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2024-04-22gnu: r-openssl: Update to 2.1.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-openssl): Update to 2.1.2. Change-Id: I7d949c4c617940b729d07478902e1ccedcd28c2d
2024-04-22gnu: r-keras: Update to 2.15.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-keras): Update to 2.15.0. Change-Id: Iff6a980dbe3fb2c118f80029708d3afc8739f0f5
2024-04-22gnu: r-tfruns: Update to 1.5.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-tfruns): Update to 1.5.3. Change-Id: I2c3008b81c269021f8259583e94c7bb8b324b22e
2024-04-22gnu: r-gsa: Update to 1.03.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-gsa): Update to 1.03.3. Change-Id: I2c3712958bfa15c32dac86a4c254c64f4e8dfad0
2024-04-22gnu: r-pkgdown: Update to 2.0.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-pkgdown): Update to 2.0.9. Change-Id: I06dd2f13fd5fb215e0fa3c9482af75049d6955d8
2024-04-22gnu: r-tune: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-tune): Update to 1.2.1. Change-Id: I9167af6ef9f2d7046765ff818c836ba962f6cc7e
2024-04-22gnu: r-flexsurv: Update to 2.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-flexsurv): Update to 2.3. Change-Id: If44f31a0171ec910b617e56bc3470e71ab3e1ee1
2024-04-22gnu: r-tolerance: Update to 3.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-tolerance): Update to 3.0.0. [propagated-inputs]: Remove r-rgl; add r-plotly. Change-Id: I7edd308af3937baa3384428cab531367e936b637
2024-04-22gnu: r-uwot: Update to 0.2.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-uwot): Update to 0.2.2. [propagated-inputs]: Add r-rspectra. Change-Id: Iece11fdfb68660f64adc1544eb52f9912335a8af
2024-04-22gnu: r-pamr: Update to 1.56.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-pamr): Update to 1.56.2. Change-Id: I2235d5e24cd2a18c79374d03f5e9225f9a2d9d7f
2024-04-22gnu: r-apcluster: Update to 1.4.12.Ricardo Wurmus
* gnu/packages/cran.scm (r-apcluster): Update to 1.4.12. Change-Id: I31b8791336e14c04da776f70617ac5443a6946a4
2024-04-22gnu: r-tm: Update to 0.7-13.Ricardo Wurmus
* gnu/packages/cran.scm (r-tm): Update to 0.7-13. Change-Id: I970c336d647911efbfa4e554ef717c732c3a6bba
2024-04-22gnu: r-targets: Update to 1.7.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-targets): Update to 1.7.0. [propagated-inputs]: Remove r-digest. Change-Id: I72c95351da2fe453014d25e4403a979dba9b35ec
2024-04-22gnu: r-tarchetypes: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-tarchetypes): Update to 0.9.0. [propagated-inputs]: Remove r-digest; add r-secretbase. Change-Id: Ie164cebdf0bab4ef128f0023dbe73a0711893a8c
2024-04-22gnu: r-factominer: Update to 2.11.Ricardo Wurmus
* gnu/packages/cran.scm (r-factominer): Update to 2.11. Change-Id: Id24133b66e55ef6b41710dbc98cbb3daf2ef4b9f
2024-04-22gnu: r-seriation: Update to 1.5.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-seriation): Update to 1.5.5. Change-Id: I1632302f747d4f64e0b26baf9213525c05b6bacb
2024-04-22gnu: python-commonroad-io: Relax requirements.Ricardo Wurmus
* gnu/packages/simulation.scm (python-commonroad-io)[arguments]: Accept 3.20.2 when 3.20.1 is wanted. Change-Id: I5ad0689f827eda8ec1a7ec74008d04fb6d9f5870
2024-04-22gnu: python-omegaconf: Fix build system errors.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-omegaconf)[arguments]: Fix syntax error in version specification; do not trigger errors on deprecation warnings. Change-Id: Ida873c11255ffb65d888378cdd77a9205163016a
2024-04-22gnu: python-deeptools: Replace python-nose with python-pytest.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Replace python-nose with python-pytest. Change-Id: Icba4ed3a464bfa36616aabe2cbbb26bfabec40aa
2024-04-22gnu: java-easymock-class-extension: Use java-asm-8.Ricardo Wurmus
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
2024-04-22gnu: python-pydantic-2: Ignore sensitive tests.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pydantic-2)[arguments]: Ignore north star tests. Change-Id: Ic305f95f8d1399a4d777dad35fcee9e28f16c907
2024-04-22gnu: python-asdf-astropy: Add missing test inputs.Ricardo Wurmus
* gnu/packages/astronomy.scm (python-asdf-astropy)[native-inputs]: Add python-pytest and python-pytest-xdist. Change-Id: I1b08cf3937d4d17e034bebf6c1e971e43ca79839
2024-04-22gnu: python-zarr: Update to 2.17.2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-zarr): Update to 2.17.2. [arguments]: Delete two flaky tests. Change-Id: I1ab1c90f17d17a03c6cd76bbeb9112df741cc9c6
2024-04-22gnu: python-xarray-dataclasses: Add missing test input.Ricardo Wurmus
* gnu/packages/python-science.scm (python-xarray-dataclasses)[native-inputs]: Add python-pytest. Change-Id: I137d49380d772f11f75837aa9a915ced85cfc1a2
2024-04-22gnu: cpplint: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/cpp.scm (cpplint)[build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase. Change-Id: I270de2cafe75ef2d7280dee884a0aeb060f2aa32
2024-04-22gnu: python-pandas-2: Skip expensive tests.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Set PANDAS_CI variable. Change-Id: I7c400ff260b3c833be1a55a30de021a81a5cbacb
2024-04-22gnu: Add python-pandas-2.Nicolas Graves
* gnu/packages/python-science.scm (python-pandas-2): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I7f0510f9021d4eac3c981e5e58f73dc3ec7efd2f
2024-04-22gnu: Add python-pytest-next.Nicolas Graves
* gnu/packages/check.scm (python-pytest-next): New variable.
