Debugging Issue for CITE-seq analysis with totalVI juytper notebook tutorial

Help scvi-tools
, ,
1

I am having issues addressing a error when trying to go through the CITE-seq analysis with totalVI notebook on my personal computer.

An error surfaces when I try to run the following cell block:

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AttributeError                            Traceback (most recent call last)
Cell In[9], line 1
----> 1 scvi.model.TOTALVI.setup_mudata(
      2     mdata,
      3     rna_layer="counts",
      4     protein_layer=None,
      5     batch_key="batch",
      6     modalities={
      7         "rna_layer": "rna_subset",
      8         "protein_layer": "protein",
      9         "batch_key": "rna_subset",
     10     },
     11 )

AttributeError: type object 'TOTALVI' has no attribute 'setup_mudata'

Besides a few NumbaDeprecationWarning and UserWarning outputs, all former cell blocks ran succesfully.

I have followed the instructions for installations and made sure everything was installed without error. I using a Apple M2 MAX.

2

What version of scvi-tools do you have? Latest is 1.0.0

1 Like
3

how do we check what version we have? I made sure to run ‘pip install scvi-tools’ and not ‘pip install scvi’

4

You can run pip show scvi-tools

1 Like
5

ok so the version that comes up is actually shown as Version: 0.16.3 which is odd because I thought when I ran ‘pip install scvi-tools’ it would be based on the latest version based on the tutorial instructions.

How can we update to 1.0.0?

6

You can use pip install -U scvi-tools

7

also ensure you are using python >=3.9. Ideally python 3.10