MVC model structure in Python
There is an inconsistency in your specification. You say Database.py needs to import all Model classes to do ORM but then you say the User class need access to the Database to do queries.
Think of these as layers of an API. The Database class provides an API (maybe object-oriented) to some physical persistence layer (such as DB-API 2.0). The Model classes, like User, use the Database layer to load and save their state. There is no reason for the Database.py class to import all the Model classes, and in fact you wouldn't want that because you'd have to modify Database.py each time you created a new Model class - which is a code smell.
I'm having problems structuring classes in the Model part of an MVC pattern in my Python app. No matter how I turn things, I keep running into circular imports. Here's what I have:
Model/__init__p.y

should hold all Model class names so
I can do a "from Model import User"
e.g. from a Controller or a unit
test case

Model/Database.py 

holds Database class
needs to import all Model classes to do ORM
initialization should be performed on first module import, i.e. no extra init calls or instantiations (all methods on Database class are @classmethods)

Model/User.py

contains User model class
needs access to Database class to do queries
should inherit from base class common to all Model classes to share functionality (database persistency methods, parameter validation code etc.)

I have yet to see a real world Python app employing MVC, so my approach is probably un-Pythonic (and possibly a language-agnostic mess on top of that...) - any suggestions on how to solve this?
Thanks, Simon