Merge branch 'style-polishing' into 'master'

Style polishing

Closes #56, #48, and #24

See merge request !44

AUTHORS

-FIXME: list authors' names and email addresses.
\ No newline at end of file

AUTHORS.md

+---
+layout: page
+title: Authors
+---
+
+This material is the product of contributions from the following people:
+
+* Aliaksandr Halavatyi
+* Jean-Karim Hériché
+* Toby Hodges
+* Julius Hossain
+* Dominik Kutra
+* Constantin Pape
+* Christian Tischer
+
+The material also owes much to [The Carpentries](https://carpentries.org):
+the site theme is based on
+[The Carpentries lesson style](https://github.com/carpentries/styles/)
+and the concept-focussed style of the modules is inspired by material taught in
+[The Carpentries Instructor Training](https://carpentries.github.io/instructor-training/).

CITATION

-FIXME: describe how to cite this lesson.
\ No newline at end of file

CITATION.md

+---
+layout: page
+title: Citation
+---
+
+Citation info coming soon.

CONTRIBUTING.md

 ---
-layout: default
+layout: page
+title: Guidelines for Contributing
 ---
-# Guidelines for Contributing
 
 Contributions to this project are very welcome.
 Changes should be submitted by merge request from a new branch to `master`.

LICENSE.md

+---
+layout: page
+title: License
+---
+
 This 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].
@@ -35,7 +40,7 @@ Notices:
   permissions necessary for your intended use. For example, other
   rights such as publicity, privacy, or moral rights may limit how you
   use the material.
-  
+
 [cc-by-human]: https://creativecommons.org/licenses/by/4.0/
 [cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
-[our-gitlab-repo]: https://git.embl.de/grp-bio-it/image-analysis-training-resources/
\ No newline at end of file
+[our-gitlab-repo]: https://git.embl.de/grp-bio-it/image-analysis-training-resources/

TEACHING.md

-# Teaching tips
-
-## White-boards
-
-- Try to frequently use white-board, because:
-	- It makes teaching more interactive.
-	- It slows down teaching, because you have to draw.
-- Make sure you have good pens with high contrast.
-- Have two white-boards:
-	- One for tidy concept maps.
-	- One for messy notes.
-
-## Stand
-
-- Try not to sit, because:
-	- Teaching will be more dynamic.
-	- People can see and hear you better.
-- Construct something to have your computer up, such that you can stand in front of it.
-

_config.yml

@@ -19,6 +19,7 @@ life_cycle: "pre-alpha"
 kind: "lesson"
 
 # Sites
+repository: "https://git.embl.de/grp-bio-it/image-analysis-training-resources"
 repo_url: "https://git.embl.de/grp-bio-it/image-analysis-training-resources"
 cc_by_human: "https://creativecommons.org/licenses/by/4.0/"
 

_extras/about.md

 ---
+layout: page
 title: About
 ---
-{% include carpentries.html %}
+
+TODO
+
 {% include links.md %}

_extras/figures.md

 ---
+layout: page
 title: Figures
 ---
 
@@ -6,17 +7,17 @@ title: Figures
 
 <script>
   window.onload = function() {
-    var lesson_episodes = [
-    {% for episode in site.episodes %}
-    "{{ episode.url }}"{% unless forloop.last %},{% endunless %}
+    var lesson_modules = [
+    {% for module in site.modules %}
+    "{{ module.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++) {
+    for (i=0; i < lesson_modules.length; i++) {
 
       xmlHttp[i] = new XMLHttpRequest();
-      xmlHttp[i].episode = lesson_episodes[i];  /* To enable use this later. */
+      xmlHttp[i].module = lesson_modules[i];  /* To enable use this later. */
       xmlHttp[i].onreadystatechange = function() {
 
         if (this.readyState == 4 && this.status == 200) {
@@ -24,7 +25,7 @@ title: Figures
           var htmlDoc = parser.parseFromString(this.responseText,"text/html");
           var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0];
 
