fix bug for code_index

Author: Zongwei9888

tools/code_indexer.py

@@ -28,6 +28,7 @@
 from mcp_agent.workflows.llm.augmented_llm_openai import OpenAIAugmentedLLM
 import yaml
 
+
 def get_preferred_llm_class(config_path: str = "mcp_agent.secrets.yaml"):
     """
     Automatically select the LLM class based on API key availability in configuration.
@@ -1534,8 +1535,10 @@ async def main():
     api_config_file = "DeepCode/mcp_agent.secrets.yaml"
 
     # You can override these parameters or let them be read from config
-    code_base_path = "DeepCode/deepcode_lab/papers/1/code_base/" # Will use config file value if None
-    output_dir = "DeepCode/deepcode_lab/papers/1/indexes/"  # Will use config file value if None
+    code_base_path = "DeepCode/deepcode_lab/papers/1/code_base/"  # Will use config file value if None
+    output_dir = (
+        "DeepCode/deepcode_lab/papers/1/indexes/"  # Will use config file value if None
+    )
 
     # Target structure - this should be customized for your specific project
     target_structure = """
@@ -1592,7 +1595,9 @@ async def main():
         # Display configuration information
         print(f"📁 Code base path: {indexer.code_base_path}")
         print(f"📂 Output directory: {indexer.output_dir}")
-        print(f"🤖 Default models: Anthropic={indexer.default_models['anthropic']}, OpenAI={indexer.default_models['openai']}")
+        print(
+            f"🤖 Default models: Anthropic={indexer.default_models['anthropic']}, OpenAI={indexer.default_models['openai']}"
+        )
         print(f"🔧 Preferred LLM: {get_preferred_llm_class(api_config_file).__name__}")
         print(
             f"⚡ Concurrent analysis: {'enabled' if indexer.enable_concurrent_analysis else 'disabled'}"

workflows/agent_orchestration_engine.py

@@ -437,7 +437,7 @@ async def paper_reference_analyzer(paper_dir: str, logger) -> str:
 Focus on:
 1. **References section analysis** - Extract all citations from the References/Bibliography part
 2. References with high-quality GitHub implementations
-3. Papers cited for methodology, algorithms, or core techniques  
+3. Papers cited for methodology, algorithms, or core techniques
 4. Related work that shares similar technical approaches
 5. Implementation references that could provide code patterns
 
@@ -579,9 +579,7 @@ async def orchestrate_reference_intelligence_agent(
             return f.read()
 
     # Execute reference analysis
-    reference_result = await paper_reference_analyzer(
-        dir_info["paper_dir"], logger
-    )
+    reference_result = await paper_reference_analyzer(dir_info["paper_dir"], logger)
 
     # Save reference analysis result
     with open(reference_path, "w", encoding="utf-8") as f: