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Author SHA1 Message Date
Ricardo Wurmus 332a8fa4bc
gnu: python-cooler: Update to 0.9.3. 
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.3.

Change-Id: I4b89d552a424e74f76cda0c527dc7b712b8c9f31
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 57f265f1ea
gnu: python-dask: Do not reference pyarrow_hotfix. 
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Add 'patch-pyproject
phase.

Change-Id: Idd173b72b1467540c295224072f3740c7f42b0a8
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 262df6c607
gnu: python-dask: Disable some tests. 
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Disable ORC tests and
those that fail due to differences in job id.

Change-Id: I272a77c8291b121b57b02750916f520b52185bbe
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 78d5fb1720
gnu: python-dask: Propagate python-dask-expr. 
* gnu/packages/python-xyz.scm (python-dask/bootstrap): New variable.
(python-dask)[propagated-inputs]: Add python-dask-expr.
* gnu/packages/python-science.scm (python-dask-expr)[propagated-inputs]:
Remove python-dask.
[native-inputs]: Add python-dask/bootstrap.

Change-Id: I1196641425421c7dde94c6fea8d573e78db9c402
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus a237ba5378
gnu: python-umap-learn: Disable failing test. 
* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Disable
one failing test.

Change-Id: Ic8f5f60f7d7bea0c24b417932daab3d54813d5fd
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus ba92122e53
gnu: python-umap-learn: Update to 0.5.6. 
* gnu/packages/machine-learning.scm (python-umap-learn): Update to 0.5.6.

Change-Id: If05cf1a9c7ad1d9fd0439bc888983608d70aea75
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 3c0579849c
gnu: python-pandas-stubs: Accept numpy 1.23. 
* gnu/packages/python-science.scm (python-pandas-stubs)[arguments]: Add phase
'relax-requirements.

Change-Id: I62e04574d53abd7d67068d08475522dd8989dcca
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 22eeb8f16e
gnu: python-dask: Disable all tokenize tests. 
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Ignore the test file.

Change-Id: Icbd4845361aa57c493f473ab87a15ade8a20a65f
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 1295abd0af
Revert "gnu: python-numpy: Update to 1.26.0." 
numba cannot use numpy > 1.24.

This reverts commit 6b8efd211fbd619e80628d2a78f99c6afc18723e.
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 5450886934
gnu: python-numpy: Update to 1.26.0. 
* gnu/packages/python-xyz.scm (python-numpy): Update to 1.26.0.
[build-system]: Use pyproject-build-system.
[arguments]: Move test flags to #:test-flags; add phase
'use-setuptools-backend.
[native-inputs]: Remove gfortran; add replace python-cython with
python-cython-3; add meson/newer and ninja.

Change-Id: I783bbca58624bf6f047056ba21d838f5ecb09ac2
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 2a7e513803
gnu: python-tabulate: Enable tests and fix version string. 
* gnu/packages/python-xyz.scm (python-tabulate)[arguments]: Enable tests.
[native-inputs]: Add python-pytest and python-setuptools-scm.

Change-Id: I14073151916fd637d83905c03e76b96c390db917
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 92259a5d4b
gnu: python-pandas-stubs: Update tests. 
This is a follow-up to adding ORC support to pyarrow.

* gnu/packages/python-science.scm (python-pandas-stubs)[arguments]: Disable
more tests that are due to enabling ORC support to pyarrow.

Change-Id: I8c3ca6afff8128792738251c85a1dba3dc3b0569
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 53b2fe2973
gnu: python-scikit-bio: Update to 0.6.0. 
* gnu/packages/patches/python-scikit-bio-1887.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.6.0.
[source]: Remove patch.
[arguments]: Disable skbio.diversity doctest; remove 'compatibility phase.
[propagated-inputs]: Add python-biom-format; remove python-ipython and
python-matplotlib.

Change-Id: I9bd9e0fd72f5f1b80ef6ff61c52da5fd56a715ed
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus e9d70b85eb
gnu: python-biom-format: Untangle from python-scikit-bio. 
* gnu/packages/bioinformatics.scm (python-biom-format)[arguments]: Add phase
'pandas-compatibility; disable tests that need sciki-bio.
[propagated-inputs]: Remove python-scikit-bio.

Change-Id: Ifd528d256a1c75962fb05aef5602edbf67a5af26
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 24bf2329a4
gnu: python-anndata: Update to 0.10.7. 
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.10.7.
[arguments]: Patch conftest.py; adjust tests; remove old patch for version
string; add phase 'set-numba-cache-dir.
[native-inputs]: Add python-awkward, python-dask, python-distributed,
python-hatchling, python-hatch-vcs, python-loompy, python-matplotlib,
python-pytest-doctestplus, and python-pytest-xdist.
[propagated-inputs]: Add python-array-api-compat and python-exceptiongroup.

