Fix Pattern/Molecule equality and mutable default arguments - #81

Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom
wshlavacek:modelapi-pattern-equality-and-defaults
May 11, 2026
Merged

Fix Pattern/Molecule equality and mutable default arguments#81
jrfaeder merged 1 commit into
RuleWorld:mainfrom
wshlavacek:modelapi-pattern-equality-and-defaults

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@wshlavacek

@wshlavacekwshlavacek commented May 10, 2026

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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

  • Existing CI passes
  • Construct two `Pattern`s with different molecule counts; `==` returns False both directions
  • Construct two `Molecule`s, call `add_component` on one, verify the other doesn't see the new component

@wshlavacek
Fix Pattern/Molecule equality and mutable default arguments
4f725c3
`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.
@jrfaeder
jrfaeder merged commit 613a526 into RuleWorld:mainMay 11, 2026
17 checks passed
@wshlavacek
wshlavacek deleted the modelapi-pattern-equality-and-defaults branch May 11, 2026 17:07
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Skip to content
Fix Pattern/Molecule equality and mutable default arguments - #81
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
May 11, 2026
Merged
Fix Pattern/Molecule equality and mutable default arguments#81
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 10, 2026

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Contributor
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
  •  Existing CI passes
  •  Construct two `Pattern`s with different molecule counts; `==` returns False both directions
  •  Construct two `Molecule`s, call `add_component` on one, verify the other doesn't see the new component
@wshlavacek
Fix Pattern/Molecule equality and mutable default arguments
4f725c3
`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.
@jrfaeder
jrfaeder
merged commit 613a526
into
RuleWorld:mainMay 11, 2026

17 checks passed

@wshlavacek
wshlavacek
deleted the

modelapi-pattern-equality-and-defaults

branch
May 11, 2026 17:07
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Skip to content
Fix Pattern/Molecule equality and mutable default arguments - #81
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
May 11, 2026
Merged
Fix Pattern/Molecule equality and mutable default arguments#81
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 10, 2026

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Contributor
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
  •  Existing CI passes
  •  Construct two `Pattern`s with different molecule counts; `==` returns False both directions
  •  Construct two `Molecule`s, call `add_component` on one, verify the other doesn't see the new component
@wshlavacek
Fix Pattern/Molecule equality and mutable default arguments
4f725c3
`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.
@jrfaeder
jrfaeder
merged commit 613a526
into
RuleWorld:mainMay 11, 2026

17 checks passed

@wshlavacek
wshlavacek
deleted the

modelapi-pattern-equality-and-defaults

branch
May 11, 2026 17:07
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Skip to content
Fix Pattern/Molecule equality and mutable default arguments - #81
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
May 11, 2026
Merged
Fix Pattern/Molecule equality and mutable default arguments#81
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 10, 2026

Copy link


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Contributor
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
  •  Existing CI passes
  •  Construct two `Pattern`s with different molecule counts; `==` returns False both directions
  •  Construct two `Molecule`s, call `add_component` on one, verify the other doesn't see the new component
@wshlavacek
Fix Pattern/Molecule equality and mutable default arguments
4f725c3
`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.
@jrfaeder
jrfaeder
merged commit 613a526
into
RuleWorld:mainMay 11, 2026

17 checks passed

@wshlavacek
wshlavacek
deleted the

modelapi-pattern-equality-and-defaults

branch
May 11, 2026 17:07
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Skip to content
Fix Pattern/Molecule equality and mutable default arguments - #81
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
May 11, 2026
Merged
Fix Pattern/Molecule equality and mutable default arguments#81
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 10, 2026

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Contributor
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
  •  Existing CI passes
  •  Construct two `Pattern`s with different molecule counts; `==` returns False both directions
  •  Construct two `Molecule`s, call `add_component` on one, verify the other doesn't see the new component
@wshlavacek
Fix Pattern/Molecule equality and mutable default arguments
4f725c3
`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.
@jrfaeder
jrfaeder
merged commit 613a526
into
RuleWorld:mainMay 11, 2026

17 checks passed

@wshlavacek
wshlavacek
deleted the

modelapi-pattern-equality-and-defaults

branch
May 11, 2026 17:07
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Skip to content
Fix Pattern/Molecule equality and mutable default arguments - #81
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
May 11, 2026
Merged
Fix Pattern/Molecule equality and mutable default arguments#81
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 10, 2026

Copy link


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Contributor
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
  •  Existing CI passes
  •  Construct two `Pattern`s with different molecule counts; `==` returns False both directions
  •  Construct two `Molecule`s, call `add_component` on one, verify the other doesn't see the new component
@wshlavacek
Fix Pattern/Molecule equality and mutable default arguments
4f725c3
`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.
@jrfaeder
jrfaeder
merged commit 613a526
into
RuleWorld:mainMay 11, 2026

17 checks passed

@wshlavacek
wshlavacek
deleted the

modelapi-pattern-equality-and-defaults

branch
May 11, 2026 17:07
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Skip to content
Fix Pattern/Molecule equality and mutable default arguments - #81
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jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
May 11, 2026
Merged
Fix Pattern/Molecule equality and mutable default arguments#81
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
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@wshlavacek
@wshlavacekwshlavacek
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May 10, 2026

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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
  •  Existing CI passes
  •  Construct two `Pattern`s with different molecule counts; `==` returns False both directions
  •  Construct two `Molecule`s, call `add_component` on one, verify the other doesn't see the new component
@wshlavacek
Fix Pattern/Molecule equality and mutable default arguments
4f725c3
`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.
@jrfaeder
jrfaeder
merged commit 613a526
into
RuleWorld:mainMay 11, 2026

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@wshlavacek
wshlavacek
deleted the

modelapi-pattern-equality-and-defaults

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May 11, 2026 17:07
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Fix Pattern/Molecule equality and mutable default arguments - #81
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
May 11, 2026
Merged
Fix Pattern/Molecule equality and mutable default arguments#81
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:modelapi-pattern-equality-and-defaults
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 10, 2026

Copy link


Copy Markdown

Contributor
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
  •  Existing CI passes
  •  Construct two `Pattern`s with different molecule counts; `==` returns False both directions
  •  Construct two `Molecule`s, call `add_component` on one, verify the other doesn't see the new component
@wshlavacek
Fix Pattern/Molecule equality and mutable default arguments
4f725c3
`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.
@jrfaeder
jrfaeder
merged commit 613a526
into
RuleWorld:mainMay 11, 2026

17 checks passed

@wshlavacek
wshlavacek
deleted the

modelapi-pattern-equality-and-defaults

branch
May 11, 2026 17:07
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2 participants

@wshlavacek@jrfaeder