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Author SHA1 Message Date
Wilko Meyer da41a8f5e8
gnu: linux-libre 4.19: Update to 4.19.313. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.313.
(linux-libre-4.19-pristine-source): Update hash.

Change-Id: I22e9d175b537164efcde4cec5188c26bae8d2fca
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-05-05 23:15:59 -04:00
Wilko Meyer 44d28d102b
gnu: linux-libre 5.4: Update to 5.4.275. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.275.
(linux-libre-5.4-pristine-source): Update hash.

Change-Id: Ifcd296510ae1c7e81a4a5fa3c8eb6e304e2d662d
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-05-05 23:15:59 -04:00
Wilko Meyer 5d51f8897c
gnu: linux-libre 5.10: Update to 5.10.216. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.216.
(linux-libre-5.10-pristine-source): Update hashes.

Change-Id: Ia14fa905e109c81cc8397d1151cc327d6e1ea25a
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-05-05 23:15:58 -04:00
Wilko Meyer 5ea5d677fe
gnu: linux-libre 5.15: Update to 5.15.158. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.158.
(linux-libre-5.15-pristine-source): Update hash.

Change-Id: Ib2b12fac8301ced17e6e068a1e68768e200d5a24
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-05-05 23:15:58 -04:00
Wilko Meyer ef0cf6ae85
gnu: linux-libre 6.1: Update to 6.1.90. 
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.90.
(linux-libre-6.1-pristine-source): Update hash.

Change-Id: Ic1ef7176af2055db78b58458bb9327bce5789d48
 2024-05-05 23:15:58 -04:00
Wilko Meyer 98e368f660
gnu: linux-libre 6.6: Update to 6.6.30. 
* gnu/packages/linux.scm (linux-libre-6.6-version): Update to 6.6.30.
(linux-libre-6.6-pristine-source): Update hash.

Change-Id: Ic261985e2c199a80068e2898684d522939b98a89
 2024-05-05 23:15:58 -04:00
Wilko Meyer c2fdac2262
gnu: linux-libre-6.8-gnu-revision: Update to 6.8.9. 
* gnu/packages/linux.scm (linux-libre-6.8-version): Update to 6.8.9.
(linux-libre-6.8-pristine-source): Update hash.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: I4f8031b1db5e19e98e5f61377a45912f91d403f7
 2024-05-05 23:15:57 -04:00
Maxim Cournoyer dae5eecd47
gnu: Add mupen64plus-video-gliden64. 
* gnu/packages/emulators.scm (mupen64plus-video-gliden64): New variable.

Change-Id: I09782d0c793062c3fa448b5376a97a5f3356ea5c
 2024-05-05 22:58:13 -04:00
Maxim Cournoyer 79a51c910c
gnu: mupen64plus-ui-console: Modernize. 
* gnu/packages/emulators.scm (mupen64plus-ui-console)
[propagated-inputs]: Remove legacy mupen64plus-video-glide64 plugin.
[arguments]: Use gexps.

Change-Id: I33ce0ef1e7ea87b382f74aae07098bcf0e5f30e0
 2024-05-05 22:58:13 -04:00
Maxim Cournoyer 3a1737aaa2
gnu: mupen64plus-video-rice: Adjust synopsis. 
* gnu/packages/emulators.scm (mupen64plus-video-rice): Adjust synopsis.

Change-Id: I3708c46593a096f632d9268200c312a434525331
 2024-05-05 22:58:13 -04:00
Maxim Cournoyer 726b076658
gnu: mupen64plus-video-glide64mk2: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-video-glide64mk2): Fix synopsis.

Change-Id: I6f41e9a4b70faa0e2342a4ffc2803873a8dc8f08
 2024-05-05 22:58:13 -04:00
Maxim Cournoyer 8c25cab988
gnu: mupen64plus-video-glide64: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-video-glide64): Fix synopsis.

Change-Id: I0b2b4630dcf3c5dc5ee385e82c71f92694cf2abe
 2024-05-05 22:58:12 -04:00
Maxim Cournoyer e21c9f337e
gnu: mupen64plus-video-arachnoid: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-video-arachnoid): Fix synopsis.

