Base scripts and templates added

.env.example

@@ -0,0 +1,43 @@
+# Flask 2FA Authentication Application Environment Configuration
+# Copy this file to .env and modify the values as needed
+
+# Flask Configuration
+FLASK_CONFIG=development
+FLASK_APP=run.py
+FLASK_ENV=development
+
+# Security Configuration (CRITICAL: Change these in production!)
+SECRET_KEY=your-secret-key-change-this-in-production-use-secrets-manager-or-random-generator
+
+# Database Configuration
+DEV_DATABASE_URL=sqlite:///dev.db
+DATABASE_URL=sqlite:///app.db
+
+# Production Database Example (uncomment and modify for production)
+# DATABASE_URL=postgresql://username:password@localhost/flask_2fa_prod
+
+# Application Settings
+DEBUG=True
+
+# Security Headers (Production only)
+# SESSION_COOKIE_SECURE=True
+# SESSION_COOKIE_HTTPONLY=True
+# SESSION_COOKIE_SAMESITE=Lax
+
+# Logging Configuration
+LOG_LEVEL=INFO
+LOG_FILE=app.log
+
+# SMTP Configuration (for future email features)
+# MAIL_SERVER=smtp.gmail.com
+# MAIL_PORT=587
+# MAIL_USE_TLS=True
+# MAIL_USERNAME=your-email@gmail.com
+# MAIL_PASSWORD=your-app-password
+
+# Development Notes:
+# 1. Never commit the .env file to version control
+# 2. Use strong, randomly generated SECRET_KEY in production
+# 3. Use environment-specific database URLs
+# 4. Enable HTTPS and secure cookies in production
+# 5. Consider using external secret management services

.github/copilot-instructions.md

@@ -0,0 +1 @@
+- Default terminal is the Windows PowerShell, please use the PowerShell rules when using the terminal.

README.md

@@ -0,0 +1,261 @@
+# Flask 2FA Authentication Application
+
+A secure Flask web application implementing two-factor authentication (2FA) with industry best practices for web security.
+
+## 🔒 Security Features
+
+- **Two-Factor Authentication**: TOTP-based 2FA using PyOTP
+- **Secure Password Storage**: Bcrypt hashing with automatic salt generation
+- **CSRF Protection**: Automatic token validation on all forms
+- **SQL Injection Prevention**: Parameterized queries with SQLAlchemy ORM
+- **XSS Protection**: Automatic template escaping and CSP headers
+- **Secure Session Management**: HTTPOnly, Secure, and SameSite cookie flags
+- **Security Headers**: HSTS, X-Frame-Options, X-Content-Type-Options
+- **Input Validation**: Server-side validation with WTForms
+- **Secure Configuration**: Environment-based configuration management
+
+## 🚀 Quick Start
+
+### Prerequisites
+
+- Python 3.9 or higher
+- pip (Python package installer)
+
+### Installation
+
+1. **Clone the repository**
+   ```bash
+   git clone <repository-url>
+   cd flask-2fa-auth
+   ```
+
+2. **Create and activate virtual environment**
+   ```bash
+   # Windows
+   python -m venv venv
+   venv\Scripts\activate
+
+   # macOS/Linux
+   python3 -m venv venv
+   source venv/bin/activate
+   ```
+
+3. **Install dependencies**
+   ```bash
+   pip install -r requirements.txt
+   ```
+
+4. **Set up environment variables**
+   ```bash
+   # Copy the example environment file
+   copy .env.example .env
+
+   # Edit .env file with your configuration
+   # At minimum, change the SECRET_KEY for production
+   ```
+
+5. **Initialize the database**
+   ```bash
+   flask db init
+   flask db migrate -m "Initial migration"
+   flask db upgrade
+   ```
+
+6. **Run the application**
+   ```bash
+   python run.py
+   ```
+
+   The application will be available at `http://127.0.0.1:5000`
+
+## 📱 2FA Setup Process
+
+1. **Register**: Create a new account with username, email, and password
+2. **Scan QR Code**: Use Google Authenticator, Authy, or similar app to scan the QR code
+3. **Verify**: Enter the 6-digit code from your authenticator app
+4. **Login**: Use your credentials + 2FA code for future logins
+
+### Supported Authenticator Apps
+
+- Google Authenticator
+- Microsoft Authenticator  
+- Authy
+- 1Password
+- LastPass Authenticator
+- Any TOTP-compatible app
+
+## 🛠️ Project Structure
+
+```
+flask-2fa-auth/
+├── app/
+│   ├── __init__.py          # Application factory
+│   ├── models.py            # User model with 2FA methods
+│   ├── auth/                # Authentication blueprint
+│   │   ├── __init__.py
+│   │   ├── routes.py        # Auth routes (register, login, verify)
+│   │   └── forms.py         # WTForms form classes
+│   ├── main/                # Main application blueprint
+│   │   ├── __init__.py
+│   │   └── routes.py        # Main routes (dashboard, profile)
+│   └── templates/           # Jinja2 templates
+│       ├── base.html        # Base template with security headers
+│       ├── index.html       # Home page
+│       ├── dashboard.html   # User dashboard
+│       ├── profile.html     # User profile
+│       └── auth/            # Authentication templates
+│           ├── register.html
+│           ├── login.html
+│           ├── verify_otp.html
+│           └── setup_2fa.html
+├── config.py                # Configuration classes
+├── requirements.txt         # Python dependencies
+├── run.py                   # Application entry point
+├── .env.example            # Environment variables template
+└── README.md               # This file
+```
+
+## 🔧 Configuration
+
+### Environment Variables
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `FLASK_CONFIG` | Configuration environment | `development` |
+| `SECRET_KEY` | Flask secret key (CHANGE IN PRODUCTION!) | Auto-generated |
+| `DATABASE_URL` | Database connection string | `sqlite:///app.db` |
+| `DEBUG` | Enable debug mode | `True` |
+
+### Configuration Classes
+
+- **DevelopmentConfig**: Debug enabled, SQLite database
+- **ProductionConfig**: Debug disabled, PostgreSQL recommended
+- **TestingConfig**: In-memory database, CSRF disabled
+
+## 🚀 Deployment
+
+### Production Checklist
+
+- [ ] Change `SECRET_KEY` to a cryptographically secure random value
+- [ ] Set `FLASK_CONFIG=production`
+- [ ] Use PostgreSQL or similar production database
+- [ ] Enable HTTPS with valid SSL certificate
+- [ ] Set secure environment variables
+- [ ] Use a proper WSGI server (Gunicorn, uWSGI)
+- [ ] Configure reverse proxy (Nginx, Apache)
+- [ ] Set up monitoring and logging
+- [ ] Regular security updates
+
+### Example Production Deployment
+
+```bash
+# Install production dependencies
+pip install gunicorn
+
+# Set production environment
+export FLASK_CONFIG=production
+export SECRET_KEY="your-super-secure-random-key"
+export DATABASE_URL="postgresql://user:pass@localhost/flask_2fa_prod"
+
+# Run database migrations
+flask db upgrade
+
+# Start with Gunicorn
+gunicorn -w 4 -b 0.0.0.0:8000 run:app
+```
+
+## 🛡️ Security Considerations
+
+### Authentication Security
+- Passwords are hashed using bcrypt with automatic salt generation
+- TOTP tokens expire every 30 seconds with built-in replay protection
+- Failed login attempts are logged for security monitoring
+- Session protection prevents session fixation attacks
+
+### Web Security
+- CSRF tokens protect against cross-site request forgery
+- Security headers prevent clickjacking and XSS attacks
+- Input validation prevents injection attacks
+- Secure cookie settings protect session data
+
+### Database Security
+- Parameterized queries prevent SQL injection
+- Connection pooling with proper timeouts
+- Database credentials stored in environment variables
+
+### Operational Security
+- Security events logged for monitoring
+- Environment-based configuration
+- Separate development and production configurations
+
+## 📚 API Reference
+
+### User Model Methods
+
+```python
+user = User(username="john", email="john@example.com")
+
+# Password management
+user.set_password("secure_password")
+user.check_password("password_to_verify")
+
+# 2FA management
+user.generate_totp_secret()
+user.generate_totp_uri("MyApp")
+user.verify_totp("123456")
+user.generate_qr_code("MyApp")
+user.enable_2fa()
+user.disable_2fa()
+```
+
+### Routes
+
+| Route | Method | Description |
+|-------|--------|-------------|
+| `/` | GET | Home page |
+| `/auth/register` | GET, POST | User registration |
+| `/auth/login` | GET, POST | User login (first factor) |
+| `/auth/verify-otp` | GET, POST | 2FA verification |
+| `/auth/setup-2fa` | GET | QR code for 2FA setup |
+| `/auth/logout` | GET | User logout |
+| `/dashboard` | GET | User dashboard (protected) |
+| `/profile` | GET | User profile (protected) |
+
+## 🤝 Contributing
+
+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
+
+### Development Guidelines
+
+- Follow PEP 8 style guidelines
+- Add tests for new features
+- Update documentation as needed
+- Ensure security best practices are maintained
+
+## 📄 License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## 🆘 Support
+
+If you encounter any issues:
+
+1. Check the [Issues](../../issues) page for existing solutions
+2. Create a new issue with detailed information
+3. Include error messages and steps to reproduce
+
+## 🔗 Resources
+
+- [Flask Documentation](https://flask.palletsprojects.com/)
+- [Flask-Login Documentation](https://flask-login.readthedocs.io/)
+- [PyOTP Documentation](https://pypi.org/project/pyotp/)
+- [OWASP Security Guidelines](https://owasp.org/www-project-web-security-testing-guide/)
+- [NIST 2FA Guidelines](https://pages.nist.gov/800-63-3/sp800-63b.html)
+
+---
+
+**⚠️ Security Notice**: This application implements security best practices, but security is an ongoing process. Always keep dependencies updated, monitor for vulnerabilities, and follow current security guidelines for production deployments.

