Adding links to linkage mapper publications

.gitignore

@@ -15,4 +15,7 @@ _book
 *.mobi
 *.pdf
 
-.jekyll-cache
+# Jekyll
+_site/
+*-cache/
+.jekyll-metadata

_config.yml

@@ -31,9 +31,13 @@ plugins:
 # Header pages
 header_pages:
   - linkage-mapper.md
+  - linkage-mapper-history.md
+  - linkage-mapper-team.md
   - linkage-mapper-tools.md
-  - about-the-linkage-mapper-team.md
+  - references.md
   - downloads.md
+  - support.md
+  - services.md
 # Exclude from processing.
 # The following items will not be processed, by default. Create a custom list
 # to override the default setting.

_includes/footer.html

@@ -35,8 +35,10 @@ <h2 class="footer-heading">{{ site.title | escape }}</h2>
   -->
 
   <div style="display: flex;justify-content: center;">
-    <button > <a style="font-size: 20px;text-decoration: none;color:black"   href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
-    <button style="margin-left:10px"> <a style="font-size: 20px;text-decoration: none;color:black"  href=" https://donorbox.org/linkage-mapper">Donate</a></button>
+    <button > <a style="font-size: 20px;text-decoration: none;color:black"  target="_blank"  href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
+    <button style="margin-left:10px"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://donorbox.org/linkage-mapper">Donate</a></button>
+    <button style="margin-left:10px"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href="https://mailchi.mp/dec0c5cf084d/linkagemapper1?e=67ba4eafbf">Newsletter</a></button>
+
   </div>
 
 </footer>

_includes/form.html

@@ -13,7 +13,7 @@
   >
     <div id="mc_embed_signup_scroll">
       <h2>
-        Download the Linkage Mapper v 3.0.0. Toolbox, and Subscribe to the
+        Download the Linkage Mapper v 3.1.0. Toolbox, and Subscribe to the
         Newsletter
       </h2>
       <div class="indicates-required">
@@ -124,11 +124,11 @@ <h2>
       </div>
     </div>
   </form>
-  <div id="button-group" style="display: none">
-    <button style="padding: 5px; margin-left: 10px">
-      <a
-        style="text-decoration: none; color: black"
-        href="../downloads/linkage_mapper_3_0_0.zip"
+    <div id="button-group" style="display: none">
+    <button style="padding: 10px 20px; margin-left: 10px; font-size: 18px; font-weight: bold">
+      <a 
+        style="text-decoration: none; color: black; font-size: 18px; font-weight: bold"
+        href="../downloads/linkage_mapper_3_1_0.zip"
         >Download</a
       >
     </button>
@@ -8355,6 +8355,7 @@ <h2>
           var msg;
           try {
             var parts = resp.msg.split(" - ", 2);
+
             if (parts[1] == undefined) {
               msg = resp.msg;
             } else {
@@ -8376,8 +8377,12 @@ <h2>
             // If index is -1 if means we don't have data on specifically which field was invalid.
             // Just lump the error message into the generic response div.
             if (index == -1) {
+              console.log(msg);
               $("#mce-" + resp.result + "-response").show();
-              $("#mce-" + resp.result + "-response").html(msg);
+              $("#mce-" + resp.result + "-response").html(
+                'Linkage Mapper 3.0.0 is <a href="https://linkagemapper.org/downloads/linkage_mapper_3_0_0.zip">here</a>. Also, ' +
+                  msg
+              );
             } else {
               var fieldName = $("input[name*='" + fnames[index] + "']").attr(
                 "name"

_includes/head.html

@@ -28,6 +28,13 @@
       left: 37%;
     }
 
+    #newsletter {
+      float: left;
+      position: relative;
+      top: 10px;
+      left: 39%;
+    }
+
     @media only screen and (max-width: 600px) {
       #survey {
         position: revert;
@@ -49,6 +56,15 @@
 
