Read-Me/github.Rmd at master · martonelab/Read-Me · GitHub

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---
title: "Setting Up GitHub"
author: "Jasmine"
date: '2019-04-29'
output: html_document
---

## Prerequisites
- have a github account http://github.com
- windows users - have powershell or some application to access the terminal
- have an up to date version of Rstudio installed for insturctions, see - https://happygitwithr.com/install-r-rstudio.html

## Acknowledgements
https://happygitwithr.com/

## Objectives
- Get a github account
- Install git on the computer
- Setup Github for Rstudio and create a SSH connections
- be able to pull commit push to GitHub

## (6) Install Git
In Shell find out where Git is (if at all) installed
```{bash}
which git
```

check in the terminal for the version
```{bash}
#git --version
```

follow additional instructions on https://happygitwithr.com/install-git.html depending on your operating system

## Skipping over the command line part
- but if you are interested: https://happygitwithr.com/push-pull-github.html#push-pull-github

## Pull Commit Push Terminology
1. `pull` - make it a habit to pull everytime before you start working on anything
2. `commit`- the staging area, also make sure you have an informative commit message
3. `push` - you

#### Terminology cheat sheet
- `repo` / `repository` - a "folder"
- `fork` - copy over a repo
- `pull request` / `pr` - when you submit some changes to be reviewed and integrate into the files
- `clone` - think of it as copying that entire folder
- `branches` - an alternate timeline for the original dile
- `issue` - you can use this as a chat board/ forum for discussing problems associated with this repo
- `merge conflict`

### Make your own repo
you will need to do this everytime you want to create something new

1. go to your account
2. go to the `repositories` tab
3. click the green `new` button
4. fill in the (a) repository name, (b) description, (c) choose public or privatate, (d) check initialize with README
5. `Create Repository`

### Just downloading the file
1. Go to the repository
2. Click the green `Clone or download` button
3. Choose the `Download ZIP` option to download the zipfile on to your computer

### Clone your repo using Rstudio
#### Create the project
1. go to File > New project > Version Control > Git
2. in repository URL paste in the provided URL from the box that pops up fromt he green `clone or download` button

__Pro tip__
- make a directory (ie. tmp) where it is easy to add all your github repos to
- you should be removing the repo when you are done with it as good practice
- pull the repo down to your computer when you need it

#### Changes, Save, Commit
1. change the `README.md` file
2. save the file
3. go to the `Git` tab on the upper right box
4. check the box under `staged` associated with github.rmd
5. click the `commit` button to open a popup window
6. type an informative description in the `commit message` text box (this is used to track what you have changed)
7. press the `commit` button associated with the box
8. press the green arrow (push) button * you may be promted for a username and password here
9. check your repo to see the changes reflected

__Pro tip __ Try following chapter 10 to cache your credentials to avoid logging in each time you push or pull to github - https://happygitwithr.com/credential-caching.html#credential-caching

## Using the Martone Lab repositories
- how to deal with other people's files

#### Fork over a repo
- for cases when you want to use other people's code or collaborate

1. Go to https://github.com/martonelab
2. Go to the Read-Me repository
3. Click Fork (makes a copy to your GitHub Account)
- allows people to attribute credit
- tracks changes
- your changes will not be integrated until you say so
- it's like making alternative universes and timelines (less of a concern for less complicated projects)
4. Clone your repository
__This part is the same as cloning your own__

#### Adding your changes
1. go to your repo that you forked to your account
2. click new pull request
3. click create pull request
4. write something informative in the title and comments
5. click create pull request
6. now you need to wait for the owner of the repo to merge (approve of) your changes

Congrats! Now you can push new lesson repos into the Lab github and pull lessons people have made available!