What are the best practices for implementing two-factor authentication in PHP login systems?

Implementing two-factor authentication in PHP login systems adds an extra layer of security by requiring users to provide two forms of identification before accessing their account. This can help prevent unauthorized access even if a user's password is compromised. One common method is to use a time-based one-time password (TOTP) generated by a mobile app like Google Authenticator.

// Generate a secret key for the user
$secretKey = 'your_secret_key_here';

// Generate a QR code for the user to scan with their authenticator app
$qrCodeUrl = 'https://api.qrserver.com/v1/create-qr-code/?data=' . urlencode('otpauth://totp/YourApp:' . $username . '?secret=' . $secretKey . '&issuer=YourApp');

// Save the secret key in the database for the user
// This should be securely stored and not displayed to the user

// Verify the TOTP entered by the user
$otp = $_POST['otp'];
$tolerance = 1; // Tolerance in seconds to account for clock drift
$totp = new OTPHP\TOTP($secretKey);
$isValid = $totp->verify($otp, null, $tolerance);

if ($isValid) {
    // User successfully authenticated
} else {
    // Invalid TOTP entered
}