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Author SHA1 Message Date
Ricardo Wurmus
699b443c86
gnu: python-bx-python: Update to 0.8.12. 
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.8.12.
[propagated-inputs]: Remove python-six.
[arguments]: Remove.  Tests are still not run, though.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
4b4ab4ce4d
gnu: Remove pbtranscript-tofu. 
Upstream has disappeared and it depends on Python 2, which is no longer
supported.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
b452d7c2cf
gnu: python-pyfit-sne: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1.
[arguments]: Disable tests explicitly.
 2021-12-07 11:51:09 +01:00
Julien Lepiller
05deb26be9
gnu: guile-netlink: Update to 1.1.1. 
* gnu/packages/guile.scm (guile-netlink): Update to 1.1.1.
 2021-12-07 00:09:35 +01:00
Nicolas Goaziou
e21b422f7f
gnu: emacs-csv-mode: Update to 1.17. 
* gnu/packages/emacs-xyz.scm (emacs-csv-mode): Update to 1.17.
 2021-12-06 22:01:31 +01:00
Pierre Langlois
4afacd4546
gnu: helm: Fix build with GCC 9 and later. 
* gnu/packages/music.scm (helm)[origin]: Add patch.
* gnu/packages/patches/helm-fix-gcc-9-build.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2021-12-06 20:41:18 +00:00
Marius Bakke
757a2eb970
tests: patchwork: Use the default PostgreSQL. 
* gnu/tests/web.scm (patchwork-os)[services]: Change from POSTGRESQL-10 to
POSTGRESQL.
 2021-12-06 21:17:31 +01:00
Marius Bakke
8662057130
gnu: patchwork: Adjust for python-build-system change. 
This is a follow-up to commit db5646d957, et.al.

* gnu/packages/patchutils.scm (patchwork)[arguments]: Adapt one more
site-packages call.
 2021-12-06 21:15:42 +01:00
Ricardo Wurmus
ca2f851da1
gnu: f-seq: Update name of commons-cli JAR. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of
commons-cli JAR.
 2021-12-06 18:48:01 +01:00
Ricardo Wurmus
f0763fba5c
gnu: f-seq: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from
build phase.
 2021-12-06 18:48:01 +01:00
Ricardo Wurmus
1310879fb0
gnu: f-seq: Simplify snippet. 
* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
 2021-12-06 18:48:01 +01:00
Leo Famulari
404f695385
gnu: Go 1.17: Update to 1.17.4. 
* gnu/packages/golang.scm (go-1.17): Update to 1.17.4.
 2021-12-06 12:40:38 -05:00
Leo Famulari
e4d8f2fe31
gnu: Go 1.16: Update to 1.16.11. 
* gnu/packages/golang.scm (go-1.16): Update to 1.16.11.
 2021-12-06 12:40:38 -05:00
Leo Famulari
4e282bc934
gnu: Syncthing: Update to 1.18.4. 
* gnu/packages/syncthing.scm (syncthing): Update to 1.18.4.
[arguments]: Build with Go 1.17.
 2021-12-06 12:10:12 -05:00
Mathieu Othacehe
3b6a7693fa
gnu: osinfo-db-next: Fix uri. 
* gnu/packages/virtualization.scm (osinfo-db-next)[source]: Fix URI.
 2021-12-06 17:28:22 +01:00
Efraim Flashner
30c776a6a8
gnu: go-gopkg-in-yaml-v2: Update to 2.4.0. 
* gnu/packages/golang.scm (go-gopkg-in-yaml-v2): Update to 2.4.0.
 2021-12-06 14:45:50 +02:00
Efraim Flashner
c569430b6c
gnu: go-gopkg-in-yaml-v2: Fix test suite on 32-bit systems. 
* gnu/packages/golamg.scm (go-gopkg-in-yaml-v2)[source]: Add snippet to
no longer cause integer overflow on 32-bit systems during test suite.
 2021-12-06 14:43:17 +02:00
Efraim Flashner
b6a726222a
gnu: go-github-com-golang-snappy: Adjust test-suite on 32-bit systems. 
* gnu/packages/syncthing.scm (go-github-com-golang-snappy)[source]: Add
patch to skip a test on 32-bit systems.
* gnu/packages/patches/go-github-com-golang-snappy-32bit-test.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2021-12-06 14:04:30 +02:00
Ludovic Courtès
f4d4c40500
gnu: python-kivy: Add missing dependencies. 
* gnu/packages/python-xyz.scm (python-kivy)[arguments]: Add 'set-home'
phase.
[inputs]: Add PYTHON-DOCUTILS, PYTHON-KIVY-GARDEN, and PYTHON-PYGMENTS.
[synopsis, description]: Tweak.
 2021-12-06 11:49:06 +01:00
Ludovic Courtès
7e40d0ee90
gnu: Add python-kivy-garden. 
* gnu/packages/python-xyz.scm (python-kivy-garden): New variable.
 2021-12-06 11:48:47 +01:00
Ludovic Courtès
9478a25250
gnu: openssh: Remove libfido2 dependency on GNU/Hurd. 
* gnu/packages/ssh.scm (openssh)[inputs]: Remove LIBFIDO2 when
'hurd-target?'.
[arguments]: Likewise for "--with-security-key-builtin".
 2021-12-06 10:56:01 +01:00
Ludovic Courtès
93e9f0bc7f
ci: Cross-build the 'guix' package. 
* gnu/ci.scm (%core-packages): Add GUIX.
 2021-12-06 10:56:01 +01:00
jgart
326e532177
gnu: Add git-absorb. 
* gnu/packages/rust-apps.scm (git-absorb): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-06 10:47:09 +01:00
Efraim Flashner
96416e4256
gnu: poke: Remove generated files. 
* gnu/packages/engineering.scm (poke)[source]: Add snippet to remove
generated files.
 2021-12-06 11:39:08 +02:00
Efraim Flashner
c70df3c467
gnu: poke: Update to 1.4. 
* gnu/packages/engineering.scm (poke): Update to 1.4.
[native-inputs]: Remove clisp, perl, python-2, and python-3.
 2021-12-06 11:39:07 +02:00
Efraim Flashner
e050ddad0b
gnu: poke: Update metadata. 
* gnu/packages/engineering.scm (poke)[home-page]: Use GNU home-page.
[synopsis]: Use upstream synopsis.
[description]: Reflow.
 2021-12-06 11:39:07 +02:00
Ricardo Wurmus
cf32c21ecd
gnu: perl-math-cephes: Build reproducibly. 
* gnu/packages/perl-maths.scm (perl-math-cephes)[source]: Sort result of
readdir.
 2021-12-06 10:12:13 +01:00
Ludovic Courtès
f72db02a6a
gnu: fpm2: Build with '-fcommon'. 
* gnu/packages/password-utils.scm (fpm2)[arguments]: Add #:configure-flags.
 2021-12-06 10:01:32 +01:00
Ludovic Courtès
3686780f31
gnu: xnee: Build with '-fcommon'. 
* gnu/packages/xnee.scm (xnee)[arguments]: New field.
 2021-12-06 10:01:15 +01:00
Leo Famulari
764be13ee6
gnu: isync: Update to 1.4.4 [fixes CVE-2021-{3657,44143}]. 
* gnu/packages/mail.scm (isync): Update to 1.4.4.
 2021-12-05 23:36:42 -05:00
Ludovic Courtès
c162f8582b
gnu: libsoup: Simplify inputs. 
Obtained by running "guix style --input-simplification=always" and by
using 'modify-inputs' instead of list primitives.

* gnu/packages/gnome.scm (libsoup-minimal, libsoup-minimal-2, libsoup):
Simplify inputs.
 2021-12-05 23:53:40 +01:00
Ludovic Courtès
0dc42f5bbf
gnu: librsvg: Simplify inputs. 
Obtained by running "guix style --input-simplification=always".

* gnu/packages/gnome.scm (librsvg, librsvg-2.40): Simplify inputs.
 2021-12-05 23:39:29 +01:00
Ludovic Courtès
dcf308a8bf
gnu: gtk+: Simplify inputs. 
Obtained by running:

  guix style --input-simplification=always gtk+ gtk+@2

* gnu/packages/gtk.scm (gtk+-2, gtk+): Simplify inputs.
 2021-12-05 23:24:48 +01:00
Ludovic Courtès
597119937d
gnu: gtk+@2: Use 'librsvg-for-system'. 
* gnu/packages/gtk.scm (gtk+-2)[propagated-inputs]: Use
'librsvg-for-system' unconditionally.
 2021-12-05 23:15:24 +01:00
Ludovic Courtès
90570b5e9f
gnu: libsoup: Remove unneeded dependency on PHP. 
* gnu/packages/gnome.scm (libsoup-minimal)[native-inputs]: Remove PHP.
 2021-12-05 23:10:44 +01:00
Ludovic Courtès
2561f2720f
gnu: gtk+: Use 'librsvg-for-system'. 
This brings back SVG support on non-x86_64 platforms.

* gnu/packages/gtk.scm (gtk+)[inputs]: Use 'librsvg-for-system'
unconditionally.
[arguments]: In 'disable-failing-tests' phase, remove conditional
substitutions aimed for non-x86_64 targets lacking librsvg support.
* gnu/packages/gnome.scm (libhandy)[arguments]: Likewise, remove
'skip-test-that-requires-svg' phase.
 2021-12-05 22:42:26 +01:00
Ludovic Courtès
3bd7ce6053
gnu: emacs: Use 'librsvg-for-system'. 
* gnu/packages/emacs.scm (emacs)[inputs]: Use 'librsvg-for-system'
unconditionally.
 2021-12-05 22:42:26 +01:00
Ludovic Courtès
c789d00b5f
gnu: openbox: Use 'librsvg-for-system'. 
* gnu/packages/openbox.scm (openbox)[inputs]: Use 'librsvg-for-system'
unconditionally.
 2021-12-05 22:42:26 +01:00
Ludovic Courtès
efbaa5fcc8
gnu: mate: Depend on 'librsvg-for-system'. 
* gnu/packages/mate.scm (engrampa)[inputs]: Replace LIBRSVG by
LIBRSVG-FOR-SYSTEM.
(libmatekbd)[inputs]: Likewise.
(mate-panel)[inputs]: Likewise.
(mate-screensaver)[inputs]: Likewise.
(mate-utils)[inputs]: Likewise.
(mate-control-center)[inputs]: Likewise.
(eom)[inputs]: Likewise, and remove duplicate
[license]: Remove unnecessary list.
 2021-12-05 22:42:25 +01:00
Ludovic Courtès
c19f968cbd
gnu: librsvg@2.40: Depend on the default Pango version. 
This avoids conflicts where, say, gtk+ would pull pango@1.44 whereas
mate-control-center would additionally pull pango@1.42 via librsvg@2.40
on i686-linux.

* gnu/packages/gnome.scm (librsvg-2.40)[arguments]: In
'remove-failing-tests' phase, remove two additional tests.
[inputs]: Change PANGO-1.42 to PANGO.
 2021-12-05 22:42:25 +01:00
Thiago Jung Bauermann
a9d426c492
gnu: Add texlive-latex-luatex. 
When TeX Live was updated to version 2021 the ‘lualatex’ format started
being generated with the LuaHBTeX engine, but the ‘lualatex’ command still
uses the LuaTeX engine. This causes the command to fail:

  user@popigai:~$ lualatex hello.tex
  This is LuaTeX, Version 1.13.0 (TeX Live 2021/GNU Guix)
  restricted system commands enabled.

  ---! lualatex.fmt was written by luahbtex
  (Fatal format file error; I'm stymied)user@popigai:~$

The correct way to fix this problem would be either to change texlive-bin
to make ‘lualatex’ use the LuaHBTeX engine, or to change texlive-latex-base
to generate ‘lualatex.fmt’ with LuaTeX. Both options would rebuild large
parts of the world.

Ricardo Wurmus suggested creating a new package to provide ‘lualatex.fmt’
for LuaTeX as a workaround. This is what this package does.

