Syntax error while running scvi.model.AUTOZI(pbmc)

Help scvi-tools
1

Hi there,

I am trying to follow the tutorial for zero inflation gene identification (AUTOZI):

https://docs.scvi-tools.org/en/stable/user_guide/notebooks/AutoZI_tutorial.html

Installation went smoothly. However while executing the following I got the error:

vae = scvi.model.AUTOZI(pbmc)
vae.train(max_epochs=200, plan_kwargs = {‘lr’:1e-2})
Traceback (most recent call last):
File “”, line 1, in
File “/home/qwang178/.local/lib/python3.6/site-packages/scvi/core/models/vaemixin.py”, line 64, in train
**kwargs,
File “/home/qwang178/.local/lib/python3.6/site-packages/scvi/core/trainers/inference.py”, line 89, in init
super().init(model, adata, **kwargs)
TypeError: init() got an unexpected keyword argument ‘max_epochs’

I understand it should be some other modules/packages dependency issue. Could you please help me pinpoint where the problem is and the possible fix?

Thanks.

2

What version of scvi-tools do you have?

import scvi
scvi.__version__
3

Hi there,

Here is what is seen on the system:

$ python
Python 3.6.8 |Anaconda custom (64-bit)| (default, Dec 30 2018, 01:22:34)

[GCC 7.3.0] on linux

Type “help”, “copyright”, “credits” or “license” for more information.

import scvi

scvi.version

‘0.8.1’

4

This should be a version issue. You should upgrade scvi-tools (exact command depends on how you installed it). The correct version is 0.12.1