Fundamentals of Data Science for EESS

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# Fundamentals of Data Science for EESS

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## R session 03 - Git

2021-01-20

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# Outline

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# Intro to Git

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## What is Git ?

* VCS: Version control system
* Created by Linus Torvald in 2005

## What Git useful for ?

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* Keep traces of all changes done to your work
    * Undo changes
    * Perform test on software you are developing 
    * Backup your work (`GitHub`)
* Team work
    * Collaborate with a small team (`GitHub`)
    * Participate into software development (`GitHub`)
    * Write paper in collaborative way (`Overleaf` - On-line Latex)
    * Provide supplementary data for your papers (`Figshare`)
...

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* Pro GIT: https://git-scm.com/book/en/v2
* GitHub guide: https://guides.github.com
* Happy Git with R: https://happygitwithr.com/

## Software

* Git: https://git-scm.com
* Git desktop: https://github.com
* GitHub account: https://desktop.github.com

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<img src="img/Git-progit2.png" width="70%" style="display: block; margin: auto;" />
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## Version control system (VCS) - Traditional

<img src="img/git-storage-traditional.png" width="60%" style="display: block; margin: auto;" />
 
* Store data as changes to a base version of each file
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## Version control system (VCS) - Git

* Git takes a snapshot at each time
* Only stores what has changed
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* Changes are stored in a **local database** inside your directory (.git)

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## Three states for a file: committed, modified, and staged

<img src="img/git-structure.png" width="30%" style="display: block; margin: auto;" />
* Need to be familiar with the vocabulary
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* **Committed**: data is safely stored in your local database. 
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* **Modified**: file changed BUT not committed in your database yet. 
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* **Staged**: modified file is marked to go into your next commit snapshot.

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# Local Git - Committing

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## Three different ways of committing
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* Using R studio interface
* Using GitHub Desktop (my prefered)
* Using Git bash - The hard way
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## Create R project and initialize Git

.student[
* Create project in a new directory : git_01
* Create a new project
* Select "Create git repository"
* You can also change Project Options (Tools/Project Options/Git/Git)
* Create a new Rmd file and save it
]
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.student[
* On top-right window go Git tab
* Stage the files you want to commit
* Commit
    * Must write a message explaining what you changed
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## Commiting changes with R
.student[
* Make a new change to the Rmd file
* Stage and Commit
* R shows the differences
* Enter new comment and commit
]

.student[
* Click on history
* Each commit has a **hash** value
    * a80df29cc709e25db49cdfed11c0c1b0399d4a72
* Can open first version of the Rmd file
]
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## Commit with GitHub Desktop
.student[
* Make a new change under R
* Save
* Open GitHub Desktop
]

--
.student[
* File/New repository
* Add existing repository
* Navigate to directory
]
--
.student[
* Commit change
* You can check in R the Commit
]
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## Commit with Git bash

```shell
$ git status
$ git add git-01.Rmd
$ git status
$ git commit
```
.student[
* Surprise, surprise you are in the VIM editor
  * Enter the commit message
  * ESC - : - x - ENTER
* Check in GitHub Desktop
]
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# Local Git - Reverting

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## Revert Commit with GitHub Desktop

.student[
* History
* Right-click : Revert Commit
]
--
.student[
* Go back to R
* Magic the changes have been reverted...
* Examine history (refresh if necessary)
* In fact revert is a **new commit**
]

## [Next slide: GitHub](#GitHub)

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## Revert Commit with Git bash

```shell
$ git log
$ git revert <hash>
$ git revert a80df29cc709e25db49cdfed11c0c1b0399d4a72
```
.student[
* Check in Rstudio the reversal
]
]
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# Local Git - Branching

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## Why create branches ?

.font150[
* Testing: Do not destroy your own work
* Collaborative work: Different people can contribute and fix bugs
]

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## How the data are stored

<img src="img/git-commit-00.png" width="40%" style="display: block; margin: auto;" />
 
Three elements:
* **blobs** - contain the contents of the different files
* **tree** - pointer to the list of the blobs
* **commit** - pointer to the tree
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## Commit

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## The master branch

<img src="img/git-commit-02.png" width="60%" style="display: block; margin: auto;" />
 
A branch in Git is simply a movable **pointer** to one commit.

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## Create a new branch

```shell
$ git branch testing
```

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## Move the HEAD to the new branch

```shell
$ git checkout testing
```

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## Make one commit on the testing branch

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## Move the HEAD back to the master branch

```shell
$ git checkout master
```

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## Do one commit on the master branch

<img src="img/git-branch-05.png" width="50%" style="display: block; margin: auto;" />
 
* Now we have two diverging branches

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## Merging

```shell
$ git checkout master
```

* Merging

```shell
$ git merge testing
Auto-merging README
Merge made by the 'recursive' strategy.
 README | 1 +
 1 file changed, 1 insertion(+)
```
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## After merging

* Now can delete the branch `testing`

```shell
$ git branch -d testing
```

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## Let's do it using R studio
Could be done also with GitHub Desktop or Git bash

.student[
* Go to Git tab
* Create a new branch `test`or the name you want
]
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* Notice that R creates the branch and switch to the branch

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.student[
* Make some change in the Rmd file and save
* While on branch `test`, commit
* Go back and forth between the two branches `master` and `test`
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* Observe how the Rmd file changes back and forth...
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.student[
* Go to branch `master`
* Make some change in the Rmd file (elsewhere e.g. Plot) and save
* While on branch `master`, commit
]

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## Merge back
Could be done also with Git bash

.student[
* Make sure you are on branch `master`
* Go to GitHub Desktop
* Branch / Merge into Current Branch
* Select the `master`
]

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* There can be conflicts
    * You need to edit file to solve the conflict

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# GitHub

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name: GitHub

## Upload your project to GitHub

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## GitHub

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## Edit on GitHub

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## Computer <--> Server synchronization

* How are we going to synchronize these changes back to our computer ?

* **Pull**: from server to computer
* **Push**: from computer to server

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## Pull from server

* If you make commits locally you need to **push** to server
* You can push several commits at once

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## Cloning a project from GitHub

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## Pull request
* You work on a project with someone else
* You cloned the project into your computer
* You created a new branch and made some change
* You want to merge back into the project

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.student[
* R
    * Create a new branch `test2` and switch
    * Make some changes
    * Save and commit
* GitHub Desktop
    * Push changes to GitHub
    * Branch / Create a Pull Request
* GitHub
    * Validate the Changes and Merge into `master`
    * Delete the branch `test2`
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# Recap

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* Save and Commit
* Push and Pull
* Branching and merging (use only in multiuser projects)
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