Ci/add ruff format to openfe protocols

[atravitz]

it's a big one!
for whoever is reviewing: i recommend going through by commit, since I split it into more digestible chunks that are "skimmable" vs "alyssa made some choices here"

related to #1478

Checklist

• Added a news entry

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[codecov]

Codecov Report

❌ Patch coverage is 89.18367% with 53 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.88%. Comparing base (135393e) to head (67ab0ab).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
openfe/protocols/openmm_utils/omm_settings.py	80.00%	11 Missing ⚠️
openfe/analysis/plotting.py	65.51%	10 Missing ⚠️
openfe/protocols/openmm_rfe/equil_rfe_methods.py	86.36%	9 Missing ⚠️
openfe/protocols/openmm_afe/base.py	86.36%	6 Missing ⚠️
openfe/protocols/openmm_utils/omm_compute.py	66.66%	4 Missing ⚠️
openfe/protocols/openmm_utils/system_creation.py	81.81%	2 Missing ⚠️
...protocols/restraint_utils/openmm/omm_restraints.py	66.66%	2 Missing ⚠️
...e/protocols/openmm_afe/equil_binding_afe_method.py	92.30%	1 Missing ⚠️
...protocols/openmm_afe/equil_solvation_afe_method.py	98.52%	1 Missing ⚠️
openfe/protocols/openmm_md/plain_md_methods.py	97.22%	1 Missing ⚠️
... and 6 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1604      +/-   ##
==========================================
- Coverage   95.33%   92.88%   -2.45%     
==========================================
  Files         183      183              
  Lines       15765    15765              
==========================================
- Hits        15030    14644     -386     
- Misses        735     1121     +386     

Flag	Coverage Δ
fast-tests	92.88% <89.18%> (?)
slow-tests	?

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[atravitz]

I believe I've addressed all your comments @IAlibay . Thanks for the feedback, and I'll carry these conventions through to the rest of the code.

[atravitz]

trailing comma is a black convention thing! https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html#trailing-commas @IAlibay

[mikemhenry]

Are we waiting to do isort on a seperate PR?

[atravitz]

yep! first comes formatting, then linting will be later.

[github-actions]

No API break detected ✅