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Author SHA1 Message Date
Ricardo Wurmus
3ad93a9458
gnu: r-pkgload: Update to 1.3.4. 
* gnu/packages/cran.scm (r-pkgload): Update to 1.3.4.

Change-Id: I5aa683b1ce91c3fd6ee9ed5015f9a0dabda88b9e
 2024-01-17 23:09:46 +01:00
Ricardo Wurmus
d38f1e5013
gnu: r-ggvenndiagram: Update to 1.5.0. 
* gnu/packages/cran.scm (r-ggvenndiagram): Update to 1.5.0.
[propagated-inputs]: Remove r-tidyr; add r-venn and r-yulab-utils.

Change-Id: Ic065aaf5f8e62f8c1f23e6c845dde88bbc682f69
 2024-01-17 23:09:45 +01:00
Ricardo Wurmus
612a24a7b8
gnu: r-proj4: Update to 1.0-14. 
* gnu/packages/cran.scm (r-proj4): Update to 1.0-14.

Change-Id: I97575fc9f094b0e3cedb33dc83bbea286ed6c63d
 2024-01-17 23:09:45 +01:00
Ricardo Wurmus
7f7ca62e27
gnu: r-ggstatsplot: Update to 0.12.2. 
* gnu/packages/cran.scm (r-ggstatsplot): Update to 0.12.2.

Change-Id: Iafe26006e36b482da64afa5c1ae88176ba2590d0
 2024-01-17 23:09:45 +01:00
Ricardo Wurmus
e1d3131080
gnu: r-cplm: Update to 0.7-12. 
* gnu/packages/cran.scm (r-cplm): Update to 0.7-12.

Change-Id: I59dee59bdf25589ffe866f69996facfe39234b39
 2024-01-17 23:09:44 +01:00
Ricardo Wurmus
9605247199
gnu: r-collapse: Update to 2.0.9. 
* gnu/packages/cran.scm (r-collapse): Update to 2.0.9.

Change-Id: I748bd138cb79ea3af4d90788544e8f1cecb91440
 2024-01-17 23:09:44 +01:00
Ricardo Wurmus
dd4f952366
gnu: Add r-venn. 
* gnu/packages/cran.scm (r-venn): New variable.

Change-Id: I6ec3e890cab6e9042686148b7c52988f0dbb878e
 2024-01-17 23:06:31 +01:00
Ricardo Wurmus
b94047cf81
import/cran: Accept optional alternative download procedure. 
This is useful for cached mass imports.

* guix/import/cran.scm (fetch-description-from-tarball): Accept optional
download keyword.
(fetch-description): Accept optional replacement-download argument.

Change-Id: Ic917074656ac34a24c8e7eea3d3e0528fc5180b3
 2024-01-17 22:59:11 +01:00
Ricardo Wurmus
270570f090
gnu: python-snaptools: Disable tests. 
* gnu/packages/bioinformatics.scm (python-snaptools)[arguments]: Disable
tests.

Change-Id: I4934bda3cfbaf42a87f57035ec12d084112dcc24
 2024-01-17 21:41:45 +01:00
Wilko Meyer
95a3aaf7ad
gnu: Add linux-libre 6.7. 
* gnu/packages/linux.scm (linux-libre-6.7-version, linux-libre-6.7-gnu-revision,
deblob-scripts-6.7, linux-libre-6.7-pristine-source, linux-libre-6.7-source,
linux-libre-headers-6.7, linux-libre-6.7): New variables.
* gnu/packages/aux-files/linux-libre/6.7-arm.conf,
gnu/packages/aux-files/linux-libre/6.7-arm64.conf,
gnu/packages/aux-files/linux-libre/6.7-i686.conf,
gnu/packages/aux-files/linux-libre/6.7-x86.conf: New files.
* Makefile.am (AUX_FILES): Add them.
* Makefile.am: Update my copyright header.

Change-Id: I88b633933875f64bd2859774419e077d8f36d75b
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-01-17 15:23:35 -05:00
cage
8ca490e660
gnu: gmid: Update to 2.0. 
* gnu/packages/web.scm (gmid): Update it.

