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Author SHA1 Message Date
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
Ricardo Wurmus b1bd997d50
gnu: python-bbknn: Add missing input. 
* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add
python-scikit-learn.
 2021-12-05 17:32:50 +01:00
Ricardo Wurmus 19f6b770dc
gnu: velvet: Add missing TeX package. 
* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add
texlive-fonts-ec.
 2021-12-05 17:22:11 +01:00
Ricardo Wurmus fe0f8c627a
gnu: velvet: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from
build phases.
 2021-12-05 17:21:39 +01:00
Ricardo Wurmus f2b99e3aaf
gnu: python-bwapy: Remove pre-built object files. 
* gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files
in a snippet.
 2021-12-05 15:04:05 +01:00
Ricardo Wurmus 57f278ffc4
gnu: metabat: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T
from build phases.
 2021-12-05 15:04:05 +01:00
Ricardo Wurmus c13046cb68
gnu: clapack: Pass -fcommon to compiler. 
* gnu/packages/maths.scm (clapack)[arguments]: Set CFLAGS.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus ae0acf6b6d
gnu: clapack: Remove trailing #T. 
* gnu/packages/maths.scm (clapack)[arguments]: Remove trailing #T from build
phases.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus 1d53c697b3
gnu: tla2tools: Remove remaining reference to %output. 
This is a follow-up to commit 7e6ee16d49.

* gnu/packages/java.scm (tla2tools)[arguments]: Remove remaining reference to
%output.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus 8ae33d6844
gnu: kraken2: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (kraken2)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus c973107a25
gnu: methyldackel: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove reference
to %outputs by using a gexp.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus d531dc6761
gnu: phast: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (phast)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-05 15:04:03 +01:00