Improver api changes (#2031)

* missing improver_api_changes

* Update to StandardiseMetadata class init arguments

improver/api/__init__.py

@@ -73,6 +73,7 @@
     "LightningFromCapePrecip": "improver.lightning",
     "LightningMultivariateProbability_USAF2024": "improver.lightning",
     "ManipulateReliabilityTable": "improver.calibration.reliability_calibration",
+    "maximum_in_height": "improver.utilities.cube_manipulation",
     "MaxInTimeWindow": "improver.cube_combiner",
     "MergeCubes": "improver.utilities.cube_manipulation",
     "MergeCubesForWeightedBlending": "improver.blending.weighted_blend",

improver/cli/standardise.py

@@ -57,11 +57,10 @@ def process(
     """
     from improver.standardise import StandardiseMetadata
 
-    return StandardiseMetadata()(
-        cube,
+    return StandardiseMetadata(
         new_name=new_name,
         new_units=new_units,
         coords_to_remove=coords_to_remove,
         coord_modification=coord_modification,
         attributes_dict=attributes_config,
-    )
+    )(cube)

improver/standardise.py

@@ -28,6 +28,46 @@
 class StandardiseMetadata(BasePlugin):
     """Plugin to standardise cube metadata"""
 
+    def __init__(
+        self,
+        new_name: Optional[str] = None,
+        new_units: Optional[str] = None,
+        coords_to_remove: Optional[List[str]] = None,
+        coord_modification: Optional[Dict[str, float]] = None,
+        attributes_dict: Optional[Dict[str, Any]] = None,
+    ):
+        """
+        Instantiate our class for standardising cube metadata.
+
+        Args:
+            new_name:
+                Optional rename for output cube
+            new_units:
+                Optional unit conversion for output cube
+            coords_to_remove:
+                Optional list of scalar coordinates to remove from output cube
+            coord_modification:
+                Optional dictionary used to directly modify the values of
+                scalar coordinates. To be used with extreme caution.
+                For example this dictionary might take the form:
+                {"height": 1.5} to set the height coordinate to have a value
+                of 1.5m (assuming original units of m).
+                This can be used to align e.g. temperatures defined at slightly
+                different heights where this difference is considered small
+                enough to ignore. Type is inferred, so providing a value of 2
+                will result in an integer type, whilst a value of 2.0 will
+                result in a float type.
+            attributes_dict:
+                Optional dictionary of required attribute updates. Keys are
+                attribute names, and values are the required changes.
+                See improver.metadata.amend.amend_attributes for details.
+        """
+        self._new_name = new_name
+        self._new_units = new_units
+        self._coords_to_remove = coords_to_remove
+        self._coord_modification = coord_modification
+        self._attributes_dict = attributes_dict
+
     @staticmethod
     def _rm_air_temperature_status_flag(cube: Cube) -> Cube:
         """
@@ -198,15 +238,7 @@ def _discard_redundant_cell_methods(cube: Cube) -> None:
 
         cube.cell_methods = updated_cms
 
-    def process(
-        self,
-        cube: Cube,
-        new_name: Optional[str] = None,
-        new_units: Optional[str] = None,
-        coords_to_remove: Optional[List[str]] = None,
-        coord_modification: Optional[Dict[str, float]] = None,
-        attributes_dict: Optional[Dict[str, Any]] = None,
-    ) -> Cube:
+    def process(self, cube: Cube) -> Cube:
         """
         Perform compulsory and user-configurable metadata adjustments.  The
         compulsory adjustments are:
@@ -220,27 +252,6 @@ def process(
         Args:
             cube:
                 Input cube to be standardised
-            new_name:
-                Optional rename for output cube
-            new_units:
-                Optional unit conversion for output cube
-            coords_to_remove:
-                Optional list of scalar coordinates to remove from output cube
-            coord_modification:
-                Optional dictionary used to directly modify the values of
-                scalar coordinates. To be used with extreme caution.
-                For example this dictionary might take the form:
-                {"height": 1.5} to set the height coordinate to have a value
-                of 1.5m (assuming original units of m).
-                This can be used to align e.g. temperatures defined at slightly
-                different heights where this difference is considered small
-                enough to ignore. Type is inferred, so providing a value of 2
-                will result in an integer type, whilst a value of 2.0 will
-                result in a float type.
-            attributes_dict:
-                Optional dictionary of required attribute updates. Keys are
-                attribute names, and values are the required changes.
-                See improver.metadata.amend.amend_attributes for details.
 