Fixes https://issues.guix.gnu.org/51252.

* gnu/packages/tex.scm (texlive-latex-luatex): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-05 22:42:25 +01:00
Ludovic Courtès
85c07e330c
gnu: gtranslator: Fix URL. 
Reported by Vivien Kraus.

* gnu/packages/gnome.scm (gtranslator)[source]: Change
'version-major+minor' to 'version-major'.
 2021-12-05 22:42:25 +01:00
Ricardo Wurmus
0f2a77e14f
gnu: Add libnftnl/fixed. 
* gnu/packages/linux.scm (libnftnl/fixed): New variable.
 2021-12-05 22:26:26 +01:00
Demis Balbach
d8401fb508
gnu: Add phonesim. 
* gnu/packages/telephony.scm (phonesim): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 21:56:53 +01:00
jgart
026ac3c010
gnu: Add pounce. 
* gnu/packages/messaging.scm (pounce): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 21:51:39 +01:00
Luis Felipe
f856c8f1b0
gnu: Add python-django-svg-image-form-field. 
* gnu/packages/django.scm (python-django-svg-image-form-field): New
variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 21:44:51 +01:00
jgart
648db3ad2b
gnu: Add litterbox. 
* gnu/packages/irc.scm (litterbox): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 21:35:13 +01:00
Nicolas Goaziou
6a8d2499ae
gnu: emacs-telega: Update to 0.7.031. 
* gnu/packages/emacs-xyz.scm (emacs-telega-server): Update to 0.7.031.
 2021-12-05 21:32:42 +01:00
Nicolas Goaziou
e0e9aa116e
gnu: emacs-geiser: Update to 0.19. 
* gnu/packages/emacs-xyz.scm (emacs-geiser): Update to 0.19.
 2021-12-05 21:22:43 +01:00
jgart
a3dea002c1
gnu: Add hex. 
* gnu/packages/rust-apps.scm (hex): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 19:46:10 +01:00
jgart
13f2f2d14d
gnu: Add rust-no-color-0.1. 
* gnu/packages/crates-io.scm (rust-no-color-0.1): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 19:44:26 +01:00
simendsjo
c4699914c9
gnu: font-iosevka: Update to 11.2.0. 
* gnu/packages/fonts.scm (font-iosevka): Update to 11.2.0

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 19:40:09 +01:00
Aleksandr Vityazev
df4debda05
gnu: sbcl-slynk: Update to 1.0.43-5.0470c02 
* gnu/packages/lisp-xyz.scm (sbcl-slynk): Update to 1.0.43-5.0470c02.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 19:37:59 +01:00
Aleksandr Vityazev
23e1f3e4f6
gnu: emacs-sly: Update to 1.0.43-5.0470c02 
* gnu/packages/emacs-xyz.scm (emacs-sly): Update to 1.0.43-5.0470c02.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 19:37:58 +01:00
Ricardo Wurmus
9bc0f45df5
Merge remote-tracking branch 'origin/master' into core-updates-frozen 2021-12-05 19:17:41 +01:00
Nicolas Goaziou
b4e97063ba
gnu: trezor-agent: Fix hash. 
* gnu/packages/finance.scm (trezor-agent): Update hash.

Hash was not updated when committing
c7c4f80881.
 2021-12-05 19:17:01 +01:00
Ricardo Wurmus
6db3c536e8
gnu: python-bwapy: Remove sanity-check. 
* gnu/packages/bioinformatics.scm (python-bwapy)[arguments]: Add phase
'relax-requirements to accept a slightly older version of wheel; remove the
'sanity-check phase.
 2021-12-05 17:38:15 +01:00
Ricardo Wurmus
dd67154e5d
gnu: Remove python2-plastid. 
* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.
 2021-12-05 17:37:05 +01:00
Ricardo Wurmus
98264531be
gnu: Remove python2-twobitreader. 
* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.
 2021-12-05 17:36:43 +01:00
Ricardo Wurmus
4202f4d58a
gnu: python-bbknn: Fix sanity-check phase. 
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'do-not-fail-to-find-sklearn, which prevents the 'sanity-check phase from
failing.
 2021-12-05 17:33:17 +01:00
Ricardo Wurmus
b1bd997d50
gnu: python-bbknn: Add missing input. 
* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add
python-scikit-learn.
 2021-12-05 17:32:50 +01:00
Ricardo Wurmus
19f6b770dc
gnu: velvet: Add missing TeX package. 
* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add
texlive-fonts-ec.
 2021-12-05 17:22:11 +01:00
Ricardo Wurmus
fe0f8c627a
gnu: velvet: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from
build phases.
 2021-12-05 17:21:39 +01:00
Ricardo Wurmus
f2b99e3aaf
gnu: python-bwapy: Remove pre-built object files. 
* gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files
in a snippet.
 2021-12-05 15:04:05 +01:00
Ricardo Wurmus
57f278ffc4
gnu: metabat: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T
from build phases.
 2021-12-05 15:04:05 +01:00
Ricardo Wurmus
c13046cb68
gnu: clapack: Pass -fcommon to compiler. 
* gnu/packages/maths.scm (clapack)[arguments]: Set CFLAGS.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
ae0acf6b6d
gnu: clapack: Remove trailing #T. 
* gnu/packages/maths.scm (clapack)[arguments]: Remove trailing #T from build
phases.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
1d53c697b3
gnu: tla2tools: Remove remaining reference to %output. 
This is a follow-up to commit 7e6ee16d49.

* gnu/packages/java.scm (tla2tools)[arguments]: Remove remaining reference to
%output.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
8ae33d6844
gnu: kraken2: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (kraken2)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
c973107a25
gnu: methyldackel: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove reference
to %outputs by using a gexp.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
d531dc6761
gnu: phast: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (phast)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
2b1e53850f
gnu: libsbml: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (libsbml)[arguments]: Remove references to
%build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
dc4b4d4d95
gnu: ataqv: Remove references to %outputs and %build-inputs. 
* gnu/packages/bioinformatics.scm (ataqv)[arguments]: Remove references to
%outputs and %build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
03ca627b09
gnu: adapterremoval: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (adapterremoval)[arguments]: Remove
reference to %outputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
fac4c98699
gnu: bbmap: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
b798d90bee
gnu: intervaltree: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (intervaltree)[arguments]: Remove reference
to %outputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
c9892edceb
gnu: biobambam2: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (biobambam2)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
a8b60bd475
gnu: sjcount: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
4c6cb448fd
gnu: sjcount: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove trailing #T
from build phases.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
c1fe074915
gnu: dropseq-tools: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove reference
to %build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
1462e5c919
gnu: dropseq-tools: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove
trailing #T from build phases...
[source]: ...and from the snippet.
 2021-12-05 15:04:02 +01:00
Marius Bakke
10554e0a57
gnu: python-django-netfields: Update to 1.2.4. 
* gnu/packages/django.scm (python-django-netfields): Update to 1.2.4.
 2021-12-05 14:40:08 +01:00
Marius Bakke
50fff94b5a
gnu: python-django: Update to 3.2.9. 
* gnu/packages/django.scm (python-django): Update to 3.2.9.
 2021-12-05 14:40:08 +01:00
Marius Bakke
e166e6acf6
gnu: drbd-utils: Update to 9.19.1. 
* gnu/packages/cluster.scm (drbd-utils): Update to 9.19.1.
 2021-12-05 14:40:07 +01:00
Nicolas Goaziou
21e2be5968
gnu: emacs-peg: Update to 0.10.3. 
* gnu/packages/emacs-xyz.scm (emacs-peg): Update to 0.10.3.
 2021-12-05 14:20:16 +01:00
Marius Bakke
c61e49aa94
gnu: tbb: Update to 2021.4.0. 
* gnu/packages/tbb.scm (tbb): Update to 2021.4.0.
 2021-12-05 14:02:10 +01:00
Marius Bakke
db5646d957
gnu: Adjust for python-build-system behavior change. 
Commit cb72f9a773 changed the semantics of
SITE-PACKAGES, but did not adjust all callers.

* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Adjust for
missing trailing slash.
* gnu/packages/maths.scm (nomad-optimizer)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchwork)[arguments]: Likewise.
 2021-12-05 14:02:10 +01:00
Marius Bakke
b507cc49ab
gnu: python-pyvcf: Fix bytecode compilation. 
* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Add phase to
patch sample script.
 2021-12-05 14:02:10 +01:00
Marius Bakke
a2584a08be
gnu: python-whisper: Update to 1.1.8. 
* gnu/packages/monitoring.scm (python-whisper): Update to 1.1.8.
 2021-12-05 14:02:10 +01:00
Marius Bakke
0d196ab9bd
gnu: python-mailman-hyperkitty: Update to 1.2.0. 
* gnu/packages/mail.scm (python-mailman-hyperkitty): Update to 1.2.0.
[source](patches): Remove.
 2021-12-05 14:02:10 +01:00
Marius Bakke
3f9d122dcb
gnu: python-hyperkitty: Update to 1.3.5. 
* gnu/packages/mail.scm (python-hyperkitty): Update to 1.3.5.
[arguments]: Add pythonpath in test invokation.
[propagated-inputs]: Add PYTHON-MISTUNE-NEXT.  Change from PYTHON-DJANGO-2.2
to PYTHON-DJANGO.
[native-inputs]: Add PYTHON-LXML.
 2021-12-05 14:02:10 +01:00
Marius Bakke
b0ce8bdb39
gnu: Add python-mistune-next. 
* gnu/packages/python-xyz.scm (python-mistune-next): New variable.
 2021-12-05 14:02:09 +01:00
Marius Bakke
f457fb19dd
gnu: python-django-haystack: Update to 3.1.1. 
* gnu/packages/django.scm (python-django-haystack): Update to 3.1.1.
[arguments]: Adjust substitution.
 2021-12-05 14:02:09 +01:00
Marius Bakke
eb8619a5a6
gnu: python-alembic: Update to 1.7.5. 
* gnu/packages/databases.scm (python-alembic): Update to 1.7.5.
[propagated-inputs]: Remove PYTHON-IMPORTLIB-RESOURCES.
 2021-12-05 14:02:09 +01:00
Marius Bakke
d801827b84
gnu: ganeti: Add the output directory on GUIX_PYTHONPATH. 
This is a follow-up to commit 1ed567c872.

* gnu/packages/virtualization.scm (ganeti)[arguments]: Adjust wrap phase to
include Ganetis own site-packages on $GUIX_PYTHONPATH.
 2021-12-05 14:02:09 +01:00
Marius Bakke
846bd3d083
gnu: python-webassets: Patch for Python 3.9. 
* gnu/packages/python-web.scm (python-webassets)[arguments]: Add
substitution.
 2021-12-05 14:02:09 +01:00
Marius Bakke
9f5b9d18d8
gnu: python-django-mailman3: Update to 1.3.7. 
* gnu/packages/mail.scm (python-django-mailman3): Update to 1.3.7.
 2021-12-05 14:02:09 +01:00
Marius Bakke
837688e505
gnu: python-mailmanclient: Update to 3.3.3. 
* gnu/packages/mail.scm (python-mailmanclient): Update to 3.3.3.
 2021-12-05 14:02:09 +01:00
Marius Bakke
97edcf2e63
gnu: python-django-url-filter: Adjust phase order. 
* gnu/packages/django.scm (python-django-url-filter)[arguments]: Move
substitution to after the unpack phase, so that it does not end up in the egg
info.
 2021-12-05 14:02:09 +01:00
Marius Bakke
458e972484
gnu: python-django-netfields: Propagate psycopg2. 
* gnu/packages/django.scm (python-django-netfields)[propagated-inputs]: Add
PYTHON-PSYCOPG2.
 2021-12-05 14:02:09 +01:00
Marius Bakke
63975ea51c
gnu: python-django-logging-json: Disable sanity check. 
* gnu/packages/django.scm (python-django-logging-json)[arguments]: Add
 #:phases.
 2021-12-05 14:02:09 +01:00
Marius Bakke
19520996f0
gnu: python-django-appconf: Fix tests. 
* gnu/packages/django.scm (python-django-appconf): Invoke django-admin with
custom pythonpath.
 2021-12-05 14:02:09 +01:00
Marius Bakke
88e9e9e697
gnu: python-django-pipeline: Fix tests. 
* gnu/packages/django.scm (python-django-pipeline): Provide pythonpath to
django-admin.
 2021-12-05 14:02:09 +01:00
Marius Bakke
e73f565445
gnu: python-django-sortedm2m: Fix tests. 
This is a follow-up to commit 283d5ac97f.

