Addresses review comments

MPAS-Dev · Nov 1, 2024 · b427336 · b427336
1 parent 2b3ccad
commit b427336
Show file tree

Hide file tree

Showing 6 changed files with 30 additions and 29 deletions.
diff --git a/compass/ocean/tests/global_ocean/files_for_e3sm/remap_sea_surface_salinity_restoring.py b/compass/ocean/tests/global_ocean/files_for_e3sm/remap_sea_surface_salinity_restoring.py
@@ -29,8 +29,8 @@ def __init__(self, test_case):
                          ntasks=512, min_tasks=1)
 
         self.add_input_file(
-            filename='woa_decav_0.25_sss_monthly_extrap.20241031.nc',
-            target='woa_decav_0.25_sss_monthly_extrap.20241031.nc',
+            filename='woa23_decav_0.25_sss_monthly_extrap.20241031.nc',
+            target='woa23_decav_0.25_sss_monthly_extrap.20241031.nc',
             database='initial_condition_database')
 
         self.add_output_file(filename='sss.WOA23_monthlyClimatology.nc')

diff --git a/compass/ocean/tests/utility/__init__.py b/compass/ocean/tests/utility/__init__.py
@@ -1,7 +1,7 @@
 from compass.ocean.tests.utility.combine_topo import CombineTopo
 from compass.ocean.tests.utility.cull_restarts import CullRestarts
 from compass.ocean.tests.utility.extrap_woa import ExtrapWoa
-from compass.ocean.tests.utility.create_salinity_restoring import CreateSalinRestoring
+from compass.ocean.tests.utility.create_salin_restoring import CreateSalinRestoring
 from compass.testgroup import TestGroup
 
 

diff --git a/...ity/create_salinity_restoring/__init__.py → ...tility/create_salin_restoring/__init__.py b/...ity/create_salinity_restoring/__init__.py → ...tility/create_salin_restoring/__init__.py
@@ -1,5 +1,5 @@
-from compass.ocean.tests.utility.create_salinity_restoring.salinity_restoring import Salinity
-from compass.ocean.tests.utility.create_salinity_restoring.extrap_salin import ExtrapSalin
+from compass.ocean.tests.utility.create_salin_restoring.salinity_restoring import Salinity
+from compass.ocean.tests.utility.create_salin_restoring.extrap_salin import ExtrapSalin
 from compass.testcase import TestCase
 
 
@@ -19,7 +19,7 @@ def __init__(self, test_group):
         test_group : compass.ocean.tests.utility.Utility
             The test group that this test case belongs to
         """
-        super().__init__(test_group=test_group, name='create_salinity_restoring')
+        super().__init__(test_group=test_group, name='create_salin_restoring')
 
         self.add_step(Salinity(test_case=self))
         self.add_step(ExtrapSalin(test_case=self))
diff --git a/...create_salinity_restoring/extrap_salin.py → ...ty/create_salin_restoring/extrap_salin.py b/...create_salinity_restoring/extrap_salin.py → ...ty/create_salin_restoring/extrap_salin.py
@@ -1,5 +1,6 @@
 import numpy as np
 import xarray as xr
+from datetime import datetime
 from scipy.signal import convolve2d
 
 from compass.step import Step
@@ -8,7 +9,7 @@
 class ExtrapSalin(Step):
     """
     Extrapolate WOA 2023 monthly sea surface salinity data into missing ocean
-	regions, including ice cavities and coasts
+    regions, including ice cavities and coasts
 
     Attributes
     ----------
@@ -22,7 +23,7 @@ def __init__(self, test_case):
 
         Parameters
         ----------
-        test_case : compass.ocean.tests.utility.extrap_woa.ExtrapWoa
+        test_case : compass.ocean.tests.utility.create_salin_restoring.CreateSalinRestoring
             The test case this step belongs to
 
         """
@@ -39,7 +40,12 @@ def setup(self):
         """
         Determine the output filename
         """
-        self.woa_filename = 'woa_surface_salinity_monthly_extrap.nc'
+
+        now = datetime.now()
+
+        datestring = now.strftime("%Y%m%d")
+
+        self.woa_filename = f'woa23_decav_0.25_sss_monthly_extrap.{datestring}.nc'
         self.add_output_file(self.woa_filename)
 
     def run(self):
@@ -48,9 +54,9 @@ def run(self):
         cavities.
         """
         # extrapolate horizontally using the ocean mask
-        _extrap_level(self.woa_filename)
+        _extrap(self.woa_filename)
 
-def _extrap_level(out_filename):
+def _extrap(out_filename):
 
     in_filename = 'woa_surface_salinity_monthly.nc'
     ds = xr.open_dataset(in_filename)

diff --git a/..._salinity_restoring/salinity_restoring.py → ...ate_salin_restoring/salinity_restoring.py b/..._salinity_restoring/salinity_restoring.py → ...ate_salin_restoring/salinity_restoring.py
@@ -9,7 +9,7 @@ class Salinity(Step):
     """
     A step for combining January through December sea surface salinity
     data into a single file for salinity restoring in G-cases.
-    The top level data of the monthly woa is utilized.
+    The top level data of the monthly WOA23 is utilized.
     """
 
     def __init__(self, test_case):
@@ -18,7 +18,7 @@ def __init__(self, test_case):
 
         Parameters
         ----------
-        test_case : compass.ocean.tests.utility.extrap_woa.ExtraWoa
+        test_case : compass.ocean.tests.utility.create_salin_restoring.CreateSalinRestoring
             The test case this step belongs to
         """
         super().__init__(test_case, name='salinity_restoring', ntasks=1, min_tasks=1)
@@ -84,29 +84,28 @@ def run(self):
         ds_out['s_an'] = xr.concat(slices, dim='time')
         ds_out['s_an'].attrs = ds_jan['s_an'].attrs
 
-        #Change names of variables and alter attributes
+        # Change names of variables and alter attributes
         ds_out = ds_out.rename_dims({'time':'Time'})
         ds_out = ds_out.rename_vars({'s_an':'SALT'})
-        #ds_out.SALT.attrs['coordinates'] = "Time lat lon"
         ds_out = ds_out.drop_vars('time')
 
         # Create a time index
-        time_var = np.arange(1,12.1,1)
+        time_var = np.arange(1, 12.1, 1)
         ds_out = ds_out.assign(Time=xr.DataArray(time_var, dims=['Time']))
 
         # Create a xtime array
         xtime_list = []
-        for i in range(1,13):
+        for i in range(1, 13):
             xtime_string = f"0000-{i:02d}-15_00:00:00"
             xtime_list.append(xtime_string)
         xtime_out = np.array(xtime_list,dtype='S64')
 
         ds_out = ds_out.assign(xtime=xr.DataArray(xtime_out, dims=['Time']))
 
-        #Change attributes to be consistent with PHC restoring file
+        # Change attributes to be consistent with PHC restoring file
         ds_out.Time.attrs['long_name'] = "Month Index"
         ds_out.Time.attrs['units'] = "month"
         ds_out.Time.attrs['axis'] = "T"
 
-        #Save file and change time dimension to unlimited
-        write_netcdf(ds_out,'woa_surface_salinity_monthly.nc')
+        # Save file and change time dimension to unlimited
+        write_netcdf(ds_out, 'woa_surface_salinity_monthly.nc')
diff --git a/compass/ocean/tests/utility/extrap_woa/extrap_step.py b/compass/ocean/tests/utility/extrap_woa/extrap_step.py
@@ -35,16 +35,12 @@ def __init__(self, test_case):
                          min_cpus_per_task=1, openmp_threads=1)
 
         self.add_input_file(
-            filename='woa_surface_salinity_monthly.nc',
-            target='../salinity_restoring/woa_surface_salinity_monthly.nc')
+            filename='woa.nc',
+            target='../combine/woa_combined.nc')
 
-#        self.add_input_file(
-#            filename='woa.nc',
-#            target='../combine/woa_combined.nc')
-
-#        self.add_input_file(
-#            filename='topography.nc',
-#            target='../remap_topography/topography_remapped.nc')
+        self.add_input_file(
+            filename='topography.nc',
+            target='../remap_topography/topography_remapped.nc')
 
         self.woa_filename = None