Add uniform, automated linting

[mattwthompson]

I find it difficult to read some changesets in this project, owing largely to things like long lines and inconsistent text wrapping. Enter (standard set of tools). The https://pre-commit.ci/ would make this a little smoother but is not necessary.

The changes here are mostly automated, though I had to make some manual fixes and I've also nested a few questions inside the code itself.

Happy to take responsibility for rebasing other PRs.

[mikemhenry]

I will merge this in once I get the other PRs merged in, run the pre-commit on the whole code base, squash in the commits, then add a file so the web-ui knows to skip that commit in the blame

[mikemhenry]

just updated the oe license and re-started CI

[mattwthompson]

Merging upstream changing in now ...

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 42.67782% with 137 lines in your changes are missing coverage. Please review.

Project coverage is 52.98%. Comparing base (016c836) to head (85a7b7f).

Files	Patch %	Lines
...penmmforcefields/generators/template_generators.py	37.50%	125 Missing :warning:
openmmforcefields/generators/system_generators.py	62.96%	10 Missing :warning:
openmmforcefields/utils.py	80.00%	2 Missing :warning:

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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #319      +/-   ##
==========================================
+ Coverage   52.80%   52.98%   +0.18%     
==========================================
  Files           5        5              
  Lines         820      804      -16     
==========================================
- Hits          433      426       -7     
+ Misses        387      378       -9     

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