Can the number of backticks used for Jupyter notebook code cell be specified?

[jackgerrits]

Bug description

I have a code cell in a notebook which contains a string with a markdown code block in it. This breaks the rendering of the outputted markdown content. Is it possible to configure the number of backticks that are used when outputting a code cell form a notebook to markdown? (In my case docusaurus, so mdx)

Steps to reproduce

The following would be the contents of the cell:

message = """
content
```python
print("Hello")
```
"""

Which gets rendered is:

```python
message = """
content
```python
print("Hello")
```
"""
```

This does not render correctly

Expected behavior

No response

Actual behavior

No response

Your environment

• CLI, MacOS 14.3.1

Quarto check output

Quarto 1.4.549
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.11: OK
      Dart Sass version 1.69.5: OK
      Deno version 1.37.2: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.4.549
      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: 3.11.7
      Path: /Users/jackgerrits/w/autogen/.venv/bin/python3
      Jupyter: 5.7.1
      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/

[mcanouil]

That's unrelated to Quarto.
It's Markdown, the same will happen on any Markdown document/services such as GitHub.

Note that your example has no code cells. Code cells describe a Markdown code block where its8 content can be used for computation.

See below.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ```  The end. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ```  The end. ````

[mcanouil]

For more help:

Could you share a small self-contained "working" (reproducible) example to work with, i.e., a complete Quarto document or a Git repository? Thanks.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ```  The end. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ```  The end. ````

Additionally and if not already given, please share the output of quarto check within a code blocks (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.

[jackgerrits]

Sorry my example was not very clear. I am using quarto render in a docusaurus website to render jupyter notebooks to mdx.

What happens is when the notebook contains a code cell, the produced mdx file contains the markdown representation of that code cell using 3 backticks as the fence.

The issue is that the code cell itself contained a string with 3 backticks too, which breaks the rendering. Normally, I would make the outer codefence use 4 or more backticks to resolve this but quarto (or pandoc?) is the one doing this translation I can't seem to do that.

[mcanouil]

I am using quarto render in a docusaurus website to build

I know, I saw "(In my case docusaurus, so mdx)", but knowing this does not make your example more reproducible.

[jackgerrits]

Sent the message too soon - see the updated content above.

[jackgerrits]

If this is the cell in the notebook:

Then the rendered content I am getting is:

```python
message = """
Content
```python
print("Hello, world!")
```
"""
```

It would be great if there was some way to specify an option saying use 4 backticks for cell code blocks to avoid this issue. Then ideally I could get something like the following out of quarto render:

````python
message = """
Content
```python
print("Hello, world!")
```
"""
````

[cscheid]

Yeah, this is definitely a bug on our side.

[jackgerrits]

I think its related to docusaurus because when I was trying to get a standalone repro (just jupyter -> markdown) it was correctly using 4 instead of 3 backticks in the above example. But in the more complex situation of file being inside of a docusaurus site I was seeing the issue

[jackgerrits]

For the markdown only example that did work I get the following output:

pandoc
  to: >-
    markdown_strict+raw_html+all_symbols_escapable+backtick_code_blocks+fenced_code_blocks+space_in_atx_header+intraword_underscores+lists_without_preceding_blankline+shortcut_reference_links
  output-file: repro.md
  standalone: true
  default-image-extension: png

Output created: repro.md

But the docusaurus version outputs:

pandoc
  to: >-
    markdown_strict+raw_html+all_symbols_escapable+backtick_code_blocks+fenced_code_blocks+space_in_atx_header+intraword_underscores+lists_without_preceding_blankline+shortcut_reference_links+autolink_bare_uris+emoji+footnotes+gfm_auto_identifiers+pipe_tables+strikeout+task_lists+tex_math_dollars+pipe_tables+tex_math_dollars+header_attributes+raw_html+all_symbols_escapable+backtick_code_blocks+fenced_code_blocks+space_in_atx_header+intraword_underscores+lists_without_preceding_blankline+shortcut_reference_links
  output-file: jupyter-code-executor.mdx
  standalone: true
  default-image-extension: png
  wrap: none
  html-math-method: webtex

metadata
  quarto-custom-format: docusaurus
  title: Jupyter Code Executor

Output created: jupyter-code-executor.mdx

Does quarto-custom-format: docusaurus affect things?

[cscheid]

It does, but you don't need that. Here's another instance of the issue:

$ cat bug.ipynb
{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "d02a6fa3",
   "metadata": {},
   "outputs": [],
   "source": [
    "message = \"\"\"\n",
    "Content\n",
    "```python\n",
    "print(\"Hello, world!\")\n",
    "```\n",
    "\"\"\""
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.13"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}
$ quarto convert bug.ipynb
$ cat bug.qmd
---
jupyter: python3
---

```{python}
message = """
Content
```python
print("Hello, world!")
```
"""
```

That's already broken.

[jackgerrits]

I can confirm that rendering the same notebook and just ensuring the target format is md instead of the default mdx it uses the correct code fence (4 backticks when it needs it)

quarto render docs/jupyter-code-executor.ipynb --to md

pandoc
  to: >-
    markdown_strict+raw_html+all_symbols_escapable+backtick_code_blocks+fenced_code_blocks+space_in_atx_header+intraword_underscores+lists_without_preceding_blankline+shortcut_reference_links
  output-file: jupyter-code-executor.md
  standalone: true
  default-image-extension: png

metadata
  title: Jupyter Code Executor

Output created: jupyter-code-executor.md

[jackgerrits]

Oh awesome, that repro is much better then

[jackgerrits]

With your example if you run it like this:

quarto render bug.ipynb --to md

It works, but if you convert it like you said it doesn't work.

[cscheid]

Funnily enough, it's two bugs. I fixed the first one in a branch and yet the following is still broken:

$ quarto convert bug.ipynb
...
$ cat bug.qmd
---
jupyter: python3
---

````{python}
message = """
Content
```python
print("Hello, world!")
```
"""
````
$ quarto render bug.ipynb --to docusaurus-md
$ cat bug.mdx



```python
message = """
Content
```python
print("Hello, world!")
```
"""
```

[cscheid]

Fixed on main.