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Author SHA1 Message Date
Mădălin Ionel Patrașcu 263f235cd0
gnu: Add python-mgatk. 
* gnu/packages/bioinformatics.scm (python-mgatk): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2023-05-12 15:30:44 +02:00
宋文武 40310efde9
system: default-skeletons: Merge search-paths of multiple profiles. 
Fixes <https://issues.guix.gnu.org/20255>.

* gnu/system/shadow.scm (default-skeletons)[bash_profile, zprofile]:
Merge search-paths from multiple profiles via "guix package".
 2023-05-12 20:27:06 +08:00
宋文武 6419ca7fd7
gnu: Add Free as in Freedom (2.0). 
* gnu/packages/fsf.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2023-05-12 20:22:02 +08:00
Pierre Neidhardt b363fab46f
gnu: sbcl-serapeum: Update to 20230511. 
* gnu/packages/lisp-xyz.scm (sbcl-serapeum): Update to 20230511.
 2023-05-12 11:56:20 +02:00
Ricardo Wurmus e3e011a081
gnu: python-lightning-cloud: Use older version of fastapi. 
The variant of the fastapi package must match that of
python-pytorch-lightning.

* gnu/packages/machine-learning.scm (python-lightning-cloud)
[propagated-inputs]: Replace python-fastapi with
python-fastapi-for-pytorch-lightning.
 2023-05-12 10:50:01 +02:00
Mădălin Ionel Patrașcu a070eb7a15
gnu: Add python-optparse-pretty. 
* gnu/packages/python-xyz.scm (python-optparse-pretty): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-05-12 09:43:20 +02:00
Mădălin Ionel Patrașcu 9d05f9a9f5
gnu: Add r-dropletutils. 
* gnu/packages/bioconductor.scm (r-dropletutils): New variable.
 2023-05-12 09:36:26 +02:00
Mădălin Ionel Patrașcu a5bae9c748
gnu: Add r-ggpattern. 
* gnu/packages/cran.scm (r-ggpattern): New variable.
 2023-05-12 09:17:07 +02:00
Mădălin Ionel Patrașcu 6c6e2b5fbc
gnu: Add r-gridpattern. 
* gnu/packages/cran.scm (r-gridpattern): New variable.
 2023-05-12 09:17:07 +02:00
Greg Hogan d07342b166
gnu: texlive-datetime2: Add needed propagated-inputs. 
Required packages can be seen with:
$ rg RequirePackage $(guix build texlive-datetime2)

* gnu/packages/tex.scm (texlive-datetime2)[propagated-inputs]: Add
TEXLIVE-ETOOLBOX, TEXLIVE-LATEX-XKEYVAL, and TEXLIVE-TRACKLANG.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2023-05-11 23:56:24 +02:00
Fabio Natali 277c24442c
gnu: Add emacs-framemove. 
* gnu/packages/emacs-xyz.scm (emacs-framemove): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2023-05-11 23:55:43 +02:00
Simon Tournier 60cf9866cf
gnu: texlive-ddphonism: Replace deprecated input. 
* gnu/packages/tex.scm (texlive-ddphonism)[propagated-inputs]: Replace
deprecated texlive-latex-tools by texlive-tools.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-05-11 22:33:28 +02:00
Simon Tournier 713f4e57f7
gnu: texlive-totpages: Replace deprecated input. 
* gnu/packages/tex.scm (texlive-totpages)[propagated-inputs]: Replace
deprecated texlive-latex-graphics by texlive-graphics.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-05-11 22:33:28 +02:00
Simon Tournier 012a514edb
gnu: texlive-totcount: Replace deprecated input. 
* gnu/packages/tex.scm (texlive-totcount)[propagated-inputs]: Replace
deprecated texlive-latex-graphics by texlive-graphics.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-05-11 22:33:27 +02:00
Simon Tournier 43c0bf757a
gnu: texlive-ncctools: Replace deprecated input. 
* gnu/packages/tex.scm (texlive-ncctools)[propagated-inputs]: Replace
deprecated texlive-latex-graphics by texlive-graphics.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-05-11 22:33:27 +02:00
Simon Tournier b924254163
gnu: texlive-soulutf8: Replace deprecated inputs. 
* gnu/packages/tex.scm (texlive-soulutf8)[propagated-inputs]: Replace
deprecated texlive-generic-etexcmds by texlive-etexcmds and deprecated
texlive-generic-infwarerr by texlive-infwarerr.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-05-11 22:33:26 +02:00
Simon Tournier 345ec9f33a
gnu: texlive-xetex: Replace deprecated inputs. 
* gnu/packages/tex.scm (texlive-xetex)[propagated-inputs]: Replace deprecated
texlive-generic-atbegshi by texlive-atbegshi and deprecated
texlive-latex-atveryend by texlive-atveryend.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-05-11 22:33:24 +02:00
Ricardo Wurmus 6a02462ba2
gnu: python-skranger: Install library. 
* gnu/packages/python-xyz.scm (python-skranger)[arguments]: Install the
library that we've just built.
 2023-05-11 20:55:54 +02:00
Ricardo Wurmus 642b73a029
gnu: Add python-skranger. 
* gnu/packages/python-xyz.scm (python-skranger): New variable.
 2023-05-11 20:41:16 +02:00
Ricardo Wurmus ee4d9a74b2
Revert "gnu: Add python-pytest-enabler." 
This reverts commit 0a8c46e89f.

