quarto-dev / quarto-dev/quarto-cli

in quarto convert failing to convert R cells?

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Description

Bug description

HI I think quite convert is failing when sed iwht r cells?

I am trying to cover .qmd to .ipynb on Mac, quarto: 1.6.40, r: .4.4.1

this is my qmd file"

---
title: 'test conversion'
---

```{r}
library(tinyplot)
```

# Introduction

This document is a test...

```{r}
a <- rnorm(100)
hist(a)
```

Does it work? I don't know?

which generates this .ipynb (pasting raw .json but basically the entire thing is in one big markdown cell):

{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"---\n",
"title: 'test conversion'\n",
"---\n",
"\n",
"{r}\n", "library(tinyplot)\n", "\n",
"\n",
"# Introduction\n",
"\n",
"This document is a test...\n",
"\n",
"{r}\n", "a <- rnorm(100)\n", "hist(a)\n", "\n",
"\n",
"Does it work? I don't know?\n"
]
}
],
"metadata": {
"kernelspec": {
"name": "python3",
"language": "python",
"display_name": "Python 3 (ipykernel)",
"path": "/Users/michelnivard/miniconda3/share/jupyter/kernels/python3"
}
},
"nbformat": 4,
"nbformat_minor": 4
}

the expected behaviour here would be a series of:

1 raw cells with the yaml
1 code cell: library(tinyplot)
1 markdown cell:
Introduction

This document is a test...
1 code cell:
a <- rnorm(100)
hist(a)
1 markdown cell:
Does it work? I don't know?

I think its failing because the conversion expects only python cells?

Conversion work fine if I change the r cells to python cells...

Steps to reproduce

No response

Expected behavior

No response

Actual behavior

No response

Your environment

No response

Quarto check output

quarto check
Quarto 1.6.40
[✓] Checking environment information...
Quarto cache location: /Users/michelnivard/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: 1.6.40
Path: /Applications/quarto/bin

[✓] Checking tools....................OK
TinyTeX: v2023.01
Chromium: (not installed)

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

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

[✓] Checking Python 3 installation....OK
Version: 3.10.8 (Conda)
Path: /Users/michelnivard/miniconda3/bin/python
Jupyter: 5.7.1
Kernels: ir, python3

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

[✓] Checking R installation...........OK
Version: 4.4.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
knitr: 1.48
rmarkdown: 2.27

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

(base) michelnivard@michels-MacBook-Air resolve-demo-doc %

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

Reproduce the reported conversion with the provided .qmd example and Quarto 1.6.40, then trace the convert-to-.ipynb path for fenced R cells. Done means the YAML is represented as raw cells, R fences become code cells, and surrounding prose remains in markdown cells.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, r
Domain
tooling
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
45/100

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