Git and GitHub

If it’s not in source control, it doesn’t exist.

Collaborative research

Data scientists and statisticians, as opposed to closet mathematicians, rarely do things in vacuum.

• We talk to scientists/clients about their data and questions.

• We write code (a lot!) together with team members or coauthors.

• We run code/program on different platforms.

• We write manuscripts/reports with co-authors.

• We distribute software so potential users have access to your methods.

In every project you have at least one other collaborator, future-you. You don’t want future-you to curse past-you.

Hadley Wickham

Why version control?

• A centralized repository helps coordinate multi-person projects.

• Time machine. Keep track of all the changes and revert back easily (reproducible).

• Storage efficiency.

• Synchronize files across multiple computers and platforms.

• GitHub is becoming a de facto central repository for open source development. E.g., all packages in Julia are distributed through GitHub; Hadley Wickham also recommends Git/GitHub as the best practices for R package development.

• Advertise yourself through GitHub.

• AmStat article: What Is Data Science Specialization, and What Can It Do for You?

What should an employer look for when they see a certification on a résumé?

For our program, and likely data science in general, they should look at the applicant’s GitHub page. They should see interesting project and code contributions.

Available version control tools

• Open source: Git, Apache subversion (aka svn), cvs, mercurial.

• Proprietary: Visual SourceSafe (VSS), etc.

• Dropbox? Mostly for file backup and sharing, limited version control (1 month?).

We use Git in this course.

Git

• Currently the most popular version control system according to Google Trend.

• Initially designed and developed by Linus Torvalds in 2005 for Linux kernel development. Git is the British English slang for unpleasant person.

I’m an egotistical bastard, and I name all my projects after myself. First ‘Linux’, now ‘git’.

Linus Torvalds

Centralized vs distributed version control

Svn is a centralized version control system:

Git is a distributed version control system:

What do I need to use Git?

• A Git server enabling multi-person collaboration through a centralized repository.

  • github.com: unlimited public repositories, private repositories costs $, but unlimited private repositories for free from Student Developer Pack.

  • bitbucket.org: unlimited public repositories, unlimited private repositories for academic account (register for free using your edu email).

  • We use github.com in this course for developing and submitting homework.

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• A Git client on your own machine.

  • Linux: Git client program is shipped with many Linux distributions, e.g., Ubuntu and CentOS. If not, install using a package manager, e.g., yum install git on CentOS.

  • Mac: follow instructions at https://www.atlassian.com/git/tutorials/install-git.

  • Windows: Git for Windows (GUI) aka Git Bash.

• RStudio supports Git.

• Do not totally rely on GUI or IDE. Learn to use Git on command line, which is needed for cluster and cloud computing.

Git workflow

Git survival commands

• Synchronize local Git directory with remote repository:

  git pull

  same as git fetch plus git merge.

• Modify files in local working directory.

• Add snapshots to staging area:

  git add FILES

• Commit: store snapshots permanently to (local) Git repository

  git commit -m "MESSAGE"

• Push commits to remote repository:

  git push

Git basic usage

• Register for an account on a Git server, e.g., github.com.

• Upload your SSH public key to the server.

• Identify yourself at local machine, e.g.,

  git config --global user.name "Your Name"
  git config --global user.email "your_email@ucla.edu"

  Name and email appear in each commit you make.

• Initialize a project.

  • Create a repository, e.g., biostat-203b-2020-winter on GitHub.

  • Clone the repository to your local machine:

  git clone git@github.com:[USERNAME]/biostat-203b-2020-winter.git

• Working with your local copy.

  • git pull: update local Git repository with remote repository (fetch + merge).

  • git log FILENAME: display the current status of working directory.

  • git diff: show differences (by default difference from the most recent commit).

  • git add file1 file2 ...: add file(s) to the staging area.

  • git commit: commit changes in staging area to Git directory.

  • git push: publish commits in local Git repository to remote repository.

  • git reset --soft HEAD~1: undo the last commit.

  • git checkout FILENAME: go back to the last commit, discarding all changes made.

  • git rm FILENAME: remove files from git control.

Branching in Git

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• For this course, you need to have two branches:

  • develop for your own development.

  • master for releases, i.e., homework submission.

  • Note master is the default branch when you initialize the project; create and switch to develop branch immediately after project initialization.

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• Commonly used commands:

  • git branch branchname: create a branch.

  • git branch: show all project branches.

  • git checkout branchname: switch to a branch.

  • git tag: show tags (major landmarks).

  • git tag tagname: create a tag.

Sample session | Getting started with homework

On GitHub.com:

• Obtain Student Developer Pack.

• Create a private repository biostat-203b-2020-winter. Add Hua-Zhou and juhkim111 as your collaborators with write permission.

On your local machine:

• Clone the repository, create develop branch, where your work on solutions.

  # clone the project
  git clone git@github.com:biostat-203b-2020-winter.git
  # enter project folder
  cd biostat-203b-2020-winter
  # what branches are there?
  git branch
  # create develop branch
  git branch develop
  # switch to the develop branch
  git checkout develop
  # create folder for HW1
  mkdir hw1
  cd hw1
  # let's write solutions
  echo "sample solution" > hw1.Rmd
  echo "some bug" >> hw1.Rmd
  # commit the code
  git add hw1.Rmd
  git commit -m "start working on problem #1"
  # push to remote repo
  git push

• Submit and tag HW1 solution to master branch.

  # which branch are we in?
  git branch
  # change to the master branch
  git checkout master
  # merge develop branch to master branch
  # git pull origin develop 
  git merge develop
  # push to the remote master branch
  git push
  # tag version hw1
  git tag hw1
  git push --tags

• RStudio has good Git integration. But practice command line operations also.

Etiquettes of using Git

• Be judicious what to put in repository.

  • Not too less: Make sure collaborators or yourself can reproduce everything on other machines.

  • Not too much: No need to put all intermediate files in repository. Make good use of the .gitignore file.

  • Strictly version control system is for source files only. E.g. only xxx.Rmd, xxx.bib, and figure files are necessary to produce a pdf file. Pdf file doesn’t need to be version controlled or, if version controlled, doesn’t need to be frequently committed.

• Commit early, commit often and don’t spare the horses.

• Adding an informative message when you commit is not optional. Spending one minute on commit message saves hours later for your collaborators and yourself. Read the following sentence to yourself 3 times:

Write every commit message like the next person who reads it is an axe-wielding maniac who knows where you live.