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* gnu: python-scanpy: Set PYTHONPATH variable.Ricardo Wurmus2021-11-21
| | | | | | | | This is a follow-up to commit 664721422cd17c151df00b9ecab268d1aa18e3b3. * gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Set PYTHONPATH variable during the build as GUIX_PYTHONPATH does not have the intended effect.
* gnu: python-scanpy: Update to 1.8.2.Ricardo Wurmus2021-11-21
| | | | | * gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.2. [arguments]: Disable test_clustermap test.
* gnu: xfce-weather-plugin: Fix build by depending on libsoup2.Kaelyn Takata2021-11-21
| | | | | | | * gnu/packages/xfce.scm (xfce-weather-plugin)[inputs]: Replace libsoup with libsoup-minimal-2. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: python-libvirt: Update to 7.9.0.Jack Hill2021-11-21
| | | | | | * gnu/packages/virtualization.scm (python-libvirt): Update to 7.9.0. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: python-seaborn: Update to 0.11.2.Ricardo Wurmus2021-11-21
| | | | * gnu/packages/python-xyz.scm (python-seaborn): Update to 0.11.2.
* gnu: emacs-elpy: More aggressively trim nondeterministic tests.Maxim Cournoyer2021-11-20
| | | | | | | | | More failing tests keep appearing sparingly, a few at a time. With the following change, the build succeeded 20 rounds. * gnu/packages/emacs-xyz.scm (emacs-elpy) [phases]{disable-broken-tests}: Disable whole tests families affected by nondeterministic failures rather than individual tests.
* gnu: perl-cworld-dekker: Use GUIX_PYTHONPATH.Ricardo Wurmus2021-11-21
| | | | | * gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use GUIX_PYTHONPATH.
* gnu: python-scanpy: Use GUIX_PYTHONPATH.Ricardo Wurmus2021-11-21
| | | | | * gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Use GUIX_PYTHONPATH instead of PYTHONPATH.
* gnu: python-numpy: Alias to python-numpy-1.20.Ricardo Wurmus2021-11-21
| | | | | | | | | | | | | | Numpy 1.20 is required by numba and umap-learn. Attempts to rename numpy 1.20 to allow it to coexist with numpy 1.21 in the same environment have not been successful. * gnu/packages/python-xyz.scm (python-numpy): Rename to... (python-numpy-next): ...this variable. (python2-numpy): Use python-numpy-next package as parent. (python-numpy-1.20): Inherit from python-numpy-next. (python-numpy): New variable pointing to python-numpy-1.20. (python-numba)[propagated-inputs]: Replace python-numpy-1.20 with python-numpy.
* gnu: multiqc: Remove sanity check.Ricardo Wurmus2021-11-21
| | | | * gnu/packages/bioinformatics.scm (multiqc)[arguments]: Delete 'sanity-check phase.
* gnu: multiqc: Use GUIX_PYTHONPATH.Ricardo Wurmus2021-11-21
| | | | | * gnu/packages/bioinformatics.scm (multiqc)[arguments]: Replace PYTHONPATH with GUIX_PYTHONPATH.
* gnu: libmp4v2: Build with '-std=c++03'.Ludovic Courtès2021-11-20
| | | | * gnu/packages/video.scm (libmp4v2)[arguments]: Add #:configure-flags.
* gnu: python-qtconsole: Add dependency on python-pyqt.Ludovic Courtès2021-11-20
| | | | | * gnu/packages/python-xyz.scm (python-qtconsole)[propagated-inputs]: Add PYTHON-PYQT.
* vm: <virtual-machine> defaults to using 'qemu-minimal'.Ludovic Courtès2021-11-20
| | | | | | | 'qemu-minimal' is enough for system tests, which is the main (only?) use of <virtual-machine>. * gnu/system/vm.scm (<virtual-machine>)[qemu]: Default to QEMU-MINIMAL.
* gnu: tcp-wrappers: Allow compilation with glibc 2.33.Ludovic Courtès2021-11-20
| | | | * gnu/packages/networking.scm (tcp-wrappers)[source]: Add 'snippet'.
* gnu: grafx2: Build with '-fcommon'.Ludovic Courtès2021-11-20
| | | | | * gnu/packages/game-development.scm (grafx2)[arguments]: Add '-fcommon' to #:make-flags.
* gnu: grafx2: Add 'file-name' field to source.Ludovic Courtès2021-11-20
| | | | | | | | | Without a file name ending in ".tgz" (or similar), the 'unpack' phase wouldn't extract it (as implemented in commit cfcead2e515c0dae02127e5a76496463898be6b6). * gnu/packages/game-development.scm (grafx2)[source]: Add 'file-name' field.
