I think the problem is caused by #39206.

On Sunday, January 19, 2025 at 12:47:55 PM UTC-8 [email protected] 
wrote:

> I have the same problem (on MacOS 14.6.1), and the problem remains in 
> beta4: checking "git status" after "./configure" gives me a message that 
> conftest.py was deleted.
>
> Should this be a github issue?
>
> PS Executing "git restore conftest.py" makes the error go away, but I know 
> almost nothing about git (or the build system) so I don't know whether that 
> causes some other problem.
>
> On Monday, January 6, 2025 at 8:35:15 PM UTC-7 John H Palmieri wrote:
>
>> Something is broken in ./configure because I end up with a non-clean git 
>> repo:
>>
>>
>> % make configure
>>   ...
>> % ./configure --with-python=`which python3.12`
>>   ...
>> % git status
>> On branch develop
>> Your branch is up to date with 'upstream/develop'.
>>
>> Changes not staged for commit:
>>   (use "git add/rm <file>..." to update what will be committed)
>>   (use "git restore <file>..." to discard changes in working directory)
>> deleted:    conftest.py
>>
>> no changes added to commit (use "git add" and/or "git commit -a")
>>
>>
>> On Saturday, January 4, 2025 at 4:34:48 PM UTC-8 Volker Braun wrote:
>>
>>> As always, you can get the latest beta version from the "develop" git 
>>> branch. Alternatively, the self-contained source tarball is at 
>>> http://www.sagemath.org/download-latest.html
>>>
>>>
>>> 1be0a589260 (tag: 10.6.beta3, github/develop) Updated SageMath version 
>>> to 10.6.beta3
>>> a2ba1f943f8 gh-39238: Modify build using meson guideline
>>> c3fc1406c17 gh-39236: minor details in modular symbols / boundary
>>> 181d8c89219 gh-39235: fixing a few typos
>>> 32ac5a343fd gh-39232: minor tweaks in Ore polynomials
>>> bfa809d7334 gh-39231: fix and activate some checks in ruff-minimal
>>> e2723af3f2a gh-39230: refresh MacMahon Omega file
>>> 14d7322cd8f gh-39229: fixing pycodestyle E222 in many cython files
>>> 751bf5ab5d1 gh-39227: deprecate fully the auld class IntegralDomain
>>> 13648155bc8 gh-39222: Remove outdated note from docstring of 
>>> `cliques_maximal`
>>> c3e0637cc2a gh-39219: Faster conversion from numpy array to matrix mod 2
>>> 6c348ba7550 gh-39217: improve graph traversal methods
>>> 3aaabb590c7 gh-39210: Switch devcontainer to use meson
>>> 266a69ffa3e gh-39209: Fix docstring formatting to use raw string 
>>> literals in multiple files
>>> 8cf2231f896 gh-39206: Pytest: Improve doctest integration
>>> 65a38a534cc gh-39194: Reimplement release creation workflow
>>> a5c4b485074 gh-39193: Some improvements to findstat._submit
>>> 3950c7d00d7 gh-39190: Update the copyright year in README.md
>>> dbdc77f1798 gh-39187: Fix tests output for Python 3.13
>>> 2080c581d46 gh-39179: Fix CremonaDatabase constructor
>>> d4c7335cd3b gh-39178: Fix test failure with giac 1.9.0.998
>>> 598ba045511 gh-39176: Improve Meson CI workflow
>>> 1981422da99 gh-39175: `build/pkgs`: Remove `libtheora`
>>> a501d590613 gh-39157: Mark artin_symbol doctest as random to avoid 
>>> failure
>>> bc8b841ac19 gh-39146: simplify some call of isinstance in pyx files
>>> 02feb6a5bef gh-39127: Minor docfix of interpolation() method
>>> 1c613f65173 gh-39099: Fix more ruff issues in ̀ sage.manifolds`
>>> c52929320d9 gh-39027: Make Sequence pretty-printed in IPython
>>> 902059743e4 gh-39011: Correctly print import errors in `sage.all`
>>> a2de302be55 gh-38993: Meson: find more dependencies via pkg-config
>>> a796b441e26 gh-38946: Allow Cython compilation to open a web browser 
>>> containing the annotated HTML file
>>> c9dd1e85118 (tag: 10.6.beta2) Updated SageMath version to 10.6.beta2
>>>
>>

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