dependencies update required

[janursa]

updated: if installed using git, it imports successfully. seems like the new updates are not published to pip

On python=3.10, installed pip install scgen, when i import scgen, i get

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/beegfs/desy/user/nourisaj/miniforge3/lib/python3.10/site-packages/scgen/__init__.py", line 3, in <module>
    from ._scgenvae import SCGENVAE
  File "/beegfs/desy/user/nourisaj/miniforge3/lib/python3.10/site-packages/scgen/_scgenvae.py", line 4, in <module>
    from scvi._compat import Literal
ModuleNotFoundError: No module named 'scvi._compat'

[alinaselega]

Same error on python=3.11 with pip install scgen installation

[lxzcpro]

I use python=3.9 and torch=2.1 with
pip install git+https://github.com/theislab/scgen.git
and the tutorial works on my local server

[steamed-stuffed-bun]

@lxzcpro I can't find your tutorial work in your GitHub repository. Can you tell me the full path to the tutorial work?

[lxzcpro]

@lxzcpro I can't find your tutorial work in your GitHub repository. Can you tell me the full path to the tutorial work?

It has been a long time since I used this repo. But I think just the environmental problem that prevents the scgen work. You may try creating a new conda environment with python=3.9 and then install torch 2.1 and pip install git+https://github.com/theislab/scgen.git to run the tutorial in Jupyter notebook? And then it works for me.