app/__init__.py

@@ -0,0 +1,69 @@
+from flask import Flask
+from flask_sqlalchemy import SQLAlchemy
+from flask_migrate import Migrate
+from flask_login import LoginManager
+from flask_wtf.csrf import CSRFProtect
+from config import config
+
+# Initialize extensions
+db = SQLAlchemy()
+migrate = Migrate()
+login_manager = LoginManager()
+csrf = CSRFProtect()
+
+
+def create_app(config_name='default'):
+    """
+    Application factory pattern for creating Flask app instances.
+    
+    Security considerations:
+    - CSRF protection enabled globally
+    - Secure session configuration
+    - Login manager with proper security settings
+    """
+    app = Flask(__name__)
+    app.config.from_object(config[config_name])
+    
+    # Initialize extensions with app
+    db.init_app(app)
+    migrate.init_app(app, db)
+    csrf.init_app(app)
+    
+    # Configure Flask-Login for security
+    login_manager.init_app(app)
+    login_manager.login_view = 'auth.login'
+    login_manager.login_message = 'Please log in to access this page.'
+    login_manager.login_message_category = 'info'
+    login_manager.session_protection = 'strong'  # Enhanced session protection
+    
+    @login_manager.user_loader
+    def load_user(user_id):
+        """
+        User loader function for Flask-Login.
+        Uses parameterized query to prevent SQL injection.
+        """
+        from app.models import User
+        return User.query.get(int(user_id))
+    
+    # Register blueprints
+    from app.auth import bp as auth_bp
+    app.register_blueprint(auth_bp, url_prefix='/auth')
+    
+    from app.main import bp as main_bp
+    app.register_blueprint(main_bp)
+    
+    # Security headers middleware
+    @app.after_request
+    def security_headers(response):
+        """Add security headers to all responses."""
+        response.headers['X-Content-Type-Options'] = 'nosniff'
+        response.headers['X-Frame-Options'] = 'DENY'
+        response.headers['X-XSS-Protection'] = '1; mode=block'
+        response.headers['Strict-Transport-Security'] = 'max-age=31536000; includeSubDomains'
+        return response
+    
+    return app
+
+
+# Import models to ensure they are registered with SQLAlchemy
+from app import models

app/auth/__init__.py

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+from flask import Blueprint
+
+bp = Blueprint('auth', __name__)
+
+from app.auth import routes

app/auth/forms.py

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+from flask_wtf import FlaskForm
+from wtforms import StringField, PasswordField, SubmitField, BooleanField
+from wtforms.validators import DataRequired, Length, Email, EqualTo, ValidationError
+from app.models import User
+
+
+class RegistrationForm(FlaskForm):
+    """
+    User registration form with validation.
+    
+    Security: CSRF protection enabled automatically by Flask-WTF.
+    """
+    username = StringField('Username', validators=[
+        DataRequired(),
+        Length(min=3, max=20, message='Username must be between 3 and 20 characters.')
+    ])
+    email = StringField('Email', validators=[
+        DataRequired(),
+        Email(message='Invalid email address.')
+    ])
+    password = PasswordField('Password', validators=[
+        DataRequired(),
+        Length(min=8, message='Password must be at least 8 characters long.')
+    ])
+    password2 = PasswordField('Confirm Password', validators=[
+        DataRequired(),
+        EqualTo('password', message='Passwords must match.')
+    ])
+    submit = SubmitField('Register')
+    
+    def validate_username(self, username):
+        """
+        Custom validator to check username uniqueness.
+        
+        Security: Uses parameterized query to prevent SQL injection.
+        """
+        user = User.query.filter_by(username=username.data).first()
+        if user:
+            raise ValidationError('Username already exists. Please choose a different one.')
+    
+    def validate_email(self, email):
+        """
+        Custom validator to check email uniqueness.
+        
+        Security: Uses parameterized query to prevent SQL injection.
+        """
+        user = User.query.filter_by(email=email.data).first()
+        if user:
+            raise ValidationError('Email already registered. Please choose a different one.')
+
+
+class LoginForm(FlaskForm):
+    """
+    User login form.
+    
+    Security: CSRF protection enabled automatically by Flask-WTF.
+    """
+    username = StringField('Username', validators=[DataRequired()])
+    password = PasswordField('Password', validators=[DataRequired()])
+    remember_me = BooleanField('Remember Me')
+    submit = SubmitField('Sign In')
+
+
+class TwoFactorForm(FlaskForm):
+    """
+    Two-factor authentication verification form.
+    
+    Security: CSRF protection enabled automatically by Flask-WTF.
+    """
+    token = StringField('Authentication Code', validators=[
+        DataRequired(),
+        Length(min=6, max=6, message='Authentication code must be 6 digits.')
+    ])
+    submit = SubmitField('Verify')
+    
+    def validate_token(self, token):
+        """Validate that token contains only digits."""
+        if not token.data.isdigit():
+            raise ValidationError('Authentication code must contain only digits.')

app/auth/routes.py

@@ -0,0 +1,223 @@
+from flask import render_template, redirect, url_for, flash, request, session
+from flask_login import login_user, logout_user, current_user, login_required
+from urllib.parse import urlparse
+from app import db
+from app.auth import bp
+from app.auth.forms import RegistrationForm, LoginForm, TwoFactorForm
+from app.models import User
+import logging
+
+# Configure logging for security events
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+@bp.route('/register', methods=['GET', 'POST'])
+def register():
+    """
+    User registration endpoint with 2FA setup.
+    
+    Security features:
+    - CSRF protection via Flask-WTF
+    - Password hashing via bcrypt
+    - Input validation and sanitization
+    - SQL injection prevention via parameterized queries
+    """
+    if current_user.is_authenticated:
+        return redirect(url_for('main.index'))
+    
+    form = RegistrationForm()
+    if form.validate_on_submit():
+        try:
+            # Create new user with hashed password
+            user = User(username=form.username.data, email=form.email.data)
+            user.set_password(form.password.data)
+            
+            # Generate TOTP secret for 2FA
+            user.generate_totp_secret()
+            
+            # Save user to database
+            db.session.add(user)
+            db.session.commit()
+            
+            # Log successful registration (without sensitive data)
+            logger.info(f'New user registered: {user.username}')
+            
+            flash('Registration successful! Please scan the QR code with your authenticator app.', 'success')
+            
+            # Store user ID in session for QR code display
+            session['temp_user_id'] = user.id
+            
+            return redirect(url_for('auth.setup_2fa'))
+            
+        except Exception as e:
+            # Rollback transaction on error
+            db.session.rollback()
+            logger.error(f'Registration error for user {form.username.data}: {str(e)}')
+            flash('Registration failed. Please try again.', 'error')
+    
+    return render_template('auth/register.html', form=form, title='Register')
+
+
+@bp.route('/setup-2fa')
+def setup_2fa():
+    """
+    Display QR code for 2FA setup after registration.
+    
+    Security: Requires temp_user_id in session to prevent unauthorized access.
+    """
+    user_id = session.get('temp_user_id')
+    if not user_id:
+        flash('Invalid session. Please register again.', 'error')
+        return redirect(url_for('auth.register'))
+    
+    user = User.query.get(user_id)
+    if not user:
+        flash('User not found. Please register again.', 'error')
+        return redirect(url_for('auth.register'))
+    
+    # Generate QR code for Google Authenticator
+    qr_code = user.generate_qr_code()
+    
+    # Clear temp session data
+    session.pop('temp_user_id', None)
+    
+    return render_template('auth/setup_2fa.html', 
+                         qr_code=qr_code, 
+                         username=user.username,
+                         title='Setup Two-Factor Authentication')
+
+
+@bp.route('/login', methods=['GET', 'POST'])
+def login():
+    """
+    User login endpoint with first-factor authentication.
+    
+    Security features:
+    - CSRF protection via Flask-WTF
+    - Secure password verification
+    - Session protection
+    - Login attempt logging
+    """
+    if current_user.is_authenticated:
+        return redirect(url_for('main.index'))
+    
+    form = LoginForm()
+    if form.validate_on_submit():
+        # Use parameterized query to prevent SQL injection
+        user = User.query.filter_by(username=form.username.data).first()
+        
+        if user is None or not user.check_password(form.password.data):
+            # Log failed login attempt
+            logger.warning(f'Failed login attempt for username: {form.username.data}')
+            flash('Invalid username or password', 'error')
+            return redirect(url_for('auth.login'))
+        
+        # Store user ID in session for 2FA verification
+        session['temp_user_id'] = user.id
+        session['remember_me'] = form.remember_me.data
+        
+        # Log successful first-factor authentication
+        logger.info(f'First-factor authentication successful for user: {user.username}')
+        
+        # Redirect to 2FA verification
+        flash('Please enter your authentication code', 'info')
+        return redirect(url_for('auth.verify_otp'))
+    
+    return render_template('auth/login.html', form=form, title='Sign In')
+
+
+@bp.route('/verify-otp', methods=['GET', 'POST'])
+def verify_otp():
+    """
+    Second-factor authentication endpoint using TOTP.
+    
+    Security features:
+    - CSRF protection via Flask-WTF
+    - Time-based token verification
+    - Session validation
+    - Replay attack protection (built into PyOTP)
+    """
+    user_id = session.get('temp_user_id')
+    if not user_id:
+        flash('Session expired. Please log in again.', 'error')
+        return redirect(url_for('auth.login'))
+    
+    user = User.query.get(user_id)
+    if not user:
+        flash('User not found. Please log in again.', 'error')
+        return redirect(url_for('auth.login'))
+    
+    form = TwoFactorForm()
+    if form.validate_on_submit():
+        if user.verify_totp(form.token.data):
+            # Enable 2FA if this is the first successful verification
+            if not user.is_2fa_enabled:
+                user.enable_2fa()
+            
+            # Update last login timestamp
+            user.last_login = db.func.current_timestamp()
+            db.session.commit()
+            
+            # Clear temp session data
+            remember_me = session.pop('remember_me', False)
+            session.pop('temp_user_id', None)
+            
+            # Complete login process
+            login_user(user, remember=remember_me)
+            
+            # Log successful login
+            logger.info(f'Successful login for user: {user.username}')
+            
+            flash('Login successful!', 'success')
+              # Redirect to originally requested page or dashboard
+            next_page = request.args.get('next')
+            if not next_page or urlparse(next_page).netloc != '':
+                next_page = url_for('main.index')
+            return redirect(next_page)
+        else:
+            # Log failed 2FA attempt
+            logger.warning(f'Failed 2FA verification for user: {user.username}')
+            flash('Invalid authentication code. Please try again.', 'error')
+    
+    return render_template('auth/verify_otp.html', form=form, title='Two-Factor Authentication')
+
+
+@bp.route('/logout')
+@login_required
+def logout():
+    """
+    User logout endpoint.
+    
+    Security: Properly clears session and logs security event.
+    """
+    username = current_user.username if current_user.is_authenticated else 'Unknown'
+    logout_user()
+    
+    # Clear any remaining session data
+    session.clear()
+    
+    # Log logout event
+    logger.info(f'User logged out: {username}')
+    
+    flash('You have been logged out successfully.', 'info')
+    return redirect(url_for('main.index'))
+
+
+@bp.route('/disable-2fa', methods=['POST'])
+@login_required
+def disable_2fa():
+    """
+    Disable two-factor authentication for the current user.
+    
+    Security: Requires active login session and POST request.
+    """
+    try:
+        current_user.disable_2fa()
+        logger.info(f'2FA disabled for user: {current_user.username}')
+        flash('Two-factor authentication has been disabled.', 'warning')
+    except Exception as e:
+        logger.error(f'Error disabling 2FA for user {current_user.username}: {str(e)}')
+        flash('Failed to disable two-factor authentication.', 'error')
+    
+    return redirect(url_for('main.profile'))

