[MAINT] Apply pre-commit fixes and clean up Ruff issues

[mcsitter]

Summary

I want to contribute type hints to make progress on #1130. Since adding a type checker and thus introducing new tooling, I first wanted to resolve the current issues reported by the existing tooling.

This PR applies the pre-commit fixes and resolves the current Ruff issues so the repository starts from a clean baseline.

Validation

• tox run -e full
• tox run -e docs
• tox run -e noqa-budget
• pre-commit run --all-files

[codecov]

Codecov Report

❌ Patch coverage is 84.61538% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.63%. Comparing base (3565eb5) to head (7e0b905).

Files with missing lines	Patch %	Lines
src/bids/utils.py	81.81%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1269      +/-   ##
==========================================
- Coverage   89.63%   89.63%   -0.01%     
==========================================
  Files          71       71              
  Lines        8036     8035       -1     
  Branches      977      977              
==========================================
- Hits         7203     7202       -1     
  Misses        591      591              
  Partials      242      242              

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[mcsitter]

I already have the return types for all public functions typed out. The work is on this branch.

If you’d prefer the type annotations to be included in this PR rather than a separate follow-up, I can update the PR accordingly.