Fixes for Python 3.12

[bennybp]

This fixes versioneer to be compatible with python 3.12. This also adds python 3.11 and 3.12 to the Github Actions tests.

The fix to versioneer is somewhat hacky (rather than vendor a new versioneer.py from the not-yet-released versioneer package).

This also replaces the use of distutils in nifty. distutils was removed in python 3.12 (but is still available from setuptools). The copytree command from distutils (with dirs_exist_ok=True) should be equivalent for python 3.8+. A test was added for the copy_tree_over function.

Fixes issue #173

[leeping]

Thank you, Ben. I don't see any issue with merging this into master. :)

[leeping]

Thanks a lot for the recent fixes. Is it possible to use importlib.metadata instead of packaging? Because geomeTRIC has only two critical dependencies (only numpy and networkx), I would prefer not to introduce a dependency on a third-party package in order to keep an existing functionality. I believe importlib.metadata also allows one to access version numbers of installed packages: https://docs.python.org/3/library/importlib.metadata.html .

We would need to drop Python 3.7 in the next release if we go this route and I'm okay with that.

[bennybp]

Actually, it's used in one place, to check the version of networkX.

The check is to see if networkX is > 2.0, which was released in 2017. It is probably safe to remove that check, since that is a pretty old version now. It's likely if you try to install 2.0 other things will break before geometric does.

There's one more thing that likely needs a fix: In the test-conda.yml github action, setup-miniconda should probably be used rather than adding $CONDA to the path and installing mamba manually. We've found it to be much more robust (as seen with this failure)

[leeping]

If you merge the latest changes from master, the Conda environment should now be set up correctly.

[leeping]

The tests indicate the optimization log file is not being generated for an OpenMM test. (The other OpenMM tests do not involve parsing the log file). Did the logging behavior change somehow?

[bennybp]

Wow sorry, that's me being sloppy. My latest commit hopefully fixes all those

[leeping]

The latest changes all look good!

[bennybp]

Great! You can probably squash and make this cleaner when you merge

[leeping]

LGTM!

Sounds good regarding the squash, I'll do that.

[effigies]

The versioneer issue has been resolved for some time, but an old versioneer is vendored here. Upgrade with pipx run versioneer install.

See https://github.com/python-versioneer/python-versioneer/blob/master/UPGRADING.md for any migration issues.