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32 hoursgnu: snakemake: Improve dependents bootstrap.Nicolas Graves1-7/+17
* gnu/packages/python-science.scm (python-snakemake-interface-logger-plugins-bootstrap): Add package. (python-snakemake-logger-plugin-rich-bootstrap): Likewise. (python-snakemake-interface-logger-plugins)[native-inputs]: Replace python-snakemake-logger-plugin-rich by python-snakemake-logger-plugin-rich-bootstrap. (python-snakemake-logger-plugin-rich)[propagated-inputs]: Replace python-snakemake-interface-logger-plugins-bootstrap by python-snakemake-interface-logger-plugins. [native-inputs]: Remove unused python-pytest. Merges: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: snakemake: Update to 9.25.1.Nicolas Graves1-33/+34
* gnu/packages/python-science.scm (snakemake): Update to 9.25.1. [source]: Switch to git-fetch. [arguments]{test-flags}: Refresh them. {phases}: Add phase 'relax-requirements, drop phase 'call-wrapper-not-wrapped-snakemake, which was not effective for some time already. [propagated-inputs]: Add python-snakemake-interface-logger-plugins, python-snakemake-interface-scheduler-plugins, python-snakemake-interface-software-deployment-plugins, python-sqlmodel. [native-inputs]: Add python-pytest, python-setuptools-scm, python-snakemake-interface-software-deployment-plugin-container, spython-snakemake-interface-logger-plugin-envmodules. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: Add python-snakemake-storage-plugin-http.Nicolas Graves1-0/+33
* gnu/packages/python-science.scm (python-snakemake-storage-plugin-http): New variable. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: Add python-snakemake-software-deployment-plugin-envmodules-bootstrap.Nicolas Graves1-0/+14
* gnu/packages/python-science.scm (python-snakemake-software-deployment-plugin-envmodules-bootstrap): New variable. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: Add python-snakemake-software-deployment-plugin-envmodules.Nicolas Graves1-0/+31
* gnu/packages/python-science.scm (python-snakemake-software-deployment-plugin-envmodules): New variable. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: Add python-snakemake-software-deployment-plugin-container.Nicolas Graves1-0/+32
* gnu/packages/python-science.scm (python-snakemake-software-deployment-plugin-container): New variable. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: Add python-snakemake-logger-plugin-rich.Nicolas Graves1-0/+36
* gnu/packages/python-science.scm (python-snakemake-logger-plugin-rich): New variable. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: python-snakemake-interface-storage-plugins: Update to 4.4.1.Nicolas Graves1-7/+11
* gnu/packages/python-science.scm (python-snakemake-interface-storage-plugins): Update to 4.4.1. [propagated-inputs]: Refresh them, add python-humanfriendly, remove python-reretry. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: Add python-snakemake-interface-scheduler-plugins.Nicolas Graves1-0/+32
* gnu/packages/python-science.scm (python-snakemake-interface-scheduler-plugins): New variable. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: python-snakemake-interface-software-deployment-plugins: Update to 0.18.6.Nicolas Graves1-12/+10
* gnu/packages/python-science.scm (python-snakemake-interface-software-deployment-plugins): Update to 0.18.6. [arguments]{phases}: Replace them with {test-flags}. [native-inputs]: Add python-hatchling, python-pytest, python-snakemake-software-deployment-plugin-envmodules-bootstrap. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: Add python-snakemake-interface-logger-plugins.Nicolas Graves1-0/+31