Change-Id: I3099cbfbb1865743c75d32243be9e5a59df1507d
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus eb866b3699
gnu: Add python-array-api-compat. 
* gnu/packages/python-xyz.scm (python-array-api-compat): New variable.

Change-Id: Ibfd701630b41f860c7ad4df57fd3624d9c5b7752
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus a3ff747a48
gnu: Add python-awkward. 
* gnu/packages/python-xyz.scm (python-awkward): New variable.

Change-Id: Ie4f9b12d3662b9029f6e042f9c3a4d547073a6e7
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus fe780b55b4
gnu: Add python-awkward-cpp. 
* gnu/packages/python-xyz.scm (python-awkward-cpp): New variable.

Change-Id: I68f7e314aa6b575eb7135aa5308c327d5f6bf3ea
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus d4c62ff301
gnu: Add python-scikit-build-core. 
* gnu/packages/python-science.scm (python-scikit-build-core): New variable.

Change-Id: If234d19d720afe88f6893bdd36fcc4955a45c5d3
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 07c7b342bb
gnu: python-distributed: Update to 2024.4.2. 
* gnu/packages/python-science.scm (python-distributed): Update to 2024.4.2.
[propagated-inputs]: Add python-dask-expr.
[arguments]: Adjust tests.

Change-Id: I9d3b45d14ae052f3a5a5dec3587bc01d13e4b71f
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus f3a80df770
gnu: Add python-dask-expr. 
* gnu/packages/python-science.scm (python-dask-expr): New variable.

Change-Id: I691593ab713fe865c771aa68b5521c4c10cc58f6
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus cc67370ca1
gnu: python-partd: Update to 1.4.1. 
* gnu/packages/python-xyz.scm (python-partd): Update to 1.4.1.
[propagated-inputs]: Remove python-blosc.

Change-Id: I3aff28899339f9ffaa47b6f5c81e0e68ce660963
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus dff3357bb6
gnu: python-dask: Update to 2024.4.2. 
* gnu/packages/python-xyz.scm (python-dask): Update to 2024.4.2.
[arguments]: Disable a few tests.

Change-Id: I759ddee2ec49fbf74f368c3313f7215906b0e5a2
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus fef6edecbc
gnu: python-tables: Update to 3.7.0. 
* gnu/packages/python-xyz.scm (python-tables): Update to 3.7.0.
[propagated-inputs]: Add python-packaging and python-py-cpuinfo.

Change-Id: I8653bef9a07bb898933b249aad92ddb2b79b8d85
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus dd6f87e492
gnu: python-pyarrow: Build with ORC support. 
* gnu/packages/databases.scm (python-pyarrow)[propagated-inputs]: Add
apache-orc.
[arguments]: Set PYARROW_WITH_ORC variable.

Change-Id: Ic35cd1db75349ecb51d35815d710d8ca3a303b00
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 8647aaaa14
gnu: apache-arrow: Build with ORC. 
* gnu/packages/databases.scm (apache-arrow)[arguments]: Set options needed to
build with ORC support; remove unused options
-DBENCHMARK_ENABLE_GTEST_TESTS=OFF and -DARROW_GLOG=ON.
[inputs]: Add apache-orc.

Change-Id: Icabe6e3a73478c8464ea1e8efc103899da8e5a86
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 442eba98be
gnu: Add apache-orc. 
* gnu/packages/databases.scm (apache-orc): New variable.

Change-Id: I9e7df4a03a5d2f258ff44d9705f539f9fc925a99
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus adf54dea4e
gnu: python-pandas-stub: Update to 2.1.1.230928. 
This is a follow-up to commit ff2d0ecfca.

* gnu/packages/python-science.scm (python-pandas-stub): Update to
2.1.1.230928.

Change-Id: I2e8ce18bd25399b467a6ff2a6fb846f8bb969e4c
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 9953207f3e
gnu: python-tabulate: Update to 0.9.0. 
* gnu/packages/python-xyz.scm (python-tabulate): Update to 0.9.0.
[build-system]: Use pyproject-build-system.

Change-Id: If360e5be6433b35308b76bd1284bb6ddb74008e8
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 5e7da50260
gnu: python-pandas-2: Fix version. 
* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Write version
string to "_version.py", not "_version_meson.py" to avoid reporting the
version as "0+unknown".

Change-Id: I1a18814e37c023102714326bc8bd505705234205
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus b343aef5aa
gnu: python-scikit-learn: Update to 1.4.2. 
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 1.4.2.
[native-inputs]: Replace python-cython-0.29.35 with python-cython-3.

Change-Id: Id8be08f931bf250a8ecb8bc46b44d7148b4c4a2f
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 6be3c24d82
gnu: python-cython-3: Update to 3.0.8. 
* gnu/packages/python-xyz.scm (python-cython-3): Update to 3.0.8.

