Merge pull request #562 from ESMValGroup/fix_hybrid_height

Added various fixes for hybrid height coordinates
ESMValGroup · Apr 1, 2020 · 6624825 · 6624825
2 parents 8e694c0 + 995d674
commit 6624825
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Showing 79 changed files with 2,096 additions and 449 deletions.
diff --git a/esmvalcore/cmor/_fixes/cmip5/access1_0.py b/esmvalcore/cmor/_fixes/cmip5/access1_0.py
@@ -1,27 +1,28 @@
 """Fixes for the ACCESS1-0 model."""
-
-from cf_units import Unit
 import iris
+from cf_units import Unit
+
+from ..common import ClFixHybridHeightCoord
 from ..fix import Fix
 
 
-# noinspection PyPep8
 class AllVars(Fix):
     """Common fixes to all vars."""
 
     def fix_metadata(self, cubes):
         """
         Fix metadata.
 
-        Fixes wrong calendar 'gregorian' instead of 'proleptic_gregorian'
+        Fixes wrong calendar 'gregorian' instead of 'proleptic_gregorian'.
 
         Parameters
         ----------
-        cube: iris.cube.Cube
+        cubes : iris.cube.CubeList
+            Input cubes which need to be fixed.
 
         Returns
         -------
-        iris.cube.Cube
+        iris.cube.CubeList
 
         """
         for cube in cubes:
@@ -32,3 +33,28 @@ def fix_metadata(self, cubes):
             else:
                 time.units = Unit(time.units.name, 'gregorian')
         return cubes
+
+
+class Cl(ClFixHybridHeightCoord):
+    """Fixes for ``cl``."""
+
+    def fix_metadata(self, cubes):
+        """Remove attributes from ``vertical coordinate formula term: b(k)``.
+
+        Additionally add pressure level coordiante.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes which need to be fixed.
+
+        Returns
+        -------
+        iris.cube.CubeList
+
+        """
+        cubes = super().fix_metadata(cubes)
+        cube = self.get_cube_from_list(cubes)
+        coord = cube.coord(long_name='vertical coordinate formula term: b(k)')
+        coord.attributes = {}
+        return cubes
diff --git a/esmvalcore/cmor/_fixes/cmip5/access1_3.py b/esmvalcore/cmor/_fixes/cmip5/access1_3.py
@@ -1,26 +1,30 @@
 """Fixes for ACCESS1-3 model."""
-
-from cf_units import Unit
 import iris
+from cf_units import Unit
+
 from ..fix import Fix
+from .access1_0 import Cl as BaseCl
+
+
+Cl = BaseCl
 
 
 class AllVars(Fix):
     """Common fixes to all vars."""
 
     def fix_metadata(self, cubes):
-        """
-        Fix metadata.
+        """Fix metadata.
 
         Fixes wrong calendar 'gregorian' instead of 'proleptic_gregorian'
 
         Parameters
         ----------
-        cube: iris.cube.Cube
+        cubes : iris.cube.CubeList
+            Input cubes which need to be fixed.
 
         Returns
         -------
-        iris.cube.Cube
+        iris.cube.CubeList
 
         """
         for cube in cubes:

diff --git a/esmvalcore/cmor/_fixes/cmip5/bcc_csm1_1_m.py b/esmvalcore/cmor/_fixes/cmip5/bcc_csm1_1_m.py
@@ -1,10 +1,9 @@
 """Fixes for bcc-csm1-1-m."""
-from .bcc_csm1_1 import Tos as BaseTos
 from ..common import ClFixHybridPressureCoord
+from .bcc_csm1_1 import Tos as BaseTos
 
 
 Cl = ClFixHybridPressureCoord
 
 
-class Tos(BaseTos):
-    """Fixes for tos."""
+Tos = BaseTos
diff --git a/esmvalcore/cmor/_fixes/cmip5/bnu_esm.py b/esmvalcore/cmor/_fixes/cmip5/bnu_esm.py
@@ -1,27 +1,31 @@
-
-"""Fixes for BNU ESM model."""
+"""Fixes for BNU-ESM model."""
 from cf_units import Unit
 from dask import array as da
 
+from ..common import ClFixHybridPressureCoord
 from ..fix import Fix
 
 
+Cl = ClFixHybridPressureCoord
+
+
 class FgCo2(Fix):
     """Fixes for fgco2."""
 
     def fix_metadata(self, cubes):
         """
         Fix metadata.
 
-        Fixes cube units
+        Fixes cube units.
 
         Parameters
         ----------
-        cube: iris.cube.CubeList
+        cubes : iris.cube.CubeList
+            Input cubes to fix.
 
         Returns
         -------
-        iris.cube.Cube
+        iris.cube.CubeList
 
         """
         self.get_cube_from_list(cubes).units = Unit('kg m-2 s-1')
@@ -31,11 +35,12 @@ def fix_data(self, cube):
         """
         Fix data.
 
-        Fixes cube units
+        Fixes cube units.
 
         Parameters
         ----------
         cube: iris.cube.Cube
+            Input cube to fix.
 
         Returns
         -------
@@ -55,11 +60,12 @@ def fix_metadata(self, cubes):
         """
         Fix metadata.
 
-        Fixes cube units
+        Fixes cube units.
 
         Parameters
         ----------
-        cubes: iris.cube.CubeList
+        cubes : iris.cube.CubeList
+            Input cubes to fix.
 
         Returns
         -------
@@ -73,11 +79,13 @@ def fix_data(self, cube):
         """
         Fix metadata.
 
-        Fixes cube units
+        Fixes cube units.
 
         Parameters
         ----------
         cube: iris.cube.Cube
+            Input cube to fix.
+
 
         Returns
         -------
@@ -97,11 +105,12 @@ def fix_metadata(self, cubes):
         """
         Fix metadata.
 
