[FIXED] Jupyter notebook does not load variables from bash_profile or zshrc

Issue

I am running Jupyter notebook using VSCode. In order to run rpy2, I have to insert the following code in my notebook:

import os
os.environ['R_HOME'] = '/Library/Frameworks/R.framework/Resources/'

I would prefer not to insert this into my scripts or notebooks every time as I am collaborating with others and I'm not sure if the above path is universal.

Anyway, I added the line

export R_HOME=/Library/Frameworks/R.framework/Resources/

in my .bash_profile and .zshrc. I already applied source to these configuration files. However, Jupyter notebook still complains.

How can I modify what os.environ returns outside of my notebook? Can anyone direct me the path of the file that is being loaded by os.environ ? This way, I'll just export the variable R_HOME. I am using a conda environment too if that matters.

Advice greatly appreciated.

Solution

you can set environment variables for your conda environment, so create a .env file in the root directory and add this line:

R_HOME=/Library/Frameworks/R.framework/Resources/

this will specifically set the R_HOME variable for your conda environment, and also to find the loaded file path for os.environ, you can use the inspect module and modify that file to set the R_HOME variable.

import inspect
import os

print(inspect.getfile(os))

Answered By - Freeman