[maintenance] Some minor hygiene changes

[MHultman]

A lot of minor changes.

• Refactor type hints to use built-in generic types and general formating.
• Fixed some configuration connected to pre-commit-config.
• pyproject.toml now use new format instead of old

[MHultman]

will you please set a lable for me? Not able to do it.

[github-actions]

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