Add pre-commit

[NMertsch]

Summary

Bundle all code checks with pre-commit.

Fixes #148

Added pre-commit checks

built-in hooks:

• Ensure trailing newlines
• Remove trailing whitespace
• Check toml and yaml syntax
• Prevent addition of large files (>500 KB)

uv:

• Check if uv.lock is up to date

ruff:

• Fix import and code formatting
• Run ruff check

custom:

• Run pytest

Other changes

• Replace lint and test CI workflows with a single pre-commit invocation to avoid configuration drift
• Set explicit workflow permissions (following a GitHub security warning)
• Update package versions
• Update documentation
• Fix pre-commit findings (add trailing newlines, remove trailing whitespace)

[NMertsch]

pre-commit.ci run

[NMertsch]

@egeakman I hope this is what you imagined. I tried pre-commit.ci, but removed it again for these reasons:

• pre-commit.ci cannot run pytest, so it would require separate local and CI configurations.
• I consider server-side code modifications an accessibility issue. For beginners, git is already complex enough without merge conflicts induced by post-push modifications.

[egeakman]

Hey Niklas! Thanks for the PR; it looks great overall!

If I understand correctly, this checks whether uv.lock is up to date and updates it if it's not. Since Dependabot already manages updates to uv.lock, I'd prefer to avoid making manual or local changes, assuming we trust our tests to catch any issues.

[NMertsch]

Thank you Ege, that's a valid point. Fixed in ff112e4.