prez.Rmd

---
title: "Introduction to Git and GitHub with RStudio"
author: "Olivier Gimenez"
date: "15/09/2020"
output:
  xaringan::moon_reader:
    css: [default, metropolis, assets/css/footer.css, metropolis-fonts, assets/css/metropolis-ak_dc.css]
    lib_dir: libs
    nature:
      beforeInit: "https://platform.twitter.com/widgets.js"
      highlightStyle: github
      titleSlideClass: [middle, left]
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---
layout: true

<div class="my-footer"><span> HAIR meeting    
&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;
&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;
                    @oaggimenez <a href="https://twitter.com/oaggimenez">`r shiny::icon("twitter")` </a>
                    oliviergimenez <a href="https://github.com/oliviergimenez">`r shiny::icon("github-alt")` </a>
                    </span></div>

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(magrittr)
```

---

# Rings a bell? 

<center>

<img src="http://www.phdcomics.com/comics/archive/phd101212s.gif" height="500px">
 
</center>
 
---

# Is your workflow...

<center>

<img src="assets/definitions.jpg" width="700px" />

</center>



---

# Why reproducible science?

<center>

<img src="assets/natureCapture.png" width="700px" />

</center>


---

# Why reproducible science?

<center>

<img src="assets/leMonde_science.png" width="700px" />

</center>



---

# Version Control

### What is it? `r emo::ji("thinking")`

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.

---

# Git, Github & RStudio

#### Before: git only through the terminal `r emo::ji("cry")`

--

***

## Now: RStudio + `usethis` `r emo::ji("package")` == `r emo::ji("heart")` `Git` & `GitHub` `r emo::ji("star_struck")`

.center[
![](https://media.giphy.com/media/GA2FNpP1kAQNi/giphy.gif)
]


---
# Configure git & GitHub

### Configure git

**Check your configuration**

```{r, eval=FALSE}
usethis::git_sitrep()
```


**Set your configuration**

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

```{r, eval=FALSE}
usethis::use_git_config(
    user.name = "Jane",
    user.email = "jane@example.org")
```

---
# Configure GitHub authentication

### Get GITHUB Personal Authorisation Token

```{r, eval=F}
usethis::browse_github_pat()
```


<img src="assets/browse_github.png" height="300px">

---

### Store in `.Renviron` file

```{r, eval=F}
usethis::edit_r_environ()
```

<img src="assets/GITHUB_PAT.png" height="400px">


---
# Initialise git


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

It's now **a repository**

<img src="assets/project_git.png" height="200px">



---

# RStudio Projects

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

<br>
 
.pull-left[
- **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
]

.pull-right.center[

**File > New Project > New Directory**

<img src="assets/new_project.png" height=200px>
]




---
# Git panel

## Integrated graphical user interface

<br>

.center[
<img src="assets/git_tab.png" height="300px">
]


---
# Git terms

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

<br>

* (*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)

---
# Git RStudio workflow

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

#### stage files
<img src="assets/git_add.png" height="150px">
]

.pull-right[
#### commit changes
<img src="assets/git_commit.png" width="600px">
]
---

# Share on GitHub

#### Create repo


```{r, eval=FALSE}
usethis::use_github(protocol = "https")
```

<img src="assets/my_awesome_repo.png" width="750px">

#### Push further changes

<img src="assets/push_github.png" height="50px">


---

# 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()`

---
# GitHub issues

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

<img src="assets/github_issues.png" width="800px">

---

# 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)


---
# Resources

<br>

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

<br>

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

<br>

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

<br>

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

---

# Virtuous research cycle

<center>

<img src="assets/researchcycle.jpg" width="700px" />

</center>