Pertpy: AttributeError: module 'pertpy.plot' has no attribute 'coda'

Help
1

Pertpy works fine if install with

pip install pertpy

However when installed from github

gh repo clone theislab/pertpy
cd pertpy
pip install .

When running pertpy.pl.coda.boxplots(), I keep encountering the following error

AttributeError: module 'pertpy.plot' has no attribute 'coda'

The installed packages are as follows

scanpy==1.9.5 anndata==0.10.2 umap==0.5.4 numpy==1.24.4 scipy==1.11.3 pandas==2.1.2 scikit-learn==1.3.2 statsmodels==0.14.0 igraph==0.10.8 pynndescent==0.5.10

The errors occur both in apple silicon macos sonoma and intel linux platform.
The only available plot modules are
Screenshot 2023-10-31 at 02.10.31
Is this because some packages are in conflict? How can I solve this problem?

2

Dear @hmnzo5gy,

thank you for using pertpy! Could you please try: pip install .[coda] when installing from source and report back?

3

Thank you for the response. I tried pip install .[coda] and pip seem to be not able to find coda.

zsh: no matches found: .[coda]

the pip version I used is pip-23.3.1 in python 3.10 conda environment.

4

I downgraded the pertpy from 0.6.0 to 0.5.0 and the problem is resolved.

5

When I install pertpy from source using the latest github deposit the problem was resolved.