deploy: 22c5e89

Author: jordibc

_modules/ete4/smartview/explorer.html

@@ -370,6 +370,7 @@ <h1>Source code for ete4.smartview.explorer</h1><div class="highlight"><pre>
     <span class="n">response</span><span class="o">.</span><span class="n">status</span> <span class="o">=</span> <span class="mi">201</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="s1">&#39;ids&#39;</span><span class="p">:</span> <span class="n">ids</span><span class="p">}</span>
 
+<span class="c1"># TODO: Remove from here and add it as an example of how to use the explorer.</span>
 <span class="nd">@post</span><span class="p">(</span><span class="s1">&#39;/load&#39;</span><span class="p">)</span>
 <span class="k">def</span><span class="w"> </span><span class="nf">callback</span><span class="p">():</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Load a tree from a given path.&quot;&quot;&quot;</span>

reference/reference_operations.html

@@ -115,8 +115,11 @@
 
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.core.operations.closest_relative">
-<span class="sig-name descname"><span class="pre">closest_relative</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">leaf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selector</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_leaf_fn</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">topological</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.closest_relative" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">closest_relative</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">leaf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selector</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_leaf_fn</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">topological</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.closest_relative" title="Link to this definition">¶</a></dt>
 <dd><p>Return the closest relative leaf to the given leaf.</p>
+<p>Note that “relative” is a topological term. If you use
+topological=False, the “relative” will be the one with the
+shortest distance.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
@@ -125,8 +128,8 @@
 If None, all leaves will be selected.</p></li>
 <li><p><strong>is_leaf_fn</strong> – Function that takes a node and returns True if it is
 considered a leaf. If None, node.is_leaf is used.</p></li>
-<li><p><strong>topological</strong> – If True, the distance between nodes will be the
-number of nodes between them (instead of the sum of branch lenghts).</p></li>
+<li><p><strong>topological</strong> – If False, the distance between nodes will be the sum
+of the branch distances between them (instead of the number of steps).</p></li>
 </ul>
 </dd>
 </dl>

reference/reference_tree.html

@@ -151,8 +151,11 @@
 
 <dl class="py method">
 <dt class="sig sig-object py" id="ete4.core.tree.Tree.closest_relative">
-<span class="sig-name descname"><span class="pre">closest_relative</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">leaf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selector</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_leaf_fn</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">topological</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.tree.Tree.closest_relative" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">closest_relative</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">leaf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selector</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_leaf_fn</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">topological</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.tree.Tree.closest_relative" title="Link to this definition">¶</a></dt>
 <dd><p>Return the closest relative leaf to the given leaf.</p>
+<p>Note that “relative” is a topological term. If you use
+topological=False, the “relative” will be the one with the
+shortest distance.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
@@ -161,8 +164,8 @@
 If None, all leaves will be selected.</p></li>
 <li><p><strong>is_leaf_fn</strong> – Function that takes a node and returns True if it is
 considered a leaf. If None, node.is_leaf is used.</p></li>
-<li><p><strong>topological</strong> – If True, the distance between nodes will be the
-number of nodes between them (instead of the sum of branch lenghts).</p></li>
+<li><p><strong>topological</strong> – If False, the distance between nodes will be the sum
+of the branch distances between them (instead of the number of steps).</p></li>
 </ul>
 </dd>
 </dl>