gnu: python-reportlab: Update to 4.0.8.

* 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

gnu: python-pegasusio: Disable tests.

* gnu/packages/bioinformatics.scm (python-pegasusio)[arguments]: Disable
tests.

Change-Id: I6b32ed416b562b47088dbc34eb7bcb0b8e2cc414

gnu: python-pyani: Disable tests.

There are none.

* gnu/packages/bioinformatics.scm (python-pyani)[arguments]: Disable tests.

Change-Id: I6862082c8335e5d487da6d1705ed094922f14e47

gnu: tadbit: Add missing input.

* gnu/packages/bioinformatics.scm (tadbit)[native-inputs]: Add glib.

Change-Id: Ia1f79e2a30f5b57616cf3d1f7b6438f07451fbbf

gnu: python-captum: Update to 0.7.0.

* gnu/packages/machine-learning.scm (python-captum): Update to 0.7.0.
[propagated-inputs]: Add python-tqdm.

Change-Id: I8917b6e294fe08077a3af4423deefa9769ba9384

gnu: python-poliastro: Make compatible with latest matplotlib.

* gnu/packages/astronomy.scm (python-poliastro)[arguments]: Add phase
'matplotlib-compatibility; disable test_porkchop_plotting.

Change-Id: Ie70673c69d4bdfa424e324d2848e9567360b03ef

gnu: python-cleanlab: Disable test_aux_inputs, enable other tests.

* 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

gnu: python-scanpy: Update to 1.9.6.

* 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

gnu: Add python-pytest-nunit.

* gnu/packages/check.scm (python-pytest-nunit): New variable.

Change-Id: Ic67c973460f09b15bf683f70040a3f5e4381108d

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

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

gnu: Add python-contourpy.

* gnu/packages/python-xyz.scm (python-contourpy): New variable.

Change-Id: Icbbe4a358242095fae36639c5c039c029eea4ee3

gnu: python-kiwisolver: Update to 1.4.5.

* 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

gnu: Add python-cppy.

* gnu/packages/python-xyz.scm (python-cppy): New variable.

Change-Id: I584fcddc3430960098d65f1916278a7473249a87

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

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

gnu: python-scikit-learn: Update to 1.3.2.

* 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

gnu: python-matplotx: Disable test_png test.

* gnu/packages/python-xyz.scm (python-matplotx)[arguments]: Disable test_png
test.

Change-Id: I19a954786d828a1b717c9c4021ad7f5c6172366c

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

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