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GIT

GIT is a decentralized versioning system.

Tracking Changes

# show changes in a file relative to last commit
git diff FILE          # if unstaged/unadded
git diff --staged FILE # if staged  /added

# show git diff with colors in less
git diff --color=always FILE | less -R

# show the git diff of the same file in different branches
# while in 'main'
git diff <other_branch> FILE

In the output, lines marked with + and - show changed lines:

- , typically red, show state of that line in previous commit + , typically green, show current state of that line

File Management

# undo all changes that were made to a file since the last commit
git restore FILE

Branch Management

# show branches in a simple list
git branch -l  # local
git branch -r  # remote
git branch -a  # all
git branch -v  # verbose
git branch -vv # more verbose

# create new branch with <branchname>
git branch BranchName

# create a new branch and immediately checkout to it
git checkout -b BranchName
git switch -c BranchName # since git 2.23

# delete <branch>
git branch -d BranchName

# check what branches are available on the remote
git ls-remote --heads origin
git remote show origin

# update your local repo's "knowledge" of remote branches
git fetch origin

# create and switch to new local copy of remote branch
git switch BranchName

# fetch branch from remote
git fetch origin <branch_name>:<branch_name>

# graphical overview of your branches
git log --all --oneline --graph --decorate

Create a new branch and push it to the remote

# on your local repo do
git switch -c BranchName

# create your changes, and then do
git add ChangedFile

# commit the changes
git commit -m "commit message"

# then push to origin
git push origin BranchName

Update your featurebranch with the latest changes in the main/other branch

# update our main branch with the remote main
git checkout main
git pull origin main

# update our feature branch with the remote feature branch
git checkout FeatureBranch
git pull origin FeatureBranch

# fix any conflicts if there are any

# merge into the feature branch,
# make sure you are in the feature branch
# with git branch -v
git merge main

# this will create a merge commit in the feature branch,
# but not in the main branch

Stashing Changes

Stashing changes is very useful if you need to switch to another branch before you are ready to make a commit.

Git normally doesn't allow you to switch branches if you have uncommitted changes, because you would lose your uncomitted changes if you do change branch. To save your uncomitted changes, you can make use of git stash:

# you are in branch 'bugfix', you've made some uncommitted changes
# then for whatever reason you need to move to the main branch
# git stash temporarily saves your changes
git stash

git switch main
# you work on main
# you are now ready to go back to 'bugfix'
git switch bugfix

# re-apply your saved uncommitted changes
git stash pop

Various Snippets

# check the changes in a particular commit
git show HEAD
git show 081870e

# change the commit message of the last commit, if you haven't pushed it to the remote yet
git commit --amend -m "new commit message"


# undo an accidental git add
git reset FILE

# delete the latest commit
git reset --hard HEAD~1
git init					Initiate a local git repository
git config --global user.name "Joran Martijn"
git config --global user.email joran.martijn@icm.uu.se
git config -l					Some general configuration information of account and repository
git clone https://github.com/novigit/brocode	"Clone" the repository to current directory
git status					Check what has been changed since last update
git add <file|dir> <file|dir> <etc>		"Stage" files for commit, or "add" files to the "staging area", where files are tracked
git add .					Adds all changed files for commit
git commit -m "commit message"			"Commit" the files to your repository
git commit -a -m "commit message"		Will automatically add all tracked files with changes. Will not add untracked files
git log	 					Check your commit log
git show HEAD					Show all changes in the last commit, and the commit details (SHA etc)
git remote -v					Lists remote repositories
git checkout <branch>				Change to a specific branch
git checkout HEAD <file>			Restore <file> to state it was in before last commit. In the working directory
git reset HEAD <file>				Restore staged <file> to state it was in, in the last commit, and remove it from staging area. In the staging area
git reset <commit_SHA>				Restore repository to state it was in, after <commit_SHA>
git push origin master				"Push" changes into repository
git fetch origin master				Downloads the latest master branch to the branch origin/master
git pull origin master				Fetch ánd merge the current master branch with your local copy
git merge <branch>				Merge <branch> with branch you are currently on
git --version					Shows current version of git

GITHUB

Setting up your GitHub SSH-key

# generate a private/public key pair
ssh-keygen -t ed25519 -C "joranmartyn@gmail.com"

# save as '~/.ssh/github_ed25519'

# nevermind a passphrase

# edit your '~/.ssh/config'
Host github.com
    IdentityFile ~/.ssh/github_ed25519
    HostName github.com

# now copy the exact contents of '~/.ssh/github_ed25519.pub'
# (the public key) onto your GitHub account

# Settings -> SSH and GPG keys -> New SSH key -> Add a title -> Paste the public key -> Add SSH key

# in your known_hosts, make sure you have
github.com ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIOMqqnkVzrm0SdG6UOoqKLsabgH5C9okWi0dh2l9GKJl
github.com ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBEmKSENjQEezOmxkZMy7opKgwFB9nkt5YRrYMjNuG5N87uRgg6CLrbo5wAdT/y6v0mKV0U2w0WZ2YB/++Tpockg=
github.com ssh-rsa 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

Cloning a repo that contains links to other repos

They are called 'submodules' and can be downloaded using --recursive

git clone --recursive git@github.com:iqtree/iqtree3.git