Fastapi Project Structure

FastAPI Project Structure Skill

Production-ready FastAPI project scaffolding templates and best practices for building scalable, maintainable backend applications with MCP integration support.

Instructions

1. Choose Project Template

Select the appropriate project template based on your use case:

• minimal: Basic FastAPI app structure (single file, quick prototypes)
• standard: Standard production structure (API routes, models, services)
• mcp-server: FastAPI app with MCP server integration
• full-stack: Complete backend with auth, database, background tasks
• microservice: Microservice-ready structure with health checks, metrics

2. Generate Project Structure

Use the setup script to scaffold a new FastAPI project:

cd /home/gotime2022/.claude/plugins/marketplaces/ai-dev-marketplace/plugins/fastapi-backend/skills/fastapi-project-structure
./scripts/setup-project.sh <project-name> <template-type>

Template types: minimal, standard, mcp-server, full-stack, microservice

Example:

./scripts/setup-project.sh my-api-service standard

What This Creates:

• Complete directory structure
• Configuration files (pyproject.toml, .env.example)
• Main application entry point
• Settings management system
• Docker configuration (for production templates)
• README with setup instructions

3. Configure Application Settings

The skill uses Pydantic Settings for configuration management:

Settings Structure:

# app/core/config.py
from pydantic_settings import BaseSettings

class Settings(BaseSettings):
    # App Configuration
    PROJECT_NAME: str = "FastAPI App"
    VERSION: str = "1.0.0"
    DEBUG: bool = False

    # Server Configuration
    HOST: str = "0.0.0.0"
    PORT: int = 8000

    # Database Configuration (if needed)
    DATABASE_URL: str

    # Security
    SECRET_KEY: str
    ALLOWED_ORIGINS: list[str] = ["*"]

    class Config:
        env_file = ".env"
        case_sensitive = True

Environment Variables: Copy .env.example to .env and customize:

cp .env.example .env
# Edit .env with your configuration

4. Project Structure Patterns

Standard Structure

my-api-service/
├── app/
│   ├── __init__.py
│   ├── main.py              # Application entry point
│   ├── core/
│   │   ├── __init__.py
│   │   ├── config.py        # Settings management
│   │   └── dependencies.py  # Dependency injection
│   ├── api/
│   │   ├── __init__.py
│   │   ├── routes/          # API route handlers
│   │   │   ├── __init__.py
│   │   │   ├── health.py
│   │   │   └── users.py
│   │   └── deps.py          # Route dependencies
│   ├── models/              # Pydantic models
│   │   ├── __init__.py
│   │   └── user.py
│   ├── schemas/             # Request/Response schemas
│   │   ├── __init__.py
│   │   └── user.py
│   └── services/            # Business logic
│       ├── __init__.py
│       └── user_service.py
├── tests/
│   ├── __init__.py
│   ├── conftest.py
│   └── test_api/
├── .env.example
├── .gitignore
├── pyproject.toml
├── README.md
└── Dockerfile (optional)

MCP Server Integration Structure

my-mcp-api/
├── app/
│   ├── main.py              # FastAPI + MCP server
│   ├── core/
│   │   ├── config.py
│   │   └── mcp_config.py    # MCP-specific settings
│   ├── api/
│   │   └── routes/
│   ├── mcp/
│   │   ├── __init__.py
│   │   ├── server.py        # MCP server instance
│   │   ├── tools/           # MCP tools
│   │   ├── resources/       # MCP resources
│   │   └── prompts/         # MCP prompts
│   └── services/
├── .mcp.json                # MCP configuration
├── pyproject.toml
└── README.md

5. Validate Project Structure

Run validation to ensure proper structure and dependencies:

./scripts/validate-structure.sh <project-directory>

Validation Checks:

• Directory structure compliance
• Required files present (main.py, config.py, pyproject.toml)
• Python syntax validation
• Dependency declarations
• Environment variable configuration
• Import structure validity
• Type hints presence

6. Development Setup

Initialize the development environment:

# Navigate to project
cd <project-name>

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

# Install dependencies
pip install -e ".[dev]"

# Run development server
uvicorn app.main:app --reload --host 0.0.0.0 --port 8000

7. MCP Server Integration (Optional)

For projects with MCP server support:

# Configure MCP settings
cp templates/mcp-config-template.json .mcp.json

# Edit MCP configuration
# Add tools, resources, and prompts

# Run as MCP server (STDIO mode)
python -m app.main --mcp

# Run as HTTP server
uvicorn app.main:app --host 0.0.0.0 --port 8000

Available Templates

Core Templates

• pyproject.toml: Modern Python project configuration with dependencies
• main.py: Application entry point with FastAPI initialization
• config.py: Pydantic Settings-based configuration management
• dependencies.py: Dependency injection patterns
• health.py: Health check endpoints with database/service checks
• docker-template: Multi-stage Docker build for production
• nginx-template: Nginx reverse proxy configuration

MCP Integration Templates

• mcp-server.py: MCP server initialization with FastAPI
• mcp-tool-template.py: MCP tool implementation pattern
• mcp-resource-template.py: MCP resource pattern
• mcp-config.json: MCP server configuration

Settings & Configuration

• .env.example: Environment variables template
• settings-dev.py: Development-specific settings
• settings-prod.py: Production-specific settings
• logging-config.yaml: Structured logging configuration

Key Features

Settings Management

• Pydantic-based type-safe configuration
• Environment-specific settings (dev, staging, prod)
• Automatic validation and type conversion
• Secret management with environment variables
• Nested configuration support

