docs: add limitations related to downlit

[mcanouil]

This PR adds limitations notes with the use of downlit via code-link: true.

Fixes #6199

[cderv]

Thanks.

I added some comments because I don't think that the addition really clarifies the situations.

Basically the current limitation due to downlit procesing is that
code-link: true has no effect when code-line-numbers or code-annotations features are used.

But both code-line-numbers and code-annotations features works well. Do you have an example where they don't work ?

This is a limitation for code-linking features which uses R packages and this is for now added to
https://quarto.org/docs/output-formats/html-code.html#code-linking

We could also add mention of code-annotations impact in there IMO.

[mcanouil]

As suggested, I made a companion PR:

• docs: downlit (code-link) limitations quarto-web#793

[cderv]

Don't know if you tried but slight side effect.... setting code-annotations: false does also prevent code linking it seems if the annotations are present in the chunk.

Basically, if one wants code linking in a cells, it should not contains any annotation using # <1> syntax.

I don't know why code-annotations: false make code linking not work because I would have thought the HTML would not be changed in that case. (which is the underlying issue with downlit)

I would say that the advice would be

• For code-link to work properly, code-line-numbers should not be activated on the cell and No code annotations syntax added.

But again, probably a bug that code-annotations still do something... unless this is the # <1> syntax that makes downlit fails... 🤔

Are you observing like me ?

[mcanouil]

FYI, I made a repository to check various combinations (but only when defining the option in the yaml frontmatter): https://github.com/mcanouil/quarto--code-link--code-annotations

[mcanouil]

After checking, code linking is not preventing by the use of code annotations, it is the other way around as I initially described, i.e., code annotation does not work properly when code-linking: true.

[mcanouil]

FYI, for code-line-numbers, see https://github.com/mcanouil/quarto--code-link--code-line-numbers.
This indeed prevents code linking.

[cderv]

Really weird - I can indeed reproduce and see that code links works in your example, but I maintain that in my previous example it still does not. Did you try ? #6297 (comment)

Simplified example

---
format: 
  html:
    code-link: true
    code-annotations: true
---

```r
stats::rnorm(1) # <1>
stats::rnorm(2) # <2>
```

1. Test 1
2. Test 2 

So we should definitely try every possible case and check how that works - for now I don't understand why this would work in the above and not in your case. Looking into it.

Thanks for the repo by the way !

[cderv]

Sorry it has been a while. Do we need to check more cases for theses options before merging ?

[mcanouil]

I have to say, indeed it's been a while and I did not update https://github.com/mcanouil/quarto--code-link--code-line-numbers with your last example.
I'll have to add those tests and check the results.