SheffieldR : Quarto for Slides

Neil Shephard

n.shephard@sheffield.ac.uk

RSE, University of Sheffield

Scan This!

View Slides : ns-rse.github.io/SheffieldR-quarto-for-slides

You can go the URL ns-rse.github.io/SheffieldR-quarto-for-slides to view the slides or if you use a browser on your phone which is synced with your desktop then you can scan this QR code and send it to your laptops browser and it will take you to these slides.

Overview

• Background
• Prerequisites
• Using a template
  • Necessary Changes
  • Initial Publish
• Markdown (briefly)
• Modifying slides
• Publishing

I thought it might be useful to cover a bit of history with regards to the philosophy that underpins Quarto, then go over a live example of how to use a template to make RevealJS Slides that are hosted on GitHub Pages and edit the Markdown.

This isn’t an exposition of Markdown and writing Quarto documents, its more focused on working with and publishing slides on GitHub.

Literate Programming - Origins

a computer program is given as an explanation of how it works in a natural language, such as English, interspersed (embedded) with snippets of macros and traditional source code, from which compilable source code can be generated.¹

Literate Programming - Donald Knuth

Quarto and other languages like it such as RMarkdown and Org-mode are literate programming languages which may be an unfamiliar term so I’ve borrowed the definition from Wikipedia.

The idea was originally proposed and developed the computer scientist Donald Knuth, and he literally wrote the book on it.

1. Wikipedia - Literate programming

Literate Programming - Better Programmes

My programs are not only explained better than ever before; they also are better programs, because the new methodology encourages me to do a better job.¹

Literate Programming - Donald Knuth

Whilst originating in computer science the principle has seen wide spread adoption in data science because it encourages reproducible research and facilitates open access to research.

As Knuth found when he adopted the practice it improved the quality of the programmes he wrote and I’ve found the same is true when writing documents myself since adopting the practice over 20 years ago.

1. Knuth (1984)

Background - Pedigree

• WEB (Knuth & Levy (2001))
• noweb
• S (Becker, Chambers & Wilks (1988))
• Sweave (Leisch F. (2002a); Leisch F (2002b); Leisch F (2003))
• RMarkdown (R Markdown: The Definitive Guide)

• 🎉 Quarto 🎉

Quarto has a long pedigree and is the latest form of literate programming. Knuths WEB language was followed by a number of variants most of which worked with his document preparation system TeX. One of these dialects was noweb and noweb underpinned an early integration of Tex/LaTeX and S code (S being the original language specification by Becker, Chambers and Wilks which R is an implementation of) this was developed by Freidrich Liesch who wrote and maintained the Sweave package.

More recently with the rise in popularity of Markdown, a simple form of markup language and the increase in popularity of R saw the development of RMarkdown which some of you might be familiar with.

The last year or two have seen the development of and release of Quarto which is the next iteration and allows embedding of not just R code within the document but other languages such as Python, Julia and Observable a data analysis and visualisation language in JavaScript.

Part of the flexibility of Quarto is that its underpinned by Pandoc which is a powerful tool for converting documents between different markup languages, including PDF and HTML.

Pre-requisites

Need a few things to get going…

• Git
• GitHub account (ideally academic @<somewhere>.ac.uk).
• RStudio configured with Git¹ (or similar e.g. Emacs/ESS/Magit or VSCode).
• Jupyter if using Python.
• Quarto installed.

Ok, now that I’ve covered some of the background going to move on and hopefully demonstrate how to use Quarto to write RevealJS slides that are hosted on GitHub and can be viewed in a web-browser. This has a number of advantages as you’ll never have to worry about getting your slides to meeting organisers, you just need a working internet connection which these days is fairly common. As a consequence you can keep on working on your slides right up to the last minute (as long as you remember to publish the changes!).

There are however a few pre-requisities for using this system. You need Git installed and a academic email address I’d recommend signing up with that, you get a few more features that are usually reserved for paying customers.

You also need a development environment which will help make some of the tasks of editing files and working with Git easier.

If you’re not already set up with one I’d recommend RStudio which I’m going using today.

There is a really useful site from Jenny Bryan on how to setup and configure RStudio and Git which I would recommend.

There are of course alternatives, personally I use Emacs with Emacs Speaks Statistics and Magit, another popular choice is VSCode, but what you use is somewhat secondary, what I hope to convey to you is the essence of the workflow and the principles of working in this manner.

Perhaps most importantly a willingness to learn comes in pretty handy, if you’re new to this approach it will seem frustrating to start with, but persevere, it gets easier and is a lot faster than copying and pasting figures and tables into Word documents and then tweaking them or replacing them when data changes. As Donald Knuth said, its fun!

1. Let’s Git started | Happy Git and GitHub for the useR

Quarto RevealJS Template

Quarto RevealJS Template includes…

• Sample slides with many examples.
• GitHub Workflowto publish pages.
• Instructions on usage.
• Thanks to David Wilby and Alex Coleman.

github.com/ns-rse/quarto-revealjs-template

To make it simple to use this workflow there is a Quarto RevealJS template in my GitHub repository that can be used.

It uses a GitHub Workflow and the README.md on the front page has instructions on usage and I’m hoping to take you through this process today.

I have to say this isn’t all my own work, I used a workflow my colleague David Wilby originally setup in for slides I prepared for a talk I was invited to give in Leeds on using pre-commit. The person who invited me, Alex Coleman, liked the setup and used my slides as a basis for making a Template and I’ve then borrowed that back and extended it to its current state.

Using Quarto RevealJS Template

• Go to github.com/ns-rse/quarto-revealjs-template
• Make a copy to your account using the “Use This Template” button.
• Give repository a unique name.

Cloning the template

The first step to using this template is to make a copy to your GitHub account.

To do this go to the repository and find the Use This Template which is on the top right in green, click on it and you’ll be prompted to give your repository a new and unique name. You can use anything you want as long as you don’t already have a repository with that name in your GitHub account.

Configuring Repository

• Settings > Actions > General > Workflow Permissions > Read and write

A key change after cloning the repository is that you need to change the permissions so that the site will be published automatically when you push changes to GitHub.

I’ll explain more about how this works bit but because this is important and you’re in GitHub after using the template I find it good practice to make the change now so I don’t forget to do it later and then end up scratching my head as to why the slides haven’t been published.

So you go to Settings tab along the top, then in the menu on the left selection Actions > General. Scroll down and you can change the Workflow Permissions to Read and Write permissions which allows [GitHub Workflows])(https://docs.github.com/en/actions/using-workflows) to read and write to branches.

Cloning - URL

• Code button

Getting repository URL for cloning

Now that you have copied the template to your account and have a repository of your own you will want to get a copy of the files locally on your own computer. In Git parlance this is called cloning and on GitHub the green button at the top of the front page of the repository allows you to copy links to clone a repository.

Whether use use https or ssh depends on how you’ve setup RStudio but the safest option is to use https (although long term I would recommend configuring and using SSH keys as they are faster and easier).

RStudio Cloning - New Project

• File > New Project > Version Control > Git.¹

New Project

You now need to start a new Project in RStudio, from the File menu select New Project and the following dialog will appear, select Version Control.

1. Let’s Git started | Happy Git and GitHub for the useR

RStudio Cloning - Version Control

• File > New Project > Version Control > Git.¹

New Project

…and you progress to the next dialog. We are cloning a Git repository rather than Subversion so select Git.

1. Let’s Git started | Happy Git and GitHub for the useR

RStudio Cloning - Git

• File > New Project > Version Control > Git.¹

New Project

You now need to use the URL you copied from GitHub and paste it into the Repository URL field, you should give a Project directory name and typically this would be the same name that you gave your repository when you used the template (you can copy and paste the last bit of the URL, removing the .git if you want).

The last field required is where to create the project and clone the repository to, this will depend on where you keep your files.

1. Let’s Git started | Happy Git and GitHub for the useR

Restore renv

• renv used for required packages.
• Required packages in renv.lock.

# Bootstrapping renv 1.0.3 ---------------------------------------------------
- Downloading renv ... OK
- Installing renv  ... OK

- Project '~/work/git/hub/slackline/quarto-live-demo' loaded. [renv 1.0.3]
- One or more packages recorded in the lockfile are not installed.
- Use `renv::status()` for more details.
> renv::restore()
The following package(s) will be updated:

# CRAN -----------------------------------------------------------------------
- lattice        [0.22-4 -> 0.21-8]
- base64enc      [* -> 0.1-3]
- bslib          [* -> 0.5.1]
- cachem         [* -> 1.0.8]
- cli            [* -> 3.6.1]
- colorspace     [* -> 2.1-0]
- ellipsis       [* -> 0.3.2]
- evaluate       [* -> 0.21]
- fansi          [* -> 1.0.4]
- farver         [* -> 2.1.1]
- fastmap        [* -> 1.1.1]
- fontawesome    [* -> 0.5.2]
- ggplot2        [* -> 3.4.3]
- glue           [* -> 1.6.2]
- gtable         [* -> 0.3.4]
- highr          [* -> 0.10]
- htmltools      [* -> 0.5.6]
- isoband        [* -> 0.2.7]
- jquerylib      [* -> 0.1.4]
- labeling       [* -> 0.4.3]
- lifecycle      [* -> 1.0.3]
- magrittr       [* -> 2.0.3]
- memoise        [* -> 2.0.1]
- mime           [* -> 0.12]
- munsell        [* -> 0.5.0]
- pillar         [* -> 1.9.0]
- pkgconfig      [* -> 2.0.3]
- R6             [* -> 2.5.1]
- rappdirs       [* -> 0.3.3]
- RColorBrewer   [* -> 1.1-3]
- rmarkdown      [* -> 2.25]
- sass           [* -> 0.4.7]
- scales         [* -> 1.2.1]
- stringi        [* -> 1.7.12]
- stringr        [* -> 1.5.0]
- tibble         [* -> 3.2.1]
- tinytex        [* -> 0.46]
- utf8           [* -> 1.2.3]
- viridisLite    [* -> 0.4.2]
- withr          [* -> 2.5.0]
- yaml           [* -> 2.3.7]

# RSPM -----------------------------------------------------------------------
- digest         [* -> 0.6.33]
- fs             [* -> 1.6.3]
- jsonlite       [* -> 1.8.7]
- knitr          [* -> 1.44]
- rlang          [* -> 1.1.1]
- vctrs          [* -> 0.6.3]
- xfun           [* -> 0.40]

Do you want to proceed? [Y/n]: y

# Installing packages --------------------------------------------------------
- Installing lattice ...                        OK [linked from cache]
- Installing R6 ...                             OK [linked from cache]
- Installing RColorBrewer ...                   OK [linked from cache]
- Installing base64enc ...                      OK [linked from cache]
- Installing rlang ...                          OK [linked from cache]
- Installing fastmap ...                        OK [linked from cache]
- Installing cachem ...                         OK [linked from cache]
- Installing digest ...                         OK [linked from cache]
- Installing ellipsis ...                       OK [linked from cache]
- Installing htmltools ...                      OK [linked from cache]
- Installing jquerylib ...                      OK [linked from cache]
- Installing jsonlite ...                       OK [linked from cache]
- Installing memoise ...                        OK [linked from cache]
- Installing mime ...                           OK [linked from cache]
- Installing fs ...                             OK [linked from cache]
- Installing rappdirs ...                       OK [linked from cache]
- Installing sass ...                           OK [linked from cache]
- Installing bslib ...                          OK [linked from cache]
- Installing cli ...                            OK [linked from cache]
- Installing colorspace ...                     OK [linked from cache]
- Installing evaluate ...                       OK [linked from cache]
- Installing fansi ...                          OK [linked from cache]
- Installing farver ...                         OK [linked from cache]
- Installing fontawesome ...                    OK [linked from cache]
- Installing glue ...                           OK [linked from cache]
- Installing lifecycle ...                      OK [linked from cache]
- Installing gtable ...                         OK [linked from cache]
- Installing isoband ...                        OK [linked from cache]
- Installing labeling ...                       OK [linked from cache]
- Installing munsell ...                        OK [linked from cache]
- Installing viridisLite ...                    OK [linked from cache]
- Installing scales ...                         OK [linked from cache]
- Installing magrittr ...                       OK [linked from cache]
- Installing utf8 ...                           OK [linked from cache]
- Installing vctrs ...                          OK [linked from cache]
- Installing pillar ...                         OK [linked from cache]
- Installing pkgconfig ...                      OK [linked from cache]
- Installing tibble ...                         OK [linked from cache]
- Installing withr ...                          OK [linked from cache]
- Installing ggplot2 ...                        OK [linked from cache]
- Installing xfun ...                           OK [linked from cache]
- Installing highr ...                          OK [linked from cache]
- Installing yaml ...                           OK [linked from cache]
- Installing knitr ...                          OK [linked from cache]
- Installing stringi ...                        OK [linked from cache]
- Installing stringr ...                        OK [linked from cache]
- Installing tinytex ...                        OK [linked from cache]
- Installing rmarkdown ...                      OK [linked from cache]
>

As this is an R user group its pertinent to focus on using Quarto with R, even though it supports embedding code in other languages such as Python, Julia and Obesrvable, but the principles transcend the language as most rely heavily on packages and for work to be reproducible you need to install the packages that are used.

In R this is done using the renv package which creates a renv.lock detailing the installed packages along with a .Rprofile which runs a script renv/activate.R that together restore environments on loading a new project. However, your system needs to install the required packages within the directory initially and this is done using renv::restore().

This may take a little while depending on your system and its possible, if you use Windows and have an old, outdated version of R installed that it won’t install at all since Microsoft stopped providing all package version for all versions of R on their MRAN archive. If this happens try updating to the latest version of R and repeating this step.

Perhaps this is a natural point to have a short pause and ask if there are any questions?

If there aren’t any then we can carry on and instal themes and extensions locally.

Install Themes and Extensions

• Themes and extensions need installing

quarto install --no-prompt extension jmbuhr/quarto-qrcode
quarto install --no-prompt extension grantmcdermott/quarto-revealjs-clean
quarto install --no-prompt extension ArthurData/quarto-confetti

These slides use some extensions for generating QR codes and making Confetti and a custom theme. I’ll explain more about extensions and themes in a bit but before you can proceed you need to install the themes on your computer.

Configuration : _quarto.yaml

• Define project type (website)
• Set title, site-url and description

Before

project:
  type: website

website:
  title: "<TITLE>"
  site-url: https://<YOUR_GITHUB_USERNAME>.github.io/<NAME_OF_REPOSITORY>
  description: "Using Quarto to make slides"

After

project:
  type: website

website:
  title: "SheffieldR - Live Demo!"
  site-url: https://slackline.github.io/quarto-live-demo
  description: "A Live Demo of How to use Quarto RevealJS Template"

You will want to configure the slides to your own taste or preferences.

This is done via two files the first is _quarto.yaml file which allows you to define the project type, which in this case is a website and you can set the title, site-url and description.

index.qmd YAML Header

---
title: "SheffieldR - Live Demo!"
author:
  - name: Neil Shephard
    orcid: 0000-0001-8301-6857
    email: n.shephard@sheffield.ac.uk
    affiliations: RSE, University of Sheffield
from: markdown+emoji
format:
  clean-revealjs:
    incremental: false
    scrollable: true
    slide-number: true
    show-slide-number: speaker
    auto-stretch: false
    chalkboard: true
    # embed-resources: true
    # standalone: true
revealjs-plugins:
  - confetti
footer: "**Slides** : [**slackline.github.io/quarto-live-demo**](https://slackline.github.io/quarto-live-demo)"
project:
  preview:
    port: 7864
    host: localhost
    watch-inputs: true

---

The other file that settings reside in is the YAML header of index.qmd such as the author details, footer, what extensions or plugins are used and so forth. So open up the `index.qmd** and start editing this header.

Put your name, your ORCiD number, email address and affiliation. The rest you can mostly leave in place but you will probably want to change the footer as its useful for the audience to see the URL where they can view the slides at all times.

You also use this file to define other common slide properties such as the theme, whether bullet points are to appear incrementally, whether to include the chalkboard feature which is enabled for these slides and introduces a button here to bring up a chalk board which you can write on. You also define common footers in this file.

NB I have two git accounts with different SSH keys so need to tweak my .git/config to make sure the correct key is used.

[core]
    sshCommand = ssh -i ~/.ssh/id_ed25519 -F /dev/null

Initial Publish

❱ quarto publish
? Provider:
  Quarto Pub
❯ GitHub Pages
  Posit Connect
  Netlify
  Confluence

❱ quarto publish
? Provider: › GitHub Pages
? Publish site to https://slackline.github.io/quarto-live-demo using gh-pages? (Y/n) › Yes
Saved working directory and index state WIP on main: 822f892 Initial commit
Switched to a new branch 'gh-pages'
[gh-pages (root-commit) 02fbb7b] Initializing gh-pages branch
remote:
remote: Create a pull request for 'gh-pages' on GitHub by visiting:
remote:      https://github.com/slackline/quarto-live-demo/pull/new/gh-pages
remote:
To github.com:slackline/quarto-live-demo.git
 * [new branch]      HEAD -> gh-pages
Your branch is up to date with 'origin/main'.
Switched to branch 'main'
On branch main
Your branch is up to date with 'origin/main'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
        modified:   .gitignore
        modified:   _quarto.yml
        modified:   index.qmd

Untracked files:
  (use "git add <file>..." to include in what will be committed)
        quarto-live-demo.Rproj

no changes added to commit (use "git add" and/or "git commit -a")
From github.com:slackline/quarto-live-demo
 * branch            gh-pages   -> FETCH_HEAD
Rendering for publish:



processing file: index.qmd
1/5
2/5 [fig-airquality]
3/5
4/5 [fig-airquality2]
5/5
output file: index.knit.md

pandoc
  to: revealjs
  from: markdown+emoji
  output-file: index.html
  standalone: true
  title-prefix: SheffieldR - Live Demo!
  wrap: none
  default-image-extension: png
  html-math-method:
    method: mathjax
    url: >-
      https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS_HTML-full
  slide-level: 2
  incremental: false

metadata
  link-citations: true
  width: 1050
  height: 700
  margin: 0.1
  center: false
  navigationMode: linear
  controlsLayout: edges
  controlsTutorial: false
  hash: true
  history: true
  hashOneBasedIndex: false
  fragmentInURL: false
  transition: none
  backgroundTransition: none
  pdfSeparateFragments: false
  lang: en
  auto-stretch: false
  theme:
    - default
    - _extensions/grantmcdermott/clean/clean.scss
  menu:
    side: left
  slideNumber: true
  date-format: long
  revealjs-plugins:
    - confetti
  title: 'Quarto Live Demo! :tada:'
  author:
    - name: Neil Shephard
      orcid: 0000-0001-8301-6857
      email: n.shephard@sheffield.ac.uk
      affiliations: 'RSE, University of Sheffield'
  footer: '**Slides** : [**slackline.github.io/quarto-live-demo**](https://github-username.github.io/<repository>)'
  showSlideNumber: speaker
  chalkboard: true

