Improve gracefully filling warning (SciTools#3171)

* Realise that running the tests is simpler than I thought

* Make Gracefully warning only appear when filling is required

* Add tests of warnings

* Get rid of install changes, they are in SciTools#3170

* Update after review

* Add whatsnew entry

docs/iris/src/conf.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2010 - 2017, Met Office
+# (C) British Crown Copyright 2010 - 2018, Met Office
 #
 # This file is part of Iris.
 #

docs/iris/src/whatsnew/contributions_2.2.0/bugfix_2018-Sep-19_gracefully-filling-warning-only-when-masked.txt

@@ -0,0 +1 @@
+* Gracefully filling warnings are only issued when the co-ordinate or bound data is actually masked.

lib/iris/analysis/_regrid.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2014 - 2017, Met Office
+# (C) British Crown Copyright 2014 - 2018, Met Office
 #
 # This file is part of Iris.
 #

lib/iris/fileformats/_pyke_rules/fc_rules_cf.krb

@@ -40,7 +40,7 @@ fc_default
 
 #
 # Context:
-#   This rule will trigger iff a grid_mapping() case specific fact 
+#   This rule will trigger iff a grid_mapping() case specific fact
 #   has been asserted that refers to a rotated pole.
 #
 # Purpose:
@@ -120,7 +120,7 @@ fc_provides_grid_mapping_mercator
 
 #
 # Context:
-#   This rule will trigger iff a grid_mapping() case specific fact 
+#   This rule will trigger iff a grid_mapping() case specific fact
 #   has been asserted that refers to a stereographic.
 #
 # Purpose:
@@ -199,10 +199,10 @@ fc_provides_grid_mapping_albers_equal_area
 #
 # Context:
 #   This rule will trigger iff a coordinate() case specific fact
-#   has been asserted that refers to a CF latitude coordinate.     
+#   has been asserted that refers to a CF latitude coordinate.
 #
 # Purpose:
-#   Assert that the CF latitude coordinate exists.    
+#   Assert that the CF latitude coordinate exists.
 #
 fc_provides_coordinate_latitude
     foreach
@@ -435,10 +435,10 @@ fc_build_auxiliary_coordinate_longitude_rotated
 #
 # Context:
 #   This rule will trigger for each auxiliary_coordinate() case specific fact
-#   that is not a spatio-temporal related auxiliary coordinate. 
+#   that is not a spatio-temporal related auxiliary coordinate.
 #
 # Purpose:
-#   Add the auxiliary coordinate to the cube.    
+#   Add the auxiliary coordinate to the cube.
 #
 fc_build_auxiliary_coordinate
     foreach
@@ -457,7 +457,7 @@ fc_build_auxiliary_coordinate
 #   This rule will trigger for each cell_measure case specific fact.
 #
 # Purpose:
-#   Add the cell measures attribute to the cube.  
+#   Add the cell measures attribute to the cube.
 #
 fc_build_cell_measure
     foreach
@@ -549,7 +549,7 @@ fc_build_coordinate_longitude_rotated
         python build_dimension_coordinate(engine, cf_coord_var,
                                           coord_name=CF_VALUE_STD_NAME_GRID_LON,
                                           coord_system=engine.provides['coordinate_system'])
-        python engine.rule_triggered.add(rule.name)        
+        python engine.rule_triggered.add(rule.name)
 
 
 #
@@ -597,7 +597,7 @@ fc_build_coordinate_longitude_nocs
                                           coord_system=None)
         python engine.rule_triggered.add(rule.name)
 
