First Steps in Learning the Use of Git and GitHub in RStudio

class: title-slide, center, top
background-image: url(img/git_github.png)
background-position: 90% 75%, 75% 75%
background-size: 20%, contain

**Mouna Belaid**<br>
October 25th, 2022
]

---
name: about-me
layout: false
class: about-me-slide, inverse, middle, center

# About me

## Mouna Belaid

### Business Intelligence Consultant<br>Prime Analytics - Paris, France<br>Organizer of R-Ladies Paris

[<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"></path></svg>mounabelaid.netlify.app/](https://mounabelaid.netlify.app/)
[<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path></svg>@mounaa_belaid](https://twitter.com/mounaa_belaid)
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[<svg viewBox="0 0 576 512" style="position:relative;display:inline-block;top:.1em;height:1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M549.655 124.083c-6.281-23.65-24.787-42.276-48.284-48.597C458.781 64 288 64 288 64S117.22 64 74.629 75.486c-23.497 6.322-42.003 24.947-48.284 48.597-11.412 42.867-11.412 132.305-11.412 132.305s0 89.438 11.412 132.305c6.281 23.65 24.787 41.5 48.284 47.821C117.22 448 288 448 288 448s170.78 0 213.371-11.486c23.497-6.321 42.003-24.171 48.284-47.821 11.412-42.867 11.412-132.305 11.412-132.305s0-89.438-11.412-132.305zm-317.51 213.508V175.185l142.739 81.205-142.739 81.201z"></path></svg> Mouna Belaid](https://www.youtube.com/channel/UCID33pDULsQg2y4FVlv4CnQ)

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<a class="footer-link" href="https://bit.ly/3f4moca">bit.ly/3f4moca; Mouna Belaid</a>

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# Session Outline

.pull-left[
1) Overview of Version Control, benefits of version control, and popular version control systems

2) What is Git?

3) What is GitHub?

4) Getting the most out of GitHub and Git
  - Connect a new RStudio project started from scratch to GitHub
  - Learn about GitHub fundamentals
  - Clone an existing GitHub Repository to an RStudio Project
  - Make commits
]

5) Submission of a new Cheatsheet to the ["Cheatsheets" GitHub Repository](https://github.com/rstudio/cheatsheets) maintained by RStudio
]

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# Requirements

--
template: requirements

.pull-left-narrow[
.center[<img src="img/r-rstudio.png" width="180%"/>]]
.pull-right-wide[### .black[R and RStudio installed]]

.pull-left-narrow[
.center[<img src="img/logo-Git.png" width="50%"/>]]
.pull-right-wide[### .black[Git installed]]

.pull-left-narrow[
.center[<svg viewBox="0 0 496 512" style="position:relative;display:inline-block;top:.1em;height:2em;" xmlns="http://www.w3.org/2000/svg">  <path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg>]]
.pull-right-wide[### .black[Free GitHub account]]

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template: question

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## What is version control?

.panelset[
.panel[.panel-name[Definition]
.pull-left[
Version control, also known as **source control**, is the practice of tracking and managing changes to software code.

Version control systems are software tools that help software teams manage changes to source code over time. 
]
.pull-right[
.center[
![:scale 140%](img/project-history.png)
<font size="-0.5"> The Turing Way project illustration by Scriberia. Used under a CC-BY 4.0
licence. DOI: <a href="https://doi.org/10.5281/zenodo.3332807">10.5281/zenodo.3332807</a> </font>
]
]
]

.panel[.panel-name[Benefits of version control]
.pull-left[
- A complete .my-red[long-term] change history of every file

- Branching and merging

- Ability to make your work more .my-red[reproducible]
]

.pull-right[
.center[
![:scale 140%](img/illustration1.png)
<font size="-0.5"> GitHub illustrated series by Allison Horst and Julie Lowndes.
A collaboration around open science, coding, teaching, and art.
<a href="https://www.openscapes.org/blog/2022/05/27/github-illustrated-series/">openscapes.org/blog/2022/05/27/github-illustrated-series/</a> </font>
]
]

]

---
template: question

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## What is Git?