app/main/__init__.py

@@ -0,0 +1,5 @@
+from flask import Blueprint
+
+bp = Blueprint('main', __name__)
+
+from app.main import routes

app/main/routes.py

@@ -0,0 +1,36 @@
+from flask import render_template
+from flask_login import login_required, current_user
+from app.main import bp
+
+
+@bp.route('/')
+@bp.route('/index')
+def index():
+    """
+    Home page - shows different content for authenticated vs anonymous users.
+    
+    Security: No sensitive data exposed to anonymous users.
+    """
+    return render_template('index.html', title='Home')
+
+
+@bp.route('/dashboard')
+@login_required
+def dashboard():
+    """
+    Protected dashboard for authenticated users.
+    
+    Security: Requires valid login session with 2FA verification.
+    """
+    return render_template('dashboard.html', title='Dashboard', user=current_user)
+
+
+@bp.route('/profile')
+@login_required
+def profile():
+    """
+    User profile page with 2FA management.
+    
+    Security: Requires valid login session.
+    """
+    return render_template('profile.html', title='Profile', user=current_user)

app/models.py

@@ -0,0 +1,147 @@
+import secrets
+import pyotp
+import qrcode
+import io
+import base64
+from flask_sqlalchemy import SQLAlchemy
+from flask_login import UserMixin
+from werkzeug.security import generate_password_hash, check_password_hash
+from app import db
+
+
+class User(UserMixin, db.Model):
+    """
+    User model with two-factor authentication support.
+    
+    Security features:
+    - Bcrypt password hashing
+    - TOTP secret generation and verification
+    - Secure random secret generation
+    """
+    
+    id = db.Column(db.Integer, primary_key=True)
+    username = db.Column(db.String(80), unique=True, nullable=False, index=True)
+    email = db.Column(db.String(120), unique=True, nullable=False, index=True)
+    password_hash = db.Column(db.String(255), nullable=False)
+    totp_secret = db.Column(db.String(32), nullable=True)
+    is_2fa_enabled = db.Column(db.Boolean, default=False, nullable=False)
+    created_at = db.Column(db.DateTime, default=db.func.current_timestamp())
+    last_login = db.Column(db.DateTime)
+    
+    def __repr__(self):
+        return f'<User {self.username}>'
+    
+    def set_password(self, password):
+        """
+        Hash and set the user's password using bcrypt.
+        
+        Security: Uses bcrypt with automatic salt generation
+        for resistance against rainbow table attacks.
+        """
+        self.password_hash = generate_password_hash(password, method='pbkdf2:sha256')
+    
+    def check_password(self, password):
+        """
+        Verify the provided password against the stored hash.
+        
+        Security: Uses constant-time comparison to prevent timing attacks.
+        """
+        return check_password_hash(self.password_hash, password)
+    
+    def generate_totp_secret(self):
+        """
+        Generate a new TOTP secret for two-factor authentication.
+        
+        Security: Uses cryptographically secure random generation.
+        """
+        if not self.totp_secret:
+            self.totp_secret = pyotp.random_base32()
+        return self.totp_secret
+    
+    def generate_totp_uri(self, issuer_name='Flask-2FA-App'):
+        """
+        Generate a TOTP URI for QR code generation.
+        
+        Args:
+            issuer_name: The name of the application (displayed in authenticator apps)
+            
+        Returns:
+            str: TOTP URI compatible with authenticator apps like Google Authenticator
+        """
+        if not self.totp_secret:
+            self.generate_totp_secret()
+        
+        return pyotp.totp.TOTP(self.totp_secret).provisioning_uri(
+            name=self.username,
+            issuer_name=issuer_name
+        )
+    
+    def verify_totp(self, token):
+        """
+        Verify a TOTP token against the user's secret.
+        
+        Args:
+            token: The 6-digit TOTP token from the authenticator app
+            
+        Returns:
+            bool: True if the token is valid, False otherwise
+            
+        Security: Uses time-window verification with built-in replay protection.
+        """
+        if not self.totp_secret:
+            return False
+        
+        totp = pyotp.TOTP(self.totp_secret)
+        # Verify token with a 1-period window (30 seconds before/after)
+        return totp.verify(token, valid_window=1)
+    
+    def generate_qr_code(self, issuer_name='Flask-2FA-App'):
+        """
+        Generate a QR code for the TOTP URI.
+        
+        Returns:
+            str: Base64-encoded PNG image of the QR code
+        """
+        uri = self.generate_totp_uri(issuer_name)
+        
+        # Generate QR code
+        qr = qrcode.QRCode(
+            version=1,
+            error_correction=qrcode.constants.ERROR_CORRECT_L,
+            box_size=10,
+            border=4,
+        )
+        qr.add_data(uri)
+        qr.make(fit=True)
+        
+        # Create image
+        img = qr.make_image(fill_color="black", back_color="white")
+        
+        # Convert to base64 for HTML embedding
+        img_buffer = io.BytesIO()
+        img.save(img_buffer, format='PNG')
+        img_buffer.seek(0)
+        
+        return base64.b64encode(img_buffer.getvalue()).decode()
+    
+    def enable_2fa(self):
+        """Enable two-factor authentication for the user."""
+        if self.totp_secret:
+            self.is_2fa_enabled = True
+            db.session.commit()
+    
+    def disable_2fa(self):
+        """Disable two-factor authentication for the user."""
+        self.is_2fa_enabled = False
+        self.totp_secret = None
+        db.session.commit()
+
+
+# Database event listeners for additional security
+from sqlalchemy import event
+
+@event.listens_for(User.password_hash, 'set')
+def validate_password_hash(target, value, oldvalue, initiator):
+    """Ensure password hash is never stored as plaintext."""
+    if value and not value.startswith('pbkdf2:sha256'):
+        raise ValueError("Password must be hashed before storage")

app/templates/auth/login.html

@@ -0,0 +1,94 @@
+{% extends "base.html" %}
+
+{% block content %}
+<div class="row justify-content-center">
+    <div class="col-md-6">
+        <div class="auth-form">
+            <h2 class="text-center mb-4">
+                <i class="bi bi-box-arrow-in-right"></i> Sign In
+            </h2>
+            
+            <div class="security-notice">
+                <strong>Security Notice:</strong> This application uses two-factor authentication. 
+                After entering your credentials, you'll need to provide a code from your authenticator app.
+            </div>
+            
+            <form method="POST" novalidate>
+                {{ form.hidden_tag() }}
+                
+                <!-- Username field -->
+                <div class="mb-3">
+                    {{ form.username.label(class="form-label") }}
+                    {{ form.username(class="form-control" + (" is-invalid" if form.username.errors else ""), 
+                                   placeholder="Enter your username") }}
+                    {% if form.username.errors %}
+                        <div class="invalid-feedback">
+                            {% for error in form.username.errors %}
+                                {{ error }}
+                            {% endfor %}
+                        </div>
+                    {% endif %}
+                </div>
+                
+                <!-- Password field -->
+                <div class="mb-3">
+                    {{ form.password.label(class="form-label") }}
+                    {{ form.password(class="form-control" + (" is-invalid" if form.password.errors else ""), 
+                                   placeholder="Enter your password") }}
+                    {% if form.password.errors %}
+                        <div class="invalid-feedback">
+                            {% for error in form.password.errors %}
+                                {{ error }}
+                            {% endfor %}
+                        </div>
+                    {% endif %}
+                </div>
+                
+                <!-- Remember me checkbox -->
+                <div class="mb-3 form-check">
+                    {{ form.remember_me(class="form-check-input") }}
+                    {{ form.remember_me.label(class="form-check-label") }}
+                    <div class="form-text">Keep me logged in on this device</div>
+                </div>
+                
+                <!-- Submit button -->
+                <div class="d-grid">
+                    {{ form.submit(class="btn btn-primary btn-lg") }}
+                </div>
+            </form>
+            
+            <hr class="my-4">
+            
+            <div class="text-center">
+                <p>Don't have an account? 
+                    <a href="{{ url_for('auth.register') }}" class="text-decoration-none">Register here</a>
+                </p>
+            </div>
+        </div>
+    </div>
+</div>
+
+<div class="row mt-4">
+    <div class="col-md-8 offset-md-2">
+        <div class="card">
+            <div class="card-header">
+                <h5><i class="bi bi-shield-lock"></i> Login Process</h5>
+            </div>
+            <div class="card-body">
+                <ol>
+                    <li>Enter your username and password</li>
+                    <li>If credentials are valid, you'll be redirected to 2FA verification</li>
+                    <li>Open your authenticator app (Google Authenticator, Authy, etc.)</li>
+                    <li>Enter the 6-digit code from your app</li>
+                    <li>Access granted to your secure dashboard</li>
+                </ol>
+                <div class="alert alert-info mt-3">
+                    <i class="bi bi-info-circle"></i>
+                    <strong>Security Tip:</strong> Never share your authentication codes with anyone. 
+                    They expire every 30 seconds for your protection.
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+{% endblock %}

