summaryrefslogtreecommitdiff
path: root/gnu
AgeCommit message (Collapse)Author
2026-01-25gnu: python-scikit-survival: Fix indentation.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-survival): Fix indentation. Change-Id: Iff0ab38a0b484938613df08ffb0fbd83da489289 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-scikit-survival: Update to 0.26.0.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-scikit-survival): Update to 0.26.0. [native-inputs]: Add python-pytest-xdist. Change-Id: If92ba627c894cb65976b7687062e738656b06e96 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Remove python-dask-expr.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-dask/bootstrap) (python-dask-expr): Delete variables. Fixes: guix/guix#4766 Change-Id: I8243329353fe41b0ffff35fd4383a9a09047cd52 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: openmm: Update to 8.4.0.Sharlatan Hellseher
* gnu/packages/machine-learning.scm (openmm): Update to 8.4.0. Change-Id: If91f5557966b7982b3504800d7761cc9b79b3af2 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Remove fanc.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (fanc): Delete variable. Change-Id: I6ecb68155c021a67ff548bb2bd3bb6052676dc3a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Remove ginga-qt5.Sharlatan Hellseher
* gnu/packages/astronomy.scm (ginga-qt5): Delete variable. Change-Id: I86a926bd8af1a999780c64e4bd435238d7dd3c85 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Remove python-webbpsf.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-webbpsf): Delete variable. Change-Id: I87374a9f04ad87eb940a9ad2751a217f779e5ea3 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Remove python-watchgod.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-watchgod): Delete variable. Change-Id: I52cbd0577de38bb21094ed8f6ee5ef14741634e0 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Remove python-statannot.Sharlatan Hellseher
A message from upstream: "This repository is not maintained anymore. I recommend using the forked package trevismd/statannotations, which has a cleaner API and further extends the functionalities of statannot." * gnu/packages/python-science.scm (python-statannot): Delete variable. Fixes: guix/guix#5355 Change-Id: Ib3347ff2077f62d4e97c0f9dc437b419d260c4b5 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-perfplot: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-perfplot): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: Ib7ea70587df75876a01e44899b7aebdd121f19fb Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-peaks2utr: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-peaks2utr): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I9aacc181e7fd2330c7ed46f14902701aba843fe8 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pandapower: Update to 3.3.0.Sharlatan Hellseher
* gnu/packages/engineering.scm (python-pandapower): Update to 3.3.0. [source]: Switch to git-fetch. [arguments] <test-flags>: Run tests in parallel, supported by upstream. <phases>: Add 'relax-requirements. [propagated-inputs]: Add python-pandera, python-geopandas, python-lxml, python-matplotlib, python-openpyxl, python-pyproj, and python-shapely. [native-inputs]: Remove python-pyproj, python-wheel, and unzip; add python-nbmake and python-pytest-xdist. Change-Id: I26e0f5ab3efa299beb1acf6ced4dfa3d15f7df3f Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-deepdiff: Update to 8.6.1.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-deepdiff): Update to 8.6.1. [native-inputs]: Add python-uuid6. Change-Id: Ife7367c5772c8bba067e698f01b974cf2bfb4bfb Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-uuid6.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-uuid6): New variable. Change-Id: I3bf9d83706763ac3ed360005831dbfa3f775c368 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-orthopy: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/maths.scm (python-orthopy): [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-wheel. Change-Id: I574e885dd7ef3522160cb287e4094c6ed4a05181 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-numpysane: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-numpysane): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I9fa1bf6e8b8110350d5524740653e02d99e36a91 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-metpy: Update to 1.7.1.Sharlatan Hellseher
* gnu/packages/geo.scm (python-metpy): Update to 1.7.1. Change-Id: I93c3600f1549d70c18acdb0b8652ffc3fbe7642c Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-mathics-core: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/maths.scm (python-mathics-core): [arguments] <tests?>: Disable for now. [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I39be334cd670b0e747429887f5a92505bd7be154 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pysm3: Relax requirements for NumPy and SciPy.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-pysm3): [phases] {relax-requirements}: New phase. Change-Id: I856c43fe9aa7d83cdb9fc71aa8687bf6648e0ba6 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-lifelines: Simplify tests.Sharlatan Hellseher
