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Teichlab / bbknn

Batch balanced KNN
MIT License
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scanpy update incompatibility #26

Closed bjstewart1 closed 4 years ago

bjstewart1 commented 4 years ago

calling bbknn either from scanpy.external (or bbknn direct) yields:

Error in py_call_impl(callable, dots$args, dots$keywords) : AttributeError: 'tuple' object has no attribute 'tocsr'

this is reported on scanpy https://github.com/theislab/scanpy/issues/1249 where the solution maybe is downgrading umap, but that's not ideal...

umap-learn 0.4.3 bbknn 1.3.4 scanpy 1.5.1 anndata 0.7.3

Any ideas?

ktpolanski commented 4 years ago

The solution is instead upgrading bbknn. The exact fix needed has been introduced in 1.3.8.