conda issue- import scvi about scvi-tools HOT 5 CLOSED

Hi, what kind of import error are you getting?

from scvi-tools.

Thank you for your fast reply. I copied it below. I am not sure why when I try to import scvi it attempts to read an h5ad file.

[sir@lm602-20 scvi_folder]$ conda activate py-env
(/user/conda-environments/py-env) [sir@lm602-20 scvi_folder]$ python
Python 3.8.6 | packaged by conda-forge | (default, Oct 7 2020, 19:08:05)
[GCC 7.5.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
import scanpy as sc
import scvi
Traceback (most recent call last):
File "/user/conda-environments/py-env/lib/python3.8/site-packages/anndata/_io/utils.py", line 156, in func_wrapper
return func(elem, *args, **kwargs)
File "/user/conda-environments/py-env/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 510, in read_group
EncodingVersions[encoding_type].check(
File "/user/conda-environments/py-env/lib/python3.8/enum.py", line 355, in getitem
return cls.member_map[name]
KeyError: 'dict'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "", line 1, in
File "/user/brainref/scvi_folder/scvi.py", line 5, in
ref_adata=sc.read_h5ad('/user/brainref/a5463d8f-07df-4870-8cae-bc504de762c8.h5ad')
File "/user/conda-environments/py-env/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 413, in read_h5ad
d[k] = read_attribute(f[k])
File "/user/conda-environments/py-env/lib/python3.8/functools.py", line 875, in wrapper
return dispatch(args[0].class)(*args, **kw)
File "/user/conda-environments/py-env/lib/python3.8/site-packages/anndata/_io/utils.py", line 162, in func_wrapper
raise AnnDataReadError(
anndata._io.utils.AnnDataReadError: Above error raised while reading key '/layers' of type <class 'h5py._hl.group.Group'> from /.

from scvi-tools.

What version of scvi-tools is it installing? We don't support Python 3.8 in our latest versions. This might be the source of the issue, I'd recommend making sure that you're installing scvi-tools>=1.1.0

from scvi-tools.

It says that you have a file called scvi in your folder. Please rename this file: /user/brainref/scvi_folder/scvi.py. Local files have a higher priority during import than installed modules.

from scvi-tools.

To add, you currently can't read this file as there is a version conflict between anndata (likely your current environment has an older version of anndata than the one used to create the file).

from scvi-tools.