gnu: behave: Replace python-pathpy by python-path.

* gnu/packages/check.scm (behave)[native-inputs]: Replace
python-pathpy by python-path.

Change-Id: I949a67d7beb9e047719a9e6e0d2b04ec0e67e3ed
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-cucumber-tag-expressions: Improve native-inputs.

* gnu/packages/python-check.scm (python-cucumber-tag-expressions)
[native-inputs]: Replace python-pathpy by python-path.  Remove
python-wheel.

Change-Id: I6bf242bd9f2abb8aeb1a1b17411e6ff9db4afcd7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Deprecate python-pip-run-bootstrap in favor of python-pip-run.

* gnu/packages/python-xyz.scm (python-pip-run-bootstrap): Deprecate
variable, which is not necessary anymore, was hidden, and is not used.
(python-pip-run): Rewrite it without inheritance.
[arguments]<#:test-flags>: Ignore additional failing test.
[native-inputs]: Add python-setuptools.
[propagated-inputs]: Add python-pip.

Change-Id: I5ba111f89c771a8d83dd222eb29bf88c652304f6
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Deprecate python-path-bootstrap in favor of python-path.

* gnu/packages/python-xyz.scm (python-path-bootstrap): Deprecate
variable, which is not necessary anymore, was hidden, and is not used.
(python-pathpy): Switch to DEFINE-DEPRECATED/PUBLIC-ALIAS.
(python-path): Rewrite it without inheritance.

Change-Id: I95647b7a12ddede97846ffcc89793855fac8beea
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-idna-ssl: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-idna-ssl):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.
[synopsis, description]: Improve them.

Change-Id: I5ef0c6d0276d90e887849d7db54f04b147100774
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pylru: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-pylru):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Remove 'check phase replacement in favor of
<#:test-backend, #:test-flags>.
[native-inputs]: Add python-pytest, python-setuptools.

Change-Id: I69ab2418da3cdc3043fd54a5a08f078f86f252c9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-llfuse: Update to 1.5.1.

* gnu/packages/python-xyz.scm (python-llfuse): Update to 1.5.1.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:test-flags>: Disable failing test.
<#:phases>: Add phase 'build-cython.
[native-inputs]: Add python-cython, python-setuptools.
[home-page]: Update it.

Change-Id: I7da8047a8157e7e77433b13856b1bbff7c37b1b7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-gorilla: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-gorilla):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:test-backend>: Set it.
[native-inputs]: Add python-setuptools.

Change-Id: Ie923f6c866c7e5b9f89d7cee3042f0593f551535
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-stopit: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-stopit):
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: I7557d16fb3e6a314553e8bac06fbd6a5f3ab82f7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-ly: Update to 0.9.9.

* gnu/packages/python-xyz.scm (python-ly): Update to 0.9.9.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.
[description]: Improve style.

Change-Id: I909000c3dba536c3bea1f1160630f5b6fd097485
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-quart-trio: Adjust inputs.

* gnu/packages/python-web.scm (python-quart-trio)[propagated-inputs]:
Remove python-hypercorn; add hypercorn.

Change-Id: I2a5bdcf7e1ec2b033f8bbda676084792c151e4f1

gnu: python-cython-3: Mark as deprecated.

This is a followup to 941b6ff1c11be3ba73e4e67bc661bd0eed3e9d58 commit.

Replace all python-cython-3 occurrences with python-cython.

* gnu/packages/python-xyz.scm (python-cython-3): Deprecate variable.