branch 'gh-pages' set up to track 'origin/gh-pages'.
HEAD is now at 02fbb7b Initializing gh-pages branch
Preparing worktree (resetting branch 'gh-pages'; was at 02fbb7b)
fatal: pathspec '.' did not match any files
[gh-pages d22f205] Built site for gh-pages
 125 files changed, 15420 insertions(+)
 create mode 100644 .nojekyll
 create mode 100644 img/OSC_Sheffield.png
 create mode 100644 index.html
 create mode 100644 index_files/figure-revealjs/fig-airquality2-1.png
 create mode 100644 robots.txt
 create mode 100644 search.json
 create mode 100644 site_libs/clipboard/clipboard.min.js
 create mode 100644 site_libs/quarto-contrib/qrcodejs-v1.0.0/qrcode.js
 create mode 100644 site_libs/quarto-html/light-border.css
 create mode 100644 site_libs/quarto-html/popper.min.js
 create mode 100644 site_libs/quarto-html/quarto-html.min.css
 create mode 100644 site_libs/quarto-html/quarto-syntax-highlighting.css
 create mode 100644 site_libs/quarto-html/tabby.min.js
 create mode 100644 site_libs/quarto-html/tippy.css
 create mode 100644 site_libs/quarto-html/tippy.umd.min.js
 create mode 100644 site_libs/revealjs/dist/reset.css
 create mode 100644 site_libs/revealjs/dist/reveal.css
 create mode 100644 site_libs/revealjs/dist/reveal.esm.js
 create mode 100644 site_libs/revealjs/dist/reveal.esm.js.map
 create mode 100644 site_libs/revealjs/dist/reveal.js
 create mode 100644 site_libs/revealjs/dist/reveal.js.map
 create mode 100644 site_libs/revealjs/dist/theme/fonts/league-gothic/LICENSE
 create mode 100644 site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.css
 create mode 100755 site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.eot
 create mode 100755 site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.ttf
 create mode 100755 site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.woff
 create mode 100644 site_libs/revealjs/dist/theme/fonts/source-sans-pro/LICENSE
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.eot
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.ttf
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.woff
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.eot
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.ttf
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.woff
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.eot
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.ttf
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.woff
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.eot
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.ttf
 create mode 100755 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff
 create mode 100644 site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro.css
 create mode 100644 site_libs/revealjs/dist/theme/quarto.css
 create mode 100644 site_libs/revealjs/plugin/highlight/highlight.esm.js
 create mode 100644 site_libs/revealjs/plugin/highlight/highlight.js
 create mode 100644 site_libs/revealjs/plugin/highlight/monokai.css
 create mode 100644 site_libs/revealjs/plugin/highlight/plugin.js
 create mode 100644 site_libs/revealjs/plugin/highlight/zenburn.css
 create mode 100644 site_libs/revealjs/plugin/markdown/markdown.esm.js
 create mode 100644 site_libs/revealjs/plugin/markdown/markdown.js
 create mode 100755 site_libs/revealjs/plugin/markdown/plugin.js
 create mode 100755 site_libs/revealjs/plugin/math/katex.js
 create mode 100644 site_libs/revealjs/plugin/math/math.esm.js
 create mode 100644 site_libs/revealjs/plugin/math/math.js
 create mode 100644 site_libs/revealjs/plugin/math/mathjax2.js
 create mode 100644 site_libs/revealjs/plugin/math/mathjax3.js
 create mode 100644 site_libs/revealjs/plugin/math/plugin.js
 create mode 100644 site_libs/revealjs/plugin/notes/notes.esm.js
 create mode 100644 site_libs/revealjs/plugin/notes/notes.js
 create mode 100644 site_libs/revealjs/plugin/notes/plugin.js
 create mode 100644 site_libs/revealjs/plugin/notes/speaker-view.html
 create mode 100644 site_libs/revealjs/plugin/pdf-export/pdfexport.js
 create mode 100644 site_libs/revealjs/plugin/pdf-export/plugin.yml
 create mode 100644 site_libs/revealjs/plugin/quarto-line-highlight/line-highlight.css
 create mode 100644 site_libs/revealjs/plugin/quarto-line-highlight/line-highlight.js
 create mode 100644 site_libs/revealjs/plugin/quarto-line-highlight/plugin.yml
 create mode 100644 site_libs/revealjs/plugin/quarto-support/footer.css
 create mode 100644 site_libs/revealjs/plugin/quarto-support/plugin.yml
 create mode 100644 site_libs/revealjs/plugin/quarto-support/support.js
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/README.md
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/LICENSE.txt
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/css/all.css
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/css/brands.css
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/css/fontawesome.css
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/css/regular.css
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/css/solid.css
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/css/svg-with-js.css
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/css/v4-shims.css
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/css/v4-shims.min.css
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-brands-400.eot
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-brands-400.svg
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-brands-400.ttf
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-brands-400.woff
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-brands-400.woff2
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-regular-400.eot
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-regular-400.svg
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-regular-400.ttf
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-regular-400.woff
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-regular-400.woff2
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-solid-900.eot
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-solid-900.svg
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-solid-900.ttf
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-solid-900.woff
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-solid-900.woff2
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/blackboard.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/boardmarker-black.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/boardmarker-blue.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/boardmarker-green.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/boardmarker-orange.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/boardmarker-purple.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/boardmarker-red.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/boardmarker-yellow.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/chalk-blue.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/chalk-green.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/chalk-orange.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/chalk-purple.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/chalk-red.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/chalk-white.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/chalk-yellow.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/sponge.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/img/whiteboard.png
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/plugin.js
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/plugin.yml
 create mode 100644 site_libs/revealjs/plugin/reveal-chalkboard/style.css
 create mode 100644 site_libs/revealjs/plugin/reveal-confetti/confetti.js
 create mode 100644 site_libs/revealjs/plugin/reveal-menu/menu.css
 create mode 100644 site_libs/revealjs/plugin/reveal-menu/menu.js
 create mode 100644 site_libs/revealjs/plugin/reveal-menu/plugin.yml
 create mode 100644 site_libs/revealjs/plugin/reveal-menu/quarto-menu.css
 create mode 100644 site_libs/revealjs/plugin/reveal-menu/quarto-menu.js
 create mode 100644 site_libs/revealjs/plugin/search/plugin.js
 create mode 100644 site_libs/revealjs/plugin/search/search.esm.js
 create mode 100644 site_libs/revealjs/plugin/search/search.js
 create mode 100644 site_libs/revealjs/plugin/zoom/plugin.js
 create mode 100644 site_libs/revealjs/plugin/zoom/zoom.esm.js
 create mode 100644 site_libs/revealjs/plugin/zoom/zoom.js
 create mode 100644 sitemap.xml
origin  git@github.com:slackline/quarto-live-demo.git (fetch)
origin  git@github.com:slackline/quarto-live-demo.git (push)
To github.com:slackline/quarto-live-demo.git
   02fbb7b..d22f205  HEAD -> gh-pages

