Setting up git for (solo) data science workflow
1 Introduction
Version Control for biostatistics/data-science data analysis is the challenge.
Lets take it one step at a time.
Scenario 1: git user @rgt47 has been working on a data analysis for some ADNI data. Its moderately complex and uses lots of packages. He’s ready to ask his team to join the analysis process. What are the first steps to do that?
Start by adding the first github user @rgt4748 to the project.
2 Methods
2.1 Invite a colleague to collaborate on a github repository
Start by logging into Github and navigating to the repository to be shared, say x24. Select settings (in top row of tabs) and then the collaborators tab (in the left panel)
Select green “add people” button, then “invite collaborator”, then “add rgt4748 to this repository”, in the center of the page.
Enter the github user name (rgt4748) and select “Add rgt4748” t Now rgt4748 should login and accept invitation:
click “message” icon in upper right corner.
Select “Invitation to join rgt47/x23 from rgt47”, then “Accept Invitation” green button in center of page.
They’ll be taken to the rgt47/x24 repo.
Now on their workstation they can clone repository with the following code:
> git clone https://github.com/rgt4748/x24.git> cd x24
> git branch myedits
> git checkout myedits
> vim x24.Rmdmodify title: "R2" to title: "changed R2" and save edits.
> git add .
> git commit -m "sample edit"
> git push origin myedits #(?)
> git checkout master
> git merge myedits
> git branch -d myedits #(delete branch)Click contribute button, then open pull request, create pull request, enter title and description.
login as rgt47. you’ll see one notification. check files changed
3 Appendix. GIT for nitwits
git init
git add fname
git status #see what happens on commit git commit -am “commit message”
git push
git branch work
git checkout work
… make changes … git add * git commit -m “something”
git checkout master
git merge work
git branch -d work
git log #see all commits
git checkout HASH #Restore old branch
Consider editing ./.git/config
View file in master branch. git show master:a101.Rmd | mvim -
Copy file from other branch (master) git checkout master uw.png
4 Appendix: Tips
Troubleshooting git pull –allow-unrelated-histories
Rule 6: Use the Imperative mood
A valuable practice involves crafting commit messages with the underlying understanding that the commit, when implemented, will achieve a precise action. Construct your commit message in a manner that logically completes the sentence “If applied, this commit will…”. For instance, rather than,git commit -m “Fixed the bug on the layout page” . use this git commit -m “Fix the bug on the layout page” ✔
In other words, if this commit were to be applied, it would indeed fix the bug on the layout page.
Rule 7: Explain “What” and “Why”, but not “How”.
Limiting commit messages to “what” and “why” creates concise yet informative explanations of each change. Developers seeking “How” the code was implemented can refer directly to the codebase. Instead, highlight what was altered and the rationale for the change, including which component or area was affected.
Case Study: Angular’s Commit Message Practices
Angular stands as a prominent illustration of effective commit messaging practices. The Angular team advocates for the use of specific prefixes when crafting commit messages. These prefixes include “chore: ,” “docs: ,” “style: ,” “feat: ,” “fix: ,” “refactor: ,” and “test: .” By incorporating these prefixes, the commit history becomes a valuable resource for understanding the nature of each commit. Tips
Remember to prioritize clear and meaningful communication through your commit messages. A well-crafted commit message serves as a story that explains ‘what,’ ‘why,’ but not ‘how’ a change was made. Remember, your commit history is a collaborative resource that future you and your team will rely on. Make it a habit to create commit messages that stand as informative, concise, and consistent narratives.
Interested in deepening your understanding of Git and evolving into a proficient “version controller”? Explore these exceptional resources:
- https://git-scm.com/doc
- https://git-scm.com/book/en/v2
- https://lab.github.com/
- https://www.atlassian.com/git/tutorials
- https://learngitbranching.js.org/
- https://www.gitkraken.com/git-cheat-sheet
- https://www.git-tower.com/learn/
5 References:
Best way to manage your dotfiles.
Git Basics — All You Need To Know as a New Developer. | by Gabriel Bonfim | Sep, 2023 | Medium
Reuse
Citation
@online{(ryy) glenn thomas2024,
author = {(Ryy) Glenn Thomas, Ronald},
title = {Setting up Git for (Solo) Data Science Workflow},
date = {2024-02-23},
url = {https://focusonr.org/posts/setupgit},
langid = {en}
}