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

Browse source 
This is a followup to 941b6ff1c1 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
This commit is contained in:
Sharlatan Hellseher 2025-10-24 09:22:20 +01:00
parent 180425422c
commit cbad86a985
No known key found for this signature in database
GPG key ID: 76D727BFF62CD2B5
21 changed files with 67 additions and 66 deletions
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4
gnu/packages/algebra.scm
View file

@ -237,7 +237,7 @@ the real span of the lattice.")
(inputs
(list fplll gmp mpfr pari-gp))
(propagated-inputs
(list python-cysignals python-cython-3 python-flake8 python-numpy))
(list python-cysignals python-cython python-flake8 python-numpy))
(home-page "https://github.com/fplll/fpylll")
(synopsis "Python interface for fplll")
(description "fpylll is a Python wrapper for fplll.")
@ -550,7 +550,7 @@ fast arithmetic.")
(native-inputs
(list meson-python
pkg-config
python-cython-3
python-cython
python-pytest))
(inputs
(list gmp

32
gnu/packages/astronomy.scm
View file

@ -2893,7 +2893,7 @@ constraints (i.e., altitude, airmass, moon separation/illumination, etc.)
(native-inputs
(list nss-certs-for-test
pkg-config
python-cython-3
python-cython
python-extension-helpers
python-objgraph
python-pytest
@ -3051,7 +3051,7 @@ celestial-to-terrestrial coordinate transformations.")
(native-inputs
(list nss-certs-for-test
pkg-config
python-cython-3
python-cython
python-extension-helpers
python-setuptools-scm))
(propagated-inputs
@ -3155,7 +3155,7 @@ online Astronomical data. Each web service has its own sub-package.")
(make-file-writable "astroscrappy/_compiler.c")
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(native-inputs
(list python-cython-3
(list python-cython
python-extension-helpers
python-pytest-astropy
python-scipy
@ -4798,7 +4798,7 @@ default) to world coordinates.")
(setenv "HOME" "/tmp")
(apply invoke "pytest" "-vv" test-flags))))))))
(native-inputs
(list python-cython-3
(list python-cython
python-extension-helpers
python-pytest
python-pytest-astropy
@ -4884,7 +4884,7 @@ sensitivity or energy density
(native-inputs
(list nss-certs-for-test
pkg-config
python-cython-3
python-cython
python-pytest
python-pytest-astropy-header
python-pytest-cython
@ -5538,7 +5538,7 @@ quantification of galaxies, quasar-host galaxy decomposition and much more.")
(setenv "TEMPO2_PREFIX" tempo2)
(setenv "TEMPO2" tempo2-runtime)))))))
(native-inputs
(list python-cython-3
(list python-cython
python-numpy
python-pytest
python-setuptools
@ -5607,7 +5607,7 @@ emission lines in 1-D spectra, especially galaxy and quasar spectra.")
(arguments
(list #:tests? #f)) ; no tests provided
(native-inputs
(list python-cython-3
(list python-cython
python-setuptools
python-wheel))
(propagated-inputs
@ -5649,7 +5649,7 @@ solutions generated by NDPPP.")
;; <.github/workflows/python.yml>.
(invoke "python" "tools/losoto_test.py")))))))
(native-inputs
(list python-cython-3
(list python-cython
python-setuptools
python-wheel))
(propagated-inputs
@ -5962,7 +5962,7 @@ photometry, segmentations, Petrosian profiling, and Sérsic fitting.")
(with-directory-excursion "/tmp"
(apply invoke "pytest" "-vv" test-flags))))))))
(native-inputs
(list python-cython-3
(list python-cython
python-extension-helpers
python-pytest-astropy
python-pytest-xdist
@ -7082,7 +7082,7 @@ Virtual observatory (VO) using Python.")
python-unyt
python-yt))
(native-inputs
(list python-cython-3
(list python-cython
python-setuptools
python-setuptools-scm
python-wheel))
@ -7302,7 +7302,7 @@ solar physics.")
python-scipy
python-shapely))
(native-inputs
(list python-cython-3
(list python-cython
python-extension-helpers
python-pytest-arraydiff
python-pytest-astropy
@ -7404,7 +7404,7 @@ setup(ext_modules=get_extensions())")))))
python-shapely
python-zarr))
(native-inputs
(list python-cython-3
(list python-cython
python-extension-helpers
python-asdf
python-gwcs
@ -7889,7 +7889,7 @@ framework of lens modelling software lenstronomy.")
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(native-inputs
(list ;; python-iminuit ; not packed, optional
python-cython-3
python-cython
python-pytest
python-pytest-astropy
python-setuptools
@ -7950,7 +7950,7 @@ to make such analysis both as flexible and clear as possible.")
" and not "))))
(native-inputs
(list nss-certs-for-test
python-cython-3
python-cython
python-poetry-core
python-pytest))
(propagated-inputs
@ -8497,7 +8497,7 @@ and CAS statistics), as well as fitting 2D Sérsic profiles.")
;; might not set the version correctly.
((".*opencv-python-headless.*") "")))))))
(native-inputs
(list python-cython-3
(list python-cython
python-psutil
python-pytest
python-pytest-xdist
@ -9565,7 +9565,7 @@ using (multivariate) polynomials.")
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(native-inputs
(list nss-certs-for-test
python-cython-3
python-cython
python-pyaml
python-pytest
python-pytest-mpl

