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Git & GitHub Cheat Sheet - For Researchers

Getting Started

Command What It Does
git init Start tracking a folder with Git
git clone <url> Download a repo from GitHub to your laptop
git status See what's changed (run this often!)

The Core Workflow

 Edit files → git add → git commit → git push
              (stage)    (snapshot)   (upload)
Command What It Does
git add <file> Stage a file for the next snapshot
git add . Stage everything that's changed
git commit -m "message" Save a snapshot with a description
git push Upload your snapshots to GitHub
git pull Download your collaborator's changes

Seeing History

Command What It Does
git log --oneline Compact list of all snapshots
git log --oneline --graph --all Visual branch diagram
git diff See what you changed (before staging)
git diff --staged See what's about to be committed
git diff HEAD~2 Compare with 2 commits ago

Branching & Collaboration

Command What It Does
git branch List branches (* = current)
git checkout -b <name> Create a new branch and switch to it
git checkout main Switch back to main
git push origin <branch> Push a branch to GitHub
git merge <branch> Merge a branch into current branch

Resolving Merge Conflicts

When Git can't auto-merge, it marks the file:

<<<<<<< HEAD
Your version of the line
=======
Their version of the line
>>>>>>> branch-name

To resolve: Edit the file to keep what you want, remove the markers, then: 

git add <file>
git commit -m "Resolve merge conflict in <file>"

Undoing Things

Command What It Does
git checkout -- <file> Discard uncommitted changes to a file
git reset HEAD <file> Unstage a file (keep changes)
git revert <commit> Create a new commit that undoes a previous one

When in doubt, ask before you force-push. git push --force rewrites history and can destroy your collaborator's work.

Commit Message Guide

Good Messages

Add regression analysis for hypothesis 2
Fix off-by-one error in date range filtering
Clean temperature data: remove stations with >30% missing
Update README with methods section and citation

Bad Messages

update
fix
asdf
changes
WIP

Formula: Start with a verb. Say what AND why.

Research-Specific Patterns

Branch Naming for Research

experiment/new-regression-model
feature/add-visualisation
fix/data-cleaning-bug
docs/update-methods-section

Tagging Submissions

git tag -a v1.0-submitted-to-nature -m "Submitted to Nature, May 2026"
git push origin --tags

Getting a DOI for Your Code

  1. Connect your GitHub repo to Zenodo (zenodo.org)
  2. Create a Release on GitHub
  3. Zenodo automatically archives it and assigns a DOI
  4. Add the DOI badge to your README

Git + Jupyter Notebooks

Notebooks (.ipynb) are stored as JSON, which makes Git diffs messy.

Tips

  • Strip output before committing: Use nbstripout to automatically remove cell outputs 
    pip install nbstripout
nbstripout --install    # sets up a Git filter automatically
  • Always add to .gitignore: 
    .ipynb_checkpoints/
  • Consider jupytext: Syncs notebooks with plain .py files for cleaner diffs 
    pip install jupytext
jupytext --set-formats ipynb,py:percent notebook.ipynb
  • Rule of thumb: Use notebooks for exploration, .py files for reusable functions

.gitignore Essentials for Research

# Large data files
data/*.csv
data/*.h5
*.parquet

# Notebook checkpoints
.ipynb_checkpoints/

# Python environment
__pycache__/
*.pyc
.venv/

# Secrets and credentials
.env
credentials.json

# OS clutter
.DS_Store
Thumbs.db

Generate a starter .gitignore: https://www.toptal.com/developers/gitignore

Useful GitHub Features

Feature How It Helps Research
Issues Track experiments, TODOs, bugs
Pull Requests Propose and review changes with collaborators
Pages Publish project documentation as a website
Actions Automate tests, builds, deployments on every push
Releases Archive specific versions (great for paper submissions)
Organizations Set up a shared space for your lab group

Getting Help

Resource URL
Pro Git book (free) git-scm.com/book
GitHub Skills skills.github.com
Software Carpentry Git lesson swcarpentry.github.io/git-novice
GitHub Docs docs.github.com
git help <command> Built-in help in your terminal