embed-resources returns a libs folder

[cscheid]

I think we're forwarding self-contained: true to pandoc's embed-resources: true but we're not passing embed-resources directly. This is a bug, right?

Discussed in #3436

^{Originally posted by dmacoritto November 23, 2022}
Hello everyone,

I am trying to switch from RMarkdown to Quarto and I have run into a challenge with the embed-resources YAML option. I would like to output an HTML document which is a standalone document with no dependencies.

Below is a screenshot of the YAML options for my document.

My issue is that, despite having included the "embed-resources: true" in the YAML, I get an external *_files folder that includes the required libraries to run the document (see below). My charts are indeed embedded in my HTML document but not my libraries. Is there a way to get a complete self-contained document with no dependencies to a *_files folder ?

Thank you very much for your help.

Darko

[cscheid]

I think we're forwarding self-contained: true to pandoc's embed-resources: true but we're not passing embed-resources directly. This is a bug, right?

This is incorrect. That MWE shows a _files folder with either option set. So it's something else going on.

[cscheid]

The interesting thing happening here is that _files is created, but is never referenced in the HTML. So I think what's happening here is that we're not appropriately cleaning up the generated HTML _files folder in case of embed-resources.

[cderv]

@cscheid I think we just don't clean when keep-*: true . And here keep-md: true

If you remove it in example it should work.

[cscheid]

Oh, that makes sense. Should be cleaned when embed-resources: true? It's not referred to anywhere in the .html file...

[cderv]

My understanding is that we clean always when embed-resources: true unless keep-md: true is asked.

quarto-cli/src/command/render/cleanup.ts

Lines 48 to 55 in 6917a2d

	// if we aren't keeping the markdown or text and we are instructed to
	// clean supporting files then do it
	if (
	!format.execute[kKeepMd] &&
	!format.render[kKeepTex] &&
	!format.render[kKeepTyp] &&
	supporting
	) {

When embed-resources: false we never clean.

If we do clean always when embed-resources: true, then I don't think there is a case where keep-md matters.

I believe this is important with plots rather than libs, because HTML dependencies don't end up in the markdown file. But if you do

---
title: "Test"
format:
  html:
    keep-md: true
    embed-resources: true
---

```{r}
plot(cars)
```

no sign of *_files in the HTML file because it is embeded, however, in the md you get

::: {.cell-output-display}
![](index_files/figure-html/unnamed-chunk-1-1.png){width=672}
:::

And so you may not want the *_files folder with the plot being deleted when keep-md: true is set, because the file will be missing.

I believe this is why it makes sense to have the cleaning depends on keep-md and not just embed-resources

[cscheid]

Ah yes, the intermediate files make total sense, of course. Closing this one as notabug!