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Author SHA1 Message Date
Sharlatan Hellseher
6bba63234b
gnu: python-vaex-core: Relax upper limit for dask version. 
* gnu/packages/python-science.scm (python-vaex-core) [arguments]
<phases>: Add 'relax-requirement.

Change-Id: Iae12fbafc6d235c99df4781521cb4fac965f7f3f
 2025-07-06 18:44:04 +01:00
Sharlatan Hellseher
0955a504b5
gnu: Add python-narwhals. 
* gnu/packages/python-science.scm (python-narwhals): New variable.

Change-Id: Iae0e6a3260ffb066172377c464a645bcb126b17b
 2025-07-06 18:44:04 +01:00
Sharlatan Hellseher
0fb7ae747f
gnu: python-scikit-image: Fix tests. 
In some cases there could be an issue to test compiled Cython library
which is not available in local checkout working directory.  This change
is inspired by the way NixOS packages scikit-image and run tests from
the output with "--pyargs" option where compiled library is available.

See: <https://github.com/NixOS/nixpkgs/blob/nixos-25.05/\
pkgs/development/python-modules/scikit-image/default.nix>.

* gnu/packages/python-science.scm (python-scikit-image) [arguments]
<test-flags>: Run tests from {#$output}, add "--pyargs" option and skip
one more problematic test.
<phases>: Use default 'check; add 'pre-check and post-check.

Change-Id: I60f58359f59b371854f4963e2f7c65c9221a0924
 2025-07-06 18:44:04 +01:00
Benoit Martin
d7c5315913
gnu: python-distributed: Update to 2024.12.1. 
* gnu/packages/python-science.scm (python-distributed): Update to 2024.12.1.

Change-Id: Ia557e7d87e48a709298bf7024ee01b08098f5842
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-06 18:44:04 +01:00
Benoit Martin
3cfcbae75a
gnu: python-dask-expr: Update to 1.1.21. 
* gnu/packages/python-science.scm (python-dask-expr): Update to 1.1.21.

Change-Id: Iaee50368ffafc473164865249e2a51732b1ea54f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-06 18:44:04 +01:00
Sharlatan Hellseher
fe3159ce7a
gnu: python-plotly: Move to python-science. 
This package is not related to Graph at all and imported by
bioinformatics and astronomy modules only which are Science disciplines.
This change moves it closer to related packages and preserves copyright
header records extracted from git log.

* gnu/packages/graph.scm (python-plotly): Move from here ...
* gnu/packages/python-science.scm: ... to here.

Change-Id: I5544ebdf1f545b2d7740dd56cab2d04bbe9d7715
 2025-07-06 00:44:38 +01:00
Sharlatan Hellseher
a03d6d1bd6
gnu: python-distributed: Move up. 
* gnu/packages/python-science.scm (python-distributed): Sort variable
alphabetically.

Change-Id: I6b0b6ab2932b7cc1edf6097a6387ee633e537d88
 2025-06-30 13:35:10 +01:00
Sharlatan Hellseher
26a8b63ec3
gnu: packages/python-science: Sort packages. 
* gnu/packages/python-science.scm: (python-deepdish, python-modin,
python-msgpack-numpy, python-pyamg, python-pyet, python-vaex-core): Sort
variables alphabetically.

Change-Id: I37db89f459242c6bfed8dce559539f8249c67192
 2025-06-30 00:00:45 +01:00
Sharlatan Hellseher
638777f627
gnu: packages/python-science: Sort packages. 
* gnu/packages/python-science.scm (python-bottleneck, python-dask-expr,
python-mpsplines, python-salib, python-unyt, python-vedo): Sort
variables alphabetically.

Change-Id: I767f6959dd5727cee22e07d49de28af244985c22
 2025-06-30 00:00:45 +01:00
Sharlatan Hellseher
0f10ad2f3d
gnu: packages/python-science: Sort packages. 
* gnu/packages/python-science.scm: (python-climin, python-fastcluster,
python-libneuroml, python-nibabel, python-opt-einsum, python-pynetdicom,
python-ruffus, python-simple-pid): Sort variables alphabetically.

