Cannot import modules in jupyter notebook; wrong sys.path

Question

I am having a problem importing modules in my iPython/Jupyter notebook. The problem fundamentally lies in where the sys.path is pointing to.

From the iPython/Jupyter notebook, sys.executable returns:

'/usr/bin/python'

However, from the command line, it returns:

'//anaconda/bin/python'

I have tried un-installing and re-installing anacondas, but the problem still remains.

I have also tried augmenting $PYTHONPATH in my bash_profile to include //anaconda/bin/python, but this doesn't resolve it.

Is there anyway to change the sys.path in my jupyter notebook permanently, without simply using sys.path.append(...)?

Answer 1

1. Open a new terminal window and see if this helps. If not, proceed with 2.

2. Start a standard Python session from the terminal and type this:

   >>> import sys
   >>> sys.executable
   

3. Do the same in the notebook:

   In [1]: import sys
           sys.executable
   

4. Compare the results. Hopefully, this gives you a clue what is going on.

Answer 2

I had the same issue. After going through many (like way too many) solutions to this issue found elsewhere, I manage to figure out a solution that at least works in my case.

Step1: check the correct executable path of the anaconda environment.

Go on command line, activate the conda environment that is problematic, and check the correct executable path for the environment.

conda activate {envronment name};
then on python console, (>>>)import sys;sys.executable

For instance on Linux it will be /media/{username}/{path-to}/anaconda3/envs/{environment name}/bin/python

Step2: correct the executable path for jupyter sessions.

From command line, check the path where kernel.json of your problematic conda environment is located.

jupyter kernelspec list

For instance on Linux it will be: /home/{username}/.local/share/jupyter/kernels/{environment name}

Open the kernel.json located in that folder and replace the incorrect executable path, as shown below.

{
 "argv": [
  "REPLACE-THIS-WITH-THE-CORRECT-EXECUTABLE-PATH",
  "-m",
  "ipykernel_launcher",
  "-f",
  "{connection_file}"
 ],
 "display_name": "heterodimers",
 "language": "python"
}

Hope this works in your case too.