Fix Pattern/Molecule equality and mutable default arguments#81
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wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
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Fix Pattern/Molecule equality and mutable default arguments#81wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
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`Pattern.__eq__` and `Molecule.__eq__` only checked subset membership of molecules / components, so a pattern was considered equal to a strict superset (a one-molecule pattern would compare equal to a two-molecule pattern that happened to contain it). Add explicit length checks so the directions are symmetric. Replace mutable default args (`molecules=[]`, `components=[]`, `states=[]`) on `Pattern.__init__`, `Molecule.__init__`, `Molecule._add_component`, and `Molecule.add_component` with the standard `None` plumbing, so fresh `Pattern` / `Molecule` instances and `add_component` calls no longer share the same list across instances. Also drops a stale `# TODO: Implement __contains__` comment on `Pattern` — `__contains__` has been implemented for some time.
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Summary
Two related fixes in `bionetgen/modelapi/pattern.py`:
Equality is one-way
`Pattern.eq` and `Molecule.eq` only check subset membership of molecules / components, so a pattern is considered equal to a strict superset (a one-molecule pattern compares equal to a two-molecule pattern that happens to contain it). Add explicit length checks so the directions are symmetric.
Mutable default args
`Pattern.init`, `Molecule.init`, `Molecule._add_component`, and `Molecule.add_component` use mutable list literals as default arguments (`molecules=[]`, `components=[]`, `states=[]`). The classic Python pitfall: every call without those args reuses the SAME list, so `add_component` calls on different molecules can silently leak components into each other.
Replace the literals with the standard `None` plumbing so each instance gets its own list.
Also drops a stale `# TODO: Implement contains` comment — `contains` has been implemented for some time.
Test plan