.pull-left-narrow[
.center[<img src="img/logo-Git.png" width="100%"/>]]
.pull-right-wide[### .black[Git is an open source software for version control, initially developed in 2005 by Linus Torvalds, the creator of the Linux operating system kernel]]

--
.pull-right-wide[### .black[Git is a distributed version control tool to track the changes in the source code of a project]]

--
.pull-right-wide[### .black[Git's key design objectives are functionality, performance, security, and flexibility]]

---
template: question

---

## What is GitHub?

.pull-left-narrow[
.center[<img src="img/github.png" width="50%"/>]]
.pull-right-wide[### .black[GitHub is the most popular hosting service for collaborating on code using Git. Other hosting services include Bitbucket, and Gitlab.]]

--
.pull-right-wide[### .black[GitHub is a collaboration platform.]]

--
.pull-right-wide[### .black[GitHub uses <img src="img/logo-Git.png" width="20%"/> the most popular open source version control software, to track every contribution and contributor to a defined project.]]

---
.center[
![:scale 80%](img/illustration2.png)
<font size="-0.2"> GitHub illustrated series by Allison Horst and Julie Lowndes.
A collaboration around open science, coding, teaching, and art.
<a href="https://www.openscapes.org/blog/2022/05/27/github-illustrated-series/">openscapes.org/blog/2022/05/27/github-illustrated-series/</a> </font>
]

---
template: question
🚀
# Getting Started with Git

---

## Getting Started with Git

.panelset[
.panel[.panel-name[Check that Git is installed]
**Step 1.** In	the Terminal of RStudio, enter the following code

```r
which git
```

You can check the version of Git

```r
git --version
```
]

.panel[.panel-name[Communicate with GitHub via HTTPS]
.pull-left[
**Step 2.** Go to [https://github.com/settings/tokens](https://github.com/settings/tokens) and click *Generate token*

![:scale 100%](img/token1.png)

**Step 3.** Copy the generated PAT to your clipboard. Or leave that browser window open and available for a little while, so you can come back to copy the PAT. 
]

![:scale 100%](img/token2.png)
Or, from RStudio, do the following:

```r
usethis::create_github_token()
gitcreds::gitcreds_set()
```

]
]

.panel[.panel-name[Tell Git who you are]
**Step 4.** In RStudio, click *Tools* -> *Shell* and type each line separately:

```r
git config --global user.email "jack.bel@gmail.com" # use your mail address instead
git config --global user.name "jack.bel" # use your GitHub username instead
```
]
]

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template: question

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## Getting the most out of GitHub and Git

.panelset[
.panel[.panel-name[1) Create	a	new	RStudio	Project	and	push it	to GitHub]
🚀 **Learning objectives**
               
- Create a new repository on GitHub
             
- Make commits
             
- Link a remote GitHub repository to a local repository
]

.panel[.panel-name[2) Clone	an	existing	GitHub	Repository	to	an	RStudio	Project]
🚀 **Learning objectives**

- Connect a new RStudio project started from scratch to GitHub

- GitHub fundamentals

- Explore a GitHub repository
] 
]

---
template: question

---

## GitHub Knowledge Base

---

## GitHub Knowledge Base

---

## GitHub Knowledge Base

---

## GitHub Knowledge Base

---

## GitHub Knowledge Base

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## GitHub Knowledge Base

---

## GitHub Knowledge Base

---

## GitHub Knowledge Base

.pull-left[
.my-blue[Commands] | .my-blue[Operations]
-------------           | -------------
`git init <directory>`  | Create empty Git repo in specified directory
`git clone <repository>` | Clone a repository located at <repository> your local machine
`git config user.name <username>` | Define author name to be used for all commits in current repository
`git add <directory>` | Stage all changes in <directory> for the next commit
]

