Updates underlying template to match swcarpentry/styles v9.2.4

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,9 @@
+Please delete the text below before submitting your contribution. 
+
+---
+
+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.  
+
+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]).  
+
+---

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,9 @@
+Please delete the text below before submitting your contribution. 
+
+---
+
+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.  
+
+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]).  
+
+---

CITATION

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

CITATION.md

@@ -6,6 +6,13 @@ permalink: /citation/
 Please cite as:
 
 Some Body (ed.):
+
+
 "Software Carpentry Extra UNIX Shell Material"
-Version ?.?, May 2016.  https://github.com/someuser/somerepo. DOI pending.
+
+Version ?.?, May 2016. 
+
+https://github.com/someuser/somerepo.
+
+DOI pending.
 

CONDUCT.md

@@ -32,13 +32,14 @@ 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.
+that are not aligned to our [Code of Conduct][coc].
 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.
+may be reported by following our [reporting guidelines][coc-reporting].
 
-This Code of Conduct is adapted from
-the [Contributor Covenant][contrib-covenant] Version 1.0.0.
+
+- [Software and Data Carpentry Code of Conduct][coc]
+- [Code of Conduct Reporting Guide][coc-reporting]
 
 {% include links.md %}

CONTRIBUTING.md

@@ -54,7 +54,7 @@ and to meet some of our community members.
     please work in <https://github.com/swcarpentry/shell-extras>,
     which can be viewed at <https://swcarpentry.github.io/shell-extras>.
 
-2.  If you wish to change this example lesson,
+2.  If you wish to change the example lesson,
     please work in <https://github.com/swcarpentry/lesson-example>,
     which documents the format of our lessons
     and can be viewed at <https://swcarpentry.github.io/lesson-example>.
@@ -111,7 +111,7 @@ you may want to look at
 [How to Contribute to an Open Source Project on GitHub][how-contribute].
 In brief:
 
-1.  The published copy of the lesson is in the [episodes][episodes] directory in the `gh-pages` branch of the repository
+1.  The published copy of the lesson is in the `gh-pages` branch of the repository
     (so that GitHub will regenerate it automatically).
     Please create all branches from that,
     and merge the [master repository][repo]'s `gh-pages` branch into your `gh-pages` branch
@@ -155,4 +155,3 @@ You can also [reach us by email][contact].
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
 [swc-lessons]: http://software-carpentry.org/lessons/
 [swc-site]: http://software-carpentry.org/
-[episodes]: _episodes

_config.yml

@@ -2,14 +2,16 @@
 # Values for this lesson.
 #------------------------------------------------------------
 
-# Which carpentry is this ("swc" or "dc")?
+# Which carpentry is this ("swc", "dc", or "lc")?
 carpentry: "swc"
 
 # Overall title for pages.
 title: "Extra Unix Shell Material"
 
-# Contact email address.
-email: [email protected]
+# Contact.  This *must* include the protocol: if it's an email
+# address, it must look like "mailto:[email protected]",
+# or if it's a URL, "https://gitter.im/username/ProjectName".
+contact: "mailto:[email protected]"
 
 # Default web-server Index page (can be blank)
 index: "index.html"
@@ -31,6 +33,7 @@ dc_site: "http://datacarpentry.org"
 swc_github: "https://github.com/swcarpentry"
 swc_site: "https://software-carpentry.org"
 swc_pages: "https://swcarpentry.github.io"
+lc_site: "http://librarycarpentry.github.io/"
 template_repo: "https://github.com/swcarpentry/styles"
 example_repo: "https://github.com/swcarpentry/lesson-example"
 example_site: "https://swcarpentry.github.com/lesson-example"
@@ -41,8 +44,9 @@ training_site: "https://swcarpentry.github.io/instructor-training"
 # Surveys.
 pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="
 post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id="
+training_post_survey: "https://www.surveymonkey.com/r/post-instructor-training"
 
-# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am)
+# 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.

