Update documentation

_sources/topics/contributing.rst.txt

@@ -64,13 +64,16 @@ Pull Request Process
 Community Guidelines
 ====================
 
-We follow the Python Community Code of Conduct, which, in essence, means that we
-expect community members
+We follow an adaptation of the Contributor Covenant Code of Conduct, which, 
+in essence, means that we expect community members to
 
 - **Be respectful** of different viewpoints and experience levels.
 - **Gracefully accept constructive criticism**.
 - **Focus on what is best for the community**.
 
+For more detailed information about our community guidelines, please see the
+`Code of Conduct <https://github.com/mggg/GerryChain/blob/main/CODE_OF_CONDUCT.md>`_ 
+page of the main repository.
 
 
 Thank You

_sources/user/install.rst.txt

@@ -134,7 +134,8 @@ adjacencies or reading in shapefiles, then run
 This approach sometimes fails due to compatibility issues between our
 different Python GIS dependencies, like ``geopandas``, ``pyproj``,
 ``fiona``, and ``shapely``. If you run into this issue, try installing
-the dependencies using the `geo_settings.txt <./geo_settings.txt>`_
+the dependencies using the 
+`geo_settings.txt <https://github.com/mggg/GerryChain/blob/main/docs/geo_settings.txt>`_
 file. To do this, run ``pip install -r geo_settings.txt`` from the
 command line.
 

api.html

@@ -155,7 +155,7 @@ <h2><a class="toc-backref" href="#id6">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='140360704862096'&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='140260702472032'&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">
@@ -211,7 +211,7 @@ <h2><a class="toc-backref" href="#id6">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='140360704862096'&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><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='140260702472032'&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><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
@@ -311,7 +311,7 @@ <h2><a class="toc-backref" href="#id6">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='140360704862096'&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='140260702472032'&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">
@@ -1328,7 +1328,7 @@ <h2><a class="toc-backref" href="#id8">Markov chains</a><a class="headerlink" hr
 
 <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='140360704862192'&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='140260702472128'&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">

full_ref.html

@@ -1585,7 +1585,7 @@ <h2>Graph<a class="headerlink" href="#graph" title="Permalink to this headline">
 
 <dl class="function">
 <dt>
-<code class="sig-prename descclassname">gerrychain.graph.adjacency.</code><code class="sig-name descname">neighbors</code><span class="sig-paren">(</span><em class="sig-param">df: &lt;Mock name='mock.GeoDataFrame' id='140360705323360'&gt;</em>, <em class="sig-param">adjacency: str</em><span class="sig-paren">)</span> &#x2192; Dict<a class="reference internal" href="_modules/gerrychain/graph/adjacency.html#neighbors"><span class="viewcode-link">[source]</span></a></dt>
+<code class="sig-prename descclassname">gerrychain.graph.adjacency.</code><code class="sig-name descname">neighbors</code><span class="sig-paren">(</span><em class="sig-param">df: &lt;Mock name='mock.GeoDataFrame' id='140260702400816'&gt;</em>, <em class="sig-param">adjacency: str</em><span class="sig-paren">)</span> &#x2192; Dict<a class="reference internal" href="_modules/gerrychain/graph/adjacency.html#neighbors"><span class="viewcode-link">[source]</span></a></dt>
 <dd></dd></dl>
 
 <dl class="function">
@@ -1691,7 +1691,7 @@ <h2>Graph<a class="headerlink" href="#graph" title="Permalink to this headline">
 
 <dl class="function">
 <dt>
-<code class="sig-prename descclassname">gerrychain.graph.geo.</code><code class="sig-name descname">identify_utm_zone</code><span class="sig-paren">(</span><em class="sig-param">df: &lt;Mock name='mock.GeoDataFrame' id='140360705323360'&gt;</em><span class="sig-paren">)</span> &#x2192; int<a class="reference internal" href="_modules/gerrychain/graph/geo.html#identify_utm_zone"><span class="viewcode-link">[source]</span></a></dt>
+<code class="sig-prename descclassname">gerrychain.graph.geo.</code><code class="sig-name descname">identify_utm_zone</code><span class="sig-paren">(</span><em class="sig-param">df: &lt;Mock name='mock.GeoDataFrame' id='140260702400816'&gt;</em><span class="sig-paren">)</span> &#x2192; int<a class="reference internal" href="_modules/gerrychain/graph/geo.html#identify_utm_zone"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Given a GeoDataFrame, identify the Universal Transverse Mercator zone
 number for the centroid of the geometries in the dataframe.</p>
 </dd></dl>
@@ -1851,7 +1851,7 @@ <h2>Graph<a class="headerlink" href="#graph" title="Permalink to this headline">
 </div>
 <dl class="method">
 <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='140360704862096'&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></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='140260702472032'&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></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">
@@ -1912,7 +1912,7 @@ <h2>Graph<a class="headerlink" href="#graph" title="Permalink to this headline">
 
