Advanced GitHub

Task List

Set up a GitHub organisation for the 2025 Rostock Open Science Workshop attendees
Add all of the workshop attendees as members
Create your own GitHub repository in this org
Fork your own repo to your own account
Clone the repo to your own computer
Create a simple webpage using quarto
Commit the changes to your computer
Push the changes to your forked repo
Set up GitHub Pages on the forked repo
Send a pull request to the base repo on the org
Merge the pull request
Set up GitHub Pages on the base repo
Set up GitHub actions to render your quarto website
Make a pull request to someone else’s repo

GitHub Org

Lisa will create a new organisation
Everyone send your github username in the chat
Accept the membership request

Create Your GitHub Repo

Fork

Fork your own repository to your own account
You can preface the name with rostock- if there is a conflict

Clone the Repo

RStudio

usethis::create_from_github("debruine/rostock-debruine")

Command Line

git clone https://github.com/debruine/rostock-debruine

Create a Website

Create a file called index.qmd
Add some markdown content
Create a file called _quarto.yml

Add the following text:

project:
  type: website
  output-dir: docs

website:
  title: "Lisa's Advanced Github Notes"

format:
  html:
    theme: slate

Render the website
```
quarto render
```

Commit and Push

Save your files
Check and stage the files
```
git status
git add *
```
Commit the new files
```
git commit -m "First commit"
```
Push the commit
```
git push
```

GitHub Pages

Go to the GitHub repo online
Go to Settings and then Pages
Select main as the branch
Select /docs as the folder, and save

Pull Request

Open a pull request to send changes to the base repo
Merge the pull request from the base repo

GitHub Pages (again)

Go to the base repo online
Go to Settings and then Pages
Select main as the branch
Select /docs as the folder, and save

GitHub Actions

Set up gh-pages branch
```
quarto publish gh-pages
```
Create a file .github/workflow/quarto.yml

Add the following text

name: Render and Publish
on:
  push:
    branches:
      - main  

jobs:
  build-deploy:
      runs-on: ubuntu-latest
      permissions:
        contents: write
      steps:
        - name: Check out repository
          uses: actions/checkout@v4

        - name: Set up Quarto
          uses: quarto-dev/quarto-actions/setup@v2
          with:
            version: 1.5.57

        - name: Publish to GitHub Pages (and render)
          uses: quarto-dev/quarto-actions/publish@v2
          with:
            target: gh-pages
          env:
            QUARTO_PROFILE: website
            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

Save, commit, and push

Base Repo

Create a new branch called gh-pages on the base repo
Send a pull request from your forked repo
Merge the pull request into your base repo
Check the actions

Pull Request Another Repo

Look at the other repos in the org
Make a change to one of the index.qmd files
Send a pull request
Review and accept any pull requests on your repo

Advanced GitHub

Task List

GitHub Org

Create Your GitHub Repo

Fork

Clone the Repo

RStudio

Command Line

Create a Website

Commit and Push

GitHub Pages

Pull Request

GitHub Pages (again)

GitHub Actions

Base Repo

Pull Request Another Repo

Further Resources

Thank You!