Fix species rename from thermo library for reaction-generated species

7318b37 introduced a `rename` flag to `generate_thermo` to prevent
user-labelled initial species from being silently renamed by a library
match.  However, it called `generate_thermo(spec)` (rename=False) inside
`make_new_species`, caching `spec.thermo` before the rename-enabled call
in `apply_thermo_to_species` could run — so the `if not spc.thermo` guard
in `generate_thermo` always short-circuited the rename for reaction
products, leaving them with SMILES labels (e.g. "O=O") instead of their
library names (e.g. "O2(S)").

Fix: pass `rename=not bool(spec.label)` so that reaction-generated species
(no label yet) are renamed from the library entry, while user-labelled
initial species are left unchanged.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: rwest

rmgpy/rmg/model.py

@@ -365,10 +365,11 @@ def make_new_species(self, object, label="", reactive=True, check_existing=True,
         spec.molecular_weight = Quantity(spec.molecule[0].get_molecular_weight() * 1000.0, "amu")
 
         if generate_thermo:
-            self.generate_thermo(spec)
+            # Rename from thermo library label only if no user-provided label exists yet.
+            self.generate_thermo(spec, rename=not bool(spec.label))
 
         # If the species still does not have a label, set initial label as the SMILES
-        # This may change later after getting thermo in self.generate_thermo()
+        # (applies when generate_thermo is False, or when no library match was found)
         if not spec.label:
             spec.label = spec.smiles