flowchart TB;
Collaborations --> _["Data Science"] & DevOps & Healthcare & HPC & MIRSG & WebDev;
_["Data Science"] -.-> data_science_responsibilities["
AI
Machine learning
Signal processing
Statistics
"];
DevOps -.-> ?;
Healthcare -.-> healthcare_responsibilities["
EMAP
Hospital projects
"];
HPC -.-> hpc_responsibilities["
C++
FPGAs
Fortran
GPUs
MPI
OpenMP
"];
MIRSG -.-> mirsg_responsibilities["
Medical imaging
OMERO
XNAT
"];
WebDev -.-> webdev_responsibilities["
CSS
HTML
JavaScript
"];
Quarto: Making Talks
2025-09-02
Scan to view the slides
Talk Motivation
- Always found making presentations tedious.
- Prefer non-WYSIWYG editors since discovering LaTeX.
- LaTeX Beamer presentations are heavy duty and look rubbish.
- Wanted to be able to version control my slides.
- Was never sure where to store my slides.
- No real record of my talks, so little motivation to give them.
- Quarto allows me to make lightweight, distributable slides that look great.
Promised this talk before.
Quarto
What is Quarto
An open source scientific and technical publishing system
What is Quarto
- Author using
Jupyternotebooks or with plain text markdown in your favourite editor. - Create dynamic content with
Python,R,Julia, andObservable. - Publish reproducible, production quality articles, presentations, dashboards, websites, blogs, and books in
HTML,PDF,Microsoft Word,ePub, and more.
What is Quarto
- Share knowledge and insights organisation-wide by publishing to
Posit Connect,Confluence, or other publishing systems. - Write using
Pandocmarkdown, including equations, citations, crossrefs, figure panels, callouts, advanced layout, and more.
Why Quarto for Presentations
- Markdown Simplicity: Write slides using intuitive Markdown syntax.
- Code Integration: Seamlessly embed and run code (R, Python, and so on) directly in your slides, displaying both code and output.
- Reproducibility: Your entire presentation, including analyses and visualisations, is reproducible from its source.
Why Quarto for Presentations
- Dynamic Content: Easily include plots, tables, and even interactive elements generated by your code.
- Customisation: Extensive options for styling, themes, and layouts.
- Open Source: Free to use and backed by a vibrant community.
Traditional Presentation Tools
PowerPoint/Google Slides
- Manual copy-pasting of figures/tables.
- Updates requires manual changes in many places.
- Limited version control.
- Limited integration with code execution.
- Proprietary formats.
Quarto reveal.js
- Automated generation of figures/tables.
- One source file for content and code.
- Git-friendly plain text files..
- Live code execution.
- Open standard for universal access.
reveal.js
- Quarto leverages
reveal.js, a powerful HTML presentation framework. - Provides smooth transitions, animations, and interactive features by default.
- Browser-based: easy to share and view on any device with a web browser.
- Supports many navigation modes (linear, vertical stacks).
- Plugins and extensibility for advanced functionalities.
Core Quarto Concepts
.qmdfile: The source file (Quarto Markdown Document).- YAML Header: Configuration settings (title, and so on).
- Markdown: For text, headings, lists, images, links.
- Code Chunks: For example
{python}for executable code. - Rendering: Converting the
.qmdfile to the output format (quarto render my-slides.qmd). - Themes: Predefined visual styles for your presentation.
- Fragments: Revealing content incrementally on a slide.
Benefits: Audience and Presenter
Audience
- Engaging and dynamic presentations.
- Clear and consistent visuals.
- Reproducible results if shared (for example, accompanying code).
- Accessible (can be viewed in any browser).
Presenter
- Streamlined workflow for data-driven talks.
- Reduced manual effort and errors.
- Easy version control and collaboration.
- Flexibility to output to other formats from the same source.
Repository Contents
My setup. In the order the repository files appear on GitHub. Most of these are optional unless you are a fellow pedant.
/.github/workflows/add-to-project.yaml
GitHub Action to add issues to project board.
---
name: Add issues to project board
on:
issues:
types:
- opened
pull_request:
types:
- opened
jobs:
add-issue-to-project:
runs-on: ubuntu-latest
steps:
# yamllint disable-line rule:line-length
- uses: paddyroddy/.github/actions/add-to-project@61f147d3eb8b0e4f7c91c701a1950e7900f3ac77 # v0
with:
project-token: ${{ secrets.PROJECT_PAT }}/.github/workflows/links.yaml
GitHub Action to perform link checking with lychee.
---
name: Links
on:
push:
branches:
- main
- renovate/**
pull_request:
jobs:
links:
runs-on: ubuntu-latest
timeout-minutes: 2
steps:
# yamllint disable-line rule:line-length
- uses: paddyroddy/.github/actions/links@61f147d3eb8b0e4f7c91c701a1950e7900f3ac77 # v0
with:
github-token: ${{ secrets.GITHUB_TOKEN }}/.github/workflows/linting.yaml
GitHub Action to perform linting with pre-commit and Vale.
---
name: Linting
on:
push:
branches:
- main
- renovate/**
pull_request:
jobs:
linting:
runs-on: ubuntu-latest
steps:
# yamllint disable-line rule:line-length
- uses: paddyroddy/.github/actions/linting@61f147d3eb8b0e4f7c91c701a1950e7900f3ac77 # v0
with:
pre-commit-config: ./.pre-commit-config.yaml
# yamllint disable-line rule:line-length
- uses: paddyroddy/.github/actions/vale@61f147d3eb8b0e4f7c91c701a1950e7900f3ac77 # v0
with:
github-token: ${{ secrets.GITHUB_TOKEN }}/.github/workflows/publish.yaml
GitHub Action to publish the Quarto website to GitHub Pages.
---
name: Quarto Publish
on:
push:
branches:
- main
- renovate/**
pull_request:
jobs:
build-and-deploy:
runs-on: ubuntu-latest
permissions:
contents: write
steps:
# yamllint disable-line rule:line-length
- uses: paddyroddy/.github/actions/github-pages/quarto@61f147d3eb8b0e4f7c91c701a1950e7900f3ac77 # v0
with:
github-token: ${{ secrets.GITHUB_TOKEN }}
requirements-txt: ${{ github.workspace }}/requirements.txt/_extensions/
Extensions are a powerful way to change and extend the behaviour of Quarto. Can be installed with quarto add <extension>, which must be committed to the repository. Extensions can be updated through quarto update <extension>.
- jmbuhr/qrcode: provides shortcodes for qrcodejs in Quarto.
- quarto-ext/fontawesome: provides support including free icons provided by Font Awesome.
/_filters/slugify.lua
If the base features of Pandoc and Quarto do not do exactly what you need, you can likely create a Pandoc Filter that bridges the gap. This filter slugifies the given title to be used within a URL.
/_includes/qr-code.qmd
This snippet is included at the start of every presentation with {{< /_includes/qr-code.qmd >}}.
/assets/images/favicon.ico
Specified in the Quarto configuration, a favicon is a small icon that serves as branding for your website.
/.gitignore
Ignore standard Quarto and Vale files.
/.pre-commit-config.yaml
My custom pre-commit hooks. They include: adrienverge/yamllint, crate-ci/typos, igorshubovych/markdownlint-cli, JohnnyMorganz/StyLua, Lucas-C/pre-commit-hooks, pappasam/toml-sort, pre-commit/pre-commit-hooks, rbubley/mirrors-prettier, rhysd/actionlint, shellcheck-py/shellcheck-py.
/.prettierrc.yaml
Configures Prettier to treat Quarto files as Markdown.
/.renovaterc.json5
Inherits my custom Renovate configuration. See my earlier talk on Renovate.
/.typos.toml
Configures known exemptions from the typos spell checker.
/.vale.ini
My Vale configuration to lint prose. See my earlier talk on Vale.
StylesPath = .github/styles
# https://github.com/errata-ai/packages
Packages = proselint,\
RedHat,\
write-good
[formats]
qmd = md
[*.{md,qmd}]
BasedOnStyles = proselint,\
RedHat,\
Vale,\
write-good
# Disable
RedHat.Definitions = NO
RedHat.Ellipses = NO
RedHat.GitLinks = NO
RedHat.Headings = NO
RedHat.PascalCamelCase = NO
RedHat.PassiveVoice = NO
RedHat.ReadabilityGrade = NO
RedHat.Slash = NO
RedHat.Spelling = NO
RedHat.TermsErrors = NO
Vale.Spelling = NO
write-good.E-Prime = NO
write-good.Passive = NO
write-good.TooWordy = NO
# `vale sync` in CI means the packages are then linted, so turn them off
[.github/styles/**]
BasedOnStyles =/404.qmd
A HTTP 404 page for the Quarto website.
/LICENCE.txt
Creative Commons Attribution Share Alike 4.0 International licence.
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Creative Commons may be contacted at creativecommons.org./README.md
The repository README, needs some work…
/_quarto.yaml
Any document rendered within the project directory will automatically inherit the metadata defined at the project level.
