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-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: 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>

gnu: python-slugid: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-slugid):
[build-system]: Switch to pyproject-build-system.
[arguments]: Replace <#:phases> by <#:test-backend>.
[native-inputs]: Add python-setuptools.  Replace python-nose by
python-pynose.
[description]: Improve style.

Change-Id: I784cb883f6ca4564e05635c89d18f173831c5a13
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-rarfile: Update to 4.2.

* gnu/packages/python-xyz.scm (python-rarfile): Update to 4.2.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style.
<#:phases>: Replace 'check phase with <#:test-backend, #:test-flags>.
Improve style of phase 'patch.
[native-inputs]: Add python-setuptools.
[description]: Improve style.

Change-Id: I754bd26e631110f7644f542028b5657ab9d328e7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Use ‘define-deprecated-package’ for deprecated packages.

Use ‘define-deprecated-package’ instead of (define x (deprecated-package …))
throughout gnu/packages/*.scm.

Change-Id: I4e176da9ac660327489dab256ca4d12c4e78fe8d

gnu: python-trio-websocket: Move to python-web.

* gnu/packages/python-xyz.scm (python-trio-websocket): Move from here ...
* gnu/packages/python-web.scm: ... to here.

Change-Id: Ifffadaa04808a64dc443b912a8bccfd4c7dcb8dd

gnu: python-trio-websocket: Update to 0.12.2.

* gnu/packages/python-xyz.scm (python-trio-websocket): Update to 0.12.2.
[arguments]: Drop all.
[propagated-inputs]: Remove python-async-generator; add python-outcome.
[native-inputs]: Remove python-wheel.

Change-Id: If494daa01c785ce59bed9b6b2fffb2de652c4375

gnu: python-twine: Update to 6.2.0.

* gnu/packages/python-xyz.scm (python-twine): Update to 6.2.0.
[arguments] <test-flags>: Skip one test.

Change-Id: Iec53cac9426e60946e83343f135198ef07790a34

gnu: Remove python-skranger.

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

Fixes: guix/guix#2921
Change-Id: I19b5ab9df38e4d41e3b01fe4fd9183a282bf9287

gnu: python-proselint: Update to 0.14.0.

* gnu/packages/python-xyz.scm (python-proselint): Update to 0.14.0.
[build-system]: Switch to pyproject-build-system.
[arguments] <tests?>: Enable.
[propagated-inputs]: Remove python-future and python-six.
[native-inputs]: Add python-poetry-core and python-pytest.

Change-Id: I8cf993f491a0445399040816c432ae59a2922ee9

gnu: python-nampa: Update to 1.0.0-0.cb6a63a

* gnu/packages/python-xyz.scm (python-nampa): Update to
cb6a63aae64324f57bdc296064bc6aa2b99ff99a commit.
[source]: Switch to git-fetch.
[arguments] <#:test-flags>: Disable test that uses yield.
<#:modify-phases>: Add 'patch-tests phase.
[native-inputs]: Remove python-wheel; add python-pytest.

Change-Id: I4d439370c6cc5ef8737944143b4c5c789c219bcb
Reviewed-by: Sören Tempel <soeren@soeren-tempel.net>
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pythondialog: Rename and update to 3.5.3.

* gnu/packages/python-xyz.scm
(python-pythondialog): Define in terms of 'deprecated-package'.
(python-dialog): New variable, formerly known as "python-pythondialog".
[source]: Update to 3.5.3. Improve style. Remove "doc" directory.
[build-system]: Switch to pyproject-build-system.
[arguments]<#phases>: Rewrite phase 'patch-path entirely.
[native-inputs]: Add python-setuptools.
[description]: Improve style.

Change-Id: I1360b4988e59b94e8c3d8e734ee2d58b56cd0baf
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-jsbeautifier: Update to 1.15.3.

* gnu/packages/python-xyz.scm (python-jsbeautifier): Update to 1.15.3.
[source, description]: Improve style.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Remove phase 'patch-python-six-requirements.
Rename setup-js.py in phase 'chdir.
[native-inputs]: Add python-setuptools.

Change-Id: Ic4be59402b3a1fe2a6a7eb670cd79cb28682b8f2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>