Change-Id: I8f1bcd36130a63d07e934093b5b12cc01a6d5022
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-17 18:30:28 +01:00
kiasoc5
14e93b5f5a
gnu: perl-image-exiftool: Update to 12.70. 
* gnu/packages/photo.scm (perl-image-exiftool): Update to 12.70.

Change-Id: If8e26b7e92cb530391cdd1dd12e78b371494a6b3
 2024-01-17 18:30:27 +01:00
Artyom V. Poptsov
903386f872
gnu: Add go-github-com-charmbracelet-harmonica. 
* gnu/packages/golang.scm (go-github-com-charmbracelet-harmonica): New
  variable.

Change-Id: I7e08006571be4e6b21eb4df3df8f3c92a412c0ca
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-17 18:30:27 +01:00
Tomas Volf
aa74e0bf17
gnu: ngtcp2: Build libngtcp2_crypto_gnutls. 
* gnu/packages/networking.scm (ngtcp2)[arguments]<#:configure-flags>: Add
--with-gnutls.
[native-inputs]: Add pkg-config.
[inputs]: Add gnutls.

Change-Id: Id3a9210992d203a57a9b791f3c3752f2ebd3e634
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-17 18:30:27 +01:00
Tomas Volf
a17a900589
gnu: ngtcp2: Update to 1.1.0. 
* gnu/packages/networking.scm (ngtcp2): Update to 1.1.0.

Change-Id: I7f6b08952ba508207c8dedbd68c7c48dd17dd0ff
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-17 18:30:27 +01:00
Tomas Volf
685399c27d
gnu: Add nghttp3. 
* gnu/packages/web.scm (nghttp3): New variable.

Change-Id: I4ed318506f6d3bdd0c47a367b1dcc1b4454c09b2
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-17 18:30:27 +01:00
Tomas Volf
dcc6f0537f
gnu: web: Delete trailing whitespace. 
* gnu/packages/web.scm (krona-tools): Delete trailing whitespace.

Change-Id: Ide601b011d3e2c3c736bf041571f9ab00b5b5b1d
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-17 18:30:27 +01:00
nafkhamdc
7bbb329060
gnu: Add r-caic4. 
* gnu/packages/cran.scm (r-caic4): New variable.

Change-Id: Ifdfb6e69c7d1801b347ce16b4ee48a4950963fe4
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-01-17 17:23:24 +01:00
Ian Eure
b3e0a973bc
gnu: powertop: Correct package description. 
* gnu/packages/linux.scm (powertop): Correct package description.

Change-Id: Ifc81ed62158df8b3c235d335731590e977dcc725
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-17 11:18:00 +01:00
spacecadet
8fbda358ab
gnu: Add tgif. 
* gnu/packages/image.scm (tgif): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
Change-Id: I4fd6bf5ae25806775e75dcca680a067f5d80ef5e
 2024-01-17 11:18:00 +01:00
Troy Figiel
dac977ea4e
gnu: Add python-pandera. 
* gnu/packages/python-science.scm (python-pandera): New variable.
 2024-01-17 11:18:00 +01:00
Troy Figiel
23cb6187f6
gnu: Add python-pandas-stubs. 
* gnu/packages/python-science.scm (python-pandas-stubs): New variable.
 2024-01-17 11:18:00 +01:00
Troy Figiel
6c34d33cde
gnu: Add python-typeguard-4. 
* gnu/packages/python-xyz.scm (python-typeguard-4): New variable.

Change-Id: Ic5728766e8171dc31a82056f55a8c00680db5870
 2024-01-17 11:17:59 +01:00
Troy Figiel
1e0b80b9e1
gnu: Add python-concurrent-log-handler. 
* gnu/packages/python-xyz.scm (python-concurrent-log-handler): New variable.
 2024-01-17 11:17:59 +01:00
Troy Figiel
4acaa72e7b
gnu: Add python-pdf2image. 
* gnu/packages/python-xyz.scm (python-pdf2image): New variable.
 2024-01-17 11:17:59 +01:00
Tomas Volf
21989dd57d
image: Consider grub-efi-removable-bootloader to be EFI bootloader. 
Without this change, trying to create a system image with efi-raw type while
using grub-efi-removable-bootloader fails with fairly confusing message:

    EFI bootloader required with GPT partitioning

* gnu/system/image.scm (system-disk-image): Consider
grub-efi-removable-bootloader to be EFI bootloader.