Change-Id: Ic560e6780965526723907aff9d2af6c48f580508
 2024-05-05 22:58:12 -04:00
Maxim Cournoyer 8fbc8e7a65
gnu: mupen64plus-rsp-z64: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-rsp-z64): Fix synopsis.

Change-Id: I97d5b8e70949f2a5198ce45b0a1fe24a089078ba
 2024-05-05 22:58:12 -04:00
Maxim Cournoyer 376fe82015
gnu: mupen64plus-rsp-hle: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-rsp-hle): Fix synopsis.

Change-Id: I7235da472ecd1856fdc33ed08d92f9f05b29ba3a
 2024-05-05 22:58:12 -04:00
Maxim Cournoyer 721e44d419
gnu: mupen64plus-audio-sdl: Fix synopsis. 
* gnu/packages/emulators.scm (mupen64plus-audio-sdl): Fix synopsis.

Change-Id: I08b2778cf625699d72d5fbab2b23d86ff06a1be0
 2024-05-05 22:58:12 -04:00
nafkhamdc e33bf0bbe6
gnu: Add python-pyahocorasick. 
* gnu/packages/bioinformatics.scm (python-pyahocorasick): New variable.

Change-Id: I468bed450351b49cf81344a328841cd77f67cb4e
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-05-06 00:07:40 +02:00
nafkhamdc a710ebec1d
gnu: Add r-memes. 
* gnu/packages/bioconductor.scm (r-memes): New variable.

Change-Id: Ibdf5173d35ef81d27da6831148e66be83f856deb
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-05-06 00:06:19 +02:00
Ricardo Wurmus a4ad0a46ef
gnu: python-graphtools: Fix tests. 
* gnu/packages/graph.scm (python-graphtools)[arguments]: Add 'patch-tests
phase.

Change-Id: I5ffb4321ddd7e33e812bcb1cf67cee069b07b5f8
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 1b44a23503
gnu: python-gpy: Update to 1.13.1. 
* gnu/packages/python-science.scm (python-gpy): Update to 1.13.1.
[source]: Remove snippet.
[build-system]: Use pyproject-build-system.
[arguments]: Remove phase 'remove-plotting-tests; add phase 'compatibility.
[native-inputs]: Remove python-nose and python-climin; add python-pytest,
python-matplotlib, and python-pods.

Change-Id: I1ed95e3ad2e8444979fd2cf272d7f3104b1bf2ec
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus a4039b6994
gnu: python-pygsp: Add missing input. 
* gnu/packages/graph.scm (python-pygsp)[native-inputs]: Add python-pytest.

Change-Id: I94cd4e160dcbecfbb491c0d101bcbeb761189876
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 9d615b915b
gnu: python-paramz: Update to 0.9.6. 
* gnu/packages/python-science.scm (python-paramz): Update to 0.9.6.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-nose.

Change-Id: I62a2f7ecf600f48da74f4d233e108360a583d5ca
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 041ea43a86
gnu: python-pingouin: Update to 0.5.4. 
* gnu/packages/python-science.scm (python-pingouin): Update to 0.5.4.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'sklearn-compatibility phase;
skip one test.

Change-Id: I8d13f15558eadee0547f04bc4bb89a0fd0e0767b
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 99bf1b1002
gnu: python-liana-py: Update to 1.1.0. 
* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.1.0.
[arguments]: Adjust tests; add phase 'relax-requirements.
[propagated-inputs]: Remove python-mofax; add python-numpy.
[native-inputs]: Remove python-numpy; add python-poetry-core.

Change-Id: I279be08ac3ac73d9a724f59652f2f0d333607696
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 4d65083bf8
gnu: python-plotnine: Fix version string. 
* gnu/packages/python-science.scm (python-plotnine)[native-inputs]: Add
python-setuptools-scm.