* gnu/packages/statistics.scm (python-lifelines): [arguments] <test-flags>: Rework skipped tests to improve determinism of them. [native-inputs]: Remove python-pytest-xdist and python-wheel; add python-jinja2. Change-Id: Ia468acbfff3714662620e1196f4ea8fe72a308df Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pytoolconfig: Reduce closure size.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-pytoolconfig): Update to 1.3.1. [propagated-inputs]: Remove python-pydantic, python-sphinx, python-sphinx-autodoc-typehints, python-sphinx-rtd-theme, and python-tabulate. Change-Id: Ifd1831f64dcb14afaddf9a1b6d445b0b67e94bbd Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pandas-stubs: Update to 2.3.3.251219.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pandas-stubs): Update to 2.3.3.251219. [arguments]: Drop all but 2 skipped tests. [propagated-inputs]: Add python-numpy. [native-inputs]: Remove python-tables, which, xclip, xorg-server-for-tests, and xsel; add python-beautifulsoup4, python-fsspec, python-html5lib, python-jinja2, python-loguru, python-mypy, python-numexpr, python-openpyxl, python-typing-extensions, python-xlrd, python-xlsxwriter, and tzdata-for-tests. Change-Id: I7b7b85c1ce9b1e575069a79321db4ff515372942 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-liana-py: Update to 1.6.1.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.6.1. [arguments] <test-flags>: Skip 2 more tests. Change-Id: Ic73e742be564798cc349b91966beeeb6561a72fa Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-decoupler: Update to 2.1.2.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-decoupler): Update to 2.1.2. [phases]{relax-requirements}: New phases. Change-Id: Iaa57b2d4ef96d661a68310c64c6f2e2b8aee520b Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-iced: Update to 0.6.0.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-iced): Update to 0.6.0. [native-inputs]: Remove python-wheel; add python-cython. Change-Id: I9fa0c3f1e1e4972349007d82095ddda7ae65e0b1 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-hyperopt: Fix build.Sharlatan Hellseher
* gnu/packages/machine-learning.scm (python-hyperopt): [arguments] <test-flags>: Move test logic from custom 'check phase here. <phases>: Use default 'check. [propagated-inputs]: Remove python-numpy; add python-numpy-1 and python-scikit-learn. Change-Id: Ic5b8b5a2ed37417e4869b8b00110367778b2c632 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-tortoise-orm: Update to 0.25.3.Sharlatan Hellseher
* gnu/packages/databases.scm (python-tortoise-orm): Update to 0.25.3. [arguments] <test-flags>: Skip only one test, run them in parallel. [propagated-inputs]: Remove python-asyncmy, and python-rapidjson; add python-anyio, python-asyncodbc, python-orjson, python-psycopg, python-psycopg-pool, and python-pyodbc. [native-inputs]: Remove python-ayncodbc, python-psycopg, python-psycopg-pool, python-pyodbc, and python-poetry-core; add python-cython, and python-pdm-backend, python-pytest-xdist. Change-Id: I4e2c7b8f083bd649c313c26b77c0dd2110a9689c Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pypika-tortoise: Update to 0.6.3.Sharlatan Hellseher
* gnu/packages/databases.scm (python-pypika-tortoise): Update to 0.6.3. [arguments]<test-flags>: Skip one test. [native-inputs]: Remove python-poetry-core; add python-pdm-backend. Change-Id: Id29435ec6f4c5962f32020e3cfaadac0911cd373 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pyreadstat: Update to 1.3.2.Sharlatan Hellseher
* gnu/packages/statistics.scm (python-pyreadstat): Update to 1.3.2. [arguments] <test-backend, test-flags>: Move custom 'check phase logic here. <phases>: Remove 'change-home-dir; add 'pre-check. [inputs]: Add readstat. [propagated-inputs]: Add python-narwhals-minimal and python-numpy. * gnu/packages/patches/python-pyreadstat-link-libiconv.patch: Refresh patch for 1.3.2. Change-Id: I478c67cb48574178483b6dfe97b5ed7bf9b4c783 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-narwhals: Update to 2.15.0.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-narwhals): Update to 2.15.0. [propagated-inputs]: Add python-duckdb, python-packaging, and python-rich. [native-inputs]: Remove python-duckdb. Change-Id: I0af82e4cbe2b3c2b3ae3803b77cde5f6c921a1a6 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: Add python-narwhals-minimal.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-narwhals-minimal): New variable. Change-Id: I972010ea88c649d41227c51256b739a022a350df Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-watchfiles: Update to 1.1.1.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-watchfiles): Update to 1.1.1. * gnu/packages/rust-crates.scm: (rust-syn-2.0.60, rust-proc-macro2-1.0.81, rust-filetime-0.2.24, rust-crossbeam-utils-0.8.19, rust-cc-1.0.96, rust-bitflags-2.7.0): New variables. (lookup-cargo-inputs)[python-watchfiles]: Remove rust-autocfg-1.4.0, rust-bitflags-2.9.0, rust-cc-1.2.19, rust-crossbeam-utils-0.8.21, rust-filetime-0.2.25, rust-indoc-2.0.6, rust-inotify-0.10.2, rust-instant-0.1.13, rust-libc-0.2.172, rust-log-0.4.27, rust-notify-7.0.0, rust-notify-types-1.0.1, rust-portable-atomic-1.11.0, rust-proc-macro2-1.0.95, rust-pyo3-0.24.1, rust-pyo3-build-config-0.24.1, rust-pyo3-ffi-0.24.1, rust-pyo3-macros-0.24.1, rust-pyo3-macros-backend-0.24.1, rust-python3-dll-a-0.2.13, rust-quote-1.0.40, rust-redox-syscall-0.5.11, rust-shlex-1.3.0, rust-syn-2.0.100, rust-unicode-ident-1.0.18, and rust-unindent-0.2.4; add rust-autocfg-1.3.0, rust-bitflags-2.7.0, rust-cc-1.0.96, rust-crossbeam-utils-0.8.19, rust-filetime-0.2.24, rust-indoc-2.0.5, rust-inotify-0.11.0, rust-libc-0.2.169, rust-log-0.4.22, rust-notify-8.0.0, rust-notify-types-2.0.0, rust-portable-atomic-1.6.0, rust-proc-macro2-1.0.81, rust-pyo3-0.26.0, rust-pyo3-build-config-0.26.0, rust-pyo3-ffi-0.26.0, rust-pyo3-macros-0.26.0, rust-pyo3-macros-backend-0.26.0, rust-python3-dll-a-0.2.14, rust-quote-1.0.36, rust-redox-syscall-0.5.3, rust-syn-2.0.60, rust-unicode-ident-1.0.12, and rust-unindent-0.2.3. Change-Id: I197939e4c9061d59708f51bfb8667d81555ea17a Change-Id: Iec394c08dad5aa5fe063bc06b927e05089231f84 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-libneuroml: Update to 0.6.7.