Python/Jupyter notebook in VSCode does not use the right environment

Question

The situation

I use Anaconda 3 on Windows 10.

I have a Visual Studio Code workspace (my_workspace) than contains a Jupyter notebook (my_notebook.ipynb). VSCode has the Python extension installed.

The file my_workspace/settings.json contains:

{
    "python.pythonPath": "C:\\Users\\Me\\Anaconda3\\envs\\my_env\\python.exe"
}

my_env is an existing Anaconda environment. I can activate it and work with it in a shell, and if I run jupyter lab in such a shell, the code inside the notebooks can import my_env's packages as expected.

If I open my_workspace in VSCode, then my_notebook.ipynb in a tab, my_env is also mentioned in VSCode's status bar ("Python 3.7.6 64-bit ('my_env': conda)"), and my_env is automatically activated when I open a PowerShell prompt in VSCode's console (I ran conda init once).

The problem

When the notebook is opened in VSCode, the Jupyter kernel seems to use the base environment's Python interpreter instead of the one in my_env. When importing a package installed in my_env, but not in base, I get this error:

>>> import keras
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'keras'

This happens for all packages, not just keras.

In the notebook tab in VSCode, if I click on the interpreter's name in the top-right corner, then choose the correct interpreter (the one in my_env), then the notebook runs correctly in my_env. But I have to do this every time I re-open VSCode.

How to make the default kernel respect the environment chosen in settings.json?

Solution

I think there is no parameter right now to control that in the settings.json. I had similar problems with the environments in which the notebook is launched and I was able to fix this modifying the kernelspec section in the IPython notebook.

Basically, open the notebook as a JSON file and remove the kernelspec section. When the notebook is launched from vscode, that part will be filled with the default python environment kernel for the workspace. In my case, is filled with the pipenv environment.

Comments

[R Chiodo]

We (I work on the extension) try to use the kernelspec in the notebook if it's there. So if the kernelspec references a valid kernel, we'll use that to start the IPython kernel under the covers. Unfortunately as @pablosjv noticed, this doesn't use your selected python environment. It literally just runs the python specified in the kernel.json as if you started it from an empty command shell. However if you erase the kernelspec from the notebook, we'll instead generate a new kernelspec that matches the environment you have selected in VS code. That's why pablosjv fix works.

[Shai Cohen]

strangely, this also works for c# notebooks! a "language-agnostic" solution should definitely have a special badge.

[user8491363]

@RChiodo VSCode Jupyter & Python are wonderful extensions but I think this behavior can be improved by explicitly letting the user know which kernel interpreter it is using. I had to dig around for a while to find out why import torch was not working on VSCode's Jupyter when it worked just fine on the native Jupyter env.