Notebooks need to be updated

It looks like most of the notebooks no longer run:
 * ggplot no longer works with pandas (ggplot seems dead, maybe plotnine or seaborn or pandas's built-in plotting would be fine)
 * the animated plotting seems to no longer work (some import issues there)
 * the cython code may work, but we should work out how to make this more general (avoid hardcoding paths).