04_git_basics.Rmd

---
title: "Git Basics"
author: "Dietmar Rieder, Gregor Sturm"
output:
  ioslides_presentation: default
---


## What is Git? 

* Source code management (SCM) tool 
* Developed by Linus Torvalds for the Linux kernel 
* Keep track of source code in *commits* and *branches*
   * *Commit = “unit of code change”*
   
   
   
![](images/branch-model.png)
   
## Why should I use git? 

* Backup your code
* Synchronize between laptop and HPC
* Know what you did 2 months ago

<br />

> - Git is an industry standard
> - Collaborate with others
> - Share your code

## A git repository...

...is just a folder with a special `.git` directory. 

<br />

Create a repository by typing

```bash
git init
```

within a directory. 

## The four git states

```{r, fig.cap="Figure from http://git-scm.com/book/en/v2/Git-Basics-Recording-Changes-to-the-Repository", echo=FALSE}
knitr::include_graphics("images/git-states.png")
```

## The four git states

Display modified files and their states:
```bash
git status
git diff
```

Add a modified file to the *staging area*:
```bash
git add <FILE>
```

Commit all *staged* files:
```bash
git commit
```

Browse history
```bash
git log
```

## Working with branches

List branches
```
git branch -v
```

Create a new branch from current commit
```
git branch <NAME>
```

Switch to another branch
```
git switch <NAME>
```

## Ignoring files

Create a file named `.gitignore` in the git repository.

Example: 

```
.Rhistory
.RData

*.nb.html
plots/*.pdf
```

## Configuring git

Configuration file at `~/.gitconfig`. Modify with text-editor or with `git config` command. 

When collaborating online, it is important to set your identity -- it will be associated with every commit: 

```bash
git config --global user.name "Your name"
git config --global user.email "mail@example.com"
```




## Links

 * [ICBI Gitlab (for internal projects)](gitlab.i-med.ac.at)
 * [ICBI GitHub (for published projects)](github.com/icbi-lab)
 * [Git Cheatsheet by GitLab](https://about.gitlab.com/images/press/git-cheat-sheet.pdf)