[Debian-med-packaging] Bug#1081624: FTBFS with Python 3.13

[Stefano Rivera]

Source: python-bx
Version: 0.12.0-1
Severity: normal
User: debian-python at lists.debian.org
Usertags: python3.13
Forward: https://github.com/bxlab/bx-python/issues/102

This package failed build from source when test-built against a version of
python3-defaults that incudes 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:

[1/1] Cythonizing lib/bx/_seqmapping.pyx
building 'bx._seqmapping' extension
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 lib/bx/_seqmapping.c -o build/temp.linux-aarch64-cpython-313/lib/bx/_seqmapping.o
lib/bx/_seqmapping.c: In function ‘__pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_6translate’:
lib/bx/_seqmapping.c:3609:15: error: implicit declaration of function ‘PyObject_AsWriteBuffer’; did you mean ‘PyObject_GetBuffer’? [-Wimplicit-function-declaration]
 3609 |   __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 54, __pyx_L1_error)
      |               ^~~~~~~~~~~~~~~~~~~~~~
      |               PyObject_GetBuffer
lib/bx/_seqmapping.c: In function ‘__pyx_pf_2bx_11_seqmapping_15IntToIntMapping_6translate’:
lib/bx/_seqmapping.c:5309:15: error: implicit declaration of function ‘PyObject_AsReadBuffer’; did you mean ‘PyObject_GetBuffer’? [-Wimplicit-function-declaration]
 5309 |   __pyx_t_1 = PyObject_AsReadBuffer(__pyx_v_src, ((void const **)(&__pyx_v_s_buf)), (&__pyx_v_s_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 134, __pyx_L1_error)
      |               ^~~~~~~~~~~~~~~~~~~~~
      |               PyObject_GetBuffer
error: command '/usr/bin/aarch64-linux-gnu-gcc' failed with exit code 1

ERROR Backend subprocess exited when trying to invoke build_wheel
E: pybuild pybuild:389: build: plugin pyproject failed with: exit code=1: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_bx-python  

If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/709365/

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