Why is Quarto duplicating .bib files when rendering a manuscript project?

[arnaudgallou]

Description

I've a simple Quarto manuscript project with the following files:

manuscript
├── _quarto.yml
├── index.qmd
└── references
    ├── main.bib
    └── pkrt.bib

On rendering, Quarto adds the following folders and files:

manuscript
├── _manuscript
│   ├── _tex
│   │   ├── index.tex
│   │   └── references
│   │       ├── main.bib
│   │       └── pkrt.bib
│   └── index.pdf
.
.

As you can see, there's a copy of the .bib files below _tex/. Maybe I'm missing something but what's the purpose of duplicating these files?

Also, note that I was using keep-tex: false in _quarto.yml, so I was a bit surprised that Quarto kept the .tex file.

[mcanouil]

Could you share a small self-contained "working" (reproducible) example to work with, i.e., a complete Quarto document or a Git repository? The goal is to make it as easy as possible for us to recreate your problem so that we can fix it: please help us help you! Thanks.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code blocks (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.

[arnaudgallou]

Here's an example repo and the quarto check:

Quarto 1.5.56
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.2.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.5.56
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/arnaudgallou/Library/TinyTeX/bin/universal-darwin
      Version: 2024

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

[✓] Checking Python 3 installation....OK
      Version: 3.9.12
      Path: /usr/local/opt/[email protected]/bin/python3.9
      Jupyter: 5.7.1
      Kernels: python3

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

[✓] Checking R installation...........OK
      Version: 4.3.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library
      knitr: 1.45
      rmarkdown: 2.27

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

I edited my message when you posted yours. I'm using keep-tex: false so I presume there's a bug somewhere anyway.

[mcanouil]

keep-tex: false is the default.

[mcanouil]

I think you miss-understood the purpose of the Manuscript project type and what keep-tex is for.

keep-tex is for debugging, it allows to keep the LaTeX file produced by Quarto/Pandoc to investigate it when needed, thus it is not enabled by default.

Manuscript main goal is publishing articles. _tex is what you need to publish your document, so Quarto is making sure all the pieces are there. _manuscript directory only contains outputs.

[arnaudgallou]

I think here Quarto chose the more conservative approach which aopparently does not account for the framework used for the citations. This would be a feature request.

Alright. In the meantime I'll simply delete the duplicated file with:

post-render: rm _manuscript/_tex/references.bib

I'd be interested to know the exact rationale behind that feature if a maintainer reads this.

It seems keep-tex cannot be used inside Manuscript project but I don't know if that's intentional or a side effect of the copy of the LaTeX files to the output directory.

That certainly the latter, which would make sense to avoid an unnecessary duplication of file. That's what confused me though because I then thought that keep-tex was set to true by default. I usually have invalid options being underlined but that wasn't the case for keep-tex so I assumed it was bugged.

[mcanouil]

I'd be interested to know the exact rationale behind that feature if a maintainer reads this.

Clearly the rational is to allow users to use cite-method: biblatex (or using natbib) and still get a full usable output.
Now, it's not necessary to keep the bib file when the cite-method is citeproc, so as I said, this could be an enhancement.

[mcanouil]

That certainly the latter, which would make sense to avoid an unnecessary duplication of file. > That's what confused me though because I then thought that keep-tex was set to true by default. I usually have invalid options being underlined but that wasn't the case for keep-tex so I assumed it was bugged.

As I said keep-tex does not output to output location, it keeps the files in place next to the Quarto document that originates them.
See https://quarto.org/docs/output-formats/pdf-basics.html#latex-output.

will also create a .tex file alongside it that you can do subsequent processing on.

[mcanouil]

For reference:

• BIB files should be copied only when needed in Manuscript #10515