[Debian-med-packaging] Bug#1055709: python-bx ftbfs with Python 3.12

[Matthias Klose]

Package: src:python-bx
Version: 0.9.0-1
Severity: important
Tags: sid trixie
User: debian-python at lists.debian.org
Usertags: python3.12

Error compiling Cython file:
------------------------------------------------------------
...
         #p_rval[i] = NIB_I2C_TABLE[ p_data[0] & 0xF ]
         p_rval[i] = NIB_I2C_TABLE_SECOND[ p_data[0] ]
         p_data = p_data + 1
         i = 1
     # Two output values for each input value
     for j from 0 <= j < (length-i)/2:
                                   ^
------------------------------------------------------------

lib/bx/seq/_nib.pyx:45:34: Cannot assign type 'double' to 'int'
Compiling lib/bx/seq/_nib.pyx because it changed.
[1/1] Cythonizing lib/bx/seq/_nib.pyx
Traceback (most recent call last):
   File "/<<PKGBUILDDIR>>/setup.py", line 193, in <module>
     main()
   File "/<<PKGBUILDDIR>>/setup.py", line 37, in main
     setup(**metadata)
   File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 
107, in setup
     return distutils.core.setup(**attrs)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
   File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", 
line 185, in setup
     return run_commands(dist)
            ^^^^^^^^^^^^^^^^^^
   File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", 
line 201, in run_commands
     dist.run_commands()
   File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", 
line 969, in run_commands
     self.run_command(cmd)
   File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 1233, 
in run_command
     super().run_command(command)
   File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", 
line 988, in run_command
     cmd_obj.run()
   File 
"/usr/lib/python3/dist-packages/setuptools/_distutils/command/build.py", 
line 131, in run
     self.run_command(cmd_name)
   File "/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py", 
line 318, in run_command
     self.distribution.run_command(command)
   File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 1233, 
in run_command
     super().run_command(command)
   File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", 
line 988, in run_command
     cmd_obj.run()
   File 
"/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", 
line 345, in run
     self.build_extensions()
   File 
"/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", 
line 467, in build_extensions
     self._build_extensions_serial()
   File 
"/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", 
line 493, in _build_extensions_serial
     self.build_extension(ext)
   File "/usr/lib/python3/dist-packages/Cython/Distutils/build_ext.py", 
line 130, in build_extension
     new_ext = cythonize(
               ^^^^^^^^^^
   File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", 
line 1154, in cythonize
     cythonize_one(*args)
   File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", 
line 1321, in cythonize_one
     raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: lib/bx/seq/_nib.pyx
E: pybuild pybuild:395: build: plugin distutils failed with: exit 
code=1: /usr/bin/python3 setup.py build
dh_auto_build: error: pybuild --build -i python{version} -p "3.12 3.11" 
returned exit code 13