More accessibility changes

assets/js/academic-search.js

@@ -0,0 +1,185 @@
+/*************************************************
+ *  Academic
+ *  https://github.com/gcushen/hugo-academic
+ *
+ *  In-built Fuse based search algorithm.
+ **************************************************/
+
+/* ---------------------------------------------------------------------------
+* Configuration.
+* --------------------------------------------------------------------------- */
+
+// Configure Fuse.
+let fuseOptions = {
+  shouldSort: true,
+  includeMatches: true,
+  tokenize: true,
+  threshold: search_config.threshold,  // Set to ~0.3 for parsing diacritics and CJK languages.
+  location: 0,
+  distance: 100,
+  maxPatternLength: 32,
+  minMatchCharLength: search_config.minLength,  // Set to 1 for parsing CJK languages.
+  keys: [
+    {name:'title', weight:0.99}, /* 1.0 doesn't work o_O */
+    {name:'summary', weight:0.6},
+    {name:'authors', weight:0.5},
+    {name:'content', weight:0.2},
+    {name:'tags', weight:0.5},
+    {name:'categories', weight:0.5}
+  ]
+};
+
+// Configure summary.
+let summaryLength = 60;
+
+/* ---------------------------------------------------------------------------
+* Functions.
+* --------------------------------------------------------------------------- */
+
+// Get query from URI.
+function getSearchQuery(name) {
+  return decodeURIComponent((location.search.split(name + '=')[1] || '').split('&')[0]).replace(/\+/g, ' ');
+}
+
+// Set query in URI without reloading the page.
+function updateURL(url) {
+  if (history.replaceState) {
+    window.history.replaceState({path:url}, '', url);
+  }
+}
+
+// Pre-process new search query.
+function initSearch(force, fuse) {
+  let query = $("#search-query").val();
+
+  // If query deleted, clear results.
+  if ( query.length < 1) {
+    $('#search-hits').empty();
+  }
+
+  // Check for timer event (enter key not pressed) and query less than minimum length required.
+  if (!force && query.length < fuseOptions.minMatchCharLength)
+    return;
+
+  // Do search.
+  $('#search-hits').empty();
+  searchAcademic(query, fuse);
+  let newURL = window.location.protocol + "//" + window.location.host + window.location.pathname + '?q=' + encodeURIComponent(query) + window.location.hash;
+  updateURL(newURL);
+}
+
+// Perform search.
+function searchAcademic(query, fuse) {
+  let results = fuse.search(query);
+  // console.log({"results": results});
+
+  if (results.length > 0) {
+    $('#search-hits').append('<h2 class="mt-0">' + results.length + ' ' + i18n.results + '</h2>');
+    parseResults(query, results);
+  } else {
+    $('#search-hits').append('<div class="search-no-results">' + i18n.no_results + '</div>');
+  }
+}
+
+// Parse search results.
+function parseResults(query, results) {
+  $.each( results, function(key, value) {
+    let content_key = value.item.section;
+    let content = "";
+    let snippet = "";
+    let snippetHighlights = [];
+
+    // Show abstract in results for content types where the abstract is often the primary content.
+    if (["publication", "talk"].includes(content_key)) {
+      content = value.item.summary;
+    } else {
+      content = value.item.content;
+    }
+
+    if ( fuseOptions.tokenize ) {
+      snippetHighlights.push(query);
+    } else {
+      $.each( value.matches, function(matchKey, matchValue) {
+        if (matchValue.key == "content") {
+          let start = (matchValue.indices[0][0]-summaryLength>0) ? matchValue.indices[0][0]-summaryLength : 0;
+          let end = (matchValue.indices[0][1]+summaryLength<content.length) ? matchValue.indices[0][1]+summaryLength : content.length;
+          snippet += content.substring(start, end);
+          snippetHighlights.push(matchValue.value.substring(matchValue.indices[0][0], matchValue.indices[0][1]-matchValue.indices[0][0]+1));
+        }
+      });
+    }
+
+    if (snippet.length < 1) {
+      snippet += value.item.summary;  // Alternative fallback: `content.substring(0, summaryLength*2);`
+    }
+
+    // Load template.
+    let template = $('#search-hit-fuse-template').html();
+
+    // Localize content types.
+    if (content_key in content_type) {
+      content_key = content_type[content_key];
+    }
+
+    // Parse template.
+    let templateData = {
+      key: key,
+      title: value.item.title,
+      type: content_key,
+      relpermalink: value.item.relpermalink,
+      snippet: snippet
+    };
+    let output = render(template, templateData);
+    $('#search-hits').append(output);
+
+    // Highlight search terms in result.
+    $.each( snippetHighlights, function(hlKey, hlValue){
+      $("#summary-"+key).mark(hlValue);
+    });
+
+  });
+}
+
+function render(template, data) {
+  // Replace placeholders with their values.
+  let key, find, re;
+  for (key in data) {
+    find = '\\{\\{\\s*' + key + '\\s*\\}\\}';  // Expect placeholder in the form `{{x}}`.
+    re = new RegExp(find, 'g');
+    template = template.replace(re, data[key]);
+  }
+  return template;
+}
+
+/* ---------------------------------------------------------------------------
+* Initialize.
+* --------------------------------------------------------------------------- */
+
+// If Academic's in-built search is enabled and Fuse loaded, then initialize it.
+if (typeof Fuse === 'function') {
+// Wait for Fuse to initialize.
+  $.getJSON(search_config.indexURI, function (search_index) {
+    let fuse = new Fuse(search_index, fuseOptions);
+
+    // On page load, check for search query in URL.
+    if (query = getSearchQuery('q')) {
+      $("body").addClass('searching');
+      $('.search-results').css({opacity: 0, visibility: "visible"}).animate({opacity: 1},200);
+      $("#search-query").val(query);
+      $("#search-query").focus();
+      initSearch(true, fuse);
+    }
+
+    // On search box key up, process query.
+    $('#search-query').keyup(function (e) {
+      clearTimeout($.data(this, 'searchTimer')); // Ensure only one timer runs!
+      if (e.keyCode == 13) {
+        initSearch(true, fuse);
+      } else {
+        $(this).data('searchTimer', setTimeout(function () {
+          initSearch(false, fuse);
+        }, 250));
+      }
+    });
+  });
+}