Change-Id: Ic2696630a49868c5a657dea3a3be353fd50d7a88
 2025-06-30 00:00:45 +01:00
Sharlatan Hellseher
ef5cc8ea79
gnu: packages/python-science: Sort packages. 
* gnu/packages/python-science.scm: (python-asap3, python-baycomp,
python-clarabel, python-hist, python-numpoly, python-particle,
python-uhi, python-vector): Sort variables alphabetically.

Change-Id: Idd202a03a518774d204de6292d74fbe53ea5761e
 2025-06-30 00:00:45 +01:00
Sharlatan Hellseher
4f2c0a5638
gnu: packages/python-science: Sort packages. 
*gnu/packages/python-science.scm (python-ase, python-geosketch,
python-histoprint, python-meshzoo, python-ndindex, python-scipy,
python-traittypes, python-upsetplot): Sort variables alphabetically.

Change-Id: I1fc194b17e3babf084c961bf09596d27e834fd6a
 2025-06-30 00:00:45 +01:00
Sharlatan Hellseher
f1c56803ea
gnu: packages/python-science: Sort packages. 
* gnu/packages/python-science.scm: (python-aplus,
python-boost-histogram, python-corner, python-decaylanguage,
python-fast-histogram, python-hepunits, python-mpl-scatter-density,
python-numpy-groupies): Sort variables alphabetically.

Change-Id: I026c5a409ebab46c844db7ffe17aa9f5293c36ea
 2025-06-30 00:00:36 +01:00
Vinicius Monego
8696eca5c0
gnu: python-pyjanitor: Update to 0.31.0. 
* gnu/packages/python-science.scm (python-pyjanitor): Update to 0.31.0.
[arguments]<#:test-flags>: Skip tests depending on Polars. Enable
previously failing test.
<#:phases>: Delete unnecessary phase 'pandas-compat'.

Change-Id: I2991e06fafea2928bb6ea45c42624bf372da2eba
 2025-06-22 12:41:00 -03:00
Vinicius Monego
e660638d0d
gnu: python-pingouin: Update to 0.5.5. 
* gnu/packages/python-science.scm (python-pingouin): Update to 0.5.5.
[arguments]<#:test-flags>: Enable previously failing test. Skip two more
failing tests.
<#:phases>: Delete unnecessary phases 'loosen-requirements',
'remove-outdated-check', 'sklearn-compatibility'.

Change-Id: Iac44747d65c9be52831ae792a24b9cc5604c54dc
 2025-06-22 12:41:00 -03:00
Vinicius Monego
d32e619d47
gnu: python-simple-pid: Update to 2.0.1. 
* gnu/packages/python-science.scm (python-simple-pid): Update to 2.0.1.
[source]: Update URI.
[build-system]: Use pyproject-build-system.
[arguments]<#:phases>: Do not override the 'check' phase.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.

Change-Id: I26c7b3097d30ac067a370c8a3a0600779d13efb6
 2025-06-22 12:41:00 -03:00
Vinicius Monego
4a38059258
gnu: python-pandas-flavor: Update to 0.7.0. 
* gnu/packages/python-science.scm (python-pandas-flavor): Update to
0.7.0.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-pytest.

Change-Id: Ie582c778d84b342eab41f8bc88f2c4bb410bbbb6
 2025-06-22 12:40:59 -03:00
Vinicius Monego
5b983cd239
gnu: python-baycomp: Update to 1.0.3. 
* gnu/packages/python-science.scm (python-baycomp): Update to 1.0.3.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.

Change-Id: I2249fc981a91ebc175a5e0ff221bb6243126fb6f
 2025-06-22 12:40:59 -03:00
Nguyễn Gia Phong
c8218094c4
gnu: Add python-apted. 
* gnu/packages/python-science.scm (python-apted): New variable.

Change-Id: Ifd79f12b6be4d593106805f714a6545226e59479
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-14 17:19:45 +01:00
Mark Walker
e9b8d0653e
gnu: Add python-pyzx. 
* gnu/packages/python-science.scm (python-pyzx): New variable.

Change-Id: I69895a9deb5739db9c0d5e793e3f864c800f4504
Reviewed-by: @lilyp
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-11 23:13:34 +01:00
Sharlatan Hellseher
74d1cf2583
gnu: Move all snakemake variants to python-science. 
* gnu/packages/python-xyz.scm (snakemake-5, snakemake-6, snakemake-7):
Move from here ...
* gnu/packages/python-science.scm: ... to here.

