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

gnu: python-peaks2utr: Update to 1.4.1 and fix build.

* gnu/packages/bioinformatics.scm (python-peaks2utr): Update to 1.4.1.
[arguments] <test-flags>: Skip 2 more similar failing test.
<phases>: Add 'relax-requirements.

Change-Id: Ia26903116915c4ef031b4a6bdb5dae64d109a1f4

gnu: python-gffutils: Update to 0.13 and fix build.

* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.13.
[build-system]: Swap to pypproject-build-system.
[arguments] <phases>: Use default 'check, add 'set-HOME.
[propagated-inputs]: Remove python-six.
[native-inputs]: Remove python-nose; add python-pytest,
python-setuptools, and python-wheel.

Change-Id: I77b1ed5be8750bdd2f2cdff3135430207b80f6fc

gnu: python-parabam: Add a maintenance note.

* gnu/packages/bioinformatics.scm (python-parabam): Add a maintenance
note on package build issue, reported upstream.

Change-Id: I447fa2354a2318b19d0eca5acf844a574e49db09

gnu: python-astroml: Disable more tests.

* gnu/packages/astronomy.scm (python-astroml) [arguments] <test-flags>:
Disable tests requiring NumPy, reported upstream.

Change-Id: I30693e2f3550ba8aab012b54d3d838508038c762

gnu: python-pyopenssl: Skip TestDTLS::test_timeout.

With the changes currently on the python-team branch, this seems to fail at
least on aarch64-linux, presumably due to faketime being used.

* gnu/packages/python-crypto.scm (python-pyopenssl)[arguments]: Skip
TestDTLS::test_timeout.

Change-Id: Ifca6dc323141219a01b9aff7baad8c712ac56b02

gnu: python-autograd: Fix indentation.

* gnu/packages/machine-learning.scm (python-autograd): Fix indentation.

Change-Id: I67b1c01d323e2458b49447969bb4164f71d1571b

gnu: python-autograd: Update to 1.7.0.

* gnu/packages/machine-learning.scm (python-autograd): Update to 1.7.0.
[source]: Use the latest version tag.
[native-inputs]: Remove python-nose, python-setuptools, and
python-wheel; add python-hatchling.

Change-Id: I42cd6b9ce621c1509f459fb947b09d05635fb79b

gnu: python-aiosmtpd: Update to 1.4.6.

* gnu/packages/mail.scm (python-aiosmtpd): Update to 1.4.6.
[build-system]: Switch to pyproject.
[arguments]{phases}: Delete it.
{test-flags}: Switch a QA test.
[native-inputs]: Remove python-flufl-testing, python-node.  Add
python-pytest, python-pytest-asyncio, python-pytest-cov,
python-pytest-mock, python-setuptools, python-wheel.

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

gnu: python-netaddr: Update to 1.3.0.

* gnu/packages/python-web.scm (python-netaddr): Update to 1.3.0.
[build-system]: Switch to pyproject.
[native-inputs]: Add python-poetry-core, python-pytest,
python-setuptools, python-wheel.

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

gnu: python-netaddr: Move to (gnu packages python-web).

* gnu/packages/python-xyz.scm (python-netaddr): Move from here…
* gnu/packages/python-web.scm (python-netaddr): …to here.

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