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133703 commits

Author SHA1 Message Date
Vivien Kraus 939bd33365
gnu: zathura: Update to 0.5.4.
Build with updated girara.

* gnu/packages/pdf.scm (zathura): Update to 0.5.4.
* gnu/packages/patches/zathura-use-struct-initializers.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it here.
* gnu/packages/pdf.scm (zathura): Use it here.

Change-Id: I5975d993b92a1a77ed35df2206acb93219138cff
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-03-16 10:55:28 +00:00
Vivien Kraus aa9aebce61
gnu: telegram-desktop: Build with glibmm@2.76.
* gnu/packages/telegram.scm (telegram-desktop): Use glibmm-2.76 instead of
glibmm.

Change-Id: I0ec4ebc549dd867db22d68ee6317d1630cf1bfd8
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-03-16 10:35:11 +00:00
Vivien Kraus c6b653f24c
gnu: Add glibmm-2.76.
* gnu/packages/glib.scm (glibmm-2.76): New variable.

Change-Id: I6d38e7640f9362ca7b6d26611db914da74ead53d
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-03-16 10:34:08 +00:00
Vivien Kraus 64785a7941
gnu: libgda: Disable failing tests.
* gnu/packages/patches/libgda-disable-data-proxy-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it here.
* gnu/packages/gnome.scm (libgda): Use it here.

Change-Id: I0a86fb75b1ad048eca99408750b26f4b8ff448c1
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-03-16 10:26:47 +00:00
Christopher Baines 618cae45dc
Merge remote-tracking branch 'savannah/master' into gnome-team
Change-Id: I775274c2693536e2efa36c9abca4c54c5c458e26
2024-03-16 10:19:30 +00:00
Marco Rimoldi 00bf07eccc
gnu: frescobaldi: Make it display icons with qtsvg-5.
* gnu/packages/music.scm (frescobaldi)
[origin]<uri>: Updated to avoid automatic redirect.
[arguments]<phases>: Add 'wrap-executable to export QT_PLUGIN_PATH.
[inputs]: Add qtsvg-5, bash-minimal.

Change-Id: I55b3c56d41bd60e4ba4c938109ff41631e211ad2
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-03-16 10:08:14 +00:00
Marco Rimoldi 82bb2ed9c9
gnu: portmidi: Add variant portmidi-2 updated to release 2.0.4.
Tested with package Frescobaldi.  Other packages dependent on the old 217
version still need to be tested and updated so that it can be phased out.

* gnu/packages/music.scm (portmidi): Add variant portmidi-2.
[version]: Change to new scheme, jumping from 217 to 2.0.4.
[source]: Change origin from Sourceforge to GitHub.
* gnu/packages/music.scm (python-pyportmidi) [inputs]: Change portmidi to portmidi-2.
* gnu/packages/music.scm (frescobaldi) [inputs]: Change portmidi to portmidi-2.

Change-Id: I2530d206e19e885082a95f1aac65348e7a51d4ca
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-03-16 10:05:23 +00:00
Marco Rimoldi cf0f8918f6
gnu: python-pyportmidi: Update to 0.0.7-0.d9e5ee0.
When the PortMidi project moved to GitHub in 2021, changing version numbering
scheme, the Python bindings were moved to a separate repository and marked as
needing a new maintainer.  The chosen revision, dated June 2023, is the first
to allow the package to build successfully in the temporary lack of an
official new release.

* gnu/packages/music.scm (python-pyportmidi): Source moved, fix build.
[version]: Change to new scheme, jumping from 217 to 0.0.7.
[source]: Change origin from Sourceforge to GitHub.

Change-Id: Ibe02edca39731f3f3c9001818665d2da97df9465
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-03-16 10:03:55 +00:00
Marco Rimoldi d99cec308c
gnu: python-poppler-qt5: Update to 21.3.0.
* gnu/packages/pdf.scm (python-poppler-qt5): Update to 21.3.0.
[build-system]: Change to pyproject.
[inputs]: Change SIP to current version variant.
* gnu/packages/patches/python-poppler-qt5-fix-build.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): De-register said patch.

Change-Id: I30d6e2a3180505091d8072ed452211b0bb3a0178
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-03-16 10:03:47 +00:00
Andy Tai 9d8a52d3bd
gnu: freeipmi: Update to 1.6.14.
* gnu/packages/freeipmi.scm (freeipmi): Update to 1.6.14.

Change-Id: I4c729baaf2a45391f95b6f96441a96d2b0f58f40
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-03-16 09:55:17 +00:00
Christopher Baines 5e1e789ffe
gnu: guix-data-service: Update to 0.0.1-46.b4583bb.
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-46.b4583bb.

