initialise lesson

.travis.yml

+# Travis CI is only used to check the lesson and is not involved in its deployment
+dist: xenial  # Ubuntu 16.04 (required for python 3.7)
+language: python
+python: 3.7
+branches:
+  only:
+  - gh-pages
+  - /.*/
+before_install:
+  - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
+  - echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/" | sudo tee -a /etc/apt/sources.list
+  - sudo apt-get update -y
+  - sudo apt-get install -y r-base
+  - sudo Rscript -e "install.packages('knitr', repos = 'https://', dependencies = TRUE)"
+  - sudo Rscript -e "install.packages('stringr', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
+  - sudo Rscript -e "install.packages('checkpoint', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
+  - sudo Rscript -e "install.packages('ggplot2', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
+  - rvm default
+  - gem install json kramdown jekyll bundler
+install:
+  - pip install pyyaml
+script:
+  - make lesson-check-all
+  - make --always-make site

AUTHORS

+Toby Hodges: toby.hodges@embl.de

CITATION

+No citation info yet.

CONTRIBUTING.md

+# Contributing
+
+[The Carpentries][c-site] ([Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]) are open source projects,
+and we welcome contributions of all kinds:
+new lessons,
+fixes to existing material,
+bug reports,
+and reviews of proposed changes are all welcome.
+
+## Contributor Agreement
+
+By contributing,
+you agree that we may redistribute your work under [our license](LICENSE.md).
+In exchange,
+we will address your issues and/or assess your change proposal as promptly as we can,
+and help you become a member of our community.
+Everyone involved in [The Carpentries][c-site]
+agrees to abide by our [code of conduct](CODE_OF_CONDUCT.md).
+
+## How to Contribute
+
+The easiest way to get started is to file an issue
+to tell us about a spelling mistake,
+some awkward wording,
+or a factual error.
+This is a good way to introduce yourself
+and to meet some of our community members.
+
+1.  If you do not have a [GitHub][github] account,
+    you can [send us comments by email][email].
+    However,
+    we will be able to respond more quickly if you use one of the other methods described below.
+
+2.  If you have a [GitHub][github] account,
+    or are willing to [create one][github-join],
+    but do not know how to use Git,
+    you can report problems or suggest improvements by [creating an issue][issues].
+    This allows us to assign the item to someone
+    and to respond to it in a threaded discussion.
+
+3.  If you are comfortable with Git,
+    and would like to add or change material,
+    you can submit a pull request (PR).
+    Instructions for doing this are [included below](#using-github).
+
+## Where to Contribute
+
+1.  If you wish to change this lesson,
+    please work in <https://github.com/swcarpentry/FIXME>,
+    which can be viewed at <https://swcarpentry.github.io/FIXME>.
+
+2.  If you wish to change the example lesson,
+    please work in <https://github.com/carpentries/lesson-example>,
+    which documents the format of our lessons
+    and can be viewed at <https://carpentries.github.io/lesson-example>.
+
+3.  If you wish to change the template used for workshop websites,
+    please work in <https://github.com/carpentries/workshop-template>.
+    The home page of that repository explains how to set up workshop websites,
+    while the extra pages in <https://carpentries.github.io/workshop-template>
+    provide more background on our design choices.
+
+4.  If you wish to change CSS style files, tools,
+    or HTML boilerplate for lessons or workshops stored in `_includes` or `_layouts`,
+    please work in <https://github.com/carpentries/styles>.
+
+## What to Contribute
+
+There are many ways to contribute,
+from writing new exercises and improving existing ones
+to updating or filling in the documentation
+and submitting [bug reports][issues]
+about things that don't work, aren't clear, or are missing.
+If you are looking for ideas, please see the 'Issues' tab for
+a list of issues associated with this repository,
+or you may also look at the issues for [Data Carpentry][dc-issues], 
+[Software Carpentry][swc-issues], and [Library Carpentry][lc-issues] projects.
+
+Comments on issues and reviews of pull requests are just as welcome:
+we are smarter together than we are on our own.
+Reviews from novices and newcomers are particularly valuable:
+it's easy for people who have been using these lessons for a while
+to forget how impenetrable some of this material can be,
+so fresh eyes are always welcome.
+
+## What *Not* to Contribute
+
+Our lessons already contain more material than we can cover in a typical workshop,
+so we are usually *not* looking for more concepts or tools to add to them.
+As a rule,
+if you want to introduce a new idea,
+you must (a) estimate how long it will take to teach
+and (b) explain what you would take out to make room for it.
+The first encourages contributors to be honest about requirements;
+the second, to think hard about priorities.
+
+We are also not looking for exercises or other material that only run on one platform.
+Our workshops typically contain a mixture of Windows, macOS, and Linux users;
+in order to be usable,
+our lessons must run equally well on all three.
+
+## Using GitHub
+
+If you choose to contribute via GitHub, you may want to look at
+[How to Contribute to an Open Source Project on GitHub][how-contribute].
+To manage changes, we follow [GitHub flow][github-flow].
+Each lesson has two maintainers who review issues and pull requests or encourage others to do so.
+The maintainers are community volunteers and have final say over what gets merged into the lesson.
+To use the web interface for contributing to a lesson:
+
+1.  Fork the originating repository to your GitHub profile.
+2.  Within your version of the forked repository, move to the `gh-pages` branch and
+create a new branch for each significant change being made.
+3.  Navigate to the file(s) you wish to change within the new branches and make revisions as required.
+4.  Commit all changed files within the appropriate branches.
+5.  Create individual pull requests from each of your changed branches
+to the `gh-pages` branch within the originating repository.
+6.  If you receive feedback, make changes using your issue-specific branches of the forked
+repository and the pull requests will update automatically.
+7.  Repeat as needed until all feedback has been addressed.
+
+When starting work, please make sure your clone of the originating `gh-pages` branch is up-to-date
+before creating your own revision-specific branch(es) from there.
+Additionally, please only work from your newly-created branch(es) and *not*
+your clone of the originating `gh-pages` branch.
+Lastly, published copies of all the lessons are available in the `gh-pages` branch of the originating
+repository for reference while revising.
+
+## Other Resources
+
+General discussion of [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
+happens on the [discussion mailing list][discuss-list],
+which everyone is welcome to join.
+You can also [reach us by email][email].
+
+[email]: mailto:admin@software-carpentry.org
+[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
+[dc-lessons]: http://datacarpentry.org/lessons/
+[dc-site]: http://datacarpentry.org/
+[discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
+[github]: https://github.com
+[github-flow]: https://guides.github.com/introduction/flow/
+[github-join]: https://github.com/join
+[how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
+[issues]: https://guides.github.com/features/issues/
+[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
+[swc-lessons]: https://software-carpentry.org/lessons/
+[swc-site]: https://software-carpentry.org/
+[c-site]: https://carpentries.org/
+[lc-site]: https://librarycarpentry.org/
+[lc-issues]: https://github.com/issues?q=user%3Alibrarycarpentry

