Migration to pyproject

[Sparks29032]

Issue relating to GIL related to subtype_dealloc of a CovalentRadiiTable object. Still looking into exactly where. While looking for the error, I made a few changes to the source and build code.

• Fix an error due to numpy update (numpy.complex128)
• Remove deprecated pkgutils and numpy.distutils usage
• Move as much of setup.py to pyproject.toml as possible (extensions must remain in setup.py)

Build has been tested on the GCP (works and pytest tests pass for 3.9+ disregarding the GIL issues). Some instructions on common errors have been written to the group wiki.

[artsiommiksiuk]

I have an issue with installation. It says no module found "numpy" on install, if using venv (numpy is installed actually). Does this PR solves it?

[Sparks29032]

I have an issue with installation. It says no module found "numpy" on install, if using venv (numpy is installed actually). Does this PR solves it?

No, this update fixes errors with build. It is possible if you are using the new Mac chips that this program is not currently compatible. Othsrwise, check that your numpy is installed with the correct python binary (python -m pip install numpy) and that your installed NumPy package directory is part of the PYTHONPATH.

[artsiommiksiuk]

Were you able to identify the GIL issue? I've build this lib for own use case and for python 3.10.14. I had to build latest build for it specifically and rebuild libdiffpy as well. It's running now on latest macos for me but I'm also faicing this issue:

Fatal Python error: PyThreadState_Get: the function must be called with the GIL held, but the GIL is released (the current Python thread state is NULL)

Interesting enough, following your lead of that this is caused by CovalentRadiiTable, and commenting it out GIL issue is gone. I can't for now as well figure out what's the cause, but maybe you already have, or can share some of your findings?

[Sparks29032]

Unfortunately, this is where I am stuck too. I will report any findings to this thread, and feel free to do so as well if you find anything new. Hope to get this resolved together!

[pavoljuhas]

Please see #28 for the Python GIL error fix.