The problem though is that Alembic doesn't want to engineer itself around implementing the tooling because it's so painful (and the author of that tool is himself asking for this kind of alter table support) and sqlalchemy-migrate breaks all the time. And sqlalchemy-migrate breaks all the time, and when I used South and django-migrations (granted, that was years ago), those also broke all the time too. The external migrations path isn't working.
So write and apply such modification scripts manually. It's not difficult, and you can tailor it to your table's unique or unusual properties, as needed.
I've seen too many people waste far too much time and effort with automated migration systems, for what amounts to very little saving even in the cases where it does work well.
