2f7287b3a7
gnu: hisat: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from
build phase.
2021-12-07 11:51:09 +01:00
9dc727f827
gnu: hisat: Remove invalid characters.
...
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
2021-12-07 11:51:09 +01:00
478e3e714a
gnu: crossmap: Update to 0.6.1.
...
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1.
[source]: Add snippet to remove generated files.
2021-12-07 11:51:09 +01:00
b5c9afb7c5
gnu: Remove python2-bx-python.
...
* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
2021-12-07 11:51:09 +01:00
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
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
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
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
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
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
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
8662057130
gnu: patchwork: Adjust for python-build-system change.
...
This is a follow-up to commit db5646d957
2021-12-06 21:15:42 +01:00
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
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
1310879fb0
gnu: f-seq: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
2021-12-06 18:48:01 +01:00
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
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
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
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
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
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
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
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
7e40d0ee90
gnu: Add python-kivy-garden.
...
* gnu/packages/python-xyz.scm (python-kivy-garden): New variable.
2021-12-06 11:48:47 +01:00
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
93e9f0bc7f
ci: Cross-build the 'guix' package.
...
* gnu/ci.scm (%core-packages): Add GUIX.
2021-12-06 10:56:01 +01:00
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
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
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
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
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
f72db02a6a
gnu: fpm2: Build with '-fcommon'.
...
* gnu/packages/password-utils.scm (fpm2)[arguments]: Add #:configure-flags.
2021-12-06 10:01:32 +01:00
3686780f31
gnu: xnee: Build with '-fcommon'.
...
* gnu/packages/xnee.scm (xnee)[arguments]: New field.
2021-12-06 10:01:15 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
0f2a77e14f
gnu: Add libnftnl/fixed.
...
* gnu/packages/linux.scm (libnftnl/fixed): New variable.
2021-12-05 22:26:26 +01:00
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
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
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
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
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
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
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
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
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
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
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
9bc0f45df5
Merge remote-tracking branch 'origin/master' into core-updates-frozen
2021-12-05 19:17:41 +01:00
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
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
dd67154e5d
gnu: Remove python2-plastid.
...
* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.
2021-12-05 17:37:05 +01:00
98264531be
gnu: Remove python2-twobitreader.
...
* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.
2021-12-05 17:36:43 +01:00
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
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
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
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
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
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
c13046cb68
gnu: clapack: Pass -fcommon to compiler.
...
* gnu/packages/maths.scm (clapack)[arguments]: Set CFLAGS.
2021-12-05 15:04:04 +01:00
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
1d53c697b3
gnu: tla2tools: Remove remaining reference to %output.
...
This is a follow-up to commit 7e6ee16d49
2021-12-05 15:04:04 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
db5646d957
gnu: Adjust for python-build-system behavior change.
...
Commit cb72f9a773
2021-12-05 14:02:10 +01:00
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
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
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
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
b0ce8bdb39
gnu: Add python-mistune-next.
...
* gnu/packages/python-xyz.scm (python-mistune-next): New variable.
2021-12-05 14:02:09 +01:00
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
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
d801827b84
gnu: ganeti: Add the output directory on GUIX_PYTHONPATH.
...
This is a follow-up to commit 1ed567c872
2021-12-05 14:02:09 +01:00
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
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
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
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
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
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
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
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
e73f565445
gnu: python-django-sortedm2m: Fix tests.
...
This is a follow-up to commit 283d5ac97f
2021-12-05 14:02:08 +01:00
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
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
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
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
0b6f4be0fa
gnu: Django packages propagate Django, after all.
...
This reverts commit d7922f488b
2021-12-05 14:02:08 +01:00
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
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
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
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
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
e70e26423b
gnu: minimap2: Update to 2.23.
...
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23.
2021-12-05 11:51:10 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
f044ffc1c4
gnu: ocaml4.07-ppx-let: Make 'properties' an alist.
...
The incorrect 'properties' value was introduced in
3649c56a5f
2021-12-04 21:57:27 +01:00
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
39e2a84f52
gnu: sailfish: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (sailfish)[source]: Remove trailing #T from
snippet.
2021-12-04 19:54:28 +01:00
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
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
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
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
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
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
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
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
8a446f5e41
gnu: preseq: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (preseq)[source]: Simplify snippet.
2021-12-04 19:54:27 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
a6b6084649
gnu: mash: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
2021-12-04 00:30:44 +01:00
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
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
5cb2920b8d
gnu: jellyfish: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp.
2021-12-04 00:19:08 +01:00
7c2ee27360
gnu: fastp: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp.
2021-12-04 00:16:10 +01:00
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
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
62e0641892
gnu: fxtract: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp.
2021-12-04 00:02:20 +01:00
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
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
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
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
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
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
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
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
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
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
dcf857e486
gnu: Add r-fpeek.
...
* gnu/packages/cran.scm (r-fpeek): New variable.
2021-12-03 22:29:40 +01:00
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
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
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
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
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
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
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
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
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
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
d0aa14a43d
gnu: Add vbz-compression.
...
* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
2021-12-03 14:55:38 +01:00
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
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
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
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
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
673cc29908
gnu: bamutils: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
2021-12-03 13:56:01 +01:00
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
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
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
b7aaf6c418
gnu: ivar: Disable parallel tests.
...
* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
2021-12-03 13:48:41 +01:00
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
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
3e9dc2754e
gnu: icecat: Remove vestigial icecat-78-makeicecat.patch.
...
This is a followup to commit a63231003e
2021-12-03 04:45:15 -05:00
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
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
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
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
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
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
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
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
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
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
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
32d5fb01f8
gnu: python-biom-format: Update to 2.1.10.
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* 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
fab80c3672
gnu: Add trayer-srg.
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* 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
28ad55a59d
gnu: pardre: Update to 2.2.5.
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* 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
fc20fad6f7
gnu: pardre: Use C++ bindings for MPI.
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* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with
openmpi-c++.
2021-12-02 15:40:46 +01:00
2d6be35ea2
gnu: Add openmpi-c++.
...
* gnu/packages/mpi.scm (openmpi-c++): New variable.
2021-12-02 15:40:45 +01:00
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
2d92b3bbb6
gnu: shotcut: Update to 21.10.31.
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* 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
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
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
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
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
e080e35dc1
gnu: glade: Remove dependency on GJS on non-x86_64.
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* 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
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
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
8477a6d743
gnu: librsvg: Reintroduce version 2.40.
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* gnu/packages/gnome.scm (librsvg-2.40): New variable.
2021-12-02 14:59:56 +01:00
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
5723503f9f
gnu: python-ipython: Remove trailing #T.
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* gnu/packages/python-xyz.scm (python-ipython)[arguments]: Remove trailing #T
from build phases.
2021-12-02 13:42:17 +01:00
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
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
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
052f56e5a6
gnu: guix: Update to 8cc099b.
...
* gnu/packages/package-management.scm (guix): Update to 8cc099b
2021-12-02 12:52:59 +01:00
a8fff63daa
gnu: Add python-mygene.
...
* gnu/packages/bioinformatics.scm (python-mygene): New variable.
2021-12-02 11:57:28 +01:00
b15a525703
gnu: Add python-biothings-client.
...
* gnu/packages/bioinformatics.scm (python-biothings-client): New variable.
2021-12-02 11:57:13 +01:00
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
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
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
a33ca53492
gnu: python2-matplotlib: Remove trailing #T.
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* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Remove
trailing #T from build phase.
2021-12-02 10:29:59 +01:00
c14ab97a03
Revert "gnu: Change source file-name suffix in rust packages."
...
This reverts commit 07a80e30a1
2021-12-02 11:10:37 +02:00
e577889828
gnu: tor: Limit test suite adjustments to affected architectures.
...
This is a follow-up to 68d090002a
2021-12-02 11:07:18 +02:00
c2c63a00de
gnu: Add r-scdblfinder.
...
* gnu/packages/bioconductor.scm (r-scdblfinder): New variable.
2021-12-02 10:03:07 +01:00
24832d2ebd
gnu: python2-numpy: Delete file that depends on deleted test.
...
This is a follow-up to commit ec4892c742
2021-12-02 09:45:24 +01:00
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
bef86fed3e
Revert "gnu: godot: Update to 3.4."
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This reverts commit dd4365efa1https://debbugs.gnu.org/cgi/bugreport.cgi?bug=52233#20
2021-12-02 01:27:12 -05:00
934a246409
gnu: cl-tooter: Update to 1.0.0-3.ec97bee.
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* 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
e9e2204897
gnu: cl-i18n: Update to 0.5.1-1.4216fe9.
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* 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
dd4365efa1
gnu: godot: Update to 3.4.
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* 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
ec4892c742
gnu: python2-numpy: Do not inherit native-inputs.
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* 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
7a171235af
gnu: linux-libre 4.19: Update to 4.19.219.
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* 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
6f18f35297
gnu: linux-libre 5.4: Update to 5.4.163.
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* 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
f01588736c
gnu: linux-libre 5.10: Update to 5.10.83.
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* 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
c3ec5eaa75
gnu: linux-libre: Update to 5.15.6.
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* 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
d53679c531
gnu: Remove couger.
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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
cd40978a4b
gnu: randomjungle: Fix compatibility errors.
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* 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
36f18626a9
gnu: petsc-{complex,openmpi,complex-openmpi}: Use gexps.
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This is a followup to 07ac13a26a
2021-12-01 23:30:15 +01:00
725d35aa9a
gnu: scalapack: Update to 2.1.0.
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* 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
a63231003e
gnu: icecat: Remove leftovers of release 78.
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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
52cb5cf5b8
gnu: icedove: Update to 91.3.2.
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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
f1a2e90409
gnu: Add nspr@4.32.
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Required for icecat/icedove 91.
* gnu/packages/nss.scm (nspr-4.32): New variable.
2021-12-01 22:06:54 +01:00
d7d7b57965
gnu: emacs-citar: Remove unnecessary input.
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* gnu/packages/emacs-xyz.scm (emacs-citar)[propagated-inputs]: Remove emacs-helm-bibtex.
2021-12-01 22:00:45 +01:00
2b08cc968b
gnu: bullet: Update to 3.17.
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* 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
d64b78ef0c
installer: parted: Use the swap-space record.
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* gnu/installer/parted.scm (user-partitions->configuration): Use the
swap-space record.
2021-12-01 20:59:06 +01:00
05c747ea6b
tests: install: Use the swap-space record.
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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
c7c4f80881
gnu: Update Trezor support.
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* 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
508200d66a
gnu: python-daemon: Update to 2.3.0.
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* 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
8cc099b425
gnu: openssh: Add support for ecdsa-sk, ed25519-sk ssh keys.
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* 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
3aaef047a6
gnu: Add libfido2.
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* gnu/packages/security-token.scm (libfido2): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:53:27 +01:00
083a710cbb
gnu: Add libcbor.
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* gnu/packages/compression.scm (libcbor): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:53:27 +01:00
b5d0029771
gnu: Add vim-nerdtree.
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* gnu/packages/vim.scm (vim-nerdtree): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:53:27 +01:00
a955e4d7f6
gnu: Add smplayer.
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* gnu/packages/video.scm (smplayer): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:51:38 +01:00
5ff34d596d
gnu: Add python-codespell.
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* 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
a82e9f45fd
installer: Make LUKS2 the default format for encrypted devices
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* 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
adce91a3ec
gnu: system: Add LUKS2 support for the root file system.
