Implementation of UGRID (part 2 of 2): Write

Changelog.rst

@@ -1,4 +1,13 @@
 Version NEXTVERSION
+----------------
+
+**2026-03-??**
+
+* Write UGRID datasets with `cfdm.write`
+  (https://github.com/NCAS-CMS/cfdm/issues/271)
+
+Version 1.12.4.0
+----------------
 
 **2026-01-??**
 
@@ -9,10 +18,10 @@ Version NEXTVERSION
   `cfdm.read` (https://github.com/NCAS-CMS/cfdm/issues/355)
 * New function `cfdm.dataset_flatten` that replaces the deprecated
   `cfdm.netcdf_flatten` (https://github.com/NCAS-CMS/cfdm/issues/355)
-* New optional dependency: ``zarr>=3.1.3``
-* Removed dependency (now optional): ``zarr>=3.0.8``
 * Reduce the time taken to import `cfdm`
   (https://github.com/NCAS-CMS/cfdm/issues/361)
+* New optional dependency: ``zarr>=3.1.3``
+* Removed dependency (now optional): ``zarr>=3.0.8``
 
 ----
 

cfdm/cellconnectivity.py

@@ -4,6 +4,7 @@
 
 class CellConnectivity(
     mixin.NetCDFVariable,
+    mixin.NetCDFConnectivityDimension,
     mixin.Topology,
     mixin.PropertiesData,
     mixin.Files,

cfdm/cfdmimplementation.py

@@ -419,6 +419,25 @@ def get_bounds_ncvar(self, parent, default=None):
 
         return self.nc_get_variable(bounds, default=default)
 
+    def get_cell_connectivities(self, parent):
+        """Return the cell connectivities from a parent.
+
+        .. versionadded:: (cfdm) NEXTVERSION
+
+        :Parameters:
+
+            parent: `Field` or `Domain`
+                The parent object.
+
+        :Returns:
+
+            `dict`
+                A dictionary whose values are cell connectivity
+                objects, keyed by unique identifiers.
+
+        """
+        return parent.cell_connectivities(todict=True)
+
     def get_cell_measures(self, field):
         """Return all of the cell measure constructs of a field.
 
@@ -1012,6 +1031,25 @@ def get_domain_axis_size(self, field, axis):
         """
         return field.domain_axes(todict=True)[axis].get_size()
 
+    def get_domain_topologies(self, parent):
+        """Return the domain topologies from  a parent.
+
+        .. versionadded:: (cfdm) NEXTVERSION
+
+        :Parameters:
+
+            parent: `Field` or `Domain`
+                The parent object.
+
+        :Returns:
+
+            `dict`
+                A dictionary whose values are domain topology objects,
+                keyed by unique identifiers.
+
+        """
+        return parent.domain_topologies(todict=True)
+
     def get_sample_dimension_position(self, construct):
         """Returns the position of the compressed data sample dimension.
 
@@ -1983,16 +2021,23 @@ def get_tie_points(self, construct, default=None):
 
         return data.source(default)
 
-    def initialise_AuxiliaryCoordinate(self):
+    def initialise_AuxiliaryCoordinate(self, **kwargs):
         """Return an auxiliary coordinate construct.
 
+        :Parameters:
+
+            kwargs: optional
+                Parameters with whcih to intialising the object.
+
+                .. versionadded:: (cfdm) NEXTVERSION
+
         :Returns:
 
             `AuxiliaryCoordinate`
 
         """
         cls = self.get_class("AuxiliaryCoordinate")
-        return cls()
+        return cls(**kwargs)
 
     def initialise_Bounds(self):
         """Return a bounds component.
@@ -3421,26 +3466,6 @@ def set_dependent_tie_points(self, construct, tie_points, dimensions):
         )
         construct.set_data(data)
 
-    def set_mesh_id(self, parent, mesh_id):
-        """Set a mesh identifier.
-
-        .. versionadded:: (cfdm)  1.11.0.0
-
-        :Parameters:
-
-            parent: construct
-                The construct on which to set the mesh id
-
-            mesh_id:
-                The mesh identifier.
-
-        :Returns:
-
-            `None`
-
-        """
-        parent.set_mesh_id(mesh_id)
-
     def nc_set_external(self, construct):
         """Set the external status of a construct.
 

cfdm/data/data.py

@@ -737,12 +737,6 @@ def __getitem__(self, indices):
         # ------------------------------------------------------------
         new._set_dask(dx, clear=self._ALL ^ self._CFA, in_memory=None)
 
-        if 0 in new.shape:
-            raise IndexError(
-                f"Index [{original_indices}] selects no elements from "
-                f"data with shape {original_shape}"
-            )
-
         # ------------------------------------------------------------
         # Get the axis identifiers for the subspace
         # ------------------------------------------------------------

cfdm/data/mixin/compressedarraymixin.py

@@ -5,49 +5,6 @@ class CompressedArrayMixin:
 
     """
 
-    def _lock_file_read(self, array):
-        """Try to return an array that doesn't support concurrent reads.
-
-        .. versionadded:: (cfdm) 1.11.2.0
-
-        :Parameters:
-
-            array: array_like
-                The array to process.
-
-        :Returns"
-
-            `dask.array.Array` or array_like
-                The new `dask` array, or the orginal array if it
-                couldn't be ascertained how to form the `dask` array.
-
-        """
-        try:
-            return array.to_dask_array()
-        except AttributeError:
-            pass
-
-        try:
-            chunks = array.chunks
-        except AttributeError:
-            chunks = "auto"
-
-        try:
-            array = array.source()
-        except (ValueError, AttributeError):
-            pass
-
-        try:
-            array.get_filename()
-        except AttributeError:
-            pass
-        else:
-            import dask.array as da
-
-            array = da.from_array(array, chunks=chunks, lock=True)
-
-        return array
-
     def to_dask_array(self, chunks="auto"):
         """Convert the data to a `dask` array.
 
