Quarto execution output ignores cell magics

[skwde]

Bug description

Output of cell magics is ignored (in some cases).

Note, in some cases the output is shown, e.g. when using memory_profiler's %memit. I guess it depends on how the magic is implemented.

Steps to reproduce

Use test.qmd with content

---
title: "Quarto Basics"
format: pdf
jupyter: python3
---

```{python}
#| echo: false
#| output: true
import re
print("While it outputs print statements, it doesn't output all cell magics")
%psource re.compile

and run via

```sh
quarto preview test.qmd --no-browser

Expected behavior

The output of the %psource magic should be displayed as it is in the jupyter notebook.

I.e. I expect to see

def compile(pattern, flags=0):
    "Compile a regular expression pattern, returning a Pattern object."
    return _compile(pattern, flags)

Actual behavior

%psource output is not displayed

Your environment

• VSCode: 1.92.0
• quarto runs on debian bookworm in a devcontainer on MacOS

Quarto check output

# quarto check
Quarto 1.5.54
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.2.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.5.54
      Path: /opt/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: v2024.07.03
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /root/.TinyTeX/bin/x86_64-linux
      Version: 2024

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

[✓] Checking Python 3 installation....OK
      Version: 3.12.4 (Conda)
      Path: /opt/conda/bin/python
      Jupyter: 5.7.2
      Kernels: python3

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

[✓] Checking R installation...........(None)

      Unable to locate an installed version of R.
      Install R from https://cloud.r-project.org/

[cscheid]

Unfortunately, that magic doesn't emit anything: see the keep-ipynb: true output. So there's nothing Quarto can do about it.

[skwde]

@cscheid, not quite sure I get what the problem is here.

In any case, using %psource as above in ipython or in a jupyter-notebook shows the function definition.

[cderv]

I believe this is the same issue as

• https://github.com/quarto-dev/quarto-cli/issues/7644

And this relates to nbconvert execution of notebook having no output for the cell magic.

If you do the following

• Execute the ipynb first
• Then use quarto render on the ipynb source, then the prior execution results will stay and you'll get output.
• If you execute using --execute flag, quarto will use nbconvert and you won't get any.

To mimic this you can do

quarto convert index.qmd
jupyter nbconvert --to notebook --execute index.ipynb

you can reproduce the problem.

So possibly a nbconvert issue.