deploy: 887993b

Author: jordibc

_modules/ete4/smartview/explorer.html

@@ -331,7 +331,8 @@ <h1>Source code for ete4.smartview.explorer</h1><div class="highlight"><pre>
         <span class="n">t</span> <span class="o">=</span> <span class="n">load_tree</span><span class="p">(</span><span class="n">tree_id</span><span class="p">)</span>
         <span class="n">node_id</span><span class="p">,</span> <span class="n">content</span> <span class="o">=</span> <span class="n">req_json</span><span class="p">()</span>
         <span class="n">node</span> <span class="o">=</span> <span class="n">t</span><span class="p">[</span><span class="n">node_id</span><span class="p">]</span>
-        <span class="n">node</span><span class="o">.</span><span class="n">props</span> <span class="o">=</span> <span class="n">newick</span><span class="o">.</span><span class="n">get_props</span><span class="p">(</span><span class="n">content</span><span class="p">,</span> <span class="n">is_leaf</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="n">node</span><span class="o">.</span><span class="n">props</span> <span class="o">=</span> <span class="n">newick</span><span class="o">.</span><span class="n">read_props</span><span class="p">(</span><span class="n">content</span><span class="o">+</span><span class="s1">&#39;;&#39;</span><span class="p">,</span> <span class="n">pos</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">is_leaf</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+                                       <span class="n">parser</span><span class="o">=</span><span class="n">newick</span><span class="o">.</span><span class="n">PARSER_DEFAULT</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
         <span class="n">ops</span><span class="o">.</span><span class="n">update_sizes_all</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
         <span class="k">return</span> <span class="p">{</span><span class="s1">&#39;message&#39;</span><span class="p">:</span> <span class="s1">&#39;ok&#39;</span><span class="p">}</span>
     <span class="k">except</span> <span class="p">(</span><span class="ne">AssertionError</span><span class="p">,</span> <span class="n">newick</span><span class="o">.</span><span class="n">NewickError</span><span class="p">)</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
@@ -794,6 +795,8 @@ <h1>Source code for ete4.smartview.explorer</h1><div class="highlight"><pre>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Add tree, layouts, etc to the global variables, and return its name.&quot;&quot;&quot;</span>
     <span class="n">name</span> <span class="o">=</span> <span class="n">name</span> <span class="ow">or</span> <span class="n">make_name</span><span class="p">()</span>  <span class="c1"># in case we didn&#39;t receive one</span>
 
+    <span class="k">assert</span> <span class="s1">&#39;,&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">name</span><span class="p">,</span> <span class="s1">&#39;name cannot have &quot;,&quot;&#39;</span>  <span class="c1"># we use it for subtrees</span>
+
     <span class="n">ops</span><span class="o">.</span><span class="n">update_sizes_all</span><span class="p">(</span><span class="n">tree</span><span class="p">)</span>  <span class="c1"># update all internal sizes (ready to draw!)</span>
 
     <span class="n">g_trees</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">tree</span>  <span class="c1"># add tree to the global dict of trees</span>

reference/reference_parsers.html

@@ -215,7 +215,7 @@ <h1>Parsers<a class="headerlink" href="#parsers" title="Link to this heading">¶
 
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.parser.newick.read_props">
-<span class="sig-name descname"><span class="pre">read_props</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">unicode</span> <span class="pre">text</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long</span> <span class="pre">pos</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_leaf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dict</span> <span class="pre">parser</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_req</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.parser.newick.read_props" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">read_props</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">unicode</span> <span class="pre">text</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long</span> <span class="pre">pos</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_leaf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dict</span> <span class="pre">parser</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_req=False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.parser.newick.read_props" title="Link to this definition">¶</a></dt>
 <dd><p>Return the properties from the content of a node, and where it ends.</p>
 <dl class="simple">
 <dt>Example (for the default format of a leaf node):</dt><dd><p>‘abc:123[&amp;&amp;NHX:x=foo]’  -&gt;  {‘name’: ‘abc’, ‘dist’: 123, ‘x’: ‘foo’}</p>