Change-Id: I9129a7837cefea0b95b0a3c3cdf73997d91f7484
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 6962b32a2b
gnu: python-pyjanitor: Update to 0.27.0. 
* gnu/packages/python-science.scm (python-pyjanitor): Update to 0.27.0.
[arguments]: Disable a few more tests; add phase 'pandas-compat.

Change-Id: Ia8891971a687342166f30ded11f9e341a208d95e
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 5def84031f
gnu: tadbit: Use G-expression. 
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Use G-expression.

Change-Id: I4fe4afc41eb3442f243b0e415ddcb363be36ce7f
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 8f8cee9ed9
gnu: r-reticulate: Update to 1.36.1. 
* gnu/packages/cran.scm (r-reticulate): Update to 1.36.1.

Change-Id: I7119ca05b8411209c617be318806b3ff4bc3b530
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus 297e88edff
gnu: python-xarray: Disable tests that are known to fail. 
* gnu/packages/python-science.scm (python-xarray)[arguments]: Disable two
tests.

Change-Id: I70954173e0aca5a377cf19476e9390a97febadc7
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus 74dd2def7f
gnu: python-pandas: Default to version 2.x. 
* gnu/packages/python-science.scm (python-pandas): Define as alias for
python-pandas-2; rename existing definition to...
(python-pandas-1): ...this new variable.

Change-Id: If359e3b2d42c683d7d0152b1757bbc5a979c999b
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus d85a19a29c
gnu: python-scikit-opt: Add missing input. 
* gnu/packages/python-science.scm (python-scikit-opt)[propagated-inputs]: Add
python-pytorch.

Change-Id: I037cc43bedeaebb05bf038c0bca72919f8c27c40
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus da4006d474
gnu: python-plastid: Replace nose with pytest. 
* gnu/packages/bioinformatics.scm (python-plastid)[native-inputs]: Replace
python-nose with python-pytest.

Change-Id: Ie0e5362d2304d3af0bcb1405fa0c1ad36fb2ace6
 2024-05-05 22:38:15 +02:00
Marco Baggio 854c42e30c
gnu: Add python-metacells. 
* gnu/packages/bioinformatics.scm (python-metacells): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I4fc760dc4317bde79c815f441ad0cc453248990a
 2024-05-05 22:38:15 +02:00
Marco Baggio da18b8620f
gnu: Add python-cvxpy. 
* gnu/packages/python-science.scm (python-cvxpy): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I440ab3768cbc4e78364dc31cf9484effd9670f49
 2024-05-05 22:38:15 +02:00
Marco Baggio 2c0cf38f04
gnu: Add python-ecos. 
* gnu/packages/python-science.scm (python-ecos): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I83d9b746f5f3563f417efc5d18911f2eb04f201c
 2024-05-05 22:38:15 +02:00
Marco Baggio a0971243bc
gnu: Add python-osqp. 
* gnu/packages/python-science.scm (python-osqp): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: Id6f1665505469fd6543046636b82d0730b319df3
 2024-05-05 22:38:15 +02:00
Marco Baggio d051ef0913
gnu: Add python-qdldl. 
* gnu/packages/python-science.scm (python-qdldl): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I523ecb2292c9b514b548e2130d0d43bb77317b00
 2024-05-05 22:38:15 +02:00
Marco Baggio d470a9aa54
gnu: Add python-scs. 
* gnu/packages/python-science.scm (python-scs): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I6c5ecdac4b558aab4b8ee396dff1dfc9cdec07f0
 2024-05-05 22:38:15 +02:00
Marco Baggio 670dcc8e4c
gnu: Add python-fastcluster. 
* gnu/packages/python-science.scm (python-fastcluster): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: Ifc5229a4d00f581eb358a1f41fc3479fd1c33c2e
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus c4eccd2066
gnu: Add python-clarabel. 
* gnu/packages/python-science.scm (python-clarabel): New variable.

Change-Id: I28459162460ca9bf9e9557122f611c677afadc27
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus 94ea83d9ef
gnu: Add rust-amd-0.2. 
* gnu/packages/crates-io.scm (rust-amd-0.2): New variable.

Change-Id: I28d4e0d6bd9b590ca61df9152f91641408e48e5a
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus d1eda517f3
gnu: Add python-param. 
* gnu/packages/python-xyz.scm (python-param): New variable.

Change-Id: Idad928488d7c306c969b4484a3cd22661c41d488
 2024-05-05 22:38:15 +02:00
Ricardo Wurmus 83262c971e
gnu: Add python-multiscale-spatial-image. 
* gnu/packages/python-xyz.scm (python-multiscale-spatial-image): New variable.

Change-Id: I05a0b3a93091148917fade831faefb88c13bbc6f
 2024-05-05 22:38:15 +02:00