A lot of our apps use Flyway and it works pretty well, though it tries to do everything in a transaction. Normally that's desirable -- we don't want a migration to partially succeed -- but we would often use CREATE INDEX CONCURRENTLY in Postgres databases, which can't run in a transaction. In those cases we would need to manually run the migrations and update Flyway's schema_version table, which is annoyingly complex (11 columns, some with no obvious purpose).