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* 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
1a0696e0a6
gnu: sdrangel: Add missing input.
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QtQuick is required by some runtime features.
* gnu/packages/radio.scm (sdrangel)[inputs]: Add qtquickcontrols2.
2021-12-01 17:30:45 +01:00
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
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
0c3acb247a
gnu: python-lsp-jsonrpc: Add deprecated alias.
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* 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
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
46e030764d
gnu: python-jedi: Update to 0.18.1.
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* 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
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
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
d9956e9383
gnu: yggdrasil: Update to 0.4.1.
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* 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
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
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
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
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
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
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
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
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
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
8e7e839c98
gnu: cl-unix-opts: Update to 0.1.7-1.0e61f34.
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* 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
854120d01f
gnu: Remove duplicated patch.
...
* gnu/local.mk (dist_patch_DATA): Remove duplicated line.
2021-12-01 09:23:51 +01:00
3411f8d512
gnu: Add r-fmcsr.
...
* gnu/packages/bioconductor.scm (r-fmcsr): New variable.
2021-11-30 22:48:07 +01:00
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
2d0c5e2477
gnu: Remove vtk-8.
...
* gnu/packages/image-processing.scm (vtk-8): Remove it.
2021-11-30 21:27:13 +01:00
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
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
3b74b41498
gnu: Add python-polling2.
...
* gnu/packages/python-xyz.scm (python-polling2): New variable.
2021-11-30 20:49:10 +01:00
1a13968210
gnu: Add python-js2py.
...
* gnu/packages/python-web.scm (python-js2py): New variable.
2021-11-30 20:48:34 +01:00
e35cfeb253
gnu: Add python-pyjsparser.
...
* gnu/packages/python-web.scm (python-pyjsparser): New variable.
2021-11-30 20:48:22 +01:00
53a16a2143
gnu: Add r-seuratdata.
...
* gnu/packages/cran.scm (r-seuratdata): New variable.
2021-11-30 20:30:02 +01:00
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
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
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
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
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
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
21bf500ee9
gnu: Add r-gistr.
...
* gnu/packages/cran.scm (r-gistr): New variable.
2021-11-30 16:46:18 +01:00
78f2fe7da8
gnu: r-crul: Update to 1.2.0.
...
* gnu/packages/cran.scm (r-crul): Update to 1.2.0.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-11-30 16:46:17 +01:00
16d7f26fed
gnu: Add python-woob.
...
* gnu/packages/python-web.scm (python-woob): New variable.
2021-11-30 16:46:17 +01:00
bfaf7b559e
gnu: Add python-xunitparser.
...
* gnu/packages/python-check.scm (python-xunitparser): New variable.
2021-11-30 16:46:17 +01:00
173a2998d9
gnu: r-umi4cpackage: Embed references to perl and bowtie2.
...
* gnu/packages/bioinformatics.scm (r-umi4cpackage)[arguments]: Add build
phases to patch calls of bowtie2 and perl.
[inputs]: Add perl and bowtie.
[synopsis]: Remove trailing period.
2021-11-30 16:46:17 +01:00
d95a982cdd
gnu: coq: Update to 8.14.0.
...
* gnu/packages/coq.scm (coq): Update to 8.14.0.
(coq-bignums): Update to 8.14.0.
(coq-equations): Update to 1.3.
* gnu/packages/patches/coq-fix-envvars.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2021-11-30 03:52:00 +01:00
189501bf3b
gnu: proof-general: Update to latest commit.
...
* gnu/packages/coq.scm (proof-general): Update to latest commit.
[license]: Change to glp3+.
2021-11-30 03:19:33 +01:00
bcd4c7ae6a
gnu: coq-semantics: Update to 8.14.0.
...
* gnu/packages/coq.scm (coq-semantics): Update to 8.14.0.
2021-11-30 03:19:21 +01:00
892f1b7273
services: Accept <inferior-package>s in lieu of <package>s.
