314 commits

Author	SHA1	Message	Date
Sharlatan Hellseher	1208fe94e0	gnu: python-pyglm: Update to 2.8.1. ... * gnu/packages/python-science.scm (python-pyglm): Update to 2.8.1. [native-inputs]: Add python-pytest, python-setuptools, and python-wheel. Change-Id: I38ebaa301c3f08f1c011b8695a5595fffbebc06e	2025-04-16 11:46:32 +02:00
Nicolas Graves	ac5a45243a	gnu: python-vaex-core: Update to 4.17.1. ... * gnu/packages/python-science.scm (python-vaex-core): Update to 4.17.1. * gnu/packages/patches/python-vaex-core-fix-tsl-use.patch: Add patch. * gnu/local.mk: Record patch. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>	2025-04-16 11:46:27 +02:00
Nicolas Graves	58ca499bff	gnu: python-pytensor: Update to 2.28.3. ... * gnu/packages/python-science.scm (python-pytensor): Update to 2.28.3. [arguments]{test-flags}: Use field. {phases}: Remove 'check phase replacement. Simplify 'versioneer. Add phase 'pre-check. Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com> Change-Id: I8f324863438356ebc1ad3d62e86b5b17c416cd02 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>	2025-04-16 11:46:26 +02:00
Sharlatan Hellseher	bc4c4b0a88	gnu: python-numdifftools: Skip some tests. ... * gnu/packages/python-science.scm (python-numdifftools) [arguments] <test-flags>: Skip 7 tests failing with a NumPy 1.26.2. Change-Id: I5dc5865d0ac1ba47e79aac57d4e1768ecdb590be	2025-04-16 11:46:26 +02:00
Nicolas Graves	a41f421b66	gnu: python-unyt: Avoid deprecation failure in tests. ... * gnu/packages/python-science.scm (python-unyt)[arguments] {test-flags}: Ignore failing test. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>	2025-04-16 11:46:15 +02:00
Ricardo Wurmus	d97df2b206	gnu: python-opt-einsum: Use pyproject-build-system. ... * gnu/packages/python-science.scm (python-opt-einsum)[build-system]: Use pyproject-build-system. [arguments]: Remove. [native-inputs]: Remove python-pytest-pep8; add python-setuptools and python-wheel. Change-Id: I6da632c3c7e02ec13ab61124ce2984aa2675d996	2025-04-16 11:46:13 +02:00
Sharlatan Hellseher	c8bd224e07	gnu: python-paramz: Fix tests. ... * gnu/packages/python-science.scm (python-paramz) [arguments] <test-flags>: Make them compatible with Pytest to allow some adjustments. [native-inputs]: Remove python-nose; add python-pytest. Change-Id: I66fbd374ce30e80f02fe43784740389a33783011	2025-04-16 11:46:12 +02:00
Ricardo Wurmus	dead8b3a52	gnu: Update references to python3.10 directory. ... * gnu/packages/admin.scm (ansible)[native-search-paths]: Refer to python3.11 directory. * gnu/packages/bioinformatics.scm (scvelo)[arguments]: Same. * gnu/packages/ebook.scm (calibre)[arguments]: Same. * gnu/packages/engineering.scm (cadabra2)[arguments]: Same. * gnu/packages/gnuzilla.scm (make-l10n-package)[arguments]: Same. * gnu/packages/machine-learning.scm (python-vosk)[arguments]: Same. * gnu/packages/python-science.scm (python-pandas-2)[arguments]: Same. * gnu/packages/version-control.scm (mercurial)[native-search-paths]: Same. * gnu/packages/irc.scm (go-gopkg-in-irc-v3): Update comment. Change-Id: If2ea1060b42b137474d5cfda6611df6e6fc85270	2025-04-16 11:46:08 +02:00
