Five ways to use GitHub to automate scholarly work

In this presentation I explain how GitHub's API and GitHub Actions can be used to automate common scholarly tasks and improve the reliability of our work.

Transcript

1. Five ways to use GitHub to automate scholarly work GitHub Presented by @arfon
2. GitHub
3. GitHub
4. Platform APIs REST (v3) GraphQL https://docs.github.com/en/rest https://docs.github.com/en/graphql
5. GitHub Actions – Platform Automation
6. Automated scholarly documents 1
7. Markdown paper in repository
8. GitHub Action configured to compile paper
9. Pull request triggers recompilation
10. Paper compiled and available to download
11. Notebook CI 2
12. Jupyter Notebooks for JWST data analysis
13. Contributing a notebook
14. Fixing the notebook ‘build’
15. Jupyter Notebooks for JWST data analysis
16. Archiving repositories with Zenodo 3
17. Powered by the GitHub API (webhooks) https://guides.github.com/activities/citable-code/
18. Zenodo landing page https://guides.github.com/activities/citable-code/
19. DOI per-release https://guides.github.com/activities/citable-code/
20. DOI per-release https://guides.github.com/activities/citable-code/
21. Reproducible compute environments 4
22. repo2docker https://github.com/jupyterhub/repo2docker
23. Define dependencies, add binder badge
24. Build Docker container image and launch
25. Interactive versioned compute environment
26. Flat 5
27. Automatically sync data with GitHub https://octo.github.com/projects/flat-data
28. GitHub Action to sync data from sources https://github.com/marketplace/actions/flat-data
29. Cron job periodically syncs data https://github.com/marketplace/actions/flat-data
30. Live, always up to date COVID dashboard https://githubocto.github.io/flat-demo-covid-dashboard/state/new-york
31. Thanks! arfon@github.com @arfon