Update documentation

latest/_modules/compass/ocean/tests/global_ocean/files_for_e3sm/diagnostic_masks.html

@@ -201,7 +201,7 @@ <h1>Source code for compass.ocean.tests.global_ocean.files_for_e3sm.diagnostic_m
 
     <span class="n">gf</span> <span class="o">=</span> <span class="n">GeometricFeatures</span><span class="p">()</span>
     <span class="n">region_groups</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;Antarctic Regions&#39;</span><span class="p">,</span> <span class="s1">&#39;Arctic Ocean Regions&#39;</span><span class="p">,</span>
-                     <span class="s1">&#39;Arctic Sea Ice Regions&#39;</span><span class="p">,</span> <span class="s1">&#39;Greenland Regions&#39;</span><span class="p">,</span>
+                     <span class="s1">&#39;Arctic Sea Ice Regions&#39;</span><span class="p">,</span> <span class="s1">&#39;ISMIP6 Greenland Regions&#39;</span><span class="p">,</span>
                      <span class="s1">&#39;Ocean Basins&#39;</span><span class="p">,</span> <span class="s1">&#39;Ocean Subbasins&#39;</span><span class="p">,</span> <span class="s1">&#39;ISMIP6 Regions&#39;</span><span class="p">]</span>
 
     <span class="k">if</span> <span class="n">with_ice_shelf_cavities</span><span class="p">:</span>

latest/developers_guide/generated/compass.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width.html

@@ -155,9 +155,9 @@ <h1>compass.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width<a class="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>lon</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – longitude in degrees (length n and between -180 and 180)</p></li>
-<li><p><strong>lat</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – longitude in degrees (length m and between -90 and 90)</p></li>
-<li><p><strong>cell_width</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – m x n array of cell width in km</p></li>
+<li><p><strong>lon</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – longitude in degrees (length n and between -180 and 180)</p></li>
+<li><p><strong>lat</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – longitude in degrees (length m and between -90 and 90)</p></li>
+<li><p><strong>cell_width</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – m x n array of cell width in km</p></li>
 </ul>
 </dd>
 </dl>

latest/developers_guide/landice/generated/compass.landice.mesh.build_mali_mesh.html

@@ -135,7 +135,7 @@ <h1>compass.landice.mesh.build_mali_mesh<a class="headerlink" href="#compass-lan
 <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>cell_width</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – Desired width of MPAS cells calculated by <a class="reference internal" href="compass.landice.mesh.build_cell_width.html#compass.landice.mesh.build_cell_width" title="compass.landice.mesh.build_cell_width"><code class="xref py py-func docutils literal notranslate"><span class="pre">build_cell_width()</span></code></a>
+<li><p><strong>cell_width</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – Desired width of MPAS cells calculated by <a class="reference internal" href="compass.landice.mesh.build_cell_width.html#compass.landice.mesh.build_cell_width" title="compass.landice.mesh.build_cell_width"><code class="xref py py-func docutils literal notranslate"><span class="pre">build_cell_width()</span></code></a>
 based on mesh density functions define in <a class="reference internal" href="compass.landice.mesh.set_cell_width.html#compass.landice.mesh.set_cell_width" title="compass.landice.mesh.set_cell_width"><code class="xref py py-func docutils literal notranslate"><span class="pre">set_cell_width()</span></code></a>
 to pass to
 <code class="xref py py-func docutils literal notranslate"><span class="pre">mpas_tools.mesh.creation.build_mesh.build_planar_mesh()</span></code>.</p></li>

latest/developers_guide/landice/generated/compass.landice.mesh.get_dist_to_edge_and_gl.html

@@ -134,11 +134,11 @@ <h1>compass.landice.mesh.get_dist_to_edge_and_gl<a class="headerlink" href="#com
 <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>thk</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – Ice thickness field from gridded dataset,
+<li><p><strong>thk</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – Ice thickness field from gridded dataset,
 usually after trimming to flood fill mask</p></li>
-<li><p><strong>topg</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – Bed topography field from gridded dataset</p></li>
-<li><p><strong>x</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – x coordinates from gridded dataset</p></li>
-<li><p><strong>y</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – y coordinates from gridded dataset</p></li>
+<li><p><strong>topg</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – Bed topography field from gridded dataset</p></li>
+<li><p><strong>x</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – x coordinates from gridded dataset</p></li>
+<li><p><strong>y</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – y coordinates from gridded dataset</p></li>
 <li><p><strong>section_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><em>str</em></a>) – Section of the config file from which to read parameters. The
 following options to be set in the given config section:
 <code class="docutils literal notranslate"><span class="pre">levels</span></code>, <code class="docutils literal notranslate"><span class="pre">x_min</span></code>, <code class="docutils literal notranslate"><span class="pre">x_max</span></code>, <code class="docutils literal notranslate"><span class="pre">y_min</span></code>, <code class="docutils literal notranslate"><span class="pre">y_max</span></code>,

latest/developers_guide/landice/generated/compass.landice.mesh.gridded_flood_fill.html

@@ -135,7 +135,7 @@ <h1>compass.landice.mesh.gridded_flood_fill<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>field</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – Array from gridded dataset to use for flood-fill.
+<li><p><strong>field</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – Array from gridded dataset to use for flood-fill.
 Usually ice thickness.</p></li>
 <li><p><strong>iStart</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a>) – x index from which to start flood fill for field.
 Defaults to the center x coordinate.</p></li>

latest/developers_guide/landice/generated/compass.landice.mesh.mpas_flood_fill.html

@@ -131,12 +131,12 @@ <h1>compass.landice.mesh.mpas_flood_fill<a class="headerlink" href="#compass-lan
 <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>seed_mask</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – Integer array of locations from which to flood fill
+<li><p><strong>seed_mask</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – Integer array of locations from which to flood fill
 0 = invalid, 1 = valid</p></li>
-<li><p><strong>grow_mask</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – Integer array of locations valid for growing into
+<li><p><strong>grow_mask</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – Integer array of locations valid for growing into
 0 = invalid, 1 = valid</p></li>
-<li><p><strong>cellsOnCell</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – cellsOnCell array from the mpas mesh</p></li>
-<li><p><strong>nEdgesOnCell</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – nEdgesOnCell array from the mpas mesh</p></li>
+<li><p><strong>cellsOnCell</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – cellsOnCell array from the mpas mesh</p></li>
+<li><p><strong>nEdgesOnCell</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – nEdgesOnCell array from the mpas mesh</p></li>
 <li><p><strong>grow_iters</strong> (<em>integer</em>) – optional argument limiting the number of iterations
 over which to extend the mask</p></li>
 </ul>

latest/developers_guide/landice/generated/compass.landice.mesh.preprocess_ais_data.html

@@ -133,7 +133,7 @@ <h1>compass.landice.mesh.preprocess_ais_data<a class="headerlink" href="#compass
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>source_gridded_dataset</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><em>str</em></a>) – name of NetCDF file containing original AIS gridded datasets</p></li>
-<li><p><strong>floodFillMask</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – 0/1 mask of flood filled ice region</p></li>
+<li><p><strong>floodFillMask</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – 0/1 mask of flood filled ice region</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>

latest/developers_guide/landice/generated/compass.landice.mesh.set_cell_width.html

@@ -141,20 +141,20 @@ <h1>compass.landice.mesh.set_cell_width<a class="headerlink" href="#compass-land
 <code class="docutils literal notranslate"><span class="pre">use_dist_to_edge</span></code>, <code class="docutils literal notranslate"><span class="pre">use_dist_to_grounding_line</span></code>, and <code class="docutils literal notranslate"><span class="pre">use_bed</span></code>.
 See the Land-Ice Framework section of the Users or Developers guide
 for more information about these options and their uses.</p></li>
-<li><p><strong>thk</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – Ice thickness field from gridded dataset,
+<li><p><strong>thk</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – Ice thickness field from gridded dataset,
 usually after trimming to flood fill mask</p></li>
-<li><p><strong>bed</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – Bed topography from gridded dataset</p></li>
-<li><p><strong>vx</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a><em>, </em><em>optional</em>) – x-component of ice velocity from gridded dataset,
+<li><p><strong>bed</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – Bed topography from gridded dataset</p></li>
+<li><p><strong>vx</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a><em>, </em><em>optional</em>) – x-component of ice velocity from gridded dataset,
 usually after trimming to flood fill mask. Can be set to <code class="docutils literal notranslate"><span class="pre">None</span></code>
 if <code class="docutils literal notranslate"><span class="pre">use_speed</span> <span class="pre">==</span> <span class="pre">False</span></code> in config file.</p></li>
-<li><p><strong>vy</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a><em>, </em><em>optional</em>) – y-component of ice velocity from gridded dataset,
+<li><p><strong>vy</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a><em>, </em><em>optional</em>) – y-component of ice velocity from gridded dataset,
 usually after trimming to flood fill mask. Can be set to <code class="docutils literal notranslate"><span class="pre">None</span></code>
 if <code class="docutils literal notranslate"><span class="pre">use_speed</span> <span class="pre">==</span> <span class="pre">False</span></code> in config file.</p></li>
-<li><p><strong>dist_to_edge</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a><em>, </em><em>optional</em>) – Distance from each cell to ice edge, calculated in separate function.
+<li><p><strong>dist_to_edge</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a><em>, </em><em>optional</em>) – Distance from each cell to ice edge, calculated in separate function.
 Can be set to <code class="docutils literal notranslate"><span class="pre">None</span></code> if <code class="docutils literal notranslate"><span class="pre">use_dist_to_edge</span> <span class="pre">==</span> <span class="pre">False</span></code> in config file
 and you do not want to set large <code class="docutils literal notranslate"><span class="pre">cell_width</span></code> where cells will be
 culled anyway, but this is not recommended.</p></li>
-<li><p><strong>dist_to_grounding_line</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a><em>, </em><em>optional</em>) – Distance from each cell to grounding line, calculated in separate
+<li><p><strong>dist_to_grounding_line</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a><em>, </em><em>optional</em>) – Distance from each cell to grounding line, calculated in separate
 function.  Can be set to <code class="docutils literal notranslate"><span class="pre">None</span></code> if
 <code class="docutils literal notranslate"><span class="pre">use_dist_to_grounding_line</span> <span class="pre">==</span> <span class="pre">False</span></code> in config file.</p></li>
 <li><p><strong>flood_fill_iStart</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a><em>, </em><em>optional</em>) – x-index location to start flood-fill when using bed topography</p></li>

latest/developers_guide/ocean/generated/compass.ocean.tests.sphere_transport.process_output.compute_convergence_rates.html

@@ -134,9 +134,9 @@ <h1>compass.ocean.tests.sphere_transport.process_output.compute_convergence_rate
 <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>dlambda</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – approximate mesh size</p></li>
-<li><p><strong>linf</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – linf relative error associated with each mesh size</p></li>
-<li><p><strong>l2</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><em>numpy.ndarray</em></a>) – l2 relative error associated with each mesh size</p></li>
+<li><p><strong>dlambda</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – approximate mesh size</p></li>
+<li><p><strong>linf</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – linf relative error associated with each mesh size</p></li>
+<li><p><strong>l2</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – l2 relative error associated with each mesh size</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>