gnu: python-pyquery: Update to 2.0.1.

* gnu/packages/python-xyz.scm (python-pyquery): Update to 2.0.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore a test that requires network access.
[native-inputs]: Add python-pytest, python-pytest-cov,
python-requests, python-setuptools, python-webob, python-webtest,
python-wheel.
[propagated-inputs]: Sort inputs.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Remove python-anyjson.

This package is a leaf package in Guix, is stale for 13 years, and its
upstream repository is not even up anymore.

* gnu/packages/python-xyz.scm (python-anyjson): Delete variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Remove python-parameterizedtestcase.

This package is a leaf package in Guix, has been abandonned for 11
years (aside from a License change).

* gnu/packages/python-check.scm (python-parameterizedtestcase): Delete variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pyvcf: Use the fork python-pyvcf3.

* gnu/packages/bioinformatics.scm (python-pyvcf): Define in terms of
'deprecated-package'.
(python-pyvcf3): New variable.
(python-nanosv): Replace python-pyvcf by python-pyvcf3.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-jsonargparse: Update to 4.37.0.

* gnu/packages/python-xyz.scm (python-jsonargparse): Update to 4.37.0.
[arguments]{test-flags}: Remove uneeded test-flags.
[propagated-inputs]: Remove python-contextvars,
python-docstring-parser, python-pyyaml, python-typeshed-client.
[native-inputs]: Add python-pypa-build. Remove python-coverage,
python-pycodestyle, python-tox, python-types-requests.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-databricks-cli: Update to 0.18.0.

* gnu/packages/python-web.scm (python-databricks-cli): Update to
0.18.0.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style, use gexps.
[native-inputs]: Add python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-cchardet: Update to 2.2.0a2.

* gnu/packages/freedesktop.scm (python-cchardet): Update to 2.2.0a2.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-zeroc-ice: Update to 3.7.10.1.

* gnu/packages/python-xyz.scm (python-zeroc-ice): Update to 3.7.10.1.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-css-parser: Update to 1.0.10.

* gnu/packages/python-web.scm (python-css-parser): Update to 1.0.10.

Change-Id: I2775f4f7871582d066ed5d4bb1831bb666f730aa

gnu: abjad-ext-rmakers: Adjust inputs.

* gnu/packages/music.scm (abjad-ext-rmakers): [native-inputs]: Add
python-pytest-cov.

Change-Id: I33dd4f77533172acfbf5fb56ed0c7787845be60c

gnu: python-uqbar: Update to 0.7.2.

* gnu/packages/graphviz.scm (python-uqbar): Update to 0.7.2.
[arguments] <test-flags>: Run all tests; provide "--pyargs" option.
[propagated-inputs]: Remove python-sphinx-5 and python-sphinx-rtd-theme;
add python-sphinx.
[native-inputs]: Remove python-flake8, python-isort, and python-mypy;
add python-defusedxml and python-typing-extensions.

Change-Id: I530799178e6d99ec097325b05c65770d3af8f732

gnu: python-ont-fast5-api: Update to 4.1.3.

* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.1.3.

Change-Id: I8dc6f2a911624b62fbf419b28cfad840200a207c

gnu: python-js2py: Update to 0.74.

* gnu/packages/python-web.scm (python-js2py): Update to 0.74.
[build-system]: Swap to pyproject-build-system.
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.
[propagated-inputs]: Remove python-six; add python-numpy.

Change-Id: I0b2a31241fd2c075c8555a921b805e254436de6a

gnu: python-iced: Update to 0.5.13.

* gnu/packages/bioinformatics.scm (python-iced): Update to 0.5.13.
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.

Change-Id: I2251b0ba37dab29bf82a2db73be1e05fee11c34e

gnu: labelme: Update to 5.2.1, fix build.

* gnu/packages/image-processing.scm (labelme): Update to 5.2.1, improve
package style.
[source] <uri>: Remove trailing ".git" from URL.
[build-system]: Swap to pyproject-build-system.
[arguments]: Use G-expressions.
<test-flags>: Utilize it.
<phases>: Use default 'check, remove 'loosen-requirements
[propagated-inputs]: Add python-natsort.
[description]: Fix indentation.

Change-Id: I9552637358ea7b6335d99f49a63cbedbe4984302

gnu: python-docrepr: Disable tests.

* gnu/packages/documentation.scm: Add (guix build-system pyproject)
and (gnu packages python-build).
(python-docrepr) [build-system]: Swap to pyproject-build-system.
[arguments] <test?>: Disable them as all fail.
<phases>: Use default 'check.
[native-inputs]: Remove python-pytest and python-pytest-asyncio; add
python-setuptools and python-wheel.

Change-Id: I27fc1b56cb44efc2c261896c1429200ce83cc080

gnu: python-fastparquet: Update to 2024.11.0, fix build.

* gnu/packages/databases.scm (python-fastparquet): Update to 2024.11.0.
[native-inputs]: Remove python-pytest-runner; add python-pytest, python-setuptools,
and python-wheel.

Change-Id: I4a798972077cd1646e48cea28b4bc369a7a68fd1

gnu: python-crosshair: Update to 0.0.84, fix build.

* gnu/packages/check.scm (python-crosshair): Update to 0.0.84.
[phases] {fix-dependencies}: Adjust version check for z3-solver.
[propagated-inputs]: Add python-importlib-metadata, python-packaging,
and python-typing-extensions.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I31a1ee4dbd57aa6c3382006c7f02772ff205277f

gnu: python-quadpy: Deselect one failing test.

* gnu/packages/maths.scm (python-quadpy) [arguments] <test-flags>:
Deselect one failing test.

Change-Id: I29ab3db45afb70928125773644b8704f9b731ada

gnu: python-orthopy: Skip some tests, fix build.

* gnu/packages/maths.scm (python-orthopy) [arguments] <test-flags>: Skip
5 failing tests.

Change-Id: Ic5e55d9a8a054eaba9f685e134a366dbfaa9bd8d