* gnu/packages/django.scm (python-django-sortedm2m): Invoke django-admin with
pythonpath and test settings.
 2021-12-05 14:02:08 +01:00
Marius Bakke
ddea9e32e7
gnu: python-django-contact-form: Update to 1.9. 
* gnu/packages/django.scm (python-django-contact-form): Update to 1.9.
 2021-12-05 14:02:08 +01:00
Marius Bakke
6b458747da
gnu: python-django-jinja: Update to 2.9.1. 
* gnu/packages/django.scm (python-django-jinja): Update to 2.9.1.
 2021-12-05 14:02:08 +01:00
Marius Bakke
de5a8b26f2
gnu: python-django-haystack: Disable sanity check. 
* gnu/packages/django.scm (python-django-haystack)[arguments]: Delete one
phase.  While at it, remove trailing #t's.
 2021-12-05 14:02:08 +01:00
Marius Bakke
acbc01940b
gnu: python-fakeredis: Update to 1.7.0. 
* gnu/packages/databases.scm (python-fakeredis): Update to 1.7.0.
 2021-12-05 14:02:08 +01:00
Marius Bakke
0b6f4be0fa
gnu: Django packages propagate Django, after all. 
This reverts commit d7922f488b.  Mainly to
placate the new 'sanity-check' phase, and because --with-input and friends
makes it easy to override.

* gnu/packages/django.scm (python-django-extensions,
python-django-simple-math-captcha, python-django-taggit,
python-easy-thumbnails, python-django-haystack, python-django-allauth,
python-django-debug-toolbar, python-django-debug-toolbar-alchemy,
python-django-assets, python-django-jinja, python-django-picklefield,
python-django-bulk-update, python-django-contact-form,
python-django-contrib-comments, python-django-pipeline, python-django-redis,
python-django-rq, python-django-q, python-django-sortedm2m,
python-django-appconf, python-django-statici18n, python-djangorestframework,
python-django-sekizai, python-django-crispy-forms,
python-django-override-storage, python-django-auth-ldap,
python-django-logging-json, python-django-netfields,
python-django-url-filter)[propagated-inputs]: Add PYTHON-DJANGO.
[native-inputs]: Remove it.
 2021-12-05 14:02:08 +01:00
Sharlatan Hellseher
bf9a1dfd59
gnu: Add imppg 
* gnu/packages/astronomy.scm: (imppg): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 12:35:55 +01:00
dissent
c663d037aa
gnu: Add pqiv. 
* gnu/packages/image-viewers.scm (pqiv): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 12:27:02 +01:00
jgart
66a2d3830c
gnu: Add pudb. 
* gnu/packages/python-xyz.scm (pudb): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 12:18:24 +01:00
Nicolas Goaziou
53afb3cf2a
gnu: leo: Use GIT-VERSION. 
* gnu/packages/web-browsers.scm (leo)[source]: Use `git-version' instead of
crafting version string.  Also fix indentation.
 2021-12-05 12:08:16 +01:00
jgart
2149515808
gnu: Add leo. 
* gnu/packages/web-browsers.scm (leo): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 11:03:14 +01:00
Efraim Flashner
e70e26423b
gnu: minimap2: Update to 2.23. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23.
 2021-12-05 11:51:10 +02:00
Artyom V. Poptsov
030d9b261f
gnu: Add guile-ini. 
* gnu/packages/guile-xyz.scm (guile-ini): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-05 09:53:59 +01:00
Vivien Kraus
f8490817e7
gnu: evolution: Build with libsoup 2. 
* gnu/packages/gnome.scm (evolution) [phase adjust-webkitgtk-version]: Remove
it.
[inputs]: Depend on webkitgtk-with-libsoup2 instead of webkitgtk.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-05 08:42:03 +01:00
Ricardo Wurmus
7e6ee16d49
gnu: tla2tools: Remove reference to %output. 
* gnu/packages/java.scm (tla2tools)[arguments]: Bind OUTPUTS in build phase
'install to remove reference to %output.
 2021-12-05 01:11:38 +01:00
Ricardo Wurmus
ad1dc0cad3
gnu: java-log4j-core: Remove reference to %outputs. 
* gnu/packages/java.scm (java-log4j-core)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-05 01:04:29 +01:00
Ricardo Wurmus
87e7ed77da
gnu: java-log4j-api: Remove reference to %outputs. 
* gnu/packages/java.scm (java-log4j-api)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-05 01:04:03 +01:00
Ricardo Wurmus
9485578570
gnu: java-native-access: Use older GCC. 
* gnu/packages/java.scm (java-native-access)[native-inputs]: Add gcc-7 to fix
the build.
 2021-12-05 01:03:31 +01:00
Ricardo Wurmus
48235c37db
gnu: java-commons-math3: Remove trailing #T. 
* gnu/packages/java.scm (java-commons-math3)[arguments]: Remove trailing #T
from build phase.
 2021-12-05 00:49:06 +01:00
Ricardo Wurmus
1e7bd5e679
gnu: salmon: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Use a gexp to remove
reference to %build-inputs.
 2021-12-05 00:49:06 +01:00
Ryan Desfosses
20d525a842
gnu: Add libphonenumber 
* gnu/package/messaging.scm (libphonenumber): New variable

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-04 23:03:54 +01:00
Artyom V. Poptsov
ac872546fc
gnu: Add guile-smc 
* gnu/packages/guile-xyz.scm (guile-smc): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-04 22:45:27 +01:00
Ludovic Courtès
3ee142ebd6
gnu: libhandy: Skip test that requires librsvg on non-x86_64. 
* gnu/packages/gnome.scm (libhandy)[arguments]: Add
'skip-test-that-requires-svg' phase on non-x86_64.
 2021-12-04 22:39:47 +01:00
Ludovic Courtès
73f78d556b
gnu: gtranslator: Update to 40.0. 
* gnu/packages/gnome.scm (gtranslator): Update to 40.0.
[inputs]: Add LIBHANDY.
 2021-12-04 22:39:46 +01:00
Ludovic Courtès
d4c4348d83
gnu: gtranslator: Fix compilation. 
* gnu/packages/gnome.scm (gtranslator)[inputs]: Replace LIBSOUP with
LIBSOUP-MINIMAL-2.
[arguments]: Pass #:meson.
 2021-12-04 22:39:46 +01:00
Ludovic Courtès
3f03f502ee
gnu: libgda: Do not use the bundled sqlite. 
* gnu/packages/gnome.scm (libgda)[source]: Add snippet.
[arguments]: Pass "--enable-system-sqlite".
[inputs]: Add SQLITE.
 2021-12-04 22:39:46 +01:00
Julien Lepiller
634b46a469
gnu: java-commons-math3: Remove references to %build-inputs. 
* gnu/packages/java.scm (java-commons-math3)[arguments]: Use a gexp
to remove references to %build-inputs.
 2021-12-04 22:07:26 +01:00
Julien Lepiller
ba5cb6456d
gnu: java-commons-collections4: Remove references to %build-inputs. 
* gnu/packages/java.scm (java-commons-collections4)[arguments]: Use a gexp
to remove references to %build-inputs.
 2021-12-04 22:07:17 +01:00
Julien Lepiller
035fec27fc
gnu: java-commons-exec-1.1: Remove references to %build-inputs. 
* gnu/packages/java.scm (java-commons-exec-1.1)[arguments]: Use a gexp
to remove references to %build-inputs.
 2021-12-04 22:07:11 +01:00
Julien Lepiller
5a4ad372ef
gnu: java-commons-exec: Remove references to %build-inputs. 
* gnu/packages/java.scm (java-commons-exec)[arguments]: Use a gexp to
remove references to %build-inputs.
 2021-12-04 22:06:49 +01:00
Julien Lepiller
2aee138485
gnu: maven-components-parent-pom-22: Remove references to %build-inputs. 
* gnu/packages/maven-parent-pom.scm (maven-components-parent-pom-22)
[arguments]: Use a gexp to remove references to %build-inputs.
 2021-12-04 22:06:41 +01:00
Julien Lepiller
d29f14aca2
gnu: java-sonatype-oss-parent-pom-9: Remove references to %build-inputs. 
* gnu/packages/maven-parent-pom.scm (java-sonatype-oss-parent-pom-9)
[arguments]: Use a gexp to remove references to %build-inputs.
 2021-12-04 22:06:23 +01:00
Ludovic Courtès
f044ffc1c4
gnu: ocaml4.07-ppx-let: Make 'properties' an alist. 
The incorrect 'properties' value was introduced in
3649c56a5f.

