command not found when I try execute shell script in jupyter cell

Environment data

• VS Code version: 1.67.0
• Jupyter Extension version (available under the Extensions sidebar): 2022.4.1001271738
• Python Extension version (available under the Extensions sidebar): 2022.6.0
• OS (Windows | Mac | Linux distro) and version: Mac
• Python and/or Anaconda version: python3.9
• Type of virtual environment used (N/A | venv | virtualenv | conda | …): poetry
• Jupyter server running: Local

Expected behaviour

Actual behaviour

Steps to reproduce:

[NOTE: Self-contained, minimal reproducing code samples are extremely helpful and will expedite addressing your issue]

This is due to my personal setup in zsh https://github.com/ztlevi/dotty-config/blob/652cff7fae4abadaa8016847933c71c235250b2d/env#L81

• To reproduce, you’ll probably need to set zsh as default terminal in macOS. Newer macOS already use zsh by default.
• Add the following code to your zshrc

function _load_all() {
  mkdir -p $HOME/Downloads
  local topics=($(ls $HOME/Downloads))
}
_load_all

Logs

Output for Jupyter in the Output panel (View→Output, change the drop-down the upper-right of the Output panel to Jupyter)

info 17:27:20.562: Execute Cell 5 xxx.ipynb
info 17:27:21.148: Cell 5 executed with state Success

[ztlevi]

Thanks. This one doesn’t work for me. I have to tweak a little bit.

  "jupyter.runStartupCommands": ["import os", "os.environ['PATH'] += os.pathsep+'/bin'"],

[DonJayamanne]

@ztlevi thanks for getting back with the information. The path variables are inherited from the VS Code process. As you haven’t launched vscode from a shell process, the environment variables are completely different. Basically the vscode application (& other desktop applications) don’t initialize any shell scripts and use any of the initialization shell scripts. Jupyter application on the other hand is launched from a terminal, hence the difference in the bahaviour and values of the path variable.

As a temporary work around you could:

• Open your user settings.json file and add the following contents

  "jupyter.runStartupCommands": [
    "import sys",
    "sys.path.append('/bin')"
  ]

Please note, this is only a work around and we’ll be looking into a more permanent fix as part of #9682