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2024-01-16gnu: python-fit-nbinom: Disable tests.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-fit-nbinom)[arguments]: Disable tests. Change-Id: I980480a3326dccc67930d34474832712005d1bb2
2024-01-16gnu: scvelo: Make compatible with latest matplotlib.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Add phase 'matplotlib-compatibility. Change-Id: Ia761821c8aa1e516525cff7c680db471a5908e5f
2024-01-16gnu: python-cartopy: Update to 0.22.0.Ricardo Wurmus
* 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
2024-01-16gnu: python-demuxem: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-demuxem)[arguments]: Disable tests, because there aren't any. Change-Id: I50364ca6744cf9d2704d4b75a8c79c4fdc4ada6e
2024-01-16gnu: python-pint: Update to 0.23.Ricardo Wurmus
* 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
2024-01-16gnu: python-cooler: Update to 0.9.1.Ricardo Wurmus
* 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
2024-01-16gnu: python-plastid: Update to 0.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.1. [arguments]: Disable four tests. Change-Id: If0225f226e702e89d451e2955d0f76691a8816c0
2024-01-16gnu: cnvkit: Update to 0.9.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.10. [arguments]: Remove. [inputs]: Add r-minimal. Change-Id: Iaa27fd3dddc507c7a955441f066d4b0e3b8f1757
2024-01-16gnu: python-reportlab: Update to 4.0.8.Ricardo Wurmus
* 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
2024-01-16gnu: python-pegasusio: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pegasusio)[arguments]: Disable tests. Change-Id: I6b32ed416b562b47088dbc34eb7bcb0b8e2cc414
2024-01-16gnu: python-pyani: Disable tests.Ricardo Wurmus
There are none. * gnu/packages/bioinformatics.scm (python-pyani)[arguments]: Disable tests. Change-Id: I6862082c8335e5d487da6d1705ed094922f14e47
2024-01-16gnu: tadbit: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit)[native-inputs]: Add glib. Change-Id: Ia1f79e2a30f5b57616cf3d1f7b6438f07451fbbf
2024-01-16gnu: python-captum: Update to 0.7.0.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-captum): Update to 0.7.0. [propagated-inputs]: Add python-tqdm. Change-Id: I8917b6e294fe08077a3af4423deefa9769ba9384
2024-01-16gnu: python-poliastro: Make compatible with latest matplotlib.Ricardo Wurmus
* gnu/packages/astronomy.scm (python-poliastro)[arguments]: Add phase 'matplotlib-compatibility; disable test_porkchop_plotting. Change-Id: Ie70673c69d4bdfa424e324d2848e9567360b03ef
2024-01-16gnu: python-cleanlab: Disable test_aux_inputs, enable other tests.Ricardo Wurmus
* 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
2024-01-16gnu: python-scanpy: Update to 1.9.6.Ricardo Wurmus
* 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
2024-01-16gnu: Add python-pytest-nunit.Ricardo Wurmus
* gnu/packages/check.scm (python-pytest-nunit): New variable. Change-Id: Ic67c973460f09b15bf683f70040a3f5e4381108d
2024-01-16gnu: python-seaborn: Update to 0.13.1.Ricardo Wurmus
* 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
2024-01-16gnu: python-matplotlib: Update to 3.8.2.Ricardo Wurmus
* 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
2024-01-16gnu: Add python-contourpy.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-contourpy): New variable. Change-Id: Icbbe4a358242095fae36639c5c039c029eea4ee3
2024-01-16gnu: python-kiwisolver: Update to 1.4.5.Ricardo Wurmus
* 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
2024-01-16gnu: Add python-cppy.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-cppy): New variable. Change-Id: I584fcddc3430960098d65f1916278a7473249a87
2024-01-16gnu: python-umap-learn: Update to 0.5.5.Ricardo Wurmus
* 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
2024-01-16gnu: python-pynndescent: Update to 0.5.11.Ricardo Wurmus
* 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
2024-01-16gnu: python-scikit-learn: Update to 1.3.2.Ricardo Wurmus
* 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
