deepcode-hku 1.0.1__tar.gz → 1.0.2__tar.gz

{deepcode_hku-1.0.1/deepcode_hku.egg-info → deepcode_hku-1.0.2}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: deepcode-hku
-Version: 1.0.1
-Summary: (
+Version: 1.0.2
+Summary: AI Research Engine - Transform research papers into working code automatically
 Home-page: https://github.com/HKUDS/DeepCode
 Author: DeepCodeTeam
 Project-URL: Documentation, https://github.com/HKUDS/DeepCode
@@ -76,7 +76,7 @@ Dynamic: summary
 <p>
   <a href="https://github.com/HKUDS/DeepCode/stargazers"><img src='https://img.shields.io/github/stars/HKUDS/DeepCode?color=00d9ff&style=for-the-badge&logo=star&logoColor=white&labelColor=1a1a2e' /></a>
   <img src="https://img.shields.io/badge/🐍Python-3.13-4ecdc4?style=for-the-badge&logo=python&logoColor=white&labelColor=1a1a2e">
-  <a href="https://pypi.org/project/deepcode/"><img src="https://img.shields.io/pypi/v/deepcode.svg?style=for-the-badge&logo=pypi&logoColor=white&labelColor=1a1a2e&color=ff6b6b"></a>
+  <a href="https://pypi.org/project/deepcode-hku/"><img src="https://img.shields.io/pypi/v/deepcode-hku.svg?style=for-the-badge&logo=pypi&logoColor=white&labelColor=1a1a2e&color=ff6b6b"></a>
 </p>
 <p>
   <a href="https://discord.gg/yF2MmDJyGJ"><img src="https://img.shields.io/badge/💬Discord-Community-7289da?style=for-the-badge&logo=discord&logoColor=white&labelColor=1a1a2e"></a>
@@ -288,11 +288,11 @@ Advanced retrieval-augmented generation combining semantic vector embeddings wit
 
 ### 🔧 **Core Techniques**
 
-- 🧠 **Intelligent Orchestration Agent** Central decision-making system that coordinates workflow phases and analyzes requirements. Employs dynamic planning algorithms to adapt execution strategies in real-time based on evolving project complexity. Dynamically selects optimal processing strategies for each implementation step. <br>
+- 🧠 **Intelligent Orchestration Agent**: Central decision-making system that coordinates workflow phases and analyzes requirements. Employs dynamic planning algorithms to adapt execution strategies in real-time based on evolving project complexity. Dynamically selects optimal processing strategies for each implementation step. <br>
 
-- **💾 Efficient Memory Mechanism: Advanced context engineering system that manages large-scale code contexts efficiently. Implements hierarchical memory structures with intelligent compression for handling complex codebases. This component enables instant retrieval of implementation patterns and maintains semantic coherence across extended development sessions. <br>
+- 💾 **Efficient Memory Mechanism**: Advanced context engineering system that manages large-scale code contexts efficiently. Implements hierarchical memory structures with intelligent compression for handling complex codebases. This component enables instant retrieval of implementation patterns and maintains semantic coherence across extended development sessions. <br>
 
-- **🔍 Advanced CodeRAG System**: Global code comprehension engine that analyzes complex inter-dependencies across repositories. Performs cross-codebase relationship mapping to understand architectural patterns from a holistic perspective. This module leverages dependency graphs and semantic analysis to provide globally-aware code recommendations during implementation.
+- 🔍 **Advanced CodeRAG System**: Global code comprehension engine that analyzes complex inter-dependencies across repositories. Performs cross-codebase relationship mapping to understand architectural patterns from a holistic perspective. This module leverages dependency graphs and semantic analysis to provide globally-aware code recommendations during implementation.
 