...
* gnu/services/authentication.scm (fprintd-configuration)
(nslcd-configuration): Substitute file-like objects for package ones.
* gnu/services/cgit.scm (cgit-configuration, opaque-cgit-configuration):
Likewise.
* gnu/services/cups.scm (package-list?, cups-configuration): Likewise.
* gnu/services/dns.scm (verify-knot-configuration)
(ddclient-configuration): Likewise.
* gnu/services/docker.scm (docker-configuration): Likewise.
* gnu/services/file-sharing.scm (transmission-daemon-configuration): Likewise.
* gnu/services/getmail.scm (getmail-configuration): Likewise.
* gnu/services/mail.scm (dovecot-configuration)
(opaque-dovecot-configuration): Likewise.
* gnu/services/messaging.scm (prosody-configuration)
(opaque-prosody-configuration): Likewise.
* gnu/services/monitoring.scm (zabbix-server-configuration)
(zabbix-agent-configuration): Likewise.
* gnu/services/networking.scm (opendht-configuration): Likewise.
* gnu/services/pm.scm (tlp-configuration): Likewise.
* gnu/services/telephony.scm (jami-configuration): Likewise.
* gnu/services/virtualization.scm (libvirt-configuration)
(qemu-guest-agent-configuration): Likewise.
* gnu/services/vpn.scm (openvpn-client-configuration): Likewise.
2021-11-30 01:08:55 +01:00
dc9be12eaf
gnu: squashfs-tools: Update to 4.5.
...
* gnu/packages/compression.scm (squashfs-tools): Update to 4.5.
2021-11-30 01:08:55 +01:00
cdf7b3daa3
gnu: toybox: Update to 0.8.5.
...
* gnu/packages/busybox.scm (toybox): Update to 0.8.5.
[arguments]: Add a new 'fix-or-skip-broken-tests phase.
Don't explicitly return #t from the other phases.
2021-11-30 01:08:55 +01:00
a392ad8302
gnu: indi: Update to 1.9.3.
...
* gnu/packages/astronomy.scm (indi): Update to 1.9.3.
2021-11-30 01:08:55 +01:00
4c62406371
gnu: simdjson: Update to 1.0.2.
...
* gnu/packages/cpp.scm (simdjson): Update to 1.0.2.
2021-11-30 01:08:54 +01:00
c6a15cf756
gnu: diffoscope: Update to 194.
...
* gnu/packages/diffoscope.scm (diffoscope): Update to 194.
2021-11-30 01:08:54 +01:00
588698c92b
gnu: lttoolbox: Omit static libraries.
...
* gnu/packages/dictionaries.scm (lttoolbox)[arguments]:
Add "--disable-static" to #:configure-flags.
2021-11-30 01:08:54 +01:00
d51c5d032e
gnu: lttoolbox: Update to 3.5.4.
...
* gnu/packages/dictionaries.scm (lttoolbox): Update to 3.5.4.
2021-11-30 01:08:54 +01:00
795e8c7a7c
gnu: quazip@1: Update to 1.2.
...
* gnu/packages/compression.scm (quazip): Update to 1.2.
2021-11-30 01:08:54 +01:00
26787a7034
gnu: thefuck: Update to 3.31.
...
* gnu/packages/admin.scm (thefuck): Update to 3.31.
[arguments]: Don't call buggy settings.init() during test suite.
2021-11-30 01:08:54 +01:00
3848dafeb1
gnu: xa: Update to 2.3.12.
...
* gnu/packages/assembly.scm (xa): Update to 2.3.12.
2021-11-30 01:08:53 +01:00
39631cefa8
gnu: rxvt-unicode: Update to 9.30.
...
* gnu/packages/xdisorg.scm (rxvt-unicode): Update to 9.30.
2021-11-30 01:08:53 +01:00
eb62e3e54d
gnu: ethtool: Update to 5.15.