Change-Id: I5f5e1a94e825fd29d6880c5bafb330e16a5ac962
 2024-01-17 11:17:59 +01:00
Efraim Flashner
299ce524c9
home: fontutils: Don't install fontconfig. 
* gnu/home/services/fontutils.scm (home-fontconfig-service-type): Don't
add fontconfig to the profile.

Change-Id: I28208461efdfa4a585ee61db3a23bed05eb38d02
 2024-01-17 11:13:45 +02:00
Efraim Flashner
0f967dde76
home: services: zsh: Use unified zprofile. 
* gnu/home/services/shells.scm (zsh-file-zprofile): Use the zprofile
defined in (gnu system shadow) as a base.

Change-Id: Iaf4c4f66d1ccbc0bd0166136b3d082229bdec201
 2024-01-17 11:11:10 +02:00
Efraim Flashner
5ef5095ab1
system: default-zprofile: Sync with home zprofile. 
The removed fields are already sourced in /etc/profile.

* gnu/system/shadow.scm (%default-zprofile): Sync with default zprofile
from (gnu home services shells).

Change-Id: I419eadf636344e23e8fd2f7006efa81f45527756
 2024-01-17 11:11:10 +02:00
Efraim Flashner
1e8ac2c41b
system: Add default guix-home-config. 
* gnu/system/shadow.scm (%deafult-skeleton-home-config): New variable.
(default-skeletons): Add it.

Change-Id: Ida4cca8b1b3674491a4f18d94bc1b12d426575ba
 2024-01-17 11:11:10 +02:00
Efraim Flashner
3ca02f0304
system: Export default guile config. 
* gnu/system/shadow.scm (%default-dotguile): Extract from
default-skeletons, export.
(default-skeletons): Use %default-dotguile.

Change-Id: Ibe91b3b517ae542bd28070a08e14152f87ed75ec
 2024-01-17 11:11:09 +02:00
Efraim Flashner
33136e0426
system: Export default nanorc. 
* gnu/system/shadow.scm (%default-nanorc): Extract from
default-skeletons, export.
(default-skeletons): Use %default-nanorc.

Change-Id: I0d07b13ed4894b1152a08b96d9ef8527dde073ce
 2024-01-17 11:11:09 +02:00
Efraim Flashner
eef3babfdb
system: Export default gdbinit. 
* gnu/system/shadow.scm (%default-gdbinit): Extract from
default-skeletons, export.
(default-skeletons): Use %default-gdbinit.

Change-Id: Ia5188f8083a83ad4cdb96e234dbd730b1bfe0072
 2024-01-17 11:11:09 +02:00
Efraim Flashner
7292838874
system: Export default xdefaults. 
* gnu/system/shadow.scm (%default-xdefaults): Extract from
default-skeletons, export.
(default-skeletons): Use %default-xdefaults.

Change-Id: I44018516ec3687a68d32ca5c86c41bc29507a273
 2024-01-17 11:11:09 +02:00
Efraim Flashner
6a9e4b0639
system: Export default zprofile. 
* gnu/system/shadow.scm (%default-zprofile): Extract from
default-skeletons, export.
(default-skeletons): Use %default-zprofile.

Change-Id: I6c6e158bca2e462a2eae709fbc2c25a2c7f3f8b4
 2024-01-17 11:11:09 +02:00
Efraim Flashner
cdcb2e78d2
system: Export default bash-profile. 
gnu/system/shadow.scm (%default-bash-profile): Extract from
default-skeletons, export.
(default-skeletons): Use %default-bash-profile.

Change-Id: I45641b1091daee3495a5f92bdc1a63050e0cc59e
 2024-01-17 11:11:03 +02:00
Wilko Meyer
2f3d6ff968
teams: Add Wilko Meyer to kernel. 
* etc/teams.scm: Add Wilko Meyer.

