Update core/evolution/evolution.py

core/evolution/evolution.py

@@ -155,47 +155,49 @@ class MolecularEvolution:
     def _run_evolution_loop(self):
         """Run the main evolution loop."""
         for gen in range(1, self.config.generations + 1):
+    
             self._log_generation_stats(gen)
-            
+    
+            # current population
+            population = self.population.molecules
             survivors = self.population.get_survivors()
-
-            
-        sample_smiles = []
-        
-        if survivors:
+    
+            sample_smiles = []
+    
             is_final_gen = (gen == self.config.generations)
-        
+    
             if is_final_gen:
-                # FINAL generation → show top 5 survivors
+                # FINAL generation → top 5 survivors
                 if self.config.maximize_cn:
                     sorted_survivors = sorted(survivors, key=lambda m: m.cn, reverse=True)
                 else:
                     sorted_survivors = sorted(survivors, key=lambda m: m.cn_error)
-        
+    
                 chosen = sorted_survivors[:5]
-        
+    
             else:
-                # EARLY generations → show rejected molecules
+                # EARLY generations → rejected molecules
                 survivor_smiles = set(m.smiles for m in survivors)
                 rejected = [m for m in population if m.smiles not in survivor_smiles]
-        
-                chosen = rejected[:5]  # show up to 5 rejected ones
-        
+    
+                chosen = rejected[:5]
+    
             sample_smiles = [m.smiles for m in chosen]
-            sample_smiles = list(dict.fromkeys(sample_smiles))  # remove duplicates
-        
+            sample_smiles = list(dict.fromkeys(sample_smiles))
+    
+            # ✅ APPEND HISTORY FOR EVERY GENERATION
             self.history.append({
                 "generation": gen,
                 "smiles": sample_smiles
             })
-
-            
+    
+            # produce next generation
             offspring = self._generate_offspring(survivors)
-            
-            # Create new population
+    
             new_pop = Population(self.config)
             new_pop.add_molecules(survivors + offspring)
             self.population = new_pop
+
     
     def _generate_results(self) -> Tuple[pd.DataFrame, pd.DataFrame]:
         """Generate final results DataFrames."""