formatting problems with multiple tables and echo: fenced

[richardjtelford]

Bug description

When I use echo: fenced block option and have multiple tables in the block, the second table loses the sub-caption and the bold formatting of the header row. With echo: true everything is fine.

Here is a minimal example

---
title: results
format: html
---
 
```{r}
#| echo: fenced
#| label: tbl-fenced
#| tbl-cap: "Two tables"
#| tbl-subcap: 
#|   - tab1
#|   - tab2

gt::gt(head(mtcars))
gt::gt(head(mtcars))
```

quarto --version 1.2.198
Ubuntu 18.04.6 LTS
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Ubuntu Bionic

Checklist

• Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
• Please format your issue so it is easier for us to read the bug report.
• Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
• Please document the operating system you're running. If on Linux, please provide the specific distribution.

[cscheid]

@cderv I think this might be a knitr issue? Check this out:

If we render with echo: fenced, only one cell-output-display div is created. The following .qmd:

```{r}
#| echo: fenced
#| label: tbl-fenced
#| tbl-cap: "Two tables"
#| tbl-subcap: 
#|   - tab1
#|   - tab2

gt::gt(head(mtcars, 1))
gt::gt(head(mtcars, 1))
```

produces this .md:

::: {#tbl-fenced .cell tbl-cap='Two tables' tbl-subcap='["tab1","tab2"]'}

````{.cell-code}
```{{r}}
#| label: tbl-fenced
#| tbl-cap: "Two tables"
#| tbl-subcap:
#|   - tab1
#|   - tab2

gt::gt(head(mtcars, 1))
gt::gt(head(mtcars, 1))
```
````

::: {.cell-output-display}

```{=html}
<div id="ocowdyeuyg" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
... gt output here
</div>
```

```{=html}
<div id="jmmgxvohco" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
... gt output here
</div>
```

:::
:::

But if we use, instead, this:

```{{r}}
#| label: tbl-fenced-2
#| tbl-cap: "Two tables"
#| tbl-subcap: 
#|   - tab1
#|   - tab2

gt::gt(head(mtcars, 1))
gt::gt(head(mtcars, 1))
```

```{r}
#| echo: false
#| label: tbl-fenced-2
#| tbl-cap: "Two tables"
#| tbl-subcap: 
#|   - tab1
#|   - tab2

gt::gt(head(mtcars, 1))
gt::gt(head(mtcars, 1))
```

(that is, emulating echo: fenced manually) then we get two divs with cell-output-display:

```{{r}}
#| label: tbl-fenced-2
#| tbl-cap: "Two tables"
#| tbl-subcap: 
#|   - tab1
#|   - tab2

gt::gt(head(mtcars, 1))
gt::gt(head(mtcars, 1))
```


::: {#tbl-fenced-2 .cell tbl-cap='Two tables' tbl-subcap='["tab1","tab2"]'}
::: {.cell-output-display}

```{=html}
<div id="zrbclxuqta" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
...
</div>
```

:::

::: {.cell-output-display}

```{=html}
<div id="jmduetdahk" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
...
</div>
```

:::
:::

[cderv]

I don't think it is a knitr issue directly. echo: fenced is not a native knitr option and only available in Quarto. We have a special option hook that will change the default knitr behavior

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

Lines 30 to 48 in 3db01ff

	# propagate echo: fenced to echo: true / fenced.echo
	opts_hooks[["echo"]] <- function(options) {
	if (identical(options[["echo"]], "fenced")) {
	options[["echo"]] <- TRUE
	options[["fenced.echo"]] <- TRUE
	} else if (isTRUE(options[["chunk.echo"]])) {
	options[["fenced.echo"]] <- FALSE
	}
	# fenced.echo implies hold (if another explicit override isn't there)
	if (isTRUE(options[["fenced.echo"]])) {
	if (identical(options[["fig.show"]], "asis")) {
	options[["fig.show"]] <- "hold"
	}
	if (identical(options[["results"]], "markup")) {
	options[["results"]] <- "hold"
	}
	}
	options
	}

So if you want to emulate it, you also need to set fig.show: hold and results: hold and this will explain the behavior

---
title: results
format: html
keep-md: true
---
 
```{{r}}
#| label: tbl-fenced-2
#| tbl-cap: "Two tables"
#| tbl-subcap: 
#|   - tab1
#|   - tab2
#| fig-show: hold
#| results: hold

gt::gt(head(mtcars, 1))
gt::gt(head(mtcars, 1))
```

```{r}
#| echo: false
#| label: tbl-fenced-2
#| tbl-cap: "Two tables"
#| tbl-subcap: 
#|   - tab1
#|   - tab2
#| fig-show: hold
#| results: hold

gt::gt(head(mtcars, 1))
gt::gt(head(mtcars, 1))
```

You'll get the same - only one cell output display (because of results: hold)

We have results: hold by default for this feature otherwise we would get the code block with option twice

With echo: fenced, I believe we want to have the whole code chunk not spit and all results after the code chunk. Hence the results: hold option.

So we need to "fix" our echo: fenced feature to output what we need for our filters, or handle this special case in our filters for subcaption and all.

What do you think ? Does it clarify or did I missed something else which make you think this is knitr issue ?

[cscheid]

What do you think ? Does it clarify or did I missed something else which make you think this is knitr issue ?

Thank you, I think you're exactly right. I apologize for missing the additional knitr context. I thought it was a bug because I saw the conversion from fenced: true to fenced.echo: true. I missed the additional hold context.

Unless this is a very small, trivial fix, I think this is a sufficiently niche situation. I'm comfortable with leaving this bug open for a bit, and telling people that echo: fenced only works with a single output for now. Do you agree?

[cderv]

Unless this is a very small, trivial fix, I think this is a sufficiently niche situation. I'm comfortable with leaving this bug open for a bit, and telling people that echo: fenced only works with a single output for now. Do you agree?

I don't see a trivial fix for now. I believe this is something to solve in Quarto where we need to align echo: fenced results with our filter that requires / expects one ::: {.cell-output-display} per table or figure for cross reference.

I need to see if we can tweak the hooks we have for knitr in Quarto to account for that. So for now I would say

echo: fenced does not work with cross referencing well when multi figures or tables. Workaround is to split in two chunk: One unevaluated and one evaluated with no echo.

Regarding niche situation that could be as I am surprised this was not found earlier.