So I've made significant headway on cythonizing a pdist function that ignores NaNs. You can see the results here: http://nbviewer.ipython.org/gist/Midnighter/b81d5732a0ef88f2e185

Two questions remain:

1) Can I somehow make use of the distance measures defined in scipy/spatial/src/distance.c?

2) Does anyone know if numexpr could be used to compute the above pairwise distances in parallel?

Thank you again.