212 gnu: opencl-headers: Remove old versions. 
There are no references left to these variables anywhere in the code.

* gnu/packages/opencl.scm (make-opencl-headers, opencl-headers-1.0,
opencl-headers-1.1, opencl-headers-1.1, opencl-headers-2.0,
opencl-headers-2.1, opencl-headers-2.2): Remove variables.

Change-Id: I4afdac98e7156f3b38eecb36503a13f5a425634c
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-08-08 10:32:39 +02:00
Andreas Enge
89766e6e60 gnu: sbcl-wayflan: Update to 0.1.0. 
* gnu/packages/lisp-xyz.scm (sbcl-wayflan): Update to 0.1.0.

Change-Id: Id847d9239b1525faac47a95e09826cf33bd805d1
 2025-08-08 09:31:59 +02:00
Andreas Enge
e9772c442f gnu: daemontools: Fix build with gcc-14. 
* gnu/packages/patches/daemontools-gcc14.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register patch.
* gnu/packages/admin.scm (daemontools)[origin]: Use patch.

Change-Id: Ica243ab00e20242e04be0281e3285d24fe7ff574
 2025-08-08 09:24:36 +02:00
Cayetano Santos
0697809d64 gnu: opensta: Update to 2.7.0-0.cda3044. 
Tests expect a hard coded path to the binary under source/build/sta.

* gnu/packages/electronics.scm (opensta): Update to 2.7.0-0.cda3044 and build locally.
<#:out-of-source?>: Set to #f.
<#:configure-flags>: Add build dir.
<#:phases>{check}: Correct relative path.
{create-build-dir}: Produce build dir.

Change-Id: I2b888675364290b28b7f29789c7807f9a42d9f5a
 2025-08-08 13:50:47 +09:00
jgart
3dbee76eee gnu: visidata: Update to 3.2. 
* gnu/packages/spreadsheet.scm (visidata): Update to 3.2.
[source]: Use GitHub source repo since missing required file on PyPI.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I34043ee551c8b77549eb241facf46dd02116875a
 2025-08-07 17:28:57 -05:00
Sharlatan Hellseher
6981f0adbf gnu: ivar: Update to 1.4.4, fix build with gcc@14. 
* gnu/packages/bioinformatics.scm (ivar): Update to 1.4.4.

Change-Id: Ia7ec6adb465e3256d3f4dfd7e2fb51ae3334261f
 2025-08-07 18:33:39 +01:00
Sharlatan Hellseher
e60839c316 gnu: mcl: Fix build with gcc@14. 
* gnu/packages/machine-learning.scm (mcl) [arguments] <configure-flags>:
Add extra option to relax GCC strictness.

Change-Id: I466786efced727f4f23540639453b5f4a2457ddb
 2025-08-07 18:33:39 +01:00
Sharlatan Hellseher
702b64e41e gnu: python-liana-py: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.6.0.
  [arguments] <test-flags>: Skip more problematic tests. Adjust pathe
  for "--ignore" option.
  <phases>: Remove 'relax-requirements.
  [propagated-inputs]: Remove python-decoupler-py; add python-decoupler.
  [native-inputs]: Remove python-black, python-poetry-core, and
  python-pytest-cov; add python-hatchling.

Change-Id: Icfec6a217f828b5e68cccde88fc889b2ee3e32f3
 2025-08-07 18:33:39 +01:00
Sharlatan Hellseher
962948f2a4 gnu: Add python-decoupler. 
This package is a successor of python-decoupler-py with reworked tests
and inputs. Project has changed the license from GPL3+ to BSD-3.

See: <https://github.com/scverse/decoupler/blob/main/CHANGELOG.md#200>

* gnu/packages/bioinformatics.scm (python-decoupler): New variable based
  on python-decoupler-py.
  [source] <url>: Fix permanent redirect.
  [arguments] <test-flags>: Rework skipped tests.
  <phases>: Remove 'relax-requirements.
  [propagated-inputs]: Remove python-ipython, python-matplotlib,
  python-nbsphinx, python-numpy, python-numpydoc, python-omnipath,
  python-scanpy, python-scikit-learn, python-skranger, and
  python-typing-extensions; add python-dcor, python-docrep,
  python-igraph, python-ipywidgets, python-marsilea, python-requests,
  python-session-info2, and python-xgboost.
  [native-inputs]: Remove python-poetry-core; add nss-certs-for-test,
  python-hatchling, python-gseapy, python-memory-profiler, and
  python-scanpy.
  [home-page]: Fix permanent redirect.
  [licenses]: Switch to bsd-3.

(python-decoupler-py): Deprecate package.

Change-Id: Ia517db074c7ac405408731c9a8cfe00e56b8107b
 2025-08-07 18:33:39 +01:00
Sharlatan Hellseher
018b8a474e gnu: Add python-marsilea. 
* gnu/packages/python-science.scm (python-marsilea): New variable.

Change-Id: I2f02691e45c57783edbd3c4654fdf4f8bafafb17
 2025-08-07 18:33:39 +01:00
Sharlatan Hellseher
d10e1abebb gnu: Add python-legendkit. 
* gnu/packages/python-science.scm (python-legendkit): New variable.

Change-Id: I98f9eb01b9162dec907b7b4a7423d718e2437fdd
 2025-08-07 18:33:39 +01:00
Sharlatan Hellseher
bf812960e5 gnu: Add python-dcor. 
* gnu/packages/statistics.scm (python-dcor): New variable.

Change-Id: I87d8562b9e0cc3a6d2faf28f38c8d9b3f757c618
 2025-08-07 18:33:38 +01:00
Sharlatan Hellseher
6e38e8ab54 gnu: python-scanpy: Update to 1.11.2. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.11.2.
  [arguments] <test-flags>: Run tests in parallel, supported
  upstream. Skipp some more problematic tests.
  <phases>: Remove 'set-numba-cache-dir; add combined 'pre-check.
  [propagated-inputs]: Remove python-session-info; add python-session-info2.
  [native-inputs]: Add python-flaky, python-pytest-xdist, and python-scanorama.

Change-Id: I6a13a7c3449b0d60801daf49e40e6f1fcc48f0c0
 2025-08-07 18:33:38 +01:00
Sharlatan Hellseher
3d7c49157b gnu: python-seaborn: Update to 0.13.2. 
* gnu/packages/python-xyz.scm (python-seaborn): Update to 0.13.2.
  [arguments] <test-flags>: Run tests in parallel, supported upstream.
  [native-inputs]: Remove python-flake8, python-ipykernel,
  python-nbconvert, python-numpydoc, python-mypy, python-pytest-cov, and
  python-pyyaml.

Change-Id: Ie8df114f7b617a8c5ce0999242b47e84f8255fa6
 2025-08-07 18:33:38 +01:00
Sharlatan Hellseher
debc80b4d4 gnu: python-statsmodels: Update to 0.14.4. 
* gnu/packages/statistics.scm (python-statsmodels): Update to 0.14.4.
  [native-inputs]: Remove python-colorama, python-cython, python-flake8,
  python-isort, python-joblib, python-pytest, python-pytest-randomly,
  python-pytest-xdist, python-setuptools, and python-wheel; add
  python-cython-3 and python-setuptools-next.

Change-Id: I59164ed861224bfb8230686b2133639a7d1c649e
 2025-08-07 18:33:38 +01:00
Sharlatan Hellseher
c22b6731d4 gnu: Add python-session-info2. 
* gnu/packages/python-xyz.scm (python-session-info2): New variable.

Change-Id: I8773329702f7ef7c6c9a929317cc3d5295b8b507
 2025-08-07 18:33:38 +01:00
Sharlatan Hellseher
c1aa803542 gnu: Add python-hatch-docstring-description. 
* gnu/packages/python-build.scm (python-hatch-docstring-description): New variable.

