[Python] Quarto cannot find nbformat and nbclient

I am trying to compile the following example (which uses the diagram filter):

---
title: Test
author:
- John Due
filters:
- diagram
format:
beamer: default
---

## Test
```tikz
\begin{tikzpicture}
\node (i) at (0, 0) {i};
\end{tikzpicture}
```


but it fails. The problem seems to come from Jupyter (although I do not know why it is involved as I have no python code nor jupyter notebook) as it shows here:

quarto check jupyter
Quarto 1.7.31
[✓] Checking Python 3 installation....OK
Version: 3.12.3
Path: /usr/bin/python3
Jupyter: 5.3.2
Kernels: python3

(/) Checking Jupyter engine render....Traceback (most recent call last):
File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module>
from notebook import notebook_execute, RestartKernel
File "/opt/quarto/share/jupyter/notebook.py", line 19, in <module>
import nbformat
ModuleNotFoundError: No module named 'nbformat'
[✓] Checking Jupyter engine render....OK


I tried to install the package nbformat as mentioned in this stackoverflow question. Running pipx list shows that it is installed in a virtual environment (does quarto have access to this?):

pipx list
venvs are in /home/John-Due/.local/share/pipx/venvs
apps are exposed on your $PATH at /home/John-Due/.local/bin
manual pages are exposed at /home/John-Due/.local/share/man
package nbclient 0.10.2, installed using Python 3.12.3
- jupyter-execute
package nbformat 5.10.4, installed using Python 3.12.3
- jupyter-trust
package radian 0.6.15, installed using Python 3.12.3
- radian


I also ran quarto capabilities and it shows that nbformat and nbclients are not installed:

quarto capabilities
{
"formats": [
"html",
"pdf",
"docx",
"odt",
"pptx",
"beamer",
"revealjs",
"gfm",
"epub",
"dashboard",
"email",
"ansi",
"asciidoc",
"asciidoc_legacy",
"asciidoctor",
"chunkedhtml",
"commonmark",
"commonmark_x",
"context",
"djot",
"docbook",
"docbook4",
"docbook5",
"dokuwiki",
"dzslides",
"epub2",
"epub3",
"fb2",
"haddock",
"html4",
"html5",
"icml",
"ipynb",
"jats",
"jats_archiving",
"jats_articleauthoring",
"jats_publishing",
"jira",
"json",
"latex",
"man",
"markdown",
"markdown_github",
"markdown_mmd",
"markdown_phpextra",
"markdown_strict",
"markua",
"mediawiki",
"ms",
"muse",
"native",
"opendocument",
"opml",
"org",
"plain",
"rst",
"rtf",
"s5",
"slideous",
"slidy",
"tei",
"texinfo",
"textile",
"typst",
"xwiki",
"zimwiki"
],
"themes": [
"default",
"spacelab",
"united",
"morph",
"materia",
"sandstone",
"cyborg",
"slate",
"superhero",
"sketchy",
"darkly",
"lux",
"vapor",
"yeti",
"cosmo",
"litera",
"flatly",
"zephyr",
"minty",
"solar",
"simplex",
"lumen",
"cerulean",
"quartz",
"pulse",
"journal"
],
"python": {
"versionMajor": 3,
"versionMinor": 12,
"versionPatch": 3,
"versionStr": "3.12.3 (main, Feb 4 2025, 14:48:35) [GCC 13.3.0]",
"conda": false,
"execPrefix": "/usr",
"executable": "/usr/bin/python3",
"jupyter_core": "5.3.2",
"nbformat": null,
"nbclient": null,
"ipykernel": null,
"shiny": null,
"pyLauncher": false,
"kernels": [
{
"name": "python3",
"language": "python",
"display_name": "Python 3 (ipykernel)",
"path": "/home/John-Due/.local/share/jupyter/kernels/python3"
}
],
"venv": true
}
}%


Any idea on how to solve this problem?

In case of, here is the error returned in the shell:

** (org.inkscape.Inkscape:20806): WARNING **: 12:04:31.085: No pages selected, getting first page only.
Error running filter /opt/quarto/share/filters/main.lua:
string expected, got nil
while retrieving function argument root
while retrieving arguments for function make_relative
stack traceback:
.../share/pandoc/datadir/../../filters/modules/mediabag.lua:20: in function 'modules/mediabag.with_mediabag_contents'
(...tail calls...)
/opt/quarto/share/filters/main.lua:2943: in local 'fn'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:34: in upvalue 'run_filter_function'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:223: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202>
(...tail calls...)
[C]: in function 'pandoc.List.map'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:125: in upvalue 'recurse'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in local 'jogger'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:98: in upvalue 'recurse'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202>
(...tail calls...)
[C]: in function 'pandoc.List.map'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:125: in upvalue 'recurse'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in local 'jogger'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:171: in upvalue 'recurse'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202>
(...tail calls...)
/opt/quarto/share/filters/main.lua:572: in function </opt/quarto/share/filters/main.lua:550>
(...tail calls...)
/opt/quarto/share/filters/main.lua:1318: in local 'callback'
/opt/quarto/share/filters/main.lua:1336: in upvalue 'run_emulated_filter_chain'
/opt/quarto/share/filters/main.lua:1372: in function </opt/quarto/share/filters/main.lua:1369>


I know it does not mention the python stuff discussed above, but I started to have the ModuleNotFoundError: No module named 'nbformat' problem first.

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