squeryl can specify composite keys, but can't make a composite key the table's primary key.

It would be nice to be able to generate e.g. this sql to make a composite primary key.
alter table samples add primary key(time, kind);

in mysql innodb, identifying primary keys are important for the storage layout of indices. See: http://dev.mysql.com/doc/refman/5.1/en/innodb-index-types.html

As long as there's only one unique non-null index, mysql will pick it as the primary key. But eventually someone will want more indexes and the ability to specify a composite as the primary.