filter check_mass_balance zeros with a floating point comparison

release-notes/next-release.md

@@ -9,6 +9,8 @@ Fixes failures of GPR.copy() in Python 3.13.
 Fix compartment not being stored for metabolites created during
 reaction.build_reaction_from_string
 
+Fix `reaction.check_mass_balance` giving incorrect results for reactions with floating point coefficients.
+
 ## Other
 
 ## Deprecated features

src/cobra/core/reaction.py

@@ -5,7 +5,7 @@
 from collections import defaultdict
 from copy import copy, deepcopy
 from functools import partial
-from math import isinf
+from math import isclose, isinf
 from operator import attrgetter
 from typing import (
     TYPE_CHECKING,
@@ -1451,7 +1451,11 @@ def check_mass_balance(self) -> Dict[str, float]:
             for element, amount in metabolite.elements.items():
                 reaction_element_dict[element] += coefficient * amount
         # filter out 0 values
-        return {k: v for k, v in reaction_element_dict.items() if v != 0}
+        return {
+            k: v
+            for k, v in reaction_element_dict.items()
+            if not isclose(v, 0.0, abs_tol=config.tolerance)
+        }
 
     @property
     def compartments(self) -> Set:

tests/test_core/test_core_reaction.py

@@ -333,6 +333,9 @@ def test_mass_balance(model: Model) -> None:
     imbalance = reaction.check_mass_balance()
     assert "H" in imbalance
     assert imbalance["H"] == 1
+    # Should be balanced even when coefficients are non-integer
+    reaction_scaled = model.reactions.get_by_id("ATPS4r") * 1.3
+    assert len(reaction_scaled.check_mass_balance()) == 0
 
 
 def test_build_from_string(model: Model) -> None: