Move more settings into pyproject.toml

[jsignell]

Description:

Just a little driveby maintenance PR to get rid of more top-level files.

PR Checklist:

• pre-commit hooks pass locally
• Tests pass (run scripts/test)
• Documentation has been updated to reflect changes, if applicable
• This PR maintains or improves overall codebase code coverage.
• Changes are added to the CHANGELOG. See the docs for information about adding to the changelog. Don't think this is needed

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (967ce91) 91.11% compared to head (912d73f) 91.11%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1284   +/-   ##
=======================================
  Coverage   91.11%   91.11%           
=======================================
  Files          51       51           
  Lines        6986     6986           
  Branches      999      999           
=======================================
  Hits         6365     6365           
  Misses        444      444           
  Partials      177      177           

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