Fix mypy issues in calculators and schema modules

[AitElBadaoui]

Summary of Changes

Fixed mypy issues in the calculators and schema modules.

FYI: @Andrew-S-Rosen, we reduced the number of mypy errors from 320 to 160. There are still over 130 errors in types.py, which I will try to fix in another PR.

The remaining issues are linked to design problems such as:

• The Atoms used in Quacc for the moment overload the ASE Atoms class with attributes and functions like charges, as_dict(), and from_dict(), which mypy does not accept. Should we ignore these, or create a QuaccAtom class with the necessary attributes and functions? what do you think ?

Requirements

• My PR is focused on a single feature addition or bugfix.
• My PR has relevant, comprehensive unit tests.
• My PR is on a custom branch (i.e. is not named main).

Notes

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[buildbot-princeton]

Can one of the admins verify this patch?

[codecov]

Codecov Report

Attention: Patch coverage is 86.44068% with 8 lines in your changes missing coverage. Please review.

Project coverage is 98.86%. Comparing base (6b2ef31) to head (6087629).
Report is 1 commits behind head on main.

Files	Patch %	Lines
src/quacc/calculators/vasp/vasp.py	60.00%	2 Missing ⚠️
src/quacc/calculators/vasp/vasp_custodian.py	60.00%	2 Missing ⚠️
src/quacc/runners/ase.py	87.50%	1 Missing ⚠️
src/quacc/schemas/ase.py	80.00%	1 Missing ⚠️
src/quacc/utils/dicts.py	80.00%	1 Missing ⚠️
src/quacc/wflow_tools/customizers.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2326      +/-   ##
==========================================
- Coverage   99.06%   98.86%   -0.20%     
==========================================
  Files          85       85              
  Lines        3520     3533      +13     
==========================================
+ Hits         3487     3493       +6     
- Misses         33       40       +7     

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[Andrew-S-Rosen]

@AitElBadaoui: Thank you very much for your edits once again!

I have several questions below. Would you be able to address them when you get a chance? Again, most of these are genuine questions rather than critiques.

[Andrew-S-Rosen]

The Atoms used in Quacc for the moment overload the ASE Atoms class with attributes and functions like charges, as_dict(), and from_dict(), which mypy does not accept. Should we ignore these, or create a QuaccAtom class with the necessary attributes and functions? what do you think ?

Interesting. I think this is a fair point. We do that patching here and perhaps a few other places. This is a technical necessity for some workflow tools and is very niche. For now, I would be okay with ignoring them to be honest. This whole business is coming from the fact that sometimes an Atoms object is being used and sometimes it is "secretly" an MSONAtoms object. Probably not worth digging into here, but... ignoring it seems wise for now.

[Andrew-S-Rosen]

@buildbot-princeton test this please

[AitElBadaoui]

Interesting. I think this is a fair point. We do that patching here and perhaps a few other places. This is a technical necessity for some workflow tools and is very niche. For now, I would be okay with ignoring them to be honest. This whole business is coming from the fact that sometimes an Atoms object is being used and sometimes it is "secretly" an MSONAtoms object. Probably not worth digging into here, but... ignoring it seems wise for now.

Sounds good. I've already ignored this type of error.

[Andrew-S-Rosen]

@buildbot-princeton test this please

[Andrew-S-Rosen]

Thank you, @AitElBadaoui!! This should be good to go. I will merge later this evening :)