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MPAS-Dev · Sep 28, 2023 · afff398 · afff398
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diff --git a/latest/_modules/compass/ocean/tests/isomip_plus/viz/plot.html b/latest/_modules/compass/ocean/tests/isomip_plus/viz/plot.html
@@ -1045,7 +1045,7 @@ <h1>Source code for compass.ocean.tests.isomip_plus.viz.plot</h1><div class="hig
         <span class="n">vertices</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1e-3</span> <span class="o">*</span> <span class="n">xVertex</span><span class="p">[</span><span class="n">vertexIndices</span><span class="p">]</span>
         <span class="n">vertices</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1e-3</span> <span class="o">*</span> <span class="n">yVertex</span><span class="p">[</span><span class="n">vertexIndices</span><span class="p">]</span>
 
-        <span class="n">polygon</span> <span class="o">=</span> <span class="n">Polygon</span><span class="p">(</span><span class="n">vertices</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
+        <span class="n">polygon</span> <span class="o">=</span> <span class="n">Polygon</span><span class="p">(</span><span class="n">vertices</span><span class="p">,</span> <span class="n">closed</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
         <span class="n">patches</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">polygon</span><span class="p">)</span>
 
     <span class="n">p</span> <span class="o">=</span> <span class="n">PatchCollection</span><span class="p">(</span><span class="n">patches</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">1.</span><span class="p">)</span>

diff --git a/latest/developers_guide/ocean/generated/compass.ocean.haney.compute_haney_number.html b/latest/developers_guide/ocean/generated/compass.ocean.haney.compute_haney_number.html
@@ -137,9 +137,9 @@ <h1>compass.ocean.haney.compute_haney_number<a class="headerlink" href="#compass
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.8.1.dev0)"><em>xarray.Dataset</em></a>) – A dataset with the MPAS-Ocean mesh</p></li>
-<li><p><strong>layer_thickness</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.8.1.dev0)"><em>xarray.DataArray</em></a>) – A data array with layer thicknesses</p></li>
-<li><p><strong>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.8.1.dev0)"><em>xarray.DataArray</em></a>) – A data array with sea surface height</p></li>
+<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.9.1.dev0)"><em>xarray.Dataset</em></a>) – A dataset with the MPAS-Ocean mesh</p></li>
+<li><p><strong>layer_thickness</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.9.1.dev0)"><em>xarray.DataArray</em></a>) – A data array with layer thicknesses</p></li>
+<li><p><strong>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.9.1.dev0)"><em>xarray.DataArray</em></a>) – A data array with sea surface height</p></li>
 <li><p><strong>show_progress</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.11)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to show a progress bar</p></li>
 </ul>
 </dd>

diff --git a/...ers_guide/ocean/generated/compass.ocean.iceshelf.compute_land_ice_pressure_and_draft.html b/...ers_guide/ocean/generated/compass.ocean.iceshelf.compute_land_ice_pressure_and_draft.html
@@ -137,8 +137,8 @@ <h1>compass.ocean.iceshelf.compute_land_ice_pressure_and_draft<a class="headerli
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.8.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height (the ice draft)</p></li>
-<li><p><strong>modify_mask</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.8.1.dev0)"><em>xarray.DataArray</em></a>) – A mask that is 1 where <code class="docutils literal notranslate"><span class="pre">landIcePressure</span></code> can be deviate from 0</p></li>
+<li><p><strong>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.9.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height (the ice draft)</p></li>
+<li><p><strong>modify_mask</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.9.1.dev0)"><em>xarray.DataArray</em></a>) – A mask that is 1 where <code class="docutils literal notranslate"><span class="pre">landIcePressure</span></code> can be deviate from 0</p></li>
 <li><p><strong>ref_density</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.11)"><em>float</em></a>) – A reference density for seawater displaced by the ice shelf</p></li>
 </ul>
 </dd>

