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

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Tom Mock: Reproducible Publications with Python and Quarto

Resources
- slides: https://thomasmock.quarto.pub/python-...

Full transcript
https://blog.dataumbrella.org/quarto-...

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:   / thomas_mock  
- GitHub: https://github.com/jthomasmock

#python #quarto #rstats