Merge branch 'open-life-science:main' into OLS_index

open-life-science · Oct 20, 2023 · 21871eb · 21871eb
2 parents 3ffd762 + b659e4b
commit 21871eb
Show file tree

Hide file tree

Showing 27 changed files with 408 additions and 70 deletions.
diff --git a/Gemfile b/Gemfile
@@ -6,5 +6,6 @@ gem 'html-proofer'
 gem 'jekyll'
 gem 'jekyll-redirect-from'
 gem 'jekyll-github-metadata'
+gem 'jekyll-toc'
 gem 'nokogiri'
 gem 'webrick'
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -68,6 +68,9 @@ GEM
       jekyll (>= 3.3, < 5.0)
     jekyll-sass-converter (3.0.0)
       sass-embedded (~> 1.54)
+    jekyll-toc (0.18.0)
+      jekyll (>= 3.9)
+      nokogiri (~> 1.12)
     jekyll-watch (2.2.1)
       listen (~> 3.0)
     kramdown (2.3.2)
@@ -132,8 +135,9 @@ DEPENDENCIES
   jekyll
   jekyll-github-metadata
   jekyll-redirect-from
+  jekyll-toc
   nokogiri
   webrick
 
 BUNDLED WITH
-   2.4.19
+   2.4.19
diff --git a/_config.yml b/_config.yml
@@ -41,8 +41,14 @@ collections:
     permalink: /openseeds/ols-8/:path/
     output: true
 
+toc:
+  min_level: 1 # default: 1
+  max_level: 3 # default: 6
+  list_class: menu-list
+
 includes_dir: .
 
 plugins:
   - jekyll-redirect-from
   - jekyll-github-metadata
+  - jekyll-toc
diff --git a/_includes/toc.html b/_includes/toc.html
diff --git a/_layouts/page.html b/_layouts/page.html
@@ -4,6 +4,20 @@
 
 <section>
     <div class="article-post">
+        {% if page.toc %}
+        <div class="columns columns-toc">
+            <div class="column is-one-fifth" id="cohort-toc">
+                <h3 id="no_toc">Table of content<h3>
+                <aside class="menu">
+                    {{ content | toc_only }} 
+                </aside>
+            </div>
+            <div class="column">
+                {{ content | inject_anchors }}
+            </div>
+        </div>
+        {% else %}
         {{ content }}
+        {% endif %}
     </div>
 </section>
diff --git a/bin/prepare_website_data.py b/bin/prepare_website_data.py
diff --git a/css/custom.scss b/css/custom.scss
@@ -489,4 +489,16 @@ code {
 
 .columns-toc {
   margin-top: 2em;
+
+  .column.is-one-fifth {
+    height: 90vh;
+    overflow: auto;
+  }
+}
+
+@media (min-width: 780px) {
+  .column.is-one-fifth {
+    position: sticky;
+    top: 50px;
+  }
 }
diff --git a/images/three-pillars-icons/open-incubator-icon.png b/images/three-pillars-icons/open-incubator-icon.png
diff --git a/images/three-pillars-icons/open-research-icon.png b/images/three-pillars-icons/open-research-icon.png
diff --git a/images/three-pillars-icons/open-science-training-icon.png b/images/three-pillars-icons/open-science-training-icon.png
diff --git a/library.md b/library.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: Open Seeds Video Library
 image: https://images.unsplash.com/photo-1481137344492-d5a150a97f8b?ixlib=rb-4.0.3&ixid=MnwxMjA3fDB8MHxwaG90by1wYWdlfHx8fGVufDB8fHx8&auto=format&fit=crop&w=2940&q=80
 photos:
@@ -98,25 +99,9 @@ photos:
 
 {% assign speaker_nb = all-speakers | remove_first: ',' | split: "," | uniq | sort | size %}
 
-<p>This page shows you the full library of available videos from talks in Open Seeds cohort calls: <strong>{{ video_nb }} videos</strong> by <strong>{{ speaker_nb }} speakers</strong>.</p>
+This page shows you the full library of available videos from talks in Open Seeds cohort calls: **{{ video_nb }} videos** by **{{ speaker_nb }} speakers**.
 
