uPTI -> PTI; black formatting; improved comments

[mattersoflight]

@talonchandler this PR is ready for review and merging. Sorry, I missed merging the main into this branch and ended up creating some conflicts in README.md. Please bring back the pypi tags and any other improvements you think are needed, approve, and merge.

[talonchandler]

This PR is ready to merge into main (merging is blocked w/o an approving review @mattersoflight).

Since you last saw it I:

• fixed a couple typos
• applied black formatting to the core files (your changes to waveorder_reconstructor.py applied black formatting, so I figured I might as well make it uniform)
• merged in mains README, double checking that all of your updates were preserved. The only remaining mention of uPTI is in the preprint's title.
• Quickly tested on hummingbird that recOrder runs smoothly when depending on this branch (I'm paranoid about black reformatting accidentally breaking functionality...unnecessary paranoia so far 👍)

[talonchandler]

After this merges I'll tag and release it as 1.0.0rc1.