Tuesday, May 14, 2024

Troubleshooting Module Import Issues in Jupyter Notebook

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[8], line 5
      1 import warnings
      3 warnings.filterwarnings("ignore")
----> 5 import pyscenic
      6 import loompy as lp
      7 import scanpy as sc

ModuleNotFoundError: No module named 'pyscenic'



If you're running a package (pyscenic in my case now) in a Jupyter notebook and encountering issues with importing modules from a specific conda environment, it's essential to ensure that the Jupyter notebook is using the correct kernel associated with your pyscenic environment. 

Steps to Resolve the Issue:

1. Identify the Current Jupyter-Lab Path:

    $ which jupyter-lab 
/home/ramadatta/.local/bin/jupyter-lab

2. Install Jupyter in Your Conda Environment:
$ conda install jupyter

3. Verify the Jupyter-Lab Path Again:
$ which jupyter-lab                                                         
/home/ramadatta/anaconda3/envs/pyscenic/bin/jupyter-lab    


You can see that the path for jupyter-lab changed from the local one to the conda environment. This was causing an issue and which was why although I installed pyscenic in the environment. After installing Jupyter in your conda environment, the path should reflect the conda environment instead of the local path.

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