Remove flake8, autopep8 and use ruff for linting

[c-randall]

Description

Start using ruff for linting and quick formatting fixes. Note that this is a minimal implementation and does not use black to format the code, avoiding more opinionated styling.

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.