Решение
In alembic/env.py or migrations/env.py:
def include_object(object, name, type_, reflected, compare_to):
if (type_ == "table" and object.schema == "exclude_from_migrations"):
return False
else:
return True
def run_migrations_online():
....
context.configure(connection=connection,
target_metadata=target_metadata,
include_object = include_object,
process_revision_directives=process_revision_directives,
**current_app.extensions['migrate'].configure_args)
...
В таблицах
class MyClass(db.Model):
__tablename__='my_class'
__table_args__ = {"schema": "exclude_from_migrations"}
