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135125 Commits (47a31f95e2f18d1644adc66a83c29b7bc4272610)

Author SHA1 Message Date
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
Ricardo Wurmus fbfd58b5bf
gnu: Add python-pims. 
* gnu/packages/image-processing.scm (python-pims): New variable.

Change-Id: I33e89dd865a38b526a1f766cf321a6c67a170a36
 2024-04-22 11:29:30 +02:00
Ricardo Wurmus 7ca1a02030
gnu: Add python-spatial-image. 
* gnu/packages/image-processing.scm (python-spatial-image): New variable.

Change-Id: I0e2bbfb94499aca71b33703153ad408530b60658
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus 81eb92105f
gnu: Add python-xarray-datatree. 
* gnu/packages/python-science.scm (python-xarray-datatree): New variable.

Change-Id: I403f241b6daae8b5c835f4517a1dceca0393f8e6
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus 3c00ef084b
gnu: Add python-xarray-dataclasses. 
* gnu/packages/python-science.scm (python-xarray-dataclasses): New variable.

Change-Id: I55f258e36ea70a2efb142bd652a81d70771a457c
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus 15f4363df0
gnu: Add python-slicerator. 
* gnu/packages/python-xyz.scm (python-slicerator): New variable.

Change-Id: I9f24707f16cb34d25f6423b03fd07ea122d55064
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus 5ac831d81b
gnu: python-nbclient: Update to 0.6.6. 
* gnu/packages/jupyter.scm (python-nbclient): Update to 0.6.6.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Remove python-nest-asyncio; add python-jupyter-core.

Change-Id: Idb70e781c508be389f08c0cab439644852b81577
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus d1e66d2ddf
gnu: Add python-ipfsspec. 
* gnu/packages/python-xyz.scm (python-ipfsspec): New variable.

Change-Id: I1fe0c2523616b9567501ef369c07b61fcacbee81
 2024-04-22 11:29:29 +02:00
Alexis Simon 78d24b78d3
gnu: Add python-cyvcf2. 
* gnu/packages/bioinformatics.scm (python-cyvcf2): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I0db07e7b5840f5c1f5c68512ffabb3d6b39ab95c
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus 8e5186ca9f
gnu: r-bayseq: Update to 2.36.2. 
* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.36.2.

Change-Id: Ic709181286a25fb2540d73991196cd54302f6fa2
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus 1ee8d23e8f
gnu: r-gsva: Update to 1.50.5. 
* gnu/packages/bioconductor.scm (r-gsva): Update to 1.50.5.

Change-Id: I18584e8766e8377f18321b4a4991edbbc933cbe2
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus 32ff790ac4
gnu: r-alevinqc: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.18.1.

Change-Id: I84abb3751c44f4679ebf6c5c39f3b7d0027f002e
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus fa8472f5be
gnu: r-lme4: Update to 1.1-35.3. 
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-35.3.

Change-Id: I20c5839dd74fc596406e129086cf58fb78d06297
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus 26ebfaa9e4
gnu: r-diptest: Update to 0.77-1. 
* gnu/packages/statistics.scm (r-diptest): Update to 0.77-1.

Change-Id: I4f8c677984f68d3d8a093d5bdd497352e4c8d4c4
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus 35b317eaa2
gnu: r-matrixstats: Update to 1.3.0. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 1.3.0.

Change-Id: I660f58800789f1e7e0a2380f3503597b62c0e5ba
 2024-04-22 11:29:29 +02:00
Ricardo Wurmus de274b5b72
gnu: r-rcpparmadillo: Update to 0.12.8.2.1. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.12.8.2.1.

Change-Id: Ibfc58ce4512ee1c50f9041708ae18b296f3987b1
 2024-04-22 11:29:29 +02:00