 ---
 
@@ -455,7 +455,7 @@ Implementation Generation • Testing • Documentation
 
 ```bash
 # 🚀 Install DeepCode package directly
-pip install deepcode
+pip install deepcode-hku
 
 # 🔑 Download configuration files
 curl -O https://raw.githubusercontent.com/HKUDS/DeepCode/main/mcp_agent.config.yaml
@@ -520,6 +520,34 @@ pip install -r requirements.txt
 
 </details>
 
+#### 🪟 **Windows Users: Additional MCP Server Configuration**
+
+If you're using Windows, you may need to configure MCP servers manually in `mcp_agent.config.yaml`:
+
+```bash
+# 1. Install MCP servers globally
+npm i -g @modelcontextprotocol/server-brave-search
+npm i -g @modelcontextprotocol/server-filesystem
+
+# 2. Find your global node_modules path
+npm -g root
+```
+
+Then update your `mcp_agent.config.yaml` to use absolute paths:
+
+```yaml
+mcp:
+  servers:
+    brave:
+      command: "node"
+      args: ["C:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-brave-search/dist/index.js"]
+    filesystem:
+      command: "node"
+      args: ["C:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js", "."]
+```
+
+> **Note**: Replace the path with your actual global node_modules path from step 2.
+
 ### ⚡ **Step 2: Launch Application**
 
 #### 🚀 **Using Installed Package (Recommended)**

{deepcode_hku-1.0.1 → deepcode_hku-1.0.2}/README.md

@@ -32,7 +32,7 @@
 <p>
   <a href="https://github.com/HKUDS/DeepCode/stargazers"><img src='https://img.shields.io/github/stars/HKUDS/DeepCode?color=00d9ff&style=for-the-badge&logo=star&logoColor=white&labelColor=1a1a2e' /></a>
   <img src="https://img.shields.io/badge/🐍Python-3.13-4ecdc4?style=for-the-badge&logo=python&logoColor=white&labelColor=1a1a2e">
-  <a href="https://pypi.org/project/deepcode/"><img src="https://img.shields.io/pypi/v/deepcode.svg?style=for-the-badge&logo=pypi&logoColor=white&labelColor=1a1a2e&color=ff6b6b"></a>
+  <a href="https://pypi.org/project/deepcode-hku/"><img src="https://img.shields.io/pypi/v/deepcode-hku.svg?style=for-the-badge&logo=pypi&logoColor=white&labelColor=1a1a2e&color=ff6b6b"></a>
 </p>
 <p>
   <a href="https://discord.gg/yF2MmDJyGJ"><img src="https://img.shields.io/badge/💬Discord-Community-7289da?style=for-the-badge&logo=discord&logoColor=white&labelColor=1a1a2e"></a>
@@ -244,11 +244,11 @@ Advanced retrieval-augmented generation combining semantic vector embeddings wit
 
 ### 🔧 **Core Techniques**
 
-- 🧠 **Intelligent Orchestration Agent** Central decision-making system that coordinates workflow phases and analyzes requirements. Employs dynamic planning algorithms to adapt execution strategies in real-time based on evolving project complexity. Dynamically selects optimal processing strategies for each implementation step. <br>
+- 🧠 **Intelligent Orchestration Agent**: Central decision-making system that coordinates workflow phases and analyzes requirements. Employs dynamic planning algorithms to adapt execution strategies in real-time based on evolving project complexity. Dynamically selects optimal processing strategies for each implementation step. <br>
 
-- **💾 Efficient Memory Mechanism: Advanced context engineering system that manages large-scale code contexts efficiently. Implements hierarchical memory structures with intelligent compression for handling complex codebases. This component enables instant retrieval of implementation patterns and maintains semantic coherence across extended development sessions. <br>
+- 💾 **Efficient Memory Mechanism**: Advanced context engineering system that manages large-scale code contexts efficiently. Implements hierarchical memory structures with intelligent compression for handling complex codebases. This component enables instant retrieval of implementation patterns and maintains semantic coherence across extended development sessions. <br>
 
-- **🔍 Advanced CodeRAG System**: Global code comprehension engine that analyzes complex inter-dependencies across repositories. Performs cross-codebase relationship mapping to understand architectural patterns from a holistic perspective. This module leverages dependency graphs and semantic analysis to provide globally-aware code recommendations during implementation.
+- 🔍 **Advanced CodeRAG System**: Global code comprehension engine that analyzes complex inter-dependencies across repositories. Performs cross-codebase relationship mapping to understand architectural patterns from a holistic perspective. This module leverages dependency graphs and semantic analysis to provide globally-aware code recommendations during implementation.
 
 ---
 
@@ -411,7 +411,7 @@ Implementation Generation • Testing • Documentation
 
 ```bash
 # 🚀 Install DeepCode package directly
-pip install deepcode
+pip install deepcode-hku
 
