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Preface

Prerequisites
Setup

Reproducibility Principles and Practices

1. Principles of Reproducibility
2. Primary Practices
3. Secondary Practices
4. Case-by-case Practices
5. Appendix: References

Introduction to the Command Line

6. Interacting with Computers
7. Command Line Basics
8. Navigating File Systems
9. Editing Files
10. Appendix: References

Installing Software with Pixi

11. Environment Managers
12. Pixi Basics
13. Unit A: Configuring the Shell
14. Unit B: UC Davis HPC Modules
15. Unit C: Python Packages
16. Unit D: Tasks

Introduction to Version Control

17. Version Control Systems
18. Git Basics
19. Remote Repositories
20. The Git Workflow

Git for Teams

21. Branches & Merges
22. Working with GitHub
23. Making Git Comfortable

Repository
Open issue

Index

By Nick Ulle, Carl Stahmer, Tyler Shoemaker, and Wesley Brooks