Add some type annotations

[ab5424]

Summary

• Added some type hints, mostly return types
• Ran pyupgrade --py39-plus
• Added pygrep-hooks rule and fixed some errors

Checklist

• Code is in the standard Python style.
  The easiest way to handle this is to run the following in the correct sequence on
  your local machine. Start with running black on your new code. This will
  automatically reformat your code to PEP8 conventions and removes most issues. Then run
  ruff.
• Docstrings have been added in the Numpy docstring format.
  Run ruff on your code.
• Type annotations are highly encouraged. Run mypy to
  type check your code.
• Tests have been added for any new functionality or bug fixes.
• All linting and tests pass.

[janosh]

Any schema files that define pydantic models cannot use future type annotations until atomate2 is 3.10+. That won't happen for at least another year.

You can revert all schema files with something like (untested!)

git checkout main -- **/schema/* **/schemas.py

[janosh]

Also, feel free to add yourself to contributors.md.

[JaGeo]

Also, feel free to add yourself to contributors.md.

I added @ab5424 yesterday (contributor to phonon workflow)

[codecov]

Codecov Report

Merging #578 (aa22dd2) into main (4e3d156) will decrease coverage by 0.31%.
Report is 4 commits behind head on main.
The diff coverage is 80.00%.

❗ Current head aa22dd2 differs from pull request most recent head c3d6a4e. Consider uploading reports for the commit c3d6a4e to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #578      +/-   ##
==========================================
- Coverage   75.62%   75.31%   -0.31%     
==========================================
  Files          80       80              
  Lines        6711     6722      +11     
  Branches      992      992              
==========================================
- Hits         5075     5063      -12     
- Misses       1330     1354      +24     
+ Partials      306      305       -1     

Files	Coverage Δ
src/atomate2/amset/jobs.py	0.00% <ø> (ø)
src/atomate2/common/files.py	81.00% <ø> (ø)
src/atomate2/common/flows/defect.py	81.57% <100.00%> (ø)
src/atomate2/common/jobs/phonons.py	84.70% <ø> (ø)
src/atomate2/common/schemas/cclib.py	77.55% <100.00%> (ø)
src/atomate2/common/schemas/defects.py	87.91% <100.00%> (ø)
src/atomate2/common/schemas/elastic.py	88.65% <100.00%> (ø)
src/atomate2/common/schemas/phonons.py	97.12% <100.00%> (ø)
src/atomate2/cp2k/drones.py	53.57% <100.00%> (ø)
src/atomate2/cp2k/jobs/base.py	89.23% <100.00%> (ø)
... and 52 more

... and 1 file with indirect coverage changes

[janosh]

I'm surprised the tests pass! Maybe the pydantic restriction I mentioned no longer applies. Looks like the recent migration from pydantic 1 to 2 did away with that.