assets/scss/custom.scss

@@ -183,10 +183,39 @@ html {
 }
 
 #TableOfContents li a,
-.toc-top li a {
+.toc-top li a,
+.toc-top span a
+{
   color: rgb(89, 89, 89);
 }
 
+.toc-top {
+  padding-left: 0;
+}
+
+// TOC indentation for each level.
+#TableOfContents div div {
+  padding-left: 0.8rem;
+}
+
+#TableOfContents span {
+  display: block;
+}
+
+#TableOfContents span a,
+.toc-top span a {
+  display: block;
+  padding: .125rem 1.5rem;
+  font-size: 0.7rem;
+}
+
+#TableOfContents span a:hover,
+.toc-top span a:hover
+{
+  color: $sta-primary;
+  text-decoration: none;
+}
+
 footer {
   display: flex;
   justify-content: flex-start;
@@ -230,6 +259,25 @@ footer {
   display: none;
 }
 
+.docs-sidebar .nav>span>a {
+  display: block;
+  padding: .25rem 1.5rem;
+  font-size: 0.8rem;
+  color: rgba(0, 0, 0, .65);
+}
+
+.docs-sidebar .nav>span>a:hover {
+  color: rgba(0, 0, 0, .85);
+  text-decoration: none;
+  background-color: transparent;
+}
+
+.docs-sidebar .nav>span>a:hover {
+  color: rgba(0, 0, 0, .85);
+  text-decoration: none;
+  background-color: transparent;
+}
+
 .dark {
 
   .site-footer-logo-dark {
@@ -241,6 +289,10 @@ footer {
     display: none;
   }
 
+  .docs-sidebar .nav > span:not(.active) > a {
+    color: rgb(248, 248, 242);
+  }
+
   .btn-primary, .btn.btn-primary.active, .btn-light {
     color: white;
   }
@@ -254,14 +306,27 @@ footer {
   }
 
