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---
title: "Introduction to GitHub"
author: Alexa Fredston-Hermann, PhD Student, Bren School, fredstonhermann@ucsb.edu <br> Elise Wall, Associate Specialist, IEE, ekwall@ucsb.edu <br>
<br> Special thanks to Dr. Julie Stewart Lowndes who created this presentation
output:
ioslides_presentation: default
slidy_presentation: default
beamer_presentation: default
---
## Does this look familiar?
<p align = 'center'>
## Why learn and use GitHub?
**Version control** Track all of your changes clearly, without breeding files or losing old versions. Used for many programming languages.
## Why learn and use GitHub?
**Version control** Track all of your changes clearly, without breeding files or losing old versions. Used for many programming languages.
Helps multiple people can work on code together, but is also a fantastic organizational tool for individuals.
GitHub allows you to back up code, easily switch between computers, undo mistakes, 'comment' on changes, and much more.
## What is GitHub?
Similar to Dropbox, certain folders on your local computer will be 'watched', with any changes able to be synced online.
## What is GitHub?
Similar to Dropbox, certain folders on your local computer will be 'watched', with any changes able to be synced online.
You have more control about what is synced, and how often. You can store, share, track changes and collaboratively edit many filetypes (including this presentation!) using any application.
## What is GitHub?
Similar to Dropbox, certain folders on your local computer will be 'watched', with any changes able to be synced online.
You have more control about what is synced, and how often. You can store, share, track changes and collaboratively edit many filetypes (including this presentation!) using any application.
It is possible to revert back to any previous version, and who is responsible for line-by-line changes.
Other great features too! (Issues, a to-do list you can share and assign tasks)
## git and GitHub
<p align = 'center'>
(definition from [GitHub.com](https://guides.github.com/introduction/getting-your-project-on-github))
## Workshop Outline
1. GitHub Structure
2. GitHub Workflow and Vocabulary
3. RStudio Practice
4. Resources
## GitHub Structure
Files are stored in **repositories**, owned by **users** / **organizations**.
<p align = 'center'>
## GitHub Structure
Files are stored in **repositories**, owned by **users** / **organizations**.
Repositories ('repos') are essentially folders containing files pertaining to a specific project. Repositories are version controlled so that any modifications to files, additions or deletions, are tracked and attributed to contributors with the correct permissions.
Same structure across all orgs/repos: familiar, easy to navigate.
GitHub is so great for creating and sharing code, lots of things you rely on already use it:
* **repositories**: [github-intro](https://github.com/eco-data-science/github-intro), [dplyr](https://github.com/hadley/dplyr), [ggplot2]()
* **users**: [jules32](https://github.com/jules32), [hadley](https://github.com/hadley), [jennybc](https://github.com/jennybc)
* **organizations**: [twitter](https://github.com/twitter), [netflix](https://github.com/netflix), [rstudio](https://github.com/rstudio), [nceas](https://github.com/nceas), [ohi-science](https://github.com/ohi-science)
## GitHub Workflow and Vocabulary
Let's discuss how this works first, and then we're going to practice with RStudio.
## GitHub Workflow and Vocabulary
Let's discuss how this works first, and then we're going to practice with RStudio.
There are lots of ways you'd get into GitHub... group project, new job, want to contribute to/use someone's neat idea.
## GitHub Workflow and Vocabulary
Let's discuss how this works first, and then we're going to practice with RStudio.
There are lots of ways you'd get into GitHub... group project, new job, want to contribute to/use someone's neat idea.
First, it'd be nice if the files were on your computer.
## GitHub Workflow and Vocabulary
* **clone**: download an identical copy - a 'clone' - of a repository to your local computer. Cloned repositories can still be synced with the online version(s) at your whim.
## GitHub Workflow and Vocabulary
Now that you have a local copy of this code, you have some ideas. When you're at a good stopping point and want to save your progress, you 'commit' the code with a message describing the changes.
Commit = the GitHub version of 'I did a thing!'
...Like 'save', but you also get to add a comment.
## GitHub Workflow and Vocabulary
* **commit**: message associated with your changes ([best practices](http://r-pkgs.had.co.nz/git.html#commit-best-practices))
## GitHub Workflow and Vocabulary
* **commit**: message associated with your changes ([best practices](http://r-pkgs.had.co.nz/git.html#commit-best-practices))
## GitHub Workflow and Vocabulary
But wait! What if, in the meantime, someone else changed the original (bug fixes, for example)? To download new changes to the code from others, you 'pull' from GitHub. **This is also how you can switch computers and easily work on the same code.**
## GitHub Workflow and Vocabulary
But wait! What if, in the meantime, someone else changed the original (bug fixes, for example)? To download new changes to the code from others, you 'pull' from GitHub. **This is also how you can switch computers and easily work on the same code.**
If there are differences that can be easily resolved (e.g., the R package developer fixed a bug by adding a line of code), your repository will be 'merged' accordingly. If the differences *conflict*, you have to resolve them manually by telling GitHub which changes to keep and which to ignore.
## Github Workflow and Vocabulary
* **pull**: sync a repo on your computer with the online version. Do this frequently to avoid **merge conflicts** or working on outdated code.
## GitHub Workflow and Vocabulary
After committing your changes and pulling the repository again, you're ready to 'upload' your version of the code to GitHub. To do this, you 'push' the code.
* **push**: sync the online repo with your version, only possible after committing
## GitHub Workflow: branches
What if you want to try something crazy, but stay organized?
[guides.github.com/introduction/flow](https://guides.github.com/introduction/flow)
## Github Workflow: branches
There are (at least) two ways to work on an existing repository:
* Clone it, then push and pull directly from the original ('master') - suitable for small group collaborations. Create 'branches' for big ideas.
## Github Workflow: branches
There are (at least) two ways to work on an existing repository:
* Clone it, then push and pull directly from the original ('master') - suitable for small group collaborations. Create 'branches' for big ideas.
* Create a 'fork' in the branch so that you can make any changes to all of the repository contents without affecting the other branches, such as the master branch. This is suitable for when you just want to copy code, or for very large collaborations.
## GitHub Workflow: sync with branch
**sync ~ pull + commit + pull + push**
All collaborators work independently but sync regularly
## GitHub Workflow: fork and pull
**fork + pull + commit + push + pull request**
## Github Workflow and Vocabulary: Summary
1. **fork a repo** to your user account
2. **clone the repo** to your computer
3. **edit a file**, inspect differences
4. **commit** changes
5. **pull**
6. **push**
7. repeat!
## RStudio Practice
In order to follow the demo, [git](https://git-scm.com/downloads) and [RStudio](https://www.rstudio.com/) must be installed on your laptop, and you must have a [GitHub](https://github.com/) account. Don't worry, they're all free!
Open RStudio and navigate to tools -> Global Options. Go to Git/SVN and click 'enable version control interface for RStudio projects'. If you have any issues, flag one of us down or check the [RStudio help page](https://support.rstudio.com/hc/en-us/articles/200532077-Version-Control-with-Git-and-SVN).
One more thing: To use the GitHub interface in RStudio, you'll need to work with R projects. R projects are associated with working directories and they help with version control and with switching between projects. [more info](https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects)
## RStudio Practice
Try finding this repository, `github-intro-2`, on the [eco-data-science GitHub](https://github.com/eco-data-science).
Remember, you can *clone* if you want a local copy on your computer, from which you can contribute changes to my project, or *fork* if you want your own branch to mess with.
Click 'fork' on the top right. You will see a copy of this same repository, but rather than eco-data-science/github-intro-2, it's called yourusername/github-intro-2, and it shows where it was forked from.
Now, it's yours! To clone this repository so you can edit it in R, click the green 'clone or download button', and then the clipboard icon to copy the URL.
## RStudio Practice
Open RStudio and go to file -> new project. Then click version control, then git, and paste the URL you just cloned into the first box.
The second box is for the name of the project, and the new directory you're creating on your computer. I almost always use the same name as the repository (in this case, `github-intro-2`).
## RStudio Practice
Finally, tell RStudio where to put this repo. It is **strongly** recommended that you create a directory in your home directory called 'github', and put all your repositories and code there. To do this, put '~/github' in the third box. Finally, click 'create project'. (If you get an error doing this, there could be many reasons, but the first thing I try is going back to the repository on GitHub, clicking 'use SSH' or 'use HTTPS' under the green 'clone' button (whichever you didn't use last time), and repeating everything on this slide. You might also have to manually create a 'github' folder in your home directory.)
## RStudio Practice
Congratulations, you just cloned a repository from GitHub! It's now yours to edit in RStudio. Under 'files' in the bottom right window, you'll see everything in this repository, including this presentation. Open practicescript.R, make any edit you like, and save it.
You'll notice the top right pane has a tab called 'git'. Click on it, and you'll see all the files in this directory. Check the box next to practicescript.R and click 'commit' above. Enter a message describing your changes in the box on the top right and click 'commit'.
Don't forget to pull before you push! Because no one else should be editing your forked repository, there shouldn't be any changes when you pull. Finally, push your commit, and then go back to GitHub to see the changes in the repository.
## RStudio Practice
If you wanted to create a new repository, you would go to the GitHub home page, click 'new repository' and follow the prompts, and then use the same process we just covered to clone it and start editing code in RStudio. You can drag and drop files from other locations into the repo directory on your local machine and then push them to GitHub, if they aren't too big.
## Non-R Options: Creating Repositories
**On GitHub.com**, you can create new repos
**On your computer**, you can create new repos in several ways:
* [**GitHub Desktop**](https://desktop.github.com/)
* [**RStudio**](www.rstudio.com)
* **shell/command line**
## Non-R Options: Syncing
**On GitHub.com**, you can clone a repo to your computer.
**On your computer**, you can clone/sync repos in several ways:
* [**GitHub Desktop**](https://desktop.github.com/)
* **RStudio**
* **shell/command line**
When you work on your computer, any edits you make to any files in your repo, using any program, will be tracked.
## Best Practices
**Pull often!**
**Commit frequently**
**Be mindful of filepaths**
* We work from a in a folder in our home directory called ***'github'*** (all lowercase!), so that everyone can access the repo with the filepath beginning in `~/github`:
* **Windows**: `Users\[User]\Documents\github\`
* **Mac**: `Users/[User]/github/`
## Thanks
## Thanks
If you have any questions, now or ever:
* Email me (fredstonhermann@ucsb.edu)
* Create an 'issue' on [eco-data-science](https://github.com/eco-data-science/eco-data-science.github.io) (Google or ask me how!)
* Tweet #rstats and #github
* Contact anyone in the eco-data-science community
## GitHub and science (and beyond)
hello?
- [GitHub gets its science on](http://readwrite.com/2014/05/15/github-science-doi-academia-repository)
- [Making your code citable](https://guides.github.com/activities/citable-code/)
- [Choosing an open source license](https://github.com/blog/1530-choosing-an-open-source-license)
<p align = 'center'>
- [Ways to use GitHub that aren't coding](http://readwrite.com/2013/11/08/seven-ways-to-use-github-that-arent-coding)
## Resources
**Learn more about GitHub:**
* [**GitHub Guides**](https://guides.github.com/) by GitHub
* [**Git and GitHub**](http://r-pkgs.had.co.nz/git.html) by Hadley Wickham
* [**Good Resources for Learning Git and GitHub**](https://help.github.com/articles/good-resources-for-learning-git-and-github/) by GitHub
* [**Learn Git Branching**](http://pcottle.github.io/learnGitBranching/) by Peter Cottle
* [**Git/GitHub Guide**](http://kbroman.org/github_tutorial/) by Karl Broman
* [**Git & GitHub**](http://htmlpreview.github.io/?https://github.com/eco-data-science/ds-git/blob/gh-pages/index.html) by Ben Best
Just Google 'GitHub Tutorial...'