Update script_for_automation.py

script_for_automation.py

@@ -404,20 +404,25 @@ def generate_markdown_output(df):
             markdown += f"| Machine Generated | ```json\n{machine}\n``` |\n"
 
     # 6. Side-by-Side YAML Comparisons
-    markdown = "\n## Gold Standard vs Machine Generated YAML\n"
+    markdown += "\n## Gold Standard vs Machine Generated YAML\n"
     for _, row in df.iterrows():
         markdown += f"\n### Recipe ID: {row['Recipe_ID']}\n"
         for key in ["planting", "interactions", "trials"]:
-            gold = yaml.dump(row['Gold_Standard_YAML'].get(key, {}), default_flow_style=False, sort_keys=True)
-            machine = yaml.dump(row['Machine_Generated_YAML'].get(key, {}), default_flow_style=False, sort_keys=True)
-            
+            # Safely get YAML data
+            gold_yaml = yaml.dump(row['Gold_Standard_YAML'].get(key, {}), default_flow_style=False, sort_keys=True)
+            machine_yaml = yaml.dump(row['Machine_Generated_YAML'].get(key, {}), default_flow_style=False, sort_keys=True)
+    
+            # Add proper line breaks between YAML blocks
+            gold_yaml = "\n".join([line for line in gold_yaml.splitlines()])  # Ensure clean output
+            machine_yaml = "\n".join([line for line in machine_yaml.splitlines()])
+    
             # Add Markdown table
             markdown += f"#### {key.capitalize()}\n"
             markdown += "| Type | YAML Content |\n"
             markdown += "|------|--------------|\n"
-            markdown += f"| Gold Standard | ```yaml\n{gold}\n``` |\n"
-            markdown += f"| Machine Generated | ```yaml\n{machine}\n``` |\n"
-
+            markdown += f"| Gold Standard | ```yaml\n{gold_yaml}\n``` |\n"
+            markdown += f"| Machine Generated | ```yaml\n{machine_yaml}\n``` |\n"
+    
     return markdown