quarto-dev / quarto-dev/quarto-cli

Quarto execution output ignores cell magics

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engines-jupyter enhancement
Dominant language
JavaScript
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Forks
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Merged PRs (30d)
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Description

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

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/

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the supplied test.qmd reproduction and run quarto preview test.qmd --no-browser, comparing the rendered result with the expected notebook output. Trace how Python cell-magic output is handled during Quarto's Jupyter execution, and consider the issue done when %psource output is displayed while existing print and %memit behavior remains intact.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter, python
Domain
tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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