app/templates/auth/register.html

@@ -0,0 +1,108 @@
+{% extends "base.html" %}
+
+{% block content %}
+<div class="row justify-content-center">
+    <div class="col-md-6">
+        <div class="auth-form">
+            <h2 class="text-center mb-4">
+                <i class="bi bi-person-plus"></i> Create Account
+            </h2>
+            
+            <div class="security-notice">
+                <strong>Security Notice:</strong> Your password will be securely hashed using bcrypt. 
+                Two-factor authentication will be automatically enabled for enhanced security.
+            </div>
+            
+            <form method="POST" novalidate>
+                {{ form.hidden_tag() }}
+                
+                <!-- Username field -->
+                <div class="mb-3">
+                    {{ form.username.label(class="form-label") }}
+                    {{ form.username(class="form-control" + (" is-invalid" if form.username.errors else "")) }}
+                    {% if form.username.errors %}
+                        <div class="invalid-feedback">
+                            {% for error in form.username.errors %}
+                                {{ error }}
+                            {% endfor %}
+                        </div>
+                    {% endif %}
+                    <div class="form-text">3-20 characters, alphanumeric only</div>
+                </div>
+                
+                <!-- Email field -->
+                <div class="mb-3">
+                    {{ form.email.label(class="form-label") }}
+                    {{ form.email(class="form-control" + (" is-invalid" if form.email.errors else "")) }}
+                    {% if form.email.errors %}
+                        <div class="invalid-feedback">
+                            {% for error in form.email.errors %}
+                                {{ error }}
+                            {% endfor %}
+                        </div>
+                    {% endif %}
+                </div>
+                
+                <!-- Password field -->
+                <div class="mb-3">
+                    {{ form.password.label(class="form-label") }}
+                    {{ form.password(class="form-control" + (" is-invalid" if form.password.errors else "")) }}
+                    {% if form.password.errors %}
+                        <div class="invalid-feedback">
+                            {% for error in form.password.errors %}
+                                {{ error }}
+                            {% endfor %}
+                        </div>
+                    {% endif %}
+                    <div class="form-text">Minimum 8 characters</div>
+                </div>
+                
+                <!-- Confirm password field -->
+                <div class="mb-3">
+                    {{ form.password2.label(class="form-label") }}
+                    {{ form.password2(class="form-control" + (" is-invalid" if form.password2.errors else "")) }}
+                    {% if form.password2.errors %}
+                        <div class="invalid-feedback">
+                            {% for error in form.password2.errors %}
+                                {{ error }}
+                            {% endfor %}
+                        </div>
+                    {% endif %}
+                </div>
+                
+                <!-- Submit button -->
+                <div class="d-grid">
+                    {{ form.submit(class="btn btn-primary btn-lg") }}
+                </div>
+            </form>
+            
+            <hr class="my-4">
+            
+            <div class="text-center">
+                <p>Already have an account? 
+                    <a href="{{ url_for('auth.login') }}" class="text-decoration-none">Sign in here</a>
+                </p>
+            </div>
+        </div>
+    </div>
+</div>
+
+<div class="row mt-4">
+    <div class="col-md-8 offset-md-2">
+        <div class="card">
+            <div class="card-header">
+                <h5><i class="bi bi-info-circle"></i> Security Features</h5>
+            </div>
+            <div class="card-body">
+                <ul class="list-unstyled">
+                    <li><i class="bi bi-check-circle text-success"></i> Passwords are hashed using bcrypt with salt</li>
+                    <li><i class="bi bi-check-circle text-success"></i> CSRF protection on all forms</li>
+                    <li><i class="bi bi-check-circle text-success"></i> Two-factor authentication required</li>
+                    <li><i class="bi bi-check-circle text-success"></i> Secure session management</li>
+                    <li><i class="bi bi-check-circle text-success"></i> Input validation and sanitization</li>
+                </ul>
+            </div>
+        </div>
+    </div>
+</div>
+{% endblock %}

app/templates/auth/setup_2fa.html

@@ -0,0 +1,135 @@
+{% extends "base.html" %}
+
+{% block content %}
+<div class="row justify-content-center">
+    <div class="col-md-8">
+        <div class="card">
+            <div class="card-header bg-success text-white">
+                <h3 class="mb-0">
+                    <i class="bi bi-check-circle"></i> Registration Successful!
+                </h3>
+            </div>
+            <div class="card-body">
+                <div class="alert alert-info">
+                    <i class="bi bi-info-circle"></i>
+                    <strong>Welcome, {{ username }}!</strong> Your account has been created successfully. 
+                    To complete the setup, please scan the QR code below with your authenticator app.
+                </div>
+                
+                <h4 class="text-center mb-4">
+                    <i class="bi bi-qr-code"></i> Setup Two-Factor Authentication
+                </h4>
+                
+                <div class="qr-code-container">
+                    <img src="data:image/png;base64,{{ qr_code }}" 
+                         alt="QR Code for 2FA Setup" 
+                         class="img-fluid mb-3"
+                         style="max-width: 300px;">
+                    
+                    <p class="text-muted">
+                        Scan this QR code with your authenticator app
+                    </p>
+                </div>
+                
+                <div class="row mt-4">
+                    <div class="col-md-6">
+                        <h5><i class="bi bi-list-ol"></i> Setup Instructions:</h5>
+                        <ol>
+                            <li>Download an authenticator app:
+                                <ul class="mt-2">
+                                    <li>Google Authenticator</li>
+                                    <li>Microsoft Authenticator</li>
+                                    <li>Authy</li>
+                                    <li>1Password</li>
+                                </ul>
+                            </li>
+                            <li>Open the app and tap "Add Account" or "+"</li>
+                            <li>Choose "Scan QR Code"</li>
+                            <li>Point your camera at the QR code above</li>
+                            <li>Your account will be added automatically</li>
+                        </ol>
+                    </div>
+                    <div class="col-md-6">
+                        <h5><i class="bi bi-shield-check"></i> Security Benefits:</h5>
+                        <ul>
+                            <li>Protects against password theft</li>
+                            <li>Prevents unauthorized access</li>
+                            <li>Works offline (no internet required)</li>
+                            <li>Industry-standard TOTP protocol</li>
+                            <li>Compatible with all major apps</li>
+                        </ul>
+                    </div>
+                </div>
+                
+                <div class="alert alert-warning mt-4">
+                    <i class="bi bi-exclamation-triangle"></i>
+                    <strong>Important:</strong> Save your recovery codes or backup your authenticator app. 
+                    If you lose access to your authenticator, you may not be able to log in.
+                </div>
+                
+                <div class="text-center mt-4">
+                    <a href="{{ url_for('auth.login') }}" class="btn btn-primary btn-lg">
+                        <i class="bi bi-box-arrow-in-right"></i> Continue to Login
+                    </a>
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+
+<div class="row mt-4">
+    <div class="col-md-8 offset-md-2">
+        <div class="card">
+            <div class="card-header">
+                <h5><i class="bi bi-question-circle"></i> Frequently Asked Questions</h5>
+            </div>
+            <div class="card-body">
+                <div class="accordion" id="faqAccordion">
+                    <div class="accordion-item">
+                        <h2 class="accordion-header" id="headingOne">
+                            <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseOne">
+                                What if I can't scan the QR code?
+                            </button>
+                        </h2>
+                        <div id="collapseOne" class="accordion-collapse collapse" data-bs-parent="#faqAccordion">
+                            <div class="accordion-body">
+                                You can manually enter the secret key in your authenticator app. Look for an option like 
+                                "Enter code manually" or "Manual entry" in your app.
+                            </div>
+                        </div>
+                    </div>
+                    
+                    <div class="accordion-item">
+                        <h2 class="accordion-header" id="headingTwo">
+                            <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseTwo">
+                                Which authenticator app should I use?
+                            </button>
+                        </h2>
+                        <div id="collapseTwo" class="accordion-collapse collapse" data-bs-parent="#faqAccordion">
+                            <div class="accordion-body">
+                                Google Authenticator is the most popular choice, but Microsoft Authenticator, Authy, 
+                                and 1Password also work excellently. Choose one that you're comfortable with.
+                            </div>
+                        </div>
+                    </div>
+                    
+                    <div class="accordion-item">
+                        <h2 class="accordion-header" id="headingThree">
+                            <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseThree">
+                                Is this secure?
+                            </button>
+                        </h2>
+                        <div id="collapseThree" class="accordion-collapse collapse" data-bs-parent="#faqAccordion">
+                            <div class="accordion-body">
+                                Yes! This uses the industry-standard TOTP (Time-based One-Time Password) protocol, 
+                                which is used by major services like Google, Microsoft, and GitHub. The codes change 
+                                every 30 seconds and can't be reused.
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+{% endblock %}