Sharlatan Hellseher	5b4368e5ce	gnu: Add python-numdifftools. ... * gnu/packages/python-science.scm (python-numdifftools): New variable. Change-Id: I0b5899e0bff10b488df5377c274eca63b26f9751	2025-03-31 21:04:11 +01:00
Sharlatan Hellseher	34411663a9	gnu: Add python-algopy. ... * gnu/packages/python-science.scm (python-algopy): New variable. Change-Id: I6630f4677e0bd33f321cce9e6d1f40a6bf36c625	2025-03-31 21:04:10 +01:00
Vinicius Monego	b4b6d20d66	gnu: python-bottleneck: Update to 1.4.2. ... * gnu/packages/python-science.scm (python-bottleneck): Update to 1.4.2. [source]: Update URI. [build-system]: Use pyproject-build-system. [arguments]: Use G-Expressions. <#:phases>: Add phase 'rebuild-ext before 'check. Do not override the 'check phase. [native-inputs]: Remove python-hypothesis, python-pytest-runner. Add python-setuptools, python-wheel. Change-Id: I7a79b126d2bd069eaa4e3cf7d5f05bcb482fb67c	2025-03-30 23:19:55 -03:00
Sharlatan Hellseher	f6147d476d	gnu: python-vedo: Update to 2025.5.3. ... fenics is no longer required and it fails to build, see #77195. * gnu/packages/python-science.scm (python-vedo): Update to 2025.5.3, fix build. [build-system]: Swap to pyproject-build-system. [arguments] <tests?>: Disable as depend on remote data. <phases>: Remove 'fix-tests, 'mpi-setup, use default 'check, keep 'sanity-check; add 'relax-requirements. [propagated-inputs]: Remove fenics; add python-pygments. [native-inputs]: Add python-setuptools and python-wheel. Change-Id: Ifbe63d794f592083f2e65366404f152fda9b3136	2025-03-23 00:12:27 +00:00
Sharlatan Hellseher	42db14eee2	gnu: python-tdda: Update to 2.2.17. ... * gnu/packages/python-science.scm (python-tdda): Update to 2.2.17. [arguments] <test-flags>: Skip one failing test. <phases>: Use default 'check, add 'fix-Python3.11-datetime.UTC. [native-inputs]: Add python-chardet, python-pyarrow, python-pytest, and python-rich. Change-Id: I9d268a8656f51484c3d6c59a86b7537e50f864dc	2025-03-23 00:12:27 +00:00
Sharlatan Hellseher	77a8c240e0	gnu: python-gpy: Move to machine-learning. ... * gnu/packages/python-science.scm (python-gpy): Move from here ... * gnu/packages/machine-learning.scm: ... to here. Change-Id: Id1c8574c166014c87ffa484ea84f798eb7f53844	2025-03-23 00:12:27 +00:00
Sharlatan Hellseher	6ac3bc012f	gnu: python-gpy: Update to 1.13.2. ... * gnu/packages/python-science.scm (python-gpy): Update to 1.13.2. Fix build and refresh package style. [native-inputs]: Add python-setuptools and python-wheel. Change-Id: I446821dace8cc9c99543f0940e400ca4fc081b08	2025-03-23 00:12:27 +00:00
Sharlatan Hellseher	aa06cb2819	gnu: python-pint: Move to python-science. ... * gnu/packages/python-xyz.scm (python-pint): Move from here ... * gnu/packages/python-science.scm: ... to here. Change-Id: Iabfce6ac788e01d42307a678979077cd61618693	2025-03-16 20:29:23 +00:00
Lars Bilke	f203028ef8	gnu: python-trimesh: Skip tests requiring network. ... * gnu/packages/python-science (python-trimesh)[arguments]<#:test-flags>: Skip network tests. Change-Id: I82389eca3baf14322875daa9aa33f74a1066c8e3 Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>	2025-03-03 14:53:43 +01:00
Efraim Flashner	162179e787	gnu: python-pandas: Skip some tests on 32bit systems. ... * gnu/packages/python-science.scm (python-pandas)[arguments]: Adjust the test-flags when not building on a 64bit system to skip some incompatible tests. Change-Id: Ic581cc6bf4ade2d92425c38df10bc45beaf4009e	2025-03-03 14:19:59 +02:00
Sharlatan Hellseher	3731cc5012	gnu: Add python-mpsplines. ... * gnu/packages/python-science.scm (python-mpsplines): New variable. Change-Id: I1ae05c5bff783f7716e578bfc01699a10d13c337	2025-02-28 22:44:04 +00:00
Sharlatan Hellseher	165c090c61	gnu: Add python-cmocean. ... * gnu/packages/python-science.scm (python-cmocean): New variable. Change-Id: I8b304c0280832f202714df278960493cbd3b12df	2025-02-28 22:44:03 +00:00
Sharlatan Hellseher	085c7d556f	gnu: python-mpl-scatter-density: Update to 0.8. ... * gnu/packages/python-science.scm (python-mpl-scatter-density): Update to 0.8. [source] <uri>: Adjust it as PyPI archive name has been changed upstream. Change-Id: Ic049ea153503cfa92c5d19b272afb00e64f7a28e	2025-02-28 22:44:01 +00:00
Ricardo Wurmus	9b2569e2c9	gnu: python-vaex-core: Update to 4.17.1. ... * gnu/packages/python-science.scm (python-vaex-core): Update to 4.17.1. [arguments]: Remove phase 'patch-for-pydantic. [native-inputs]: Use python-cython-3 instead of python-cython. Change-Id: I5fdb8f19b5d334058c5ece215a288ac4abd7647f	2025-02-27 13:58:23 +01:00
Ricardo Wurmus	0729d415e6	gnu: python-pandera: Use Pydantic 2. ... * gnu/packages/python-science.scm (python-pandera)[propagated-inputs]: Replace python-pydantic with python-pydantic-2. [arguments]: Disable one test. Change-Id: Ie222a484f4d8a540ffdf6db6da09e600723169d7	2025-02-27 09:59:50 +01:00
Ricardo Wurmus	2d5b2060e3	gnu: python-vaex-core: Use pyproject-build-system and Pydantic 2. ... * gnu/packages/python-science.scm (python-vaex-core)[build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase; add phase 'patch-for-pydantic. [propagated-inputs]: Replace python-pydantic with python-pydantic-2; add python-pydantic-settings. [native-inputs]: Add python-setuptools and python-wheel. Change-Id: I0e3d4d30940f55e234a5971431dc1c3fec2abce3	2025-02-27 09:59:50 +01:00
reza	14a7cb000c	gnu: python-pyvista: Update to 0.44.2. ... * gnu/packages/python-science.scm (python-pyvista): Update to 0.44.2 [build-system]: Change to pyproject-build-system. [native-inputs]: Add native-inputs for testing. [modify-phases]: Enable sanity-check and check phase, disable failing tests and vtk dependency check and redirect $HOME variable. Change-Id: I4293e99be12d096e639e47b8066116ba519909a8 Signed-off-by: Christopher Baines <mail@cbaines.net>	2025-02-25 10:57:51 +00:00
Efraim Flashner	66daf46b41	gnu: Fix some misspellings. ... Change-Id: I316652aff7418af4b8e83bea24638b1513f8aa97	2025-02-19 11:21:47 +02:00
Ricardo Wurmus	f1d34da912	gnu: python-plotnine: Update to 0.14.5. ... * gnu/packages/python-science.scm (python-plotnine): Update to 0.14.5. [arguments]: Disable more image tests; add phase 'pretend-version. Change-Id: I7ba5cc47ff93187785b0d8c2f5e294e0d08c9f54	2025-02-15 21:56:40 +01:00
