Fix residue naming

[hannahbaumann]

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• Added a news entry, or the changes are not user-facing.
• Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

• GPU integration tests
• example notebook testing
• packaging tests: run this for any large feature PRs or PRs that add test data.

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/.

[hannahbaumann]

pre-commit.ci autofix

[codecov]

Codecov Report

❌ Patch coverage is 98.92473% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 90.61%. Comparing base (541e1ca) to head (91fde04).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...s/protocols/openmm_rfe/test_hybrid_top_protocol.py	98.21%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2042      +/-   ##
==========================================
- Coverage   94.95%   90.61%   -4.35%     
==========================================
  Files         217      218       +1     
  Lines       20768    20864      +96     
==========================================
- Hits        19720    18905     -815     
- Misses       1048     1959     +911     

Flag	Coverage Δ
fast-tests	90.61% <98.92%> (?)
slow-tests	?

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[hannahbaumann]

pre-commit.ci autofix

[github-actions]

No API break detected ✅

View workflow run

Griffe output

$ griffe check "openfe" -s src --no-inspection --no-color --verbose -a origin/main

$ griffe check "openfecli" -s src --no-inspection --no-color --verbose -a origin/main