         Returns:
             The processed cube
@@ -249,16 +260,16 @@ def process(
         cube = self._rm_air_temperature_status_flag(cube)
         cube = self._collapse_scalar_dimensions(cube)
 
-        if new_name:
-            cube.rename(new_name)
-        if new_units:
-            cube.convert_units(new_units)
-        if coords_to_remove:
-            self._remove_scalar_coords(cube, coords_to_remove)
-        if coord_modification:
-            self._modify_scalar_coord_value(cube, coord_modification)
-        if attributes_dict:
-            amend_attributes(cube, attributes_dict)
+        if self._new_name:
+            cube.rename(self._new_name)
+        if self._new_units:
+            cube.convert_units(self._new_units)
+        if self._coords_to_remove:
+            self._remove_scalar_coords(cube, self._coords_to_remove)
+        if self._coord_modification:
+            self._modify_scalar_coord_value(cube, self._coord_modification)
+        if self._attributes_dict:
+            amend_attributes(cube, self._attributes_dict)
         self._discard_redundant_cell_methods(cube)
 
         # this must be done after unit conversion as if the input is an integer

improver_tests/standardise/test_StandardiseMetadata.py

@@ -25,14 +25,13 @@ class HaltExecution(Exception):
 def test_as_cubelist_called(mock_as_cube):
     mock_as_cube.side_effect = HaltExecution
     try:
-        StandardiseMetadata()(
-            sentinel.cube,
+        StandardiseMetadata(
             new_name=sentinel.new_name,
             new_units=sentinel.new_units,
             coords_to_remove=sentinel.coords_to_remove,
             coord_modification=sentinel.coord_modification,
             attributes_dict=sentinel.attributes_dict,
-        )
+        )(sentinel.cube)
     except HaltExecution:
         pass
     mock_as_cube.assert_called_once_with(sentinel.cube)
@@ -51,12 +50,11 @@ def setUp(self):
             time_bounds=[datetime(2019, 10, 10, 23), datetime(2019, 10, 11)],
             frt=datetime(2019, 10, 10, 18),
         )
-        self.plugin = StandardiseMetadata()
 
     def test_null(self):
         """Test process method with default arguments returns an unchanged
         cube"""
-        result = self.plugin.process(self.cube.copy())
+        result = StandardiseMetadata().process(self.cube.copy())
         self.assertIsInstance(result, iris.cube.Cube)
         self.assertArrayAlmostEqual(result.data, self.cube.data)
         self.assertEqual(result.metadata, self.cube.metadata)
@@ -72,7 +70,7 @@ def test_standardise_time_coords(self):
                 np.float64
             )
         self.cube.coord("forecast_period").convert_units("hours")
-        result = self.plugin.process(self.cube)
+        result = StandardiseMetadata().process(self.cube)
         self.assertEqual(result.coord("forecast_period").units, "seconds")
         self.assertEqual(result.coord("forecast_period").points.dtype, np.int32)
         self.assertEqual(result.coord("forecast_period").bounds.dtype, np.int32)
@@ -86,13 +84,13 @@ def test_standardise_time_coords_missing_fp(self):
             np.float64
         )
         self.cube.remove_coord("forecast_period")
-        result = self.plugin.process(self.cube)
+        result = StandardiseMetadata().process(self.cube)
         self.assertEqual(result.coord("time").points.dtype, np.int64)
 
     def test_collapse_scalar_dimensions(self):
         """Test scalar dimension is collapsed"""
         cube = iris.util.new_axis(self.cube, "time")
-        result = self.plugin.process(cube)
+        result = StandardiseMetadata().process(cube)
         dim_coord_names = [coord.name() for coord in result.coords(dim_coords=True)]
         aux_coord_names = [coord.name() for coord in result.coords(dim_coords=False)]
         self.assertSequenceEqual(result.shape, (5, 5))
@@ -104,7 +102,7 @@ def test_realization_not_collapsed(self):
         realization = AuxCoord([1], "realization")
         self.cube.add_aux_coord(realization)
         cube = iris.util.new_axis(self.cube, "realization")
-        result = self.plugin.process(cube)
+        result = StandardiseMetadata().process(cube)
         dim_coord_names = [coord.name() for coord in result.coords(dim_coords=True)]
         self.assertSequenceEqual(result.shape, (1, 5, 5))
         self.assertIn("realization", dim_coord_names)
@@ -129,14 +127,14 @@ def test_metadata_changes(self):
         # Modifier for scalar height coordinate
         coord_modification = {"height": 2.0}
 
