Git & GitHub

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# Git & GitHub
### Bruna Wundervald
### PhD Candidate in Statistics, Hamilton Institute, Maynooth University
### October, 2018

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## What are git and GitHub?

- **Git**: the most widely used modern version control system 
in the world today 
    - Originally developed in 2005 by Linus Torvalds

- **Github**: a web-based hosting service for version 
  control using git.
  
  
<b>  
<img src="https://www.enriquedans.com/wp-content/uploads/2018/06/GitHub-Octocat.jpg" width="30%" height="50%" style="display: block; margin: auto;" />

[Git Cheatsheet here!](https://www.atlassian.com/git/tutorials/atlassian-git-cheatsheet)
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## Starting

- [Download](https://git-scm.com/downloads) and
install git. 
- Create a [GitHub](http://github.com) account.
  - Note that students are eligible to one year
  of premium account for free!
  
- Connect you GitHub account to your local git using
the SSH keys. **But what is a SSH key?**

> An SSH key is an access credential in the SSH protocol. Its function is similar to that of user names and passwords, but the keys are primarily used for automated processes and for implementing single sign-on by system administrators and power users.

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## Connecting local git and GitHub

1. Open the GitHub website and go to `Settings` -> `SSH and GPG keys` -> `New SSH key` 
  
  2. Open terminal and run (with your email, of course): 
  `ssh-keygen -t rsa -b 4096 -C "your_email@example.com"`
  
  3. Press enter till the end of the process.
  
  4. On terminal, run `eval "$(ssh-agent -s)"`
  and `ssh-add ~/.ssh/id_rsa`.

Now you have generated the key. The next step is to 
copy and paste it in GitHub:

5. Open the file created in `~/.ssh` and copy it
  to GitHub. 
  
More details here: https://help.github.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/

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# Basic git commands

First, create a repository in GitHub, by clicking
"Start a project".

1. Clone it in the path you want with terminal
  by running `git clone username/repositoryname`
    - If you don't have the permission to clone
    the repository, git you tell you!
  2. Starting editing the folder!

To push your changes to git, there are basically four steps:

1. Check what changed with `git status`
  
  2. Add your changes with `git add changed_file.extension`
    - You can use `git add .` to add all of them!
    
  3. Commit your changes with `git commit -m "commit message"`
  
  4. Push your changes with `git push`

Update git repositories with `git pull`!
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## Branches

- Branches are used to develop isolated functionalities
  in a git repository.
  
<img src="https://cdn-images-1.medium.com/max/1600/1*iB8lNrITmLvKeL8mnp3qAA.png" width="70%" height="50%" style="display: block; margin: auto;" />

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# Using branches

1. Create a new branch in the repo with `git checkout -b branch_name`
  
  2. Now you're working on this branch. 
  
  3. Add your changes normally, except by the push step: now you need
  to use `git push branch_name` to identify where the changes are
  coming from. 
  
  4. Return to the master branch with git `checkout master`
  
**At this point, the changes made using the branch are not**
**available in the master folder. If everything is ok with**
**the branch, you can `merge` ("accept") it with `git merge branch_name`** 
  
  - This depends on the branch having no conflicts with the
  master branch. If conflicts exist, you might need to deal
  with them manually. 
  
It is possible to check the differences between branches with
`git diff <origin branch> <destin branch>`

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## Contributing to existing repositories

Suppose you want to add changes to an existing repository - example:
to discontinuated `R` packages. The steps to do that are:

1.  `fork` the repository into your github account.
  
  
<img src="https://github-images.s3.amazonaws.com/help/bootcamp/Bootcamp-Fork.png" width="40%" height="40%" style="display: block; margin: auto;" />

2. Clone it (from your github account, e.g. `github.com/your_user/forked_repository`), make the changes 
  and push it. 
  
  3. Make a `pull request` into the original repository, a.k.a.
  ask for your changes to be added by the owner of the repository.

**Some repositories have their own contributing guide!**

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# Contributing scheme
<img src="http://jlord.us/git-it/assets/imgs/clone.png" width="90%" height="70%" style="display: block; margin: auto;" />

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## Acknowledgments

This work was supported by a Science Foundation Ireland Career Development Award grant number: 17/CDA/4695

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# Thanks!

<b>

[@brunaw](https://github.com/brunaw)