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135703 Commits (21b9cd035536f4875b4f0a1b526a385b17d08d63)

Author SHA1 Message Date
chris d6a39f3e89
gnu: highlight: Update to 4.11. 
* gnu/packages/pretty-print.scm (highlight): Update to 4.11.
[source]: Switch to git-fetch.
[home-page]: Switch to html page.
[arguments]<#:make-flags>: Use #$output replace %output.
<#:phases>: Use ‘this-package-input‘ to find lua and perl.

Reviewed-by: Dale Mellor <guix-devel-0brg6a@rdmp.org>
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

Change-Id: I0c402fcea5708c4882b52309b3e072301f0a5614
 2024-05-06 13:44:24 +02:00
Daniel Ziltener 7ed5a336bd
gnu: hwdata: Update to 0.378. 
* gnu/packages/pciutils.scm (hwdata): Update to 0.378.

Reviewed-by: Dale Mellor <guix-devel-0brg6a@rdmp.org>
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Change-Id: I7200477ce06280913802e94cd5ef6d9639b8de9f
 2024-05-06 13:42:50 +02:00
Arjan Adriaanse a8f0e8a31d
gnu: pcsc-lite: Update to 2.1.0. 
* gnu/packages/security-token.scm (pcsc-lite): Update to 2.1.0.

Reviewed-by: Christina O'Donnell <cdo@mutix.org>

Change-Id: I133fd056afb84259cf5cb1f3e9c664ac336e50b9
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2024-05-06 13:41:57 +02:00
Rovanion Luckey 3bc4f32058
gnu: musescore: Propagate alsa-plugins pulseaudio to runtime. 
In order for libasound_module_conf_pulse.so to be present at runtime of
MuseScore the alsa-plugins output "pulseaudio" must be present.

Playback of scores was not working, at least on a foreign distro like
Debian. When running on Debian, MuseScore complained that
libasound_module_conf_pulse.so was missing at startup. This patch was
tested on Debian 12 and fixed the issue.

* gnu/packages/music.scm (musescore): Propagate alsa-plugins pulseaudio to runtime

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Change-Id: I4e2db8e45fdf33987817cef41bcd336526b16d90
 2024-05-06 13:41:11 +02:00
James Smith 20cb45a502
gnu: leocad: Update to 23.03 
* gnu/packages/lego.scm (leocad): Update to 23.03

Change-Id: I0fc566e0325aa992440cf4f895b5780df7e49632
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-05-06 13:26:16 +02:00
Timotej Lazar e4090a558f
gnu: msmtp: Update to 1.8.26. 
* gnu/packages/mail.scm (msmtp): Update to 1.8.26.

Change-Id: I85eea2d64944a3e1b7b4ed3022772190ee5787c2
 2024-05-06 13:24:42 +02:00
Sergey Trofimov bdba291a72
gnu: emacs-telega: Update to 0.8.255. 
* gnu/packages/emacs-xyz.scm (emacs-telega): Update to 0.8.255.
* gnu/packages/patches/emacs-telega-path-placeholder.patch: Update patch.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I8cec5a5170318f0ae99116a98afcefe31203b585
 2024-05-06 13:22:29 +02:00
Ricardo Wurmus f736a784e1
gnu: trust4: Update to 1.1.0. 
* gnu/packages/bioinformatics.scm (trust4): Update to 1.1.0.

Change-Id: I4780038a5db110514e27f07a576166def4063da7
 2024-05-06 12:36:53 +02:00
Mădălin Ionel Patrașcu 709e87caff
gnu: Add trust4. 
gnu/packages/bioinformatics.scm (trust4): New variable.

Change-Id: I6a0fd339a0f761a473f50c7da74c26cfac7b1caf
 2024-05-06 11:47:05 +02:00
Mădălin Ionel Patrașcu 57769fb0b3
gnu: Add r-seraster. 
* gnu/packages/bioinformatics.scm (r-seraster): New variable.

Change-Id: I9f9fd24a9aa563f7c74154e613b85dee46bdcf79
 2024-05-06 11:38:17 +02:00
Mădălin Ionel Patrașcu fc51a747fa
gnu: Add r-rearrr. 
* gnu/packages/cran.scm (r-rearrr): New variable.

Change-Id: I41e06b24e565a4070f570b7fd5c656f185aacfa9
 2024-05-06 11:38:08 +02:00
Mădălin Ionel Patrașcu 64fcc49dc5
gnu: Add r-metadeconfoundr. 
* gnu/packages/bioinformatics.scm (r-metadeconfoundr): New variable.

Change-Id: I733fb464d2a3c7fd1335826be9f23e2610e6fd60
 2024-05-06 11:26:54 +02:00
Mădălin Ionel Patrașcu 2c52bbd16d
gnu: Add r-detectseparation. 
* gnu/packages/cran.scm (r-detectseparation): New variable.

Change-Id: I6c795719c22a6ff929785e799f749ce053e83fbe
 2024-05-06 11:24:57 +02:00
Mădălin Ionel Patrașcu 458cd1e1d8
gnu: Add r-roi-plugin-lpsolve. 
* gnu/packages/cran.scm (r-roi-plugin-lpsolve): New variable.

Change-Id: Ia3f47ba0b414ecd9273c101977ec8d14916fa656
 2024-05-06 11:24:56 +02:00
Mădălin Ionel Patrașcu 112ecacba3
gnu: Add r-roi. 
* gnu/packages/cran.scm (r-roi): New variable.

Change-Id: I58cbb4be238a5cc9f861ee9dafea03a133f7c0f1
 2024-05-06 11:24:56 +02:00
Mădălin Ionel Patrașcu 2b7e9239c0
gnu: Add r-lpsolveapi. 
* gnu/packages/cran.scm (r-lpsolveapi): New variable.

Change-Id: I6a93603a5814df0eb43a214b5c2a0f4865901bcd
 2024-05-06 11:24:56 +02:00
nafkhamdc 00aa6b5a3c
gnu: Add python-pyrodigal. 
* gnu/packages/bioinformatics.scm (python-pyrodigal): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

Change-Id: Iaa0bdb4b918d93f990d5b904f1df3a3f910726b0
 2024-05-06 10:37:41 +02:00
nafkhamdc a5fef66b34
gnu: Add python-archspec. 
* gnu/packages/python-xyz.scm (python-archspec): New variable.

Change-Id: Icb15a681d7f339ab25cb0a91feeaacc6a3e8cd6a
 2024-05-06 10:37:41 +02:00
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