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Phenograph supports now Leiden algorithm for community detection.
The new feature can be called from phenograph.cluster, by choosing leiden as the clustering algorithm.
Few adjustments to the code including black formatting.
Include simple parallel implementation of brute force nearest neighbors search using scipy's cdist and multiprocessing. This may be more efficient than kdtree on very large high-dimensional data sets
and avoids memory issues that arise in sklearn's implementation.
Refactor parallel_jaccard_kernel to remove unnecessary use of ctypes and multiprocessing.Array.