dev

davidhassell · davidhassell · commit 672cb9804649 · 2023-09-13T16:19:33.000+01:00
diff --git a/cf/auxiliarycoordinate.py b/cf/auxiliarycoordinate.py
@@ -36,9 +36,7 @@ class AuxiliaryCoordinate(
 
     {{netCDF variable}}
 
-    The netCDF variable group structure may be accessed with the
-    `nc_set_variable`, `nc_get_variable`, `nc_variable_groups`,
-    `nc_clear_variable_groups` and `nc_set_variable_groups` methods.
+    {{netCDF UGRID node coordinate}}
 
     """
 
diff --git a/cf/cellconnectivity.py b/cf/cellconnectivity.py
@@ -20,11 +20,11 @@ class CellConnectivity(mixin.PropertiesData, cfdm.CellConnectivity):
     connectivity, and properties to describe the data. There must be a
     property indicating the condition by which the connectivity is
     derived from the domain topology. The array spans the domain axis
-    construct with the addition of a ragged dimension that indexes a
-    unique identity for the cell as well as the identities of all
-    other cells to which it is connected. The cell identity must be
-    recorded in the first element of the ragged dimension, otherwise
-    the order is arbitrary. Note that the connectivity array for point
+    construct with the addition of a ragged dimension. For each cell,
+    the first element along the ragged dimension contains the unique
+    identity of the cell, and the following elements contain in
+    arbitrary order the identities of all the other cells to which the
+    cell is connected. Note that the connectivity array for point
     cells is, by definition, equivalent to the array of the domain
     topology construct.
 
@@ -38,7 +38,6 @@ class CellConnectivity(mixin.PropertiesData, cfdm.CellConnectivity):
     UGRID mesh topology variable. The construct array is supplied
     either indirectly by any of the UGRID variables that are used to
     define a domain topology construct, or directly by the UGRID
-    "edge_edge_connectivity" variable (for edge cells) or
     "face_face_connectivity" variable (for face cells). In the direct
     case, the integer indices contained in the UGRID variable may be
     used as the cell identities, although the CF data model attaches
diff --git a/cf/constructs.py b/cf/constructs.py
@@ -47,6 +47,8 @@ class Constructs(cfdm.Constructs):
     * dimension coordinate constructs
     * domain ancillary constructs
     * domain axis constructs
+    * domain topology constructs
+    * cell connectivity constructs
     * cell method constructs
     * field ancillary constructs
 
@@ -126,9 +128,6 @@ def _flip(self, axes):
                 ]
                 construct.flip(iaxes, inplace=True)
 
-    # ----------------------------------------------------------------
-    # Methods
-    # ----------------------------------------------------------------
     def close(self):
         """Close all files referenced by the metadata constructs.
 
diff --git a/cf/data/array/boundsfromnodesarray.py b/cf/data/array/boundsfromnodesarray.py
@@ -1,11 +1,11 @@
 import cfdm
 
 from ...mixin_container import Container
-from .mixin import ArrayMixin, CompressedArrayMixin, MeshArrayMixin
+from .mixin import ArrayMixin, CompressedArrayMixin #, MeshArrayMixin
 
 
 class BoundsFromNodesArray(
-    MeshArrayMixin,
+#    MeshArrayMixin,
     CompressedArrayMixin,
     ArrayMixin,
     Container,
diff --git a/cf/data/array/cellconnectivityarray.py b/cf/data/array/cellconnectivityarray.py
@@ -1,11 +1,11 @@
 import cfdm
 
 from ...mixin_container import Container
-from .mixin import ArrayMixin, CompressedArrayMixin, MeshArrayMixin
+from .mixin import ArrayMixin, CompressedArrayMixin #, MeshArrayMixin
 
 
 class CellConnectivityArray(
-    MeshArrayMixin,
+#    MeshArrayMixin,
     CompressedArrayMixin,
     ArrayMixin,
     Container,
@@ -14,8 +14,8 @@ class CellConnectivityArray(
     """A connectivity array derived from a UGRID connectivity variable.
 
     A UGRID connectivity variable contains indices which map each cell
-    to its neighbours, as found in a UGRID "edge_edge_connectivty",
-    "face_face_connectivty", or "volume_volume_connectivty" variable.
+    to its neighbours, as found in a UGRID "face_face_connectivty" or
+    "volume_volume_connectivty" variable.
 
