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rnakato / ShortCake

A docker image for single-cell analysis
https://hub.docker.com/r/rnakato/shortcake
GNU General Public License v3.0
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ImportError for cellrank #5

Closed qisun2 closed 2 years ago

qisun2 commented 2 years ago

Using your latest docker image rnakato/singlecell_jupyter:2022.08, I got an error message when "import cellrank as cr".

ImportError: cannot import name 'Iterable' from 'collections' (/opt/conda/envs/CellRank/lib/python3.10/collections/init.py)

I googled this error. The reason is "the Iterable abstract class was removed from collections in Python 3.10". You might have to set Python to 3.9?

Qi

rnakato commented 2 years ago

Hi Qi, Thank you for the report. I modified the 2022.08 image to use Python3.9 for CellRank. Could you pull the image again and try CellRank?

qisun2 commented 2 years ago

It works now. Thank your for the prompt fix, and for maintaining this very useful resource!