[✓] Deploying gh-pages branch to website (this may take a few minutes)
[✓] Published to https://slackline.github.io/quarto-live-demo

Next we’re going to use the quarto publish command which makes the initial publishing for us, creating the gh-pages branch, rendering the pages and pushing them to GitHub. This should complete ok and once its done you can navigate to your repository and look at the Actions tab and hopefully see the pages being deployed.

Once this completes you should have a browser tab open up with your pages in them.

For those following along have how many have been able to publish their slides?

Slides : index.qmd

• Now you can write your slides!
• index.qmd is the main file to work on.
• Template includes many examples.

Ok we’ve cloned the template and customised it to work under our account, setup a gh-pages branch and pushed the changes and they are published and we have our website, now you are finally ready to start writing your slides and customising them.

In addition to the YAML header the index.qmd contains the contents of your slides.

The body is written in Quarto Markdown which is pretty similar to general Markdown.

Markdown

• Simple markup language.
• Separate content from style.
• Write in ASCII plain text.
• Simple to version control.

Ok we’ll now make a very brief digression into Markdown because Quarto uses its own dialect of Markdown which is a relatively simple markup language.

Markup languages differ from Word Processor software such as Microsoft Word and Google Docs as they separate the content that you are writing from the style, which is how it looks because you write in ASCII plain text and adorn the text with markers which indicate what it should look like and then apply themes to say what certain features should look like.

Plain text files have the advantage that they are simple to keep under version control which also means they are easy to work on collaboratively using tools such as GitHub or GitLab.

Basic Markdown

+ **Bold**
+ _Italics_
+ ~~Strikethrough~~
+ [Search](https://duckduckgo.com)

• Bold
• Italics
• Strikethrough
• Search

Quarto documentation is excellent.

QR Code Extension

• quarto-qrcode extension is really useful.

Before

\{{< qrcode https://ns-rse.github.io/quarto-revealjs-template qr1 width=400 height=400 >}\}

[ns-rse.github.io/quarto-revealjs-template](https://ns-rse.github.io/quarto-revealjs-template)

After

\{{< qrcode https://ns-rse.github.io/quarto-live-demo qr1 width=400 height=400 >}\}

[slackline.github.io/quarto-live-demo](https://slackline.github.io/quarto-live-demo)

NB The \ before the \{ and \} are NOT required, I had to escape them to get them to render.

We can update the QR-code references to point to our new site as we wouldn’t want viewers going to the wrong site!

Images

• Embed Images (any image on the internet or locally)

Before

![Relaxing in the mountains](https://live.staticflickr.com/65535/53144704609_c5e6fa8c77_k.jpg){width=700}

After

![SheffieldR Hex](https://raw.githubusercontent.com/SheffieldR/SheffieldR.github.io/main/images/SheffieldR_hex.png){width=400}

On line 162 there is an image embedded, a picture I snapped whilst relaxing on a hiking holiday in the Julian Alps this summer.

