github.md

GitHub and Git Cheatsheet

Repository Setup

# clone a GitHub repository
git clone https://github.com/USER/REPO.git

# move into the cloned repository
cd REPO

# show the remote repository URLs
git remote -v

# add a GitHub remote named origin
git remote add origin https://github.com/USER/REPO.git

# change the origin remote URL
git remote set-url origin https://github.com/USER/REPO.git

Status and History

# show changed files and the current branch
git status

# show a compact commit history
git log --oneline --graph --decorate --all

# show changes that are not staged
git diff

# show staged changes
git diff --staged

# show the current branch name
git branch --show-current

Stage, Commit, and Push

# stage all changed files
git add .

# stage one file
git add path/to/file

# commit staged changes
git commit -m "describe the change"

# push the current branch
git push

# push a new branch and set upstream tracking
git push -u origin branch-name

Pull and Sync

# pull newest changes for the current branch
git pull

# fetch remote changes without merging
git fetch

# pull using rebase for a linear local history
git pull --rebase

# show local branches and remote tracking info
git branch -vv

Submodules

# add another GitHub repository as a submodule
git submodule add https://github.com/USER/SUBMODULE_REPO.git path/to/submodule

# commit the new submodule link and .gitmodules file
git add .gitmodules path/to/submodule
git commit -m "Add submodule"

# clone a repository and include all submodules
git clone --recurse-submodules https://github.com/USER/REPO.git

# initialize submodules after a normal clone
git submodule update --init --recursive

# show submodule status and commit pointers
git submodule status

# one-time setup: make a submodule follow a specific branch
git config -f .gitmodules submodule.SUBMODULE_NAME.branch main
git submodule sync --recursive
git add .gitmodules
git commit -m "Track submodule main branch"

# update one submodule to the newest commit from its tracked branch and merge it
git submodule update --remote --merge path/to/submodule

# update all submodules to newest commits from tracked branches
git submodule update --remote --merge --recursive

# example: update a PyOncoplot submodule from the parent repo
git submodule update --remote --merge code_library/PyOncoplot
git add code_library/PyOncoplot
git commit -m "Update PyOncoplot submodule"
git push

# manually update a submodule from inside its folder
cd path/to/submodule
git pull
cd -

# commit the updated submodule pointer in the parent repo
git add path/to/submodule
git commit -m "Update submodule"

Branches

# list local branches
git branch

# create and switch to a new branch
git switch -c branch-name

# switch to an existing branch
git switch branch-name

# rename the current branch
git branch -m new-branch-name

# delete a local branch
git branch -d branch-name

# delete a remote branch
git push origin --delete branch-name

Merge Basics

# switch to the branch that should receive changes
git switch main

# merge another branch into the current branch
git merge branch-name

# stop a merge with conflicts before committing
git merge --abort

# continue after fixing conflicts
git add .
git commit

Undo Common Mistakes

# unstage a file but keep edits
git restore --staged path/to/file

# discard unstaged edits in one file
git restore path/to/file

# amend the most recent commit message
git commit --amend -m "new message"

# create a new commit that reverses an old commit
git revert COMMIT_SHA

GitHub CLI

# authenticate GitHub CLI
gh auth login

# create a pull request
gh pr create --fill

# list pull requests
gh pr list

# view checks for the current pull request
gh pr checks

# open the current repo in the browser
gh repo view --web