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Author SHA1 Message Date
Ricardo Wurmus 42e9e8ba2e
gnu: Add homer. 
* gnu/packages/bioinformatics.scm (homer): New variable.
 2023-05-08 18:50:38 +02:00
Maxim Cournoyer 4228d3c358
Partly reinstate "doc: Update all menus." 
This partly reinstates commit 9719d7d ("doc: Update all menus."), omitting the
hunk touching doc/contributing.texi.

* doc/guix.texi: Update all menus.
 2023-05-08 09:57:09 -04:00
Efraim Flashner e15d2655cb
gnu: python-bleach: Don't vendor python-html5lib. 
* gnu/packages/python-xyz.scm (python-bleach)[source]: Add snippet to
remove vendored library and references to it.
[propagated-inputs]: Add python-html5lib.
 2023-05-08 15:45:44 +03:00
Ricardo Wurmus 030a90bf9c
gnu: python-bleach: Update to 5.0.1. 
* gnu/packages/python-xyz.scm (python-bleach): Update to 5.0.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase.
 2023-05-08 14:31:09 +02:00
Ricardo Wurmus e118b92cfe
gnu: Add r-seurat5. 
* gnu/packages/cran.scm (r-seurat5): New variable.
 2023-05-08 11:53:29 +02:00
Ricardo Wurmus c2a2d40e6d
gnu: Add r-seurat5object. 
* gnu/packages/cran.scm (r-seurat5object): New variable.
 2023-05-08 11:53:29 +02:00
Efraim Flashner 12c529c071
gnu: python-bottleneck: Honor #:tests? flag. 
* gnu/packages/python-science.scm (python-bottleneck)[arguments]: Adjust
custom 'check phase to honor the #:tests? flag.
 2023-05-08 12:42:10 +03:00
Efraim Flashner 4a23812c7c
gnu: python-bottleneck: Update to 1.3.7. 
* gnu/packages/python-science.scm (python-bottleneck): Update to 1.3.7.
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher 02dbaa0311
gnu: python-astropy: Update to 5.2.2. 
* gnu/packages/astronomy.scm (python-astropy): Update to 5.2.2.
[arguments]<phases>{check}: Skip 2 more failing tests.
[native-inputs]: Add python-colorlog, python-h5py, python-pandas,
python-pyarrow, python-pytest-astropy-header, python-scikit-image,
python-scipy, python-timezonefinder.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher 596f3beeb7
gnu: python-pytest-mpl: Update to 0.16.1. 
* gnu/packages/python-check.scm (python-pytest-mpl): Update to 0.16.1.
[build-system]: Use pyproject-build-system.
[arguments]<phases>: Simplify phases by removing redundant modification
and use <test-flags> instead.
[propagated-inputs]: Add python-jinja2, python-packaging.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher 3a5c78b287
gnu: python-pytest-arraydiff: Update to 0.5.0. 
* gnu/packages/python-check.scm (python-pytest-arraydiff): Update to
0.5.0.
[native-inputs]: Add python-setuptools-scm.
[propagated-inputs]: Remove python-six.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher 16e83296d7
gnu: python-pytest-remotedata: Update to 0.4.0. 
* gnu/packages/python-check.scm (python-pytest-remotedata): Update to
0.4.0.
[build-system]: Use pyproject-build-system.
[arguments]<phases>: Simplify by removing not required phase
modification and use <test-flags> instead.
[native-inputs]: Add python-setuptools-scm.
[propagated-inputs]: Delete python-six, add python-packaging.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher a1baa54b8a
gnu: python-skyfield: Update to 1.46. 
* gnu/packages/astronomy.scm (python-skyfield): Update to 1.46.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher e48105bc55
gnu: python-jplephem: Update to 2.18. 
* gnu/packages/astronomy.scm (python-jplephem): Update to 2.18.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher 450185df4e
gnu: python-extension-helpers: Update to 1.0.0. 
* gnu/packages/python-xyz.scm (python-extension-helpers): Update to
1.0.0.
[build-system]: Use pyproject-build-system.
[arguments]<tests>: Disable them, as pytest can't load the test suite.
[native-inputs]: Add python-setuptools-scm.
[home-page]: Re-point to actual project home page.
[synopsis]: Adjust it to cover actual project.
[description]: ... as above.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher 2f9173430f
gnu: python-pytest-astropy: Simplify package. 
* gnu/package/python-check.scm (python-pytest-astropy): Simplify package.
[arguments]<phases>: Remove remove-requirement phase.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher 735513e93e
gnu: python-pytest-filter-subpackage: Update to 0.1.2. 
* gnu/packages/python-check.scm (python-pytest-filter-subpackage):
Update to 0.1.2.
[build-system]: Use pyproject-build-system.
[arguments]: Drop no more required phases.
[native-inputs]: Add python-setuptools-scm.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher 5a70b9b924
gnu: Add python-timezonefinder. 
* gnu/packages/time.scm (python-timezonefinder): New variable.
* gnu/packages/geo.scm (h3-3, python-h3-3): New variables. The latest
compatible versions to build python-timezonefinder.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher 424ba87292
gnu: Add python-h3. 
* gnu/packages/geo.scm (python-h3): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:09 +03:00
Sharlatan Hellseher af3742b160
gnu: Sort use-module alphabetically in (gnu packages geo). 
* gnu/packages/geo.scm: Sort use-module alphabetically to ease
maintenance.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:08 +03:00
Sharlatan Hellseher 53809e5f4b
gnu: Add h3. 
* gnu/packages/geo.scm (h3): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:08 +03:00
Sharlatan Hellseher bb38261b5d
gnu: python-pytest-doctestplus: Update to 0.12.1. 
* gnu/packages/python-check.scm (python-pytest-doctestplus): Update to
0.12.1.
[build-system]: Use pyproject-build-system.
[arguments]<phases>: Remove modify-phases and add test-flags option
instead.
[native-inputs]: Add python-numpy.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:08 +03:00
Raphaël Mélotte 476f764f07
gnu: tio: Update to 2.5. 
* gnu/packages/terminals.scm (tio): Update to 2.5.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:08 +03:00
Yovan Naumovski 8bd5b3a373
gnu: openttd-engine: Update to 13.1. 
* gnu/packages/games.scm (openttd-engine): Update to 13.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-08 12:42:08 +03:00
Mădălin Ionel Patrașcu 0e09e8ab15
gnu: Add r-multibac. 
* gnu/packages/bioconductor.scm (r-multibac): New variable.
 2023-05-08 10:34:06 +02:00
Maxim Cournoyer b7e7744626
Revert "doc: Update all menus." 
This reverts commit 9719d7d2b0.  It breaks Guix
pull, building the 'guix-manual' for reasons that currently escape me.
 2023-05-07 22:49:29 -04:00
Maxim Cournoyer 9719d7d2b0
doc: Update all menus. 
Automated via 'M-x texinfo-all-menus-update' in Emacs, and dropping
the *Contributing menu removal, which is erroneously removed because defined
in a different Texinfo file.

