Improve module layout

Gemfile.lock

+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.6.0)
+      public_suffix (>= 2.0.2, < 4.0)
+    colorator (1.1.0)
+    commonmarker (0.17.13)
+      ruby-enum (~> 0.5)
+    concurrent-ruby (1.1.5)
+    ffi (1.11.1)
+    forwardable-extended (2.6.0)
+    i18n (1.6.0)
+      concurrent-ruby (~> 1.0)
+    jekyll (3.4.0)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      jekyll-sass-converter (~> 1.0)
+      jekyll-watch (~> 1.1)
+      kramdown (~> 1.3)
+      liquid (~> 3.0)
+      mercenary (~> 0.3.3)
+      pathutil (~> 0.9)
+      rouge (~> 1.7)
+      safe_yaml (~> 1.0)
+    jekyll-commonmark (1.2.0)
+      commonmarker (~> 0.14)
+      jekyll (>= 3.0, < 4.0)
+    jekyll-commonmark-ghpages (0.1.0)
+      commonmarker (~> 0.17.6)
+      jekyll-commonmark (~> 1)
+    jekyll-sass-converter (1.5.2)
+      sass (~> 3.4)
+    jekyll-watch (1.5.1)
+      listen (~> 3.0)
+    kramdown (1.17.0)
+    liquid (3.0.6)
+    listen (3.1.5)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+      ruby_dep (~> 1.2)
+    mercenary (0.3.6)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    public_suffix (3.1.0)
+    rb-fsevent (0.10.3)
+    rb-inotify (0.10.0)
+      ffi (~> 1.0)
+    rouge (1.11.1)
+    ruby-enum (0.7.2)
+      i18n
+    ruby_dep (1.5.0)
+    safe_yaml (1.0.5)
+    sass (3.7.4)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  jekyll (= 3.4.0)
+  jekyll-commonmark-ghpages
+  tzinfo-data
+
+RUBY VERSION
+   ruby 2.6.2p47
+
+BUNDLED WITH
+   2.0.1

_layouts/module.html

@@ -91,8 +91,11 @@ window.onload = set_view_defaults;
 </header>
 {% if page.prerequisites %}
 <div class="prerequisites">
+  <br>
+  <br>
   <h2>Prerequisites</h2>
-  Before starting this lesson, you should be familiar with:
+  Before starting this lesson, you should be familiar with:<br>
+  <br>
   <ul>
     {% for prereq in page.prerequisites %}
 <li>{{ prereq | markdownify }}</li>
@@ -101,8 +104,11 @@ window.onload = set_view_defaults;
 </div>
 {% endif %}
 <div class="learning-objectives">
+  <br>
+  <br>
   <h2>Learning Objectives</h2>
-  After completing this lesson, learners should be able to:
+  After completing this lesson, learners should be able to:<br>
+  <br>
   <ul>
     {% for objective in page.objectives %}
 <li>{{ objective | markdownify }}</li>
@@ -110,15 +116,21 @@ window.onload = set_view_defaults;
   </ul>
 </div>
 
+<br>
+<br>
 <h2>Motivation</h2>
 
 {{ page.motivation | markdownify }}
 
+<br>
+<br>
 <h2>Concept map</h2>
 <div class="mermaid">
 {{ page.concept_map }}
 </div>
 
+<br>
+<br>
 <h2>Example</h2>
 
 <figure>
@@ -132,6 +144,8 @@ window.onload = set_view_defaults;
 {{ content }}
 </div>
 
+<br>
+<br>
 <h2>Activity</h2>
 
 {% if page.activity_preface %}
@@ -139,7 +153,7 @@ window.onload = set_view_defaults;
 {% endif %}
 
 {% if page.activities %}
-Choose a platform to display instructions for: <select id="id_activity_platform" name="activityplatformlist" onchange="change_activity_content_by_platform('id_activity_platform');return false;">
+Show activity for: <select id="id_activity_platform" name="activityplatformlist" onchange="change_activity_content_by_platform('id_activity_platform');return false;">
   {% assign first = true %}
 {% endif %}
 {% for platform in page.activities %}
@@ -158,7 +172,6 @@ Choose a platform to display instructions for: <select id="id_activity_platform"
 {% for platform in page.activities %}
 <div id="{{ platform[0] | slugify }}-activity-div">
 &nbsp; <br>
-&nbsp; <br>
 <h3>{{ platform[0] }}</h3>
 {% assign includefile = platform[1] %}
 {% capture activity %}{% include {{ includefile }} %}{% endcapture %}
@@ -167,6 +180,9 @@ Choose a platform to display instructions for: <select id="id_activity_platform"
 {% endfor %}
 