* gnu/packages/ocaml.scm (ocaml4.07-ppx-let)[properties]: Turn into an
alist.
 2021-12-04 21:57:27 +01:00
Ricardo Wurmus
98d2abe523
gnu: sailfish: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use a gexp to remove
references to %build-inputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
39e2a84f52
gnu: sailfish: Simplify snippet. 
* gnu/packages/bioinformatics.scm (sailfish)[source]: Remove trailing #T from
snippet.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
b0fd09f856
gnu: piranha: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (piranha)[arguments]: Use gexp to remove
references to %build-inputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
01d2e2b334
gnu: piranha: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (piranha)[arguments]: Remove trailing #T
from build phases.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
502538c6e4
gnu: emboss: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use gexp to remove
reference to %build-inputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
2657bdc100
gnu: vcftools: Replace references to %outputs. 
* gnu/packages/bioinformatics.scm (vcftools)[arguments]: Use gexp to remove
references to %outputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
eec1bdcd9e
gnu: seqan-1: Use gexp for builder. 
* gnu/packages/bioinformatics.scm (seqan-1)[arguments]: Use a gexp to remove
references to %build-inputs and %outputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
2c1c75a56c
gnu: seqan-2: Use gexp for builder. 
* gnu/packages/bioinformatics.scm (seqan-2)[arguments]: Use a gexp to remove
references to %build-inputs and %outputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
f41576c09f
gnu: sra-tools: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use a gexp instead
of referencing %build-inputs.
 2021-12-04 19:54:27 +01:00
Ricardo Wurmus
f33e490334
gnu: preseq: Remove references to %outputs and %build-inputs. 
* gnu/packages/bioinformatics.scm (preseq)[arguments]: Replace references to
%outputs and %build-inputs by using a gexp.
 2021-12-04 19:54:27 +01:00
Ricardo Wurmus
8a446f5e41
gnu: preseq: Simplify snippet. 
* gnu/packages/bioinformatics.scm (preseq)[source]: Simplify snippet.
 2021-12-04 19:54:27 +01:00
zimoun
bd746917a2
gnu: julia-forwarddiff: Disable tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-forwarddiff)[arguments]<#:tests?>:
Conditionally disable tests.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:33 +02:00
zimoun
82586916be
gnu: julia-geometrybasics: Fix tests on i686-linux. 
* gnu/packages/julia-xyz (julia-geometrybasics)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:33 +02:00
zimoun
eb4f1fcf74
gnu: julia-structarrays: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-structarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in the test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:32 +02:00
zimoun
afd35e8e9c
gnu: julia-mutablearithmetics: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-mutablearithmetics)[arguments]<#:phases>:
Conditionally disable the failing test.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:32 +02:00
zimoun
630824a238
gnu: julia-woodburymatrices: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-woodburymatrices)[arguments]<#:phases>:
Conditionally disable the failing test.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:32 +02:00
zimoun
828012ed9f
gnu: julia-intervalsets: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-intervalsets)[arguments]<#:phases>:
Conditionally disable the failing test.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:32 +02:00
zimoun
29c0410086
gnu: julia-reversediff: Disable tests on i686-linux. 
* gnu/packages/julia-xyz (julia-reversediff)[arguments]<#:tests?>:
Conditionally disable tests.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:31 +02:00
zimoun
28d530ea44
gnu: julia-interpolations: Disable tests in i686-linux. 
* gnu/packages/julia-xyz.scm (julia-interpolations)[arguments]<#:tests?>:
Conditionally disable tests.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:31 +02:00
zimoun
e3c15b0bfc
gnu: julia-arrayinterface: Disable tests for i686. 
* gnu/packages/julia-xyz.scm (julia-arrayinterface)[arguments]<#:tests?>:
Conditionally disable tests.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:31 +02:00
zimoun
7c8e9cbfa9
gnu: julia-mappedarrays: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-mappedarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:30 +02:00
zimoun
dcd7c950c6
gnu: julia-blockarrays: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-blockarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:30 +02:00
zimoun
557caa4e2c
gnu: julia-lazyarrays: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-lazyarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:30 +02:00
zimoun
dbad333481
gnu: julia-configurations: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-configurations)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:30 +02:00
zimoun
a31a4517b6
gnu: julia-finitedifferences: Fix tests on i686-linux. 
* gnu/packages/julia-xyz (julia-finitedifferences)[arguments]<#:phases>:
Conditionnally disable the failing test.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:29 +02:00
zimoun
2a749f34e5
gnu: julia-benchmarktools: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-benchmarktools)[arguments]<#:phases>:
Conditionnally disable the failing tests.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:29 +02:00
zimoun
7fee8a46fb
gnu: julia-datastructures: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-datastructures)[arguments]<#:phases>:
Conditionnally disable the failing test.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:29 +02:00
zimoun
9112bed608
gnu: libunwind-julia: Fix build on i686-linux. 
* gnu/packages/julia.scm (libunwind)[origin]<patches>: Add patch.
* gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch: New file.
* gnu/local/mk (dist_patch_DATA): Register it.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:33:30 +02:00
Nicolas Goaziou
f199427c1b
gnu: emacs-org-roam-bibtex: Update to 0.6.1. 
* gnu/packages/emacs-xyz.scm (emacs-org-roam-bibtex): Update to 0.6.1.
 2021-12-04 16:17:58 +01:00
Ricardo Wurmus
cc491eab7e
gnu: plink-ng: Enable tests. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Replace 'check phase
to run tests; do not disable tests via arguments.
[native-inputs]: Add diffutils, plink, and python.
 2021-12-04 16:00:08 +01:00
Ricardo Wurmus
e28b8a9cea
gnu: plink-ng: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-04 15:35:28 +01:00
Ricardo Wurmus
88bb81b515
gnu: plink: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (plink)[arguments]: Use a gexp to replace
reference to %build-inputs.
 2021-12-04 15:31:31 +01:00
Ricardo Wurmus
e920101141
gnu: plink: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (plink)[arguments]: Remove trailing #T from
build phase.
 2021-12-04 15:31:08 +01:00
Ricardo Wurmus
a4e7475edc
gnu: rsem: Update to 1.3.3. 
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3.
[arguments]: Build with gnu++11 standard; patch sources for compatibility.
 2021-12-04 15:27:39 +01:00
Ricardo Wurmus
c45c909026
gnu: rsem: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Remove trailing #T from
build phases.
 2021-12-04 15:26:48 +01:00
Ricardo Wurmus
5e0bcba57b
gnu: rsem: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Use a gexp.
 2021-12-04 15:26:01 +01:00
Ricardo Wurmus
23975fe27a
gnu: rsem: Remove trailing #T from snippet. 
* gnu/packages/bioinformatics.scm (rsem)[source]: Remove trailing #T.
 2021-12-04 15:25:26 +01:00
Ricardo Wurmus
cfaf37d10b
gnu: prodigal: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (prodigal)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-04 15:13:11 +01:00
Ricardo Wurmus
09ae51f7b8
gnu: prank: Bind INPUTS in 'install phase. 
* gnu/packages/bioinformatics.scm (prank)[arguments]: Bind INPUTS in 'install
phase to remove references to %build-inputs.
 2021-12-04 15:11:28 +01:00
Ricardo Wurmus
e128839a94
gnu: prank: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (prank)[arguments]: Remove trailing #T from
build phases.
 2021-12-04 15:11:04 +01:00
jgart
da70132ee9
gnu: janet: Update to 1.19.0. 
* gnu/packages/lisp.scm (janet): Update to 1.19.0.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-04 13:51:49 +01:00
cage
612fe425b4
gnu: tinmop: Update to 0.9.2. 
* gnu/packages/web-browsers.scm (tinmop): Update to 0.9.2.
  [inputs]: Move nano, openssl and xdg-utils to...
  [native-inputs]: ... here. Add automake, autoconf and mandoc. Remove curl
  and gnupg.
  [arguments]: Add 'fix-configure.ac' phase.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-04 13:44:17 +01:00
Ricardo Wurmus
18a85213ae
gnu: pigx-sars-cov2-ww: Update to 0.0.4. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4.
[inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils.
 2021-12-04 12:42:51 +01:00
Ricardo Wurmus
114eb987cb
gnu: mash: Replace references to %build-inputs. 
* gnu/packages/bioinformatics.scm (mash)[arguments]: Use a gexp.
 2021-12-04 00:32:01 +01:00
Ricardo Wurmus
22d9097b5e
gnu: mash: Move htslib and capnproto to regular inputs. 
* gnu/packages/bioinformatics.scm (mash)[native-inputs]: Move htslib and
capnproto from here...
[inputs]: ...to here.
 2021-12-04 00:31:20 +01:00
Ricardo Wurmus
a6b6084649
gnu: mash: Simplify snippet. 
* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
 2021-12-04 00:30:44 +01:00
Ricardo Wurmus
31409a4af7
gnu: mafft: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Remove trailing #T from
build phase.
 2021-12-04 00:22:27 +01:00
Ricardo Wurmus
630671d2e8
gnu: mafft: Replace references to %build-inputs and %outputs. 
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Replace references to
%outputs with a gexp; replace reference to %build-inputs in the 'wrap-programs
phase by binding INPUTS.
 2021-12-04 00:21:27 +01:00
Ricardo Wurmus
5cb2920b8d
gnu: jellyfish: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp.
 2021-12-04 00:19:08 +01:00
Ricardo Wurmus
7c2ee27360
gnu: fastp: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp.
 2021-12-04 00:16:10 +01:00
Ricardo Wurmus
64aafe4bc5
gnu: java-picard: Replace reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (java-picard): Use a gexp.
 2021-12-04 00:06:43 +01:00
Ricardo Wurmus
a3b00a21c0
gnu: java-htsjdk: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (java-htsjdk)[arguments]: Use a gexp.
 2021-12-04 00:03:54 +01:00
Ricardo Wurmus
62e0641892
gnu: fxtract: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp.
 2021-12-04 00:02:20 +01:00
Ricardo Wurmus
4f03151ca4
gnu: delly: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (delly)[arguments]: Replace reference to
%outputs with a gexp.
 2021-12-04 00:00:26 +01:00
Ricardo Wurmus
3601fcbf65
gnu: libbigwig: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (libbigwig)[arguments]: Replace reference to
%outputs with a gexp.
 2021-12-03 23:57:24 +01:00
Ricardo Wurmus
fd607a9efa
gnu: cd-hit: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Replace reference to
%outputs with gexp.
 2021-12-03 23:56:11 +01:00
Ricardo Wurmus
c40852a227
gnu: bowtie1: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-03 23:54:10 +01:00
Ricardo Wurmus
a47a90b900
gnu: bowtie: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace reference to
%outputs with a gexp.
 2021-12-03 23:52:43 +01:00
Ricardo Wurmus
f5c38ee45f
gnu: bless: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (bless)[arguments]: Replace reference to
%build-inputs with a gexp.  Use the dynamic library of zlib while we're at it.
[inputs]: Remove zlib:static.
 2021-12-03 23:51:16 +01:00
Ricardo Wurmus
dd19c8da88
gnu: bless: Remove trailing #T from snippet and build phases. 
* gnu/packages/bioinformatics.scm (bless)[source, arguments]: Remove all
trailing #Ts.
 2021-12-03 23:48:46 +01:00
Ricardo Wurmus
0e09065460
gnu: bedtools: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use a gexp instead of
referencing %outputs.
 2021-12-03 23:36:18 +01:00
Ricardo Wurmus
a5663a7c8a
gnu: qtltools: Replace references to %build-inputs. 
* gnu/packages/bioinformatics.scm (qtltools)[arguments]: Use a gexp instead of
referencing %build-inputs.
 2021-12-03 23:26:48 +01:00
Ricardo Wurmus
ce9bfcddb5
gnu: imp: Update to 2.15.0. 
* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0.
[arguments]: Disable one more test.
 2021-12-03 22:29:52 +01:00
Ricardo Wurmus
dcf857e486
gnu: Add r-fpeek. 
* gnu/packages/cran.scm (r-fpeek): New variable.
 2021-12-03 22:29:40 +01:00
Liliana Marie Prikler
15404ff19b
gnu: emacs: Load package descriptors from packages referenced by subdirs.el 
* gnu/packages/aux-files/emacs/guix-emacs.el
(guix-emacs--non-core-load-path): New procedure.
(guix-emacs-autoload-packages): Use it here.
(guix-emacs-load-package-descriptors): New procedure.
* gnu/packages/emacs.scm (emacs)[install-site-start]: Install advice to run
‘guix-emacs-load-package-descriptors’.
 2021-12-03 21:39:50 +01:00
Liliana Marie Prikler
4baeb72717
gnu: emacs: Make DocView PDF work out of the box. 
* gnu/packages/emacs.scm (emacs)[patch-program-file-names]: Add patches for
the programs “gs”, “dvipdf”, “ps2pdf” and “pdftotext”.
[inputs]: Add ghostscript and poppler.
 2021-12-03 21:39:49 +01:00
Liliana Marie Prikler
f725279cdd
gnu: emacs: Find real GVFS processes. 
* gnu/packages/emacs.scm (emacs)[#:phases]<patch-program-file-names>: Expand
calls to “tramp-compat-process-running-p” so that Guix wrappers are also
matched.
 2021-12-03 21:39:49 +01:00
phodina
269baba919
gnu: Add valeronoi. 
* gnu/packages/engineering.scm (valeronoi): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-03 21:38:30 +01:00
jgart
19528e39bb
gnu: st: Install terminfo files. 
* gnu/packages/suckless.scm (st)[native-inputs]: Add ncurses.
[make-flags](TERMINFO): New flag.
[phases](inhibit-terminfo-install): Remove phase.

Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>
 2021-12-03 15:27:41 -05:00
Morgan Smith
170cb4c881
gnu: emacs-org: Preserve version information. 
* gnu/packages/emacs-xyz.scm (emacs-org)[#:phases]: Prevent install phase from
deleting the version information.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-03 21:14:25 +01:00
Nicolas Goaziou
85ed37c170
gnu: emacs-consult-notmuch: Update to 0.6. 
* gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.6.
 2021-12-03 19:43:12 +01:00
Nicolas Goaziou
6557f17000
gnu: emacs-helm: Update to 3.8.2. 
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.2.
 2021-12-03 19:41:27 +01:00
Nicolas Goaziou
a7776d5ac0
gnu: emacs-vertico: Update to 0.17. 
* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.17.
 2021-12-03 19:36:35 +01:00
Ricardo Wurmus
b8d6e77476
gnu: python-ont-fast5-api: Update to 4.0.0. 
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0.
[source]: Remove bundled plugin binaries.
[arguments]: Install plugin from inputs.
[inputs]: Add vbz-compression.
[propagated-inputs]: Remove python-six; add python-packaging.
 2021-12-03 14:55:38 +01:00
Ricardo Wurmus
d0aa14a43d
gnu: Add vbz-compression. 
* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
 2021-12-03 14:55:38 +01:00
Mathieu Othacehe
3354e41c1e
system: vm: Remove the vga argument. 
* gnu/system/vm.scm (common-qemu-options): Remove the "-vga std" argument that
is the default since QEMU 2.2.