diff --git a/...velopers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_geom.html b/...velopers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_geom.html
@@ -138,8 +138,8 @@ <h1>compass.ocean.tests.isomip_plus.geom.interpolate_geom<a class="headerlink" h
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.8.1.dev0)"><em>xarray.Dataset</em></a>) – An MPAS-Ocean mesh</p></li>
-<li><p><strong>ds_geom</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.8.1.dev0)"><em>xarray.Dataset</em></a>) – Ice-sheet topography produced by
+<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.9.1.dev0)"><em>xarray.Dataset</em></a>) – An MPAS-Ocean mesh</p></li>
+<li><p><strong>ds_geom</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.9.1.dev0)"><em>xarray.Dataset</em></a>) – Ice-sheet topography produced by
 <a class="reference internal" href="compass.ocean.tests.isomip_plus.process_geom.ProcessGeom.html#compass.ocean.tests.isomip_plus.process_geom.ProcessGeom" title="compass.ocean.tests.isomip_plus.process_geom.ProcessGeom"><code class="xref py py-class docutils literal notranslate"><span class="pre">compass.ocean.tests.isomip_plus.process_geom.ProcessGeom</span></code></a></p></li>
 <li><p><strong>min_ocean_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.11)"><em>float</em></a>) – The minimum ocean fraction after interpolation, below which the cell
 is masked as land (which is not distinguished from grounded ice)</p></li>

diff --git a/...rs_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask.html b/...rs_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask.html
@@ -140,8 +140,8 @@ <h1>compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask<a class="headerl
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.8.1.dev0)"><em>xarray.Dataset</em></a>) – An MPAS-Ocean mesh</p></li>
-<li><p><strong>ds_geom</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.8.1.dev0)"><em>xarray.Dataset</em></a>) – Ice-sheet topography produced by
+<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.9.1.dev0)"><em>xarray.Dataset</em></a>) – An MPAS-Ocean mesh</p></li>
+<li><p><strong>ds_geom</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.9.1.dev0)"><em>xarray.Dataset</em></a>) – Ice-sheet topography produced by
 <a class="reference internal" href="compass.ocean.tests.isomip_plus.process_geom.ProcessGeom.html#compass.ocean.tests.isomip_plus.process_geom.ProcessGeom" title="compass.ocean.tests.isomip_plus.process_geom.ProcessGeom"><code class="xref py py-class docutils literal notranslate"><span class="pre">compass.ocean.tests.isomip_plus.process_geom.ProcessGeom</span></code></a></p></li>
 <li><p><strong>min_ocean_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.11)"><em>float</em></a>) – The minimum ocean fraction after interpolation, below which the cell
 is masked as land (which is not distinguished from grounded ice)</p></li>

diff --git a/...velopers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.html b/...velopers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.html
@@ -170,8 +170,8 @@ <h1>compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter<a class="headerlink" h
 <li><p><strong>expt</strong> (<em>{'Ocean0'</em><em>, </em><em>'Ocean1'</em><em>, </em><em>'Ocean2'}</em>) – The name of the experiment</p></li>
 <li><p><strong>sectionY</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.11)"><em>float</em></a>) – The location along the y axis of a transect in the x-z plane to
 plot</p></li>
-<li><p><strong>dsMesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.8.1.dev0)"><em>xarray.Dataset</em></a>) – The MPAS mesh</p></li>
-<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.8.1.dev0)"><em>xarray.Dataset</em></a>) – The time series output</p></li>
+<li><p><strong>dsMesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.9.1.dev0)"><em>xarray.Dataset</em></a>) – The MPAS mesh</p></li>
+<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.9.1.dev0)"><em>xarray.Dataset</em></a>) – The time series output</p></li>
 <li><p><strong>showProgress</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.11)"><em>bool</em></a>) – Whether to show a progressbar</p></li>
 </ul>
 </dd>

diff --git a/...ers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.TimeSeriesPlotter.html b/...ers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.TimeSeriesPlotter.html
@@ -155,8 +155,8 @@ <h1>compass.ocean.tests.isomip_plus.viz.plot.TimeSeriesPlotter<a class="headerli
 <li><p><strong>inFolder</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a><em>, </em><em>optional</em>) – The folder with simulation results</p></li>
 <li><p><strong>outFolder</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a><em>, </em><em>optional</em>) – The folder where images will be written</p></li>
 <li><p><strong>expt</strong> (<em>{'Ocean0'</em><em>, </em><em>'Ocean1'</em><em>, </em><em>'Ocean2'}</em><em>, </em><em>optional</em>) – The name of the experiment</p></li>
-<li><p><strong>dsMesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.8.1.dev0)"><em>xarray.Dataset</em></a><em>, </em><em>optional</em>) – The MPAS mesh</p></li>
-<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.8.1.dev0)"><em>xarray.Dataset</em></a><em>, </em><em>optional</em>) – The time series output</p></li>
+<li><p><strong>dsMesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.9.1.dev0)"><em>xarray.Dataset</em></a><em>, </em><em>optional</em>) – The MPAS mesh</p></li>
+<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.9.1.dev0)"><em>xarray.Dataset</em></a><em>, </em><em>optional</em>) – The time series output</p></li>
 </ul>
 </dd>
 </dl>

