# Run directly with uvx (no installation needed)
uvx anydocs-mcp-server

# Run with custom configuration
uvx anydocs-mcp-server --config config.yaml

# Run in debug mode
uvx anydocs-mcp-server --debug

# Install globally with uvx for repeated use
uvx install anydocs-mcp-server

# Then run anytime with:
anydocs-mcp-server --config config.yaml

# Clone the repository
git clone https://github.com/funky1688/anydocs-mcp.git
cd anydocs-mcp

# Install dependencies using uv (recommended)
pip install uv
uv pip install -e .

# Copy environment configuration
cp .env.example .env

# Copy and customize configuration
cp config.yaml my-config.yaml

# Edit configuration (add your API keys and settings)
nano .env

# Start the server (hybrid mode - MCP + Web interface)
uv run python start.py

# Create virtual environment (recommended)
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

# Install dependencies
uv pip install -e .  # for production
# OR for development:
uv pip install -e .[dev]

# Copy and configure environment
cp .env.example .env

# Edit configuration files
nano .env

# Initialize and start
uv run python start.py --mode hybrid --debug

# Run as module
python -m anydocs_mcp

# With configuration
python -m anydocs_mcp --config config.yaml

# Debug mode
python -m anydocs_mcp --debug

# Development environment
docker-compose -f docker-compose.dev.yml up -d

# Production environment
docker-compose up -d

uv run python start.py
# or explicitly:
uv run python start.py --mode hybrid

uv run python start.py --mode mcp

uv run python start.py --mode web

# Debug mode with auto-reload
uv run python start.py --debug

# Custom configuration file
uv run python start.py --config custom-config.yaml

# Skip dependency check (faster startup)
uv run python start.py --no-deps-check

# Kill occupied ports before starting
uv run python start.py --kill-ports

# Skip database initialization
uv run python start.py --no-db-init

uv run python start.py --help

# Available options:
#   --mode {mcp,web,hybrid}     Startup mode (default: hybrid)
#   --config CONFIG             Configuration file path (default: config.yaml)
#   --debug                     Enable debug mode
#   --no-deps-check            Skip dependency check
#   --no-db-init               Skip database initialization
#   --kill-ports               Kill occupied ports before starting

from mcp import ClientSession, StdioServerParameters
from mcp.client.stdio import stdio_client

# Connect to AnyDocs MCP Server
async with stdio_client(StdioServerParameters(
    command="python",
    args=["main.py"]
)) as (read, write):
    async with ClientSession(read, write) as session:
        # Initialize the connection
        await session.initialize()
        
        # List available tools
        tools = await session.list_tools()
        
        # Search documents
        result = await session.call_tool(
            "search_documents",
            arguments={"query": "authentication", "limit": 10}
        )

from anydocs_mcp.adapters.base import BaseDocumentAdapter

class CustomAdapter(BaseDocumentAdapter):
    """Custom documentation adapter implementation."""
    
    async def fetch_documents(self) -> List[Document]:
        """Fetch documents from your platform."""
        # Implementation here
        pass
    
    async def get_document_content(self, doc_id: str) -> str:
        """Get specific document content."""
        # Implementation here
        pass

# Always use uv run to ensure correct virtual environment
uv run python start.py

# If the issue persists, reinstall python-jose with cryptography extras
uv pip uninstall python-jose
uv pip install "python-jose[cryptography]"

# The dependency check has been fixed to use correct import names
# Ensure you're using the latest version
git pull origin main
uv pip install -e .