Change-Id: Ia7b85a090a4d8e81689bd137e1d12cb3708aa760
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-01-16 20:47:52 -05:00
Sharlatan Hellseher
d99670e33e
gnu: abjad-ext-ipython: Fix build. 
* gnu/packages/music.scm (abjad-ext-ipython): Fix build.
[propagated-inputs]: Add python-sphinx-autodoc-typehints.

Change-Id: Id20c0527e61b8be194c5387c6c43fdf82ab5ff09
 2024-01-16 21:43:30 +00:00
Sharlatan Hellseher
d79fd9adc3
gnu: python-deepdish: Fix build. 
* gnu/packages/python-science.scm (python-deepdish): Fix build.
[build-system]: Swap to pyproject-build-system.
[arguments]<#:test-flags>: Silent failing tests.

Change-Id: I4c4df66fc80434aaf5b95a7a62b83e0c1c02a4c6
 2024-01-16 21:43:30 +00:00
Ricardo Wurmus
01bf69177d
import/cran: Add more invalid package names and translations. 
These were encountered in a mass import of Bioconductor packages.

* guix/import/cran.scm (invalid-packages): Add "rtools".
(transform-sysname): Add aliases for Python and bioinformatics packages.

Change-Id: I97e13cee10c2ee85d4b9296d91afccbdbcec4946
 2024-01-16 22:36:39 +01:00
Ricardo Wurmus
171ac4fa4f
import/cran: Add more invalid package names and translations. 
* guix/import/cran.scm (invalid-packages): Add "build-essential".
(transform-sysname): Add aliases for openssl, libxml2, and zlib.

Change-Id: Ia142ebc388dbcd47caf3b2c5165bc21227bc1832
 2024-01-16 19:40:50 +01:00
Ricardo Wurmus
9a9f05f1f2
gnu: Add samtools-1.14. 
* gnu/packages/bioinformatics.scm (samtools-1.14): New variable.

Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f
 2024-01-16 19:35:37 +01:00
Ricardo Wurmus
e0369ba57d
gnu: samtools: Update to 1.19. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.19.
[source]: Simplify snippet.

Change-Id: If0e02bbbc8e0443eb418c078dc47525f432d7ebe
 2024-01-16 19:31:35 +01:00
Ricardo Wurmus
eda31ffaab
gnu: htslib: Update to 1.19. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.19.

Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a
 2024-01-16 19:22:03 +01:00
Ricardo Wurmus
cb1f38cc78
gnu: htscodecs: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.0.

Change-Id: Ibd5be30e8fbe7fe5d0ef494c1b1e0cd9ec3333cc
 2024-01-16 19:17:39 +01:00
Ricardo Wurmus
20606ca9af
gnu: Add python-prisma. 
* gnu/packages/databases.scm (python-prisma): New variable.

Change-Id: I7df9b5600fb49ef46a73678323bc29993f35fae2
 2024-01-16 15:40:35 +01:00
Ricardo Wurmus
224f8d543b
gnu: Add python-strenum. 
* gnu/packages/python-xyz.scm (python-strenum): New variable.

Change-Id: I6b6d64024db9358ea0a65cfd6c7cd6f94747de42
 2024-01-16 15:33:57 +01:00
Ricardo Wurmus
f4d2371808
gnu: python-readpaf: Explicitly disable tests. 
* gnu/packages/bioinformatics.scm (python-readpaf)[arguments]: Disable tests.

Change-Id: I28ddfa46675b74bd5073c12e5d33bcbf9dee8252
 2024-01-16 14:52:21 +01:00
Ricardo Wurmus
b8085c9240
gnu: python-pyls-black: Fix build. 
* gnu/packages/patches/python-pyls-black-41.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/python-xyz.scm (python-pyls-black)[source]: Add patch.
[build-system]: Use pyproject-build-system.
[arguments]: Disable one failing test.

Change-Id: I14b2982644e58c0b43d76838febc6dfceb220b15
 2024-01-16 14:52:21 +01:00
Efraim Flashner
8520f00d69
import: crate: Simplify find-crate-version. 
* guix/import/crate.scm (find-crate-version): Reuse
nonyanked-crate-versions, max-crate-version-of-semver.

Change-Id: I976a3b5a397f0d6a7d723804a98356544bfc7da3
 2024-01-16 14:24:10 +02:00