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Add DeepLabCut MyST mini-hackathon blog post (#300)
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title: MyST Mini-Hackathon with the DeepLabCut Team | ||
date: "2024-09-02" | ||
banner: | ||
image: "featured.png" | ||
authors: ["Jenny Wong", "Angus Hollands", "Chris Holdgraf"] | ||
tags: [bioscience, open source] | ||
categories: [impact] | ||
featured: false | ||
draft: false | ||
--- | ||
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## The DeepLabCut Team | ||
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![Animal pose estimation using deep neural networks. Courtesy of the DeepLabCut Jupyter Book](https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/daed7f16-527f-4150-8bdd-cbb20e267451/cheetah-ezgif.com-video-to-gif-converter.gif?format=180w "Animal pose estimation using deep neural networks. Courtesy of the [DeepLabCut Jupyter Book](https://deeplabcut.github.io/DeepLabCut/README.html)") | ||
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The [DeepLabCut team](http://www.mackenziemathislab.org/deeplabcut) is a group of researchers and developers who are working on open source tools for analyzing animal pose estimation by training deep neural networks on videos. | ||
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Chris Holdgraf visited the lab in early August to learn more about how the group were using open-source tools to document and share their work. | ||
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## Jupyter Book and MyST | ||
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Extensive documentation for using the DeepLabCut software package is already available as a [Jupyter Book](https://deeplabcut.github.io/DeepLabCut/README.html). The group was interested in adopting MyST Markdown to stay ahead of the curve and upgrade their Jupyter Book (see the related announcement [Jupyter Book 2 will be build upon the MyST-MD engine](https://executablebooks.org/en/latest/blog/2024-05-20-jupyter-book-myst/)). | ||
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Chris led a mini-hackathon to introduce the group to MyST and collect feedback on where enhancement features could be made in the future. Here's a summary of the outcomes: | ||
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- Many improvements were made to the [MyST documentation](https://mystmd.org/guide/) 📖 | ||
- The [MyST Quick Start Guide](https://mystmd.org/guide/quickstart) was used to onboard new users. Amendments were [upstreamed to the MyST docs directly](https://github.com/jupyter-book/mystmd/pull/1433) and were immediately available to all. | ||
- A [tutorial on executable documents](https://mystmd.org/guide/quickstart-executable-documents) was added to the collection of MyST tutorials. | ||
- MyST-MD installation instructions were [simplified using `mamba`](https://github.com/jupyter-book/mystmd/pull/1454). | ||
- A bunch of enhancement features were requested ✨ | ||
- [Using cell tags for labelling notebook cells](https://github.com/jupyter-book/mystmd/issues/1455) | ||
- [Support for loading user-defined CSS stylesheets for theming](https://github.com/jupyter-book/myst-theme/issues/321) | ||
- [Better UX for mult-versioned documentation](https://github.com/jupyter-book/mystmd/issues/1458) | ||
- [Bibliography styling in HTML](https://github.com/jupyter-book/mystmd/issues/1462) | ||
- [Automatic API documentation generation](https://github.com/DeepLabCut/DeepLabCut/pull/2712) | ||
- And we found a bug in the [table of contents validation](https://github.com/jupyter-book/mystmd/issues/1456) 🐞 | ||
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## Summary | ||
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Hackathons are a great way for quickly imparting knowledge and gathering feedback in a short space of time. The event spurred rapid contributions to the MyST ecosystem – embracing reuse of the MyST quick start guides saved time and effort, while engaging with users directly closed a tight feedback loop for enhancements. | ||
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## Acknowledgments | ||
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We would like to thank the [Makenzie Mathis Lab](http://www.mackenziemathislab.org/) for hosting Chris Holdgraf at EPFL, Lausanne, Switzerland. |