Bug#1057405: pynormaliz ftbfs with Python 3.12

[Torrance, Douglas]

Control: reassign -1 src:nauty  2.8.8+ds-1

On Sun 10 Dec 2023 12:08:31 AM +08, Bo YU <tsu.y...@gmail.com> wrote:

[[PGP Signed Part:Undecided]]
On Mon, Dec 04, 2023 at 02:22:43PM +0100, Matthias Klose wrote:

Package: src:pynormaliz
Version: 2.18+ds-1
Severity: serious
Tags: sid trixie
User: debian-pyt...@lists.debian.org
Usertags: python3.12

pynormaliz ftbfs with Python 3.12:


[...]
dh execute_after_dh_auto_build --buildsystem=pybuild
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
  dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:310: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build;

Error: nauty.c version mismatch
E: pybuild pybuild:395: test: plugin distutils failed with: exit

I: pybuild base:310: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build;

Error: nauty.c version mismatch
E: pybuild pybuild:395: test: plugin distutils failed with: exit

dh_auto_test: error: pybuild --test -i python{version} -p "3.12
3.11" returned exit code 13
make: *** [debian/rules:9: binary-arch] Error 25

PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build python3.12 tests/runtests.py code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build; PYTHONPATH={build_dir} {interpreter} tests/runtests.py PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build python3.11 tests/runtests.py code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; PYTHONPATH={build_dir} {interpreter} tests/runtests.py

I have spent some time looking at this and I'm more inclined to think
about that this issue has nothing to do with python3.12.

The error from (lib)nauty, unfortunately I did not find the root cause.
The error prototype is defined:
https://salsa.debian.org/science-team/nauty/-/blame/master/nauty.c?page=2#L1175

pynormaliz use libnormaliz that defined some header files in
/usr/include/libnormaliz/ which has relative with nauty.

In fact even on python3.12 the pynormaliz package can be built with
nauty 2.8.6+ds-2. Now the failed version is on nauty 2.8.8+ds-1. So if
you look at the update for nauty and then have a better understand:
https://tracker.debian.org/pkg/nauty

So I suspected the root cause is that upgrading of nauty. If someone
help me to understand the specially call chain or debug method I'm
appreciate it.

I think this is really a nauty bug, and so it's showing up in normaliz and 
consequently pynormaliz.  Here it is in normaliz, for example:


constraints 6 symbolic
x[1] >= 0;
x[2] >= 0;
x[3] >= 0;
x[1] <= 1;
x[2] <= 1;
x[3] <= 1;
EuclideanAutomorphisms


I think the underlying problem is that nauty forces all of its reverse 
dependencies to be built against the latest version with the nauty_check() 
function.  But currently, we're not bumping the SONAME version when this 
happens to trigger a transition.  Maybe we should do that.

Doug

$ cat cube_3.in amb_space 3 $ normaliz cube_3.in Error: nauty.c version mismatch

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