-        result = self.plugin.process(
-            self.cube,
+        plugin = StandardiseMetadata(
             new_name=new_name,
             new_units="degC",
             coords_to_remove=["forecast_period"],
             coord_modification=coord_modification,
             attributes_dict=attribute_changes,
         )
+        result = plugin.process(self.cube)
         self.assertEqual(result.name(), new_name)
         self.assertEqual(result.units, "degC")
         self.assertArrayAlmostEqual(result.data, expected_data, decimal=5)
@@ -150,11 +148,10 @@ def test_attempt_modify_dimension_coord(self):
 
         coord_modification = {"latitude": [0.1, 1.2, 3.4, 5.6, 7]}
         msg = "Modifying dimension coordinate values is not allowed "
+        plugin = StandardiseMetadata(coord_modification=coord_modification)
 
         with self.assertRaisesRegex(ValueError, msg):
-            self.plugin.process(
-                self.cube, coord_modification=coord_modification,
-            )
+            plugin.process(self.cube)
 
     def test_attempt_modify_multi_valued_coord(self):
         """Test that an exception is raised if the coord_modification is used
@@ -168,10 +165,9 @@ def test_attempt_modify_multi_valued_coord(self):
         coord_modification = {"kittens": [2, 3, 4, 5, 6]}
         msg = "Modifying multi-valued coordinates is not allowed."
 
+        plugin = StandardiseMetadata(coord_modification=coord_modification)
         with self.assertRaisesRegex(ValueError, msg):
-            self.plugin.process(
-                cube, coord_modification=coord_modification,
-            )
+            plugin.process(cube)
 
     def test_attempt_modify_time_coord(self):
         """Test that an exception is raised if the coord_modification targets
@@ -181,10 +177,9 @@ def test_attempt_modify_time_coord(self):
         for coord in ["time", "forecast_period", "forecast_reference_time"]:
             coord_modification = {coord: 100}
 
+            plugin = StandardiseMetadata(coord_modification=coord_modification)
             with self.assertRaisesRegex(ValueError, msg):
-                self.plugin.process(
-                    self.cube, coord_modification=coord_modification,
-                )
+                plugin.process(self.cube)
 
     def test_discard_cellmethod(self):
         """Test changes to cell_methods"""
@@ -193,7 +188,7 @@ def test_discard_cellmethod(self):
             iris.coords.CellMethod(method="point", coords="time"),
             iris.coords.CellMethod(method="max", coords="realization"),
         ]
-        result = self.plugin.process(cube,)
+        result = StandardiseMetadata().process(cube)
         self.assertEqual(
             result.cell_methods,
             (iris.coords.CellMethod(method="max", coords="realization"),),
@@ -203,7 +198,7 @@ def test_float_deescalation(self):
         """Test precision de-escalation from float64 to float32"""
         cube = self.cube.copy()
         cube.data = cube.data.astype(np.float64)
-        result = self.plugin.process(cube)
+        result = StandardiseMetadata().process(cube)
         self.assertEqual(result.data.dtype, np.float32)
         self.assertArrayAlmostEqual(result.data, self.cube.data, decimal=4)
 
@@ -213,7 +208,7 @@ def test_float_deescalation_with_unit_change(self):
         cube = set_up_variable_cube(
             np.ones((5, 5), dtype=np.int16), name="rainrate", units="mm h-1"
         )
-        result = self.plugin.process(cube, new_units="m s-1")
+        result = StandardiseMetadata(new_units="m s-1").process(cube)
         self.assertEqual(cube.dtype, np.float32)
         self.assertEqual(result.data.dtype, np.float32)
 
@@ -237,7 +232,7 @@ def test_air_temperature_status_flag_coord(self):
         # surface altitude.
         result_no_sf = cube.copy()
         result_no_sf.data[:, 0, ...] = np.nan
-        target = self.plugin.process(result_no_sf)
+        target = StandardiseMetadata().process(result_no_sf)
 
         cube_with_flags = cube.copy()
         flag_status = np.zeros((3, 3, 5, 5), dtype=np.int8)
@@ -253,7 +248,7 @@ def test_air_temperature_status_flag_coord(self):
         )
         cube_with_flags.add_aux_coord(status_flag_coord, (0, 1, 2, 3))
 
-        result = self.plugin.process(cube_with_flags)
+        result = StandardiseMetadata().process(cube_with_flags)
         self.assertArrayEqual(result.data, target.data)
         self.assertEqual(result.coords(), target.coords())
 
@@ -277,7 +272,7 @@ def test_air_temperature_status_flag_coord_without_realization(self):
         # surface altitude.
         result_no_sf = cube.copy()
         result_no_sf.data[0, ...] = np.nan
-        target = self.plugin.process(result_no_sf)
+        target = StandardiseMetadata().process(result_no_sf)
 
         cube_with_flags = cube.copy()
         flag_status = np.zeros((3, 5, 5), dtype=np.int8)
@@ -293,7 +288,7 @@ def test_air_temperature_status_flag_coord_without_realization(self):
         )
         cube_with_flags.add_aux_coord(status_flag_coord, (0, 1, 2))
 
-        result = self.plugin.process(cube_with_flags)
+        result = StandardiseMetadata().process(cube_with_flags)
         self.assertArrayEqual(result.data, target.data)
         self.assertEqual(result.coords(), target.coords())