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Fix simplicial set embedding bug
Add logging
Code cleanup
`func_mode` -> `get_mode`
Factor out `get_leiden_partition`
Refactor `knngraph_full` -> `create_knn_graph`
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Description
In this PR:
make_csrmatrix_noselfloop->prune_localkeep_all_local_dist->do_prune_local, with the opposite meaning, i.e.do_prune_local = Trueis the same askeep_all_local_dist = Falsel2_std_factoras argumentdiscard_countprune_local