> ## Documentation Index
> Fetch the complete documentation index at: https://codegeninc-fix-system-prompt-typo.mintlify.site/llms.txt
> Use this file to discover all available pages before exploring further.

# Deep Code Research with AI

This guide demonstrates how to build an intelligent code research tool that can analyze and explain codebases using Codegen's and LangChain. The tool combines semantic code search, dependency analysis, and natural language understanding to help developers quickly understand new codebases.

<Info>View the full code on [GitHub](https://github.com/codegen-sh/codegen-sdk/tree/develop/codegen-examples/examples/deep_code_research)</Info>

<Tip>This example works with any public GitHub repository - just provide the repo name in the format owner/repo</Tip>

## Overview

The process involves three main components:

1. A CLI interface for interacting with the research agent
2. A set of code analysis tools powered by Codegen
3. An LLM-powered agent that combines the tools to answer questions

Let's walk through building each component.

## Step 1: Setting Up the Research Tools

First, let's import the necessary components and set up our research tools:

```python theme={null}
from codegen import Codebase
from codegen.extensions.langchain.agent import create_agent_with_tools
from codegen.extensions.langchain.tools import (
    ListDirectoryTool,
    RevealSymbolTool,
    SearchTool,
    SemanticSearchTool,
    ViewFileTool,
)
from langchain_core.messages import SystemMessage
```

We'll create a function to initialize our codebase with a nice progress indicator:

```python theme={null}
def initialize_codebase(repo_name: str) -> Optional[Codebase]:
    """Initialize a codebase with a spinner showing progress."""
    with console.status("") as status:
        try:
            status.update(f"[bold blue]Cloning {repo_name}...[/bold blue]")
            codebase = Codebase.from_repo(repo_name)
            status.update("[bold green]✓ Repository cloned successfully![/bold green]")
            return codebase
        except Exception as e:
            console.print(f"[bold red]Error initializing codebase:[/bold red] {e}")
            return None
```

Then we'll set up our research tools:

```python theme={null}
# Create research tools
tools = [
    ViewFileTool(codebase),      # View file contents
    ListDirectoryTool(codebase),  # Explore directory structure
    SearchTool(codebase),        # Text-based search
    SemanticSearchTool(codebase), # Natural language search
    RevealSymbolTool(codebase),  # Analyze symbol relationships
]
```

Each tool provides specific capabilities:

* `ViewFileTool`: Read and understand file contents
* `ListDirectoryTool`: Explore the codebase structure
* `SearchTool`: Find specific code patterns
* `SemanticSearchTool`: Search using natural language
* `RevealSymbolTool`: Analyze dependencies and usages

## Step 2: Creating the Research Agent

Next, we'll create an agent that can use these tools intelligently. We'll give it a detailed prompt about its role:

```python theme={null}
RESEARCH_AGENT_PROMPT = """You are a code research expert. Your goal is to help users understand codebases by:
1. Finding relevant code through semantic and text search
2. Analyzing symbol relationships and dependencies
3. Exploring directory structures
4. Reading and explaining code

Always explain your findings in detail and provide context about how different parts of the code relate to each other.
When analyzing code, consider:
- The purpose and functionality of each component
- How different parts interact
- Key patterns and design decisions
- Potential areas for improvement

Break down complex concepts into understandable pieces and use examples when helpful."""

# Initialize the agent
agent = create_agent_with_tools(
    codebase=codebase,
    tools=tools,
    chat_history=[SystemMessage(content=RESEARCH_AGENT_PROMPT)],
    verbose=True
)
```

## Step 3: Building the CLI Interface

Finally, we'll create a user-friendly CLI interface using rich-click:

```python theme={null}
import rich_click as click
from rich.console import Console
from rich.markdown import Markdown

@click.group()
def cli():
    """🔍 Codegen Code Research CLI"""
    pass

@cli.command()
@click.argument("repo_name", required=False)
@click.option("--query", "-q", default=None, help="Initial research query.")
def research(repo_name: Optional[str] = None, query: Optional[str] = None):
    """Start a code research session."""
    # Initialize codebase
    codebase = initialize_codebase(repo_name)
    
    # Create and run the agent
    agent = create_research_agent(codebase)
    
    # Main research loop
    while True:
        if not query:
            query = Prompt.ask("[bold cyan]Research query[/bold cyan]")
            
        result = agent.invoke(
            {"input": query},
            config={"configurable": {"thread_id": 1}}
        )
        console.print(Markdown(result["messages"][-1].content))
        
        query = None  # Clear for next iteration
```

## Using the Research Tool

You can use the tool in several ways:

1. Interactive mode (will prompt for repo):

```bash theme={null}
python run.py research
```

2. Specify a repository:

```bash theme={null}
python run.py research "fastapi/fastapi"
```

3. Start with an initial query:

```bash theme={null}
python run.py research "fastapi/fastapi" -q "Explain the main components"
```

Example research queries:

* "Explain the main components and their relationships"
* "Find all usages of the FastAPI class"
* "Show me the dependency graph for the routing module"
* "What design patterns are used in this codebase?"

<Tip>
  The agent maintains conversation history, so you can ask follow-up questions
  and build on previous findings.
</Tip>

## Advanced Usage

### Custom Research Tools

You can extend the agent with custom tools for specific analysis needs:

```python theme={null}
from langchain.tools import BaseTool
from pydantic import BaseModel, Field

class CustomAnalysisTool(BaseTool):
    """Custom tool for specialized code analysis."""
    name = "custom_analysis"
    description = "Performs specialized code analysis"
    
    def _run(self, query: str) -> str:
        # Custom analysis logic
        return results

# Add to tools list
tools.append(CustomAnalysisTool())
```

### Customizing the Agent

You can modify the agent's behavior by adjusting its prompt:

```python theme={null}
CUSTOM_PROMPT = """You are a specialized code reviewer focused on:
1. Security best practices
2. Performance optimization
3. Code maintainability
...
"""

agent = create_agent_with_tools(
    codebase=codebase,
    tools=tools,
    chat_history=[SystemMessage(content=CUSTOM_PROMPT)],
)
```