Various cleanups

[mikix]

• Use terminology more consistently (standardized on truth and annotator)
• Use black
• Use pycodestyle (mostly just small pep8 violations that black doesn't care about like long comments)
• Use bandit (this is basically all local math code, but since it can deal with PHI directly...)

The above are all different commits for ease of review. I'd look at individual commits rather than the whole PR (but grouping them makes my life easier rather than chained PRs).

Notably absent from the above list is pylint -- mostly because it'd add more noise to this PR. We can always add it later.

[mikix]

BTW I took all your nit suggestions and this is ready to land from my POV, just giving it a bit to breathe in case Andy wants to look in

[mikix]

Eh, I've got another PR I want to file, based on this. I'm going to land now