Large update.

Gemfile

@@ -1,5 +1,6 @@
 source 'https://rubygems.org'
 gem 'github-pages', group: :jekyll_plugins
+gem 'jekyll-seo-tag'
 #gem 'jekyll-sass-converter'
 
 # Avoid polling for changes

README.md

@@ -39,16 +39,19 @@ bundle exec jekyll serve
 ```
 
 ## 5. Open the local site and check your changes
-Open a browser and go to `localhost:4000/`. Any changes you make to any of the repository's files, except `_config.yml` will be reflected on the site after refreshing the page.
+Open a browser and go to `localhost:4000/`. Any changes you make to any of the repository's files, except `_config.yml`, will be reflected on the site after refreshing the page. If you edit `_config.yml`, you will need to quit the local server (`Ctrl+C`) and rebuild the site locally in order to see your changes.
 
 # How the site is set up
 The structure can be a little confusing, but I'll try to outline the basics. Just to be clear, I (TS) don't know much, and everything I do know is from playing with the site for a day and a half. Still, here is goes:
 
 The different pages (e.g., News, Papers, Team) are organized in separate folders. Each folder contains a file for the page itself (`index.html`) and a folder containing markdown files with the different entries for the page (`_posts/`). Whether adding a new lab member, paper, poster, presentation, project, or piece of news, you will generally be creating one of these markdown files.
 
-The markdown files have two sections, a header with metadata and the content below. How the post is formatted on the general page (e.g., how Taylor Salo's picture fits into the Team webpage) is determined by the `index.html` file mentioned above. How the post is formatted on its own page (e.g., Taylor Salo's member page) is determined by the theme for that post's category. Themes are saved as html files in `_includes/themes/lab/`. You can change these themes, but be aware that they will affect all other pages of the same type. For example, if you resize the photo field in the lab member theme file, then the photos of all lab members will be affected. NOTE: You might assume that the themes or similar info are in the `_layouts` folder, but that appears to be a red herring. Those pages just call the files in the `themes` folder.
+The markdown files have two sections, a header with metadata and the content below. How the post is formatted on the general page (e.g., how Taylor Salo's picture fits into the [Team webpage](https://nbclab.github.io/team/)) is determined by the `index.html` file mentioned above. How the post is formatted on its own page (e.g., [Taylor Salo's member page](https://nbclab.github.io/team/taylor-salo)) is determined by the theme for that post's category. Themes are saved as html files in `_includes/themes/lab/`. You can change these themes, but be aware that they will affect all other pages of the same type. For example, if you resize the photo field in the lab member theme file, then the photos of all lab members will be affected.
+- NOTE: You might assume that the themes or similar info are in the `_layouts` folder, but that appears to be a red herring. Those pages just call the files in the `themes` folder.
+- Ultimately, if it is possible, we would like simplify this structure.
 
 Pictures, pdfs, etc. can be placed in `assets/`. However, because GitHub repositories are limited in terms of space, I would ultimately like to shift toward using a public Google Drive folder or something similar.
+- When adding pictures of posters or presentations, please export the pdf (assuming that's what you have) to png format, and then resample to a lower resolution. For posters, we use a width of 250 pixels with whatever height scales proportionally with that, and a resolution of 72 pixels per inch. For presentations, please save just the first slide for the page thumbnail, and use a width of 1000 pixels (again, with whatever height matches this) and a resolution of 150 pixels per inch.
 
 The markdown files for the homepage, the "About the site" page, and the "Contact us" page are all located in `misc/_posts/`. I only mention this because it wasn't obvious to me when I went searching for those pages.
 

_config.yml

@@ -160,5 +160,6 @@ JB :
   # where [HELPER] is the name of the helper you are overriding.
 
 # allow page redirection
-gems:
+plugins:
   - jekyll-redirect-from
+  - jekyll-seo-tag

_includes/themes/lab/default.html

@@ -28,15 +28,14 @@
     <link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/academicons/1.8.1/css/academicons.css"/>
 
     <!-- Custom fonts and icons via Academicons, http://fortawesome.github.io/Font-Awesome/ -->
-   <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css"/>
+    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css"/>
 
     <!-- Fonts via Google -->
     <link href='http://fonts.googleapis.com/css?family=Lato:300italic,700italic,300,700' rel='stylesheet' type='text/css'/>
 
     <!-- Math via MathJax -->
     <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
-
     <!-- HTML5 Shim and Respond.js IE8 support of HTML5 elements and media queries -->
     <!-- WARNING: Respond.js doesn't work if you view the page via file:// -->
     <!--[if lt IE 9]>
@@ -57,6 +56,7 @@
     <link href="{{ BASE_PATH }}{{ site.JB.rss_path }}" type="application/rss+xml" rel="alternate" title="Sitewide RSS Feed">
     -->
 
+    {% seo %}
   </head>
 
   <body>

_includes/themes/lab/member.html

@@ -12,7 +12,7 @@
 <div class="row">
 	<div class="col-md-3">
 		<div class="media">
-			<img class="pull-left pad-right big-member-photo" src="{{ image }}">
+			<img class="pull-left pad-right big-member-photo" src="{{ image }}" style="width:250px; height:auto; padding:1px; border:1px solid #021a40;">
 		</div>
 		<div class="bigspacer"></div>
 
@@ -36,7 +36,9 @@
 			<div class="pad-left note">
 				<div class="smallspacer"></div>
 				<i class="fa fa-user fa-fw"></i>
-				<a class="off" href="{{ member.site }}">{{ member.site | remove: 'http://' | remove: 'https://' }}</a>
+				<a class="social site" href="{{ member.site }}">
+					{{ member.site | remove: 'http://' | remove: 'https://' }}
+				</a>
 			</div>
 			<div class="bigspacer"></div>
 		{% endif %}
@@ -48,7 +50,9 @@
 			<div class="pad-left note">
 				<div class="smallspacer"></div>
 				<i class="fa fa-file-text-o fa-fw"></i>
-				<a class="off" href="{{ member.cv }}">{{ member.cv | split: '/' | last }}</a>
+				<a class="social cv" href="{{ member.cv }}">
+					{{ member.cv | split: '/' | last }}
+				</a>
 			</div>
 			<div class="bigspacer"></div>
 		{% endif %}
@@ -60,7 +64,9 @@
 			<div class="pad-left note">
 				<div class="smallspacer"></div>
 				<i class="fa fa-github-alt fa-fw"></i>
-				<a class="off" href="https://github.com/{{ member.github }}">{{ member.github }}</a>
+				<a class="social github" href="https://github.com/{{ member.github }}">
+					{{ member.github }}
+				</a>
 			</div>
 			<div class="bigspacer"></div>
 		{% endif %}
@@ -72,7 +78,9 @@
 			<div class="pad-left note">
 				<div class="smallspacer"></div>
 				<i class="fa fa-twitter fa-fw"></i>
-				<a class="off" href="https://twitter.com/{{ member.twitter }}">{{ member.twitter }}</a>
+				<a class="social twitter" href="https://twitter.com/{{ member.twitter }}">
+					{{ member.twitter }}
+				</a>
 			</div>
 			<div class="bigspacer"></div>
 		{% endif %}
@@ -84,7 +92,9 @@
 			<div class="pad-left note">
 				<div class="smallspacer"></div>
 				<i class="ai ai-google-scholar"></i>
-				<a class="off" href="http://scholar.google.com/citations?user={{ member.scholar }}">{{ member.title }}</a>
+				<a class="social scholar" href="http://scholar.google.com/citations?user={{ member.scholar }}">
+					{{ member.title }}
+				</a>
 			</div>
 			<div class="bigspacer"></div>
 		{% endif %}
@@ -96,7 +106,9 @@
 			<div class="pad-left note">
 				<div class="smallspacer"></div>
 				<i class="ai ai-osf"></i>
