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181 Commits

Author SHA1 Message Date
Maxim Cournoyer
05eb9349e3
gnu: Add python-pods. 
* gnu/packages/python-science.scm (python-pods): New variable.

Change-Id: I9044baaa750ee9cb7411e41dcee1df17b57741db
 2024-03-31 21:25:51 -04:00
Sharlatan Hellseher
25d66b55c2
gnu: python-distributed: Disable parallel tests. 
As seen in <https://ci.guix.gnu.org/build/3708961/log/raw>, parallel
tests introduced package build regression.

* gnu/packages/python-science.scm (python-distributed) [arguments]
<#:test-flags>: Disable parallel tests.
[native-inputs]: Remove python-pytest-xdist.

Change-Id: I3a04098604fa03ab91ceb228dd70c34c3d84db78
 2024-03-29 19:08:08 +00:00
Sharlatan Hellseher
249f0a9c9f
gnu: python-distributed: Speed up tests. 
* gnu/packages/python-science.scm (python-distributed) [arguments]
<#:test-flags>: Add option to run tests in parallel. Disable 3 more
flaky tests.
[native-inputs]: Add python-pytest-xdist. Sort alphabetically.

Change-Id: I588c1a1dc82e3208cc1eeeefbdc58fb080775ac0
 2024-03-29 15:08:07 +00:00
nafkhamdc
d616e85ac8
gnu: python-upsetplot: Update to 0.9.0. 
* gnu/packages/python-science.scm (python-upsetplot): Update to 0.9.0.
[source]: Remove obsolete snippet.
[arguments]: Remove custom check phase.
[build-system]: Use pyproject-build-system.

Change-Id: I68bcd6840577a12594e491e9fd5e114f9261f6c7
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2024-03-28 13:37:20 +01:00
TimotheeMathieu
9474e64b09
gnu: Add python-scikit-opt. 
* gnu/packages/python-science.scm (python-scikit-opt): New variable.

Change-Id: I47d6b35d9658a37a242b4db61d293fa7efd33802
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-02-10 22:51:59 +01:00
Sharlatan Hellseher
5729b2b352
gnu: python-traittypes: Simplify package. 
* gnu/packages/python-science.scm (python-traittypes) [build-system]:
Swap to pyproject-build-system.
[arguments]: Move excluded tests to <#:test-flags>. Use standard 'check
phase.

Change-Id: I4cab0c94036a7e5f0851edf2833dfac2f675d2a0
 2024-02-06 21:11:40 +00:00
Sharlatan Hellseher
5dee582c13
gnu: python-pynrrd: Update to 1.0.0. 
* gnu/packages/python-science.scm (python-pynrrd): Update to 1.0.0.
[arguments]: Keep 'ensure-no-mtimes-pre-1980 phase as it's building with
it successfully.
[propagated-inputs]: Add python-nptyping and python-typing-extensions.

Change-Id: Ic4dcd0825e71d3eb4acd39694bee9e22e8485f9f
 2024-02-06 19:56:05 +00:00
Sharlatan Hellseher
ac18dfc675
gnu: python-pynrrd: Improve description. 
* gnu/packages/python-science.scm (python-pynrrd) [description]: Add
definition of NRRD.

Change-Id: I0335df0eb4be600d81799da64374ddfb49b06720
 2024-02-06 19:49:50 +00:00
Antero Mejr
36f5db706c
gnu: Add python-pynrrd. 
* gnu/packages/python-science.scm (python-pynrrd): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-02-06 19:40:17 +00:00
Wiktor Żelazny
a879dd8b36
gnu: Add python-pandarallel. 
* gnu/packages/python-science.scm (python-pandarallel): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-02-01 21:16:14 +00:00
Efraim Flashner
9f1ab898c3
gnu: python-scipy: Enable building on more architectures. 
* gnu/packages/python-science.scm (python-scipy)[propagated-inputs]:
Only include python-jupytext on systems where it is supported.