   #TableOfContents li a,
-  .toc-top li a {
+  .toc-top li a,
+  .toc-top span a
+  {
     color: rgb(191, 190, 193);
   }
 
+  #TableOfContents li a:hover,
+  .toc-top li a:hover,
+  .toc-top span a:hover,
+  .docs-sidebar .docs-toc-item a:hover,
+  .docs-sidenav a:hover,
+  .docs-sidebar .nav > span:not(.active) > a:hover
+  {
+    color: mix(white, $sta-primary-light, 50%);
+  }
+
   a,
   .docs-sidebar .docs-toc-item.active a,
   .docs-sidebar .nav>.active:hover>a,
-  .docs-sidebar .nav>.active>a {
+  .docs-sidebar .nav>.active>a,
+  .docs-sidebar .docs-toc-item.active span a {
     color: mix(white, $sta-primary-light, 50%);
   }
 

content/courses/fiji-image-processing/fiji-omero/index.md

@@ -182,8 +182,8 @@ Before you begin, you need to know the dataset ID that the image should be linke
 
 3. Go to OMERO webclient (http://omero.hpc.virginia.edu) and look for the uploaded image in `Orphaned Images`.
 
-	<img src="/courses/fiji-omero/leaf.png" style="float:left;width:40%;height:auto">
-	<img src="/courses/fiji-omero/fiji-omero-new-export.png" style="width:40%;height:auto">
+	<img src="./leaf.png" style="float:left;width:40%;height:auto">
+	<img src="./fiji-omero-new-export.png" style="width:40%;height:auto">
 
 
 <br>
@@ -211,15 +211,15 @@ Before you begin, you need to know the dataset ID that the image should be linke
 	a. Go to `Process` > `Filter` > `Median`.  In the popup dialog enter a `Radius` of  `3.0` and click `OK`.  This will smooth out some of the image's intrinsic noise without degrading the object outlines.
 
 	b. Go to `Image` > `Adjust Threshold`.  In the popup dialog choose the `Default` thresholding algorithm, uncheck the `Dark Background` box and click `Apply`. The image should have been converted to a binary mask with white objects ona black background.
-			<img src="/courses/fiji-omero/fiji-omero-setthreshold.png" style="float:left;width:47%;height:auto">
-			<img src="/courses/fiji-omero/fiji-omero-blobs-thresholded.png" style="width:40%;height:auto">
+			<img src="./fiji-omero-setthreshold.png" style="float:left;width:47%;height:auto">
+			<img src="./fiji-omero-blobs-thresholded.png" style="width:40%;height:auto">
 
 
 	c. Go to `Analyze` > `Set Measurements...`. In the popup dialog specify the parameters as shown in this screenshot. Click `OK`.
 
 	d. Go to `Analyze` > `Analyze Particles` and set up the parameters as shown. Click `OK`.
-			<img src="/courses/fiji-omero/fiji-omero-setmeasurements.png" style="float:left;width:40%;height:auto">
-			<img src="/courses/fiji-omero/fiji-omero-analyzeparticles.png" style="width:50%;height:auto">
+			<img src="./fiji-omero-setmeasurements.png" style="float:left;width:40%;height:auto">
+			<img src="./fiji-omero-analyzeparticles.png" style="width:50%;height:auto">
 
     e. These steps should create a `Results` and a `Summary` table.
 

content/courses/fiji-image-processing/introduction/index.md

@@ -10,7 +10,7 @@ url_dataset: data/intro-fiji-images.zip
 
 {{< figure src="/img/fiji.png" >}}
 
-{{% link-button href="/data/intro-fiji-images.zip" icon="fa fa-download" %}}Data{{% /link-button %}}
+{{% link-button href="/data/intro-fiji-images.zip" icon="fa fa-download" aria-label="Download Data" title="Download Data" %}}Data{{% /link-button %}}
 
 ## Fiji Installation
 

content/courses/fiji-image-processing/scripting/index.md

@@ -9,7 +9,7 @@ url_code: /scripts/fiji/fiji-example-scripts.zip
 
 {{< figure library="true" src="fiji.png" >}}
 
-{{% link-button href="/scripts/fiji/fiji-example-scripts.zip" icon="fa fa-download" %}}Scripts{{% /link-button %}}
+{{% link-button href="/scripts/fiji/fiji-example-scripts.zip" icon="fa fa-download" title="Download Scripts" aria-label="Download Scripts" %}}Scripts{{% /link-button %}}
 