_includes/carpentries.html

@@ -26,3 +26,19 @@
     building on learners' existing knowledge to enable them to quickly apply skills learned to their own research.
   </div>
 </div>
+<br/>
+<div class="row">
+  <div class="col-md-2" align="center">
+    <a href="{{ site.lc_site }}"><img src="{{ page.root }}/assets/img/lc-icon-black.svg" alt="Library Carpentry logo" /></a>
+  </div>
+  <div class="col-md-8">
+    Library Carpentry is made by librarians to help librarians
+    automate repetitive, boring, error-prone tasks;
+    create, maintain and analyse sustainable and reusable data;
+    work effectively with IT and systems colleagues;
+    better understand the use of software in research;
+    and much more.
+    Library Carpentry was the winner of the 2016
+    <a href="http://labs.bl.uk/British+Library+Labs+Awards">British Library Labs Teaching and Learning Award</a>.
+  </div>
+</div>

_includes/dc/intro.html

@@ -0,0 +1,18 @@
+<p>
+  <a href="{{site.dc_site}}">Data Carpentry</a>
+  aims to help researchers get their work done
+  in less time and with less pain
+  by teaching them basic research computing skills.
+  This hands-on workshop will cover basic concepts and tools,
+  including program design, version control, data management,
+  and task automation.
+  Participants will be encouraged to help one another
+  and to apply what they have learned to their own research problems.
+</p>
+<p align="center">
+  <em>
+    For more information on what we teach and why,
+    please see our paper
+    "<a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745">Best Practices for Scientific Computing</a>".
+  </em>
+</p>

_includes/dc/schedule.html

@@ -0,0 +1,24 @@
+<div class="row">
+  <div class="col-md-6">
+    <h3>Day 1</h3>
+    <table class="table table-striped">
+      <tr> <td>09:00</td>  <td>Automating tasks with the Unix shell</td> </tr>
+      <tr> <td>10:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
+      <tr> <td>13:00</td>  <td>Building programs with Python</td> </tr>
+      <tr> <td>14:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>16:00</td>  <td>Wrap-up</td> </tr>
+    </table>
+  </div>
+  <div class="col-md-6">
+    <h3>Day 2</h3>
+    <table class="table table-striped">
+      <tr> <td>09:00</td>  <td>Version control with Git</td> </tr>
+      <tr> <td>10:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
+      <tr> <td>13:00</td>  <td>Managing data with SQL</td> </tr>
+      <tr> <td>14:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>16:00</td>  <td>Wrap-up</td> </tr>
+    </table>
+  </div>
+</div>

_includes/dc/syllabus.html

@@ -0,0 +1,96 @@
+<div class="row">
+  <div class="col-md-6">
+    <h3 id="syllabus-shell">The Unix Shell</h3>
+    <ul>
+      <li>Files and directories</li>
+      <li>History and tab completion</li>
+      <li>Pipes and redirection</li>
+      <li>Looping over files</li>
+      <li>Creating and running shell scripts</li>
+      <li>Finding things</li>
+      <li><a href="{{site.swc_pages}}/shell-novice/reference/">Reference...</a></li>
+    </ul>
+  </div>
+  <div class="col-md-6">
+    <h3 id="syllabus-python">Programming in Python</h3>
+    <ul>
+      <li>Using libraries</li>
+      <li>Working with arrays</li>
+      <li>Reading and plotting data</li>
+      <li>Creating and using functions</li>
+      <li>Loops and conditionals</li>
+      <li>Defensive programming</li>
+      <li>Using Python from the command line</li>
+      <li><a href="{{site.swc_pages}}/python-novice-inflammation/reference/">Reference...</a></li>
+    </ul>
+  </div>
+  <!--
+  <div class="col-md-6">
+    <h3 id="syllabus-r">Programming in R</h3>
+    <ul>
+      <li>Working with vectors and data frames</li>
+      <li>Reading and plotting data</li>
+      <li>Creating and using functions</li>
+      <li>Loops and conditionals</li>
+      <li>Using R from the command line</li>
+      <li><a href="{{site.swc_pages}}/r-novice-inflammation/reference/">Reference...</a></li>
+    </ul>
+  </div>
+  -->
+  <!--
+  <div class="col-md-6">
+    <h3 id="syllabus-matlab">Programming in MATLAB</h3>
+    <ul>
+      <li>Working with arrays</li>
+      <li>Reading and plotting data</li>
+      <li>Creating and using functions</li>
+      <li>Loops and conditionals</li>
+      <li>Defensive programming</li>
+      <li><a href="{{site.swc_pages}}/matlab-novice-inflammation/reference/">Reference...</a></li>
+     </ul>
+   </div>
+   -->
+</div>
+
+<div class="row">
+  <div class="col-md-6">
+    <h3 id="syllabus-git">Version Control with Git</h3>
+    <ul>
+      <li>Creating a repository</li>
+      <li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
+      <li>Viewing changes: <code>status</code>, <code>diff</code>, ...</li>
+      <li>Ignoring files</li>
+      <li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
+      <li>Resolving conflicts</li>
+      <li>Open licenses</li>
+      <li>Where to host work, and why</li>
+      <li><a href="{{site.swc_pages}}/git-novice/reference/">Reference...</a></li>
+    </ul>
+  </div>
+  <!--
+  <div class="col-md-6">
+    <h3 id="syllabus-sql">Managing Data with SQL</h3>
+    <ul>
+      <li>Reading and sorting data</li>
+      <li>Filtering with <code>where</code></li>
+      <li>Calculating new values on the fly</li>
+      <li>Handling missing values</li>
+      <li>Combining values using aggregation</li>
+      <li>Combining information from multiple tables using <code>join</code></li>
+      <li>Creating, modifying, and deleting data</li>
+      <li>Programming with databases</li>
+      <li><a href="{{site.swc_pages}}/sql-novice-survey/reference/">Reference...</a></li>
+    </ul>
+  </div>
+   -->
+  <div class="col-md-6">
+    <h3 id="syllabus-r">Open Refine</h3>
+    <ul>
+      <li>Introduction to OpenRefine</li>
+      <li>Importing data</li>
+      <li>Basic functions</li>
+      <li>Advanced Functions</li>
+      <li><a href="{{site.lc_pages}}library-openrefine/reference">Reference...</a></li>
+    </ul>
+  </div>
+</div>

