Document that Footnote ids should be unique in Quarto Book when producing PDF, EPUB, and DOCX

[IULibScholComm]

Bug description

In the PDF, EPUB, and DOCX, the footnotes of my Chapter 6 (the last chapter with footnotes) of my Quarto book are treated as the footnotes of every other chapter. (I.e. the Chapter 6 footnotes, which run 1-9, replace footnotes 1-9 of the first five chapters.)

Steps to reproduce

# The Ratchet and the Red Queen {#sec-chap6}

May and Anderson concluded that the Red Queen could work, but only if parasites killed their hosts (i.e., they were maximally virulent).[^1]

[^1]: May and Anderson, for example, stated, "Our studies, in which the epidemiological details of the parasite–host interactions are treated more explicitly than in Hamilton's work, make this [the parasite] answer to the problem of sex [@ghiselin1974a; @williams1975a; @maynard1978a] less likely."

Expected behavior

The notes of Chapter 6 should appear only in Chapter 6 in the PDF, EPUB, and DOCX, not as the notes of all the chapters in those formats.

Actual behavior

The notes of Chapter 6 (1-9) appear as the notes (1-9) of every chapter in the PDF, EPUB, and DOCX versions and the notes (1-9) of Chapters 1-5 are erased; notes 10+ of Chapters 1-5, however, are correct.

Your environment

• IDE: VSCode: 1.85.0
• OS: Windows 10 Enterprise 22H2

Quarto check output

[>] Checking versions of quarto binary dependencies...
Pandoc version 3.1.9: OK
Dart Sass version 1.69.5: OK
Deno version 1.37.2: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
Version: 1.4.521
Path: C:\Program Files\Quarto\bin
CodePage: 1252 [>] Checking tools....................OK
TinyTeX: (not installed)
Chromium: (not installed) [>] Checking LaTeX....................OK
Using: Installation From Path
Path: C:\texlive\2023\bin\windows
Version: 2023 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK
Version: 3.11.4
Path: C:/Users/amazel/AppData/Local/Programs/Python/Python311/python.exe
Jupyter: 5.5.0
Kernels: ir, python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK
Version: 4.3.0
Path: C:/Users/amazel/AppData/Local/Programs/R/R-4.3.0
LibPaths:

• C:/Users/amazel/AppData/Local/R/win-library/4.3
• C:/Users/amazel/AppData/Local/Programs/R/R-4.3.0/library
• knitr: 1.43
• rmarkdown: 2.22 [>] Checking Knitr engine render......OK

[cderv]

This indeed can be reproduced and is related to scoping. We do not mention that in our doc though:
https://quarto.org/docs/authoring/footnotes-and-citations.html#footnotes

Identifier for footnotes must be unique accross all the document as I believe we will render using Pandoc on a single pass.

In your console log there should be a warning of this form

[WARNING] Duplicate note reference '1' at line 69 column 1

It is better to use specific ids for footnotes, or using inline footnote.

We may try to solve this in the future - Pandoc has a --file-scope feature but it could have some undesired side effect in Quarto book context.

@dragonstyle @cscheid can you confirm this is known limitation for single document project like PDF book, docx or EPUB document created from a Quarto Book Project ?

Or do we have already a processing (Lua or Post Process) that should have been taking care of making this right ?

[dragonstyle]

I am not aware of any post processing that we do to renumber footnotes (nor do I see any from a cursory look). Adding @jjallaire just to confirm that he doesn't recall implementing anything like that.

[jjallaire]

Yes, this is indeed the intended behavior (but should in fact be more clearly documented!). Note that when using the visual editor we automatically take care of scoped footnote numbering.

[IULibScholComm]

Thank you very much, all! Your troubleshooting and solution fixed my issue. I very much appreciate it!