Preparing for June 2016 release

.gitignore

+*~
+.DS_Store
+.sass-cache
+_site
+__pycache__

CONDUCT.md

+---
+layout: page
+title: "Contributor Code of Conduct"
+permalink: /conduct/
+---
+As contributors and maintainers of this project,
+we pledge to respect all people who contribute through reporting issues,
+posting feature requests,
+updating documentation,
+submitting pull requests or patches,
+and other activities.
+
+We are committed to making participation in this project a harassment-free experience for everyone,
+regardless of level of experience,
+gender,
+gender identity and expression,
+sexual orientation,
+disability,
+personal appearance,
+body size,
+race,
+ethnicity,
+age,
+or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or imagery,
+derogatory comments or personal attacks,
+trolling,
+public or private harassment,
+insults,
+or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct.
+Project maintainers who do not follow the Code of Conduct may be removed from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior
+may be reported by opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from
+the [Contributor Covenant][contrib-covenant] Version 1.0.0.
+
+[contrib-covenant]: http://contributor-covenant.org/

LICENSE.md

+---
+layout: page
+title: "Licenses"
+permalink: /license/
+---
+## Instructional Material
+
+All Software Carpentry and Data Carpentry instructional material is
+made available under the [Creative Commons Attribution
+license][cc-by-human]. The following is a human-readable summary of
+(and not a substitute for) the [full legal text of the CC BY 4.0
+license][cc-by-legal].
+
+You are free:
+
+* to **Share**---copy and redistribute the material in any medium or format
+* to **Adapt**---remix, transform, and build upon the material
+
+for any purpose, even commercially.
+
+The licensor cannot revoke these freedoms as long as you follow the
+license terms.
+
+Under the following terms:
+
+* **Attribution**---You must give appropriate credit (mentioning that
+  your work is derived from work that is Copyright © Software
+  Carpentry and, where practical, linking to
+  http://software-carpentry.org/), provide a [link to the
+  license][cc-by-human], and indicate if changes were made. You may do
+  so in any reasonable manner, but not in any way that suggests the
+  licensor endorses you or your use.
+
+**No additional restrictions**---You may not apply legal terms or
+technological measures that legally restrict others from doing
+anything the license permits.  With the understanding that:
+
+Notices:
+
+* You do not have to comply with the license for elements of the
+  material in the public domain or where your use is permitted by an
+  applicable exception or limitation.
+* No warranties are given. The license may not give you all of the
+  permissions necessary for your intended use. For example, other
+  rights such as publicity, privacy, or moral rights may limit how you
+  use the material.
+
+## Software
+
+Except where otherwise noted, the example programs and other software
+provided by Software Carpentry and Data Carpentry are made available under the
+[OSI][osi]-approved
+[MIT license][mit-license].
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+## Trademark
+
+"Software Carpentry" an "Data Carpentry" and their respective logos
+are registered trademarks of [NumFOCUS][numfocus].
+
+[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
+[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
+[mit-license]: http://opensource.org/licenses/mit-license.html
+[numfocus]: http://numfocus.org/
+[osi]: http://opensource.org

