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Background and Design

There are a few things you need to know in order to understand why this template is organized the way it is:

  1. Git uses the term clone to mean "a copy of a repository". GitHub uses 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 remote called origin that points to the original repo; other remotes can be added manually.

  2. A user on GitHub can only have one fork of a particular repo. This is a problem for us because an author may be involved in writing several lessons, each of which has its own website repo. Those website repositories ought to be forks of this one, but since GitHub doesn't allow that, we've had to find a workaround.

  3. If a repository has a branch called gh-pages (which stands for "GitHub pages"), then GitHub uses the HTML and Markdown files in that branch to create a website for the repository. If the repository's URL is http://github.com/darwin/finches, the URL for the website is http://darwin.github.io/finches.

  4. We use Markdown for writing pages 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 use something else to author their lessons (e.g., IPython Notebooks), it's up to them to generate and commit Markdown formatted according to the rules below.

    Note: we do not prescribe what tools instructors should use when actually teaching. The IPython Notebook, Python IDEs like Spyder, and the GOCLI (Good Ol' Command Line Interpreter) are all equally welcome up on stage --- all we specify is the format of the lesson notes.

  5. We use Pandoc to process pages instead of Jekyll (GitHub's default conversion tool) because Pandoc supports a much richer dialect of Markdown than Jekyll. Like Jekyll, Pandoc looks for a header at the top of each page 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 this. Lesson authors will usually not have to worry about this.

  6. Using Pandoc instead of Jekyll means that we have to compile our Markdown into HTML on our own machines and commit it to the gh-pages branch of the lesson's GitHub repository.

    It's considered bad practice to put computer-generated files under version control, but the HTML pages put into the lesson's root directory by Pandoc must be committed to version control in order for the lesson to be displayed properly on GitHub.

    It's also considered bad practice to put generated files in the same directory as source files. We do it because some authors may use auxiliary source files such as R Markdown and IPython Notebook files which are executable, and contain paths to things like images and data files. If we put our source files in a sub-directory, those paths won't work (or conversely, if we put our generated files in a different directory, the paths won't work there).

  7. In order to display properly, our generated HTML pages need artwork, CSS style files, and a few bits of Javascript. We could load these from the web, but that would make offline authoring difficult. Instead, each lesson's repository has a copy of these files, and a way of updating them (and only them) on demand.

One final note: we try not to put HTML inside Markdown because it's ugly to read and write, and error-prone to process. Instead, we put things that ought to be in <div> blocks, like the learning objectives and challenge exercises, in blockquotes indented with >, and do a bit of post-processing to attach the right CSS classes to these blocks.