Add F* diagram generator to pymatgen

[jonathanjdenney]

I have written code that takes a list of symmetrized structure objects and generates an f* diagram automatically with the plotly library.

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

[janosh]

Thanks @jonathanjdenney!

Can you please check if some of the test files we already have can be used in place of new ones and for the remaining new files, please gzip them.

[jonathanjdenney]

@janosh
Everything on this pull request looks good from my end. Let me know if there are any changes you want me to make.

[janosh]

As I mentioned earlier, please try to minimize the number of new test files and compress the remaining.

[jonathanjdenney]

@janosh
I got the tests to work with just one cif that is already in the test files directory. Please let me know if there are other changes you would like.

[janosh]

@jonathanjdenney There are still 33 changed files and 23k changed lines which make this PR very hard to review. The purpose of these 3 files is obvious.

Could you either explain the purpose of or remove the other 30 files?

[jonathanjdenney]

@janosh
Sorry, I didn't realize it thinks I changed/added all those files. The ones you highlighted are the only ones I deliberately added. I'm guessing the others are the remnants of some merge error or something. I will get rid of them.

[jonathanjdenney]

@janosh Sorry, I didn't realize it thinks I changed/added all those files. The ones you highlighted are the only ones I deliberately added. I'm guessing the others are the remnants of some merge error or something. I will get rid of them.

I'm looking through the extra files and in all of them they are treated as changed files but the addition and deletion lines are identical. I don't what happened, but the files are supposed to be there as they are in the main pymatgen code as well. I'm not quite sure how to move forward. Should I just delete those files from my local version and make that as a pull request? I feel like that would have the same problem of showing as 30 edited files.

[janosh]

I think you need to run sth like

git checkout master -- space/separated paths/to/files you/want/to/revert

[janosh]

@jonathanjdenney I removed all the excess files and gzipped pymatgen/analysis/fstar/neutron_factors.csv. The tests look a bit meagre. Maybe you can think of more things to test? E.g. uncovered edge cases?

[jonathanjdenney]

@jonathanjdenney I removed all the excess files and gzipped pymatgen/analysis/fstar/neutron_factors.csv. The tests look a bit meagre. Maybe you can think of more things to test? E.g. uncovered edge cases?

I added a few ValueError messages for situations I know won't work. Specifically structures with less than 3 unique sites, and neutron scattering for atomic numbers greater than 96. I'm having trouble thinking of any more edge cases than that. I'm not sure of any specific tests I can add.

Also I would like to set up a tutorial for this, as some of it's features are not all that intuitive. What would be the best way to go about setting that up?