I am adding another answer here since this is the kind of resource I was originally looking for.
The Journal of Inquiry Based Learning has a book on mathematical modelling. The abstract says the following:
This is a set of notes for a one semester course in Mathematical
Modeling. The topics covered are difference equations, Markov chains,
Monte Carlo ...
A great example in this vein is Lorena Barba's CFDPython also known as "12 Steps to Navier Stokes", which consists of a sequence of jupyter notebooks that go from really basic numerical analysis up through more complex problems.
One project I have discovered since I initially asked this question is the following:
It is still a work in progress, but is building up a set of problems that can aid in learning computational science.
For a similar resource that focuses primarily on bioinformatics we have Rosalind: