Contents shortcode does not work on code-cell div with `knitr`

[mcanouil]

Bug description

It appears {{< contents ID >}} cannot move code-cells with an ID when the engine is set to knitr.

I'm not sure what the limitation actually is:

Currently, {{< contents >}} itself does not work inside code elements. We may lift that limitation in the future.

Steps to reproduce

	Jupyter (works)	knitr (does not work)
Div	--- title: "Quarto Playground" format: html engine: jupyter --- ## Section 1 ```{python} #| label: my-figure import matplotlib.pyplot as plt plt.plot([1,2,3]) ``` ## Section 2 {{< contents my-figure >}}	--- title: "Quarto Playground" format: html engine: knitr --- ## Section 1 ```{r} #| label: my-figure plot(1:10) ``` ## Section 2 {{< contents my-figure >}}
Cross-ref Div	--- title: "Quarto Playground" format: html engine: jupyter --- ## Section 1 ```{python} #| label: fig-figure import matplotlib.pyplot as plt plt.plot([1,2,3]) ``` ## Section 2 {{< contents fig-figure >}}	--- title: "Quarto Playground" format: html engine: knitr --- ## Section 1 ```{r} #| label: fig-figure plot(1:10) ``` ## Section 2 {{< contents fig-figure >}}

Expected behavior

Content is moved without warning.

Actual behavior

WARNING (/Users/mcanouil/Projects/quarto/quarto-cli/src/resources/filters/./quarto-pre/contentsshortcode.lua:79) [Malformed document] Found `contents` shortcode without a corresponding div with id: my-figure.
This might happen because the shortcode is used in div context, while the id corresponds to a span.
Removing from document.

WARNING (/Users/mcanouil/Projects/quarto/quarto-cli/src/resources/filters/./quarto-pre/contentsshortcode.lua:79) [Malformed document] Found `contents` shortcode without a corresponding div with id: fig-figure.
This might happen because the shortcode is used in div context, while the id corresponds to a span.
Removing from document.

Your environment

No response

Quarto check output

Quarto 99.9.9
[✓] Checking environment information...
      Quarto cache location: /Users/mcanouil/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: 99.9.9
      commit: b822c3f5cc2b7dd57238bed2bcbbd2c2ed7688b8
      Path: /Users/mcanouil/Projects/quarto/quarto-cli/package/dist/bin

[✓] Checking tools....................OK
      TinyTeX: v2025.02
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/mcanouil/Library/TinyTeX/bin/universal-darwin
      Version: 2024

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /Applications/Brave Browser.app/Contents/MacOS/Brave Browser
      Source: QUARTO_CHROMIUM

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

[✓] Checking Python 3 installation....OK
      Version: 3.13.2
      Path: /Users/mcanouil/Projects/quarto/quarto-playground/.venv/bin/python
      Jupyter: 5.7.2
      Kernels: julia-1.11, python3

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

(|) Checking R installation...........ℹ R version 4.4.2 (2024-10-31)
! Config '~/.Rprofile' was loaded!
[✓] Checking R installation...........OK
      Version: 4.4.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Users/mcanouil/Projects/quarto/quarto-playground/renv/library/macos/R-4.4/aarch64-apple-darwin20
        - /Users/mcanouil/Library/Caches/org.R-project.R/R/renv/sandbox/macos/R-4.4/aarch64-apple-darwin20/f7156815
      knitr: 1.46
      rmarkdown: 2.29

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

[cscheid]

Knitr puts the id only in the image, and jupyter puts an id in the cell div in addition to the image. contents expects to find the cell div. Here are the relevant keep-md outputs:

knitr

---
title: "Quarto Playground"
format: html
engine: knitr
keep-md: true
---

## Section 1

::: {.cell}

```{.r .cell-code}
plot(1:10)
```

::: {.cell-output-display}
![](issue-12065_files/figure-html/fig-figure-1.png){#fig-figure width=672}
:::
:::

