Added flux.count_species_in_well()

To properly count species in cases where a species label is contained within another species label, e.g., 'NO' and 'NO2'. This is avoided when using RMG labels like 'S(1243)', but is not avoided when generating flux diagrams for non-RMG generated Cantera models

t3/utils/flux.py

@@ -894,14 +894,37 @@ def get_opposite_rxn_species(rxn: str, spc: str) -> List[str]:
     """
     arrow = ' <=> ' if ' <=> ' in rxn else ' => '
     wells = rxn.split(arrow)
-    counts = wells[0].count(spc), wells[1].count(spc)
+    counts = count_species_in_well(well=wells[0], spc=spc), count_species_in_well(well=wells[1], spc=spc)
     i = int(counts[0] > counts[1])
     species = wells[i].split(' + ')
     for token in [' + M', ' (+M)', 'M', ' + ']:
         species = [s.replace(token, '') for s in species]
     return [s for s in species if s != '']
 
 
+def count_species_in_well(well: str,
+                          spc: str,
+                          ) -> int:
+    """
+    Count the number of times a species appears in a well.
+
+    Args:
+        well (str): The well string.
+        spc (str): The species label.
+
+    Returns:
+        int: The number of times a species appears in the well.
+    """
+    count = 0
+    for token in [' + M', ' (+M)', 'M']:
+        well = well.replace(token, '')
+    splits = well.split(' + ')
+    for s in splits:
+        if s == spc:
+            count += 1
+    return count
+
+
 def unpack_stoichiometry(labels: List[str]) -> Tuple[List[str], List[int]]:
     """
     Unpack stoichiometry.