Merge pull request #698 from davidhassell/ugrid-0

Implementation of UGRID (part 1 of 2)

Author: davidhassell

.gitignore

@@ -14,6 +14,7 @@
 cf/test/dir/
 cf/test/*.nc
 cf/test/*.nca
+cf/test/*.cdl
 cf/test/*.txt
 
 # coverage reports from a running the test coverage script

Changelog.rst

@@ -3,10 +3,24 @@ version 3.16.0
 
 **2023-??-??**
 
+* Implemented the reading and manipulation of UGRID mesh topologies
+  (https://github.com/NCAS-CMS/cf-python/issues/696)
+* New methods: `cf.Field.cell_connectivity`,
+  `cf.Field.cell_connectivities`
+  (https://github.com/NCAS-CMS/cf-python/issues/696)
+* New methods: `cf.Field.domain_topology`,
+  `cf.Field.domain_topologies`
+  (https://github.com/NCAS-CMS/cf-python/issues/696)
+* New method: `cf.Data.masked-values`
+  (https://github.com/NCAS-CMS/cf-python/issues/696)
+* New method: `cf.Data.arctan2`
+  (https://github.com/NCAS-CMS/cf-python/issues/38)
 * Fix bug that caused `cf.Field.collapse` to give incorrect results
   for the "sum", "sum_of_weights" and "sum_of_weights2" methods, only
   in the case that weights have been requested
   (https://github.com/NCAS-CMS/cf-python/issues/701)
+* Changed dependency: ``1.11.0.0<=cfdm<1.11.1.0``
+* New dependency: ``scipy>=1.10.0``
 
 version 3.15.4
 --------------
@@ -283,8 +297,8 @@ version 3.11.0
 * Fix for `cf.aggregate` failures when a datum or coordinate
   conversion parameter has an array value
   (https://github.com/NCAS-CMS/cf-python/issues/230)
-* Allow for regridding using a destination field featuring size 1 dimension(s)
-  (https://github.com/NCAS-CMS/cf-python/issues/250)
+* Allow for regridding using a destination field featuring size 1
+  dimension(s) (https://github.com/NCAS-CMS/cf-python/issues/250)
 * Fix bug that sometimes caused `cf.Field.autocyclic` to fail when
   setting a construct that is cyclic and has a defined period
 * Fix bug that sometimes caused a failure when reading PP extra data

MANIFEST.in

@@ -8,6 +8,6 @@ recursive-exclude cf *.o *.so *.a .nfs*
 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 wgdos_packed.pp extra_data.pp file1.pp *.cdl
+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 wgdos_packed.pp extra_data.pp file1.pp *.cdl
 prune cf/test/dir

README.md

@@ -85,52 +85,34 @@ The `cf` package uses
 of its array manipulation and can:
 
 * read field constructs from netCDF, CDL, PP and UM datasets,
-
 * create new field constructs in memory,
-
-* write and append field constructs to netCDF datasets on disk,
-
+* write and append field and domain constructs to netCDF datasets on disk,
+* read, create, and manipulate UGRID mesh topologies,
 * read, write, and create coordinates defined by geometry cells,
-
 * read netCDF and CDL datasets containing hierarchical groups,
-
 * inspect field constructs,
-
 * test whether two field constructs are the same,
-
 * modify field construct metadata and data,
-
 * create subspaces of field constructs,
-
 * write field constructs to netCDF datasets on disk,
-
 * incorporate, and create, metadata stored in external files,
-
 * read, write, and create data that have been compressed by convention
   (i.e. ragged or gathered arrays, or coordinate arrays compressed by
   subsampling), whilst presenting a view of the data in its
   uncompressed form,
-
 * combine field constructs arithmetically,
-
 * manipulate field construct data by arithmetical and trigonometrical
   operations,
-
-* perform statistical collapses on field constructs,
-
+* perform weighted statistical collapses on field constructs,
+  including those with geometry cells and UGRID mesh topologies,
 * perform histogram, percentile and binning operations on field
   constructs,
-
 * regrid field constructs with (multi-)linear, nearest neighbour,
   first- and second-order conservative and higher order patch recovery
-  methods,
-
+  methods, to and from structured and unstructured grids,
 * apply convolution filters to field constructs,
-
 * create running means from field constructs,
-
 * apply differential operators to field constructs,
-
 * create derived quantities (such as relative vorticity).
 
 Visualization

cf/__init__.py

@@ -73,9 +73,9 @@
 
 """
 
-__Conventions__ = "CF-1.10"
-__date__ = "2023-10-10"
-__version__ = "3.15.4"
+__Conventions__ = "CF-1.11"
+__date__ = "2023-??-??"
+__version__ = "3.16.0"
 
 _requires = (
     "numpy",
@@ -86,6 +86,7 @@
     "psutil",
     "dask",
     "packaging",
+    "scipy",
 )
 
 x = ", ".join(_requires)
@@ -144,6 +145,11 @@
 except ImportError as error1:
     raise ImportError(_error0 + str(error1))
 
+try:
+    import scipy
+except ImportError as error1:
+    raise ImportError(_error0 + str(error1))
+
 # Check the version of packaging
 _minimum_vn = "20.0"
 if Version(packaging.__version__) < Version(_minimum_vn):
@@ -193,8 +199,8 @@
     )
 
 # Check the version of cfdm
-_minimum_vn = "1.10.1.2"
-_maximum_vn = "1.10.2.0"
+_minimum_vn = "1.11.0.0"
+_maximum_vn = "1.11.1.0"
 _cfdm_version = Version(cfdm.__version__)
 if not Version(_minimum_vn) <= _cfdm_version < Version(_maximum_vn):
     raise RuntimeError(
@@ -218,6 +224,14 @@
         f"or later. Got {platform.python_version()}"
     )
 
+# Check the version of scipy
+_minimum_vn = "1.10.0"
+if Version(scipy.__version__) < Version(_minimum_vn):
+    raise RuntimeError(
+        f"Bad scipy version: cf requires scipy>={_minimum_vn}. "
+        f"Got {scipy.__version__} at {scipy.__file__}"
+    )
+
 from .constructs import Constructs
 
 from .mixin import Coordinate
@@ -248,18 +262,23 @@
 from .dimensioncoordinate import DimensionCoordinate
 from .auxiliarycoordinate import AuxiliaryCoordinate
 from .coordinatereference import CoordinateReference
+from .cellconnectivity import CellConnectivity
 from .cellmethod import CellMethod
 from .cellmeasure import CellMeasure
 from .domainancillary import DomainAncillary
 from .domainaxis import DomainAxis
+from .domaintopology import DomainTopology
 from .fieldancillary import FieldAncillary
 from .field import Field
 from .data import Data
 from .data.array import (
+    BoundsFromNodesArray,
+    CellConnectivityArray,
     CFANetCDFArray,
     FullArray,
     GatheredArray,
     NetCDFArray,
+    PointTopologyArray,
     RaggedContiguousArray,
     RaggedIndexedArray,
     RaggedIndexedContiguousArray,