Pre-commit Update

**Is this pull request associated with an issue(s)?** - Pre-commit with new, stricter Python hooks were introduced with NWChemEx/pre-commit-config#2. - This PR prepares this repo so future contributors don't have to fix our tech debt. Instructions for new contributors to run pre-commit are to be added with NWChemEx/.github#173. **Description** Cleans up this repo to be compliant with the new pre-commit hooks that will need to pass before a commit can be made.