switch template to have molssi branding

Author: janash

_config.yml

@@ -7,7 +7,7 @@
 # dc: Data Carpentry
 # lc: Library Carpentry
 # cp: Carpentries (to use for instructor traning for instance)
-carpentry: "swc"
+carpentry: "molssi"
 
 # Overall title for pages.
 title: "Python Scripting for Computational Molecular Science"

_extras/about.md

@@ -10,5 +10,5 @@ title: About
   </div>
 </div>
 <br/>
-{% include carpentries.html %}
+{% include molssi.html %}
 {% include links.md %}

_includes/carpentries.html

@@ -1,4 +1,4 @@
-{% assign favicon_url = relative_root_path | append: '/assets/favicons/' | append: site.carpentry  %}
+{% assign favicon_url = site.baseurl | append: '/assets/favicons/' | append: site.carpentry | prepend: site.url %}
 
 {% if site.carpentry == 'swc' %}
 {% assign carpentry = 'Software Carpentry' %}
@@ -8,26 +8,15 @@
 {% assign carpentry = 'Library Carpentry' %}
 {% elsif site.carpentry == 'cp' %}
 {% assign carpentry = 'The Carpentries' %}
+{% elsif site.carpentry == 'molssi' %}
+{% assign carpentry = 'The Molecular Sciences Software Institute' %}
 {% endif %}
 
     <!-- Favicons for everyone -->
-    <link rel="apple-touch-icon-precomposed" sizes="57x57" href="{{ favicon_url }}/apple-touch-icon-57x57.png" />
-    <link rel="apple-touch-icon-precomposed" sizes="114x114" href="{{ favicon_url }}/apple-touch-icon-114x114.png" />
-    <link rel="apple-touch-icon-precomposed" sizes="72x72" href="{{ favicon_url }}/apple-touch-icon-72x72.png" />
-    <link rel="apple-touch-icon-precomposed" sizes="144x144" href="{{ favicon_url }}/apple-touch-icon-144x144.png" />
-    <link rel="apple-touch-icon-precomposed" sizes="60x60" href="{{ favicon_url }}/apple-touch-icon-60x60.png" />
-    <link rel="apple-touch-icon-precomposed" sizes="120x120" href="{{ favicon_url }}/apple-touch-icon-120x120.png" />
-    <link rel="apple-touch-icon-precomposed" sizes="76x76" href="{{ favicon_url }}/apple-touch-icon-76x76.png" />
-    <link rel="apple-touch-icon-precomposed" sizes="152x152" href="{{ favicon_url }}/apple-touch-icon-152x152.png" />
     <link rel="icon" type="image/png" href="{{ favicon_url }}/favicon-196x196.png" sizes="196x196" />
     <link rel="icon" type="image/png" href="{{ favicon_url }}/favicon-96x96.png" sizes="96x96" />
     <link rel="icon" type="image/png" href="{{ favicon_url }}/favicon-32x32.png" sizes="32x32" />
     <link rel="icon" type="image/png" href="{{ favicon_url }}/favicon-16x16.png" sizes="16x16" />
     <link rel="icon" type="image/png" href="{{ favicon_url }}/favicon-128.png" sizes="128x128" />
     <meta name="application-name" content="{{ carpentry }} - {{ site.title }}"/>
-    <meta name="msapplication-TileColor" content="#FFFFFF" />
-    <meta name="msapplication-TileImage" content="{{ favicon_url }}/mstile-144x144.png" />
-    <meta name="msapplication-square70x70logo" content="{{ favicon_url }}/mstile-70x70.png" />
-    <meta name="msapplication-square150x150logo" content="{{ favicon_url }}/mstile-150x150.png" />
-    <meta name="msapplication-wide310x150logo" content="{{ favicon_url }}/mstile-310x150.png" />
-    <meta name="msapplication-square310x310logo" content="{{ favicon_url }}/mstile-310x310.png" />
+    <meta name="msapplication-TileColor" content="#FFFFFF" />

