GitHub, Markdown, and Jekyll


Teaching: 10 min
Exercises: 0 min
  • How are pages published?

  • Explain how GitHub Pages produce web sites from Git repositories.

  • Explain Jekyll’s formatting rules.

This episode describes the tools we use to build and manage lessons. These simplify many tasks, but make other things more complicated.

Background Resources

Find out more about setting up a lesson and contributing changes, including information on using GitHub.

Repositories on GitHub

Our lessons are stored in Git repositories (or “repos”) on GitHub. We use the term fork to mean “a copy of a GitHub-hosted repo that is also hosted on GitHub” and the term clone to mean “a copy of a GitHub-hosted repo that’s located on someone else’s machine”. In both cases, the duplicate has a reference that points to the original repo.

In an ideal world, we would put all of the common files used by our lessons (such as the CSS style files and the image files with project logos) in a template repo. The master copy of each lesson would be a fork of that repo, and each author’s working copy would be a fork of that master:

Forking Repositories

However, GitHub only allows a user to have one fork of any particular repo. This creates a problem for us because an author may be involved in writing several lessons, each with its own repo. We therefore use GitHub Importer to create new lessons. After the lesson has been created, we manually add the template repository as a remote called template to update the lesson when the template changes.

Repository Links

GitHub Pages

If a repository has a branch called gh-pages (short for “GitHub Pages”), GitHub publishes its content to create a website for the repository. If the repository’s URL is, the website is

GitHub Pages sites can include static HTML pages, which are published as-is, or they can use Jekyll as described below to compile HTML and/or Markdown pages with embedded directives to create the pages for display.

Why Doesn’t My Site Appear?

If the root directory of a repository contains a file called .nojekyll, GitHub will not generate a website for that repository’s gh-pages branch.

We write lessons in Markdown because it’s simple to learn and isn’t tied to any specific language. (The ReStructured Text format popular in the Python world, for example, is a complete unknown to R programmers.) If authors want to write lessons in something else, such as R Markdown, they must generate HTML or Markdown that Jekyll can process and commit that to the repository. A later episode describes the Markdown we use.

Teaching Tools

We do not prescribe what tools instructors should use when actually teaching: the Jupyter Notebook, RStudio, and the good ol’ command line are equally welcome up on stage. All we specify is the format of the lesson notes.


GitHub uses Jekyll to turn Markdown into HTML. It looks for text files that begin with a header formatted like this:

variable: value
other_variable: other_value

...stuff in the page...

and inserts the values of those variables into the page when formatting it. The three dashes that start the header must be the first three characters in the file: even a single space before them will make Jekyll ignore the file.

The header’s content must be formatted as YAML, and may contain Booleans, numbers, character strings, lists, and dictionaries of name/value pairs. Values from the header are referred to in the page as page.variable. For example, this page:

name: Science
Today we are going to study {{}}.

is translated into:

    <p>Today we are going to study Science.</p>

Back in the Day…

The previous version of our template did not rely on Jekyll, but instead required authors to build HTML on their desktops and commit that to the lesson repository’s gh-pages branch. This allowed us to use whatever mix of tools we wanted for creating HTML (e.g., Pandoc), but complicated the common case for the sake of uncommon cases, and didn’t model the workflow we want learners to use.


Jekyll also reads values from a configuration file called _config.yml, which are referred to in pages as site.variable. The lesson template does not include _config.yml, since each lesson will change some of its value, which would result in merge collisions each time the lesson was updated from the template. Instead, the template contains a script called bin/ which should be run once to create an initial _config.yml file (and a few other files as well). The author should then edit the values in the top half of the file.


If several Markdown files are stored in a directory whose name begins with an underscore, Jekyll creates a collection for them. We rely on this for both lesson episodes (stored in _episodes) and extra files (stored in _extras). For example, putting the extra files in _extras allows us to populate the “Extras” menu pulldown automatically. To clarify what will appear where, we store files that appear directly in the navigation bar in the root directory of the lesson. The next episode describes these files.

Key Points

  • Lessons are stored in Git repositories on GitHub.

  • Lessons are written in Markdown.

  • Jekyll translates the files in the gh-pages branch into HTML for viewing.

  • The site’s configuration is stored in _config.yml.

  • Each page’s configuration is stored at the top of that page.

  • Groups of files are stored in collection directories whose names begin with an underscore.