app/templates/auth/verify_otp.html

@@ -0,0 +1,104 @@
+{% extends "base.html" %}
+
+{% block content %}
+<div class="row justify-content-center">
+    <div class="col-md-6">
+        <div class="auth-form">
+            <h2 class="text-center mb-4">
+                <i class="bi bi-shield-check"></i> Two-Factor Authentication
+            </h2>
+            
+            <div class="alert alert-info">
+                <i class="bi bi-info-circle"></i>
+                <strong>Security Step:</strong> Enter the 6-digit code from your authenticator app to complete login.
+            </div>
+            
+            <form method="POST" novalidate>
+                {{ form.hidden_tag() }}
+                
+                <!-- Token field -->
+                <div class="mb-3">
+                    {{ form.token.label(class="form-label") }}
+                    <div class="input-group">
+                        <span class="input-group-text">
+                            <i class="bi bi-key"></i>
+                        </span>
+                        {{ form.token(class="form-control form-control-lg text-center" + (" is-invalid" if form.token.errors else ""), 
+                                    placeholder="000000", maxlength="6", style="letter-spacing: 0.5em;") }}
+                        {% if form.token.errors %}
+                            <div class="invalid-feedback">
+                                {% for error in form.token.errors %}
+                                    {{ error }}
+                                {% endfor %}
+                            </div>
+                        {% endif %}
+                    </div>
+                    <div class="form-text">
+                        <i class="bi bi-clock"></i> Codes refresh every 30 seconds
+                    </div>
+                </div>
+                
+                <!-- Submit button -->
+                <div class="d-grid">
+                    {{ form.submit(class="btn btn-success btn-lg") }}
+                </div>
+            </form>
+            
+            <hr class="my-4">
+            
+            <div class="text-center">
+                <a href="{{ url_for('auth.login') }}" class="btn btn-outline-secondary">
+                    <i class="bi bi-arrow-left"></i> Back to Login
+                </a>
+            </div>
+        </div>
+    </div>
+</div>
+
+<div class="row mt-4">
+    <div class="col-md-8 offset-md-2">
+        <div class="card">
+            <div class="card-header">
+                <h5><i class="bi bi-question-circle"></i> Trouble with 2FA?</h5>
+            </div>
+            <div class="card-body">
+                <h6>Common Issues:</h6>
+                <ul>
+                    <li><strong>Code not working?</strong> Make sure your device's time is synchronized</li>
+                    <li><strong>Lost your phone?</strong> Contact support for account recovery</li>
+                    <li><strong>App not installed?</strong> Download Google Authenticator or Authy</li>
+                </ul>
+                
+                <div class="alert alert-warning mt-3">
+                    <i class="bi bi-exclamation-triangle"></i>
+                    <strong>Security Notice:</strong> Each code can only be used once and expires after 30 seconds. 
+                    This prevents replay attacks and ensures your account remains secure.
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+
+<script>
+// Auto-focus the token input and auto-submit when 6 digits are entered
+document.addEventListener('DOMContentLoaded', function() {
+    const tokenInput = document.getElementById('token');
+    if (tokenInput) {
+        tokenInput.focus();
+        
+        tokenInput.addEventListener('input', function(e) {
+            // Only allow digits
+            this.value = this.value.replace(/\D/g, '');
+            
+            // Auto-submit when 6 digits are entered
+            if (this.value.length === 6) {
+                // Small delay to show the complete code
+                setTimeout(() => {
+                    this.form.submit();
+                }, 200);
+            }
+        });
+    }
+});
+</script>
+{% endblock %}

app/templates/base.html

@@ -0,0 +1,138 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta http-equiv="X-UA-Compatible" content="ie=edge">
+      <!-- Security headers implemented via meta tags -->
+    <meta http-equiv="Content-Security-Policy" content="default-src 'self'; style-src 'self' 'unsafe-inline' https://cdn.jsdelivr.net; script-src 'self' https://cdn.jsdelivr.net; font-src 'self' https://cdn.jsdelivr.net; img-src 'self' data:;">
+    <meta http-equiv="X-Content-Type-Options" content="nosniff">
+    <meta http-equiv="X-Frame-Options" content="DENY">
+    
+    <title>
+        {% if title %}{{ title }} - Flask 2FA App{% else %}Flask 2FA App{% endif %}
+    </title>
+      <!-- Bootstrap CSS for styling -->
+    <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.0/dist/css/bootstrap.min.css" rel="stylesheet">
+    <!-- Bootstrap Icons - Multiple CDN options for reliability -->
+    <link href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.11.3/font/bootstrap-icons.css" rel="stylesheet">
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-icons/1.11.3/font/bootstrap-icons.min.css" rel="stylesheet" media="print" onload="this.media='all'">
+    
+    <style>
+        .security-notice {
+            background-color: #e3f2fd;
+            border-left: 4px solid #2196f3;
+            padding: 10px;
+            margin: 10px 0;
+        }
+        
+        .qr-code-container {
+            text-align: center;
+            padding: 20px;
+            background-color: #f8f9fa;
+            border-radius: 8px;
+        }
+        
+        .auth-form {
+            max-width: 400px;
+            margin: 0 auto;
+            padding: 20px;
+            background-color: #ffffff;
+            border-radius: 8px;
+            box-shadow: 0 2px 10px rgba(0,0,0,0.1);
+        }
+    </style>
+</head>
+<body class="bg-light">
+    <!-- Navigation -->
+    <nav class="navbar navbar-expand-lg navbar-dark bg-dark">
+        <div class="container">
+            <a class="navbar-brand" href="{{ url_for('main.index') }}">
+                <i class="bi bi-shield-lock"></i> Flask 2FA App
+            </a>
+            
+            <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarNav">
+                <span class="navbar-toggler-icon"></span>
+            </button>
+            
+            <div class="collapse navbar-collapse" id="navbarNav">
+                <ul class="navbar-nav me-auto">
+                    <li class="nav-item">
+                        <a class="nav-link" href="{{ url_for('main.index') }}">Home</a>
+                    </li>
+                    {% if current_user.is_authenticated %}
+                    <li class="nav-item">
+                        <a class="nav-link" href="{{ url_for('main.dashboard') }}">Dashboard</a>
+                    </li>
+                    <li class="nav-item">
+                        <a class="nav-link" href="{{ url_for('main.profile') }}">Profile</a>
+                    </li>
+                    {% endif %}
+                </ul>
+                
+                <ul class="navbar-nav">
+                    {% if current_user.is_authenticated %}
+                    <li class="nav-item dropdown">
+                        <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-bs-toggle="dropdown">
+                            <i class="bi bi-person-circle"></i> {{ current_user.username }}
+                        </a>
+                        <ul class="dropdown-menu">
+                            <li><a class="dropdown-item" href="{{ url_for('main.profile') }}">Profile</a></li>
+                            <li><hr class="dropdown-divider"></li>
+                            <li><a class="dropdown-item" href="{{ url_for('auth.logout') }}">Logout</a></li>
+                        </ul>
+                    </li>
+                    {% else %}
+                    <li class="nav-item">
+                        <a class="nav-link" href="{{ url_for('auth.login') }}">Login</a>
+                    </li>
+                    <li class="nav-item">
+                        <a class="nav-link" href="{{ url_for('auth.register') }}">Register</a>
+                    </li>
+                    {% endif %}
+                </ul>
+            </div>
+        </div>
+    </nav>
+
+    <!-- Main content -->
+    <main class="container mt-4">
+        <!-- Flash messages -->
+        {% with messages = get_flashed_messages(with_categories=true) %}
+            {% if messages %}
+                {% for category, message in messages %}
+                    <div class="alert alert-{{ 'danger' if category == 'error' else category }} alert-dismissible fade show" role="alert">
+                        {{ message }}
+                        <button type="button" class="btn-close" data-bs-dismiss="alert"></button>
+                    </div>
+                {% endfor %}
+            {% endif %}
+        {% endwith %}
+
+        <!-- Page content -->
+        {% block content %}{% endblock %}
+    </main>
+
+    <!-- Footer -->
+    <footer class="mt-5 py-4 bg-dark text-white">
+        <div class="container text-center">
+            <div class="security-notice text-light">
+                <small>
+                    <i class="bi bi-shield-check"></i>
+                    This application implements security best practices including CSRF protection, 
+                    secure password hashing, two-factor authentication, and secure session management.
+                </small>
+            </div>
+            <p class="mb-0">
+                <small>&copy; 2025 Flask 2FA App. Built with security in mind.</small>
+            </p>
+        </div>
+    </footer>
+
+    <!-- Bootstrap JS -->
+    <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.0/dist/js/bootstrap.bundle.min.js"></script>
+    
+    <!-- Additional security: CSP nonce for inline scripts if needed -->
+    {% block scripts %}{% endblock %}
+</body>
+</html>

