Merge pull request #419 from dcs4cop/forman-347-dont_reorder_lat

Workaround for some cases that end up in #347

CHANGES.md

@@ -1,7 +1,11 @@
-## Changes in 0.7.1.dev1 (in development)
-
-* Added `s3fs`  requirement that has been removed by accident.
-* Added missing requirements `requests` and `urllib3`.
+## Changes in 0.7.1
+
+* Dataset normalisation no longer includes reordering increasing
+  latitude coordinates, as this creates datasets that are no longer writable 
+  to Zarr. (#347)
+* Updated package requirements
+  - Added `s3fs`  requirement that has been removed by accident.
+  - Added missing requirements `requests` and `urllib3`.
 
 ## Changes in 0.7.0
 

test/core/test_normalize.py

@@ -12,11 +12,11 @@
 from jdcal import gcal2jd
 from numpy.testing import assert_array_almost_equal
 
+from xcube.core.normalize import adjust_spatial_attrs
+from xcube.core.normalize import adjust_temporal_attrs
 from xcube.core.normalize import normalize_coord_vars
 from xcube.core.normalize import normalize_dataset
 from xcube.core.normalize import normalize_missing_time
-from xcube.core.normalize import adjust_spatial_attrs
-from xcube.core.normalize import adjust_temporal_attrs
 
 
 # noinspection PyPep8Naming
@@ -85,25 +85,23 @@ def test_normalize_lon_lat(self):
         dataset = xr.Dataset({'first': (['latitude',
                                          'longitude'], [[1, 2, 3],
                                                         [2, 3, 4]])})
-        # Since normalization puts latitudes into descending order, we
-        # expect the rows to be swapped.
-        expected = xr.Dataset({'first': (['lat', 'lon'], [[2, 3, 4],
-                                                          [1, 2, 3]])})
+        expected = xr.Dataset({'first': (['lat', 'lon'], [[1, 2, 3],
+                                                          [2, 3, 4]])})
         actual = normalize_dataset(dataset)
         assertDatasetEqual(actual, expected)
 
         dataset = xr.Dataset({'first': (['lat', 'long'], [[1, 2, 3],
                                                           [2, 3, 4]])})
-        expected = xr.Dataset({'first': (['lat', 'lon'], [[2, 3, 4],
-                                                          [1, 2, 3]])})
+        expected = xr.Dataset({'first': (['lat', 'lon'], [[1, 2, 3],
+                                                          [2, 3, 4]])})
         actual = normalize_dataset(dataset)
         assertDatasetEqual(actual, expected)
 
         dataset = xr.Dataset({'first': (['latitude',
                                          'spacetime'], [[1, 2, 3],
                                                         [2, 3, 4]])})
-        expected = xr.Dataset({'first': (['lat', 'spacetime'], [[2, 3, 4],
-                                                                [1, 2, 3]])})
+        expected = xr.Dataset({'first': (['lat', 'spacetime'], [[1, 2, 3],
+                                                                [2, 3, 4]])})
         actual = normalize_dataset(dataset)
         assertDatasetEqual(actual, expected)
 
@@ -114,7 +112,7 @@ def test_normalize_lon_lat(self):
         actual = normalize_dataset(dataset)
         assertDatasetEqual(actual, expected)
 
-    def test_normalize_inverted_lat(self):
+    def test_normalize_does_not_reorder_increasing_lat(self):
         first = np.zeros([3, 45, 90])
         first[0, :, :] = np.eye(45, 90)
         ds = xr.Dataset({
@@ -125,18 +123,8 @@ def test_normalize_inverted_lat(self):
             'time': [datetime(2000, x, 1) for x in range(1, 4)]}).chunk(
             chunks={'time': 1})
 
-        first = np.zeros([3, 45, 90])
-        first[0, :, :] = np.flip(np.eye(45, 90), axis=0)
-        expected = xr.Dataset({
-            'first': (['time', 'lat', 'lon'], first),
-            'second': (['time', 'lat', 'lon'], np.zeros([3, 45, 90])),
-            'lat': np.linspace(88, -88, 45),
-            'lon': np.linspace(-178, 178, 90),
-            'time': [datetime(2000, x, 1) for x in range(1, 4)]}).chunk(
-            chunks={'time': 1})
-
         actual = normalize_dataset(ds)
-        xr.testing.assert_equal(actual, expected)
+        xr.testing.assert_equal(actual, ds)
 
     def test_normalize_with_missing_time_dim(self):
         ds = xr.Dataset({'first': (['lat', 'lon'], np.zeros([90, 180])),

xcube/core/normalize.py

@@ -56,34 +56,11 @@ def normalize_dataset(ds: xr.Dataset) -> xr.Dataset:
     ds = _normalize_lat_lon_2d(ds)
     ds = _normalize_dim_order(ds)
     ds = _normalize_lon_360(ds)
-
-    # xcube viewer currently requires decreasing latitude co-ordinates, so
-    # we invert them here if necessary.
-    ds = _ensure_lat_decreasing(ds)
-
     ds = normalize_missing_time(ds)
     ds = _normalize_jd2datetime(ds)
     return ds
 
 
-def _ensure_lat_decreasing(ds: xr.Dataset) -> xr.Dataset:
-    """
-    If the latitude is increasing, invert it to make it decreasing.
-    :param ds: some xarray dataset
-    :return: a normalized xarray dataset
-    """
-    try:
-        if not _is_lat_decreasing(ds.lat):
-            ds = ds.sel(lat=slice(None, None, -1))
-    except AttributeError:
-        # The dataset doesn't have 'lat', probably not geospatial
-        pass
-    except ValueError:
-        # The dataset still has an ND 'lat' array
-        pass
-    return ds
-
-
 def _normalize_lat_lon(ds: xr.Dataset) -> xr.Dataset:
     """
     Rename variables named 'longitude' or 'long' to 'lon', and 'latitude' to 'lon'.
@@ -366,7 +343,7 @@ def normalize_missing_time(ds: xr.Dataset) -> xr.Dataset:
     return ds
 
 
-def adjust_spatial_attrs(ds: xr.Dataset, allow_point: bool=False) -> xr.Dataset:
+def adjust_spatial_attrs(ds: xr.Dataset, allow_point: bool = False) -> xr.Dataset:
     """
     Adjust the global spatial attributes of the dataset by doing some
     introspection of the dataset and adjusting the appropriate attributes
@@ -692,7 +669,6 @@ def _is_lat_decreasing(lat: xr.DataArray) -> bool:
 
 
 def _normalize_dim_order(ds: xr.Dataset) -> xr.Dataset:
-
     copy_created = False
 
     for var_name in ds.data_vars:

xcube/version.py

@@ -19,4 +19,4 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-version = '0.7.1.dev1'
+version = '0.7.1'