-<p>Below are all of the individual videos, but the videos are part of cohort calls that you can watch directly from the same links. You can use these for self-study, courses, and more! </p>
-
-<div class="columns columns-toc">
-<div class="column is-one-fifth" markdown="1">
-
-### Table of content
-{:.no_toc}
-
-<aside class="menu" markdown="1">
-
-- TOC
-{:toc .menu-list}
-
-</aside>
-</div>
-
-<div class="column" markdown="1">
+Below are all of the individual videos, but the videos are part of cohort calls that you can watch directly from the same links. You can use these for self-study, courses, and more!
 
 {% for topic in library %}
     {% assign topic-name = topic[0] | slugify %}
@@ -198,5 +183,3 @@ photos:
     </div>
     {% endfor %}
 {% endfor %}
-</div>
-</div>
diff --git a/openseeds/ols-1/index.md b/openseeds/ols-1/index.md
@@ -9,6 +9,7 @@ photos:
 redirect_from:
   - /OLS-1
   - /ols-1
+toc: true
 ---
 
 {% include _includes/cohort-metadata.html cohort='ols-1' %}
@@ -28,8 +29,6 @@ and international bioinformatics communities.
 2. **Connecting** members across different communities, backgrounds, and identities by creating space in this program for them to share their experiences and expertise.
 3. **Empowering** them to become effective Open Science ambassadors in their communities.
 
-{% include _includes/toc.html %}
-
 # Goals and Learning Objectives
 
 The vision of Open Life Science program is to strengthen Open Science skills for early stage researchers and young leaders in life science.
@@ -211,3 +210,5 @@ Updates regarding new calls for applications, announcements, and final project p
 # Community Participation Guidelines
 
 {% include CODE_OF_CONDUCT.md %}
+
+</div>
diff --git a/openseeds/ols-1/schedule.md b/openseeds/ols-1/schedule.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: OLS-1 schedule
 image: https://images.unsplash.com/photo-1435527173128-983b87201f4d?ixlib=rb-1.2.1&ixid=eyJhcHBfaWQiOjEyMDd9&auto=format&fit=crop&w=1047&q=80
 photos:
@@ -30,4 +31,4 @@ redirect_from:
 
 {% assign cohort = 'ols-1' %}
 {% assign schedule = site.data.openseeds[cohort].schedule %}
-{% include _includes/schedule.md %}
+{% include _includes/schedule.md %}
diff --git a/openseeds/ols-2/index.md b/openseeds/ols-2/index.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: Welcome to the 2nd cohort of OLS program!
 image: /images/syllabus.jpg
 photos:
@@ -28,8 +29,6 @@ and international bioinformatics communities.
 2. **Connecting** members across different communities, backgrounds, and identities by creating space in this program for them to share their experiences and expertise.
 3. **Empowering** them to become effective Open Science ambassadors in their communities.
 
-{% include _includes/toc.html %}
-
 # Goals and Learning Objectives
 
 The vision of Open Life Science program is to strengthen Open Science skills for early stage researchers and young leaders in life science.
@@ -304,4 +303,4 @@ Updates regarding new calls for applications, announcements, and final project p
 
 # Community Participation Guidelines
 
-{% include CODE_OF_CONDUCT.md %}
+{% include CODE_OF_CONDUCT.md %}
diff --git a/openseeds/ols-2/schedule.md b/openseeds/ols-2/schedule.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: OLS-2 schedule
 image: https://images.unsplash.com/photo-1435527173128-983b87201f4d?ixlib=rb-1.2.1&ixid=eyJhcHBfaWQiOjEyMDd9&auto=format&fit=crop&w=1047&q=80
 photos:
@@ -11,4 +12,4 @@ redirect_from: /ols-2/schedule
 
