This repo is an initial attempt at converting the OSCA introduction sub-book to quarto. A few minor changes (listed below) is enough to get 90% of the way there and produce a decent looking render. There are some broken parts here and there. Figuring out the last 10% and how to automate the changes I did here by hand for the other sub-books will be more difficult.

Changes implemented

Changes necessary to get the document to render:

• rename "s/Rmd$/qmd/" *.Rmd

• edit chunk options to match qmd format. This usually involves

  1. moving into the chunk
  2. adding #| to the start
  3. changing an = to a :
  4. possibly adding a space after the colon
  5. possibly changing TRUE/FALSE to true/false
  6. possibly changing the option name's format e.g. fig.cap -> fig-cap
  7. possibly remove BiocStyle-specific options for now e.g. fig.wide (which is NOT the same thing as fig.width)

• fix incompatible YAML e.g. link-citations: yes -> link-citations: true

• prefix the labels of figure-producing chunks with "fig-" so that quarto can easily reference them with @fig-sce

• remove title from yml of index.qmd

• delete lines with r link(...) cross-referencing magic for now

• copy DESCRIPTION from OSCA.intro so that rebook::openingDetails() can find the opening details like author info

• add {.unnumbered} to the first top level heading in index.qmd so that it doesn't get a chapter number

• ignore multi-book structure for now

Rendering & output

Clone this repo, cd into it, then run quarto render (or quarto preview if you've previously rendered). A rendered version can be seen here.

Future steps

• Reincorporate the deleted book / rebook magic
• Investigate using the quarto freeze option (sort of like chapter-level caching instead of knitr chunk-level caching) as an alternative way of managing the execution if book/rebook turns out to be non-viable.
• Utilize fancy quarto features like switchable themes