2024-04-22gnu: python-contourpy: Update to 1.1.1.Nicolas Graves
* gnu/packages/python-xyz.scm (python-contourpy): Update to 1.1.1. Change-Id: I31ac27bb7f41f04c82baba2650012d4730a4b684
2024-04-22gnu: python-openpyxl: Update to 3.0.10.Nicolas Graves
* 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
2024-04-22gnu: python-pytest-xdist: Use pyproject-build-system.Nicolas Graves
* gnu/packages/check.scm (python-pytest-xdist): Use pyproject-build-system.
2024-04-22gnu: python-jinja2: Update to 3.1.2.Nicolas Graves
* gnu/packages/python-xyz.scm (python-jinja2): Update to 3.1.2. Format. [build-system]: Use pyproject-build-system. [arguments]: Remove uneeded argument.
2024-04-22gnu: python-pyproject-metadata: Update to 0.7.1.Nicolas Graves
* gnu/packages/python-xyz.scm (python-pyproject-metadata): Update to 0.7.1.
2024-04-22gnu: Add meson-python/newer.Ricardo Wurmus
* gnu/packages/build-tools.scm (meson-python/newer): New variable. Change-Id: I5f34a1abdffcc2e782a2956c199f1c303911069c
2024-04-22gnu: meson/newer: Update to 1.2.1.Nicolas Graves
* gnu/packages/build-tools.scm (meson/newer): Update to 1.2.1.
2024-04-22gnu: Add python-pims.Ricardo Wurmus
* gnu/packages/image-processing.scm (python-pims): New variable. Change-Id: I33e89dd865a38b526a1f766cf321a6c67a170a36
2024-04-22gnu: Add python-spatial-image.Ricardo Wurmus
* gnu/packages/image-processing.scm (python-spatial-image): New variable. Change-Id: I0e2bbfb94499aca71b33703153ad408530b60658
2024-04-22gnu: Add python-xarray-datatree.Ricardo Wurmus
* gnu/packages/python-science.scm (python-xarray-datatree): New variable. Change-Id: I403f241b6daae8b5c835f4517a1dceca0393f8e6
2024-04-22gnu: Add python-xarray-dataclasses.Ricardo Wurmus
* gnu/packages/python-science.scm (python-xarray-dataclasses): New variable. Change-Id: I55f258e36ea70a2efb142bd652a81d70771a457c
2024-04-22gnu: Add python-slicerator.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-slicerator): New variable. Change-Id: I9f24707f16cb34d25f6423b03fd07ea122d55064
2024-04-22gnu: python-nbclient: Update to 0.6.6.Ricardo Wurmus
* 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
2024-04-22gnu: Add python-ipfsspec.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-ipfsspec): New variable. Change-Id: I1fe0c2523616b9567501ef369c07b61fcacbee81
2024-04-22gnu: Add python-cyvcf2.Alexis Simon
* gnu/packages/bioinformatics.scm (python-cyvcf2): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I0db07e7b5840f5c1f5c68512ffabb3d6b39ab95c
2024-04-22gnu: r-bayseq: Update to 2.36.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.36.2. Change-Id: Ic709181286a25fb2540d73991196cd54302f6fa2
2024-04-22gnu: r-gsva: Update to 1.50.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gsva): Update to 1.50.5. Change-Id: I18584e8766e8377f18321b4a4991edbbc933cbe2
2024-04-22gnu: r-alevinqc: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.18.1. Change-Id: I84abb3751c44f4679ebf6c5c39f3b7d0027f002e
2024-04-22gnu: r-lme4: Update to 1.1-35.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-35.3. Change-Id: I20c5839dd74fc596406e129086cf58fb78d06297
2024-04-22gnu: r-diptest: Update to 0.77-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-diptest): Update to 0.77-1. Change-Id: I4f8c677984f68d3d8a093d5bdd497352e4c8d4c4
2024-04-22gnu: r-matrixstats: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-matrixstats): Update to 1.3.0. Change-Id: I660f58800789f1e7e0a2380f3503597b62c0e5ba
2024-04-22gnu: r-rcpparmadillo: Update to 0.12.8.2.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.12.8.2.1. Change-Id: Ibfc58ce4512ee1c50f9041708ae18b296f3987b1
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