python-biopython fails to build with Python 3.13.03.

  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)))
        |                    ^

According to https://docs.python.org/3.13/whatsnew/3.13.html:

Remove PyEval_CallObject(), PyEval_CallObjectWithKeywords(): use PyObject_CallNoArgs() or PyObject_Call() instead.
Warning: PyObject_Call() positional arguments must be a tuple and must not be NULL,
keyword arguments must be a dict or NULL, whereas removed functions checked arguments type and accepted NULL positional and keyword arguments.
To replace PyEval_CallObjectWithKeywords(func, NULL, kwargs) with PyObject_Call(),
pass an empty tuple as positional arguments using PyTuple_New(0).


https://docs.python.org/3.13/whatsnew/3.13.html

For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.13/fedora-rawhide-x86_64/06937513-python-biopython/

For all our attempts to build python-biopython with Python 3.13, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.13/package/python-biopython/

Testing and mass rebuild of packages is happening in copr.
You can follow these instructions to test locally in mock if your package builds with Python 3.13:
https://copr.fedorainfracloud.org/coprs/g/python/python3.13/

Let us know here if you have any questions.

Python 3.13 is planned to be included in Fedora 41.
To make that update smoother, we're building Fedora packages with all pre-releases of Python 3.13.
A build failure prevents us from testing all dependent packages (transitive [Build]Requires),
so if this package is required a lot, it's important for us to get it fixed soon.

We'd appreciate help from the people who know this package best,
but if you don't want to work on this now, let us know so we can try to work around it on our side.