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2022-01-10build-system/gnu: Make gzip files writable before resetting timestamps.Sarah Morgensen
guix/build/gnu-build-system.scm (reset-gzip-timestamps): Ensure gzip files are writable before resetting their timestamps. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: tbb-2020: Use ld.gold to work around segfaults in check phase.Maxim Cournoyer
* gnu/packages/tbb.scm (tbb-2020) [configure-flags]: Use -fuse-ld=gold in CFLAGS. [native-inputs]: Add ld-gold-wrapper.
2022-01-10gnu: python-igraph: Update to 0.9.8.Maxim Cournoyer
* gnu/packages/graph.scm (python-igraph): Update to 0.9.8. [origin]: Fetch from git. [configure-flags]: Delete argument. [phases]{build}: No longer override phase. {check}: Preserve ordering and streamline. {specify-libigraph-location}: New phase. [native-inputs]: Remove pkg-config. [home-page]: Update.
2022-01-10gnu: igraph: Update to 0.9.5.Maxim Cournoyer
* gnu/packages/graph.scm (igraph): Update to 0.9.5. [source]: Add snippet to fully unbundle. [build-system]: Use cmake-build-system. [configure-flags]: Replace all by just '-DBUILD_SHARED_LIBS=ON'. [native-inputs]: Add pkg-config. [inputs]{zlib}: Delete input. {arpack-ng, plfit, suitesparse}: New inputs.
2022-01-10gnu: Add plfit.Maxim Cournoyer
* gnu/packages/graph.scm (plfit): New variable.
2022-01-10gnu: python-pysam: Update to 0.18.0.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0. [source]: Add FIXME to clarify bundled libraries in use. [phases]{check}: Streamline. [propagated-inputs]: Use latest htslib (1.14). [native-inputs]: Use latest samtools and bcftools (1.14). Remove python-nose.
2022-01-10gnu: bcftools: Update to 1.14.Maxim Cournoyer
* 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.
2022-01-10gnu: samtools: Update to 1.14.Maxim Cournoyer
* 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.
2022-01-10gnu: htslib: Update to 1.14.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (htslib): Update to 1.14. (htslib-1.12): New variable. (htslib-1.10, htslib-1.9, htslib-1.3) (htslib-for-samtools-1.2): Normalize style.
2022-01-10gnu: python-beautifulsoup4: Update to 4.10.0.Maxim Cournoyer
* 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.
2022-01-10gnu: poetry: Update to 1.1.12.Maxim Cournoyer
* gnu/packages/python-xyz.scm (poetry): Update to 1.1.12. [phases]{patch-setup-py}: Relax packaging version requirement. [propagated-inputs]{python-msgpack-transitional}: Replace with... {python-msgpack}: ... this. {python-requests-toolbelt-0.9.1}: Replace with... {python-requests-toolbelt}: ... this. {python-msgpack-transitional}: Delete variable.
2022-01-10gnu: python-requests-toolbelt: Update to 0.9.1 and enable tests.Maxim Cournoyer
* gnu/packages/python-web.scm (pyhton-requests-toolbelt): Update to 0.9.1. [phases]{delete-problematic-tests}: New phase. (python-requests-toolbelt-0.9.1): Delete variable. (python2-requests-toolbelt): Likewise. (python-cloudscraper): Adjust accordingly.
2022-01-10gnu: python-cachecontrol: Update to 0.12.10.Maxim Cournoyer
* gnu/packages/python-web.scm (python-cachecontrol): Update to 0.12.10.
2022-01-10gnu: python-os-testr: Propagate python-testtools and python-babel.Maxim Cournoyer
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.
2022-01-10gnu: webkitgtk: Enable GStreamer GL support.Maxim Cournoyer
* gnu/packages/webkit.scm (webkitgtk)[configure-flags]: Remove the '-DUSE_GSTREAMER_GL=OFF' build option.
2022-01-10gnu: webkitgtk: Add a note about plugins in description.Maxim Cournoyer
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>
2022-01-10gnu: python2-matplotlib: Update to 2.2.5.Maxim Cournoyer
* 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.
2022-01-10gnu: python-matplotlib: Update to 3.5.1 and run tests in parallel.Maxim Cournoyer
* 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.
2022-01-10gnu: python-fonttools: Update to 4.28.5.Maxim Cournoyer
* 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.
2022-01-10gnu: Add python-zopfli.Maxim Cournoyer
* gnu/packages/python-compression.scm (python-zopfli): New variable.
2022-01-10gnu: Add zopfli.Maxim Cournoyer
* gnu/packages/compression.scm (zopfli): New variable.
2022-01-10gnu: Add python-fs.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-fs): New variable.
2022-01-10gnu: Add python-pyftpdlib.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-pyftpdlib): New variable.
2022-01-10gnu: Add python-pysendfile.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-pysendfile): New variable.
2022-01-10gnu: python-pylint: Update to 2.12.2.Maxim Cournoyer
* gnu/packages/check.scm (python-pylint): Update to 2.12.2. [phases]{check}: Override phase. [native-inputs]: Remove python-pytest-benchmark, python-pytest-runner. [propagated-inputs]: Add python-platformdirs, python-typing-extensions. [synopsis]: Streamline.
2022-01-10gnu: python-platformdirs: Update to 2.4.0, run tests and fix metadata.Maxim Cournoyer
* 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.
