I would add the Django project to that list as it's a very large, mature, and successful open source python project - https://github.com/django/django
However reading the less abstract parts may help. For instance, the paginator is pretty self contained. https://github.com/django/django/blob/master/django/core/pag...
https://github.com/django/django/blob/master/django/core/man...
I prefer sklearn like https://github.com/scikit-learn/scikit-learn/blob/master/skl...
A lot of code that does a lot.
Bottle is nice on the web dev front.
The "self.thing = bar" in one function that only gets used in some other function ( or even worse something only used in a companion class) pattern is super prevalent.
Might just be me but I think a lot of the older code suffers from massive locality problems that makes debugging framework bugs super tricky
I think a lot of the issues involving overuse of state, are primarily related to using OO when a pure function would suffice. It's just too tempting to dynamically assign attributes to mutable instances.
To be fair, when Django is used properly it isn't usually an issue. Besides the queryset/model API is extremely nice, and at this point very polished.
Whilst this wasn't a discussion on which framework is best (and I'm not a Web dev by trade either), I must say I turn to Flask, as I find the API more Pythonic.
I guess what I'm trying to say is that the Django source code is probably great, but the less heavyweight packages/frameworks the better. Learn Pythonic API design from somewhere else.