Update the init test case

Store the `inactive_top_comp_subdir` so we know what files to
compare with during validation.

Use `ds.load()` when modifying `minLevelCell` in the initial state
to prevent issues with reading from and writing to the same file.

Crop inactive top cells after writing out the modified initial
state (because we now use the modified `minLevelCell`).

Set the default to `inactive_top_cells = 0` in a new `init.cfg`
instead of the config file for the QU240 mesh.

Author: xylar

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

@@ -24,6 +24,11 @@ class Init(TestCase):
     init_subdir : str
         The subdirectory within the test group for all test cases with this
         initial condition
+
+    inactive_top_comp_subdir : str
+        If ``with_inactive_top_cells == True``, the subdirectory equivalent to
+        ``init_subdir`` for test cases without inactive top cells for use for
+        validation between tests with and without inactive top cells
     """
     def __init__(self, test_group, mesh, initial_condition,
                  with_inactive_top_cells=False):
@@ -46,6 +51,9 @@ def __init__(self, test_group, mesh, initial_condition,
         ic_dir = initial_condition
         init_subdir = os.path.join(mesh_name, ic_dir)
         if with_inactive_top_cells:
+            # Add the name of the subdir without inactive top cells whether or
+            # not is has or will be run
+            self.inactive_top_comp_subdir = init_subdir
             init_subdir = os.path.join(init_subdir, inactive_top)
         self.init_subdir = init_subdir
         subdir = os.path.join(self.init_subdir, name)

compass/ocean/tests/global_ocean/init/init.cfg

@@ -0,0 +1,5 @@
+# Options related to the vertical grid
+[vertical_grid]
+
+# no inactive top cells by default
+inactive_top_cells = 0

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

@@ -1,18 +1,18 @@
 import os
 from importlib.resources import contents
+
 import xarray
+from mpas_tools.io import write_netcdf
 
 from compass.model import run_model
+from compass.ocean.inactive_top_cells import remove_inactive_top_cells_output
 from compass.ocean.plot import plot_initial_state, plot_vertical_grid
 from compass.ocean.tests.global_ocean.metadata import (
     add_mesh_and_init_metadata,
 )
-from compass.ocean.inactive_top_cells import remove_inactive_top_cells_output
 from compass.ocean.vertical.grid_1d import generate_1d_grid, write_1d_grid
 from compass.step import Step
 
-from mpas_tools.io import write_netcdf
-
 
 class InitialState(Step):
     """
@@ -27,7 +27,7 @@ class InitialState(Step):
     initial_condition : {'WOA23', 'PHC', 'EN4_1900'}
         The initial condition dataset to use
     """
-    def __init__(self, test_case, mesh, initial_condition, 
+    def __init__(self, test_case, mesh, initial_condition,
                  with_inactive_top_cells):
         """
         Create the step
@@ -188,7 +188,7 @@ def run(self):
 
         update_pio = config.getboolean('global_ocean', 'init_update_pio')
         run_model(self, update_pio=update_pio)
- 
+
         if self.with_inactive_top_cells:
 
             logger.info("   * Updating minLevelCell for inactive top cells")
@@ -197,26 +197,32 @@ def run(self):
             out_filename = in_filename
 
             with xarray.open_dataset(in_filename) as ds:
+                ds.load()
 
                 # keep the data set with Time for output
                 ds_out = ds
 
                 ds = ds.isel(Time=0)
 
-                if ('minLevelCell' in ds):
-                    if config.has_option('vertical_grid', 
-                                         'inactive_top_cells'):
-                        offset = config.getint('vertical_grid', 
-                                               'inactive_top_cells')
-                    minLevelCell = ds.minLevelCell+offset
-                    ds_out['minLevelCell'] = minLevelCell
+                if config.has_option('vertical_grid', 'inactive_top_cells'):
+                    offset = config.getint('vertical_grid',
+                                           'inactive_top_cells')
                 else:
-                    logger.info("   - Streams missing for inactive top cells")
+                    offset = 0
 
-            remove_inactive_top_cells_output(in_filename, 
-                                             inactive_top_cells=offset)
+                if 'minLevelCell' in ds:
+                    minLevelCell = ds.minLevelCell + offset
+                    ds_out['minLevelCell'] = minLevelCell
+                else:
+                    logger.info("   - Variable minLevelCell, needed for "
+                                "inactive top cells, is missing from the "
+                                "initial condition")
 
             write_netcdf(ds_out, out_filename)
+
+            remove_inactive_top_cells_output(
+                in_filename=in_filename, out_filename='initial_state_crop.nc')
+
             logger.info("   - Complete")
 
         add_mesh_and_init_metadata(self.outputs, config,