adjusted site color to match saturation and brightness of pmbio and u…

…pdated gems

Gemfile.lock

@@ -14,75 +14,90 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (4.2.8)
+    activesupport (4.2.10)
       i18n (~> 0.7)
       minitest (~> 5.1)
       thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
-    addressable (2.5.1)
-      public_suffix (~> 2.0, >= 2.0.2)
+    addressable (2.5.2)
+      public_suffix (>= 2.0.2, < 4.0)
     colorator (1.1.0)
-    ffi (1.9.18)
+    concurrent-ruby (1.0.5)
+    em-websocket (0.5.1)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0.6.0)
+    eventmachine (1.2.5)
+    ffi (1.9.21)
     forwardable-extended (2.6.0)
     gemoji (3.0.0)
-    html-pipeline (2.5.0)
+    html-pipeline (2.7.1)
       activesupport (>= 2)
       nokogiri (>= 1.4)
-    i18n (0.8.1)
-    jekyll (3.4.3)
+    http_parser.rb (0.6.0)
+    i18n (0.9.3)
+      concurrent-ruby (~> 1.0)
+    jekyll (3.7.2)
       addressable (~> 2.4)
       colorator (~> 1.0)
+      em-websocket (~> 0.5)
+      i18n (~> 0.7)
       jekyll-sass-converter (~> 1.0)
-      jekyll-watch (~> 1.1)
-      kramdown (~> 1.3)
-      liquid (~> 3.0)
+      jekyll-watch (~> 2.0)
+      kramdown (~> 1.14)
+      liquid (~> 4.0)
       mercenary (~> 0.3.3)
       pathutil (~> 0.9)
-      rouge (~> 1.7)
+      rouge (>= 1.7, < 4)
       safe_yaml (~> 1.0)
-    jekyll-feed (0.9.2)
+    jekyll-feed (0.9.3)
       jekyll (~> 3.3)
     jekyll-mentions (1.2.0)
       activesupport (~> 4.0)
       html-pipeline (~> 2.3)
       jekyll (~> 3.0)
     jekyll-paginate (1.1.0)
-    jekyll-redirect-from (0.12.1)
+    jekyll-redirect-from (0.13.0)
       jekyll (~> 3.3)
-    jekyll-sass-converter (1.5.0)
+    jekyll-sass-converter (1.5.2)
       sass (~> 3.4)
-    jekyll-seo-tag (2.2.2)
+    jekyll-seo-tag (2.4.0)
       jekyll (~> 3.3)
     jekyll-sitemap (0.13.0)
       jekyll (~> 3.3)
-    jekyll-watch (1.5.0)
-      listen (~> 3.0, < 3.1)
-    jemoji (0.8.0)
-      activesupport (~> 4.0)
+    jekyll-watch (2.0.0)
+      listen (~> 3.0)
+    jemoji (0.9.0)
+      activesupport (~> 4.0, >= 4.2.9)
       gemoji (~> 3.0)
       html-pipeline (~> 2.2)
-      jekyll (>= 3.0)
-    kramdown (1.13.2)
-    liquid (3.0.6)
-    listen (3.0.8)
+      jekyll (~> 3.0)
+    kramdown (1.16.2)
+    liquid (4.0.0)
+    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)
-    mini_portile2 (2.1.0)
-    minitest (5.10.1)
-    nokogiri (1.7.1)
-      mini_portile2 (~> 2.1.0)
-    pathutil (0.14.0)
+    mini_portile2 (2.3.0)
+    minitest (5.11.3)
+    nokogiri (1.8.2)
+      mini_portile2 (~> 2.3.0)
+    pathutil (0.16.1)
       forwardable-extended (~> 2.6)
-    public_suffix (2.0.5)
-    rb-fsevent (0.9.8)
-    rb-inotify (0.9.8)
-      ffi (>= 0.5.0)
-    rouge (1.11.1)
+    public_suffix (3.0.1)
+    rb-fsevent (0.10.2)
+    rb-inotify (0.9.10)
+      ffi (>= 0.5.0, < 2)
+    rouge (3.1.1)
+    ruby_dep (1.5.0)
     safe_yaml (1.0.4)
-    sass (3.4.23)
+    sass (3.5.5)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
     thread_safe (0.3.6)
-    tzinfo (1.2.3)
+    tzinfo (1.2.5)
       thread_safe (~> 0.1)
 
 PLATFORMS
@@ -93,4 +108,4 @@ DEPENDENCIES
   bundler (~> 1.12)
 
 BUNDLED WITH
-   1.14.6
+   1.16.1

_config.yml

@@ -18,7 +18,7 @@ exclude:
 - alembic-jekyll-theme.gemspec
 
 # 2. Installed Gems
-gems:
+plugins:
 - jekyll-sitemap
 - jekyll-mentions
 - jekyll-paginate
@@ -77,7 +77,7 @@ defaults:
 # 7. Site settings
 encoding: utf-8 # Make sure the encoding is right
 title: "Griffith Lab" # Site name or title, also used in jekyll-seo-tag
-logo: "/assets/Site_Logo3.png" # Site logo, also used in jekyll-seo-tag
+logo: "/assets/Site_Logo3_v2.png" # Site logo, also used in jekyll-seo-tag
 logo_link: "http://www.griffithlab.org"
 description: "This resource is structured in a modular format. Users would benefit from familiarity with topics covered in previous modules however it is not a requirement unless stated otherwise." # Site description and default description, also used in jekyll-seo-tag
 url: "http://www.genviz.org/" # Site url, also used in jekyll-seo-tag

_sass/_colors.scss

@@ -4,7 +4,7 @@ $color__site--heading: #333;
 $color__site--body: darken($color__site--heading, 10%);
 $color__feature--background: darken($color__site--background, 5%);
 $color__site--captions: lighten($color__site--heading, 50%);
-$color__site--link: #05bf85;
+$color__site--link: #7BC23C;
 $color__site--link--hover: darken($color__site--link, 10%);
 $color__site--link--current: desaturate($color__site--link, 100%);
-$color__site--accent: #05bf85;
+$color__site--accent: #7BC23C;