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Author SHA1 Message Date
Ricardo Wurmus
662e2e82b1
gnu: arriba: Use SEARCH-INPUT-FILE and -DIRECTORY. 
* gnu/packages/bioinformatics.scm (arriba)[arguments]:
Use SEARCH-INPUT-DIRECTORY and SEARCH-INPUT-FILE; use G-expression; drop
trailing #T from build phases.
 2023-05-12 22:40:18 +02:00
Ricardo Wurmus
001d9b1c64
gnu: multichoose: Clean up. 
* gnu/packages/bioinformatics.scm (multichoos): Fix indentation.
[arguments]: Use G-expression.
 2023-05-12 22:33:44 +02:00
Ricardo Wurmus
6d72af0747
gnu: samblaster: Update to 0.1.26. 
* gnu/packages/bioinformatics.scm (samblaster): Update to 0.1.26.
 2023-05-12 22:31:22 +02:00
Ricardo Wurmus
6331e41cde
gnu: samblaster: Simplify. 
* gnu/packages/bioinformatics.scm (samblaster): Fix indentation.
[arguments]: Use G-expression; drop trailing #T from 'install phase.
[description]: Use double spacing between all sentences.
 2023-05-12 22:29:38 +02:00
Ricardo Wurmus
7da3ca1bd7
gnu: methyldackel: Update to 0.6.1. 
* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.6.1.
[arguments]: Set LIBBIGWIG variable instead of patching Makefile.
[inputs]: Replace htslib-1.9 with htslib.
 2023-05-12 22:27:17 +02:00
Ricardo Wurmus
7a199bb74c
gnu: methyldackel: Simplify arguments. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Use list, drop
argument list.
[native-inputs]: Drop package label.
 2023-05-12 22:24:30 +02:00
Ricardo Wurmus
5d446e439d
gnu: phast: Simplify by using G-expression. 
* gnu/packages/bioinformatics.scm (phast)[arguments]: Use G-expression and
drop trailing #T from build phases.
 2023-05-12 22:23:23 +02:00
Ricardo Wurmus
fac8721bfd
gnu: ribotaper: Simplify with G-expression. 
* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Use G-expression and
drop trailing #T from build phase.
 2023-05-12 22:21:14 +02:00
Ricardo Wurmus
0e20ed322d
gnu: sra-tools: Do link with libxml2. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use G-expression for
clarity; drop trailing #T from build phases; modify 'configure phase to
dynamically link with libxml2.
[inputs]: Drop package labels; add libxml2.
 2023-05-12 21:54:01 +02:00
Ricardo Wurmus
8ba3bf6564
gnu: ncbi-vdb: Ensure that vdb-sqlite is installed. 
The most important change here is the addition of the 'install-libs phase.
All other changes are just the result of switching to G-expressions.

* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add 'install-libs
phase; use G-expression; drop trailing #T from build phases.
[inputs]: Drop package labels.
 2023-05-12 21:51:41 +02:00
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