5  Adapting our template

If you want to use our template for your own course, you will likely want to adapt it to your branding and needs.

This page describes how you can copy this template and adapt it to your needs.

TipCiting us

If you use this template for your course, please cite us as indicated on the home page.

5.1 Copying the template

One possibility is to fork our repository, but this will create a link to our repository and keep all its history, which may not be desirable. Instead, we suggest that you copy the template without keeping any history, so you can start fresh.

  1. Make a clone of our repository:

    git clone https://github.com/cambiotraining/quarto-course-template.git genetics-course-template
cd genetics-course-template

  2. Remove the .git directory to remove the history:

    rm -rf .git

  3. Initialise a new repository:

    git init
git add .
git commit -m "Initial commit, copy of CRIT template"

5.2 Create a new GitHub repository

We will use the following as an example:

  • Username: gencam
  • Our new template repository is called genetics-course-template.

But please adapt the commands to your own username and chosen repository name.

  1. Create a new repository on GitHub called genetics-course-template (do not initialise it with a README, .gitignore or license).

  2. Go to Settings > Actions and:

    • Select “Allow all actions and reusable workflows”
    • Select “Read and write permissions”
    • Tick “Allow GitHub Actions to create and approve pull requests”

  3. Push the code to the remote repository.

    git branch -M main
git remote add origin https://github.com/gencam/genetics-course-template.git
git push -u origin main

5.3 Publish the site

  • Go to GitHub and open the “Actions” tab
    • An action called “Deploy” should be running or have finished running after you push.
    • Confirm that the action finished successfully.
    • Once it finishes a new gh-pages branch is created.
  • Go to “Settings > Pages”, and under “Build and deploy”:
    • Source: “Deploy from a branch”
    • Branch: “gh-pages” > Save
  • The page should publish to gencam.github.io/genetics-course-template/ (it may take a few minutes to appear).

5.4 Customising the theme

The template used by us uses a custom theme with our colours, logo, and fonts. If you want to adapt it to your own branding, you will need to adapt a CSS file and a few other files.

5.4.1 Add your own theme

  • In the _quarto.yml file, replace format: crit-format-html with (feel free to change some of the options as preferred, but note that the theme.scss needs to match the file set in the next step):

    format:
  html:
    theme: [default, genetics-theme/theme.scss]
    toc: true
    number-sections: true
    number-depth: 3
    code-link: true
    code-copy: true
    lightbox: true

  • Create the genetics-theme/ directory and copy our theme into it:

    mkdir genetics-theme
cp _extensions/cambiotraining/crit-format/theme.scss genetics-theme/theme.scss

  • Edit the newly copied theme.scss file to adapt it to your branding (colours, fonts, logo, etc).

  • Edit the rest of _quarto.yml to use your own title, logo, link to social media, and other details.

  • Test building the site with quarto render and check that everything looks as expected.

5.4.2 Remove CRIT branding

Our branding is included as an extension, which you can now remove from your copy.

  • Uninstall the extension:

    quarto remove cambiotraining/crit-format

  • Remove the github action that updates our extensions automatically:

    rm .github/workflows/update_extensions.yml

  • Test the local rendering again: quarto render

If everything looks good, push the changes to GitHub and check that the site builds correctly 🚀

Remember to see other sections of this documentation to adapt the content of the course to your needs.