Jeremy Cook has put together a new post showing how he got PUPUnit, Doctrine and MySQL to "play nicely" together when he was writing up some of his tests in a current application.
One of the pain points for me though has been in getting Doctrine setup with PHPUnit for testing. One of the main Doctrine contributors, Benjamin Beberlei, has written a package called DoctrineExtensions which amongst other things adds a class called DoctrineExtensionsPHPUnitOrmTestCase which extends PHPUnit's DbUnit database test case class. This all works well in principle but hits a major snag in reality: MySQL doesn't allow InnoDb tables with foreign keys to be truncated. PHUnit's database extension truncates the database tables before each test run and inserts a fresh set of data to work with.
To work around this issue Jeremy by porting over a method posted by Mike Lively over to Doctrine as a custom "MySQLTruncate" class (code included in the post). He also includes some sample code showing it in use - a basic ORM test case that calls the truncate method when its set up.