ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2024-11-07 15:36:20 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions
88883 commits 1 branch 0 tags 448 MiB
Commit graph

88883 commits

This branch
This branch
All branches
Author SHA1 Message Date
Ricardo Wurmus
224d1c5818
gnu: python-dask: Update to 2021.11.2. 
* gnu/packages/python-xyz.scm (python-dask): Update to 2021.11.2.
[source]: Fetch from github.
[arguments]: Remove phase 'disable-broken-tests.
 2021-12-07 13:07:46 +01:00
Ricardo Wurmus
ed15986a32
gnu: python-dask: Run tests conditionally. 
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Respect TESTS? option.
 2021-12-07 13:07:23 +01:00
Ricardo Wurmus
ad17046040
gnu: python-dask: Add missing input for tests. 
* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Add
python-pytest-rerunfailures.
 2021-12-07 13:06:37 +01:00
Ricardo Wurmus
899121f4d6
gnu: phylip: Update to 3.697. 
* gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
 2021-12-07 13:05:53 +01:00
Ricardo Wurmus
e86fe9801e
gnu: phylip: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
 2021-12-07 13:05:35 +01:00
Ricardo Wurmus
125fdc3ba4
gnu: phylip: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from
build phases.
 2021-12-07 13:05:15 +01:00
Ricardo Wurmus
4561ca7f4e
gnu: subread: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T
from build phases.
 2021-12-07 12:59:51 +01:00
Ricardo Wurmus
96b2be833d
gnu: subread: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
 2021-12-07 12:59:36 +01:00
Ricardo Wurmus
9a03587b62
gnu: subread: Update home page.. 
* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
 2021-12-07 12:55:08 +01:00
Ricardo Wurmus
aa25c9b1a4
gnu: subread: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
 2021-12-07 12:54:48 +01:00
Ricardo Wurmus
417299f004
gnu: python-pytest-console-scripts: Update to 1.2.1. 
* gnu/packages/python-check.scm (python-pytest-console-scripts): Update to
1.2.1.
 2021-12-07 12:41:14 +01:00
Ricardo Wurmus
6874994fa9
gnu: Add python-pytest-rerunfailures. 
* gnu/packages/python-check.scm (python-pytest-rerunfailures): New variable.
 2021-12-07 12:35:00 +01:00
Ricardo Wurmus
c25a6d39f3
gnu: mcl: Add -fcommon to compiler flags. 
* gnu/packages/machine-learning.scm (mcl)[arguments]: Set CFLAGS.
 2021-12-07 12:34:34 +01:00
Ricardo Wurmus
b214034109
gnu: python-cytoolz: Update to 0.11.2. 
* gnu/packages/python-xyz.scm (python-cytoolz): Update to 0.11.2.
[source]: Add snippet.
 2021-12-07 12:34:22 +01:00
Ricardo Wurmus
06fca01968
gnu: hisat: Update to 0.1.6. 
* gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
 2021-12-07 11:51:10 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
9dc727f827
gnu: hisat: Remove invalid characters. 
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
b5c9afb7c5
gnu: Remove python2-bx-python. 
* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
699b443c86
gnu: python-bx-python: Update to 0.8.12. 
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.8.12.
[propagated-inputs]: Remove python-six.
[arguments]: Remove.  Tests are still not run, though.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
4b4ab4ce4d
gnu: Remove pbtranscript-tofu. 
Upstream has disappeared and it depends on Python 2, which is no longer
supported.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
b452d7c2cf
gnu: python-pyfit-sne: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1.
[arguments]: Disable tests explicitly.
 2021-12-07 11:51:09 +01:00
Pierre Langlois
4afacd4546
gnu: helm: Fix build with GCC 9 and later. 
* gnu/packages/music.scm (helm)[origin]: Add patch.
* gnu/packages/patches/helm-fix-gcc-9-build.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2021-12-06 20:41:18 +00:00
Marius Bakke
8662057130
gnu: patchwork: Adjust for python-build-system change. 
This is a follow-up to commit db5646d957, et.al.

* gnu/packages/patchutils.scm (patchwork)[arguments]: Adapt one more
site-packages call.
 2021-12-06 21:15:42 +01:00
Ricardo Wurmus
ca2f851da1
gnu: f-seq: Update name of commons-cli JAR. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of
commons-cli JAR.
 2021-12-06 18:48:01 +01:00
Ricardo Wurmus
f0763fba5c
gnu: f-seq: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from
build phase.
 2021-12-06 18:48:01 +01:00
Ricardo Wurmus
1310879fb0
gnu: f-seq: Simplify snippet. 
* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
 2021-12-06 18:48:01 +01:00
Mathieu Othacehe
3b6a7693fa
gnu: osinfo-db-next: Fix uri. 
* gnu/packages/virtualization.scm (osinfo-db-next)[source]: Fix URI.
 2021-12-06 17:28:22 +01:00
Ludovic Courtès
f4d4c40500
gnu: python-kivy: Add missing dependencies. 
* gnu/packages/python-xyz.scm (python-kivy)[arguments]: Add 'set-home'
phase.
[inputs]: Add PYTHON-DOCUTILS, PYTHON-KIVY-GARDEN, and PYTHON-PYGMENTS.
[synopsis, description]: Tweak.
 2021-12-06 11:49:06 +01:00
Ludovic Courtès
7e40d0ee90
gnu: Add python-kivy-garden. 
* gnu/packages/python-xyz.scm (python-kivy-garden): New variable.
 2021-12-06 11:48:47 +01:00
Ludovic Courtès
f72db02a6a
gnu: fpm2: Build with '-fcommon'. 
* gnu/packages/password-utils.scm (fpm2)[arguments]: Add #:configure-flags.
 2021-12-06 10:01:32 +01:00
Ludovic Courtès
3686780f31
gnu: xnee: Build with '-fcommon'. 
* gnu/packages/xnee.scm (xnee)[arguments]: New field.
 2021-12-06 10:01:15 +01:00
Ludovic Courtès
c162f8582b
gnu: libsoup: Simplify inputs. 
Obtained by running "guix style --input-simplification=always" and by
using 'modify-inputs' instead of list primitives.

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

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

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

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

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

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

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

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

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

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

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

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

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

* gnu/packages/gnome.scm (gtranslator)[source]: Change
'version-major+minor' to 'version-major'.
 2021-12-05 22:42:25 +01:00
Ricardo Wurmus
0f2a77e14f
gnu: Add libnftnl/fixed. 
* gnu/packages/linux.scm (libnftnl/fixed): New variable.
 2021-12-05 22:26:26 +01:00
Ricardo Wurmus
9bc0f45df5
Merge remote-tracking branch 'origin/master' into core-updates-frozen 2021-12-05 19:17:41 +01:00
Ricardo Wurmus
6db3c536e8
gnu: python-bwapy: Remove sanity-check. 
* gnu/packages/bioinformatics.scm (python-bwapy)[arguments]: Add phase
'relax-requirements to accept a slightly older version of wheel; remove the
'sanity-check phase.
 2021-12-05 17:38:15 +01:00
Ricardo Wurmus
dd67154e5d
gnu: Remove python2-plastid. 
* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.
 2021-12-05 17:37:05 +01:00
Ricardo Wurmus
98264531be
gnu: Remove python2-twobitreader. 
* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.
 2021-12-05 17:36:43 +01:00
Ricardo Wurmus
4202f4d58a
gnu: python-bbknn: Fix sanity-check phase. 
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'do-not-fail-to-find-sklearn, which prevents the 'sanity-check phase from
failing.
 2021-12-05 17:33:17 +01:00