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
5d446e439d
gnu: phast: Simplify by using G-expression.
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* gnu/packages/bioinformatics.scm (phast)[arguments]: Use G-expression and
drop trailing #T from build phases.
2023-05-12 22:23:23 +02:00
fac8721bfd
gnu: ribotaper: Simplify with G-expression.
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* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Use G-expression and
drop trailing #T from build phase.
2023-05-12 22:21:14 +02:00
0e20ed322d
gnu: sra-tools: Do link with libxml2.
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* 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
8ba3bf6564
gnu: ncbi-vdb: Ensure that vdb-sqlite is installed.
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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
263f235cd0
gnu: Add python-mgatk.
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* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-05-12 15:30:44 +02:00
40310efde9
system: default-skeletons: Merge search-paths of multiple profiles.
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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
6419ca7fd7
gnu: Add Free as in Freedom (2.0).
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* gnu/packages/fsf.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
2023-05-12 20:22:02 +08:00
b363fab46f
gnu: sbcl-serapeum: Update to 20230511.
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* gnu/packages/lisp-xyz.scm (sbcl-serapeum): Update to 20230511.
2023-05-12 11:56:20 +02:00
e3e011a081
gnu: python-lightning-cloud: Use older version of fastapi.
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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
a070eb7a15
gnu: Add python-optparse-pretty.
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* 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
9d05f9a9f5
gnu: Add r-dropletutils.
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* gnu/packages/bioconductor.scm (r-dropletutils): New variable.
2023-05-12 09:36:26 +02:00
a5bae9c748
gnu: Add r-ggpattern.
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* gnu/packages/cran.scm (r-ggpattern): New variable.
2023-05-12 09:17:07 +02:00
6c6e2b5fbc
gnu: Add r-gridpattern.
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* gnu/packages/cran.scm (r-gridpattern): New variable.
2023-05-12 09:17:07 +02:00
d07342b166
gnu: texlive-datetime2: Add needed propagated-inputs.
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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
277c24442c
gnu: Add emacs-framemove.
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* 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
60cf9866cf
gnu: texlive-ddphonism: Replace deprecated input.
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* 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
713f4e57f7
gnu: texlive-totpages: Replace deprecated input.
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* 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
012a514edb
gnu: texlive-totcount: Replace deprecated input.
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* 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
43c0bf757a
gnu: texlive-ncctools: Replace deprecated input.
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* 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
b924254163
gnu: texlive-soulutf8: Replace deprecated inputs.
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* 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
345ec9f33a
gnu: texlive-xetex: Replace deprecated inputs.
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* 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
6a02462ba2
gnu: python-skranger: Install library.
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* gnu/packages/python-xyz.scm (python-skranger)[arguments]: Install the
library that we've just built.
2023-05-11 20:55:54 +02:00
642b73a029
gnu: Add python-skranger.
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* gnu/packages/python-xyz.scm (python-skranger): New variable.
2023-05-11 20:41:16 +02:00
ee4d9a74b2
Revert "gnu: Add python-pytest-enabler."
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This reverts commit 0a8c46e89f
2023-05-11 20:41:16 +02:00
f3a23fed20
gnu: lagrange: Update to 1.15.9.
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* gnu/packages/web-browsers.scm (lagrange): Update to 1.15.9.
2023-05-11 21:33:05 +03:00
b9a87d02e8
gnu: mutt: Update to 2.2.10.
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* gnu/packages/mail.scm (mutt): Update to 2.2.10.
2023-05-11 21:33:05 +03:00
ce6a1b29bd
gnu: qiv: Update to 2.3.3.
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* gnu/packages/image-viewers.scm (qiv): Update to 2.3.3.
2023-05-11 21:33:05 +03:00
7120dc6e16
gnu: git-annex: Update to 10.20230407.
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* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20230407.
2023-05-11 21:33:05 +03:00
96e013f964
gnu: global: Update to 6.6.10.
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* gnu/packages/code.scm (global): Update to 6.6.10.
2023-05-11 21:33:02 +03:00
d6f6b57766
tests: vnstat: Avoid call to 'getservbyname'.
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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
f43c029041
.guix-authorizations: Authorize Josselin Poiret.
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* .guix-authorizations (jpoiret): Add OpenPGP key fingerprint.
2023-05-11 11:18:48 -04:00
23a575f97c
gnu: Add python-omnipath.
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* gnu/packages/python-web.scm (python-omnipath): New variable.
2023-05-11 17:12:54 +02:00
6cac909c95
gnu: Add python-inflect.
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* gnu/packages/python-xyz.scm (python-inflect): New variable.
2023-05-11 17:12:54 +02:00
0616939641
gnu: Add python-docrep.
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* gnu/packages/python-xyz.scm (python-docrep): New variable.
2023-05-11 17:12:54 +02:00
0a8c46e89f
gnu: Add python-pytest-enabler.
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* gnu/packages/python-check.scm (python-pytest-enabler): New variable.
2023-05-11 17:12:54 +02:00
5e07608a30
gnu: Add python-adjusttext.
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* gnu/packages/python-xyz.scm (python-adjusttext): New variable.
2023-05-11 17:12:54 +02:00
1e4c45b0dc
tests: Add vnstat tests.
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* 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
ca52cdd647
services: inetd: Export accessors.
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* 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
0e3bb48d36
services: Add vnstat-service-type.
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* 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
2ecf4a9ba3
doc: Update dicod-configuration example
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* 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
b8e912c35f
gnu: barrier: Include NULL compatibility.
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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
92a7817fcb
gnu: git: Update to 2.40.1 [security fixes].
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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
b984ac16dc
gnu: laby: Add patch for being able to execute game code.
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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
8cb6fc32a6
gnu: laby: Make laby function in pure environments.
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* 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
420b6a8555
gnu: laby: Use new package style.
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* 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
199218e372
doc: Clarify substitute* docstring with an example.
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* 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
61031dd32f
services: dhcp-client-configuration: Add 'shepherd-requirement' field.
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* 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
8d442e8a53
gnu: home: services: fontutils: Add support for SXML fragments.
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* 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
ef0aa7ff8b
.guix-authorizations: Authorize Simon Tournier.
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* .guix-authorizations (zimoun): Add OpenPGP key fingerprint.
2023-05-11 10:35:16 -04:00
Ricardo Wurmus
Mădălin Ionel Patrașcu
宋文武
Pierre Neidhardt
Greg Hogan
Fabio Natali
Simon Tournier
Efraim Flashner
Ludovic Courtès
Maxim Cournoyer
Bruno Victal
Nathaniel Nicandro
Ivana Drazovic
Gabriel Wicki
Sergey Trofimov
Andrew Patterson