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title: Doc-MCP Documentation RAG System emoji: 📚 colorFrom: indigo colorTo: purple sdk: gradio sdk_version: "5.34.2" app_file: app.py pinned: true license: mit short_description: GitHub docs into queryable RAG knowledge bases

Doc-MCP — Documentation RAG System

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Transform any GitHub documentation repository into an intelligent, queryable knowledge base — in minutes.

Live Demo · Report Bug · Request Feature

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What is Doc-MCP?

Doc-MCP is an open-source Retrieval-Augmented Generation (RAG) system purpose-built for software documentation. Point it at any public GitHub repository, and within minutes you can ask natural language questions and receive precise, cited answers — all powered by state-of-the-art vector embeddings and large language models.

It also exposes its search capabilities as MCP (Model Context Protocol) tools, meaning any MCP-compatible AI assistant (like Claude Desktop) can query your documentation knowledge base directly, without manual copy-paste.

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Features

Feature	Description
Semantic Search	Find answers across thousands of docs using natural language — no keyword matching required
AI-Powered Q&A	Get intelligent, contextual responses with exact source file citations
Batch Processing	Ingest entire repositories with real-time progress tracking
Incremental Updates	SHA-based change detection — only re-embeds files that actually changed
Repository Management	Full CRUD: view stats, delete repositories, manage ingested content
MCP Integration	Expose documentation search as tools for any MCP-compatible AI agent
Gradio Web UI	Clean, intuitive browser interface — no CLI knowledge required

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Architecture

┌─────────────────────────────────────────────────────────────┐
│                        Gradio Web UI                        │
│   (Ingestion Tab | Q&A Tab | Management Tab | MCP Info)     │
└─────────────────┬───────────────────────────────────────────┘
                  │
         ┌────────▼────────┐
         │  GitHub Loader  │  ← Async file fetching with rate-limit handling
         └────────┬────────┘
                  │ Markdown files
         ┌────────▼────────┐
         │  Text Chunker   │  ← Header-aware recursive splitting (CHUNK_SIZE=3072)
         └────────┬────────┘
                  │ Text chunks
         ┌────────▼────────┐
         │   Nebius AI     │  ← BAAI/bge-en-icl embeddings (4096 dims)
         │   Embeddings    │
         └────────┬────────┘
                  │ Vectors
         ┌────────▼────────┐
         │  MongoDB Atlas  │  ← Vector Search index (cosine similarity)
         │  Vector Store   │
         └────────┬────────┘
                  │ Top-K results
         ┌────────▼────────┐
         │   Nebius LLM    │  ← Meta-Llama-3.1-70B-Instruct
         │  (Answer Gen)   │
         └─────────────────┘

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Quick Start

Prerequisites

• Python 3.13+
• MongoDB Atlas account with Vector Search enabled
• Nebius AI API key (for embeddings + LLM)
• GitHub Personal Access Token (optional — increases rate limit from 60 to 5,000 req/hr)

Installation

# Clone the repository
git clone https://github.com/tirth1263/doc-mcp.git
cd doc-mcp

# Create virtual environment
python -m venv .venv
source .venv/bin/activate      # Linux/Mac
# .venv\Scripts\activate       # Windows

# Install dependencies
pip install -r requirements.txt

Configuration

# Copy environment template
cp .env.example .env

Edit .env with your credentials:

# Required
NEBIUS_API_KEY=your_nebius_api_key_here
MONGODB_URI=mongodb+srv://username:password@cluster.mongodb.net/

# Optional
GITHUB_API_KEY=your_github_token_here
CHUNK_SIZE=3072
SIMILARITY_TOP_K=5
GITHUB_CONCURRENT_REQUESTS=10

MongoDB Atlas Setup

1. Create a free cluster at cloud.mongodb.com
2. Enable Vector Search in your cluster
3. Run the database setup script:

python scripts/db_setup.py setup

This automatically creates:

• doc_rag — document chunks with embeddings
• ingested_repos — repository metadata
• Vector search index on the embedding field

Launch

python main.py

Visit http://localhost:7860 to access the web interface.

