From 4f725c3b11f9c5f07311defa364a381fe88244c7 Mon Sep 17 00:00:00 2001
From: Bill Hlavacek <bill.hlavacek@gmail.com>
Date: Sun, 10 May 2026 15:56:22 -0600
Subject: [PATCH] Fix Pattern/Molecule equality and mutable default arguments
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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.
---
 bionetgen/modelapi/pattern.py | 33 ++++++++++++++++++++++++---------
 1 file changed, 24 insertions(+), 9 deletions(-)

diff --git a/bionetgen/modelapi/pattern.py b/bionetgen/modelapi/pattern.py
index 6ef7d929..d0b37fc8 100644
--- a/bionetgen/modelapi/pattern.py
+++ b/bionetgen/modelapi/pattern.py
@@ -58,9 +58,14 @@ class Pattern:
     """
 
     def __init__(
-        self, molecules=[], bonds=None, compartment=None, label=None, canonicalize=False
+        self,
+        molecules=None,
+        bonds=None,
+        compartment=None,
+        label=None,
+        canonicalize=False,
     ):
-        self.molecules = molecules
+        self.molecules = list(molecules) if molecules is not None else []
         self._bonds = bonds
         self.compartment = compartment
         self.label = label
@@ -287,6 +292,12 @@ def __eq__(self, other):
                             other.canonical_label is not None
                         ):
                             return self.canonical_label == other.canonical_label
+                        if len(self.molecules) != len(other.molecules):
+                            logger.debug(
+                                f"molecule count differs: {len(self.molecules)} vs {len(other.molecules)}",
+                                loc=loc,
+                            )
+                            return False
                         # now we can check contents
                         for molecule in self:
                             if molecule not in other.molecules:
@@ -374,8 +385,6 @@ def __getitem__(self, key):
     def __iter__(self):
         return self.molecules.__iter__()
 
-    # TODO: Implement __contains__
-
 
 class Molecule:
     """
@@ -402,9 +411,9 @@ class Molecule:
         (for molecule types) "states"
     """
 
-    def __init__(self, name="0", components=[], compartment=None, label=None):
+    def __init__(self, name="0", components=None, compartment=None, label=None):
         self._name = name
-        self._components = components
+        self._components = list(components) if components is not None else []
         self._compartment = compartment
         self._label = label
         self.canonical_order = None
@@ -435,6 +444,12 @@ def __eq__(self, other):
                     # we can check canonical labels
                     if self.canonical_label != other.canonical_label:
                         return False
+                if len(self.components) != len(other.components):
+                    logger.debug(
+                        f"component count differs: {len(self.components)} vs {len(other.components)}",
+                        loc=loc,
+                    )
+                    return False
                 # check components now
                 for component in self:
                     if component not in other.components:
@@ -547,14 +562,14 @@ def label(self, value):
         # print("Warning: Logical checks are not complete")
         self._label = value
 
-    def _add_component(self, name, state=None, states=[]):
+    def _add_component(self, name, state=None, states=None):
         comp_obj = Component()
         comp_obj.name = name
         comp_obj.state = state
-        comp_obj.states = states
+        comp_obj.states = list(states) if states is not None else []
         self.components.append(comp_obj)
 
-    def add_component(self, name, state=None, states=[]):
+    def add_component(self, name, state=None, states=None):
         # TODO: Add built-in logic here
         # print("Warning: Logical checks are not complete")
         self._add_component(name, state, states)