[flavio81]

I understand that Numpy is fast in CPython because it relies on high speed code being done in C.

What you could do is much simpler --- :

Split your Python application in two parts:

1. Keep your functions that make heavy use of Numpy and Scipy under CPython; expose your algorithms/functions as a web service/REST service/etc running under CPython.

2. The rest of the application, which of course needs to call the functions in (1), can be written in PyPy and call the web service in (1). This is where you would put the general-purpose stuff like web, graphics, database access, and of course all symbolic manipulations that do not require Numpy/Scipy.

I think this is a simple, workable solution.