fix merge conflicts

Author: davidhassell

Changelog.rst

@@ -1,8 +1,10 @@
-version 3.17.0
+version 3.16.1
 --------------
 
-**2024-??-??**
+**2024-03-01**
 
+* Allow DSG tractories with identical `trajectory_id` values to be
+  aggregated (https://github.com/NCAS-CMS/cf-python/issues/723)
 * New methods: `cf.Field.pad_missing` and `cf.Data.pad_missing`
   (https://github.com/NCAS-CMS/cf-python/issues/717)
 * Fix occasional bug when calculating UGRID cell areas when

DOCUMENTATION.md

@@ -5,7 +5,7 @@
   sphinx-copybutton==0.5.1
   sphinx-toggleprompt==0.2.0
   sphinxcontrib-spelling==4.3.0
-  serializinghtml-serializinghtml==1.1.5
+  sphinxcontrib.serializinghtml==1.1.5
   sphinx==2.4.5
 
 * The `.py` files to generate recipes are stored in `docs/source/recipes/`.

cf/__init__.py

@@ -74,8 +74,8 @@
 """
 
 __Conventions__ = "CF-1.11"
-__date__ = "2023-12-06"
-__version__ = "3.16.0"
+__date__ = "2023-03-01"
+__version__ = "3.16.1"
 
 _requires = (
     "numpy",

cf/aggregate.py

@@ -54,6 +54,7 @@
         "add_offset",
         "calendar",
         "cell_methods",
+        "featureType",
         "_FillValue",
         "flag_masks",
         "flag_meanings",
@@ -210,6 +211,7 @@ class _Meta:
         (
             "Type",
             "Identity",
+            "featureType",
             "Units",
             "Cell_methods",
             "Data",
@@ -389,6 +391,10 @@ def __init__(
         if field_identity:
             self.identity = f.get_property(field_identity, None)
 
+        # Set the DSG featureType
+        featureType = f.get_property("featureType", None)
+        self.featureType = featureType
+
         construct_axes = f.constructs.data_axes()
 
         # ------------------------------------------------------------
@@ -502,6 +508,7 @@ def __init__(
                         "identity": dim_identity,
                         "key": dim_coord_key,
                         "units": units,
+                        "cf_role": None,
                         "hasdata": dim_coord.has_data(),
                         "hasbounds": hasbounds,
                         "coordrefs": self.find_coordrefs(axis),
@@ -539,11 +546,18 @@ def __init__(
                     aux_coord, aux_identity, relaxed_units=relaxed_units
                 )
 
+                # Set the cf_role for DSGs
+                if not featureType:
+                    cf_role = None
+                else:
+                    cf_role = aux_coord.get_property("cf_role", None)
+
                 info_aux.append(
                     {
                         "identity": aux_identity,
                         "key": key,
                         "units": units,
+                        "cf_role": cf_role,
                         "hasdata": aux_coord.has_data(),
                         "hasbounds": aux_coord.has_bounds(),
                         "coordrefs": self.find_coordrefs(key),
@@ -586,12 +600,14 @@ def __init__(
 
                     return
 
+                identity = f"ncvar%{identity}"
                 size = domain_axis.get_size()
 
             axis_identities = {
                 "ids": "identity",
                 "keys": "key",
                 "units": "units",
+                "cf_role": "cf_role",
                 "hasdata": "hasdata",
                 "hasbounds": "hasbounds",
                 "coordrefs": "coordrefs",
@@ -1773,6 +1789,9 @@ def structural_signature(self):
         Cell_methods = self.cell_methods
         Data = self.has_field_data
 
+        # DSG FeatureType
+        featureType = self.featureType
+
         # Properties
         Properties = self.properties
 
