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This is a Python implementation of cover trees, a data structure for finding nearest neighbors in a general metric space (e.g., a 3D box with periodic boundary conditions). Cover trees are described in two papers hosted here: http://hunch.net/~jl/projects/cover_tree/cover_tree.html The implementation here owes a great deal to PyCoverTree, by Thomas Kollar, Nil Geisweiller, Emanuele Olivetti, which can be found here: http://github.com/emanuele/PyCoverTree The API follows that of Anne M. Archibald's KD-tree implementation for scipy (scipy.spatial.kdtree). Other than specifying a distance function in the constructor, this module can be used as a drop-in replacement for kdtree.