Merge pull request #3320 from znicholls/collections-deprecation-warning

Update in preparation for Python3.8 deprecation of importing ABCs from collections

Author: ajdawson

lib/iris/_constraints.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2010 - 2017, Met Office
+# (C) British Crown Copyright 2010 - 2019, Met Office
 #
 # This file is part of Iris.
 #
@@ -23,7 +23,10 @@
 from six.moves import (filter, input, map, range, zip)  # noqa
 import six
 
-import collections
+try:  # Python 3
+    from collections.abc import Iterable, Mapping
+except:  # Python 2.7
+    from collections import Iterable, Mapping
 import operator
 
 import numpy as np
@@ -98,7 +101,7 @@ def __init__(self, name=None, cube_func=None, coord_values=None, **kwargs):
             raise TypeError('cube_func must be None or callable, got %r'
                             % cube_func)
         if not (coord_values is None or isinstance(coord_values,
-                                                   collections.Mapping)):
+                                                   Mapping)):
             raise TypeError('coord_values must be None or a '
                             'collections.Mapping, got %r' % coord_values)
 
@@ -258,7 +261,7 @@ def extract(self, cube):
         try_quick = False
         if callable(self._coord_thing):
             call_func = self._coord_thing
-        elif (isinstance(self._coord_thing, collections.Iterable) and
+        elif (isinstance(self._coord_thing, Iterable) and
                 not isinstance(self._coord_thing,
                                (six.string_types, iris.coords.Cell))):
             desired_values = list(self._coord_thing)

lib/iris/analysis/__init__.py

@@ -50,7 +50,11 @@
 from six.moves import (filter, input, map, range, zip)  # noqa
 import six
 
-import collections
+from collections import OrderedDict
+try:  # Python 3
+    from collections.abc import Iterable
+except:  # Python 2.7
+    from collections import Iterable
 from functools import wraps
 
 import dask.array as da
@@ -715,7 +719,7 @@ def post_process(self, collapsed_cube, data_result, coords, **kwargs):
         names = [coord.name() for coord in coords]
         coord_name = '{}_over_{}'.format(self.name(), '_'.join(names))
 
-        if not isinstance(points, collections.Iterable):
+        if not isinstance(points, Iterable):
             points = [points]
 
         # Decorate a collapsed cube with a scalar additive coordinate
@@ -764,7 +768,7 @@ def aggregate_shape(self, **kwargs):
         points = kwargs[self._args[0]]
         shape = ()
 
-        if not isinstance(points, collections.Iterable):
+        if not isinstance(points, Iterable):
             points = [points]
 
         points = np.array(points)
@@ -1089,7 +1093,7 @@ def _percentile(data, axis, percent, fast_percentile_method=False,
 
     # Ensure to unflatten any leading dimensions.
     if shape:
-        if not isinstance(percent, collections.Iterable):
+        if not isinstance(percent, Iterable):
             percent = [percent]
         percent = np.array(percent)
         # Account for the additive dimension.
@@ -1207,7 +1211,7 @@ def _weighted_percentile(data, axis, weights, percent, returned=False,
 
     # Ensure to unflatten any leading dimensions.
     if shape:
-        if not isinstance(percent, collections.Iterable):
+        if not isinstance(percent, Iterable):
             percent = [percent]
         percent = np.array(percent)
         # Account for the additive dimension.
@@ -1877,10 +1881,10 @@ def __init__(self, groupby_coords, shared_coords=None):
         self.coords = []
         self._groupby_coords = []
         self._shared_coords = []
-        self._slices_by_key = collections.OrderedDict()
+        self._slices_by_key = OrderedDict()
         self._stop = None
         # Ensure group-by coordinates are iterable.
-        if not isinstance(groupby_coords, collections.Iterable):
+        if not isinstance(groupby_coords, Iterable):
             raise TypeError('groupby_coords must be a '
                             '`collections.Iterable` type.')
 
@@ -1891,7 +1895,7 @@ def __init__(self, groupby_coords, shared_coords=None):
         # coordinates.
         if shared_coords is not None:
             # Ensure shared coordinates are iterable.
-            if not isinstance(shared_coords, collections.Iterable):
+            if not isinstance(shared_coords, Iterable):
                 raise TypeError('shared_coords must be a '
                                 '`collections.Iterable` type.')
             # Add valid shared coordinates.

lib/iris/coords.py

@@ -24,7 +24,11 @@
 import six
 
 from abc import ABCMeta, abstractproperty
-import collections
+from collections import namedtuple
+try:  # Python 3
+    from collections.abc import Iterator
+except:  # Python 2.7
+    from collections import Iterator
 import copy
 from itertools import chain
 from six.moves import zip_longest
@@ -48,10 +52,10 @@
 from iris.util import points_step
 
 
-class CoordDefn(collections.namedtuple('CoordDefn',
-                                       ['standard_name', 'long_name',
-                                        'var_name', 'units',
-                                        'attributes', 'coord_system'])):
+class CoordDefn(namedtuple('CoordDefn',
+                           ['standard_name', 'long_name',
+                            'var_name', 'units',
+                            'attributes', 'coord_system'])):
     """
     Criterion for identifying a specific type of :class:`DimCoord` or
     :class:`AuxCoord` based on its metadata.
@@ -86,11 +90,11 @@ def _sort_key(defn):
         return _sort_key(self) < _sort_key(other)
 
 
-class CoordExtent(collections.namedtuple('_CoordExtent', ['name_or_coord',
-                                                          'minimum',
-                                                          'maximum',
-                                                          'min_inclusive',
-                                                          'max_inclusive'])):
+class CoordExtent(namedtuple('_CoordExtent', ['name_or_coord',
+                                              'minimum',
+                                              'maximum',
+                                              'min_inclusive',
+                                              'max_inclusive'])):
     """Defines a range of values for a coordinate."""
 
     def __new__(cls, name_or_coord, minimum, maximum,
@@ -139,8 +143,8 @@ def __new__(cls, name_or_coord, minimum, maximum,
 
 
 # Private named tuple class for coordinate groups.
-_GroupbyItem = collections.namedtuple('GroupbyItem',
-                                      'groupby_point, groupby_slice')
+_GroupbyItem = namedtuple('GroupbyItem',
+                          'groupby_point, groupby_slice')
 
 
 def _get_2d_coord_bound_grid(bounds):
@@ -184,7 +188,7 @@ def _get_2d_coord_bound_grid(bounds):
     return result
 
 
-class Cell(collections.namedtuple('Cell', ['point', 'bound'])):
+class Cell(namedtuple('Cell', ['point', 'bound'])):
     """
     An immutable representation of a single cell of a coordinate, including the
     sample point and/or boundary position.
@@ -2315,7 +2319,7 @@ def xml_element(self, doc):
 
 
 # See Coord.cells() for the description/context.
-class _CellIterator(collections.Iterator):
+class _CellIterator(Iterator):
     def __init__(self, coord):
         self._coord = coord
         if coord.ndim != 1:
@@ -2331,7 +2335,7 @@ def __next__(self):
 
 
 # See ExplicitCoord._group() for the description/context.
-class _GroupIterator(collections.Iterator):
+class _GroupIterator(Iterator):
     def __init__(self, points):
         self._points = points
         self._start = 0

lib/iris/cube.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2010 - 2018, Met Office
+# (C) British Crown Copyright 2010 - 2019, Met Office
 #
 # This file is part of Iris.
 #
@@ -24,7 +24,19 @@
 from six.moves import (filter, input, map, range, zip)  # noqa
 import six
 
-import collections
+from collections import namedtuple, OrderedDict
+try:  # Python 3
+    from collections.abc import (Iterable,
+                                 Container,
+                                 Mapping,
+                                 MutableMapping,
+                                 Iterator)
+except:  # Python 2.7
+    from collections import (Iterable,
+                             Container,
+                             Mapping,
+                             MutableMapping,
+                             Iterator)
 import copy
 from copy import deepcopy
 import datetime
@@ -58,13 +70,13 @@
 __all__ = ['Cube', 'CubeList', 'CubeMetadata']
 
 
-class CubeMetadata(collections.namedtuple('CubeMetadata',
-                                          ['standard_name',
-                                           'long_name',
-                                           'var_name',
-                                           'units',
-                                           'attributes',
-                                           'cell_methods'])):
+class CubeMetadata(namedtuple('CubeMetadata',
+                              ['standard_name',
+                               'long_name',
+                               'var_name',
+                               'units',
+                               'attributes',
+                               'cell_methods'])):
     """
     Represents the phenomenon metadata for a single :class:`Cube`.
 
@@ -495,7 +507,7 @@ def concatenate_cube(self, check_aux_coords=True):
             raise ValueError("can't concatenate an empty CubeList")
 
         names = [cube.metadata.name() for cube in self]
-        unique_names = list(collections.OrderedDict.fromkeys(names))
+        unique_names = list(OrderedDict.fromkeys(names))
         if len(unique_names) == 1:
             res = iris._concatenate.concatenate(
                 self, error_on_mismatch=True,
@@ -629,7 +641,7 @@ def _is_single_item(testee):
 
     """
     return (isinstance(testee, six.string_types) or
-            not isinstance(testee, collections.Iterable))
+            not isinstance(testee, Iterable))
 
 
 class Cube(CFVariableMixin):
@@ -952,7 +964,7 @@ def _check_multi_dim_metadata(self, metadata, data_dims):
         # Convert to a tuple of integers
         if data_dims is None:
             data_dims = tuple()
-        elif isinstance(data_dims, collections.Container):
+        elif isinstance(data_dims, Container):
             data_dims = tuple(int(d) for d in data_dims)
         else:
             data_dims = (int(data_dims),)
@@ -1064,7 +1076,7 @@ def _add_unique_dim_coord(self, dim_coord, data_dim):
             raise ValueError('The dim_coord may not be an AuxCoord instance.')
 
