Most of the content is written in GitHub Flavored Markdown with some metadata (or variables) found in YAML files. Everything is stored on a GitHub repository: https://github.com/galaxyproject/training-material.

The process of development of new content is open and transparent, using git and following the GitHub flow:

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1. Create a fork
2. Clone your fork of this repository to create a local copy on your computer
3. Create a new branch in your local copy for each significant change
4. Commit the changes in that branch
5. Push that branch to your fork on GitHub
6. Submit a pull request from that branch to the original repository
7. If you receive feedback, make changes in your local clone and push them to your branch on GitHub: the pull request will update automatically
8. Pull requests will be merged by the training team members after at least one other person has reviewed the Pull request and approved it.

Agenda

In this tutorial, you will learn how to contribute to the GitHub repository:

1. Create a fork of this repository on GitHub
2. Clone the GitHub repository on your computer
3. Create a new branch
4. Make your changes on this branch
5. Push your branch on your GitHub repository
6. Open a pull request
7. Make the requested changes
8. Check the automatic tests
9. Stay up to date
10. Close the Pull Request
11. Conclusion

Create a fork of this repository on GitHub

A fork is a copy of a repository. Forking a repository allows you to freely experiment with changes without affecting the original project:

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Forking a repository is a simple two-step process:

Hands-on: Fork the repository

1. Go on the GitHub repository: https://github.com/galaxyproject/training-material

2. Click on Fork (top-right corner of the page)

   

Comment

When you click the Fork button GitHub will show you a list with your user account and any groups where you can create a fork of this repository (starting with @). If you see yourself only below “You have existing forks of this repository:”, it means you already have a fork and you have nothing to do.

Clone the GitHub repository on your computer

To modify the content of the repository, you need a copy of it on your computer. This step of importing a git repository is called “cloning”:

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Hands-on: Clone the GitHub repository

1. Get the URL of your fork. You can find this on the main page of your fork under the green button:

   1. Click on Code (right)

      

   2. Copy the URL

      It should be something like https://github.com/< Your GitHub Username >/training-material.git

2. Open a terminal
3. Navigate with cd to the folder in which you will clone the repository

4. Clone the repository with the command:

   $ git clone https://github.com/< Your GitHub Username >/training-material.git
   

5. Navigate to the repository

   $ cd training-material
   

Comment

If you already have a local copy of the GitHub repository, you need to update it before doing any changes. To learn how to do that, please follow the last section.

Create a new branch

You have now your repository locally and you want to modify it. For this example tutorial, you will add yourself as contributor of the project to appear on the Hall of Fame.

In GitHub flow, there is a concept: one new feature or change = one branch.

When you’re working on a project, you’re going to have a bunch of different features or ideas in progress at any given time – some of which are ready to go, and others which are not. Branching exists to help you manage this workflow. You should develop different features on different branches to help keep the changes you make simple and easy to review.

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Here for this tutorial, you will create a branch called “my_new_branch” in which you will modify the CONTRIBUTORS.yaml file, the file used to generate the Hall of Fame.

Hands-on: Create a branch

1. List the existing branch

   $ git branch
     * main
   

   The branch on which you are is shown with the *

2. Create a new branch

   $ git checkout -b my_new_branch
   Switched to a new branch 'my_new_branch'
   

3. List the existing branch to check that the branch has been created and you are now on it

This branch is added to your local copy:

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Make your changes on this branch

You have created your first branch! Now you want to make the change in the CONTRIBUTING.yaml file. By changing a file in this branch, it will diverge from the main branch. It will contain data that is only on this new branch:

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Hands-on: Make changes in a branch

1. Open with your favorite text editor the CONTRIBUTORS.yaml file that is on your computer

2. Add yourself in the CONTRIBUTORS.yaml file

   You should use your GitHub username and add it followed by : at the correct position given the alphabetical order

3. Save the file

4. Check the changes you made

   $ git status
   On branch my_new_branch
   Changes not staged for commit:
     (use "git add/rm <file>..." to update what will be committed)
     (use "git checkout -- <file>..." to discard changes in working directory)
   
       modified:   CONTRIBUTORS.yaml
   
   no changes added to commit (use "git add" and/or "git commit -a")
   

5. Add the file and commit the changes

   $ git add CONTRIBUTORS.yaml
   $ git commit -m "Add ..."
   

