style: update style tooling and linting + run on codebase

[jsstevenson]

close #56

• this is slightly less opinionated than our internal lab template, ideally lowering the number of nitpicks that a volunteer community member might have to step over to get a PR merged
• I might make 1-2 final tweaks as I get through the end of the HGVS codebase, but I'm putting this up for review now because I think it's close enough

[reece]

@jsstevenson I can't tell what's supposed to happen with this PR and the failing tests. Can you please clarify?

[korikuzma]

@reece Branch just needed to be updated. Tests are passing

[jsstevenson]

Ah, thanks @korikuzma. @reece this was an issue relating to the pytest-optional-dependencies library -- something about the build/release for that package was broken, causing pytest runs to fail (regardless of whether the package was even used). This was creating failures in this repo as well as bioutils and seqrepo. I think we have now pushed out fixes to all affected repos.

[jsstevenson]

Ok, I need to update to handle this week's changes and then I can put back up. I have implementation PRs up on bioutils, seqrepo, and anyvar.

[jsstevenson]

redoing in #72