In the first part of this lab, we will learn about Git and GitHub for managing projects.
Git is software that you will install on your computer that helps manage versions of documents. It is an example of version control software. At this point some editors have version control built in (Google Docs, for example, allows you to click backwards in the history).
Once installed, you will be able to create your own repository (directory), add files, and tag versions. You can have complete ownership over your repository, and is especially good if you have a long-term project and you may want to be able to go back to earlier versions (thesis, anyone??).
Git is a command line tool, but we will access it using GitHub Desktop. You will tag versions of a file (for example, file.py above) by first adding the changed file:
git add file.py
This stages the file for a commit, which prepares git for tagging this version. You can add multiple files to commit a bunch at once. Then, to commit that version, you write
git commit -m "informational message about the changes"
This tags all files that have been added with a version number, and you can always revisit these versions.
GitHub is a code hosting platform that uses Git as the underlying version control software. Let's add me (Anna) and the class to this picture:
For your programming assignments and labs, I have created a repository on GitHub (just like this URL). It contains some files (this README.md, for example). You can clone this repo onto your own computer. These files will be in a directory and you can open them and modify them.
Now, suppose you'd like to contribute your changes to the repository. (We'll be doing this in the future during group projects, which will work from a single repo). First, you need to add & commit your files on your computer. These are local changes that track the version control of YOUR files. Second, you will push these commits to the repository in GitHub.
Alright great. But what if another student wants to contribute their changes? They will be able to add & commit their files on their computers. But, when they push their commits to the repository, it will be rejected by GitHub.
This is because other edits have been made since the student last checked the repo, and they must first fetch your edits (and merge any conflicts - we'll see that a bit later). Once they do that, then students can push their commits to the repository.
Once the class has finished the project, I will be able to pull the changes in the repo onto my local computer. All done! For another overview of using GitHub (including forking and branching), see this quick tutorial - we won't need this though.
We will use GitHub Desktop to manage repositories. If you are already using Git and GitHub, then keep doing what you're doing and skip to Step 3. For the rest of us, read on...
Make a GitHub account here. These accounts are free but you cannot make private repositories. If you plan to make repositories outside of this class, I'd encourage you to apply for a student account (which gets you private repositories and a bunch of other stuff).
Send Anna your GitHub username through the chat when this is done.
GitHub Desktop will install both git and a desktop application for managing GitHub repositories. There are options for both Macs and [Windows](https://central.github.com/deployments/desktop/desktop/latest/win32].
You will be asked to log into GitHub in order to connect the Desktop App to your account.
Click "Clone Repository" and add Reed-CompBio/BIO331-F20-Lab6.1-GitHub to the URL. You will also specify the Local Path - the location that this repository will be cloned on YOUR computer.
You have cloned this repository! The buttons on the right hand panel allow you to open the files in an editor (e.g. Atom), show the location of these files on your local machine (e.g. to open them in Spyder), or open the GitHub webpage in your browser.
Save a copy of copy-me.txt with your name (e.g. Anna.txt). You can modify the contents of the file.
You then need to commit the file. Remember that this is a Git command that saves the version on your local computer. Checking the files in the left-hand pane is like typing git add README.md in a terminal. Typing a message and hitting commit to main is like typing git commit -m "message here".
Once you've committed the file, you need to push those commits to GitHub.
a) If you have a Push origin button, click it to put these changes in the GitHub repository.
b) If you cannot push your commits, that means someone else has made modifications to the repository that you do not have yet. You may have to Fetch origin before you are able to push.
Great! The GitHub Repository now has your new file. Go to the GitHub website to confirm.
Now, you will edit the modify-me.txt file by adding your name under the existing names. Complete the same procedure to add & commit the file and then push it to GitHub.
❓ You may get a conflict!! This happens when multiple people are editing the same part of a file. You need to fix the merge (by including everyone's names), then commit it again. After this you will be able to push to the GitHub repository.
The class will be using a GitHub repository for the programming assignment in the next module. Keep these instructions handy.