fgpyo
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chore: Modernize mypy config
Summary
This PR adds the mypy configuration used by our template and addresses resulting type errors.
Most of the changes are a consequence of setting strict_optional = true, a setting recommended by the mypy developers.
Mypy checks are failing on 3.9. I wonder if this is related to our decision to not enforce a python version in the mypy config.
TBH I'd prefer to drop support for 3.9 (https://github.com/fulcrumgenomics/fgpyo/issues/247) since it EOLs next month anyways, rather than spend time fixing.