Update documentation

_sources/full_ref.rst.txt

@@ -27,33 +27,6 @@ Chain
     :show-inheritance:
     :noindex:
 
-Grid
-----
-
-.. automodule:: gerrychain.grid
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :noindex:
-
-Metagraph
----------
-
-.. automodule:: gerrychain.metagraph
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :noindex:
-
-Tree
-----
-
-.. automodule:: gerrychain.tree
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :noindex:
-
 Constraints
 -----------
 
@@ -81,6 +54,7 @@ Constraints
     :show-inheritance:
     :noindex:
 
+
 Graph
 -----
 
@@ -102,6 +76,15 @@ Graph
     :show-inheritance:
     :noindex:
 
+Grid
+----
+
+.. automodule:: gerrychain.grid
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
 Meta
 ----
 
@@ -111,6 +94,15 @@ Meta
     :show-inheritance:
     :noindex:
 
+Metagraph
+---------
+
+.. automodule:: gerrychain.metagraph
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
 Metrics
 -------
 
@@ -126,6 +118,22 @@ Metrics
     :show-inheritance:
     :noindex:
 
+Optimization
+------------
+
+.. automodule:: gerrychain.optimization
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+
+.. automodule:: gerrychain.gingleator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
 Partition
 ---------
 
@@ -174,6 +182,16 @@ Proposals
     :show-inheritance:
     :noindex:
 
+Tree
+----
+
+.. automodule:: gerrychain.tree
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+
 Updaters
 --------
 

api.html

@@ -157,7 +157,7 @@ <h2><a class="toc-backref" href="#id10">Adjacency graphs</a><a class="headerlink
 </div>
 <dl class="method">
 <dt id="gerrychain.graph.graph.Graph.add_data">
-<code class="sig-name descname">add_data</code><span class="sig-paren">(</span><em class="sig-param">df: &lt;Mock name='mock.DataFrame' id='139977221999200'&gt;</em>, <em class="sig-param">columns: Optional[Iterable[str]] = None</em><span class="sig-paren">)</span> &#x2192; None<a class="reference internal" href="_modules/gerrychain/graph/graph.html#Graph.add_data"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gerrychain.graph.graph.Graph.add_data" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">add_data</code><span class="sig-paren">(</span><em class="sig-param">df: &lt;Mock name='mock.DataFrame' id='140044217018976'&gt;</em>, <em class="sig-param">columns: Optional[Iterable[str]] = None</em><span class="sig-paren">)</span> &#x2192; None<a class="reference internal" href="_modules/gerrychain/graph/graph.html#Graph.add_data"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gerrychain.graph.graph.Graph.add_data" title="Permalink to this definition">¶</a></dt>
 <dd><p>Add columns of a DataFrame to a graph as node attributes
 by matching the DataFrame’s index to node ids.</p>
 <dl class="field-list simple">
@@ -213,7 +213,7 @@ <h2><a class="toc-backref" href="#id10">Adjacency graphs</a><a class="headerlink
 
