Convert to jupyter-book

callum-jpg commented 2 years ago

Changes made:

Authors are now shown at the bottom of every page
ToC parts are defined in _toc.yml rather than inside .Rmd files themselves
Added 'Getting Started' to first part in ToC
Instead of subsections (define by ##, ### etc.) being shown in the left ToC pane, they are shown in the right pane upon selection of a particular chapter
- I think to have subsections shown in the left pane would require each subsection to be a distinct file
All files were converted from .Rmd to .md
- This was because the best way to replace the 'note' sections (eg in 03-setup-images.md was to use the jupyter-book {note} directive
  - However, this directive isn't available for .Rmd files converted with jupytex it seems, hence the conversion
Changing to .md alters the method for lists and linking to other pages, which have also been updated
Paragraphs of text added to one line
Can't find a replacement for appendix specific numbering
- eg A1, A2 etc.
gh-pages branch (and therefore the website) will be updated on any pushes to master branch by github actions

bethac07 commented 2 years ago

You can check out what it looks like on his fork here

bethac07 commented 2 years ago

@shntnu Ok to just go ahead and pull this?

bethac07 commented 2 years ago

Actually @callum-jpg looks like you forked off the next to last commit, we need to rebase this onto the last commit. If you need help, happy to have you throw time on my calendar!

shntnu commented 2 years ago

@shntnu Ok to just go ahead and pull this?

Yes, certainly!

Over to @callum-jpg and you https://github.com/cytomining/profiling-handbook/pull/66#issuecomment-1085916815

cytomining / profiling-handbook

Convert to jupyter-book #66