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Merge remote-tracking branch 'upstream/gh-pages' into our-stuff
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‎.github/ISSUE_TEMPLATE.md

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Please delete the text below before submitting your contribution.
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---
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Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.
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Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum. If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck ([email protected]).
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‎.github/PULL_REQUEST_TEMPLATE.md

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Please delete the text below before submitting your contribution.
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---
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Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.
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Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum. If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck ([email protected]).
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‎CONDUCT.md

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title: "Contributor Code of Conduct"
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permalink: /conduct/
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---
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As contributors and maintainers of this project,
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we pledge to respect all people who contribute through reporting issues,
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posting feature requests,
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updating documentation,
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submitting pull requests or patches,
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and other activities.
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The CWL Project is dedicated to providing a harassment-free experience for everyone, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, age, race, or religion. We do not tolerate harassment of participants in any form.
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‎_includes/carpentries.html

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<br/>
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<div class="row">
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<div class="col-md-2" align="center">
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<a href="{{ site.lc_site }}"><img src="{{ page.root }}/assets/img/lc-icon-black.svg" alt="Library Carpentry logo" /></a>
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<a href="{{ site.lc_site }}"><img src="{{ page.root }}/assets/img/lc-icon-black.png" alt="Library Carpentry logo" /></a>
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</div>
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<div class="col-md-8">
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Library Carpentry is made by librarians to help librarians
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<a href="{{ site.lc_site }}">Library Carpentry</a> is made by librarians to help librarians
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automate repetitive, boring, error-prone tasks;
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create, maintain and analyse sustainable and reusable data;
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work effectively with IT and systems colleagues;

‎_includes/dc/intro.html

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<p>
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<a href="{{site.dc_site}}">Data Carpentry</a>
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aims to help researchers get their work done
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in less time and with less pain
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by teaching them basic research computing skills.
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This hands-on workshop will cover basic concepts and tools,
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including program design, version control, data management,
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and task automation.
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Participants will be encouraged to help one another
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and to apply what they have learned to their own research problems.
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</p>
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<p align="center">
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<em>
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For more information on what we teach and why,
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please see our paper
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"<a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745">Best Practices for Scientific Computing</a>".
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</em>
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</p>

‎_includes/dc/schedule.html

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<div class="row">
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<div class="col-md-6">
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<h3>Day 1</h3>
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<table class="table table-striped">
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<tr> <td>09:00</td> <td>Automating tasks with the Unix shell</td> </tr>
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<tr> <td>10:30</td> <td>Coffee</td> </tr>
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<tr> <td>12:00</td> <td>Lunch break</td> </tr>
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<tr> <td>13:00</td> <td>Building programs with Python</td> </tr>
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<tr> <td>14:30</td> <td>Coffee</td> </tr>
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<tr> <td>16:00</td> <td>Wrap-up</td> </tr>
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</table>
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</div>
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<div class="col-md-6">
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<h3>Day 2</h3>
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<table class="table table-striped">
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<tr> <td>09:00</td> <td>Version control with Git</td> </tr>
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<tr> <td>10:30</td> <td>Coffee</td> </tr>
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<tr> <td>12:00</td> <td>Lunch break</td> </tr>
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<tr> <td>13:00</td> <td>Managing data with SQL</td> </tr>
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<tr> <td>14:30</td> <td>Coffee</td> </tr>
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<tr> <td>16:00</td> <td>Wrap-up</td> </tr>
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</table>
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</div>
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</div>

