There are now a number of upper-level computational physics books that use Python and  VPython.  These include:

A Survey of Computational Physics: Introductory Computational Science, Rubin H. Landau, Manual J. Paez, Cristian Bordeianu (2011), Princeton.

Computational Physics with Python, Mark Newman (2012), Createspace.

An Introduction to Statistical Mechanics and Thermodynamics, Robert H. Swendsen (2012), Oxford.

Equilibrium Statistical Physics With Computer Simulations in Python, Leonard M. Sander (2013), Createspace.

Computational Modeling and Visualization of Physical Systems with Python,  Jay Wang (2016), Wiley.