scverse / scverse/scanpy

TypeError: bbknn() got an unexpected keyword argument 'n_trees'

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Description

Hello, When I use sc.external.pp.bbknn(adata, batch_key='group'), group is batch in my datasets. something wrongs :

TypeError                                 Traceback (most recent call last)
/tmp/ipykernel_173326/699274021.py in <module>
----> 1 sc.external.pp.bbknn(adata, batch_key='group')

~/.local/lib/python3.7/site-packages/scanpy/external/pp/_bbknn.py in bbknn(adata, batch_key, approx, metric, copy, n_pcs, trim, n_trees, use_faiss, set_op_mix_ratio, local_connectivity, **kwargs)
    118         set_op_mix_ratio=set_op_mix_ratio,
    119         local_connectivity=local_connectivity,
--> 120         **kwargs,
    121     )

~/.local/lib/python3.7/site-packages/bbknn/__init__.py in bbknn(adata, batch_key, use_rep, approx, use_annoy, metric, copy, **kwargs)
    123         #call BBKNN proper
    124 	bbknn_out = bbknn_matrix(pca=pca, batch_list=batch_list, approx=approx,
--> 125 							 use_annoy=use_annoy, metric=params['metric'], **kwargs)
    126         #store the parameters in .uns['neighbors']['params'], add use_rep and batch_key
    127         adata.uns['neighbors'] = {}

TypeError: bbknn() got an unexpected keyword argument 'n_trees'

How to deal with it ?

Contributor guide

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First steps

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Research direction

The traceback points to scanpy/external/pp/_bbknn.py and the installed bbknn/init.py; start by comparing the versions and function signatures used at those entry points. Reproduce the sc.external.pp.bbknn call and confirm the selected dependency versions handle n_trees without raising TypeError.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
28/100

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