First of all, from my experience this kind of workflow is not particularly customary outside web development. However, there are a couple of options that come at least close to what you ask for.
You may want to use some sort of automated build tool like SCons. The Cython developers even provide a build tool for it.
Then there is setuptools/distutils, which are mostly for packaging Python software but also support building C extensions. I think, this is even the canonical way of building Cython source into shared objects.
There is another alternative also part of Cython itself: using pyximport you can simply import Cython modules like so:
import pyximport; pyximport.install()
import foo
You don't have to worry about compilation then, since pyximport automatically compiles the module on import if necessary.
I hope one of these options at least resembles what you were looking for ;)