@@ -1812,6 +1831,7 @@ def structural_signature(self):
                         ]
                     ),
                 ),
+                ("cf_role", axis[identity]["cf_role"]),
                 ("hasdata", axis[identity]["hasdata"]),
                 ("hasbounds", axis[identity]["hasbounds"]),
                 ("coordrefs", axis[identity]["coordrefs"]),
@@ -1918,6 +1938,7 @@ def structural_signature(self):
         self.signature = self._structural_signature(
             Type=Type,
             Identity=Identity,
+            featureType=featureType,
             Units=Units,
             Cell_methods=Cell_methods,
             Data=Data,
@@ -4147,6 +4168,15 @@ def _hash_values(m):
 
         hash0 = hash1
 
+        # If 'count' is 0 then all of the 1-d coordinates have the
+        # same values across fields. However, for a DSG featureType
+        # axis we can still aggregate it, because it's OK to aggregate
+        # featureTypes with the timeseries_id, profile_id, or
+        # trajectory_id.
+        if not count and dsg_feature_type_axis(m0, axis):
+            a_identity = axis
+            count = 1
+
         if count == 1:
             # --------------------------------------------------------
             # Exactly one axis has different 1-d coordinate values
@@ -4248,10 +4278,22 @@ def _hash_values(m):
             # aggregate anything in this entire group.
             # --------------------------------------------------------
             if info:
-                meta[
-                    0
-                ].message = (
-                    "Some fields have identical sets of 1-d coordinates."
+                coord_ids = []
+                for k, v in m0.axis.items():
+                    coord_ids.extend([repr(i) for i in v["ids"]])
+
+                if len(coord_ids) > 1:
+                    coord_ids = (
+                        f"{', '.join(coord_ids[:-1])} and {coord_ids[-1]}"
+                    )
+                elif coord_ids:
+                    coord_ids = coord_ids[0]
+                else:
+                    coord_ids = ""
+
+                meta[0].message = (
+                    f"Some fields have identical sets of 1-d {coord_ids} "
+                    "coordinates."
                 )
 
             return ()
@@ -4839,6 +4881,19 @@ def _aggregate_2_fields(
 
 
 def f_identity(meta):
+    """Return the field identity for logging strings.
+
+    :Parameters:
+
+        meta: `_Meta`
+            The `_Meta` instance containing the field.
+
+    :Returns:
+
+        `str`
+            The identity.
+
+    """
     identity = meta.identity
     f_identity = meta.field.identity()
     if f_identity == identity:
@@ -4847,3 +4902,38 @@ def f_identity(meta):
         identity = f"{meta.identity!r} ({f_identity})"
 
     return identity
+
+
+def dsg_feature_type_axis(meta, axis):
+    """True if the given axis is a DSG featureType axis.
+
+    A DSG featureType axis has no dimension coordinates and at least
+    one 1-d auxiliary coordinate with a ``cf-role`` property.
+
+    :Parameters:
+
+        meta: `_Meta`
+            The `_Meta` instance
+
+        axis: `str`
+            One of the axes in ``meta.axis_ids``.
+
+    :Returns:
+
+        `bool`
+            `True` if the given axis is a DSG featureType axis.
+
+    """
+    if not meta.featureType:
+        # The field/domain is not a DSG
+        return False
+
+    coords = meta.axis[axis]
+    if coords["dim_coord_index"] is not None:
+        # The axis has dimension coordinates
+        return False
+
+    # Return True if one of the 1-d auxiliary coordinates has a
+    # cf_role property
+    cf_role = coords["cf_role"]
+    return cf_role.count(None) != len(cf_role)

cf/field.py

@@ -2385,27 +2385,27 @@ def cell_area(
                 constructs are considered for cell area
                 creation. Otherwise they are ignored.
 
-                .. versionadded:: 3.17.0
+                .. versionadded:: 3.16.1
 
             coordinates: `bool`, optional
                 If True, the default, then coordinate constructs are
                 considered for cell area creation. Otherwise they are
                 ignored.
 
-                .. versionadded:: 3.17.0
+                .. versionadded:: 3.16.1
 
             methods: `bool`, optional
                 If True, then return a dictionary describing the method
                 used to create the cell areas instead of the default,
                 a field construct.
 
-                .. versionadded:: 3.17.0
+                .. versionadded:: 3.16.1
 
             return_cell_measure: `bool`, optional
                 If True, then return a cell measure construct instead
                 of the default, a field construct.
 
-                .. versionadded:: 3.17.0
+                .. versionadded:: 3.16.1
 
             insert: deprecated at version 3.0.0
 
@@ -3507,15 +3507,15 @@ def weights(
                 ``'volume'``. If False then cell measure constructs
                 are ignored for these *weights*.
 