Suggested-by: Attila Lendvai <attila@lendvai.name>
 2021-12-03 14:25:57 +01:00
Attila Lendvai
b42bfbdfe5
guix system vm: Add --no-graphic CLI argument. 
It configures QEMU to use the tty it was started in for IO (as opposed to
opening a separate graphical window).  This enables copy-pasting and
scrollback.  Exit QEMU with C-a x.

* gnu/system/vm.scm (system-qemu-image/shared-store-script): Also add the
'-nographic' QEMU argument when called with #:graphic? #false.
* guix/scripts/system.scm (system-derivation-for-action): Propagate
the #:graphic? keyword arg.
(perform-action): Add and propagate the #:graphic? keyword arg.
(show-help): Add --no-graphic CLI arg.
(%options): Process the new --no-graphic CLI arg.
(process-action): Feed in the CLI arg through the #:graphic? keyword arg.
* doc/guix.texi (Invoking guix system): Add example to combine guix system and
invoking the vm start script into one command.  Split the description of the
various options into separate paragraphs.  Add a paragraph to describe
--no-graphic.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-03 14:18:32 +01:00
Charles
5a18cf3604
gnu: cl-coalton: Update to 0.0.1-2.012f6c8. 
* gnu/packages/lisp-xyz.scm (sbcl-coalton): Update to 0.0.1-2.012f6c8.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-03 14:08:14 +01:00
Charles
6e0c4a28b9
gnu: cl-float-features: Update to 1.0.0-2.c1f86ae. 
* gnu/packages/lisp-xyz.scm (sbcl-float-features): Update to 1.0.0-2.c1f86ae.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-03 13:59:46 +01:00
Ricardo Wurmus
6d4f260166
gnu: bamutils: Update to 1.0.14. 
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.14.
[arguments]: Patch DATE for reproducibility; prepare sources of libstatgen.
[native-inputs]: Add sources of libstatgen.
 2021-12-03 13:56:02 +01:00
Ricardo Wurmus
673cc29908
gnu: bamutils: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
361e0d9f27
gnu: bamm: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (bamm)[arguments]: Use gexp instead of
%build-inputs.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
4f536c4607
gnu: python2-openpyxl: Explicitly build with Python 2. 
* gnu/packages/python-xyz.scm (python2-openpyxl)[arguments]: Add value
for #:python field.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
7fb5bfc54f
gnu: python-plastid: Update to 0.5.1. 
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.5.1.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
b7aaf6c418
gnu: ivar: Disable parallel tests. 
* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
 2021-12-03 13:48:41 +01:00
Ricardo Wurmus
aa2d5ca02e
gnu: Remove python2-biom-format. 
There are no users of this variant, and the current version of biom-format
does not support Python 2.

* gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable.
(python-biom-format)[properties]: Remove field.
 2021-12-03 13:31:32 +01:00
Ricardo Wurmus
8fa7de386c
gnu: r-flowclust: Add gsl. 
* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally
committed comment character.
 2021-12-03 13:31:32 +01:00
Mark H Weaver
3e9dc2754e
gnu: icecat: Remove vestigial icecat-78-makeicecat.patch. 
This is a followup to commit a63231003e.

* gnu/packages/patches/icecat-78-makeicecat.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-12-03 04:45:15 -05:00
Mathieu Othacehe
c0d9ba22d0
gnu: cuirass: Update to 1.1.0-6.df8837c. 
* gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c.
 2021-12-03 10:41:37 +01:00
jgart
fcf7e6513c
gnu: python-pandocfilters: Update to 1.5.0. 
* gnu/packages/textutils.scm (python-pandocfilters): Update to 1.5.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-03 10:41:37 +01:00
Mark H Weaver
d49e7a592f
gnu: icecat: Fix CVE-2021-43527. 
* gnu/packages/patches/icecat-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gnuzilla.scm (icecat-source): Apply it.
 2021-12-03 04:37:42 -05:00
Mark H Weaver
080a5de2ee
gnu: nss: Fix CVE-2021-43527 via graft. 
* gnu/packages/patches/nss-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/nss.scm (nss/fixed): New variable
(nss)[replacement]: New field.
 2021-12-03 04:37:21 -05:00
Ricardo Wurmus
345b341919
gnu: openjdk16: Use MAKE-FILE-WRITABLE. 
* gnu/packages/java.scm (openjdk16)[arguments]: Do not shell out to "chmod".
 2021-12-02 23:58:56 +01:00
Arne Babenhauserheide
68e71fbb17
gnu: Add openjdk17. 
* gnu/packages/java.scm (openjdk17): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-02 23:58:53 +01:00
Ricardo Wurmus
1f5c1bc024
gnu: python2-decorator: Downgrade to 4.3.0 
* gnu/packages/python-xyz.scm (python2-decorator): Keep at 4.3.0.
(python-decorator)[properties]: Add python2-variant.
 2021-12-02 18:56:29 +01:00
Ricardo Wurmus
a2423c0ca4
gnu: ribodiff: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T
from build phase.
 2021-12-02 18:32:33 +01:00
Ricardo Wurmus
1123d25830
gnu: ribodiff: Disable broken test. 
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase
'disable-plot-test.
 2021-12-02 18:32:10 +01:00
Ricardo Wurmus
f28f5be11d
gnu: python2-statsmodels: Downgrade to 0.9.0. 
* gnu/packages/statistics.scm (python2-statsmodels): Downgrade to 0.9.0.
 2021-12-02 18:31:38 +01:00
Ricardo Wurmus
31d372cd8a
gnu: khmer: Fix build with Python 3.8. 
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T.
[arguments]: Remove trailing #T from build phases; add build phase
'python-3.8-compatibility.
 2021-12-02 18:24:31 +01:00
Ricardo Wurmus
32d5fb01f8
gnu: python-biom-format: Update to 2.1.10. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10.
[source]: Simplify snippet.
[arguments]: Add phase 'relax; remove trailing #T from other build phases.
[propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with
python-pandas.
 2021-12-02 18:02:07 +01:00
jgart
fab80c3672
gnu: Add trayer-srg. 
* gnu/packages/wm.scm (trayer-srg): New variable.

Co-authored-by: Disseminate Dissent <disseminatedissent@protonmail.com>
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:44:31 +01:00
Ricardo Wurmus
28ad55a59d
gnu: pardre: Update to 2.2.5. 
* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5.
[arguments]: Remove trailing #T and update comment about tests.
 2021-12-02 15:40:46 +01:00
Ricardo Wurmus
fc20fad6f7
gnu: pardre: Use C++ bindings for MPI. 
* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with
openmpi-c++.
 2021-12-02 15:40:46 +01:00
Ricardo Wurmus
2d6be35ea2
gnu: Add openmpi-c++. 
* gnu/packages/mpi.scm (openmpi-c++): New variable.
 2021-12-02 15:40:45 +01:00
Liliana Marie Prikler
df4f960cb8
gnu: Add libconfini. 
* gnu/packages/cpp.scm (libconfini): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:38:17 +01:00
Vinicius Monego
2d92b3bbb6
gnu: shotcut: Update to 21.10.31. 
* gnu/packages/video.scm (shotcut): Update to 21.10.31.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:29:33 +01:00
Vinicius Monego
82e5a1b4c3
gnu: kdenlive: Update to 21.08.3. 
* gnu/packages/kde.scm (kdenlive): Update to 21.08.3.
[arguments]: Pass "-DBUILD_TESTING=off" to #:configure-flags as tests are
currently disabled.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:29:33 +01:00
Vinicius Monego
6fc0cfe1b5
gnu: mlt: Update to 7.2.0. 
* gnu/packages/video.scm (mlt): Update to 7.2.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:29:33 +01:00
jgart
e8d5dd5c9b
gnu: ccls: Update to 0.20210330. 
* gnu/packages/cpp.scm (ccls): Update to 0.20210330.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:26:05 +01:00
Artyom V. Poptsov
a4cc1ae446
gnu: guile-udev: Update to 0.2.0 
* gnu/packages/guile-xyz.scm (guile-udev): Update to 0.2.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:05:28 +01:00
Ludovic Courtès
e080e35dc1
gnu: glade: Remove dependency on GJS on non-x86_64. 
* gnu/packages/gnome.scm (glade3)[arguments]: Add optional
'skip-gjs-test' phase.
[native-inputs]: Provide GJS only when 'target-x86-64?'.
 2021-12-02 14:59:57 +01:00
Ludovic Courtès
689d141cd8
gnu: Remove librsvg@2.50 from the Xfce dependency graph. 
This allows us to build Xfce on non-x86_64 platforms.

* gnu/packages/gstreamer.scm (gst-plugins-good)[inputs]: Use
'librsvg-for-system' instead of 'librsvg'.
* gnu/packages/gtk.scm (guile-rsvg)[inputs]: Likewise.
* gnu/packages/xfce.scm (xfce4-xkb-plugin)[inputs]: Likewise.
 2021-12-02 14:59:57 +01:00
Ludovic Courtès
d371abbd0f
gnu: librsvg: Add 'librsvg-for-system' procedure. 
* gnu/packages/gnome.scm (librsvg-for-system): New procedure.
 2021-12-02 14:59:56 +01:00
Ludovic Courtès
8477a6d743
gnu: librsvg: Reintroduce version 2.40. 
* gnu/packages/gnome.scm (librsvg-2.40): New variable.
 2021-12-02 14:59:56 +01:00
Ricardo Wurmus
46b73fd22d
gnu: python-ipython: Update to 7.20.0. 
* gnu/packages/python-xyz.scm (python-ipython): Update to 7.20.0.
 2021-12-02 13:42:17 +01:00
Ricardo Wurmus
5723503f9f
gnu: python-ipython: Remove trailing #T. 
* gnu/packages/python-xyz.scm (python-ipython)[arguments]: Remove trailing #T
from build phases.
 2021-12-02 13:42:17 +01:00
Efraim Flashner
923a121751
gnu: yggdrasil: Simplify build phases. 
* gnu/packages/networking.scm (yggdrasil)[arguments]: Rewrite custom
'build phase reusing go-build-system 'build phase. Remove custom
'install phase.
 2021-12-02 14:28:06 +02:00
Efraim Flashner
d19e646c83
gnu: go-golang-zx2c4-com-wireguard: Fix downloading source. 
* gnu/packages/golang.scm (go-golang-zx2c4-com-wireguard)[source]:
Adjust commit string in git-reference.
 2021-12-02 14:13:27 +02:00
Efraim Flashner
e0755470f8
gnu: go-github-com-vividcortex-ewma: Adjust import-path. 
* gnu/packages/golang.scm (go-github-com-vividcortex-ewma)[arguments]:
Adjust import-path to location other go packages expect it to be.
 2021-12-02 14:12:31 +02:00
Ludovic Courtès
052f56e5a6
gnu: guix: Update to 8cc099b. 
* gnu/packages/package-management.scm (guix): Update to 8cc099b.
 2021-12-02 12:52:59 +01:00
Ricardo Wurmus
a8fff63daa
gnu: Add python-mygene. 
* gnu/packages/bioinformatics.scm (python-mygene): New variable.
 2021-12-02 11:57:28 +01:00
Ricardo Wurmus
b15a525703
gnu: Add python-biothings-client. 
* gnu/packages/bioinformatics.scm (python-biothings-client): New variable.
 2021-12-02 11:57:13 +01:00
Ricardo Wurmus
37c475ebc0
gnu: prinseq: Fix use of SEARCH-INPUT-FILE. 
* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Pass missing argument
to SEARCH-INPUT-FILE.
 2021-12-02 11:26:55 +01:00
Ricardo Wurmus
f1fd313e48
gnu: gnome-shell: Do not wrap in LD_LIBRARY_PATH. 
Fixes <https://bugs.gnu.org/37123>.

