Merge pull request #38 from GMOD/update_dash

Upgrade dash and dash-browse dependencies
GMOD · Apr 8, 2022 · 4899962 · 4899962
2 parents b23dd28 + b690e5c
commit 4899962
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Showing 25 changed files with 89 additions and 74 deletions.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -51,6 +51,7 @@ $ python -m pytest tests/
 ```
 We use flake8 for linting. You can run 
 ```
+$ pip install flake8
 $ flake8 --count
 ```
 from the root of this repo to see any lint errors

diff --git a/README.md b/README.md
@@ -61,11 +61,10 @@ $ pip install jbrowse-jupyter
 ![Launching hg19 CGV in python notebook](https://github.com/GMOD/jbrowse-jupyter/raw/main/images/notebook2.png)
 *JBrowse Linear Genome view in python Dash application*
 ```python
-import dash
-import dash_html_components as html
+from dash import html, Dash
 from jbrowse_jupyter import create, create_component
 
-app = dash.Dash(__name__)
+app = Dash(__name__)
 
 jbrowse_conf = create("LGV", genome="hg38")
 

diff --git a/docs/docs/doctrees/contact.doctree b/docs/docs/doctrees/contact.doctree
diff --git a/docs/docs/doctrees/environment.pickle b/docs/docs/doctrees/environment.pickle
diff --git a/docs/docs/doctrees/index.doctree b/docs/docs/doctrees/index.doctree
diff --git a/docs/docs/doctrees/installation.doctree b/docs/docs/doctrees/installation.doctree
diff --git a/docs/docs/doctrees/jbrowse_jupyter.doctree b/docs/docs/doctrees/jbrowse_jupyter.doctree
diff --git a/docs/docs/doctrees/modules.doctree b/docs/docs/doctrees/modules.doctree
diff --git a/docs/docs/doctrees/quickstart.doctree b/docs/docs/doctrees/quickstart.doctree
diff --git a/docs/docs/doctrees/tutorial.doctree b/docs/docs/doctrees/tutorial.doctree
diff --git a/docs/docs/doctrees/util.doctree b/docs/docs/doctrees/util.doctree
diff --git a/docs/docs/html/.buildinfo b/docs/docs/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 43a7918517821381983e049c73d75535
+config: 0925fe609f33614d2923588cc7a96bc2
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/docs/html/_sources/quickstart.md.txt b/docs/docs/html/_sources/quickstart.md.txt
@@ -34,11 +34,10 @@ Using the package, we can create a Dash JBrowse LinearGenomeView  to embed in a
 3. Use `create_component` to create a Dash JBrowse Linear Genome View component. The example below uses dash and dash_html_components to create a python application.
 
 ```python
-import dash
-import dash_html_components as html
+from dash import html, Dash
 from jbrowse_jupyter import create, create_component
 
-app = dash.Dash(__name__)
+app = Dash(__name__)
 
 jbrowse_conf = create("LGV", genome="hg38")
 

diff --git a/docs/docs/html/_static/doctools.js b/docs/docs/html/_static/doctools.js
@@ -154,9 +154,7 @@ var Documentation = {
     this.fixFirefoxAnchorBug();
     this.highlightSearchWords();
     this.initIndexTable();
-    if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
-      this.initOnKeyListeners();
-    }
+    this.initOnKeyListeners();
   },
 
   /**
@@ -269,6 +267,13 @@ var Documentation = {
     window.history.replaceState({}, '', url);
   },
 
+   /**
+   * helper function to focus on search bar
+   */
+  focusSearchBar : function() {
+    $('input[name=q]').first().focus();
+  },
+
   /**
    * make the url absolute
    */
@@ -291,27 +296,54 @@ var Documentation = {
   },
 
   initOnKeyListeners: function() {
+    // only install a listener if it is really needed
+    if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS &&
+        !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS)
+        return;
+
     $(document).keydown(function(event) {
       var activeElementType = document.activeElement.tagName;
       // don't navigate when in search box, textarea, dropdown or button
       if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
-          && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey
-          && !event.shiftKey) {
-        switch (event.keyCode) {
-          case 37: // left
-            var prevHref = $('link[rel="prev"]').prop('href');
-            if (prevHref) {
-              window.location.href = prevHref;
-              return false;
-            }
-            break;
-          case 39: // right
-            var nextHref = $('link[rel="next"]').prop('href');
-            if (nextHref) {
-              window.location.href = nextHref;
-              return false;
-            }
-            break;
+          && activeElementType !== 'BUTTON') {
+        if (event.altKey || event.ctrlKey || event.metaKey)
+          return;
+
+          if (!event.shiftKey) {
+            switch (event.key) {
+              case 'ArrowLeft':
+                if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS)
+                  break;
+                var prevHref = $('link[rel="prev"]').prop('href');
+                if (prevHref) {
+                  window.location.href = prevHref;
+                  return false;
+                }
+                break;
+              case 'ArrowRight':
+                if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS)
+                  break;
+                var nextHref = $('link[rel="next"]').prop('href');
+                if (nextHref) {
+                  window.location.href = nextHref;
+                  return false;
+                }
+                break;
+              case 'Escape':
+                if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS)
+                  break;
+                Documentation.hideSearchWords();
