At the end of this exercise, you will be able to:
1. Create a new repository on GitHub and link it to GitHub
Desktop.
2. Improve the aesthetics and information about your repository.
3. Use GitHub Desktop to manage your repository.
4. Commit, push and pull files on GitHub.
GitHub is a file storage and management site used by programmers. Programmers upload code to repositories (folders) and make it publicly available. We will use Github to store our work and manage workflows in BIS 15L. We have a main repository for our class datascibiol. You should Star this repository for future reference.
Since we will use GitHub for assignments and projects, you need to have a personal BIS 15L repository. If you followed the setup instructions then you should be ready to make a repository using the instructions below. Please Email your GitHub user name to Bry.
BIS15L_W26_yourfirstinitialyourlastname. Mine looks like
this: BIS15L_W26_jmledfordThe easiest way to manage your GitHub repository is to use GitHub desktop. This is a helpful tool that will allow you to manage all of your files. Open the program and login using your GitHub account.
In GitHub desktop, you will see your personal repository as an option
under clone repository. Clone your repository to the
desktop. Once you have done this any changes you make to files will be
recorded and easily uploaded. Do not move this folder from your
desktop.
In order to keep track of the class files, the last thing you need to
do is make a copy of the class repository. I will make regular changes
to the class repository including the addition of files and data that
you will need. Do a search for datascibiol and download a
copy to the desktop. You do this by navigating to the repository then
going to the small green code button at top right. Click on the code
button then go to Download ZIP.
Copy the lab1 folder from the class repository and paste
it into your personal repository. By doing this, you have created your
own copies of lab materials for lab 1.
You will use your repository to store all of your notes and work.
There are three terms that we need to define:
1. Commit takes a snapshot of your current progress.
2. Pull this is the same as download.
3. Push this is the same as upload.
If you setup GitHub
desktop, then you will see that it automatically tracks your
changes. Clicking the Commit to master button in the bottom
left corner means that you are recording a snapshot of your edits
locally. Once this is done, you need to upload your changes to GitHub.
This is done by clicking Push origin. Once you have pushed
your changes you can double check by looking at your repository on
github.com.
The file format we use in class is called a markdown file. RMarkdown
files have the extension .Rmd and can be created in RStudio
by going to File > New File > RMarkdown. RMarkdown
files allow you to combine text, code, and output in a single
document.
RMarkdown files need to be knit in order to produce a
final document. This is done by clicking the Knit button at
the top of the RStudio window. Knitting produces a final document in
HTML format. You will turn in all homework assignments as knitted HTML
files. If your code does not work, then the file will not knit.
Since you will use your GitHub repository extensively in class, we
need to practice.
1. Navigate to your repository and find the file dummy_push
in the lab 1 folder.
2. Open dummy_push.
3. Add your name under author at the top of the page.
4. Save this file.
5. Knit the file.
6. Use GitHub Desktop to first Commit to master and then
Push origin to your GitHub repository.