What is the difference between these two algorithms?
Currently, both have almost same APIs, and cKDTree is faster than KDTree.
So, In the near future, SciPy developers are planning to remove KDTree, and cKDTree will be renamed to KDTree in a backwards-compatible way.
Ref: Detailed SciPy Roadmap — SciPy v1.6.0.dev Reference Guide http://scipy.github.io/devdocs/roadmap-detailed.html#spatial