Switch to Ruff

[flying-sheep]

Fixes #142.

Rendered docs

TODO:

• Once done, update docs/template_usage.md#pre-commit-checks to link to ruff docs

At time of writing, Ruff supports the following out of all the flake8 plugins we use:

• flake8-tidy-imports
• flake8-docstrings (as pydocstyle/D)
• flake8-rst-docstrings
• flake8-comprehensions
• flake8-bugbear
• flake8-blind-except

Therefore at the time of writing this PR has only one regression: flake8-rst-docstrings would be gone without replacement. Is there something similar we could use?

There’s many more good plugins we can consider, activating e.g.

• https://beta.ruff.rs/docs/rules/#pep8-naming-n
• https://beta.ruff.rs/docs/rules/#flake8-import-conventions-icn
• https://beta.ruff.rs/docs/rules/#flake8-pytest-style-pt
• https://beta.ruff.rs/docs/rules/#pyupgrade-up
• https://beta.ruff.rs/docs/rules/#flake8-use-pathlib-pth (I took the freedom to already add this)

[github-actions]

A PR has been generated to the instance repo:
scverse/cookiecutter-scverse-instance#38

You can check out the PR to preview your changes
in an instance of the cookiecutter template. The PR will be kept in sync with
this PR automatically.

[grst]

Therefore at the time of writing this PR has only one regression: flake8-rst-docstrings would be gone without replacement. Is there something similar we could use?

I think we could do without flake8-rst-docstrings for now. Maybe it gets eventually implemented in ruff.

https://beta.ruff.rs/docs/rules/#pyupgrade-up

We already have a separate hook for pyupgrade. So there's not reason not to switch this to ruff I guess?

[flying-sheep]

We should switch that one to Ruff as well then! I mentioned why here: #142 (comment)

[flying-sheep]

OK! Speed gains:

• main branch:
  
• this PR without caching:
  
• this PR with caching:
  

On my machine, cd ../pre-commit-instance; pre-commit run --all-files --verbose yields:

main branch: 0.42s

• isort: 0.07s
• yesqa: 0.03s
• autoflake: 0.08s
• flake8: 0.19s
• pyupgrade: 0.04s

this PR: 0.02s

• ruff: 0.02s

[grst]

Nice!

What do you think about integrating nbqa (#141) in this PR as well?

[flying-sheep]

Let’s do that after, it’s already changing a lot, and I still need to do the doc changes

[flying-sheep]

This is ready from my side!

[ivirshup]

Reviewed with some minor changes, questions

[flying-sheep]

All addressed, only one two qs left!