Consolidate Python config files

[mattwthompson]

Description

I don't like TOML

[codecov]

Codecov Report

Attention: Patch coverage is 66.66667% with 6 lines in your changes missing coverage. Please review.

Project coverage is 93.36%. Comparing base (78460a1) to head (734613f).
Report is 19 commits behind head on main.

Files with missing lines	Patch %	Lines
openff/interchange/foyer/_create.py	66.66%	2 Missing ⚠️
openff/interchange/foyer/_guard.py	60.00%	2 Missing ⚠️
openff/interchange/foyer/_nonbonded.py	66.66%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1104      +/-   ##
==========================================
- Coverage   93.45%   93.36%   -0.09%     
==========================================
  Files          68       69       +1     
  Lines        5985     5997      +12     
==========================================
+ Hits         5593     5599       +6     
- Misses        392      398       +6     

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[mattwthompson]

Unfortunately, is looking at openff/interchange/foyer/*.py and not the proper location when doing from foyer import ...

This is probably the cause?

[tool.setuptools.packages.find]
where = ["openff/interchange"]

[mattwthompson]

Well that was (not) fun. Some things I baked in here

• Setting code coverage option at the project level conflicts with my desire to not track coverage in examples. Hence -c /dev/null
• Having a module named foyer/__init__.py should be fine but I ran into some issues which were hard to pinpoint or absolve away. I know not to have a foyer.py file, but I thought modules were okay.
  • This can cause a sort of false positive of has_package("foyer") which picks up something from the wrong path and returns True, so at a few points I look to see if I can grab from foyer.forcefield import Forcefield or something like that and store it as a boolean.
• I'm still not sure what tool.setuptools.packages.find does
• tool.mypy.python_version only sets what Python version is used when mypy is called and can be updated whenever