* gnu/packages/algebra.scm (python-fpylll, python-flint)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/astronomy.scm (python-astropy, python-astroscrappy,
python-halotools, python-healpy, python-libstempo, python-lofar-h5plot,
python-losoto, python-photutils, python-pyxsim, python-regions,
python-reproject, python-sncosmo, python-sndata, python-stcal,
python-yt)[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/bioinformatics.scm (macs-3, python-pyrodigal):
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/build-tools.scm (meson-python)[propagated-inputs]: Remove
python-cython-3; add python-cython.
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/databases.scm: (python-adbc-driver-manager,
python-psycopg, python-pyarrow)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/finance.scm (python-ta-lib)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/game-development.scm (python-pygame-ce)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/geo.scm (python-pyogrio, python-cf-units)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/machine-learning.scm: (python-scikit-learn,
python-opentsne)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/maths.scm: (python-cylp, python-petsc4py,
python-primecountpy, python-slepc4py)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/python-check.scm (python-line-profiler)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-compression.scm (python-blosc2)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-graphics.scm (python-vispy)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-science.scm: (python-pykdtree, python-qutip,
python-scikit-misc, python-scikit-surprise, python-pandas-2,
python-vaex-core)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/python-web.scm: (python-aiohttp, python-falcon,
python-yarl, python-uvloop)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/python-xyz.scm: (python-logbook, python-netcdf4,
python-pyyaml, python-propcache, python-pywavelets, python-symengine,
python-cysignals, python-pyemd, python-rbfly)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/sagemath.scm: (python-cypari2, python-pplpy, sage)
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/sphinx.scm (python-sphinx)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/statistics.scm: (python-statsmodels, python-pyreadstat):
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/tor.scm (onionshare-cli)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/xorg.scm (xpra)[native-inputs]: Remove python-cython-3;
add python-cython.

Change-Id: I38038d2ab18e6a7b549070083d6e4c5beb8b0293

gnu: python-pillow-heif: Update to 1.1.1.

* gnu/packages/python-xyz.scm (python-pillow-heif): Update to 1.1.1.
[native-inputs]: Remove python-coverage, python-pre-commit, python-pylint, and
python-wheel.

Change-Id: I2d0380ab52969fe4852f20ef2a72587283e5ef9c

gnu: python-pika: Update to 1.3.2.

* gnu/packages/python-xyz.scm (python-pika): Update to 1.3.2.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:test-flags>: Ignore failing tests.
<#:phases>: Replace 'check phase by 'configure-tests.
[native-inputs]: Add python-pytest, python-setuptools.  Remove
python-mock, python-nose2.

Change-Id: I06bf9f879a71b2718c2743cf305be2f06cb6c9ff
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-fastimport: Update to 0.9.16.

* gnu/packages/python-xyz.scm (python-fastimport): Update to 0.9.16.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:test-backend>: Set it.
[native-inputs]: Add python-setuptools.
[description]: Improve style.

Change-Id: Ie7888990f96ef1ffd01ef5bad02f54f81c1d1929
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-tftpy: Update to 0.8.6.

* gnu/packages/python-xyz.scm (python-tftpy): Update to 0.8.6.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:test-backend, #:test-flags, #:phases>: Replace 'check
phase replacement with these keywords.
[native-inputs]: Add python-setuptools.
[description]: Improve style.

Change-Id: Ic2e825e42e06eef1f570a7030b3461283ad2df86
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-py3status: Update to 3.62.

* gnu/packages/python-xyz.scm (python-py3status): Update to 3.62.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-hatchling.

Change-Id: Ia8bb3e6221d5a090e2f05b676e18719fa374670e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pkgconfig: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-pkgconfig):
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: I9cc62942bd9f1cc999e872b0278ef2ced4c29775
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: beancount: Ignore network-related failing tests.

* gnu/packages/finance.scm (beancount)[arguments]<#:test-flags>:
Ignore network-related failing tests.

Change-Id: Id6688a6b57bfb9e609d2e158fce57f4fe59022c2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-magic: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-magic):
[source]<modules, snippet>: Move them in phases.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:test-backend, #:test-flags>: Run tests.
<#:phases>: Remove 'check phase replacement.  Import phase 'fix-tests
from [source].  Improve style of phase 'hard-code-path-to-libmagic.
[native-inputs]: Add python-setuptools.
[description]: Improve style.

Change-Id: I0496e7e3b6f800e8358c133066e366ee144a24b3
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>