Multi-leg HybridTop Protocols

[IAlibay]

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes / no
If yes, please provide details here: Yes, worked with claude Sonnet 4.6 to help with the refactor.

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.
• Filled in the AI generated code disclosure.

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/.

[IAlibay]

pre-commit.ci autofix

[codecov]

Codecov Report

❌ Patch coverage is 52.61044% with 236 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.49%. Comparing base (7ff38c9) to head (a4b3315).

Files with missing lines	Patch %	Lines
...openfe/protocols/openmm_rfe/hybridtop_protocols.py	40.32%	148 Missing ⚠️
...protocols/openmm_rfe/hybridtop_protocol_results.py	25.25%	74 Missing ⚠️
src/openfe/protocols/openmm_rfe/hybridtop_units.py	81.08%	14 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2093      +/-   ##
==========================================
- Coverage   95.13%   89.49%   -5.64%     
==========================================
  Files         213      213              
  Lines       20878    21252     +374     
==========================================
- Hits        19862    19020     -842     
- Misses       1016     2232    +1216     

Flag	Coverage Δ
fast-tests	89.49% <52.61%> (?)
slow-tests	?

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[IAlibay]

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[github-actions]

🚨 API breaking changes detected! 🚨

View workflow run

Griffe output

$ griffe check "openfe" -s src --no-inspection --no-color --verbose -a origin/main
src/openfe/protocols/openmm_rfe/hybridtop_units.py:1827: HybridTopologyMultiStateSimulationUnit:
Base class was removed:
  Old: [gufe.ProtocolUnit, openfe.protocols.openmm_rfe.hybridtop_units.HybridTopologyUnitMixin]
  New: [openfe.protocols.openmm_rfe.hybridtop_units.BaseHybridTopologyMultiStateSimulationUnit]

src/openfe/protocols/openmm_rfe/hybridtop_units.py:1834: HybridTopologyMultiStateAnalysisUnit:
Base class was removed:
  Old: [gufe.ProtocolUnit, openfe.protocols.openmm_rfe.hybridtop_units.HybridTopologyUnitMixin]
  New: [openfe.protocols.openmm_rfe.hybridtop_units.BaseHybridTopologyMultiStateAnalysisUnit]

src/openfe/protocols/openmm_afe/afe_protocol_results.py:0: AbsoluteBindingProtocolResult.bound_state:
Public object was removed

src/openfe/protocols/openmm_afe/afe_protocol_results.py:0: AbsoluteBindingProtocolResult.unbound_state:
Public object was removed

src/openfe/protocols/openmm_afe/afe_protocol_results.py:0: AbsoluteSolvationProtocolResult.bound_state:
Public object was removed

src/openfe/protocols/openmm_afe/afe_protocol_results.py:0: AbsoluteSolvationProtocolResult.unbound_state:
Public object was removed

src/openfe/protocols/openmm_afe/afe_protocol_results.py:0: AbsoluteProtocolResultMixin.bound_state:
Public object was removed

src/openfe/protocols/openmm_afe/afe_protocol_results.py:0: AbsoluteProtocolResultMixin.unbound_state:
Public object was removed


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