[FEATURE]: Add dependencies to pre-commit mypy hook and fix issues

[tomvothecoder]

Is your feature request related to a problem?

I noticed that (1) mypy xcdat and (2) pre-commit run mypy --all-files produce different results.
I learned that (2) runs in an isolated virtualenv without dependencies installed, so we must add an array of dependencies in the additional_dependencies settings under .pre-commit-config.yaml to capture a complete log of issues.

More info: pre-commit/pre-commit#1580 (comment)

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