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GitHub

Version Control is an important component in software development which manages changes to documents, websites, code, or other digital information. Version control can save you when code changes break things. Web hosting of your code repositories lets you share and work on code together and save your work in the event of a hardware failure.

The most commmon version control software in data science are git, svn, cvs, and bzr.

Given the limited amount of time we have this week, we are only going to cover Git and one web-based hosting service (GitHub) in this camp.

In this lesson you will learn how to:

• Interact with git via GitHub

  • Using a browser
  • Using the command line

• Add collaborators to your organization

• Initialize a git repository on the command line and push it to GitHub

  • Push/pull files
  • Commit to GitHub

• Learn about versions

  • Forks
  • Branches
  • Merges
  • Revert
  • Releases
  • Badging

Important

GitHub is not really intended for storing or manipulating data

Navigating & Interacting with GitHub

Basic Layout

The basic layout includes:

• Profile
• Organizations
• Teams
• Repositories
• Projects
• Followers
• Contributions
• Watch / Unwatch repos

Add a Collaborator

Online only

1. Go to your Organization
2. Click “people”
3. Invite someone!

OR

1. Can add collaborators under “Settings” -> “Collaborators”

Create a Repo Online & Locally

Online

1. Go to your dasboard
2. Click “New”
3. Name the repository
4. Initialize with “README” - form of metadata - this tells you and the those looking at the repository what it is about
5. Go to “Clone or Download” and clone to local folder / directory titled “Lab”
6. Can delete repo under “Settings” -> “Options”

Command Line

1. Locate or create a local folder / directory structure titled “Lab”

cd
mkdir -p github/lab
cd github/lab

2. Initialize folder as a repository with git

git init
echo "This is a test repo" >> README.md #append to file
git add . #add all the files in the current directory
git commit -m "initial project"

Note

Documentation is vital You will be doing this for YOU 6 months from now

Interact with GitHub

Clone a repo

This is used to work locally rather than online.

Online

1. Click the down arrow “Clone or download”
2. Click “Open in Desktop”
3. Select where to save it - Create a folder for GitHub repos on your computer locally

Command Line

cd path/to/location
git clone <url> [rename]
#URL of thte repository on GitHub
#rename the directory (optional)

Commit

Online

1. Create a file by clicking “Create a new file”
2. Name file (/name)
3. Write commit message
4. Press “Commit”

OR

1. Create a file locally
2. Click “Upload files”
3. Select file(s) within a folder

Command Line

1. Create a file

cd path/to/repo
touch file.txt

2. Add file(s)

git add -A #adds all the new files
git push
git commit -m "added file" #-m initiates a message

Tip

It is good practice to write commmit messages to remember what you added or fixed.

Create an Issue

Issues are great for tracking decisions made or to-do lists

Online only

1. Click on the repository you just created.
2. Click on “Issues”
3. Click on “New issue”
4. Create a title (# and issue number for reference)
5. Assign to someone, or create a label
6. Submit new issue
7. Close issue

Version Control

Online

1. Click on file
2. Click “History”

Command Line

git log
git log --stat #gives abbreviated stats for each commit
git log --pretty=oneline #can also add options: short, full, fuller
git log --pretty=format:"%h - %an, %ar : %s #lots of options for pretty=format
q #to quit

Create a branch

Branches are useful to working on code etc. without disturbing the master branch.

Online

1. Select the down arrow on the repository page that says “Branch:master”
2. Create a new branch name

OR

1. Add new file or edit existing file.
2. Write a commit message.
3. Select “Create a new branch”

Command Line

1. Create a new branch

cd path/to/repo
#common practice to pull before commiting anything
git pull #does a fetch for you
git checkout -b new-branch #creates a new branch and puts you on that branch
#set new branch upstream
git push --set-upstream origin new-branch

2. Edit some files

#edit files
vi path/to/file
q #to quit

3. Commit changes

git pull
git add
commit -am "changed a file" #stage changes and write a message
git push

Make a pull request

Pull requests are useful to have another set of eyes to review changes before merging them with the master branch.

Online Only

1. From your branch, create a new file
2. Commit file to your branch
3. Hit “Compare & pull request”
4. Go to pull requests
5. Set it on the master branch

Merge

Online

1. Go to “Pull requests”
2. Select down arrow of “Merge pull request” (if no conflicts)
3. Delete branch
4. Leave comment if need be
5. Close pull request

Command Line

cd path/to/repo
git pull
git checkout new-branch
git merge master #testing to see if merging breaks anythin
git checkout master
git merge new-branch #now repull it all into master

Revert

Command Line

git log
#copy tag for last working commit
git revert <tag to last working commit>
#will make it look like a new commit
git add -A
git commit -m "changed things back to <commit tag>"
git push

Advanced

Fork

Online

1. Go to a new repository
2. Click fork
3. Save to personal repository.
4. Clone to Desktop.
5. Interact via online or in Desktop.
6. If want to make suggestions, can create a pull request.

Command Line

git close <github-repo>
cd <new-folder>
git fork

Etc.

These are Online only

• Versioning

  1. Go to “Releases”
  2. Click “Create a new release”
  3. Tag version: Version #
  4. Release title: I usually put the date of the release, but any system can work

• Reactions:

  1. Create a new pull request
  2. Looking at the messages, click the smiley face to give a reaction

• Badges

  1. Go find a badge!
  2. Copy badge code into README:

Git cheat sheet

Here is a list of the most important commands in Git:

Git Task	Command	Description
Set up your profile locally	git config --global user.name "Cy Unicorn"	Set your user name
	git config --global user.email Cy1@cyverse.org	Set your email address
Create a Repository locally	git init	Initialize a folder as a git repository
Get an existing repository from a web service	git clone ssh://git@github.com/[username]/[repository-name].git	Create a local copy of a remote repository

Branching & Merging	Description
git branch	List branches (the asterisk denotes the current branch)
git branch -a	List all branches (local and remote)
git branch [branch name]	Create a new branch
git branch -d [branch name]	Delete a branch
git push origin --delete [branch name]	Delete a remote branch
git checkout -b [branch name]	Create a new branch and switch to it
git checkout -b [branch name] origin/[branch name]	Clone a remote branch and switch to it
git checkout [branch name]	Switch to a branch
git checkout -	Switch to the branch last checked out
git checkout -- [file-name.txt]	Discard changes to a file
git merge [branch name]	Merge a branch into the active branch
git merge [source branch] [target branch]	Merge a branch into a target branch
git stash	Stash changes in a dirty working directory
git stash clear	Remove all stashed entries

Sharing & Updating Projects	Description
git push origin [branch name]	Push a branch to your remote repository
git push -u origin [branch name]	Push changes to remote repository (and remember the branch)
git push	Push changes to remote repository (remembered branch)
git push origin --delete [branch name]	Delete a remote branch
git pull	Update local repository to the newest commit
git pull origin [branch name]	Pull changes from remote repository
git remote add origin ssh://git@github.com/[username]/[repository-name].git	Add a remote repository
git remote set-url origin ssh://git@github.com/[username]/[repository-name].git	Set a repository’s origin branch to SSH

Inspection & Comparison	Description
git log	View changes
git log --summary	View changes (detailed)
git diff [source branch] [target branch]	Preview changes before merging