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Teichlab / bbknn

Batch balanced KNN
MIT License
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ModuleNotFoundError #21

Closed mvfki closed 4 years ago

mvfki commented 4 years ago

A ModuleNotFoundError raised for me when I was trying bbknn.bbknn(adata) function, at ./bbknn/__init__.py line 262, where you wrote 

start = logg.info(...)

I know that this logg came from line 10 

from scanpy import logging as logg

Here you are using a "try/except" syntax, such that you are allowing the nonexistence of scanpy. But in the core function (line 262) it seems still mandatory.

Simply installing scanpy has already fixed it, I am just writing this down in case anyone else new to all these pipelines encounters a similar issue.

ktpolanski commented 4 years ago

Not a bug. bbknn.bbknn() operates on an AnnData object, so having scanpy around seems logical. bbknn.bbknn_pca_matrix(), on the other hand, does not use scanpy logging, and would work fine.