Species Interaction Data Workshop: Background and Design

There are a few things you need to know in order to understand why we do things the way we do. Some of them are specific to GitHub, rather than Git itself.

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 instructor may be involved in several workshops, each of which has its own website repo. To avoid this issue, we use the template functionality (you could also use the import.github.com functionality).

3. If a repository has a file called README.md in its root directory, GitHub displays the contents of that file on the repository’s home page.

4. 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.

5. If an HTML or Markdown file has a header consisting of three dashes, some data about the page, and three more dashes:

   ---
   key: value
   other_key: other_value
   ---
   content of the page
   

   then GitHub doesn’t just copy the file over verbatim. Instead, it runs the file through a translator called Jekyll that looks for specially-formatted commands embedded in the file and uses them to fill in the page.

6. Commands can be embedded in the body of a page. One is {% include something.html %}, which tells Jekyll to copy the contents of something.html into the file being translated; this is used to create standard headers and footers for pages. Another is {{variable}}: when Jekyll sees this, it replaces it with the value of variable. This is used to insert things like a contact email address and the URL for our Twitter account.

7. Jekyll gets variables from two places: a file called _config.yml located in the repo’s root directory, and the header of each individual page. Variables from _config.yml are put in an object called site, and referred to as site.variable, so that (for example) {{site.swc_site}} in a page is replaced by the URL of the main Software Carpentry web site (https://software-carpentry.org). Variables from the page’s header are put in an object called page, and referred to as page.variable, so if a page’s header defines a variable called venue, {{page.venue}} is replaced by “Euphoric State University” (or whatever value the variable has).

8. If a page uses {% include something.html %} to include a snippet of HTML, Jekyll looks in a directory called _includes to find something.html. It always looks there, and nowhere else, so anything we want people to be able to include in their pages has to be stored in _includes.

9. A repository can have another special directory called _layouts. If a page like index.html has a variable called layout, and that variable’s value is standard.html, Jekyll loads the file _layouts/standard.html and copies the content of index.html into it, then expands the result. This is used to give the pages in a site a uniform appearance. We have created two layouts for workshop pages:

   • workshop.html is used for workshops’ home pages, and is the layout for the index.html page in your repo’s root directory. That index.html page’s header must define several variables as specified in the the customization instructions in order for your workshop to be included in our main website.

   • page.html is used for any other pages you want to create. Note: if you create extra pages, you must edit the values in the top section of _config.yml as described in the lesson template documentation.

Extra Directories

This workshop template shares resources with the template used for Carpentry lessons. As a result, your workshop website’s repository contains directories that most workshops don’t need, but which can be used to store extra material when necessary:

• _extras/: extra pages (like this one).
• _episodes/: lesson episodes (which workshops usually don’t have).
• _episodes_rmd/: R Markdown lesson episodes (if any).
• code/: for code samples.
• data/: for data files.
• fig/: for figures and other images.
• files/: for miscellaneous files.

For more information on these, please see the documentation for the lesson template.