Change-Id: Iad913c9e7abc43855e8b7964e7753438df6e2300
2024-03-16 09:54:25 +00:00
Christopher Baines 8a53a71cbd
gnu: bffe: Update to 0-5.bdfaab9.
* gnu/packages/package-management.scm (bffe): Update to 0-5.bdfaab9.

Change-Id: I7483026b61971e6420eab5257f0ef8afd54d032d
2024-03-16 09:51:11 +00:00
Christopher Baines 6ef846b9dc
gnu: guix-build-coordinator: Update to 0-99.d802b81.
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-99.d802b81.

Change-Id: I82067857ed358c0895162b4f2fb7a775ede12e7d
2024-03-16 09:32:14 +00:00
Sharlatan Hellseher 6f05c96f96
gnu: go-github-com-bwesterb-go-ristretto: Move to golang-crypto.
* gnu/packages/golang.scm (go-github-com-bwesterb-go-ristretto): Move
from here ...
* gnu/packages/golang-crypto.scm: ... to here.

Change-Id: Ia028e4c5ccceaec3f0ceb828a147eff72cf6a20f
2024-03-15 23:54:12 +00:00
Sharlatan Hellseher 5b59c149e0
gnu: go-github-com-beorn7-perks-quantile: Move to golang-xyz.
* gnu/packages/syncthing.scm (go-github-com-beorn7-perks-quantile): Move
from here ...
* gnu/packages/golang-xyz.scm: ... to here.

Change-Id: I09a2080b78fd3273af75cbbbb49718bb8eec86e5
2024-03-15 23:43:58 +00:00
Sharlatan Hellseher 47f2a8c14b
gnu: kubo: Unbundle more packages.
* gnu/packages/ipfs.scm (kubo) [snippet]: Remove more available vendor
packages.
[inputs]: Add go-github-com-benbjohnson-clock and
go-github-com-blang-semver-v4. Remove go-github-com-cheggaaa-pb-v3,
fail over to vendor package explicitly as v3 is not required.

Change-Id: I8317ea656120b034a98d180278b928f0744f5fbb
2024-03-15 23:33:13 +00:00
Sharlatan Hellseher 9e2d8ed8fd
gnu: go-github-com-beorn7-perks-quantile: Fix indentation.
* gnu/packages/syncthing.scm (go-github-com-beorn7-perks-quantile): Fix
indentation.

Change-Id: Id159b4314fc25ecebc0737221995823e28045626
2024-03-15 23:33:13 +00:00
Sharlatan Hellseher 2f0aba1fd4
gnu: go-github-com-beorn7-perks-quantile: Update to 1.0.1.
* gnu/packages/syncthing.scm (go-github-com-beorn7-perks-quantile):
Update to 1.0.1.

Change-Id: Ie8c864dbc15b3aef3e4575337b940b625d6f9bbf
2024-03-15 23:33:12 +00:00
Sharlatan Hellseher 62fa7ac31e
gnu: kubo: Sort inputs alphabetically.
* gnu/packages/ipfs.scm (kudo) [inputs]: Sort alphabetically to ease
maintenance.

Change-Id: Icb95464b5b8cf7d6e26285628198cfcd5c90e695
2024-03-15 23:33:12 +00:00
Sharlatan Hellseher 024a0e2288
gnu: Add go-github-com-blang-semver-v4.
* gnu/packages/golang-xyz.scm (go-github-com-blang-semver-v4): New variable.

Change-Id: I87132b1b727b7e6ef4d46bb08dc5ad509db4e2e4
2024-03-15 23:33:12 +00:00
Sharlatan Hellseher f59f85bdeb
gnu: go-github-com-blang-semver: Fix indentation.
* gnu/packages/golang-xyz.scm (go-github-com-blang-semver): Fix
indentation.

Change-Id: I9b5e792f2ef859ad7a9d799ba1e369f96e53294b
2024-03-15 23:33:12 +00:00
Sharlatan Hellseher 74cab6cd03
gnu: go-github-com-blang-semver: Update to 3.8.0.
* gnu/packages/golang-xyz.scm (go-github-com-blang-semver): Update to 3.8.0.

Change-Id: I5f1eec936236e4f8984d6aabbab9a9ce99e291a3
2024-03-15 23:33:12 +00:00
Ilya Chernyshov 868e21bb76
gnu: guile-scheme-json-rpc: Update to 0.4.5a.
Shift some inputs requiring during runtime.