Change-Id: Ic085094e4e3977e4c0698e8c03de09ee8e70f144
 2024-01-30 13:43:32 +02:00
Troy Figiel
cde0adaacd
gnu: Add python-pyjanitor. 
* gnu/packages/python-science.scm (python-pyjanitor): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-29 21:40:59 +00:00
Troy Figiel
343f4f1d70
gnu: Add python-unyt. 
* gnu/packages/python-science.scm (python-unyt): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-29 21:12:12 +00:00
Sharlatan Hellseher
77a07a968f
gnu: python-pyamg: Regenerate bundled files. 
* gnu/packages/python-science.scm (python-pyamg) [source]: Delete
auto-generated files.
[arguments] <#:phases>: Add 'amg-core-bind-them phase to
re-generate *_bind.cpp files deleted in snippet.
[native-inputs]: Add python-cppheaderparser and python-pyyaml.
[description]: Improve style, omit implementation details.

Change-Id: I6f68914cd912e6f4592e51c21b129847e73be847
 2024-01-28 22:44:30 +00:00
Sharlatan Hellseher
42c7b50e23
gnu: python-trimesh: Enable tests. 
* gnu/packages/python-science.scm (python-trimesh): Enable tests and
apply new package style.
[source]: Use git checkout which has working test suit.
[arguments] <#:test-flags>: Disable tests requiring optional Python
modules.
[propagated-inputs]: Add python-chardet, python-colorlog python-httpx
python-jsonschema python-lxml python-networkx python-pillow
python-requests python-rtree python-scipy python-setuptools
python-shapely python-sympy and python-xxhash.

Change-Id: I1aa363053c2d736bc44b8f9071c637256cc2d952
 2024-01-28 22:39:22 +00:00
Sharlatan Hellseher
a01afbd300
gnu: python-trimesh: Update to 4.0.10. 
* gnu/packages/python-science.scm (python-trimesh): Update to 4.0.10.
[build-system]: Swap to pyproject-build-system.

Change-Id: I757b4c27db9969d42021434883a057debbbc83fd
 2024-01-28 22:38:05 +00:00
Vinicius Monego
a4c9766108
gnu: python-xarray-einstats: Update to 0.7.0. 
* gnu/packages/python-science.scm (python-xarray-einstats): Update to 0.7.0.

Change-Id: Iddd1fca8c37f05a928d20b90f9f95814f31435b2
 2024-01-24 20:02:51 -03:00
Ricardo Wurmus
afd0fe50b0
gnu: python-pyts: Update to 0.13.0. 
* gnu/packages/python-science.scm (python-pyts): Update to 0.13.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; enable all tests.
[propagated-inputs]: Remove python-matplotlib.

Change-Id: Iafcc047d8bb14e1eef514fd92aa53f8fda38eab0
 2024-01-24 11:34:35 +01:00
Sharlatan Hellseher
3419c216b4
gnu: python-pydicom: Update to 2.4.4. 
* gnu/packages/python-science.scm (python-pydicom): Update to 2.4.4.

Change-Id: I996115fb3bdf0bd61d2b2dcdb2500b31ce104597
 2024-01-23 23:57:32 +00:00
Sharlatan Hellseher
b537437af7
gnu: python-pydicom: Simplify package style. 
* gnu/packages/python-science.scm (python-pydicom)[build-system]: Swap
to pyproject-build-system.
[description]: Simplify wording, indent.

Change-Id: I7ef413ea2da6cbb83eb33424c559f7ac5ed549cb
 2024-01-23 23:54:44 +00:00
Sharlatan Hellseher
5a616cc14b
gnu: python-pynetdicom: Simplify package style. 
* gnu/package/python-science.scm (python-pynetdicom)[build-system]: Swap
to pyproject-build-system.
[description]: Simplify wording, indent.

Change-Id: If4e80d06edb0080685d0695f30abc2f9db669f45
 2024-01-23 23:51:48 +00:00
Antero Mejr
e71abbc643
gnu: Add python-pynetdicom. 
* gnu/packages/python-science.scm (python-pynetdicom): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-23 23:38:02 +00:00
Ricardo Wurmus
994817bfdc
gnu: python-scipy: Update to 1.12.0. 
* gnu/packages/python-science.scm (python-scipy): Update to 1.12.0.
[propagated-inputs]: Add python-jupytext, python-mpmath, python-mypy,
python-numpydoc, python-pydata-sphinx-theme, python-pydevtool,
python-rich-click, python-sphinx, python-threadpoolctl, and
python-typing-extensions; remove python-pyparsing.
[native-inputs]: Add python-hypothesis, python-pycodestyle, python-pytest-cov,
and python-pytest-xdist; remove python-threadpoolctl.

