xnetcdf and 2-d lat/lon coordinates

.github/workflows/run-test-suite.yml

@@ -100,13 +100,6 @@ jobs:
         cd ${{ github.workspace }}/main
         pip install --no-deps -e .
 
-    # Make UMRead library
-    - name: Make UMRead
-      shell: bash -l {0}
-      run: |
-        cd ${{ github.workspace }}/main/cf/umread_lib/c-lib
-        make
-
     # Install the coverage library
     # We do so with conda which was setup in a previous step.
     - name: Install coverage

.gitignore

@@ -21,11 +21,6 @@ cf/test/*.txt
 cf/test/.coverage
 cf/test/cf_coverage_report/
 
-# C object files generated by tests under cf/umread_lib/ and its sub-dirs:
-cf/umread_lib/c-lib/*.o
-cf/umread_lib/c-lib/*.so
-cf/umread_lib/c-lib/type-dep/*.o
-
 # packaging-related files changing with environment adjustments:
 *.egg-info/
 

Changelog.rst

@@ -3,6 +3,24 @@ Version NEXTVERSION
 
 **2026-08-??**
 
+* New keywords to `cf.read`: ``backend``, ``backend_options``,
+  ``cfa_filesystem``, ``cfa_backend``, ``cfa_backend_options``
+  (https://github.com/NCAS-CMS/cf-python/issues/961)
+* Deprecated keyword to `cfdm.read`: ``netcdf_backend``
+  (https://github.com/NCAS-CMS/cf-python/issues/961)
+* Dataset reads are now entirely managed by `xnetcdf` and its backend
+  libraries (via `cfdm.read`)
+  (https://github.com/NCAS-CMS/cf-python/issues/961)
+* Read with `cf.read` anything that can be read by `xarray`
+  (https://github.com/NCAS-CMS/cf-python/issues/961)
+* Convert `xarray.Dataset` and `xarray.DataTree` to `cf.Field` via
+  `cf.read` (https://github.com/NCAS-CMS/cf-python/issues/961)
+* Convert `pyfive.File`, `zarr.Group`, `h5py.File`, `umfile.File`, and
+  `xnetcdf.Dataset` to `cf.Field` via `cf.read`
+  (https://github.com/NCAS-CMS/cf-python/issues/961)
+* Extend `cf.Field.create_latlon_coordinates` to allow the creation of
+  2-d latitudes/longitudes from plane projection and rotated pole
+  coordinates (https://github.com/NCAS-CMS/cf-python/issues/962)
 * Automatically create consolidated HDF5 metadata with `cf.write`.
   New keywords to `cf.write`: ``hdf5_consolidated_metadata`` and
   ``hdf5_expansion_factor``
@@ -17,6 +35,7 @@ Version NEXTVERSION
 * New output format for `cf.write` that creates an `xarray` dataset in
   memory: ``'XARRAY'``
   (https://github.com/NCAS-CMS/cf-python/issues/933)
+* New optional dependency: ``umfive>=0.3.0``
 * New optional dependency: ``xarray>=2026.7.0``
 
 ----

MANIFEST.in

@@ -9,7 +9,7 @@ recursive-exclude cf/data *.rst
 prune cf/test
 recursive-include cf/test __init__.py test_*.py 
 recursive-include cf/test cfa_test.sh run_tests.py setup_create_field.py create_test_files*.py individual_tests.sh
-recursive-include cf/test test_file.nc test_file[2-4].nc file.nc file[1-9].nc ugrid_global_1.nc ugrid_global_2.nc create_test_files.npz create_test_files_2.npz wgdos_packed.pp extra_data.pp file1.pp *.cdl create_test_files.npz create_test_files_2.npz example_field_0.nc cell_measures.nc
+recursive-include cf/test test_file.nc test_file[2-4].nc file.nc file[1-9].nc ugrid_global_1.nc ugrid_global_2.nc create_test_files.npz create_test_files_2.npz wgdos_packed.pp extra_data.pp file1.pp rotated_pole.pp *.cdl create_test_files.npz create_test_files_2.npz example_field_0.nc cell_measures.nc
 recursive-include cf/test/example_field_0.zarr[23] *
 include cf/test/example_field_0.kerchunk
 prune cf/test/dir