We can modify this and change the embeded image by simply changing the target URL for the image.

Here I insert the Sheffield R Hex image instead https://github.com/SheffieldR/SheffieldR.github.io/blob/main/images/SheffieldR_hex.png?raw=true

Lets change the first slide to show an image.

Previewing

• Preview slides locally whenever you want using quarto preview.
• Renders files locally and opens them in a new browser tab.
• Use regularly when writing your slides!

Starting python3 kernel...Done

Executing 'index.ipynb'

pandoc
  to: revealjs
  from: markdown+emoji
  output-file: index.html
  standalone: true
  title-prefix: SheffieldR - Quarto for Slides
  wrap: none
  default-image-extension: png
  html-math-method:
    method: mathjax
    url: >-
      https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS_HTML-full
  slide-level: 2
  incremental: false

metadata
  link-citations: true
  width: 1050
  height: 700
  margin: 0.1
  center: false
  navigationMode: linear
  controlsLayout: edges
  controlsTutorial: false
  hash: true
  history: true
  hashOneBasedIndex: false
  fragmentInURL: false
  transition: none
  backgroundTransition: none
  pdfSeparateFragments: false
  lang: en
  auto-stretch: false
  theme:
    - default
    - _extensions/grantmcdermott/clean/clean.scss
  menu:
    side: left
  slideNumber: true
  date-format: long
  revealjs-plugins:
    - confetti
  title: 'SheffieldR : Quarto for Slides'
  author:
    - name: Neil Shephard
      orcid: 0000-0001-8301-6857
      email: n.shephard@sheffield.ac.uk
      affiliations: 'RSE, University of Sheffield'
  footer: '**Slides** : [**ns-rse.github.io/SheffieldR-quarto-for-slides**](https://ns-rse.github.io/SheffieldR-quarto-for-slides)'
  showSlideNumber: speaker
  chalkboard: true

Output created: _site/index.html

Watching files for changes
Browse at http://localhost:4431/index.html

Now you could stage, commit and push your changes to GitHub and the Workflow Action would kick in and render the pages for you but that takes a little bit of time as it requires the GitHub runners to setup the environment for you.

Fortunately you can render your slides locally, there is a button to do this but I prefer to switch to a terminal and use quarto preview command. This makes the HTML files from your source markdown and start a web-server for you to view the pages before you push them to GitHub. By running it at the terminal the penultimate line where it says Watching files for changes actually works and you can make changes to and save index.qmd and they appear in the preview.

This is a great way of developing your slides as you write them and I’d recommend getting in the habit of previewing your slides regularly before committing and pushing them to GitHub as that way you catch any errors before they are published (this just makes the feedback loop shorter).

R Code

Before

library(ggplot2)

ggplot(airquality, aes(Temp, Ozone)) +
  geom_point() +
  geom_smooth(method = "loess")

After

library(ggplot2)
library(ggdark)

ggplot(airquality, aes(Temp, Ozone)) +
  geom_point() +
  geom_smooth(method = "loess") +
  ggdark::dark_theme_grey()

> renv::install("ggdark")

On line 186 we have a slide that shows a plot of air quality as measured by Ozone concentration and temperature Ok here is where I actually modify some R code, we have a slide defined on line 183 that plots the temperature v’s Ozone. The default theme is used with a white background.

We’re going to change this to use the ggdark theme instead, but in the rendering we get an error message as we haven’t installed the package.

We have to load the library and then we can apply the dark theme.

Update renv

• When adding code you probably have the libraries installed locally.
• Must update renv.lock to include these so that they are installed when rendering in the Workflow.

renv::settings$snapshot.type("all")
## Updating
renv::upgrade()
renv::update()
renv::snapshot()

When you add code to your slides that use new packages you probably already have them installed locally so the preview will render. But this won’t be the case in the GitHub environment where you slides will be built on-line.

To get round this you must update the renv.lock. I’ve found it can be useful to change the settings for the snapshot.type to all and it can be a good opportunity to update any installed packages locally as typically the most recent version of packages are installed when the GitHub action runs so its useful to have the same versions installed locally.

You can do that running renv::Settings$snapshot.type("all") and then renv::upgrade(), renv::update() and finally taking a renv::snapshot().

Speaker Notes

• Add additional notes for yourself.

::: {.notes}
I have a terrible memory so rely on speaker notes to remind me what I want to say.
:::

A nice feature of RevealJS common to many slide presentation software is the ability to add speaker notes to the bottom of every slide.

These can then be viewed by pressing s when viewing slides and a new browser window pops up and you can see the current slide and its notes and a preview of the next slide.

Changing Themes

Before…

format:
  clean-revealjs:
    incremental: false
    slide-number: true
    show-slide-number: speaker
    auto-stretch: false

After…

format:
  # clean-revealjs:
  revealjs:
    theme: dark
    incremental: false
    slide-number: true
    show-slide-number: speaker
    auto-stretch: false

Its straight-forward to change themes by editing the relevant section in the YAML header of index.qmd.

