Restored/removed all ESMValCore-related files

esmvaltool/cmor/_fixes/CMIP5/GFDL_ESM2G.py

@@ -1,48 +1,49 @@
 # pylint: disable=invalid-name, no-self-use, too-few-public-methods
-"""Fixes for GFDL ESM2G."""
+"""Fixes for GFDL ESM2G"""
 import iris
-
+from iris.coords import AuxCoord
 from ..fix import Fix
 
 
-def _get_and_remove(cubes, long_name):
-    try:
-        cube = cubes.extract_strict(long_name)
-        cubes.remove(cube)
-    except iris.exceptions.ConstraintMismatchError:
-        pass
-
-
 class allvars(Fix):
     """Common fixes."""
 
     def fix_metadata(self, cubes):
-        """Fix metadata.
+        """
+        Fix metadata.
 
-        Fixes bad standard names.
+        Fixes bad standard names
 
         Parameters
         ----------
         cubes: iris.cube.CubeList
 
         Returns
         -------
-        iris.cube.CubeList
+        iris.cube.Cube
 
         """
-        _get_and_remove(cubes, 'Start time for average period')
-        _get_and_remove(cubes, 'End time for average period')
-        _get_and_remove(cubes, 'Length of average period')
+        self._get_and_remove(cubes, 'Start time for average period')
+        self._get_and_remove(cubes, 'End time for average period')
+        self._get_and_remove(cubes, 'Length of average period')
         return cubes
 
+    def _get_and_remove(self, cubes, long_name):
+        try:
+            cube = cubes.extract_strict(long_name)
+            cubes.remove(cube)
+        except iris.exceptions.ConstraintMismatchError:
+            pass
+
 
 class co2(Fix):
     """Fixes for co2."""
 
     def fix_data(self, cube):
-        """Fix data.
+        """
+        Fix data.
 
-        Fixes discrepancy between declared units and real units.
+        Fixes discrepancy between declared units and real units
 
         Parameters
         ----------
@@ -57,25 +58,3 @@ def fix_data(self, cube):
         cube *= 1e6
         cube.metadata = metadata
         return cube
-
-
-class fgco2(Fix):
-    """Fixes for fgco2."""
-
-    def fix_metadata(self, cubes):
-        """Fix metadata.
-
-        Remove unnecessary variables prohibiting cube concatenation.
-
-        Parameters
-        ----------
-        cubes: iris.cube.CubeList
-
-        Returns
-        -------
-        iris.cube.CubeList
-
-        """
-        _get_and_remove(cubes, 'Latitude of tracer (h) points')
-        _get_and_remove(cubes, 'Longitude of tracer (h) points')
-        return cubes

esmvaltool/cmor/tables/custom/CMOR_nbp_grid.dat

@@ -6,11 +6,11 @@ modeling_realm:    land
 !----------------------------------
 ! Variable attributes:
 !----------------------------------
-standard_name:
-units:             kg s-1
+standard_name:     
+units:             kg m-2 s-1
 cell_methods:      time: mean area: mean
 cell_measures:     area: areacella
-long_name:         Carbon Mass Flux out of Atmosphere due to Net Biospheric Production on Land per grid cell
+long_name:         Carbon Mass Flux out of Atmosphere due to Net Biospheric Production on Land (relative to grid cell area)
 comment:           This is the net mass flux of carbon between land and atmosphere calculated as photosynthesis MINUS the sum of  plant and soil respiration, carbonfluxes  from fire, harvest, grazing  and land use change. Positive flux  is into the land.
 !----------------------------------
 ! Additional variable information:

esmvaltool/preprocessor/_derive/__init__.py

@@ -52,8 +52,8 @@ def get_required(short_name):
         and occasionally mip or fx_files.
 
     """
-    derived_variable = ALL_DERIVED_VARIABLES[short_name]
-    variables = deepcopy(derived_variable().required)
+    DerivedVariable = ALL_DERIVED_VARIABLES[short_name]
+    variables = deepcopy(DerivedVariable().required)
     return variables
 
 
@@ -107,8 +107,8 @@ def derive(cubes,
                     "'%s' not found", fx_var, short_name)
 
     # Derive variable
-    derived_variable = ALL_DERIVED_VARIABLES[short_name]
-    cube = derived_variable().calculate(cubes)
+    DerivedVariable = ALL_DERIVED_VARIABLES[short_name]
+    cube = DerivedVariable().calculate(cubes)
 
     # Set standard attributes
     cube.var_name = short_name

esmvaltool/preprocessor/_derive/_shared.py

@@ -1,23 +1,6 @@
 """Auxiliary derivation functions used for multiple variables."""
 
