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Author SHA1 Message Date
Ricardo Wurmus
6c9bbf8071
gnu: python-scanpy: Update to 1.8.2. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.2.
[arguments]: Disable test_clustermap test.
 2021-11-21 09:07:50 +01:00
Kaelyn Takata
4c4d53ed52
gnu: xfce-weather-plugin: Fix build by depending on libsoup2. 
* gnu/packages/xfce.scm (xfce-weather-plugin)[inputs]: Replace libsoup with
libsoup-minimal-2.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-11-21 09:07:50 +01:00
Jack Hill
9f8a4760e8
gnu: python-libvirt: Update to 7.9.0. 
* gnu/packages/virtualization.scm (python-libvirt): Update to 7.9.0.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-11-21 09:07:50 +01:00
Ricardo Wurmus
00127cbca7
gnu: python-seaborn: Update to 0.11.2. 
* gnu/packages/python-xyz.scm (python-seaborn): Update to 0.11.2.
 2021-11-21 09:07:49 +01:00
Maxim Cournoyer
d8b429ddb7
gnu: emacs-elpy: More aggressively trim nondeterministic tests. 
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.
 2021-11-20 22:29:53 -05:00
Julien Lepiller
348f1f7cb5
gnu: camlboot: Update to latest commit. 
* gnu/packages/ocaml.scm (camlboot): Update to latest commit.
 2021-11-21 04:14:49 +01:00
Ricardo Wurmus
1a9665743b
gnu: perl-cworld-dekker: Use GUIX_PYTHONPATH. 
* gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use
GUIX_PYTHONPATH.
 2021-11-21 00:40:34 +01:00
Ricardo Wurmus
664721422c
gnu: python-scanpy: Use GUIX_PYTHONPATH. 
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Use
GUIX_PYTHONPATH instead of PYTHONPATH.
 2021-11-21 00:39:57 +01:00
Ricardo Wurmus
a22fb2d164
gnu: python-numpy: Alias to python-numpy-1.20. 
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.
 2021-11-21 00:39:09 +01:00
Ricardo Wurmus
55870e86d9
gnu: multiqc: Remove sanity check. 
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Delete 'sanity-check phase.
 2021-11-21 00:39:09 +01:00
Ricardo Wurmus
e2ca652c98
gnu: multiqc: Use GUIX_PYTHONPATH. 
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Replace PYTHONPATH
with GUIX_PYTHONPATH.
 2021-11-21 00:39:05 +01:00
Ludovic Courtès
b2bfedcdb3
gnu: libmp4v2: Build with '-std=c++03'. 
* gnu/packages/video.scm (libmp4v2)[arguments]: Add #:configure-flags.
 2021-11-20 23:11:45 +01:00
Ludovic Courtès
27ceda472a
gnu: python-qtconsole: Add dependency on python-pyqt. 
* gnu/packages/python-xyz.scm (python-qtconsole)[propagated-inputs]: Add
PYTHON-PYQT.
 2021-11-20 23:11:45 +01:00
Ludovic Courtès
aaf210888c
vm: <virtual-machine> defaults to using 'qemu-minimal'. 
'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.
 2021-11-20 23:11:44 +01:00
Ludovic Courtès
ce67634629
gnu: tcp-wrappers: Allow compilation with glibc 2.33. 
* gnu/packages/networking.scm (tcp-wrappers)[source]: Add 'snippet'.
 2021-11-20 23:11:44 +01:00
Ludovic Courtès
83010a08bc
gnu: grafx2: Build with '-fcommon'. 
* gnu/packages/game-development.scm (grafx2)[arguments]: Add '-fcommon'
to #:make-flags.
 2021-11-20 23:11:44 +01:00
Ludovic Courtès
c34bb6b310
gnu: grafx2: Add 'file-name' field to source. 
Without a file name ending in ".tgz" (or similar), the 'unpack' phase
wouldn't extract it (as implemented in commit
cfcead2e51).

* gnu/packages/game-development.scm (grafx2)[source]: Add 'file-name'
field.
 2021-11-20 23:11:44 +01:00
Julien Lepiller
0846e7d326
gnu: Add ocaml-charinfo-width. 
* gnu/packages/ocaml.scm (ocaml4.07-charinfo-width): Replace with...
(ocaml-charinfo-width): ...this. Use latest ocaml package.
