diff --git a/latest/_modules/compass/ocean/tests/global_ocean/files_for_e3sm/remap_iceberg_climatology.html b/latest/_modules/compass/ocean/tests/global_ocean/files_for_e3sm/remap_iceberg_climatology.html
index 9fe38ca53..17f599ecf 100644
--- a/latest/_modules/compass/ocean/tests/global_ocean/files_for_e3sm/remap_iceberg_climatology.html
+++ b/latest/_modules/compass/ocean/tests/global_ocean/files_for_e3sm/remap_iceberg_climatology.html
@@ -163,6 +163,8 @@ <h1>Source code for compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceber
 <span class="sd">        Run this step of the test case</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">with_ice_shelf_cavities</span><span class="p">:</span>
+            <span class="k">return</span>
         <span class="n">logger</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">logger</span>
         <span class="n">config</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span>
         <span class="n">ntasks</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ntasks</span>
diff --git a/latest/developers_guide/landice/generated/compass.landice.tests.mismipplus.setup_mesh.mark_cull_cells_for_MISMIP.html b/latest/developers_guide/landice/generated/compass.landice.tests.mismipplus.setup_mesh.mark_cull_cells_for_MISMIP.html
index 845dc91ea..52feb1a9f 100644
--- a/latest/developers_guide/landice/generated/compass.landice.tests.mismipplus.setup_mesh.mark_cull_cells_for_MISMIP.html
+++ b/latest/developers_guide/landice/generated/compass.landice.tests.mismipplus.setup_mesh.mark_cull_cells_for_MISMIP.html
@@ -134,7 +134,7 @@ <h1>compass.landice.tests.mismipplus.setup_mesh.mark_cull_cells_for_MISMIP<a cla
 <span class="sig-prename descclassname"><span class="pre">compass.landice.tests.mismipplus.setup_mesh.</span></span><span class="sig-name descname"><span class="pre">mark_cull_cells_for_MISMIP</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ds_mesh</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/compass/landice/tests/mismipplus/setup_mesh.html#mark_cull_cells_for_MISMIP"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#compass.landice.tests.mismipplus.setup_mesh.mark_cull_cells_for_MISMIP" title="Link to this definition">¶</a></dt>
 <dd><dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><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 v2024.5.1.dev0)"><em>xarray.Dataset</em></a>)</p>
+<dd class="field-odd"><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 v2024.6.1.dev0)"><em>xarray.Dataset</em></a>)</p>
 </dd>
 </dl>
 </dd></dl>
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
index 0cc70b59c..cacc3f4f4 100644
--- 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
@@ -136,9 +136,9 @@ <h1>compass.ocean.haney.compute_haney_number<a class="headerlink" href="#compass
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></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 v2024.5.1.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 v2024.5.1.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 v2024.5.1.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 v2024.6.1.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 v2024.6.1.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 v2024.6.1.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 v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to show a progress bar</p></li>
 </ul>
 </dd>
diff --git a/latest/developers_guide/ocean/generated/compass.ocean.iceshelf.compute_land_ice_pressure_and_draft.html b/latest/developers_guide/ocean/generated/compass.ocean.iceshelf.compute_land_ice_pressure_and_draft.html
index c965bc3ab..3bd6811a2 100644
--- a/latest/developers_guide/ocean/generated/compass.ocean.iceshelf.compute_land_ice_pressure_and_draft.html
+++ b/latest/developers_guide/ocean/generated/compass.ocean.iceshelf.compute_land_ice_pressure_and_draft.html
@@ -136,8 +136,8 @@ <h1>compass.ocean.iceshelf.compute_land_ice_pressure_and_draft<a class="headerli
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></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 v2024.5.1.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 v2024.5.1.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 v2024.6.1.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 v2024.6.1.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 v3.12)"><em>float</em></a>) – A reference density for seawater displaced by the ice shelf</p></li>
 </ul>
 </dd>
diff --git a/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_geom.html b/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_geom.html
index 461bee856..1790adaa4 100644
--- a/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_geom.html
+++ b/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_geom.html
@@ -137,8 +137,8 @@ <h1>compass.ocean.tests.isomip_plus.geom.interpolate_geom<a class="headerlink" h
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></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 v2024.5.1.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 v2024.5.1.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 v2024.6.1.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 v2024.6.1.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 v3.12)"><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/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask.html b/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask.html
index e3db370fc..5fcedfe0c 100644
--- a/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask.html
+++ b/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask.html
@@ -139,8 +139,8 @@ <h1>compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask<a class="headerl
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></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 v2024.5.1.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 v2024.5.1.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 v2024.6.1.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 v2024.6.1.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 v3.12)"><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/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.html b/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.html
index f1d65ea37..e14680b12 100644
--- a/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.html
+++ b/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.html
@@ -169,8 +169,8 @@ <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 v3.12)"><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 v2024.5.1.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 v2024.5.1.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 v2024.6.1.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 v2024.6.1.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 v3.12)"><em>bool</em></a>) – Whether to show a progressbar</p></li>
 </ul>
 </dd>
diff --git a/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.TimeSeriesPlotter.html b/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.TimeSeriesPlotter.html
index 1e366355f..6bbdc5000 100644
--- a/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.TimeSeriesPlotter.html
+++ b/latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.TimeSeriesPlotter.html
@@ -154,8 +154,8 @@ <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 v3.12)"><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 v3.12)"><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 v2024.5.1.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 v2024.5.1.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 v2024.6.1.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 v2024.6.1.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
index 652d38668..2c65fc1e0 100644
--- 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
@@ -169,7 +169,7 @@ <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 v2024.5.1.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 v2024.6.1.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/latest/developers_guide/ocean/generated/compass.ocean.vertical.partial_cells.alter_bottom_depth.html b/latest/developers_guide/ocean/generated/compass.ocean.vertical.partial_cells.alter_bottom_depth.html
index 4ee7b30a9..9a0741bbe 100644
--- a/latest/developers_guide/ocean/generated/compass.ocean.vertical.partial_cells.alter_bottom_depth.html
+++ b/latest/developers_guide/ocean/generated/compass.ocean.vertical.partial_cells.alter_bottom_depth.html
@@ -139,9 +139,9 @@ <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 v2024.5.1.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 v2024.5.1.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 v2024.5.1.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 v2024.6.1.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 v2024.6.1.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 v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the bottom valid level</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></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
index c568e536d..19dbf410a 100644
--- 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
@@ -139,9 +139,9 @@ <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 v2024.5.1.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 v2024.5.1.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 v2024.5.1.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 v2024.6.1.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 v2024.6.1.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 v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the top valid level</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
diff --git a/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_min_max_level_cell.html b/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_min_max_level_cell.html
index 864c91199..94e9676dc 100644
--- a/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_min_max_level_cell.html
+++ b/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_min_max_level_cell.html
@@ -137,10 +137,10 @@ <h1>compass.ocean.vertical.zlevel.compute_min_max_level_cell<a class="headerlink
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>refTopDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – A 1D array of positive-down depths of the top of each z level</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 v2024.5.1.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>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height</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 v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – The positive-down depth of the seafloor</p></li>
+<li><p><strong>refTopDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – A 1D array of positive-down depths of the top of each z level</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 v2024.6.1.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>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height</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 v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The positive-down depth of the seafloor</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
diff --git a/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_z_level_layer_thickness.html b/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_z_level_layer_thickness.html
index 3eeee2122..baafdf92d 100644
--- a/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_z_level_layer_thickness.html
+++ b/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_z_level_layer_thickness.html
@@ -136,12 +136,12 @@ <h1>compass.ocean.vertical.zlevel.compute_z_level_layer_thickness<a class="heade
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>refTopDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – A 1D array of positive-down depths of the top of each z level</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 v2024.5.1.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>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height</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 v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – The positive-down depth of the seafloor</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 v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the top valid 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 v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the bottom valid level</p></li>
+<li><p><strong>refTopDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – A 1D array of positive-down depths of the top of each z level</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 v2024.6.1.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>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height</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 v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The positive-down depth of the seafloor</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 v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the top valid 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 v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the bottom valid level</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
diff --git a/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_z_level_resting_thickness.html b/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_z_level_resting_thickness.html
index ea92c1ae7..33477f7d4 100644
--- a/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_z_level_resting_thickness.html
+++ b/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.compute_z_level_resting_thickness.html
@@ -137,11 +137,11 @@ <h1>compass.ocean.vertical.zlevel.compute_z_level_resting_thickness<a class="hea
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>layerThickness</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – The thickness of each layer (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 v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height</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 v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – The positive-down depth of the seafloor</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 v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the top valid 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 v2024.5.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the bottom valid level</p></li>
+<li><p><strong>layerThickness</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The thickness of each layer (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 v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height</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 v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The positive-down depth of the seafloor</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 v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the top valid 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 v2024.6.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the bottom valid level</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
diff --git a/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.init_z_level_vertical_coord.html b/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.init_z_level_vertical_coord.html
index 01e818e13..cb83f7f3a 100644
--- a/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.init_z_level_vertical_coord.html
+++ b/latest/developers_guide/ocean/generated/compass.ocean.vertical.zlevel.init_z_level_vertical_coord.html
@@ -169,7 +169,7 @@ <h1>compass.ocean.vertical.zlevel.init_z_level_vertical_coord<a class="headerlin
 <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 v2024.5.1.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 v2024.6.1.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/latest/developers_guide/ocean/generated/compass.ocean.vertical.zstar.init_z_star_vertical_coord.html b/latest/developers_guide/ocean/generated/compass.ocean.vertical.zstar.init_z_star_vertical_coord.html
index 8fed9aa72..7e04fe8df 100644
--- a/latest/developers_guide/ocean/generated/compass.ocean.vertical.zstar.init_z_star_vertical_coord.html
+++ b/latest/developers_guide/ocean/generated/compass.ocean.vertical.zstar.init_z_star_vertical_coord.html
@@ -169,7 +169,7 @@ <h1>compass.ocean.vertical.zstar.init_z_star_vertical_coord<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>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.5.1.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 v2024.6.1.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/latest/developers_guide/organization.html b/latest/developers_guide/organization.html
index 76d8ebfc3..a5578ef3f 100644
--- a/latest/developers_guide/organization.html
+++ b/latest/developers_guide/organization.html
@@ -1317,7 +1317,7 @@ <h2>Directory structure<a class="headerlink" href="#directory-structure" title="
 </div>
 <p>Without going into all the details of this method, it creates a mesh that
 is periodic in x (but not y), then adds a vertical grid and an initial
-condition to an <a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.5.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">xarray.Dataset</span></code></a>, which is then written out to
+condition to an <a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.6.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">xarray.Dataset</span></code></a>, which is then written out to
 the file <code class="docutils literal notranslate"><span class="pre">ocean.nc</span></code>.</p>
 <p>In the example step we’ve been using,
 <a class="reference internal" href="ocean/generated/compass.ocean.tests.baroclinic_channel.forward.Forward.run.html#compass.ocean.tests.baroclinic_channel.forward.Forward.run" title="compass.ocean.tests.baroclinic_channel.forward.Forward.run"><code class="xref py py-func docutils literal notranslate"><span class="pre">compass.ocean.tests.baroclinic_channel.forward.Forward.run()</span></code></a> looks
diff --git a/latest/tutorials/dev_porting_legacy.html b/latest/tutorials/dev_porting_legacy.html
index c8d5912bd..145a2b027 100644
--- a/latest/tutorials/dev_porting_legacy.html
+++ b/latest/tutorials/dev_porting_legacy.html
@@ -792,13 +792,13 @@ <h3>Defining the run method<a class="headerlink" href="#defining-the-run-method"
 tool <code class="docutils literal notranslate"><span class="pre">planar_hex</span></code>, but <code class="docutils literal notranslate"><span class="pre">compass</span></code> will typically use the
 <a class="reference external" href="http://mpas-dev.github.io/MPAS-Tools/stable/generated/mpas_tools.planar_hex.make_planar_hex_mesh.html#mpas_tools.planar_hex.make_planar_hex_mesh" title="(in mpas_tools vstable)"><code class="xref py py-func docutils literal notranslate"><span class="pre">mpas_tools.planar_hex.make_planar_hex_mesh()</span></code></a> function instead to
 avoid the complexity of <code class="docutils literal notranslate"><span class="pre">subprocess</span></code> calls and unnecessary file I/O.  The
-result is an <a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.5.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">xarray.Dataset</span></code></a> containing the mesh.</p>
+result is an <a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.6.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">xarray.Dataset</span></code></a> containing the mesh.</p>
 <p>Second, we make sure any land cells are culled by calling the cell culler.
 In legacy COMPASS, this is done with the command-line tool <code class="docutils literal notranslate"><span class="pre">MpasCellCuller.x</span></code>
 but in <code class="docutils literal notranslate"><span class="pre">compass</span></code>, the same can be achieved with
 <a class="reference external" href="http://mpas-dev.github.io/MPAS-Tools/stable/generated/mpas_tools.mesh.conversion.cull.html#mpas_tools.mesh.conversion.cull" title="(in mpas_tools vstable)"><code class="xref py py-func docutils literal notranslate"><span class="pre">mpas_tools.mesh.conversion.cull()</span></code></a> (which is a wrapper around a
 <code class="docutils literal notranslate"><span class="pre">subprocess`</span></code> call to <code class="docutils literal notranslate"><span class="pre">MpasCellCuller.x</span></code>).  <code class="docutils literal notranslate"><span class="pre">cull()</span></code> has
-<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.5.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">xarray.Dataset</span></code></a> objects as its input an return value, and also
+<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.6.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">xarray.Dataset</span></code></a> objects as its input an return value, and also
 takes a “logger” where it can write output (sometimes a log file and sometimes
 directly to the terminal via stdout).  You should always pass <code class="docutils literal notranslate"><span class="pre">self.logger</span></code>
 so <code class="docutils literal notranslate"><span class="pre">compass</span></code> can figure out whether a file or stdout is the right place for