-import logging
-
-import dask.array as da
 import iris
-from iris import Constraint
-
-logger = logging.getLogger(__name__)
-
-
-def var_name_constraint(var_name):
-    """:mod:`iris.Constraint` using `var_name` of a :mod:`iris.cube.Cube`."""
-    return Constraint(cube_func=lambda c: c.var_name == var_name)
-
-
-def shape_is_broadcastable(shape_1, shape_2):
-    """Check if two :mod:`numpy.array' shapes are broadcastable."""
-    return all((m == n) or (m == 1) or (n == 1)
-               for (m, n) in zip(shape_1[::-1], shape_2[::-1]))
 
 
 def cloud_area_fraction(cubes, tau_constraint, plev_constraint):
@@ -37,95 +20,3 @@ def cloud_area_fraction(cubes, tau_constraint, plev_constraint):
         new_cube = new_cube.collapsed('air_pressure', iris.analysis.SUM)
 
     return new_cube
-
-
-def _get_fx_cube(cubes, standard_name, fx_land_name, fx_sea_name=None):
-    """Extract desired fx cubes from list of cubes."""
-    cube = cubes.extract_strict(Constraint(name=standard_name))
-    fx_cube = None
-    invert = False
-    if fx_sea_name is not None:
-        try:
-            fx_cube = cubes.extract_strict(var_name_constraint(fx_sea_name))
-        except iris.exceptions.ConstraintMismatchError:
-            logger.debug(
-                "Cannot correct cube '%s' with '%s', fx file not found",
-                standard_name, fx_sea_name)
-        else:
-            if not shape_is_broadcastable(fx_cube.shape, cube.shape):
-                fx_cube = None
-                invert = True
-                logger.debug(
-                    "Cannot broadcast fx cube '%s' to cube '%s', trying '%s'",
-                    fx_sea_name, standard_name, fx_land_name)
-            else:
-                logger.debug("Using fx cube '%s' to fix '%s'", fx_sea_name,
-                             standard_name)
-    if fx_cube is None:
-        try:
-            fx_cube = cubes.extract_strict(var_name_constraint(fx_land_name))
-        except iris.exceptions.ConstraintMismatchError:
-            logger.debug(
-                "Cannot correct cube '%s' with '%s', fx file not found",
-                standard_name, fx_land_name)
-        else:
-            if not shape_is_broadcastable(fx_cube.shape, cube.shape):
-                fx_cube = None
-                invert = False
-                logger.debug("Cannot broadcast fx cube '%s' to cube '%s'",
-                             fx_land_name, standard_name)
-            else:
-                logger.debug("Using fx cube '%s' to fix '%s'", fx_land_name,
-                             standard_name)
-    return (fx_cube, invert)
-
-
-def grid_area_correction(cubes, standard_name, integrate=True, sea_var=False):
-    """Correct (flux) variable defined relative to land area and integrate."""
-    cube = cubes.extract_strict(Constraint(name=standard_name))
-    core_data = cube.core_data()
-
-    # Area fraction
-    (fraction_cube, invert) = _get_fx_cube(
-        cubes,
-        standard_name,
-        fx_land_name='sftlf',
-        fx_sea_name='sftof' if sea_var else None)
-    if fraction_cube is not None:
-        if not invert:
-            core_data *= fraction_cube.core_data() / 100.0
-        else:
-            fraction = (da.ones_like(fraction_cube.core_data()) -
-                        fraction_cube.core_data() / 100.0)
-            core_data *= fraction
-
-    # Area
-    if integrate:
-        (area_cube, _) = _get_fx_cube(
-            cubes,
-            standard_name,
-            fx_land_name='areacella',
-            fx_sea_name='areacello' if sea_var else None)
-        if area_cube is not None:
-            core_data *= area_cube.core_data()
-            cube.units *= area_cube.units
-        else:
-            try:
-                logger.debug(
-                    "Area files for cube '%s' not found, trying to calculate "
-                    "area using cell bounds", standard_name)
-                for coord_name in ('latitude', 'longitude'):
-                    if not cube.coord(coord_name).has_bounds():
-                        cube.coord(coord_name).guess_bounds()
-                area = iris.analysis.cartography.area_weights(cube)
-                core_data *= area
-            except iris.exceptions.CoordinateMultiDimError as exc:
-                logger.error(
-                    "Cannot integrate irregular cube '%s', necessary area "
-                    "files not found", standard_name)
-                logger.error(cube)
-                raise exc
-
-    # Return cube
-    cube = cube.copy(core_data)
-    return cube