* gnu/packages/gnome.scm (gnome-shell)[arguments]: Remove LD_LIBRARY_PATH from
wrapper.
 2021-12-02 10:52:45 +01:00
Ricardo Wurmus
e1cb787870
gnu: python2-matplotlib: Disable sanity-check. 
* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Delete
'sanity-check phase.
 2021-12-02 10:30:40 +01:00
Ricardo Wurmus
a33ca53492
gnu: python2-matplotlib: Remove trailing #T. 
* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Remove
trailing #T from build phase.
 2021-12-02 10:29:59 +01:00
Efraim Flashner
c14ab97a03
Revert "gnu: Change source file-name suffix in rust packages." 
This reverts commit 07a80e30a1.

This commit affects rust crates that are inputs to librsvg, which causes
many packages to be rebuilt.
 2021-12-02 11:10:37 +02:00
Efraim Flashner
e577889828
gnu: tor: Limit test suite adjustments to affected architectures. 
This is a follow-up to 68d090002a.

* gnu/packages/tor.scm (tor)[arguments]: Only add custom
'adjust-test-suite phase on aarch64, powerpc32.
 2021-12-02 11:07:18 +02:00
Ricardo Wurmus
c2c63a00de
gnu: Add r-scdblfinder. 
* gnu/packages/bioconductor.scm (r-scdblfinder): New variable.
 2021-12-02 10:03:07 +01:00
Ricardo Wurmus
24832d2ebd
gnu: python2-numpy: Delete file that depends on deleted test. 
This is a follow-up to commit ec4892c742.

* gnu/packages/python-xyz.scm (python2-numpy)[arguments]: Also delete a second
test file that depends on the previously deleted test file.
 2021-12-02 09:45:24 +01:00
Z572
07a80e30a1
gnu: Change source file-name suffix in rust packages. 
* gnu/packages/rust-apps.scm (rust-cbindgen)[source]: Change source
file-name suffix from '.crate' to '.tar.gz'.
* gnu/packages/crates-graphics.scm (rust-ansi-term-0.12): Likewise.
(rust-ansi-term-0.11): Likewise.
(rust-rgb-0.8): Likewise.

* gnu/packages/crates-io.scm (rust-adler32-1): Likewise.
(rust-antidote-1): Likewise.
(rust-atty-0.2): Likewise.
(rust-autocfg-0.1): Likewise.
(rust-backtrace-sys-0.1): Likewise.
(rust-base-x-0.2): Likewise.
(rust-bencher-0.1): Likewise.
(rust-bitflags-1): Likewise.
(rust-blas-sys-0.7): Likewise.
(rust-cargon-0.0): Likewise.
(rust-cblas-sys-0.1): Likewise.
(rust-cc-1): Likewise.
(rust-cfg-if-0.1): Likewise.
(rust-clang-sys-0.26): Likewise.
(rust-clap-2): Likewise.
(rust-clicolors-control-1): Likewise.
(rust-cloudabi-0.1): Likewise.
(rust-cloudabi-0.0): Likewise.
(rust-cmake-0.1): Likewise.
(rust-compiler-builtins-0.1): Likewise.
(rust-constant-time-eq-0.1): Likewise.
(rust-core-foundation-sys-0.6): Likewise.
(rust-data-encoding-2): Likewise.
(rust-defmac-0.2): Likewise.
(rust-defmac-0.1): Likewise.
(rust-dirs-1): Likewise.
(rust-discard-1): Likewise.
(rust-doc-comment-0.3): Likewise.
(rust-dtoa-0.4): Likewise.
(rust-dtoa-0.2): Likewise.
(rust-fallible-iterator-0.2): Likewise.
(rust-filetime-0.2): Likewise.
(rust-findshlibs-0.5): Likewise.
(rust-fixedbitset-0.2): Likewise.
(rust-fixedbitset-0.1): Likewise.
(rust-fnv-1): Likewise.
(rust-foreign-types-shared-0.2): Likewise.
(rust-fs-extra-1): Likewise.
(rust-fuchsia-cprng-0.1): Likewise.
(rust-fuchsia-zircon-0.3): Likewise.
(rust-fuchsia-zircon-sys-0.3): Likewise.
(rust-futures-0.1): Likewise.
(rust-futures-core-preview-0.3): Likewise.
(rust-futures-cpupool-0.1): Likewise.
(rust-futures-io-preview-0.3): Likewise.
(rust-futures-sink-preview-0.3): Likewise.
(rust-getopts-0.2): Likewise.
(rust-glob-0.3): Likewise.
(rust-glob-0.2): Likewise.
(rust-heapsize-0.4): Likewise.
(rust-heapsize-0.3): Likewise.
(rust-heapsize-plugin-0.1): Likewise.
(rust-heck-0.3): Likewise.
(rust-hex-0.3): Likewise.
(rust-hex-0.2): Likewise.
(rust-hostname-0.1): Likewise.
(rust-iovec-0.1): Likewise.
(rust-itoa-0.4): Likewise.
(rust-itoa-0.1): Likewise.
(rust-json-0.11): Likewise.
(rust-kernel32-sys-0.2): Likewise.
(rust-language-tags-0.2): Likewise.
(rust-lazy-static-1): Likewise.
(rust-libloading-0.5): Likewise.
(rust-lock-api-0.1): Likewise.
(rust-log-0.4): Likewise.
(rust-maplit-1): Likewise.
(rust-matches-0.1): Likewise.
(rust-matrixmultiply-0.2): Likewise.
(rust-matrixmultiply-0.1): Likewise.
(rust-md5-0.7): Likewise.
(rust-md5-0.6): Likewise.
(rust-memmap-0.7): Likewise.
(rust-memmap-0.6): Likewise.
(rust-mime-0.3): Likewise.
(rust-miniz-oxide-0.3): Likewise.
(rust-miniz-sys-0.1): Likewise.
(rust-miow-0.3): Likewise.
(rust-miow-0.2): Likewise.
(rust-modifier-0.1): Likewise.
(rust-net2-0.2): Likewise.
(rust-nodrop-0.1): Likewise.
(rust-nodrop-union-0.1): Likewise.
(rust-num-traits-0.1): Likewise.
(rust-numtoa-0.1): Likewise.
(rust-openssl-probe-0.1): Likewise.
(rust-owning-ref-0.4): Likewise.
(rust-parity-wasm-0.40): Likewise.
(rust-peeking-take-while-0.1): Likewise.
(rust-percent-encoding-2): Likewise.
(rust-percent-encoding-1): Likewise.
(rust-permutohedron-0.2): Likewise.
(rust-pico-sys-0.0): Likewise.
(rust-pkg-config-0.3): Likewise.
(rust-plain-0.2): Likewise.
(rust-plugin-0.2): Likewise.
(rust-pocket-resources-0.3): Likewise.
(rust-ppv-lite86-0.2): Likewise.
(rust-proc-macro2-1): Likewise.
(rust-quick-error-2): Likewise.
(rust-quick-error-1): Likewise.
(rust-quote-1): Likewise.
(rust-rand-0.7): Likewise.
(rust-rand-0.6): Likewise.
(rust-rand-0.3): Likewise.
(rust-rand-chacha-0.1): Likewise.
(rust-rand-core-0.4): Likewise.
(rust-rand-core-0.3): Likewise.
(rust-rand-hc-0.2): Likewise.
(rust-rand-hc-0.1): Likewise.
(rust-rand-isaac-0.1): Likewise.
(rust-rand-jitter-0.1): Likewise.
(rust-rand-os-0.1): Likewise.
(rust-rand-pcg-0.3): Likewise.
(rust-rand-pcg-0.2): Likewise.
(rust-rand-pcg-0.1): Likewise.
(rust-rand-xorshift-0.1): Likewise.
(rust-rawpointer-0.2): Likewise.
(rust-rawpointer-0.1): Likewise.
(rust-rdrand-0.4): Likewise.
(rust-redox-syscall-0.1): Likewise.
(rust-redox-termios-0.1): Likewise.
(rust-resolv-conf-0.6): Likewise.
(rust-rustc-demangle-0.1): Likewise.
(rust-rustc-serialize-0.3): Likewise.
(rust-rustc-std-workspace-core-1): Likewise.
(rust-ryu-1): Likewise.
(rust-safemem-0.3): Likewise.
(rust-same-file-1): Likewise.
(rust-schannel-0.1): Likewise.
(rust-scoped-threadpool-0.1): Likewise.
(rust-scoped-tls-1): Likewise.
(rust-scoped-tls-0.1): Likewise.
(rust-scopeguard-1): Likewise.
(rust-scopeguard-0.3): Likewise.
(rust-security-framework-sys-0.3): Likewise.
(rust-semver-parser-0.9): Likewise.
(rust-semver-parser-0.7): Likewise.
(rust-serde-derive-1): Likewise.
(rust-shlex-1): Likewise.
(rust-shlex-0.1): Likewise.
(rust-slab-0.4): Likewise.
(rust-socket2-0.3): Likewise.
(rust-sourcefile-0.1): Likewise.
(rust-spin-0.5): Likewise.
(rust-stacker-0.1): Likewise.
(rust-static-assertions-1): Likewise.
(rust-static-assertions-0.3): Likewise.
(rust-stdweb-internal-runtime-0.1): Likewise.
(rust-stdweb-internal-test-macro-0.1): Likewise.
(rust-streaming-stats-0.2): Likewise.
(rust-strsim-0.9): Likewise.
(rust-strsim-0.8): Likewise.
(rust-synstructure-test-traits-0.1): Likewise.
(rust-tar-0.4): Likewise.
(rust-tempdir-0.3): Likewise.
(rust-tempfile-3): Likewise.
(rust-term-0.4): Likewise.
(rust-term-0.2): Likewise.
(rust-termcolor-1): Likewise.
(rust-termion-1): Likewise.
(rust-termios-0.3): Likewise.
(rust-thread-id-3): Likewise.
(rust-thread-local-1): Likewise.
(rust-thread-local-0.3): Likewise.
(rust-threadpool-1): Likewise.
(rust-time-0.1): Likewise.
(rust-tokio-mock-task-0.1): Likewise.
(rust-toml-0.5): Likewise.
(rust-tracing-core-0.1): Likewise.
(rust-traitobject-0.1): Likewise.
(rust-try-from-0.3): Likewise.
(rust-try-lock-0.2): Likewise.
(rust-typeable-0.1): Likewise.
(rust-typemap-0.3): Likewise.
(rust-typenum-1): Likewise.
(rust-ucd-trie-0.1): Likewise.
(rust-ucd-util-0.1): Likewise.
(rust-unicode-xid-0.2): Likewise.
(rust-unicode-xid-0.1): Likewise.
(rust-unreachable-1): Likewise.
(rust-unsafe-any-0.4): Likewise.
(rust-untrusted-0.7): Likewise.
(rust-vcpkg-0.2): Likewise.
(rust-vec-map-0.8): Likewise.
(rust-version-check-0.9): Likewise.
(rust-version-check-0.1): Likewise.
(rust-void-1): Likewise.
(rust-wasi-0.5): Likewise.
(rust-wasm-bindgen-shared-0.2): Likewise.
(rust-wasm-bindgen-test-macro-0.2): Likewise.
(rust-widestring-0.4): Likewise.
(rust-winapi-0.3): Likewise.
(rust-winapi-0.2): Likewise.
(rust-winapi-build-0.1): Likewise.
(rust-winapi-util-0.1): Likewise.
(rust-wincolor-1): Likewise.
(rust-winutil-0.1): Likewise.
(rust-ws2-32-sys-0.2): Likewise.
(rust-xattr-0.2): Likewise.
(rust-xdg-2): Likewise.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-02 10:24:17 +02:00
Leo Famulari
bef86fed3e
Revert "gnu: godot: Update to 3.4." 
This reverts commit dd4365efa1.