     The connectivity array has one more column than the corresponding
     UGRID variable. The extra column, in the first position, contains
diff --git a/cf/data/array/gatheredarray.py b/cf/data/array/gatheredarray.py
@@ -32,11 +32,6 @@ def __repr__(self):
         """
         return super().__repr__().replace("<", "<CF ", 1)
 
-    def subarray_parameters(self):
-        """TODOUGRID"""
-        return {}
-
-
 #    def to_dask_array(self, chunks="auto"):
 #        """Convert the data to a `dask` array.
 #
diff --git a/cf/data/array/mixin/__init__.py b/cf/data/array/mixin/__init__.py
@@ -1,6 +1,3 @@
 from .arraymixin import ArrayMixin
 from .compressedarraymixin import CompressedArrayMixin
 from .filearraymixin import FileArrayMixin
-from .mesharraymixin import MeshArrayMixin
-
-# from .raggedarraymixin import RaggedArrayMixin
diff --git a/cf/data/array/mixin/compressedarraymixin.py b/cf/data/array/mixin/compressedarraymixin.py
@@ -50,10 +50,6 @@ def _lock_file_read(self, array):
 
         return array
 
-    def subarray_parameters(self):
-        """TODOUGRID"""
-        raise NotImplementedError("TODOUGRID")
-
     def to_dask_array(self, chunks="auto"):
         """Convert the data to a `dask` array.
 
@@ -92,8 +88,7 @@ def to_dask_array(self, chunks="auto"):
 
         context = partial(config.set, scheduler="synchronous")
 
-        compressed_dimensions = self.compressed_dimensions()
-        conformed_data = self.conformed_data()
+#        compressed_dimensions = self.compressed_dimensions() TODOUGRID
 
         # If possible, convert the compressed data to a dask array
         # that doesn't support concurrent reads. This prevents
@@ -103,12 +98,10 @@ def to_dask_array(self, chunks="auto"):
         # TODO: This won't be necessary if this is refactored so that
         #       the compressed data is part of the same dask graph as
         #       the compressed subarrays.
+        conformed_data = self.conformed_data()
         conformed_data = {
             k: self._lock_file_read(v) for k, v in conformed_data.items()
         }
-
-        # TODO: When the minimum version is Python 3.9, replace with
-        # `subarray_kwargs = conformed_data | self.subarray_parameters()`
         subarray_kwargs = {**conformed_data, **self.subarray_parameters()}
 
         # Get the (cfdm) subarray class
@@ -129,14 +122,13 @@ def to_dask_array(self, chunks="auto"):
             subarray = Subarray(
                 indices=c_indices,
                 shape=u_shape,
-                compressed_dimensions=compressed_dimensions,
+#                compressed_dimensions=compressed_dimensions, # TODOUGRID
                 context_manager=context,
                 **subarray_kwargs,
             )
 
             key = f"{subarray_name}-{tokenize(subarray)}"
             dsk[key] = subarray
-
             dsk[name + chunk_location] = (getter, key, Ellipsis, False, False)
 
         # Return the dask array
diff --git a/cf/data/array/mixin/mesharraymixin.py b/cf/data/array/mixin/mesharraymixin.py
@@ -1,15 +1,15 @@
-class MeshArrayMixin:
-    """Mixin class for data based on a UGRID connectivity array.
-
-    .. versionadded:: UGRIDVER
-
-    """
-
-    def subarray_parameters(self):
-        """TODOUGRID"""
-        return {"start_index": self.get_start_index()}
-
-
+#class MeshArrayMixin:
+#    """Mixin class for data based on a UGRID connectivity array.
+#
+#    .. versionadded:: UGRIDVER
+#
+#    """
+#
+#    def subarray_parameters(self):
+#        """TODOUGRID"""
+#        return {"start_index": self.get_start_index()}
+#
+#
 #    def to_dask_array(self, chunks="auto"):
 #        """Convert the data to a `dask` array.
 #
diff --git a/cf/data/array/pointtopologyarray.py b/cf/data/array/pointtopologyarray.py
@@ -1,11 +1,11 @@
 import cfdm
 
