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>

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: ableton-link: Fix build.

This addresses issue #3784.

* gnu/packages/audio.scm (ableton-link)[propagated-inputs]: Replace asio with asio-1.28.

Change-Id: Ic2571e89c5db461f2a54dd4f00c21725639dbe69
Signed-off-by: Gabriel Wicki <gabriel@erlikon.ch>

gnu: xlispstat: Fix compilation with modern GCC versions.

Package compilation would fail with modern GCC due to deprecated features that
are used in the package source code.  This patch updates the package to
modernize the source code to fix compilation errors (see
<https://github.com/jhbadger/xlispstat/pull/1>.)

* gnu/packages/statistics.scm (xlispstat): Fix compilation with GCC version 14
or newer.
[source]: Add a patch.
* gnu/packages/patches/xlispstat-fix-compilation-with-modern-gcc.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Register the patch.

Change-Id: I0f8b194887298fff196be7426a0de7eb247a8c48

gnu: guile-fibers: Update url.

* gnu/packages/guile-xyz.scm (guile-fibers): Update url to guile/fibers.

Change-Id: I1da9493f582710a7ff2f56b62c4ebcadf3faa68b

gnu: sosage: Update to 1.6.1.

* gnu/packages/games.scm (sosage): Update to 1.6.1.

Change-Id: I0b5fbb1ce5263c43f29b6b561ef278996d0d4f57