6. Check that there are no more changes to commit with git status

Push your branch on your GitHub repository

The changes you made on your branch are only on the local copy of the repository. To propagate them online, you need to push them on your fork on GitHub:

Hands-on: Push the changes

1. Push the changes to the GitHub repository

   $ git push origin my_new_branch
   

   Details: "push origin"

   When you git pushed, you specified origin. Git repositories can know that forks exist in multiple places. When you clone one, it creates a “remote” (a remote repository) which it names origin, set to the URL that you used when you cloned. By having multiple remotes, you can manage more complex workflows.

2. Go to your GitHub repository
3. Change to the “my_new_branch” branch:

   1. Click on Branch: main (left)

      

   2. Select the branch “my_new_branch”

4. Check that your name is in the CONTRIBUTORS.yaml file

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Open a pull request

You pushed your changes to GitHub, but currently they are only on your fork. You want to have these changes in the main GitHub repository in order to appear on our Hall of Fame online. You can’t add or push directly the main GitHub repository, so you need to create what we call a pull request:

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Hands-on: Create a pull request

1. Go to your GitHub repository

2. Click on Compare & pull request

   

3. Check that the selected branch are correct: main on the left and your branch name on the right

   

4. Fill in the pull request description

   

   1. Add a title for the Pull Request
   2. Add a message explaining the changes you made (Be kind )

   3. Click on Create pull request or switch to Create draft pull request from the dropdown menu

      

      Details: "Draft pull requests"

      Creating a pull request as a draft serves as an indication that you are still working on the content. Reviewers may comment on the current state and give general feedback, but they will know that they are not looking at the final version of your contribution.

      In the Galaxy Training Material repository we have also disabled the computationally most expensive automated tests on draft pull requests, and we encourage you to use the draft stage as a small contribution to sustainable computing.

5. Go to Pull requests to check if it is there

Once the pull is open, it will be reviewed. There are two possible outcomes:

1. Your pull request is accepted. Congratulations! Your changes will be merged into the main branch of the original repository. The website will be re-built and you will be in the Hall of Fame
2. Your pull request needs modifications: the reviewers will ask for some changes, possibly because the automatic tests are failing.

Make the requested changes

One of the reviewers of your pull request asked you to add your name after your GitHub username in the CONTRIBUTORS.yaml file

Hands-on: Make further changes

1. Make the requested changes in the CONTRIBUTORS.yaml file

   It should look like

   bebatut:
        name: Bérénice Batut
   

2. Check the changes that you made

   $ git status
   On branch my_new_branch
   Changes not staged for commit:
     (use "git add/rm <file>..." to update what will be committed)
     (use "git checkout -- <file>..." to discard changes in working directory)
   
       modified:   CONTRIBUTORS.yaml
   
   no changes added to commit (use "git add" and/or "git commit -a")
   

3. Add the file and commit the changes

   $ git add CONTRIBUTORS.yaml
   $ git commit -m "Add ..."
   

4. Check that there are no more changes to commit with git status

5. Push the new changes to GitHub

   $ git push origin my_new_branch
   

   The pull request should be automatically updated

6. Check that the new changes are added to the pull request on GitHub

Check the automatic tests

When a pull request is opened, some automated tests are automatically launched on Travis to be sure that the changes do not break the website, the URL are valid, etc.

On the bottom of your pull request, you can see the status of the tests:

• Yellow (with circle)

  

  The tests are still running

• Red (with cross)

  

  When it is red, you can investigate why by clicking on Details. You will be redirected on Travis where you can see the logs of the tests. Get in touch with us on Gitter if you need help to understand the issue.

• Green (with tick)

  

  The tests passed. Good job!

  Even it is green, we recommend to check the result of the tests, as some of tests are allowed to fail (to avoid too much noise).

Stay up to date

You now want to work on a new tutorial or make some other new changes. However since you get a local copy, some changes have happened to the original GitHub repository. You need then to update your local copy of the repository before changing anything.

Hands-on: Update the local copy

1. Move to the main branch

   $ git checkout main
   

2. Add a reference to the original GitHub repository

   $ git remote add upstream https://github.com/galaxyproject/training-material.git
   

   Comment: Error "remote upstream already exists"

   If you have done step 2 before and try to remote add again, git will tell you that a “remote upstream already exists”. In this case you can safely continue to step 4.

