Reproducible Tests

<?php
use Phalcon\Di\FactoryDefault;
use Phalcon\Db\Adapter\Pdo\Mysql;
$container = new FactoryDefault();
$container->setShared(
    'db', 
    function () {
        return new Mysql(
            [
                'host'     => '127.0.0.1',
                'username' => 'root',
                'password' => '',
                'dbname'   => 'test',
                'charset'  => 'utf8',
            ]
        );
    }
);
$result = $container['db']->query('SELECT * FROM customers');

Include models and controllers as part of the test:

<?php
use Phalcon\Di\FactoryDefault;
use Phalcon\Mvc\Application;
use Phalcon\Mvc\Controller;
use Phalcon\Mvc\Model;
$container = new FactoryDefault();
// other services
$application->setDI($container);
class IndexController extends Controller
{
    public function indexAction() { 
          /* your content here */
    }
}
class Users extends Model
{
}
$response = $application->handle(
    $_SERVER["REQUEST_URI"]
);
echo $response->getContent();

<?php
use Phalcon\Di;
use Phalcon\Db\Adapter\Pdo\Mysql as Connection;
use Phalcon\Events\Manager as EventsManager;
use Phalcon\Mvc\Model;
use Phalcon\Mvc\Model\Manager as ModelsManager;
use Phalcon\Mvc\Model\Metadata\Memory as ModelsMetaData;
$eventsManager = new EventsManager();
$container     = new Di();
$connection    = new Connection(
    [
        'host'     => 'localhost',
        'username' => 'root',
        'password' => '',
        'dbname'   => 'test',
    ]
);
$eventsManager->attach(
    'db:beforeQuery',
    function ($event, $connection) {
        echo $connection->getSqlStatement(), '<br>' . PHP_EOL;
    }
);
$container['db']             = $connection;
$container['modelsManager']  = new ModelsManager();
$container['modelsMetadata'] = new ModelsMetadata();
if (true !== $connection->tableExists('user', 'test')) {
    $connection->execute(
        'CREATE TABLE user (id integer primary key auto_increment, email varchar(120) not null)'
    );
}
class User extends Model
{
    public $id;
    public $email;
    public static function createNewUserReturnId()
    {
        $newUser = new User();
        $newUser->email = 'test';
        if (false === $newUser->save()) {
            return false;
        }
        return $newUser->id;
    }
}
echo User::createNewUserReturnId();