SQLAlchemy, Alembic and new instances
If you know the state of the database you can just stamp the revision you were at when you created in the instance.

setup instance
run create_all
alembic heads (to determine latest version available in scripts dir)
alembic stamp  

Here is the doc from the commandline:
stamp               'stamp' the revision table with the given revision;
                        don't run any migrations.
In a platform using Flask, SQLAlchemy, and Alembic, we constantly need to create new separate instances with their own set of resources, including a database.
When creating a new instance, SQLAlchemy's create_all gives us a database with all the updates up to the point when the instance is created, but this means that this new instance does not have the migrations history that older instances have. It doesn't have an Alembic revisions table pointing to the latest migration.
So when the time comes to update both older instances (with migrations histories) and a newer instance without migrations history we have to either give the newer instance a custom set of revisions (ignoring older migrations than the database itself) or create a fake migrations history for it and use a global set of migrations. For the couple of times that this has happened, we have done the latter.
Is making a root migration that sets up the entire database as it was before the first migration and then running all migrations instead of create_all a better option for bootstrapping the database of new instances?
I'm concerned for the scalability of this as migrations increase in number.
Is there perhaps another option altogether?