Merge pull request #24 from AnthonyChristidis/main

Fix package dependencies, also add css file.
ccb-hms · Mar 14, 2024 · 48e8927 · 48e8927
2 parents 081d2fb + 5db43f4
commit 48e8927
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -16,7 +16,7 @@ Encoding: UTF-8
 LazyData: true
 URL: https://github.com/ccb-hms/scDiagnostics
 BugReports: https://github.com/ccb-hms/scDiagnostics/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends:
  R (>= 4.2.0),
  SingleCellExperiment,
@@ -33,7 +33,8 @@ Suggests:
     scater,
     gridExtra,
     ggplot2,
-    SummarizedExperiment
+    SummarizedExperiment,
+    BiocStyle
 VignetteBuilder: knitr
 Imports:
     isotree
diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css
@@ -0,0 +1,60 @@
+/*!
+ * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
+ * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
+
+/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */
+
+/* All levels of nav */
+nav[data-toggle='toc'] .nav > li > a {
+  display: block;
+  padding: 4px 20px;
+  font-size: 13px;
+  font-weight: 500;
+  color: #767676;
+}
+nav[data-toggle='toc'] .nav > li > a:hover,
+nav[data-toggle='toc'] .nav > li > a:focus {
+  padding-left: 19px;
+  color: #563d7c;
+  text-decoration: none;
+  background-color: transparent;
+  border-left: 1px solid #563d7c;
+}
+nav[data-toggle='toc'] .nav > .active > a,
+nav[data-toggle='toc'] .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav > .active:focus > a {
+  padding-left: 18px;
+  font-weight: bold;
+  color: #563d7c;
+  background-color: transparent;
+  border-left: 2px solid #563d7c;
+}
+
+/* Nav: second level (shown on .active) */
+nav[data-toggle='toc'] .nav .nav {
+  display: none; /* Hide by default, but at >768px, show it */
+  padding-bottom: 10px;
+}
+nav[data-toggle='toc'] .nav .nav > li > a {
+  padding-top: 1px;
+  padding-bottom: 1px;
+  padding-left: 30px;
+  font-size: 12px;
+  font-weight: normal;
+}
+nav[data-toggle='toc'] .nav .nav > li > a:hover,
+nav[data-toggle='toc'] .nav .nav > li > a:focus {
+  padding-left: 29px;
+}
+nav[data-toggle='toc'] .nav .nav > .active > a,
+nav[data-toggle='toc'] .nav .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav .nav > .active:focus > a {
+  padding-left: 28px;
+  font-weight: 500;
+}
+
+/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */
+nav[data-toggle='toc'] .nav > .active > ul {
+  display: block;
+}
diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js
@@ -0,0 +1,159 @@
+/*!
+ * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
+ * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
+(function() {
+  'use strict';
+
+  window.Toc = {
+    helpers: {
+      // return all matching elements in the set, or their descendants
+      findOrFilter: function($el, selector) {
+        // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/
+        // http://stackoverflow.com/a/12731439/358804
+        var $descendants = $el.find(selector);
+        return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])');
+      },
+
+      generateUniqueIdBase: function(el) {
+        var text = $(el).text();
+        var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-');
+        return anchor || el.tagName.toLowerCase();
+      },
+
+      generateUniqueId: function(el) {
+        var anchorBase = this.generateUniqueIdBase(el);
+        for (var i = 0; ; i++) {
+          var anchor = anchorBase;
+          if (i > 0) {
+            // add suffix
+            anchor += '-' + i;
+          }
+          // check if ID already exists
+          if (!document.getElementById(anchor)) {
+            return anchor;
+          }
+        }
+      },
+
+      generateAnchor: function(el) {
+        if (el.id) {
+          return el.id;
+        } else {
+          var anchor = this.generateUniqueId(el);
+          el.id = anchor;
+          return anchor;
+        }
+      },
+
+      createNavList: function() {
+        return $('<ul class="nav"></ul>');
+      },
+
+      createChildNavList: function($parent) {
+        var $childList = this.createNavList();
+        $parent.append($childList);
+        return $childList;
+      },
+
+      generateNavEl: function(anchor, text) {
+        var $a = $('<a></a>');
+        $a.attr('href', '#' + anchor);
+        $a.text(text);
+        var $li = $('<li></li>');
+        $li.append($a);
+        return $li;
+      },
+
+      generateNavItem: function(headingEl) {
+        var anchor = this.generateAnchor(headingEl);
+        var $heading = $(headingEl);
+        var text = $heading.data('toc-text') || $heading.text();
+        return this.generateNavEl(anchor, text);
+      },
+
+      // Find the first heading level (`<h1>`, then `<h2>`, etc.) that has more than one element. Defaults to 1 (for `<h1>`).
