gnu: tombo: Switch to pyproject.

* gnu/packages/bioinformatics.scm (tombo) [build-system]: Switch to
pyproject-build-system.
[native-inputs]: Remove python-cython and python-nose2; add python-cython-0 and
python-setuptools.

Change-Id: Ib647da2feba5f0614428c9b70d7b18532b0a9e1c

gnu: python-rpy2: Delete sanity-check.

* gnu/packages/statistics.scm (python-rpy2) [arguments] <phases>: Delete
'sanity-check.
[propagated-inputs]: Remove python-six.
[native-inputs]: Remove python-coverage, python-ipython, python-numpy,
python-pandas, python-pytest-cov, and python-wheel.

Change-Id: Iac85261a8236d5b9746671a373da7fd6824c1a70

gnu: python-pyopengl-accelerate: Update to 3.1.10.

* gnu/packages/python-graphics.scm (python-pyopengl-accelerate): Update to 3.1.10.

Change-Id: I92b6b3ed8b18a5e07c647d209d8aa00840b5f7e9

gnu: python-hdbscan: Update to 0.8.40.

* gnu/packages/machine-learning.scm (python-hdbscan): Update to 0.8.40.
[arguments] <test-flags>: Ignore 3 test files.
<phases>: Add 'pre-check.
[native-inputs]: Remove python-nose, python-pandas, python-networkx, and
python-wheel; add python-numpy.

Change-Id: I38813d1cc16d4e90b5f0875dc93728bb42f4fa5d

gnu: python-kivy: Fix build.

* gnu/packages/python-graphics.scm (python-kivy)[native-inputs]:
Remove python-cython; add python-cython-0.

Change-Id: Ic37de9f525576a7a5dd8551c2db215f960c6dcf8

gnu: python-pygame-sdl2: Fix build.

* gnu/packages/game-development.scm (python-pygame-sdl2)
[native-inputs]: Remove python-cython; add python-cython-0.

Change-Id: I6b72a665daf0206c61a33fb30f4f775bf3977693

gnu: python-pybbi: Update to 0.4.1.

* gnu/packages/bioinformatics.scm (python-pybbi): Update to 0.4.1. Use
G-Expressions.
[build-system]: Switch to pyproject-build-system.
[arguments] <test-flags>: Skip tests requiring network access.
<phases>: Use default 'check; add 'remove-local-bbi.
[propagated-inputs]: Remove python-cython, python-pandas, and python-six.
[native-inputs]: Add python-cython, python-pandas, and python-setuptools.

Change-Id: I580999a2aa7ba3511752ba00f3c923a26ab2c426

gnu: python-pillow-simd: Don't inherit from python-pillow.

* gnu/packages/python-xyz.scm (python-pillow-simd): Don't inherit from
python-pillow.
[arguments] <test-flags>: Skip one more test.
[inputs]: Add freetype, lcms, libimagequant, libjpeg-turbo, libraqm,
libtiff, libwebp, openjpeg, and zlib.
[native-inputs]: Add python-check-manifest, python-defusedxml,
python-markdown2, python-olefile, python-packaging, python-pytest,
python-pytest-timeout, python-setuptools, and python-trove-classifiers.

Change-Id: Ie2473266b4d1447ece70b4da12cc17a9e7fbcf4a

gnu: python-pyaes: Disable tests.

* gnu/packages/python-crypto.scm (python-pyaes)[arguments] <tests?>:
Disable for now.
[native-inputs]: Remove python-wheel.

Change-Id: I6b1be9e4dab156ed36ddb2a57b080824f6388f11

gnu: python-js2py: Fix build.

* gnu/packages/python-web.scm (python-js2py) [propagated-inputs]: Remove
python-numpy; add python-six.
[native-inputs]: Remove python-pytest and python-wheel.

Change-Id: I5e18ac4c7eff8de3aa8858021d530b967c1a3529

gnu: python-memory-allocator: Disable tests.

* gnu/packages/sagemath.scm (python-memory-allocator)[arguments]
<tests?>: No tests provided.
[native-inputs]: Remove python-wheel.

Change-Id: I9568b8847e808ef3f61add0d14d8c2a6aa6a07c1

gnu: python-lightning-utilities: Disable tests.

* gnu/packages/machine-learning.scm (python-lightning-utilities)[arguments]
<tests?>: Most tests are broken.
[native-inputs]: Remove python-wheel.

Change-Id: I73e90cadff07d662e43dfced6227f0023382b76c

gnu: python-gpy: Fix tests.

* gnu/packages/machine-learning.scm (python-gpy)[arguments]
<test-flags>: Ignore 2 test files.

Change-Id: Ic529f0e913aaa7977503476f812c1d1293f5d2fc

gnu: python-yt-astro-analysis: Update to 1.1.4.

* gnu/packages/astronomy.scm (python-yt-astro-analysis): Update to 1.1.4.
[native-inputs]: Remove python-tomli, and python-wheel.

Change-Id: I877d19cb921b39970fb6125cad4a5055f4547c2f

gnu: onionshare-cli: Don't check wheel in sanity check.

python-wheel is less likely required during runtime at all, adjust
relaxation and remove it from native inputs completely.

* gnu/packages/tor.scm (onionshare-cli)[phases]{relax-requirements}:
Remove check for wheel package
[native-inputs]: Remove python-wheel; add python-setuptools.

Change-Id: Ifa6af72d70af364f744e93f84820d00bff6fd267

gnu: python-efl: Fix bulid.

* gnu/packages/enlightenment.scm (python-efl)[native-inputs]: Remove
python-cython; add python-cython-0.

Change-Id: I6899a268a0019774709e1e318ccf3966239e7098

gnu: python-yt: Skip some tests.

* gnu/packages/astronomy.scm (python-yt)[arguments]<test-flags>: Skip
one more test which fails on deprecation, ignore some documentation
tests.

Change-Id: I231adf3a785e8340523e4d2bf7291f8f13ffc116

gnu: python-txacme: Update to 0.9.3-0.ac18f92, fix build.

* gnu/packages/python-xyz.scm (python-txacme): Update to 0.9.3-0.ac18f92.
[source]: Switch to git-fetch and use the latest commit from trunk
branch.
[arguments] <test-backend>: Use 'custom.
<test-flags>: Provide option to run tests with twisted.
[native-inputs]: Remove python-fixtures, python-hypothesis, python-mock,
python-service-identity, python-testrepository, python-testscenarios,
and python-testtools; add python-setuptools.

Change-Id: Ifd7feb33bbca051e61f9eddf7b6e1a5026ec5568

gnu: breezy: Fix build with gcc-14.

* gnu/packages/version-control.scm (breezy)[arguments] <phases>: Add
'relax-gcc-14-strictness.
[phases]{check}: Skip one more test.
[native-inputs]: Remove python-cython; add python-cython-0.

Change-Id: Ibdaf1851d49b01e1a7f7c168ca9962e92155cfe7

gnu: python-mando: Update to 0.8.2.

* gnu/packages/python-xyz.scm (python-mando): Update to 0.8.2. Improve
style.
[bulid-system]: Switch to pyproject-bulid-system.
[arguments]: Drop all.
[propagated-inputs]: Remove python-rst2ansi and python-six.
[native-inputs]: Add python-setuptools.

Change-Id: I2ef5ca1c19e209404491be4a4fd616080d6ca744