         # Convert data_dim to a single integer
-        if isinstance(data_dim, collections.Container):
+        if isinstance(data_dim, Container):
             if len(data_dim) != 1:
                 raise ValueError('The supplied data dimension must be a'
                                  ' single number.')
@@ -1366,7 +1378,7 @@ def coords(self, name_or_coord=None, standard_name=None,
                                     if guess_axis(coord_) == axis]
 
         if attributes is not None:
-            if not isinstance(attributes, collections.Mapping):
+            if not isinstance(attributes, Mapping):
                 msg = 'The attributes keyword was expecting a dictionary ' \
                       'type, but got a %s instead.' % type(attributes)
                 raise ValueError(msg)
@@ -1396,7 +1408,7 @@ def attr_filter(coord_):
                                     self.coord_dims(coord_)]
 
         if dimensions is not None:
-            if not isinstance(dimensions, collections.Container):
+            if not isinstance(dimensions, Container):
                 dimensions = [dimensions]
             dimensions = tuple(dimensions)
             coords_and_factories = [coord_ for coord_ in coords_and_factories
@@ -3185,7 +3197,7 @@ def collapsed(self, coords, aggregator, **kwargs):
                                 for coord in coords]
 
             # Remove duplicate dimensions.
-            new_dims = collections.OrderedDict.fromkeys(
+            new_dims = OrderedDict.fromkeys(
                 d for dim in dims_to_collapse for d in dim)
             # Reverse the dimensions so the order can be maintained when
             # reshaping the data.
@@ -3753,7 +3765,7 @@ def regrid(self, grid, scheme):
         return regridder(self)
 
 
-class ClassDict(collections.MutableMapping, object):
+class ClassDict(MutableMapping, object):
     """
     A mapping that stores objects keyed on their superclasses and their names.
 
@@ -3839,7 +3851,7 @@ def sorted_axes(axes):
 
 
 # See Cube.slice() for the definition/context.
-class _SliceIterator(collections.Iterator):
+class _SliceIterator(Iterator):
     def __init__(self, cube, dims_index, requested_dims, ordered):
         self._cube = cube
 

lib/iris/fileformats/cf.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2010 - 2018, Met Office
+# (C) British Crown Copyright 2010 - 2019, Met Office
 #
 # This file is part of Iris.
 #
@@ -30,7 +30,11 @@
 import six
 
 from abc import ABCMeta, abstractmethod
-from collections import Iterable, MutableMapping
+
+try:  # Python 3
+    from collections.abc import Iterable, MutableMapping
+except:  # Python 2.7
+    from collections import Iterable, MutableMapping
 import os
 import re
 import warnings

lib/iris/io/format_picker.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2010 - 2015, Met Office
+# (C) British Crown Copyright 2010 - 2019, Met Office
 #
 # This file is part of Iris.
 #
@@ -25,7 +25,7 @@
     import matplotlib.pyplot as plt
     fagent = fp.FormatAgent()
     png_spec = fp.FormatSpecification('PNG image', fp.MagicNumber(8),
-                                      0x89504E470D0A1A0A, 
+                                      0x89504E470D0A1A0A,
                                       handler=lambda filename: plt.imread(filename),
                                       priority=5
                                       )
@@ -55,7 +55,10 @@
 from six.moves import (filter, input, map, range, zip)  # noqa
 import six
 
-import collections
+try:  # Python 3
+    from collections.abc import Callable
+except:  # Python 2.7
+    from collections import Callable
 import functools
 import os
 import struct
@@ -126,12 +129,12 @@ def get_spec(self, basename, buffer_obj):
                 if buffer_obj is not None and buffer_obj.tell() != 0:
                     # reset the buffer if tell != 0
                     buffer_obj.seek(0)
- 
+
                 element_cache[repr(fmt_elem)] = \
                     fmt_elem.get_element(basename, buffer_obj)
 
             # If we have a callable object, then call it and tests its result, otherwise test using basic equality
-            if isinstance(fmt_elem_value, collections.Callable):
+            if isinstance(fmt_elem_value, Callable):
                 matches = fmt_elem_value(element_cache[repr(fmt_elem)])
             elif element_cache[repr(fmt_elem)] == fmt_elem_value:
                 matches = True
@@ -255,14 +258,14 @@ def __init__(self, requires_fh=True):
 
         """
         self.requires_fh = requires_fh
-    
+
     def get_element(self, basename, file_handle):
         """Called when identifying the element of a file that this FileElement is representing."""
         raise NotImplementedError("get_element must be defined in a subclass")
-        
+
     def __hash__(self):
         return hash(repr(self))
-    
+
     def __repr__(self):
         return '{}()'.format(self.__class__.__name__)