sciware

Sciware

Intro to GitHub

https://sciware.flatironinstitute.org/33_SummerIntro

Sciware goal

Activities where participants all actively work to foster an environment which encourages participation across experience levels, coding language fluency, technology choices*, and scientific disciplines.

*though sometimes we try to expand your options

Sciware website

Previous sciwares available here https://sciware.flatironinstitute.org

Password for videos is…

Getting help

• #code-help on SF Intern Slack
• #sciware on SF Slack

Today’s Agenda

Collaborating on GitHub

• Forking
• Pull Requests
• Reviewing
• Branches

Collaborating with others

• We need something more than a single repo, if we want to…
  • make changes separately from a main project
  • take an existing project in a new direction
  • make and track changes to repositories we don’t have permissions to push to

Forking Workflow

1. Fork the repository on github
2. Clone your new fork from github to local
3. Make changes to the code
4. Push to your fork
5. Open a Pull Request (PR) from your fork to the upstream repo
6. Wait for upstream to approve and merge your changes
7. Keep your fork up to date

Step 0: A clean start

• If you already have a copy of this repo from the last workshop, navigate to the directory above it and rename it.
• Normally you'd re-use this repository, but just to make sure everyone's on the same page...

> mv sciware33-git-intro/ sciware33-git-intro-day1/

Step 1: Fork

<img width=80% src=”./assets/Learn-Git-Graphics/Forking%20a%20Repo.png”>

Step 1: Fork

First we need to fork the repo https://github.com/flatironinstitute/sciware33-git-intro

Step 2: Clone

<img width=80% src=”./assets/Learn-Git-Graphics/Clone%20the%20Fork.png”>

Step 2: Clone

Next, we clone our fork of the repo:

> git clone git@github.com:your_user_name/sciware33-git-intro.git

Step 3: Add Your Code

• Add a file in the student_info/ directory called firstName_lastName.csv with the following info:
  • Your full name
  • Your center
  • Your research focus
  • A fun fact

> cd student_info/
> nano

Step 3: Add Your Code

Example contents of robert_blackwell.csv:

    
Name,Center,Research Focus,Fun Fact
Robert Blackwell,SCC,high performance computing,violin!
    

Save the file.

Step 4: Push to Your Fork

<img width=80% src=”./assets/Learn-Git-Graphics/Push%20to%20the%20Fork.png”>

Step 4: Push to Your Fork

• Add the file
• Commit the file
• Push the commit to your fork

       > git status

> git add student_info/robert_blackwell.csv
> git commit -m "Adding info for Robert Blacwell"

   > git push origin main

Break

Step 5: Open a Pull Request

Step 5: Open a Pull Request

• Using your browser, navigate to your forked repository
• It should look something like this:

• Click on the Contribute button

Step 5: Open a Pull Request

• Click on the Open pull request button

PR Case Study

Here’s an example of a PR without a helpful description:

PR Case Study

Here’s an example of a PR with a helpful description:

<img height=70% width=60% src=”./assets/pr_case_study_good.png”>

Step 5: Open a Pull Request

Things to think about when making pull requests (PR):

• PRs are a way for someone else to review your changes before they are merged into the "upstream" version.
• PRs usually contain many commits.
• The first comment in the PR should be more narrative than the commit messages and should describe why you're making the PR and summarize the changes you made.
• PRs are a valuable record, similar to a lab notebook.

Step 5: Open a Pull Request

Finish up your pull request and click “Create Pull Request”

Step 6: Wait for your PR to be merged

Someone else will merge your PR.

In practice, someone might leave comments on your PR and/or request changes before merging.

Reviewing a Pull Request

As other folks make PRs, go to the pull requests tab on GitHub.

Reviewing a Pull Request

Choose another student’s PR and click on it.

Click on the commit to see the diff of their changes and hover over a line until you see the + symbol.

Step 7: Pull Other’s Changes

<img width=80% src=”./assets/fetch-upstream-3.png”>

Step 7: Pull Other’s Changes to your Fork

Sync.

<img width=80% src=”./assets/fetch-upstream-1.png”>

Step 7: Pull Other’s Changes to your Fork (Sync)

Sync.

<img width=80% src=”./assets/fetch-upstream-4.png”>

Step 8: Pull Other’s Changes to your Local

    > git pull origin main

Step 8: Pull Other’s Changes to your Local

Confirm that you have the changes locally.

      > git log
      > ls student_info/
    

Advanced: Branching

• A branch is like a fork within a repository
• You can create a local branch that is only on your local computer
• You can push this branch to your remote to have multiple branches on your github repo

Create a local branch

• git checkout can be used to switch branches

> git branch -v
> git checkout -b newbranch
> git branch -v
> git checkout main

Make a commit on a branch

• Checkout your branch: git checkout newbranch
• Create/edit a file, add, and commit
• Push this branch to github: git push origin newbranch

Open a PR

• On your own github repo, create a PR to merge newbranch into main

Merge into main

> git branch -v
> git checkout main
> git merge newbranch
> git push origin main

Check your new PR!

Extra Resources

Check out and bookmark these tutorials for more information about git and the forking workflow:

• Bitbucket: Making a Pull Request
• CodeRefinery: Distributed version control and forking workflow

Survey