.pull-right[
.my-blue[Commands] | .my-blue[Operations]
------------- | -------------
`git commit -m <"message">` | Commit the staged snapshot, but instead of launching a text editor, use <"message"> as the commit message
`git status` | List which files are staged, unstaged, and untracked
`git log` | Display the entire commit history using the default format
]

---

## GitHub Knowledge Base

.my-blue[Commands] | .my-blue[Operations]
------------- | -------------
`git pull <remote>` | Fetch the specified remote’s copy of current branch and immediately merge it into the local copy
`git push <remote> <branch>` | Upload local repository content to a remote repository

**Pull requests** are proposed changes to a repository submitted by a user and accepted or rejected by a repository's collaborators. Pull requests each have their own discussion forum.

**Issues** are suggested improvements, tasks or questions related to the repository. Issues can be created by anyone (for public repositories), and are moderated by repository collaborators. Each issue contains its own discussion thread.

---

---

## 1) Create	a	new	RStudio	Project	and	push	it	to	GitHub

.pull-left[
**Step 1.** In	RStudio	click	*File*	>	*New	Project*	>	*New	Directory* > *New	Project*
![:scale 100%](img/project.png)
![:scale 100%](img/project2.png)
]
.pull-right[
**Step 2.** Give a name to the project in the *Directory name* tab and select	*Create	a	git	repository* then click on *Create Project*
![:scale 100%](img/project3.png)
]

---

## 1) Create	a	new	RStudio	Project	and	push	it	to	GitHub

.pull-left[
**Step 3.** Create a new	R script. In the next steps, this script will be	added	to a repository on GitHub by using Git.
![:scale 100%](img/project4.png)
]
.pull-right[
**Step 4.** The *Welcome.R* script is created and is saved in the project directory. It	should also	appear in	the Git tab	next to	the	*Environment*	or the *History*	tab. You need to select	this R script on the Git panel.	
![:scale 100%](img/project5.png)
]

---
name: repository
## 1) Create	a	new	RStudio	Project	and	push	it	to	GitHub

.pull-left[
**Step 5.** Now	click *Commit*. A new window is open. Enter	an	identifying	
message	in the *Commit	message* tab.
![:scale 100%](img/project6.png)
You	have	now	committed	the	current	version	of	this	*Welcome.R* script	to	your	repository	on	your	computer. Now	you	want	to push the	contents	of	this	commit	to	GitHub,	so	it	is	also	backed-up	off	site	and	available to	collaborators.
]
.pull-right[
**Step 6.** Go	to [GitHub](https://github.com/).	Create	a	*New	repository*,	and	name	it
]

---

## 1) Create	a	new	RStudio	Project	and	push	it	to	GitHub

**Step 7.** In the *Terminal* tab, type	the following three lines of code	and	click	enter

```r
git remote add origin https://github.com/MounaBelaid/Test.git # Test is the repository name that I've created on GitHub
git branch -M main
git push -u origin main
```

![:scale 100%](img/project7.png)

---
template: question

---

## 2) Clone	an	existing	GitHub	Repository	to	an	RStudio	Project

.pull-left[
**Step 1.** In	RStudio	click	*File*	>	*New	Project*	>	*Version Control* > *Git*
![:scale 100%](img/PR_Clone1.png)
]
.pull-right[
**Step 2.** Go	to	the	Resporitory	on GitHub and	click	on *Code* and make a copy of the  git link in order to clone this repository i.e to get a copy of this existing	Git respository into your local machine.
![:scale 100%](img/PR_Clone2.png)
]

---

## 2) Clone	an	existing	GitHub	Repository	to	an	RStudio	Project

**Step 3.** Go back to you R session and enter the link	in *Respository	URL* then click on *Create Project*

![:scale 45%](img/PR_Clone3.png)

---
template: question