Ricardo Wurmus
186aa138a6
gnu: python-metpy: Update to 1.6.0.
...
* gnu/packages/geo.scm (python-metpy): Update to 1.6.0.
[arguments]: Add phases 'fix-version-check and 'hide-imp-deprecation-warnings.
[native-inputs]: Add python-packaging; remove python-shapely and
python-cartopy.
Change-Id: I4a46a5e60b1904699475608146f2a09aefc07624
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
0c6db478ec
gnu: python-pint: Add missing input.
...
This is a follow-up to commit 23b8601cd2cf90ed11a51ca6db133083433e74d8.
Without this input the version string will be 0.0.0.
* gnu/packages/python-xyz.scm (python-pint)[native-inputs]: Add
python-setuptools-scm.
Change-Id: Id621e459f119d7268cdcc41ef93bcae135e842d1
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
cda0f029d6
gnu: python-hicexplorer: Make compatible with latest scipy.
...
* gnu/packages/bioinformatics.scm (python-hicexplorer)[arguments]: Add
'scipy-compatibility phase.
Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
3ce25c212f
gnu: python-hicmatrix: Update to 17.1.
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* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 17.1.
[arguments]: Remove.
Change-Id: I6b1230d703d0dc1a88ee61a84cc6cd95f7eeb6f9
2024-01-16 12:44:36 +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snippet to fix outdated use of "max_features" option.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
50dbb9561f
gnu: python-fit-nbinom: Disable tests.
...
* gnu/packages/python-xyz.scm (python-fit-nbinom)[arguments]: Disable tests.
Change-Id: I980480a3326dccc67930d34474832712005d1bb2
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
6b4c911a99
gnu: scvelo: Make compatible with latest matplotlib.
...
* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Add phase
'matplotlib-compatibility.
Change-Id: Ia761821c8aa1e516525cff7c680db471a5908e5f
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
e833d3abf8
gnu: python-cartopy: Update to 0.22.0.
...
* gnu/packages/geo.scm (python-cartopy): Update to 0.22.0.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-expression; use #:test-flags; update list of disabled
tests; add phase 'remove-endpoint.
[propagated-inputs]: Add python-packaging; remove python-pykdtree.
[native-inputs]: Add python-coveralls and python-pytest-xdist; remove
python-flufl-lock.
Change-Id: I353fff0ceade648286ef552effdc35671032c62c
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
3118d95b56
gnu: python-demuxem: Disable tests.
...
* gnu/packages/bioinformatics.scm (python-demuxem)[arguments]: Disable tests,
because there aren't any.
Change-Id: I50364ca6744cf9d2704d4b75a8c79c4fdc4ada6e
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
745b208767
gnu: python-pint: Update to 0.23.
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* gnu/packages/python-xyz.scm (python-pint): Update to 0.23.
[arguments]: Disable "test_load_definitions_stage_2" test.
[native-inputs]: Remove python-dask, python-distributed,
python-importlib-metadata, python-setuptools-scm, python-sparse,
python-uncertainties, and python-xarray; add python-pytest-benchmark.
[propagated-inputs]: Add python-uncertainties.
Change-Id: I98baae3369e5ffeea96355d9509296771c33dc50
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
1c01f7e5c6
gnu: python-cooler: Update to 0.9.1.
...
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom build phases; disable tests via #:test-flags.
[propagated-inputs]: Remove python-six and python-sparse.
[native-inputs]: Remove python-codecov, python-mock, and python-pytest-flake8;
add python-coverage, python-hatchling, and python-isort.
Change-Id: I48b6a9c07a2bc1c213971585d7191573fd5d5aca
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
3d3a55ec19
gnu: python-plastid: Update to 0.6.1.
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* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.1.
[arguments]: Disable four tests.
Change-Id: If0225f226e702e89d451e2955d0f76691a8816c0
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
3a58a3ef05
gnu: cnvkit: Update to 0.9.10.
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* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.10.
[arguments]: Remove.
[inputs]: Add r-minimal.
Change-Id: Iaa27fd3dddc507c7a955441f066d4b0e3b8f1757
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
5a7f7156a2
gnu: python-reportlab: Update to 4.0.8.