diff --git a/latest/developers_guide/ocean/generated/compass.ocean.vertical.init_vertical_coord.html b/latest/developers_guide/ocean/generated/compass.ocean.vertical.init_vertical_coord.html
@@ -170,7 +170,7 @@ <h1>compass.ocean.vertical.init_vertical_coord<a class="headerlink" href="#compa
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>config</strong> (<a class="reference internal" href="../../generated/compass.config.CompassConfigParser.html#compass.config.CompassConfigParser" title="compass.config.CompassConfigParser"><em>compass.config.CompassConfigParser</em></a>) – Configuration options with parameters used to construct the vertical
 grid</p></li>
-<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.8.1.dev0)"><em>xarray.Dataset</em></a>) – A data set containing <code class="docutils literal notranslate"><span class="pre">bottomDepth</span></code> and <code class="docutils literal notranslate"><span class="pre">ssh</span></code> variables used to
+<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2023.9.1.dev0)"><em>xarray.Dataset</em></a>) – A data set containing <code class="docutils literal notranslate"><span class="pre">bottomDepth</span></code> and <code class="docutils literal notranslate"><span class="pre">ssh</span></code> variables used to
 construct the vertical coordinate</p></li>
 </ul>
 </dd>

diff --git a/...lopers_guide/ocean/generated/compass.ocean.vertical.partial_cells.alter_bottom_depth.html b/...lopers_guide/ocean/generated/compass.ocean.vertical.partial_cells.alter_bottom_depth.html
@@ -140,9 +140,9 @@ <h1>compass.ocean.vertical.partial_cells.alter_bottom_depth<a class="headerlink"
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>config</strong> (<a class="reference internal" href="../../generated/compass.config.CompassConfigParser.html#compass.config.CompassConfigParser" title="compass.config.CompassConfigParser"><em>compass.config.CompassConfigParser</em></a>) – Configuration options with parameters used to construct the vertical
 grid</p></li>
-<li><p><strong>bottomDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.8.1.dev0)"><em>xarray.DataArray</em></a>) – The positive-down depth of the seafloor</p></li>
-<li><p><strong>refBottomDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.8.1.dev0)"><em>xarray.DataArray</em></a>) – A 1D array of positive-down depths of the bottom of each z level</p></li>
-<li><p><strong>maxLevelCell</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.8.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the bottom valid level</p></li>
+<li><p><strong>bottomDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.9.1.dev0)"><em>xarray.DataArray</em></a>) – The positive-down depth of the seafloor</p></li>
+<li><p><strong>refBottomDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.9.1.dev0)"><em>xarray.DataArray</em></a>) – A 1D array of positive-down depths of the bottom of each z level</p></li>
+<li><p><strong>maxLevelCell</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.9.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the bottom valid level</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>

diff --git a/latest/developers_guide/ocean/generated/compass.ocean.vertical.partial_cells.alter_ssh.html b/latest/developers_guide/ocean/generated/compass.ocean.vertical.partial_cells.alter_ssh.html
@@ -140,9 +140,9 @@ <h1>compass.ocean.vertical.partial_cells.alter_ssh<a class="headerlink" href="#c
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>config</strong> (<a class="reference internal" href="../../generated/compass.config.CompassConfigParser.html#compass.config.CompassConfigParser" title="compass.config.CompassConfigParser"><em>compass.config.CompassConfigParser</em></a>) – Configuration options with parameters used to construct the vertical
 grid</p></li>
-<li><p><strong>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.8.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height</p></li>
-<li><p><strong>refBottomDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.8.1.dev0)"><em>xarray.DataArray</em></a>) – A 1D array of positive-down depths of the bottom of each z level</p></li>
-<li><p><strong>minLevelCell</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.8.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the top valid level</p></li>
+<li><p><strong>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.9.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height</p></li>
+<li><p><strong>refBottomDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.9.1.dev0)"><em>xarray.DataArray</em></a>) – A 1D array of positive-down depths of the bottom of each z level</p></li>
+<li><p><strong>minLevelCell</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2023.9.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the top valid level</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>