Allow rendering of manuscript notebook files in other formats

[bethanyhgardner]

Description

I'm testing out manuscripts for a new paper, and overall I'm a fan! Ideally I would like to be able to render notebook files in PDF/docx, not just HTML. I think my ideal use case would be to have one or more of the notebook files be the manuscript supplement (generally includes more tables/figures etc), so it would be great to have the option of rendering in the same format(s) as the manuscript, since I'm going to have collaborators/journal submission portals that want a PDF, not an HTML file or link to site hosted on GitHub. Currently, adding additional formats to the YAML header of a notebook file or specifying an output format when rendering from command line don't have any effect.

[mcanouil]

I am not sure to follow.

Below is the default Manuscript project YAML file _quarto.yml.
As you can see there are several formats.

project:
  type: manuscript

manuscript:
  article: index.qmd

format:
  html:
    comments:
      hypothesis: true
  docx: default
  jats: default

  # (other formats)
  # pdf: default

execute:
  freeze: true

You can also use Quarto CLI directly: quarto render my-file.qmd --to docx.

Could you share some minimal example we can use to play around and check what you tried and did not work? It's possible, there is a bug, but without code we can't know.

[MitchellAcoustics]

Not sure if it's what @bethanyhgardner had in mind, but I'd love for the other formats to show up as a download option on the notebook page like they do on the main manuscript. As an example, my manuscript site here has the main page with docx, pdf, and MECA bundle links at the top and the notebook links on the side. But even though those notebooks have the same format settings, there's no link to download a pdf format.

Locally it works fine and I render them to PDF there to submit as supplementary material to the journal, but it would be nice to include it on the manuscript site as well.

[bethanyhgardner]

Yes, this is what I had in mind! For manuscript submissions, I need a PDF/DOCX of the manuscript and then all of the supplements combined. I don't know how complicated it is to add this feature, but if it's doable I think it would be a useful bridge between how manuscripts are traditionally edited/submitted/reviewed/published and publishing the code using quarto.

[MitchellAcoustics]

To my understanding, it shouldn't be difficult, since the notebook pages run through the renderer anyway to get to html. I haven't looked into it, but it seems like the manuscript render is actually just ignoring the yaml header for the notebooks which sets a pdf format. I'm not sure why this is the default, but I would certainly like it to also output whatever formats are set in the notebook header. For your use, it would then be simple to get the rendered PDFs and just combine them in Acrobat or some other PDF reader as the supplementary material.