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* gnu/packages/pdf.scm (python-reportlab): Update to 4.0.8.
[arguments]: Update configure flags and 'find-libraries phase.
[inputs]: Remove freetype and libart-lgpl.
[propagated-inputs]: Add python-chardet.
Change-Id: I626ef4c71a0b867ec4e1c74a71e45843349f46ef
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
b8e4be02eb
gnu: python-pegasusio: Disable tests.
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* gnu/packages/bioinformatics.scm (python-pegasusio)[arguments]: Disable
tests.
Change-Id: I6b32ed416b562b47088dbc34eb7bcb0b8e2cc414
2024-01-16 12:44:36 +01:00
Ricardo Wurmus
c620c8ae81
gnu: python-pyani: Disable tests.
...
There are none.
* gnu/packages/bioinformatics.scm (python-pyani)[arguments]: Disable tests.
Change-Id: I6862082c8335e5d487da6d1705ed094922f14e47
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
b460f89d93
gnu: tadbit: Add missing input.
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* gnu/packages/bioinformatics.scm (tadbit)[native-inputs]: Add glib.
Change-Id: Ia1f79e2a30f5b57616cf3d1f7b6438f07451fbbf
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
c085139bc9
gnu: python-captum: Update to 0.7.0.
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* gnu/packages/machine-learning.scm (python-captum): Update to 0.7.0.
[propagated-inputs]: Add python-tqdm.
Change-Id: I8917b6e294fe08077a3af4423deefa9769ba9384
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
efd98a9c45
gnu: python-poliastro: Make compatible with latest matplotlib.
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* gnu/packages/astronomy.scm (python-poliastro)[arguments]: Add phase
'matplotlib-compatibility; disable test_porkchop_plotting.
Change-Id: Ie70673c69d4bdfa424e324d2848e9567360b03ef
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
2c94760dcb
gnu: python-cleanlab: Disable test_aux_inputs, enable other tests.
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* gnu/packages/machine-learning.scm (python-cleanlab)[arguments]: Remove
'disable-bad-tests phase and ignore test files in #:test-flags instead;
disable test_aux_inputs test, but re-enable tests from
test_multilabel_classification.py.
[native-inputs]: Add python-pytest-lazy-fixture.
Change-Id: I77a16768ff61215e918c98bccd3efa216fb30d7f
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
447876fa0d
gnu: python-scanpy: Update to 1.9.6.
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* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.6.
[arguments]: Update test flags.
[native-inputs]: Add python-hatchling, python-hatch-vcs, and
python-pytest-nunit.
Change-Id: I6d4dcd267a076c5697ed103650841f520dc9917f
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
6a2f1863e7
gnu: Add python-pytest-nunit.
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* gnu/packages/check.scm (python-pytest-nunit): New variable.
Change-Id: Ic67c973460f09b15bf683f70040a3f5e4381108d
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
c647bd42a3
gnu: python-seaborn: Update to 0.13.1.
...
* gnu/packages/python-xyz.scm (python-seaborn): Update to 0.13.1.
[propagated-inputs]: Add python-ipykernel, python-mypy, python-nbconvert,
python-numpydoc, python-pyyaml, and python-statsmodels.
[native-inputs]: Add python-flake8, python-pre-commit, python-pytest-cov, and
python-pytest-xdist; remove python-pypa-build.
Change-Id: Id1ed6cfaf7e0950e99c06900fd68fb1ab884bee0
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
82b7c3077f
gnu: python-matplotlib: Update to 3.8.2.
...
* gnu/packages/python-xyz.scm (python-matplotlib): Update to 3.8.2.
[build-system]: Use pyproject-build-system.
[arguments]: Enable more tests; simplify custom 'check phase.
[propagated-inputs]: Remove gobject-introspection, python-cairocffi,
python-certifi, python-pygobject, python-pytz, python-six, and
python-wxpython; add python-contourpy and python-importlib-resources.
[native-inputs]: Add pybind11.
Change-Id: Ie34826882fdcc20fac3b09130bcd0f4ad4f76b07
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
c7646437a2
gnu: Add python-contourpy.
...
* gnu/packages/python-xyz.scm (python-contourpy): New variable.
