GitHub (and co) is a web platform to host and share projects tracked by git
In other words:
You do not need GitHub to use git but you cannot use GitHub without using git
git as a CLI
RStudio and git
Git main panel
RStudio and git
Stage files, view differences and commit changes
View history and versions
Using git
How does git work?
git takes a sequence of snapshots
Each snapshot can contain changes for one or many file(s)
User chooses which files to ‘save’ in a snapshot and when (!= file hosting services like Dropbox, Google Drive, etc.)
In the git universe, a snapshot is a version, i.e. the state of the whole project at a specific point in time
A snapshot is a two-step process:
Stage files: select which files to add to the version
Commit changes: save the version and add metadata (commit message)
Basic workflow
Initialize git in a (empty) folder (repository)
git init
The three areas of a gitrepository:
working copy: current state of the directory (what you actually see)
staging area: selected files that will be added to the next version
repository: area w/ all the versions (the .git/ subdirectory)
Basic workflow
Add new files in the repository
git status# On branch main# # No commits yet# # Untracked files:# README.md# analyses.R# data.csv# # Nothing added to commit but untracked files present# Use "git add <file>..." to track
Basic workflow
Stage (select) one file
git add data.csv
git status# On branch main# # No commits yet# # Changes to be committed:# (use "git rm --cached <file>..." to unstage)# new file: data.csv# # Untracked files:# (use "git add <file>..." to track)# README.md# analyses.R
Basic workflow
Stage (select) several files
git add data.csv analyses.R
git status# On branch main# # No commits yet# # Changes to be committed:# (use "git rm --cached <file>..." to unstage)# new file: analyses.R# new file: data.csv# # Untracked files:# (use "git add <file>..." to track)# README.md
Basic workflow
Stage (select) all files
git add .
git status# On branch main# # No commits yet# # Changes to be committed:# (use "git rm --cached <file>..." to unstage)# new file: analyses.R# new file: data.csv# new file: README.md
Basic workflow
Commit changes to create a new version
git commit -m"a good commit message"
Basic workflow
Now we are up-to-date
git status# On branch main# nothing to commit, working tree clean
The status of a file
With git a file can be untracked or tracked1. If it’s tracked, it can be:
unmodified
modifed and unstaged
modified and staged
The status of a file
When you create a new file, by default it’s untracked.
The status of a file
To tell git to track this new file, you have to stage it.
The status of a file
After commiting your changes, the file becomes unmodified (up-to-date with the latest version).
The status of a file
If you edit tracked file, it becomes modified.
The status of a file
When you decide to create a new version, stage the modified file.
The status of a file
After commiting your changes, the file becomes unmodified (up-to-date with the latest version).
The .gitignore
We can also tell git to ignore specific files: it’s the purpose of the .gitignore file
Which files? For instance:
passwords, tokens and other secrets
temporary files
large files
The .gitignore
We can also tell git to ignore specific files: it’s the purpose of the .gitignore file
Which files? For instance:
passwords, tokens and other secrets
temporary files
large files
The syntax is simple:
# Ignore a specific fileREADME.html# Ignore all PDF*.pdf# Ignore a folderdata/# Ignore a subfolderdata/raw-data/# Ignore a specific file in a subfolderdata/raw-data/raw-data.csv
git status# On branch main# Your branch is up to date with 'origin/main'## Untracked files:# README.md# # Nothing added to commit but untracked files present# Use "git add <file>..." to track
Working w/ GitHub
Stage changes
git add .
git status# On branch main# Your branch is up to date with 'origin/main'## Changes to be committed:# (use "git restore --staged <file>..." to unstage)# new file: README.md
Working w/ GitHub
Commit changes
git commit -m"add README"
git status# On branch main# Your branch is ahead of 'origin/main' by 1 commit.# (use "git push" to publish your local commits)# # nothing to commit, working tree clean
Working w/ GitHub
Push changes to remote
git push# Sometimes, you'll need to use:git push -u origin main
git status# On branch main# Your branch is up to date with 'origin/main'.# # nothing to commit, working tree clean
Working w/ GitHub
Pull changes from remote
Working w/ GitHub
Pull changes from remote
git pull
git status# On branch main# Your branch is up to date with 'origin/main'.# # nothing to commit, working tree clean
Help me, I can’t push!
When you try to push, you might see this following error message:
git push# To github.com:ahasverus/projectname.git# ! [rejected] main -> main (fetch first)## error: failed to push some refs to 'github.com:ahasverus/projectname.git'## hint: Updates were rejected because the remote contains work that you do# hint: not have locally. This is usually caused by another repository pushing# hint: to the same ref. You may want to first integrate the remote changes# hint: (e.g., 'git pull ...') before pushing again.# hint: See the 'Note about fast-forwards' in 'git push --help' for details.
Just git pull and try to git push again
Help me, I can’t pull!
When you try to pull, you might see this following error message:
git pull# [...]# Auto-merging README.md# CONFLICT (content): Merge conflict in README.md## error: could not apply b8302e6... edit README## hint: Resolve all conflicts manually, mark them as resolved with# hint: "git add/rm <conflicted_files>", then run "git rebase --continue".# hint: You can instead skip this commit: run "git rebase --skip".# hint: To abort and get back to the state before "git rebase", # hint: run "git rebase --abort".
Welcome to the wonderful world of gitconflicts
Resolving conflicts
What is a (lexical) conflict?
A git conflict appears when two versions cannot be merged by git because changes have been made to the same lines.
README.md - Version A
# The SURPRISE pizzaAn amazing surprise of the dev team dedicated just to your fancythirst for fortune and originality.
README.md - Version B
# The Surprise PizzaAn amazing surprise of the dev team dedicated just to your fancythirst for fortune and originality.
Git will identify conflicts in files:
<<<<<<< HEAD# The SURPRISE pizza=======# The Surprise Pizza>>>>>>> b8302e6 (edit README)An amazing surprise of the dev team dedicated just to your fancythirst for fortune and originality.
You have to decide which version you want to keep.
Resolving conflicts
What is a (lexical) conflict?
A git conflict appears when two versions cannot be merged by git because changes have been made to the same lines.
README.md - Version A
# The SURPRISE pizzaAn amazing surprise of the dev team dedicated just to your fancythirst for fortune and originality.
README.md - Version B
# The Surprise PizzaAn amazing surprise of the dev team dedicated just to your fancythirst for fortune and originality.
Git will identify conflicts in files:
<<<<<<< HEAD# The SURPRISE pizza=======# The Surprise Pizza>>>>>>> b8302e6 (edit README)An amazing surprise of the dev team dedicated just to your fancythirst for fortune and originality.
README.md - Final version
# My wonderful pizzaAn amazing surprise of the dev team dedicated just to your fancythirst for fortune and originality.
You have to decide which version you want to keep.
