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Author SHA1 Message Date
Florian Pelz e5c0ea22e6
news: Update news and commit for nss-certs change. 
As discussed in
<https://lists.gnu.org/archive/html/guix-devel/2024-04/msg00211.html>.

* etc/news.scm: Update.

Change-Id: Id893abe6642de3939f7993267075764e4bb5d820
 2024-04-23 08:01:51 +02:00
Fabio Natali 67a3a83170
doc: Fix mentions of 'nss-certs'. 
* doc/guix.texi (Using the Configuration System): Fix mention of 'nss-certs'
after the package has been added to '%default-packages' (see
'65e8472a4b6fc6f66871ba0dad518b7d4c63595e').

* doc/guix.texi (Web Services): Fix mention of 'nss-certs' after the package has
been added to '%default-packages' (see
'65e8472a4b6fc6f66871ba0dad518b7d4c63595e').

Change-Id: Iecdecb8deb440cdea224f3e9e7ce54e89dd575a2
Signed-off-by: Florian Pelz <pelzflorian@pelzflorian.de>
 2024-04-23 07:13:38 +02:00
Matthew Trzcinski b8ccbc942e
doc: Fix typo. 
* doc/guix.texi (Installing Guix in a VM): Change indefinite article.

Signed-off-by: Florian Pelz <pelzflorian@pelzflorian.de>
 2024-04-22 21:08:41 +02:00
Ricardo Wurmus 02df0a8a7d
gnu: Add r-saige. 
* gnu/packages/bioinformatics.scm (r-saige): New variable.

Change-Id: Id5bda4d25ca61fe26d11bae0af19900fd0f0080e
 2024-04-22 16:35:31 +02:00
Ricardo Wurmus 4a5a23aceb
gnu: Add savvy. 
* gnu/packages/bioinformatics.scm (savvy): New variable.

Change-Id: I48dcfad2c6c769778bd79dffa084332da53991ad
 2024-04-22 16:35:31 +02:00
Ricardo Wurmus 81d6fe1672
gnu: Add streambuf-shrinkwrap. 
* gnu/packages/compression.scm (streambuf-shrinkwrap): New variable.

Change-Id: I3405b777e18cfd7b505f6de06019353d6c49a797
 2024-04-22 16:35:30 +02:00
Ricardo Wurmus b829aeefb8
gnu: Add r-metaskat. 
* gnu/packages/cran.scm (r-metaskat): New variable.

Change-Id: I9f9917ca4ecf4a15a8926df0b6dfad0f517a31dd
 2024-04-22 16:35:30 +02:00
Ricardo Wurmus 2082dfde93
gnu: Add r-skat. 
* gnu/packages/cran.scm (r-skat): New variable.

Change-Id: Ia16c9214dea6ef83081f60d1e93c5849f96ab8f2
 2024-04-22 16:35:30 +02:00
Ricardo Wurmus f941e51ca3
gnu: Add r-spatest. 
* gnu/packages/cran.scm (r-spatest): New variable.

Change-Id: I0bece84e911e6e57dda0f0075e953304f1e25167
 2024-04-22 16:35:30 +02:00
Wilko Meyer 30de275109
gnu: linux-libre 5.15: Update to 5.15.156. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.156.
(linux-libre-5.15-pristine-source): Update hashes.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: I33e9832611372321e9bedb3ae0c1da657ccc5c79
 2024-04-22 07:46:13 -04:00
Wilko Meyer 63728df4ec
gnu: linux-libre 6.1: Update to 6.1.87. 
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.87.
(linux-libre-6.1-pristine-source): Update hashes.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: I9246f882bbb9f4572a88fef3b1eafc1caffc9fec
 2024-04-22 07:46:12 -04:00
Wilko Meyer 5c43d0ba0d
gnu: linux-libre 6.6: Update to 6.6.28. 
* gnu/packages/linux.scm (linux-libre-6.6-version): Update to 6.6.28.
(linux-libre-6.6-pristine-source): Update hashes.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: Ifa0dd02a61e07efcfdf733e8fb12b5bcf5a430ca
 2024-04-22 07:46:12 -04:00
Wilko Meyer ab0f220e9f
gnu: linux-libre 6.8: Update to 6.8.7. 
* gnu/packages/linux.scm (linux-libre-6.8-version): Update to 6.8.7.
(linux-libre-6.8-pristine-source): Update hashes.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: I8b04b4af1bc62d336366b8f0e7281c9249fc6d7d
 2024-04-22 07:46:07 -04:00
Ricardo Wurmus 28e41dc3bc
gnu: r-tclust: Update to 2.0-3. 
* gnu/packages/statistics.scm (r-tclust): Update to 2.0-3.
[propagated-inputs]: Remove r-cluster, r-mclust, r-mvtnorm, and r-sn; add r-doparallel,
r-foreach, r-mass, r-rcpp, and r-rcpparmadillo.

