PDF book: chapters are falsely grouped within a "part" (hierarchy wise)

[pat-s]

Checklist

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Issue

References listed at the same hierarchy level as a part are getting grouped within the last "Part" instead of appearing at the same level (in the Toc).

Reprex

1. quarto create-project mybook --type book
2. Adjust _quarto.yml with content below
3. quarto render --to pdf

project:
  type: book

book:
  title: "mybook"
  author: "Jane Doe"
  date: "6/6/2022"
  chapters:
    - index.qmd
    - part: intro.qmd
      chapters:
      - summary.qmd
    - references.qmd

bibliography: references.bib

format:
  pdf:
    documentclass: book

Metadata

quarto check

[✓] Checking Quarto installation......OK
      Version: 0.9.515
      Path: /Applications/quarto/bin

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.9.13
      Path: /opt/homebrew/opt/python@3.9/bin/python3.9
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

[✓] Checking R installation...........OK
      Version: 4.2.0
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Users/pjs/Library/R/arm64/4.2/library
        - /opt/R/4.2.0-arm64/Resources/site-library
        - /opt/R/4.2.0-arm64/Resources/library
      rmarkdown: 2.14

[✓] Checking Knitr engine render......OK

[jjallaire]

I wonder if there is a whitespace issue in your YAML? When I make this change I get this output:

Here is my _quarto.yml:

book:
  title: "mybook42"
  author: "Jane Doe"
  date: "6/6/2022"
  chapters:
    - index.qmd
    - part: intro.qmd
      chapters: 
        - summary.qmd
    - references.qmd

[pat-s]

Only applies to PDF, HTML output is fine.

[jjallaire]

This gets into some LaTeX that is beyond what I'm familiar with (it seems like by default w/o hacks that LaTeX does indeed slurp up subsequent chapters into previous parts as \part exists at the global level not in a hierarchy). Here is some related discussion:

https://tex.stackexchange.com/questions/355472/how-can-i-exclude-a-chapter-from-part-in-hyperref-bookmarks

@dragonstyle Could you have a look at this when its convenient to see if there is any special incantation we can make to exclude subsequent chapters from the part.

@pat-s If you want to hack on this as well just add keep-tex: true to the pdf format and then you can play with the generated LaTeX (the RStudio Compile PDF command or any LaTeX editor's similar command should be able to render the keep-tex output to PDF.

[pat-s]

Thanks JJ!

I assumed that I had to play around here a bit for an optimal solution.
The tex.stackexchange answer is great! Turns out all it needs it a

\bookmarksetup{startatroot}

above the \chapter{} call in question within the respective .qmd file. Will only be used in PDF outputs and ignored in HTML. Great!

[jjallaire]

Thanks! We'll see if we can make this automatic.

[pat-s]

Just found out that in a vanilla setup (e.g. CI/CD), the following is required in addition so that the bookmark pkg is getting installed

format:
  pdf:
    include-in-header:
      - text: |
          \usepackage{bookmark}

[dragonstyle]

Thanks for reporting and providing a great solution and diagnosis. This should be automatic for you now!

[pat-s]

Thanks.
In v0.9.531 I now see

Error running filter /Applications/quarto/share/filters/quarto-post/quarto-post.lua:
Block expected, got Attr
        while retrieving MetaValue
        while retrieving value
        while retrieving key-value pair
        while retrieving Map
        while retrieving MetaValue
        while retrieving value
        while retrieving key-value pair
        while retrieving Map
        while retrieving MetaValue
        while retrieving index 1
        while retrieving list
        while retrieving MetaValue
        while retrieving value
        while retrieving key-value pair
        while retrieving Map
        while retrieving Meta
        while retrieving function argument meta
        while retrieving arguments for function Pandoc
stack traceback:
        ...cations/quarto/share/filters/quarto-post/quarto-post.lua:1166: in function 'compileTemplate'
        ...cations/quarto/share/filters/quarto-post/quarto-post.lua:1770: in local 'fn'
        ...cations/quarto/share/filters/quarto-post/quarto-post.lua:1063: in function <...cations/quarto/share/filters/quarto-post/quarto-post.lua:1057>
make: *** [pdf] Error 1

My config is like

book:
  chapters:
    - part: part.qmd
      chapters:
        - chapter1.qmd
        - chapter3.qmd
    - references.qmd