Fixed bug reading complicated Newick labels

niemasd · Jul 28, 2019 · 00004b1 · 00004b1
1 parent 4c5d7f7
commit 00004b1
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Showing 26 changed files with 922 additions and 1,611 deletions.
diff --git a/docs/.buildinfo b/docs/.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: aa3f3270dabdc76838123769ce828643
+config: 39554576fa41e4dbf8cbe9ad62a111f9
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -1,19 +1,19 @@
 
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
 
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
-    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta charset="utf-8" />
     <title>Overview: module code &#8212; TreeSwift  documentation</title>
     <link rel="stylesheet" href="../_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+
     <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
     <script type="text/javascript" src="../_static/jquery.js"></script>
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
-    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <script type="text/javascript" src="../_static/language_data.js"></script>
+
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
   </head><body>
@@ -46,13 +46,11 @@ <h1>All modules for which code is available</h1>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
 <div id="searchbox" style="display: none" role="search">
-  <h3>Quick search</h3>
+  <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../search.html" method="get">
-      <input type="text" name="q" />
+      <input type="text" name="q" aria-labelledby="searchlabel" />
       <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
     </form>
     </div>
 </div>
@@ -75,7 +73,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, Niema Moshiri.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.6.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 2.1.2.
     </div>
   </body>
 </html>
diff --git a/docs/_modules/treeswift/Node.html b/docs/_modules/treeswift/Node.html
@@ -1,19 +1,19 @@
 
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
 
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
-    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta charset="utf-8" />
     <title>treeswift.Node &#8212; TreeSwift  documentation</title>
     <link rel="stylesheet" href="../../_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+
     <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
     <script type="text/javascript" src="../../_static/jquery.js"></script>
     <script type="text/javascript" src="../../_static/underscore.js"></script>
     <script type="text/javascript" src="../../_static/doctools.js"></script>
-    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <script type="text/javascript" src="../../_static/language_data.js"></script>
+
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
   </head><body>
@@ -419,13 +419,11 @@ <h1>Source code for treeswift.Node</h1><div class="highlight"><pre>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
 <div id="searchbox" style="display: none" role="search">
-  <h3>Quick search</h3>
+  <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" />
+      <input type="text" name="q" aria-labelledby="searchlabel" />
       <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
     </form>
     </div>
 </div>
@@ -449,7 +447,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, Niema Moshiri.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.6.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 2.1.2.
     </div>
   </body>
 </html>
diff --git a/docs/_modules/treeswift/Tree.html b/docs/_modules/treeswift/Tree.html
@@ -1,19 +1,19 @@
 
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
 
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
-    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta charset="utf-8" />
     <title>treeswift.Tree &#8212; TreeSwift  documentation</title>
     <link rel="stylesheet" href="../../_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+
     <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
     <script type="text/javascript" src="../../_static/jquery.js"></script>
     <script type="text/javascript" src="../../_static/underscore.js"></script>
     <script type="text/javascript" src="../../_static/doctools.js"></script>
-    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <script type="text/javascript" src="../../_static/language_data.js"></script>
+
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
   </head><body>
@@ -50,6 +50,12 @@ <h1>Source code for treeswift.Tree</h1><div class="highlight"><pre>
 <span class="n">INVALID_NEXML</span> <span class="o">=</span> <span class="s2">&quot;Invalid valid NeXML File&quot;</span>
 <span class="n">EULER_GAMMA</span> <span class="o">=</span> <span class="mf">0.5772156649015328606065120900824024310421</span>
 