2024-01-16gnu: python-matplotx: Disable test_png test.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-matplotx)[arguments]: Disable test_png test. Change-Id: I19a954786d828a1b717c9c4021ad7f5c6172366c
2024-01-16gnu: python-pypng: Update to 0.20220715.0.Ricardo Wurmus
* 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
2024-01-16gnu: python-scikit-image: Update to 0.22.0.Ricardo Wurmus
* 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
2024-01-16gnu: python-imageio: Update to 2.33.1.Ricardo Wurmus
* 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
2024-01-16gnu: python-lazy-loader: Update to 0.3.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-lazy-loader): Update to 0.3. [native-inputs]: Add python-pre-commit. Change-Id: Id4f8b61e6e60dd6da04beb8c1e4d064dc34d994c
2024-01-16gnu: python-tifffile: Update to 2023.12.9.Ricardo Wurmus
* 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
2024-01-16gnu: python-scipy: Update to 1.11.4.Ricardo Wurmus
* 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
2024-01-16gnu: meson-python: Update to 0.15.0.Ricardo Wurmus
* 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
2024-01-16gnu: Add python-pydevtool.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pydevtool): New variable. Change-Id: I325b81fa6421094a5a64084c06e66b8fa136e270
2024-01-16gnu: Add python-pyproject-metadata-0.7.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pyproject-metadata-0.7): New variable. Change-Id: I7c47c911fa2a33c0b5711b0009f31b3e32c1c1d7
2024-01-16gnu: python-doit: Update to 0.36.0.Ricardo Wurmus
* 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
2024-01-16gnu: Add pybind11-2.10.Ricardo Wurmus
* gnu/packages/python-xyz.scm (pybind11-2.10): New variable. Change-Id: Ia7915af3baca36b0677d3f762046585abc473f56
2024-01-16gnu: Add python-cython-0.29.35.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-cython-0.29.35): New variable. Change-Id: I09ec851a2051e885f6417524bbeeb81b743bef0b
2024-01-16gnu: Add python-pydoc-markdown.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pydoc-markdown): New variable. Change-Id: I03e45c2b87f626f7a8113d785c72c14a301d79be
2024-01-16gnu: python-yapf: Update to 0.32.0.Ricardo Wurmus
* 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
2024-01-16gnu: Add python-docspec-python.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-docspec-python): New variable. Change-Id: Ic607d0a34a8601dd464251edd8c8509314b7489c
2024-01-16gnu: Add python-nr-util.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-nr-util): New variable. Change-Id: I26dda5e5bc03334fb476e3f1fd2fa6aaf93a91c3
2024-01-15gnu: go-github-com-arceliar-ironwood: Update to ↵Artyom V. Poptsov
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>
2024-01-15gnu: yggdrasil: Update to 0.5.4.Artyom V. Poptsov
* gnu/packages/networking.scm (yggdrasil): Update to 0.5.4. Change-Id: I4f386e1b69627b0c5a6095c42274b8a8bff8bfd9 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-15gnu: hypercorn: Reformat with guix style.Troy Figiel
* gnu/packages/python-web.scm (hypercorn): Reformat with guix style.
2024-01-15gnu: hypercorn: Adjust inputs.Troy Figiel
* gnu/packages/python-web.scm (hypercorn)[propagated-inputs]: Add python-exceptiongroup and python-tomli. Remove python-toml and python-typing-extensions. [native-inputs]: Remove python-mock.
2024-01-15gnu: Remove python-tslearn.Ricardo Wurmus
This package now lives in the guix-science channel. * gnu/packages/machine-learning.scm (python-tslearn): Remove variable. Change-Id: I655df3417d258cb1231746626817fde9628e9569
2024-01-15gnu: Add python-docspec.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-docspec): New variable. Change-Id: I3103bde3483273a335156b38de742f493fd366f1
2024-01-15gnu: Add python-databind-json.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-databind-json): New variable. Change-Id: Iaab64e28ba6772c14704ff67cffab21a2f555460
2024-01-15gnu: Add python-databind-core.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-databind-core): New variable. Change-Id: I45bf0ec5ef123ea20c50e2ca3caf930bfba45eea
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