Reproducibility & Data Science in R – Collaborate With GitHub

Review

Word Bank

A collection of files tracked by git
A snapshot of the state of a repository
git ___ is used to tell git to track a file
For example, a repo on GitHub
git ____ is used to synchronize changes on your computer with a remote

Review

What difficulties did you have while putting your repo on GitHub?

Collaborating with GitHub

Example repo

Everyone practice cloning this example repo as a new RStudio project: https://github.com/cct-datascience/demo-repo-2024 ¹
Need one volunteer to edit the README.md and practice commit + push

Dealing with Conflicts

What happens when two people make conflicting edits to a file and push them?
Creates a merge conflict

Ok, try `git pull`

Merge, rebase, fast-forward??

These are alternative ways to deal with conflicts—we won’t get into the details
For now, we recommend you stick with the “merge” option

Use:

git config pull.rebase false

Or, if you want to set this option for all future repos too

git config --global pull.rebase false

Fixing a Merge Conflict

Resolve the conflict however you want (i.e. keep one of the two sections)
Delete all lines with <<<<<<<, >>>>>>>, or =======
Save and commit

Avoid merge conflicts by working on branches

Each person works on a “branch”—an independent series of commits that can be merged back into the “main” branch.

Working on a Branch

Make a new branch using RStudio’s Git pane (for this demo, use your name)
Make some edits (e.g. to README.md), save, add, commit.
You can go back to the “main” version of your project at any time.

Working on a Branch

Push your branch to GitHub
View changes on GitHub

Pull Requests

A request to merge changes into the main branch

Need another volunteer to share screen and be guided through making a pull request
This time, everyone can follow along!

Forks

What if you don’t have permission to push to a GitHub repo but you want to contribute?

Make a fork!

Collaborating with Forks

To contribute to a repo you don’t have push permission for:

Fork the repo to your own GitHub
Clone the fork to your local computer
Make commits (ideally on a branch)
Make a pull request to the upstream repo

Tip

Learn more, including handy usethis shortcuts: https://happygitwithr.com/fork-and-clone

Practice

Exercise

In pairs, practice forking and cloning a demo repo you do not have permission to push to: https://github.com/cct-datascience/demo-repo-fork-2024.
Make a new branch, make commits, and make a pull request to the upstream repo.

Resources

Forking and cloning
Pull request helpers in usethis
#git channel in UA Data Science Slack

Your Tasks

For the next update to your colloquium project, practice using a branch and and pull request on GitHub
Clone a repo you do not have permission to push to without forking it and see what happens when you try to use git push
Fork and clone a repo on GitHub to explore it (e.g. a lab mate’s code, a research compendium, your favorite R package)

References

Bryan, Jennifer. 2018. “Excuse Me, Do You Have a Moment to Talk about Version Control?” The American Statistician 72 (1): 2027. https://doi.org/10.1080/00031305.2017.1399928.