 # 🔑 Download configuration files
 curl -O https://raw.githubusercontent.com/HKUDS/DeepCode/main/mcp_agent.config.yaml
@@ -476,6 +476,34 @@ pip install -r requirements.txt
 
 </details>
 
+#### 🪟 **Windows Users: Additional MCP Server Configuration**
+
+If you're using Windows, you may need to configure MCP servers manually in `mcp_agent.config.yaml`:
+
+```bash
+# 1. Install MCP servers globally
+npm i -g @modelcontextprotocol/server-brave-search
+npm i -g @modelcontextprotocol/server-filesystem
+
+# 2. Find your global node_modules path
+npm -g root
+```
+
+Then update your `mcp_agent.config.yaml` to use absolute paths:
+
+```yaml
+mcp:
+  servers:
+    brave:
+      command: "node"
+      args: ["C:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-brave-search/dist/index.js"]
+    filesystem:
+      command: "node"
+      args: ["C:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js", "."]
+```
+
+> **Note**: Replace the path with your actual global node_modules path from step 2.
+
 ### ⚡ **Step 2: Launch Application**
 
 #### 🚀 **Using Installed Package (Recommended)**

{deepcode_hku-1.0.1 → deepcode_hku-1.0.2}/__init__.py

@@ -5,12 +5,9 @@ DeepCode - AI Research Engine
 ⚡ Transform research papers into working code automatically
 """
 
-__version__ = "1.0.1"
+__version__ = "1.0.2"
 __author__ = "DeepCode Team"
 __url__ = "https://github.com/HKUDS/DeepCode"
-__description__ = (
-    "AI Research Engine - Transform research papers into working code automatically"
-)
 
 # Import main components for easy access
 from utils import FileProcessor, DialogueLogger
@@ -21,5 +18,4 @@ __all__ = [
     "__version__",
     "__author__",
     "__url__",
-    "__description__",
 ]

{deepcode_hku-1.0.1 → deepcode_hku-1.0.2}/deepcode.py

@@ -190,11 +190,11 @@ def main():
             "--theme.base",
             "dark",
             "--theme.primaryColor",
-            "#4dd0e1",
+            "#3b82f6",
             "--theme.backgroundColor",
-            "#0a0e27",
+            "#0f1419",
             "--theme.secondaryBackgroundColor",
-            "#1a1f3a",
+            "#1e293b",
         ]
 
         subprocess.run(cmd, check=True)

{deepcode_hku-1.0.1 → deepcode_hku-1.0.2/deepcode_hku.egg-info}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: deepcode-hku
-Version: 1.0.1
-Summary: (
+Version: 1.0.2
+Summary: AI Research Engine - Transform research papers into working code automatically
 Home-page: https://github.com/HKUDS/DeepCode
 Author: DeepCodeTeam
 Project-URL: Documentation, https://github.com/HKUDS/DeepCode
@@ -76,7 +76,7 @@ Dynamic: summary
 <p>
   <a href="https://github.com/HKUDS/DeepCode/stargazers"><img src='https://img.shields.io/github/stars/HKUDS/DeepCode?color=00d9ff&style=for-the-badge&logo=star&logoColor=white&labelColor=1a1a2e' /></a>
   <img src="https://img.shields.io/badge/🐍Python-3.13-4ecdc4?style=for-the-badge&logo=python&logoColor=white&labelColor=1a1a2e">
-  <a href="https://pypi.org/project/deepcode/"><img src="https://img.shields.io/pypi/v/deepcode.svg?style=for-the-badge&logo=pypi&logoColor=white&labelColor=1a1a2e&color=ff6b6b"></a>
+  <a href="https://pypi.org/project/deepcode-hku/"><img src="https://img.shields.io/pypi/v/deepcode-hku.svg?style=for-the-badge&logo=pypi&logoColor=white&labelColor=1a1a2e&color=ff6b6b"></a>
 </p>
 <p>
   <a href="https://discord.gg/yF2MmDJyGJ"><img src="https://img.shields.io/badge/💬Discord-Community-7289da?style=for-the-badge&logo=discord&logoColor=white&labelColor=1a1a2e"></a>
@@ -288,11 +288,11 @@ Advanced retrieval-augmented generation combining semantic vector embeddings wit
 