+<span class="c1"># store bracket open/close for convenience in label parsing</span>
+<span class="n">BRACKET</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;[&#39;</span><span class="p">:</span> <span class="s1">&#39;]&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;{&#39;</span><span class="p">:</span> <span class="s1">&#39;}&#39;</span><span class="p">,</span>
+<span class="p">}</span>
+
 <div class="viewcode-block" id="Tree"><a class="viewcode-back" href="../../index.html#treeswift.Tree">[docs]</a><span class="k">class</span> <span class="nc">Tree</span><span class="p">:</span>
     <span class="sd">&#39;&#39;&#39;``Tree`` class&#39;&#39;&#39;</span>
     <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">is_rooted</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
@@ -1305,8 +1311,12 @@ <h1>Source code for treeswift.Tree</h1><div class="highlight"><pre>
                     <span class="n">ls</span> <span class="o">+=</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">];</span> <span class="n">i</span> <span class="o">+=</span> <span class="mi">1</span>
                 <span class="n">n</span><span class="o">.</span><span class="n">edge_length</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">ls</span><span class="p">);</span> <span class="n">i</span> <span class="o">-=</span> <span class="mi">1</span>
             <span class="k">else</span><span class="p">:</span>
-                <span class="n">label</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
-                <span class="k">while</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;:&#39;</span> <span class="ow">and</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;,&#39;</span> <span class="ow">and</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;;&#39;</span> <span class="ow">and</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;)&#39;</span><span class="p">:</span>
+                <span class="n">label</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span><span class="p">;</span> <span class="n">bracket</span> <span class="o">=</span> <span class="kc">None</span>
+                <span class="k">while</span> <span class="n">bracket</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="ow">in</span> <span class="n">BRACKET</span> <span class="ow">or</span> <span class="p">(</span><span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;:&#39;</span> <span class="ow">and</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;,&#39;</span> <span class="ow">and</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;;&#39;</span> <span class="ow">and</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;)&#39;</span><span class="p">):</span>
+                    <span class="k">if</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="ow">in</span> <span class="n">BRACKET</span> <span class="ow">and</span> <span class="n">bracket</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                        <span class="n">bracket</span> <span class="o">=</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+                    <span class="k">elif</span> <span class="n">bracket</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">==</span> <span class="n">BRACKET</span><span class="p">[</span><span class="n">bracket</span><span class="p">]:</span>
+                        <span class="n">bracket</span> <span class="o">=</span> <span class="kc">None</span>
                     <span class="n">label</span> <span class="o">+=</span> <span class="n">ts</span><span class="p">[</span><span class="n">i</span><span class="p">];</span> <span class="n">i</span> <span class="o">+=</span> <span class="mi">1</span>
                 <span class="n">i</span> <span class="o">-=</span> <span class="mi">1</span><span class="p">;</span> <span class="n">n</span><span class="o">.</span><span class="n">label</span> <span class="o">=</span> <span class="n">label</span>
             <span class="n">i</span> <span class="o">+=</span> <span class="mi">1</span>
@@ -1492,13 +1502,11 @@ <h1>Source code for treeswift.Tree</h1><div class="highlight"><pre>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
 <div id="searchbox" style="display: none" role="search">
-  <h3>Quick search</h3>
+  <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" />
+      <input type="text" name="q" aria-labelledby="searchlabel" />
       <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
     </form>
     </div>
 </div>
@@ -1522,7 +1530,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, Niema Moshiri.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.6.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 2.1.2.
     </div>
   </body>
 </html>
diff --git a/docs/_static/ajax-loader.gif b/docs/_static/ajax-loader.gif
diff --git a/docs/_static/basic.css b/docs/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -81,6 +81,10 @@ div.sphinxsidebar input {
     font-size: 1em;
 }
 
+div.sphinxsidebar #searchbox form.search {
+    overflow: hidden;
+}
+
 div.sphinxsidebar #searchbox input[type="text"] {
     float: left;
     width: 80%;
@@ -227,6 +231,16 @@ a.headerlink {
     visibility: hidden;
 }
 
+a.brackets:before,
+span.brackets > a:before{
+    content: "[";
+}
+
+a.brackets:after,
+span.brackets > a:after {
+    content: "]";
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -275,6 +289,12 @@ img.align-center, .figure.align-center, object.align-center {
   margin-right: auto;
 }
 
+img.align-default, .figure.align-default {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
+
 .align-left {
     text-align: left;
 }
@@ -283,6 +303,10 @@ img.align-center, .figure.align-center, object.align-center {
     text-align: center;
 }
 
+.align-default {
+    text-align: center;
+}
+
 .align-right {
     text-align: right;
 }
@@ -354,6 +378,11 @@ table.align-center {
     margin-right: auto;
 }
 
+table.align-default {
+    margin-left: auto;
+    margin-right: auto;
+}
+
 table caption span.caption-number {
     font-style: italic;
 }
@@ -387,6 +416,16 @@ table.citation td {
     border-bottom: none;
 }
 
+th > p:first-child,
+td > p:first-child {
+    margin-top: 0px;
+}
+
+th > p:last-child,
+td > p:last-child {
+    margin-bottom: 0px;
+}
+
 /* -- figures --------------------------------------------------------------- */
 
 div.figure {
@@ -427,6 +466,13 @@ table.field-list td, table.field-list th {
     hyphens: manual;
 }
 
+/* -- hlist styles ---------------------------------------------------------- */
+
+table.hlist td {
+    vertical-align: top;
+}
+
+
 /* -- other body styles ----------------------------------------------------- */
 
 ol.arabic {
@@ -449,11 +495,57 @@ ol.upperroman {
     list-style: upper-roman;
 }
 
+li > p:first-child {
+    margin-top: 0px;
+}
+
+li > p:last-child {
+    margin-bottom: 0px;
+}
+
+dl.footnote > dt,
+dl.citation > dt {
+    float: left;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+    margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+    content: "";
+    clear: both;
+}
+
+dl.field-list {
+    display: flex;
+    flex-wrap: wrap;
+}
+
+dl.field-list > dt {
+    flex-basis: 20%;
+    font-weight: bold;
+    word-break: break-word;
+}
+
+dl.field-list > dt:after {
+    content: ":";
+}
+
+dl.field-list > dd {
+    flex-basis: 70%;
+    padding-left: 1em;
+    margin-left: 0em;
+    margin-bottom: 0em;
+}
+
 dl {
     margin-bottom: 15px;
 }
 
-dd p {
+dd > p:first-child {
     margin-top: 0px;
 }
 
@@ -526,6 +618,12 @@ dl.glossary dt {
     font-style: oblique;
 }
 
+.classifier:before {
+    font-style: normal;
+    margin: 0.5em;
+    content: ":";
+}
+
 abbr, acronym {
     border-bottom: dotted 1px;
     cursor: help;

diff --git a/docs/_static/classic.css b/docs/_static/classic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- classic theme.
  *
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/docs/_static/comment-bright.png b/docs/_static/comment-bright.png
diff --git a/docs/_static/comment-close.png b/docs/_static/comment-close.png
diff --git a/docs/_static/comment.png b/docs/_static/comment.png