clean up + reorganize repo for Quarto

[nehamoopen]

refer to the python workshop as a basis: https://github.com/UtrechtUniversity/workshop-introduction-to-python

keep the following structure:

• a book directory to contain all the Quarto book files
• a docs directory to contain the rendered Quarto book files in HTML
• a slides directory to contain both the Rmd & HTML files for the slides
• eventually we can implement a GitHub Actions workflow to render the book, so the docs folder may become redundant - but let's make a start here.

test locally with a minimal example:

• make a branch of main and remove all the content except for index.qmd and one book chapter (perhaps project setup) and the corresponding slides...
• embedding slides could work with the following code chunk (example):

<iframe class="slide-deck" src="slides/index.html"></iframe>

[nehamoopen]

Figured it out! This code chunk works with Xaringan slides:

{r embed-xaringan-1, echo=FALSE}
xaringanExtra::embed_xaringan(url = "../slides/slides_introduction.html", ratio = "4:3")

[DorienHuijser]

It's pushed to the quarto-test branch now. A few notes:

• "book" directory is called "bookfiles" instead. I got a weird build error with the name "book"

Yet to do:

• [ ] the slides refer to the correct htmls but they still lost their formatting somehow. Needs to be figured out
• [ ] check internal links / crosslinks within the book. There were some errors that images could not be found. This is probably because the "chapters" are now moved to a subfolder
• [ ] Read in CSS file for styling
• [ ] Divide sections of chapters in separate qmd files
• [ ] Do something with renv? Do we want to keep it in the repo?
• [ ] Organize the separate files (now in to-be-deleted) and figure out how the exercises fit into the book

In all, work in progress, but the basics seem to work :)