         /* float: left; */
       }
+
+      #newsletter {
+        position: revert;
+        position: relative;
+        top: 10px;
+        left: revert;
+        left: 5px;
+        width: fit-content;
+      }
     }
     /* Add your own Mailchimp form style overrides in your site stylesheet or in this style block.
     We recommend moving this block and the preceding CSS link to the HEAD of your HTML file. */

_includes/header.html

@@ -5,8 +5,9 @@
     {%- assign page_paths = site.header_pages | default: default_paths -%}
     <a class="site-title" rel="author" href="{{ "/" | relative_url }}">{{ site.title | escape }}</a>
 
-    <button id="survey"> <a style="font-size: 20px;text-decoration: none;color:black"   href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
-    <button id="donate"> <a style="font-size: 20px;text-decoration: none;color:black"  href=" https://donorbox.org/linkage-mapper">Donate</a></button>
+    <button id="survey"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
+    <button id="donate"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://donorbox.org/linkage-mapper">Donate</a></button>
+    <button id="newsletter"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://mailchi.mp/dec0c5cf084d/linkagemapper1?e=67ba4eafbf">Newsletter</a></button>
 
 
     {%- if page_paths -%}

_sass/minima/_layout.scss

@@ -9,7 +9,12 @@
   // Positioning context for the mobile navigation icon
   position: relative;
 }
-
+  // The nav has 8 items and won't fit in the default 800px content width,
+  // so give the header its own wider wrapper to keep everything on one line.
+  .wrapper {
+    max-width: -webkit-calc(1120px - (#{$spacing-unit} * 2));
+    max-width:         calc(1120px - (#{$spacing-unit} * 2));
+  }
 .site-title {
   @include relative-font-size(1.625);
   font-weight: 300;
@@ -39,7 +44,9 @@
   .page-link {
     color: $text-color;
     line-height: $base-line-height;
-
+    // Keep multi-word titles like "Linkage Mapper Tools" from breaking
+    // across lines when the nav wraps.
+    white-space: nowrap;
     // Gaps between nav items, but not on the last one
     &:not(:last-child) {
       margin-right: 20px;

_site/404.html

@@ -9,11 +9,11 @@
 <meta property="og:locale" content="en_US" />
 <meta name="description" content="Linkage Mapper" />
 <meta property="og:description" content="Linkage Mapper" />
-<link rel="canonical" href="https://linkagescape.org/404.html" />
-<meta property="og:url" content="https://linkagescape.org/404.html" />
+<link rel="canonical" href="http://localhost:4000/404.html" />
+<meta property="og:url" content="http://localhost:4000/404.html" />
 <meta property="og:site_name" content="Linkage Mapper" />
 <script type="application/ld+json">
-{"description":"Linkage Mapper","@type":"WebPage","url":"https://linkagescape.org/404.html","headline":"Linkage Mapper","@context":"https://schema.org"}</script>
+{"description":"Linkage Mapper","@type":"WebPage","headline":"Linkage Mapper","url":"http://localhost:4000/404.html","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->
 <link rel="stylesheet" href="/assets/main.css">
   <link
@@ -40,6 +40,13 @@
       left: 37%;
     }
 
+    #newsletter {
+      float: left;
+      position: relative;
+      top: 10px;
+      left: 39%;
+    }
+
     @media only screen and (max-width: 600px) {
       #survey {
         position: revert;
@@ -61,16 +68,26 @@
 
         /* float: left; */
       }
+
+      #newsletter {
+        position: revert;
+        position: relative;
+        top: 10px;
+        left: revert;
+        left: 5px;
+        width: fit-content;
+      }
     }
     /* Add your own Mailchimp form style overrides in your site stylesheet or in this style block.
     We recommend moving this block and the preceding CSS link to the HEAD of your HTML file. */
-  </style><link type="application/atom+xml" rel="alternate" href="https://linkagescape.org/feed.xml" title="Linkage Mapper" /></head>
+  </style><link type="application/atom+xml" rel="alternate" href="http://localhost:4000/feed.xml" title="Linkage Mapper" /></head>
 <body><header class="site-header" role="banner">
 