‎_includes/dc/syllabus.html

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<div class="row">
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<div class="col-md-6">
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<h3 id="syllabus-shell">The Unix Shell</h3>
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<ul>
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<li>Files and directories</li>
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<li>History and tab completion</li>
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<li>Pipes and redirection</li>
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<li>Looping over files</li>
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<li>Creating and running shell scripts</li>
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<li>Finding things</li>
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<li><a href="{{site.swc_pages}}/shell-novice/reference/">Reference...</a></li>
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</ul>
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</div>
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<div class="col-md-6">
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<h3 id="syllabus-python">Programming in Python</h3>
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<ul>
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<li>Using libraries</li>
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<li>Working with arrays</li>
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<li>Reading and plotting data</li>
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<li>Creating and using functions</li>
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<li>Loops and conditionals</li>
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<li>Defensive programming</li>
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<li>Using Python from the command line</li>
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<li><a href="{{site.swc_pages}}/python-novice-inflammation/reference/">Reference...</a></li>
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</ul>
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</div>
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<!--
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<div class="col-md-6">
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<h3 id="syllabus-r">Programming in R</h3>
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<ul>
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<li>Working with vectors and data frames</li>
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<li>Reading and plotting data</li>
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<li>Creating and using functions</li>
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<li>Loops and conditionals</li>
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<li>Using R from the command line</li>
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<li><a href="{{site.swc_pages}}/r-novice-inflammation/reference/">Reference...</a></li>
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</ul>
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</div>
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-->
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<!--
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<div class="col-md-6">
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<h3 id="syllabus-matlab">Programming in MATLAB</h3>
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<ul>
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<li>Working with arrays</li>
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<li>Reading and plotting data</li>
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<li>Creating and using functions</li>
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<li>Loops and conditionals</li>
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<li>Defensive programming</li>
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<li><a href="{{site.swc_pages}}/matlab-novice-inflammation/reference/">Reference...</a></li>
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</ul>
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</div>
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-->
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</div>
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<div class="row">
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<div class="col-md-6">
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<h3 id="syllabus-git">Version Control with Git</h3>
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<ul>
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<li>Creating a repository</li>
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<li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
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<li>Viewing changes: <code>status</code>, <code>diff</code>, ...</li>
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<li>Ignoring files</li>
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<li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
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<li>Resolving conflicts</li>
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<li>Open licenses</li>
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<li>Where to host work, and why</li>
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<li><a href="{{site.swc_pages}}/git-novice/reference/">Reference...</a></li>
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</ul>
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</div>
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<!--
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<div class="col-md-6">
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<h3 id="syllabus-sql">Managing Data with SQL</h3>
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<ul>
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<li>Reading and sorting data</li>
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<li>Filtering with <code>where</code></li>
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<li>Calculating new values on the fly</li>
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<li>Handling missing values</li>
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<li>Combining values using aggregation</li>
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<li>Combining information from multiple tables using <code>join</code></li>
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<li>Creating, modifying, and deleting data</li>
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<li>Programming with databases</li>
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<li><a href="{{site.swc_pages}}/sql-novice-survey/reference/">Reference...</a></li>
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</ul>
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</div>
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-->
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<div class="col-md-6">
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<h3 id="syllabus-r">Open Refine</h3>
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<ul>
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<li>Introduction to OpenRefine</li>
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<li>Importing data</li>
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<li>Basic functions</li>
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<li>Advanced Functions</li>
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<li><a href="{{site.lc_pages}}library-openrefine/reference">Reference...</a></li>
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</ul>
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</div>
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</div>

‎_includes/dc/who.html

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<p id="who">
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<strong>Who:</strong>
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The course is aimed at graduate students and other researchers.
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<strong>
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You don't need to have any previous knowledge of the tools
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that will be presented at the workshop.
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</strong>
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</p>

‎_includes/episode_navbar.html

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<div class="col-md-10">
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{% if include.episode_navbar_title %}
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<h3 class="maintitle"><a href="{{ page.root }}/">{{ site.title }}</a></h3>
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<h1 class="maintitle">{{ page.title }}</h1>
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{% endif %}
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</div>
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<div class="col-md-1">

‎_includes/episode_title.html

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{% comment %}
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Find previous and next episodes (if any).
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{% endcomment %}
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{% for episode in site.episodes %}
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{% if episode.url == page.url %}
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{% unless forloop.first %}
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{% assign prev_episode = prev %}
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{% endunless %}
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{% unless forloop.last %}
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{% assign next_episode = site.episodes[forloop.index] %}
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{% endunless %}
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{% endif %}
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{% assign prev = episode %}
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{% endfor %}
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{% comment %}
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Display title and prev/next links.
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{% endcomment %}
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<div class="row">
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<div class="col-md-1">
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<h3>
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{% if prev_episode %}
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<a href="{{ page.root }}{{ prev_episode.url }}"><span class="glyphicon glyphicon-menu-left"></span></a>
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{% else %}
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<a href="{{ page.root }}"><span class="glyphicon glyphicon-menu-up"></span></a>
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{% endif %}
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</h3>
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</div>
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<div class="col-md-10">
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<h3 class="maintitle"><a href="{{ page.root }}/">{{ site.title }}</a></h3>
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<h1 class="maintitle">{{ page.title }}</h1>
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</div>
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<div class="col-md-1">
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<h3>
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{% if next_episode %}
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<a href="{{ page.root }}{{ next_episode.url }}"><span class="glyphicon glyphicon-menu-right"></span></a>
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{% else %}
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<a href="{{ page.root }}"><span class="glyphicon glyphicon-menu-up"></span></a>
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{% endif %}
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</h3>
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</div>
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</div>

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