...
* gnu/packages/networking.scm (ethtool): Update to 5.15.
2021-11-30 01:08:53 +01:00
01f08d5f82
gnu: btrfs-progs: Update to 5.15.1.
...
* gnu/packages/linux.scm (btrfs-progs): Update to 5.15.1.
2021-11-30 01:08:53 +01:00
1e9d70e42e
gnu: powerstat: Update to 0.02.27.
...
* gnu/packages/linux.scm (powerstat): Update to 0.02.27.
2021-11-30 01:08:53 +01:00
c1546d8a68
gnu: powerstat: Fetch sources from Git.
...
* gnu/packages/linux.scm (powerstat)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
2021-11-30 01:08:53 +01:00
2397cc097c
gnu: usbutils: Update to 014.
...
* gnu/packages/linux.scm (usbutils): Update to 014.
[arguments]: Remove obsolete autogen.sh substitution.
Don't explicitly return #t from phases.
2021-11-30 01:08:53 +01:00
215524a116
gnu: xfsprogs: Omit static library.
...
* gnu/packages/linux.scm (xfsprogs)[arguments]:
Add "--disable-static" to #:configure-flags.
(xfsprogs-static)[arguments]: Undo it.
2021-11-30 01:08:52 +01:00
3ec27a7436
gnu: xfsprogs: Update to 5.14.0.
...
* gnu/packages/linux.scm (xfsprogs): Update to 5.14.0.
[inputs]: Add liburcu.
2021-11-30 01:08:52 +01:00
72c3763653
gnu: kexec-tools: Update to 2.0.23.
...
* gnu/packages/linux.scm (kexec-tools): Update to 2.0.23.
2021-11-30 01:08:52 +01:00
7e3151c19e
gnu: Add inkbox.
...
* gnu/packages/qt.scm (inkbox): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-11-29 22:18:30 +01:00
daa6c67fb4
gnu: guix-build-coordinator: Update to 0-40.226ec0f.
...
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-40.226ec0f.
* doc/guix.texi (Guix Build Coordinator): Remove note about the service being
considered experimental, it's been stable for a while now.
2021-11-29 21:01:26 +00:00
653bcab96d
gnu: Add python-pysox.
...
* gnu/packages/audio.scm (python-pysox): New variable.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2021-11-29 21:34:24 +05:30
f22dfba530
gnu: agg: Fix build.
...
* gnu/packages/patches/agg-2.5-gcc8.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/graphics.scm (agg)[source]: Use it.
2021-11-29 14:58:39 +01:00
3d54f24156
gnu: darktable: Build with OpenEXR 3.
...
* gnu/packages/photo.scm (darktable)[arguments]<#:phases>: Rename
'set-LDFLAGS-and-CPATH to 'set-LDFLAGS. Don't set CPATH.
[inputs]: Remove ilmbase. Add imath. Replace openexr-2 with openexr.
Signed-off-by: Leo Famulari <leo@famulari.name>
2021-11-28 21:51:12 -05:00
91ed051149
gnu: darktable: Build with libsoup 2.
...
* gnu/packages/photo.scm (darktable)[inputs]: Change libsoup to
libsoup-minimal-2.
Signed-off-by: Leo Famulari <leo@famulari.name>
2021-11-28 21:51:08 -05:00
5b4d1e57b6
gnu: slepc: Update to 3.16.1.
...
* gnu/packages/maths.scm (slepc): Update to 3.16.1.
[native-inputs]: Use PYTHON instead of PYTHON-2. Add WHICH.
[properties]: New field.
2021-11-29 00:04:03 +01:00
07ac13a26a
gnu: petsc: Update to 3.16.1.
...
* gnu/packages/maths.scm (petsc): Update to 3.16.1.
[native-inputs]: Use PYTHON instead of PYTHON-2. Add WHICH.