4
gnu/packages/bioinformatics.scm
View file

@ -9989,7 +9989,7 @@ sequencing tag position and orientation.")
python-scikit-learn
python-scipy))
(native-inputs
(list python-cython-3
(list python-cython
python-pytest
python-setuptools
python-wheel
@ -20056,7 +20056,7 @@ bgzipped text file that contains a pair of genomic coordinates per line.")
(propagated-inputs (list python-archspec))
(native-inputs
(list cmake-minimal
python-cython-3
python-cython
python-scikit-build-core))
(home-page "https://github.com/althonos/pyrodigal")
(synopsis "Cython bindings and Python interface for Prodigal")

4
gnu/packages/build-tools.scm
View file

@ -371,7 +371,7 @@ resembles Python.")
(list meson
ninja/pinned
python-colorama
python-cython-3
python-cython
python-pyproject-metadata
python-tomli
python-typing-extensions
@ -381,7 +381,7 @@ resembles Python.")
git-minimal/pinned
patchelf
pkg-config
python-cython-3
python-cython
python-gitpython
python-pytest
python-pytest-cov

6
gnu/packages/databases.scm
View file

@ -828,7 +828,7 @@ the API, and provides features such as:
#:tests? #f
#:build-backend "setuptools.build_meta"))
(native-inputs
(list python-cython-3
(list python-cython
python-setuptools
python-wheel))
(propagated-inputs
@ -4772,7 +4772,7 @@ with the @code{psycopg} PostgreSQL driver.")
(invoke "psql" "-h" dbdir "-d" "postgres"
"-c" "CREATE DATABASE nixbld;"))))))))
(native-inputs
(list python-cython-3
(list python-cython
python-mypy
python-psycopg-pool
python-pytest
@ -5582,7 +5582,7 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
(native-inputs
(list cmake ;needs 3.25
pkg-config
python-cython-3
python-cython
python-pytest
python-pytest-runner
python-setuptools-scm))

2
gnu/packages/finance.scm
View file

@ -2437,7 +2437,7 @@ interactive controls. This package provides a GTK+ graphical user interface
(invoke "make" "cython"))))))
(inputs (list ta-lib))
(propagated-inputs (list python-numpy))
(native-inputs (list python-cython-3
(native-inputs (list python-cython
python-pandas
python-pytest
python-setuptools

2
gnu/packages/game-development.scm
View file

@ -1684,7 +1684,7 @@ developed mainly for Ren'py.")
(setenv "SDL_AUDIODRIVER" "disk"))))))
(native-inputs (list meson-python
pkg-config
python-cython-3
python-cython
python-numpy
python-pytest
python-setuptools))

