theislab/scvelo

Dependency problem on packages optax & chex

jasonleongbio opened this issue · 1 comments

I recently newly installed scVelo in my virtual environment.
However, loading scvelo was not successful

import scvelo as scv

which showed the following the error message:

module 'chex' has no attribute 'warn_deprecated_function'

This error has been reported in another single-cell tool cellrank, but it seems that this has not been reported here in scVelo
theislab/cellrank#1186

and a solution suggested by the post was that to downgrade the package optax from 0.2.2 (current ver) to 0.2.0. I tried it with my virtual environment for scVelo and it worked.

mamba install optax=0.2.0

Hope this will help the community to solve the problem.

Best,
Jason.

...

# paste your code here, if applicable
# see above
Error output
# paste the error output here, if applicable
# see above
Versions
# paste the ouput of scv.logging.print_versions() here

# This actually generated another error message but it seems the code using `scvelo` works fine
Running scvelo 0.0.0 (python 3.11.4) on 2024-06-26 15:55.
ERROR: XMLRPC request failed [code: -32500]
RuntimeError: PyPI no longer supports 'pip search' (or XML-RPC search). Please use https://pypi.org/search (via a browser) instead. See https://warehouse.pypa.io/api-reference/xml-rpc.html#deprecated-methods for more information.

# pacakge info from mamba
# scvelo                    0.3.2              pyhd8ed1ab_1    conda-forge

Thanks, @jasonleongbio! The jax dependecies will be removed in the future s.t. this issue should no longer occur.