Change-Id: Ia771b316049f375183025e7617e6d0ddf06f99ff
 2025-05-26 17:36:37 +01:00
Danny Milosavljevic
27b615acbe
gnu: Add python-asap3@3.13.7. 
* gnu/packages/python-science.scm (python-asap3): New variable.

Change-Id: Idea83eaf0475f14aa2ea443c81463ab8279694b6
 2025-05-25 21:25:30 +02:00
Danny Milosavljevic
1e9def3dac
gnu: Add python-ase@3.25.0. 
* gnu/packages/python-science.scm (python-ase): New variable.

Change-Id: If868c0e83cf04f9d0c3108304ec77619e28ee2d4
 2025-05-25 21:24:45 +02:00
Sharlatan Hellseher
5a7170e7ed
gnu: python-einops: Update to 0.8.1. 
* gnu/packages/python-science.scm (python-einops): Update to 0.8.1.
[native-inputs]: Remove jupyter.

Change-Id: I2d5c710990a77ca0fef480eaed4b59da6a10db27
 2025-05-08 12:05:04 +01:00
Sharlatan Hellseher
32d17c83e0
gnu: python-adjusttext: Move to python-science. 
* gnu/packages/python-xyz.scm (python-adjusttext): Move from here ...
* gnu/packages/python-science.scm: ... to here.

Change-Id: If8c5fa89736dbf8ae29169fb317d43d2c2fbd682
 2025-05-08 11:06:39 +01:00
Vinicius Monego
f72ce07fa3
gnu: Add python-vector. 
* gnu/packages/python-science.scm (python-vector): New variable.

Change-Id: I77d72b0c18a0bc215cb2198ce5447e587b13d0fe
 2025-05-04 08:16:28 -03:00
Vinicius Monego
c1c7d09bf3
gnu: Add python-decaylanguage. 
* gnu/packages/python-science.scm (python-decaylanguage): New variable.

Change-Id: I5c709016f80b19cef22105bff42ca62b8f384f1b
 2025-05-04 08:16:28 -03:00
Vinicius Monego
dae5362436
gnu: Add python-particle. 
* gnu/packages/python-science.scm (python-particle): New variable.

Change-Id: Ib2462e25aadba797532c005a3b4d4e4a238a611e
 2025-05-04 08:16:28 -03:00
Vinicius Monego
1c17f30d9b
gnu: Add python-hepunits. 
* gnu/packages/python-science.scm (python-hepunits): New variable.

Change-Id: I174495c4fdacd21491e9e7d5abdd7d5dd0e5ffe8
 2025-05-04 08:16:28 -03:00
Vinicius Monego
d08134c28e
gnu: Add python-hist. 
* gnu/packages/python-science.scm (python-hist): New variable.

Change-Id: Ia3495b6d94a620b797318ffce162aa1d58e79049
 2025-05-04 08:16:27 -03:00
Vinicius Monego
f534495d41
gnu: Add python-histoprint. 
* gnu/packages/python-science.scm (python-histoprint): New variable.

Change-Id: I1ace11116c39e2c803afd10849c107c3f232273e
 2025-05-04 08:16:27 -03:00
Vinicius Monego
36de5a4047
gnu: Add python-uhi. 
* gnu/packages/python-science.scm (python-uhi): New variable.

Change-Id: I12e802cfc9dd6473cac9657dc477e470238f1bbc
 2025-05-04 08:16:27 -03:00
Vinicius Monego
eb6a1d9317
gnu: Add python-boost-histogram. 
* gnu/packages/python-science.scm (python-boost-histogram): New variable.

Change-Id: I91e73a0a3e3a698197b2d309bd5bdf388fd2697a
 2025-05-04 08:16:27 -03:00
Vinicius Monego
a786cd333c
gnu: python-scikit-build-core: Update to 0.11.2. 
* gnu/packages/python-science.scm (python-scikit-build-core): Update to
0.11.2.

Change-Id: I66d04ba5ed89d3a9eb57df1e9491b8170d5b1571
 2025-05-04 08:16:27 -03:00
Sharlatan Hellseher
3e055916bf
gnu: python-pyqtgraph: Move to python-science. 
* gnu/packages/python-xyz.scm (python-pyqtgraph): Move from here ...
* gnu/packages/python-science.scm: ... to here.

