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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>Using with </title>
<meta charset="utf-8" />
<meta name="author" content="Maxime Jaunatre" />
<script src="libs/header-attrs/header-attrs.js"></script>
<link href="libs/remark-css/default.css" rel="stylesheet" />
<link href="libs/remark-css/metropolis.css" rel="stylesheet" />
<link href="libs/remark-css/metropolis-fonts.css" rel="stylesheet" />
</head>
<body>
<textarea id="source">
class: center, middle, inverse, title-slide
.title[
# Using <svg viewBox="0 0 448 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M100.59 334.24c48.57 3.31 58.95 2.11 58.95 11.94 0 20-65.55 20.06-65.55 1.52.01-5.09 3.29-9.4 6.6-13.46zm27.95-116.64c-32.29 0-33.75 44.47-.75 44.47 32.51 0 31.71-44.47.75-44.47zM448 80v352a48 48 0 0 1-48 48H48a48 48 0 0 1-48-48V80a48 48 0 0 1 48-48h352a48 48 0 0 1 48 48zm-227 69.31c0 14.49 8.38 22.88 22.86 22.88 14.74 0 23.13-8.39 23.13-22.88S258.62 127 243.88 127c-14.48 0-22.88 7.84-22.88 22.31zM199.18 195h-49.55c-25-6.55-81.56-4.85-81.56 46.75 0 18.8 9.4 32 21.85 38.11C74.23 294.23 66.8 301 66.8 310.6c0 6.87 2.79 13.22 11.18 16.76-8.9 8.4-14 14.48-14 25.92C64 373.35 81.53 385 127.52 385c44.22 0 69.87-16.51 69.87-45.73 0-36.67-28.23-35.32-94.77-39.38l8.38-13.43c17 4.74 74.19 6.23 74.19-42.43 0-11.69-4.83-19.82-9.4-25.67l23.38-1.78zm84.34 109.84l-13-1.78c-3.82-.51-4.07-1-4.07-5.09V192.52h-52.6l-2.79 20.57c15.75 5.55 17 4.86 17 10.17V298c0 5.62-.31 4.58-17 6.87v20.06h72.42zM384 315l-6.87-22.37c-40.93 15.37-37.85-12.41-37.85-16.73v-60.72h37.85v-25.41h-35.82c-2.87 0-2 2.52-2-38.63h-24.18c-2.79 27.7-11.68 38.88-34 41.42v22.62c20.47 0 19.82-.85 19.82 2.54v66.57c0 28.72 11.43 40.91 41.67 40.91 14.45 0 30.45-4.83 41.38-10.2z"></path></svg> with <svg viewBox="0 0 581 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg>
]
.author[
### Maxime Jaunatre
]
.institute[
### LESSEM | INRAE
]
.date[
### 2022-12-01 (updated: 2022-12-01)
]
---
exclude: true
class: inverse, center, middle
# Introduction
---
class: inverse, center, middle
# Practice
<!-- Ces slides présentent l'utilisation de Git avec Rstudio, Github Desktop, R et bien sur Git Bash qui est un terminal de commande. -->
<!-- Bien que tout ces outils permettent de faire des dépots Git et de commit, plus on va avancer, plus il deviendra pertinent d'utiliser le terminal. -->
<!-- Il est donc préférable de lire cette partie de [Happy git for Ruser](https://happygitwithr.com/shell.html) afin d'appréhender cet outils qui offre toute la puissance de git. -->
<!-- Afin de ne pas paniquer, une [cheatsheet](https://services.github.com/on-demand/downloads/github-git-cheat-sheet.pdf) est également disponible ici pour comprendre la plupart des options. -->
---
# Config git account !
In Git Bash terminal :
```bash
$ git config --global user.name 'Maxime Jaunatre'
$ git config --global user.email 'myveryownmail@mail.com'
$ git config --global --list
```
Or using the `{usethis}` package in R terminal :
```r
## install if needed (do this exactly once):
## install.packages("usethis")
library(usethis)
use_git_config(user.name = "Maxime Jaunatre",
user.email = "myveryownmail@mail.com")
```
This allow to sign the commits
---
# Initiate git
## Create a new folder (Rstudio project)
In Git Bash terminal :
```bash
$ cd
$ git init tuto_git
Initialized empty Git repository in path/to/your/directory/tuto/.git/
```
<!-- Avec Github Desktop (GHD) : File > New Repository > Type name > Create repository -->
With Rstudio : File > New Directory > R project > Type name + check "Create git repository"
---
# Initiate git
## You can also add git to an existing project
In Git Bash terminal :
```bash
$ cd path/to/directory
$ git init
Initialized empty Git repository in path/to/your/directory/tuto/.git/
```
In R terminal :
```r
usethis::use_git()
# Read the messages !
```
<!-- Avec Github Desktop (GHD) : File > New Repository > Type name > Create repository -->
With Rstudio : Tools > Project Options … > Git/SVN. Under “Version control system”, choose “Git”. Confirm New Git Repository? Yes!
???
Basically the same thing but from an existing directory.
---
# Adding files to git repository
Once the file is saved (Ctrl+S), **git** will observe the change!
Check this in the Git tab or in the command terminal:
```bash
$ git status
```
We can also see that in the Git tab which indicates a small *A* next to our file.
???
We can set Rstudio to show the git bash terminal! And that's handy
---
# First commit
We can make our first commit!!!
It happens in 2 steps: add the files to the index and make the commit.
