Equation labels not properly handled when pandoc 2.0 is used with gitbook output

[dataopt]

Here is a minimal example for a minimal book with the following index.Rmd

---
title: "A Book"
author: "Frida Gomam"
site: bookdown::bookdown_site
documentclass: book
output:
  bookdown::gitbook:
    split_by: section
  bookdown::pdf_book: default
---

# Test labels {-}

Second equation label is not replaced with proper tag when using pandoc 2.0

\begin{equation}
x \in \mathbb{R} (\#eq:real)
\end{equation}
Hello
\begin{equation}
y \in \mathbb{Z} (\#eq:integer)
\end{equation}

Screenshot of the generated gitbook:

[yihui]

Could you add empty lines before and after Hello so that the equation can be in its own paragraph?

[dataopt]

Unfortunately, making the equation a paragraph results in too much space in the latex output. Below are screenshots of before and after putting empty lines around Hello.

[yihui]

The spacing issue is easier to solve. A quick google search: https://tex.stackexchange.com/q/224987/9128

[dataopt]

Thanks for the suggestion. Unfortunately, using setlength is more a hack than a solution to the problem since to get the desired spacing, I have to specify a negative value for abovedisplayskip. As the Rmd file contains perfectly valid syntax, the problem is probably a bug in bookdown.

[yihui]

I know exactly what the problem is in this case, and I also know to fix it. I just hope I don't have to touch it, for three reasons: (1) I often have too many other things to do; (2) there is a workaround (i.e. this issue does not really block you); (3) fixing bugs can introduce new problems.

[dataopt]

I now also know exactly what the problem is. I'm making a pull request to pandoc to add newlines around inlined display math. This should solve the problem. I hope the PR gets accepted.

EDIT: I discovered a simpler solution that requires no changes in bookdown and pandoc. It is to add the following option:
pandoc_args: "--wrap=preserve"

Should this option become a default?

[yihui]

It is great to know --wrap=preserve fixed the issue. It is probably a reasonable default.

[yihui]

I just made --wrap=preserve the default for Pandoc 2.0. Thanks a lot!

[github-actions]

This old thread has been automatically locked. If you think you have found something related to this, please open a new issue by following the issue guide (https://yihui.org/issue/), and link to this old issue if necessary.