gnu: python-annotated-types: Update to 0.7.0.

* gnu/packages/python-xyz.scm (python-annotated-types): Update to 0.7.0.

Change-Id: I610b144339841768b4ce861d5457cf4184f756a2

gnu: macs-3: Add missing input.

* gnu/packages/bioinformatics.scm (macs-3)[native-inputs]: Add python-wheel.

Change-Id: I22b8d8e144434ae537af7c113f4719392933e90c

gnu: python-httpretty: Enable tests.

* gnu/packages/web.scm (python-httpretty)[arguments]: Enable most tests.
[native-inputs]: Add nss-certs-for-test, python-freezegun, python-httplib2,
and python-pyparsing.

Change-Id: I08d2c14a2e81559d41dc38f0eeb34c2d6c59125a

gnu: python-dulwich: Update to 0.21.7.

* gnu/packages/python-xyz.scm (python-dulwich): Update to 0.21.7.
[build-system]: Use pyproject-build-system.
[arguments]: Use #:test-flags; fix tests after 'unpack phase, split off
'pre-check phase.
[native-inputs]: Replace git with git-minimal/pinned; add python-mypy,
python-paramiko, python-pytest, python-requests, python-setuptools, and
python-wheel; remove python-mock and python-gpg.

Change-Id: I642de3e7707d545672066c6e59c9bcc2b5926097

gnu: python-geventhttpclient: Update to 2.3.3.

* gnu/packages/python-web.scm (python-geventhttpclient): Update to 2.3.3.
[source]: Fetch from git repository; remove snippet.
[build-system]: Use pyproject-build-system.
[arguments]: Use #:test-flags; remove all custom phases.
[native-inputs]: Add python-requests, python-setuptools, and python-wheel.
[propagated-inputs]: Remove python-six.

Change-Id: Ide97ffb7d656f58dd6693bd59ff82706bfea6caa

gnu: python-gevent: Propagate greenlet.

* gnu/packages/python-xyz.scm (python-gevent)[native-inputs]: Move
python-greenlet from here...
[propagated-inputs]: ...to here.
[arguments]: Adjust.

Change-Id: I5ebac1dd5e8c16b11e4855da78972c98f10cd285

gnu: python-eventlet: Update to 0.38.2.

* gnu/packages/python-xyz.scm (python-eventlet): Update to 0.38.2.
[native-inputs]: Add python-pre-commit.
[arguments]: Disable one more test.

Change-Id: I73638abba7d5363538d7c65254e610e704fbe5d0

gnu: python-gevent: Update to 24.11.1.

* gnu/packages/python-xyz.scm (python-gevent): Update to 24.11.1.
[build-system]: Use pyproject-build-system.
[arguments]: Use #:test-flags; enable more tests; rename
'add-greenlet-on-C_INCLUDE_PATH to 'augment-C_INCLUDE_PATH.
[propagated-inputs]: Remove python-greenlet.
[native-inputs]: Add python-cffi, python-coverage, python-greenlet,
python-idna, python-requests, python-setuptools, and python-wheel.
[inputs]: Add libuv.

Change-Id: Idd09ca01caf2977783c5a05eac2817b5630df327

gnu: python-pandas-2: Restrict number of test processes.

* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Restrict to at
most four processes.

Change-Id: I8ee4cb29ad922e9b853515b5f0e8f8aabca52c92

gnu: python-pandas-2: Remove X.

These tests are not run anyway, so there is no need to launch an X server.

* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Rename
'prepare-x phase to 'pre-check.
[native-inputs]: Remove xorg-server-for-tests.

Change-Id: Ib85883360397d2715a1893b74435d96a1d119f9e

gnu: python-pythran: Update to 0.17.0.

* gnu/packages/python-science.scm (python-pythran): Update to 0.17.0.
[build-system]: Use pyproject-build-system.
[source]: Remove obsolete snippet.
[arguments]: Remove phase 'do-not-install-third-parties and custom 'check
phase; use #:test-flags and add 'pre-check phase.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I49ebdd21cfb0668dd84f0d12c460a86ed694c7d6

gnu: python-beniget: Update to 0.4.2.post1.

* gnu/packages/python-xyz.scm (python-beniget): Update to 0.4.2.post1.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I03c53e97f1bb4ae7c13a4af2c7e4434137f764d6

gnu: python-gast: Update to 0.6.0.

* gnu/packages/python-xyz.scm (python-gast): Update to 0.6.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase.
[native-inputs]: Add python-setuptools and python-wheel.
[propagated-inputs]: Remove.

Change-Id: I3cc17b2c5434e637435f76482e0dcaf54c75c0dd

gnu: linkchecker: Update to 10.5.0.

* gnu/packages/web.scm (linkchecker): Update to 10.5.0. Improve package
style. Fix bulid.
[build-system]: Swap to pyproject-build-system.
[arguments]<test-flags>: Skip 2 tests.
<phases>: Add 'set-version. Use default 'check.
[inputs]: Remove python-pyxdg.
[native-inputs]: Remove lables. Remove gettext-minimal, python-miniboa,
and python-parameterized; add python-hatch-vcs, python-hatchling, and
python-setuptools-scm.

Change-Id: I2292be0305e8ad3991680ced6b154c48571e3efc

gnu: python-email-validator: Update to 2.2.0.

* gnu/packages/python-xyz.scm (python-email-validator): Update to
2.2.0. Improve style.
[build-system]: Swap to pyrpoject-build-system.
[arguments]<test-flags>: Skip one test.
<phases>: Remove 'use-dnspython as removed in
<https://github.com/JoshData/python-email-validator/pull/13>.
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.

Change-Id: Idc51ad58fe734071aa66f44bce0fb7cbf84831b6

gnu: python-dnspython: Update to 2.7.0.

* gnu/packages/python-xyz.scm (python-dnspython): Update to
2.7.0. Improve style.
[source]: PyPI archive has been swapped from .zip to .tar.gz.
[build-system]: Swap to pyproject-build-system.
[arguments]<test-flags>: Skip 2 tests.
[propagated-inputs]: Add python-cryptography, python-aioquic, python-h2,
python-httpcore, python-httpx, python-idna, and python-trio.
[native-inputs]: Remove unzip; add python-hatchling and python-pytest.

Change-Id: I726a9d68c61435089c1e7a846e8aa7c8b41f8378

gnu: python-joblib: Disable one additional test.

* gnu/packages/python-xyz.scm (python-joblib)[arguments]: Disable one more
test.

Change-Id: Id0b99ba3abb37bf49d26434b6719a7f6f77ee00a

gnu: python-starlette: Update to 0.42.0.

* gnu/packages/python-web.scm (python-starlette): Update to 0.42.0.

Change-Id: I2cdfadf4856e460f7b7cae9f8654a1806839b9ea

gnu: python-pydantic: Fix build.

As pyproject-build system now reads pytest config from pyproject.toml or
pytest.ini files it starts highlighting enabled "fail on warnings" which
were ignored before, this change silent it again.

* gnu/packages/python-xyz.scm (python-pydantic) [arguments]<test-flags>:
Skip 5 tests.
[phases]{pre-check}: Ignore all pytest warnings set in pyproject.toml.

Change-Id: I8551ba672d095b56f90955e4203c8a2aac270a4b

gnu: python-tox: Simplify.

* gnu/packages/python-check.scm (python-tox)[arguments]: Enable more tests;
remove phase 'virtualenv-compatibility.

Change-Id: I39a637cfc2385da74c11fc82ea811a26cf5f849a