[Debian-med-packaging] Bug#1081665: FTBFS with Python 3.13

[Stefano Rivera]

Source: python-biopython
Version: 1.83+dfsg1-4
Severity: normal
Tags: upstream patch fixed-upstream
User: debian-python at lists.debian.org
Usertags: python3.13
Forwarded: https://github.com/biopython/biopython/pull/4706

This package failed build from source when test-built against a version of
python3-defaults that includes 3.13 as a supported version.

To reproduce this issue, build against python3-defaults (python3-all-dev etc.)
from Debian experimental.

What's new in Python 3.13:
https://docs.python.org/3.13/whatsnew/3.13.html

Log snippet:

aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c Bio/cpairwise2module.c -o build/temp.linux-aarch64-cpython-313/Bio/cpairwise2module.o
Bio/cpairwise2module.c: In function ‘_get_match_score’:
Bio/cpairwise2module.c:60:22: error: implicit declaration of function ‘PyEval_CallObject’; did you mean ‘PyObject_CallObject’? [-Wimplicit-function-declaration]
   60 |     if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist)))
      |                      ^~~~~~~~~~~~~~~~~
      |                      PyObject_CallObject
Bio/cpairwise2module.c:60:20: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   60 |     if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist)))
      |                    ^
error: command '/usr/bin/aarch64-linux-gnu-gcc' failed with exit code 1
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3.13 setup.py build 


If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/712092/

This bug has been filed at "normal" severity, as we haven't started the
transition to add 3.13 as a supported version, yet. This will be raised to RC
as soon as that happens, hopefully well before trixie.

Thanks,

Stefano