Sorry, I was not aware that configure writes files in the root directory. contest.py is indeed the standard pytest name, so shouldnt be used by configure

I've checked that in ./configure one has

rm -f configure*

in a lot of places; these rm come from standard autoconf macros and it's unrealistic to fix them.

So what we can do is to use a shell analog of Python atexit facility to rename conftest.py to something safe, and then rename it back at ./configure shell exit.

Or perhaps tell pytest to look for conftest.py somewhere else, but I don't know how.

Here is the answer I got on the autoconf mailing list:
https://lists.gnu.org/archive/html/autoconf/2025-01/msg00013.html

tl;dr; no luck fixing it and preserving the way we do things now. They suggest a split build - I'll try, but I'm not hopeful.

No, of course, split build (running configure+make in a subdirectory) can't be done without (major?) changes of what we do now.

How about going with a wrapper? Say, we have a script called Configure which makes a copy of configure.py, calls configure passing all the parameters, and finally restores configure.py ?