Jupyter notebook doesn't load env variables

[ListIndexOutOfRange]

Does this issue occur when all extensions are disabled?: Can't check because i only have a remote ssh access to the concerned computer.

• VS Code Version:
  Version: 1.62.1
  Commit: f4af3cbf5a99787542e2a30fe1fd37cd644cc31f
  Date: 2021-11-05T10:56:50.217Z
  Electron: 13.5.2
  Chrome: 91.0.4472.164
  Node.js: 14.16.0
  V8: 9.1.269.39-electron.0
  OS: Linux x64 5.4.0-89-generic snap (Ubuntu 18.04.5 LTS)

I'm not sure how to reproduce this issue since it mysteriously stopped working overnight. Anyway, here what happens:

• I'm running vs-code remotely via SSH. I'm running python inside a venv. I have a variable inside my .bashrc file alike:

export SOME_VARIABLE=/some/path/

so that in a python file, os.getenv('SOME_VARIABLE') works just fine.

• However inside a jupyter notebook (with the good kernel), this variable is set to None. If it can help, the PYTHONPATH is:
  /path/to/my/home/.vscode-server/extensions/ms-toolsai.jupyter-2021.10.1101450599/pythonFiles:/path/to/my/home/.vscode-server/extensions/ms-toolsai.jupyter-2021.10.1101450599/pythonFiles/lib/python

• I tried setting:

    "terminal.integrated.inheritEnv": true,
    "terminal.integrated.defaultProfile.linux": "bash",

in the json settings file but it didn't change anything.

I guess this is a jupyter bug since it works in a python file.

[rchiodo]

Thanks for the bug.

Can you include the output of the 'jupyter' output tab? We should be starting the venv the same way as normal python but something might not be working.

[Bai-YunHan]

Having the same issue.
Both python/ipython interactive console can read the environment variable.
And the environment variable is also accessible through echo $SOME_VARIABLE in terminal
But Jupiter fails to get the environment variable set in .bashrc.

[heatxg]

Having the same issue.
Has anyone come across a solution?

[rchiodo]

We don't run your bash rc script before starting a kernel. You'd need to launch VS code from a bash shell and then it should inherit it.

[heatxg]

@rchiodo Even if I export the environment variables through the terminal within VSCode before or while the jupyter notebook is active, I am unable to access them.

[rchiodo]

Even if I export the environment variables through the terminal within VSCode before or while the jupyter notebook is active, I am unable to access them.

Sorry I'm not following what you're doing here.

VS code itself has to be started from a terminal with the environment variables set. Like so:

rich@CORTANA:~/test$ export FOO=BAR
rich@CORTANA:~/test$ code . <-- This is launching VS code from this folder. It will inherit FOO=BAR

[heatxg]

@rchiodo I am ssh into a remote machine with VSCode, not launching from the machine. Then I open the notebook and attempt to access the environment variables. I have tried:

• setting them in .bashrc
• exporting them through a terminal in VSCode before opening the jupyter notebook
• exporting them through a terminal in VSCode after opening the jupyter notebook

I am having no success with any of those approaches.

[rchiodo]

Sorry but that's not supported. Your .bashrc won't be run before we start a kernel.

You could workaround this by setting this value to set some environment variables:

"jupyter.runStartupCommands": []

Or we could change this issue to an enhancement and add an option to run a kernel from a shell script instead of launching it directly.

[rchiodo]

This issue is likely relevant too. It seems weird to me to run a kernel from a shell script, but an .env should work.

[heatxg]

I agree, that feels weird. Thank you for the redirect. I will take a look.

[onnoeberhard]

I'm not sure if this is the same problem, but for me in a notebook in VS Code import os; print(os.environ['PATH']) outputs /Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/Users/onno/mpi/.venv/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
(a ridiculous output)

In the integrated terminal, with the same virtual environment activated, python -c "import os; print(os.environ['PATH'])" outputs /Users/onno/mpi/.venv/bin:/Users/onno/.pyenv/shims:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/homebrew/bin:/opt/homebrew/sbin.

(Critically, the TeX directory is missing in the notebook. This is not set in .zshrc, but in /etc/profile). When I open a jupyter notebook in the browser from the terminal, I get the correct path, the same as Python in the terminal gives me. I even started VS Code by typing code .

I'm not sure what to do.. I tried restarting everything including my computer, but nothing changed.

Update: Apparently this is related to a different issue. This comment helped me solve the problem: #9774 (comment)

[AminnimAMoh]

@rchiodo That is the Perfect answer. The content of .bashrc used to be pre-loaded to the Jupyter before, but it stopped working for some reason. Lunching VSCode from a bash terminal fixed the issue for me. Many thanks.

[nateGeorge]

I find it amazing that something as basic as using ~/.bashrc to load env variables in a remote VS code server with Azure cloud ML is made so difficult it's basically impossible. Instead you can use python-dotenv:

from dotenv import load_dotenv

load_dotenv()

You need a .env file in the directory you're running this from (or specify the path I think in load_dotenv). The file should have pairs like API_KEY="12345".

[nickovchinnikov]

The same issue was reproduced again, and the solution is in this comment
#9774 (comment)