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Author SHA1 Message Date
Ricardo Wurmus
2b3a21c55f
gnu: Add r-experimenthubdata. 
* gnu/packages/bioconductor.scm (r-experimenthubdata): New variable.

Change-Id: I5faf26f483898b162bc1f863a4aceb6f46c52c18
 2024-01-20 19:52:05 +01:00
Ricardo Wurmus
c4838027b4
gnu: Add r-jaspar2016. 
* gnu/packages/bioconductor.scm (r-jaspar2016): New variable.

Change-Id: Ib2970791207b426c39bd0226e01107a35fec0bb2
 2024-01-20 19:50:13 +01:00
Ricardo Wurmus
6f93502ced
gnu: Add r-genomicstate. 
* gnu/packages/bioconductor.scm (r-genomicstate): New variable.

Change-Id: I1b86c8e849af7b69b5fa9ea2a0e43b4e3e1850b2
 2024-01-20 19:45:26 +01:00
Ricardo Wurmus
4e706e6b18
gnu: Add r-shinymeta. 
* gnu/packages/cran.scm (r-shinymeta): New variable.

Change-Id: I35e1c032283cdc010e4551c0d33f9d4202d9deee
 2024-01-20 19:45:26 +01:00
Ricardo Wurmus
c410d4e268
gnu: Add r-ensdb-hsapiens-v79. 
* gnu/packages/bioconductor.scm (r-ensdb-hsapiens-v79): New variable.

Change-Id: I773615df66194ddb195f013f7000d175ac07d095
 2024-01-20 19:45:26 +01:00
Maxim Cournoyer
9c367ee196
gnu: Add rust-rustc-demangle-capi-0.1. 
* gnu/packages/crates-io.scm (rust-rustc-demangle-capi-0.1): New variable.

Change-Id: I98afb19ed4bdbcb9107a1ab30af49b055802b8b0

Reviewed-by: Efraim Flashner <efraim@flashner.co.il>
Change-Id: Ifeaefa5a377600320c3fd2a637aefaf29707e3b7
 2024-01-19 22:57:27 -05:00
Maxim Cournoyer
b509dedf83
gnu: guile-hall: Update to 0.4.1-1.7558ba9. 
* gnu/packages/guile-xyz.scm (guile-hall): Update to 0.4.1-1.7558ba9.
[arguments] <modules>: Remove (ice-9 match) and (ice-9 ftw) modules.
Add (guix build guile-build-system).
<phases>: Use gexps.  Streamline hall-wrap-binaries phase.
[native-inputs]: Add guile-3.0 and gettext-minimal.
[propagated-inputs]: Delete field, moving guile-config to...
[inputs]: ... here.  Add bash-minimal and guile-lib.

Change-Id: Idef796dc3ba9ca3fa4df8114efe91af7c5cf7be0
 2024-01-19 22:57:15 -05:00
Maxim Cournoyer
c66a1a0f0f
gnu: reuse: Update to 3.0.1. 
* gnu/packages/license.scm (reuse): Update to 3.0.1.
[arguments]: New field.

Change-Id: Ibbc5ae8cfa0e0e62b6c64bd90387022e88f9c933
 2024-01-19 22:50:24 -05:00
Vinicius Monego
dae418afd7
gnu: symengine: Update to 0.11.2. 
* gnu/packages/algebra.scm (symengine): Update to 0.11.2.

Change-Id: I34c24dd8591e306a7740f0a3d51077aceec67fab
 2024-01-19 22:01:31 -03:00
Vinicius Monego
a185dd97e4
gnu: python-metpy: Update to 1.6.1. 
* gnu/packages/geo.scm (python-metpy): Update to 1.6.1.

Change-Id: Id8d8d6db3e31307242e56c494b6dee7c2ffab8f1
 2024-01-19 22:01:31 -03:00
Vinicius Monego
a6b249bd67
gnu: python-deepxde: Update to 1.10.1. 
* gnu/packages/machine-learning.scm (python-deepxde): Update to 1.10.1.

Change-Id: If3515735d4adee8a2f1e9460d6ccb72c6ce26321
 2024-01-19 22:01:31 -03:00
Vinicius Monego
826b4331d3
gnu: python-mapie: Update to 0.8.2. 
* gnu/packages/statistics.scm (python-mapie): Update to 0.8.2.

Change-Id: I82098caa8ed5d3bf68eec9f374f600d203d6b178
 2024-01-19 22:01:31 -03:00
Vinicius Monego
b482a6c768
gnu: libngspice: Update to 42. 
* gnu/packages/engineering.scm (libngspice, ngspice): Update to 42.

