[Debian-med-packaging] Bug#1056047: python-skbio ftbfs with Python 3.12 (and cython 3.0.5)

[Matthias Klose]

Package: src:python-skbio
Version: 0.5.8-4
Severity: important
Tags: sid trixie
User: debian-python at lists.debian.org
Usertags: python3.12

python-skbio ftbfs with Python 3.12 (and cython 3.0.5):

[...]
dh_auto_configure
I: pybuild base:310: python3.12 setup.py config
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: 
FutureWarning: Cython directive 'language_level' not set, using '3str' 
for now (Py3). This has changed from earlier releases! File: 
/<<PKGBUILDDIR>>/skbio/alignment/_ssw_wrapper.pyx
   tree = Parsing.p_module(s, pxd, full_module_name)

Error compiling Cython file:
------------------------------------------------------------
...
         else:
             matrix = self._convert_dict2d_to_matrix(substitution_matrix)
         # Set up our mask_length
         # Mask is recommended to be max(query_sequence/2, 15)
         if mask_auto:
             self.mask_length = len(query_sequence) / 2
                                                    ^
------------------------------------------------------------

skbio/alignment/_ssw_wrapper.pyx:584:51: Cannot assign type 'double' to 
'int32_t'
[1/6] Cythonizing skbio/alignment/_ssw_wrapper.pyx
Traceback (most recent call last):
   File "/<<PKGBUILDDIR>>/setup.py", line 129, in <module>
     extensions = cythonize(extensions, force=True)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
   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: skbio/alignment/_ssw_wrapper.pyx
E: pybuild pybuild:395: configure: plugin distutils failed with: exit 
code=1: python3.12 setup.py config