another try at fixing broken links

bartonlab · Mar 28, 2023 · a2d3a96 · a2d3a96
1 parent f1e1fc1
commit a2d3a96
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Showing 13 changed files with 110 additions and 110 deletions.
diff --git a/_config.yml b/_config.yml
@@ -16,7 +16,7 @@ destination:   docs
 
 title:         Barton lab at Pitt CSB
 description:   Research in pathogen evolution, computational immunology, and statistical inference
-url:           https://bartonlab.github.io
+url:           bartonlab.github.io
 baseurl:       /docs
 author:        John P Barton
 logo:          favicon.ico

diff --git a/_data/members.yml b/_data/members.yml
@@ -6,7 +6,7 @@
   scholar: ItAcAOMAAAAJ
   image: assets/img/members/john-barton.jpg
   cv: cv.html
-  blurb: '<b><a href="/menu/about.html">John Barton</a></b> is an Associate Professor of Computational and Systems Biology at the University of Pittsburgh. He <a href="/menu/research.html">studies</a> pathogen evolution and immunology using methods inspired by statistical physics.'
+  blurb: '<b>John Barton</b> is an Associate Professor of Computational and Systems Biology at the University of Pittsburgh. He studies pathogen evolution and immunology using methods inspired by statistical physics.'
 
 - name: Liz Finney
   position: GSR

diff --git a/_includes/footer.html b/_includes/footer.html
@@ -2,5 +2,5 @@
   {% for item in site.data.settings.social %}
     <a href="{{ item.link }}" target="_blank"><i class="fa fa-{{ item.icon }}" aria-hidden="true"></i></a>
   {% endfor %}
-  <div class="post-date"><a href="{{ "/menu/about.html" | relative_url }}">{{ site.data.settings.title }} | {{ site.data.settings.tagline }}</a></div>
+  <div class="post-date"><a href="{{ '/menu/about.html' | relative_url }}">{{ site.data.settings.title }} | {{ site.data.settings.tagline }}</a></div>
 </footer>
diff --git a/_includes/head.html b/_includes/head.html
@@ -15,8 +15,8 @@
     <meta charset="UTF-8">
 
     <!-- Main style -->
-    <link rel="stylesheet" href="{{ "/assets/css/main.css" | relative_url }}">
-    <link rel="stylesheet" href="{{ "/assets/css/syntax.css" | relative_url }}">
+    <link rel="stylesheet" href="{{ '/assets/css/main.css' | relative_url }}">
+    <link rel="stylesheet" href="{{ '/assets/css/syntax.css' | relative_url }}">
 
     <!-- Google fonts -->
     <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Avenir">
@@ -34,9 +34,9 @@
     -->
 
     <!-- KaTeX + auto render -->
-    <script src="{{ "/assets/js/katex.min.js" | relative_url }}" type="text/javascript"></script>
-    <link href="{{ "/assets/css/katex.min.css" | relative_url }}" rel="stylesheet" type="text/css">
-    <script src="{{ "/assets/js/auto-render.min.js" | relative_url }}" type="text/javascript"></script>
+    <script src="{{ '/assets/js/katex.min.js' | relative_url }}" type="text/javascript"></script>
+    <link href="{{ '/assets/css/katex.min.css' | relative_url }}" rel="stylesheet" type="text/css">
+    <script src="{{ '/assets/js/auto-render.min.js' | relative_url }}" type="text/javascript"></script>
     <script>
       document.addEventListener("DOMContentLoaded", function() {
         renderMathInElement(document.body);

diff --git a/_includes/header.html b/_includes/header.html
@@ -1,6 +1,6 @@
 <header class="masthead">
   <h3 class="masthead-title">
-    <a href="{{ "/menu/about.html" | relative_url }}" class="masthead-lab">{{ site.data.settings.title }}</a>
+    <a href="{{ '/menu/about.html' | relative_url }}" class="masthead-lab">{{ site.data.settings.title }}</a>
     <small class="masthead-subtitle">{{ site.data.settings.tagline }}</small>
     {% include menu.html %}
   </h3>

diff --git a/_layouts/cv.html b/_layouts/cv.html
@@ -3,7 +3,7 @@
 
 <head>
   <title></title>
-  <link rel="stylesheet" href="{{ "/assets/css/cv.css" | relative_url }}">
+  <link rel="stylesheet" href="{{ '/assets/css/cv.css' | relative_url }}">
 </head>
 
