cellrank: Unable to import scvelo as scv

After installing cellrank with conda and creating the cellrank environment, I activate the environment, and in python I try to import scvelo but I can’t import it at all.

Python 3.9.2 | packaged by conda-forge | (default, Feb 21 2021, 05:02:46)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scvelo as scv
Illegal instruction (core dumped)
$

Python 3.9.2 | packaged by conda-forge | (default, Feb 21 2021, 05:02:46)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scvelo as scv
Illegal instruction (core dumped)
$

Versions:

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About this issue

Original URL
State: closed
Created 3 years ago
Comments: 17

Most upvoted comments

Hi @mihem ,

The problem seems to be this line in scvelo: https://github.com/theislab/scvelo/blob/master/scvelo/settings.py#L300 The quick workaround is to use:

scv.settings.set_figure_params('scvelo', ipython_format=None)

this will cause an Exception to be raised which is caught immediatelly afterwards. I’ve created an issue on scvelo https://github.com/theislab/scvelo/issues/437. The reason why you’re getting this after installing CellRank is that in our requirements, we have ipywidgets, which also pulls the ipython, which causes this. If there’s not IPython installed, style='scvelo' works just fine. The ipywidgets requirement from our side has already been removed on the dev branch in https://github.com/theislab/cellrank/pull/571.

michalk8 on May 1, 2021

Yes, when I install numba==‘0.52.0’, the pipeline can run.

numba is pinned in https://github.com/theislab/cellrank/blob/master/requirements.txt#L9 to >=0.52.2,<0.53.0

michalk8 on Apr 7, 2021

finish with numba==‘0.52.0’, fail in numba==‘0.53.1’

millersan on Apr 2, 2021