 {% assign cohort = 'ols-2' %}
 {% assign schedule = site.data.openseeds[cohort].schedule %}
-{% include _includes/schedule.md %}
+{% include _includes/schedule.md %}
diff --git a/openseeds/ols-3/index.md b/openseeds/ols-3/index.md
@@ -9,6 +9,7 @@ photos:
 redirect_from:
   - /OLS-3
   - /ols-3
+toc: true
 ---
 
 {% include _includes/cohort-metadata.html cohort='ols-3' %}
@@ -28,8 +29,6 @@ and international bioinformatics communities.
 2. **Connecting** members across different communities, backgrounds, and identities by creating space in this program for them to share their experiences and expertise.
 3. **Empowering** them to become effective Open Science ambassadors in their communities.
 
-{% include _includes/toc.html %}
-
 # Goals and Learning Objectives
 
 The vision of Open Life Science program is to strengthen Open Science skills for early stage researchers and young leaders in life science.
@@ -394,4 +393,4 @@ Updates regarding new calls for applications, announcements, and final project p
 
 # Community Participation Guidelines
 
-{% include CODE_OF_CONDUCT.md %}
+{% include CODE_OF_CONDUCT.md %}
diff --git a/openseeds/ols-3/schedule.md b/openseeds/ols-3/schedule.md
@@ -7,8 +7,9 @@ photos:
   license: CC BY
   url: https://unsplash.com/photos/FoKO4DpXamQ
 redirect_from: /ols-3/schedule
+toc: true
 ---
 
 {% assign cohort = 'ols-3' %}
 {% assign schedule = site.data.openseeds[cohort].schedule %}
-{% include _includes/schedule.md %}
+{% include _includes/schedule.md %}
diff --git a/openseeds/ols-4/index.md b/openseeds/ols-4/index.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: Welcome to the 4th cohort of OLS program!
 image: /images/syllabus.jpg
 photos:
@@ -28,8 +29,6 @@ and international bioinformatics communities.
 2. **Connecting** members across different communities, backgrounds, and identities by creating space in this program for them to share their experiences and expertise.
 3. **Empowering** them to become effective Open Science ambassadors in their communities.
 
-{% include _includes/toc.html %}
-
 # Goals and Learning Objectives
 
 The vision of Open Life Science program is to strengthen Open Science skills for early stage researchers and young leaders in life science.
@@ -379,4 +378,4 @@ Updates regarding new calls for applications, announcements, and final project p
 
 # Community Participation Guidelines
 
-{% include CODE_OF_CONDUCT.md %}
+{% include CODE_OF_CONDUCT.md %}
diff --git a/openseeds/ols-4/schedule.md b/openseeds/ols-4/schedule.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: OLS-4 schedule
 image: https://images.unsplash.com/photo-1435527173128-983b87201f4d?ixlib=rb-1.2.1&ixid=eyJhcHBfaWQiOjEyMDd9&auto=format&fit=crop&w=1047&q=80
 photos:
@@ -11,4 +12,4 @@ redirect_from: /ols-4/schedule
 
 {% assign cohort = 'ols-4' %}
 {% assign schedule = site.data.openseeds[cohort].schedule %}
-{% include _includes/schedule.md %}
+{% include _includes/schedule.md %}
diff --git a/openseeds/ols-5/index.md b/openseeds/ols-5/index.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: Welcome to the 5th cohort of OLS program!
 image: /images/syllabus.jpg
 photos:
@@ -28,8 +29,6 @@ and international bioinformatics communities.
 2. **Connecting** members across different communities, backgrounds, and identities by creating space in this program for them to share their experiences and expertise.
 3. **Empowering** them to become effective Open Science ambassadors in their communities.
 
