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

1 files changed, 11 insertions, 10 deletions

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