A migration tool applies changes to your database. I like to keep things simple:

#!/usr/bin/env php
<?php

require __DIR__.'/../vendor/autoload.php';

$dotenv = new Dotenv\Dotenv(__DIR__.'/../');
$dotenv->load();
$dotenv->required([
    'DSN',
    'DATABASE_USERNAME',
    'DATABASE_PASSWORD',
    'MIGRATIONS_FOLDER',
]);

$pdo = new PDO(
    getenv('DSN'),
    getenv('DATABASE_USERNAME'),
    getenv('DATABASE_PASSWORD')
);

$pdo->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
$pdo->setAttribute(PDO::ATTR_DEFAULT_FETCH_MODE, PDO::FETCH_ASSOC);

$pdo->query('create table if not exists migration (name varchar(255))');

$folder = getenv('MIGRATIONS_FOLDER');

foreach (new DirectoryIterator($folder) as $file) {
    if ($file->getFilename() === '.' || $file->getFilename() === '..')
        continue;

    $migrations[] = $file->getFilename();
}

sort($migrations);

array_map(function ($migration) use ($pdo, $folder) {

    $stmt = $pdo->prepare('select * from migration where name=:name');
    $stmt->execute(['name' => $migration]);

    if (empty($stmt->fetchAll())) {

        print "Migrating $migration \n";

        $pdo->query(file_get_contents($folder . $migration));

        $pdo->prepare('insert into migration values (:name)')
            ->execute(['name' => $migration]);
    }
}, $migrations);

The tool runs new migrations once. The migrations are .sql files e.g. 2017-05-01-create-initial-tables.sql:

create table contact(
    id int NOT NULL AUTO_INCREMENT,
    name varchar(255) NOT NULL,
    email varchar(255) NOT NULL unique,
    PRIMARY KEY (id)
);

The tool has one dependency: composer require vlucas/phpdotenv.