Merge pull request #27 from SlavovLab/stable

Restoring deleted files

.github/ISSUE_TEMPLATE/bug_report-ORHUN.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

docs/_config.yml

@@ -26,12 +26,14 @@ search_enabled: true
 
 # Aux links for the upper right navigation
 aux_links:
-  "JPR Articles":
+  "DO-MS Articles":
     - "https://do-ms.slavovlab.net/#research-articles"
   "GitHub Repository":
     - "https://github.com/SlavovLab/DO-MS"
   "Slavov Lab":
-    - "http://slavovlab.net"
+    - "https://slavovlab.net"
+  "SCP Hub":
+    - "https://scp.slavovlab.net"
 
 github_link: https://github.com/SlavovLab/DO-MS
 preprint_link: https://www.biorxiv.org/content/10.1101/2023.02.02.526809v1

docs/_layouts/default.html

@@ -12,7 +12,7 @@
         {% include nav.html %}
       </div>
       <footer role="contentinfo" class="site-footer">
-        <p class="text-small text-grey-dk-000 mb-0">This site uses <a href="https://github.com/pmarsceill/just-the-docs">Just the Docs</a>, a documentation theme for Jekyll.</p>
+        <p class="text-small text-grey-dk-000 mb-0">Resources from the <a href="https://slavovlab.net">Slavov Lab</a></p>
       </footer>
     </div>
     <div class="main-content-wrap js-main-content" tabindex="0">

docs/assets/js/just-the-docs.js

@@ -0,0 +1,176 @@
+// Event handling
+
+function addEvent(el, type, handler) {
+    if (el.attachEvent) el.attachEvent('on'+type, handler); else el.addEventListener(type, handler);
+}
+function removeEvent(el, type, handler) {
+    if (el.detachEvent) el.detachEvent('on'+type, handler); else el.removeEventListener(type, handler);
+}
+
+// Show/hide mobile menu
+
+function toggleNav(){
+  const nav = document.querySelector('.js-main-nav');
+  const auxNav = document.querySelector('.js-aux-nav');
+  const navTrigger = document.querySelector('.js-main-nav-trigger');
+  const search = document.querySelector('.js-search');
+
+  addEvent(navTrigger, 'click', function(){
+    var text = navTrigger.innerText;
+    var textToggle = navTrigger.getAttribute('data-text-toggle');
+
+    nav.classList.toggle('nav-open');
+    auxNav.classList.toggle('nav-open');
+    navTrigger.classList.toggle('nav-open');
+    search.classList.toggle('nav-open');
+    navTrigger.innerText = textToggle;
+    navTrigger.setAttribute('data-text-toggle', text);
+    textToggle = text;
+  })
+}
+
+// Site search
+
+function initSearch() {
+  var index = lunr(function () {
+    this.ref('id');
+    this.field('title', { boost: 20 });
+    this.field('content', { boost: 10 });
+    this.field('url');
+  });
+
+  // Get the generated search_data.json file so lunr.js can search it locally.
+
+  sc = document.getElementsByTagName("script");
+  source = '';
+
+  for(idx = 0; idx < sc.length; idx++)
+  {
+    s = sc.item(idx);
+
+    if(s.src && s.src.match(/just-the-docs\.js$/))
+    { source = s.src; }
+  }
+
+  jsPath = source.replace('just-the-docs.js', '');
+
+  jsonPath = jsPath + 'search-data.json';
+
+  var request = new XMLHttpRequest();
+  request.open('GET', jsonPath, true);
+
+  request.onload = function() {
+    if (request.status >= 200 && request.status < 400) {
+      // Success!
+      var data = JSON.parse(request.responseText);
+      var keys = Object.keys(data);
+
+      for(var i in data) {
+        index.add({
+          id: data[i].id,
+          title: data[i].title,
+          content: data[i].content,
+          url: data[i].url
+        });
+      }
+      searchResults(data);
+    } else {
+      // We reached our target server, but it returned an error
+      console.log('Error loading ajax request. Request status:' + request.status);
+    }
+  };
+
+  request.onerror = function() {
+    // There was a connection error of some sort
+    console.log('There was a connection error');
+  };
+
+  request.send();
+
+  function searchResults(dataStore) {
+    var searchInput = document.querySelector('.js-search-input');
+    var searchResults = document.querySelector('.js-search-results');
+    var store = dataStore;
+
+    function hideResults() {
+      searchResults.innerHTML = '';
+      searchResults.classList.remove('active');
+    }
+
+    addEvent(searchInput, 'keyup', function(e){
+      var query = this.value;
+
+      searchResults.innerHTML = '';
+      searchResults.classList.remove('active');
+
+      if (query === '') {
+        hideResults();
+      } else {
+        var results = index.search(query);
+
+        if (results.length > 0) {
+          searchResults.classList.add('active');
+          var resultsList = document.createElement('ul');
+          searchResults.appendChild(resultsList);
+
+          for (var i in results) {
+            var resultsListItem = document.createElement('li');
+            var resultsLink = document.createElement('a');
+            var resultsUrlDesc = document.createElement('span');
+            var resultsUrl = store[results[i].ref].url;
+            var resultsRelUrl = store[results[i].ref].relUrl;
+            var resultsTitle = store[results[i].ref].title;
+
+            resultsLink.setAttribute('href', resultsUrl);
+            resultsLink.innerText = resultsTitle;
+            resultsUrlDesc.innerText = resultsRelUrl;
+
+            resultsList.classList.add('search-results-list');
+            resultsListItem.classList.add('search-results-list-item');
+            resultsLink.classList.add('search-results-link');
+            resultsUrlDesc.classList.add('fs-2','text-grey-dk-000','d-block');
+
+            resultsList.appendChild(resultsListItem);
+            resultsListItem.appendChild(resultsLink);
+            resultsLink.appendChild(resultsUrlDesc);
+          }
+        }
+
+        // When esc key is pressed, hide the results and clear the field
+        if (e.keyCode == 27) {
+          hideResults();
+          searchInput.value = '';
+        }
+      }
+    });
+
+    addEvent(searchInput, 'blur', function(){
+      setTimeout(function(){ hideResults() }, 300);
+    });
+  }
+}
+
+function pageFocus() {
+  var mainContent = document.querySelector('.js-main-content');
+  mainContent.focus();
+}
+
+
+// Document ready
+
+function ready(){
+  toggleNav();
+  pageFocus();
+  if (typeof lunr !== 'undefined') {
+    initSearch();
+  }
+}
+
+// in case the document is already rendered
+if (document.readyState!='loading') ready();
+// modern browsers
+else if (document.addEventListener) document.addEventListener('DOMContentLoaded', ready);
+// IE <= 8
+else document.attachEvent('onreadystatechange', function(){
+    if (document.readyState=='complete') ready();
+});

