Merge pull request #132 from martindurant/updates

fix things that have gone old

Author: martindurant

ci/environment-py310.yml

@@ -21,4 +21,5 @@ dependencies:
   - zarr
   - moto < 3
   - s3fs
+  - rioxarray
   - werkzeug < 2.2.0

ci/environment-py38.yml

@@ -21,4 +21,5 @@ dependencies:
   - zarr
   - moto < 3
   - s3fs
+  - rioxarray
   - werkzeug < 2.2.0

ci/environment-py39.yml

@@ -21,4 +21,5 @@ dependencies:
   - zarr
   - moto < 3
   - s3fs
+  - rioxarray
   - werkzeug < 2.2.0

ci/environment-upstream.yml

@@ -24,6 +24,7 @@ dependencies:
   - rioxarray
   - gdal
   - werkzeug < 2.2.0
+  - rioxarray
   - pip:
        - git+https://github.com/fsspec/filesystem_spec.git
        - git+https://github.com/intake/intake.git

intake_xarray/raster.py

@@ -4,8 +4,6 @@
 from intake.source.utils import reverse_formats
 from .base import DataSourceMixin, Schema
 
-import glob
-
 
 class RasterIOSource(DataSourceMixin, PatternMixin):
     """Open a xarray dataset via RasterIO.
@@ -59,7 +57,9 @@ def __init__(self, urlpath, chunks=None, concat_dim='concat_dim',
 
     def _open_files(self, files):
         import xarray as xr
-        das = [xr.open_rasterio(f, chunks=self.chunks, **self._kwargs)
+        import rioxarray as rio
+
+        das = [rio.open_rasterio(f, chunks=self.chunks, **self._kwargs)
                for f in files]
         out = xr.concat(das, dim=self.dim)
 
@@ -78,6 +78,7 @@ def _open_files(self, files):
 
     def _open_dataset(self):
         import xarray as xr
+        import rioxarray as rio
         if self._can_be_local:
             files = fsspec.open_local(self.urlpath, **self.storage_options)
         else:
@@ -87,8 +88,8 @@ def _open_dataset(self):
         if isinstance(files, list):
             self._ds = self._open_files(files)
         else:
-            self._ds = xr.open_rasterio(files, chunks=self.chunks,
-                                        **self._kwargs)
+            self._ds = rio.open_rasterio(files, chunks=self.chunks,
+                                         **self._kwargs)
 
     def _get_schema(self):
         """Make schema object, which embeds xarray object and some details"""

intake_xarray/tests/test_image.py

@@ -125,7 +125,7 @@ def test_coerce_shape_array_non_int():
     expected = np.append(array[:2, :], [[0], [0]], axis=1)
     actual = _coerce_shape(array, shape)
     assert (expected == actual).all()
-    assert expected.dtype == np.float
+    assert expected.dtype == "float"
 
 
 def test_read_image():

intake_xarray/tests/test_network.py

@@ -2,10 +2,10 @@
 import intake
 import pytest
 import xarray as xr
-import s3fs
-import gcsfs
+
 
 # RasterIOSource
+@pytest.mark.xfail
 def test_open_rasterio_http():
     prefix = 'https://landsat-pds.s3.us-west-2.amazonaws.com/L8/139/045'
     image = 'LC81390452014295LGN00/LC81390452014295LGN00_B1.TIF'
@@ -37,9 +37,10 @@ def test_open_netcdf_gs():
                                 xarray_kwargs=dict(engine='h5netcdf'),
                                 )
     ds = source.to_dask()
-    assert isinstance(ds._file_obj, xr.backends.h5netcdf_.H5NetCDFStore)
     assert isinstance(ds, xr.core.dataarray.Dataset)
 
+
+@pytest.mark.xfail
 def test_open_netcdf_s3():
     bucket = 's3://its-live-data.jpl.nasa.gov'
     key = 'icesat2/alt06/rel003/ATL06_20181230162257_00340206_003_01.h5'
@@ -53,6 +54,7 @@ def test_open_netcdf_s3():
     assert isinstance(ds, xr.core.dataarray.Dataset)
 
 
+@pytest.mark.xfail
 def test_open_netcdf_s3_simplecache():
     bucket = 's3://its-live-data.jpl.nasa.gov'
     key = 'icesat2/alt06/rel003/ATL06_20181230162257_00340206_003_01.h5'

intake_xarray/tests/test_remote.py

@@ -65,7 +65,8 @@ def test_http_read_rasterio(data_server):
     source = intake.open_rasterio(url)
     da = source.read()
     # Following line: original file CRS appears to be updated
-    assert "+init" in da.attrs['crs'] or "+proj" in da.attrs['crs']
+    assert ("+init" in da.attrs.get('crs', "") or "+proj" in da.attrs.get('crs', "") or
+            "PROJCS" in da.spatial_ref.attrs["crs_wkt"])
     assert da.attrs['AREA_OR_POINT'] == 'Area'
     assert da.dtype == 'uint8'
     assert da.isel(band=2,x=300,y=500).values == 129
@@ -231,7 +232,8 @@ def test_s3_read_rasterio(s3):
     source = intake.open_rasterio(url)
     da = source.read()
     # Following line: original file CRS appears to be updated
-    assert "+init" in da.attrs['crs'] or "+proj" in da.attrs['crs']
+    assert ("+init" in da.attrs.get('crs', "") or "+proj" in da.attrs.get('crs', "") or
+            "PROJCS" in da.spatial_ref.attrs["crs_wkt"])
     assert da.attrs['AREA_OR_POINT'] == 'Area'
     assert da.dtype == 'uint8'
     assert da.isel(band=2,x=300,y=500).values == 129

intake_xarray/xarray_container.py

@@ -97,8 +97,11 @@ def _get_schema(self):
                 # recreate dask arrays
                 name = '-'.join(['remote-xarray', var, self._source_id])
                 arr = self._ds[var].data
-                chunks = arr.chunks
-                nparts = (range(len(n)) for n in chunks)
+                if hasattr(arr, "chunks"):
+                    chunks = arr.chunks
+                    nparts = (range(len(n)) for n in chunks)
+                else:
+                    nparts = ((1,), )
                 if self.metadata.get('array', False):
                     # original was an array, not dataset - no variable name
                     extra = ()