 {% if page.exercises_preface or page.exercises %}
+
+<br>
+<br>
 <h2>Formative assessment</h2>
 {% endif %}
 
@@ -175,7 +191,7 @@ Choose a platform to display instructions for: <select id="id_activity_platform"
 {% endif %}
 
 {% if page.exercises %}
-Choose a platform to display instructions for: <select id="id_exercises_platform" name="exercisesplatformlist" onchange="change_exercises_content_by_platform('id_exercises_platform');return false;">
+Perform additional excercises for: <select id="id_exercises_platform" name="exercisesplatformlist" onchange="change_exercises_content_by_platform('id_exercises_platform');return false;">
   {% assign first = true %}
 {% endif %}
 {% for platform in page.exercises %}
@@ -192,6 +208,7 @@ Choose a platform to display instructions for: <select id="id_exercises_platform
 {% endif %}
 {% for platform in page.exercises %}
 <div id="{{ platform[0] | slugify }}-exercises-div">
+&nbsp; <br>
 <h3>{{ platform[0] }}</h3>
 {% assign includefile = platform[1] %}
 {% capture exercise %}{% include {{ includefile }} %}{% endcapture %}
@@ -199,6 +216,8 @@ Choose a platform to display instructions for: <select id="id_exercises_platform
 </div>
 {% endfor %}
 
+<br>
+<br>
 <h2>Follow-up material</h2>
 
 <ul>
@@ -207,6 +226,8 @@ Choose a platform to display instructions for: <select id="id_exercises_platform
 {% endfor %}
 </ul>
 
+<br>
+<br>
 <h2>Learn more</h2>
 
 <ul>

_site/Gemfile

+source "https://rubygems.org"
+ruby RUBY_VERSION
+
+# This will help ensure the proper Jekyll version is running.
+gem "jekyll", "3.4.0"
+
+# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
+gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]
+
+# install GH-flavoured MD plugin
+group :jekyll_plugins do
+  gem 'jekyll-commonmark-ghpages'
+end

_site/Gemfile.lock

+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.6.0)
+      public_suffix (>= 2.0.2, < 4.0)
+    colorator (1.1.0)
+    commonmarker (0.17.13)
+      ruby-enum (~> 0.5)
+    concurrent-ruby (1.1.5)
+    ffi (1.11.1)
+    forwardable-extended (2.6.0)
+    i18n (1.6.0)
+      concurrent-ruby (~> 1.0)
+    jekyll (3.4.0)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      jekyll-sass-converter (~> 1.0)
+      jekyll-watch (~> 1.1)
+      kramdown (~> 1.3)
+      liquid (~> 3.0)
+      mercenary (~> 0.3.3)
+      pathutil (~> 0.9)
+      rouge (~> 1.7)
+      safe_yaml (~> 1.0)
+    jekyll-commonmark (1.2.0)
+      commonmarker (~> 0.14)
+      jekyll (>= 3.0, < 4.0)
+    jekyll-commonmark-ghpages (0.1.0)
+      commonmarker (~> 0.17.6)
+      jekyll-commonmark (~> 1)
+    jekyll-sass-converter (1.5.2)
+      sass (~> 3.4)
+    jekyll-watch (1.5.1)
+      listen (~> 3.0)
+    kramdown (1.17.0)
+    liquid (3.0.6)
+    listen (3.1.5)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+      ruby_dep (~> 1.2)
+    mercenary (0.3.6)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    public_suffix (3.1.0)
+    rb-fsevent (0.10.3)
+    rb-inotify (0.10.0)
+      ffi (~> 1.0)
+    rouge (1.11.1)
+    ruby-enum (0.7.2)
+      i18n
+    ruby_dep (1.5.0)
+    safe_yaml (1.0.5)
+    sass (3.7.4)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  jekyll (= 3.4.0)
+  jekyll-commonmark-ghpages
+  tzinfo-data
+
+RUBY VERSION
+   ruby 2.6.2p47
+
+BUNDLED WITH
+   2.0.1

_site/LICENSE.md

+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].
+
+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 ©
+  European Molecualr Biology Laboratory and, where practical, link to
+  the [source project repository][our-gitlab-repo]) and [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.
+  
+[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

