Linting, CI, dependencies, and infrastructure updates

[rkingsbury]

This PR contains a series of updates to the linting, CI, and dependency management systems to make package maintenance easier and to harmonize our practices with other MP ecosystem packages, notably pymatgen and custodian.

Specifically:

• replace flake8, pycodestyle, pydocstyle, and isort dependencies with ruff (note that pydocstyle was in the requirements but never invoked in CI or pre-commit). Ruff is substantially faster than flake8, etc., and replaces many popular tools by re-implementing rules from pycodestyle, pydocstyle, flake8, isort, etc. into a single dependency. The ruff configuration closely tracks that implemented by @materialsproject/pymatgen-maintainers for custodian and pymatgen (see Add ruff linter custodian#278)
• add ruff linting to CI (replacing Flake8)
• replace setup.cfg with pyproject.toml
• add GitHub workflow to periodically update dependencies in a single PR (alternative to dependabot). See https://www.oddbird.net/2022/06/01/dependabot-single-pull-request/
• lint whole project with ruff, which required moving some mypy imports from inline comments (e.g., # type: Any) to normal type hints and making use of teh __all__ variable in empty __init__.py files.
• update .pre-commit action to current repo and version
• add pre-commit auto fixes to CI
• updated PR template to sync more closely with pymatgen
• misc. spelling fixes

[codecov]

Codecov Report

Patch coverage: 87.30% and project coverage change: +0.06% 🎉

Comparison is base (ad355cf) 88.09% compared to head (cbaefa6) 88.15%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #810      +/-   ##
==========================================
+ Coverage   88.09%   88.15%   +0.06%     
==========================================
  Files          44       44              
  Lines        3629     3589      -40     
==========================================
- Hits         3197     3164      -33     
+ Misses        432      425       -7     

Files Changed	Coverage Δ
src/maggma/__init__.py	100.00% <ø> (ø)
src/maggma/api/API.py	81.81% <ø> (ø)
src/maggma/api/query_operator/core.py	100.00% <ø> (ø)
src/maggma/api/query_operator/pagination.py	100.00% <ø> (+4.00%)	⬆️
src/maggma/api/resource/core.py	83.72% <ø> (+3.72%)	⬆️
src/maggma/api/resource/s3_url.py	58.33% <0.00%> (ø)
src/maggma/api/resource/utils.py	80.76% <0.00%> (ø)
src/maggma/core/validator.py	100.00% <ø> (ø)
src/maggma/utils.py	94.01% <60.00%> (-1.71%)	⬇️
src/maggma/cli/distributed.py	81.09% <63.63%> (ø)
... and 28 more

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[janosh]

Looks great! Thanks @rkingsbury.

and making use of teh all variable in empty init.py files.

I'm curious what you mean by that. Is this about unused import errors?

Yes, initially when running ruff it did not like using __init__.py to collect imports, so I placed all imported classes inside the __all__ variable. This was before I duplicated your ruleset; I think your per-file-ignore "__init__.py" = ["F401"] takes care of it.

[rkingsbury]

@munrojm I disabled a few ruff rules in api because I didn't want to inadvertently screw anything up. You may want to examine and see if any can be fixed

[rkingsbury]

@munrojm any concerns about the migration to pyproject.toml, or other changes here? I'll wait to hear from you before merging since this touches a lot of the CI infrastructure.

[munrojm]

Nope! No concerns on my end. I'm glad to have these changes. Thanks for making them.