PATH not updated correctly from conda activate in VSCode's terminal

Question

I am using VSCodes terminal pane. I activate a conda environment. For some reason, the python command is still set to /usr/bin/python, instead of the correct path to the conda environment.

% conda activate myenv
% which python
/usr/bin/python

The correct anaconda environment directory does seem to be in the $PATH variable, but /usr/bin seems above it in priority.

When I open a standard terminal through the OS, the behavior is as I expect.

% conda activate myenv
% which python
/Users/cpl/anaconda3/envs/myenv/bin/python

Please note: I have already set the VSCode preferences key python.pythonPath to /Users/cpl/anaconda3/envs/myenv/bin/python, and I think that it works correctly. When I run a file through right-clicking and selecting Run Python File In Terminal, the correct python (from the conda environment) is executed. My problem is using the VSCode terminal directly to execute python.

My shell is zsh, and I am using OSX. Any advice?

Answer 1

This behavior is explained in the VSCode docs: Why are there duplicate paths in the terminal's $PATH environment variable and/or why are they reversed?#

It sounds like VSCode will run your .zshrc twice in MacOS, conflicting with the conda-generated PATH variable definitions.

There are two solutions listed in the link above. The one that works for me is to set the VSCode setting "terminal.integrated.inheritEnv": false. The documentation warns that all of your environmental variables will be stripped if you do this. However, I find I still have my custom variables defined in the .zshrc file.

It is worth noting that recent versions of VSCode will prompt you when it detects you are using a conda environment, and suggests making this change.

Answer 2

I don't use zsh, but I've run into this issue in bash and I believe the cause is the same.

Conda has recently changed the "official" method of activating environments, as described in this issue: https://github.com/Microsoft/vscode-python/issues/1882

Before, you needed to modify your .bashrc/.zshrc to prepend PATH with the directory of conda's activate script, and then activate specific environments by typing source activate name_of_env. VSCode-Python activates conda terminals by sending this command to the shell — with visible echo, like you typed it yourself.

The new method is to source $HOME/anaconda3/etc/profile.d/conda.sh in .bashrc and then activate environments with conda activate name_of_env, which is the behavior you're seeing work correctly in a dedicated terminal. VSCode-Python does not yet support this, and there appear to be issues with cross-platform support on Windows that are complicating the transition.

The best solution for now is to ignore the "correct" method of conda activate and consistently use the older source activate name_of_env, which still works (if your PATH is set to include $HOME/anaconda3/bin).

Answer 3

A dark magic below may work:-

In my Big Sur, I added the following empty entry to my settings.json -- can be found at File(Windows)/Code(Mac)>Preferences>Settings -- click on any link stated "Edit in settings.json"

"terminal.integrated.env.osx": {
        "PATH": ""
}

All the best!