Change-Id: I859fbd0beb3a31c812c818caf0eabc75e55df9b8
 2025-08-07 18:33:38 +01:00
Sharlatan Hellseher
80e27d57bf gnu: blast+: Update to 2.17.0. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.17.0.

Change-Id: I37b460e057b392a88934a03f9a41d2b445e08f20
 2025-08-07 18:33:38 +01:00
Sharlatan Hellseher
f470fc04d4 gnu: java-cisd-jhdf5: Fix build with gcc@14. 
* gnu/packages/java.scm (java-cisd-jhdf5): [phases]
{build-native-library}: Add "-Wno-error=implicit-function-declaration"
option to relax GCC strictness.

Change-Id: Icee8001a4908e9124b76bf1ffb27d2659868e32d
 2025-08-07 18:33:38 +01:00
Sharlatan Hellseher
51e8d1cb95 gnu: salmon: Update to 1.10.3, fix build. 
* gnu/packages/bioinformatics.scm (salmon): Update to 1.10.3.
[inputs]: Update pufferfish sources.

Change-Id: Iba95cc2bc61bbd8bddd1c9b679c9705e260a1364
 2025-08-07 18:33:37 +01:00
Sharlatan Hellseher
e3a90b8150 gnu: lmms: Fix build. 
Fixes guix/guix#1802

* gnu/packages/music.scm (lmms) [arguments] <phases>: Add
'fix-carla-export.

Change-Id: I763418c78068388c76066a62b7bf9277afe3a355
 2025-08-07 18:33:37 +01:00
Sharlatan Hellseher
659d44ce19 gnu: r-voltron: Fix tests. 
* gnu/packages/bioinformatics.scm (r-voltron): [inputs]: Add which.

Change-Id: Id16ef6a5810f592a349249f1327dc747db9a66b1
 2025-08-07 18:33:37 +01:00
Sharlatan Hellseher
4dbe551971 gnu: r-stringfish: Update to 0.17.0, fix build with gcc@14. 
* gnu/packages/cran.scm (r-stringfish): Update to 0.17.0.
  [arguments] <phases>: Add 'use-system-tbb, and
  'relax-gcc-14-strictness.
  [inputs]: Add tbb-2020.

Change-Id: Ibb7b7fface988727b185763b47cf7074119088f0
 2025-08-07 18:33:37 +01:00
Sharlatan Hellseher
41df2ab16d gnu: r-hdf5dataframe: Update to 0.0.0-2.1e30e6b. 
* gnu/packages/bioinformatics.scm (r-hdf5dataframe): Update to 0.0.0-2.1e30e6b.
[native-inputs]: Add r-testthat.

Change-Id: I4b7b933dd8fe668d03f3e04ccd78336b4efa7e5f
 2025-08-07 18:33:37 +01:00
Sharlatan Hellseher
e716c800b6 gnu: python-mudata: Update to 0.3.2. 
* gnu/packages/bioinformatics.scm (python-mudata): Update to 0.3.2.

Change-Id: I60c2b5d16dd1afddafc5f06231d6c5bf28a4b20c
 2025-08-07 18:33:37 +01:00
Sharlatan Hellseher
b91c64a3a5 gnu: python-anndata: Update to 0.12.1. 
* gnu/packages/python-science.scm (python-anndata): Update to 0.12.1.
  [arguments] <test-flags>: Rework ignored and skipped tests.
  [propagated-inputs]: Remove python-exceptiongroup and
  python-numcodecs; add python-legacy-api-wrap.
  [native-inputs]: Remove python-pytest-doctestplus, python-toml, and
  python-flit.