3. Update the local copy of the repository by “pulling” in the content of the original GitHub repository

   $ git pull upstream main
   

You can now restart the GitHub flow to propose new changes: start by creating a new branch.

Close the Pull Request

Great! You now know how to make pull request on GitHub, and how to make changes after a review. Reviewers can now approve and merge your pull request.

Because this was just a practice pull request, let’s close it again.

Hands-on: Close the Pull Request

Once you have run through all these steps, please close the pull request again.

1. Go to the list of pull request tab on GitHub
2. Click on your pull request
3. Scroll to the bottom of the page
4. Click on “Close pull request” button

Whenever you add your first real contribution, you can add yourself to the CONTRIBUTORS.yaml file in that PR.

Conclusion

With this tutorial, you have learned some basics git commands and principles:

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You also learned the GitHub flow and its cycle:

1. Create a new branch in your local copy
2. Commit the changes in that branch
3. Push that branch to your fork on GitHub
4. Submit a pull request from that branch to the main repository
5. Wait for feedbacks and make requested changes
6. Update your local copy
7. Restart the cycle

You can now contribute and help us to improve our tutorials!

Details: Git in Depth

This tutorial was a quick introduction to explain the basics of contributing to the training material. We recommend that everyone follow a more detailed git tutorials:

• Software Carpentry tutorial which explains a bit more in detail some git commands and the concept of remote, local and stagging
• Learn Git Branching by GitHub to test the different git commands

You should also download, print and keep always with you the Git Cheat Sheet

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• Work on your fork

• 1 branch = 1 feature

• 1 pull request = 1 branch

• Be careful of the branch you’re working on

• Check the automated tests

Frequently Asked Questions

Feedback

Did you use this material as an instructor? Feel free to give us feedback on how it went.
Did you use this material as a learner or student? Click the form below to leave feedback.

Citing this Tutorial

1. Cyril Monjeaud, Bérénice Batut, Contributing with GitHub via command-line (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/contributing/tutorials/github-command-line-contribution/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{contributing-github-command-line-contribution,
author = "Cyril Monjeaud and Bérénice Batut",
	title = "Contributing with GitHub via command-line (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/contributing/tutorials/github-command-line-contribution/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Developing GTN training material

This tutorial is part of a series to develop GTN training material, feel free to also look at:

1. Contributing with GitHub via command-line
2. Overview of the Galaxy Training Material
3. Creating Interactive Galaxy Tours
4. Including a new topic
5. Teaching Python
6. GTN Metadata
7. Tools, Data, and Workflows for tutorials
8. Running the GTN website online using GitHub CodeSpaces
9. Adding Quizzes to your Tutorial
10. Adding auto-generated video to your slides
11. Principles of learning and how they apply to training and teaching
12. Design and plan session, course, materials
13. Running the GTN website online using GitPod
14. Contributing with GitHub via its interface
15. Updating diffs in admin training
16. Generating PDF artefacts of the website
17. Running the GTN website locally using the command line
18. Creating a new tutorial
19. Single Cell Publication - Data Plotting
20. FAIR Galaxy Training Material
21. Single Cell Publication - Data Analysis
22. Creating content in Markdown
23. Creating Slides
24. Updating tool versions in a tutorial

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/github-command-line-contribution/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

Feedback

5 stars	6

May 2021

• 5 stars: Liked: That it is a step by step <3 Disliked: The master branch on my side is called main

October 2020

• 5 stars: Liked: Very clear directions - thank you! The key points at the end are a great concise summary.

April 2020

• 5 stars: Liked: Liked the clean explanation with visuals. Great Job. In clears the process flow for beginners. Disliked: 1) In situations where I'm working on a feature "F1" in branch "B1", while I prepare to make a PR, do I need to keep my local up-to date with Upstream before PR? 2) After deciding my feature branch is good to go for PR, can I checkout to Master and pull my feature first? What's the process for updating my Master with my new feature I developed? Please answer this. I always have this confusion. Thanks.
• 5 stars: Liked: The presentation was very clear

August 2019

• 5 stars: Liked: Every thing was great especially the graphics. Thanks for all the help!! Disliked: Every thing is fine and up to date though I am not an expert!
• 5 stars: Liked: It's easy to understand Disliked: More diagrams