-                .. versionadded:: 3.17.0
+                .. versionadded:: 3.16.1
 
             coordinates: `bool`, optional
                 If True, the default, then coordinate constructs are
                 considered for weights creation for *weights* of
                 `True` or ``'area'``. If False then coordinate
                 constructs are ignored for these *weights*.
 
-                .. versionadded:: 3.17.0
+                .. versionadded:: 3.16.1
 
             kwargs: deprecated at version 3.0.0.
 
@@ -8719,7 +8719,7 @@ def insert_dimension(
                 metadata constructs that don't already include it. By
                 default, metadata constructs are not changed.
 
-                .. versionadded:: 3.17.0
+                .. versionadded:: 3.16.1
 
             {{inplace: `bool`, optional}}
 
@@ -11960,7 +11960,7 @@ def pad_missing(self, axis, pad_width=None, to_size=None, inplace=False):
          The field's data and all metadata constructs that span the
          axis are padded.
 
-        .. versionadded:: 3.17.0
+        .. versionadded:: 3.16.1
 
         :Parameters:
 
@@ -11978,13 +11978,13 @@ def pad_missing(self, axis, pad_width=None, to_size=None, inplace=False):
 
              {{inplace: `bool`, optional}}
 
-         :Returns:
+        :Returns:
 
-             `Field` or `None`
-                 The padded field construct, or `None` if the operation
-                 was in-place.
+            `Field` or `None`
+                The padded field construct, or `None` if the operation
+                was in-place.
 
-        **Examples*
+        **Examples**
 
         >>> f = cf.example_field(6)
         >>> print(f)

cf/regrid/regrid.py

@@ -1707,6 +1707,12 @@ def create_esmpy_mesh(grid, mask=None):
     node_count = node_ids.size
     node_owners = np.zeros(node_count)
 
+    # Make sure that node IDs are >= 1, as needed by newer versions of
+    # esmpy
+    min_id = node_ids.min()
+    if min_id < 1:
+        node_ids += min_id + 1
+
     # Add nodes. This must be done before `add_elements`.
     esmpy_mesh.add_nodes(
         node_count=node_count,

cf/test/test_aggregate.py

@@ -649,6 +649,21 @@ def test_aggregate_ugrid(self):
         d += 0.1
         self.assertEqual(len(cf.aggregate([f, g])), 2)
 
+    def test_aggregate_trajectory(self):
+        """Test DSG trajectory aggregation"""
+        # Test that aggregation occurs when the tractory_id axes have
+        # identical 1-d auxiliary coordinates
+        f = cf.example_field(11)
+        g = cf.aggregate([f, f], relaxed_identities=True)
+        self.assertEqual(len(g), 1)
+
+        g = g[0]
+        self.assertTrue(
+            g.subspace(**{"cf_role=trajectory_id": [0]}).equals(
+                g.subspace(**{"cf_role=trajectory_id": [1]})
+            )
+        )
+
 
 if __name__ == "__main__":
     print("Run date:", datetime.datetime.now())

docs/source/class/cf.AuxiliaryCoordinate.rst

@@ -262,6 +262,7 @@ Data
    :template: method.rst
 
    ~cf.AuxiliaryCoordinate.halo
+   ~cf.AuxiliaryCoordinate.pad_missing
 
 .. rubric:: *Data array mask*
 

docs/source/class/cf.Bounds.rst

@@ -170,6 +170,16 @@ Data
    ~cf.Bounds.swapaxes
    ~cf.Bounds.transpose
 
+.. rubric:: *Expanding the data*
+
+.. autosummary::
+   :nosignatures:
+   :toctree: ../method/
+   :template: method.rst
+
+   ~cf.Bounds.halo
+   ~cf.Bounds.pad_missing
+
 .. rubric:: *Data array mask*
 
 .. autosummary::
@@ -205,7 +215,6 @@ Data
    :template: method.rst
 
    ~cf.Bounds.__setitem__
-   ~cf.Bounds.halo
    ~cf.Bounds.masked_invalid
    ~cf.Bounds.subspace
    ~cf.Bounds.where