_includes/dc/who.html

@@ -0,0 +1,8 @@
+<p id="who">
+  <strong>Who:</strong>
+  The course is aimed at graduate students and other researchers.
+  <strong>
+    You don't need to have any previous knowledge of the tools
+    that will be presented at the workshop.
+  </strong>
+</p>

_includes/episode_navbar.html

@@ -14,7 +14,6 @@ <h3>
   <div class="col-md-10">
     {% if include.episode_navbar_title %}
     <h3 class="maintitle"><a href="{{ page.root }}/{{ site.index }}">{{ site.title }}</a></h3>
-    <h1 class="maintitle">{{ page.title }}</h1>
     {% endif %}
   </div>
   <div class="col-md-1">

_includes/episode_title.html

@@ -0,0 +1,9 @@
+<div class="row">
+  <div class="col-md-1">
+  </div>
+  <div class="col-md-10">
+    <h1 class="maintitle">{{ page.title }}</h1>
+  </div>
+  <div class="col-md-1">
+  </div>
+</div>

_includes/lc/intro.html

@@ -0,0 +1,19 @@
+<p>
+  <a href="{{site.lc_site}}">Library Carpentry</a>
+  is made by librarians, for librarians to help you:
+</p>
+<ul>
+  <li>automate repetitive, boring, error-prone tasks</li>
+  <li>create, maintain and analyse sustainable and reusable data</li>
+  <li>work effectively with IT and systems colleagues</li>
+  <li>better understand the use of software in research</li>
+  <li>and much more...</li>
+</ul>
+<p align="center">
+  <em>
+    Library Carpentry introduces you to the fundamentals of computing
+    and provides you with a platform for further self-directed learning.
+    For more information on what we teach and why, please see our paper
+    "<a href="http://doi.org/10.18352/lq.10176">Library Carpentry: software skills training for library professionals</a>".
+  </em>
+</p>

_includes/lc/schedule.html

@@ -0,0 +1,24 @@
+<div class="row">
+  <div class="col-md-6">
+    <h3>Day 1</h3>
+    <table class="table table-striped">
+      <tr> <td>09:00</td>  <td>Data Intro for Librarians</td> </tr>
+      <tr> <td>10:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
+      <tr> <td>13:00</td>  <td>Shell Lessons for Libraries</td> </tr>
+      <tr> <td>14:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>16:00</td>  <td>Wrap-up</td> </tr>
+    </table>
+  </div>
+  <div class="col-md-6">
+    <h3>Day 2</h3>
+    <table class="table table-striped">
+      <tr> <td>09:00</td>  <td>Git Intro for Librarians</td> </tr>
+      <tr> <td>10:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
+      <tr> <td>13:00</td>  <td>OpenRefine for Librarians</td> </tr>
+      <tr> <td>14:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>16:00</td>  <td>Wrap-up</td> </tr>
+    </table>
+  </div>
+</div>