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-libneuroml): Update to 0.6.7. [native-inputs]: Remove python-wheel. Change-Id: I7ef49953a922116bd2c1aeb12ea548d0dd8afb18 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-imagecodecs: Fix build.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-imagecodecs): [inputs]: Remove python-blosc2; add c-blosc2. Change-Id: I28487d0a93c8098620b68c5d46caf6d6f55ca108 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-quadpy: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/maths.scm (python-quadpy): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I103cc604f51d1af3e4030c64b3bc3cda9fadc77d Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-accupy: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/maths.scm (python-accupy): [propagated-inputs]: Add python-numpy-1. [native-inputs]: Remove python-wheel. Change-Id: I9df15444696ef365861b2fdf40011b86dc0afb1a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pyfma: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pyfma): [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-wheel. Change-Id: I8236576e39b7e6f8b981126cbf67fc55f35db83c Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-salib: Update to 1.5.2.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-salib): Update to 1.5.2. [phases]{set-version}: New phase. [native-inputs]: Remove python-pytest-cov; add python-hatch-vcs. Change-Id: Ibff2633efa0f7657a40b580a3028cb71f57b923d Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-muon: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-muon): [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-pytest-flake8. Change-Id: I6b16e7ce8d26ba874d1065766fac875e880f51f2 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pyamg: Update to 5.3.0.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pyamg): Update to 5.3.0. [arguments] <test-flags>: Remove local source instead in phase.. <phases>: Add 'pre-check. [native-inputs]: Remove python-wheel. Change-Id: I3f231c1201013b4cbc7a8fbda14937aa0685827e Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pygenometracks: Update to 3.9.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.9. [source]: Switch to git-fetch. [arguments] <tests?, test-flags>: Enable them. <phases>: Remove 'remove-invalid-syntax; adjust 'relax-requirements. [propagated-inputs]: Add python-bx-python, python-pybedtools, and python-pyfaidx. [native-inputs]: Remove python-wheel; add python-setuptools. Change-Id: I364255a3e4d072535a871340588cdff0f30b83ff Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-hicmatrix: Update to 17.2.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 17.2. [arguments] <test-flags>: Skip one test. <phases>: Remove 'find-blosc2. [inputs]: Remove c-blosc2. [native-inputs]: Remove python-wheel. Change-Id: I45972befc224d9c85858d1c1ac9be885f63cdf01 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: pigx-scrnaseq: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): [inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I3bd24084626d2c1720c899a2bae6e9be4ab99c09 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-sbpy: Skip one doc test.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-sbpy) [arguments] <test-flags>: Skip one test. Change-Id: Ie3c929d9367f596561f67e34f7bebf9024641654 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: scvelo: Update to 0.3.3.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (scvelo): Update to 0.3.3. [source]: Switch to git-fetch. [arguments] <test-flags>: Run all tests in "tests/core" <phases>: Remove 'matplotlib-compatibility; add 'set-version. Change-Id: Iea4f9e9b7d385033b1131644c0145a5fdc3a7db7 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-hic2cool: Fix tests.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-hic2cool) [arguments] <test-backend, test-flags>: Use custom. Change-Id: I1bfacc5b91a31e3bcd9434589d1d9e1a7b4d4076 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-hdf5storage: Use pythno-numpy@1.Sharlatan Hellseher
* gnu/packages/python-xyz.scm (python-hdf5storage): [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-wheel. Change-Id: I1d2e3d4d5b654e4025aa16f4d1aa9230c10a3e0a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-dcor: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/statistics.scm (python-dcor): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: Ida842dda2adea1e6a2085ae219b7e95988c14f85 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: coda: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/maths.scm (coda): [native-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I1419ec3eb9cb4f25b1078908e305c99ec8bd59c4 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: dolphin-emu: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/emulators.scm (dolphin-emu)[native-inputs]: Remove python-numpy, add python-numpy-1. Change-Id: I1693aa1af04d8c2abca4781b81143cb9a22275d8 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
generated by cgit v1.3 (git 2.53.0) at 2026-08-03 13:52:34 +0000