Vinicius Monego	5ff5a2b2cf	gnu: Add python-imagehash. ... * gnu/packages/python-science.scm (python-imagehash): New variable. Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Change-Id: Ie773b4504d97ac2678e0776a27eb661d909fed47	2025-02-11 16:04:52 +00:00
Vinicius Monego	19f092e8e8	gnu: Add python-nibabel. ... * gnu/packages/python-science.scm (python-nibabel): New variable. Change-Id: I27d3841def6f360ae3996aacb787142bcfa92291 Signed-off-by: Andreas Enge <andreas@enge.fr>	2025-02-10 14:27:57 +01:00
Ricardo Wurmus	c467d3d292	gnu: python-pandas-1: Disable failing test. ... * gnu/packages/python-science.scm (python-pandas-1):[arguments]: Disable failing test_nat_comparisons. Change-Id: Ifdd3cfb244e03b9412c7caa458557ce3fd30e38a	2025-02-07 13:47:34 +01:00
Sharlatan Hellseher	a7a9c10d6e	gnu: python-unyt: Update to 3.0.3, fix build. ... * gnu/packages/python-science.scm (python-unyt): Update to 3.0.3. Fix build. Change-Id: Ic894ddfa982b9d41b40fc7e18149de099dd705f6	2025-01-28 22:28:37 +00:00
Ricardo Wurmus	6083002133	gnu: Add python-scikit-misc. ... * gnu/packages/python-science.scm (python-scikit-misc): New variable. Change-Id: I8fb3c46fe8a927e5d2fbd3222a423330e771379e	2025-01-28 21:27:13 +01:00
Sharlatan Hellseher	a35e975e16	gnu: python-deepdish: Fix indentation. ... * gnu/packages/python-science.scm (python-deepdish): Fix indentation. Change-Id: Idf8a0b5cdb9e371cb5d1f5f51f993da6209342d5	2025-01-27 21:22:32 +00:00
Sharlatan Hellseher	b17657ee86	gnu: python-deepdish: Update to 0.3.7-0.3f2dff7, fix build. ... * gnu/packages/python-science.scm (python-deepdish): Update to 0.3.7-0.3f2dff7. [source]: Swap to git checkout containing fixes for NumPy. [native-inputs]: Add python-pytest. Change-Id: Icbc8c0895bcac0bdfede65ac7b6006186c684a70	2025-01-27 21:22:32 +00:00
Sharlatan Hellseher	ab46e9fb53	gnu: python-pods: Update to 0.1.17. ... * gnu/packages/python-science.scm (python-pods): Update to 0.1.17. [native-inputs]: Remove python-setuptools and python-wheel; add python-poetry-core. Change-Id: I68db152ec47c54ffb92528863e9faedec11440ac	2025-01-27 21:22:31 +00:00
Sharlatan Hellseher	13b6dc1467	gnu: python-paramz: Add missing inputs, fix build. ... * gnu/packages/python-science.scm (python-paramz): [native-inputs]: Add python-setuptools and python-wheel. Change-Id: I3d33d04f523a214995e82d03d5bb1ce669962398	2025-01-27 21:22:20 +00:00
Felix Gruber	91cd3bc17f	gnu: python-pods: Fix build. ... * gnu/packages/python-science.scm (python-pods): Fix build. [native-inputs]: Add python-setuptools and python-wheel. Change-Id: I758d7a45e8e7baf436abe3c0b2ad92241c0bab48	2025-01-27 19:53:01 +08:00
Sharlatan Hellseher	8a490d8b7c	gnu: python-libneuroml: Update to 0.6.5. ... * gnu/packages/python-science.scm (python-libneuroml): Update to 0.6.5. Fix build. [propagated-inputs]: Remove python-six; add python-natsort and python-networkx. Change-Id: I750f90cebdeba46286239b18569300a2e4ce8c80	2025-01-20 21:38:04 +01:00
Ricardo Wurmus	4ea986c35c	gnu: python-modin: Update to 0.32.0. ... * gnu/packages/python-science.scm (python-modin): Update to 0.32.0. [build-system]: Use pyproject-build-system. [arguments]: Remove phase 'make-files-writable; disable one test; update custom 'check phase. [propagated-inputs]: Add python-s3fs. [native-inputs]: Add python-boto3 and python-wheel. Change-Id: I1d74013902e3387945586192b88c1e4fd8256733	2025-01-20 21:38:03 +01:00
