To be fair with respect to the pattern, MVC is not tied to web applications. I think due to trends in Internet support over the past couple of years, this link between MVC and web applications could increase. In other words, a web application can use MVC, but using MVC does not necessarily mean that you have a web application.
If you want to use the framework, you can try to use the one closest to your intended controller. I am not aware of MVC structures with a command line as an interface, but some platforms with an independent GUI platform that use it, like GTK + or QT : both have python bindings.
From a personal point of view, I used to use Django . Although technical cleanliness may be the subject of discussion, when choosing a structure, no one forces you to use all the infrastructure components. Django has a good ORM that I liked so much that I made it the basis for the SSH interface. This may be redundant, but there was an advantage for me that I could reuse my knowledge of the system instead of learning a new, once-used infrastructure.
In conclusion, it all comes down to discipline. Even the best frames cannot stop you from breaking coding standards and cutting corners ...
PS, if you are running Linux, you can use the python curses module for the command line interface.
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