An older version of python-pytest-enabler already exists in (gnu packages
check).
 2023-05-11 20:41:16 +02:00
Efraim Flashner f3a23fed20
gnu: lagrange: Update to 1.15.9. 
* gnu/packages/web-browsers.scm (lagrange): Update to 1.15.9.
 2023-05-11 21:33:05 +03:00
Efraim Flashner b9a87d02e8
gnu: mutt: Update to 2.2.10. 
* gnu/packages/mail.scm (mutt): Update to 2.2.10.
 2023-05-11 21:33:05 +03:00
Efraim Flashner ce6a1b29bd
gnu: qiv: Update to 2.3.3. 
* gnu/packages/image-viewers.scm (qiv): Update to 2.3.3.
 2023-05-11 21:33:05 +03:00
Efraim Flashner 7120dc6e16
gnu: git-annex: Update to 10.20230407. 
* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20230407.
 2023-05-11 21:33:05 +03:00
Efraim Flashner 96e013f964
gnu: global: Update to 6.6.10. 
* gnu/packages/code.scm (global): Update to 6.6.10.
 2023-05-11 21:33:02 +03:00
Ludovic Courtès d6f6b57766
tests: vnstat: Avoid call to 'getservbyname'. 
This would break "make as-derivation" because /etc/services is
unavailable in the build environment:

  [ 38/ 80] loading...	 95.0% of 40 filesBacktrace:
  In guix/build/compile.scm:
      249:8 19 (compile-files "." "/gnu/store/s5nadqd6hkzivkxp33svwqslfn608ng5-guix-system-tests" ("gnu/tests/audio.scm" "gnu/tests/base.scm" "gnu/tests/ci.scm" "gnu/tests/cups.scm" "gnu/tests/d…" …) …)
  […]
  In unknown file:
	     0 (getserv "discard" "tcp")

  ERROR: In procedure getserv:
  In procedure getserv: no such service discard
  builder for `/gnu/store/…-guix-system-tests.drv' failed with exit code 1

* gnu/tests/vnstat.scm (run-vnstat-test): Hard-code 'guest-port' instead
of calling 'getservbyname'.
 2023-05-11 18:09:45 +02:00
Maxim Cournoyer f43c029041
.guix-authorizations: Authorize Josselin Poiret. 
* .guix-authorizations (jpoiret): Add OpenPGP key fingerprint.
 2023-05-11 11:18:48 -04:00
Ricardo Wurmus 23a575f97c
gnu: Add python-omnipath. 
* gnu/packages/python-web.scm (python-omnipath): New variable.
 2023-05-11 17:12:54 +02:00
Ricardo Wurmus 6cac909c95
gnu: Add python-inflect. 
* gnu/packages/python-xyz.scm (python-inflect): New variable.
 2023-05-11 17:12:54 +02:00
Ricardo Wurmus 0616939641
gnu: Add python-docrep. 
* gnu/packages/python-xyz.scm (python-docrep): New variable.
 2023-05-11 17:12:54 +02:00
Ricardo Wurmus 0a8c46e89f
gnu: Add python-pytest-enabler. 
* gnu/packages/python-check.scm (python-pytest-enabler): New variable.
 2023-05-11 17:12:54 +02:00
Ricardo Wurmus 5e07608a30
gnu: Add python-adjusttext. 
* gnu/packages/python-xyz.scm (python-adjusttext): New variable.
 2023-05-11 17:12:54 +02:00
Bruno Victal 1e4c45b0dc
tests: Add vnstat tests. 
* gnu/tests/vnstat.scm: New file.
* gnu/local.mk: Register it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:29 +02:00
Bruno Victal ca52cdd647
services: inetd: Export accessors. 
* gnu/services/networking.scm: Export inetd-configuration?,
inetd-configuration-program, inetd-configuration-entries, inetd-entry?,
inetd-entry-node, inetd-entry-name, inetd-entry-socket-type,
inetd-entry-protocol, inetd-entry-wait?, inetd-entry-user, inetd-entry-program
and inetd-entry-arguments.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:29 +02:00
Bruno Victal 0e3bb48d36
services: Add vnstat-service-type. 
* gnu/services/monitoring.scm (vnstat-service-type): New variable.
* doc/guix.texi (Monitoring Services): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:29 +02:00
Nathaniel Nicandro 2ecf4a9ba3
doc: Update dicod-configuration example 
* doc/guix.texi (Dictionary Service): Update dicod-configuration example to
fix outdated WordNet database configuration.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:29 +02:00
Simon Tournier b8e912c35f
gnu: barrier: Include NULL compatibility. 
Fixes <https://bugs.gnu.org/63244>.
Reported by <john@fremlin.org>

* gnu/packages/barrier.scm (barrier)[arguments]: Use G-exp, add phases
including NULL macro.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:28 +02:00
Greg Hogan 92a7817fcb
gnu: git: Update to 2.40.1 [security fixes]. 
Fixes CVE-2023-25652 and CVE-2023-29007.