 ### 🔧 **Core Techniques**
 
-- 🧠 **Intelligent Orchestration Agent** Central decision-making system that coordinates workflow phases and analyzes requirements. Employs dynamic planning algorithms to adapt execution strategies in real-time based on evolving project complexity. Dynamically selects optimal processing strategies for each implementation step. <br>
+- 🧠 **Intelligent Orchestration Agent**: Central decision-making system that coordinates workflow phases and analyzes requirements. Employs dynamic planning algorithms to adapt execution strategies in real-time based on evolving project complexity. Dynamically selects optimal processing strategies for each implementation step. <br>
 
-- **💾 Efficient Memory Mechanism: Advanced context engineering system that manages large-scale code contexts efficiently. Implements hierarchical memory structures with intelligent compression for handling complex codebases. This component enables instant retrieval of implementation patterns and maintains semantic coherence across extended development sessions. <br>
+- 💾 **Efficient Memory Mechanism**: Advanced context engineering system that manages large-scale code contexts efficiently. Implements hierarchical memory structures with intelligent compression for handling complex codebases. This component enables instant retrieval of implementation patterns and maintains semantic coherence across extended development sessions. <br>
 
-- **🔍 Advanced CodeRAG System**: Global code comprehension engine that analyzes complex inter-dependencies across repositories. Performs cross-codebase relationship mapping to understand architectural patterns from a holistic perspective. This module leverages dependency graphs and semantic analysis to provide globally-aware code recommendations during implementation.
+- 🔍 **Advanced CodeRAG System**: Global code comprehension engine that analyzes complex inter-dependencies across repositories. Performs cross-codebase relationship mapping to understand architectural patterns from a holistic perspective. This module leverages dependency graphs and semantic analysis to provide globally-aware code recommendations during implementation.
 