_includes/favicons.html

@@ -10,25 +10,25 @@
     <div class="col-md-6 help-links" align="right">
 	{% if page.source %}
 	{% if page.source == "Rmd" %}
-	<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Edit on GitHub</a>
+	<a href="{{site.github.repository_url}}/edit/gh-pages/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}">Edit on GitHub</a>
 	{% endif %}
 	{% else %}
-	<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path}}" data-checker-ignore>Edit on GitHub</a>
+	<a href="{{site.github.repository_url}}/edit/gh-pages/{{page.path}}">Edit on GitHub</a>
 	{% endif %}
 	/
-	<a href="{{ repo_url }}/blob/{{ source_branch }}/CONTRIBUTING.md" data-checker-ignore>Contributing</a>
+	<a href="{{ site.github.repository_url }}/blob/gh-pages/CONTRIBUTING.md">Contributing</a>
 	/
 	<a href="{{ site.github.repository_url }}/">Source</a>
 	/
-	<a href="{{ repo_url }}/blob/{{ source_branch }}/CITATION" data-checker-ignore>Cite</a>
+	<a href="{{ site.github.repository_url }}/blob/gh-pages/CITATION">Cite</a>
 	/
 	<a href="mailto:{{ site.email }}">Contact</a>
     </div>
   </div>
   <div class="row">
     <div class="col-md-12" align="center">
-      Using <a href="https://github.com/carpentries/styles/">The Carpentries style</a>
+      Using a MolSSI modification of <a href="https://github.com/carpentries/styles/">The Carpentries style</a>
       version <a href="https://github.com/carpentries/styles/releases/tag/v9.5.0">9.5.0</a>.
     </div>
   </div>
-</footer>
+</footer>

_includes/lesson_footer.html

@@ -0,0 +1,29 @@
+{% comment %}
+  General description of The Molecular Sciences Software Institute.
+{% endcomment %}
+<div class="row">
+  <div class="col-md-2" align="center">
+    <a href="https://molssi.org/"><img src="{{ page.root }}/assets/img/molssi_main_logo.png" alt="MolSSI logo" width="100%" /></a>
+  </div>
+  <div class="col-md-8">    
+    Since its launch in 2016, <a href="https://molssi.org/">The Molecular Sciences Software Institute</a>, has served as a nexus for the 
+    broad computational molecular sciences community by providing software expertise, community engagement and leadership, and education 
+    and training. Through a broad array of software infrastructure projects, teaching workshops, and community outreach, the MolSSI is 
+    catalyzing the scientific advances needed to solve emerging scientific computing Grand Challenges.
+  </div>
+</div>
+
+<div class="row">
+  <div class="col-md-10">    
+    <p>Education of students, post-docs, and faculty on programming and Best Practices in Software Development is a large part of MolSSI's mission. 
+      Our education program consists of our cohorts of <a href="https://molssi.org/molssi-software-fellows/">Software Fellows</a>, 
+      <a href="https://molssi-education.github.io/resources.html">online training materials</a>, 
+      and <a href="https://molssi-education.github.io/request.html">multiple workshops online or in-person at various locations each year</a>.
+    </p>
+    <p>MolSSI’s education techniques and practices are modeled after <a href="https://software-carpentry.org/">The Software Carpentries</a> 
+      style to teaching novice software best practices. This approach teaches subjects that not only increase a student’s scientific 
+      capability and efficiency, but also his/her future marketability in both scientific and non-scientific fields. 
+    </p>
+  </div>
+</div>
+

_includes/molssi.html

@@ -10,6 +10,7 @@ $color-brand:       #2b3990 !default;
 
 // code boxes
 $color-error:       #bd2c00 !default;
+$color-warning:     #cda01d !default;
 $color-output:      #303030 !default;
 $color-source:      #360084 !default;
 
@@ -36,9 +37,10 @@ $color-testimonial: #fc8dc1 !default;
     border-radius: 4px 0 0 4px;
 }
 