* gnu/packages/guile-xyz.scm (guile-scheme-json-rpc): Update to 0.4.5a.
[inputs]: Remove guile-srfi-145 and guile-srfi-180.
[propagated-inputs]: Add guile-srfi-145 and guile-srfi-180.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: If1c6ffaf6269c36ec857fd6f0aec444869468d24
2024-03-15 23:24:56 +00:00
Ricardo Wurmus 10345d2f63
gnu: r-clusterprofiler: Update to 4.10.1.
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.10.1.

Change-Id: I05b41c27d1e1ac8b2887845df5a4a75d45513929
2024-03-15 23:54:35 +01:00
Ricardo Wurmus 48e458e662
gnu: r-zlibbioc: Update to 1.48.2.
* gnu/packages/bioconductor.scm (r-zlibbioc): Update to 1.48.2.
[native-inputs]: Add r-knitr.

Change-Id: Iee1c599473d30532660eb3770cf471ff979530dd
2024-03-15 23:54:35 +01:00
Ricardo Wurmus b11f7c18bd
gnu: r-stringdb: Update to 2.14.3.
* gnu/packages/bioconductor.scm (r-stringdb): Update to 2.14.3.
[propagated-inputs]: Remove r-rcurl; add r-httr.

Change-Id: Id46873bee69cdd1047002db3505ff5420097e9e9
2024-03-15 23:54:35 +01:00
Ricardo Wurmus 74066baa0b
gnu: r-gsva: Update to 1.50.1.
* gnu/packages/bioconductor.scm (r-gsva): Update to 1.50.1.

Change-Id: Ib298992cb9ea4615fe3888e799c332e778a7b5be
2024-03-15 23:54:35 +01:00
Ricardo Wurmus 7416d0f273
gnu: r-genomicfeatures: Update to 1.54.4.
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.54.4.
[propagated-inputs]: Remove r-rcurl; add r-httr and r-rjson.

Change-Id: Iaed5177d04bc1c292dfad607f82401f45cfd02bc
2024-03-15 23:54:35 +01:00
Ricardo Wurmus df26e72fd6
gnu: r-genomeinfodb: Update to 1.38.7.
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.38.7.
[propagated-inputs]: Remove r-rcurl.

Change-Id: Ifc265a49ed946f3548ff279b930a8346c42025a8
2024-03-15 23:54:35 +01:00
Ricardo Wurmus b49398487c
gnu: r-deseq2: Update to 1.42.1.
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.42.1.

Change-Id: Ida0b7ad662c44b2b12af487bb6aa8364874ce3da
2024-03-15 23:54:35 +01:00
Ricardo Wurmus db7d9e6cab
gnu: r-biostrings: Update to 2.70.3.
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.70.3.

Change-Id: I4a921a148d9f54be13967ed0e3092353a683f20f
2024-03-15 23:54:35 +01:00
Ricardo Wurmus f97a8a8650
gnu: r-coregx: Update to 2.6.1.
* gnu/packages/bioconductor.scm (r-coregx): Update to 2.6.1.

Change-Id: Icb0eb5a7697811f4272cda3d42d3c428bb59bd23
2024-03-15 23:54:35 +01:00
Ricardo Wurmus 900ad49572
gnu: r-asics: Update to 2.18.1.
* gnu/packages/bioconductor.scm (r-asics): Update to 2.18.1.

Change-Id: I760771fd8fe57984ae1d0c96b72cb63562a1b43e
2024-03-15 23:54:35 +01:00
Luis Felipe 999bfa0d54
doc: build: Update paths to style sheets.
The Guix website style sheets are now organized in themes. This change
makes the documentation builder use the resources provided by a theme
called "initial" (See https://issues.guix.gnu.org/69783).

* doc/build.scm (syntax-highlighted-html): Update path to CSS.
(html-manual-indexes): Likewise.
(stylized-html): Likewise, and update path to language picker image.

Change-Id: Ib2d51fcfdec42ad827add1ead1cfee4c9c4e65b7
Signed-off-by: Florian Pelz <pelzflorian@pelzflorian.de>
2024-03-15 23:22:45 +01:00
Clément Lassieur 93aefca7ba
gnu: alacritty: Fix loading of libxkbcommon-x11.so.
* gnu/packages/terminals.scm (alacritty)[arguments]: Handle
libxkbcommon-x11.so in the ‘add-absolute-library-references’ phase.

This fixes this error:

thread 'main' panicked at /tmp/guix-build-alacritty-0.13.1.drv-0/source/guix-vendor/rust-xkbcommon-dl-0.4.1.tar.gz/src/x11.rs:59:28:
Library libxkbcommon-x11.so could not be loaded.
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Change-Id: Ifbf19b4962bc3d9eeba6acdf32ca66b0c662f493
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2024-03-15 10:32:03 +02:00
Sharlatan Hellseher 646810ab6a
gnu: python-pycurl: Disable one failing test.
* gnu/packages/python-web.com (python-pycurl) [arguments]
<#:test-flags>: Disable one more failing test which occurs on CI with
CPU thread count more than 16.