Ricardo Wurmus	d8c294e880	gnu: python-pynetdicom: Update to 2.1.1. ... * gnu/packages/python-science.scm (python-pynetdicom): Update to 2.1.1. [native-inputs]: Add python-codespell, python-coverage, python-poetry-core, python-pytest-cov, python-pytest-xdist, python-sphinx, and python-sphinx-rtd-theme; remove python-pyfakefs, python-setuptools, and python-wheel. [propagated-inputs]: Add python-mypy, python-numpydoc, and python-pyfakefs. Change-Id: Ic0089df89cd34b50c31370581db7a6e88884199c	2025-01-20 21:38:03 +01:00
宋文武	c24968b12c	gnu: python-spin: Fix build. ... * gnu/packages/python-science.scm (python-spin)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: Ieeaa5f7186e51a16022910da89704e8cc282d935	2025-01-20 21:37:50 +01:00
Ricardo Wurmus	d1597a7b02	gnu: python-xarray-schema: Add missing inputs. ... * gnu/packages/python-science.scm (python-xarray-schema)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: I7cecc17468f94c9987ed349b0dd0d319e175e399	2025-01-20 21:37:47 +01:00
Ricardo Wurmus	7b20f39e19	gnu: python-xarray-datatree: Add missing inputs. ... * gnu/packages/python-science.scm (python-xarray-datatree)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: I5c2d5ec44b13c82e7400687accccf81427aa0da9	2025-01-20 21:37:47 +01:00
Ricardo Wurmus	b221e34953	gnu: python-fastcluster: Add missing inputs. ... * gnu/packages/python-science.scm (python-fastcluster)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: I2fa034054f5183e04c2f1e673f841f07799a7b94	2025-01-20 21:37:39 +01:00
Ricardo Wurmus	c43c0d06e3	gnu: python-cvxpy: Add missing input. ... * gnu/packages/python-science.scm (python-cvxpy)[native-inputs]: Add python-wheel. Change-Id: I66f4f504a0a4101abc845b7b7d0a0fccbd6b91b9	2025-01-20 21:37:39 +01:00
Ricardo Wurmus	f874d80a36	gnu: python-scikit-survival: Add missing input. ... * gnu/packages/python-science.scm (python-scikit-survival)[native-inputs]: Add python-setuptools. Change-Id: I52e98c787cec226590f21c98e4287a41fb41f3d3	2025-01-20 21:37:39 +01:00
Ricardo Wurmus	440cd7d571	gnu: python-qdldl: Add missing input. ... * gnu/packages/python-science.scm (python-qdldl)[native-inputs]: Add python-wheel. Change-Id: I6bca560b20a9c259eae95c09edcf10ead685ec21	2025-01-20 21:37:39 +01:00
Ricardo Wurmus	322e03c807	gnu: python-osqp: Add missing inputs. ... * gnu/packages/python-science.scm (python-osqp)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: Ief43d97442a98935dea1499c67e022e9beb5359e	2025-01-20 21:37:39 +01:00
Ricardo Wurmus	7b70b21379	gnu: python-scikit-fuzzy: Add missing inputs. ... * gnu/packages/python-science.scm (python-scikit-fuzzy)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: Idbaf5fa622b3584f8fd348ec0783605936d3bf41	2025-01-20 21:37:39 +01:00
Ricardo Wurmus	b752a03e8b	gnu: python-scikit-allel: Update to 1.3.13. ... * gnu/packages/python-science.scm (python-scikit-allel): Update to 1.3.13. [propagated-inputs]: Remove python-click. [native-inputs]: Remove python-scipy. Change-Id: I3c29bd3d9f87d0866da747c344740bad71cae1c3	2025-01-20 21:37:39 +01:00