Defaults files cannot specify order between filter and citeproc

[wenkokke]

You cannot specify the relative ordering of filters and citeproc in a defaults file.
For instance, with the following set up:

• defaults.yaml

  input-file: sample.md
  output-file: sample.html
  filters: ["${.}/include-files.lua"]
  citeproc: true

• sample.md

  ---
  bibliography: sample.bib
  ---
  ```{.include}
  chapters/chapter1.md
  ```

• sample.bib

  @book{BenjaminHornigold,
    author = {Benjamin Hornigold},
    title  = {A proof of Pirate ipsum},
    year   = {1680},
  }

• chapters/chapter1.md

  We all love @BenjaminHornigold's famous proof.
  But is it real?
  No. Probably not.

• include-files.lua from pandoc/lua-filters

The expected output of pandoc -d defaults.yaml would be something like:

<p>
  We all love
  <span class="citation" data-cites="BenjaminHornigold">Hornigold (1680)</span
  >’s famous proof. But is it real? No. Probably not.
</p>
<div id="refs" class="references csl-bib-body hanging-indent" role="list">
  <div id="ref-BenjaminHornigold" class="csl-entry" role="listitem">
    Hornigold, Benjamin. 1680. <em>A Proof of Pirate Ipsum</em>.
  </div>
</div>

However, the actual the result is:

<p>
  We all love
  <span class="citation" data-cites="BenjaminHornigold">@BenjaminHornigold</span
  >’s famous proof. But is it real? No. Probably not.
</p>

Pandoc version?
I'm using Pandoc 3.1.1 on macOS.

$ pandoc --version
pandoc 3.1.1
Features: +server +lua
Scripting engine: Lua 5.4
User data directory: /Users/keri/.local/share/pandoc
Copyright (C) 2006-2023 John MacFarlane. Web:  https://pandoc.org
This is free software; see the source for copying conditions. There is no
warranty, not even for merchantability or fitness for a particular purpose.

[wenkokke]

A zip archive with the files described above: bug-report.zip

[wenkokke]

The solution is to omit the citeproc: true key and define a Lua filter that runs citeproc...

-- File: citeproc.lua
function Pandoc (doc)
  return pandoc.utils.citeproc(doc)
end

...which you can then include in a specific position in your filters list:

# File: defaults.yaml
filters:
- "${.}/include-files.lua"
- "${.}/citeproc.lua"

[tarleb]

Thank you for this excellent report. The intended way to do this is the following (the type for the Lua filter can be omitted):

filters:
  - type: lua
    path: '${.}/include-files.lua'
  - type: citeproc

It seems that we need to make this more obvious in the manual, so I'll categorize this as a documentation bug.

[jgm]

Also the docs entry for filters still has an example with pandoc-citeproc, which may be confusing.

[wlupton]

Doesn't this also work?

filters:
  - '${.}/include-files.lua'
  - citeproc