Update linting/formatting/etc

[jsstevenson]

• Ensure use of latest ruff lint/format + configs
• Update GHA if necessary
• Add precommit checks if necessary
• Pull out unused stuff
• Update makefile

Honestly most/all of this might be done, I haven't really looked in a while

[reece]

@jsstevenson I think this is done and now demonstrated in biocommons/bioutils#83.

Agree? If yes, please close this issue

[github-actions]

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