make tests pass

intake_stac/catalog.py

@@ -2,7 +2,6 @@
 import warnings
 
 import satstac
-import yaml
 from intake.catalog import Catalog
 from intake.catalog.local import LocalCatalogEntry
 from pkg_resources import get_distribution
@@ -68,12 +67,9 @@ def serialize(self):
 
         Returns
         -------
-        A string with the yaml-formatted catalog.
+        A string with the yaml-formatted catalog (just top-level).
         """
-        output = {'metadata': self.metadata, 'sources': {}}
-        for key, entry in self.items():
-            output['sources'][key] = yaml.safe_load(entry.yaml())['sources']
-        return yaml.dump(output)
+        return self.yaml()
 
 
 class StacCatalog(AbstractStacCatalog):
@@ -268,13 +264,20 @@ def _get_band_info(self):
                 )
         return band_info
 
-    def stack_bands(self, bands, regrid=False):
+    def stack_bands(self, bands):
         """
         Stack the listed bands over the ``band`` dimension.
 
         This method only works for STAC Items using the 'eo' Extension
         https://github.com/radiantearth/stac-spec/tree/master/extensions/eo
 
+        NOTE: This method is not aware of geotransform information. It *assumes*
+        bands for a given STAC Item have the same coordinate reference system (CRS).
+        This is usually the case for a given multi-band satellite acquisition.
+        Coordinate alignment is performed automatically upon calling the
+        `to_dask()` method to load into an Xarray DataArray if bands have diffent
+        ground sample distance (gsd) or array shapes.
+
         Parameters
         ----------
         bands : list of strings representing the different bands
@@ -307,7 +310,7 @@ def stack_bands(self, bands, regrid=False):
                 if info is not None:
                     band = info.get('id', info.get('name'))
 
-            if band not in assets or (regrid is False and info is None):
+            if band not in assets or info is None:
                 valid_band_names = []
                 for b in band_info:
                     valid_band_names.append(b.get('id', b.get('name')))
@@ -331,17 +334,6 @@ def stack_bands(self, bands, regrid=False):
                     'band info in a fixed section of the url'
                 )
 
-            if regrid is False:
-                gsd = info.get('gsd')
-                if 'gsd' not in item:
-                    item['gsd'] = gsd
-                elif item['gsd'] != gsd:
-                    raise ValueError(
-                        f'Stacking failed: {band} has different ground '
-                        f'sampling distance ({gsd}) than other bands '
-                        f'({item["gsd"]})'
-                    )
-
             titles.append(band)
             item['urlpath'].append(href)
 

intake_stac/tests/test_catalog.py

@@ -55,11 +55,13 @@ def test_init_catalog_from_url(stac_cat_url):
     assert isinstance(cat, intake.catalog.Catalog)
     assert cat.name == 'stac-catalog'
     assert cat.discover()['container'] == 'catalog'
+    assert int(cat.metadata['stac_version'][0]) >= 1
 
     cat = StacCatalog.from_url(stac_cat_url)
     assert isinstance(cat, intake.catalog.Catalog)
     assert cat.name == 'stac-catalog'
     assert cat.discover()['container'] == 'catalog'
+    assert int(cat.metadata['stac_version'][0]) >= 1
 
     # test kwargs are passed through
     cat = StacCatalog.from_url(stac_cat_url, name='intake-stac-test')
@@ -88,7 +90,6 @@ def test_init_catalog_with_bad_url_raises():
         StacCatalog('foo.bar')
 
 
-@pytest.mark.xfail(reason='need to fix serialization')
 def test_serialize(cat):
     cat_str = cat.serialize()
     assert isinstance(cat_str, str)
@@ -121,75 +122,58 @@ def test_cat_from_item(stac_item_obj):
     assert 'B5' in cat
 
