Jupyter-book: HTML comments ahead of raw HTML tag cause garbled HTML output

Created on 13 Nov 2020  路  4Comments  路  Source: executablebooks/jupyter-book

I am attempting to include in my book a Markdown file (.md) that has been generated from a RMarkdown file (.Rmd) by the R knitr package. I am using the R gt package to create formatted tables, and it inserts a HTML comment on the same line as it's HTML <style> tag, i.e. something like this:

<!--html_preserve--><style>
    .myclass {
        font-weight: bold;
        color: red
    }
</style>

<span class="myclass">Hello world</span><!--/html_preserve-->

The leading comment, <!--html_preserve-->, causes the final HTML file outputted by Jupyter Book to include HTML tags within the <style> section which cause it to no longer work. In this case you would get:

<!--html_preserve--><style>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>.myclass {
    font-weight: bold;
    color: red
}
</pre></div>
</div>
</style>

However, the rmarkdown::render() command in R will process this correctly. The comment looks like it is probably generated by the htmltools::htmlPreserve function:

htmlPreserve <- function(x) {
  x <- paste(x, collapse = "\n")
  if (nzchar(x))
    sprintf("<!--html_preserve-->%s<!--/html_preserve-->", x)
  else
    x
}

Since this package (hmltools) is potentially used by many other R packages the issue is likely going to be widespread when dealing with inputs generated by R.

Environment

  • Python Version: 3.7.5
  • Package versions or output of jupyter-book --version: 0.8.3
  • Operating System: MacOS
bug
Source
picture abielr

Most helpful comment

Thanks @mmcky, if I understand right what you are suggesting is to insert the {raw} block around the original HTML in the .md file generated by knitr. If so, probably the easier thing is just open the file and do a find and replace for those HTML comments, replacing them with an empty string and writing out the new file. Sphinx seems to have no issue parsing the resulting file.

Hi @choldgraf, to clarify, I believe this behavior is a function of the R htmltools package, not RStudio. This package is imported into a wide range of other R packages, such that many other R packages could potentially generate similar issues.

Note: I've only raised an issue with the htmltools project here so they are aware of this.

picture abielr on 22 Nov 2020
👍2

All 4 comments

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welcome[bot] picture welcome[bot] on 13 Nov 2020

hi @abielr maybe you could try using the raw directive to pass this html through to the HTML writer.

```{raw} html <html> ```

to ensure the html is unaltered as it is passed through to html.

mmcky picture mmcky on 16 Nov 2020

more generally, I wonder whether the markdown behavior that @abielr mentions at the top is CommonMark-compliant or if it something specific to RStudio. If it's the former, then we should find a way to support it, but if it isn't then I think @mmcky's suggestion is the way to go

choldgraf picture choldgraf on 16 Nov 2020
👍1

Thanks @mmcky, if I understand right what you are suggesting is to insert the {raw} block around the original HTML in the .md file generated by knitr. If so, probably the easier thing is just open the file and do a find and replace for those HTML comments, replacing them with an empty string and writing out the new file. Sphinx seems to have no issue parsing the resulting file.

Hi @choldgraf, to clarify, I believe this behavior is a function of the R htmltools package, not RStudio. This package is imported into a wide range of other R packages, such that many other R packages could potentially generate similar issues.

Note: I've only raised an issue with the htmltools project here so they are aware of this.

abielr picture abielr on 22 Nov 2020
👍2
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