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
gnu: unbound: Update to 1.24.1. [security-fixes] This security release fixes CVE-2025-11411. * gnu/packages/dns.scm (unbound): Update to 1.24.1. [native-inputs]: Add pkg-config. Change-Id: Ife2840c8657e75e19810634454b20e6cb90c0675 Signed-off-by: Andreas Enge <andreas@enge.fr>
gnu: ruby-3.4: Update to 3.4.7. Includes an update to the uri gem addressing CVE-2025-61594. * gnu/packages/ruby.scm (ruby-3.4): Update to 3.4.7. Change-Id: Ib5892b938e9ccabf38fc8110ce137f130e0b5031 Signed-off-by: Andreas Enge <andreas@enge.fr>
gnu: quodlibet: Correct deprecated input. * gnu/packages/music.scm (quodlibet)[inputs]: Replace keybinder-3.0 by keybinder. Change-Id: Ie0b4cd7b4676791116d6c3ce9f5432bd2eda0953
gnu: musikcube: Update to 3.0.5. * gnu/packages/music.scm (musikcube): Update to 3.0.5. [inputs]: Remove ffmpeg-4; add ffmpeg. Change-Id: I63b41bf43b3b4c0bec506ccaaad68eaad3443528
gnu: stringtie: Update to 3.0.2. * gnu/packages/bioinformatics.scm (stringtie): Update to 3.0.2. Change-Id: Ie35084c70ad6c91b9e03b09ec6fe4f825bd39dcd