Change-Id: I81a4831e3d94c58416f7d35ec47de90370b88210
 2024-01-23 13:36:47 +01:00
Troy Figiel
6f6cfb8365
gnu: python-tdda: Remove relax-requirements phase. 
* gnu/packages/python-science.scm (python-tdda)[arguments]<#:phases>: Remove relax-requirements phase.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-22 21:48:28 +00:00
Sharlatan Hellseher
b9e74d092d
gnu: python-scikit-fem: Update to 9.0.1. 
* gnu/packages/python-science.scm (python-scikit-fem): Update to 9.0.1.
[arguments]<#:test-flags>: Drop it to activate all tests.
[native-inputs]: Add python-autograd, python-pyamg, and python-shapely.

Change-Id: Ic4706196026bd5756b4db8230b15efacdca7d463
 2024-01-21 17:40:18 +00:00
Felix Gruber
5f93aa182a
gnu: Add python-pyamg. 
* gnu/packages/python-science.scm (python-pyamg): New variable.

Change-Id: Ibf39fecd14d4e6fd72078b217737e5e5cbbf2321
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-21 17:18:29 +00:00
Troy Figiel
e1d3be4113
gnu: python-pandera: Fix build. 
* gnu/packages/python-science.scm (python-pandera): Fix build.
[source]: Delete tests/modin directory.
[native-inputs]: Remove python-modin.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-20 22:03:03 +00:00
Troy Figiel
7c540ed106
gnu: python-pandas-stubs: Update to 1.5.3.230321. 
* gnu/packages/python-science.scm (python-pandas-stubs): Update to
1.5.3.230321.
[arguments]<#:test-flags>: Ignore tests that require a version of
python-pyarrow with ORC integration.
[native-inputs]: Add python-odfpy.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-20 22:02:49 +00:00
Troy Figiel
0118fe6f85
gnu: python-plotnine: Reformat with guix style. 
* gnu/packages/python-science.scm (python-plotnine): Reformat with guix style.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-18 21:04:21 +00:00
Troy Figiel
662ae5eac2
gnu: python-plotnine: Fix build. 
* gnu/packages/python-science.scm (python-plotnine): Fix build.
[arguments]<#:test-flags>: Add test_custom_shape to ignored tests.

Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-18 20:56:59 +00:00
Troy Figiel
dac977ea4e
gnu: Add python-pandera. 
* gnu/packages/python-science.scm (python-pandera): New variable.
 2024-01-17 11:18:00 +01:00
Troy Figiel
23cb6187f6
gnu: Add python-pandas-stubs. 
* gnu/packages/python-science.scm (python-pandas-stubs): New variable.
 2024-01-17 11:18:00 +01:00
Sharlatan Hellseher
d79fd9adc3
gnu: python-deepdish: Fix build. 
* gnu/packages/python-science.scm (python-deepdish): Fix build.
[build-system]: Swap to pyproject-build-system.
[arguments]<#:test-flags>: Silent failing tests.

Change-Id: I4c4df66fc80434aaf5b95a7a62b83e0c1c02a4c6
 2024-01-16 21:43:30 +00:00
Ricardo Wurmus
e31e5928ae
gnu: python-xarray: Update to 2023.12.0. 
* gnu/packages/python-science.scm (python-xarray): Update to 2023.12.0.
[arguments]: Ignore one test file.
[propagated-inputs]: Add python-packaging.

Change-Id: I6b70f59670f7bc8b56787fe3436579db8ac113bb
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
a8c1d812a0
gnu: python-pandas: Update to 1.5.3. 
* gnu/packages/python-science.scm (python-pandas): Update to 1.5.3.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-expression; move test flags to #:test-flags; add phase
'patch-build-system; fix substitution of "which" executable; remove
'enable-parallel-build; remove custom 'check phase; add 'pre-check phase.
[propagated-inputs]: Add python-matplotlib.
[native-inputs]: Replace python-cython with python-cython-0.29.35.

Change-Id: I9d09971f707b925f469e29be67fe040c181314ff
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
998df6e047
gnu: python-scikit-optimize: Make compatible with latest sklearn. 
* gnu/packages/python-science.scm (python-scikit-optimize)[source]: Add
snippet to fix outdated use of "max_features" option.