 2021-11-20 19:39:57 +01:00
Julien Lepiller
f9bf7de5b4
gnu: Add ocaml-gsl. 
* gnu/packages/ocaml.scm (ocaml4.07-gsl): Replace with...
(ocaml-gsl): ...this. Use latest ocaml package.
(ocaml4.07-gsl-1): Adapt accordingly.
 2021-11-20 19:39:54 +01:00
Julien Lepiller
0481810ebf
gnu: Add ocaml-fftw3. 
* gnu/packages/ocaml.scm (ocaml4.07-fftw3): Replace with...
(ocaml-fftw3) ...this. Use latest ocaml package.
 2021-11-20 19:39:52 +01:00
Julien Lepiller
e9d3f3656b
gnu: Add ocaml-lacaml. 
* gnu/packages/ocaml.scm (ocaml4.07-lacaml): Replace with...
(ocaml-lacaml): ...this.  Use latest ocaml package.
 2021-11-20 19:39:25 +01:00
John Kehayias
c51667d52e
gnu: ledger: Remove failing test output. 
* gnu/packages/finance.scm (ledger)[source]: Add snippet to remove a failing
  test.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-11-20 19:23:50 +01:00
Guillaume Le Vaillant
89eb1f2a76
gnu: sdrangel: Update to 6.17.3. 
* gnu/packages/radio.scm (sdrangel): Update to 6.17.3.
  [arguments]: Add 'fix-boost-compatibility' phase.
 2021-11-20 19:18:44 +01:00
Leo Famulari
40239e23e8
gnu: linux-libre 5.10: Update to 5.10.80. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.80.
(linux-libre-5.10-pristine-source): Update hash.
 2021-11-20 13:15:11 -05:00
Leo Famulari
d2f5bc7da8
gnu: linux-libre: Update to 5.14.20. 
* gnu/packages/linux.scm (linux-libre-5.14-version): Update to 5.14.20.
(linux-libre-5.14-pristine-source): Update hash.
 2021-11-20 13:15:07 -05:00
Guillaume Le Vaillant
4d02165992
gnu: opencpn: Update to 5.2.4. 
* gnu/packages/geo.scm (opencpn): Update to 5.2.4.
  [arguments]: Update 'configure-flag' and 'fix-build' phase.
 2021-11-20 18:23:15 +01:00
Julien Lepiller
0a4656f1c1
gnu: ocaml-version: Update to 3.4.0. 
* gnu/packages/ocaml.scm (ocaml-version): Update to 3.4.0.
 2021-11-20 17:09:03 +01:00
Julien Lepiller
4378eb9a15
gnu: ocaml-tyxml: Update to 4.5.0. 
* gnu/packages/ocaml.scm (ocaml-tyxml): Update to 4.5.0.
 2021-11-20 17:08:55 +01:00
Julien Lepiller
c2242284ab
gnu: ocaml-topkg: Update to 1.0.4. 
* gnu/packages/ocaml.scm (ocaml-topkg): Update to 1.0.4.
 2021-11-20 17:08:50 +01:00
Julien Lepiller
972c6fe87b
gnu: ocaml-stdlib-shims: Update to 0.3.0. 
* gnu/packages/ocaml.scm (ocaml-stdlib-shims): Update to 0.3.0.
 2021-11-20 17:08:47 +01:00
Julien Lepiller
5a3fcf0cac
gnu: ocaml-sedlex: Update to 2.4. 
* gnu/packages/ocaml.scm (ocaml-sedlex): Update to 2.4.
[native-inputs]: Remove ocamlbuild.
[propagated-inputs]: Remove ocaml-ppx-tools-versioned.
(ocaml4.07-sedlex)[propagated-inputs]: Add ocaml-ppx-tools-versioned.
 2021-11-20 17:08:37 +01:00
Julien Lepiller
40f7eb975b
gnu: ocaml-qtest: Update to 2.11.2. 
* gnu/packages/ocaml.scm (ocaml-qtest): Update to 2.11.2.
 2021-11-20 17:08:33 +01:00
Julien Lepiller
b0e76b0828
gnu: ocaml-qcheck: Update to 0.18. 
* gnu/packages/ocaml.scm (ocaml-qcheck): Update to 0.18.
* gnu/packages/patches/ocaml-qcheck-fix-test-whitespace.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2021-11-20 17:08:06 +01:00
Julien Lepiller
0df82727a6
gnu: ocaml-ppx-variants-conv: Update to 0.14.2. 
* gnu/packages/ocaml.scm (ocaml-ppx-variants-conv): Update to 0.14.2.
[origin]: Remove patch.
* gnu/packages/patches/ocaml-ppx-variants-ppxlib-api-change.patch:
Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-11-20 17:07:50 +01:00
Julien Lepiller
97fd67edea
gnu: ocaml-ppx-js-style: Update to 0.14.1. 
* gnu/packages/ocaml.scm (ocaml-ppx-js-style): Update to 0.14.1.
 2021-11-20 17:07:44 +01:00
Julien Lepiller
95e6a977fa
gnu: ocaml-odoc: Update to 2.0.0. 
* gnu/packages/ocaml.scm (ocaml-odoc): Update to 2.0.0.
[inputs, native-inputs]: Adjust inputs.
(ocaml4.07-odoc)[inputs, native-inputs]: Keep previous inputs.
 2021-11-20 17:07:24 +01:00
Julien Lepiller
1277bd9fc0
gnu: ocaml-ocplib-endian: Update to 1.2. 
* gnu/packages/ocaml.scm (ocaml-ocplib-endian): Update to 1.2.
 2021-11-20 17:07:14 +01:00
Julien Lepiller
e46621ca6c
gnu: ocaml-mtime: Update to 1.3.0. 
* gnu/packages/ocaml.scm (ocaml-mtime): Update to 1.3.0.
 2021-11-20 17:07:10 +01:00
Julien Lepiller
63e5e127cb
gnu: ocaml-mdx: Remove unneeded dependency. 
* gnu/packages/ocaml.scm (ocaml-mdx)[inputs]: remove
ocaml-migrate-parsetree.
 2021-11-20 17:06:59 +01:00
Julien Lepiller
e7bf93e5cc
gnu: ocaml-integers: Update to 0.5.1. 2021-11-20 17:06:50 +01:00
Julien Lepiller
426faa76d1
gnu: ocaml-fmt: Update to 0.9.0. 
* gnu/packages/ocaml.scm (ocaml-fmt): Update to 0.9.0.
(ocaml4.07-fmt): New variable.
 2021-11-20 17:06:30 +01:00
Ricardo Wurmus
c618f4a9cc
gnu: pigx-bsseq: Update to 0.1.6. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.6.
 2021-11-20 16:31:32 +01:00
Ricardo Wurmus
b182e13638
gnu: python-scikit-learn: Update to 1.0.1. 
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 1.0.1.
[arguments]: Disable one failing network test.
 2021-11-20 16:22:53 +01:00
Ricardo Wurmus
3d56b8af90
gnu: python-scikit-learn: Run tests conditionally. 
* gnu/packages/machine-learning.scm (python-scikit-learn)[arguments]: Respect
TESTS? in 'check phase.
 2021-11-20 16:22:53 +01:00
Ricardo Wurmus
7ca5dc370d
gnu: python-joblib: Update to 1.1.0. 
* gnu/packages/python-xyz.scm (python-joblib): Update to 1.1.0.
[arguments]: Disable one test.
 2021-11-20 16:22:53 +01:00
Ricardo Wurmus
f407e4b0f9
gnu: python2-joblib: Do not inherit source from python-joblib. 
* gnu/packages/python-xyz.scm (python2-joblib)[version]: Explicitly set to
0.14.1.
[source]: Do not inherit.
 2021-11-20 16:22:49 +01:00
Maxim Cournoyer
76df1ad3df
gnu: gtk: Guard against timeouts in the test suite. 
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.
 2021-11-20 08:57:02 -05:00
Maxim Cournoyer
58c42ce41d
gnu: libnice: Disable the 'test-bsd' test. 
* gnu/packages/networking.scm (libnice)
[phases]{disable-failing-test}: Rename to...
{disable-failing-tests}: ... this, plural.  Disable 'test-bsd'.
 2021-11-20 08:57:02 -05:00
Maxim Cournoyer
cb09adc093
gnu: wayland: Use native-inputs unconditionally 
* gnu/packages/freedesktop.scm (wayland): Remove trailing #t.
[phases]: Use native-inputs unconditionally.
 2021-11-20 08:57:02 -05:00
Maxim Cournoyer
afacad8b67
gnu: gnome-shell: Update to 41.0. 
* 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.
 2021-11-20 08:57:01 -05:00