We reverted this commit because it broke the operation of the only
package in Guix that depends on Godot, SuperStarfighter:

https://debbugs.gnu.org/cgi/bugreport.cgi?bug=52233#20
 2021-12-02 01:27:12 -05:00
cage
934a246409
gnu: cl-tooter: Update to 1.0.0-3.ec97bee. 
* gnu/packages/lisp-xyz.scm (cl-tooter): Update to 1.0.0-3.ec97bee.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-12-02 00:12:58 -05:00
cage
e9e2204897
gnu: cl-i18n: Update to 0.5.1-1.4216fe9. 
* gnu/packages/lisp-xyz.scm (cl-i18n): Update to 0.5.1-1.4216fe9.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-12-02 00:12:57 -05:00
Andy Tai
dd4365efa1
gnu: godot: Update to 3.4. 
* gnu/packages/game-development.scm (godot): Update to 3.4.
[source]: Add new bundled dependencies to the origin snippet.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-12-02 00:02:47 -05:00
Ricardo Wurmus
ec4892c742
gnu: python2-numpy: Do not inherit native-inputs. 
* gnu/packages/python-xyz.scm (python2-numpy)[native-inputs]: Do not inherit
from Python 3 variant; use only python2-cython, python2-pytest, and gfortran.
[arguments]: Add phase 'delete-failing-test.
 2021-12-02 01:20:43 +01:00
Leo Famulari
7a171235af
gnu: linux-libre 4.19: Update to 4.19.219. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.219.
(linux-libre-4.19-pristine-source): Update hash.
 2021-12-01 18:43:05 -05:00
Leo Famulari
6f18f35297
gnu: linux-libre 5.4: Update to 5.4.163. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.163.
(linux-libre-5.4-pristine-source): Update hash.
 2021-12-01 18:43:05 -05:00
Leo Famulari
f01588736c
gnu: linux-libre 5.10: Update to 5.10.83. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.83.
(linux-libre-5.10-pristine-source): Update hash.
 2021-12-01 18:43:05 -05:00
Leo Famulari
c3ec5eaa75
gnu: linux-libre: Update to 5.15.6. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.6.
(linux-libre-5.15-pristine-source): Update hash.
 2021-12-01 18:43:02 -05:00
Ricardo Wurmus
d53679c531
gnu: Remove couger. 
This package has been moved to the Guix Past channel.

* gnu/packages/bioinformatics.scm (couger): Remove variable.
 2021-12-02 00:32:12 +01:00
Ricardo Wurmus
cd40978a4b
gnu: randomjungle: Fix compatibility errors. 
* gnu/packages/machine-learning.scm (randomjungle)[arguments]: Add build phase
'fix-compatibility-errors to patch type errors.
 2021-12-02 00:32:12 +01:00
Ludovic Courtès
36f18626a9
gnu: petsc-{complex,openmpi,complex-openmpi}: Use gexps. 
This is a followup to 07ac13a26a, which
omitted to switch to gexps in packages that inherit from 'petsc'.

Reported by Mathieu Othacehe <othacehe@gnu.org>.

* gnu/packages/maths.scm (petsc-complex)[arguments]: Use gexps.
(petsc-openmpi)[arguments]: Likewise.
(petsc-complex-openmpi)[arguments]: Likewise.
 2021-12-01 23:30:15 +01:00
Ludovic Courtès
725d35aa9a
gnu: scalapack: Update to 2.1.0. 
* gnu/packages/maths.scm (scalapack): Update to 2.1.0.
[source]: Remove "scalapack-blacs-mpi-deprecations.patch" and add
"scalapack-gcc-10-compilation.patch".
[arguments]: Add 'skip-faulty-test' phase.
* gnu/packages/patches/scalapack-blacs-mpi-deprecations.patch: Remove.
* gnu/packages/patches/scalapack-gcc-10-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
 2021-12-01 23:30:15 +01:00
Jonathan Brielmaier
a63231003e
gnu: icecat: Remove leftovers of release 78. 
No longer required as icedove is now based on the 91 branch.

* gnu/packages/gnuzilla.scm (mozilla-78-compare-locales): Remove.
(all-mozilla-78-locales): Remove.
(%icecat-78-version): Remove.
(icecat-78-source): Remove.
 2021-12-01 22:07:00 +01:00
Jonathan Brielmaier
52cb5cf5b8
gnu: icedove: Update to 91.3.2. 
The profile folder moved from `~/.icedove` to `~/.thunderbird`. You may
need to migrate (copy) your profile over.

* gnu/packages/gnuzilla.scm (icedove): Update to 91.3.2.
[source]: Switch back to icecat-source.
[arguments]: `obj-x86_64-pc-linux-gnu` folder is now generated during
build, so it can't deleted in front. Remove surounding `'` from
MOZ_DEDICATED_PROFILES to follow source code. MOZ_APP_BASENAME and
MOZ_APP_DISPLAYNAME are no longer set in `comm/mail/confvars.sh`. Update
path of `customizeToolbar.js`.
Delete `'bootstrap` phase and no longer set AUTOCONF variable as the
autoconf build part was removed. Set MACH_USE_SYSTEM_PYTHON and
MOZ_APP_NAME, the latter is the binary name.
`--enable-calendar` flag got removed. Use bundled NSS until
core-updates merge.
[inputs]: Update to `icu4c-69` and `nspr-4.32`. Use bundled NSS for now.
[native-inputs]: Switch to comm-esr91 branch. Remove autoconf, add m4.
Update rust and cargo to 1.51. Use `rust-cbindgen-0.19`.
 2021-12-01 22:07:00 +01:00
Jonathan Brielmaier
f1a2e90409
gnu: Add nspr@4.32. 
Required for icecat/icedove 91.

* gnu/packages/nss.scm (nspr-4.32): New variable.
 2021-12-01 22:06:54 +01:00
Nicolas Goaziou
d7d7b57965
gnu: emacs-citar: Remove unnecessary input. 
* gnu/packages/emacs-xyz.scm (emacs-citar)[propagated-inputs]: Remove emacs-helm-bibtex.
 2021-12-01 22:00:45 +01:00
Andy Tai
2b08cc968b
gnu: bullet: Update to 3.17. 
* gnu/packages/game-development.scm (bullet): Update to 3.17.
[arguments]<#:configure-flags>: Disable access to third-party libs.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 21:54:41 +01:00
Mathieu Othacehe
d64b78ef0c
installer: parted: Use the swap-space record. 
* gnu/installer/parted.scm (user-partitions->configuration): Use the
swap-space record.
 2021-12-01 20:59:06 +01:00
Mathieu Othacehe
05c747ea6b
tests: install: Use the swap-space record. 
This fixes the following error:

In gnu/services/base.scm:
  2228:56  4 (_ #<<uuid> type: dce bv: #vu8(17 17 17 17 34 34 51 51 …>)
In gnu/build/file-systems.scm:
   239:13  3 (swap-space->flags-bit-mask #<<uuid> type: dce bv: #vu8…>)
In ice-9/boot-9.scm:
  1685:16  2 (raise-exception _ #:continuable? _)
  1685:16  1 (raise-exception _ #:continuable? _)
  1685:16  0 (raise-exception _ #:continuable? _)

ice-9/boot-9.scm:1685:16: In procedure raise-exception:
In procedure swap-space-priority: Wrong type argument: #<<uuid> type: dce bv: #vu8(17 17 17 17 34 34 51 51 68 68 18 52 86 120 154 188)>

* gnu/tests/install.scm (installation-target-os-for-gui-tests): Use the
swap-space record.
 2021-12-01 19:23:12 +01:00
Attila Lendvai
c7c4f80881
gnu: Update Trezor support. 
* gnu/packages/patches/python-trezor-agent-fix-argv0.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Apply previous removal.
* gnu/packages/finance.scm (python-trezor-agent): Update to 0.14.4.
[source]: Remove now useless patch.
(python-mnemonic): Update to 0.20.
(python-trezor): Update to 0.12.4
(trezor-agent): Update to 0.11.0-1.
[source]: Add file-name field.
[arguments]: Remove trailing #T in phases.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 18:05:26 +01:00
Attila Lendvai
508200d66a
gnu: python-daemon: Update to 2.3.0. 
* gnu/packages/python-xyz.scm (python-daemon): Update to 2.3.0.
[native-inputs]: Add python-coverage and python-twine.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 17:58:33 +01:00
Ahmad Jarara
8cc099b425
gnu: openssh: Add support for ecdsa-sk, ed25519-sk ssh keys. 
* gnu/packages/ssh.scm (openssh)[inputs]: Add LIBFIDO2.
[arguments]: Pass "--with-security-key-builtin".

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-01 17:53:27 +01:00
Ahmad Jarara
3aaef047a6
gnu: Add libfido2. 
* gnu/packages/security-token.scm (libfido2): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-01 17:53:27 +01:00
Ahmad Jarara
083a710cbb
gnu: Add libcbor. 
* gnu/packages/compression.scm (libcbor): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-01 17:53:27 +01:00
Foo Chuan Wei
b5d0029771
gnu: Add vim-nerdtree. 
* gnu/packages/vim.scm (vim-nerdtree): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-01 17:53:27 +01:00
Attila Lendvai
a955e4d7f6
gnu: Add smplayer. 
* gnu/packages/video.scm (smplayer): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-01 17:51:38 +01:00
Felix Gruber
5ff34d596d
gnu: Add python-codespell. 
* gnu/packages/python-xyz.scm (python-codespell): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-01 17:51:37 +01:00
Josselin Poiret
a82e9f45fd
installer: Make LUKS2 the default format for encrypted devices 
* gnu/installer/parted.scm (luks-format-and-open): Change it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-01 17:51:37 +01:00
Josselin Poiret
adce91a3ec
gnu: system: Add LUKS2 support for the root file system. 
* gnu/bootloader/grub.scm (grub-configuration-file): Add 'insmod
luks2'.
* gnu/system/mapped-devices.scm (open-luks-device): Create
'/run/cryptsetup/' directory.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-01 17:51:37 +01:00
Guillaume Le Vaillant
1a0696e0a6
gnu: sdrangel: Add missing input. 
QtQuick is required by some runtime features.

* gnu/packages/radio.scm (sdrangel)[inputs]: Add qtquickcontrols2.
 2021-12-01 17:30:45 +01:00
jgart via Guix-patches via
e7ead42383
gnu: python-language-server: Add deprecated alias. 
* gnu/packages/python-xyz.scm (python-language-server): New variable.

Add deprecated alias for package removed in the parent commit.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 17:13:41 +01:00
jgart via Guix-patches via
7907ddbc3a
gnu: Add python-lsp-server. 
* gnu/packages/python-xyz.scm (python-language-server): Delete variable.
* gnu/packages/python-xyz.scm (python-lsp-server): New variable.

Removes deprecated python-language-server package and adds maintained
fork.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 17:13:27 +01:00
jgart via Guix-patches via
0c3acb247a
gnu: python-lsp-jsonrpc: Add deprecated alias. 
* gnu/packages/python-xyz.scm (python-jsonrpc-server): New variable.

Add deprecated alias for package removed in the parent commit.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 17:13:10 +01:00
jgart via Guix-patches via
869c7d6703
gnu: Add python-lsp-jsonrpc. 
* gnu/packages/python-xyz.scm (python-jsonrpc-server): Delete variable.
* gnu/packages/python-xyz.scm (python-lsp-jsonrpc): New variable.

