Ci/add ruff format part3

[atravitz]

part 3 of 4 - I'll do the cli tests in a follow-up

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 87.47300% with 116 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.88%. Comparing base (25933de) to head (43c9c7a).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
...s/protocols/openmm_rfe/test_hybrid_top_protocol.py	85.11%	32 Missing ⚠️
...tests/protocols/openmm_rfe/test_hybrid_top_slow.py	9.09%	20 Missing ⚠️
.../tests/protocols/openmm_septop/test_septop_slow.py	27.77%	13 Missing ⚠️
...fe/tests/protocols/openmm_md/test_plain_md_slow.py	14.28%	12 Missing ⚠️
openfe/tests/protocols/conftest.py	79.48%	8 Missing ⚠️
...enfe/tests/protocols/openmm_ahfe/test_ahfe_slow.py	11.11%	8 Missing ⚠️
...enfe/tests/protocols/openmm_abfe/test_abfe_slow.py	22.22%	7 Missing ⚠️
...ests/protocols/openmm_md/test_plain_md_protocol.py	86.11%	5 Missing ⚠️
.../tests/protocols/openmm_ahfe/test_ahfe_settings.py	50.00%	4 Missing ⚠️
.../tests/protocols/openmm_abfe/test_abfe_energies.py	40.00%	3 Missing ⚠️
... and 2 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1622      +/-   ##
==========================================
- Coverage   95.33%   92.88%   -2.45%     
==========================================
  Files         183      183              
  Lines       15765    15763       -2     
==========================================
- Hits        15030    14642     -388     
- Misses        735     1121     +386     

Flag	Coverage Δ
fast-tests	92.88% <87.47%> (?)
slow-tests	?

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[github-actions]

No API break detected ✅

[IAlibay]

Totally just skimmed, but nothing hurt my eyes so I say it's fine.