-				<a class="off" href="http://osf.io/{{ member.osf }}">{{ member.title }}</a>
+				<a class="social osf" href="http://osf.io/{{ member.osf }}">
+					{{ member.title }}
+				</a>
 			</div>
 			<div class="bigspacer"></div>
 		{% endif %}
@@ -107,8 +119,10 @@
 			</div>
 			<div class="pad-left note">
 				<div class="smallspacer"></div>
-				<i class="ai ai-researchgate"></i>
-				<a class="off" href="https://www.researchgate.net/profile/{{ member.researchgate }}">{{ member.researchgate }}</a>
+					<i class="ai ai-researchgate"></i>
+					<a class="social researchgate" href="https://www.researchgate.net/profile/{{ member.researchgate }}">
+						{{ member.researchgate }}
+					</a>
 			</div>
 			<div class="bigspacer"></div>
 		{% endif %}
@@ -120,7 +134,9 @@
 			<div class="pad-left note">
 				<div class="smallspacer"></div>
 				<i class="ai ai-orcid"></i>
-				<a class="off" href="http://orcid.org/{{ member.orcid }}">{{ member.orcid }}</a>
+				<a class="social orcid" href="http://orcid.org/{{ member.orcid }}">
+					{{ member.orcid }}
+				</a>
 			</div>
 			<div class="bigspacer"></div>
 		{% endif %}
@@ -132,7 +148,9 @@
 			<div class="pad-left note">
 				<div class="smallspacer"></div>
 				<i class="ai ai-publons"></i>
-				<a class="off" href="https://publons.com/author/{{ member.publons }}">{{ member.title }}</a>
+				<a class="social publons" href="https://publons.com/author/{{ member.publons }}">
+					{{ member.title }}
+				</a>
 			</div>
 			<div class="bigspacer"></div>
 		{% endif %}
@@ -176,10 +194,15 @@
 			{% endfor %}
 
 			{% for poster in site.categories.posters %}
+			<!-- Disabling first-author check for now
 				{% assign split_authors = poster.authors | split: ", " %}
 				{% if split_authors[0] contains lastname %}
 					{% assign postersq = true %}
 				{% endif %}
+			-->
+				{% if poster.authors contains lastname %}
+					{% assign postersq = true %}
+				{% endif %}
 			{% endfor %}
 
 			<!-- Add section divider -->
@@ -216,6 +239,8 @@
 		              <a href="{{ paper.url }}" class="off">[PREPRINT] {{ paper.title }}</a>
 		            {% elsif paper.tags contains "chapter" %}
 		              <a href="{{ paper.url }}" class="off">[CHAPTER] {{ paper.title }}</a>
+								{% elsif paper.tags contains "correspondence" %}
+			              <a href="{{ paper.url }}" class="off">[CORRESPONDENCE] {{ paper.title }}</a>
 		            {% else %}
 		              <a href="{{ paper.url }}" class="off">{{ paper.title }}</a>
 		            {% endif %}
@@ -226,12 +251,13 @@
 			{% endif %}
 
 			<!-- Only show presentations on first author's page -->
+			<!-- Disabling for now -->
 			{% if presentationsq == true %}
 				<div class="bigspacer"></div>
 				<div class="head">Presentations</div>
 				<div class="spacer"></div>
 				{% for pres in site.categories.presentations %}
-					{% assign split_authors = pres.authors | split: ", " %}
+				  {% assign split_authors = pres.authors | split: ", " %}
 					{% if split_authors[0] contains lastname %}
 					  <div class="pad-left note"><p>
 						<a href="{{ pres.url }}" class="off">{{ pres.title }}</a>
@@ -246,8 +272,7 @@
 				<div class="head">Posters</div>
 				<div class="spacer"></div>
 				{% for poster in site.categories.posters %}
-					{% assign split_authors = poster.authors | split: ", " %}
-					{% if split_authors[0] contains lastname %}
+					{% if poster.authors contains lastname %}
 					  <div class="pad-left note"><p>
 						<a href="{{ poster.url }}" class="off">{{ poster.title }}</a>
 						</p></div>

_includes/themes/lab/paper.html

@@ -14,7 +14,7 @@
 <div class="row">
 	<div class="col-md-3">
 		<div class="media">
-			<img class="pull-left pad-right media-object paper-image" src="{{ image }}">