Change-Id: Ib7b72724f8f46ce376bd6517cb2652c870edcb0d
 2024-01-19 22:01:31 -03:00
Vinicius Monego
9c67673d7b
gnu: darktable: Update to 4.6.0. 
* gnu/packages/photo.scm (darktable): Update to 4.6.0.

Change-Id: Ic64b02e8d191ba91fde1b95b9bcb4321a471dcba
 2024-01-19 22:01:31 -03:00
Vinicius Monego
946cd84d57
gnu: darktable: Enable more optional features. 
* gnu/packages/photo.scm (darktable)[inputs]: Add libjxl, portmidi.

Change-Id: I7747dfc2e88379a13182590f87514951bdd70e0c
 2024-01-19 22:01:30 -03:00
Vinicius Monego
e7d14578ad
gnu: darktable: Build with GCC. 
* gnu/packages/photo.scm (darktable)[arguments][#:phases]: Delete the
'prepare-build-environment phase.
[native-inputs]: Remove clang. Add gcc-13.

Change-Id: Ia0dc1c6a717ccd00cd31d378aa51ce63fbf1806a
 2024-01-19 22:01:30 -03:00
Vinicius Monego
5073187524
gnu: gmic: Update to 3.3.3. 
gmic was integrated into Krita 5+.

* gnu/packages/image-processing.scm (gmic, gmic-qt): Update to 3.3.3.
(gmic-qt-krita): Delete variable.

Change-Id: I44e33b570bcf3e1df3eba5eb9ede1f333f8a177a
 2024-01-19 22:01:30 -03:00
Vinicius Monego
53096bb5a0
gnu: labplot: Update to 2.10.1. 
* gnu/packages/kde.scm (labplot): Update to 2.10.1.
[source]<origin>: Update URI.

Change-Id: I03d24410304fb14daa20f7a75f6947caed63ab84
 2024-01-19 22:01:22 -03:00
Vinicius Monego
9f918e9c48
gnu: python-symengine: Update to 0.11.0. 
* gnu/packages/python-xyz.scm (python-symengine): Update to 0.11.0.
[native-inputs]: Replace python-cython with python-cython-3.

Change-Id: Ieab464491e3df6e2bdb5b552cbf48ebf67ff81e4
 2024-01-19 21:56:37 -03:00
Ricardo Wurmus
eb1d80ac77
gnu: Add r-trnadbimport. 
* gnu/packages/bioconductor.scm (r-trnadbimport): New variable.

Change-Id: I5a232b50c08ef999f691566ccf5c0fbaf0eb21ea
 2024-01-19 23:55:43 +01:00
Ricardo Wurmus
74ce9d7e3b
gnu: Add r-trna. 
* gnu/packages/bioconductor.scm (r-trna): New variable.

Change-Id: Ifce902910fa75ddc471d8a25cc974307c19fd1d0
 2024-01-19 23:55:43 +01:00
Ricardo Wurmus
1d56a24509
gnu: Add r-modstrings. 
* gnu/packages/bioconductor.scm (r-modstrings): New variable.

Change-Id: Ia61816213a7d128ab50a9ae2b2c8879e6ac00499
 2024-01-19 23:55:43 +01:00
Ricardo Wurmus
5c10649a50
gnu: Add r-structstrings. 
* gnu/packages/bioconductor.scm (r-structstrings): New variable.

Change-Id: I9759520a03ee8178432591c48bf56fb25a379f27
 2024-01-19 23:55:43 +01:00
Ricardo Wurmus
d084e9d036
gnu: Add python-mediapy. 
* gnu/packages/python-xyz.scm (python-mediapy): New variable.

Change-Id: I2e55c018670053c662ae2d896feefab3b505b139
 2024-01-19 23:55:43 +01:00
Ricardo Wurmus
d8c718d44c
gnu: Add r-flames. 
* gnu/packages/bioconductor.scm (r-flames): New variable.

Change-Id: I551a8f9d7de16e2281898b9541572dd244aadc36
 2024-01-19 23:55:43 +01:00
Artyom V. Poptsov
f7c0ccb186
gnu: kubo: Update to 0.16.0. 
* gnu/packages/ipfs.scm (kubo): Update to 0.16.0.
  [arguments]: Use go-1.18.
  [home-page]: Set to "https://ipfs.tech".

Change-Id: I06239354b0c9c23294d5aeac6d01f67636d5d3a5
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-19 21:51:35 +00:00
Maxim Cournoyer
c0f423bf1a
gnu: emacs-evil-quickscope: Skip failing test. 
* gnu/packages/emacs-xyz.scm (emacs-evil-quickscope)
[arguments]: Use gexps.  Add disable-failing-tests phase.

