Software Carpentry Bootcamps

This repository's gh-pages branch is the starting point for a bootcamp website. It contains a template for your bootcamp's home page, and the shared lesson materials we have developed. The sections below explain how GitHub turns a repository into a web site, how you can build a website for your bootcamp using this repo as a starting point, what lessons we have, where they're located, and how you can incorporate them into your teaching. To contribute corrections or additions to this repository, see the contributing guidelines.

Note: If you are teaching Git in your bootcamp, you should create two repositories: one for your bootcamp's website, and one for learners to clone and update during your lessons. You should not try to use the same repo for both purposes because:

1. your website repo is probably going to be fairly large, and
2. you really don't want a learner accidentally overwriting your lessons while you're trying to teach.

Table of Contents

Background
Getting Started
Previewing the Site
Layout and Variables
Include Files
Instructors and Sponsors
Lesson Material
Other Lesson Material FAQ

Background

There are a few things you need to know in order to understand why we do things the way we do. Most 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 bootcamps, 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. HTML files and images are simply copied over; Markdown files are translated into HTML for copying.

4. If an HTML or Markdown file has a header consisting of three dashes, some data about the page, and three more dashes, 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. One of these commands is {% include somefile.html %}, which tells Jekyll to copy the contents of somefile.html into the file being translated; this is used to create standard headers and footers for pages. Another command is {{variable}}, which Jekyll replaces with the value of variable; this is used to insert things like a contact email address and the URL for our Twitter account.

5. 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 {{site.twitter_name}} in a page is replaced by @swcarpentry. 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).

6. 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 (or in a directory within _includes).

7. A repo 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 standard layouts for bootcamp pages. The first, bootcamp.html, is used for bootcamps' home pages: it is the layout for the index.html page in your repo's root directory. Its header defines several variables that must be present in order for your bootcamp to be included in our main website.

The second layout, lesson.html, can be used to lay out pages for individual lessons. You don't have to use it, but all of the pages in this repo's lessons directory do.

Getting Started

To create a website for a new bootcamp:

1. Create a new repository on GitHub with a name like YYYY-MM-DD-site, e.g., 2014-03-31-esu. This repository must not be a fork of an existing repository (because as mentioned earlier, GitHub only allows a user to fork a repository once, but many instructors are involved in several bootcamps). Please use the same ID for your bootcamp that the Software Carpentry admins are using to identify it, i.e., if the admins called the bootcamp 2014-03-31-esu, please don't call your repo euphoric-march-2014.
2. Clone this new repository to your local machine and cd into it. You can ignore the warning about cloning an empty repository: it won't stay empty long.

3. Add the template repository https://github.com/swcarpentry/bc.git as a remote named swcarpentry:

   git remote add swcarpentry https://github.com/swcarpentry/bc.git
   

4. Create a new branch in the local clone named gh-pages.

   git checkout -b gh-pages
   

5. Pull content from the GitHub template repository into your desktop repository:

   git pull swcarpentry gh-pages
   

6. Edit index.html to create the bootcamp home page (see below). Please double-check the information in the page's header (described below), as it is used to update the main website.

7. Preview your changes (see below).

8. (Optional) Delete these instructions from your bootcamp's README.md file and replace them with a paragraph describing your bootcamp.

9. Push content to your YYYY-MM-DD-site repository:

   git push origin gh-pages
   

As soon as your repo has been pushed to GitHub, GitHub will render your pages at the url:

http://{your-github-username}.github.io/YYYY-MM-DD-site/

You may update your bootcamp's website whenever you want.

Previewing the Site

To preview your bootcamp's page(s), go into its root directory and run:

make check

This will run jekyll to create the directory ./_site with your rendered pages. The ./_site/README.html file this produces will not have any CSS styling applied: GitHub will do that when the page is uploaded. The ./_site/index.html page, on the other hand, should have the Software Carpentry look and feel and the information about your bootcamp.

Note: you will need to install Jekyll 1.0.3 or later in order to preview things locally. If you have Ruby installed on your computer, this should be as simple as:

gem install github-pages

or if that doesn't work:

gem install jekyll
gem install kramdown

(We use Kramdown for translating Markdown instead of the default Redcarpet because Kramdown will handle Markdown inside HTML blocks). On OS X, we suggest you use a recent Ruby to get access to these. If you don't have Homebrew or MacPorts installed, here's a quick recipe to get started using HomeBrew.

ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
brew install ruby

and then gem install as above. If you don't have make in your machine, you can build the preview with:

jekyll -t build -d _site

Layout and Variables

The _layouts directory contains two files:

• bootcamp.html: the layout for bootcamp home pages. The material in your bootcamp's index.html is used to fill in the {{content}} section of this page.
• lesson.html: a minimal page for previewing lesson content.

Your bootcamp's index.html page (which uses the bootcamp.html layout) must define the following values in its YAML header:

• layout must be bootcamp.
• root is the path to the repository's root directory. This is '.' if the page is in the root directory, '..' if it is one directory down, and so on. If you create subdirectories for different rooms in your bootcamp, or for different lessons, set root accordingly.
• venue is the name of the institution or group hosting the bootcamp.
• address is the bootcamp venue's street address.
• country must be a hyphenated country name like 'United-States'. This is used to look up flags for display in the main web site; see the assets/flags directory in the site repo for a full list of valid names.
• latlng is the latitude and longitude of the bootcamp site (so we can put a pin on our map).
• humandate is the human-friendly dates for the bootcamp (e.g., July 3-4, 2015).
• startdate is the bootcamp's starting date in YYYY-MM-DD format.
• enddate is the bootcamp's ending date in the same format.
• registration is open (if anyone is allowed to sign up) or restricted (if only some people are allowed to take part). Please do not put HTML or links in here to explain who's allowed to enrol or how to go about doing it; that should go in the main body of your page.
• instructor is a comma-separated list of instructor names. This must be enclosed in square brackets, as in ["Alan Turing","Grace Hopper"]
• contact is the contact email address to use for your bootcamp.

