Conda activate is failing when conda is in '/usr/bin/' folder

[junrrein]

Environment data

• VS Code version: 1.43.2
• Extension version (available under the Extensions sidebar): 2020.3.71113
• OS and version: Fedora 31
• Python version (& distribution if applicable, e.g. Anaconda): 3.7.7
• Type of virtual environment used (N/A | venv | virtualenv | conda | ...): conda
• Relevant/affected Python packages and their versions: n/a

Workspace Settings

{
    "python.pythonPath": "/home/julian/.conda/envs/pdi-practica2020/bin/python"
}

Actual behavior

Starting a Jupyter Notebook server fails with error:

Activating Python 3.7.7 64-bit ('pdi-practica2020': conda) to run Jupyter failed with Error: Command failed: . /usr/bin/activate pdi-practica2020 && echo 'e8b39361-0157-4923-80e1-22d70d46dee6' && python /home/julian/.vscode/extensions/ms-python.python-2020.3.71113/pythonFiles/printEnvVariables.py bash: /usr/bin/activate: No such file or directory .

Expected behavior

The extension should use plain conda activate to activate the conda environment, as the extension does (I think?) when opening a terminal.

Steps to reproduce:

1. Install conda using the package manager: sudo dnf install conda
2. Create an environment that includes Jupyter: conda create --name vscode-test notebook
3. Open a folder with VSCode.
4. Use the "Select Interpreter" command to activate the vscode-test environment.
5. Use the "Create New Blank Jupyter Notebook" command.
6. Add code to the first cell (for example import sys) and run it.

Notes

May be related to #2315 and #7671 and the way they were solved.

[rchiodo]

Conda activate is not DS specific, removing DS label.

[junrrein]

@rchiodo This only fails for the Jupyter Server. Everywhere else the conda environment seems to be applied fine.

[rchiodo]

What does 'Select Interpreter to start Jupyter' show as the current selection? Does it match your python path? And does the selection box indicate it thinks the interpreter is a conda interpreter (the selection box should show something like so for the item you have selected)

Those should be all true, but for some reason the code we run doesn't realize that python path is a conda environment.

[junrrein]

@rchiodo

What does 'Select Interpreter to start Jupyter' show as the current selection?

Does it match your python path?

The one I intend to be selected is the pdi-practica2020: conda one. Even when I select that one, when I use 'Select Interpreter to start Jupyter' the first item in the list is highlighted, and no settings seem to be changed for the workspace.

When using 'Python: Select Interpreter' (not the Jupyter one), here also the first item in the list is the one highlighted, but selecting an interpreter does modify the .vscode/settings.json file in the workspace, and the Python extension does pick up that environment.

[junrrein]

@rchiodo

When using 'Select Interpreter to start Jupyter' to select the 'base' environment, where I don't have Jupyter installed, the extension correctly shows me an error about that: Data Science libraries jupyter and notebook are not installed in interpreter Python 3.7.6 64-bit ('base': conda).

When selecting my custom environment, nothing seems to happen, but presumably the extension does see that Jupyter is installed. Just in case, here is my environment.yml file.

[rchiodo]

The 'jupyter' interpreter is not saved in your settings. It's in a different spot. But regardless, it thinks it's a conda environment, so it should be launching it with conda activate. It looks to me like there's a bug somewhere in this code here:
https://github.com/microsoft/vscode-python/blob/master/src/client/common/terminal/environmentActivationProviders/condaActivationProvider.ts

In the function getUnixCommands it looks like the 'condaFile' is actually found in /usr/bin instead of some conda folder and that's why it's running '/usr/bin/activate'. Perhaps there's a conda in '/usr/bin'?

[junrrein]

@rchiodo

There is indeed a conda binary script in my /usr/bin path, and it was installed by my package manager.

Just in case, my bash shell seems to need a plain conda command to use it. Invoking /usr/bin/conda doesn't work:

bash-5.0$ /usr/bin/conda activate pdi-practica2020

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

bash-5.0$ conda activate pdi-practica2020

bash-5.0$ conda env list
# conda environments:
#
pdi-practica2020      *  /home/julian/.conda/envs/pdi-practica2020
base                     /usr

Note: conda init bash was actually used beforehand. It just seems that a direct invocation to /usr/bin/conda doesn't work.

[ericsnowcurrently]

@junrrein, we just published a new release of the extension. Please verify you are still seeing the problem after updating. Thanks!

[junrrein]

@ericsnowcurrently, I'm now using version 2020.5.78807 of the extension.

