Backporting from UMAP 0.4dev

[jlmelville]

In https://github.com/lmcinnes/pynndescent/pull/16, there was mention of the UMAP 0.4dev branch having diverged substantially from pynndescent for the sparse code.

The non-sparse code doesn't seem to have been changed as much, though. The main change is in the nearest neighbor descent code; apart from that there is some variance in numba decoration, but that's about it.

If there is interest in porting UMAP 0.4dev code from utils.py, nn_descent.py and rp_trees.py back into pynndescent separately from the sparse or threaded code, I am happy to create a PR, so at least there are some diffs which can be examined to work out which bits to use from each code base.

[tomwhite]

Thanks for opening this issue @jlmelville. My goal is really to remove duplication, and have umap use the nn-descent code from this project at some point.

I am happy to create a PR, so at least there are some diffs which can be examined to work out which bits to use from each code base.

That sounds like it would be useful.