Move to ruff for linting

[c-randall]

Description

Move to using ruff for linting and formatting instead of flake8 and autopep8. Also, currently following an issue requesting linting for Cython in ruff here, which will be beneficial to have some day.

Type of change

• New feature (non-breaking change which adds functionality)
• Optimization (back-end change that improves speed/readability/etc.)
• Bug fix (non-breaking change which fixes an issue)
• Chore (any other clean up, maintenance, etc.)

Key checklist

• No style issues: $ nox -s linter [-- format]
• Code is free of misspellings: $ nox -s codespell [-- write]
• All tests pass: $ nox -s tests
• Badges are updated: $ nox -s badges

Further checks:

• The documentation builds: $ nox -s docs.
• Code is commented, particularly in hard-to-understand areas.
• Tests are added that prove fix is effective or that feature works.