.pull-left[
**Git Bash**
```bash
$ git add Notes_Maxime.Rmd
$ git commit
```
This will open a text editor! (We can write whatever we want here.
]
.pull-right[
**Rstudio**
* Click on Commit
* Check the *Staged* box
* Write the commit
]
.pull-left[
**R**
```r
usethis::use_git(
message = "Initial commit"
)
# or
git2r::add(repo, "test.txt")
git2::commit(repo, "Commit message")
```
]
.pull-right[
<img src="CSU_RepRo_files/figure-html/rstudio_commit.png" width="85%" style="display: block; margin: auto;" />
]
???
Tab allows auto completion of file names !
---
# Repeat the operation
Now we can modify the file and start again:
**Edit -> Save -> Add to index -> Commit**
--
You can check the status with *Diff* and the history with *log*.
.pull-left[
**Git Bash**
```bash
$ git status
$ git diff
$ git log
```
]
.pull-right[
**Rstudio**
* Status -> Diff
* log -> Clock icon
]
.pull-left[
**R**
```r
git2r::status()
```
]
.pull-right[
<img src="CSU_RepRo_files/figure-html/git_stage.png" width="85%" style="display: block; margin: auto;" />
]
Let's make some commits... Add some files to test!
---
class: inverse, center, middle
# Clone remote repository from github/gitlab
---
# Config Github Token (PAT) !
Github does not work anymore with passwords -> security !
Create a token by going to [https://github.com/settings/tokens](https://github.com/settings/tokens) and -> "Generate token".
Or in R :
```r
usethis::create_github_token()
```
Validate the boxes "repo", "user" and "workflow". Don't forget to copy the key !
It will be requested the next time you use git and need it.
You can even store it with R :
```r
gitcreds::gitcreds_set() # interactive command
```
---
# Clone a github repository
We will copy a remote repository to disk: **https://github.com/Ifremer-IAM/Tutorat_git**
.pull-left[
**Git Bash**
```bash
$ git clone <URL>
```
]
.pull-right[
**R**
For once R doesn't do everything...
]
.pull-left[
**Rstudio**
* File -> New Project
* Version Control -> Git
* URL : copy the url
]
.pull-right[
<img src="CSU_RepRo_files/figure-html/clone_repo.png" width="85%" style="display: block; margin: auto;" />
]
--
[Happy Git for the useR](https://happygitwithr.com/usage-intro.html) explains other cases than this one.
???
Take the time for everyone to pull and commit, because there will be conflicts!
---
# Commit -> Pull -> Push
<img src="git_exo_files/figure-html/diag-1.png" style="display: block; margin: auto;" />
---
# Create a new branch
.pull-left[
**Git Bash**
```bash
$ git checkout -b <NOM>
```
]
.pull-right[
**R**
```r
git2r::branch_create(name = <NOM>)
```
]
.pull-left[
**Rstudio**
* Onglet Git -> Symbole violet
]
.pull-right[
<img src="CSU_RepRo_files/figure-html/new_branch.png" width="85%" style="display: block; margin: auto;" />
]
---
# Navigate in the history
Once a certain number of commits have been defined, you can go back or change branches.
## Change branch
.pull-left[
**Git Bash**
You just have to give the name of the branch. We can list them as follows:
```bash
$ git branch
```
Switch to the *main* branch
```bash
$ git checkout main
```
]
.pull-right[
**Rstudio**
* Git tab -> Next to the creation of branches you can choose which one to look at
]
You can change branches if all files are **committed** or ignored.
---
# Navigate in the history
Once a certain number of commits are defined, you can go back or change branches.
## Change commit
.pull-left[
**Git Bash**
You just have to give the SHA of the commit. We can list them as follows:
```bash
$ git log --oneline
$ git checkout <SHA>
```
]
.pull-right[
**Rstudio**
I haven't done this with Rstudio yet, if anyone finds it...
```r
# git2r::checkout()
```
]
You can change commits if all files are **commit** or ignored.
Another way to observe the past is to use **Github** which allows to easily visualize the history of a repository : see the article of [Happy Git for Ruser](https://happygitwithr.com/time-travel-see-past.html).
---
# Explanation
**git checkout** allows to move **HEAD**, which corresponds to what is presented on your computer.
.pull-left[
<img src="git_exo_files/figure-html/head_act-1.png" style="display: block; margin: auto;" />
]
.pull-right[
<img src="git_exo_files/figure-html/head_branch-1.png" style="display: block; margin: auto;" />
]
--
.pull-left[
Reverting allows to see the state but you can also start a new branch re-commit from a past commit.
Example:
```bash
$ git checkout -b test A
$ git add ... ; git commit -m 'F'
```
]
.pull-right[
<img src="git_exo_files/figure-html/head_past-1.png" style="display: block; margin: auto;" />
]
---
# Merging branches
Once the code is working we can do a **merge** of the branches.
.pull-left[
<img src="git_exo_files/figure-html/branch_pre-1.png" style="display: block; margin: auto;" />
]
.pull-right[
<img src="git_exo_files/figure-html/branch_premerge-1.png" style="display: block; margin: auto;" />
]
.pull-left[
A merge is always done from the target branch (*main*) by incorporating the external branch (here *dev*)
```bash
$ git checkout main
$ git merge dev
```
]
.pull-right[
<img src="git_exo_files/figure-html/branch merge-1.png" style="display: block; margin: auto;" />
]
In the case where each branch has commits, a new commit *merge* will be created with the opportunity to resolve conflicts. This commit belongs to both branches *main* and *dev*.
</textarea>
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