Change-Id: I3a39e707461de2aef4bcccc11bb839e8b273f15b
 2024-04-22 12:34:18 +02:00
Ricardo Wurmus b0f21308d2
gnu: r-segmented: Update to 2.0-4. 
* gnu/packages/statistics.scm (r-segmented): Update to 2.0-4.

Change-Id: Iae911494c64b04540c877e2eb31efb933d4d94c6
 2024-04-22 12:34:18 +02:00
Ricardo Wurmus 47a31f95e2
gnu: r-openssl: Update to 2.1.2. 
* gnu/packages/statistics.scm (r-openssl): Update to 2.1.2.

Change-Id: I7d949c4c617940b729d07478902e1ccedcd28c2d
 2024-04-22 12:34:18 +02:00
Ricardo Wurmus 1991848db4
gnu: r-keras: Update to 2.15.0. 
* gnu/packages/cran.scm (r-keras): Update to 2.15.0.

Change-Id: Iff6a980dbe3fb2c118f80029708d3afc8739f0f5
 2024-04-22 12:34:18 +02:00
Ricardo Wurmus 628c2d9624
gnu: r-tfruns: Update to 1.5.3. 
* gnu/packages/cran.scm (r-tfruns): Update to 1.5.3.

Change-Id: I2c3008b81c269021f8259583e94c7bb8b324b22e
 2024-04-22 12:34:18 +02:00
Ricardo Wurmus 95e8e95b19
gnu: r-gsa: Update to 1.03.3. 
* gnu/packages/cran.scm (r-gsa): Update to 1.03.3.

Change-Id: I2c3712958bfa15c32dac86a4c254c64f4e8dfad0
 2024-04-22 12:34:18 +02:00
Ricardo Wurmus a79bacf8b0
gnu: r-pkgdown: Update to 2.0.9. 
* gnu/packages/cran.scm (r-pkgdown): Update to 2.0.9.

Change-Id: I06dd2f13fd5fb215e0fa3c9482af75049d6955d8
 2024-04-22 12:34:17 +02:00
Ricardo Wurmus 8a7eea118f
gnu: r-tune: Update to 1.2.1. 
* gnu/packages/cran.scm (r-tune): Update to 1.2.1.

Change-Id: I9167af6ef9f2d7046765ff818c836ba962f6cc7e
 2024-04-22 12:34:17 +02:00
Ricardo Wurmus 3989dca8a1
gnu: r-flexsurv: Update to 2.3. 
* gnu/packages/cran.scm (r-flexsurv): Update to 2.3.

Change-Id: If44f31a0171ec910b617e56bc3470e71ab3e1ee1
 2024-04-22 12:34:17 +02:00
Ricardo Wurmus 3b1f8972fa
gnu: r-tolerance: Update to 3.0.0. 
* gnu/packages/cran.scm (r-tolerance): Update to 3.0.0.
[propagated-inputs]: Remove r-rgl; add r-plotly.

Change-Id: I7edd308af3937baa3384428cab531367e936b637
 2024-04-22 12:34:16 +02:00
Ricardo Wurmus c4f40ee0ff
gnu: r-uwot: Update to 0.2.2. 
* gnu/packages/cran.scm (r-uwot): Update to 0.2.2.
[propagated-inputs]: Add r-rspectra.

Change-Id: Iece11fdfb68660f64adc1544eb52f9912335a8af
 2024-04-22 12:34:16 +02:00
Ricardo Wurmus 21473fe5b5
gnu: r-pamr: Update to 1.56.2. 
* gnu/packages/cran.scm (r-pamr): Update to 1.56.2.

