ENH: Remove deepcopies when slicing cubes and copying coords

docs/iris/example_code/General/SOI_filtering.py

@@ -52,6 +52,9 @@ def low_pass_weights(window, cutoff):
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # Enable a future option, to ensure that the netcdf load works the same way
     # as in future Iris versions.
     iris.FUTURE.netcdf_promote = True

docs/iris/example_code/General/anomaly_log_colouring.py

@@ -36,6 +36,9 @@
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # Enable a future option, to ensure that the netcdf load works the same way
     # as in future Iris versions.
     iris.FUTURE.netcdf_promote = True

docs/iris/example_code/General/cross_section.py

@@ -15,6 +15,9 @@
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # Enable a future option, to ensure that the netcdf load works the same way
     # as in future Iris versions.
     iris.FUTURE.netcdf_promote = True

docs/iris/example_code/General/custom_aggregation.py

@@ -65,6 +65,9 @@ def count_spells(data, threshold, axis, spell_length):
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # Enable a future option, to ensure that the netcdf load works the same way
     # as in future Iris versions.
     iris.FUTURE.netcdf_promote = True

docs/iris/example_code/General/inset_plot.py

@@ -17,6 +17,9 @@
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # Load the data
     with iris.FUTURE.context(netcdf_promote=True):
         cube1 = iris.load_cube(iris.sample_data_path('ostia_monthly.nc'))

docs/iris/example_code/General/lineplot_with_legend.py

@@ -11,6 +11,9 @@
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     fname = iris.sample_data_path('air_temp.pp')
 
     # Load exactly one cube from the given file.

docs/iris/example_code/General/orca_projection.py

@@ -22,6 +22,9 @@
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # Enable a future option, to ensure that the netcdf load works the same way
     # as in future Iris versions.
     iris.FUTURE.netcdf_promote = True

docs/iris/example_code/General/polynomial_fit.py

@@ -16,6 +16,9 @@
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # Enable a future option, to ensure that the netcdf load works the same way
     # as in future Iris versions.
     iris.FUTURE.netcdf_promote = True

docs/iris/example_code/Meteorology/COP_1d_plot.py

@@ -36,6 +36,9 @@
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # Enable a future option, to ensure that the netcdf load works the same way
     # as in future Iris versions.
     iris.FUTURE.netcdf_promote = True

docs/iris/example_code/Meteorology/COP_maps.py

@@ -50,6 +50,9 @@ def cop_metadata_callback(cube, field, filename):
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # Load e1 and a1 using the callback to update the metadata
     e1 = iris.load_cube(iris.sample_data_path('E1.2098.pp'),
                         callback=cop_metadata_callback)

docs/iris/example_code/Meteorology/deriving_phenomena.py

@@ -38,6 +38,9 @@ def limit_colorbar_ticks(contour_object):
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     fname = iris.sample_data_path('colpex.pp')
 
     # The list of phenomena of interest

docs/iris/example_code/Meteorology/hovmoller.py

@@ -17,6 +17,9 @@
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # Enable a future option, to ensure that the netcdf load works the same way
     # as in future Iris versions.
     iris.FUTURE.netcdf_promote = True

docs/iris/example_code/Meteorology/lagged_ensemble.py

@@ -44,6 +44,9 @@ def realization_metadata(cube, field, fname):
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # extract surface temperature cubes which have an ensemble member
     # coordinate, adding appropriate lagged ensemble metadata
     surface_temp = iris.load_cube(

docs/iris/example_code/Oceanography/atlantic_profiles.py

@@ -22,6 +22,9 @@
 
 
 def main():
+    # Use new behaviour of data-sharing behaviour on indexing.
+    iris.FUTURE.share_data = True
+
     # Enable a future option, to ensure that the netcdf load works the same way
     # as in future Iris versions.
     iris.FUTURE.netcdf_promote = True

docs/iris/src/whatsnew/contributions_1.13/deprecate_2017-Feb-17_share_data.txt

@@ -0,0 +1,3 @@
+* Deprecated the data-copying behaviour of Cube indexing.
+ The `share_data` attribute of `iris.FUTURE` can be used to switch to
+ the new data-sharing behaviour  See :class:`iris.Future`.

lib/iris/__init__.py

@@ -145,7 +145,7 @@ class Future(threading.local):
 
     def __init__(self, cell_datetime_objects=False, netcdf_promote=False,
                  strict_grib_load=False, netcdf_no_unlimited=False,
-                 clip_latitudes=False):
+                 clip_latitudes=False, share_data=False):
         """
         A container for run-time options controls.
 
@@ -200,20 +200,27 @@ def __init__(self, cell_datetime_objects=False, netcdf_promote=False,
         :meth:`iris.coords.Coord.guess_bounds()` method limits the
         guessed bounds to [-90, 90] for latitudes.
 
+        The option `share_data` controls whether indexing a Cube returns
+        a Cube whose data is a view onto the original Cube's data, as
+        opposed to a independent copy of the relevant data.  Conversely, when
+        share_data=False (currently the default), an indexed partial cube
+        always contains fully independent, copied data arrays.
+
         """
         self.__dict__['cell_datetime_objects'] = cell_datetime_objects
         self.__dict__['netcdf_promote'] = netcdf_promote
         self.__dict__['strict_grib_load'] = strict_grib_load
         self.__dict__['netcdf_no_unlimited'] = netcdf_no_unlimited
         self.__dict__['clip_latitudes'] = clip_latitudes
+        self.__dict__['share_data'] = share_data
 
     def __repr__(self):
         msg = ('Future(cell_datetime_objects={}, netcdf_promote={}, '
                'strict_grib_load={}, netcdf_no_unlimited={}, '
-               'clip_latitudes={})')
+               'clip_latitudes={}, share_data={})')
         return msg.format(self.cell_datetime_objects, self.netcdf_promote,
                           self.strict_grib_load, self.netcdf_no_unlimited,
-                          self.clip_latitudes)
+                          self.clip_latitudes, self.share_data)
 
     deprecated_options = {
         'strict_grib_load': ('This is because "iris.fileformats.grib" is now '

lib/iris/coords.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2010 - 2016, Met Office
+# (C) British Crown Copyright 2010 - 2017, Met Office
 #
 # This file is part of Iris.
 #
@@ -522,8 +522,13 @@ def copy(self, points=None, bounds=None):
             raise ValueError('If bounds are specified, points must also be '
                              'specified')
 
-        new_coord = copy.deepcopy(self)
         if points is not None:
+            # We do not perform a deepcopy when we supply new points so as to
+            # not unnecessarily copy the old points.
+            new_coord = copy.copy(self)
+            new_coord.attributes = copy.deepcopy(self.attributes)
+            new_coord.coord_system = copy.deepcopy(self.coord_system)
+
             # Explicitly not using the points property as we don't want the
             # shape the new points to be constrained by the shape of
             # self.points
@@ -533,6 +538,8 @@ def copy(self, points=None, bounds=None):
             # points will result in new bounds, discarding those copied from
             # self.
             new_coord.bounds = bounds
+        else:
+            new_coord = copy.deepcopy(self)
 
         return new_coord
 
@@ -1502,7 +1509,7 @@ def points(self):
 
     @points.setter
     def points(self, points):
-        points = np.array(points, ndmin=1)
+        points = np.array(points, ndmin=1, copy=False)
         # If points are already defined for this coordinate,
         if hasattr(self, '_points') and self._points is not None:
             # Check that setting these points wouldn't change self.shape
@@ -1538,7 +1545,7 @@ def bounds(self):
     def bounds(self, bounds):
         if bounds is not None:
             # Ensure the bounds are a compatible shape.
-            bounds = np.array(bounds, ndmin=2)
+            bounds = np.array(bounds, ndmin=2, copy=False)
             if self.shape != bounds.shape[:-1]:
                 raise ValueError(
                     "The shape of the bounds array should be "

lib/iris/cube.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2010 - 2016, Met Office
+# (C) British Crown Copyright 2010 - 2017, Met Office
 #
 # This file is part of Iris.
 #
@@ -2153,6 +2153,14 @@ def __getitem__(self, keys):
         requested must be applicable directly to the cube.data attribute. All
         metadata will be subsequently indexed appropriately.
 
+        .. deprecated:: 1.13
+            In future, the `data` attribute of the indexing result may be a
+            view onto the original data array, to avoid unnecessary copying.
+            For the present, however, indexing always produces a full
+            independent copy.  The `share_data` attribute of `iris.FUTURE`
+            should be set to True to enable this new data-sharing behaviour
+            (if not, a deprecation warning will be issued).
+
         """
         # turn the keys into a full slice spec (all dims)
         full_slice = iris.util._build_full_slice_given_keys(keys,
@@ -2177,7 +2185,7 @@ def new_cell_measure_dims(cm_):
         try:
             first_slice = next(slice_gen)
         except StopIteration:
-            first_slice = None
+            first_slice = Ellipsis if iris.FUTURE.share_data else None
 
         if first_slice is not None:
             data = self._my_data[first_slice]
@@ -2187,10 +2195,18 @@ def new_cell_measure_dims(cm_):
         for other_slice in slice_gen:
             data = data[other_slice]
 
-        # We don't want a view of the data, so take a copy of it if it's
-        # not already our own.
-        if isinstance(data, biggus.Array) or not data.flags['OWNDATA']:
-            data = copy.deepcopy(data)
+        if not iris.FUTURE.share_data:
+            # We don't want a view of the data, so take a copy of it if it's
+            # not already our own.
+            msg = ('The `data` attribute of the indexing result is currently '
+                   'a copy of the original data array.  This behaviour was '
+                   'deprecated in v1.13.0 and will be replaced with views '
+                   'onto the original data array where possible.  Set '
+                   'iris.FUTURE.share_data=True to switch to the new '
+                   'behaviour.')
+            warn_deprecated(msg)
+            if isinstance(data, biggus.Array) or not data.flags['OWNDATA']:
+                    data = copy.deepcopy(data)
 
         # We can turn a masked array into a normal array if it's full.
         if isinstance(data, ma.core.MaskedArray):
@@ -3108,7 +3124,7 @@ def add_history(self, string):
 
         .. deprecated:: 1.6
             Add/modify history metadata within
-            attr:`~iris.cube.Cube.attributes` as needed.
+            :attr:`~iris.cube.Cube.attributes` as needed.
 