   <div class="wrapper"><a class="site-title" rel="author" href="/">Linkage Mapper</a>
 
-    <button id="survey"> <a style="font-size: 20px;text-decoration: none;color:black"   href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
-    <button id="donate"> <a style="font-size: 20px;text-decoration: none;color:black"  href=" https://donorbox.org/linkage-mapper">Donate</a></button><nav class="site-nav">
+    <button id="survey"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
+    <button id="donate"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://donorbox.org/linkage-mapper">Donate</a></button>
+    <button id="newsletter"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://mailchi.mp/dec0c5cf084d/linkagemapper1?e=67ba4eafbf">Newsletter</a></button><nav class="site-nav">
         <input type="checkbox" id="nav-trigger" class="nav-trigger" />
         <label for="nav-trigger">
           <span class="menu-icon">
@@ -134,8 +151,10 @@ <h2 class="footer-heading">Linkage Mapper</h2>
   -->
 
   <div style="display: flex;justify-content: center;">
-    <button > <a style="font-size: 20px;text-decoration: none;color:black"   href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
-    <button style="margin-left:10px"> <a style="font-size: 20px;text-decoration: none;color:black"  href=" https://donorbox.org/linkage-mapper">Donate</a></button>
+    <button > <a style="font-size: 20px;text-decoration: none;color:black"  target="_blank"  href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
+    <button style="margin-left:10px"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://donorbox.org/linkage-mapper">Donate</a></button>
+    <button style="margin-left:10px"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href="https://mailchi.mp/dec0c5cf084d/linkagemapper1?e=67ba4eafbf">Newsletter</a></button>
+
   </div>
 
 </footer>

_site/Downloads/index.html

@@ -9,11 +9,11 @@
 <meta property="og:locale" content="en_US" />
 <meta name="description" content="Linkage Mapper" />
 <meta property="og:description" content="Linkage Mapper" />
-<link rel="canonical" href="https://linkagescape.org/Downloads/" />
-<meta property="og:url" content="https://linkagescape.org/Downloads/" />
+<link rel="canonical" href="http://localhost:4000/Downloads/" />
+<meta property="og:url" content="http://localhost:4000/Downloads/" />
 <meta property="og:site_name" content="Linkage Mapper" />
 <script type="application/ld+json">
-{"description":"Linkage Mapper","@type":"WebPage","url":"https://linkagescape.org/Downloads/","headline":"Downloads","@context":"https://schema.org"}</script>
+{"description":"Linkage Mapper","@type":"WebPage","headline":"Downloads","url":"http://localhost:4000/Downloads/","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->
 <link rel="stylesheet" href="/assets/main.css">
   <link
@@ -40,6 +40,13 @@
       left: 37%;
     }
 
+    #newsletter {
+      float: left;
+      position: relative;
+      top: 10px;
+      left: 39%;
+    }
+
     @media only screen and (max-width: 600px) {
       #survey {
         position: revert;
@@ -61,16 +68,26 @@
 
         /* float: left; */
       }
+
+      #newsletter {
+        position: revert;
+        position: relative;
+        top: 10px;
+        left: revert;
+        left: 5px;
+        width: fit-content;
+      }
     }
     /* Add your own Mailchimp form style overrides in your site stylesheet or in this style block.
     We recommend moving this block and the preceding CSS link to the HEAD of your HTML file. */
-  </style><link type="application/atom+xml" rel="alternate" href="https://linkagescape.org/feed.xml" title="Linkage Mapper" /></head>
+  </style><link type="application/atom+xml" rel="alternate" href="http://localhost:4000/feed.xml" title="Linkage Mapper" /></head>
 <body><header class="site-header" role="banner">
 