* gnu/packages/python-science.scm (python-snakemake-interface-logger-plugins): New variable. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: python-snakemake-interface-report-plugins: Update to 1.3.0.Nicolas Graves1-12/+8
* gnu/packages/python-science.scm (python-snakemake-interface-report-plugins): Update to 1.3.0. [arguments]{phases}: Replace them with {test-backend, test-flags}. [propagated-inputs]: Remove python-pytest. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: python-snakemake-interface-executor-plugins: Update to 9.4.0.Nicolas Graves1-14/+8
* gnu/packages/python-science.scm (python-snakemake-interface-executor-plugins): Update to 9.4.0. [arguments]{phases}: Replace them with {test-backend, test-flags}. [propagated-inputs]: Remove python-argparse-dataclass, python-throttler. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: python-snakemake-interface-common: Update to 1.23.0-0.d585b5c.Nicolas Graves1-12/+19
* gnu/packages/python-science.scm (python-snakemake-interface-common): Update to 1.23.0-0.d585b5c. [arguments]{phases}: Replace them with {test-backend, test-flags}. [propagated-inputs]: Add python-packaging. [native-inputs]: Replace python-poetry-core by python-setuptools. Relates-to: guix/guix!10625 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
32 hoursgnu: Add python-typedunits.Spencer King1-0/+39
* gnu/packages/python-science.scm (python-typedunits): New variable. Relates-to: guix/guix!10789 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-19gnu: maturin: Move to (gnu packages build-tools).Sharlatan Hellseher1-1/+0
Authors were parsed from git history with the following command: git log --all --grep="maturin:" \ --pretty=format:";;; Copyright © %as %aN <%aE>" * gnu/packages/rust-apps.scm (vtracer, uv)[native-inputs]: Replace maturing with (@ (gnu packages build-tools) maturin). (maturing): Deprecate variable and move from here ... * gnu/packages/build-tools.scm: ... to here. * gnu/packages/embedded.scm: Replace rust-apps with build-tools module. * gnu/packages/python-crypto.scm: Likewise. * gnu/packages/python-web.scm: Likewise. * gnu/packages/time.scm: Likewise. * gnu/packages/machine-learning.scm: Remove rust-apps module. * gnu/packages/python-compression.scm: Likewise. * gnu/packages/python-science.scm: Likewise. * gnu/packages/python-xyz.scm: Likewise. Signed-off-by: Maxim Cournoyer <maxim@guixotic.coop>
2026-08-14gnu: python-adjusttext: Update to 1.4.0.Sharlatan Hellseher1-6/+8
* gnu/packages/python-science.scm (python-adjusttext): Update to 1.4.0. [source]: Switch to git-fetch. [native-inputs]: Remove python-wheel. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-14gnu: python-pandas-stubs: Update to 3.0.3.260530.Nguyễn Gia Phong1-3/+22
* gnu/packages/python-science.scm (python-pandas-stubs): Update to 3.0.3.260530. [arguments]<#:test-flags>: Deselect additional failing tests. [native-inputs]: Add python-pytz and python-tables. Merges: guix/guix!10525 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-14gnu: packages/python-science: Sort variables.Sharlatan Hellseher1-1897/+1896
* gnu/packages/python-science.scm: Sort all variables in alphabetical order. Adjust module footer comment.
2026-08-08gnu: python-flox: Update to 0.11.2-0.d2857f3.Sharlatan Hellseher1-29/+63
* gnu/packages/python-science.scm (python-flox): Update to d2857f323a3f5b7c737b34e8cfc09492cc9ef2bf commit. [arguments] <#:test-flags>: Rework ignored and skipped tests. [propagated-inputs]: Add python-cachey, python-cftime, python-dask, python-lxml, python-matplotlib, python-numba, python-numbagg, python-sparse, python-xarray, and python-zarr. [native-inputs]: Remove python-dask, python-numbagg, python-sparse, and python-xarray. [description]: Start from a new line, fix fill column indentation.
