Cannot import cell2location

[elisulvaran]

Dear cell2location team,
I am trying to do analyze Visium data I have but I can't successfully import the library. I am running the following code:

import os
os.environ["THEANO_FLAGS"] = 'device=cuda,floatX=float32,force_device=True
import cell2location

But I am getting the following error:

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Input In [6], in <cell line: 3>()
      1 import os
      2 os.environ["THEANO_FLAGS"] = 'device=cuda,floatX=float32,force_device=True'
----> 3 import cell2location

File ~/miniconda3/lib/python3.9/site-packages/cell2location/__init__.py:5, in <module>
      2 from pyro.distributions.transforms import SoftplusTransform
      3 from torch.distributions import biject_to, transform_to
----> 5 from .run_c2l import run_cell2location
      6 from .run_colocation import run_colocation
      7 from .run_regression import run_regression

File ~/miniconda3/lib/python3.9/site-packages/cell2location/run_c2l.py:18, in <module>
     15 import scipy
     16 import theano
---> 18 import cell2location.models as models
     19 import cell2location.plt as c2lpl
     20 from cell2location.cluster_averages import compute_cluster_averages, select_features

File ~/miniconda3/lib/python3.9/site-packages/cell2location/models/__init__.py:1, in <module>
----> 1 from ._cell2location_model import Cell2location
      2 from .downstream import CoLocatedGroupsSklearnNMF
      3 from .pymc3.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormGeneAlpha import (
      4     LocationModelLinearDependentWMultiExperimentLocationBackgroundNormGeneAlpha,
      5 )

File ~/miniconda3/lib/python3.9/site-packages/cell2location/models/_cell2location_model.py:11, in <module>
      9 from pyro import clear_param_store
     10 from pyro.nn import PyroModule
---> 11 from scvi import _CONSTANTS
     12 from scvi.data._anndata import get_from_registry
     13 from scvi.model.base import BaseModelClass, PyroSampleMixin, PyroSviTrainMixin

ImportError: cannot import name '_CONSTANTS' from 'scvi' (/Users/elisulvarang/miniconda3/lib/python3.9/site-packages/scvi/__init__.py)

I do have scvi-tools installed, this is the output when I run print(scvi.__version__):
0.15.4

Same thing with pyro: print(pyro.__version__)
1.8.0

I do not get any errors when I want to import any of these two libraries.

And this is the output when I run python -V:
Python 3.9.7

Thanks!

[vitkl]

Hi @elisulvaran

Please make sure that you install cell2location as described in README https://github.com/BayraktarLab/cell2location#installation and follow the latest tutorial https://cell2location.readthedocs.io/en/latest/notebooks/cell2location_tutorial.html. It could help to create a clean conda environment by following those installation steps and theano options are no longer relevant. The error you observe originates from a version mismatch between cell2location and scvi-tools which should go away if you recreate conda environemnt.

[vitkl]

Also good to try this solution #142 (comment)