Change-Id: Icbbe4a358242095fae36639c5c039c029eea4ee3
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
037cb397c1
gnu: python-kiwisolver: Update to 1.4.5.
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* gnu/packages/maths.scm (python-kiwisolver): Update to 1.4.5.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Add python-typing-extension.
[native-inputs]: Add python-cppy, python-pytest, and python-setuptools-scm.
Change-Id: Iea75440dc58fa342dcf4a2a381b6dcc17e71e618
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
9ea9346168
gnu: Add python-cppy.
...
* gnu/packages/python-xyz.scm (python-cppy): New variable.
Change-Id: I584fcddc3430960098d65f1916278a7473249a87
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
fa5d8c839a
gnu: python-umap-learn: Update to 0.5.5.
...
* gnu/packages/machine-learning.scm (python-umap-learn): Update to 0.5.5.
[build-system]: Use pyproject-build-system.
[arguments]: Remove 'numpy-compatibility and custom 'check phases.
Change-Id: I2123f66519730d43e454d9536e8cb7b6c4569d56
2024-01-16 12:44:35 +01:00
Ricardo Wurmus
ca1749c243
gnu: python-pynndescent: Update to 0.5.11.
...
* gnu/packages/machine-learning.scm (python-pynndescent): Update to 0.5.11.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
[propagated-inputs]: Add python-importlib-metadata.
Change-Id: I14f15ea98157ed15b360971c30fe00c5f00af4a7
2024-01-16 12:44:34 +01:00
Ricardo Wurmus
247c427302
gnu: python-scikit-learn: Update to 1.3.2.
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* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 1.3.2.
[build-system]: Use pyproject-build-system.
[arguments]: Move test flags to #:test-flags.
[native-inputs]: Replace python-cython with python-cython-0.29.35.
Change-Id: Iac6107dae752c42d9f57448a66eed0526974d57e
2024-01-16 12:44:34 +01:00
Ricardo Wurmus
e759380796
gnu: python-matplotx: Disable test_png test.
...
* gnu/packages/python-xyz.scm (python-matplotx)[arguments]: Disable test_png
test.
Change-Id: I19a954786d828a1b717c9c4021ad7f5c6172366c
2024-01-16 12:44:34 +01:00
Ricardo Wurmus
2057f778a4
gnu: python-pypng: Update to 0.20220715.0.
...
* gnu/packages/python-xyz.scm (python-pypng): Update to 0.20220715.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add 'pre-check phase.
[native-inputs]: Add python-pytest.
Change-Id: Ic47c653f94a688048383eba216f01d7987625680
2024-01-16 12:44:34 +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
32edfc4a85
gnu: python-imageio: Update to 2.33.1.
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* gnu/packages/python-xyz.scm (python-imageio): Update to 2.33.1.
[propagated-inputs]: Remove python-psutil; add python-tifffile.
[native-inputs]: Add python-black, python-flake8, python-fsspec, and
python-pytest-cov.
Change-Id: I5c64d939f5ee94ac9ec8fdbd7b51cd978b7df0fb
2024-01-16 12:44:34 +01:00
Ricardo Wurmus
6fbbffd6ef
gnu: python-lazy-loader: Update to 0.3.
...
* gnu/packages/python-xyz.scm (python-lazy-loader): Update to 0.3.
[native-inputs]: Add python-pre-commit.
Change-Id: Id4f8b61e6e60dd6da04beb8c1e4d064dc34d994c
2024-01-16 12:44:34 +01:00
Ricardo Wurmus
299455fef2
gnu: python-tifffile: Update to 2023.12.9.
...
* gnu/packages/python-xyz.scm (python-tifffile): Update to 2023.12.9.
[propagated-inputs]: Remove python-imagecodecs.
[native-inputs]: Add python-pytest.
Change-Id: I2567bef390e286ed4399cc67b80a9df503f53c0a
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
22c5d2d835
gnu: meson-python: Update to 0.15.0.
...
* gnu/packages/build-tools.scm (meson-python): Update to 0.15.0.
[arguments]: Add phase 'delete-directory.
[propagated-inputs]: Add python-cython, python-pyproject-metadata-0.7, and
python-typing-extensions.
[native-inputs]: Add python-pytest-cov.
