A snippet for getting Alembic to recognize multiple model classes in multiple modules

env.py

# Inspired by http://liuhongjiang.github.io/hexotech/2015/10/14/alembic-support-multiple-model-files/

def combine_metadata():
    from sqlalchemy import MetaData
    import models  # models file into which all models are imported

    model_classes = []
    for model_name in models.__all__:
        model_classes.append(getattr(models, model_name))

    m = MetaData()
    for model in model_classes:
        for t in model.metadata.tables.values():
            t.tometadata(m)

    return m

target_metadata = combine_metadata()

Since Alembic 0.9.0 we can simply do this: target_metadata = [Model1Base.metadata, Model2Base.metadata].