+      getTopLevel: function($scope) {
+        for (var i = 1; i <= 6; i++) {
+          var $headings = this.findOrFilter($scope, 'h' + i);
+          if ($headings.length > 1) {
+            return i;
+          }
+        }
+
+        return 1;
+      },
+
+      // returns the elements for the top level, and the next below it
+      getHeadings: function($scope, topLevel) {
+        var topSelector = 'h' + topLevel;
+
+        var secondaryLevel = topLevel + 1;
+        var secondarySelector = 'h' + secondaryLevel;
+
+        return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
+      },
+
+      getNavLevel: function(el) {
+        return parseInt(el.tagName.charAt(1), 10);
+      },
+
+      populateNav: function($topContext, topLevel, $headings) {
+        var $context = $topContext;
+        var $prevNav;
+
+        var helpers = this;
+        $headings.each(function(i, el) {
+          var $newNav = helpers.generateNavItem(el);
+          var navLevel = helpers.getNavLevel(el);
+
+          // determine the proper $context
+          if (navLevel === topLevel) {
+            // use top level
+            $context = $topContext;
+          } else if ($prevNav && $context === $topContext) {
+            // create a new level of the tree and switch to it
+            $context = helpers.createChildNavList($prevNav);
+          } // else use the current $context
+
+          $context.append($newNav);
+
+          $prevNav = $newNav;
+        });
+      },
+
+      parseOps: function(arg) {
+        var opts;
+        if (arg.jquery) {
+          opts = {
+            $nav: arg
+          };
+        } else {
+          opts = arg;
+        }
+        opts.$scope = opts.$scope || $(document.body);
+        return opts;
+      }
+    },
+
+    // accepts a jQuery object, or an options object
+    init: function(opts) {
+      opts = this.helpers.parseOps(opts);
+
+      // ensure that the data attribute is in place for styling
+      opts.$nav.attr('data-toggle', 'toc');
+
+      var $topContext = this.helpers.createChildNavList(opts.$nav);
+      var topLevel = this.helpers.getTopLevel(opts.$scope);
+      var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
+      this.helpers.populateNav($topContext, topLevel, $headings);
+    }
+  };
+
+  $(function() {
+    $('nav[data-toggle="toc"]').each(function(i, el) {
+      var $nav = $(el);
+      Toc.init($nav);
+    });
+  });
+})();
diff --git a/docs/docsearch.css b/docs/docsearch.css
@@ -0,0 +1,148 @@
+/* Docsearch -------------------------------------------------------------- */
+/*
+  Source: https://github.com/algolia/docsearch/
+  License: MIT
+*/
+
+.algolia-autocomplete {
+  display: block;
+  -webkit-box-flex: 1;
+  -ms-flex: 1;
+  flex: 1
+}
+
+.algolia-autocomplete .ds-dropdown-menu {
+  width: 100%;
+  min-width: none;
+  max-width: none;
+  padding: .75rem 0;
+  background-color: #fff;
+  background-clip: padding-box;
+  border: 1px solid rgba(0, 0, 0, .1);
+  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+}
+
+@media (min-width:768px) {
+  .algolia-autocomplete .ds-dropdown-menu {
+      width: 175%
+  }
+}
+
+.algolia-autocomplete .ds-dropdown-menu::before {
+  display: none
+}
+
+.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+  padding: 0;
+  background-color: rgb(255,255,255);
+  border: 0;
+  max-height: 80vh;
+}
+
+.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
+  margin-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion {
+  padding: 0;
+  overflow: visible
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
+  padding: .125rem 1rem;
+  margin-top: 0;
+  font-size: 1.3em;
+  font-weight: 500;
+  color: #00008B;
+  border-bottom: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
+    float: none;
+    padding-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
+  float: none;
+  width: auto;
+  padding: 0;
+  text-align: left
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content {
+  float: none;
+  width: auto;
+  padding: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content::before {
+  display: none
+}
+
+.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
+  padding-top: .75rem;
+  margin-top: .75rem;
+  border-top: 1px solid rgba(0, 0, 0, .1)
+}
+
+.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+  display: block;
+  padding: .1rem 1rem;
+  margin-bottom: 0.1;
+  font-size: 1.0em;
+  font-weight: 400
+  /* display: none */
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--title {
+  display: block;
+  padding: .25rem 1rem;
+  margin-bottom: 0;
+  font-size: 0.9em;
+  font-weight: 400
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text {
+  padding: 0 1rem .5rem;
+  margin-top: -.25rem;
+  font-size: 0.8em;
+  font-weight: 400;
+  line-height: 1.25
+}
+
+.algolia-autocomplete .algolia-docsearch-footer {
+  width: 110px;
+  height: 20px;
+  z-index: 3;
+  margin-top: 10.66667px;
+  float: right;
+  font-size: 0;
+  line-height: 0;
+}
+
+.algolia-autocomplete .algolia-docsearch-footer--logo {
+  background-image: url("data:image/svg+xml;utf8,<svg viewBox='0 0 130 18' xmlns='http://www.w3.org/2000/svg'><defs><linearGradient x1='-36.868%' y1='134.936%' x2='129.432%' y2='-27.7%' id='a'><stop stop-color='%2300AEFF' offset='0%'/><stop stop-color='%233369E7' offset='100%'/></linearGradient></defs><g fill='none' fill-rule='evenodd'><path d='M59.399.022h13.299a2.372 2.372 0 0 1 2.377 2.364V15.62a2.372 2.372 0 0 1-2.377 2.364H59.399a2.372 2.372 0 0 1-2.377-2.364V2.381A2.368 2.368 0 0 1 59.399.022z' fill='url(%23a)'/><path d='M66.257 4.56c-2.815 0-5.1 2.272-5.1 5.078 0 2.806 2.284 5.072 5.1 5.072 2.815 0 5.1-2.272 5.1-5.078 0-2.806-2.279-5.072-5.1-5.072zm0 8.652c-1.983 0-3.593-1.602-3.593-3.574 0-1.972 1.61-3.574 3.593-3.574 1.983 0 3.593 1.602 3.593 3.574a3.582 3.582 0 0 1-3.593 3.574zm0-6.418v2.664c0 .076.082.131.153.093l2.377-1.226c.055-.027.071-.093.044-.147a2.96 2.96 0 0 0-2.465-1.487c-.055 0-.11.044-.11.104l.001-.001zm-3.33-1.956l-.312-.311a.783.783 0 0 0-1.106 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