@@ -87,18 +44,7 @@ def to_dask_array(self, chunks="auto"):
 
         context = partial(config.set, scheduler="synchronous")
 
-        # If possible, convert the compressed data to a dask array
-        # that doesn't support concurrent reads. This prevents
-        # "compute called by compute" failures problems at compute
-        # time.
-        #
-        # 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()
-        }
         subarray_kwargs = {**conformed_data, **self.subarray_parameters()}
 
         # Get the (cfdm) subarray class

cfdm/data/netcdfindexer.py

@@ -249,13 +249,15 @@ def __getitem__(self, index):
             # E.g.     index : (1, np.newaxis, slice(1, 5))
             #      =>  index1: (1, slice(1, 5))
             #      and index2: (slice(None), np.newaxis, slice(None))
-        except ValueError:
+        except (ValueError, TypeError):
             # Something went wrong, which is indicative of the
             # variable not supporting the appropriate slicing method
             # (e.g. `h5netcdf` might have returned "ValueError: Step
-            # must be >= 1 (got -2)"). Therefore we'll just get the
-            # entire array as a numpy array, and then try indexing
-            # that.
+            # must be >= 1 (got -2)" or "TypeError: Indexing elements
+            # must be in increasing order").
+            #
+            # Therefore we'll just get the entire array as a numpy
+            # array, and then try indexing that.
             data = self._index(Ellipsis)
             data = self._index(index, data=data)
 

cfdm/data/subarray/cellconnectivitysubarray.py

@@ -40,6 +40,7 @@ def __getitem__(self, indices):
             stop += 1
 
         data = self._select_data(check_mask=True)
+
         if np.ma.isMA(data):
             empty = np.ma.empty
         else:

cfdm/data/subarray/mixin/pointtopology.py

@@ -25,7 +25,29 @@ def __getitem__(self, indices):
         from cfdm.functions import integer_dtype
 
         start_index = self.start_index
-        node_connectivity = self._select_data(check_mask=False)
+        node_connectivity = self._select_data(check_mask=True)
+
+        # ------------------------------------------------------------
+        # E.g. For faces, 'node_connectivity' might be (two
+        #      quadrilaterals and one triangle):
+        #
+        #      [[3 4 2 1 ]
+        #       [5 6 4 3 ]
+        #       [7 2 4 --]]
+        #
+        # E.g. For nine edges of the above faces, 'node_connectivity'
+        #      is
+        #
+        #      [[2 7]
+        #       [4 7]
+        #       [4 2]
+        #       [1 2]
+        #       [3 1]
+        #       [3 4]
+        #       [3 5]
+        #       [6 5]
+        #       [4 6]]
+        # ------------------------------------------------------------
 
         masked = np.ma.isMA(node_connectivity)
 
@@ -49,8 +71,15 @@ def __getitem__(self, indices):
         cols_extend = cols.extend
         u_extend = u.extend
 
+        unique_nodes = np.unique(node_connectivity)
+        if masked:
+            # Remove the missing value from unique nodes
+            unique_nodes = unique_nodes[:-1]
+
+        unique_nodes = unique_nodes.tolist()
+
         # WARNING (TODO): This loop is a potential performance bottleneck.
-        for node in np.unique(node_connectivity).tolist():
+        for node in unique_nodes:
             # Find the collection of all nodes that are joined to this
             # node via links in the mesh, including this node itself
             # (which will be at the start of the list).
@@ -62,10 +91,11 @@ def __getitem__(self, indices):
             cols_extend(range(n_nodes))
             u_extend(nodes)
 
+        del unique_nodes
+
         u = np.array(u, dtype=integer_dtype(largest_node_id))
         u = csr_array((u, cols, pointers))
         u = u.toarray()
-
         if any(map(isnan, self.shape)):
             # Store the shape, now that is it known.
             self._set_component("shape", u.shape, copy=False)
@@ -76,6 +106,20 @@ def __getitem__(self, indices):
         # Mask all zeros
         u = np.ma.where(u == 0, np.ma.masked, u)
 
+        # ------------------------------------------------------------
+        # E.g. For both of the face and edges examples above, 'u' is
+        #      now
+        #
+        #      [[1 2 3 -- --]
+        #       [2 1 4  7 --]
+        #       [3 1 4  5 --]
+        #       [4 2 3  6  7]
+        #       [5 3 6 -- --]
+        #       [6 4 5 -- --]
+        #       [7 2 4 -- --]]
+        #
+        # ------------------------------------------------------------
+
         if not start_index:
             # Subtract 1 to get back to zero-based node identities
             u -= 1