   <div class="wrapper"><a class="site-title" rel="author" href="/">Linkage Mapper</a>
 
-    <button id="survey"> <a style="font-size: 20px;text-decoration: none;color:black"   href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
-    <button id="donate"> <a style="font-size: 20px;text-decoration: none;color:black"  href=" https://donorbox.org/linkage-mapper">Donate</a></button><nav class="site-nav">
+    <button id="survey"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
+    <button id="donate"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://donorbox.org/linkage-mapper">Donate</a></button>
+    <button id="newsletter"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://mailchi.mp/dec0c5cf084d/linkagemapper1?e=67ba4eafbf">Newsletter</a></button><nav class="site-nav">
         <input type="checkbox" id="nav-trigger" class="nav-trigger" />
         <label for="nav-trigger">
           <span class="menu-icon">
@@ -97,7 +114,7 @@ <h1 class="post-title">Downloads</h1>
   <form style="border: 1px solid black" action="https://linkagemapper.us5.list-manage.com/subscribe/post?u=41706d728d514adf01eae0389&amp;id=bd94a02d76" method="post" id="mc-embedded-subscribe-form" name="mc-embedded-subscribe-form" class="validate" target="_blank" novalidate="">
     <div id="mc_embed_signup_scroll">
       <h2>
-        Download the Linkage Mapper v 3.0.0. Toolbox, and Subscribe to the
+        Download the Linkage Mapper v 3.1.0. Toolbox, and Subscribe to the
         Newsletter
       </h2>
       <div class="indicates-required">
@@ -158,7 +175,7 @@ <h2>
   </form>
   <div id="button-group" style="display: none">
     <button style="padding: 5px; margin-left: 10px">
-      <a style="text-decoration: none; color: black" href="../downloads/linkage_mapper_3_0_0.zip">Download</a>
+      <a style="text-decoration: none; color: black" href="../downloads/linkage_mapper_3_1_0.zip">Download</a>
     </button>
     <br />
   </div>
@@ -8383,6 +8400,7 @@ <h2>
           var msg;
           try {
             var parts = resp.msg.split(" - ", 2);
+
             if (parts[1] == undefined) {
               msg = resp.msg;
             } else {
@@ -8404,8 +8422,12 @@ <h2>
             // If index is -1 if means we don't have data on specifically which field was invalid.
             // Just lump the error message into the generic response div.
             if (index == -1) {
+              console.log(msg);
               $("#mce-" + resp.result + "-response").show();
-              $("#mce-" + resp.result + "-response").html(msg);
+              $("#mce-" + resp.result + "-response").html(
+                'Linkage Mapper 3.0.0 is <a href="https://linkagemapper.org/downloads/linkage_mapper_3_0_0.zip">here</a>. Also, ' +
+                  msg
+              );
             } else {
               var fieldName = $("input[name*='" + fnames[index] + "']").attr(
                 "name"
@@ -8509,41 +8531,28 @@ <h2>
 
 <!--End mc_embed_signup-->
 
-<p>Circuitscape to be used with Linkage mapper 3.0.0: <a href="../downloads/Circuitscape-4.0.7-x64-setup.exe.zip">Circuitscape 4.0.7</a></p>
+<p>Circuitscape to be used with Linkage mapper 3.1.0: <a href="../downloads/Circuitscape-4.0.7-x64-setup.exe.zip">Circuitscape 4.0.7</a></p>
+
+<p>Extras: <a href="downloads/LM_Lab_V2.zip">Lab Excercise: Linkage Pathways, Pinchpoints, and Barriers </a></p>
 
-<h3 id="whats-new-in-version-300">What’s new in Version 3.0.0</h3>
+<h3 id="whats-new-in-version-310">What’s new in Version 3.1.0</h3>
 