Change-Id: I46c46c73f3a232345cc029d79b1018290505f5af
 2025-08-07 18:33:37 +01:00
Sharlatan Hellseher
123ec7f705 gnu: python-zarr: Update to 2.18.7. 
* gnu/packages/python-xyz.scm (python-zarr): Update to 2.18.7.
[native-inputs]: Remove python-pytest-doctestplus, python-sphinx,
python-sphinx-copybutton, python-sphinx-design, and
python-sphinx-issues.

Change-Id: I9db3ffe51bb9daba53b0759a4c6a5814ff285b83
 2025-08-07 18:33:37 +01:00
Nicolas Graves
e3c7460568 gnu: python-case: Deprecate package. 
* gnu/packages/python-check.scm (python-case): Deprecate variable.
* gnu/packages/python-xyz.scm (python-kombu, python-billiard,
python-celery)[native-inputs]: Remove python-case.

Change-Id: I98d19e88aa5b8fa2b47f347a4d0c958d71096e4e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:36 +01:00
Nicolas Graves
35f2fd68b0 gnu: python-case: Move to (gnu packages python-check). 
* /gnu/packages/python-xyz.scm (python-case): Move from here…
* gnu/packages/python-check.scm (python-case): …to here.

Change-Id: I59379226031edbd4dc63c70f15725b488668d05c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:36 +01:00
Nicolas Graves
2484aec81e gnu: python-curtsies: Update to 0.4.3. 
* gnu/packages/terminals.scm (python-curtsies): Update to 0.4.3.

Change-Id: I516134ed9a3a02be805498f76b552a8ab1e4411d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:36 +01:00
Nicolas Graves
4fda9a96ff gnu: python-pyte: Update to 0.8.2. 
* gnu/packages/terminals.scm (python-pyte): Update to 0.8.2.

Change-Id: I6255a5598d86cb02f74c36c393e58d09f6a9b9a9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:36 +01:00
Nicolas Graves
3a3573fae8 gnu: python-rchitect: Update to 0.4.8. 
* gnu/packages/statistics.scm (python-rchitect): Update to 0.4.8.

Change-Id: If96584dc8ebec144ddb2ea9c0743b5ec36105abf
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:36 +01:00
Nicolas Graves
1679d70724 gnu: python-py2bit: Update to 0.3.3. 
* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.3.
[native-inputs]: Add python-setuptools-scm.

Change-Id: Ib7e9d701595501e5da76288e5a8cae32e1dc6739
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:36 +01:00
Nicolas Graves
0dba518cb1 gnu: python-radian: Update to 0.6.15. 
* gnu/packages/statistics.scm (python-radian): Update to 0.6.15.

Change-Id: Ic0b3227884ff7fef0b9b9a3b166da14ddc90dcb3
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:36 +01:00
Nicolas Graves
bac69decd3 gnu: python-pyro-api: Switch to pyproject. 
* gnu/packages/machine-learning.scm (python-pyro-api):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: Iab866450e9ab7104ecba8ff21bf34e8a4226e1b2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:36 +01:00
Nicolas Graves
fc194e7755 gnu: python-pytest-isort: Switch to pyproject. 
* gnu/packages/python-check.scm (python-pytest-isort):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]: Remove them.
[native-inputs]: Add python-poetry-core.
[home-page]: Refresh.

Change-Id: I712fcdd2bb659b5f9d2a8fbfca2d8cd0d2cdb127
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:36 +01:00
Nicolas Graves
77faad4aa2 gnu: python-pyte: Switch to pyproject. 
* gnu/packages/terminals.scm (python-pyte):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]: Remove them.
[native-inputs]: Add python-setuptools, python-wheel.  Remove
python-pytest-runner.

Change-Id: I6467cc03b9d71de5a5b70f39def7f409a64bdfce
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:35 +01:00
Nicolas Graves
2f1dd4f326 gnu: python-asyncmy: Update to 0.2.10. 
* gnu/packages/databases.scm (python-asyncmy): Update to 0.2.10.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Disable them for now.
<#:phases>: Replace 'check phase. Add a 'cleanup phase.
[native-inputs]: Add mysql, python-poetry-core, python-pytest,
python-pytest-asyncio, python-setuptools, python-wheel.

