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

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

gnu: python-fit-nbinom: Disable tests.

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

Change-Id: I980480a3326dccc67930d34474832712005d1bb2

gnu: scvelo: Make compatible with latest matplotlib.

* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Add phase
'matplotlib-compatibility.

Change-Id: Ia761821c8aa1e516525cff7c680db471a5908e5f

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

gnu: python-demuxem: Disable tests.

* gnu/packages/bioinformatics.scm (python-demuxem)[arguments]: Disable tests,
because there aren't any.

Change-Id: I50364ca6744cf9d2704d4b75a8c79c4fdc4ada6e

gnu: python-pint: Update to 0.23.

* 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

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

gnu: python-plastid: Update to 0.6.1.

* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.1.
[arguments]: Disable four tests.

Change-Id: If0225f226e702e89d451e2955d0f76691a8816c0

gnu: cnvkit: Update to 0.9.10.

* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.10.
[arguments]: Remove.
[inputs]: Add r-minimal.

Change-Id: Iaa27fd3dddc507c7a955441f066d4b0e3b8f1757

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