Merge pull request #120 from rgaiacs/gh-pages

Upgrade to styles v9.2.3
aschuerch · May 6, 2017 · 87996d0 · 87996d0
2 parents 9be02b8 + 6cbc024
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diff --git a/.github/ISSUE_TEMPLATE.md b/.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]).  
+
+---
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.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]).  
+
+---
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -45,18 +45,22 @@ and to meet some of our community members.
 
 ## Where to Contribute
 
-1.  If you wish to change this example lesson,
-    please work in <https://github.com/swcarpentry/lesson-example>.
-    This lesson documents the format of our lessons,
+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/swcarpentry/lesson-example>,
+    which documents the format of our lessons
     and can be viewed at <https://swcarpentry.github.io/lesson-example>.
 
-2.  If you wish to change the template used for workshop websites,
+3.  If you wish to change the template used for workshop websites,
     please work in <https://github.com/swcarpentry/workshop-template>.
     The home page of that repository explains how to set up workshop websites,
     while the extra pages in <https://swcarpentry.github.io/workshop-template>
     provide more background on our design choices.
 
-3.  If you wish to change CSS style files, tools,
+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/swcarpentry/styles>.
 
@@ -102,8 +106,7 @@ 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
@@ -137,14 +140,12 @@ You can also [reach us by email][contact].
 [dc-lessons]: http://datacarpentry.org/lessons/
 [dc-site]: http://datacarpentry.org/
 [discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
-[example-site]: https://swcarpentry.github.io/lesson-example/
 [github]: http://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://github.com/swcarpentry/lesson-example/issues/
-[repo]: https://github.com/swcarpentry/lesson-example/
+[issues]: https://github.com/swcarpentry/FIXME/issues/
+[repo]: https://github.com/swcarpentry/FIXME/
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
 [swc-lessons]: http://software-carpentry.org/lessons/
 [swc-site]: http://software-carpentry.org/
-[episodes]: _episodes
diff --git a/_includes/dc/intro.html b/_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>
diff --git a/_includes/dc/schedule.html b/_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>
diff --git a/_includes/dc/syllabus.html b/_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>
diff --git a/_includes/dc/who.html b/_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>
diff --git a/_includes/episode_navbar.html b/_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.title }}</a></h3>
-    <h1 class="maintitle">{{ page.title }}</h1>
     {% endif %}
   </div>
   <div class="col-md-1">

diff --git a/_includes/episode_title.html b/_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>
diff --git a/_includes/lc/intro.html b/_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>
diff --git a/_includes/lc/schedule.html b/_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>
diff --git a/_includes/lc/syllabys.html b/_includes/lc/syllabys.html
@@ -0,0 +1,69 @@
+<div class="row">
+  <div class="col-md-6">
+    <h3 id="syllabus-python">Data Intro</h3>
+    <ul>
+      <li>Intro to data</li>
+      <li>Jargon busting</li>
+      <li>Keyboard shortcuts</li>
+      <li>Plain text formats</li>
+      <li>Naming files</li>
+      <li>Regular expressions</li>
+      <li><a href="http://data-lessons.github.io/library-data-intro/reference/">Reference...</a></li>
+    </ul>
+  </div>
+  <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>Counting and sorting contents in files</li>
+      <li>Pipes and redirection</li>
+      <li>Mining or searching in files</li>
+      <li><a href="http://data-lessons.github.io/library-shell/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>Configuring git</li>
+      <li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
+      <li>Viewing state changes with <code>status</code></li>
+      <li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
+      <li>Where to host work, and why</li>
+      <li><a href="http://data-lessons.github.io/library-git/reference">Reference...</a></li>
+    </ul>
+  </div>
+  <div class="col-md-6">
+    <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="http://data-lessons.github.io/library-openrefine/reference">Reference...</a></li>
+      </ul>
+    </div>
+  </div>
+</div>
+<!--div class="row">
+  <div class="col-md-6">
+    <h3 id="syllabus-sql">SQL Intro</h3>
+    <ul>
+      <li>What is SQL?</li>
+      <li>Intro to SQLite Manager</li>
+      <li>Importing a database</li>
+      <li>Reading and sorting data</li>
+      <li>Filtering with <code>where</code></li>
+      <li>Combining values using aggregation</li>
+      <li>Combining information from multiple tables using <code>join</code></li>
+      <li><a href="http://data-lessons.github.io//library-sql/reference/">Reference...</a></li>
+    </ul>
+  </div>
+</div>
+-->
diff --git a/_includes/lc/who.html b/_includes/lc/who.html
@@ -0,0 +1,8 @@
+<p id="who">
+  <strong>Who:</strong>
+  The course is for librarians, archivists, and other information workers.
+  <strong>
+    You don't need to have any previous knowledge of the tools that
+    will be presented at the workshop.
+  </strong>
+</p>
diff --git a/_includes/links.md b/_includes/links.md
@@ -31,3 +31,5 @@
 [training]: http://swcarpentry.github.io/instructor-training/
 [workshop-repo]: {{ site.workshop_repo }}
 [yaml]: http://yaml.org/
+[coc]: https://software-carpentry.org/conduct/
+[coc-reporting]: https://software-carpentry.org/CoC-reporting/