Change-Id: I759a85d29372b0d50c2d8992ee303724b7462958
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:35 +01:00
Nicolas Graves
11902d484c gnu: python-css-html-js-minify: Update to 2.5.5-0.8f72452. 
* gnu/packages/python-web.scm (python-css-html-js-minify): Update to 2.5.5-0.8f72452.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Add phase 'relax-requirements.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: I54bbaee60b8f7291f8bac14edf2ac83c23149efb
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:35 +01:00
Nicolas Graves
ea571d67f4 gnu: python-pytimeparse: Switch to pyproject. 
* gnu/packages/time.scm (python-pytimeparse):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Add a 'cleanup phase. Replace the check phase.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: Ic8aa640789556b8583e24069291003063c794a29
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:35 +01:00
Nicolas Graves
483ac59d8f gnu: python-sphinxcontrib-programoutput: Switch to pyproject. 
* gnu/packages/sphinx.scm (python-sphinxcontrib-programoutput):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Add a cleanup phase to avoid pytest
malfunction.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.
[home-page]: Update and reorder field.

Change-Id: I38a290fc6b7868db39b57dd75ed9d0ae3e9c5147
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:35 +01:00
Nicolas Graves
c43023090a gnu: python-nbsphinx: Switch to pyproject. 
* gnu/packages/sphinx.scm (python-nbsphinx):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Disable them.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: I37beb7447618f8aec8f8b6df897aa86ac454dd2a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:35 +01:00
Nicolas Graves
99f7b8fcf9 gnu: python-test-utils: Switch to pyproject. 
* gnu/packages/python-check.scm (python-test-utils):
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: Ifc02d90691e1d72cff5ba9034ee99718ebff2051
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:35 +01:00
Nicolas Graves
d7d35b6b75 gnu: python-launchpadlib: Update to 2.1.0. 
* gnu/packages/python-web.scm (python-launchpadlib): Update to 2.1.0.
[build-system]: Switch to pyproject-build-system.
[propagated-inputs]: Remove python-keyring.
[native-inputs]: Add python-setuptools, python-wheel. Replace
python-mock by python-pytest.
[home-page]: Refresh.

Change-Id: If64e97b0a3a98757683e02c30992d688dfa12074
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:35 +01:00
Nicolas Graves
406592b117 gnu: python-py7zr: Ignore benchmark tests. 
* gnu/packages/python-compression.scm (python-py7zr):
[arguments]<#:test-flags>: Ignore benchmark tests.
[native-inputs]: Remove python-coverage, python-coveralls,
python-pytest-cov.

Change-Id: Iad630ff9d406f2c059cded3af3d2c59c7928e549
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:35 +01:00
Nicolas Graves
2eb2d3ba23 gnu: python-pyzstd: Switch to pyproject. 
* gnu/packages/python-compression.scm (python-pyzstd):
[build-system]: Switch to pyproject-build-system.
[arguments]<#:configure-flags>: Migrate option.
<#:phases>: Remove them.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.
[home-page]: Refresh.

Change-Id: I9a2fb36bfce24a81be9c70983781da5a3decc5a2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:34 +01:00
Nicolas Graves
4bf7fec9b0 gnu: python-pytest-sugar: Update to 1.0.0. 
* gnu/packages/check.scm (python-pytest-sugar): Update to 1.0.0.

Change-Id: I46d4fa51c89bdc59f26626e63d7d4e1e0c1c183a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:34 +01:00
Nicolas Graves
b29b245166 gnu: python-pytest-sugar: Switch to pyproject. 
* gnu/packages/check.scm (python-pytest-sugar):
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: Ia5b6f5ce5f8a122cc8d73c5c6e32401488ee700a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-07 18:33:34 +01:00