Python: cannot deactivate environments in Terminal

[isabelizimm]

Positron Version:

Positron dev

Steps to reproduce the issue:

1. Start up Terminal
2. Try to deactivate current environment/activate a new one
3. See output

I believe this is a side effect of python.terminal.activateEnvironment setting. By the time I have tried to activate one environment, I have 3 environments displayed, and the one I have activated is not actually the one in use.

What did you expect to happen?

Python environments to deactivate properly.

Were there any error messages in the output or Developer Tools console?

None

[seeM]

Could you please share more about your environment management setup? Specifically, what's executed in your bashrc/zshrc and corresponding _profile files?

What happens if you repeat this in VSCode (ensuring the same python.terminal.activateEnvironment setting and that you opt into the same experiment we do)? I recall seeing issues about deactivation in the upstream repo so may also be worth exploring those.

[isabelizimm]

In VSCode, with python.terminal.activateEnvironment, conda (base) is activated automatically every new terminal I open. This occurs in Positron as well, since it is being activated in my .zshrc/.bash_profile. The difference is, in Positron, the pyenv interpreter is also activated + nested automatically.

In VSCode:

### START OF TERMINAL:
(base) ➜   pyenv activate positron
pyenv-virtualenv: prompt changing will be removed from future release. configure `export PYENV_VIRTUALENV_DISABLE_PROMPT=1' to simulate the behavior.
(positron) (base) ➜   pyenv activate pydemo  
pyenv-virtualenv: prompt changing will be removed from future release. configure `export PYENV_VIRTUALENV_DISABLE_PROMPT=1' to simulate the behavior.
(pydemo) (base) ➜   which python
/Users/isabelzimmerman/.pyenv/versions/3.11.4/bin/python
(pydemo) (base) ➜   

In Positron:

### START OF TERMINAL:
((positron) ) (base) ➜  pyenv activate pydemo
pyenv-virtualenv: virtualenv `/Users/isabelzimmerman/.pyenv/versions/3.10.7/envs/positron' is already activated
((positron) ) (base) ➜  pyenv deactivate     
((positron) ) (base) ➜  pyenv activate pydemo
pyenv-virtualenv: prompt changing will be removed from future release. configure `export PYENV_VIRTUALENV_DISABLE_PROMPT=1' to simulate the behavior.
(pydemo) ((positron) ) (base) ➜  which python
/Users/isabelzimmerman/.pyenv/versions/3.10.7/envs/positron/bin/python
(pydemo) ((positron) ) (base) ➜   

Do note that neither of these are really doing what I want them to; pydemo is Python 3.9.12, positron is Python 3.10.7, and my global pyenv is Python 3.11.4. My startup interpreter is positron. In that sense, Positron is actually closer to choosing the right Python than VSCode 😅

I suppose my largest issues here are

1. conda is activated, even when it is not my selected interpreter (maybe that is not something Positron can/should do, if it includes overwriting zshrc/bashrc settings)
2. multiple interpreters showing when i try to activate/deactivate
3. nested interpreters (potentially fixed upstream, see related issues)

---

Related upstream discussions:

• Respect VIRTUAL_ENV_PROMPT when calculating PS1 microsoft/vscode-python#23080
• Double parantheses: "((.venv) )" microsoft/vscode-python#23193
• Fix duplicated venv prompt parenthesis microsoft/vscode-python#23201

---

With pyenv AND conda installed, I do have a bit of a mess in these files.

I've pulled out the pyenv + conda pieces for the following files:

~/.zshrc

export PYENV_ROOT="$HOME/.pyenv"
command -v pyenv >/dev/null || export PATH="$PYENV_ROOT/bin:$PATH"
eval "$(pyenv init -)"
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/Users/isabelzimmerman/miniconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/Users/isabelzimmerman/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/Users/isabelzimmerman/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/Users/isabelzimmerman/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

~/.bashrc

nothing pyenv or conda related

~/.zprofile

nothing pyenv or conda related

~/.bash_profile

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/opt/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/opt/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/opt/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

[jthomasmock]

Also ran into this:

Not sure if this is same, but I have observed this behavior, where it looks like you are in a venv, but unable to deactivate.

# initial load of a new zsh shell
# ------

(.venv) 

~/demo-video [🐍pyenv 3.12.0 (.venv)][2024-18-06  8:56AM]
❯ which python
/Users/thomasmock/demo-video/.venv/bin/python
(.venv) 

~/demo-video [🐍pyenv 3.12.0 (.venv)][2024-18-06  8:56AM]
❯ deactivate
zsh: permission denied: deactivate
(.venv) 

~/demo-video [🐍pyenv 3.12.0 (.venv)][2024-18-06  8:56AM]
❯ source .venv/bin/activate
(.venv) 

~/demo-video [🐍pyenv 3.12.0 (.venv)][2024-18-06  8:56AM]
❯ which python             
/Users/thomasmock/demo-video/.venv/bin/python
(.venv) 

~/demo-video [🐍pyenv 3.12.0 (.venv)][2024-18-06  8:56AM]
❯ deactivate               
(.venv) 

~/demo-video [2024-18-06  8:56AM]
❯ which python
/Users/thomasmock/demo-video/.venv/bin/python
(.venv) 

[jthomasmock]

On Workbench, I'm also seeing some errors like this in the Python output:

2024-11-26 20:35:22.276 [error] Failed to initialize deactivate script /bin/bash [Error: "/usr/lib/rstudio-server/bin/positron-server/extensions/positron-python/python_files/deactivate/bash/envVars.txt" file not created
	at Timeout.<anonymous> (/usr/lib/rstudio-server/bin/positron-server/extensions/positron-python/dist/client/extension.js:2:326102)
	at listOnTimeout (node:internal/timers:573:17)
	at process.processTimers (node:internal/timers:514:7)]

And the inability to deactivate out of a .venv:

$ deactivate
grep: /usr/lib/rstudio-server/bin/positron-server/extensions/positron-python/python_files/deactivate/bash/envVars.txt: No such file or directory
grep: /usr/lib/rstudio-server/bin/positron-server/extensions/positron-python/python_files/deactivate/bash/envVars.txt: No such file or directory
grep: /usr/lib/rstudio-server/bin/positron-server/extensions/positron-python/python_files/deactivate/bash/envVars.txt: No such file or directory

[isabelizimm]

I am no longer able to reproduce this state; switching between interpreters, including mixing pyenv, venv, and conda acts as expected. There has been work on this bug upstream, which looks like it fixed this.

@jthomasmock if this continues to be a problem on workbench, feel free to open another issue!

[jthomasmock]

Thanks! I just tried on the candidate 2024.12.1 patch, and it seems to be working 🎉

thomas@session---positron-pro-sessio6z7sc:~/2024-11-26-notebooks$ source .venv/bin/activate
(.venv) thomas@session---positron-pro-sessio6z7sc:~/2024-11-26-notebooks$ deactivate
thomas@session---positron-pro-sessio6z7sc:~/2024-11-26-notebooks$