 ---
 
@@ -455,7 +455,7 @@ Implementation Generation • Testing • Documentation
 
 ```bash
 # 🚀 Install DeepCode package directly
-pip install deepcode
+pip install deepcode-hku
 
 # 🔑 Download configuration files
 curl -O https://raw.githubusercontent.com/HKUDS/DeepCode/main/mcp_agent.config.yaml
@@ -520,6 +520,34 @@ pip install -r requirements.txt
 
 </details>
 
+#### 🪟 **Windows Users: Additional MCP Server Configuration**
+
+If you're using Windows, you may need to configure MCP servers manually in `mcp_agent.config.yaml`:
+
+```bash
+# 1. Install MCP servers globally
+npm i -g @modelcontextprotocol/server-brave-search
+npm i -g @modelcontextprotocol/server-filesystem
+
+# 2. Find your global node_modules path
+npm -g root
+```
+
+Then update your `mcp_agent.config.yaml` to use absolute paths:
+
+```yaml
+mcp:
+  servers:
+    brave:
+      command: "node"
+      args: ["C:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-brave-search/dist/index.js"]
+    filesystem:
+      command: "node"
+      args: ["C:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js", "."]
+```
+
+> **Note**: Replace the path with your actual global node_modules path from step 2.
+
 ### ⚡ **Step 2: Launch Application**
 
 #### 🚀 **Using Installed Package (Recommended)**

{deepcode_hku-1.0.1 → deepcode_hku-1.0.2}/mcp_agent.config.yaml

@@ -31,35 +31,35 @@ mcp:
       # Use `npm i -g @modelcontextprotocol/server-filesystem` to install the server globally.
       # Use `npm -g root` to find the global node_modules path.`
       # command: "node"
-      # args: ["c:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js","./agent_folder"]
+      # args: ["c:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js","."]
       command: "npx"
       args: ["-y", "@modelcontextprotocol/server-filesystem"]
     fetch:
       command: "uvx"
       args: ["mcp-server-fetch"]
     github-downloader:
-      command: "python3"
+      command: "python"
       args: ["tools/git_command.py"]
       env:
         PYTHONPATH: "."
     file-downloader:
-      command: "python3"
+      command: "python"
       args: ["tools/pdf_downloader.py"]
       env:
         PYTHONPATH: "."
     command-executor:
-      command: "python3"
+      command: "python"
       args: ["tools/command_executor.py"]
       env:
         PYTHONPATH: "."
     code-implementation:
-      command: "python3"
+      command: "python"
       args: ["tools/code_implementation_server.py"]
       env:
         PYTHONPATH: "."
       description: "Paper code reproduction tool server - provides file operations, code execution, search and other functions"
     code-reference-indexer:
-      command: "python3"
+      command: "python"
       args: ["tools/code_reference_indexer.py"]
       env:
         PYTHONPATH: "."

{deepcode_hku-1.0.1 → deepcode_hku-1.0.2}/setup.py

@@ -13,7 +13,7 @@ def read_long_description():
 
 # Retrieving metadata from __init__.py
 def retrieve_metadata():
-    vars2find = ["__author__", "__version__", "__url__", "__description__"]
+    vars2find = ["__author__", "__version__", "__url__"]
     vars2readme = {}
 
     # Use definitive path relative to setup.py location
@@ -62,7 +62,7 @@ setuptools.setup(
     url=metadata["__url__"],
     version=metadata["__version__"],
     author=metadata["__author__"],
-    description=metadata["__description__"],
+    description="AI Research Engine - Transform research papers into working code automatically",
     long_description=long_description,
     long_description_content_type="text/markdown",
     packages=setuptools.find_packages(

{deepcode_hku-1.0.1 → deepcode_hku-1.0.2}/tools/code_indexer.py

@@ -6,10 +6,11 @@ identifying file relationships and reusable components for implementation.
 
 Features:
 - Recursive file traversal
-- LLM-powered code similarity analysis
+- LLM-powered code similarity analysis using augmented LLM classes
 - JSON-based relationship storage
 - Configurable matching strategies
 - Progress tracking and error handling
+- Automatic LLM provider selection based on API key availability
 """
 
 import asyncio
@@ -22,6 +23,78 @@ from pathlib import Path
 from dataclasses import dataclass, asdict
 from typing import List, Dict, Any
 
+# MCP Agent imports for LLM
+from mcp_agent.workflows.llm.augmented_llm_anthropic import AnthropicAugmentedLLM
+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.
+
+    Reads from YAML config file and returns AnthropicAugmentedLLM if anthropic.api_key
+    is available, otherwise returns OpenAIAugmentedLLM.
+
+    Args:
+        config_path: Path to the YAML configuration file
+
+    Returns:
+        class: The preferred LLM class
+    """
+    try:
+        # Try to read the configuration file
+        if os.path.exists(config_path):
+            with open(config_path, "r", encoding="utf-8") as f:
+                config = yaml.safe_load(f)
+
+            # Check for anthropic API key in config
+            anthropic_config = config.get("anthropic", {})
+            anthropic_key = anthropic_config.get("api_key", "")
+
+            if anthropic_key and anthropic_key.strip() and not anthropic_key == "":
+                return AnthropicAugmentedLLM
+            else:
+                return OpenAIAugmentedLLM
+        else:
+            print(f"🤖 Config file {config_path} not found, using OpenAIAugmentedLLM")
+            return OpenAIAugmentedLLM
+
+    except Exception as e:
+        print(f"🤖 Error reading config file {config_path}: {e}")
+        print("🤖 Falling back to OpenAIAugmentedLLM")
+        return OpenAIAugmentedLLM
