githubtutorial

A simple toy repository for introducing Git/GitHub, testing/demonstrating features, etc.

Learning objectives

1. Understanding of the purpose and use of core GitHub collaboration features
2. Ability to clone an existing repository locally, create a personal branch, and generate a pull request to update the original master

Instructions

1. Clone the repository to your device.
2. Create a personal branch, make some edits, and commit.
3. Make a pull request!

Resources

Literature

• Lowdes et al. 2017. "Our path to better science in less time using open data science tools." Nature Ecology & Evolution 1, 0160: https://www.nature.com/articles/s41559-017-0160

Examples

• Grant McDermott's blueparadox repository: This is a simple example of a "finished" repository for a specific publication. Grant (and co-authors) provide STATA and R code to replicate the figures and core results for McDermott, Meng, et al. (PNAS, 2018): "The blue paradox: Preemptive overfishing in marine reserves". It includes great READMEs in important places that clearly lay out the purpose and use of different components. Grant includes one pull request as an update to address a comment on the original publication, highlighting a use-case for the branching/PR/merging features.
• Grant McDermott's sceptic-priors repository: In this example, Grant shares an in-progress analysis. The READMEs still do a good job of explaining what each piece does and how to execute the program. The repository includes several (now closed) pull requests, including one submitted by a student. In this example, Grant reviews Alex's (@jungangl) branch at the point the PR was created (see the Files changed page for the PR). On the Conversation page, he asks Alex to make a few additional changes to ensure the repository still functions properly, demonstrating how the flow and structure of the Pull Request collaboration features.

Tutorials

• Eli Holmes's "Practical Workflow for Scientists" series: Week 1 (basic intro to installing Git/GitHub/RStudio and getting them talking to each other), Week 2 (a guide to cloning someone else's repository), and Week 7 (merge conflicts and using branches effectively) are directly relevant to Git/GitHub best practices.

Acknowledgements

Thanks to Allison Horst (@allisonhorst) for the palmerpenguins data, via Palmer Station LTER. These data are provided here under the CC0 1.0 Universal associated with the palmerpenguins package.