Makefile

+## ========================================
+## Commands for both workshop and lesson websites.
+
+# Settings
+MAKEFILES=Makefile $(wildcard *.mk)
+JEKYLL=jekyll
+DST=_site
+
+# Controls
+.PHONY : commands clean files
+all : commands
+
+## commands       : show all commands.
+commands :
+	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
+
+## serve          : run a local server.
+serve :
+	${JEKYLL} serve --config _config.yml,_config_dev.yml
+
+## site           : build files but do not run a server.
+site :
+	${JEKYLL} build --config _config.yml,_config_dev.yml
+
+## figures        : re-generate inclusion displaying all figures.
+figures :
+	@bin/extract_figures.py -s _episodes -p bin/markdown-ast.rb > _includes/all_figures.html
+
+## clean          : clean up junk files.
+clean :
+	@rm -rf ${DST}
+	@rm -rf .sass-cache
+	@rm -rf bin/__pycache__
+	@find . -name .DS_Store -exec rm {} \;
+	@find . -name '*~' -exec rm {} \;
+	@find . -name '*.pyc' -exec rm {} \;
+
+## ----------------------------------------
+## Commands specific to workshop websites.
+
+.PHONY : workshop-check
+
+## workshop-check : check workshop homepage.
+workshop-check :
+	@bin/workshop_check.py .
+
+## ----------------------------------------
+## Commands specific to lesson websites.
+
+.PHONY : lesson-check lesson-files lesson-fixme lesson-single
+
+# Lesson source files in the order they appear in the navigation menu.
+SRC_FILES = \
+  index.md \
+  CONDUCT.md \
+  setup.md \
+  $(wildcard _episodes/*.md) \
+  reference.md \
+  $(wildcard _extras/*.md) \
+  LICENSE.md
+
+# Generated lesson files in the order they appear in the navigation menu.
+HTML_FILES = \
+  ${DST}/index.html \
+  ${DST}/conduct/index.html \
+  ${DST}/setup/index.html \
+  $(patsubst _episodes/%.md,${DST}/%/index.html,$(wildcard _episodes/*.md)) \
+  ${DST}/reference/index.html \
+  $(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \
+  ${DST}/license/index.html
+
+## lesson-check   : validate lesson Markdown.
+lesson-check :
+	@bin/lesson_check.py -s . -p bin/markdown-ast.rb
+
+unittest :
+	python bin/test_lesson_check.py
+
+## lesson-files   : show expected names of generated files for debugging.
+lesson-files :
+	@echo 'source:' ${SRC_FILES}
+	@echo 'generated:' ${HTML_FILES}
+
+## lesson-fixme   : show FIXME markers embedded in source files.
+lesson-fixme :
+	@fgrep -i -n FIXME ${SRC_FILES} || true
+
+#-------------------------------------------------------------------------------
+# Include extra commands if available.
+#-------------------------------------------------------------------------------
+
+-include commands.mk

_config_dev.yml

+#------------------------------------------------------------
+# This config-file is only needed for development. Instead of changing
+# the url everytime you work locally on the project, run a server with
+# both configuration files:
+#
+#    jekyll serve --config _config.yml,_config_dev.yml
+#------------------------------------------------------------
+
+# Is this production or development? (Overrides _config.yml.)
+is_production: false
+
+# Override root so that CSS and other resources will load locally.
+github:
+  url: http://0.0.0.0:4000

_includes/all_keypoints.html

+{% comment %}
+  Display key points of all episodes for reference.
+{% endcomment %}
+<h2>Key Points</h2>
+<table class="table table-striped">
+{% for episode in site.episodes %}
+  {% unless episode.break %}
+    <tr>
+      <td class="col-md-3">
+        <a href="{{ site.github.url }}{{ episode.url }}">{{ episode.title }}</a>
+      </td>
+      <td class="col-md-9">
+        <ul>
+  	{% for keypoint in episode.keypoints %}
+  	<li>{{ keypoint }}</li>
+  	{% endfor %}
+        </ul>
+      </td>
+    </tr>
+  {% endunless %}
+{% endfor %}
+</table>

_includes/carpentries.html

+<div class="row">
+  <div class="col-md-2" align="center">
+    <a href="{{ site.swc_site }}"><img src="{{ site.github.url }}/assets/img/swc-icon-blue.svg" alt="Software Carpentry logo" /></a>
+  </div>
+  <div class="col-md-8">
+    Since 1998,
+    <a href="{{ site.swc_site }}">Software Carpentry</a>
+    has been teaching researchers in science, engineering, medicine, and related disciplines
+    the computing skills they need to get more done in less time and with less pain.
+    Its volunteer instructors have run hundreds of events
+    for thousands of learners in the past two and a half years.
+  </div>
+</div>
+<br/>
+<div class="row">
+  <div class="col-md-2" align="center">
+    <a href="{{ site.dc_site }}"><img src="{{ site.github.url }}/assets/img/dc-icon-black.svg" alt="Data Carpentry logo" /></a>
+  </div>
+  <div class="col-md-8">
+    <a href="{{ site.dc_site }}">Data Carpentry</a> develops and teaches workshops on the fundamental data skills needed to conduct research.
+    Its target audience is researchers who have little to no prior computational experience,
+    and its lessons are domain specific,
+    building on learners' existing knowledge to enable them to quickly apply skills learned to their own research.
+  </div>
+</div>
+
+

_includes/episode_break.html

+{% comment %}
+  Display information about a break.
+{% endcomment %}
+<p>Break: {{page.break}} min</p>

_includes/episode_find_prev_next.html

+{% comment %}
+    Find previous and next episodes (if any).
+{% endcomment %}
+{% for episode in site.episodes  %}
+  {% if episode.url == page.url %}
+    {% unless forloop.first %}
+      {% assign prev_episode = prev %}
+    {% endunless %}
+    {% unless forloop.last %}
+      {% assign next_episode = site.episodes[forloop.index] %}
+    {% endunless %}
+  {% endif %}
+  {% assign prev = episode %}
+{% endfor %}

_includes/episode_keypoints.html

+<blockquote class="keypoints">
+  <h2>Key Points</h2>
+  <ul>
+    {% for keypoint in page.keypoints %}
+    <li>{{ keypoint }}</li>
+    {% endfor %}
+  </ul>
+</blockquote>

_includes/episode_overview.html

+{% comment %}
+    Display an episode's timings and learning objectives.
+{% endcomment %}
+<blockquote class="objectives">
+  <h2>Overview</h2>
+
+  <div class="row">
+    <div class="col-md-3">
+      <strong>Teaching:</strong> {{ page.teaching }} min
+      </br>
+      <strong>Exercises:</strong> {{ page.exercises }} min
+    </div>
+    <div class="col-md-9">
+      <strong>Questions</strong>
+      <ul>
+	{% for question in page.questions %}
+	<li>{{ question }}</li>
+	{% endfor %}
+      </ul>
+    </div>
+  </div>
+  
+  <div class="row">
+    <div class="col-md-3">
+    </div>
+    <div class="col-md-9">
+      <strong>Objectives</strong>
+      <ul>
+	{% for objective in page.objectives %}
+	<li>{{ objective }}</li>
+	{% endfor %}
+      </ul>
+    </div>
+  </div>
+  
+</blockquote>

_includes/episode_title.html

+{% include episode_find_prev_next.html %}
+<div class="row">
+  <div class="col-md-1">
+    <h3>
+      {% if prev_episode %}
+      <a href="{{ site.github.url }}{{ prev_episode.url }}"><span class="glyphicon glyphicon-menu-left"></span></a>
+      {% else %}
+      <a href="{{ site.github.url }}"><span class="glyphicon glyphicon-menu-up"></span></a>
+      {% endif %}
+    </h3>
+  </div>
+  <div class="col-md-10">
+    <h3 class="maintitle"><a href="{{ site.github.url }}/">{{ site.title }}</a></h3>
+    <h1 class="maintitle">{{ page.title }}</h1>
+  </div>
+  <div class="col-md-1">
+    <h3>
+      {% if next_episode %}
+      <a href="{{ site.github.url }}{{ next_episode.url }}"><span class="glyphicon glyphicon-menu-right"></span></a>
+      {% else %}
+      <a href="{{ site.github.url }}"><span class="glyphicon glyphicon-menu-up"></span></a>
+      {% endif %}
+    </h3>
+  </div>
+</div>

_includes/footer.html

+{% comment %}
+  Generic footer.  Links to repository, not to generated website, so
+  we do a bit of a dance to get the right URL.
+{% endcomment %}
+{% if site.is_production %}
+  {% capture repo_url %}{{ site.github.repository_url }}{% endcapture %}
+{% else %}
+  {% capture repo_url %}https://github.com/{{ site.account }}/{{ site.project }}{% endcapture %}
+{% endif %}
+<hr/>
+<footer>
+  <div class="row">
+    <div class="col-md-6" align="left">
+      <h4>
+	Copyright &copy; 2016
+	{% if site.carpentry == "swc" %}<a href="{{ site.swc_site }}">Software Carpentry Foundation</a>{% endif %}
+	{% if site.carpentry == "dc" %}<a href="{{ site.dc_site }}">Data Carpentry</a>{% endif %}
+      </h4>
+    </div>
+    <div class="col-md-6" align="right">
+      <h4>
+	<a href="{{ repo_url }}">Source</a>
+	/
+	<a href="{{ repo_url }}/blob/gh-pages/CONTRIBUTING.md">Contributing</a>
+	/
+	<a href="mailto:{{ site.email }}">Contact</a>
+      </h4>
+    </div>
+  </div>
+</footer>

_includes/javascript.html

+<script src="{{ site.github.url }}/assets/js/jquery.min.js"></script>
+<script src="{{ site.github.url }}/assets/js/bootstrap.min.js"></script>
+<script src="{{ site.github.url }}/assets/js/lesson.js"></script>

_includes/main_title.html

+<h1 class="maintitle"><a href="{{ site.github.url }}/">{{ site.title }}</a>{% if page.title %}: {{ page.title }}{% endif %}</h1>

_includes/navbar.html

+<nav class="navbar navbar-default">
+  <div class="container-fluid">
+    <div class="navbar-header">
+      {% if page.carpentry == "swc" %}
+      <a href="{{ site.swc_site }}" class="pull-left">
+        <img class="navbar-logo" src="{{ site.github.url }}/assets/img/swc-icon-blue.svg" alt="Software Carpentry logo" />
+      </a>
+      {% elsif page.carpentry == "dc" %}
+      <a href="{{ site.dc_site }}" class="pull-left">
+        <img class="navbar-logo" src="{{ site.github.url }}/assets/img/dc-icon-black.svg" alt="Data Carpentry logo" />
+      </a>
+      {% elsif site.carpentry == "swc" %}
+      <a href="{{ site.swc_site }}" class="pull-left">
+        <img class="navbar-logo" src="{{ site.github.url }}/assets/img/swc-icon-blue.svg" alt="Software Carpentry logo" />
+      </a>
+      {% elsif site.carpentry == "dc" %}
+      <a href="{{ site.dc_site }}" class="pull-left">
+        <img class="navbar-logo" src="{{ site.github.url }}/assets/img/dc-icon-black.svg" alt="Data Carpentry logo" />
+      </a>
+      {% endif %}
+      <a class="navbar-brand" href="{{ site.github.url }}/">Home</a>
+    </div>
+    <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
+      <ul class="nav navbar-nav">
+        <li><a href="{{ site.github.url }}/conduct/">Code of Conduct</a></li>
+        {% if site.kind == "lesson" %}
+        <li><a href="{{ site.github.url }}/setup/">Setup</a></li>
+        <li class="dropdown">
+          <a href="{{ site.github.url }}/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Episodes <span class="caret"></span></a>
+          <ul class="dropdown-menu">
+            {% for episode in site.episodes %}
+            <li><a href="{{ site.github.url }}{{ episode.url }}">{{ episode.title }}</a></li>
+            {% endfor %}
+          </ul>
+        </li>
+        <li class="dropdown">
+          <a href="{{ site.github.url }}/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Extras <span class="caret"></span></a>
+          <ul class="dropdown-menu">
+            {% for extra in site.extras %}
+            <li><a href="{{ site.github.url }}{{ extra.url }}">{{ extra.title }}</a></li>
+            {% endfor %}
+          </ul>
+        </li>
+        <li><a href="{{ site.github.url }}/reference/">Reference</a></li>
+        {% endif %}
+        <li><a href="{{ site.github.url }}/license/">License</a></li>
+      </ul>
+      <form class="navbar-form navbar-right" role="search" id="search" onsubmit="google_search(); return false;">
+        <div class="form-group">
+          <input type="text" id="google-search" placeholder="Search...">
+        </div>
+      </form>
+    </div>
+  </div>
+</nav>

_includes/syllabus.html

+{% comment %}
+  Display syllabus in tabular form.
+  Days are displayed if at least one episode has 'start = true'.
+{% endcomment %}
+<div class="syllabus">
+  <h2>Schedule</h2>
+
+  {% assign day = 0 %}
+  {% assign multiday = false %}
+  {% for episode in site.episodes %}
+    {% if episode.start %}{% assign multiday = true %}{% break %}{% endif %}
+  {% endfor %}
+  {% assign current = site.start_time %}
+
+  <table class="table table-striped">
+  {% for episode in site.episodes %}
+    {% if episode.start %} {% comment %} Starting a new day? {% endcomment %}
+      {% assign day = day | plus: 1 %}
+      {% if day > 1 %} {% comment %} If about to start day 2 or later, show finishing time for previous day {% endcomment %}
+        {% assign hours = current | divided_by: 60 %}
+        {% assign minutes = current | modulo: 60 %}
+        <tr>
+          {% if multiday %}<td></td>{% endif %}
+          <td class="col-md-1">{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}</td>
+          <td class="col-md-3">Finish</td>
+          <td class="col-md-7"></td>
+        </tr>
+      {% endif %}
+      {% assign current = site.start_time %} {% comment %}Re-set start time of this episode to general daily start time {% endcomment %}
+    {% endif %}
+    {% assign hours = current | divided_by: 60 %}
+    {% assign minutes = current | modulo: 60 %}
+    <tr>
+      {% if multiday %}<td class="col-md-1">{% if episode.start %}Day {{ day }}{% endif %}</td>{% endif %}
+      <td class="col-md-1">{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}</td>
+      <td class="col-md-3">
+        <a href="{{ site.github.url }}{{ episode.url }}">{{ episode.title }}</a>
+      </td>
+      <td class="col-md-7">
+        {% if episode.break %}
+          Break
+        {% else %}
+          {% if episode.questions %}
+            {{ episode.questions | join: '<br/>' }}
+          {% endif %}
+        {% endif %}
+      </td>
+    </tr>
+    {% assign current = current | plus: episode.teaching | plus: episode.exercises | plus: episode.break %}
+  {% endfor %}
+  {% assign hours = current | divided_by: 60 %}
+  {% assign minutes = current | modulo: 60 %}
+  <tr>
+    {% if multiday %}<td></td>{% endif %}
+    <td class="col-md-1">{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}</td>
+    <td class="col-md-3">Finish</td>
+    <td class="col-md-7"></td>
+  </tr>
+  </table>
+</div>

_includes/workshop_ad.html

+<div class="jumbotron">
+  <div class="row">
+    <div class="col-md-10 col-md-offset-1">
+      <h2>{{page.venue}}</h2>
+      <div class="row">
+        <div class="col-md-6">
+          <p>{{page.humandate}}</p>
+          <p>{% if page.humantime %}{{page.humantime}}{% endif %}</p>
+        </div>
+        <div class="col-md-6">
+          <p>
+          <strong>Instructors:</strong>
+          {% if page.instructor %}
+          {{page.instructor | join: ', ' %}}
+          {% else %}
+          to be announced.
+          {% endif %}
+          </p>
+          {% if page.helper %}
+          <p>
+          <strong>Helpers:</strong>
+          {{page.helper | join: ', ' %}}
+          </p>
+          {% endif %}
+        </div>
+      </div>
+    </div>
+  </div>
+</div>