---
title: "Git and GitHub"
author: "Dr. Hua Zhou"
date: "Jan 16, 2018"
output:
  ioslides_presentation: default
subtitle: Biostat M280
bibliography: ../bib-HZ.bib
---

## {.flexbox .vcenter}
> If it's not in source control, it doesn't exist.

<p align="center">
  <img src="./screenshot_versioncontrolcartoon.png" height="375">
</p>

## Collaborative research

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.

## {.flexbox .vcenter}

> 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](github.com) is becoming a de facto central repository for open source development. E.g., all packages in Julia are distributed through GitHub; [Hadley Wickham](http://r-pkgs.had.co.nz) also recommends Git/GitHub as the best practices for R package development.

- Advertise yourself through GitHub.

## 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](https://trends.google.com/trends/explore?date=all&q=%2Fm%2F05vqwg,%2Fm%2F012ct9,%2Fm%2F08441_,%2Fm%2F08w6d6,%2Fm%2F09d6g&hl=en-US&tz=&tz=).

- Initially designed and developed by [Linus Torvalds](http://en.wikipedia.org/wiki/Linus_Torvalds) in 2005 for Linux kernel development. Git is the British English slang for unpleasant person.

<div class="centered">

> I'm an egotistical bastard, and I name all my projects after myself. First 'Linux', now 'git'.
> 
> Linus Torvalds

</div>

## Centralized version control

Svn is a **centralized** version control system:

<p align="center">
  <img src="./centralized_vcs.png" height="375">
</p>

## Distributed version control

Git is a **distributed** version control system:

<p align="center">
  <img src="./distributed_vcs.png" height="400">
</p>

## What do I need to use Git?

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

    - [github.com](github.com): unlimited public repositories, private repositories costs $, but unlimited private repositories for free from [Student Developer Pack](https://education.github.com/pack).

    - [bitbucket.org](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.

----

- A **Git client** on your own machine.

    - Linux: shipped with many Linux distributions, e.g., Ubuntu. If not, install using a package manager, e.g., `yum install git` on CentOS.

    - Mac: install by `port install git` or other package managers.

    - Windows: [GitHub Desktop](https://desktop.github.com) (GUI), [TortoiseGIT](https://tortoisegit.org) (is this good?).
    
- Don't totally rely on GUI or IDE. Learn to use Git on command line, which is needed for cluster and cloud computing.

## Git workflow

<p align="center">
  <img src="./git_workflow.png" height="450">
</p>

## Git survival commands {.smaller}

- Synchronize local Git directory with remote repository:
    ```{bash, eval=FALSE}
    git pull
    ```
same as `git fetch` plus `git merge`.

- Modify files in local working directory.

- Add snapshots to staging area:
    ```{bash, eval=FALSE}
    git add FILES
    ```

- Commit: store snapshots permanently to (local) Git repository
    ```{bash, eval=FALSE}
    git commit -m "MESSAGE"
    ```

- Push commits to remote repository:
    ```{bash, eval=FALSE}
    git push
    ```

## Git basic usage {.smaller}

- 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.,
    ```{bash, eval=FALSE}
    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-m280-2018-winter` on the server.
    
    - Clone the repository to your local machine:
    ```{bash, eval=FALSE}
    git clone git@github.com:biostat-m280-2018-winter.git
    ```

## {.smaller}

- 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

<p align="center">
  <img src="./git_branching.png" height="450">
</p>

----

- 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.
    
<p align="center">
  <img src="./git_branching_simplified.png" height="250">
</p>

----

- 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

- Obtain [Student Developer Pack](https://education.github.com/pack).

- Create a private repository `biostat-m280-2018-winter`. Add `Hua-Zhou` and `juhkim111` as your collaborators with write permission.

## {.smaller}

On your local machine: 

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

    ```{bash, eval=FALSE}
    # clone the project
    git clone git@github.com:biostat-m280-2018-winter.git
    # enter project folder
    cd biostat-m280-2018-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
    ```

## {.smaller}

- Submit and tag HW1 solution to master branch.

    ```{bash, eval=FALSE}
    # 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 {.smaller}

- 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.**