 <dl class="method">
 <dt id="gerrychain.graph.graph.Graph.from_geodataframe">
-<em class="property">classmethod </em><code class="sig-name descname">from_geodataframe</code><span class="sig-paren">(</span><em class="sig-param">dataframe: &lt;Mock name='mock.DataFrame' id='139977221999200'&gt;</em>, <em class="sig-param">adjacency: str = 'rook'</em>, <em class="sig-param">cols_to_add: Optional[List[str]] = None</em>, <em class="sig-param">reproject: bool = False</em>, <em class="sig-param">ignore_errors: bool = False</em>, <em class="sig-param">crs_override: Union[str</em>, <em class="sig-param">int</em>, <em class="sig-param">None] = None</em><span class="sig-paren">)</span> &#x2192; gerrychain.graph.graph.Graph<a class="reference internal" href="_modules/gerrychain/graph/graph.html#Graph.from_geodataframe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gerrychain.graph.graph.Graph.from_geodataframe" title="Permalink to this definition">¶</a></dt>
+<em class="property">classmethod </em><code class="sig-name descname">from_geodataframe</code><span class="sig-paren">(</span><em class="sig-param">dataframe: &lt;Mock name='mock.DataFrame' id='140044217018976'&gt;</em>, <em class="sig-param">adjacency: str = 'rook'</em>, <em class="sig-param">cols_to_add: Optional[List[str]] = None</em>, <em class="sig-param">reproject: bool = False</em>, <em class="sig-param">ignore_errors: bool = False</em>, <em class="sig-param">crs_override: Union[str</em>, <em class="sig-param">int</em>, <em class="sig-param">None] = None</em><span class="sig-paren">)</span> &#x2192; gerrychain.graph.graph.Graph<a class="reference internal" href="_modules/gerrychain/graph/graph.html#Graph.from_geodataframe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gerrychain.graph.graph.Graph.from_geodataframe" title="Permalink to this definition">¶</a></dt>
 <dd><p>Creates the adjacency <a class="reference internal" href="#gerrychain.graph.graph.Graph" title="gerrychain.graph.graph.Graph"><code class="xref py py-class docutils literal notranslate"><span class="pre">Graph</span></code></a> of geometries described by <cite>dataframe</cite>.
 The areas of the polygons are included as node attributes (with key <cite>area</cite>).
 The shared perimeter of neighboring polygons are included as edge attributes
@@ -315,7 +315,7 @@ <h2><a class="toc-backref" href="#id10">Adjacency graphs</a><a class="headerlink
 
 <dl class="method">
 <dt id="gerrychain.graph.graph.Graph.join">
-<code class="sig-name descname">join</code><span class="sig-paren">(</span><em class="sig-param">dataframe: &lt;Mock name='mock.DataFrame' id='139977221999200'&gt;</em>, <em class="sig-param">columns: Optional[List[str]] = None</em>, <em class="sig-param">left_index: Optional[str] = None</em>, <em class="sig-param">right_index: Optional[str] = None</em><span class="sig-paren">)</span> &#x2192; None<a class="reference internal" href="_modules/gerrychain/graph/graph.html#Graph.join"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gerrychain.graph.graph.Graph.join" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">join</code><span class="sig-paren">(</span><em class="sig-param">dataframe: &lt;Mock name='mock.DataFrame' id='140044217018976'&gt;</em>, <em class="sig-param">columns: Optional[List[str]] = None</em>, <em class="sig-param">left_index: Optional[str] = None</em>, <em class="sig-param">right_index: Optional[str] = None</em><span class="sig-paren">)</span> &#x2192; None<a class="reference internal" href="_modules/gerrychain/graph/graph.html#Graph.join"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gerrychain.graph.graph.Graph.join" title="Permalink to this definition">¶</a></dt>
 <dd><p>Add data from a dataframe to the graph, matching nodes to rows when
 the node’s <cite>left_index</cite> attribute equals the row’s <cite>right_index</cite> value.</p>
 <dl class="field-list simple">
@@ -1356,7 +1356,7 @@ <h2><a class="toc-backref" href="#id12">Markov chains</a><a class="headerlink" h
 
 <dl class="class">
 <dt id="gerrychain.updaters.DataTally">
-<em class="property">class </em><code class="sig-prename descclassname">gerrychain.updaters.</code><code class="sig-name descname">DataTally</code><span class="sig-paren">(</span><em class="sig-param">data: Union[Dict, &lt;Mock name='mock.Series' id='139977221999392'&gt;, str], alias: str</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gerrychain/updaters/tally.html#DataTally"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gerrychain.updaters.DataTally" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">gerrychain.updaters.</code><code class="sig-name descname">DataTally</code><span class="sig-paren">(</span><em class="sig-param">data: Union[Dict, &lt;Mock name='mock.Series' id='140044217019120'&gt;, str], alias: str</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gerrychain/updaters/tally.html#DataTally"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gerrychain.updaters.DataTally" title="Permalink to this definition">¶</a></dt>
 <dd><p>An updater for tallying numerical data that is not necessarily stored as
 node attributes</p>
 <dl class="field-list simple">