README.md

+# Building Websites with Jekyll and GitHub/GitLab
+
+Lesson material.
+
+
+## Maintainer(s)
+
+Current maintainer of this lesson is
+
+* Toby Hodges
+
+## Authors
+
+A list of contributors to the lesson can be found in [AUTHORS](AUTHORS)
+
+## Citation
+
+To cite this lesson, please consult with [CITATION](CITATION)
+
+[lesson-example]: https://carpentries.github.io/lesson-example

_config.yml

+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this ("swc", "dc", "lc", or "cp")?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor traning for instance)
+carpentry: none
+
+# Overall title for pages.
+title: "Building Websites with Jekyll and GitHub/GitLab"
+
+# Life cycle stage of the lesson
+# possible values: "pre-alpha", "alpha", "beta", "stable"
+life_cycle: "pre-alpha"
+
+#------------------------------------------------------------
+# Generic settings (should not need to change).
+#------------------------------------------------------------
+
+# What kind of thing is this ("workshop" or "lesson")?
+kind: "lesson"
+
+# Magic to make URLs resolve both locally and on GitHub.
+# See https://help.github.com/articles/repository-metadata-on-github-pages/.
+# Please don't change it: <USERNAME>/<PROJECT> is correct.
+repository: <USERNAME>/<PROJECT>
+
+# Email address, no mailto:
+email: "toby.hodges@embl.de"
+
+# Sites.
+amy_site: "https://amy.carpentries.org/workshops"
+carpentries_github: "https://github.com/carpentries"
+carpentries_pages: "https://carpentries.github.io"
+carpentries_site: "https://carpentries.org/"
+dc_site: "https://datacarpentry.org"
+example_repo: "https://github.com/carpentries/lesson-example"
+example_site: "https://carpentries.github.io/lesson-example"
+lc_site: "https://librarycarpentry.org/"
+swc_github: "https://github.com/swcarpentry"
+swc_pages: "https://swcarpentry.github.io"
+swc_site: "https://software-carpentry.org"
+template_repo: "https://github.com/carpentries/styles"
+training_site: "https://carpentries.github.io/instructor-training"
+workshop_repo: "https://github.com/carpentries/workshop-template"
+workshop_site: "https://carpentries.github.io/workshop-template"
+cc_by_human: "https://creativecommons.org/licenses/by/4.0/"
+
+# Surveys.
+pre_survey: "https://carpentries.typeform.com/to/wi32rS?slug="
+post_survey: "https://carpentries.typeform.com/to/UgVdRQ?slug="
+instructor_pre_survey: "https://www.surveymonkey.com/r/instructor_training_pre_survey?workshop_id="
+instructor_post_survey: "https://www.surveymonkey.com/r/instructor_training_post_survey?workshop_id="
+
+
+# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
+start_time: 0
+
+# Specify that things in the episodes collection should be output.
+collections:
+  episodes:
+    output: true
+    permalink: /:path/index.html
+  extras:
+    output: true
+    permalink: /:path/index.html
+
+# Set the default layout for things in the episodes collection.
+defaults:
+  - values:
+      root: .
+      layout: page
+  - scope:
+      path: ""
+      type: episodes
+    values:
+      root: ..
+      layout: episode
+  - scope:
+      path: ""
+      type: extras
+    values:
+      root: ..
+      layout: page
+
+# Files and directories that are not to be copied.
+exclude:
+  - Makefile
+  - bin/
+  - .Rproj.user/
+  - .vendor/
+  - .docker-vendor/
+
+# Turn on built-in syntax highlighting.
+highlighter: rouge

