gnu: python-opt-einsum: Use pyproject-build-system.

* gnu/packages/python-science.scm (python-opt-einsum)[build-system]: Use
pyproject-build-system.
[arguments]: Remove.
[native-inputs]: Remove python-pytest-pep8; add python-setuptools and
python-wheel.

Change-Id: I6da632c3c7e02ec13ab61124ce2984aa2675d996

gnu: python-pytest-flakes: Use pyproject-build-system.

* gnu/packages/check.scm (python-pytest-flakes)[build-system]: Use
pyproject-build-system.
[arguments]: Remove custom 'check phase; use #:test-flags instead.
[native-inputs]: Remove python-pytest-pep8; add python-setuptools and
python-wheel.

Change-Id: I510ed41d7750e4024c404322c60deae4291dc9b7

gnu: d-feet: Deprecate.

d-feet is no longer maintained and depends on the unmaintained python-pep8,
which is slated for removal.

* gnu/packages/gnome.scm (d-feet): Deprecate in favor of d-spy.

Change-Id: I57908295e78aeb9013a2d3290b53981fb687e283

gnu: python-shortuuid: Update to 1.0.13.

* gnu/packages/python-xyz.scm (python-shortuuid): Update to 1.0.13.
[native-inputs]: Remove python-pep8; add python-poetry-core and python-pytest.
[build-system]: Use pyproject-build-system.

Change-Id: If854af9296fa378c505e83d87bacf609978edf9f

gnu: python-multiprocess: Update to 0.70.17.

* gnu/packages/python-xyz.scm (python-multiprocess): Update to 0.70.17.
[arguments]{phases}: Use gexps. Remove phase
'disable-broken-tests. Improve phase 'check.

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

gnu: python-dill: Update to 0.3.9.

* gnu/packages/python-xyz.scm (python-dill): Update to 0.3.9.
[arguments]{phases}: Rewrite using gexp. Adapt 'check phase.
[native-inputs]: Remove python-nose.

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

gnu: Remove python-flake8-pie.

* gnu/packages/python-xyz.scm (python-flake8-pie): Delete variable.

Change-Id: I094d1b46090473f4cdb19bf40088d717c574f778

gnu: python-protobuf: Update to 3.20.3.

* gnu/packages/protobuf.scm (python-protobuf): Update to 3.20.3.
[inputs]: Use protobuf-3.20.
[arguments]: Do not use C++ implementation.

Change-Id: I21d140ce2959b009026847b1ad73c15dfa23fd91

gnu: protobuf: Update to 3.20.3.

* gnu/packages/protobuf.scm (protobuf): Update to 3.20.3.

Change-Id: I451913a3f379f7bad1f6cea56fb6b028627984bb

gnu: python-ml-collections: Update to 1.0.0.

* gnu/packages/machine-learning.scm (python-ml-collections): Update to 1.0.0.
[source]: Fetch from git repository.
[arguments]: Remove custom 'check phase; use test-flags instead.
[propagated-inputs]: Remove python-six.
[native-inputs]: Remove python-mock, python-setuptools, and python-wheel; add
python-pylint, python-pytest-xdist, and python-flit-core.

Change-Id: Icdd340d138a14eaa5b1972d53b4a788a2a0e830e

gnu: Remove python-contextlib2.

This was a backport of the Python 3.10 version of contextlib.

* gnu/packages/python-xyz.scm (python-contextlib2): Remove variable.
* gnu/packages/machine-learning.scm (python-ml-collections)
[propagated-inputs]: Remove it.

Change-Id: I47e4eccf98d8caa18235008e94a0849e21975a68

gnu: Remove python-pyblake2.

This package no longer builds with Python 3.11.  Since Python 3.6 and later
have native support for BLAKE2 in hashlib derived from this implementation,
with compatible API, it is no big loss to remove this package.

* gnu/packages/python-crypto.scm (python-pyblake2): Remove variable.

Change-Id: Ia540ce0ee2cae10ee5fb5527b5fc90bb6db2be9b

gnu: python-astropy: Skip one more test.

* gnu/packages/astronomy.scm (python-astropy) [arguments] <test-flags>:
Skip one more failing test.

Change-Id: Iea781139001dedac966365da2e7c3fca7094ec81

gnu: python-paramz: Fix tests.

* gnu/packages/python-science.scm (python-paramz)
[arguments] <test-flags>: Make them compatible with Pytest to allow some
adjustments.
[native-inputs]: Remove python-nose; add python-pytest.

Change-Id: I66fbd374ce30e80f02fe43784740389a33783011

gnu: python-pywavelets: Update to 1.8.0.

* gnu/packages/python-xyz.scm (python-pywavelets): Update to 1.8.0.
[source]: Remove obsolete snippet.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'pre-check phase.
[native-inputs]: Replace python-cython with python-cython-3; remove
python-matplotlib; add meson, ninja, pkg-config, python-meson-python, and
python-numpy.
[propagated-inputs]: Add python-scipy.

Change-Id: I1d157775a2079e2a218dea89ab46bbd01685d91a

gnu: python-cmd2: Update to 2.5.11.

* gnu/packages/python-xyz.scm (python-cmd2): Update to 2.5.11.
[propagated-inputs]: Remove python-attrs and python-colorama.
[native-inputs]: Remoe python-invoke and python-mock.

Change-Id: I97b98a7eb39e8dd2c83e837cd08ab52965b8a58c

gnu: python-wcwidth: Update to 0.2.13.

* gnu/packages/python-xyz.scm (python-wcwidth): Update to 0.2.13.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-pytest, python-pytest-cov, python-setuptools, and
python-wheel.

Change-Id: I50b427532a834026ca5dac869440df1216148cad

gnu: python-numpy: Update to 1.26.2.

* gnu/packages/python-xyz.scm (python-numpy): Update to 1.26.2.
[arguments] <phases>: Add 'hide-gfortran.
[native-inputs]: Remove python-cython.

Change-Id: I1f02d45dd5c5bc7ad248dbbdc63a8e6a7a21ca9f
Reviewed-by: Ludovic Courtès <ludo@gnu.org>

gnu: mozjs-78: Fix build with Python 3.11.

* gnu/packages/gnuzilla.scm (mozjs-78):[arguments]: Add phase
'python-3.11-compatibility.

Change-Id: I9178a2f8a6880bbcc2d712a1a9ccecd300242370

gnu: mozjs: Fix build with Python 3.11.

* gnu/packages/gnuzilla.scm (mozjs):[arguments]: Add phase
'python-3.11-compatibility.

Change-Id: I0d02ff98f69bab9df405550c75d5e13a741389d6