You can then preview the slides locally to see what they look like, if you’re happy then you stage and commit the changes to Git and push them to GitHub.

GitHub Actions

• GitHub Action uses .github/workflows/quarto-publish.yaml to publish.
• Install extensions.
• Install R/Python and any packages.

on:
  push:
    branches: main

name: Render and Publish

jobs:
  build-deploy:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository
        uses: actions/checkout@v3

      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2
        with:
          # To install LaTeX to build PDF book
          tinytex: true
          # uncomment below and fill to pin a version
          # version: 1.2.335

      - name: Install Quarto Extensions
        run: |
          quarto install --no-prompt extension jmbuhr/quarto-qrcode
          quarto install --no-prompt extension grantmcdermott/quarto-revealjs-clean
          quarto install --no-prompt extension ArthurData/quarto-confetti

      - name: Install Python and Dependencies
        uses: actions/setup-python@v4.3.0
        with:
          python-version: '3.10'
          cache: 'pip'
      - run: pip install -r requirements.txt

      - name: Install R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.2.0'

      - name: Install R Dependencies
        uses: r-lib/actions/setup-renv@v2
        with:
          cache-version: 1

      - name: Publish to GitHub Pages (and render)
        uses: quarto-dev/quarto-actions/publish@v2
        with:
          target: gh-pages
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # this secret is always available for github actions

Because we want to get all of these changes onto GitHub and we are version controlling our slides you have to stage, commit and push your changes to GitHub.

There is a special file which I mentioned earlier with regards to extensions that controls the building and rendering of the slides. This is .github/workflows/quarto-publish.yaml. There are a few key sections here that are important beyond making sure any extensions you are using are installed.

Extensions - GitHub Action

• GitHub Action uses .github/workflows/quarto-publish.yaml

      - name: Install Quarto Extensions
        run: |
          quarto install --no-prompt extension jmbuhr/quarto-qrcode
          quarto install --no-prompt extension grantmcdermott/quarto-revealjs-clean
          quarto install --no-prompt extension ArthurData/quarto-confetti

For the GitHub Action the theme and extensions that are used are already included in the template are already there, but if you add any extensions you should add them to the section that Installs Quarto Extensions.

Software Dependencies

• R packages you use locally need installing on GitHub.
• A step in GitHub Action called Install R.
• r-lib/actions/setup-r@v2 installs R.
• r-lib/actions/setup-renv@v2 installs packages.
• Use renv in your project to define packages.

Any packages that you have loaded and used in your work will need installing in the computer that builds the website and renders it on GitHub.

This is configured through a step called Install R which uses two actions from r-lib, the setup-renv and renv.

We have already made sure our renv is up-to-date locally but we have to make sure we include everything in the git commit and push the changes to GitHub otherwise the new R package ggdark won’t be installed.

Publish!

• Stage, commit and push to GitHub!
• If on main branch Action kicks in.

git commit -u
git commit -m "Updating slides in real time"
git push

You can stage, commit and push your changes, we can review all the changes we have made locally and add the .Rproj file too. Once happy we add a commit message and then push the changes up-stream.

If we go to GitHub page and look at the Action tab we can see our commit has triggered an action to run.

This takes a little while to run but it should complete and when it does we can look at our web-page.

Whilst waiting if we go to the Code tab

BONUS - Linting with pre-commit

• Includes pre-commit hook to lint Markdown.
• Ensures consistent style used.
• Configuration via .markdownlint-cli2.yaml.
• Automatically fixes mistakes where possible.
• Pre-commit : Protecting your future self¹

The repository includes configuration to use pre-commit hooks to link your Markdown. Linting is the principle of using a consistent style when writing code and markup so that it is easier for others to read and modify and its really important when working collaboratively as might be the case when writing slides in this manner. Simple things like ensuring a consistent line length is used, links are all correctly formatted and so forth.

Configuration of the Markdown linting is via the markdownlint-cli2.yaml file and it will automatically fix errors it finds where possible.

pre-commit itself is a Python programme and as such you need to install it on your system, if you’re using Linux chances are you can install it from your package manager, if you’re using OSX then you can install it using Homebrew. On either of these operating systems or if you are using Windows you can install a virtual environment, and if you’re not familiar with this you can see the notes from the course Conda environments for effective and reproducible research.

1. More posts on my blog

Links

• Quarto
• Slide Template
• GitHub Workflows
• SheffieldR

• Pre-commit : Protecting your future self
• RSE blog
• My blog!

Q&A

Thank you for attending this session. 🙏


Feel free to ask anything; no question is too small or too big. Your curiosity and engagement make this session even more valuable. We’re eager to assist you.

Future Meetings and Feedback

Volunteer to talk:

Feedback: