De-carpentryfy the lesson look

Author: mkuzak

.travis.yml

@@ -0,0 +1,24 @@
+# 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

@@ -0,0 +1 @@
+FIXME: list authors' names and email addresses.

CITATION

@@ -0,0 +1 @@
+FIXME: describe how to cite this lesson.

CONTRIBUTING.md

@@ -0,0 +1,151 @@
+# 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:[email protected]
+[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

@@ -0,0 +1,40 @@
+# FIXME Lesson title
+
+[![Create a Slack Account with us](https://img.shields.io/badge/Create_Slack_Account-The_Carpentries-071159.svg)](https://swc-slack-invite.herokuapp.com/)
+
+This repository generates the corresponding lesson website from [The Carpentries](https://carpentries.org/) repertoire of lessons. 
+
+## Contributing
+
+We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any
+questions, concerns, or experience any difficulties along the way.
+
+We'd like to ask you to familiarize yourself with our [Contribution Guide](CONTRIBUTING.md) and have a look at
+the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even
+how to write new episodes.
+
+Please see the current list of [issues][FIXME] for ideas for contributing to this
+repository. For making your contribution, we use the GitHub flow, which is
+nicely explained in the chapter [Contributing to a Project](http://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) in Pro Git
+by Scott Chacon.
+Look for the tag ![good_first_issue](https://img.shields.io/badge/-good%20first%20issue-gold.svg). This indicates that the maintainers will welcome a pull request fixing this issue.  
+
+
+## Maintainer(s)
+
+Current maintainers of this lesson are 
+
+* FIXME
+* FIXME
+* FIXME
+
+
+## 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

_episodes/01-introduction.md

@@ -0,0 +1,15 @@
+---
+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

@@ -0,0 +1,5 @@
+---
+title: About
+---
+{% include escience_academy.html %}
+{% include links.md %}

_extras/discuss.md

@@ -0,0 +1,6 @@
+---
+title: Discussion
+---
+FIXME
+
+{% include links.md %}

_extras/figures.md

@@ -0,0 +1,79 @@
+---
+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

@@ -0,0 +1,6 @@
+---
+title: "Instructor Notes"
+---
+FIXME
+
+{% include links.md %}