Change-Id: I2235d5e24cd2a18c79374d03f5e9225f9a2d9d7f
 2024-04-22 12:34:16 +02:00
Ricardo Wurmus 926d240167
gnu: r-apcluster: Update to 1.4.12. 
* gnu/packages/cran.scm (r-apcluster): Update to 1.4.12.

Change-Id: I31b8791336e14c04da776f70617ac5443a6946a4
 2024-04-22 12:34:15 +02:00
Ricardo Wurmus 0b507db3c0
gnu: r-tm: Update to 0.7-13. 
* gnu/packages/cran.scm (r-tm): Update to 0.7-13.

Change-Id: I970c336d647911efbfa4e554ef717c732c3a6bba
 2024-04-22 12:34:15 +02:00
Ricardo Wurmus f5c0f54bdb
gnu: r-targets: Update to 1.7.0. 
* gnu/packages/cran.scm (r-targets): Update to 1.7.0.
[propagated-inputs]: Remove r-digest.

Change-Id: I72c95351da2fe453014d25e4403a979dba9b35ec
 2024-04-22 12:34:15 +02:00
Ricardo Wurmus 8011581794
gnu: r-tarchetypes: Update to 0.9.0. 
* gnu/packages/cran.scm (r-tarchetypes): Update to 0.9.0.
[propagated-inputs]: Remove r-digest; add r-secretbase.

Change-Id: Ie164cebdf0bab4ef128f0023dbe73a0711893a8c
 2024-04-22 12:34:15 +02:00
Ricardo Wurmus 6a960987ce
gnu: r-factominer: Update to 2.11. 
* gnu/packages/cran.scm (r-factominer): Update to 2.11.

Change-Id: Id24133b66e55ef6b41710dbc98cbb3daf2ef4b9f
 2024-04-22 12:34:14 +02:00
Ricardo Wurmus d6ee393bad
gnu: r-seriation: Update to 1.5.5. 
* gnu/packages/cran.scm (r-seriation): Update to 1.5.5.

Change-Id: I1632302f747d4f64e0b26baf9213525c05b6bacb
 2024-04-22 12:34:14 +02:00
Ricardo Wurmus 22030634ef
gnu: python-commonroad-io: Relax requirements. 
* gnu/packages/simulation.scm (python-commonroad-io)[arguments]: Accept 3.20.2
when 3.20.1 is wanted.

Change-Id: I5ad0689f827eda8ec1a7ec74008d04fb6d9f5870
 2024-04-22 11:29:31 +02:00
Ricardo Wurmus c0c713be66
gnu: python-omegaconf: Fix build system errors. 
* gnu/packages/python-xyz.scm (python-omegaconf)[arguments]: Fix syntax error
in version specification; do not trigger errors on deprecation warnings.

Change-Id: Ida873c11255ffb65d888378cdd77a9205163016a
 2024-04-22 11:29:31 +02:00
Ricardo Wurmus a78de8f792
gnu: python-deeptools: Replace python-nose with python-pytest. 
* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Replace
python-nose with python-pytest.

Change-Id: Icba4ed3a464bfa36616aabe2cbbb26bfabec40aa
 2024-04-22 11:29:31 +02:00
Ricardo Wurmus f0268853de
gnu: java-easymock-class-extension: Use java-asm-8. 
This is necessary to avoid invalid instructions coming from the incompatible
build of java-asm.

* gnu/packages/java.scm (java-easymock-class-extension)[inputs]: Replace
java-asm with java-asm-8.

Change-Id: Iff11a54fe62ba71a6d5e62fe80c08b1539c6cee0
 2024-04-22 11:29:31 +02:00
Ricardo Wurmus d6af13222e
gnu: python-pydantic-2: Ignore sensitive tests. 
* gnu/packages/python-xyz.scm (python-pydantic-2)[arguments]: Ignore north
star tests.

Change-Id: Ic305f95f8d1399a4d777dad35fcee9e28f16c907
 2024-04-22 11:29:31 +02:00
Ricardo Wurmus 2632660295
gnu: python-asdf-astropy: Add missing test inputs. 
* gnu/packages/astronomy.scm (python-asdf-astropy)[native-inputs]: Add
python-pytest and python-pytest-xdist.

