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Author SHA1 Message Date
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
Ricardo Wurmus 2b1e53850f
gnu: libsbml: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (libsbml)[arguments]: Remove references to
%build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus dc4b4d4d95
gnu: ataqv: Remove references to %outputs and %build-inputs. 
* gnu/packages/bioinformatics.scm (ataqv)[arguments]: Remove references to
%outputs and %build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus 03ca627b09
gnu: adapterremoval: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (adapterremoval)[arguments]: Remove
reference to %outputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus fac4c98699
gnu: bbmap: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus b798d90bee
gnu: intervaltree: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (intervaltree)[arguments]: Remove reference
to %outputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus c9892edceb
gnu: biobambam2: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (biobambam2)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus a8b60bd475
gnu: sjcount: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus 4c6cb448fd
gnu: sjcount: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove trailing #T
from build phases.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus c1fe074915
gnu: dropseq-tools: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove reference
to %build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus 1462e5c919
gnu: dropseq-tools: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove
trailing #T from build phases...
[source]: ...and from the snippet.
 2021-12-05 15:04:02 +01:00
Marius Bakke 10554e0a57
gnu: python-django-netfields: Update to 1.2.4. 
* gnu/packages/django.scm (python-django-netfields): Update to 1.2.4.
 2021-12-05 14:40:08 +01:00
Marius Bakke 50fff94b5a
gnu: python-django: Update to 3.2.9. 
* gnu/packages/django.scm (python-django): Update to 3.2.9.
 2021-12-05 14:40:08 +01:00
Marius Bakke f63fb61d0c
import: PyPI: Validate GPG signatures when applicable. 
* guix/import/pypi.scm (<distribution>): Fix funny typo.
(latest-release): When the distribution has a cryptographic signature, pass it
along to UPSTREAM-SOURCE.
 2021-12-05 14:40:08 +01:00
Marius Bakke e166e6acf6
gnu: drbd-utils: Update to 9.19.1. 
* gnu/packages/cluster.scm (drbd-utils): Update to 9.19.1.
 2021-12-05 14:40:07 +01:00
Nicolas Goaziou 21e2be5968
gnu: emacs-peg: Update to 0.10.3. 
* gnu/packages/emacs-xyz.scm (emacs-peg): Update to 0.10.3.
 2021-12-05 14:20:16 +01:00
Marius Bakke c61e49aa94
gnu: tbb: Update to 2021.4.0. 
* gnu/packages/tbb.scm (tbb): Update to 2021.4.0.
 2021-12-05 14:02:10 +01:00
Marius Bakke db5646d957
gnu: Adjust for python-build-system behavior change. 
Commit cb72f9a773 changed the semantics of
SITE-PACKAGES, but did not adjust all callers.

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

* gnu/packages/virtualization.scm (ganeti)[arguments]: Adjust wrap phase to
include Ganetis own site-packages on $GUIX_PYTHONPATH.
 2021-12-05 14:02:09 +01:00
Marius Bakke 846bd3d083
gnu: python-webassets: Patch for Python 3.9. 
* gnu/packages/python-web.scm (python-webassets)[arguments]: Add
substitution.
 2021-12-05 14:02:09 +01:00
Marius Bakke 9f5b9d18d8
gnu: python-django-mailman3: Update to 1.3.7. 
* gnu/packages/mail.scm (python-django-mailman3): Update to 1.3.7.
 2021-12-05 14:02:09 +01:00
Marius Bakke 837688e505
gnu: python-mailmanclient: Update to 3.3.3. 
* gnu/packages/mail.scm (python-mailmanclient): Update to 3.3.3.
 2021-12-05 14:02:09 +01:00