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Author SHA1 Message Date
Ricardo Wurmus a4ad0a46ef
gnu: python-graphtools: Fix tests. 
* gnu/packages/graph.scm (python-graphtools)[arguments]: Add 'patch-tests
phase.

Change-Id: I5ffb4321ddd7e33e812bcb1cf67cee069b07b5f8
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 1b44a23503
gnu: python-gpy: Update to 1.13.1. 
* gnu/packages/python-science.scm (python-gpy): Update to 1.13.1.
[source]: Remove snippet.
[build-system]: Use pyproject-build-system.
[arguments]: Remove phase 'remove-plotting-tests; add phase 'compatibility.
[native-inputs]: Remove python-nose and python-climin; add python-pytest,
python-matplotlib, and python-pods.

Change-Id: I1ed95e3ad2e8444979fd2cf272d7f3104b1bf2ec
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus a4039b6994
gnu: python-pygsp: Add missing input. 
* gnu/packages/graph.scm (python-pygsp)[native-inputs]: Add python-pytest.

Change-Id: I94cd4e160dcbecfbb491c0d101bcbeb761189876
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 9d615b915b
gnu: python-paramz: Update to 0.9.6. 
* gnu/packages/python-science.scm (python-paramz): Update to 0.9.6.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-nose.

Change-Id: I62a2f7ecf600f48da74f4d233e108360a583d5ca
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 041ea43a86
gnu: python-pingouin: Update to 0.5.4. 
* gnu/packages/python-science.scm (python-pingouin): Update to 0.5.4.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'sklearn-compatibility phase;
skip one test.

Change-Id: I8d13f15558eadee0547f04bc4bb89a0fd0e0767b
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 99bf1b1002
gnu: python-liana-py: Update to 1.1.0. 
* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.1.0.
[arguments]: Adjust tests; add phase 'relax-requirements.
[propagated-inputs]: Remove python-mofax; add python-numpy.
[native-inputs]: Remove python-numpy; add python-poetry-core.

Change-Id: I279be08ac3ac73d9a724f59652f2f0d333607696
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 4d65083bf8
gnu: python-plotnine: Fix version string. 
* gnu/packages/python-science.scm (python-plotnine)[native-inputs]: Add
python-setuptools-scm.

Change-Id: I0fc2f3ad7edcdaaa5e3bf9774bc6840c8fbeb727
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 02ca781c03
gnu: python-plotnine: Disable test because of harmless warning. 
* gnu/packages/python-science.scm (python-plotnine)[arguments]: Disable
test_save_method which prints an unexpected warning..

Change-Id: I28a20b85ee549311bed534efbf801db930419ca9
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus f678884b4a
gnu: python-mapie: Disable strict tests. 
* gnu/packages/statistics.scm (python-mapie)[arguments]: Disable two tests.

Change-Id: I2c72f6f2d0136db5f97ba709a468a3aebd447d5d
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus c226d12856
gnu: python-scikit-learn-extra: Disable a validation test. 
* gnu/packages/machine-learning.scm (python-scikit-learn-extra)[arguments]:
Disable one test.

Change-Id: I1309cb6a82dee1a714ddec59aa90692ccfcd885b
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 1ea0e3e6dd
gnu: python-cooltools: Update to 0.7.0. 
* gnu/packages/bioinformatics.scm (python-cooltools): Update to 0.7.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.

Change-Id: I4112bf0cbc309df551087b8bb3cb1d37af7f751d
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus d14d5147b1
gnu: python-bioframe: Update to 0.6.4. 
* gnu/packages/bioinformatics.scm (python-bioframe): Update to 0.6.4.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'pre-check phase.  Use
 #:test-flags to disable tests that require internet access.
[native-inputs]: Add python-hatchling.
[propagated-inputs]: Add python-pyyaml.

Change-Id: Iad1c8c6ef8f52886e398e9c4d2d384c5fce075c6
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 317be75d1d
gnu: python-verde: Add missing input. 
* gnu/packages/geo.scm (python-verde)[native-inputs]: Add python-pytest.

Change-Id: I82b844627f27cfe60e42050bb37d092b3d9a43c1
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus ffffc0227a
gnu: python-statmake: Adjust tests and version checks. 
* gnu/packages/fontutils.scm (python-statmake)[arguments]: Disable broken
test; relax check for cattrs.

Change-Id: Ibd479743160d3591088d17635e26484e7de5250f
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus cb9ec4c5c5
gnu: python-decoupler-py: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.6.0.
[arguments]: Do not disable test_plot_volcano test.

Change-Id: I44a31d30e8a03d2d1ffd86383c8bc6db79628def
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus 0e24635033
gnu: python-omnipath: Update to 1.0.8. 
* gnu/packages/python-web.scm (python-omnipath): Update to 1.0.8.
[arguments]: Disable tests that need internet access.
[native-inputs]: Add python-pytest-socket.

Change-Id: Ib5856a1a25835d43918d9fe565d0262dded70eed
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 7c938c232c
gnu: barectf: Use python-termcolor-1. 
* gnu/packages/instrumentation.scm (barectf)[propagated-inputs]: Use
python-termcolor-1.

