Address mypy errors

[underchemist]

Related to #5 and #26, which introduces mypy as a pre-commit hook with configuration defined in pyproject.toml. Currently this is set to ignore all errors but disabling this option and running mypy -p oaff or pre-commit run --all-files results in a large number of errors. See here for an example mypy output.

This issue is meant to track work required to resolve errors produced by mypy.

A question I'm not sure the answer to:
Is ignore_missing_imports=true appropriate here? even with mypy --install-types there are multiple packages without type stubs.