MCP SSE endpoint: http://127.0.0.1:7860/gradio_api/mcp/sse

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Usage Guide

1. Ingest Documentation

1. Navigate to the 📥 Documentation Ingestion tab
2. Enter a GitHub repository URL:
   • langchain-ai/langchain
   • https://github.com/facebook/react
   • owner/repo
3. Click Load Files — the system fetches the full file tree
4. Select which markdown files to include
5. Click Ingest Selected Files — watch the progress bar as files are chunked and embedded

2. Ask Questions

1. Go to the 🤖 AI Documentation Assistant tab
2. Select your ingested repository from the dropdown
3. Type any natural language question
4. Get an AI-generated answer with source file citations

Example questions:

• "How do I set up authentication?"
• "What are the available configuration options?"
• "Show me an example of streaming responses"
• "What's the difference between X and Y?"

3. Manage Repositories

Use the 🗂️ Repository Management tab to:

• View statistics (file count, chunk count, last ingested date)
• Delete repositories to free up storage
• Refresh the repository list

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MCP Integration

Connect any MCP-compatible AI assistant to query your documentation:

Claude Desktop Configuration

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "doc-mcp": {
      "url": "http://127.0.0.1:7860/gradio_api/mcp/sse"
    }
  }
}

Available MCP Tools

search_documentation

Semantic similarity search across ingested documentation.

{
  "repo": "langchain-ai/langchain",
  "query": "how to use memory in chains",
  "top_k": 5
}

ask_documentation

AI-powered Q&A with source citations.

{
  "repo": "langchain-ai/langchain",
  "question": "What is the difference between LLMChain and ConversationChain?"
}

list_available_repos

List all ingested repositories.

{}

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Configuration Reference

Variable	Default	Description
NEBIUS_API_KEY	—	Required. Nebius AI API key
MONGODB_URI	—	Required. MongoDB Atlas connection string
GITHUB_API_KEY	—	Optional. GitHub token for higher rate limits
CHUNK_SIZE	3072	Maximum characters per text chunk
SIMILARITY_TOP_K	5	Number of chunks retrieved per query
GITHUB_CONCURRENT_REQUESTS	10	Parallel GitHub API requests

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Project Structure

doc-mcp/
├── app.py                  # Hugging Face Spaces entry point
├── main.py                 # Local development entry point
├── requirements.txt
├── .env.example
├── scripts/
│   └── db_setup.py         # Database initialization & status utility
└── src/
    ├── config.py           # Environment & constants
    ├── github_loader.py    # Async GitHub file fetching
    ├── embeddings.py       # Nebius embeddings + LLM answer generation
    ├── vector_store.py     # MongoDB Atlas vector operations
    ├── mcp_server.py       # MCP tool definitions
    └── ui.py               # Gradio web interface

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Troubleshooting

Rate limit errors from GitHub

Add a GITHUB_API_KEY to your .env. Authenticated requests get 5,000/hr vs 60/hr unauthenticated.

No results returned from search

The MongoDB Atlas Vector Search index may still be building (can take 2-5 minutes after first setup). Check status with:

python scripts/db_setup.py status

Memory / OOM errors during ingestion

Reduce CHUNK_SIZE in your .env (e.g., CHUNK_SIZE=1024).

MongoDB connection errors

1. Verify your IP is whitelisted in Atlas Network Access
2. Confirm Vector Search is enabled on your cluster tier (M10+)
3. Double-check the connection string format in .env

Embedding API errors

Verify your NEBIUS_API_KEY is valid and has sufficient credits.

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Tech Stack

Component	Technology
Web UI	Gradio 5
Embeddings	BAAI/bge-en-icl via Nebius AI
LLM	Meta-Llama-3.1-70B-Instruct via Nebius AI
Vector DB	MongoDB Atlas Vector Search
GitHub API	aiohttp (async)
Protocol	Model Context Protocol (MCP)

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Contributing

Contributions are welcome! Please:

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Commit your changes (git commit -m 'Add amazing feature')
4. Push to the branch (git push origin feature/amazing-feature)
5. Open a Pull Request

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License

Distributed under the MIT License. See LICENSE for details.

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Built with Python, Gradio, MongoDB Atlas, and Nebius AI

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