-        
+
 #
 # Context:
 #   This rule will trigger iff a projection_x_coordinate coordinate exists and
@@ -917,8 +917,8 @@ fc_attribute_ukmo__process_flags
         python attr_value = engine.cf_var.ukmo__process_flags
         python engine.cube.attributes['ukmo__process_flags'] = tuple([x.replace("_", " ") for x in attr_value.split(" ")])
         python engine.rule_triggered.add(rule.name)
-        
-        
+
+
 #
 # Context:
 #   This rule will trigger iff a formula term that refers to a
@@ -1076,8 +1076,8 @@ fc_extras
     import iris.std_names
     import iris.util
     from iris._lazy_data import as_lazy_data
-    
-    
+
+
     #
     # UD Units Constants (based on Unidata udunits.dat definition file)
     #
@@ -1087,7 +1087,7 @@ fc_extras
     UD_UNITS_LON = ['degrees_east', 'degree_east', 'degree_e', 'degrees_e',
                     'degreee', 'degreese', 'degrees', 'degrees east',
                     'degree east', 'degree e', 'degrees e']
-    
+
     #
     # CF Dimensionless Vertical Coordinates
     #
@@ -1119,7 +1119,7 @@ fc_extras
     CF_GRID_MAPPING_STEREO = 'stereographic'
     CF_GRID_MAPPING_TRANSVERSE = 'transverse_mercator'
     CF_GRID_MAPPING_VERTICAL = 'vertical_perspective'
-    
+
     #
     # CF Attribute Names.
     #
@@ -1149,7 +1149,7 @@ fc_extras
     CF_ATTR_LONG_NAME = 'long_name'
     CF_ATTR_UNITS = 'units'
     CF_ATTR_CELL_METHODS = 'cell_methods'
-    
+
     #
     # CF Attribute Value Constants.
     #
@@ -1158,11 +1158,11 @@ fc_extras
     CF_VALUE_AXIS_Y = 'y'
     CF_VALUE_AXIS_T = 't'
     CF_VALUE_AXIS_Z = 'z'
-    
-    
+
+
     # Attribute - positive.
     CF_VALUE_POSITIVE = ['down', 'up']
-    
+
     # Attribute - standard_name.
     CF_VALUE_STD_NAME_LAT = 'latitude'
     CF_VALUE_STD_NAME_LON = 'longitude'
@@ -1213,7 +1213,7 @@ fc_extras
             msg = msg.replace('variable', 'variable {!r}'.format(name))
             warnings.warn(message=msg, category=UnknownCellMethodWarning)
 
-        # Set the cube global attributes. 
+        # Set the cube global attributes.
         for attr_name, attr_value in six.iteritems(cf_var.cf_group.global_attributes):
             try:
                 if six.PY2 and isinstance(attr_value, six.text_type):
@@ -1242,7 +1242,7 @@ fc_extras
 
         # Check for a default spherical earth.
         if major is None and minor is None and inverse_flattening is None:
-            major = getattr(cf_grid_var, CF_ATTR_GRID_EARTH_RADIUS, None) 
+            major = getattr(cf_grid_var, CF_ATTR_GRID_EARTH_RADIUS, None)
 
         return major, minor, inverse_flattening
 
@@ -1344,7 +1344,7 @@ fc_extras
                 inverse_flattening is not None:
             ellipsoid = iris.coord_systems.GeogCS(major, minor,
                                                   inverse_flattening)
-						  
+
 	cs = iris.coord_systems.LambertConformal(
             latitude_of_projection_origin, longitude_of_central_meridian,
             false_easting, false_northing, standard_parallel,
@@ -1401,7 +1401,7 @@ fc_extras
         # values for false_easting, false_northing,
         # scale_factor_at_projection_origin and standard_parallel. These are
         # checked elsewhere.
-      
+
         ellipsoid = None
         if major is not None or minor is not None or \
                 inverse_flattening is not None:
@@ -1621,7 +1621,7 @@ fc_extras
         attr_units = get_attr_units(cf_coord_var, attributes)
         points_data = cf_coord_var[:]
         # Gracefully fill points masked array.
-        if ma.isMaskedArray(points_data):
+        if ma.is_masked(points_data):
             points_data = ma.filled(points_data)
             msg = 'Gracefully filling {!r} dimension coordinate masked points'
             warnings.warn(msg.format(str(cf_coord_var.cf_name)))
@@ -1631,7 +1631,7 @@ fc_extras
         if cf_bounds_var is not None:
             bounds_data = cf_bounds_var[:]
             # Gracefully fill bounds masked array.
-            if ma.isMaskedArray(bounds_data):
+            if ma.is_masked(bounds_data):
                 bounds_data = ma.filled(bounds_data)
                 msg = 'Gracefully filling {!r} dimension coordinate masked bounds'
                 warnings.warn(msg.format(str(cf_coord_var.cf_name)))
@@ -1696,7 +1696,7 @@ fc_extras
             else:
                 # Scalar coords are placed in the aux_coords container.
                 cube.add_aux_coord(coord, data_dims)
-            
+
         # Update the coordinate to CF-netCDF variable mapping.
         engine.provides['coordinates'].append((coord, cf_coord_var.cf_name))
 
@@ -1739,7 +1739,7 @@ fc_extras
         # and the coordinate being built.
         common_dims = [dim for dim in cf_coord_var.dimensions
                        if dim in cf_var.dimensions]
-        data_dims = None    
+        data_dims = None
         if common_dims:
             # Calculate the offset of each common dimension.
             data_dims = [cf_var.dimensions.index(dim) for dim in common_dims]
@@ -1763,7 +1763,7 @@ fc_extras
         # Update the coordinate to CF-netCDF variable mapping.
         engine.provides['coordinates'].append((coord, cf_coord_var.cf_name))
 
