Reaction kinetics: split setRate into rate/probability/binding_radius properties#161
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dilawar wants to merge 2 commits into
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Reaction kinetics: split setRate into rate/probability/binding_radius properties#161dilawar wants to merge 2 commits into
setRate into rate/probability/binding_radius properties#161dilawar wants to merge 2 commits into
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…properties Reaction.setRate was a single method doing three jobs based on a rate<0 sentinel, mirroring libsmoldyn's overloaded smolSetReactionRate(..., isinternal). Replace it with three property setters, one per kinetic quantity, each routing to setReactionRate with the correct isinternal value: - .rate -> isinternal=0 (macroscopic rate) - .reaction_probability -> isinternal=1 (unimol) or 2 (bimol) - .binding_radius -> isinternal=1 (bimolecular only) probability and binding_radius have no C-side getter (libsmoldyn exposes no smolGetReactionProbability or smolGetReactionBindingRadius), so their property getters return last-set values cached on the instance. setRate stays as a deprecated shim with the old sentinel semantics preserved, so back-compat callers still work but get a DeprecationWarning. Reaction.__init__ now uses the properties directly rather than setRate.
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setRateintorate/probability/binding_radiusproperties #161 (this PR) — Reaction kinetics property refactorSummary
The Python wrapper's
Reaction.setRate(rate, reaction_probability, binding_radius)was a single method doing three jobs, dispatched via arate < 0sentinel — mirroring libsmoldyn's overloadedsmolSetReactionRate(..., isinternal). This PR splits the Python surface into three single-purpose property setters:r.ratesmolSetReactionRate(..., isinternal=0)r.reaction_probabilitysmolSetReactionRate(..., isinternal=1)(unimol) or2(bimol)r.binding_radiussmolSetReactionRate(..., isinternal=1)(bimol only, asserted)smolSetReactionRateis unchanged — the C API stays as-is, the wrapper just stops exposing its polymorphic shape.Notes
setRateremains as a back-compat shim that emitsDeprecationWarning. The oldrate < 0sentinel semantics are preserved inside the shim.reaction_probabilityandbinding_radiushave no C-side getter (libsmoldyn exposes nosmolGetReactionProbabilityorsmolGetReactionBindingRadius), so their property getters return last-set values cached on the instance.smolGetReactionRateC function andgetReactionRatepybind11 binding that land in More unit tests and some fixes #160.Test plan
pytest tests/test_reaction.py— 31 tests pass (was 17 in More unit tests and some fixes #160, +14 new for property setters + deprecation shim)make lint(mypy --strict + flake8) cleanmake fix(added in More unit tests and some fixes #160) leaves the file unchanged