upgrade to be compatible with newer version dependencies (#1389)

* fix broken parts due to xarray updates

* update for shapely and numpy

---------

Co-authored-by: Emma Ai <emma.ai@ga.gov.au>

conda-environment.yml

@@ -32,5 +32,5 @@ dependencies:
   - rasterio >=1.3.2
   - sqlalchemy
   - GeoAlchemy2
-  - xarray >=0.9,!=2022.6.0
+  - xarray >=0.9
   - toolz

datacube/api/grid_workflow.py

@@ -17,14 +17,13 @@
 def _fast_slice(array, indexers):
     data = array.values[indexers]
     dims = [dim for dim, indexer in zip(array.dims, indexers) if isinstance(indexer, slice)]
-    variable = xarray.Variable(dims, data, attrs=array.attrs, fastpath=True)
     coords = OrderedDict((dim,
                           xarray.Variable((dim,),
                                           array.coords[dim].values[indexer],
                                           attrs=array.coords[dim].attrs,
                                           fastpath=True))
                          for dim, indexer in zip(array.dims, indexers) if isinstance(indexer, slice))
-    return xarray.DataArray(variable, coords=coords, fastpath=True)
+    return xarray.DataArray(data, dims=dims, coords=coords, attrs=array.attrs)
 
 
 class Tile(object):

datacube/utils/geometry/_base.py

@@ -17,7 +17,7 @@
 import xarray as xr
 from affine import Affine
 import rasterio                    # type: ignore[import]
-from shapely import geometry, ops  # type: ignore[import]
+from shapely import geometry, ops, from_wkt  # type: ignore[import]
 from shapely.geometry import base  # type: ignore[import]
 from pyproj import CRS as _CRS
 from pyproj.enums import WktVersion
@@ -438,7 +438,7 @@ def short_enough(p1, p2):
 
 
 def _clone_shapely_geom(geom: base.BaseGeometry) -> base.BaseGeometry:
-    return type(geom)(geom)
+    return from_wkt(geom.wkt)
 
 
 class Geometry:
@@ -604,7 +604,10 @@ def wkt(self) -> str:
 
     @property
     def __array_interface__(self):
-        return self.geom.__array_interface__
+        """
+        Should consider to deprecate this interface as shapely > 1.8 does
+        """
+        return numpy.array(self.geom.coords)
 
     @property
     def __geo_interface__(self):
@@ -710,7 +713,7 @@ def split(self, splitter: 'Geometry') -> Iterable['Geometry']:
         if splitter.crs != self.crs:
             raise CRSMismatchError(self.crs, splitter.crs)
 
-        for g in ops.split(self.geom, splitter.geom):
+        for g in ops.split(self.geom, splitter.geom).geoms:
             yield Geometry(g, self.crs)
 
     def __iter__(self) -> Iterator['Geometry']:

datacube/virtual/impl.py

@@ -543,6 +543,7 @@ def statistic(coords, value):
             data = self._input.fetch(value, **load_settings)
             result = self._statistic.compute(data)
             result.coords[dim] = coords[dim]
+            result = result.drop_indexes(dim, errors="ignore")
             return result
 
         groups = list(xr_map(grouped.box, statistic))

docker/constraints.in

@@ -1,5 +1,5 @@
 # datacube dependencies
-Sphinx
+Sphinx<6.0.0 # be compatible to sphinx_rtd_theme
 affine
 attrs>=18.1
 # boto is too huge, need to set lower bound
@@ -37,8 +37,7 @@ sphinx_autodoc_typehints
 sphinx_rtd_theme
 sqlalchemy
 toolz
-# FOR INVESTIGATION: xarray 2022.6.0 breaks virtual products tests.
-xarray>=0.18,!=2022.6.0
+xarray>=0.18
 
 # Previous pins were to very old versions
 # pytest Py3.10 requires >6.2.5