RStudio and Git

# RStudio and Git
## <a href="https://privefl.github.io/R-presentation/rstudio-git.html" class="uri">https://privefl.github.io/R-presentation/rstudio-git.html</a>
### Florian Privé & Magali Richard
### January 18, 2017

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# RStudio

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## 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**

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## 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()`)

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## 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.

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## 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/

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## More

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

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# Version control (Git)

## tracks changes to your code

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## You don't use version control?

<br>

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## 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.

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## Why should you use version control?

### Version control for the researcher

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## Why should you use version control?

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

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## Why should you use version control?

### To work from anywhere

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## 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)]

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## Why should you use version control?

### To get a nice mosaic on GitHub

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## 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.

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## 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..

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## 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

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

<br>

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

### When you open a project, always pull

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

### Before you close a project, always push

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## Help with Git

- [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)

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# Demo: RStudio & GitHub

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

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## 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

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## 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)

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## 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)

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## 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

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## 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)
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## 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)

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# 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)