-          var article_here = document.getElementById(this.episode);
+          var article_here = document.getElementById(this.module);
           var images = htmlDocArticle.getElementsByTagName("img");
 
           if (images.length > 0) {
@@ -52,17 +53,17 @@ title: Figures
           }
         }
       }
-      episode_url = "{{ relative_root_path }}" + lesson_episodes[i];
-      xmlHttp[i].open("GET", episode_url);
+      module_url = "{{ relative_root_path }}" + lesson_modules[i];
+      xmlHttp[i].open("GET", module_url);
       xmlHttp[i].send(null);
     }
   }
 </script>
 {% comment %}
-Create anchor for each one of the episodes.
+Create anchor for each one of the modules.
 {% endcomment %}
-{% for episode in site.episodes %}
-<article id="{{ episode.url }}" class="figures"></article>
+{% for module in site.modules %}
+<article id="{{ module.url }}" class="figures"></article>
 {% endfor %}
 
 {% include links.md %}

_extras/guide.md

 ---
 title: "Instructor Notes"
+layout: page
 ---
-FIXME
+
+## White-boards
+
+- Try to frequently use white-board, because:
+	- It makes teaching more interactive.
+	- It slows down teaching, because you have to draw.
+- Make sure you have good pens with high contrast.
+- Have two white-boards:
+	- One for tidy concept maps.
+	- One for messy notes.
+
+## Stand
+
+- Try not to sit, because:
+	- Teaching will be more dynamic.
+	- People can see and hear you better.
+- Construct something to have your computer up, such that you can stand in front of it.
 
 {% include links.md %}

_includes/dc/intro.html

-<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

-<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

-<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

-<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/lc/intro.html

-<p>
-  <a href="{{site.lc_site}}">Library Carpentry</a>
-  is made by people working in library- and information-related roles to help you:
-</p>
-<ul>
-  <li>automate repetitive, boring, error-prone tasks</li>
-  <li>create, maintain and analyze 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="https://doi.org/10.18352/lq.10176">Library Carpentry: software skills training for library professionals</a>".
-  </em>
-</p>

_includes/lc/schedule.html

-<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>

_includes/lc/syllabus.html

-<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="https://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="https://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="https://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="https://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="https://data-lessons.github.io//library-sql/reference/">Reference...</a></li>
-    </ul>
-  </div>
-</div>
--->

_includes/lc/who.html

-<p id="who">
-  <strong>Who:</strong>
-  The course is for people working in library- and information-related roles.
-  <strong>
-    You don't need to have any previous knowledge of the tools that
-    will be presented at the workshop.
-  </strong>
-</p>

_includes/lesson_footer.html

@@ -2,7 +2,7 @@
   Footer for lesson pages.
 {% endcomment %}
 
-{% include gh_variables.html %}
+<!-- {% include gh_variables.html %} -->
 
 <footer>
   <div class="row">
@@ -33,14 +33,14 @@
 	<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Edit on GitHub</a>
 	{% endif %}
 	{% else %}
-	<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path}}" data-checker-ignore>Edit on GitHub</a>
+	<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path}}" data-checker-ignore>Edit source file</a>
 	{% endif %}
 	/
-	<a href="{{ repo_url }}/blob/{{ source_branch }}/CONTRIBUTING.md" data-checker-ignore>Contributing</a>
+	<a href="{{ repo_url }}/blob/{{ source_branch }}/contributing" data-checker-ignore>Contributing</a>
 	/
 	<a href="{{ repo_url }}/">Source</a>
-	/
-	<a href="{{ repo_url }}/blob/{{ source_branch }}/CITATION" data-checker-ignore>Cite</a>
+	<!-- /
+	<a href="{{ repo_url }}/blob/{{ source_branch }}/CITATION" data-checker-ignore>Cite</a> -->
 	/
 	<a href="mailto:{{ site.email }}">Contact</a>
     </div>

_includes/sc/intro.html

-<p>
-  <a href="{{site.swc_site}}">Software 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/sc/schedule.html

-<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/sc/syllabus.html

-<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>