Add mesh and out filename when cropping inactive top

Use `minLevelCell` instead of an argument to determine the number
of inactive top levels.

Author: xylar

compass/ocean/inactive_top_cells.py

@@ -4,7 +4,8 @@
 from mpas_tools.io import write_netcdf
 
 
-def remove_inactive_top_cells_output(in_filename, inactive_top_cells=1):
+def remove_inactive_top_cells_output(in_filename, out_filename=None,
+                                     mesh_filename=None):
     """
     Remove inactive top cells from the output netCDF file
 
@@ -13,16 +14,32 @@ def remove_inactive_top_cells_output(in_filename, inactive_top_cells=1):
     in_filename : str
         Filename for the netCDF file to be cropped
 
-    inactive_top_cells : str, optional
-        The number of inactive top cell layers. It should be equal to
-        ``config.inactive_top_cells``.
+    out_filename : str, optional
+        Filename for the netCDF file after cropping.  Tbe default name is the
+        original file name with ``_crop`` appended before the extension
+
+    mesh_filename : str, optional
+        Filename for an MPAS mesh if not included in the file to be cropped
+
     """
     if not os.path.exists(in_filename):
-        raise OSError('File {} does not exist.'.format(in_filename))
+        raise OSError(f'File {in_filename} does not exist.')
 
-    out_filename = in_filename.split('.')[0] + '_crop.nc'
+    if out_filename is None:
+        basename, ext = os.path.splitext(in_filename)
+        out_filename = f'{basename}_crop{ext}'
 
     with xarray.open_dataset(in_filename) as ds_in:
-        ds_out = ds_in.isel(nVertLevels=slice(1, None))
+        if mesh_filename is None:
+            ds_mesh = ds_in
+        else:
+            ds_mesh = xarray.open_dataset(mesh_filename)
+        minLevelCell = ds_mesh.minLevelCell
+        minval = minLevelCell.min().values
+        maxval = minLevelCell.max().values
+        if minval != maxval:
+            raise ValueError('Expected minLevelCell to have a constant '
+                             'value for inactive top cell tests')
+        ds_out = ds_in.isel(nVertLevels=slice(minval-1, None))
 
     write_netcdf(ds_out, out_filename)

compass/ocean/tests/global_ocean/init/__init__.py

@@ -100,12 +100,24 @@ def validate(self):
                           filename1='initial_state/initial_state.nc')
 
         if self.with_inactive_top_cells:
-            variables = [
-                'temperature', 'salinity', 'layerThickness', 'normalVelocity']
-            compare_variables(test_case=self, variables=variables,
-                              filename1='initial_state/initial_state_crop.nc',
-                              filename2='initial_state/initial_state_comp.nc',
-                              quiet=False, check_outputs=False)
+            # construct the work directory for the other test
+            filename2 = os.path.join(self.base_work_dir, self.mpas_core.name,
+                                     self.test_group.name,
+                                     self.inactive_top_comp_subdir,
+                                     'init/initial_state/initial_state.nc')
+            if os.path.exists(filename2):
+                variables = ['temperature', 'salinity', 'layerThickness',
+                             'normalVelocity']
+                compare_variables(test_case=self, variables=variables,
+                                  filename1='initial_state/initial_state_crop.nc'
+                                  filename2=filename2,
+                                  quiet=False, check_outputs=False,
+                                  skip_if_step_not_run=False)
+
+            else:
+                self.logger.warn('The version of "init" without inactive top '
+                                 'cells was not run.  Skipping\n'
+                                 'validation.')
 
         if self.mesh.with_ice_shelf_cavities:
             variables = ['ssh', 'landIcePressure']

compass/ocean/tests/global_ocean/performance_test/__init__.py

@@ -73,17 +73,21 @@ def validate(self):
             compare_variables(test_case=self, variables=variables,
                               filename1=f'{step_subdir}/output.nc')
 
-            if self.config.has_option('vertical_grid', 'inactive_top_cells'):
-                offset = self.config.getint('vertical_grid', 'inactive_top_cells')
-                if offset > 0:
-                    remove_inactive_top_cells_output('forward/output.nc',
-                                                     inactive_top_cells=offset)
-                    filename2=None
-                    if os.path.exists('forward/output_comp.nc'):
-                        filename2='forward/output_comp.nc'
+            if self.init.with_inactive_top_cells:
+                # construct the work directory for the other test
+                subdir = get_forward_subdir(self.init.inactive_top_comp_subdir,
+                                            self.time_integrator, self.name)
+                filename2 = os.path.join(self.base_work_dir, self.mpas_core.name,
+                                         self.test_group.name, subdir,
+                                         'forward/output.nc')
+                if os.path.exists(filename2):
                     compare_variables(test_case=self, variables=variables,
                                       filename1='forward/output_crop.nc',
                                       filename2=filename2)
+                else:
+                    self.logger.warn('The version of "performance_test" without '
+                                     'inactive top cells was not run.\n'
+                                     'Skipping validation.')
 
             if self.mesh.with_ice_shelf_cavities:
                 variables = [