+
+
+def get_default_models(config_path: str = "mcp_agent.config.yaml"):
+    """
+    Get default models from configuration file.
+
+    Args:
+        config_path: Path to the configuration file
+
+    Returns:
+        dict: Dictionary with 'anthropic' and 'openai' default models
+    """
+    try:
+        if os.path.exists(config_path):
+            with open(config_path, "r", encoding="utf-8") as f:
+                config = yaml.safe_load(f)
+
+            anthropic_model = config.get("anthropic", {}).get(
+                "default_model", "claude-sonnet-4-20250514"
+            )
+            openai_model = config.get("openai", {}).get("default_model", "o3-mini")
+
+            return {"anthropic": anthropic_model, "openai": openai_model}
+        else:
+            print(f"Config file {config_path} not found, using default models")
+            return {"anthropic": "claude-sonnet-4-20250514", "openai": "o3-mini"}
+
+    except Exception as e:
+        print(f"Error reading config file {config_path}: {e}")
+        return {"anthropic": "claude-sonnet-4-20250514", "openai": "o3-mini"}
+
 
 @dataclass
 class FileRelationship:
@@ -78,6 +151,7 @@ class CodeIndexer:
         self.indexer_config_path = indexer_config_path
         self.api_config = self._load_api_config()
         self.indexer_config = self._load_indexer_config()
+        self.default_models = get_default_models("mcp_agent.config.yaml")
 
         # Use config paths if not provided as parameters
         paths_config = self.indexer_config.get("paths", {})
@@ -301,7 +375,7 @@ class CodeIndexer:
             return {}
 
     async def _initialize_llm_client(self):
-        """Initialize LLM client based on configured provider"""
+        """Initialize LLM client (Anthropic or OpenAI) based on API key availability"""
         if self.llm_client is not None:
             return self.llm_client, self.llm_client_type
 
@@ -312,89 +386,65 @@ class CodeIndexer:
             self.llm_client_type = "mock"
             return "mock", "mock"
 
-        # Try configured provider first
-        if self.model_provider.lower() == "anthropic":
-            try:
-                anthropic_key = self.api_config.get("anthropic", {}).get("api_key")
-                if anthropic_key:
-                    from anthropic import AsyncAnthropic
-
-                    client = AsyncAnthropic(api_key=anthropic_key)
-                    # Test connection
-                    await client.messages.create(
-                        model="claude-sonnet-4-20250514",
-                        max_tokens=10,
-                        messages=[{"role": "user", "content": "test"}],
-                    )
-                    self.logger.info("Using Anthropic API for code analysis")
-                    self.llm_client = client
-                    self.llm_client_type = "anthropic"
-                    return client, "anthropic"
-            except Exception as e:
-                self.logger.warning(f"Configured Anthropic API unavailable: {e}")
+        # Check which API has available key and try that first
+        anthropic_key = self.api_config.get("anthropic", {}).get("api_key", "")
+        openai_key = self.api_config.get("openai", {}).get("api_key", "")
 
-        elif self.model_provider.lower() == "openai":
+        # Try Anthropic API first if key is available
+        if anthropic_key and anthropic_key.strip():
             try:
-                openai_key = self.api_config.get("openai", {}).get("api_key")
-                if openai_key:
-                    from openai import AsyncOpenAI
-
-                    client = AsyncOpenAI(api_key=openai_key)
-                    # Test connection
-                    await client.chat.completions.create(
-                        model="gpt-3.5-turbo",
-                        max_tokens=10,
-                        messages=[{"role": "user", "content": "test"}],
-                    )
-                    self.logger.info("Using OpenAI API for code analysis")
-                    self.llm_client = client
-                    self.llm_client_type = "openai"
-                    return client, "openai"
-            except Exception as e:
-                self.logger.warning(f"Configured OpenAI API unavailable: {e}")
-
-        # Fallback: try other provider
-        self.logger.info("Trying fallback provider...")
-
-        # Try Anthropic as fallback
-        try:
-            anthropic_key = self.api_config.get("anthropic", {}).get("api_key")
-            if anthropic_key:
                 from anthropic import AsyncAnthropic
 
                 client = AsyncAnthropic(api_key=anthropic_key)
+                # Test connection with default model from config
                 await client.messages.create(
-                    model="claude-sonnet-4-20250514",
+                    model=self.default_models["anthropic"],
                     max_tokens=10,
                     messages=[{"role": "user", "content": "test"}],
                 )
-                self.logger.info("Using Anthropic API as fallback")
+                self.logger.info(
+                    f"Using Anthropic API with model: {self.default_models['anthropic']}"
+                )
                 self.llm_client = client
                 self.llm_client_type = "anthropic"
                 return client, "anthropic"
-        except Exception as e:
-            self.logger.warning(f"Anthropic fallback failed: {e}")
+            except Exception as e:
+                self.logger.warning(f"Anthropic API unavailable: {e}")
 