cf/__init__.py

@@ -104,8 +104,8 @@
 # Check the version of cfdm (this is worth doing because of the very
 # tight coupling between cf and cfdm, and the risk of bad things
 # happening at run time if the versions are mismatched).
-_minimum_vn = "1.13.2.1"
-_maximum_vn = "1.13.3.0"
+_minimum_vn = "1.13.3.0"
+_maximum_vn = "1.13.4.0"
 _cfdm_vn = Version(cfdm.__version__)
 if _cfdm_vn < Version(_minimum_vn) or _cfdm_vn >= Version(_maximum_vn):
     raise RuntimeError(
@@ -172,6 +172,7 @@
     ScipyNetcdfFileArray,
     SubsampledArray,
     UMArray,
+    XnetcdfArray,
     ZarrArray,
 )
 

cf/cfimplementation.py

@@ -32,16 +32,12 @@
     BoundsFromNodesArray,
     CellConnectivityArray,
     GatheredArray,
-    H5netcdfArray,
-    NetCDF4Array,
     PointTopologyArray,
-    PyfiveArray,
     RaggedContiguousArray,
     RaggedIndexedArray,
     RaggedIndexedContiguousArray,
-    ScipyNetcdfFileArray,
     SubsampledArray,
-    ZarrArray,
+    XnetcdfArray,
 )
 from .functions import CF
 
@@ -147,18 +143,14 @@ def set_construct(self, parent, construct, axes=None, copy=True, **kwargs):
     BoundsFromNodesArray=BoundsFromNodesArray,
     CellConnectivityArray=CellConnectivityArray,
     GatheredArray=GatheredArray,
-    H5netcdfArray=H5netcdfArray,
-    NetCDF4Array=NetCDF4Array,
-    ScipyNetcdfFileArray=ScipyNetcdfFileArray,
     PointTopologyArray=PointTopologyArray,
-    PyfiveArray=PyfiveArray,
     Quantization=Quantization,
     RaggedContiguousArray=RaggedContiguousArray,
     RaggedIndexedArray=RaggedIndexedArray,
     RaggedIndexedContiguousArray=RaggedIndexedContiguousArray,
     SubsampledArray=SubsampledArray,
     TiePointIndex=TiePointIndex,
-    ZarrArray=ZarrArray,
+    XnetcdfArray=XnetcdfArray,
 )
 
 
@@ -174,51 +166,5 @@ def implementation():
         `CFImplementation`
             A container for the CF data model implementation.
 
-    **Examples**
-
-    >>> i = cf.implementation()
-    >>> i
-    <CFImplementation: >
-    >>> i.classes()
-    {'AuxiliaryCoordinate': cf.auxiliarycoordinate.AuxiliaryCoordinate,
-     'BoundsFromNodesArray': cf.data.array.boundsfromnodesarray.BoundsFromNodesArray,
-     'CellConnectivity': cf.cellconnectivity.CellConnectivity,
-     'CellConnectivityArray': cf.data.array.cellconnectivityarray.CellConnectivityArray,
-     'CellMeasure': cf.cellmeasure.CellMeasure,
-     'CellMethod': cf.cellmethod.CellMethod,
-     'CoordinateReference': cf.coordinatereference.CoordinateReference,
-     'DimensionCoordinate': cf.dimensioncoordinate.DimensionCoordinate,
-     'Domain': cf.domain.Domain,
-     'DomainAncillary': cf.domainancillary.DomainAncillary,
-     'DomainAxis': cf.domainaxis.DomainAxis,
-     'DomainTopology': cf.domaintopology.DomainTopology,
-     'Field': cf.field.Field,
-     'FieldAncillary': cf.fieldancillary.FieldAncillary,
-     'Bounds': cf.bounds.Bounds,
-     'InteriorRing': cf.interiorring.InteriorRing,
-     'InterpolationParameter': cf.interpolationparameter.InterpolationParameter,
-     'CoordinateConversion': cf.coordinateconversion.CoordinateConversion,
-     'Datum': cf.datum.Datum,
-     'List': cf.list.List,
-     'Index': cf.index.Index,
-     'Count': cf.count.Count,
-     'NodeCountProperties': cf.nodecountproperties.NodeCountProperties,
-     'PartNodeCountProperties': cf.partnodecountproperties.PartNodeCountProperties,
-     'Data': cf.data.data.Data,
-     'GatheredArray': cf.data.array.gatheredarray.GatheredArray,
-     'H5netcdfArray': cf.data.array.h5netcdfarray.H5netcdfArray,
-     'NetCDF4Array': cf.data.array.netcdf4array.NetCDF4Array,
-     'ScipyNetcdfFileArray': cf.data.array.scipynetcdffilearray.ScipyNetcdfFileArray,
-     'PointTopologyArray': <class 'cf.data.array.pointtopologyarray.PointTopologyArray'>,
-     'PyfiveArray': cf.data.array.pyfivearray.PyfiveArray,
-     'Quantization': cf.quantization.Quantization,
-     'RaggedContiguousArray': cf.data.array.raggedcontiguousarray.RaggedContiguousArray,
-     'RaggedIndexedArray': cf.data.array.raggedindexedarray.RaggedIndexedArray,
-     'RaggedIndexedContiguousArray': cf.data.array.raggedindexedcontiguousarray.RaggedIndexedContiguousArray,
-     'SubsampledArray': cf.data.array.subsampledarray.SubsampledArray,
-     'TiePointIndex': cf.tiepointindex.TiePointIndex,
-     'ZarrArray': cf.data.array.zarrarray.ZarrArray,
-    }
-
     """
     return _implementation.copy()