Change-Id: I0fc2f3ad7edcdaaa5e3bf9774bc6840c8fbeb727
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 02ca781c03
gnu: python-plotnine: Disable test because of harmless warning. 
* gnu/packages/python-science.scm (python-plotnine)[arguments]: Disable
test_save_method which prints an unexpected warning..

Change-Id: I28a20b85ee549311bed534efbf801db930419ca9
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus f678884b4a
gnu: python-mapie: Disable strict tests. 
* gnu/packages/statistics.scm (python-mapie)[arguments]: Disable two tests.

Change-Id: I2c72f6f2d0136db5f97ba709a468a3aebd447d5d
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus c226d12856
gnu: python-scikit-learn-extra: Disable a validation test. 
* gnu/packages/machine-learning.scm (python-scikit-learn-extra)[arguments]:
Disable one test.

Change-Id: I1309cb6a82dee1a714ddec59aa90692ccfcd885b
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 1ea0e3e6dd
gnu: python-cooltools: Update to 0.7.0. 
* gnu/packages/bioinformatics.scm (python-cooltools): Update to 0.7.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.

Change-Id: I4112bf0cbc309df551087b8bb3cb1d37af7f751d
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus d14d5147b1
gnu: python-bioframe: Update to 0.6.4. 
* gnu/packages/bioinformatics.scm (python-bioframe): Update to 0.6.4.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'pre-check phase.  Use
 #:test-flags to disable tests that require internet access.
[native-inputs]: Add python-hatchling.
[propagated-inputs]: Add python-pyyaml.

Change-Id: Iad1c8c6ef8f52886e398e9c4d2d384c5fce075c6
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 317be75d1d
gnu: python-verde: Add missing input. 
* gnu/packages/geo.scm (python-verde)[native-inputs]: Add python-pytest.

Change-Id: I82b844627f27cfe60e42050bb37d092b3d9a43c1
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus ffffc0227a
gnu: python-statmake: Adjust tests and version checks. 
* gnu/packages/fontutils.scm (python-statmake)[arguments]: Disable broken
test; relax check for cattrs.

Change-Id: Ibd479743160d3591088d17635e26484e7de5250f
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus cb9ec4c5c5
gnu: python-decoupler-py: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.6.0.
[arguments]: Do not disable test_plot_volcano test.

Change-Id: I44a31d30e8a03d2d1ffd86383c8bc6db79628def
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 0e24635033
gnu: python-omnipath: Update to 1.0.8. 
* gnu/packages/python-web.scm (python-omnipath): Update to 1.0.8.
[arguments]: Disable tests that need internet access.
[native-inputs]: Add python-pytest-socket.

Change-Id: Ib5856a1a25835d43918d9fe565d0262dded70eed
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 7c938c232c
gnu: barectf: Use python-termcolor-1. 
* gnu/packages/instrumentation.scm (barectf)[propagated-inputs]: Use
python-termcolor-1.

Change-Id: I8284db970d3cee8988318be7f1180aa933ab461a
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 1f5eef8391
gnu: Add python-termcolor-1. 
* gnu/packages/python-xyz.scm (python-termcolor-1): New variable.

Change-Id: I1aca97b6b7976cb698131c3a0be73e4798bef6d6
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 79d13482e4
gnu: python-pytest-shutil: Disable a test. 
* gnu/packages/python-check.scm (python-pytest-shutil)[build-system]: Use
pyproject-build-system.
[arguments]: Disable test_pretty_formatter.

Change-Id: I862320feab5b3c6e375bf652deced6a631dfc575
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 360f9ea421
gnu: python-cleanlab: Update to 2.6.3. 
* gnu/packages/machine-learning.scm (python-cleanlab): Update to 2.6.3.
[arguments]: Disable tests that require "datasets" package; add phase
'remove-datasets.

Change-Id: I6af99e3e749a10515328db4874974a3504658352
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 714baf2295
gnu: python-termcolor: Update to 2.4.0. 
* gnu/packages/python-xyz.scm (python-termcolor): Update to 2.4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add 'fix-pyproject build phase.
[native-inputs]: Add python-hatch-vcs, python-hatchling, python-pytest, and
python-pytest-cov.