Change-Id: If372531778eab6e3fc164a2f63b98d6775193114
 2024-01-19 15:05:53 -05:00
Maxim Cournoyer
d6170e03e3
gnu: emacs-shx: Fix test failure. 
* gnu/packages/patches/emacs-shx-byte-compilation-test.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/emacs-xyz.scm (emacs-shx): Apply it.

Change-Id: I6d8edd3b50f99f1c4cd495216caf9648dfee4ea3
 2024-01-19 15:05:53 -05:00
Maxim Cournoyer
33f12b7dcd
gnu/local.mk: Sort Emacs patches and fix 2044 year in copyright notice. 
* gnu/local.mk: Correct 2044 copyright year.
(dist_patch_DATA): Sort emacs patches.

Change-Id: Ib9669bb1d7fb2556d6d809d62624981fa66d27f3
 2024-01-19 15:05:53 -05:00
Maxim Cournoyer
ec24673bf9
gnu: emacs-org-journal: Disable failing tests. 
* gnu/packages/emacs-xyz.scm (emacs-org-journal)
[arguments]: Add disable-failing-tests phase.

Change-Id: I466cb46613a7048ccbda66cd7855001a04871891
 2024-01-19 15:05:52 -05:00
Maxim Cournoyer
72f31a9be6
gnu: emacs-ess: Disable flaky "command-without-trailing-newline-test" test. 
* gnu/packages/statistics.scm [arguments]: Add new disable-etests syntax in
'skip-failing-tests phase, and use it to disable the
'command-without-trailing-newline-test' test.

Change-Id: I99f52685691d86dc633fe6061f9ef3332159eb4e
 2024-01-19 15:05:52 -05:00
Arun Isaac
4987618368
gnu: wfmash: Update to 0.12.5. 
* gnu/packages/bioinformatics.scm (wfmash): Update to 0.12.5.
(source): Use git-fetch. Update git repository URL.
(arguments): In check phase, symlink to "../source/data" and change wfmash
invocation arguments.
(home-page): Update URL.

Change-Id: I78f228f06a6a12e6904a58a12fd4201743e84d72
 2024-01-19 18:04:39 +00:00
Greg Hogan
15efd5a7f4
gnu: python-graph-tool: Update to 2.59. 
* gnu/packages/graph.scm (python-graph-tool): Update to 2.59.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I08ecb5fe76183fa980fedf2408fc1df93ebbc63d
 2024-01-19 17:20:04 +00:00
Christopher Baines
4d91ddf5bc
gnu: guix-build-coordinator: Update to 0-95.dc04b74. 
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-95.dc04b74.

Change-Id: I89d968e72188428d40906a7d55533dfd25c7ec25
 2024-01-19 16:45:38 +00:00
Christopher Baines
6fb4cb7ca3
gnu: bffe: Update to 0-3.1c12da4. 
* gnu/packages/package-management.scm (bffe): Update to 0-3.1c12da4.

Change-Id: I90a4231961aed434c2b4ffa07189b85e108b5c46
 2024-01-19 16:45:38 +00:00
Sharlatan Hellseher
65e7828a95
gnu: nsq: Fix build on i686-linux. 
As seen in https://ci.guix.gnu.org/build/3329277/details

* gnu/packages/high-availability.scm (nsq)[arguments]<#:phases>{check}:
Skip '-race' option during tests on i686-linux.

Change-Id: I952d7187443835d5fbcb74f0ae09b923bd6bdb29
 2024-01-19 13:57:54 +00:00
Cayetano Santos
0eadd48648
gnu: Add emacs-vhdl-mode. 
* gnu/packages/emacs-xyz.scm (emacs-vhdl-mode): New variable.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Change-Id: I7e261fc25ae011c20f22e1078ae40bacff3a6947
 2024-01-18 22:42:42 -05:00
Maxim Cournoyer
05be458f02
gnu: Add emacs-pde. 
* gnu/packages/emacs-xyz.scm (emacs-pde): New variable.

Change-Id: Icab5d8acf9d441bb4a832a82e75432d64cc77ba7
 2024-01-18 22:41:02 -05:00
Maxim Cournoyer
33783e3695
gnu: perl-b-keywords: Update to 1.26. 
* gnu/packages/perl.scm (perl-b-keywords): Update to 1.26.

Change-Id: I3fdb9acf9f257ff9583179e29b2e6a26104b7e0d
 2024-01-18 22:10:58 -05:00
Maxim Cournoyer
2d40e6f7ab
build: perl: Accept Gexps for #:module-build-flags. 
* guix/build-system/perl.scm (perl-build) [module-build-flags]: Accept gexps.