4
gnu/packages/geo.scm
View file

@ -1094,7 +1094,7 @@ for seismology.")
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(propagated-inputs (list python-certifi python-numpy python-packaging))
(inputs (list gdal))
(native-inputs (list python-cython-3
(native-inputs (list python-cython
python-pytest
python-pytest-cov
python-setuptools
@ -2043,7 +2043,7 @@ extension.")
(with-directory-excursion #$output
(apply invoke "pytest" "-vv" test-flags)))))))
(native-inputs
(list python-cython-3
(list python-cython
python-pytest
python-setuptools
python-setuptools-scm

4
gnu/packages/machine-learning.scm
View file

@ -2117,7 +2117,7 @@ computing environments.")
(native-inputs
(list gfortran
meson-python
python-cython-3
python-cython
python-pandas
python-pytest
python-pytest-xdist))
@ -2360,7 +2360,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
(setenv "NUMBA_CACHE_DIR" "/tmp")
;; Rebuild extensions to run tests.
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(native-inputs (list python-cython-3 python-pytest python-setuptools
(native-inputs (list python-cython python-pytest python-setuptools
python-wheel))
(inputs (list fftw))
(propagated-inputs (list python-numpy python-pynndescent

8
gnu/packages/maths.scm
View file

@ -3017,7 +3017,7 @@ and quadratic objectives using the Simplex algorithm.")
(propagated-inputs (list python-numpy python-pytest python-scipy))
(inputs (list cbc))
(native-inputs (list pkg-config
python-cython-3
python-cython
python-hypothesis
python-numpy
python-pytest
@ -4651,7 +4651,7 @@ can return results in exact arithmetic.")
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "test/runtests.py")))))))
(native-inputs (list python-cython-3))
(native-inputs (list python-cython))
(inputs (list petsc-openmpi python-numpy))
(home-page "https://bitbucket.org/petsc/petsc4py/")
(synopsis "Python bindings for PETSc")
@ -4681,7 +4681,7 @@ bindings to almost all functions of PETSc.")
(list #:tests? #f)) ; there are no tests
(native-inputs
(list python-cysignals
python-cython-3
python-cython
python-setuptools
python-wheel))
(inputs
@ -4948,7 +4948,7 @@ arising after the discretization of partial differential equations.")
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "test/runtests.py")))))))
(native-inputs (list python-cython-3))
(native-inputs (list python-cython))
(inputs (list python-numpy python-petsc4py petsc-openmpi slepc-openmpi))
(home-page "https://bitbucket.org/slepc/slepc4py/")
(synopsis "Python bindings for SLEPc")

2
gnu/packages/python-check.scm
View file

@ -1339,7 +1339,7 @@ result documents that can be read by tools such as Jenkins or Bamboo.")
;; sync. kernprof.line_profiler = . kernprof.__version__ = 4.2.0.
#~(list "--deselect=tests/test_cli.py::test_version_agreement")))
(native-inputs
(list python-cython-3
(list python-cython
python-pytest
python-setuptools
python-ubelt

2
gnu/packages/python-compression.scm
View file

@ -138,7 +138,7 @@ This Python package wraps the Blosc library.")
(native-inputs
(list cmake-minimal
pkg-config
python-cython-3
python-cython
python-pytest
python-scikit-build
python-setuptools))

2
gnu/packages/python-graphics.scm
View file

@ -819,7 +819,7 @@ wrappers for common SDL2 functionality.")
(setenv "HOME" "/tmp")
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(native-inputs
(list python-cython-3
(list python-cython
python-pytest
python-setuptools
python-setuptools-scm

