quarto-dev / quarto-dev/quarto-cli
"Jupyter is not available in this Python installation" when using pipx
Nobody has claimed this yet.
- Dominant language
- JavaScript
- Stars
- 6k
- Forks
- 458
- Avg merge
- 1d 9h
- Merged PRs (30d)
- 41
Description
Bug description
I use pipx to install python stuff (https://github.com/pypa/pipx). Jupyterlab works just fine, and in VScode I am able to select kernels installed this way no problem. However, when I run quarto render on a jupyter notebook, I get the following error:
quarto render r-notebook.ipynb --execute
Starting ir kernel...Traceback (most recent call last):
File "/Applications/quarto/share/jupyter/jupyter.py", line 21, in <module>
from notebook import notebook_execute, RestartKernel
File "/Applications/quarto/share/jupyter/notebook.py", line 15, in <module>
from yaml import safe_load as parse_string
ModuleNotFoundError: No module named 'yaml'
Python 3 installation:
Version: 3.13.1
Path: /opt/homebrew/opt/python@3.13/bin/python3.13
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
Jupyter is globally accessible to all environments:
> pipx list
venvs are in /Users/venpopov/.local/pipx/venvs
apps are exposed on your $PATH at /Users/venpopov/.local/bin
manual pages are exposed at /Users/venpopov/.local/share/man
package jupyterlab 4.3.4, installed using Python 3.13.1
- debugpy
- httpx
- ipython
- ipython3
- jlpm
- jsonpointer
- jsonschema
- jupyter
- jupyter-dejavu
- jupyter-events
- jupyter-execute
- jupyter-kernel
- jupyter-kernelspec
- jupyter-lab
- jupyter-labextension
- jupyter-labhub
- jupyter-migrate
- jupyter-nbconvert
- jupyter-run
- jupyter-server
- jupyter-troubleshoot
- jupyter-trust
- normalizer
- pybabel
- pygmentize
- pyjson5
- send2trash
- wsdump
- man1/ipython.1
package notebook 7.3.2, installed using Python 3.13.1
- jupyter-notebook
package radian 0.6.13, installed using Python 3.13.1
- radian
commands like jupyter work just fine in any terminal and VScode. It seems that quarto CLI tool is making erroneous assumptions about how to check for the presence of jupyter.
Steps to reproduce
the following installs jupyterlab via pipx
pipx install jupyterlab --include-deps
Expected behavior
quarto CLI should recognize the globally accessible jupyter installation
Actual behavior
No response
Your environment
- zsh terminal
- MacOS Sonoma
Quarto check output
Quarto 1.6.39
[✓] Checking environment information...
Quarto cache location: /Users/venpopov/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.4.0: OK
Dart Sass version 1.70.0: OK
Deno version 1.46.3: OK
Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.6.39
Path: /Applications/quarto/bin
[✓] Checking tools....................OK
TinyTeX: (not installed)
Chromium: (not installed)
[✓] Checking LaTeX....................OK
Tex: (not detected)
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.13.1
Path: /opt/homebrew/opt/python@3.13/bin/python3.13
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[✓] Checking R installation...........OK
Version: 4.4.2
Path: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources
LibPaths:
- /Users/venpopov/Library/R/arm64/4.4/library
- /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
knitr: 1.49
rmarkdown: 2.29
[✓] Checking Knitr engine render......OK
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the failure with pipx install jupyterlab --include-deps, then run quarto render r-notebook.ipynb --execute. Start by reading /Applications/quarto/share/jupyter/jupyter.py and notebook.py, where the reported import failure occurs. Done means Quarto recognizes the pipx-installed Jupyter environment and renders the notebook successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter, python
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100