 <body>

diff --git a/docs/feed.xml b/docs/feed.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="3.9.3">Jekyll</generator><link href="http://localhost:4000/docs/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/docs/" rel="alternate" type="text/html" /><updated>2023-03-28T12:56:11-04:00</updated><id>http://localhost:4000/docs/feed.xml</id><title type="html">Barton lab at Pitt CSB</title><subtitle>Research in pathogen evolution, computational immunology, and statistical inference</subtitle><author><name>John P Barton</name></author><entry><title type="html">New grant support</title><link href="http://localhost:4000/docs/posts/grants.html" rel="alternate" type="text/html" title="New grant support" /><published>2020-07-01T00:00:00-04:00</published><updated>2020-07-01T00:00:00-04:00</updated><id>http://localhost:4000/docs/posts/grants</id><content type="html" xml:base="http://localhost:4000/docs/posts/grants.html">&lt;p&gt;This summer we’ve been fortunate to receive two major grants to support our research.&lt;/p&gt;
+<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="3.9.3">Jekyll</generator><link href="http://localhost:4000/docs/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/docs/" rel="alternate" type="text/html" /><updated>2023-03-28T13:34:22-04:00</updated><id>http://localhost:4000/docs/feed.xml</id><title type="html">Barton lab at Pitt CSB</title><subtitle>Research in pathogen evolution, computational immunology, and statistical inference</subtitle><author><name>John P Barton</name></author><entry><title type="html">New grant support</title><link href="http://localhost:4000/docs/posts/grants.html" rel="alternate" type="text/html" title="New grant support" /><published>2020-07-01T00:00:00-04:00</published><updated>2020-07-01T00:00:00-04:00</updated><id>http://localhost:4000/docs/posts/grants</id><content type="html" xml:base="http://localhost:4000/docs/posts/grants.html">&lt;p&gt;This summer we’ve been fortunate to receive two major grants to support our research.&lt;/p&gt;
 
 &lt;p&gt;First, we received a Maximizing Investigators’ Research Award (MIRA) from the NIH. This grant will support the development of new methods to infer selection from temporal genetic data. We’re excited to begin work on this project. An advertisement for a new postdoc position supported by this grant will be posted soon!&lt;/p&gt;
 

diff --git a/docs/menu/code.html b/docs/menu/code.html
@@ -183,9 +183,9 @@ <h1>
 <ul class="code-list">
 
     <li>
-        <a class="project-title" href="/projects/paper-SARS-CoV-2-inference/">paper-SARS-CoV-2-inference</a>
+        <a class="project-title" href="/docs/projects/paper-SARS-CoV-2-inference/">paper-SARS-CoV-2-inference</a>
         <div class="smallspacer"></div>
-        <a class="project-subtitle" href="/projects/paper-SARS-CoV-2-inference/"></a>
+        <a class="project-subtitle" href="/docs/projects/paper-SARS-CoV-2-inference/"></a>
         <div class="smallspacer"></div>
         <small>
 	        Updated
@@ -202,9 +202,9 @@ <h1>
     </li>
 
     <li>
-        <a class="project-title" href="/projects/paper-MPL-inference/">paper-MPL-inference</a>
+        <a class="project-title" href="/docs/projects/paper-MPL-inference/">paper-MPL-inference</a>
         <div class="smallspacer"></div>
-        <a class="project-subtitle" href="/projects/paper-MPL-inference/"></a>
+        <a class="project-subtitle" href="/docs/projects/paper-MPL-inference/"></a>
         <div class="smallspacer"></div>
         <small>
 	        Updated
@@ -221,9 +221,9 @@ <h1>
     </li>
 
     <li>
-        <a class="project-title" href="/projects/paper-innate-immune-adaptation/">paper-innate-immune-adaptation</a>
+        <a class="project-title" href="/docs/projects/paper-innate-immune-adaptation/">paper-innate-immune-adaptation</a>
         <div class="smallspacer"></div>
-        <a class="project-subtitle" href="/projects/paper-innate-immune-adaptation/"></a>
+        <a class="project-subtitle" href="/docs/projects/paper-innate-immune-adaptation/"></a>
         <div class="smallspacer"></div>
         <small>
 	        Updated
@@ -240,9 +240,9 @@ <h1>
     </li>
 
