21 files changed, 67 insertions(+), 66 deletions(-)

M gnu/packages/algebra.scm
M gnu/packages/astronomy.scm
M gnu/packages/bioinformatics.scm
M gnu/packages/build-tools.scm
M gnu/packages/databases.scm
M gnu/packages/finance.scm
M gnu/packages/game-development.scm
M gnu/packages/geo.scm
M gnu/packages/machine-learning.scm
M gnu/packages/maths.scm
M gnu/packages/python-check.scm
M gnu/packages/python-compression.scm
M gnu/packages/python-graphics.scm
M gnu/packages/python-science.scm
M gnu/packages/python-web.scm
M gnu/packages/python-xyz.scm
M gnu/packages/sagemath.scm
M gnu/packages/sphinx.scm
M gnu/packages/statistics.scm
M gnu/packages/tor.scm
M gnu/packages/xorg.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

@@ 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

@@ 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")

@@ 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

@@ 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))

@@ 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

@@ 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))

@@ 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

@@ 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

@@ 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")

@@ 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

@@ 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))

@@ 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

@@ 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

@@ 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

@@ 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

@@ 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

@@ 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

@@ 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")

@@ 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))

@@ 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"