Change-Id: Ie772a7f096357b541cc8baa2349a524f05500e52
2024-03-15 07:48:08 +00:00
Leo Famulari e1e6116e05
Revert "gnu: linux-libre-documentation: Fix compilation."
This bug was fixed upstream in 6.7.6.

This reverts commit b6f82b9ef1.

Change-Id: Ia756a62b29ad1f342b0e7430a0cb88cc140974eb
2024-03-15 01:41:23 -04:00
Leo Famulari f28802a813
gnu: linux-libre 4.19: Update to 4.19.309.
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.309.
(linux-libre-4.19-pristine-source): Update hash.

Change-Id: If579a8179ded35cb4269e733bd96ee6f7c5d5360
2024-03-15 01:41:23 -04:00
Leo Famulari 557fc25caa
gnu: linux-libre 5.4: Update to 5.4.271.
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.271.
(linux-libre-5.4-pristine-source): Update hash.

Change-Id: Iaf7277f1f4ec3f106b8f0b82aef5a8be953972bd
2024-03-15 01:41:22 -04:00
Leo Famulari 65d12a4a97
gnu: linux-libre 5.10: Update to 5.10.212.
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.212.
(linux-libre-5.10-pristine-source): Update hash.

Change-Id: I620729ec22cd67bbe22dc808ba6b4d74d2c0479d
2024-03-15 01:41:22 -04:00
Leo Famulari cc2b28975b
gnu: linux-libre 5.15: Update to 5.15.151.
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.151.
(linux-libre-5.15-pristine-source): Update hash.

Change-Id: I83ddffad4f1ce05723faa5d243e8345b21e39edb
2024-03-15 01:41:22 -04:00
Leo Famulari c6d2fa1139
gnu: linux-libre 6.1: Update to 6.1.81.
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.81.
(linux-libre-6.1-pristine-source, deblob-scripts-6.1): Update hashes.

Change-Id: Iaec9f01a190d67bcab490c318456241ea8eabf22
2024-03-15 01:41:22 -04:00
Leo Famulari 1e568b2ed3
gnu: linux-libre 6.6: Update to 6.6.21.
* gnu/packages/linux.scm (linux-libre-6.6-version): Update to 6.6.21.
(linux-libre-6.6-pristine-source): Update hash.

Change-Id: Ic2f197add55f89196010c32957e10d3683cb8c01
2024-03-15 01:41:21 -04:00
Leo Famulari 019fb14b1e
gnu: linux-libre: Update to 6.7.9.
* gnu/packages/linux.scm (linux-libre-6.7-version): Update to 6.7.9.
(linux-libre-6.7-pristine-source): Update hash.

Change-Id: I9d3e3907623b17f1a47b78ea00e9b7a5cf428ff6
2024-03-15 01:41:21 -04:00
Sharlatan Hellseher a862a99bb3
gnu: python-pycurl: Enable tests.
* gnu/packages/python-web.scm (python-pycurl): Enable most of the tests.
[build-system]: Swap to pyproject-build-system.
[arguments] <#:tests?>: Enable them.
<#:test-arguments>: Disable some failing and hanging tests.
[native-inputs]: Add python-flaky, python-pytest, and
python-pytest-xdist.

Change-Id: Ie222aa1111720f2e39b950b79d9e707401be7e8f
2024-03-14 23:29:02 +00:00
Sharlatan Hellseher 2187ac84d0
gnu: packages: python-web: Sort use-modules alphabetically.
* gnu/packages/python-web.scm: Sort #:use-module alphabetically to ease
maintenance.

Change-Id: Id01b66ff7eaf610895c1275c2abfd9de2e537d8e
2024-03-14 23:28:52 +00:00
Troy Figiel e22175655d
gnu: Add python-zodb.
* gnu/packages/python-web.scm (python-zodb): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-03-14 22:49:59 +00:00
Troy Figiel 36da1ad73d
gnu: Add python-zodbpickle.
* gnu/packages/python-web.scm (python-zodbpickle): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-03-14 22:49:51 +00:00
Troy Figiel fb377b4af7
gnu: Add python-zconfig.
* gnu/packages/python-web.scm (python-zconfig): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-03-14 22:22:45 +00:00
Ricardo Wurmus efe62c5ed3
gnu: Add morpheus.
* gnu/packages/bioinformatics.scm (morpheus): New variable.

Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
Change-Id: I4bf14414f497ff17690b1d26420d442d236fd6b5
2024-03-14 21:01:37 +01:00