 from ...mixin_container import Container
-from .mixin import ArrayMixin, CompressedArrayMixin, MeshArrayMixin
+from .mixin import ArrayMixin, CompressedArrayMixin #, MeshArrayMixin
 
 
 class PointTopologyArray(
-    MeshArrayMixin,
+#    MeshArrayMixin,
     CompressedArrayMixin,
     ArrayMixin,
     Container,
diff --git a/cf/data/array/subsampledarray.py b/cf/data/array/subsampledarray.py
@@ -192,7 +192,6 @@ def to_dask_array(self, chunks="auto"):
 
             key = f"{subarray_name}-{tokenize(subarray)}"
             dsk[key] = subarray
-
             dsk[name + chunk_location] = (
                 getter,
                 key,
diff --git a/cf/domaintopology.py b/cf/domaintopology.py
@@ -45,17 +45,18 @@ class DomainTopology(mixin.PropertiesData, cfdm.DomainTopology):
     also has a ragged dimension, whose function depends on the spatial
     dimensionality of the cells.
 
-    For point cells, the array's ragged dimension values are composed
-    of the node identity of each cell in the first element, followed
-    in arbitrary order by the identity of each node to which it is
-    connected by a mesh link.
-
-    For edge and face cells, the array's ragged dimension values are
-    the node identities of the boundary vertices of each cell, in the
-    same order that the boundary vertices are stored by the auxiliary
-    coordinate constructs. Each boundary vertex except the last is
-    connected by a mesh link to the next vertex along the ragged
-    dimension, and the last vertex is connected to the first.
+    For each point cell, the first element along the ragged dimension
+    contains the node identity of the cell, and the following elements
+    contain in arbitrary order the identities of all the cells to
+    which it is connected by a mesh link.
+
+    For each edge or face cell, the elements along the ragged
+    dimension contain the node identities of the boundary vertices of
+    the cell, in the same order that the boundary vertices are stored
+    by the auxiliary coordinate constructs. Each boundary vertex
+    except the last is connected by a mesh link to the next vertex
+    along the ragged dimension, and the last vertex is connected to
+    the first.
 
     When a domain topology construct is present it is considered to be
     definitive and must be used in preference to the topology implied
@@ -75,6 +76,28 @@ class DomainTopology(mixin.PropertiesData, cfdm.DomainTopology):
     a variable that references the UGRID mesh topology variable,
     i.e. a data variable or a UGRID location index set variable.
 
+    A single UGRID mesh topology defines multiple domain constructs
+    and defines how they relate to each other. For instance, when
+    "face_node_connectivity" and "edge_node_connectivity" variables
+    are both present there are three implied domain constructs - one
+    each for face, edge and point cells - all of which have the same
+    mesh and so are explicitly linked (e.g. it is known which edge
+    cells define each face cell). The CF data model has no mechanism
+    for explicitly recording such relationships between multiple
+    domain constructs, however whether or not two domains have the
+    same mesh may be reliably deternined by inspection, thereby
+    allowing the creation of netCDF datasets containing UGRID mesh
+    topology variables.
+
+    The restrictions on the type of mesh that may be used with a given
+    cell spatial dimensionality excludes some meshes which can be
+    described by an undirected graph, but is consistent with UGRID
+    encoding within CF-netCDF. UGRID also describes meshes for
+    three-dimensional volume cells that correspond to a volume
+    enclosed by a set of faces, but how the nodes relate to volume
+    boundary vertices is undefined and so volume cells are currently
+    omitted from the CF data model.
+
     See CF Appendix I "The CF Data Model".
 
     **NetCDF interface**
diff --git a/cf/field.py b/cf/field.py
@@ -14740,7 +14740,7 @@ def regrids(
 
             {{weights_file: `str` or `None`, optional}}
 
-               .. versionadded:: 3.15.2
+                .. versionadded:: 3.15.2
 
             {{inplace: `bool`, optional}}
 
@@ -14980,7 +14980,7 @@ def regridc(
 
             {{weights_file: `str` or `None`, optional}}
 
-               .. versionadded:: 3.15.2
+                .. versionadded:: 3.15.2
 
             {{inplace: `bool`, optional}}
 
diff --git a/cf/regrid/regrid.py b/cf/regrid/regrid.py
diff --git a/cf/regrid/regridoperator.py b/cf/regrid/regridoperator.py
