Actually Black format everything

[MicahGale]

Description

This is a follow-on to #3222 that actually formats everything with black.

Proposed way to merge.

1. Review and approve #3222.
2. Run black locally on develop and then compare with this PR. I think this is the only way to verify nothing was snuck in with so many changes.
3. This will lead to a lot of merge conflicts for all open PRs. I would recommend that those with open PRs:
   1. Run black against their branch and commit.
   2. Merge in develop. This should eliminate almost all merge conflicts.

Fixes #2002 (actually implement.)

Checklist

• [ ] I have performed a self-review of my own code
• [ ] I have run clang-format (version 15) on any C++ source files (if applicable)
• [x] I have followed the style guidelines for Python source files (if applicable)
• [x] I have made corresponding changes to the documentation (if applicable)
• [ ] I have added tests that prove my fix is effective or that my feature works (if applicable)