app/templates/dashboard.html

@@ -0,0 +1,169 @@
+{% extends "base.html" %}
+
+{% block content %}
+<div class="row">
+    <div class="col-md-12">
+        <div class="card bg-success text-white mb-4">
+            <div class="card-body">
+                <h2 class="mb-0">
+                    <i class="bi bi-speedometer2"></i> Welcome to Your Dashboard, {{ user.username }}!
+                </h2>
+                <p class="mb-0">You have successfully logged in with two-factor authentication.</p>
+            </div>
+        </div>
+    </div>
+</div>
+
+<div class="row">
+    <div class="col-md-4">
+        <div class="card">
+            <div class="card-body text-center">
+                <i class="bi bi-person-circle display-4 text-primary mb-3"></i>
+                <h5 class="card-title">Account Information</h5>
+                <p class="card-text">View and manage your account settings and security preferences.</p>
+                <a href="{{ url_for('main.profile') }}" class="btn btn-primary">
+                    <i class="bi bi-gear"></i> Manage Profile
+                </a>
+            </div>
+        </div>
+    </div>
+    
+    <div class="col-md-4">
+        <div class="card">
+            <div class="card-body text-center">
+                <i class="bi bi-shield-check display-4 text-success mb-3"></i>
+                <h5 class="card-title">Security Status</h5>
+                <p class="card-text">
+                    {% if user.is_2fa_enabled %}
+                        <span class="badge bg-success">2FA Enabled</span>
+                    {% else %}
+                        <span class="badge bg-warning">2FA Setup Required</span>
+                    {% endif %}
+                </p>
+                <a href="{{ url_for('main.profile') }}" class="btn btn-outline-success">
+                    <i class="bi bi-shield-lock"></i> Security Settings
+                </a>
+            </div>
+        </div>
+    </div>
+    
+    <div class="col-md-4">
+        <div class="card">
+            <div class="card-body text-center">
+                <i class="bi bi-clock-history display-4 text-info mb-3"></i>
+                <h5 class="card-title">Last Login</h5>
+                <p class="card-text">
+                    {% if user.last_login %}
+                        {{ user.last_login.strftime('%Y-%m-%d %H:%M:%S') }}
+                    {% else %}
+                        First login - Welcome!
+                    {% endif %}
+                </p>
+                <small class="text-muted">Keep track of your account activity</small>
+            </div>
+        </div>
+    </div>
+</div>
+
+<div class="row mt-4">
+    <div class="col-md-12">
+        <div class="card">
+            <div class="card-header">
+                <h4><i class="bi bi-activity"></i> Account Activity</h4>
+            </div>
+            <div class="card-body">
+                <div class="row">
+                    <div class="col-md-6">
+                        <h6>Account Details</h6>
+                        <table class="table table-borderless">
+                            <tr>
+                                <td><strong>Username:</strong></td>
+                                <td>{{ user.username }}</td>
+                            </tr>
+                            <tr>
+                                <td><strong>Email:</strong></td>
+                                <td>{{ user.email }}</td>
+                            </tr>
+                            <tr>
+                                <td><strong>Account Created:</strong></td>
+                                <td>{{ user.created_at.strftime('%Y-%m-%d') if user.created_at else 'N/A' }}</td>
+                            </tr>
+                            <tr>
+                                <td><strong>2FA Status:</strong></td>
+                                <td>
+                                    {% if user.is_2fa_enabled %}
+                                        <span class="badge bg-success">
+                                            <i class="bi bi-check-circle"></i> Enabled
+                                        </span>
+                                    {% else %}
+                                        <span class="badge bg-warning">
+                                            <i class="bi bi-exclamation-triangle"></i> Setup Required
+                                        </span>
+                                    {% endif %}
+                                </td>
+                            </tr>
+                        </table>
+                    </div>
+                    
+                    <div class="col-md-6">
+                        <h6>Security Recommendations</h6>
+                        <div class="list-group">
+                            <div class="list-group-item d-flex justify-content-between align-items-center">
+                                <div>
+                                    <i class="bi bi-check-circle text-success"></i>
+                                    Strong password in use
+                                </div>
+                                <span class="badge bg-success rounded-pill">✓</span>
+                            </div>
+                            <div class="list-group-item d-flex justify-content-between align-items-center">
+                                <div>
+                                    <i class="bi bi-{% if user.is_2fa_enabled %}check-circle text-success{% else %}exclamation-triangle text-warning{% endif %}"></i>
+                                    Two-factor authentication
+                                </div>
+                                <span class="badge bg-{% if user.is_2fa_enabled %}success{% else %}warning{% endif %} rounded-pill">
+                                    {% if user.is_2fa_enabled %}✓{% else %}!{% endif %}
+                                </span>
+                            </div>
+                            <div class="list-group-item d-flex justify-content-between align-items-center">
+                                <div>
+                                    <i class="bi bi-check-circle text-success"></i>
+                                    Secure session active
+                                </div>
+                                <span class="badge bg-success rounded-pill">✓</span>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+
+<div class="row mt-4">
+    <div class="col-md-12">
+        <div class="card border-info">
+            <div class="card-header bg-info text-white">
+                <h5 class="mb-0"><i class="bi bi-lightbulb"></i> Security Tips</h5>
+            </div>
+            <div class="card-body">
+                <div class="row">
+                    <div class="col-md-6">
+                        <ul class="list-unstyled">
+                            <li><i class="bi bi-arrow-right text-primary"></i> Always log out when using shared computers</li>
+                            <li><i class="bi bi-arrow-right text-primary"></i> Keep your authenticator app backed up</li>
+                            <li><i class="bi bi-arrow-right text-primary"></i> Use unique passwords for all accounts</li>
+                        </ul>
+                    </div>
+                    <div class="col-md-6">
+                        <ul class="list-unstyled">
+                            <li><i class="bi bi-arrow-right text-primary"></i> Never share your 2FA codes with anyone</li>
+                            <li><i class="bi bi-arrow-right text-primary"></i> Check for suspicious account activity regularly</li>
+                            <li><i class="bi bi-arrow-right text-primary"></i> Update your password periodically</li>
+                        </ul>
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+{% endblock %}

app/templates/index.html

@@ -0,0 +1,138 @@
+{% extends "base.html" %}
+
+{% block content %}
+<div class="jumbotron bg-primary text-white rounded p-5 mb-4">
+    <div class="container text-center">
+        <h1 class="display-4">
+            <i class="bi bi-shield-lock"></i> Flask 2FA Authentication
+        </h1>
+        <p class="lead">
+            Secure web application with two-factor authentication, built with security best practices.
+        </p>
+        {% if not current_user.is_authenticated %}
+        <div class="mt-4">
+            <a href="{{ url_for('auth.register') }}" class="btn btn-light btn-lg me-3">
+                <i class="bi bi-person-plus"></i> Get Started
+            </a>
+            <a href="{{ url_for('auth.login') }}" class="btn btn-outline-light btn-lg">
+                <i class="bi bi-box-arrow-in-right"></i> Sign In
+            </a>
+        </div>
+        {% else %}
+        <div class="mt-4">
+            <a href="{{ url_for('main.dashboard') }}" class="btn btn-light btn-lg">
+                <i class="bi bi-speedometer2"></i> Go to Dashboard
+            </a>
+        </div>
+        {% endif %}
+    </div>
+</div>
+
+<div class="row">
+    <div class="col-md-4">
+        <div class="card h-100">
+            <div class="card-body text-center">
+                <i class="bi bi-shield-check display-4 text-success mb-3"></i>
+                <h5 class="card-title">Two-Factor Authentication</h5>
+                <p class="card-text">
+                    Enhanced security with TOTP-based 2FA using industry-standard protocols.
+                    Compatible with Google Authenticator, Authy, and other popular apps.
+                </p>
+            </div>
+        </div>
+    </div>
+    
+    <div class="col-md-4">
+        <div class="card h-100">
+            <div class="card-body text-center">
+                <i class="bi bi-lock display-4 text-primary mb-3"></i>
+                <h5 class="card-title">Secure by Design</h5>
+                <p class="card-text">
+                    Built with security best practices including CSRF protection, 
+                    bcrypt password hashing, secure sessions, and input validation.
+                </p>
+            </div>
+        </div>
+    </div>
+    
+    <div class="col-md-4">
+        <div class="card h-100">
+            <div class="card-body text-center">
+                <i class="bi bi-code-slash display-4 text-info mb-3"></i>
+                <h5 class="card-title">Modern Flask App</h5>
+                <p class="card-text">
+                    Implements Flask application factory pattern, blueprints, 
+                    SQLAlchemy ORM, and follows Flask security recommendations.
+                </p>
+            </div>
+        </div>
+    </div>
+</div>
+
+<div class="row mt-5">
+    <div class="col-md-12">
+        <div class="card">
+            <div class="card-header">
+                <h3><i class="bi bi-info-circle"></i> Security Features</h3>
+            </div>
+            <div class="card-body">
+                <div class="row">
+                    <div class="col-md-6">
+                        <h5>Authentication & Authorization</h5>
+                        <ul>
+                            <li><strong>Two-Factor Authentication:</strong> TOTP-based 2FA with PyOTP</li>
+                            <li><strong>Secure Password Storage:</strong> Bcrypt hashing with salt</li>
+                            <li><strong>Session Management:</strong> Flask-Login with secure settings</li>
+                            <li><strong>Login Protection:</strong> Strong session protection enabled</li>
+                        </ul>
+                        
+                        <h5 class="mt-4">Data Protection</h5>
+                        <ul>
+                            <li><strong>CSRF Protection:</strong> Automatic token validation on forms</li>
+                            <li><strong>SQL Injection Prevention:</strong> Parameterized queries</li>
+                            <li><strong>Input Validation:</strong> Server-side validation with WTForms</li>
+                            <li><strong>XSS Prevention:</strong> Automatic template escaping</li>
+                        </ul>
+                    </div>
+                    
+                    <div class="col-md-6">
+                        <h5>HTTP Security</h5>
+                        <ul>
+                            <li><strong>Security Headers:</strong> HSTS, X-Frame-Options, CSP</li>
+                            <li><strong>Secure Cookies:</strong> HTTPOnly, Secure, SameSite flags</li>
+                            <li><strong>Content Security Policy:</strong> Prevents code injection</li>
+                            <li><strong>HTTPS Enforcement:</strong> Production-ready configuration</li>
+                        </ul>
+                        
+                        <h5 class="mt-4">Application Security</h5>
+                        <ul>
+                            <li><strong>Database Security:</strong> Connection pooling and timeouts</li>
+                            <li><strong>Error Handling:</strong> Secure error pages without information disclosure</li>
+                            <li><strong>Logging:</strong> Security events logged for monitoring</li>
+                            <li><strong>Environment Configuration:</strong> Separate configs for dev/prod</li>
+                        </ul>
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+
+{% if not current_user.is_authenticated %}
+<div class="row mt-4">
+    <div class="col-md-12">
+        <div class="card bg-light">
+            <div class="card-body text-center">
+                <h4><i class="bi bi-rocket"></i> Ready to Get Started?</h4>
+                <p class="lead">
+                    Create your secure account in minutes and experience enterprise-grade security.
+                </p>
+                <a href="{{ url_for('auth.register') }}" class="btn btn-primary btn-lg">
+                    <i class="bi bi-person-plus"></i> Create Account Now
+                </a>
+            </div>
+        </div>
+    </div>
+</div>
+{% endif %}
+{% endblock %}

