rstudio-git.Rmd

---
title: "RStudio and Git"
subtitle: "https://privefl.github.io/R-presentation/rstudio-git.html"
author: "Florian Privé & Magali Richard"
date: "January 18, 2017"
output:
  xaringan::moon_reader:
    includes:
      after_body: include_twitter.html
    lib_dir: libs
    nature:
      highlightStyle: github
      highlightLines: true
      countIncrementalSlides: false
---

```{r setup, include=FALSE}
options(htmltools.dir.version = FALSE)
knitr::opts_chunk$set(echo = FALSE, fig.align = "center", dev = "svg")
```

class: center, middle, inverse

# RStudio

---

## RStudio Features

- everything you can expect from a good IDE

- keyboard shortcuts I use
  1. *Crtl + Space* (autocompletion)
  2. *Ctrl + Up* (command history & search)
  3. *Ctrl + Click* (function source code)
  3. *Ctrl + Enter* (execute line of code)
  4. *Ctrl + Shift + K* (knit)
  4. *Ctrl + Shift + B* (build package or website)
  4. *Ctrl + Shift + M* (pipe)
  4. *Alt + Shift + K* to see all shortcuts
  4. ...

- Panels (everything is integrated, including **Git**)

- **R Projects**

---

## Releases 

- Version 1.0 (November 1st, 2016)
<ul>
<li>Authoring tools for <a href="http://rmarkdown.rstudio.com/r_notebooks.html">R Notebooks</a>.</li>
<li>Integrated support for the <a href="http://spark.rstudio.com">sparklyr</a> package (R interface to Spark).</li>
<li>Enhanced data import tools based on the <a href="https://github.com/hadley/readr">readr</a>, <a href="https://github.com/hadley/readxl">readxl</a> and <a href="https://github.com/hadley/haven">haven</a> packages.</li>
<li>Performance profiling via integration with the <a href="https://github.com/rstudio/profvis">profvis</a> package.</li>
<li>Authoring tools for R Markdown <a href="http://rmarkdown.rstudio.com/rmarkdown_websites.html">websites</a> and the <a href="https://bookdown.org/">bookdown</a> package.</li>
</ul>

- Version 1.1.383 (October 9th, 2017)
  - integrated terminal
  - new features for connections to data bases
  - better object explorer (`View()`)

---

## R Projects

- **Meaningful structure** in one folder

- The working directory automatically switches to the project's folder.

- File tab displays the associated files and folders in the project

- History of R commands and open files.

- Any settings associated with the project, such as Git settings, are loaded.

- Note that a *set-up.R* or even a *.Rprofile* file in the project's root directory enable project-specific settings to be loaded each time people work on the project.

---

## Project-oriented workflow

<blockquote class="twitter-tweet" data-lang="fr" align="center"><p lang="en" dir="ltr">The only two things that make <a href="https://twitter.com/JennyBryan?ref_src=twsrc%5Etfw">@JennyBryan</a> 😤😠🤯. Instead use projects + here::here() <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> <a href="https://t.co/GwxnHePL4n">pic.twitter.com/GwxnHePL4n</a></p>&mdash; Hadley Wickham (@hadleywickham) <a href="https://twitter.com/hadleywickham/status/940021008764846080?ref_src=twsrc%5Etfw">11 décembre 2017</a></blockquote>
<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

Read more at https://www.tidyverse.org/articles/2017/12/workflow-vs-script/

---

## More

Chapter [*Efficient set-up*](https://bookdown.org/csgillespie/efficientR/set-up.html) of

```{r, out.width="45%"}
knitr::include_graphics("https://csgillespie.github.io/efficientR/figures/f0_web.png")
```

---

class: center, middle, inverse

# Version control (Git)

## tracks changes to your code

---

## You don't use version control?

<br>

```{r, out.width="75%"}
knitr::include_graphics("https://www.tacomaworld.com/attachments/i-also-like-to-live-dangerously-jpg.760853/")
```

---

## Why should you use version control?

Have you ever:

- **Made a change to code, realised it was a mistake and wanted to revert back?**
- **Lost code or had a backup that was too old?**
- Had to maintain multiple versions of a product?
- Wanted to see the difference between two (or more) versions of your code?
- Wanted to prove that a particular change broke or fixed a piece of code?
- Wanted to review the history of some code?
- **Wanted to submit a change to someone else's code?**
- **Wanted to share your code, or let other people work on your code?**
- Wanted to see how much work is being done, and where, when and by whom?
- Wanted to experiment with a new feature without interfering with working code?