Include Files

The _includes directory contains the following .html files:

• header.html: material for the page's head.
• banner.html: the generic banner with the Software Carpentry logo.
• footer.html: the generic footer with links to Software Carpentry's web presence.
• javascript.html: JQuery and Bootstrap Javascript.

You normally won't need to worry about these: they're included by bootcamp.html and lesson.html.

_includes/bootcamps also contains short pieces of standard text that can be included in bootcamp pages using {% include name.html %}:

• what.html: what bootcamps are.
• who.html: our intended audience
• instructors.html: creates a list of instructors' names.
• python.html: a brief point-form syllabus for a bootcamp using Python.
• r.html: a brief point-form syllabus for a bootcamp using R.
• requirements.html: what people need to bring.
• contact.html: how to reach the organizers.

If the information for your bootcamp is different, you can either modify these files or just copy their contents directly into your index.html page.

Instructors and Sponsors

The _includes directory also contains directories called people and orgs which hold short descriptions of people involved in Software Carpentry and our financial sponsors respectively. You can use {% include dir/file.html %} to include these in your bootcamp home page; they refer to head shots and logos in img/people and img/orgs, and these should be included automatically. Please send additions to the Software Carpentry administrators.

Lesson Material

Finally and most importantly, _includes contains lesson material that you can incorporate into your pages using {% include ... %}. Each lesson's material is in its own subdirectory: for example, the guide-shell lesson is the instructors' guide to the Unix shell, and contains:

• instructors.html: instructors' notes.
• opening.html: opening motivational story.
• prereq.html: discussion of pre-requisites.
• reference.html: a cheat sheet for the subject.
• summary.html: closing summary of the entire lesson.

It also contain subdirectories for various topics, each of which has:

• title.md: the topic title
• objectives.html: the topic's learning objectives
• lesson.html: a long-form prose version of the lesson
• summary.html: the key points of the lesson
• challenges.html: includes all the topic's challenge questions
• challenges/some-title.html: a single challenge question

The images that these files refer to have not yet been created; feel free to send us pull requests :-).

Other Lesson Material

Jekyll doesn't turn the files in _includes into web pages unless they're included somewhere, so we have created pages in a directory called lessons that do this. We have also put two other kinds of lesson materials in this directory:

• lessons built around IPython Notebooks, and
• lessons imported wholesale from other sources.

The file [lessons/index.html](lessons/index.html) lists all of the lessons we currently have, and includes links to the main page for each.

FAQ

• Where can I get help?
  Mail us at [email protected], or join our discussion list and ask for help there.

• Why does the bootcamp repository have to be created from scratch? Why not fork bc on GitHub?
  Because any particular user can only have one fork of a repository, but instructors frequently need to work on several bootcamps at once.

• Why are the lesson and topic files HTML instead of Markdown?
  Primarily convenience---that's what Greg Wilson had in hand to convert. These may be converted to Markdown in future. (Help would be welcome.)

• Why do files like lessons/db.html include everything explicitly?
  Because Jekyll does not support parameterized includes like:
  {% include {{lesson}}/something.html %}
  so we can't loop over a set of topics.

• Then why use Jekyll? Why not some other markup language and some other converter?
  Because they're the defaults on GitHub. If we're going to teach people to use that site, we should teach them to use it as it is, not as we wish it was.

• What do I do if I see a invalid byte sequence in ... error when I run make check?
  Declare the en_US.UTF-8 locale in your shell:

  export LC_ALL=en_US.UTF-8
  export LANG=en_US.UTF-8
  

• What do I do if I see a Conversion error when I run make check?
  The error message may look something like this:

  Configuration file: d:/OpenCourses/swc/2013-10-17-round6.4/_config.yml
          Source: d:/OpenCourses/swc/2013-10-17-round6.4
     Destination: _site
    Generating... c:/Ruby193/lib/ruby/gems/1.9.1/gems/posix-spawn-0.3.6/lib/posix/spawn.rb:162: wa
  rning: cannot close fd before spawn
  Conversion error: There was an error converting 'lessons/misc-biopython/fastq.md'.
  done.
  

  This is a problem in Pygments.rb Uninstall pygments.rb 0.5.1 or 0.5.2, install 0.5.0. For example, here's how you would uninstall pygments 0.5.2 and restore version 0.5.0:

  gem uninstall pygments.rb --version "=0.5.2"
  gem install pygments.rb --version "=0.5.0"
  

• What do I do if I see a File not found: u'nbconvert' when I run make check?
  The output of make check looks like this:

  WARNING: Unrecognized alias: 'output', it will probably have no effect.[TerminalIPythonApp] File not found: u'nbconvert'
  cp tmp/python/novice/01-numpy.html _site/python/novice/01-numpy.html
  cp: cannot stat ‘tmp/python/novice/01-numpy.html’: No such file or directory
  

  This means you don't have a recent enough version of IPython (below 1.0) and you should install a newer version. Installing a local version can be done with:

  pip install --upgrade --user ipython
  

  You might need pip that can be installed (under Ubuntu and alike) with:

  sudo apt-get install python-pip
  

• What if I get some missing packages messages when I run make check?
  Some additional packages are required. They can be installed (under Ubuntu and alike) with:

  sudo apt-get install pandoc jinja2
  

  Installation of jinja2 can also be carried on using pip.

• Where should pages go if multiple boot camps are running at a site simultaneously?
  Use subdirectories like 2013-07-01-esu/beginners, so that main directory names always follow our four-part convention.