 <dl class="method">
 <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='140360704862096'&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><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></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='140260702472032'&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><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></dt>
 <dd><p>Creates the adjacency <a class="reference internal" href="api.html#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
@@ -2012,7 +2012,7 @@ <h2>Graph<a class="headerlink" href="#graph" title="Permalink to this headline">
 
 <dl class="method">
 <dt>
-<code class="sig-name descname">join</code><span class="sig-paren">(</span><em class="sig-param">dataframe: &lt;Mock name='mock.DataFrame' id='140360704862096'&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></dt>
+<code class="sig-name descname">join</code><span class="sig-paren">(</span><em class="sig-param">dataframe: &lt;Mock name='mock.DataFrame' id='140260702472032'&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></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">
@@ -2100,7 +2100,7 @@ <h2>Graph<a class="headerlink" href="#graph" title="Permalink to this headline">
 
 <dl class="function">
 <dt>
-<code class="sig-prename descclassname">gerrychain.graph.graph.</code><code class="sig-name descname">add_boundary_perimeters</code><span class="sig-paren">(</span><em class="sig-param">graph: gerrychain.graph.graph.Graph</em>, <em class="sig-param">geometries: &lt;Mock name='mock.Series' id='140360704862192'&gt;</em><span class="sig-paren">)</span> &#x2192; None<a class="reference internal" href="_modules/gerrychain/graph/graph.html#add_boundary_perimeters"><span class="viewcode-link">[source]</span></a></dt>
+<code class="sig-prename descclassname">gerrychain.graph.graph.</code><code class="sig-name descname">add_boundary_perimeters</code><span class="sig-paren">(</span><em class="sig-param">graph: gerrychain.graph.graph.Graph</em>, <em class="sig-param">geometries: &lt;Mock name='mock.Series' id='140260702472128'&gt;</em><span class="sig-paren">)</span> &#x2192; None<a class="reference internal" href="_modules/gerrychain/graph/graph.html#add_boundary_perimeters"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Add shared perimeter between nodes and the total geometry boundary.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
@@ -2120,7 +2120,7 @@ <h2>Graph<a class="headerlink" href="#graph" title="Permalink to this headline">
 
 <dl class="function">
 <dt>
-<code class="sig-prename descclassname">gerrychain.graph.graph.</code><code class="sig-name descname">check_dataframe</code><span class="sig-paren">(</span><em class="sig-param">df: &lt;Mock name='mock.DataFrame' id='140360704862096'&gt;</em><span class="sig-paren">)</span> &#x2192; None<a class="reference internal" href="_modules/gerrychain/graph/graph.html#check_dataframe"><span class="viewcode-link">[source]</span></a></dt>
+<code class="sig-prename descclassname">gerrychain.graph.graph.</code><code class="sig-name descname">check_dataframe</code><span class="sig-paren">(</span><em class="sig-param">df: &lt;Mock name='mock.DataFrame' id='140260702472032'&gt;</em><span class="sig-paren">)</span> &#x2192; None<a class="reference internal" href="_modules/gerrychain/graph/graph.html#check_dataframe"><span class="viewcode-link">[source]</span></a></dt>
 <dd><dl class="field-list simple">
 <dt class="field-odd">Returns</dt>
 <dd class="field-odd"><p>None</p>
@@ -2516,7 +2516,7 @@ <h2>Partition<a class="headerlink" href="#partition" title="Permalink to this he
 
 <dl class="method">
 <dt>
-<code class="sig-name descname">to_series</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; &lt;Mock name='mock.Series' id='140360704862192'&gt;<a class="reference internal" href="_modules/gerrychain/partition/assignment.html#Assignment.to_series"><span class="viewcode-link">[source]</span></a></dt>
+<code class="sig-name descname">to_series</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; &lt;Mock name='mock.Series' id='140260702472128'&gt;<a class="reference internal" href="_modules/gerrychain/partition/assignment.html#Assignment.to_series"><span class="viewcode-link">[source]</span></a></dt>
 <dd><dl class="field-list simple">
 <dt class="field-odd">Returns</dt>
 <dd class="field-odd"><p>The assignment as a <code class="xref py py-class docutils literal notranslate"><span class="pre">pandas.Series</span></code>.</p>
@@ -4483,7 +4483,7 @@ <h2>Updaters<a class="headerlink" href="#updaters" title="Permalink to this head
 
 <dl class="class">
 <dt>
-<em class="property">class </em><code class="sig-prename descclassname">gerrychain.updaters.tally.</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='140360704862192'&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></dt>
+<em class="property">class </em><code class="sig-prename descclassname">gerrychain.updaters.tally.</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='140260702472128'&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></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <p>An updater for tallying numerical data that is not necessarily stored as
 node attributes</p>