gnu: python-pyvips: Update to 3.0.0.

* gnu/packages/python-xyz.scm (python-pyvips): Update to 3.0.0.
[source]: Fetch from GitHub.
[build-system]: Use pyproject-build-system.
[arguments]<#:phases>: Delete the now unnecessary 'fix-build, 'fix-paths
and custom 'check phases. Also build in API mode.
[native-inputs]: Add pkg-config, python-setuptools, python-wheel. Remove
python-pytest-flake8, python-pytest-runner.
[propagated-inputs]: Add python-pkgconfig.
(python-pyvips-for-python-scooby): Do not delete the phase that was
deleted in the parent package.

Change-Id: I8b3ac54f5b118a565f7297cf455698e690197e78

gnu: python-symengine: Update to 0.14.1.

* gnu/packages/python-xyz.scm (python-symengine): Update to 0.14.1.
[native-inputs]: Replace cmake by cmake-minimal.

Change-Id: Ib2141353862c6549136b8880bd449eebdc2651bd

gnu: python-cram: Move to python-check.

* gnu/packages/python-xyz.scm (python-cram): Move from here ...
* gnu/packages/python-check.scm: ... to here.

* gnu/packages/rcm.scm: Replace python-xyz with python-check module.
* gnu/packages/benchmark.scm: Add python-check module.

Change-Id: I0192701e4d4890735a18cc60abd2782fed8db090

gnu: python-h5py: Update to 3.13.0.

* gnu/packages/python-xyz.scm (python-h5py): Update to 3.13.0.
[build-system]: Switch to pyproject-build-system.
[arguments]: Use gexps. Move a modified 'check phase after the 'install phase.
[native-inputs]: Add python-pytest-mpi, python-setuptools and python-wheel.

Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: python-h5py: Update input.

* gnu/packages/python-xyz.scm (python-h5py)[inputs]: Remove hdf5-1.10;
add hdf5.

Change-Id: I384e9571322f7c4b71f3c0d7144fec4131d84327

gnu: python-virtualenv-clone: Skip some tests.

* gnu/packages/python-xyz.scm (python-virtualenv-clone) [build-system]:
Switch to pyproject.
[arguments] <test-flags>: Skip 5 tests.
<phases>: Use default 'check.
[native-inputs]: Remove python-tox, python-coverage, and
python-hypothesis; add python-setuptools.

Change-Id: I0ecc55f694a03c7e3a41eb5acae0817adde1c0c9

gnu: Deprecate python-hdf4.

The project has changed the name and VCS URL
<https://github.com/fhs/python-hdf4> redirects to
<https://github.com/fhs/pyhdf>, see
<https://github.com/fhs/pyhdf/pull/22>.

* gnu/packages/python-xyz.scm (python-hdf4): Deprecate variable.
(python-pyhdf): New variable.

Change-Id: I785804a57fa520109a0ceb89263b181889e18bd1

gnu: Add python-imageio-freeimage.

* gnu/packages/python-xyz.scm (python-imageio-freeimage): New variable.
(python-imageio)[arguments]<#:phases>: Remove the freeimage substitution
from the 'fix-source phase. Delete the 'fix-failing-tests phase, add
test logic in #:test-flags instead.
[inputs]: Remove freeimage.

Change-Id: I842998baea1568e1d9d1328e4387d14867bd3bb2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pyopengl: Move to python-graphics.

* gnu/packages/python-xyz.scm (python-pyopengl,
  python-pyopengl-accelerate): Move from here ...
* gnu/packages/python-graphics.scm: ... to here.

* gnu/packages/xorg.scm: Add python-graphics module.

Change-Id: I8d9e374a1948330ab37bb148a1ad6274563f9f1b

gnu: python-pyqtgraph: Move to python-science.

* gnu/packages/python-xyz.scm (python-pyqtgraph): Move from here ...
* gnu/packages/python-science.scm: ... to here.

Change-Id: I3de3c6a71fb2c5c49b76e03a026eae7deaa55840

gnu: python-pyopengl-accelerate: Update to 3.1.9.

* gnu/packages/python-xyz.scm (python-pyopengl-accelerate): Update to 3.1.9.
[inputs]: Remove mesa and python-numpy.

Change-Id: I39acd590f02853ba9c45ce40d3c2e1ace27d00b5

gnu: python-pyopengl: Update to 3.1.9.

* gnu/packages/python-xyz.scm (python-pyopengl): Update to 3.1.9.
[native-inputs]: Add python-cython and python-numpy.

Change-Id: I8088e3745cabcf52d317413be2dca3e4c5a641b8

gnu: python-concurrent-log-handler: Disable tests.

* gnu/packages/python-xyz.scm (python-concurrent-log-handler)
[arguments] <tests?>: Disable as broken, and can't be skipped.
[native-inputs]: Remove python-pytest.

Change-Id: Id1ec3c647428d833b938cde7b7f3dd1028f5b2b7

gnu: python-hdf5storage: 0.1.19-0.7ee2a96.

* gnu/packages/python-xyz.scm (python-hdf5storage): 0.1.19-0.7ee2a96.
[source]: Switch to git-fetch and use the latest commit containing
fixes.
[native-inputs]: Remove python-nose; add python-pytest.

Change-Id: I6f90d311eccd455de0335d60b776a20d25c9f328

gnu: python-omegaconf: Update to 2.3.0.

* gnu/packages/python-xyz.scm (python-omegaconf): Update to 2.3.0.

Change-Id: Ib967d173695b4e46770787fc414141366620bdb4

gnu: python-twisted: Remove test artifacts.

* gnu/packages/python-xyz.scm (python-twisted)[arguments]<phases>: Extend
check phase to clean up test artifacts.

Change-Id: Ibbf04771dea4342fe66221a740a11ad9882b6038
Signed-off-by: Christopher Baines <mail@cbaines.net>

gnu: python-pdoc3: Update to 0.11.6.

* gnu/packages/python-xyz.scm (python-pdoc3): Update to 0.11.6.
[build-system]: Switch to pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

* gnu/packages/patches/python-pdoc3-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Deregester python-pdoc3-tests.patch.

Change-Id: I1cffb6272d5de4ca7037aa761c36002bd0d03318

gnu: python-pydbus: Fix build.

* gnu/packages/python-xyz.scm (python-pydbus) [bulid-system]: Switch to
pyproject.
[arguments] <tests?>: Disable as no provided in PyPI archive.
<phases>: Add 'fix-comparability-with-pygobject.
[native-inputs]: Add python-setuptools and python-wheel.
[description]: Start from a new line.

Change-Id: Ie859207b700ed9c864b119b25bc3fcb2d1c2b8b4

gnu: python-whatever: Update to 0.7.

* gnu/packages/python-xyz.scm (python-whatever): Update to 0.7.

Change-Id: I71bfbd02cd9f9e0302805af2568c9f8b0da27472

gnu: Remove python-typed-ast.

Failing to build not compatible with Python 3.8 onward, see
<https://github.com/python/typed_ast/issues/179>.

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

Change-Id: Id602f14bc985a542ae05cbf138b9c96b89920005