cf/data/array/__init__.py

@@ -14,4 +14,5 @@
 from .raggedindexedcontiguousarray import RaggedIndexedContiguousArray
 from .subsampledarray import SubsampledArray
 from .umarray import UMArray
+from .xnetcdfarray import XnetcdfArray
 from .zarrarray import ZarrArray

cf/data/array/aggregatedarray.py

@@ -19,5 +19,5 @@ def __new__(cls, *args, **kwargs):
         """
         # Override the inherited FragmentFileArray class
         instance = super().__new__(cls)
-        instance._FragmentArray["uri"] = FragmentFileArray
+        instance._AggregatedArray__FragmentArray["uri"] = FragmentFileArray
         return instance

cf/data/array/h5netcdfarray.py

@@ -1,16 +1,15 @@
-import cfdm
-
-from ...mixin_container import Container
-from .mixin import ActiveStorageMixin
-
-
-class H5netcdfArray(
-    ActiveStorageMixin,
-    Container,
-    cfdm.H5netcdfArray,
-):
+class H5netcdfArray:
     """A netCDF array accessed with `h5netcdf` using the `h5py` backend.
 
     .. versionadded:: 3.16.3
 
     """
+
+    def __init__(self, *args, **kwargs):
+        class DeprecationError(Exception):
+            """Deprecation error."""
+
+        raise DeprecationError(
+            f"{self.__class__.__name__} was deprecated at version NEXTVERSION "
+            "and is no longer available. Use XnetcdfArray instead."
+        )

cf/data/array/netcdf4array.py

@@ -1,12 +1,11 @@
-import cfdm
-
-from ...mixin_container import Container
-from .mixin import ActiveStorageMixin
+class NetCDF4Array:
+    """A netCDF array accessed with `netCDF4`."""
 
+    def __init__(self, *args, **kwargs):
+        class DeprecationError(Exception):
+            """Deprecation error."""
 
-class NetCDF4Array(
-    ActiveStorageMixin,
-    Container,
-    cfdm.NetCDF4Array,
-):
-    """A netCDF array accessed with `netCDF4`."""
+        raise DeprecationError(
+            f"{self.__class__.__name__} was deprecated at version NEXTVERSION "
+            "and is no longer available. Use XnetcdfArray instead."
+        )

cf/data/array/pyfivearray.py

@@ -1,16 +1,15 @@
-import cfdm
-
-from ...mixin_container import Container
-from .mixin import ActiveStorageMixin
-
-
-class PyfiveArray(
-    ActiveStorageMixin,
-    Container,
-    cfdm.PyfiveArray,
-):
+class PyfiveArray:
     """A netCDF array accessed with `pyfive`.
 
     .. versionadded:: 3.20.0
 
     """
+
+    def __init__(self, *args, **kwargs):
+        class DeprecationError(Exception):
+            """Deprecation error."""
+
+        raise DeprecationError(
+            f"{self.__class__.__name__} was deprecated at version NEXTVERSION "
+            "and is no longer available. Use XnetcdfArray instead."
+        )

cf/data/array/scipynetcdffilearray.py

@@ -1,14 +1,15 @@
-import cfdm
-
-from ...mixin_container import Container
-
-
-class ScipyNetcdfFileArray(
-    Container,
-    cfdm.ScipyNetcdfFileArray,
-):
+class ScipyNetcdfFileArray:
     """A netCDF-3 array accessed with `scipy.io.netcdf_file`.
 
     .. versionadded:: 3.20.0
 
     """
+
+    def __init__(self, *args, **kwargs):
+        class DeprecationError(Exception):
+            """Deprecation error."""
+
+        raise DeprecationError(
+            f"{self.__class__.__name__} was deprecated at version NEXTVERSION "
+            "and is no longer available. Use XnetcdfArray instead."
+        )