app/templates/profile.html

@@ -0,0 +1,220 @@
+{% extends "base.html" %}
+
+{% block content %}
+<div class="row">
+    <div class="col-md-8">
+        <div class="card">
+            <div class="card-header">
+                <h3><i class="bi bi-person-circle"></i> Profile Information</h3>
+            </div>
+            <div class="card-body">
+                <div class="row">
+                    <div class="col-md-6">
+                        <h5>Account Details</h5>
+                        <table class="table table-borderless">
+                            <tr>
+                                <td><strong>Username:</strong></td>
+                                <td>{{ user.username }}</td>
+                            </tr>
+                            <tr>
+                                <td><strong>Email:</strong></td>
+                                <td>{{ user.email }}</td>
+                            </tr>
+                            <tr>
+                                <td><strong>Account ID:</strong></td>
+                                <td>{{ user.id }}</td>
+                            </tr>
+                            <tr>
+                                <td><strong>Member Since:</strong></td>
+                                <td>{{ user.created_at.strftime('%B %d, %Y') if user.created_at else 'N/A' }}</td>
+                            </tr>
+                            <tr>
+                                <td><strong>Last Login:</strong></td>
+                                <td>{{ user.last_login.strftime('%Y-%m-%d %H:%M:%S') if user.last_login else 'First login' }}</td>
+                            </tr>
+                        </table>
+                    </div>
+                    
+                    <div class="col-md-6">
+                        <h5>Quick Actions</h5>
+                        <div class="d-grid gap-2">
+                            <a href="{{ url_for('main.dashboard') }}" class="btn btn-primary">
+                                <i class="bi bi-speedometer2"></i> Dashboard
+                            </a>
+                            <button type="button" class="btn btn-outline-secondary" disabled>
+                                <i class="bi bi-pencil"></i> Edit Profile (Coming Soon)
+                            </button>
+                            <button type="button" class="btn btn-outline-secondary" disabled>
+                                <i class="bi bi-key"></i> Change Password (Coming Soon)
+                            </button>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+    
+    <div class="col-md-4">
+        <div class="card">
+            <div class="card-header">
+                <h4><i class="bi bi-shield-lock"></i> Security Settings</h4>
+            </div>
+            <div class="card-body">
+                <div class="security-status mb-3">
+                    <h6>Two-Factor Authentication</h6>
+                    {% if user.is_2fa_enabled %}
+                        <div class="alert alert-success">
+                            <i class="bi bi-check-circle"></i>
+                            <strong>Enabled</strong><br>
+                            Your account is protected with 2FA
+                        </div>
+                        
+                        <form method="POST" action="{{ url_for('auth.disable_2fa') }}" 
+                              onsubmit="return confirm('Are you sure you want to disable two-factor authentication? This will make your account less secure.');">
+                            {{ csrf_token() }}
+                            <button type="submit" class="btn btn-outline-warning btn-sm">
+                                <i class="bi bi-shield-x"></i> Disable 2FA
+                            </button>
+                        </form>
+                    {% else %}
+                        <div class="alert alert-warning">
+                            <i class="bi bi-exclamation-triangle"></i>
+                            <strong>Setup Required</strong><br>
+                            Complete 2FA setup for better security
+                        </div>
+                        
+                        <a href="{{ url_for('auth.register') }}" class="btn btn-success btn-sm">
+                            <i class="bi bi-shield-check"></i> Setup 2FA
+                        </a>
+                    {% endif %}
+                </div>
+                
+                <hr>
+                
+                <h6>Security Score</h6>
+                <div class="progress mb-2">
+                    <div class="progress-bar {% if user.is_2fa_enabled %}bg-success{% else %}bg-warning{% endif %}" 
+                         style="width: {% if user.is_2fa_enabled %}100{% else %}60{% endif %}%">
+                    </div>
+                </div>
+                <small class="text-muted">
+                    {% if user.is_2fa_enabled %}
+                        Excellent - All security features enabled
+                    {% else %}
+                        Good - Enable 2FA to reach 100%
+                    {% endif %}
+                </small>
+            </div>
+        </div>
+    </div>
+</div>
+
+<div class="row mt-4">
+    <div class="col-md-12">
+        <div class="card">
+            <div class="card-header">
+                <h4><i class="bi bi-graph-up"></i> Account Activity</h4>
+            </div>
+            <div class="card-body">
+                <div class="row">
+                    <div class="col-md-4">
+                        <div class="card bg-light">
+                            <div class="card-body text-center">
+                                <i class="bi bi-calendar-check display-6 text-primary"></i>
+                                <h6 class="mt-2">Account Age</h6>
+                                <h4>
+                                    {% if user.created_at %}
+                                        {{ ((user.created_at - user.created_at).days) if user.created_at else 0 }} days
+                                    {% else %}
+                                        New
+                                    {% endif %}
+                                </h4>
+                            </div>
+                        </div>
+                    </div>
+                    
+                    <div class="col-md-4">
+                        <div class="card bg-light">
+                            <div class="card-body text-center">
+                                <i class="bi bi-shield-check display-6 text-success"></i>
+                                <h6 class="mt-2">Security Level</h6>
+                                <h4>
+                                    {% if user.is_2fa_enabled %}
+                                        High
+                                    {% else %}
+                                        Medium
+                                    {% endif %}
+                                </h4>
+                            </div>
+                        </div>
+                    </div>
+                    
+                    <div class="col-md-4">
+                        <div class="card bg-light">
+                            <div class="card-body text-center">
+                                <i class="bi bi-clock-history display-6 text-info"></i>
+                                <h6 class="mt-2">Session Status</h6>
+                                <h4>Active</h4>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+
+<div class="row mt-4">
+    <div class="col-md-12">
+        <div class="card border-info">
+            <div class="card-header bg-info text-white">
+                <h5 class="mb-0"><i class="bi bi-info-circle"></i> Account Security Information</h5>
+            </div>
+            <div class="card-body">
+                <div class="row">
+                    <div class="col-md-6">
+                        <h6>Authentication Methods</h6>
+                        <ul class="list-group list-group-flush">
+                            <li class="list-group-item d-flex justify-content-between align-items-center">
+                                Password Authentication
+                                <span class="badge bg-success rounded-pill">Active</span>
+                            </li>
+                            <li class="list-group-item d-flex justify-content-between align-items-center">
+                                Two-Factor Authentication
+                                <span class="badge bg-{% if user.is_2fa_enabled %}success{% else %}secondary{% endif %} rounded-pill">
+                                    {% if user.is_2fa_enabled %}Active{% else %}Inactive{% endif %}
+                                </span>
+                            </li>
+                        </ul>
+                    </div>
+                    
+                    <div class="col-md-6">
+                        <h6>Security Features</h6>
+                        <ul class="list-group list-group-flush">
+                            <li class="list-group-item d-flex justify-content-between align-items-center">
+                                CSRF Protection
+                                <span class="badge bg-success rounded-pill">Active</span>
+                            </li>
+                            <li class="list-group-item d-flex justify-content-between align-items-center">
+                                Secure Session
+                                <span class="badge bg-success rounded-pill">Active</span>
+                            </li>
+                            <li class="list-group-item d-flex justify-content-between align-items-center">
+                                Password Encryption
+                                <span class="badge bg-success rounded-pill">Bcrypt</span>
+                            </li>
+                        </ul>
+                    </div>
+                </div>
+                
+                <div class="alert alert-info mt-3 mb-0">
+                    <i class="bi bi-lightbulb"></i>
+                    <strong>Security Tip:</strong> Your account benefits from multiple layers of security including 
+                    encrypted passwords, CSRF protection, secure sessions, and optional two-factor authentication. 
+                    All these features work together to keep your account safe from unauthorized access.
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+{% endblock %}

config.py

@@ -0,0 +1,66 @@
+import os
+from datetime import timedelta
+
+class Config:
+    """Base configuration class with security best practices."""
+    
+    # Security: Use environment variables for sensitive data
+    SECRET_KEY = os.environ.get('SECRET_KEY') or 'dev-key-change-in-production-use-secrets-manager'
+    
+    # CSRF Protection - enabled by default with Flask-WTF
+    WTF_CSRF_ENABLED = True
+    WTF_CSRF_TIME_LIMIT = 3600  # 1 hour CSRF token timeout
+    
+    # Database configuration with connection pooling
+    SQLALCHEMY_DATABASE_URI = os.environ.get('DATABASE_URL') or 'sqlite:///app.db'
+    SQLALCHEMY_TRACK_MODIFICATIONS = False
+    SQLALCHEMY_ENGINE_OPTIONS = {
+        'pool_pre_ping': True,  # Verify connections before use
+        'pool_recycle': 300,    # Recycle connections every 5 minutes
+    }
+    
+    # Session security settings
+    PERMANENT_SESSION_LIFETIME = timedelta(hours=1)
+    SESSION_COOKIE_SECURE = True  # HTTPS only cookies
+    SESSION_COOKIE_HTTPONLY = True  # Prevent XSS attacks
+    SESSION_COOKIE_SAMESITE = 'Lax'  # CSRF protection
+    
+    # Additional security headers
+    SEND_FILE_MAX_AGE_DEFAULT = timedelta(hours=1)
+
+
+class DevelopmentConfig(Config):
+    """Development configuration with debug enabled."""
+    DEBUG = True
+    
+    # Allow HTTP cookies in development
+    SESSION_COOKIE_SECURE = False
+    
+    # Development database
+    SQLALCHEMY_DATABASE_URI = os.environ.get('DEV_DATABASE_URL') or 'sqlite:///dev.db'
+
+
+class ProductionConfig(Config):
+    """Production configuration with enhanced security."""
+    DEBUG = False
+    
+    # Production should use PostgreSQL or similar
+    SQLALCHEMY_DATABASE_URI = os.environ.get('DATABASE_URL') or 'postgresql://user:pass@localhost/flask_2fa'
+    
+    # Stricter session settings for production
+    PERMANENT_SESSION_LIFETIME = timedelta(minutes=30)
+
+
+class TestingConfig(Config):
+    """Testing configuration."""
+    TESTING = True
+    WTF_CSRF_ENABLED = False  # Disable CSRF for testing
+    SQLALCHEMY_DATABASE_URI = 'sqlite:///:memory:'
+
+
+config = {
+    'development': DevelopmentConfig,
+    'production': ProductionConfig,
+    'testing': TestingConfig,
+    'default': DevelopmentConfig
+}

init_db.py

@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+"""
+Database initialization script for Flask 2FA Authentication Application
+
+This script creates the database tables and sets up the initial schema.
+"""
+
+import os
+import sys
+
+# Add the project root to Python path
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+
+from app import create_app, db
+from app.models import User
+
+
+def init_database():
+    """Initialize the database with tables."""
+    app = create_app('development')
+    
+    with app.app_context():
+        print("Creating database tables...")
+        
+        # Create all tables
+        db.create_all()
+        
+        print("Database tables created successfully!")
+        
+        # Show created tables
+        print("\nCreated tables:")
+        print("- User table with columns:")
+        print("  - id (Primary Key)")
+        print("  - username (Unique)")
+        print("  - email (Unique)")
+        print("  - password_hash")
+        print("  - totp_secret")
+        print("  - is_2fa_enabled")
+        print("  - created_at")
+        print("  - last_login")
+        
+        print("\nDatabase initialization complete!")
+        print("You can now run the application with: python run.py")
+
+
+if __name__ == '__main__':
+    init_database()

migrations/README

@@ -0,0 +1 @@
+Single-database configuration for Flask.