# This is fixed in the current version - ensure you have the latest code
git pull origin main

# Always use 'uv run' to ensure correct environment
uv run python start.py

# Check if you're in the right environment
which python  # Should point to your project's Python
uv pip list    # Should show installed packages

# The redundant root setup.py has been removed
# Use pyproject.toml for package management
uv pip install -e .

# Kill processes on required ports (Windows)
netstat -ano | findstr :8000
taskkill /F /PID <PID>

# Or use the built-in option
uv run python start.py --kill-ports

# Server Configuration
ANYDOCS_HOST=localhost
ANYDOCS_PORT=8000
ANYDOCS_WEB_PORT=8080
ANYDOCS_DEBUG=false

# Database
DATABASE_URL=sqlite:///data/anydocs.db
# DATABASE_URL=postgresql://user:pass@localhost/anydocs

# Authentication
JWT_SECRET_KEY=your-secret-key
API_KEY_PREFIX=anydocs_

# Document Adapters
GITBOOK_API_TOKEN=your-gitbook-token
NOTION_API_TOKEN=your-notion-token
CONFLUENCE_API_TOKEN=your-confluence-token

# Cache (Optional)
REDIS_URL=redis://localhost:6379/0

# Monitoring
ENABLE_METRICS=true
LOG_LEVEL=INFO

# config.yaml
server:
  host: localhost
  port: 8000
  web_port: 8080
  debug: false

database:
  url: sqlite:///data/anydocs.db
  pool_size: 10
  echo: false

auth:
  jwt_secret: ${JWT_SECRET_KEY}
  token_expire_minutes: 1440
  
  api_key:
    prefix: anydocs_
    length: 32

adapters:
  gitbook:
    api_token: ${GITBOOK_API_TOKEN}
    base_url: https://api.gitbook.com
    rate_limit: 100
  
  notion:
    api_token: ${NOTION_API_TOKEN}
    version: "2022-06-28"
    rate_limit: 3

# Install development dependencies
uv pip install -e .[dev]

# Setup pre-commit hooks
uv run pre-commit install

# Run tests
uv run pytest

# Run with coverage
uv run pytest --cov=src/anydocs_mcp

# Code formatting
uv run black src/ tests/
uv run isort src/ tests/

# Type checking
uv run mypy src/

# Security checks
uv run bandit -r src/

anydocs-mcp/
├── src/anydocs_mcp/          # Main package
│   ├── adapters/             # Document adapters
│   ├── auth/                 # Authentication
│   ├── config/               # Configuration management
│   ├── content/              # Content processing
│   ├── database/             # Database models and operations
│   ├── utils/                # Utilities and helpers
│   ├── web/                  # Web interface
│   └── server.py             # MCP server implementation
├── tests/                    # Test suite
├── docs/                     # Documentation
├── scripts/                  # Utility scripts
│   └── setup.py              # Development environment setup
├── pyproject.toml            # Package configuration (modern Python packaging)
├── start.py                  # Main startup script
└── main.py                   # MCP server entry point

# All tests
uv run pytest

# Unit tests only
uv run pytest tests/unit/

# Integration tests only
uv run pytest tests/integration/

# With coverage
uv run pytest --cov=src/anydocs_mcp --cov-report=html

# Performance tests
uv run pytest tests/performance/

# Check service health
curl http://localhost:8080/health

# Detailed health check
curl http://localhost:8080/health/detailed

# Application logs
tail -f anydocs_mcp.log

# Check logs in real-time
uv run python start.py --debug

# Start development environment
docker-compose -f docker-compose.dev.yml up -d

# View logs
docker-compose logs -f anydocs-mcp-dev

# Access shell
docker-compose exec anydocs-mcp-dev bash

# Build and start production environment
docker-compose up -d

# Scale services
docker-compose up -d --scale anydocs-mcp=3

# Update services
docker-compose pull && docker-compose up -d

# Start with monitoring
docker-compose --profile monitoring up -d

# Access services
# Grafana: http://localhost:3001 (admin/admin)
# Prometheus: http://localhost:9090

# Run security checks
uv run bandit -r src/

# Dependency vulnerability scan
uv run safety check

# SAST scanning
uv run bandit -r src/

# Performance testing
uv run pytest tests/performance/

# Memory profiling
uv run python -m memory_profiler start.py