Remove uses of cKDTree #2264
Description
As of scipy 1.6, we might as well use KDTree itself:
`cKDTree` is functionally identical to `KDTree`. Prior to SciPy
v1.6.0, `cKDTree` had better performance and slightly different
functionality but now the two names exist only for
backward-compatibility reasons. If compatibility with SciPy < 1.6 is not
a concern, prefer `KDTree`.
Hinting in PyCharm is much better for KDTree. Unfortunately, need to wait until December 2022 for that.