Added fixes for hybrid level coordinates of CESM2 models

esmvalcore/cmor/_fixes/cmip6/cesm2.py

@@ -1,12 +1,16 @@
 """Fixes for CESM2 model."""
 from shutil import copyfile
 
-from netCDF4 import Dataset
 import numpy as np
+from netCDF4 import Dataset
 
 from ..fix import Fix
-from ..shared import (add_scalar_depth_coord, add_scalar_height_coord,
-                      add_scalar_typeland_coord, add_scalar_typesea_coord)
+from ..shared import (
+    add_scalar_depth_coord,
+    add_scalar_height_coord,
+    add_scalar_typeland_coord,
+    add_scalar_typesea_coord,
+)
 from .gfdl_esm4 import Siconc as Addtypesi
 
 
@@ -24,27 +28,6 @@ def _fix_formula_terms(self, filepath, output_dir):
         dataset.close()
         return new_path
 
-    def fix_data(self, cube):
-        """Fix data.
-
-        Fixed ordering of vertical coordinate.
-
-        Parameters
-        ----------
-        cube: iris.cube.Cube
-            Input cube to fix.
-
-        Returns
-        -------
-        iris.cube.Cube
-
-        """
-        (z_axis,) = cube.coord_dims(cube.coord(axis='Z', dim_coords=True))
-        indices = [slice(None)] * cube.ndim
-        indices[z_axis] = slice(None, None, -1)
-        cube = cube[tuple(indices)]
-        return cube
-
     def fix_file(self, filepath, output_dir):
         """Fix hybrid pressure coordinate.
 
@@ -77,6 +60,30 @@ def fix_file(self, filepath, output_dir):
         dataset.close()
         return new_path
 
+    def fix_metadata(self, cubes):
+        """Fix ``atmosphere_hybrid_sigma_pressure_coordinate``.
+
+        See discussion in #882 for more details on that.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+
+        """
+        cube = self.get_cube_from_list(cubes)
+        lev_coord = cube.coord(var_name='lev')
+        a_coord = cube.coord(var_name='a')
+        b_coord = cube.coord(var_name='b')
+        lev_coord.points = a_coord.core_points() + b_coord.core_points()
+        lev_coord.bounds = a_coord.core_bounds() + b_coord.core_bounds()
+        lev_coord.units = '1'
+        return cubes
+
 
 Cli = Cl
 

tests/integration/cmor/_fixes/cmip6/test_cesm2.py

@@ -97,15 +97,21 @@ def test_cl_fix_file(mock_get_filepath, tmp_path, test_data_path):
 
 
 @pytest.fixture
-def cl_cube():
+def cl_cubes():
     """``cl`` cube."""
     time_coord = iris.coords.DimCoord(
         [0.0, 1.0], var_name='time', standard_name='time',
         units='days since 1850-01-01 00:00:00')
+    a_coord = iris.coords.AuxCoord(
+        [0.1, 0.2, 0.1], bounds=[[0.0, 0.15], [0.15, 0.25], [0.25, 0.0]],
+        var_name='a', units='1')
+    b_coord = iris.coords.AuxCoord(
+        [0.9, 0.3, 0.1], bounds=[[1.0, 0.8], [0.8, 0.25], [0.25, 0.0]],
+        var_name='b', units='1')
     lev_coord = iris.coords.DimCoord(
-        [0.0, 1.0, 2.0], var_name='lev',
-        standard_name='atmosphere_hybrid_sigma_pressure_coordinate', units='1',
-        attributes={'positive': 'up'})
+        [999.0, 99.0, 9.0], var_name='lev',
+        standard_name='atmosphere_hybrid_sigma_pressure_coordinate',
+        units='hPa', attributes={'positive': 'up'})
     lat_coord = iris.coords.DimCoord(
         [0.0, 1.0], var_name='lat', standard_name='latitude', units='degrees')
     lon_coord = iris.coords.DimCoord(
@@ -122,30 +128,23 @@ def cl_cube():
         standard_name='cloud_area_fraction_in_atmosphere_layer',
         units='%',
         dim_coords_and_dims=coord_specs,
+        aux_coords_and_dims=[(a_coord, 1), (b_coord, 1)],
     )
-    return cube
+    return iris.cube.CubeList([cube])
 
 
-def test_cl_fix_data(cl_cube):
-    """Test ``fix_data`` for ``cl``."""
-    fix = Cl(None)
-    out_cube = fix.fix_data(cl_cube)
-    assert out_cube.shape == cl_cube.shape
-    np.testing.assert_allclose(out_cube.data,
-                               [[[[8, 9],
-                                  [10, 11]],
-                                 [[4, 5],
-                                  [6, 7]],
-                                 [[0, 1],
-                                  [2, 3]]],
-                                [[[20, 21],
-                                  [22, 23]],
-                                 [[16, 17],
-                                  [18, 19]],
-                                 [[12, 13],
-                                  [14, 15]]]])
-    np.testing.assert_allclose(out_cube.coord(var_name='lev').points,
-                               [2.0, 1.0, 0.0])
+def test_cl_fix_metadata(cl_cubes):
+    """Test ``fix_metadata`` for ``cl``."""
+    vardef = get_var_info('CMIP6', 'Amon', 'cl')
+    fix = Cl(vardef)
+    out_cubes = fix.fix_metadata(cl_cubes)
+    out_cube = out_cubes.extract_cube(
+        'cloud_area_fraction_in_atmosphere_layer')
+    lev_coord = out_cube.coord(var_name='lev')
+    assert lev_coord.units == '1'
+    np.testing.assert_allclose(lev_coord.points, [1.0, 0.5, 0.2])
+    np.testing.assert_allclose(lev_coord.bounds,
+                               [[1.0, 0.95], [0.95, 0.5], [0.5, 0.0]])
 
 
 def test_get_cli_fix():

tests/integration/cmor/_fixes/cmip6/test_cesm2_waccm.py

@@ -7,6 +7,7 @@
 import numpy as np
 import pytest
 
+from esmvalcore.cmor._fixes.cmip6.cesm2 import Cl as BaseCl
 from esmvalcore.cmor._fixes.cmip6.cesm2 import Tas as BaseTas
 from esmvalcore.cmor._fixes.cmip6.cesm2_waccm import Cl, Cli, Clw, Tas
 from esmvalcore.cmor.fix import Fix
@@ -18,6 +19,11 @@ def test_get_cl_fix():
     assert fix == [Cl(None)]
 
 
+def test_cl_fix():
+    """Test fix for ``cl``."""
+    assert issubclass(Cl, BaseCl)
+
+
 @pytest.mark.skipif(sys.version_info < (3, 7, 6),
                     reason="requires python3.7.6 or newer")
 @unittest.mock.patch(