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Author SHA1 Message Date
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
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