12
gnu/packages/python-science.scm
View file

@ -2406,7 +2406,7 @@ Evapotranspiration using various standard methods.")
(with-directory-excursion (site-packages inputs outputs)
(for-each delete-file (find-files "." "test*"))))))))
(native-inputs
(list python-cython-3 python-pytest python-setuptools python-wheel))
(list python-cython python-pytest python-setuptools python-wheel))
(propagated-inputs
(list python-numpy))
(home-page "https://github.com/storpipfugl/pykdtree")
@ -2591,7 +2591,7 @@ factorization routine for quasi-definite linear system.")
(with-directory-excursion #$output
(apply invoke "pytest" "-vv" test-flags))))))))
(propagated-inputs (list python-numpy python-packaging python-scipy))
(native-inputs (list python-cython-3
(native-inputs (list python-cython
python-numpy
python-packaging
python-pytest
@ -2975,7 +2975,7 @@ logic, also known as grey logic.")
python-spin))
(native-inputs (list gfortran
pkg-config
python-cython-3
python-cython
python-meson-python
python-numpy
python-pytest
@ -3106,7 +3106,7 @@ be accessible and easy to use in many contexts.")
;; permission.
(setenv "HOME" "/tmp"))))))
(native-inputs
(list python-cython-3
(list python-cython
python-pandas
python-pytest
python-setuptools
@ -3839,7 +3839,7 @@ tissue-specificity metrics for gene expression.")
(native-inputs
(list meson-python
python-beautifulsoup4
python-cython-3
python-cython
python-html5lib
python-lxml
python-matplotlib
@ -4590,7 +4590,7 @@ readable.")
python-six
python-tabulate))
(native-inputs
(list python-pytest python-cython-3 python-setuptools python-wheel))
(list python-pytest python-cython python-setuptools python-wheel))
(home-page "https://www.github.com/maartenbreddels/vaex")
(synopsis "Core of Vaex library for exploring tabular datasets")
(description "Vaex is a high performance Python library for lazy

8
gnu/packages/python-web.scm
View file

@ -1828,7 +1828,7 @@ for adding, removing and dropping callbacks.")
python-yarl))
(native-inputs
(list gunicorn-bootstrap
python-cython-3
python-cython
python-freezegun
python-pytest
python-pytest-cov
@ -2790,7 +2790,7 @@ AWS S3 Service using boto3 S3 resource as a driver.")
(native-inputs
(list python-aiofiles
python-cbor2
python-cython-3 ;for faster binaries
python-cython ;for faster binaries
python-fakeredis
python-httpx
python-mujson
@ -8297,7 +8297,7 @@ name resolutions asynchronously.")
(("build_inplace=False") "build_inplace=True")))))))
(native-inputs
(list python-covdefaults
python-cython-3
python-cython
python-expandvars
python-pytest
python-pytest-cov
@ -8936,7 +8936,7 @@ hard or impossible to fix in cssselect.")
(delete-file-recursively "uvloop")))))))
(native-inputs
(list python-aiohttp
python-cython-3
python-cython
python-psutil
python-pyopenssl
python-pytest

21
gnu/packages/python-xyz.scm
View file

@ -2184,7 +2184,7 @@ easy logging and rotating to a console or a file.")
(build-system pyproject-build-system)
(native-inputs
(list python-brotli
python-cython-3
python-cython
python-pytest
python-setuptools
python-wheel))
@ -5035,7 +5035,7 @@ of the netcdf4 package before.")
(setenv "NO_CDL" "1")
(invoke "python" "run_all.py"))))))))
(native-inputs
(list python-cython-3
(list python-cython
python-setuptools
python-wheel))
(propagated-inputs
@ -8072,7 +8072,7 @@ environments and back.")
(base32 "0gmwggzm0j0iprx074g5hah91y2f68sfhhldq0f8crddj7ndk16m"))))
(build-system pyproject-build-system)
(native-inputs
(list python-cython-3
(list python-cython
python-pytest
python-setuptools
python-wheel))
@ -10418,7 +10418,8 @@ writing C extensions for Python as easy as Python itself.")
;; time of the test suite.
(setenv "CFLAGS" "-O0"))))))))
(define-public python-cython-3 python-cython)
;; It may be removed after 2026-01-24.
(define-deprecated/public-alias python-cython-3 python-cython)
;; NOTE: when upgrading numpy please make sure that python-numba,
;; python-pandas and python-scipy still build, as these three packages are
@ -11438,7 +11439,7 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.
(("build_inplace=False") "build_inplace=True")))))))
(native-inputs
(list python-covdefaults
python-cython-3
python-cython
python-expandvars
python-pytest
python-pytest-cov
@ -13246,7 +13247,7 @@ a front-end for C compilers or analysis tools.")
(list meson
ninja
pkg-config
python-cython-3
python-cython
python-meson-python
python-numpy
python-pytest))
@ -20764,7 +20765,7 @@ document.")
(invoke "nose2" "-v" "symengine.tests"))
(format #t "test suite not run~%")))))))
(native-inputs (list cmake-minimal
python-cython-3
python-cython
python-nose2
python-setuptools
python-wheel))
@ -22065,7 +22066,7 @@ codebase to support both Python 2 and Python 3 with minimal overhead.")
(build-system pyproject-build-system)
(native-inputs (list meson-python
pkg-config
python-cython-3
python-cython
python-pytest
python-sphinx))
(home-page "https://github.com/sagemath/cysignals")
@ -24770,7 +24771,7 @@ from the header, as well as section details and data available.")
(build-system pyproject-build-system)
(propagated-inputs (list python-numpy))
(native-inputs
(list python-cython-3
(list python-cython
python-pytest
python-setuptools
python-setuptools-scm
@ -27194,7 +27195,7 @@ executed more than a given number of times during a given period.")
(substitute* "pyproject.toml"
((".*addopts.*") "")))))))
(native-inputs
(list python-cython-3
(list python-cython
python-pytest
python-pytest-asyncio
python-pytest-timeout