Change-Id: I4272ffc82b4951315b74b4adee27527e8d513fca
 2024-01-16 12:44:36 +01:00
Ricardo Wurmus
e2c76bdd83
gnu: python-scikit-image: Update to 0.22.0. 
* gnu/packages/python-science.scm (python-scikit-image): Update to 0.22.0.
[source]: Fetch from git repository.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-expression; remove custom 'build phase; simplify 'check
phase; enable all tests.
[propagated-inputs]: Add python-lazy-loader.
[native-inputs]: Add meson-python, python-numpydoc, python-packaging, and
python-wheel.

Change-Id: I00ede026a7941eae36157106f753a21fb64099c3
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
accd091fff
gnu: python-scipy: Update to 1.11.4. 
* gnu/packages/python-science.scm (python-scipy): Update to 1.11.4.
[arguments]: Use mesonpy backend.
[inputs]: Replace pybind11 with pybind11-2.10.
[native-inputs]: Add python-click, python-doit, python-pooch, and
python-pydevtool; replace python-cython with python-cython-0.29.35.

Change-Id: I4b26e1b6382899bba24f84461f154e97765e08f5
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
6c453e04b8
gnu: python-distributed: Disable breaking test. 
This test times out since the merge of the mesa-updates branch.

* gnu/packages/python-science.scm (python-distributed)[arguments]: Disable
test_tell_workers_when_peers_have_left.

Change-Id: Ib65b971a3a821ea13d36a4be60658ffc366ca6ac
 2024-01-10 20:35:28 +01:00
Ricardo Wurmus
0ec25720ab
gnu: python-vaex-core: Add missing input. 
* gnu/packages/python-science.scm (python-vaex-core)[propagated-inputs]: Add
python-click.

Change-Id: Id91e925832ed107d5b346ba513a9825dc31481f6
 2023-12-15 16:13:14 +01:00
Vinicius Monego
b2d433d485
gnu: python-pytensor: Update to 2.18.1. 
* gnu/packages/python-science.scm (python-pytensor): Update to 2.18.1.

Change-Id: I7992d8a00c378c008995df3d026c3e05c235ae6d
 2023-12-05 16:41:52 -03:00
Efraim Flashner
504e621445
gnu: python-gpy: Adjust for newer python. 
* gnu/packages/python-science.scm (python-gpy)[source]: Add snippet to
adjust python module imports.

Change-Id: I0772febb97d75e0a0caa331913c9e7453d11e70d
 2023-12-05 13:43:42 +02:00
Felix Gruber
8803100072
gnu: Add python-pyfma. 
* gnu/packages/python-science.scm (python-pyfma): New variable.

Change-Id: I354d3d56f2799c8c9ac9b868fcacbf88dcc5c25d
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-12-04 22:26:37 +01:00
Felix Gruber
f76ffc3ea6
gnu: Add python-meshzoo. 
* gnu/packages/python-science.scm (python-meshzoo): New variable.

Change-Id: Ia41d62ebd6c4cb3c22ebe0668c36279a9ca191ac
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-12-04 22:26:37 +01:00
Troy Figiel
416ae9ad89
gnu: Add python-tdda. 
* gnu/packages/python-science.scm (python-tdda): New variable.

Change-Id: I456aa236b3348e5b990289d8a381c2d5276a12f1
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-11-15 18:29:38 +01:00
Vinicius Monego
43d9fa0802
gnu: python-pytensor: Update to 2.17.3. 
* gnu/packages/python-science.scm (python-pytensor): Update to 2.17.3.

Change-Id: I2843aca1df4d43883bf643e6e363bd3700202c45
 2023-11-03 19:25:36 -03:00
Vinicius Monego
a7d56852e3
gnu: Add python-salib. 
* gnu/packages/python-science.scm (python-salib): New variable.
 2023-11-03 19:25:35 -03:00
Paul A. Patience
d07e75a4ce
gnu: python-trimesh: Update to 3.23.5. 
* gnu/packages/python-science.scm (python-trimesh): Update to 3.23.5.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-10-17 10:26:55 +01:00
Paul A. Patience
4aa6a924b2
gnu: python-pyvista: Update to 0.42.3. 
* gnu/packages/python-science.scm (python-pyvista): Update to 0.42.3.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-10-17 10:26:23 +01:00
Nicolas Graves
e9c0bb0341
gnu: python-distributed: Disable failing tests. 
* gnu/packages/python-science.scm (python-distributed): Disable failing tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-10-08 23:43:50 +02:00