Bug description
This is related to #3340 and including citation keys in tables (manual ones and ones made with things like {gt})
{gt} recently added fmt_markdown(), which injects <span data-qmd="blah"></span> stuff around citations and cross references in HTML output, so that Quarto correctly processes the citations and cross references.
In #7451, Quarto added a similar feature for LaTeX output, adding a \QuartoMarkdownBase64{} command for processing/protecting citations and cross references.
\QuartoMarkdownBase64{} works for cross references, but not for citations.
Steps to reproduce
With this document:
---
title: "Citations in tables"
format:
html: default
pdf:
keep-tex: true
references:
- type: article-journal
id: Lovelace1842
author:
- family: Lovelace
given: Augusta Ada
issued:
date-parts:
- - 1842
title: >-
Sketch of the analytical engine invented by Charles Babbage, by LF Menabrea,
officer of the military engineers, with notes upon the memoir by the translator
title-short: Molecular structure of nucleic acids
container-title: Taylor’s Scientific Memoirs
volume: 3
page: 666-731
language: en-GB
---
$$
a^2 + b^2 = c^2
$${#eq-math}
```{r}
library(gt)
tibble::tribble(
~Thing, ~Citation,
1234, "@Lovelace1842",
5678, "@eq-math"
) |>
gt() |>
fmt_markdown(Citation)
```…when rendered to HTML, everything works great thanks to @rich-iannone's updates to fmt_markdown():
When rendered to PDF, though, neither of the citation keys are processed (likely because {gt} doesn't do anything with \QuartoMarkdownBase64{} yet?):
So I tried making the table manually with LaTeX:
```{=latex}
% QExvdmVsYWNlMTg0Mg==} is "@Lovelace1842" in base-64 encoding
% QGVxLW1hdGg= is "@eq-math" in base-64 encoding
\begin{tabular}{cc}
Thing & Citation \\
1234 & \QuartoMarkdownBase64{QExvdmVsYWNlMTg0Mg==} \\
5678 & \QuartoMarkdownBase64{QGVxLW1hdGg=} \\
\end{tabular}
```
Quarto emits this LaTeX:
% QExvdmVsYWNlMTg0Mg==} is "@Lovelace1842" in base-64 encoding
% QGVxLW1hdGg= is "@eq-math" in base-64 encoding
\begin{tabular}{cc}
Thing & Citation \\
1234 & @Lovelace1842 \\
5678 & Equation~\ref{eq-math} \\
\end{tabular}…and this PDF:
The @Lovelace1842 citation key is unprocessed, while the @eq-math cross reference is converted to the correct LaTeX.
Expected behavior
I was hoping that the @Lovelace1842 citation key in the table would get converted to a bibliographic reference and be processed by citeproc, but it looks like citation processing is happening at a different stage in the Quarto pipeline?
Actual behavior
The @Lovelace1842 citation key is unprocessed, while the @eq-math cross reference is converted to the correct LaTeX.
Your environment
- IDE: RStudio 2024.04.0-daily+581
- OS: macOS Sonoma 14.4.1
Quarto check output
Quarto 1.5.27
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.1.11: OK
Dart Sass version 1.70.0: OK
Deno version 1.41.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.5.27
Path: /Applications/quarto/bin
[✓] Checking tools....................OK
TinyTeX: (external install)
Chromium: (not installed)
[✓] Checking LaTeX....................OK
Using: TinyTex
Path: /Users/andrew/Library/TinyTeX/bin/universal-darwin
Version: 2023
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.11.5
Path: /opt/homebrew/opt/python@3.11/bin/python3.11
Jupyter: 5.3.0
Kernels: python3
[✓] Checking Jupyter engine render....OK
[✓] Checking R installation...........OK
Version: 4.3.2
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
knitr: 1.45
rmarkdown: 2.25
[✓] Checking Knitr engine render......OK
❯ quarto check > ~/Desktop/bloop.txt
Quarto 1.5.27
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.1.11: OK
Dart Sass version 1.70.0: OK
Deno version 1.41.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.5.27
Path: /Applications/quarto/bin
[✓] Checking tools....................OK
TinyTeX: (external install)
Chromium: (not installed)
[✓] Checking LaTeX....................OK
Using: TinyTex
Path: /Users/andrew/Library/TinyTeX/bin/universal-darwin
Version: 2023
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.11.5
Path: /opt/homebrew/opt/python@3.11/bin/python3.11
Jupyter: 5.3.0
Kernels: python3
[✓] Checking Jupyter engine render....OK
[✓] Checking R installation...........OK
Version: 4.3.2
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
knitr: 1.45
rmarkdown: 2.25
[✓] Checking Knitr engine render......OK
Bug description
This is related to #3340 and including citation keys in tables (manual ones and ones made with things like {gt})
{gt} recently added
fmt_markdown(), which injects<span data-qmd="blah"></span>stuff around citations and cross references in HTML output, so that Quarto correctly processes the citations and cross references.In #7451, Quarto added a similar feature for LaTeX output, adding a
\QuartoMarkdownBase64{}command for processing/protecting citations and cross references.\QuartoMarkdownBase64{}works for cross references, but not for citations.Steps to reproduce
With this document:
…when rendered to HTML, everything works great thanks to @rich-iannone's updates to
fmt_markdown():When rendered to PDF, though, neither of the citation keys are processed (likely because {gt} doesn't do anything with
\QuartoMarkdownBase64{}yet?):So I tried making the table manually with LaTeX:
Quarto emits this LaTeX:
…and this PDF:
The
@Lovelace1842citation key is unprocessed, while the@eq-mathcross reference is converted to the correct LaTeX.Expected behavior
I was hoping that the
@Lovelace1842citation key in the table would get converted to a bibliographic reference and be processed by citeproc, but it looks like citation processing is happening at a different stage in the Quarto pipeline?Actual behavior
The
@Lovelace1842citation key is unprocessed, while the@eq-mathcross reference is converted to the correct LaTeX.Your environment
Quarto check output