## Section 2

{{< contents fig-figure >}}

jupyter

---
title: "Quarto Playground"
format: html
engine: jupyter
keep-md: true
---

## Section 1

::: {#cell-fig-figure .cell execution_count=1}
``` {.python .cell-code}
import matplotlib.pyplot as plt
plt.plot([1,2,3])
```

::: {.cell-output .cell-output-display}
![](issue-12065-j_files/figure-html/fig-figure-output-1.png){#fig-figure width=579 height=411}
:::
:::


## Section 2

{{< contents fig-figure >}}

[cderv]

For reference, this also relates to this other issue which is about Jupyter engine

• Contents Shortcode not working for pdf output (relates to Feature 10552) #10671 (comment)

id on .cell div is part of the difference between engines. This is all about

• mini-epic: AST uniformization across engines for floats #7062
• [EPIC] Differences on generated Markdown between knitr and jupyter engine #7670

Some notes I have taken on this topic

Jupyter always add an id on .cell div

Jupyter always add one, and use #cell- prefix

quarto-cli/src/core/jupyter/jupyter.ts

Lines 909 to 922 in 7ca42c0

	// Ensure that the cell has an id - the id will be
	// unique within this notebook thanks to the index
	const cellId = (cell: JupyterCell) => {
	if (
	options && options[kCellLabel] &&
	typeof (options[kCellLabel]) === "string"
	) {
	return `cell-${options[kCellLabel]}`;
	} else if (cell.id) {
	return cell.id;
	} else {
	return `cell-${index}`;
	}
	};

Knitr does not and only sets one in some situation

knitr is supposed to add one also when a label is set on the cell

quarto-cli/src/resources/rmd/hooks.R

Lines 410 to 414 in 7ca42c0

	paste0(
	options[["indent"]], "::: {",
	labelId(label), paste(classes, collapse = " ") ,forwardAttr, "}\n", x, "\n", cell.cap ,
	options[["indent"]], ":::"
	)

quarto-cli/src/resources/rmd/hooks.R

Lines 981 to 987 in 7ca42c0

	labelId <- function(label) {
	if (!is.null(label) && !startsWith(label, "#"))
	paste0("#", label)
	else
	label
	}

Though, it will consider #fig-

quarto-cli/src/resources/rmd/hooks.R

Line 209 in 7ca42c0

label <- output_label(options)

quarto-cli/src/resources/rmd/hooks.R

Lines 1006 to 1013 in 7ca42c0

	output_label <- function(options) {
	label <- options[["label"]]
	if (!is.null(label) && grepl("^#?(fig)-", label)) {
	label
	} else {
	NULL
	}
	}

but it will only pass the fig- label if there is a caption and subcaption (as the subfigure id will be the one on each figure)

quarto-cli/src/resources/rmd/hooks.R

Lines 230 to 235 in 7ca42c0

	# caption output
	if (!is.null(fig.cap) && !is.null(fig.subcap)) {
	cell.cap <- paste0("\n", fig.cap, "\n")
	} else {
	label <- NULL
	}

Regarding prefix of id, knitr will only add a #cell- if we are preserving cell

quarto-cli/src/resources/rmd/hooks.R

Lines 214 to 219 in 7ca42c0

	# If we're preserving cells, we need provide a cell id
	cellId <- NULL
	if (isTRUE(format$render$`notebook-preserve-cells`) && !is.null(label)) {
	cellId <- paste0("cell-", label)
	}

(from d136b1e)

Other exception is when tbl- is detected to let it pass through

quarto-cli/src/resources/rmd/hooks.R

Lines 387 to 398 in 7ca42c0

	# allow table label through
	if (is_table_label(options[["label"]])) {
	label <- options[["label"]]
	}
	if (is.null(label) && !is.null(cellId)) {
	label <- cellId
	}
	if (!is.null(label)) {
	label <- paste0(label, " ")
	}

And this is part of the problem in regards to

• Teach engine about new custom crossref #7665

This is definitely something I want to work on for knitr and jupyter engine. I think a prerequisite is to sit, write down the "specs" for what the markdown syntax should be for .cell div and .cell-output-x for engine output.
Once we have that, we can then tweak our current engine to do the right thing.