In these cases, and no doubt others, a version control system should make your life easier. 

.footnote[Source: https://stackoverflow.com/a/1408464/6103040]

---

## Why should you use version control?

### Version control for the researcher

```{r, out.width="45%"}
knitr::include_graphics("http://www.datacarpentry.org/rr-version-control/fig/phd101212s.png")
```

---

## Why should you use version control?

### Version control for the data analyst: reproducible workflow

<center>
<iframe width="560" height="315" src="https://www.youtube.com/embed/s3JldKoA0zw" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
</center>

.footnote[Also, see https://stackoverflow.com/q/2712421/6103040]

---

## Why should you use version control?

### To work from anywhere

```{r, out.width="85%"}
knitr::include_graphics("git.svg")
```

---

## Why should you use version control?

### Working with GitHub, a line on your CV

<br>

> A lot of students have said to me later, even first-year undergraduates, that using GitHub has helped them a lot when they went for an internship or a research position interview.

> They are able to say, "Oh, I already have worked with GitHub. I'm familiar with it. I know how it works.” So I think they are at least able to put that on their CVs and go into a situation where there's a research or data analysis team and say, "Yeah, sure. I am actually familiar with the same tools that you use."
>
> -- Mine Cetinkaya-Rundel, Duke University, RStudio

.footnote[[Read more](https://github.com/blog/2336-invest-in-tools-students-can-grow-with-github-and-rstudio-for-data-science-at-duke-university)]

---

## Why should you use version control?

### To get a nice mosaic on GitHub

```{r, out.width="80%"}
knitr::include_graphics("webshot-mosaic-github.png")
```

---

## Why should you use version control? 

### February session: Best coding practices

A. Arnaud & J. Arbel will focus on

- coding style

- R packages (RStudio & Git are super useful for developing!!)

<br>

### June session: Make your personal webpage with R

We will focus on using R Markdown & GitHub in order to easily make websites, presentations & reports, and make them available online.



---

## Git platforms (share your code, collaborate)

- [GitHub](https://github.com/magrichard), [documentation](https://guides.github.com/activities/hello-world/) (only free for public repositories)

- [GitLab UGA](https://gricad-gitlab.univ-grenoble-alpes.fr/), [documentation](https://docs.gricad-pages.univ-grenoble-alpes.fr/help/) or just [GitLab](https://about.gitlab.com/) (open source & free)

- [Bitbucket](https://bitbucket.org/) (free with less than 5 collaborators)

- any server..

---

## 3 main commands: commit, push, and pull

- pull: update your local project with the latest version of the main project

- commit: snapshot of your code at a specified point in time

- push: merge your local modifications with the main project


---

## Simple (solo) use of git to prevent merge conflicts

<br>

```{r, out.width="90%"}
knitr::include_graphics("meme-merge-conflicts.jpg")
```

---

## Simple (solo) use of git to prevent merge conflicts

### When you open a project, always pull

```{r, out.width="60%"}
knitr::include_graphics("http://s2.quickmeme.com/img/73/730acd1051914ae6cb59ae7e751498c477bfd0191cc2a07f90682451dc1da9d5.jpg")
```

---

## Simple (solo) use of git to prevent merge conflicts

### Before you close a project, always push

```{r, out.width="80%"}
knitr::include_graphics("https://hikaruzone.files.wordpress.com/2015/10/in-case-of-fire-1-git-commit-2-git-push-3-leave-building2.png?w=800&h=559")
```