Removes deprecated python-jsonrpc-server package and adds maintained
fork.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 17:12:58 +01:00
jgart
46e030764d
gnu: python-jedi: Update to 0.18.1. 
* gnu/packages/python-xyz.scm (python-jedi): Update to 0.18.1.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 17:12:31 +01:00
jgart via Guix-patches via
6b29c3c735
gnu: python2-jedi: Remove package. 
* gnu/packages/python-xyz.scm (python2-jedi): Delete variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 17:10:34 +01:00
jgart via Guix-patches via
c56e9033f5
gnu: python-parso: Update to 0.8.2. 
* gnu/packages/python-xyz.scm (python-parso): Update to 0.8.2.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 17:10:18 +01:00
raingloom
d9956e9383
gnu: yggdrasil: Update to 0.4.1. 
* gnu/packages/networking.scm (yggdrasil): Update to 0.4.1.
* gnu/packages/patches/yggdrasil-extra-config.patch: Update for new version.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-01 17:03:34 +01:00
raingloom
f3b2af2147
gnu: yggdrasil: Update to 0.4.0. 
* gnu/packages/patches/yggdrasil-extra-config.patch: Update patch.
* gnu/packages/networking.scm (yggdrasil): Update to 0.4.0.
[arguments]: Also install genkeys.
[propagated-inputs]: Remove go-github-com-cheggaaa-pb; add go-golang-org-x-sys,
go-github-com-mattn-go-runewidth, go-github-com-mattn-go-isatty,
go-github-com-fatih-color, go-github-com-cheggaaa-pb-v3,
go-github-com-vividcortex-ewma, and go-github-com-arceliar-ironwood.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-01 17:03:34 +01:00
raingloom
dee3e337b6
gnu: Add go-github-com-arceliar-ironwood. 
* gnu/packages/golang.scm (go-github-com-arceliar-ironwood): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-01 17:03:34 +01:00
raingloom
7e4b418733
gnu: Rename go-github-com-cheggaaa-pb to go-github-com-cheggaaa-pb-v3. 
* gnu/packages/golang.scm (go-github-com-cheggaaa-pb): Rename this variable...
(go-github-com-cheggaaa-pb-v3): ...to this variable.
(go-github-com-cheggaaa-pb): New variable for deprecated package.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-01 17:03:34 +01:00
raingloom
b7e774a828
gnu: go-github-com-cheggaaa-pb: Update to 3.0.8. 
* gnu/packages/golang.scm (go-github-com-cheggaaa-pb): Update to 3.0.8.
[arguments]: Disable tests; update import path.
[native-inputs]: Move go-github-com-mattn-go-isatty from here...
[propagated-inputs]: ...to here; add go-github-com-vividcortex-ewma and
go-github-com-rivo-uniseg.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-01 17:03:34 +01:00
raingloom
660062a65b
gnu: Add go-github-com-mattn-go-runewidth. 
* gnu/packages/golang.scm (go-github-com-mattn-go-runewidth): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-01 17:03:34 +01:00
raingloom
f3861469b6
gnu: Add go-github-com-rivo-uniseg. 
* gnu/packages/golang.scm (go-github-com-rivo-uniseg): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-01 17:03:34 +01:00
raingloom
b3a9d079b8
gnu: Add go-github-com-vividcortex-ewma. 
* gnu/packages/golang.scm (go-github-com-vividcortex-ewma): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-01 17:03:34 +01:00
ZmnSCPxj via Guix-patches via
5ca0042116
gnu: Add python-mrkd. 
* gnu/packages/python-xyz.scm (python-mrkd): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 16:40:49 +01:00
cage
0a9edd23ca
gnu: telescope: Update to 0.6.1. 
* gnu/packages/web-browsers.scm (telescope): Update to 0.6.1.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-01 16:36:39 +01:00
cage
8e7e839c98
gnu: cl-unix-opts: Update to 0.1.7-1.0e61f34. 
* gnu/packages/lisp-xyz.scm (sbcl-unix-opts): Update to 0.1.7-1.0e61f34.
  [source]: Fetch using commit instead of old tag.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-01 13:26:29 +01:00
cage
0da9ae01a8
gnu: cl-croatoan: Update to 0.0.1-4.cf87513. 
* gnu/packages/lisp-xyz.scm (sbcl-croatoan): Update to 0.0.1-4.cf87513.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-01 13:16:01 +01:00
jgart
dc438820c3
gnu: Add julia-millboard. 
* gnu/packages/julia-xyz.scm (julia-millboard): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-01 14:08:46 +02:00
jgart
f303eaa31b
gnu: Add julia-jive. 
* gnu/packages/julia-xyz.scm (julia-jive): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-01 14:08:46 +02:00
jgart
2eca48e310
gnu: Add julia-softglobalscope. 
* gnu/packages/julay-xyz.scm (julia-softglobalscope): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-01 14:08:46 +02:00
Giacomo Leidi
ce6ea46d40
gnu: Add dynaconf. 
* gnu/packages/python-xyz.scm (dynaconf): New variable.
* gnu/packages/patches/dynaconf-Unvendor-dependencies.patch: New file.
* local.mk (dist_patch_DATA): Register it.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-01 13:58:07 +02:00
Giacomo Leidi
f8b1215874
gnu: Add python-dotenv-0.13.0. 
* gnu/packages/python-xyz.scm (python-dotenv-0.13.0): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-01 13:58:04 +02:00
Efraim Flashner
1e8ad167f6
gnu: python-dotenv: Run test suite. 
* gnu/packages/python-xyz.scm (python-dotenv)[arguments]: Add custom
'check phase.
 2021-12-01 13:58:04 +02:00
Giacomo Leidi
a8d62aea22
gnu: Add python-dotenv. 
* gnu/packages/python-xyz.scm (python-dotenv): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-01 13:57:59 +02:00
Ricardo Wurmus
124d76c5c2
gnu: python2-numpydoc: Update to 0.9.1. 
* gnu/packages/python-xyz.scm (python2-numpydoc): Update to 0.9.1; do not
inherit from Python 3 variant.
 2021-12-01 11:39:58 +01:00
Ricardo Wurmus
38d648655b
gnu: python-numpydoc: Update to 1.1.0. 
* gnu/packages/python-xyz.scm (python-numpydoc): Update to 1.1.0.
[arguments]: Override 'check phase to run tests.
[native-inputs]: Remove python-nose; add python-matplotlib, python-pytest, and
python-pytest-cov.
 2021-12-01 11:39:58 +01:00
Alice BRENON
6367c92c6e
gnu: Add python-mwparserfromhell. 
* gnu/packages/python-web.scm (python-mwparserfromhell): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-01 11:22:42 +01:00
Efraim Flashner
619e0627a6
gnu: ruby-mocha: Update to 1.13.0. 
* gnu/packages/ruby.scm (ruby-mocha): Update to 1.13.0.
[home-page]: Update to new location.
 2021-12-01 11:39:14 +02:00
Efraim Flashner
68d090002a
gnu: tor: Fix build issue on some architectures. 
* gnu/packages/tor.scm (tor)[arguments]: Add phase to remove sandbox
during one of the tests.
 2021-12-01 11:38:33 +02:00
Vivien Kraus
762643e0fc
gnu: gnome-builder: Use libsoup 2. 
* gnu/packages/gnome.scm (gnome-builder) [phase 'patch-meson]: Don’t search
for webkit2gtk-4.1.
[inputs]: Replace devhelp with devhelp-with-libsoup2 and
webkit with webkit-with-libsoup2.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-01 10:01:44 +01:00
Vivien Kraus
89907521ef
gnu: devhelp: Add a libsoup 2 variant. 
* gnu/packages/gnome.scm (devhelp-with-libsoup2): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-01 10:01:38 +01:00
Charles
f11605d96d
gnu: cl-yxorp: Update to 0.4. 
* gnu/packages/lisp-xyz.scm (sbcl-yxorp): Update to 0.4.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-01 09:44:03 +01:00
Sharlatan Hellseher
4beb013c84
gnu: Add cl-liballegro. 
* gnu/packages/lisp-xyz.scm: (sbcl-cl-liballegro, ecl-cl-liballegro,
  cl-liballegro): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-01 09:44:03 +01:00
Nicolas Vallet
d7477f09c3
gnu: Add r-phyloseq. 
* gnu/packages/cran.scm (r-phyloseq): New variable

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-01 09:29:26 +01:00
Mathieu Othacehe
854120d01f
gnu: Remove duplicated patch. 
* gnu/local.mk (dist_patch_DATA): Remove duplicated line.
 2021-12-01 09:23:51 +01:00
Ricardo Wurmus
3411f8d512
gnu: Add r-fmcsr. 
* gnu/packages/bioconductor.scm (r-fmcsr): New variable.
 2021-11-30 22:48:07 +01:00
Mathieu Othacehe
6805ab3290
gnu: freecad: Fix build. 
* gnu/packages/patches/freecad-boost-serialization.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/engineering.scm (freecad) [source]: Use it.
[arguments]{#:configure-flags}: Turn it into a GEXP and adapt it.
 2021-11-30 21:27:13 +01:00
Mathieu Othacehe
2d0c5e2477
gnu: Remove vtk-8. 
* gnu/packages/image-processing.scm (vtk-8): Remove it.
 2021-11-30 21:27:13 +01:00
Mathieu Othacehe
a5cdd82ecd
gnu: freecad: Switch to vtk-9. 
Switch to vtk-9 with the relevant patch to be able to get rid of vtk-8.

* gnu/packages/patches/freecad-vtk9.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/engineering.scm (freecad)[source]: Use it.
 2021-11-30 21:27:13 +01:00
Ricardo Wurmus
e4e50229f1
gnu: python-cloudscraper: Update to 1.2.58. 
* gnu/packages/python-web.scm (python-cloudscraper): Update to 1.2.58.
[source]: Do not delete as many files in snippet; fetch sources via git.
[arguments]: Add build phase 'fix-references; replace 'check phase.
[inputs]: Add node.
[propagated-inputs]: Add python-js2py, python-polling2, and python-responses.
 2021-11-30 20:49:18 +01:00
Ricardo Wurmus
3b74b41498
gnu: Add python-polling2. 
* gnu/packages/python-xyz.scm (python-polling2): New variable.
 2021-11-30 20:49:10 +01:00
Ricardo Wurmus
1a13968210
gnu: Add python-js2py. 
* gnu/packages/python-web.scm (python-js2py): New variable.
 2021-11-30 20:48:34 +01:00
Ricardo Wurmus
e35cfeb253
gnu: Add python-pyjsparser. 
* gnu/packages/python-web.scm (python-pyjsparser): New variable.
 2021-11-30 20:48:22 +01:00
Ricardo Wurmus
53a16a2143
gnu: Add r-seuratdata. 
* gnu/packages/cran.scm (r-seuratdata): New variable.
 2021-11-30 20:30:02 +01:00
Ricardo Wurmus
79bc812357
gnu: guile-wisp: Update to 1.0.6. 
* gnu/packages/guile-xyz.scm (guile-wisp): Update to 1.0.6.
 2021-11-30 20:30:02 +01:00
Ricardo Wurmus
f7db3bf277
gnu: guile-wisp: Remove trailing #T. 
* gnu/packages/guile-xyz.scm (guile-wisp)[arguments]: Remove trailing #T.
 2021-11-30 20:30:02 +01:00
Nicolas Goaziou
a47dfd0e7f
gnu: emacs-fountain-mode: Update to 3.6.0. 
* gnu/packages/emacs-xyz.scm (emacs-fountain-mode): Update to 3.6.0.
 2021-11-30 19:59:57 +01:00
Nicolas Goaziou
2ac171867a
gnu: emacs-tramp: Update to 2.5.1.5. 
* gnu/packages/emacs-xyz.scm (emacs-tramp): Update to 2.5.1.5.
 2021-11-30 19:56:16 +01:00
zimoun
afc4945d44
gnu: ghc: Fix build on i686-linux. 
* gnu/packages/haskell.scm (ghc-8.10)[arguments]<#:phases>: Disable
failing test.

Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
 2021-11-30 16:53:28 +01:00
Hong.Li@mdc-berlin.de
5bdf1b6551
gnu: Add r-rbokeh. 
* gnu/packages/cran.scm (r-rbokeh): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2021-11-30 16:46:18 +01:00