* gnu: ledger: Remove failing test output.John Kehayias2021-11-20
| | | | | | | * gnu/packages/finance.scm (ledger)[source]: Add snippet to remove a failing test. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu: sdrangel: Update to 6.17.3.Guillaume Le Vaillant2021-11-20
| | | | | * gnu/packages/radio.scm (sdrangel): Update to 6.17.3. [arguments]: Add 'fix-boost-compatibility' phase.
* gnu: opencpn: Update to 5.2.4.Guillaume Le Vaillant2021-11-20
| | | | | * gnu/packages/geo.scm (opencpn): Update to 5.2.4. [arguments]: Update 'configure-flag' and 'fix-build' phase.
* gnu: python-scikit-learn: Update to 1.0.1.Ricardo Wurmus2021-11-20
| | | | | * gnu/packages/machine-learning.scm (python-scikit-learn): Update to 1.0.1. [arguments]: Disable one failing network test.
* gnu: python-scikit-learn: Run tests conditionally.Ricardo Wurmus2021-11-20
| | | | | * gnu/packages/machine-learning.scm (python-scikit-learn)[arguments]: Respect TESTS? in 'check phase.
* gnu: python-joblib: Update to 1.1.0.Ricardo Wurmus2021-11-20
| | | | | * gnu/packages/python-xyz.scm (python-joblib): Update to 1.1.0. [arguments]: Disable one test.
* gnu: python2-joblib: Do not inherit source from python-joblib.Ricardo Wurmus2021-11-20
| | | | | | * gnu/packages/python-xyz.scm (python2-joblib)[version]: Explicitly set to 0.14.1. [source]: Do not inherit.
* gnu: gtk: Guard against timeouts in the test suite.Maxim Cournoyer2021-11-20
| | | | | | | | | | | This change piggy backs on the improvements to the meson-build-system made in dfcc96d8f48716ae5aefb383c58b153d5bcb407c; it's motivated by timeouts that occurred in the GTK test suite while building on a heavily loaded machine. * gnu/packages/gtk.scm (gtk)[parallel-tests]: New argument. [test-options]: New argument, which now includes --suite=gtk and --no-suite=gsk-compare-broadway, to match what upstream uses. [phases]{check}: Remove override.
* gnu: libnice: Disable the 'test-bsd' test.Maxim Cournoyer2021-11-20
| | | | | | * gnu/packages/networking.scm (libnice) [phases]{disable-failing-test}: Rename to... {disable-failing-tests}: ... this, plural. Disable 'test-bsd'.
* gnu: wayland: Use native-inputs unconditionallyMaxim Cournoyer2021-11-20
| | | | | * gnu/packages/freedesktop.scm (wayland): Remove trailing #t. [phases]: Use native-inputs unconditionally.
* gnu: gnome-shell: Update to 41.0.Maxim Cournoyer2021-11-20
| | | | | | | | * gnu/packages/gnome.scm (gnome-shell): Update to 41.0. [origin]: Remove patches and modules fields. [phases]{pre-check}: Set HOME. * gnu/packages/patches/gnome-shell-disable-test.patch: Delete file. * gnu/local.mk (dist_patch_DATA): De-register it.
* gnu: gsettings-desktop-schemas: Update to 41.0.Maxim Cournoyer2021-11-20
| | | | | | * gnu/packages/gnome.scm (gsettings-desktop-schemas): Update to 41.0. Reformat synopsis and description. [origin]: Fix indentation.
* gnu: gjs: Update to 1.70.0.Maxim Cournoyer2021-11-20
| | | | * gnu/packages/gnome.scm (gjs): Update to 1.70.0.
* gnu: mutter: Update to 41.0 and enable tests.Maxim Cournoyer2021-11-20
| | | | | | | | | | | | | | | | * gnu/packages/gnome.scm (mutter): Update to 41.0. [imported-modules, modules]: New arguments. [configure-flags]: Specify the gles2_libname, egl_device and wayland_eglstream options. Enable the profiler by removing the option. [phases]{patch-dlopen-calls}: New phase. {disable-problematic-tests}: Likewise. {check}: Override phase. [native-inputs]{xorg-server-for-tests}: Replace with... {xvfb-run}: ... this. {adwaita-icon-theme, libxcursor, pipewire-0.3} {python-dbus, python-dbusmock, tini}: New native inputs. [propagated-inputs]: Add libxcvt. [inputs]: Add egl-wayland and sysprof.