docs/assets/js/search-data.json

@@ -0,0 +1,12 @@
+---
+---
+{
+  {% for page in site.html_pages %}{% if page.search_exclude != true %}"{{ forloop.index0 }}": {
+    "id": "{{ forloop.index0 }}",
+    "title": "{{ page.title | replace: '&', '&' }}",
+    "content": "{{ page.content | markdownify | strip_html | escape_once | remove: 'Table of contents' | remove: '```'  | remove: '---' | replace: '\', ' ' | normalize_whitespace }}",
+    "url": "{{ page.url | absolute_url }}",
+    "relUrl": "{{ page.url }}"
+  }{% unless forloop.last %},{% endunless %}
+  {% endif %}{% endfor %}
+}

docs/assets/js/vendor/MathJax.js

@@ -0,0 +1,53 @@
+(function () {
+    var newMathJax = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js';
+    var oldMathJax = 'cdn.mathjax.org/mathjax/latest/MathJax.js';
+
+    var replaceScript = function (script, src) {
+      //
+      //  Make redirected script
+      //
+      var newScript = document.createElement('script');
+      newScript.src = newMathJax + src.replace(/.*?(\?|$)/, '$1');
+      //
+      //  Move onload and onerror handlers to new script
+      //
+      newScript.onload = script.onload; 
+      newScript.onerror = script.onerror;
+      script.onload = script.onerror = null;
+      //
+      //  Move any content (old-style configuration scripts)
+      //
+      while (script.firstChild) newScript.appendChild(script.firstChild);
+      //
+      //  Copy script id
+      //
+      if (script.id != null) newScript.id = script.id;
+      //
+      //  Replace original script with new one
+      //
+      script.parentNode.replaceChild(newScript, script);
+      //
+      //  Issue a console warning
+      //
+      console.warn('WARNING: cdn.mathjax.org has been retired. Check https://www.mathjax.org/cdn-shutting-down/ for migration tips.')
+    }
+
+    if (document.currentScript) {
+      var script = document.currentScript;
+      replaceScript(script, script.src);
+    } else {
+      //
+      // Look for current script by searching for one with the right source
+      //
+      var n = oldMathJax.length;
+      var scripts = document.getElementsByTagName('script');
+      for (var i = 0; i < scripts.length; i++) {
+        var script = scripts[i];
+        var src = (script.src || '').replace(/.*?:\/\//,'');
+        if (src.substr(0, n) === oldMathJax) {
+          replaceScript(script, src);
+          break;
+        }
+      }
+    }
+  })();