style: eliminate unused noqa statements

[aucampia]

Summary of changes

This change enables RUF100 ("Unused noqa directive") and removes all the
noqa directives that are no longer needed.

This is done with poetry run ruff check --fix ., which also removes
noqa directives that are not needed because of ruff config, like E402.

This change also removes file level ignores for some python files in
favour of noqa directives. This is to avoid removing noqa directives
that will just be added back later.

Checklist

• Checked that there aren't other open pull requests for
  the same change.
• Checked that all tests and type checking passes.
• Considered granting push permissions to the PR branch,
  so maintainers can fix minor issues and keep your PR up to date.