-        Fixes cube units
+        Fixes cube units.
 
         Parameters
         ----------
-        cubes: iris.cube.CubeList
+        cubes : iris.cube.CubeList
+            Input cubes to fix.
 
         Returns
         -------
@@ -115,11 +124,12 @@ def fix_data(self, cube):
         """
         Fix data.
 
-        Fixes cube units
+        Fixes cube units.
 
         Parameters
         ----------
         cube: iris.cube.Cube
+            Input cube to fix.
 
         Returns
         -------
@@ -139,11 +149,12 @@ def fix_data(self, cube):
         """
         Fix data.
 
-        Fixes cube units
+        Fixes cube units.
 
         Parameters
         ----------
-        cube: iris.cube.Cube
+        cube : iris.cube.Cube
+            Input cube to fix.
 
         Returns
         -------
@@ -167,7 +178,8 @@ def fix_data(self, cube):
 
         Parameters
         ----------
-        cube: iris.cube.Cube
+        cube : iris.cube.Cube
+            Input cube to fix.
 
         Returns
         -------

diff --git a/esmvalcore/cmor/_fixes/cmip5/ccsm4.py b/esmvalcore/cmor/_fixes/cmip5/ccsm4.py
@@ -21,12 +21,12 @@ def fix_data(self, cube):
 
         Parameters
         ----------
-        cubes : iris.cube.Cube
+        cube : iris.cube.Cube
             Input cube.
 
         Returns
         -------
-        iris.cube.CubeList
+        iris.cube.Cube
         """
         cube.data = da.ma.masked_equal(cube.core_data(), 1.e33)
         return cube

diff --git a/esmvalcore/cmor/_fixes/cmip5/hadgem2_es.py b/esmvalcore/cmor/_fixes/cmip5/hadgem2_es.py
@@ -1,20 +1,20 @@
-
 """Fix HadGEM2_ES."""
 import numpy as np
 
+from ..common import ClFixHybridHeightCoord
 from ..fix import Fix
 
 
 class AllVars(Fix):
     """Fix errors common to all vars."""
 
     def fix_metadata(self, cubes):
-        """
-        Fix latitude.
+        """Fix latitude.
 
         Parameters
         ----------
-        cube: iris.cube.CubeList
+        cubes : iris.cube.CubeList
+            Input cubes which need to be fixed.
 
         Returns
         -------
@@ -33,16 +33,19 @@ def fix_metadata(self, cubes):
         return cubes
 
 
+Cl = ClFixHybridHeightCoord
+
+
 class O2(Fix):
     """Fix o2."""
 
     def fix_metadata(self, cubes):
-        """
-        Fix standard and long name.
+        """Fix standard and long name.
 
         Parameters
         ----------
-        cube: iris.cube.CubeList
+        cubes : iris.cube.CubeList
+            Input cubes which need to be fixed.
 
         Returns
         -------

diff --git a/esmvalcore/cmor/_fixes/cmip6/access_cm2.py b/esmvalcore/cmor/_fixes/cmip6/access_cm2.py
@@ -0,0 +1,11 @@
+"""Fixes for ACCESS-CM2."""
+from ..common import ClFixHybridHeightCoord
+
+
+Cl = ClFixHybridHeightCoord
+
+
+Cli = ClFixHybridHeightCoord
+
+
+Clw = ClFixHybridHeightCoord
diff --git a/esmvalcore/cmor/_fixes/cmip6/access_esm1_5.py b/esmvalcore/cmor/_fixes/cmip6/access_esm1_5.py
@@ -0,0 +1,11 @@
+"""Fixes for ACCESS-ESM1-5."""
+from ..common import ClFixHybridHeightCoord
+
+
+Cl = ClFixHybridHeightCoord
+
+
+Cli = ClFixHybridHeightCoord
+
+
+Clw = ClFixHybridHeightCoord
diff --git a/esmvalcore/cmor/_fixes/cmip6/bcc_esm1.py b/esmvalcore/cmor/_fixes/cmip6/bcc_esm1.py
@@ -1,6 +1,6 @@
 """Fixes for BCC-ESM1 model."""
-from .bcc_csm2_mr import Tos as BaseTos
 from ..common import ClFixHybridPressureCoord
+from .bcc_csm2_mr import Tos as BaseTos
 
 
 Cl = ClFixHybridPressureCoord
@@ -12,5 +12,4 @@
 Clw = ClFixHybridPressureCoord
 
 
-class Tos(BaseTos):
-    """Fixes for tos."""
+Tos = BaseTos
diff --git a/esmvalcore/cmor/_fixes/cmip6/cesm2.py b/esmvalcore/cmor/_fixes/cmip6/cesm2.py
@@ -56,12 +56,10 @@ def fix_file(self, filepath, output_dir):
         return new_path
 
 
-class Cli(Cl):
-    """Fixes for ``cli``."""
+Cli = Cl
 
 
-class Clw(Cl):
-    """Fixes for ``clw``."""
+Clw = Cl
 
 
 class Fgco2(Fix):

diff --git a/esmvalcore/cmor/_fixes/cmip6/cesm2_fv2.py b/esmvalcore/cmor/_fixes/cmip6/cesm2_fv2.py
@@ -3,17 +3,13 @@
 from .cesm2 import Tas as BaseTas
 
 
-class Cl(BaseCl):
-    """Fixes for ``cl``."""
+Cl = BaseCl
 
 
-class Clw(Cl):
-    """Fixes for ``clw``."""
+Cli = Cl
 
 
-class Cli(Cl):
-    """Fixes for ``cli``."""
+Clw = Cl
 
 
-class Tas(BaseTas):
-    """Fixes for ``tas``."""
+Tas = BaseTas