2026-08-08gnu: python-pytensor: Update to 3.2.4.Nicolas Graves1-2/+2
* gnu/packages/python-science.scm (python-pytensor): Update to 3.2.4. Merges: guix/guix!10394 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: python-salib: Fix build.Nicolas Graves1-0/+10
* gnu/packages/python-science.scm (python-salib)[arguments] {phases}: Add phase fix-for-pandas-3. Relates-to: guix/guix!10394 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: python-pyts: Fix build.Nicolas Graves1-1/+11
* gnu/packages/python-science.scm (python-pyts)[arguments]{phases}: Add phase fix-scikit-learn-compat. Merges: guix/guix!10413 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: python-numbagg: Ignore failing tests.Nicolas Graves1-3/+19
* gnu/packages/python-science.scm (python-numbagg)[arguments] {test-flags}: Ignore tests failing because of Pandas@3.0. These are edge cases, they probably don't affect other dependencies. Relates-to: guix/guix!10413 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: python-formulaic: Fix tests.Nicolas Graves1-1/+2
* gnu/packages/python-science.scm (python-fomulaic)[native-inputs]: Add python-sympy. Relates-to: guix/guix!10354 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: python-pyjanitor: Update to 0.32.23.Nicolas Graves1-3/+6
* gnu/packages/python-science.scm (python-pyjanitor): Update to 0.32.23. [arguments]{test-flags}: Ignore flaky test. [propagated-inputs]: Add python-janitor-rs. Merges: guix/guix!10392 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: Add python-janitor-rs.Nicolas Graves1-0/+50
* gnu/packages/python-science.scm (python-janitor-rs): New variable. * gnu/packages/rust-crates.scm (lookup-cargo-inputs): Add janitor-rs entry. Relates-to: guix/guix!10392 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: python-numba-stats: Update to 1.12.0.Nicolas Graves1-4/+7
* gnu/packages/python-science.scm (python-numba-stats): Update to 1.12.0. [source]: Switch to git-fetch. Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-08-08gnu: python-plotnine: Ignore failing tests.Nicolas Graves1-22/+4
* gnu/packages/python-science.scm (python-plotnine)[arguments] {test-flags}: Refresh them, ignore test_geom* and test_stat* more robustly. Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-08-08gnu: python-pingouin: Update to 0.6.1.Nicolas Graves1-7/+7
* gnu/packages/python-science.scm (python-pingouin): Update to 0.6.1. [arguments]{test-flags}: Refresh them. Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-08-08gnu: python-pandarallel: Fix build.Nicolas Graves1-1/+4
* gnu/packages/patches/python-pandarallel-fix-df-applymap.patch: Add patch. * gnu/packages/patches/python-pandarallel-fix-parallel_apply.patch: Likewise. * gnu/local.mk (dist_patch_DATA): Record patches. * gnu/packages/python-science.scm (python-pandarallel) [source]{patches}: Record them. Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-08-08gnu: python-plotnine: Update to 0.15.7.Hugo Buddelmeijer1-2/+2
* gnu/packages/python-science.scm (python-plotnine): Update to 0.15.7. Relates-to: guix/guix!10013 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: python-numdifftools: Fix build.Hugo Buddelmeijer1-2/+6
Only dependency, python-pynt-pulsar builds fine, so these tests cannot be too important. * gnu/packages/python-science.scm (python-numdifftools): Fix build. [arguments]<#:test-flags>: Skip two failing tests. Relates-to: guix/guix!9909
2026-08-08gnu: python-pandera: Reduce threads even more.Hugo Buddelmeijer1-1/+1
* gnu/packages/python-science.scm (python-pandera): Reduce threads. [arguments]<#:test-flags>: Reduce numprocesses to 2. Relates-to: guix/guix!9909
2026-08-08gnu: python-decaylanguage: Update to 1.0.0.Hugo Buddelmeijer1-3/+4
* gnu/packages/python-science.scm (python-decaylanguage): Update to 1.0.0. [native-inputs]: Add python-pytest-benchmark. Relates-to: guix/guix!9885 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: python-particle: Update to 1.0.0.Hugo Buddelmeijer1-4/+3
* gnu/packages/python-science.scm (python-particle): Update to 1.0.0. [propagated-inputs]: Remove python-typing-extensions. Relates-to: guix/guix!9885 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: python-tdda: Update to 3.2.03.Hugo Buddelmeijer1-19/+16
* gnu/packages/python-science.scm (python-tdda): Update to 3.2.03. [arguments]<#:test-flags>: Update deselected tests; add comments. [native-inputs]: Add tzdata-for-tests. Relates-to: guix/guix!9885 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: python-upsetplot: Update to 0.9.0-1.e9603da.Hugo Buddelmeijer1-5/+15
* gnu/packages/python-science.scm (python-upsetplot): Update to 0.9.0-1.e9603da. [source]: Switch to git-fetch and to maintained fork. Relates-to: guix/guix!9885 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: python-cvxpy: Update to 1.7.5.Sharlatan Hellseher1-7/+14
* gnu/packages/python-science.scm (python-cvxpy): Update to 1.7.5. [source]: Switch to git-fetch. [arguments] <#:test-flags>: Skip one more test. [propagated-inputs]: Add python-cylp. [native-inputs]: Replace pybind11-2 with pybind11.
