Package: src:python-skbio
Version: 0.5.8-4
Severity: important
Tags: sid trixie
User: debian-pyt...@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