Change-Id: I3de3c6a71fb2c5c49b76e03a026eae7deaa55840
 2025-04-28 21:58:59 +01:00
Sharlatan Hellseher
201d30fb4f
gnu: python-pandera: Fix tests. 
* gnu/packages/python-science.scm (python-pandera) [source] <snippet>:
Remove tests deletion and ignore them with pytest options which are
working now.
[arguments] <test-flags> Skip some more tests; run tests in parallel up
to 8 thread, supported upstream.
[propagated-inputs]: Remove python-hypothesis; add
python-hypothesis-next and python-modin.
[native-inputs]: Add python-pytest-xdist.

Change-Id: I45482203519ceb2208a330d91c07d12b65e6ee53
 2025-04-24 12:41:43 +01:00
Sharlatan Hellseher
897d8a0d20
gnu: python-modin: Fix tests. 
* gnu/packages/python-science.scm (python-modin) [arguments]
<test-flags>: Run test in up to 8 threads to improve performance,
supported upstream.
[native-inputs]: Remove python-coverage.

Change-Id: Id298ca7ae204f87fc7b421f6dc2f80959c4c4f85
 2025-04-24 12:41:43 +01:00
Sharlatan Hellseher
233a3e9191
gnu: snakemake: Move inputs to propagated-inputs. 
* gnu/packages/python-science.scm (snakemake): Swap INPUTS to
PROPAGATED-INPUTS as the package may be included in others.

Change-Id: I034d8b18a6f4d145bf7b08584b73a5abd19f955e
 2025-04-19 10:17:34 +01:00
Nicolas Graves
6dd0d0fd90
gnu: Add snakemake. 
* gnu/packages/python-science.scm (snakemake): New variable.

Change-Id: Id61c7955684f5186b9dc884f0c9de4ec73f766ea
Signed-off-by: Steve George <steve@futurile.net>
 2025-04-16 11:46:36 +02:00
Nicolas Graves
5ae21052de
gnu: Add python-snakemake-interface-storage-plugins. 
* gnu/packages/python-science.scm
(python-snakemake-interface-storage-plugins): New variable.

Change-Id: Ie74edfdc2535f7f26f0c6210a274dfc351336129
Signed-off-by: Steve George <steve@futurile.net>
 2025-04-16 11:46:35 +02:00
Nicolas Graves
b6c69075cb
gnu: Add python-snakemake-interface-software-deployment-plugins. 
* gnu/packages/python-science.scm
(python-snakemake-interface-software-deployment-plugins): New variable.

Change-Id: Ia3f6beed3a3ea02607645ca127be52f328b429bb
Signed-off-by: Steve George <steve@futurile.net>
 2025-04-16 11:46:35 +02:00
Nicolas Graves
499eda24b3
gnu: Add python-snakemake-interface-report-plugins. 
* gnu/packages/python-science.scm
(python-snakemake-interface-report-plugins): New variable.

Change-Id: I8705ba63df668d46ffda575b18ee97bb65acdc6c
Signed-off-by: Steve George <steve@futurile.net>
 2025-04-16 11:46:35 +02:00
Nicolas Graves
ef1180807c
gnu: Add python-snakemake-interface-executor-plugins. 
* gnu/packages/python-science.scm
(python-snakemake-interface-executor-plugins): New variable.

Change-Id: I6bd9c6aec7293b8412c20dac04f82d867400d71c
Signed-off-by: Steve George <steve@futurile.net>
 2025-04-16 11:46:35 +02:00
Nicolas Graves
18ef23a5ad
gnu: Add python-snakemake-interface-common. 
* gnu/packages/python-science.scm (python-snakemake-interface-common):
New variable.

Change-Id: Iaac3acb7f57c3b6aedda7fe48daccbd952faddd5
Signed-off-by: Steve George <steve@futurile.net>
 2025-04-16 11:46:35 +02:00
Sharlatan Hellseher
4c08d7037a
gnu: python-pyglm: Move to maths. 
* gnu/packages/python-science.scm (python-pyglm): Move from here ...
* gnu/packages/maths.scm: ... to here.

* gnu/packages/gnome-xyz.scm: Add (gnu packages maths); remove (gnu
packages python-science).

Change-Id: I49ab732c1070210d005f8753c1e894c9abc3ee8b
 2025-04-16 11:46:32 +02:00
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