Adding a utility for flattening Aux Coords

.travis.yml

@@ -28,7 +28,7 @@ git:
 
 install:
   - >
-    export IRIS_TEST_DATA_REF="2f3a6bcf25f81bd152b3d66223394074c9069a96";
+    export IRIS_TEST_DATA_REF="dba47566a9147645fea586f94a138e0a8d45a48e";
     export IRIS_TEST_DATA_SUFFIX=$(echo "${IRIS_TEST_DATA_REF}" | sed "s/^v//");
 
   # Cut short doctest phase under Python 2 : now only supports Python 3
@@ -125,17 +125,20 @@ install:
     fi
 
 script:
-  - if [[ $TEST_TARGET == 'default' ]]; then
-      python -m iris.tests.runner --default-tests --system-tests --coding-tests --print-failed-images --num-processors=3;
+  # Capture install-dir: As a test command must be last for get Travis to check
+  # the RC, so it's best to start each operation with an absolute cd.
+  - INSTALL_DIR=$(pwd)
+
+  - >
+    if [[ $TEST_TARGET == 'default' ]]; then
+      export IRIS_REPO_DIR=$INSTALL_DIR;
+      python -m iris.tests.runner --default-tests --system-tests --print-failed-images --num-processors=3;
     fi
+
   - if [[ $TEST_TARGET == 'example' ]]; then
       python -m iris.tests.runner --example-tests --print-failed-images --num-processors=3;
     fi
 
-  # Capture install-dir: As a test command must be last for get Travis to check
-  # the RC, so it's best to start each operation with an absolute cd.
-  - INSTALL_DIR=$(pwd)
-
   - >
     if [[ $TEST_TARGET == 'doctest' ]]; then
       MPL_RC_DIR=$HOME/.config/matplotlib;

docs/iris/src/sphinxext/custom_class_autodoc.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.
 #
@@ -20,6 +20,8 @@
 
 from sphinx.ext import autodoc
 from sphinx.ext.autodoc import *
+from sphinx.util import force_decode
+from sphinx.util.docstrings import prepare_docstring
 
 import inspect
 

docs/iris/src/userguide/cube_statistics.rst

@@ -97,10 +97,6 @@ For an example of using this functionality, the
 in the gallery takes a zonal mean of an ``XYT`` cube by using the
 ``collapsed`` method with ``latitude`` and ``iris.analysis.MEAN`` as arguments.
 
-You cannot partially collapse a multi-dimensional coordinate. See
-:ref:`cube.collapsed <partially_collapse_multi-dim_coord>` for more
-information.
-
 .. _cube-statistics-collapsing-average:
 
 Area averaging

docs/iris/src/whatsnew/2.2.rst

@@ -66,6 +66,9 @@ Iris 2.2 Features
   discontiguous points in coordinates can be explicitly masked
   using another new feature :func:`iris.util.mask_cube`.
 
+* :func:`iris.util.array_equal` now has a 'withnans' keyword, which provides
+  a NaN-tolerant array comparison.
+
 
 Iris 2.2 Dependency updates
 =============================
@@ -89,8 +92,21 @@ Bugs Fixed
 * "Gracefully filling..." warnings are now only issued when the coordinate or
   bound data is actually masked.
 
+
+Bugs fixed in v2.2.1
+--------------------
+
 * Iris can now correctly unpack a column of header objects when saving a
   pandas DataFrame to a cube.
+
+* fixed a bug in :meth:`iris.util.new_axis` : copying the resulting cube
+  resulted in an exception, if it contained an aux-factory.
+
+* :class:`iris.coords.AuxCoord`'s can now test as 'equal' even when the points
+  or bounds arrays contain NaN values, if values are the same at all points.
+  Previously this would fail, as conventionally "NaN != NaN" in normal
+  floating-point arithmetic.
+
 
 
 Documentation Changes

lib/iris/analysis/__init__.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.
 #
@@ -1341,7 +1341,9 @@ def interp_order(length):
 
     # Collapse array to its final data shape.
     slices = [slice(None)] * array.ndim
-    slices[-1] = 0
+    endslice = slice(0, 1) if len(slices) == 1 else 0
+    slices[-1] = endslice
+    slices = tuple(slices)  # Numpy>=1.16 : index with tuple, *not* list.
 
     if isinstance(array.dtype, np.float):
         data = array[slices]

lib/iris/analysis/_interpolation.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2014 - 2017, Met Office
+# (C) British Crown Copyright 2014 - 2019, Met Office
 #
 # This file is part of Iris.
 #

lib/iris/analysis/calculus.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.
 #

lib/iris/analysis/cartography.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.
 #
@@ -717,6 +717,7 @@ def project(cube, target_proj, nx=None, ny=None):
         index = list(index)
         index[xdim] = slice(None, None)
         index[ydim] = slice(None, None)
+        index = tuple(index)  # Numpy>=1.16 : index with tuple, *not* list.
         new_data[index] = cartopy.img_transform.regrid(ll_slice.data,
                                                        source_x, source_y,
                                                        source_cs,

lib/iris/coords.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.
 #
@@ -817,11 +817,13 @@ def __eq__(self, other):
             eq = self._as_defn() == other._as_defn()
             # points comparison
             if eq:
-                eq = iris.util.array_equal(self.points, other.points)
+                eq = iris.util.array_equal(self.points, other.points,
+                                           withnans=True)
             # bounds comparison
             if eq:
                 if self.has_bounds() and other.has_bounds():
-                    eq = iris.util.array_equal(self.bounds, other.bounds)
+                    eq = iris.util.array_equal(self.bounds, other.bounds,
+                                               withnans=True)
                 else:
                     eq = self.bounds is None and other.bounds is None
 

lib/iris/experimental/stratify.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2017, Met Office
+# (C) British Crown Copyright 2017 - 2019, Met Office
 #
 # This file is part of Iris.
 #

lib/iris/fileformats/name_loaders.py

@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2013 - 2017, Met Office
+# (C) British Crown Copyright 2013 - 2019, Met Office
 #
 # This file is part of Iris.
 #