-        # Try OpenAI as fallback
-        try:
-            openai_key = self.api_config.get("openai", {}).get("api_key")
-            if openai_key:
+        # Try OpenAI API if Anthropic failed or key not available
+        if openai_key and openai_key.strip():
+            try:
                 from openai import AsyncOpenAI
 
-                client = AsyncOpenAI(api_key=openai_key)
+                # Handle custom base_url if specified
+                openai_config = self.api_config.get("openai", {})
+                base_url = openai_config.get("base_url")
+
+                if base_url:
+                    client = AsyncOpenAI(api_key=openai_key, base_url=base_url)
+                else:
+                    client = AsyncOpenAI(api_key=openai_key)
+
+                # Test connection with default model from config
                 await client.chat.completions.create(
-                    model="gpt-3.5-turbo",
+                    model=self.default_models["openai"],
                     max_tokens=10,
                     messages=[{"role": "user", "content": "test"}],
                 )
-                self.logger.info("Using OpenAI API as fallback")
+                self.logger.info(
+                    f"Using OpenAI API with model: {self.default_models['openai']}"
+                )
+                if base_url:
+                    self.logger.info(f"Using custom base URL: {base_url}")
                 self.llm_client = client
                 self.llm_client_type = "openai"
                 return client, "openai"
-        except Exception as e:
-            self.logger.warning(f"OpenAI fallback failed: {e}")
+            except Exception as e:
+                self.logger.warning(f"OpenAI API unavailable: {e}")
 
-        raise ValueError("No available LLM API for code analysis")
+        raise ValueError(
+            "No available LLM API - please check your API keys in configuration"
+        )
 
     async def _call_llm(
         self, prompt: str, system_prompt: str = None, max_tokens: int = None
@@ -426,7 +476,7 @@ class CodeIndexer:
 
                 if client_type == "anthropic":
                     response = await client.messages.create(
-                        model="claude-sonnet-4-20250514",
+                        model=self.default_models["anthropic"],
                         system=system_prompt,
                         messages=[{"role": "user", "content": prompt}],
                         max_tokens=max_tokens,
@@ -451,7 +501,7 @@ class CodeIndexer:
                     ]
 
                     response = await client.chat.completions.create(
-                        model="gpt-4-1106-preview",
+                        model=self.default_models["openai"],
                         messages=messages,
                         max_tokens=max_tokens,
                         temperature=self.llm_temperature,
@@ -1043,7 +1093,7 @@ class CodeIndexer:
                         if r.confidence_score > self.high_confidence_threshold
                     ]
                 ),
-                "analyzer_version": "1.3.0",  # Updated version to reflect concurrent support
+                "analyzer_version": "1.4.0",  # Updated version to reflect augmented LLM support
                 "pre_filtering_enabled": self.enable_pre_filtering,
                 "files_before_filtering": len(all_files),
                 "files_after_filtering": len(files_to_analyze),
@@ -1373,7 +1423,7 @@ class CodeIndexer:
         # Build statistics report
         statistics_report = {
             "report_generation_time": datetime.now().isoformat(),
-            "analyzer_version": "1.3.0",
+            "analyzer_version": "1.4.0",
             "configuration_used": {
                 "config_file": self.indexer_config_path,
                 "concurrent_analysis_enabled": self.enable_concurrent_analysis,
@@ -1481,11 +1531,14 @@ async def main():
     """Main function to run the code indexer with full configuration support"""
 
     # Configuration - can be overridden by config file
-    config_file = "deepcode-mcp/tools/indexer_config.yaml"
+    config_file = "DeepCode/tools/indexer_config.yaml"
+    api_config_file = "DeepCode/mcp_agent.secrets.yaml"
 
     # You can override these parameters or let them be read from config
-    code_base_path = None  # Will use config file value if None
-    output_dir = None  # 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 = """
@@ -1526,6 +1579,7 @@ async def main():
 
     print("🚀 Starting Code Indexer with Enhanced Configuration Support")
     print(f"📋 Configuration file: {config_file}")
+    print(f"🔑 API configuration file: {api_config_file}")
 
     # Create indexer with full configuration support
     try:
@@ -1533,6 +1587,7 @@ async def main():
             code_base_path=code_base_path,  # None = read from config
             target_structure=target_structure,  # Required - project specific
             output_dir=output_dir,  # None = read from config
+            config_path=api_config_file,  # API configuration file
             indexer_config_path=config_file,  # Configuration file
             enable_pre_filtering=True,  # Can be overridden in config
         )
@@ -1540,7 +1595,10 @@ async def main():
         # Display configuration information
         print(f"📁 Code base path: {indexer.code_base_path}")
         print(f"📂 Output directory: {indexer.output_dir}")
-        print(f"🤖 Model provider: {indexer.model_provider}")
+        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'}"
         )