* doc/guix.texi: Update all menus.
* doc/contributing.texi (Submitting Patches): Likewise.
 2023-05-07 21:51:27 -04:00
Maxim Cournoyer 26a788ae06
doc: Add some information/recommendation regarding --sysconfdir. 
* doc/contributing.texi (Building from Git): Mention sysconfdir along
localstatedir.
* doc/guix.texi (Requirements): Likewise.
 2023-05-07 21:51:27 -04:00
Maxim Cournoyer d1aba42ad4
gnu: nss-certs: Update to 3.88.1. 
* gnu/packages/certs.scm (nss-certs): Update to 3.88.1.
 2023-05-07 13:04:25 -04:00
Maxim Cournoyer 62f31c9d50
gnu: libva-utils: Update home page. 
* gnu/packages/video.scm (libva-utils) [home-page]: Update URL.
 2023-05-07 13:04:25 -04:00
Maxim Cournoyer 260bb2c320
gnu: vdpauinfo: Update to 1.5. 
* gnu/packages/video.scm (vdpauinfo): Update to 1.5.
 2023-05-07 13:04:24 -04:00
Maxim Cournoyer 69f55d1115
gnu: libva-utils: Update to 2.18.1. 
* gnu/packages/video.scm (libva-utils): Update to 2.18.1.
 2023-05-07 13:04:24 -04:00
Maxim Cournoyer 0bb691d7d3
gnu: libva: Update to 2.18.0. 
* gnu/packages/video.scm (libva): Update to 2.18.0.
 2023-05-07 13:04:24 -04:00
Kaelyn Takata 0be7838105
gnu: mesa: Update to 23.0.3. 
* gnu/packages/gl.scm (mesa): Update to 23.0.3.
[source]: Remove obsolete patch and update HTTPS url.
[arguments]: Enable the crocus gallium driver.
* gnu/packages/patches/mesa-fix-sporadic-test-failures.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2023-05-07 13:04:24 -04:00
Kaelyn Takata cf79468720
gnu: mesa: Use gexps instead of quasiquote. 
* gnu/packages/gl.scm (mesa)[arguments]: Use gexps instead of quasiquote.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-05-07 13:04:24 -04:00
Kaelyn Takata 02995444db
gnu: mesa: Fix hardware video decoding. 
* gnu/packages/gl.scm (mesa): Fix hardware video decoding.
[arguments]: Add -Dvideo-codecs to the #:configure-flags
[native-search-paths]: Add VDPAU_DRIVER_PATH so libvdpau can find the drivers.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-05-07 13:04:24 -04:00
Kaelyn Takata 61a3264424
gnu: mesa: Fix library paths in Vulkan layer manifests. 
* gnu/packages/gl.scm (mesa): Fix library paths in Vulkan layer manifests.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-05-07 13:04:23 -04:00
Antero Mejr 4c3532d7ab
gnu: Add emacs-next-pgtk-xwidgets. 
* gnu/packages/emacs.scm (emacs-next-pgtk-xwidgets): New variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2023-05-07 17:55:27 +02:00
Liliana Marie Prikler 3fc284da69
gnu: ppsspp: Update to 1.14.4. 
* gnu/packages/emulators.scm (ppsspp): Update to 1.14.4.
[source]<snippet>: Adjust accordingly.
[arguments]<#:configure-flags>: Add “-DARMIPS_USE_STD_FILESYSTEM=ON” and
“-DUSE_SYSTEM_ZSTD=ON”.
<#:phases>: Drop replacement for ‘check’ phase.
Drop ‘fix-unittest-build’.
Do not add sources for pspautotests -- they are not tested in ‘check’ and some
of them fail.
* gnu/packages/patches/ppsspp-disable-upgrade-and-gold.patch: Adjust
accordingly.
 2023-05-07 17:55:15 +02:00
Liliana Marie Prikler b2b0179ec7
gnu: armips: Update to 0.11.0-1-6719ede. 
* gnu/packages/assembly.scm (armips): Update to 0.11.0-1-6719ede.
[source]: Add snippet to fix “Core/Types.h”.
[arguments]<#:configure-flags>: Add “-DARMIPS_USE_STD_FILESYSTEM=ON”.
 2023-05-07 17:55:15 +02:00
Zongyuan Li 3e46970eab
gnu: python-sphinx-4: Fix sanity-check failure 
* gnu/packages/sphinx.scm (python-sphinx-4)[propagated-inputs]:
  Downgrades python-docutils to v0.15