[arguments]: Rewrite using gexps. Pass '--with-openblas-dir'. In
'configure' phase, modify "config/example_template.py".
2021-11-29 00:04:02 +01:00
57b62e5bb9
gnu: python2-requests: Remove dependency on python-charset-normalizer.
...
The python-charset-normalizer package is Python 3 only.
* gnu/packages/python-web.scm (python-requests)[properties]: New field.
(python2-requests): Rewrite to remove 'python-charset-normalizer' from
'propagated-inputs'.
2021-11-29 00:04:02 +01:00
8ecc99be11
gnu: python-notify2: Propagate python-dbus.
...
* gnu/packages/python-xyz.scm (python-notify2)[native-inputs]: Rename to...
[propagated-inputs]: ... this.
2021-11-29 00:04:02 +01:00
2ec5a1a576
gnu: python-dbus: Register 'python2-dbus' as the Python 2 variant.
...
This allows things like 'python2-notify2' to actually use the Python 2
variant of 'python-dbus'.
* gnu/packages/python-xyz.scm (python-dbus)[properties]: New field.
(python2-dbus)[inputs]: Remove unnecessary 'alist-delete' argument.
2021-11-29 00:04:02 +01:00
0ca73525c8
gnu: krfb: Use latest pipewire.
...
* gnu/packages/kde-systemtools.scm (krfb)[inputs]: Replace pipewire with
pipewire-0.3.
2021-11-28 23:30:46 +01:00
4883d7fe9e
gnu: guile-gitlab: Update to 0.2.1.
...
* gnu/packages/guile-xyz.scm (guile-gitlab): Update to 0.2.1.
[inputs]: Use guile2.2-json instead of guile-json-1.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-11-28 22:35:37 +01:00
9a91cc47af
gnu: pipewire-0.3: Add optional inputs.
...
* gnu/packages/linux.scm (pipewire-0.3)[inputs]: Add avahi and ldacbt.
2021-11-28 22:31:46 +01:00
f18a586a45
gnu: pipewire-0.3: Update to 0.3.40.
...
* gnu/packages/linux.scm (pipewire-0.3): Update to 0.3.40.
[arguments]: Disable session managers to avoid missing input.
2021-11-28 22:31:09 +01:00
8351f6c570
gnu: emacs-org: Update to 9.5.1.
...
* gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.5.1.
2021-11-28 22:05:57 +01:00
5ee135df5f
gnu: emacs-org: Don't use release tar.
...
* gnu/packages/emacs-xyz.scm (emacs-org):
[source]: Use git repository.
[arguments]: Add phases to help with building.
[native-inputs]: Add texinfo.
2021-11-28 21:54:02 +01:00
b8abc6c88a
gnu: trezord: Update to 2.0.31.
...
* gnu/packages/finance.scm (trezord): Update to 2.0.31.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-11-28 21:31:09 +01:00
Ricardo Wurmus
Julien Lepiller
Nicolas Goaziou
Pierre Langlois
Marius Bakke
Leo Famulari
Mathieu Othacehe
Efraim Flashner
Ludovic Courtès
jgart
Thiago Jung Bauermann
Demis Balbach
Luis Felipe
simendsjo
Aleksandr Vityazev
Sharlatan Hellseher
dissent
Artyom V. Poptsov
Vivien Kraus
Ryan Desfosses
zimoun
cage
Liliana Marie Prikler
phodina
Morgan Smith
Attila Lendvai
Charles
Mark H Weaver
Arne Babenhauserheide
Vinicius Monego
Z572
Andy Tai
Jonathan Brielmaier
Ahmad Jarara
Foo Chuan Wei
Felix Gruber
Josselin Poiret
Guillaume Le Vaillant
jgart via Guix-patches via
raingloom
Giacomo Leidi
Alice BRENON
Nicolas Vallet
Hong.Li@mdc-berlin.de
Hong Li
Tobias Geerinckx-Rice
Christopher Baines