_episodes/01-introduction.md

+---
+title: "Introduction"
+teaching: 0
+exercises: 0
+questions:
+- "Key question (FIXME)"
+objectives:
+- "First learning objective. (FIXME)"
+keypoints:
+- "First key point. Brief Answer to questions. (FIXME)"
+---
+FIXME
+
+{% include links.md %}
+

_extras/about.md

+---
+title: About
+---
+{% include carpentries.html %}
+{% include links.md %}

_extras/discuss.md

+---
+title: Discussion
+---
+FIXME
+
+{% include links.md %}

_extras/figures.md

+---
+title: Figures
+---
+
+{% include base_path.html %}
+{% include manual_episode_order.html %}
+
+<script>
+  window.onload = function() {
+    var lesson_episodes = [
+    {% for lesson_episode in lesson_episodes %}
+      {% if site.episode_order %}
+        {% assign episode = site.episodes | where: "slug", lesson_episode | first %}
+      {% else %}
+        {% assign episode = lesson_episode %}
+      {% endif %}
+    "{{ episode.url }}"{% unless forloop.last %},{% endunless %}
+    {% endfor %}
+    ];
+
+    var xmlHttp = [];  /* Required since we are going to query every episode. */
+    for (i=0; i < lesson_episodes.length; i++) {
+
+      xmlHttp[i] = new XMLHttpRequest();
+      xmlHttp[i].episode = lesson_episodes[i];  /* To enable use this later. */
+      xmlHttp[i].onreadystatechange = function() {
+
+        if (this.readyState == 4 && this.status == 200) {
+          var parser = new DOMParser();
+          var htmlDoc = parser.parseFromString(this.responseText,"text/html");
+          var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0];
+
+          var article_here = document.getElementById(this.episode);
+          var images = htmlDocArticle.getElementsByTagName("img");
+
+          if (images.length > 0) {
+            var h1text = htmlDocArticle.getElementsByTagName("h1")[0].innerHTML;
+
+            var htitle = document.createElement('h2');
+            htitle.innerHTML = h1text;
+            article_here.appendChild(htitle);
+
+            var image_num = 0;
+            for (let image of images) {
+              image_num++;
+
+              var title = document.createElement('p');
+              title.innerHTML = "<strong>Figure " + image_num + ".</strong> " + image.alt;
+              article_here.appendChild(title);
+
+              article_here.appendChild(image.cloneNode(false));
+
+              if (image_num < images.length) {
+                var hr = document.createElement('hr');
+                article_here.appendChild(hr);
+              }
+            }
+          }
+        }
+      }
+      episode_url = "{{ relative_root_path }}" + lesson_episodes[i];
+      xmlHttp[i].open("GET", episode_url);
+      xmlHttp[i].send(null);
+    }
+  }
+</script>
+
+{% comment %} Create anchor for each one of the episodes.  {% endcomment %}
+
+{% for lesson_episode in lesson_episodes %}
+  {% if site.episode_order %}
+    {% assign episode = site.episodes | where: "slug", lesson_episode | first %}
+  {% else %}
+    {% assign episode = lesson_episode %}
+  {% endif %}
+<article id="{{ episode.url }}" class="figures"></article>
+{% endfor %}
+
+{% include links.md %}

_extras/guide.md

+---
+title: "Instructor Notes"
+---
+FIXME
+
+{% include links.md %}

index.md

+---
+layout: lesson
+root: .  # Is the only page that doesn't follow the pattern /:path/index.html
+permalink: index.html  # Is the only page that doesn't follow the pattern /:path/index.html
+---
+
+- Markdown
+  - links
+  - conversion to HTML
+- GitHub Pages
+  - activating
+  - `index.md`
+  - YAML headers
+- GitLab Pages
+  - activating
+  - `gitlab-ci.yml`
+  - `index.md`
+  - YAML headers
+- Jekyll
+  - variables
+  - `_config.yml`
+  - includes
+- Themes
+  - layouts
+
+<!-- this is an html comment -->
+
+{% comment %} This is a comment in Liquid {% endcomment %}
+
+> ## Prerequisites
+>
+> - familiarity with git (add, commit, pull, push, checkout)& at least one of GitHub or GitLab
+> - familiarity with HTML & CSS
+{: .prereq}
+
+{% include links.md %}

reference.md

+---
+layout: reference
+---
+
+## Glossary
+
+FIXME
+
+{% include links.md %}

setup.md

+---
+title: Setup
+---
+FIXME
+
+
+{% include links.md %}