Mastering Quarto CLI: From Authoring to Publishing
A Hands-on Workshop
A Quarto CLI Workshop for Physalia-courses.
Overview
This comprehensive workshop provides an immersive journey through the Quarto ecosystem, designed to transform participants from newcomers to confident practitioners capable of creating sophisticated, reproducible documents and interactive publications.
Through seven structured sessions, attendees will master the complete Quarto workflow from initial setup and Markdown fundamentals to advanced theming, multi-format publishing, and professional deployment strategies. The workshop emphasises practical, hands-on learning with real-world applications, covering project architecture, computational integration across R/Python/Julia, advanced formatting techniques, and modern publishing workflows.
By the end of this workshop, participants will have developed the expertise to create polished, professional publications that seamlessly integrate narrative content with executable code whilst maintaining reproducibility across multiple output formats.
Workshop Objectives
- Establish a solid foundation in Quarto fundamentals, including installation, project types, and the command-line interface.
- Master authoring essentials through Markdown fundamentals, Quarto-specific features, and YAML configuration.
- Integrate computational workflows by embedding R, Python, and Julia code with proper execution control and caching strategies.
- Develop professional publications using advanced project structures, multi-format optimisation, and custom formatting techniques.
- Implement cohesive branding and visual identity across formats using Bootstrap theming,
brand.ymlsystems, and Pandoc templating. - Deploy projects confidently through various publishing platforms including Quarto Pub, GitHub Pages, and automated workflows.
Prerequisites
Prior to the workshop, please ensure you have the following installed on your computer.
- Quarto CLI 1.8.* or higher: https://quarto.org/docs/get-started
- Computing languages (one or more):
- R 4.5.* or higher: https://cran.r-project.org
- Python 3.13.* or higher: https://www.python.org/downloads/
- Julia 1.12.* or higher: https://julialang.org/downloads/
Alternatively, you can use GitHub Codespaces:
bash
./.devcontainer/setup.sh --what <all|r|python|julia>Program
| Session | Title |
|---|---|
| Session 1 | Introduction & Setup |
| Session 2 | Authoring Essentials |
| Session 3 | Embedding Computations & Code |
| Session | Title |
|---|---|
| Session 4 | Formats & Projects |
| Session 5 | Formatting & Branding |
| Session 6 | Publishing |
| Session 7 | Closing & Next Steps |
Instructor
- I am Mickaël CANOUIL, I hold a Ph.D. in Biostatistics, with over a decade of academic experience in the genetics of type 2 diabetes and obesity.
- My research has contributed to understanding the genetic and molecular mechanisms underlying metabolic diseases, with publications in leading journals.
- Currently, I work as a consultant in biostatistics, applying my expertise to diverse projects in multi-omics and data analysis.
- I am also deeply involved in the Quarto ecosystem, developing extensions and tools that enhance reproducibility and scientific communication.
- My contributions, including Quarto Wizard and various Quarto extensions, aim to streamline workflows for researchers and data scientists.
- You can explore my work on GitHub, my projects, and my publications.
License
This project is licensed under the CC BY-NC-SA 4.0 license.