-.error  { @include cdSetup($color-error); }
-.output { @include cdSetup($color-output); }
-.source { @include cdSetup($color-source); }
+.error   { @include cdSetup($color-error); }
+.warning { @include cdSetup($color-warning); }
+.output  { @include cdSetup($color-output); }
+.source  { @include cdSetup($color-source); }
 
 .bash, .language-bash     { @include cdSetup($color-source); }
 .make, .language-make     { @include cdSetup($color-source); }
@@ -48,6 +50,7 @@ $color-testimonial: #fc8dc1 !default;
 .sql, .language-sql       { @include cdSetup($color-source); }
 
 .error::before,
+.warning:before,
 .output::before,
 .source::before,
 .bash::before, .language-bash::before,
@@ -56,13 +59,14 @@ $color-testimonial: #fc8dc1 !default;
 .python::before, .language-python::before,
 .r::before, .language-r::before,
 .sql::before, .language-sql::before {
-  background-color: #f2eff6;
-  display: block;
-  font-weight: bold;
-  padding: 5px 10px;
+    background-color: #f2eff6;
+    display: block;
+    font-weight: bold;
+    padding: 5px 10px;
 }
 
 .error::before  { background-color: #ffebe6; content: "Error"; }
+.warning:before { background-color: #f8f4e8; content:" Warning"; }
 .output::before { background-color: #efefef; content: "Output"; }
 .source::before { content: "Code"; }
 .bash::before, .language-bash::before { content: "Bash"; }
@@ -72,7 +76,26 @@ $color-testimonial: #fc8dc1 !default;
 .r::before, .language-r::before { content: "R"; }
 .sql::before, .language-sql::before { content: "SQL"; }
 
+// Tab panels are used on Setup pages to show instructions for different Operating Systems
+.tab-pane {
+  border: solid 1px #ddd; // #ddd == @nav-tabs-active-link-hover-border-color
+  border-top: none;
+  padding: 20px 20px 10px 20px;
+  border-radius: 0 0 4px 4px; // 4px == @border-radius-base
+}
+
+// Stripe above tab panels where OS tabs are shown
+ul.nav.nav-tabs {
+  background: #E1E1E1;
+  border-radius: 4px 4px 0 0;  // 4px == @border-radius-base
+}
 
+// This color provides better contrast ratio on most backgrounds used on Carpentries websites
+// 9.24 on FFFFFF: https://webaim.org/resources/contrastchecker/?fcolor=204A6F&bcolor=FFFFFF&api (body)
+// 8.78 on F9F9F9: https://webaim.org/resources/contrastchecker/?fcolor=204A6F&bcolor=F9F9F9&api (tables)
+// 7.07 on E1E1E1: https://webaim.org/resources/contrastchecker/?fcolor=204A6F&bcolor=E1E1E1&api (tab panels)
+a { color: #ed1c24FF; }
+a:hover{ color: #393536ff; }
 //----------------------------------------
 // Specialized blockquote environments for learning objectives, callouts, etc.
 //----------------------------------------
@@ -156,13 +179,20 @@ blockquote :not(h2) + p {
 // Override Bootstrap settings.
 //----------------------------------------
 
+blockquote { font-size: inherit; }
+
 code {
   white-space: nowrap;
   padding: 2px 5px;
   color: #006cad;
   background-color: #e7e7e7;
 }
 
+samp { hyphens: none; }
+
+dt { margin-top: 20px; }
+dd { margin-left: 2em; }
+
 article img {
     display: block;
     margin: 20px auto;
@@ -197,7 +227,7 @@ article pre {
   text-align: center;
 }
 
-footer .copyright,
+footer .license,
 footer .help-links
 {
     font-size: inherit;
@@ -278,4 +308,4 @@ kbd {
     box-shadow: 0 1px 0 rgba(12,13,14,0.2), 0 0 0 2px #FFF inset;
     white-space: nowrap;
     font-style: normal;
-}
+}