2026-08-08gnu: python-pint: Update to 0.25.3.Sharlatan Hellseher1-9/+13
* gnu/packages/python-science.scm (python-pint): Update to 0.25.3. [native-inputs]: Remove python-setuptools, python-setuptools-scm, and python-wheel; add python-hatch-vcs and python-hatchling.
2026-08-08gnu: python-anndata: Update to 0.13.0rc3.Sharlatan Hellseher1-47/+10
* gnu/packages/python-science.scm (python-anndata): Update to 0.13.0rc3. [arguments] <test-flags> Simplify skipped tests by utilizing "not gpu" marker to ignore all tests requiring CUDA. [propagated-inputs]: Add python-scverse-misc and python-typing-extensions. [native-inputs]: Add python-jsonschema.
2026-08-08gnu: python-vaex-core: Relax requirements for Pandas.Sharlatan Hellseher1-2/+5
* gnu/packages/python-science.scm (python-vaex-core): [phases]{relax-requirements}: Drop higher bar for Pandas. [native-inputs]: Remove pybind11-2; add pybind11.
2026-08-08gnu: python-pandera: Update to 0.31.1.Sharlatan Hellseher1-21/+21
* gnu/packages/python-science.scm (python-pandera): Update to 0.31.1. [arguments] <test-flags>: Disable tests for Modin, enable for Polars; simplify skipped tests. [inputs]: Remove python-modin; add python-polars. [native-inputs]: Add python-black, python-mypy-for-tests, python-pytz, python-sphinx, and tzdata-for-tests. Change-Id: Ie750a3795d87fec54386c35aec6f569c7798f55f
2026-08-08gnu: python-narwhals: Fix tests.Sharlatan Hellseher1-3/+4
* gnu/packages/python-science.scm (python-narwhals): [propagated-inputs]: Remove python-modin. [native-inputs]: Add tzdata-for-tests. Change-Id: I78ce19bc5cabb511b2bf77b765dd6bdfccd88ea5
2026-08-08gnu: python-modin: Use python-pandas-2Sharlatan Hellseher1-1/+3
* gnu/packages/python-science.scm (python-modin): [propagated-inputs]: Remove python-pandas; add python-pandas-2. Relates-to: guix/guix#9336 Change-Id: I2ae9ee81e46b778f9444f3b07067bd44dd49f2bb
2026-08-08gnu: python-dask-image: Update to 2026.5.0.Sharlatan Hellseher1-15/+11
* gnu/packages/python-science.scm (python-dask-image): Update to 2026.5.0. [source]: Switch to git-source. [arguments]: Drop all. Change-Id: Iff8d1ddd63509f87ba8e0e57b24875d00e64544e
2026-08-08gnu: python-pythran: Unvendor xsimd.Sharlatan Hellseher1-1/+9
* gnu/packages/python-science.scm (python-pythran): [phases]{unvendor-xsimd}: New phase. Change-Id: I2b8a86d15720d0573099792d74e2c37bc414f850
2026-08-08gnu: python-pythran: Update to 0.18.1-0.1159b80.Hugo Buddelmeijer1-3/+9
* gnu/packages/python-science.scm (python-pythran): Update to 1159b80a09ece110a369729507ba5d0bc8e895b2 commit. Relates-to: guix/guix!9327. Change-Id: I408e718acc942dc514e8874ac161ac226f107f2f Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-08-08gnu: Add python-dask-gateway.Sharlatan Hellseher1-0/+39
* gnu/packages/python-science.scm (python-dask-gateway): New variable. Change-Id: I1b466e0d41d8d09c3b12829011b4e92acd0782e9
2026-08-08gnu: python-distributed: Update to 2026.3.0.Sharlatan Hellseher1-4/+4
* gnu/packages/python-science.scm (python-distributed): Update to 2026.3.0. Change-Id: I7f1f371f147b2deb576d2777fc77a77284db6834
generated by cgit v1.2.3 (git 2.25.1) at 2026-09-03 07:14:03 +0000