_site/css/main.css

+/**
+ * Reset some basic elements
+ */
+body, h1, h2, h3, h4, h5, h6,
+p, blockquote, pre, hr,
+dl, dd, ol, ul, figure {
+  margin: 0;
+  padding: 0; }
+
+/**
+ * Basic styling
+ */
+body {
+  font: 400 16px/1.5 "Helvetica Neue", Helvetica, Arial, sans-serif;
+  color: #111;
+  background-color: #fdfdfd;
+  -webkit-text-size-adjust: 100%;
+  -webkit-font-feature-settings: "kern" 1;
+  -moz-font-feature-settings: "kern" 1;
+  -o-font-feature-settings: "kern" 1;
+  font-feature-settings: "kern" 1;
+  font-kerning: normal; }
+
+/**
+ * Set `margin-bottom` to maintain vertical rhythm
+ */
+h1, h2, h3, h4, h5, h6,
+p, blockquote, pre,
+ul, ol, dl, figure,
+.highlight {
+  margin-bottom: 15px; }
+
+/**
+ * Images
+ */
+img {
+  max-width: 100%;
+  vertical-align: middle; }
+
+/**
+ * Figures
+ */
+figure > img {
+  display: block; }
+
+figcaption {
+  font-size: 14px; }
+
+/**
+ * Lists
+ */
+ul, ol {
+  margin-left: 30px; }
+
+li > ul,
+li > ol {
+  margin-bottom: 0; }
+
+/**
+ * Headings
+ */
+h1, h2, h3, h4, h5, h6 {
+  font-weight: 400; }
+
+/**
+ * Links
+ */
+a {
+  color: #2a7ae2;
+  text-decoration: none; }
+  a:visited {
+    color: #1756a9; }
+  a:hover {
+    color: #111;
+    text-decoration: underline; }
+
+/**
+ * Blockquotes
+ */
+blockquote {
+  color: #828282;
+  border-left: 4px solid #e8e8e8;
+  padding-left: 15px;
+  font-size: 18px;
+  letter-spacing: -1px;
+  font-style: italic; }
+  blockquote > :last-child {
+    margin-bottom: 0; }
+
+/**
+ * Code formatting
+ */
+pre,
+code {
+  font-size: 15px;
+  border: 1px solid #e8e8e8;
+  border-radius: 3px;
+  background-color: #eef; }
+
+code {
+  padding: 1px 5px; }
+
+pre {
+  padding: 8px 12px;
+  overflow-x: auto; }
+  pre > code {
+    border: 0;
+    padding-right: 0;
+    padding-left: 0; }
+
+/**
+ * Wrapper
+ */
+.wrapper {
+  max-width: -webkit-calc(800px - (30px * 2));
+  max-width: calc(800px - (30px * 2));
+  margin-right: auto;
+  margin-left: auto;
+  padding-right: 30px;
+  padding-left: 30px; }
+  @media screen and (max-width: 800px) {
+    .wrapper {
+      max-width: -webkit-calc(800px - (30px));
+      max-width: calc(800px - (30px));
+      padding-right: 15px;
+      padding-left: 15px; } }
+
+/**
+ * Clearfix
+ */
+.wrapper:after, .footer-col-wrapper:after {
+  content: "";
+  display: table;
+  clear: both; }
+
+/**
+ * Icons
+ */
+.icon > svg {
+  display: inline-block;
+  width: 16px;
+  height: 16px;
+  vertical-align: middle; }
+  .icon > svg path {
+    fill: #828282; }
+
+/**
+ * Site header
+ */
+.site-header {
+  border-top: 5px solid #424242;
+  border-bottom: 1px solid #e8e8e8;
+  min-height: 56px;
+  position: relative; }
+
+.site-title {
+  font-size: 26px;
+  font-weight: 300;
+  line-height: 56px;
+  letter-spacing: -1px;
+  margin-bottom: 0;
+  float: left; }
+  .site-title, .site-title:visited {
+    color: #424242; }
+
+.site-nav {
+  float: right;
+  line-height: 56px; }
+  .site-nav .menu-icon {
+    display: none; }
+  .site-nav .page-link {
+    color: #111;
+    line-height: 1.5; }
+    .site-nav .page-link:not(:last-child) {
+      margin-right: 20px; }
+  @media screen and (max-width: 600px) {
+    .site-nav {
+      position: absolute;
+      top: 9px;
+      right: 15px;
+      background-color: #fdfdfd;
+      border: 1px solid #e8e8e8;
+      border-radius: 5px;
+      text-align: right; }
+      .site-nav .menu-icon {
+        display: block;
+        float: right;
+        width: 36px;
+        height: 26px;
+        line-height: 0;
+        padding-top: 10px;
+        text-align: center; }
+        .site-nav .menu-icon > svg {
+          width: 18px;
+          height: 15px; }
+          .site-nav .menu-icon > svg path {
+            fill: #424242; }