Change-Id: I412af929c9e0485aa2a15e316d247f58e6f3477b
2024-01-16 12:44:34 +01:00
Ricardo Wurmus
08f48f2939
gnu: Add python-pydevtool.
...
* gnu/packages/python-xyz.scm (python-pydevtool): New variable.
Change-Id: I325b81fa6421094a5a64084c06e66b8fa136e270
2024-01-16 12:44:34 +01:00
Ricardo Wurmus
1c91d45724
gnu: Add python-pyproject-metadata-0.7.
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* gnu/packages/python-xyz.scm (python-pyproject-metadata-0.7): New variable.
Change-Id: I7c47c911fa2a33c0b5711b0009f31b3e32c1c1d7
2024-01-16 12:44:34 +01:00
Ricardo Wurmus
1fb5d95e75
gnu: python-doit: Update to 0.36.0.
...
* gnu/packages/python-xyz.scm (python-doit): Update to 0.36.0.
[build-system]: Use pyproject-build-system.
[arguments]: Disable test_execute test.
[propagated-inputs]: Remove python-pyinotify; add python-importlib-metadata.
[description]: Add missing spaces between two sentences.
Change-Id: I1d046201c9bef63477f8fb0a2f8494bffbbbc711
2024-01-16 12:44:34 +01:00
Ricardo Wurmus
1d91698478
gnu: Add pybind11-2.10.
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* gnu/packages/python-xyz.scm (pybind11-2.10): New variable.
Change-Id: Ia7915af3baca36b0677d3f762046585abc473f56
2024-01-16 12:44:33 +01:00
Ricardo Wurmus
ce451cdcb8
gnu: Add python-cython-0.29.35.
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* gnu/packages/python-xyz.scm (python-cython-0.29.35): New variable.
Change-Id: I09ec851a2051e885f6417524bbeeb81b743bef0b
2024-01-16 12:44:33 +01:00
Ricardo Wurmus
33d0a549e9
gnu: Add python-pydoc-markdown.
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* gnu/packages/python-xyz.scm (python-pydoc-markdown): New variable.
Change-Id: I03e45c2b87f626f7a8113d785c72c14a301d79be
2024-01-16 12:36:08 +01:00
Ricardo Wurmus
b05fe5c763
gnu: python-yapf: Update to 0.32.0.
...
* gnu/packages/python-xyz.scm (python-yapf): Update to 0.32.0.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-pytest.
[propagated-inputs]: Add python-importlib-metadata, python-platformdirs, and
python-tomli.
Change-Id: I30fa0b9d643f6585624da87d5c1a1edbb59425c4
2024-01-16 12:21:07 +01:00
Ricardo Wurmus
1fcf3d2a0c
gnu: Add python-docspec-python.
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* gnu/packages/python-xyz.scm (python-docspec-python): New variable.
Change-Id: Ic607d0a34a8601dd464251edd8c8509314b7489c
2024-01-16 11:56:34 +01:00
Ricardo Wurmus
8721b9c1fb
gnu: Add python-nr-util.
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* gnu/packages/python-xyz.scm (python-nr-util): New variable.
Change-Id: I26dda5e5bc03334fb476e3f1fd2fa6aaf93a91c3
2024-01-16 11:37:07 +01:00
Artyom V. Poptsov
21f5d20d68
gnu: go-github-com-arceliar-ironwood: Update to v0.0.0-20231127131626-465b82dfb5bd.
...
* gnu/packages/golang.scm (go-github-com-arceliar-ironwood): Update to
v0.0.0-20231127131626-465b82dfb5bd.
Change-Id: Ia94d7c88e54d33f7bb7b5054a757d7ef203d47c2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-15 23:18:58 +00:00
Artyom V. Poptsov
5358b308a1
gnu: yggdrasil: Update to 0.5.4.
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* gnu/packages/networking.scm (yggdrasil): Update to 0.5.4.
Change-Id: I4f386e1b69627b0c5a6095c42274b8a8bff8bfd9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-15 23:18:35 +00:00
Troy Figiel
eb0f35e16d
gnu: hypercorn: Reformat with guix style.
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* gnu/packages/python-web.scm (hypercorn): Reformat with guix style.
2024-01-15 22:43:58 +00:00