6
gnu/packages/sagemath.scm
View file

@ -199,7 +199,7 @@ represented as strings.")
"080p17yn8wjl973jnw15hz3dhxzp3db1bi4giw3c28d2brrki8qk"))))
(build-system pyproject-build-system)
(native-inputs
(list python-cython-3 python-pytest python-setuptools python-wheel))
(list python-cython python-pytest python-setuptools python-wheel))
(propagated-inputs
(list python-cysignals))
(inputs
@ -281,7 +281,7 @@ libraries GMO, MPFR and MPC.")
(base32 "1zggfj09zkfcabcsasq27vwbhdmkig4yn380gi6wykcih9n22anl"))))
(build-system pyproject-build-system)
(native-inputs
(list python-cython-3
(list python-cython
python-pytest
python-setuptools
python-wheel))
@ -381,7 +381,7 @@ database.")
(build-system pyproject-build-system)
(native-inputs
(list autoconf automake m4 pkg-config ; for ./bootstrap
python-cython-3
python-cython
python-cysignals
python-memory-allocator
python-pkgconfig

2
gnu/packages/sphinx.scm
View file

@ -152,7 +152,7 @@
(native-inputs
(list imagemagick ;for "convert"
nss-certs-for-test
python-cython-3
python-cython
python-defusedxml
python-flit-core
python-pytest

4
gnu/packages/statistics.scm
View file

@ -1403,7 +1403,7 @@ conformal prediction methods intervals.")
python-patsy
python-scipy))
(native-inputs
(list python-cython-3
(list python-cython
python-matplotlib
python-setuptools
python-setuptools-scm))
@ -3312,7 +3312,7 @@ files, including Rmarkdown files.")
(build-system python-build-system)
(propagated-inputs (list python-pandas))
(inputs (list libiconv zlib))
(native-inputs (list python-cython-3))
(native-inputs (list python-cython))
(home-page "https://github.com/Roche/pyreadstat")
(synopsis
"Read and write SAS, SPSS and Stata files into/from Pandas DataFrames")

2
gnu/packages/tor.scm
View file

@ -304,7 +304,7 @@ key, and private key are written to a new directory.")
(base32 "16yr25llnbgl2iwk458ca0rhrxsmpfx72q4gdg4a52i6g546p3hd"))))
(build-system pyproject-build-system)
(native-inputs
(list python-cython-3
(list python-cython
python-poetry-core
python-pytest
python-setuptools))

2
gnu/packages/xorg.scm
View file

@ -6616,7 +6616,7 @@ basic eye-candy effects.")
python-lz4 ; Faster compression than zlib.
python-netifaces
python-pycups))
(native-inputs (list pkg-config pandoc python-cython-3))
(native-inputs (list pkg-config pandoc python-cython))
(arguments
(list
#:configure-flags #~(list "--without-Xdummy"