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* gnu: python-schema-salad: Update to 8.2.20211116214159.Ricardo Wurmus2021-12-07
| | | | | | | | | * gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.2.20211116214159. [arguments]: Remove trailing #T. [propagated-inputs]: Replace python-cachecontrol-0.11 with python-cachecontrol. [native-inputs]: Add python-black.
* gnu: taxtastic: Update to 0.9.2.Ricardo Wurmus2021-12-07
| | | | | | * gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2. [arguments]: Delete 'sanity-check and 'python37-compatibility phases; adjust 'prepare-directory phase.
* gnu: taxtastic: Run tests conditionally.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS? option.
* gnu: python-dendropy: Update to 4.5.1.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1. [arguments]: Skip failing tests.
* gnu: python-cooler: Use python-cytoolz-for-cooler.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace python-cytoolz with python-cytoolz-for-cooler.
* gnu: Add python-cytoolz-for-cooler.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/python-xyz.scm (python-cytoolz-for-cooler): New variable.
* gnu: python-sparse: Update to 0.13.0.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/python-xyz.scm (python-sparse): Update to 0.13.0.
* gnu: python-dask: Update to 2021.11.2.Ricardo Wurmus2021-12-07
| | | | | | * gnu/packages/python-xyz.scm (python-dask): Update to 2021.11.2. [source]: Fetch from github. [arguments]: Remove phase 'disable-broken-tests.
* gnu: python-dask: Run tests conditionally.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/python-xyz.scm (python-dask)[arguments]: Respect TESTS? option.
* gnu: python-dask: Add missing input for tests.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Add python-pytest-rerunfailures.
* gnu: phylip: Update to 3.697.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
* gnu: phylip: Pass -fcommon to compiler.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
* gnu: phylip: Remove trailing #T.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from build phases.
* gnu: subread: Remove trailing #T.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T from build phases.
* gnu: subread: Update to 2.0.3.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
* gnu: subread: Update home page..Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
* gnu: subread: Pass -fcommon to compiler.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
* gnu: python-pytest-console-scripts: Update to 1.2.1.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/python-check.scm (python-pytest-console-scripts): Update to 1.2.1.
* gnu: Add python-pytest-rerunfailures.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/python-check.scm (python-pytest-rerunfailures): New variable.
* gnu: mcl: Add -fcommon to compiler flags.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/machine-learning.scm (mcl)[arguments]: Set CFLAGS.
* gnu: python-cytoolz: Update to 0.11.2.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/python-xyz.scm (python-cytoolz): Update to 0.11.2. [source]: Add snippet.
* gnu: hisat: Update to 0.1.6.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
* gnu: hisat: Remove trailing #T.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from build phase.
* gnu: hisat: Remove invalid characters.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
* gnu: crossmap: Update to 0.6.1.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1. [source]: Add snippet to remove generated files.
* gnu: Remove python2-bx-python.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
* gnu: python-bx-python: Update to 0.8.12.Ricardo Wurmus2021-12-07
| | | | | | * 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.
* gnu: Remove pbtranscript-tofu.Ricardo Wurmus2021-12-07
| | | | | | | Upstream has disappeared and it depends on Python 2, which is no longer supported. * gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
* gnu: python-pyfit-sne: Update to 1.2.1.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1. [arguments]: Disable tests explicitly.
* gnu: helm: Fix build with GCC 9 and later.Pierre Langlois2021-12-06
| | | | | | * 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.
* gnu: patchwork: Adjust for python-build-system change.Marius Bakke2021-12-06
| | | | | | | This is a follow-up to commit db5646d957895944007c1bb44fcd998ea392f168, et.al. * gnu/packages/patchutils.scm (patchwork)[arguments]: Adapt one more site-packages call.
* gnu: f-seq: Update name of commons-cli JAR.Ricardo Wurmus2021-12-06
| | | | | * gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of commons-cli JAR.
* gnu: f-seq: Remove trailing #T.Ricardo Wurmus2021-12-06
| | | | | * gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from build phase.
* gnu: f-seq: Simplify snippet.Ricardo Wurmus2021-12-06
| | | | * gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
* gnu: osinfo-db-next: Fix uri.Mathieu Othacehe2021-12-06
| | | | * gnu/packages/virtualization.scm (osinfo-db-next)[source]: Fix URI.
* gnu: python-kivy: Add missing dependencies.Ludovic Courtès2021-12-06
| | | | | | | * 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.
* gnu: Add python-kivy-garden.Ludovic Courtès2021-12-06
| | | | * gnu/packages/python-xyz.scm (python-kivy-garden): New variable.
* gnu: fpm2: Build with '-fcommon'.Ludovic Courtès2021-12-06
| | | | * gnu/packages/password-utils.scm (fpm2)[arguments]: Add #:configure-flags.
* gnu: xnee: Build with '-fcommon'.Ludovic Courtès2021-12-06
| | | | * gnu/packages/xnee.scm (xnee)[arguments]: New field.
* gnu: libsoup: Simplify inputs.Ludovic Courtès2021-12-05
| | | | | | | | 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.
* gnu: librsvg: Simplify inputs.Ludovic Courtès2021-12-05
| | | | | | Obtained by running "guix style --input-simplification=always". * gnu/packages/gnome.scm (librsvg, librsvg-2.40): Simplify inputs.
* gnu: gtk+: Simplify inputs.Ludovic Courtès2021-12-05
| | | | | | | | Obtained by running: guix style --input-simplification=always gtk+ gtk+@2 * gnu/packages/gtk.scm (gtk+-2, gtk+): Simplify inputs.
* gnu: gtk+@2: Use 'librsvg-for-system'.Ludovic Courtès2021-12-05
| | | | | * gnu/packages/gtk.scm (gtk+-2)[propagated-inputs]: Use 'librsvg-for-system' unconditionally.
* gnu: libsoup: Remove unneeded dependency on PHP.Ludovic Courtès2021-12-05
| | | | * gnu/packages/gnome.scm (libsoup-minimal)[native-inputs]: Remove PHP.
* gnu: gtk+: Use 'librsvg-for-system'.Ludovic Courtès2021-12-05
| | | | | | | | | | | 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.
* gnu: emacs: Use 'librsvg-for-system'.Ludovic Courtès2021-12-05
| | | | | * gnu/packages/emacs.scm (emacs)[inputs]: Use 'librsvg-for-system' unconditionally.
* gnu: openbox: Use 'librsvg-for-system'.Ludovic Courtès2021-12-05
| | | | | * gnu/packages/openbox.scm (openbox)[inputs]: Use 'librsvg-for-system' unconditionally.
* gnu: mate: Depend on 'librsvg-for-system'.Ludovic Courtès2021-12-05
| | | | | | | | | | | | * 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.
* gnu: librsvg@2.40: Depend on the default Pango version.Ludovic Courtès2021-12-05
| | | | | | | | | | 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.
* gnu: Add texlive-latex-luatex.Thiago Jung Bauermann2021-12-05
| | | | | | | | | | | | | | | | | | | | | | | | | | | 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>
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