Change-Id: I1b824ca6f125305169c3f64f00dbacbeb77d0ed0
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 31f57ae7df
gnu: python-hicexplorer: Update to 3.7.4. 
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.4.
[source]: Remove obsolete snippet.
[arguments]: Remove obsolete phase 'scipy-compatibility.
[propagated-inputs]: Replace python-cleanlab-1 with python-cleanlab.

Change-Id: Iac9a24cc4551b7d7e1d41d1f07a6db6d620b119e
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 9692e2bb7c
gnu: snakemake-5: Patch version string. 
* gnu/packages/python-xyz.scm (snakemake-5)[arguments]: Add phase
'patch-version.

Change-Id: I647625e9d26b2ee06274a0c5bb844ccb87035537
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 8d14b1cbb6
gnu: snakemake-5: Make compatible with tabulate 0.9.0. 
* gnu/packages/python-xyz.scm (snakemake-5)[arguments]: Add phase
'tabulate-compatibility.

Change-Id: I0b0ddafe9c2da91dbe10a584eb6fa0a3d5d62e87
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 36a1e76173
gnu: snakemake: Fetch from git repository. 
* gnu/packages/python-xyz.scm (snakemake)[source]: Fetch from git repository
to include tests.
[arguments]: Enable tests; add 'pre-check phase.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add git-minimal, python-wrapper, python-pytest,
python-pandas, and python-requests-mock.

Change-Id: I32e9d36752cc91eacb8f05138d969834dbbce817
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 6095e5b436
gnu: snakemake-7: Make compatible with tabulate 0.9.0. 
* gnu/packages/python-xyz.scm (snakemake-7)[arguments]: Add phase
'tabulate-compatibility.

Change-Id: Ie6b2a7d65bc76e3df7c3946ba4533b301f5a3610
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 6244177e79
gnu: snakemake-6: Make compatible with tabulate 0.9.0. 
* gnu/packages/python-xyz.scm (snakemake-6)[arguments]: Add phase
'tabulate-compatibility.

Change-Id: I0471726e2000af76871e2542ed347cd1727bf0c9
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus ee9720b2f0
gnu: python-jsonpickle: Update to 3.0.4. 
* gnu/packages/python-web.scm (python-jsonpickle): Update to 3.0.4.
[build-system]: Use pyproject-build-system.
[arguments]: Use test-flags; add 'pre-check phase.
[propagated-inputs]: Add python-importlib-metadata.
[native-inputs]: Add python-bson, python-ecdsa, python-feedparser,
python-pymongo, python-pytest, python-pytest-benchmark, python-pytest-cov,
python-pytest-enabler, python-setuptools, python-setuptools-scm,
python-simplejson, python-sqlalchemy, python-ujson, and tzdata-for-tests.

Change-Id: I99e41ae2652ce02b090ee2b99a7b850a19b5f353
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus d5424b12af
gnu: python-imbalanced-learn: Update to 0.12.2. 
* gnu/packages/machine-learning.scm (python-imbalanced-learn): Update to
0.12.2.
[native-inputs]: Remove python-numpydoc.

Change-Id: I8af0017f76d5ab3a2d55a96c0ace6be22d57fb66
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 2d8c81a8d7
gnu: tadbit: Add R to inputs. 
* gnu/packages/bioinformatics.scm (tadbit)[inputs]: Add r-minimal.

Change-Id: I4929dd89ddd27b4fcbd8b3a00b8ab8f3586945d2
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 93a397f8b7
gnu: tadbit: Patch for compatibility with latest scipy. 
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Add phase
'scipy-compatibility.

Change-Id: Ib25b9cde75f0505c347c4ff470e61f06fb162839
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 453b7a267b
gnu: tadbit: Update to 1.0.1-2.2838129. 
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-2.2838129.

Change-Id: I2c220ae37cd196ca508d30aefc24938cce985527
 2024-05-05 22:38:17 +02:00