Dependency Injection

• FastAPI's built-in DI system
• Reusable dependencies for auth, database, services
• Request-scoped and application-scoped dependencies
• Easy testing with dependency overrides

Project Organization

• Clear separation of concerns (routes, models, services)
• Scalable directory structure
• Consistent naming conventions
• Module-based organization for large projects

MCP Integration

• Dual-mode operation (HTTP + MCP STDIO)
• MCP tools, resources, and prompts
• Configuration management via .mcp.json
• FastMCP framework compatibility

Production-Ready

• Docker multi-stage builds
• Health check endpoints
• Structured logging
• Error handling middleware
• CORS configuration
• Security headers

Examples

See the examples directory for:

• minimal-api/: Simple FastAPI application
• crud-api/: Complete CRUD API with database
• mcp-integrated-api/: FastAPI + MCP server
• microservice-template/: Production microservice
• auth-api/: API with JWT authentication

Configuration Files Generated

pyproject.toml

[project]
name = "my-api-service"
version = "1.0.0"
description = "FastAPI application"
requires-python = ">=3.11"
dependencies = [
    "fastapi>=0.115.0",
    "uvicorn[standard]>=0.32.0",
    "pydantic>=2.0.0",
    "pydantic-settings>=2.0.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=8.0.0",
    "pytest-asyncio>=0.24.0",
    "httpx>=0.27.0",
    "ruff>=0.6.0",
    "mypy>=1.11.0",
]
mcp = [
    "mcp>=1.0.0",
]

[tool.ruff]
line-length = 100
target-version = "py311"

[tool.mypy]
python_version = "3.11"
strict = true

main.py (Standard Template)

from fastapi import FastAPI
from fastapi.middleware.cors import CORSMiddleware
from app.core.config import settings
from app.api.routes import health, users

app = FastAPI(
    title=settings.PROJECT_NAME,
    version=settings.VERSION,
    debug=settings.DEBUG,
)

# CORS
app.add_middleware(
    CORSMiddleware,
    allow_origins=settings.ALLOWED_ORIGINS,
    allow_credentials=True,
    allow_methods=["*"],
    allow_headers=["*"],
)

# Include routers
app.include_router(health.router, prefix="/health", tags=["health"])
app.include_router(users.router, prefix="/api/v1/users", tags=["users"])

@app.get("/")
async def root():
    return {"message": f"Welcome to {settings.PROJECT_NAME}"}

Dockerfile (Production Template)

FROM python:3.11-slim as builder
WORKDIR /app
COPY pyproject.toml .
RUN pip install --no-cache-dir build && \
    python -m build --wheel

FROM python:3.11-slim
WORKDIR /app
COPY --from=builder /app/dist/*.whl .
RUN pip install --no-cache-dir *.whl && rm *.whl
COPY app/ ./app/
EXPOSE 8000
CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "8000"]

Best Practices

Project Structure:

1. Keep business logic in services, not routes
2. Use schemas for request/response validation
3. Separate models (DB) from schemas (API)
4. Implement dependency injection for services
5. Use async/await for I/O-bound operations

Configuration:

1. Never commit secrets (.env in .gitignore)
2. Use Pydantic Settings for type safety
3. Separate dev/staging/prod configurations
4. Validate all environment variables at startup
5. Document required environment variables in .env.example

Code Organization:

1. One router per resource (users.py, posts.py)
2. Group related endpoints in routers
3. Keep route handlers thin (delegate to services)
4. Use consistent naming conventions
5. Type-hint all function parameters and returns

Testing:

1. Use TestClient for API testing
2. Override dependencies for mocking
3. Separate unit and integration tests
4. Use fixtures for common test data
5. Test both success and error cases

Security:

1. Validate all inputs with Pydantic
2. Implement proper CORS configuration
3. Use environment variables for secrets
4. Enable security headers middleware
5. Implement rate limiting for public APIs

Performance:

1. Use async route handlers for I/O
2. Implement connection pooling for databases
3. Add response caching where appropriate
4. Use background tasks for non-critical operations
5. Monitor with health check endpoints

Common Workflows

Creating a New API Endpoint

# 1. Generate project structure
./scripts/setup-project.sh my-api standard

# 2. Add new route file
# Create app/api/routes/items.py

# 3. Add schemas
# Create app/schemas/item.py

# 4. Add service logic
# Create app/services/item_service.py

# 5. Register router in main.py
# app.include_router(items.router, prefix="/api/v1/items")

Setting Up MCP Integration

# 1. Generate MCP-enabled project
./scripts/setup-project.sh my-mcp-api mcp-server

# 2. Configure .mcp.json
cp templates/mcp-config-template.json my-mcp-api/.mcp.json

# 3. Add MCP tools
# Copy from templates/mcp-tool-template.py to app/mcp/tools/

# 4. Run in MCP mode
cd my-mcp-api
python -m app.main --mcp

Production Deployment

# 1. Build Docker image
docker build -t my-api:latest .

# 2. Run container
docker run -d -p 8000:8000 \
  --env-file .env.prod \
  --name my-api \
  my-api:latest

# 3. Health check
curl http://localhost:8000/health

Troubleshooting

Import errors: Ensure virtual environment is activated and dependencies installed

Port already in use: Change PORT in .env or use different port with --port flag

Environment variables not loading: Check .env file location and syntax, ensure pydantic-settings installed

MCP server not starting: Verify .mcp.json configuration and mcp package installed

Type checking errors: Run mypy app/ to see detailed type errors, ensure all dependencies have type stubs

Plugin: fastapi-backend Version: 1.0.0 Category: Project Structure & Scaffolding Skill Type: Templates & Automation