* gnu/packages/version-control.scm (git): Update to 2.40.1.
(git-minimal)[arguments]: Rewrite to use gexps.  In
'remove-unusable-perl-commands' phase, make "git-add--interactive"
removal conditional.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:28 +02:00
Ivana Drazovic b984ac16dc
gnu: laby: Add patch for being able to execute game code. 
Reported upstream at https://github.com/sgimenez/laby/pull/68

* gnu/packages/patches/laby-use-tmpdir-from-runtime.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/games.scm (laby)[source]: Use it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:28 +02:00
Ivana Drazovic 8cb6fc32a6
gnu: laby: Make laby function in pure environments. 
* gnu/packages/games.scm (laby)
[build-system]: Switch to 'glib-or-gtk-build-system'.
[inputs]: Add 'gdk-pixbuf' and 'librsvg-for-system'.
[arguments]: Wrap to use SVG-enabled pixbuf loaders.cache.

Co-authored-by: Florian Pelz <pelzflorian@pelzflorian.de>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:28 +02:00
Ivana Drazovic 420b6a8555
gnu: laby: Use new package style. 
* gnu/packages/games.scm (laby)[arguments]: Use gexps.
Use "this-package-input" to locate package input.

Co-authored-by: Florian Pelz <pelzflorian@pelzflorian.de>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:28 +02:00
Gabriel Wicki 199218e372
doc: Clarify substitute* docstring with an example. 
* doc/guix.texi (Build Utilities): Update the corresponding passage.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:28 +02:00
Sergey Trofimov 61031dd32f
services: dhcp-client-configuration: Add 'shepherd-requirement' field. 
* gnu/services/networking.scm (<dhcp-client-configuration>)
[shepherd-requirement]: New field.
(dhcp-client-shepherd-service): Honor it.
(dhcp-client-configuration-shepherd-requirement): Export accessor.
* doc/guix.texi (Networking Setup): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:28 +02:00
Andrew Patterson 8d442e8a53
gnu: home: services: fontutils: Add support for SXML fragments. 
* gnu/home/services/fontutils.scm (add-fontconfig-config-file): Add
support for adding arbitrary SXML configuration into fonts.conf;
* doc/guix.texi (Fonts Services): Update the documentation.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-05-11 16:38:27 +02:00
Maxim Cournoyer ef0aa7ff8b
.guix-authorizations: Authorize Simon Tournier. 
* .guix-authorizations (zimoun): Add OpenPGP key fingerprint.
 2023-05-11 10:35:16 -04:00
zamfofex b718e42c96
gnu: Add oneDNN. 
* gnu/packages/machine-learning.scm (oneapi-dnnl): New variable.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2023-05-11 22:19:08 +08:00
zamfofex af6ed2fc14
gnu: Add ISPC. 
* gnu/packages/c.scm (ispc): New variable.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2023-05-11 22:19:08 +08:00
Ricardo Wurmus 4557c83a7d
gnu: python-distributed: Update to 2023.4.1. 
* gnu/packages/python-science.scm (python-distributed): Update to 2023.4.1.
[source]: Remove snippet.
[arguments]: Update build phase 'versioneer; restore 'sanity-check phase;
simplify custom 'check phase; add 'fix-pytest-config phase; use #:test-flags.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-importlib-metadata.
 2023-05-11 15:59:22 +02:00
Ricardo Wurmus aa17958ca9
gnu: python-zict: Update to 3.0.0. 
* gnu/packages/python-xyz.scm (python-zict): Update to 3.0.0.
[build-system]: Use pyproject-build-system.
[arguments]: Ignore optional lmdb test.
[native-inputs]: Add python-pytest-asyncio, python-pytest-repeat, and
python-pytest-timeout.
 2023-05-11 15:59:22 +02:00
Ricardo Wurmus ab91da5004
gnu: python-dask: Update to 2023.4.1. 
* gnu/packages/python-xyz.scm (python-dask): Update to 2023.4.1.
[source]: Remove snippet.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; update 'versioneer phase; add
'fix-pytest-config and 'pre-check phases; set #:test-flags.
[native-inputs]: Add python-click and python-importlib-metadata.
 2023-05-11 15:59:22 +02:00