gnu: gourmet: Add missing input.

* gnu/packages/nutrition.scm (gourmet)[inputs]: Add python-toml.

Change-Id: I53bc9b0247c6dc32c5ec6e3cc518dbc982362bd2

gnu: python-pyrdfa3: Update to 3.6.2.

* gnu/packages/rdf.scm (python-pyrdfa3): Update to 3.6.2.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom build phases.
[propagated-inputs]: Add python-requests.

Change-Id: Ie8a1a369a569d29c8f43248d03f024e6cc19c004

gnu: python-clingraph: Update to 1.1.2.

* gnu/packages/potassco.scm (python-clingraph): Update to 1.1.2.

Change-Id: I5910853d39389ff9ad981543204fd8ef1445e495

gnu: python-astroml: Make compatible with recent Matplot and Scipy.

* gnu/packages/astronomy.scm (python-astroml)[arguments]: Add phases
'matplotlib-compatibility and 'scipy-compatibility.

Change-Id: Id88cf769f705f9326f41f951403583155bcee58f

gnu: python-bbknn: Update to 1.6.0.

* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.6.0.
[arguments]: Remove phase 'do-not-fail-to-find-sklearn.
[propagated-inputs]: Add python-pynndescent.
[native-inputs]: Add python-flit-core.

Change-Id: I5fca2d6ca52e54eb7650b3bb24a34a0aa47b1782

gnu: python-geopandas: Update to 0.14.2.

* gnu/packages/geo.scm (python-geopandas): Update to 0.14.2.
[arguments]: Disable test_pandas_kind tests.

Change-Id: I2a49d6ef73a79b84751ce0225757a2b83019cd42

gnu: python-dask: Propagate click.

* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Move python-click
from here...
[propagated-inputs]: ...to here.

Change-Id: I1a1617d9cb00268d9fc26f4fe6c9ecc6d0a2e375

gnu: python-xarray: Update to 2023.12.0.

* gnu/packages/python-science.scm (python-xarray): Update to 2023.12.0.
[arguments]: Ignore one test file.
[propagated-inputs]: Add python-packaging.

Change-Id: I6b70f59670f7bc8b56787fe3436579db8ac113bb

gnu: python-telomerecat: Disable tests.

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

Change-Id: I0422ae1e563374a8cc408fc9584cfb7b0e880e95

gnu: python-mysql-connector-python: Defuse time bomb.

Additional tests fail due to expired certificates.  Disable them.

* gnu/packages/python-xyz.scm (python-mysql-connector-python)[arguments]:
Disable six additional tests.

Change-Id: I99b5f15736af89c0281ab7aca56c1bd3958d1a46

gnu: python-adjusttext: Disable tests.

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

Change-Id: Ib1002de20a6e301f43bb34f64f7299d4316d8a67

gnu: python-scikit-bio: Update to 0.5.9.

* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.5.9.
[source]: Add patch.
[arguments]: Disable one test via #:test-flags; adjust 'compatibility phase;
update 'check phase.
[propagated-inputs]: Remove python-cachecontrol, python-lockfile, and
python-scikit-learn; add python-requests.
* gnu/packages/patches/python-scikit-bio-1887.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Change-Id: Ie57b0256cf695e5ea088545cd2102335303a93e7

gnu: python-pandas: Update to 1.5.3.

* gnu/packages/python-science.scm (python-pandas): Update to 1.5.3.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-expression; move test flags to #:test-flags; add phase
'patch-build-system; fix substitution of "which" executable; remove
'enable-parallel-build; remove custom 'check phase; add 'pre-check phase.
[propagated-inputs]: Add python-matplotlib.
[native-inputs]: Replace python-cython with python-cython-0.29.35.

Change-Id: I9d09971f707b925f469e29be67fe040c181314ff

gnu: python-click-default-group: Update to 1.2.4.

* gnu/packages/python-xyz.scm (python-click-default-group): Update to 1.2.4.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-flit-core and python-pytest.

Change-Id: I7e617ee57499542b7e832bb5ea24417b70e8cf85

gnu: datasette: Update to 1.0a7.

* gnu/packages/databases.scm (datasette): Update to 1.0a7.
[propagated-inputs]: Add python-asyncinject and python-sqlite-utils.

Change-Id: If713cd0f115c8092f9cc200daa850f9a78a20f6b

gnu: Add python-asyncinject.

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

Change-Id: I2647e8340bca2efabc222d19155d330b1a5ff16f

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

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

gnu: python-hicexplorer: Make compatible with latest scipy.

* gnu/packages/bioinformatics.scm (python-hicexplorer)[arguments]: Add
'scipy-compatibility phase.

Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad

gnu: python-hicmatrix: Update to 17.1.

* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 17.1.
[arguments]: Remove.

Change-Id: I6b1230d703d0dc1a88ee61a84cc6cd95f7eeb6f9