problem in latest version of scanpy (bbknn)

[ahmedibatta]

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.
• [ ] (optional) I have confirmed this bug exists on the master branch of scanpy.

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Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.

Minimal code sample (that we can copy&paste without having any data)

import scanpy as sc
import bbknn
sc.logging.print_header()
adata = sc.read('pancreas.h5ad', backup_url='https://www.dropbox.com/s/qj1jlm9w10wmt0u/pancreas.h5ad?dl=1') 
sc.external.pp.bbknn(adata, batch_key='batch')  #error2

 tuple' object has no attribute 'tocsr'

Versions

<bbknn : 1.5.0>

umap: 0.1.1 umap-learn: 0.5.1 [Paste the output of scanpy. logging.print_versions() leaving a blank line after the details tag]

[ivirshup]

Any idea why scanpy. logging.print_versions() is reporting a different version that you've reported above it?

Could be that there's an issue with this environment. Can you replicate the issue in a fresh conda environment?

[ivirshup]

I'm assuming the :+1: means the issue is solved, please re-open if this isn't the case.