Fix conftest.py being deleted by configure script

[cxzhong]

Problem

When running make after switching branches or when reconfiguration is needed, conftest.py (the pytest configuration file) gets deleted.

Root Cause

The configure_wrapper script backs up conftest.py before running ./real_configure and restores it afterward:

trap 'mv bak_conftest.py conftest.py; trap - EXIT; exit' EXIT INT HUP TERM
cp conftest.py bak_conftest.py
./real_configure $@

However, when make triggers a reconfigure, it runs:

./config.status --recheck

The config.status file is generated by real_configure and contains a hardcoded path:

# Line 502 in config.status
set X /bin/bash './real_configure' $ac_configure_extra_args --no-create --no-recursion

This bypasses the ./configure wrapper entirely, so:

1. conftest.py is not backed up
2. real_configure runs and deletes all conftest* files
3. conftest.py is gone

When This Happens

• Running make after git checkout to a different branch
• Running make after any change that triggers reconfigure target
• Running ./config.status --recheck directly

Potential Solutions

Modify config.status generation - Patch the autoconf output to call ./configure instead of ./real_configure

📝 Checklist

• The title is concise and informative.
• The description explains in detail what this PR is about.
• I have linked a relevant issue or discussion.
• I have created tests covering the changes.
• I have updated the documentation and checked the documentation preview.

⌛ Dependencies

[github-actions]

Documentation preview for this PR (built with commit a1812a6; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

[dimpase]

seems to be the right path to fix this, finally, not sure about details

[dimpase]

On Thu, Dec 25, 2025 at 03:02:01AM -0800, Chenxin Zhong wrote: @cxzhong requested your review on: sagemath/sage#41333 Fix conftest.py being deleted by configure script.

I just tested this, by running make which triggers bootstrap+configure, and then errors out, and no, it does not work. That is, the file does not get restored. (perhaps it does if `make ` finishes normally)

[dimpase]

oops, I actually made a testing error, sorry. It seems to work all right.

[dimpase]

this is non-posix use of sed, it breaks macOS builds.
https://groups.google.com/g/sage-release/c/fG2pnz3Hfi0/m/dF2iSSIjBgAJ
@cxzhong