---

## Help with Git

```{r, out.width="30%"}
knitr::include_graphics("https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcQdltx925phiPYsw72GpjM30TBMn30YLTi8kAlf-N2sC_kTQNTiFQ")
```

- [H. Wickham's book](http://r-pkgs.had.co.nz/git.html)

- [Happy Git and GitHub for the useR](http://happygitwithr.com/)

- [Git cheatsheet](https://services.github.com/on-demand/downloads/github-git-cheat-sheet.pdf)

- [When things go wrong](https://github.com/k88hudson/git-flight-rules)

- [To fix a mistake](http://ohshitgit.com/)

- [Create a new branch with git and manage branches](https://github.com/Kunena/Kunena-Forum/wiki/Create-a-new-branch-with-git-and-manage-branches)

---

class: center, middle, inverse

# Demo: RStudio & GitHub

## [Also, see my video](https://youtu.be/8Q3fYwgyNGQ)

---

## Create a local Git repository

1 - RStudio > New Project > New directory > R packages + create a git repository

2 - Go to the git menu, on the top-right, and add your files of interest: 

- (i) save your changes, 

- (ii) open the commit window, 

- (iii) select files, 

- (iv) stage files, 

- (v) write a commit message, 

- (vi) commit

---

## Create a local Git repository 

1 - RStudio > New Project > New directory > R packages + create a git repository

2 - Go to the git menu, on the top-right, and add your files of interest: 

3 - Synchronising with GitHub. Go to RStudio > Tools > Shell

- create a new repo on [GitHub](https://github.com/new) and give it the same name as your package

- push your local respository from the command line

`git remote add origin https://github.com/magrichard/testgit.git`

`git push -u origin master`

4 - Check that your GitHub repository is updated [GitHub repo](https://github.com/magrichard/testgit)

---

## Publishing your code on GitHub (or Gitlab...)


1 - Change something (modify the hello.R file and create a new R file)

2 - Go to the git menu, on the top-right, and add your files of interest: 

- (i) save your changes, 

- (ii) open the commit window, 

- (iii) select files, 

- (iv) stage files, 

- (v) write a commit message, 

- (vi) commit

- **(vii) push**

3 - Check that your GitHub repository is updated [GitHub repo](https://github.com/magrichard/testgit)

---

## Import a GitHub repository into RStudio

1 - On GitHub: [create new repo](https://github.com/new) with a README and a description. Leave all the other options as is, then click Submit. (no license, no gitignore...)

2- **CLONE** your repository. **Copy** the web URL


3- In RStudio: Create a New Project > Version Control > Git and **paste** the web URL of the project. Congratulation, you have cloned your new repo.

- => You now have access to Git functionalities within Rstudio

---

## Collaborative work on GitHub

Option 1 - Equal collaborators: Everyone can pull, commit and push on the same 'master' branch

Option 2 - One coordinator (master branch, owns the project) and one (or more) contributor:

![workflow](workflow.png)
---

## Collaborative work on GitHub

Option 1 - Equal collaborators: Everyone can pull, commit and push on the same 'master' branch

Option 2 - One coordinator (master branch, owns the project) and one (or more) contributor:

- Fork the original repo

- Clone it, and link it to the master repo 

`git remote add upstream https://github.com/magrichard/testgit.git`

- Uptade your fork with latest changes form the master repo (fetch and merge) 

`git pull upstream master`

- Commit, push on your fork, and create a [Pull Request](https://help.github.com/articles/creating-a-pull-request/) (that will be reviewed and accepted by the master)

---

class: center, middle, inverse

# Thanks!

<br>

Presentation available at

https://privefl.github.io/R-presentation/rstudio-git.html

<br>

Twitter: [@privefl](https://twitter.com/privefl) & [@magg_richard](https://twitter.com/magg_richard)

GitHub: [@privefl](https://github.com/privefl) & [@magrichard](https://github.com/magrichard)

.footnote[Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan).]