Introduction to Git and GitHub with RStudio

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# Introduction to Git and GitHub with RStudio
### Olivier Gimenez
### 15/09/2020

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# Rings a bell?

<img src="http://www.phdcomics.com/comics/archive/phd101212s.gif" height="500px">
 
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# Is your workflow...

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# Why reproducible science?

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# Why reproducible science?

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# Version Control

### What is it? 🤔

The **management of changes** to documents, computer programs, large web sites, and other collections of information.

### Git <img src="https://git-scm.com/images/logos/downloads/Git-Logo-2Color.png" height="25px" >

Open source (free to use) **Version control software.**

### GitHub <img src="https://raw.githubusercontent.com/annakrystalli/rrresearch/master/docs/assets/github_logo.jpg" height="25px">

A **website** (https://github.com/) that allows you to **store your Git repositories online** and makes it easy to collaborate with others.

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# Git, Github & RStudio

#### Before: git only through the terminal 😢

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## Now: RStudio + `usethis` 📦 == ❤️ `Git` & `GitHub` 🤩

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# Configure git & GitHub

### Configure git

**Check your configuration**

**Set your configuration**

Use your github username and and the email you used to sign-up on GitHub

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# Configure GitHub authentication

### Get GITHUB Personal Authorisation Token

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### Store in `.Renviron` file

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# Initialise git

### Initialise **RStudio project** with Git by **just checking a box!**

It's now **a repository**

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# RStudio Projects

## Use RStudio projects to keep materials associated with a particular analysis together

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- **Self contained** and **portable**
- **Working directory set to root** of project on launch
- **Fresh session** everytime the project is launched

See Jenny Bryan's post on [**project oriented workflows**](https://www.tidyverse.org/articles/2017/12/workflow-vs-script/) for more details
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**File > New Project > New Directory**

<img src="assets/new_project.png" height=200px>
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# Git panel

## Integrated graphical user interface

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<img src="assets/git_tab.png" height="300px">
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# Git terms

* **repository** your project folder
 
* **commit** a snapshot of your repo
 
* **push** send commits to a remote
 
* **pull** get commits from a remote

* (*clone* get the repository from the remote for the first time)
* (*branch* a movable label that points to a commit)
* (*merge* combining two branches)
* (*remote* a computer with the repository on it)

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# Git RStudio workflow

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#### view file status
<img src="assets/git_view.png" height="150px">

#### stage files
<img src="assets/git_add.png" height="150px">
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#### commit changes
<img src="assets/git_commit.png" width="600px">
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# Share on GitHub

#### Create repo

#### Push further changes

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# Anatomy of a GitHub repo

- **`README`**. Explain what your project is, and how to use it. 
  + `usethis::use_readme_md()`
  + `usethis::use_readme_rmd()`

- **`LICENSE`**. Without a licence, the contents of the repository are technically closed. 
  + Examples licence [MIT](https://tldrlegal.com/license/mit-license): `usethis::use_mit_license(name = "Olivier Gimenez")`
  + `?licenses`: details of functions available to generate licenses
  + [https://choosealicense.com/](https://choosealicense.com/) help on choosing a licence.

- **`CONTRIBUTING.md`** - guidelines for contributors.
  + `usethis::use_tidy_contributing()` provides a realtively strict but instructive template

- **`CODE_OF_CONDUCT.md`** set the tone for discourse between contributors. 
  + `use_code_of_conduct()`

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# GitHub issues

### use GitHub issues to plan, record and discuss tasks.

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# Why using a remote like GitHub ?

* A backup of your repository

* Work with others (not covered)

* Increase your visibility

* Increase interactions with users

* Easy distribution of packages (without CRAN submissions)

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# Resources

#### I used many slides from [Anna Krystalli](https://annakrystalli.me/)

#### Also, see our [FRB-Cesab and GDR EcoStat Workshop on reproducible research in ecology](https://frbcesab.github.io/datatoolbox/index.html#1)

#### Check out [Happy Git and GitHub for the useR](https://happygitwithr.com/) for more

#### The British Ecological Society has [A Guide to Reproducible Code in Ecology and Evolution](https://colauttilab.github.io/Readings/BES-Reproducible-Code.pdf)

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# Virtuous research cycle

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