---
project:
type: website
format:
html:
theme: darkly
revealjs:
auto-stretch: false
callout-appearance: simple
code-copy: true
filters:
- _filters/slugify.lua
footer: "{{< meta title >}} - <https://paddyroddy.github.io/talks>"
hash-type: number
history: false
incremental: true
link-external-icon: true
mermaid:
theme: dark
menu:
hideMissingTitles: true
useTextContentForMissingTitles: false
preview-links: true
slide-number: true
theme: dark
transition: fade
website:
google-analytics: G-SCSTN0WCDT
favicon: /assets/images/favicon.ico
navbar:
tools:
- icon: house
href: https://paddyroddy.github.io
- icon: github
href: https://github.com/paddyroddy/talks
site-url: https://paddyroddy.github.io/talks
title: ""/index.qmd
Listings automatically generate the contents of a page from a list of Quarto documents or other custom data.
/requirements.txt
Some talks include executable programs. These are the dependencies for some Python code.
Demo
Will show some Quarto code and then display it on the neighbouring slide. These have not been crafted specifically for this talk, they were seen in my other talks.
Title Slide
Each talk must start with some YAML front matter metadata. Note that the listing specified in /index.qmd mapped subtitle to Events.
---
author: "[Patrick J. Roddy](https://paddyroddy.github.io)"
date: 2025-09-02
format: revealjs
subtitle: "[ARC Collaborations Hour](https://www.ucl.ac.uk/arc)"
title: "Quarto: Making Talks"
---Sections are then made with # and slides are made with ##.
Figures
Figures are included using the standard Markdown pattern.
Lists
Lists are included using the standard Markdown pattern. The incremental: true settings means they show one-by-one.
- Get automated Pull Requests to update your dependencies
- Reduce noise by running Renovate on a schedule, for example:
- on weekends
- outside of working hours
- each week
- each month
- Reduce noise by running Renovate on a schedule, for example:
- Relevant package files are discovered automatically
Code Blocks
Code blocks can have fenced code blocks syntax highlighted in the usual way. The code-line-numbers option allows for control of what numbers you want your audience to follow.
```{.json code-line-numbers="2|3,16|4|5|6,13|7-10|11|12,18-20|14|15|17|21,38|22-27|28-32|33-37"}
{
$schema: "https://docs.renovatebot.com/renovate-schema.json",
extends: [
"config:best-practices",
"schedule:weekdays",
":assignAndReview(paddyroddy)",
":automergeBranch",
":automergeDigest",
":automergeMinor",
":automergePatch",
":disableDependencyDashboard",
":enablePreCommit",
":label(renovate)",
":maintainLockFilesMonthly",
":noUnscheduledUpdates",
],
commitMessageAction: "Renovate:",
"git-submodules": {
enabled: true,
},
packageRules: [
{
description: "Only allow major updates",
enabled: false,
matchDepNames: ["renovatebot/pre-commit-hooks"],
matchUpdateTypes: ["minor", "patch", "pin"],
},
{
description: "Combine updates together",
groupName: "paddyroddy/.github",
matchDepNames: ["paddyroddy/.github"],
},
{
description: "Shorten commit titles",
commitMessageTopic: "{{depName}}",
matchManagers: ["github-actions", "pre-commit"],
},
],
}
```{
$schema: "https://docs.renovatebot.com/renovate-schema.json",
extends: [
"config:best-practices",
"schedule:weekdays",
":assignAndReview(paddyroddy)",
":automergeBranch",
":automergeDigest",
":automergeMinor",
":automergePatch",
":disableDependencyDashboard",
":enablePreCommit",
":label(renovate)",
":maintainLockFilesMonthly",
":noUnscheduledUpdates",
],
commitMessageAction: "Renovate:",
"git-submodules": {
enabled: true,
},
packageRules: [
{
description: "Only allow major updates",
enabled: false,
matchDepNames: ["renovatebot/pre-commit-hooks"],
matchUpdateTypes: ["minor", "patch", "pin"],
},
{
description: "Combine updates together",
groupName: "paddyroddy/.github",
matchDepNames: ["paddyroddy/.github"],
},
{
description: "Shorten commit titles",
commitMessageTopic: "{{depName}}",
matchManagers: ["github-actions", "pre-commit"],
},
],
}Footers
You can control the footer for a single slide as follows.
Fragments
Fragments are used to highlight or incrementally reveal individual elements on a slide.
The
[GitHub automerge](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/automatically-merging-a-pull-request)
setting is required
::: {.fragment .fade-left}
It is **highly recommended** to ensure you have tests that will operate on the
Renovate branches.
```{.yaml}
on:
push:
branches:
- main
- "renovate/**"
pull_request:
```
:::The GitHub automerge setting is required
Columns
Columns can be made using layout-ncol or the layout we saw earlier in the QR code slide.
Flowcharts
Flowcharts can be made with Mermaid.
```{mermaid}
%%| fig-align: center
flowchart TB;
Collaborations --> _["Data Science"] & DevOps & Healthcare & HPC & MIRSG & WebDev;
_["Data Science"] -.-> data_science_responsibilities["
AI
Machine learning
Signal processing
Statistics
"];
DevOps -.-> ?;
Healthcare -.-> healthcare_responsibilities["
EMAP
Hospital projects
"];
HPC -.-> hpc_responsibilities["
C++
FPGAs
Fortran
GPUs
MPI
OpenMP
"];
MIRSG -.-> mirsg_responsibilities["
Medical imaging
OMERO
XNAT
"];
WebDev -.-> webdev_responsibilities["
CSS
HTML
JavaScript
"];
```Quotes
Standard Markdown quoting.
[Wikipedia](https://en.wikipedia.org/wiki/DevOps):
> DevOps is a method in the software development and IT industry. Used as a set
> of practices and tools, DevOps integrates and automates the work of software
> development (Dev) and IT operations (Ops) as a means for improving and
> shortening the systems development life cycle. DevOps is complementary to
> agile software development; many DevOps aspects came from the agile way of
> working. Automation is an important part of DevOps. Software programmers and
> architects should use "fitness functions" to keep their software in check.DevOps is a method in the software development and IT industry. Used as a set of practices and tools, DevOps integrates and automates the work of software development (Dev) and IT operations (Ops) as a means for improving and shortening the systems development life cycle. DevOps is complementary to agile software development; many DevOps aspects came from the agile way of working. Automation is an important part of DevOps. Software programmers and architects should use “fitness functions” to keep their software in check.
Checkboxes
Standard Markdown checkboxes.
Documentation:
- [ ] **A statement of need** stating problems the software is designed to solve
and its target audience in README.
- [ ] **Installation instructions:** for the development version of the package
and any non-standard dependencies in README.
- [ ] **Vignette(s)** demonstrating major functionality that runs successfully
locally.Documentation:
Running Code
Can embed and run code to do all kinds of things. This example generates an interactive map by using the Python package ipyleaflet.
```{python}
from ipyleaflet import Map, Marker, basemap_to_tiles, basemaps
heathrow_coords = (51.4680, 0.4551)
seatac_coords = (47.4436, -122.2961)
m = Map(
basemap=basemap_to_tiles(basemaps.Esri.WorldImagery, "2017-04-08"),
center=(
(heathrow_coords[0] + seatac_coords[0]) / 2,
(heathrow_coords[1] + seatac_coords[1]) / 2,
),
zoom=3,
)
m.add_layer(Marker(location=heathrow_coords))
m.add_layer(Marker(location=seatac_coords))
m
```Website Previews
Websites can be previewed as follows.
Stack Layout
This example shows how to stack figures on top of each other.
::: {.r-hstack}
::: {.r-stack}
{.fragment height=550}
{.fragment height=550}
{.fragment height=550}
{.fragment height=550}
:::
::: {.r-stack}
{.fragment height=550}
{.fragment height=550}
{.fragment height=550}
{.fragment height=550}
:::
:::
Tables
Standard markdown tables.
| Reusable workflows | Composite actions |
| -------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
| A YAML file, similar to any standard workflow file | An action containing a bundle of workflow steps |
| Each reusable workflow is a single file in the `.github/workflows` directory of a repository | Each composite action is a separate repository, or a directory, containing an `action.yml` file and, optionally, other files || Reusable workflows | Composite actions |
|---|---|
| A YAML file, similar to any standard workflow file | An action containing a bundle of workflow steps |
Each reusable workflow is a single file in the .github/workflows directory of a repository |
Each composite action is a separate repository, or a directory, containing an action.yml file and, optionally, other files |
Callouts
Can include GitHub Markdown-like callouts.
Much of this talk holds true for personal GitHub accounts and GitHub organisations. However, it is not always the case. The focus here is solely on organisational accounts.
More Examples
Official Quarto Example Presentation
Further Examples
Conclusions
- Quarto combines Pandoc and Markdown syntax.
- Can present slides in the browser or export them as PDF and so on.
- Can extend functionality with extensions or write your own custom filters.
- Can display code line-by-line and even run code in presentations.
- Can re-use slides within a presentation.
- Easy to start, takes a little time to perfect.
- More fun.
Quarto: Making Talks - https://paddyroddy.github.io/talks