Based on material first developed by Lauren Michael
Let's say you've got a shared set of files in your research group that everyone will need to see and contribute to AND you'd like to use version control for this set of files. Instead of sending new updates of a project folder between eachother or using a department filesystem that doesn't have version control, you could use GitHub (or a group server) as the central location that each of you can pull from and push to using Git.
In this exercise, you'll each contribute to an authoritative repository within a GitHub organization. You'll first 'fork' a copy of the organization's repository in your own GitHub account and 'clone' a copy to your laptop, where you'll make changes. From then on, you'll always update your local laptop copy from the authoritative organization copy on GitHub. When you've made changes to your local copy, you'll first 'push' your changes to the repository in YOUR GitHub account, and then make a pull request from your GitHub repository to the organization's authoritative repository on GitHub.
Importantly, this type of workflow can be used extensively with a range of collaborative research work, including code development, draft writing, developing laboratory protocols, etc. In all cases, git and GitHub will keep track of which version of each file existed at various times in history, and which changes were made. (GitHub organization repositories can also be accessed from off campus and by anyone that your group decides, which might be an advantage over using a more private group server or department filesystem.)
For this example, we'll use the UW-Madison-ACI organization account for the authoritative repository. While we won't go through the details of creating and managing a new organization account in GitHub, your research group could create one through the following page: https://github.com/organizations/new
Public group repositories are FREE, but your group could opt for a private, fee-based repository, instead. For public organizations, anyone with access to GitHub can view the contents of the repositories and make pull requests (just as for GitHub user accounts). With either type of repository (public or private), the 'owners' of an organization control who has the authority to merge pull requests and otherwise directly affect repositories in the account.
More details about creating and managing organization repositories can be found in GitHub's help pages: https://help.github.com/articles/creating-a-new-organization-account/
First, let's navigate to our group repository in GitHub, in this case, the 'swcarpentry-workflows-in-practice' in the UW-Madison-ACI account, here: https://github.com/UW-Madison-ACI/swcarpentry-workflows-in-practice
Click the 'Fork' button in the top right. If GitHub wants you to choose which account to fork to, make sure to choose YOUR user account.
Now, from the repository page in YOUR GitHub account, click the green "Clone or download" button to the right and copy the address of the repository in preparation for cloning it to your computer. Use the command line to navigate to your desired directory for the repository: (The "YOU" in the below address will be replaced withyour GitHub username.)
$ git clone https://github.com/YOU/swcarpentry-workflows-in-practice.git
Now you've got a copy of the group repository on your laptop! You can check it by running the following commands:
$ cd swcarpentry-workflows-in-practice
$ ls
$ git status
Also, YOUR GitHub copy of the repository has been automatically set as the "origin" remote for the local repository. Check it with:
$ git remote -v
In order to make sure that you'll be able to pull future changes from the authoritative group repository, add it as another remote named "upstream" to represent the fact that it exists upstream from the "origin" copy you cloned from YOUR GitHub account.
$ git remote add upstream https://github.com/UW-Madison-ACI/swcarpentry-workflows-in-practice.git
$ git remote -v
Now, create a .txt file in your repository directory on your laptop, named according to your first initial and last name (like LMichael.txt) with three lines of inoccuous information about yourself, similar to the following:
Lauren Michael
I like blue skies.
Horses are cool.
If you are uncomfortable having your name and details added to our public group repository, later, you can use a made-up name or celebrity you think others will not choose.
Commit the changes to your local repository, then push to YOUR GitHub repository. Check your repository on GitHub to confirm the changes are there.
When viewing your GitHub user copy of the swcarpentry-workflows-in-practice
repository, click the "Pull requests" tab toward the top of the page. Then,
click the green "New pull request" button to start a new pull request.
Make sure that the "base fork" is the "UW-Madison-ACI" repository while the "head fork" is your own copy on GitHub, then click the green "Create pull request" button.
Confirm the pull request comment, then click the next green "Create pull request" button. You should now see your pull request! If you'd like to see the pull requests of other workshop attendees as they're added, refresh the "Pull requests" tab page.
The instructors will merge your pull request after reviewing your changes, similar to how group members would for a research group repository.
Run the following commands within your local swcarpentry-workflows-in-practice
directory to pull and view changes that were made to the group repository:
$ git pull upstream master
$ ls
You should now see everyone else's files, and have completed the basic workflow:
- Periodically pull from the authoritative group repository to update your working copy.
- Push new changes in your working copy to your repository on GitHub.
- Create a pull request to the group repository so someone can review and merge your updates.
- Repeat