* gnu/packages/bioinformatics.scm (bcftools): Update to 1.14.
(bcftools-1.12): New variable.
(bcftools-1.10): Use package/inherit and delete trailing #t.
[name]: Delete field.
* gnu/packages/bioinformatics.scm (samtools): Update to 1.14.
[modules]: Delete argument.
[phases]{install-library, install-headers}: Delete phases. This version no
longer includes the legacy library (it links to htslib directly).
(samtools-1.12): New variable.
* gnu/packages/python-xyz.scm (python-beautifulsoup4): Update to 4.10.0.
[propagated-inputs]{python-html5lib, python-lxml}: New inputs.
[arguments]: Delete field.
(python2-beautifulsoup4): Peg at version 4.9.3.
Lack of python-testtools was causing the sanity-check phase to fail.
* gnu/packages/openstack.scm (python-os-testr)
[native-inputs]{python-testtools, python-babel}: Move to...
[propagated-inputs]: ... here.
This is in response to <https://issues.guix.gnu.org/52375>.
* gnu/packages/webkit.scm (webkitgtk): Add a note about GStreamer plugins.
Reported-by: Jack Hill <jackhill@jackhill.us>
* gnu/packages/python-xyz.scm (python2-matplotlib): Update to 2.2.5.
[phases]: Use G-exp.
{install-jquery-ui}: Delete phase. JQuery is bundled in this release.
[native-inputs]: Remove all exception pkg-config.
[propagated-inputs]: Sort and explicitly specify all inputs to ease
maintenance.
* gnu/packages/python-xyz.scm (python-matplotlib): Update to 3.5.1.
[propagated-inputs]: Add python-fonttools, python-wxpython
and python-packaging.
[native-inputs]: Remove python-mock, python-wheel, unzip and jquery-ui.
Add python-pytest-timeout, python-pytest-xdist, python-setuptools-scm and
python-setuptools-scm-git-archive.
[phases]: Delete trailing #t.
{pretend-version}: New phase.
{install-jquery-ui}: Delete phase.
{check}: Honor TESTS?. Do not skip webagg tests anymore. Invoke using
'-n' argument to run tests in parallel via pytest-xdist.
{configure-environment}: Do not set LD_LIBRARY_PATH nor HOME. Rename
setup.cfg to mplsetup.cfg. Set the backend to Agg.
* gnu/packages/python-xyz.scm (python-fonttools): Update to 4.28.5 and hide
the package.
[properties]: New field.
(python-fonttools-with-tests): New variable.
* gnu/packages/python-xyz.scm (python-platformdirs): Update to 2.4.0.
[phases]{pretend-version}: New phase.
{check}: Override to run tests.
[native-inputs]{python-setuptools-scm}: New input.
* gnu/packages/python-xyz.scm (python-flit)[origin]: Fetch from pypi-uri, to
ease updating the package.
[phases]{bootstrap}: Delete phase.
{build, install}: Do a PEP 517 build using pypa-build.
{check}: New phase.
[tests?]: Enable.
[propagated-inputs]{python-pytoml, python-toml}: Remove.
{python-pypa-build, python-tomli-w, python-flit-core, python-requests}: New
inputs.
{python-docutils}: New input, moved from...
[native-inputs]: ... here. Apply guix style.
{python-testpath}: Use the regular python-testpath package.
[synopsis, description]: Re-indent.
Flit Core apparently requires tomli at runtime rather than toml. This means
we must build a toml-less python-flit-core first, for bootstrapping purposes.
* gnu/packages/python-build.scm (python-flit-core-bootstrap): New variable.
(python-flit-core): Inherit from the above, replacing the propagated
python-toml by python-tomli.
(python-tomli): Adjust accordingly.
* gnu/packages/patches/gtk-introspection-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/gtk.scm (gtk): Update to 4.4.1.
[origin]: Apply new patch.
[phases]{pre-check}: Set TZDIR.
[native-inputs]: Add graphene, python-pygobject and tzdata.
Since commit 5d20d7e1369fc7d93de19c0bd219937d697ceae6, meson no longer
propagates Python, which is the reason this change is now needed here.
* gnu/packages/gnome.scm (gsettings-desktop-schemas)
[phases]{patch-schemas}: Use 'search-input-directory'.
[native-inputs]: Use new style and add python.