Unfortunately, I'm still hitting the same issue as in the OP:

Activating Python 3.7.7 64-bit ('pdi-practica2020': conda) to run Jupyter failed with Error: Command failed: . activate pdi-practica2020 && echo 'e8b39361-0157-4923-80e1-22d70d46dee6' && python /home/julian/.vscode/extensions/ms-python.python-2020.5.78807/pythonFiles/pyvsc-run-isolated.py /home/julian/.vscode/extensions/ms-python.python-2020.5.78807/pythonFiles/printEnvVariables.py bash: activate: No such file or directory .

[Betaglutamate]

I am having the same issue I think

Command failed: . activate image_env && echo 'e8b39361-0157-4923-80e1-22d70d46dee6' && python /home/betaglutamate/.vscode/extensions/ms-python.python-2020.7.96456/pythonFiles/pyvsc-run-isolated.py /home/betaglutamate/.vscode/extensions/ms-python.python-2020.7.96456/pythonFiles/printEnvVariables.py
bash: activate: No such file or directory

I can use jupyter notebooks using base python and even conda base however it fails with all conda envs.

on further digging i found an issue with conda when creating a new env.

Preparing transaction: done
Verifying transaction: / WARNING conda.core.path_actions:verify(962): Unable to create environments file. Path not writable.
  environment location: /home/betaglutamate/.conda/environments.txt

done
Executing transaction: - WARNING conda.core.envs_manager:register_env(50): Unable to register environment. Path not writable or missing.
  environment location: /home/betaglutamate/anaconda3/envs/test
  registry file: /home/betaglutamate/.conda/environments.txt
done

I think this may be caused by installing conda as su. try uninstalling as here:

https://docs.anaconda.com/anaconda/install/uninstall/

you need to do full uninstall then reinstall without sudo this seems to have fixed my problem.

[junrrein]

@Betaglutamate

I think this may be caused by installing conda as su. try uninstalling as here:

https://docs.anaconda.com/anaconda/install/uninstall/

you need to do full uninstall then reinstall without sudo this seems to have fixed my problem.

I have installed conda using my distributions' package manager. Doing a manual 'local' install is undesirable.

[vrpascuzzi]

FWIW I'm also having this issue. For some reason, it wants to source an activate script instead of calling conda activate <...>.

[rgranit]

I'm having a very similar issue:

Command failed: . /usr/bin/activate env && echo ... bash: /usr/bin/activate: No such file or directory

My conda is in '/usr/bin/conda'

Any suggested solution?

I was able to locate the activate file using find . -name activate and copy it to my working directory.. this solved the issue for me :)

[bw-turner]

I'm having a similar issue.

I am using VS code on WSL and have installed Miniconda. I have created an environment inside a project directory, and VS Code correctly locates that environment which I can select from the interpreters list.

When I go to open an integrated terminal however, I get:

ben@Firefly:~/Projects/myproj$ source activate /home/ben/Projects/myproj/env
bash: activate: No such file or directory

For some reason source is being called in place of conda.

[brpy]

Having the same issue.
rgranit's solution fixes the issue for now.

[simozacca]

I am having the same issue; activation of the environment is using source activate instead of the proper conda activate. I have temporarily fixed it by adding the paths to the conda activate script in my PATH through my .bashrc but this is a very disruptive issue.

[simozacca]

Issue related to #8770 and #8870

[chadHGY]

Hi recently I also encounter_ similar problem,
then I find that in the latest python-extension(v2021.1.502429) comes with setting that you can manually specify the root of the conda path:

After assigning the conda path I can launch the jupyter-notebook normally

[memeplex]

The above suggestion fixes nothing for me, after setting the conda path to /usr/local/Caskroom/miniconda/base/condabin/, I'm still getting a "source activate ..." line that fails with "no such file or directory" (since the is no such file or directory there, so I'm unable to see how it could fix anything).

[memeplex]

Ok, the problem is that, at least in a brew installation, the conda executable that is in the path after sourcing:

source /usr/local/Caskroom/miniconda/base/etc/profile.d/conda.sh

is in:

/usr/local/Caskroom/miniconda/base/condabin/conda

while activate is in:

/usr/local/Caskroom/miniconda/base/activate

I don't know what is the best approach to fix this (besides manually configuring the path). Probably vscode should do conda activate instead of plain activate, since that's what the conda documentation says.

[karrtikr]

#11039 should solve this issue. The fix should already be out if you want to try it:

• Use pre-release:
  
• Add "python.experiments.optInto": ["pythonTerminalEnvVarActivation"] to User settings and reload window.
• Make sure to not be using a multiroot workspace