Lines containing, but not starting, with "#| echo: fenced" are omitted

[debruine]

Bug description

This is a tiny minor bug, but if you try to include the text #| echo: fenced in a fenced figure caption, that doesn't show up! (I found this while writing the quarto chapter of my MSc methods textbook).

I assume you just need to add regex to only omit lines that start with #| echo: fenced

Steps to reproduce

```{r}
#| echo: fenced
#| label: fig-demo
#| fig-cap: "fig-cap is invisible if it contains `#| echo: fenced`"

hist(rnorm(100000))
```

Expected behavior

The figure caption line should show in the code block

Actual behavior

The fig-cap line does not show

Your environment

• IDE: RStudio 2023.06.0+421
• quarto: 1.5.57
• R version 4.2.1 (2022-06-23)

Quarto check output

Quarto 1.5.57
[✓] 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: 1.5.57
Path: /Applications/quarto/bin

[✓] Checking tools....................OK
TinyTeX: (external install)
Chromium: (not installed)

[✓] Checking LaTeX....................OK
Using: TinyTex
Path: /Users/lisad/Library/TinyTeX/bin/universal-darwin
Version: 2021

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

[✓] Checking Python 3 installation....OK
Version: 3.9.6
Path: /Users/lisad/.virtualenvs/r-reticulate/bin/python3
Jupyter: (None)

  Jupyter is not available in this Python installation.
  Install with python3 -m pip install jupyter

[✓] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
knitr: 1.44
rmarkdown: 2.25

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

[mcanouil]

I cannot reproduce on the current development version.

[debruine]

@mcanouil You did reproduce it. The code chunk in the rendered doc has the label line, but not the fig-cap line

[mcanouil]

How you meant, it's not in the echoed code cell.

[debruine]

Super-niche bug, I know

[mcanouil]

This happens for both knitr and Python engines.

It seems to be on purpose (not only here) but maybe the "hard way" is way too hard:

• quarto-cli/src/core/handlers/base.ts

  Lines 635 to 646 in ee16c2e

  	for (const contentLine of contentLines) {
  	const commentMatch = contentLine.value.match(commentPattern);
  	if (commentMatch) {
  	if (contentLine.value.indexOf("echo: fenced") === -1) {
  	frontMatterLines.push(contentLine);
  	}
  	++inputIndex;
  	} else {
  	break;
  	}
  	}
  	const inputLines = contentLines.slice(inputIndex);

• quarto-cli/src/resources/formats/html/ojs/quarto-ojs-runtime.js

  Lines 23705 to 23728 in ee16c2e

  	// hack for "echo: fenced": remove all "//| echo: fenced" lines the hard way, but keep
  	// the right line numbers around.
  	Array.from(document.querySelectorAll("span.co"))
  	.filter((n) => n.textContent === "//| echo: fenced")
  	.forEach((n) => {
  	const lineSpan = n.parentElement;
  	const lineBreak = lineSpan.nextSibling;
  	if (lineBreak) {
  	const nextLineSpan = lineBreak.nextSibling;
  	if (nextLineSpan) {
  	const lineNumber = Number(nextLineSpan.id.split("-")[1]);
  	nextLineSpan.style = `counter-reset: source-line ${lineNumber - 1}`;
  	}
  	}
  	// update the source offset variable with the new right amount
  	const sourceDiv = lineSpan.parentElement.parentElement.parentElement;
  	const oldOffset = Number(sourceDiv.dataset.sourceOffset);
  	sourceDiv.dataset.sourceOffset = oldOffset - "//| echo: fenced\n".length;
  	lineSpan.remove();
  	lineBreak.remove();
  	});

[mcanouil]

In fact, you only need echo: fenced to be in a line starting with the special comment symbol.

Input	Output
--- title: "Quarto Playground" format: html --- ```{r} #| echo: fenced #| whatever: "echo: fenced" #| something: "echo: true" print("Hello, World!") ```

[debruine]

I hacked a fix like I describe here: #3554 (reply in thread)

[cscheid]

The echo: fenced removal is indeed super hacky on our side, and it'll be a long time before we can make it perfect. Nevertheless, we should only be a little more defensive and only pluck the lines that have no other content.

[cscheid]

FYI the specific line at play is this one:

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

Line 465 in 084df08

yamlCode <- Filter(function(line) !grepl("echo:\\s+fenced", line), yamlCode)

[cscheid]

In Jupyter, it seems that we're removing more than just the echo: fenced lines:

---
title: issue-10821
format: html
_quarto:
  tests:
    html:
      ensureHtmlElements:
        - []
        - []
---

```{python}
#| echo: fenced
#| warning: true
#| whatever: "echo: fenced"
#| something: "echo: true"
print("Hello, World!")
```

The output:

I believe what's happening is that in Jupyter, unrecognized options are not forwarded to the engine and so the engine can't print them back to us.

[cscheid]

In addition, we also seem to be stripping echo: fenced from Jupyter cells too aggressively:

---
title: issue-10821
format: html
_quarto:
  tests:
    html:
      ensureHtmlElements:
        - []
        - []
---

```{python}
#| echo: fenced
#| label: fig-1
#| fig-cap: "This figure will have 'echo: fenced' in its caption."
import matplotlib.pyplot as plt
plt.plot([1,2,3])
```

[cscheid]

In contrast,

---
title: issue-10821
format: html
_quarto:
  tests:
    html:
      ensureHtmlElements:
        - []
        - []
---

```{python}
#| echo: fenced
#| label: fig-1
#| fig-cap: "A regular caption."
import matplotlib.pyplot as plt
plt.plot([1,2,3])
```