Change-Id: I8284db970d3cee8988318be7f1180aa933ab461a
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 1f5eef8391
gnu: Add python-termcolor-1. 
* gnu/packages/python-xyz.scm (python-termcolor-1): New variable.

Change-Id: I1aca97b6b7976cb698131c3a0be73e4798bef6d6
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 79d13482e4
gnu: python-pytest-shutil: Disable a test. 
* gnu/packages/python-check.scm (python-pytest-shutil)[build-system]: Use
pyproject-build-system.
[arguments]: Disable test_pretty_formatter.

Change-Id: I862320feab5b3c6e375bf652deced6a631dfc575
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 360f9ea421
gnu: python-cleanlab: Update to 2.6.3. 
* gnu/packages/machine-learning.scm (python-cleanlab): Update to 2.6.3.
[arguments]: Disable tests that require "datasets" package; add phase
'remove-datasets.

Change-Id: I6af99e3e749a10515328db4874974a3504658352
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 714baf2295
gnu: python-termcolor: Update to 2.4.0. 
* gnu/packages/python-xyz.scm (python-termcolor): Update to 2.4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add 'fix-pyproject build phase.
[native-inputs]: Add python-hatch-vcs, python-hatchling, python-pytest, and
python-pytest-cov.

Change-Id: I1b824ca6f125305169c3f64f00dbacbeb77d0ed0
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 31f57ae7df
gnu: python-hicexplorer: Update to 3.7.4. 
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.4.
[source]: Remove obsolete snippet.
[arguments]: Remove obsolete phase 'scipy-compatibility.
[propagated-inputs]: Replace python-cleanlab-1 with python-cleanlab.

Change-Id: Iac9a24cc4551b7d7e1d41d1f07a6db6d620b119e
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 9692e2bb7c
gnu: snakemake-5: Patch version string. 
* gnu/packages/python-xyz.scm (snakemake-5)[arguments]: Add phase
'patch-version.

Change-Id: I647625e9d26b2ee06274a0c5bb844ccb87035537
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 8d14b1cbb6
gnu: snakemake-5: Make compatible with tabulate 0.9.0. 
* gnu/packages/python-xyz.scm (snakemake-5)[arguments]: Add phase
'tabulate-compatibility.

Change-Id: I0b0ddafe9c2da91dbe10a584eb6fa0a3d5d62e87
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 36a1e76173
gnu: snakemake: Fetch from git repository. 
* gnu/packages/python-xyz.scm (snakemake)[source]: Fetch from git repository
to include tests.
[arguments]: Enable tests; add 'pre-check phase.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add git-minimal, python-wrapper, python-pytest,
python-pandas, and python-requests-mock.

Change-Id: I32e9d36752cc91eacb8f05138d969834dbbce817
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 6095e5b436
gnu: snakemake-7: Make compatible with tabulate 0.9.0. 
* gnu/packages/python-xyz.scm (snakemake-7)[arguments]: Add phase
'tabulate-compatibility.

Change-Id: Ie6b2a7d65bc76e3df7c3946ba4533b301f5a3610
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 6244177e79
gnu: snakemake-6: Make compatible with tabulate 0.9.0. 
* gnu/packages/python-xyz.scm (snakemake-6)[arguments]: Add phase
'tabulate-compatibility.

Change-Id: I0471726e2000af76871e2542ed347cd1727bf0c9
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus ee9720b2f0
gnu: python-jsonpickle: Update to 3.0.4. 
* gnu/packages/python-web.scm (python-jsonpickle): Update to 3.0.4.
[build-system]: Use pyproject-build-system.
[arguments]: Use test-flags; add 'pre-check phase.
[propagated-inputs]: Add python-importlib-metadata.
[native-inputs]: Add python-bson, python-ecdsa, python-feedparser,
python-pymongo, python-pytest, python-pytest-benchmark, python-pytest-cov,
python-pytest-enabler, python-setuptools, python-setuptools-scm,
python-simplejson, python-sqlalchemy, python-ujson, and tzdata-for-tests.

Change-Id: I99e41ae2652ce02b090ee2b99a7b850a19b5f353
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus d5424b12af
gnu: python-imbalanced-learn: Update to 0.12.2. 
* gnu/packages/machine-learning.scm (python-imbalanced-learn): Update to
0.12.2.
[native-inputs]: Remove python-numpydoc.

Change-Id: I8af0017f76d5ab3a2d55a96c0ace6be22d57fb66
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 2d8c81a8d7
gnu: tadbit: Add R to inputs. 
* gnu/packages/bioinformatics.scm (tadbit)[inputs]: Add r-minimal.

Change-Id: I4929dd89ddd27b4fcbd8b3a00b8ab8f3586945d2
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 93a397f8b7
gnu: tadbit: Patch for compatibility with latest scipy. 
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Add phase
'scipy-compatibility.

Change-Id: Ib25b9cde75f0505c347c4ff470e61f06fb162839
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus 453b7a267b
gnu: tadbit: Update to 1.0.1-2.2838129. 
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-2.2838129.

Change-Id: I2c220ae37cd196ca508d30aefc24938cce985527
 2024-05-05 22:38:17 +02:00
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