+                return false;
+          }
+        }
+
+        // some keyboard layouts may need Shift to get /
+        switch (event.key) {
+          case '/':
+            if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS)
+              break;
+            Documentation.focusSearchBar();
+            return false;
         }
       }
     });

diff --git a/docs/docs/html/_static/documentation_options.js b/docs/docs/html/_static/documentation_options.js
@@ -1,12 +1,14 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.2.1',
+    VERSION: '1.2.2',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
     FILE_SUFFIX: '.html',
     LINK_SUFFIX: '.html',
     HAS_SOURCE: true,
     SOURCELINK_SUFFIX: '.txt',
-    NAVIGATION_WITH_KEYS: false
+    NAVIGATION_WITH_KEYS: false,
+    SHOW_SEARCH_SUMMARY: true,
+    ENABLE_SEARCH_SHORTCUTS: true,
 };
diff --git a/docs/docs/html/_static/searchtools.js b/docs/docs/html/_static/searchtools.js
@@ -172,10 +172,6 @@ var Search = {
       }
       // stem the word
       var word = stemmer.stemWord(tmp[i].toLowerCase());
-      // prevent stemmer from cutting word smaller than two chars
-      if(word.length < 3 && tmp[i].length >= 3) {
-        word = tmp[i];
-      }
       var toAppend;
       // select the correct list
       if (word[0] == '-') {
@@ -276,7 +272,7 @@ var Search = {
           setTimeout(function() {
             displayNextItem();
           }, 5);
-        } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+        } else if (DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY) {
           $.ajax({url: requestUrl,
                   dataType: "text",
                   complete: function(jqxhr, textstatus) {
@@ -293,7 +289,7 @@ var Search = {
                     }, 5);
                   }});
         } else {
-          // no source available, just display title
+          // just display title
           Search.output.append(listItem);
           setTimeout(function() {
             displayNextItem();

diff --git a/docs/docs/html/quickstart.html b/docs/docs/html/quickstart.html
@@ -110,11 +110,10 @@ <h2>Python Dash Application<a class="headerlink" href="#python-dash-application"
 </li>
 <li><p>Use <code class="docutils literal notranslate"><span class="pre">create_component</span></code> to create a Dash JBrowse Linear Genome View component. The example below uses dash and dash_html_components to create a python application.</p></li>
 </ol>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">dash</span>
-<span class="kn">import</span> <span class="nn">dash_html_components</span> <span class="k">as</span> <span class="nn">html</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">dash</span> <span class="kn">import</span> <span class="n">html</span><span class="p">,</span> <span class="n">Dash</span>
 <span class="kn">from</span> <span class="nn">jbrowse_jupyter</span> <span class="kn">import</span> <span class="n">create</span><span class="p">,</span> <span class="n">create_component</span>
 
-<span class="n">app</span> <span class="o">=</span> <span class="n">dash</span><span class="o">.</span><span class="n">Dash</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+<span class="n">app</span> <span class="o">=</span> <span class="n">Dash</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
 
 <span class="n">jbrowse_conf</span> <span class="o">=</span> <span class="n">create</span><span class="p">(</span><span class="s2">&quot;LGV&quot;</span><span class="p">,</span> <span class="n">genome</span><span class="o">=</span><span class="s2">&quot;hg38&quot;</span><span class="p">)</span>
 

diff --git a/docs/docs/html/searchindex.js b/docs/docs/html/searchindex.js
diff --git a/docs/docs/html/util.html b/docs/docs/html/util.html
@@ -80,19 +80,12 @@ <h1>Creating components<a class="headerlink" href="#creating-components" title="
 <dt class="sig sig-object py">
 <span class="sig-name descname"><span class="pre">create</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">view_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'LGV'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span></dt>
 <dd><p>Creates a JBrowseConfig given a view type.</p>
-<p>e.g
-create() -</p>
-<blockquote>
-<div><p>creates empty LGV JBrowseConfig</p>
-</div></blockquote>
-<dl class="simple">
-<dt>create(“CGV”) -</dt><dd><p>creates empty CGV JBrowseConfig</p>
-</dd>
-<dt>create(“LGV”, genome=”hg19”) -</dt><dd><p>creates LGV JBrowseConfig with hg19 default config</p>
-</dd>
-<dt>create(“CGV”, conf={“my”: “conf”}) -</dt><dd><p>creates CGV JBrowseConfig given a conf obj</p>
-</dd>
-</dl>
+<ul class="simple">
+<li><p>create(): creates empty LGV JBrowseConfig</p></li>
+<li><p>create(“CGV”):creates empty CGV JBrowseConfig</p></li>
+<li><p>create(“LGV”, genome=”hg19”):creates LGV JBrowseConfig w/ default genome</p></li>
+<li><p>create(“CGV”, conf={“k”: “v”}):creates CGV JBrowseConfig w/ a conf obj</p></li>
+</ul>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,7 +1,7 @@
-dash>=2.0
-dash-jbrowse>=0.0.2
-flake8>=4.0.1
-jupyter_dash>=0.4.0
+dash==2.3.0
+dash-jbrowse>=1.0.2
+jupyter_dash>=0.4.2
+Werkzeug==2.0.3
 pandas>=1.1.5
 pytest>=6.2.5
 Sphinx>=4.3.1

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -26,7 +26,7 @@
 author = 'Teresa De Jesus Martinez, JBrowse Team'
 
 # The full version, including alpha/beta/rc tags
-release = '1.2.1'
+release = '1.2.2'
 
 
 # -- General configuration ---------------------------------------------------