Using Pandoc to expand citations (without Bibliographies) in Markdown

Not very surprisingly I think, given the Zettelkasten technique originated from an academic background a number of practitioners are from the same background and thus there is quite a lot of emphasis on citing the proper sources etc. I caught that bug as well if only in that I wanted a more reliable way to track articles I would use in my Zettelkasten than just Pinboard bookmarks. That lead me to Zotero and from there it was a one short fateful step to learning about pandoc. Pandoc is rightly the “Swiss army knife of document manipulation”, but so many times while I was desperately trying to bend it to my will I really really wished I had never made the decision to investigate pandoc.

Anyway, this post is about something I learnt to do in pandoc for what will eventually become the public face of my Zettelkasten notes - a way to generate Hugo compatible Markdown files with a full citation but no bibliography sections, all via Pandoc.

Here then in all it’s glory is the final invocation I came up with (minus some other bits I will blog about in another post)

pandoc X:\path\to\source.md -f markdown --standalone --wrap=preserve --atx-headers --filter pandoc-citeproc --metadata=suppress-bibliography -t markdown_mmd+yaml_metadata_block -o X:\path\to\content\posts\target.md --bibliography="X:\path\to\Zotero\bibliography.bib" --csl="X:\path\to\chicago-full.csl"

Explanation of the options is below:

  • X:\path\to\source.md: Self-explanatory. Input file.
  • -f markdown: This just specifies that the input file uses pandoc markdown syntax. Not entirely sure if this is required since file extension will be .md.
  • --standalone: Required to ensure that YAML headers appear in the output file. It’s unclear why “draft: false” in the YAML headers of the input file gets stripped in output.
  • --wrap=preserve: Ensures line-wraps in source file are preserved. Not sure if this is required for YAML headers, but definitely needed for TOML headers.
  • --atx-headers: Ensures output markdown file uses “#” for Markdown headers rather than the “–/==” syntax.
  • --filter pandoc-citeproc: Where it all started. Makes Pandoc process any references in source file that use the Pandoc “[@]” reference syntax.
  • The Biggie --metadata=suppress-bibliography: Additional metadata option (This option take precedence over metadata supplied through “–metadata-file” and metadata inside the source file) to prevent a bibliography section from being added at the end of each output file.
  • -t markdown_mmd+yaml_metadata_block: Generates a Multimarkdown output file (which supports footnotes) while also ensuring that YAML metadata blocks in source files are retained in the output.
  • -o X:\path\to\content\posts\target.md: Path to output directory. Output file name must be supplied by the calling script.
  • --bibliography="X:\path\to\Zotero\bibliography.bib": Path to Bibliography file generated from Zotero. I’m using the Better BibTex plugin in Zotero while outputting the bibliography file. Use quotes to fix any spaces in the Path.
  • --csl="X:\path\to\chicago-full.csl: Path to Citation Style Langugage (CSL) file. I’m using the “Chicago Manual of Style 17th edition (full note)” citation style here.

Alternative (Not Tested!)