+      .site-nav .trigger {
+        clear: both;
+        display: none; }
+      .site-nav:hover .trigger {
+        display: block;
+        padding-bottom: 5px; }
+      .site-nav .page-link {
+        display: block;
+        padding: 5px 10px;
+        margin-left: 20px; }
+        .site-nav .page-link:not(:last-child) {
+          margin-right: 0; } }
+
+/**
+ * Site footer
+ */
+.site-footer {
+  border-top: 1px solid #e8e8e8;
+  padding: 30px 0; }
+
+.footer-heading {
+  font-size: 18px;
+  margin-bottom: 15px; }
+
+.contact-list,
+.social-media-list {
+  list-style: none;
+  margin-left: 0; }
+
+.footer-col-wrapper {
+  font-size: 15px;
+  color: #828282;
+  margin-left: -15px; }
+
+.footer-col {
+  float: left;
+  margin-bottom: 15px;
+  padding-left: 15px; }
+
+.footer-col-1 {
+  width: -webkit-calc(35% - (30px / 2));
+  width: calc(35% - (30px / 2)); }
+
+.footer-col-2 {
+  width: -webkit-calc(20% - (30px / 2));
+  width: calc(20% - (30px / 2)); }
+
+.footer-col-3 {
+  width: -webkit-calc(45% - (30px / 2));
+  width: calc(45% - (30px / 2)); }
+
+@media screen and (max-width: 800px) {
+  .footer-col-1,
+  .footer-col-2 {
+    width: -webkit-calc(50% - (30px / 2));
+    width: calc(50% - (30px / 2)); }
+
+  .footer-col-3 {
+    width: -webkit-calc(100% - (30px / 2));
+    width: calc(100% - (30px / 2)); } }
+@media screen and (max-width: 600px) {
+  .footer-col {
+    float: none;
+    width: -webkit-calc(100% - (30px / 2));
+    width: calc(100% - (30px / 2)); } }
+/**
+ * Page content
+ */
+.page-content {
+  padding: 30px 0; }
+
+.page-heading {
+  font-size: 20px; }
+
+.post-list {
+  margin-left: 0;
+  list-style: none; }
+  .post-list > li {
+    margin-bottom: 30px; }
+
+.post-meta {
+  font-size: 14px;
+  color: #828282; }
+
+.post-link {
+  display: block;
+  font-size: 24px; }
+
+/**
+ * Posts
+ */
+.post-header {
+  margin-bottom: 30px; }
+
+.post-title {
+  font-size: 42px;
+  letter-spacing: -1px;
+  line-height: 1; }
+  @media screen and (max-width: 800px) {
+    .post-title {
+      font-size: 36px; } }
+
+.post-content {
+  margin-bottom: 30px; }
+  .post-content h2 {
+    font-size: 32px; }
+    @media screen and (max-width: 800px) {
+      .post-content h2 {
+        font-size: 28px; } }
+  .post-content h3 {
+    font-size: 26px; }
+    @media screen and (max-width: 800px) {
+      .post-content h3 {
+        font-size: 22px; } }
+  .post-content h4 {
+    font-size: 20px; }
+    @media screen and (max-width: 800px) {
+      .post-content h4 {
+        font-size: 18px; } }
+
+/**
+ * Syntax highlighting styles
+ */
+.highlight {
+  background: #fff; }
+  .highlighter-rouge .highlight {
+    background: #eef; }
+  .highlight .c {
+    color: #998;
+    font-style: italic; }
+  .highlight .err {
+    color: #a61717;
+    background-color: #e3d2d2; }
+  .highlight .k {
+    font-weight: bold; }
+  .highlight .o {
+    font-weight: bold; }
+  .highlight .cm {
+    color: #998;
+    font-style: italic; }
+  .highlight .cp {
+    color: #999;
+    font-weight: bold; }
+  .highlight .c1 {
+    color: #998;
+    font-style: italic; }
+  .highlight .cs {
+    color: #999;
+    font-weight: bold;
+    font-style: italic; }
+  .highlight .gd {
+    color: #000;
+    background-color: #fdd; }
+  .highlight .gd .x {
+    color: #000;
+    background-color: #faa; }
+  .highlight .ge {
+    font-style: italic; }
+  .highlight .gr {
+    color: #a00; }
+  .highlight .gh {
+    color: #999; }
+  .highlight .gi {
+    color: #000;
+    background-color: #dfd; }
+  .highlight .gi .x {
+    color: #000;
+    background-color: #afa; }
+  .highlight .go {
+    color: #888; }
+  .highlight .gp {
+    color: #555; }
+  .highlight .gs {
+    font-weight: bold; }
+  .highlight .gu {
+    color: #aaa; }