Change-Id: If1daa4d9a8cf97824b75f2113f4d7d83256463ce
 2024-01-18 22:10:58 -05:00
Maxim Cournoyer
90b1fe57d0
gnu: emacs: Patch awk, find, sed and sh commands. 
Before this change, using Emacs in a pure environment, e.g. 'guix shell --pure
emacs', would cause problems such as:

  jka-compr-insert-file-contents: Uncompression program ‘sh’ not found

And other problems were found requiring the other tools.

* gnu/packages/emacs.scm (emacs-minimal) [arguments]: Extend the
patch-program-file-names phase.
[inputs]: Add findutils, gawk and sed.

Series-changes: 2
 - Patch references in place instead of wrapping via PATH

Change-Id: Ifb4fe2fc12ddc9eae387adb3da3f7821fab78e65
 2024-01-18 22:10:58 -05:00
Maxim Cournoyer
d97a6c9ba7
gnu: qt-creator: Update to 12.0.1. 
* gnu/packages/qt.scm (qt-creator): Update to 12.0.1.
[source]: Adjust snippet for the upstream removal of bundled libraries under
the unittest directory.
[arguments]: Also wrap kcachegrind tool in wrap-bin phase.
[inputs]: Add kcachegrind.

Change-Id: I63616d532be2f1a603fcee0841f493d83a138302
 2024-01-18 22:10:33 -05:00
Maxim Cournoyer
7d4a4ded8d
gnu: kcachegrind: Update to 23.08.4. 
* gnu/packages/kde.scm (kcachegrind): Update to 23.08.4.

Change-Id: I5cd0401c61325b274bfcb5c4bc914d8fe0325388
 2024-01-18 22:10:33 -05:00
Maxim Cournoyer
f3fdb4e041
gnu: mpv: Propagate most libraries. 
This is needed when packages lookup the mpv library via pkg-config, such as
done by plasmatube.

Prior to this change, the following would fail (this is what CMake's
'pkg_check_modules' does):

  $ guix shell --pure pkg-config mpv \
    -- pkg-config --print-errors --short-errors --exists mpv
  Package 'wayland-client', required by 'mpv', not found

* gnu/packages/video.scm (mpv)
[inputs]: Move alsa-lib, ffmpeg, jack-1, libass, libbluray, libcaca,
libcdio-paranoia, libdvdnav, libjpeg-turbo, libplacebo, libva, libvdpau,
libx11, libxext, libxinerama, libxpresent, libxrandr, libxscrnsaver, lua-5.2,
mesa, pulseaudio, shaderc, wayland, wayland-protocols, zimg and zlib to...
[propagated-inputs]: ... here.

Change-Id: Ia0cd4e33a8b4df4b060546c979d00be0b2b3977e
 2024-01-18 20:54:18 -05:00
Maxim Cournoyer
119f4cad81
gnu: libdvdnav: Propagate libdvdread. 
* gnu/packages/video.scm (libdvdnav) [inputs]: Move libdvdread to...
[propagated-inputs]: ... here.

Change-Id: Ifea887985f27ed1dec2c56ce2f5291862f011bed
 2024-01-18 20:54:18 -05:00
Maxim Cournoyer
4c3794f82d
gnu: libplacebo: Propagate lcms, shaderc and vulkan-loader. 
* gnu/packages/video.scm (libplacebo)
[inputs]: Move lcms, shaderc and vulkan-loader to...
[propagated-inputs]: ... here.

Change-Id: If426be3b4e32632bb775485e0a8c517e09ccbeaf
 2024-01-18 20:54:18 -05:00
Maxim Cournoyer
ee1521f67b
gnu: ktextaddons: Update to 1.5.3. 
* gnu/packages/kde-frameworks.scm (ktextaddons): Update to 1.5.3.
[inputs]: Add kio, ksyntaxhighlighting and sonnet.

Change-Id: I2c09d28f90dfcd43bf3081e2174405837798b29f
 2024-01-18 20:54:18 -05:00
Maxim Cournoyer
200d8cdf8e
gnu: pulseaudio-qt: Update to 1.4.0. 
* gnu/packages/kde-frameworks.scm (pulseaudio-qt): Update to 1.4.0.

Change-Id: I6a7a60a6da03af5591724596509292e09616ca7d
 2024-01-18 20:54:17 -05:00
Maxim Cournoyer
a413b85918
gnu: kdav: Update to 5.114.0. 
* gnu/packages/kde-frameworks.scm (kdav): Update to 5.114.0.

Change-Id: Ieceba23a043909cd88018e3f2e310d0483c7f3f8
 2024-01-18 20:54:17 -05:00
Maxim Cournoyer
b7734daf51
gnu: kross: Update to 5.114.0. 
* gnu/packages/kde-frameworks.scm (kross): Update to 5.114.0.

Change-Id: Icbfcae279178923737634f5c371e440f8c69ccd8
 2024-01-18 20:54:17 -05:00