- 
+
     ################################################################################
     def build_cell_measures(engine, cf_cm_attr, coord_name=None):
         """Create a CellMeasure instance and add it to the cube."""
@@ -1780,19 +1780,19 @@ fc_extras
         # and the coordinate being built.
         common_dims = [dim for dim in cf_cm_attr.dimensions
                        if dim in cf_var.dimensions]
-        data_dims = None    
+        data_dims = None
         if common_dims:
             # Calculate the offset of each common dimension.
             data_dims = [cf_var.dimensions.index(dim) for dim in common_dims]
 
         # Determine the standard_name, long_name and var_name
         standard_name, long_name, var_name = get_names(cf_cm_attr, coord_name, attributes)
-        
+
         # Obtain the cf_measure.
         measure = cf_cm_attr.cf_measure
-        
+
         # Create the CellMeasure
-        cell_measure = iris.coords.CellMeasure(data, 
+        cell_measure = iris.coords.CellMeasure(data,
                                                standard_name=standard_name,
                                                long_name=long_name,
                                                var_name=var_name,
@@ -1802,17 +1802,17 @@ fc_extras
 
         # Add it to the cube
         cube.add_cell_measure(cell_measure, data_dims)
-	
+
 
 
     ################################################################################
     def _is_lat_lon(cf_var, ud_units, std_name, std_name_grid, axis_name, prefixes):
         """
         Determine whether the CF coordinate variable is a latitude/longitude variable.
-        
+
         Ref: [CF] Section 4.1 Latitude Coordinate.
              [CF] Section 4.2 Longitude Coordinate.
-        
+
         """
         is_valid = False
         attr_units = getattr(cf_var, CF_ATTR_UNITS, None)
@@ -1854,7 +1854,7 @@ fc_extras
     def is_latitude(engine, cf_name):
         """Determine whether the CF coordinate variable is a latitude variable."""
         cf_var = engine.cf_var.cf_group[cf_name]
-        return _is_lat_lon(cf_var, UD_UNITS_LAT, CF_VALUE_STD_NAME_LAT, 
+        return _is_lat_lon(cf_var, UD_UNITS_LAT, CF_VALUE_STD_NAME_LAT,
                            CF_VALUE_STD_NAME_GRID_LAT, CF_VALUE_AXIS_Y, ['lat', 'rlat'])
 
 
@@ -1910,7 +1910,7 @@ fc_extras
             is_time_reference = cf_units.Unit(attr_units or 1).is_time_reference()
         except ValueError:
             is_time_reference = False
-        
+
         return is_time_reference and (attr_std_name=='time' or attr_axis.lower()==CF_VALUE_AXIS_T)
 
 
@@ -1978,7 +1978,7 @@ fc_extras
     def has_supported_mercator_parameters(engine, cf_name):
         """Determine whether the CF grid mapping variable has the supported
         values for the parameters of the Mercator projection."""
-        
+
         is_valid = True
         cf_grid_var = engine.cf_var.cf_group[cf_name]
 
@@ -2018,8 +2018,8 @@ fc_extras
     ################################################################################
     def has_supported_stereographic_parameters(engine, cf_name):
         """Determine whether the CF grid mapping variable has a value of 1.0
-        for the scale_factor_at_projection_origin attribute.""" 
-        
+        for the scale_factor_at_projection_origin attribute."""
+
         is_valid = True
         cf_grid_var = engine.cf_var.cf_group[cf_name]
 
@@ -2102,6 +2102,6 @@ fc_extras
                     if len(d[CM_NAME]) != len(comment) and len(comment) == 1:
                         comment = comment*len(d[CM_NAME])
                 d[CM_INTERVAL] = tuple(interval)
-                d[CM_COMMENT] = tuple(comment)               
+                d[CM_COMMENT] = tuple(comment)
                 cell_methods.append(iris.coords.CellMethod(d[CM_METHOD], coords=d[CM_NAME], intervals=d[CM_INTERVAL], comments=d[CM_COMMENT]))
         return tuple(cell_methods)

lib/iris/tests/integration/test_regridding.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2013 - 2017, Met Office
+# (C) British Crown Copyright 2013 - 2018, Met Office
 #
 # This file is part of Iris.
 #

lib/iris/tests/test_coordsystem.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2010 - 2017, Met Office
+# (C) British Crown Copyright 2010 - 2018, Met Office
 #
 # This file is part of Iris.
 #

lib/iris/tests/unit/fileformats/netcdf/test__load_cube.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2014 - 2017, Met Office
+# (C) British Crown Copyright 2014 - 2018, Met Office
 #
 # This file is part of Iris.
 #

lib/iris/tests/unit/fileformats/pp/test_save.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2014 - 2017, Met Office
+# (C) British Crown Copyright 2014 - 2018, Met Office
 #
 # This file is part of Iris.
 #