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-05-07 11:37:38 -04:00
Sharlatan Hellseher d16826cc32
gnu: Add python-ccdproc. 
* gnu/packages/astronomy.scm (python-ccdproc): New variable.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-05-07 10:39:26 -04:00
Sharlatan Hellseher 192426f2f6
gnu: python-astroalign: Update to 2.4.2. 
* gnu/packages/astronomy.scm (python-astroalign): Update to 2.4.2.
[source]: Use git checkout instead PyPI to enable tests.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Migrate from inputs. Remove labels. Add optional
python-bottleneck.
[native-inputs]: Add python-astropy, python-ccdproc, python-pillow.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-05-07 10:37:54 -04:00
Sharlatan Hellseher 7dac6fee5d
gnu: Add python-memory-profiler. 
* gnu/packages/python-check.scm (python-memory-profiler): New variable.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-05-07 10:37:46 -04:00
Sharlatan Hellseher 018764f165
gnu: Add python-astroscrappy. 
* gnu/packages/astronomy.scm (python-astroscrappy): New variable.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-05-07 09:28:08 -04:00
Mekeor Melire 7f8575c97a
Makefile.am: Use --add flag to "git config". 
Without the "--add" flag to "git config include.path ...", the command fails
if the user already has a configuration entry of "include.path".

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-05-07 09:12:47 -04:00
Christopher Baines 8b855dc1f4
gnu: findutils: Update XFAIL_TESTS for the hurd. 
This could do with more investigating, but this reflects what I see locally.

* gnu/packages/base.scm (findutils)[arguments]: Update XFAIL_TESTS for the
hurd.
* gnu/packages/commencement.scm (findutils-boot0): Stop clearing the
make-flags, so the above change applies to findutils-boot0.
 2023-05-07 12:16:51 +01:00
Christopher Baines aad47b1b92
Revert "gnu: gcc-11: Adapt patching for hurd to not use gexp's." 
This reverts commit 08acdd0765.

This change is now unnecessary now that gcc-boot0 uses
gexps (a795a02a9d).

* gnu/packages/gcc.scm (gcc-11)[arguments]: Use gexp for modify-phases.
[native-inputs]: Remove.
* gnu/packages/commencement.scm (gcc-boot0)[native-inputs]: Remove.
 2023-05-07 12:16:51 +01:00
Benjamin fccb48d2ce
gnu: neovim update to 0.9.0. 
* gnu/packages/vim.scm (neovim): Update to 0.9.0.
[arguments]: Adjust phase 'prevent-embedding-gcc-store-path to changes
in the source code.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-07 12:22:20 +03:00
Benjamin 23bc492dca
gnu: tree-sitter: Update to 0.20.8. 
* gnu/packages/tree-sitter.scm (tree-sitter): Update to 0.20.8.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-05-07 12:21:44 +03:00