     <li>
-        <a class="project-title" href="/projects/Python-workshop/">Python-workshop</a>
+        <a class="project-title" href="/docs/projects/Python-workshop/">Python-workshop</a>
         <div class="smallspacer"></div>
-        <a class="project-subtitle" href="/projects/Python-workshop/"></a>
+        <a class="project-subtitle" href="/docs/projects/Python-workshop/"></a>
         <div class="smallspacer"></div>
         <small>
 	        Updated
@@ -259,9 +259,9 @@ <h1>
     </li>
 
     <li>
-        <a class="project-title" href="/projects/paper-Nef-modeling/">paper-Nef-modeling</a>
+        <a class="project-title" href="/docs/projects/paper-Nef-modeling/">paper-Nef-modeling</a>
         <div class="smallspacer"></div>
-        <a class="project-subtitle" href="/projects/paper-Nef-modeling/"></a>
+        <a class="project-subtitle" href="/docs/projects/paper-Nef-modeling/"></a>
         <div class="smallspacer"></div>
         <small>
 	        Updated
@@ -278,9 +278,9 @@ <h1>
     </li>
 
     <li>
-        <a class="project-title" href="/projects/ACE/">ACE</a>
+        <a class="project-title" href="/docs/projects/ACE/">ACE</a>
         <div class="smallspacer"></div>
-        <a class="project-subtitle" href="/projects/ACE/">Fast and flexible code for solving the inverse Ising/Potts inference problem</a>
+        <a class="project-subtitle" href="/docs/projects/ACE/">Fast and flexible code for solving the inverse Ising/Potts inference problem</a>
         <div class="smallspacer"></div>
         <small>
 	        Updated
@@ -297,9 +297,9 @@ <h1>
     </li>
 
     <li>
-        <a class="project-title" href="/projects/simple-rebound-simulation/">simple-rebound-simulation</a>
+        <a class="project-title" href="/docs/projects/simple-rebound-simulation/">simple-rebound-simulation</a>
         <div class="smallspacer"></div>
-        <a class="project-subtitle" href="/projects/simple-rebound-simulation/">Simulating viral rebound from the latent reservoir</a>
+        <a class="project-subtitle" href="/docs/projects/simple-rebound-simulation/">Simulating viral rebound from the latent reservoir</a>
         <div class="smallspacer"></div>
         <small>
 	        Updated
@@ -316,9 +316,9 @@ <h1>
     </li>
 
     <li>
-        <a class="project-title" href="/projects/paper-bnAb-flexibility/">paper-bnAb-flexibility</a>
+        <a class="project-title" href="/docs/projects/paper-bnAb-flexibility/">paper-bnAb-flexibility</a>
         <div class="smallspacer"></div>
-        <a class="project-subtitle" href="/projects/paper-bnAb-flexibility/"></a>
+        <a class="project-subtitle" href="/docs/projects/paper-bnAb-flexibility/"></a>
         <div class="smallspacer"></div>
         <small>
 	        Updated
@@ -335,9 +335,9 @@ <h1>
     </li>
 
     <li>
-        <a class="project-title" href="/projects/mplot/">mplot</a>
+        <a class="project-title" href="/docs/projects/mplot/">mplot</a>
         <div class="smallspacer"></div>
-        <a class="project-subtitle" href="/projects/mplot/">Simple scripts for high quality figures using matplotlib</a>
+        <a class="project-subtitle" href="/docs/projects/mplot/">Simple scripts for high quality figures using matplotlib</a>
         <div class="smallspacer"></div>
         <small>
 	        Updated

diff --git a/docs/menu/members.html b/docs/menu/members.html
@@ -203,7 +203,7 @@ <h1>
     </p>
 	</div>
   <div class="member-right">
-    <b><a href="/menu/about.html">John Barton</a></b> is an Associate Professor of Computational and Systems Biology at the University of Pittsburgh. He <a href="/menu/research.html">studies</a> pathogen evolution and immunology using methods inspired by statistical physics.
+    <b>John Barton</b> is an Associate Professor of Computational and Systems Biology at the University of Pittsburgh. He studies pathogen evolution and immunology using methods inspired by statistical physics.
   </div>
   <p style="margin-bottom:0px; margin-top:0px;"></p>
 </div>