migrations/alembic.ini

@@ -0,0 +1,50 @@
+# A generic, single database configuration.
+
+[alembic]
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic,flask_migrate
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[logger_flask_migrate]
+level = INFO
+handlers =
+qualname = flask_migrate
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

migrations/env.py

@@ -0,0 +1,113 @@
+import logging
+from logging.config import fileConfig
+
+from flask import current_app
+
+from alembic import context
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+logger = logging.getLogger('alembic.env')
+
+
+def get_engine():
+    try:
+        # this works with Flask-SQLAlchemy<3 and Alchemical
+        return current_app.extensions['migrate'].db.get_engine()
+    except (TypeError, AttributeError):
+        # this works with Flask-SQLAlchemy>=3
+        return current_app.extensions['migrate'].db.engine
+
+
+def get_engine_url():
+    try:
+        return get_engine().url.render_as_string(hide_password=False).replace(
+            '%', '%%')
+    except AttributeError:
+        return str(get_engine().url).replace('%', '%%')
+
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+config.set_main_option('sqlalchemy.url', get_engine_url())
+target_db = current_app.extensions['migrate'].db
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def get_metadata():
+    if hasattr(target_db, 'metadatas'):
+        return target_db.metadatas[None]
+    return target_db.metadata
+
+
+def run_migrations_offline():
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url, target_metadata=get_metadata(), literal_binds=True
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online():
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+
+    # this callback is used to prevent an auto-migration from being generated
+    # when there are no changes to the schema
+    # reference: http://alembic.zzzcomputing.com/en/latest/cookbook.html
+    def process_revision_directives(context, revision, directives):
+        if getattr(config.cmd_opts, 'autogenerate', False):
+            script = directives[0]
+            if script.upgrade_ops.is_empty():
+                directives[:] = []
+                logger.info('No changes in schema detected.')
+
+    conf_args = current_app.extensions['migrate'].configure_args
+    if conf_args.get("process_revision_directives") is None:
+        conf_args["process_revision_directives"] = process_revision_directives
+
+    connectable = get_engine()
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection,
+            target_metadata=get_metadata(),
+            **conf_args
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

migrations/script.py.mako

@@ -0,0 +1,24 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
+
+
+def upgrade():
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade():
+    ${downgrades if downgrades else "pass"}

migrations/versions/4ee6bbb732e4_initial_migration_with_user_model.py

@@ -0,0 +1,46 @@
+"""Initial migration with User model
+
+Revision ID: 4ee6bbb732e4
+Revises: 
+Create Date: 2025-05-29 23:49:19.086429
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '4ee6bbb732e4'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('user',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('username', sa.String(length=80), nullable=False),
+    sa.Column('email', sa.String(length=120), nullable=False),
+    sa.Column('password_hash', sa.String(length=255), nullable=False),
+    sa.Column('totp_secret', sa.String(length=32), nullable=True),
+    sa.Column('is_2fa_enabled', sa.Boolean(), nullable=False),
+    sa.Column('created_at', sa.DateTime(), nullable=True),
+    sa.Column('last_login', sa.DateTime(), nullable=True),
+    sa.PrimaryKeyConstraint('id')
+    )
+    with op.batch_alter_table('user', schema=None) as batch_op:
+        batch_op.create_index(batch_op.f('ix_user_email'), ['email'], unique=True)
+        batch_op.create_index(batch_op.f('ix_user_username'), ['username'], unique=True)
+
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('user', schema=None) as batch_op:
+        batch_op.drop_index(batch_op.f('ix_user_username'))
+        batch_op.drop_index(batch_op.f('ix_user_email'))
+
+    op.drop_table('user')
+    # ### end Alembic commands ###

requirements.txt

@@ -0,0 +1,11 @@
+Flask>=2.3.0
+Flask-Login>=0.6.3
+Flask-WTF>=1.2.1
+Flask-SQLAlchemy>=3.1.1
+Flask-Migrate>=4.0.5
+SQLAlchemy>=2.0.0
+PyOTP>=2.9.0
+bcrypt>=4.1.2
+qrcode[pil]>=7.4.2
+python-dotenv>=1.0.0
+WTForms>=3.1.0

run.py

@@ -0,0 +1,115 @@
+#!/usr/bin/env python3
+"""
+Flask 2FA Authentication Application
+
+This is the main entry point for the Flask application with two-factor authentication.
+The application implements security best practices including:
+- CSRF protection
+- Secure password hashing with bcrypt  
+- Two-factor authentication using TOTP
+- Secure session management
+- SQL injection prevention
+- XSS protection
+
+Security considerations:
+- Never run in debug mode in production
+- Use environment variables for sensitive configuration
+- Ensure HTTPS is enabled in production
+- Regularly update dependencies for security patches
+"""
+
+import os
+from app import create_app, db
+from app.models import User
+from flask_migrate import upgrade
+
+
+def deploy():
+    """
+    Deployment function for production environments.
+    
+    This function:
+    1. Creates the application instance
+    2. Runs database migrations
+    3. Sets up initial data if needed
+    """
+    app = create_app(os.getenv('FLASK_CONFIG') or 'default')
+    
+    with app.app_context():
+        # Create database tables
+        db.create_all()
+        
+        # Run database migrations
+        upgrade()
+
+
+# Create application instance
+app = create_app(os.getenv('FLASK_CONFIG') or 'default')
+
+
+@app.shell_context_processor
+def make_shell_context():
+    """
+    Shell context processor for Flask shell command.
+    
+    Provides convenient access to common objects when using 'flask shell'.
+    """
+    return {
+        'db': db, 
+        'User': User
+    }
+
+
+@app.cli.command()
+def deploy_cmd():
+    """Flask CLI command for deployment."""
+    deploy()
+
+
+@app.cli.command()
+def create_admin():
+    """
+    Create an admin user for testing purposes.
+    
+    Security note: This is for development/testing only.
+    In production, admin users should be created through secure processes.
+    """
+    username = input("Admin username: ")
+    email = input("Admin email: ")
+    password = input("Admin password: ")
+    
+    if User.query.filter_by(username=username).first():
+        print(f"User {username} already exists!")
+        return
+    
+    admin_user = User(username=username, email=email)
+    admin_user.set_password(password)
+    admin_user.generate_totp_secret()
+    
+    db.session.add(admin_user)
+    db.session.commit()
+    
+    print(f"Admin user {username} created successfully!")
+    print("Please complete 2FA setup by registering through the web interface.")
+
+
+if __name__ == '__main__':
+    # Security warning for development
+    if app.config.get('DEBUG'):
+        print("\n" + "="*60)
+        print("WARNING: Running in DEBUG mode!")
+        print("This should NEVER be used in production.")
+        print("Set FLASK_CONFIG=production for production deployment.")
+        print("="*60 + "\n")
+    
+    # Get port from environment or default to 5000
+    port = int(os.environ.get('PORT', 5000))
+    
+    # Run the application
+    # Note: For production, use a proper WSGI server like Gunicorn
+    app.run(
+        host='127.0.0.1',  # Change to '0.0.0.0' if you need external access
+        port=port,
+        debug=app.config.get('DEBUG', False),
+        threaded=True  # Enable threading for better performance
+    )

test_app.py

@@ -0,0 +1,131 @@
+#!/usr/bin/env python3
+"""
+Test script for Flask 2FA Authentication Application
+
+This script performs basic functionality tests to ensure the application
+is working correctly.
+"""
+
+import os
+import sys
+import requests
+import time
+
+# Add the project root to Python path
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+
+from app import create_app, db
+from app.models import User
+
+
+def test_database():
+    """Test database connectivity and User model."""
+    print("Testing database connectivity...")
+    
+    app = create_app('development')
+    
+    with app.app_context():
+        try:
+            # Test database connection
+            db.create_all()
+            
+            # Test User model
+            test_user = User(username='testuser', email='test@example.com')
+            test_user.set_password('testpassword123')
+            test_user.generate_totp_secret()
+            
+            print("✓ Database connection successful")
+            print("✓ User model working correctly")
+            print("✓ Password hashing working")
+            print("✓ TOTP secret generation working")
+            
+            # Test TOTP URI generation
+            uri = test_user.generate_totp_uri()
+            print(f"✓ TOTP URI generated: {uri[:50]}...")
+            
+            # Test QR code generation
+            qr_code = test_user.generate_qr_code()
+            print(f"✓ QR code generated ({len(qr_code)} characters)")
+            
+            return True
+            
+        except Exception as e:
+            print(f"✗ Database test failed: {e}")
+            return False
+
+
+def test_application_startup():
+    """Test if the application starts without errors."""
+    print("\nTesting application startup...")
+    
+    try:
+        app = create_app('development')
+        
+        with app.test_client() as client:
+            # Test home page
+            response = client.get('/')
+            if response.status_code == 200:
+                print("✓ Home page loads successfully")
+            else:
+                print(f"✗ Home page failed: {response.status_code}")
+                return False
+            
+            # Test registration page
+            response = client.get('/auth/register')
+            if response.status_code == 200:
+                print("✓ Registration page loads successfully")
+            else:
+                print(f"✗ Registration page failed: {response.status_code}")
+                return False
+            
+            # Test login page
+            response = client.get('/auth/login')
+            if response.status_code == 200:
+                print("✓ Login page loads successfully")
+            else:
+                print(f"✗ Login page failed: {response.status_code}")
+                return False
+            
+            return True
+            
+    except Exception as e:
+        print(f"✗ Application startup test failed: {e}")
+        return False
+
+
+def run_all_tests():
+    """Run all tests."""
+    print("=" * 60)
+    print("Flask 2FA Authentication Application - Test Suite")
+    print("=" * 60)
+    
+    tests_passed = 0
+    total_tests = 2
+    
+    # Test database
+    if test_database():
+        tests_passed += 1
+    
+    # Test application startup
+    if test_application_startup():
+        tests_passed += 1
+    
+    # Results
+    print("\n" + "=" * 60)
+    print("TEST RESULTS")
+    print("=" * 60)
+    print(f"Tests passed: {tests_passed}/{total_tests}")
+    
+    if tests_passed == total_tests:
+        print("✓ All tests passed! The application is ready to use.")
+        print("\nTo start the application:")
+        print("  python run.py")
+        print("\nThen open your browser to: http://127.0.0.1:5000")
+    else:
+        print("✗ Some tests failed. Please check the errors above.")
+    
+    print("=" * 60)
+
+
+if __name__ == '__main__':
+    run_all_tests()