 This chapter is an introduction to the scripting interface of the [Fiji](https://fiji.sc) application, an open-source and enhanced version of the popular ImageJ program used for scientific image processing.  Here you will learn how to write scripts for automated execution of image processing pipelines and batch processing of multiple image files in Fiji.
 

content/landing/_index.md

@@ -5,9 +5,9 @@ subtitle = ""
 
 ## [Tutorials](/tutorials) are perfect for introducing yourself to a new topic.
 
-Some tutorials are offered as in-person and/or Zoom workshops regularly.  Find the notes or slides and download materials [here](/tutorials).
+Some tutorials are offered as in-person and/or Zoom workshops regularly.  Find the notes or slides and download materials [on the Tutorials page](/tutorials).
 
-For a list of upcoming workshops, please see our [page](https://www.rc.virginia.edu/education/workshops/) at the UVARC Website.
+For a list of upcoming workshops, please see [the Workshops page](https://www.rc.virginia.edu/education/workshops/) at the UVARC Website.
 
 ## [Short courses](/courses) are longer and more in-depth than tutorials or workshops.
 

content/notes/slurm-from-cli/_index.md

@@ -5,12 +5,13 @@ type: docs
 weight: 1
 menu: 
     slurm-from-cli:
+        name: The Slurm Resource Manager
 ---
 
-{{< figure src="/notes/slurm-from-cli/img/slurm_logo.png" width=30% >}}
+{{< figure src="/notes/slurm-from-cli/img/slurm_logo.png" width=30% alt="Slurm resource manager logo" >}}
 
 
-[Slurm](https://slurm.schedmd.com/) is a  __resource manager__ (RM), also known as a  _queueing system_.
+[Slurm](https://slurm.schedmd.com/ "The official Slurm website") is a  __resource manager__ (RM), also known as a  _queueing system_.
 
 Resource managers are used to submit _jobs_ on a computing cluster to compute nodes from an access point generally called a  login node.
 

content/notes/slurm-from-cli/section1.md

@@ -10,7 +10,7 @@ menu:
 
 ## Resources and Partitions
 
-An HPC **job** is a description of the resources required, any preparatory steps such as loading [modules](https://www.rc.virginia.edu/userinfo/rivanna/software/modules/) or otherwise setting up an environment, and the commands to run the software, along with any postprocessing that may be appropriate.
+An HPC **job** is a description of the resources required, any preparatory steps such as loading [modules](https://www.rc.virginia.edu/userinfo/rivanna/software/modules/ "The Research Computing website's modules page") or otherwise setting up an environment, and the commands to run the software, along with any postprocessing that may be appropriate.
 
 The job is specified through a special form of script often called a _batch script_.  Usually it is written in `bash`.
 
@@ -34,7 +34,7 @@ Slurm began when cpus had only one core each. Beginning around 2005, cpus began
 
 **Memory** refers to _random-access memory_.  It is not the same thing as storage.  If a process reports running out of memory, it means RAM memory. Running out of disk space will result in a different error.
 
-For more details about the structure of a computational cluster, see our [introduction](https://learning.rc.virginia.edu/notes/hpc-intro/).
+For more details about the structure of a computational cluster, see our [introduction](/notes/hpc-intro/ "Intro to High Performance Computing notes").
 ## Processes and Tasks
 
 A **process** can be envisioned an instance of an executable that is running on a particular computer.  Most executables run only a single process.  Some executables run _threads_ within the _root_ process.
@@ -44,7 +44,7 @@ Slurm refers to the root process as a **task**. By default, each task is assigne
 
 ## Slurm Resource Requests
 
-SLURM refers to queues as  __partitions__ .  We do not have a default partition; each job must request one explicitly.
+SLURM refers to queues as  __partitions__.  We do not have a default partition; each job must request one explicitly.
 
 {{< table >}}
 | Queue Name | Purpose | Job Time Limit | Max Memory / Node / Job | Max Cores / Node |