2022-01-10gnu: python-flit: Update to 3.5.1, enable tests and apply guix style.Maxim Cournoyer
* 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.
2022-01-10gnu: python-testpath: Update to 0.5.0 and enable tests.Maxim Cournoyer
* gnu/packages/check.scm (python-testpath): Update to 0.5.0. [phases]{relax-requirements}: New phase {build}: Build using pypa-build's 'build' command. {check}: Override phase. {install}: Adjust. [native-inputs]: Remove python-flit. Add python-pypa-build and python-pytest. [home-page]: Update.
2022-01-10gnu: Add python-tomli-w.Maxim Cournoyer
* gnu/packages/python-build.scm (python-tomli-w): New variable.
2022-01-10gnu: python-astroid: Update to 2.9.0.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-astroid): Update to 2.9.0. [native-inputs]: Add python-typing-extensions. [properties]: Delete field. (python2-astroid): Delete variable.
2022-01-10gnu: python-typing-extensions: Update to 4.0.1.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-typing-extensions): Update to 4.0.1. [origin]: Use git-fetch. [tests?]: Disable. [phases]{unpack, build, install}: New phases. [native-inputs]: Add python-pypa-build, python-flit-core. [home-page]: Shorten URL.
2022-01-10gnu: python-typing: Update to 3.10.0.0.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-typing): Update to 3.10.0.0.
2022-01-10gnu: python-flit-core: Propagate python-tomli instead of python-toml.Maxim Cournoyer
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.
2022-01-10gnu: python-curio: Disable newly failing 'test_timeout' test.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-prettytable) [phases]{check}: Honor TESTS? and skip the 'test_timeout' test.
2022-01-10gnu: glade3: Add python to native inputs.Maxim Cournoyer
Since commit 5d20d7e1369fc7d93de19c0bd219937d697ceae6, meson no longer propagates Python. * gnu/packages/gnome.scm (glade3)[native-inputs]: Add python.
2022-01-10gnu: python-typed-ast: Update to 1.5.1.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-typed-ast): Update to 1.5.1.
2022-01-10gnu: gjs: Build with meson-0.59 to avoid 'install_dir' error.Maxim Cournoyer
* gnu/packages/gnome.scm (gjs)[meson]: Use meson-0.59.
2022-01-10gnu: python-msgpack: Update to 1.0.3.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-msgpack): Update to 1.0.3. (python2-msgpack): Delete variable.
2022-01-10gnu: tracker: Add python to native inputs.Maxim Cournoyer
Since commit 5d20d7e1369fc7d93de19c0bd219937d697ceae6, meson no longer propagates Python. * gnu/packages/gnome.scm (tracker)[native-inputs]: Add python.
2022-01-10gnu: dconf: Add python to native inputs.Maxim Cournoyer
Since commit 5d20d7e1369fc7d93de19c0bd219937d697ceae6, meson no longer propagates Python. * gnu/packages/gnome.scm (dconf)[native-inputs]: Add python.
2022-01-10gnu: gtkmm: Add python to native inputs.Maxim Cournoyer
Since commit 5d20d7e1369fc7d93de19c0bd219937d697ceae6, meson no longer propagates Python. * gnu/packages/gtk.scm (gtkmm)[native-inputs]: Add python.
2022-01-10gnu: gtk: Update to 4.4.1.Maxim Cournoyer
* 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.
2022-01-10gnu: gusb: Add python to native inputs.Maxim Cournoyer
Since commit 5d20d7e1369fc7d93de19c0bd219937d697ceae6, meson no longer propagates Python. * gnu/packages/gnome.scm (gusb)[native-inputs]: Add python.
2022-01-10gnu: pangomm: Add python to native inputs.Maxim Cournoyer
Since commit 5d20d7e1369fc7d93de19c0bd219937d697ceae6, meson no longer propagates Python. * gnu/packages/gtk.scm (pangomm)[native-inputs]: Add python.
2022-01-10gnu: atkmm-2.28: Do not propagate two variants of glibmm.Maxim Cournoyer
* gnu/packages/gtk.scm (atkmm-2.28)[propagated-inputs]: Replace rather than append glibmm-2.64.
2022-01-10gnu: atkmm: Add python to native inputs.Maxim Cournoyer
Since commit 5d20d7e1369fc7d93de19c0bd219937d697ceae6, meson no longer propagates Python. * gnu/packages/gtk.scm (atkmm)[native-inputs]: Add python.
2022-01-10gnu: libxkbcommon: Add python to native inputs.Maxim Cournoyer
Since commit 5d20d7e1369fc7d93de19c0bd219937d697ceae6, meson no longer propagates Python. * gnu/packages/xdisorg.scm (libxkbcommon)[native-inputs]: Add python.
2022-01-10gnu: wayland-protocols: Add python to native inputs.Maxim Cournoyer
Since commit 5d20d7e1369fc7d93de19c0bd219937d697ceae6, meson no longer propagates Python. * gnu/packages/freedesktop.scm (wayland-protocols)[native-inputs]: Add python.
2022-01-10gnu: wayland: Add python to native inputs.Maxim Cournoyer
Since commit 5d20d7e1369fc7d93de19c0bd219937d697ceae6, meson no longer propagates Python. * gnu/packages/freedesktop.scm (wayland)[native-inputs]: Add python.
2022-01-10gnu: epiphany: Update to 41.2.Maxim Cournoyer
* gnu/packages/gnome.scm (epiphany): Update to 41.2.
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