Issue with epi.pp.pca : Unexpected Argument Error

[macelik]

Hello,

I encountered an issue while performing basic QC analysis for single-cell data using episcanpy. Here's what happened:

I created a new environment and installed the necessary libraries, including scanpy, episcanpy, and celltypist. When I tried to run PCA using the command epi.pp.pca(adata, n_comps=50), I received the following error:

pca() takes from 1 to 2 positional arguments but 11 were given

Initially, I thought it might be an issue with my setup, so I recreated the environment from scratch, but the error persisted. Interestingly, the same command works smoothly in my old environment. This leads me to believe that the issue might be related to the versions of the packages.

I am not sure which package version is causing this issue, but it seems to be a compatibility problem. I am attaching the list of pip libraries for both envs in here.

new_env_pip_list.txt
old_env_pip_list.txt