nafkhamdc
e33bf0bbe6
gnu: Add python-pyahocorasick.
...
* gnu/packages/bioinformatics.scm (python-pyahocorasick): New variable.
Change-Id: I468bed450351b49cf81344a328841cd77f67cb4e
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-05-06 00:07:40 +02:00
nafkhamdc
a710ebec1d
gnu: Add r-memes.
...
* gnu/packages/bioconductor.scm (r-memes): New variable.
Change-Id: Ibdf5173d35ef81d27da6831148e66be83f856deb
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-05-06 00:06:19 +02:00
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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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
