using flask-migrate with flask-script, flask-socketio and application factory
Based on the comment by Miguel I found a way which works.
For some reason the following code does not work
manager.add_command("run", socketio.run( flask.current_app, host='127.0.0.1', port=5000, use_reloader=False))
But this actually works.
@manager.commanddef run(): socketio.run(flask.current_app, host='127.0.0.1', port=5000, use_reloader=False)