Warning when using Python via pyenv

[cbrnr]

Description

I use pyenv to manage my Python environments (including virtual environments). In a Quarto project using a specific pyenv version, everything works fine (meaning that Quarto correctly uses the currently active Python environment as set by pyenv), but I get a warning e.g. when publishing (again, everything works correctly despite of this warning). The same warnings are also popping up in the output of quarto check:

Quarto 1.4.550
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.11: OK
      Dart Sass version 1.69.5: OK
      Deno version 1.37.2: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.4.550
      Path: /Users/clemens/Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/clemens/Library/TinyTeX/bin/universal-darwin
      Version: 2022

[✓] Checking basic markdown render....OK

WARNING: Specified QUARTO_PYTHON '/Users/clemens/.pyenv/versions/3.12.2/envs/python-intro-short' does not exist.
[✓] Checking Python 3 installation....OK
      Version: 3.12.2
      Path: /Users/clemens/.pyenv/versions/python-intro-short/bin/python3
      Jupyter: 5.7.1
      Kernels: python3

WARNING: Specified QUARTO_PYTHON '/Users/clemens/.pyenv/versions/3.12.2/envs/python-intro-short' does not exist.
[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.3.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
      knitr: 1.45
      rmarkdown: 2.25

[✓] Checking Knitr engine render......OK

Is this something that I should be worried about? It is a bit confusing, because everything is detected correctly, so the warning doesn't make sense to me.

[mcanouil]

Did you set QUARTO_PYTHON somewhere in your project? Perhaps in _environment? (https://quarto.org/docs/projects/environment.html)

If you did not set it, it means Quarto find this and since it is valid, go to the next location to find Python.

It should be fine, but better to not have warnings especially regarding configuration such as the Python setup.

[cbrnr]

I think the problem is really specific to the VS Code extension. In a regular terminal, the output of quarto check is fine:

[✓] Checking Python 3 installation....OK
      Version: 3.12.2
      Path: /Users/clemens/.pyenv/versions/python-intro-short/bin/python3
      Jupyter: 5.7.1
      Kernels: python3

However, when I preview a Quarto document in VS Code (by clicking on the "Preview" icon), a new terminal tab opens, and Quarto runs its preview command (quarto preview /Users/clemens/Projects/python-intro-short/12/12.qmd --no-browser --no-watch-inputs). And it's in this terminal that it shows the warning!

[mcanouil]

Did you try to run quarto within a terminal in VSCode? Maybe that's what you meant by "regular terminal" ...

When I have a bit more time, I'll try to setup a repository to reproduce this, likely using Devcontainer.

[cbrnr]

Yes, by regular terminal I mean any terminal running my default shell, including terminals opened in VS Code. It's just that Quarto Preview opens a special terminal, where Python detection produces this weird warning.

[cderv]

Let me clarifiy some things here:

QUARTO_PYTHON is supposed to point to the binary.

@mcanouil we support QUARTO_PYTHON has a directory in which the binary can be found. If a directory is provided we look for these binaries (const bin = ["python3", "python", "python3.exe", "python.exe"]). You can check the resolution of QUARTO_PYTHON in the code base.

But maybe the Quarto extension sets this? I certainly did not set it...

@cbrnr Yes in VSCODE we do set the QUARTO_PYTHON env var to use the active Python Interpreter. This can be found in the code base for the extension
https://github.com/quarto-dev/quarto/blob/f9edec34e53817e9c9f73cb349f524a82bcc6474/apps/vscode/src/core/terminal.ts#L40-L44

What is your active python interpreter in VSCODE ? Is this /Users/clemens/.pyenv/versions/3.12.2/envs/python-intro-short (probably) ?

Is this a working version in VSCODE for the python extension ? Are there binaries in /Users/clemens/.pyenv/versions/3.12.2/envs/python-intro-short ?

When QUARTO_PYTHON value is not found, it just throws a warning (that you see) and goes on with the usual detection looking for python in PATH. I believe this is where /Users/clemens/.pyenv/versions/python-intro-short/bin/python3 is found.

You should check which Python version is configured to be used in VSCODE using the python extension. This python version is meant to be used with python cells or any Python work you would do in VSCODE

Here is a doc about this Python interpreter thing: https://code.visualstudio.com/docs/python/environments

Hope it helps

[cbrnr]

Thanks @mcanouil and @cderv for your help! I think I could track it down to the currently selected Python interpreter in VS Code not being set correctly. I re-selected the same venv, and now everything works fine! Thanks a lot! 🙏

[mcanouil]

Glad you fixed your issue.
By the way, why are you setting the path in VSCode exactly?
I did not and this select the proper Python to run every single time, from Virtual Env, Conda, global.

[cbrnr]

You mean you never select the project interpreter? It prompts me every time I create a new project. This setting was set to some venv I created previously, and I'm not sure VS Code automatically picks up the correct Python env I set with a .python-version file.

[cbrnr]

I just tried setting it to python like you have, and it does seem to recognize the correct env! Thanks! 💯