Interesting to see this - we ran into a similar problem of finding points within a certain distance from amongst thousands or millions of points. We ended up using Cython[0].

Would this numpy trick work if he still needed an accurate distance calculation? Kind of underwhelming to throw away the accuracy to get speed without adding it back later.

[0] http://doublemap.github.io/blog/2015/05/29/optimizing-python...