quarto-dev / quarto-dev/quarto-cli

link-citations: true incompletely implemented in ipynb

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bug citations ipynb-format
Dominant language
JavaScript
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Description

Bug description

Using link-citations: true makes citations hyperlink to the corresponding bibliography entries. This works fine for html and pdf outputs. However, in ipynb the citation is a link, but the target is not defined.

Minimal example:

test.qmd

---
bibliography: references.bib
link-citations: true
---

Citation: a book @Author2006 and a paper @Author2020.

::: {#refs}
:::

Command:

quarto render temp.qmd --to ipynb

This results in a in notebook with a single markdown cell:

# 

Citation: a book Author1 ([2006](#ref-author2006)) and
a paper Author3 ([2020](#ref-author2020)).

Author1, X., and Z. Author2. 2006. “Some title.” In *Some journal*, 1: 100-115

Author3, A. 2020. “Another title.” *Another journal.*  2: 304-315

Expected result (I think), markdown cell:

# 

Citation: a book Author1 ([2006](#ref-author2006)) and
a paper Author3 ([2020](#ref-author2020)).

<span id="ref-author2006"></span>Author1, X., and Z. Author2. 2006. “Some title.” *Some journal*, 1: 100-115

<span id="ref-author2020"></span>Author3, A. 2020. “Another title.” *Another journal.*  2: 304-315

I am using VSCode to write qmd files, but render them on the command line (Mac OS 11.7), using quarto installed directly from the GitHub repo, commit id #82eae91a0 (which is why quarto --version gives 99.9.9)

Checklist
  • Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
  • Please format your issue so it is easier for us to read the bug report.
  • Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
  • Please document the operating system you're running. If on Linux, please provide the specific distribution.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the minimal test.qmd and references.bib example, then run quarto render temp.qmd --to ipynb and inspect the generated markdown cell. Compare the citation targets with the bibliography entries; done means each #ref-... citation target is defined in the notebook output.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
45/100

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