Change-Id: I1b08cf3937d4d17e034bebf6c1e971e43ca79839
 2024-04-22 11:29:30 +02:00
Ricardo Wurmus 789286ebd9
gnu: python-zarr: Update to 2.17.2. 
* gnu/packages/python-xyz.scm (python-zarr): Update to 2.17.2.
[arguments]: Delete two flaky tests.

Change-Id: I1ab1c90f17d17a03c6cd76bbeb9112df741cc9c6
 2024-04-22 11:29:30 +02:00
Ricardo Wurmus e6586f55e0
gnu: python-xarray-dataclasses: Add missing test input. 
* gnu/packages/python-science.scm (python-xarray-dataclasses)[native-inputs]:
Add python-pytest.

Change-Id: I137d49380d772f11f75837aa9a915ced85cfc1a2
 2024-04-22 11:29:30 +02:00
Ricardo Wurmus 7244fb26bd
gnu: cpplint: Use pyproject-build-system. 
* gnu/packages/cpp.scm (cpplint)[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase.

Change-Id: I270de2cafe75ef2d7280dee884a0aeb060f2aa32
 2024-04-22 11:29:30 +02:00
Ricardo Wurmus 061c7bc1ca
gnu: python-pandas-2: Skip expensive tests. 
* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Set PANDAS_CI
variable.

Change-Id: I7c400ff260b3c833be1a55a30de021a81a5cbacb
 2024-04-22 11:29:30 +02:00
Nicolas Graves ff2d0ecfca
gnu: Add python-pandas-2. 
* gnu/packages/python-science.scm (python-pandas-2): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I7f0510f9021d4eac3c981e5e58f73dc3ec7efd2f
 2024-04-22 11:29:30 +02:00
Nicolas Graves 2b5cb248d3
gnu: Add python-pytest-next. 
* gnu/packages/check.scm (python-pytest-next): New variable.
 2024-04-22 11:29:30 +02:00
Nicolas Graves 925e6d4072
gnu: python-contourpy: Update to 1.1.1. 
* gnu/packages/python-xyz.scm (python-contourpy): Update to 1.1.1.

Change-Id: I31ac27bb7f41f04c82baba2650012d4730a4b684
 2024-04-22 11:29:30 +02:00
Nicolas Graves 43965c93ae
gnu: python-openpyxl: Update to 3.0.10. 
* gnu/packages/python-xyz.scm (python-openpyxl): Update to 3.0.10.
[build-system]: Use pyproject-build-system.
[arguments]: Delete check phase replacement.

Change-Id: I1a537050f1e9f109189150d0d73e87bbd87dcb00
 2024-04-22 11:29:30 +02:00
Nicolas Graves 118b2f79f8
gnu: python-pytest-xdist: Use pyproject-build-system. 
* gnu/packages/check.scm (python-pytest-xdist): Use pyproject-build-system.
 2024-04-22 11:29:30 +02:00
Nicolas Graves 2528aabf6f
gnu: python-jinja2: Update to 3.1.2. 
* gnu/packages/python-xyz.scm (python-jinja2): Update to 3.1.2. Format.
[build-system]: Use pyproject-build-system.
[arguments]: Remove uneeded argument.
 2024-04-22 11:29:30 +02:00
Nicolas Graves 1039ec03be
gnu: python-pyproject-metadata: Update to 0.7.1. 
* gnu/packages/python-xyz.scm (python-pyproject-metadata): Update to 0.7.1.
 2024-04-22 11:29:30 +02:00
Ricardo Wurmus e0e224eae6
gnu: Add meson-python/newer. 
* gnu/packages/build-tools.scm (meson-python/newer): New variable.

Change-Id: I5f34a1abdffcc2e782a2956c199f1c303911069c
 2024-04-22 11:29:30 +02:00
Nicolas Graves ce953927fd
gnu: meson/newer: Update to 1.2.1. 
* gnu/packages/build-tools.scm (meson/newer): Update to 1.2.1.
 2024-04-22 11:29:30 +02:00