-{% include _includes/toc.html %}
-
 # Goals and Learning Objectives
 
 The vision of Open Life Science program is to strengthen Open Science skills for early stage researchers and young leaders in life science.
@@ -379,4 +378,4 @@ Updates regarding new calls for applications, announcements, and final project p
 
 # Community Participation Guidelines
 
-{% include CODE_OF_CONDUCT.md %}
+{% include CODE_OF_CONDUCT.md %}
diff --git a/openseeds/ols-5/schedule.md b/openseeds/ols-5/schedule.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: OLS-5 schedule
 image: https://images.unsplash.com/photo-1435527173128-983b87201f4d?ixlib=rb-1.2.1&ixid=eyJhcHBfaWQiOjEyMDd9&auto=format&fit=crop&w=1047&q=80
 photos:
@@ -9,7 +10,8 @@ photos:
 redirect_from: /ols-5/schedule
 ---
 
+
 {% assign cohort = 'ols-5' %}
 {% assign schedule = site.data.openseeds[cohort].schedule %}
 {% include _includes/overall-schedule.md %}
-{% include _includes/detailed-schedule.md %}
+{% include _includes/detailed-schedule.md %}
diff --git a/openseeds/ols-6/index.md b/openseeds/ols-6/index.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: Welcome to the 6th cohort of OLS program!
 image: /images/syllabus.jpg
 photos:
@@ -28,8 +29,6 @@ and international bioinformatics communities.
 2. **Connecting** members across different communities, backgrounds, and identities by creating space in this program for them to share their experiences and expertise.
 3. **Empowering** them to become effective Open Science ambassadors in their communities.
 
-{% include _includes/toc.html %}
-
 # Goals and Learning Objectives
 
 The vision of OLS is to strengthen Open Science skills for early stage researchers and young leaders in science.
@@ -379,4 +378,4 @@ Updates regarding new calls for applications, announcements, and final project p
 
 # Community Participation Guidelines
 
-{% include CODE_OF_CONDUCT.md %}
+{% include CODE_OF_CONDUCT.md %}
diff --git a/openseeds/ols-6/schedule.md b/openseeds/ols-6/schedule.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: OLS-6 schedule
 image: https://images.unsplash.com/photo-1435527173128-983b87201f4d?ixlib=rb-1.2.1&ixid=eyJhcHBfaWQiOjEyMDd9&auto=format&fit=crop&w=1047&q=80
 photos:

diff --git a/openseeds/ols-7/index.md b/openseeds/ols-7/index.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: Welcome to the 7th cohort of OLS program!
 image: /images/syllabus.jpg
 photos:
@@ -28,8 +29,6 @@ and international bioinformatics communities.
 2. **Connecting** members across different communities, backgrounds, and identities by creating space in this program for them to share their experiences and expertise.
 3. **Empowering** them to become effective Open Science ambassadors in their communities.
 
-{% include _includes/toc.html %}
-
 # Goals and Learning Objectives
 
 The vision of OLS program is to strengthen Open Science skills for early stage researchers and young leaders in science.
@@ -383,4 +382,4 @@ Updates regarding new calls for applications, announcements, and final project p
 
 # Community Participation Guidelines
 
-{% include CODE_OF_CONDUCT.md %}
+{% include CODE_OF_CONDUCT.md %}
diff --git a/openseeds/ols-7/schedule.md b/openseeds/ols-7/schedule.md
@@ -1,5 +1,6 @@
 ---
 layout: page
+toc: true
 title: OLS-7 schedule
 image: https://images.unsplash.com/photo-1435527173128-983b87201f4d?ixlib=rb-1.2.1&ixid=eyJhcHBfaWQiOjEyMDd9&auto=format&fit=crop&w=1047&q=80
 photos:
@@ -11,4 +12,4 @@ redirect_from: /ols-7/schedule
 
 {% assign cohort = 'ols-7' %}
 {% assign schedule = site.data.openseeds[cohort].schedule %}
-{% include _includes/schedule.md %}
+{% include _includes/schedule.md %}