* gnu: libxcursor: Add a search path for XCURSOR_PATH.Maxim Cournoyer2021-11-20
| | | | | * gnu/packages/xorg.scm (libxcursor): Fix indentation. [native-search-paths]: New field (previously commented). Update comment.
* build: syscalls: Add a SET-CHILD-SUBREAPER! procedure.Maxim Cournoyer2021-11-20
| | | | | * guix/build/syscalls.scm (PR_SET_CHILD_SUBREAPER): New variable. (set-child-subreaper!): New procedure.
* gnu: python-numba: Update to 0.54.1.Ricardo Wurmus2021-11-20
| | | | | | * gnu/packages/python-xyz.scm (python-numba): Update to 0.54.1. [propagated-inputs]: Replace python-numpy with python-numpy-1.20. [arguments]: Add phase 'disable-failing-tests.
* gnu: python-numba: Run tests conditionally.Ricardo Wurmus2021-11-20
| | | | * gnu/packages/python-xyz.scm (python-numba)[arguments]: Respect TESTS? argument.
* gnu: python-numba: Remove trailing #T.Ricardo Wurmus2021-11-20
| | | | | * gnu/packages/python-xyz.scm (python-numba)[arguments]: Remove trailing #T from build phase.
* gnu: Add python-numpy-1.20.Ricardo Wurmus2021-11-20
| | | | * gnu/packages/python-xyz.scm (python-numpy-1.20): New variable.
* gnu: repo2docker: Use GUIX_PYTHONPATH.Ricardo Wurmus2021-11-20
| | | | | * gnu/packages/jupyter.scm (repo2docker)[arguments]: Use GUIX_PYTHONPATH instead of PYTHONPATH.
* gnu: python-llvmlite: Update to 0.37.0.Ricardo Wurmus2021-11-20
| | | | | * gnu/packages/llvm.scm (python-llvmlite): Update to 0.37.0. [inputs]: Update patched LLVM.
* gnu: python-llvmlite: Remove trailing #T.Ricardo Wurmus2021-11-20
| | | | | * gnu/packages/llvm.scm (python-llvmlite)[arguments]: Remove trailing #T from build phases.
* gnu: python-pytorch: Warn of missing test inputs.Ricardo Wurmus2021-11-20
| | | | * gnu/packages/machine-learning.scm (python-pytorch): Add comment.
* gnu: python-pytorch: Add missing input.Ricardo Wurmus2021-11-20
| | | | | * gnu/packages/machine-learning.scm (python-pytorch)[propagated-inputs]: Add python-click.
* gnu: python-pytorch: Use ADD-INSTALLED-PYTHONPATH.Ricardo Wurmus2021-11-20
| | | | | * gnu/packages/machine-learning.scm (python-pytorch)[arguments]: Do not set PYTHONPATH; use add-installed-pythonpath instead.
* gnu: opendht: Use GUIX_PYTHONPATH.Ricardo Wurmus2021-11-20
| | | | * gnu/packages/networking.scm (opendht)[arguments]: Use GUIX_PYTHONPATH in the wrapper.
* gnu: elogind: Revert changes to polkit build time detection.Josselin Poiret2021-11-19
| | | | | | | | * gnu/packages/patches/elogind-revert-polkit-detection.patch: New file. * gnu/packages/freedesktop.scm (elogind): Use it. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Timothy Sample <samplet@ngyro.com>
* gnu: python-jupyter-console: Update to 6.4.0.Ludovic Courtès2021-11-19
| | | | | * gnu/packages/python-xyz.scm (python-jupyter-console): Update to 6.4.0. [native-inputs]: Add PYTHON-PYTEST.
* gnu: python-notebook: Fix tests that rely on the gio "trash" mechanism.Ludovic Courtès2021-11-19
| | | | | | | | | | | | | Previously 'test_delete' and a couple of related tests in 'test_content_api.py' would fail: https://lists.gnu.org/archive/html/guix-devel/2021-11/msg00083.html Reported by Ricardo Wurmus. * gnu/packages/python-xyz.scm (python-notebook)[arguments]: Add 'use-our-home-for-tests' phase. In 'check' phase, remove call to 'setenv' and unnecessary use of 'with-directory-excursion'.
* gnu: wlroots: Remove unneeded elogind dependency.Josselin Poiret2021-11-19
| | | | | | * gnu/packages/wm.scm (wlroots): Remove it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: seatd: Make elogind a propagated input.Josselin Poiret2021-11-19
| | | | | | * gnu/packages/freedesktop.scm (seatd): Do it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: geary: Upgrade to 40.0Vivien Kraus2021-11-19
| | | | | | * gnu/packages/gnome.scm (geary): Upgrade to 40.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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