+			<img class="pull-left pad-right media-object paper-image" src="{{ image }}" style="border:1px solid #021a40;">
 		</div>
 		<div class="bigspacer"></div>
 		<div class="glyphbox note"> <!-- DAD: what is this class? -->
@@ -142,11 +142,13 @@
 		<div class="media-body titlebox">
 			<div class="title media-heading">
 				{% if page.tags contains "preprint" %}
-				[PREPRINT] {{ page.title }}
+				  [PREPRINT] {{ page.title }}
 				{% elsif page.tags contains "chapter" %}
-				[CHAPTER] {{ page.title }}
+				  [CHAPTER] {{ page.title }}
+				{% elsif page.tags contains "correspondence" %}
+					[CORRESPONDENCE] {{ page.title }}
 				{% else %}
-				{{ page.title }}
+				  {{ page.title }}
 				{% endif %}
 			</div>
 			<p>

_includes/themes/lab/poster_or_presentation.html

@@ -20,7 +20,7 @@
 <div class="row">
 	<div class="col-md-3">
 		<div class="media">
-			<img class="pull-left pad-right media-object paper-image" src="{{ image }}">
+			<img class="pull-left pad-right media-object paper-image" src="{{ image }}" style="border:1px solid #021a40;">
 		</div>
     <div class="bigspacer"></div>
     <div class="glyphbox note"> <!-- DAD: what is this class? -->

_includes/themes/lab/project.html

@@ -14,7 +14,7 @@
 <div class="row">
 	<div class="col-md-3">
     <div class="media">
-      <img class="pull-left pad-right media-object paper-image" src="{{ image }}">
+      <img class="pull-left pad-right media-object paper-image" src="{{ image }}" style="border:1px solid #021a40;">
     </div>
     <div class="bigspacer"></div>
     {% if page.grant %}
@@ -110,7 +110,7 @@
         {% endif %}
       {% endfor %}
     {% endif %}
-		
+
 		<!-- comment out unless we want the categories and tags
     {% unless page.categories == empty %}
     <ul class="tag_box inline">

assets/themes/lab/css/style.scss

@@ -38,6 +38,61 @@ h6, .h6 { font-size: ceil($font-size-base * 0.85); }  /* ~12px */
   padding-right: 25px;
 }
 
+/* some hyperlink stuff */
+a.anchor {
+    display: block;
+    position: relative;
+    top: -45px;
+    visibility: hidden;
+}
+
+a.social {
+	color: #666;
+	-webkit-transition: all .3s ease-in-out;
+  -moz-transition: all .3s ease-in-out;
+  transition: all .3s ease-in-out;
+}
+
+/* hover colors from darjeeling limited palettes:
+https://github.com/karthik/wesanderson/blob/master/R/colors.R
+*/
+
+a.site:hover {
+	color:#FF0000;
+}
+
+a.cv:hover {
+	color:#00A08A;
+}
+
+a.github:hover {
+  color: #F2AD00;
+}
+
+a.scholar:hover {
+  color: #F98400;
+}
+
+a.twitter:hover {
+  color: #5BBCD6;
+}
+
+a.orcid:hover {
+	color: #ECCBAE;
+}
+
+a.osf:hover {
+	color: #046C9A;
+}
+
+a.researchgate:hover {
+  color: #D69C4E;
+}
+
+a.publons:hover {
+  color: #ABDDDE;
+}
+
 .pad-left {
   padding-left: 10px;
 }

index.html

@@ -85,15 +85,12 @@
 					</a>
 				</div>
 				<div class="note">
-					{{ news.excerpt }}
+					{{ news.excerpt | markdownify }}
 				</div>
 				<div class="smallspacer"></div>
 				<div class="smallnote">
 					Posted
 					{{ news.date | date_to_string }}
-					{% if author %}
-					by <a class="off" href="{{ author.url }}">{{ author.nickname }}</a>
-					{% endif %}
 				</div>
 				<div class="spacer"></div>
 				<div class="spacer"></div>
@@ -137,6 +134,8 @@
               <a href="{{ paper.url }}" class="off">[PREPRINT] {{ paper.title }}</a>
           {% elsif paper.tags contains "chapter" %}
               <a href="{{ paper.url }}" class="off">[CHAPTER] {{ paper.title }}</a>
+          {% elsif paper.tags contains "correspondence" %}
+              <a href="{{ paper.url }}" class="off">[CORRESPONDENCE] {{ paper.title }}</a>
           {% else %}
               <a href="{{ paper.url }}" class="off">{{ paper.title }}</a>
           {% endif %}