diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 4ee152d1e70..7f033fcc979 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -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 diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 2d3d005227a..7f68b110aa3 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -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 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b82ec381579..9f0fbd01351 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm index 15a072849b8..957cd5dc567 100644 --- a/gnu/packages/build-tools.scm +++ b/gnu/packages/build-tools.scm @@ -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 diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 27b6df3b86e..35306d062c6 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -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)) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 6b4fca95da0..27443b19da3 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -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 diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 394903ee2af..656df347895 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -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)) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 36d1ec1d490..02152d6719d 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -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 diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 8d918338efc..13890adfb32 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -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 diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 1d36ed00d5b..b190b74b47f 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -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") diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index 57b723c8116..03d07325bd8 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -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 diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index c4efd30ea52..c02993ededb 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -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)) diff --git a/gnu/packages/python-graphics.scm b/gnu/packages/python-graphics.scm index ae870013403..d75f0edd2ed 100644 --- a/gnu/packages/python-graphics.scm +++ b/gnu/packages/python-graphics.scm @@ -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 diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 12a0dc7d20b..cb701a0c7d5 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -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 diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 016ac6a1daa..3f86ce395a7 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -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 diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f743fd98dc2..85c3b570070 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -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 diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 4fad4d30cab..f70c5370093 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -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 diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 5d04470960b..52e898ea028 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -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 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d0d7be3ae7a..ba3b792e377 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -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") diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 2eb73704d43..b01431bba05 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -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)) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index b3162b492ee..f7e53176558 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -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"