We have a similar setup (a PostgreSQL schema per tenant), we deal with 
different database versions by running different *code versions* - i.e. if 
you need a new column you release a new code version which knows how to 
deal with the new column. Switching a tenant to that code version runs an 
Alembic migration which adds the column to their schema. Each request is 
routed to a particular code version depending on the tenant's database 
schema.

This way the old code never sees the new database structure and vice versa.

-- 
SQLAlchemy - 
The Python SQL Toolkit and Object Relational Mapper

http://www.sqlalchemy.org/

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