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Author SHA1 Message Date
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
Ricardo Wurmus
38065d8104
gnu: python-scikit-opt: Add missing input. 
* gnu/packages/python-science.scm (python-scikit-opt)[native-inputs]: Add
python-setuptools.

Change-Id: Id14e3964257e250c1ba597c6d8fe1a0410fa475f
 2025-01-20 21:37:29 +01:00
Ricardo Wurmus
1fd5f28306
gnu: python-traittypes: Fix tests. 
* gnu/packages/python-science.scm (python-traittypes)[arguments]: Add phase
'numpy-compatibility.

Change-Id: I41d55d65d0dafd44029de38b3044d9fad378db50
 2025-01-20 21:37:28 +01:00
Ricardo Wurmus
aa0d8b7e6c
gnu: python-pandas-2: Restrict number of test processes. 
* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Restrict to at
most four processes.

Change-Id: I8ee4cb29ad922e9b853515b5f0e8f8aabca52c92
 2025-01-20 21:37:24 +01:00
Ricardo Wurmus
0a7a2b24d3
gnu: python-pandas-2: Remove X. 
These tests are not run anyway, so there is no need to launch an X server.

* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Rename
'prepare-x phase to 'pre-check.
[native-inputs]: Remove xorg-server-for-tests.

Change-Id: Ib85883360397d2715a1893b74435d96a1d119f9e
 2025-01-20 21:37:24 +01:00
Ricardo Wurmus
aa0650d159
gnu: python-pythran: Update to 0.17.0. 
* gnu/packages/python-science.scm (python-pythran): Update to 0.17.0.
[build-system]: Use pyproject-build-system.
[source]: Remove obsolete snippet.
[arguments]: Remove phase 'do-not-install-third-parties and custom 'check
phase; use #:test-flags and add 'pre-check phase.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I49ebdd21cfb0668dd84f0d12c460a86ed694c7d6
 2025-01-20 21:37:24 +01:00
Ricardo Wurmus
35c5f07e96
gnu: python-scikit-build-core: Update to 0.10.7. 
* gnu/packages/python-science.scm (python-scikit-build-core): Update to
0.10.7.
[native-inputs]: Add python-pytest-subprocess.

Change-Id: I3da5a9e5d59900335deee2d4a5a1c80d1dd7c5ab
 2025-01-20 21:37:21 +01:00
Ricardo Wurmus
be60505289
gnu: python-qdldl: Add missing input. 
* gnu/packages/python-science.scm (python-qdldl)[native-inputs]: Add
python-setuptools.

Change-Id: I5f4c5b8f368da21da1f7d5c5cedd7a806dbdd709
 2025-01-20 21:37:20 +01:00
Ricardo Wurmus
3c31650d18
gnu: python-upsetplot: Add missing inputs. 
* gnu/packages/python-science.scm (python-upsetplot)[native-inputs]: Add
python-setuptools and python-wheel.

Change-Id: Ibddb6f183345af29dfce218145c7c8c83aa9c244
 2025-01-01 14:11:52 +01:00
Sharlatan Hellseher
a835ef1cbe
gnu: python-mpl-scatter-density: Fix buld. 
* gnu/packages/python-science.scm (python-mpl-scatter-density):
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ica320293019ae3e88e2b0654e356bc4d1be50626
 2024-12-21 22:07:51 +00:00
Sharlatan Hellseher
0c0c2d8815
gnu: python-supersmoother: Fix build 
* gnu/packages/python-science.scm (python-supersmoother):
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.

Change-Id: I33f151e74d54b6e0647b3cfae73c063522c35ea3
 2024-12-21 22:07:51 +00:00
Sharlatan Hellseher
e5b3deb1ec
gnu: python-trimesh: Update to 4.5.3. 
* gnu/packages/python-science.scm (python-trimesh): Update to 4.5.3, fix
build.
[arguments] <phases>: Remove 'fix-build, as resolved upstream.
Delete 'sanity-check.

Change-Id: I9320912764506a8c0d0bd7f300dca98b32ce4333
 2024-12-21 22:06:45 +00:00