UMAP 0.4.0rc1 doesn't play nice with ingest

@Koncopd, I just tried out the new release candidate for umap and get errors though out the ingest tests. It looks like umap now relies on pynndescent and some functions are no longer available. Here’s an example traceback:

------------------------------------------------------------------------------------------------------------------- Captured stderr call -------------------------------------------------------------------------------------------------------------------
running ingest
______________________________________________________________________________________________________________ test_ingest_map_embedding_umap ______________________________________________________________________________________________________________

    def test_ingest_map_embedding_umap():
        adata_ref = sc.AnnData(X)
        adata_new = sc.AnnData(T)
    
        sc.pp.neighbors(
            adata_ref, method='umap', use_rep='X', n_neighbors=4, random_state=0
        )
        sc.tl.umap(adata_ref, random_state=0)
    
>       ing = sc.tl.Ingest(adata_ref)

scanpy/tests/test_ingest.py:132: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
scanpy/tools/_ingest.py:270: in __init__
    self._init_neighbors(adata)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <scanpy.tools._ingest.Ingest object at 0x140357550>, adata = AnnData object with n_obs × n_vars = 6 × 5 
    uns: 'neighbors', 'umap'
    obsm: 'X_umap'

    def _init_neighbors(self, adata):
        from umap.distances import named_distances
>       from umap.nndescent import (
            make_initialisations,
            make_initialized_nnd_search,
        )
E       ImportError: cannot import name 'make_initialisations' from 'umap.nndescent' (/usr/local/lib/python3.7/site-packages/umap/nndescent.py)

scanpy/tools/_ingest.py:210: ImportError

[Koncopd]

@nahanoo Hi, there are 3 options for now:

1. downgrading umap to 0.39
2. installing scanpy from github
3. waiting for a new release of scanpy.

[nahanoo]

Thank you for the fast response. Building from source did the job for me.