 <ul>
-  <li>Compatibility with ArcGIS Pro</li>
-  <li>Linkage Priority Tool improvements (see next newsletter item)</li>
-  <li>User Guide improvements</li>
-  <li>Back-end engineering and code refactoring</li>
-  <li>Re-writing of the GitHub commit history to make the repository smaller</li>
-  <li>Improved Error Messages and Log Files</li>
-  <li>Climate-wise Connectivity Improvements in Version 3.0.0
-    <ul>
-      <li>There are many climate considerations that can be incorporated in
-habitat connectivity modeling and mapping. Two considerations have
-previously been modeled in isolation from each other, and yield
-quite different recommendations for linkage priority. However, we
-discovered that they are two ends of the same continuous framework,
-and Linkage Mapper Version 3.0.0 allows the user to model for one,
-or the other, or an appropriate blend between both (which we
-recommend). The first consideration is “range shift connectivity”,
-and gives linkages a higher priority for conservation if they are
-predicted to connect a core area that might become too hot/dry in
-the future with a core that is expected to be much cooler/wetter.
-The other is “climate analog connectivity” giving higher priority to
-linkages with the destination core having the same predicted climate
-at a future time (e.g. 2050), as the climate in the source core at
-the current time. We also added “preferred climate” as an optional
-parameter in differentiating among destination cores.</li>
-    </ul>
-  </li>
+  <li>Updated code to run in latest versions of ArcPro, versions 3.x (Python changed the syntax of time.)</li>
+  <li>Update that makes it possible to run tools in batch from Python scripts. Helpful for testing.</li>
+  <li>Fix to the Coarsen Raster Sizes utility to allow it to work with rasters that have file extensions not just raster grids.</li>
+  <li>Fixed a bug in Pinchpoint mapper that arises for certain edge cases.</li>
+  <li>Further refined the use of (time) in ArcPro, versions 3.x and higher</li>
 </ul>
 
+<p>Thank you to Darren Kavanagh for coding these improvements, and to Fred Watson for finding and sharing the initial solution to the ArcPro 3.0 bug.</p>
+
 <h3 id="previous-versions">Previous Versions</h3>
 
+<p><strong>Latest ArcGIS 10.7 - 10.8 Version, ArcGIS Pro</strong>: <a href="../downloads/LinkageMapper_3_0_0.zip">Linkage Mapper 3.0.0</a></p>
+
+<p>Circuitscape to be used with Linkage mapper 3.0.0: <a href="../downloads/Circuitscape-4.0.7-x64-setup.exe.zip">Circuitscape 4.0.7</a></p>
+
 <p><strong>Latest ArcGIS 10.0 - 10.6 Version</strong>: <a href="https://github.com/linkagescape/linkage-mapper/files/2204107/Linkage_Mapper_2_0_0.zip">Linkage Mapper 2.0.0</a></p>
 
 <p><strong>Latest ArcGIS 9.3 Version</strong>: <a href="../downloads/LinkageMapper_1_1_0.zip">Linkage Mapper 1.1.0</a></p>
@@ -8583,8 +8592,10 @@ <h2 class="footer-heading">Linkage Mapper</h2>
   -->
 
   <div style="display: flex;justify-content: center;">
-    <button > <a style="font-size: 20px;text-decoration: none;color:black"   href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
-    <button style="margin-left:10px"> <a style="font-size: 20px;text-decoration: none;color:black"  href=" https://donorbox.org/linkage-mapper">Donate</a></button>
+    <button > <a style="font-size: 20px;text-decoration: none;color:black"  target="_blank"  href=" https://www.surveymonkey.com/r/LinkageMapper2021">User Survey</a></button>
+    <button style="margin-left:10px"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href=" https://donorbox.org/linkage-mapper">Donate</a></button>
+    <button style="margin-left:10px"> <a style="font-size: 20px;text-decoration: none;color:black" target="_blank"  href="https://mailchi.mp/dec0c5cf084d/linkagemapper1?e=67ba4eafbf">Newsletter</a></button>
+
   </div>
 
 </footer>