[84] Reproducible Publications with Python and Quarto (Thomas Mock)

Join our Meetup group: https://www.meetup.com/data-umbrella Tom Mock: Reproducible Publications with Python and Quarto ## Resources - slides: https://thomasmock.quarto.pub/python-umbrella/#/ ## Full transcript https://blog.dataumbrella.org/quarto-blog ## About the Event Quarto is an open-source scientific and technical publishing system that builds on standard markdown with features essential for scientific communication. The system has support for reproducible embedded computations, equations, citations, crossrefs, figure panels, callouts, advanced layouts, and more. In this talk we'll explore the use of Quarto with Python, describing both integration with IPython/Jupyter and the Quarto VS Code extension. Users can author Jupyter notebooks or documents as plain text markdowns with code in Python, R, Julia or Observable. Quarto includes the ability to publish high-quality articles, reports, presentations, websites, blogs, and books in HTML, PDF, MS Word, ePub, Reveal.js and more. ## Timestamps 00:00 Data Umbrella introduction 03:41 Introduce the speaker, Thomas Mock 04:14 Thomas begins 05:14 RStudio is now Posit 05:55 What is Quarto? 07:13 Origins of Quarto 08:31 Goal: Computation Document 09:09 Goal: Scientific Markdown 10:03 Goal: Single Source Publishing 10:33 Simple example of what Quarto looks like (YAML, Markup, Markdown, code chunks) 12:29 Simple example: multi-format (output formats: html, pdf, docx, epub, pptx, revealjs) 13:16 List of what is possible with Quarto 14:02 So, what is Quarto: quarto is a language-agnostic command line interface (CLI) 15:27 Basic Quarto workflow 16:43 Difference between "render" and "preview" 17:16 IPython 18:43 Stored/frozen computation and reproducibility 20:36 A *.qmd is a plain text file 21:28 Quarto doesn't have to be plain text 22:12 Rendering pipeline 22:57 What to do with my existing .ipynb? 24:23 Comfort of your own workspace: JupyterLab, Visual Studio Code, 25:00 Auto-completion in RStudio + VSCode 26:01 Quarto Extensions and Visual / Live Editor 27:19 Quarto, unified document layout 29:54 Quarto, unified syntax across Markdown and code 31:11 Built-in vs Custom 33:01 Extending Quarto with Extensions 33:51 Interactivity, Jupyter Widgets (with plots, matplotlib, etc) 34:15 Interactivity, Observable 35:01 Interactivity, on the fly Observable "widgets" 36:24 Parameters - one source, many outputs 37:36 Rendering with parameters 38:27 Quarto Publish 38:57 Quarto, crafted with love and care (the team) 39:30 Quarto Resources (installation) 39:44 Quarto resources: video tutorials 40:13 Q: Can Quarto documents be shared like Overleaf docs and can users import article templates for specific journals into Quarto? 41:39 new! Manuscript option to bundle an entire project together (bundle can be shipped to a journal) 42:48 Q: Is Quarto git friendly? 43:28 Q: Has Quarto already been used in published scientific work? 44:14 publishing books with Quarto 44:22 Q: Any general suggestions for outputting to docx (Word)? 45:20 Q: Any tips on how Quarto can help conda users? 46:14 Q: Can you use GitHub Actions with Quarto? 47:18 Q: Can you have individual environments for each blog post? 49:50 Download CLI (command line interface) for Quarto 51:10 Example Gallery 51:44 nbdev project 53:14 Quarto blog, Shinylive extension 55:12 Q: How can I use Quarto to write scientific papers? ## About the Speaker: Tom Mock - Twitter: https://twitter.com/thomas_mock - GitHub: https://github.com/jthomasmock #python #quarto #rstats