         """
         warn_deprecated("Cube.add_history() has been deprecated - "

lib/iris/tests/test_coord_api.py

@@ -638,30 +638,44 @@ def test_get_set_points_and_bounds(self):
         coord.bounds = [[123, 456], [234, 567], [345, 678]]
         self.assertEqual(coord.shape, (3, ))
         self.assertEqual(coord.bounds.shape, (3, 2))
-        
+
 
 class TestGuessBounds(tests.IrisTest):
     def test_guess_bounds(self):
-        coord = iris.coords.DimCoord(np.array([0, 10, 20, 30]), long_name="foo", units="1")
+        coord = iris.coords.DimCoord(np.array([0, 10, 20, 30]),
+                                     long_name="foo", units="1")
         coord.guess_bounds()
-        self.assertArrayEqual(coord.bounds, np.array([[-5, 5], [5, 15], [15, 25], [25, 35]]))
-
+        self.assertArrayEqual(coord.bounds, np.array([[-5, 5],
+                                                      [5, 15],
+                                                      [15, 25],
+                                                      [25, 35]]))
+
         coord.bounds = None
         coord.guess_bounds(0.25)
-        self.assertArrayEqual(coord.bounds, np.array([[-5, 5], [5, 15], [15, 25], [25, 35]]) + 2.5)
-
+        self.assertArrayEqual(coord.bounds, np.array([[-5, 5],
+                                                      [5, 15],
+                                                      [15, 25],
+                                                      [25, 35]]) + 2.5)
+
         coord.bounds = None
         coord.guess_bounds(0.75)
-        self.assertArrayEqual(coord.bounds, np.array([[-5, 5], [5, 15], [15, 25], [25, 35]]) - 2.5)
+        self.assertArrayEqual(coord.bounds, np.array([[-5, 5],
+                                                      [5, 15],
+                                                      [15, 25],
+                                                      [25, 35]]) - 2.5)
 
         points = coord.points.copy()
         points[2] = 25
         coord.points = points
         coord.bounds = None
         coord.guess_bounds()
-        self.assertArrayEqual(coord.bounds, np.array([[-5., 5.], [5., 17.5], [17.5, 27.5], [27.5, 32.5]]))
-
+        self.assertArrayEqual(coord.bounds, np.array([[-5., 5.],
+                                                      [5., 17.5],
+                                                      [17.5, 27.5],
+                                                      [27.5, 32.5]]))
+
         # if the points are not monotonic, then guess_bounds should fail
+        points = coord.points.copy()
         points[2] = 32
         coord = iris.coords.AuxCoord.from_coord(coord)
         coord.points = points

lib/iris/tests/unit/analysis/cartography/test_project.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2014 - 2016, Met Office
+# (C) British Crown Copyright 2014 - 2017, Met Office
 #
 # This file is part of Iris.
 #
@@ -151,9 +151,9 @@ def test_no_coord_system(self):
         cube.coord('grid_latitude').coord_system = None
         with iris.tests.mock.patch('warnings.warn') as warn:
             _, _ = project(cube, ROBINSON)
-        warn.assert_called_once_with('Coordinate system of latitude and '
-                                     'longitude coordinates is not specified. '
-                                     'Assuming WGS84 Geodetic.')
+        msg = ('Coordinate system of latitude and longitude coordinates is '
+               'not specified. Assuming WGS84 Geodetic.')
+        self.assertIn(msg, warn.call_args_list[0][0][0])
 
 
 if __name__ == '__main__':

lib/iris/tests/unit/analysis/geometry/test_geometry_area_weights.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2014 - 2015, Met Office
+# (C) British Crown Copyright 2014 - 2017, Met Office
 #
 # This file is part of Iris.
 #
@@ -143,9 +143,11 @@ def test_distinct_xy_bounds_pole(self):
         with warnings.catch_warnings(record=True) as w:
             warnings.simplefilter("always")  # always trigger all warnings
             weights = geometry_area_weights(cube, geometry)
-            self.assertEqual(str(w[-1].message), "The geometry exceeds the "
-                             "cube's y dimension at the upper end.")
-            self.assertTrue(issubclass(w[-1].category, UserWarning))
+
+            msg = ("The geometry exceeds the cube's y dimension at the upper "
+                   "end.")
+            ind = [str(rec.message) for rec in w].index(msg)
+            self.assertTrue(issubclass(w[ind].category, UserWarning))
         target = np.array([
             [0, half, half, 0],
             [0, half, half, 0],