 
-@pytest.mark.xfail(reason='need to fix stack bands')
 def test_cat_item_stacking(stac_item_obj):
-    items = StacItem(stac_item_obj)
+    item = StacItem(stac_item_obj)
     list_of_bands = ['B1', 'B2']
-    new_entry = items.stack_bands(list_of_bands)
-    assert new_entry.description == 'Band 1 (coastal), Band 2 (blue)'
+    new_entry = item.stack_bands(list_of_bands)
+    assert isinstance(new_entry, StacEntry)
+    assert new_entry._description == 'B1, B2'
     assert new_entry.name == 'B1_B2'
-    new_da = new_entry.to_dask()
+    new_da = new_entry().to_dask()
     assert sorted([dim for dim in new_da.dims]) == ['band', 'x', 'y']
     assert (new_da.band == list_of_bands).all()
 
 
-@pytest.mark.xfail(reason='need to fix stack bands')
 def test_cat_item_stacking_using_common_name(stac_item_obj):
-    items = StacItem(stac_item_obj)
+    item = StacItem(stac_item_obj)
     list_of_bands = ['coastal', 'blue']
-    new_entry = items.stack_bands(list_of_bands)
-    assert new_entry.description == 'Band 1 (coastal), Band 2 (blue)'
+    new_entry = item.stack_bands(list_of_bands)
+    assert isinstance(new_entry, StacEntry)
+    assert new_entry._description == 'B1, B2'
     assert new_entry.name == 'coastal_blue'
-    new_da = new_entry.to_dask()
+    new_da = new_entry().to_dask()
     assert sorted([dim for dim in new_da.dims]) == ['band', 'x', 'y']
     assert (new_da.band == ['B1', 'B2']).all()
 
 
-@pytest.mark.xfail(reason='need to fix stack bands')
 def test_cat_item_stacking_dims_of_different_type_raises_error(stac_item_obj):
-    items = StacItem(stac_item_obj)
+    item = StacItem(stac_item_obj)
     list_of_bands = ['B1', 'ANG']
     with pytest.raises(ValueError, match=('ANG not found in list of eo:bands in collection')):
-        items.stack_bands(list_of_bands)
+        item.stack_bands(list_of_bands)
 
 
-@pytest.mark.xfail(reason='need to fix stack bands')
 def test_cat_item_stacking_dims_with_nonexistent_band_raises_error(stac_item_obj,):  # noqa: E501
-    items = StacItem(stac_item_obj)
+    item = StacItem(stac_item_obj)
     list_of_bands = ['B1', 'foo']
     with pytest.raises(ValueError, match="'B8', 'B9', 'blue', 'cirrus'"):
-        items.stack_bands(list_of_bands)
+        item.stack_bands(list_of_bands)
 
 
-@pytest.mark.xfail(reason='need to fix stack bands')
 def test_cat_item_stacking_dims_of_different_size_regrids(stac_item_obj):
-    items = StacItem(stac_item_obj)
+    item = StacItem(stac_item_obj)
     list_of_bands = ['B1', 'B8']
-    B1_da = items.B1.to_dask()
-    assert B1_da.shape == (1, 7801, 7641)
-    B8_da = items.B8.to_dask()
-    assert B8_da.shape == (1, 15601, 15281)
-    new_entry = items.stack_bands(list_of_bands, regrid=True)
-    new_da = new_entry.to_dask()
-    assert new_da.shape == (2, 15601, 15281)
+    B1_da = item.B1.to_dask()
+    assert B1_da.shape == (1, 7791, 7651)
+    B8_da = item.B8.to_dask()
+    assert B8_da.shape == (1, 15581, 15301)
+    new_entry = item.stack_bands(list_of_bands)
+    new_da = new_entry().to_dask()
+    assert new_da.shape == (2, 15581, 15301)
     assert sorted([dim for dim in new_da.dims]) == ['band', 'x', 'y']
     assert (new_da.band == list_of_bands).all()
 
 
-@pytest.mark.xfail(reason='need to fix stack bands')
-def test_cat_item_stacking_dims_of_different_size_raises_error_by_default(
-    stac_item_obj,
-):  # noqa: E501
-    items = StacItem(stac_item_obj)
-    list_of_bands = ['B1', 'B8']
-    B1_da = items.B1.to_dask()
-    assert B1_da.shape == (1, 7801, 7641)
-    B8_da = items.B8.to_dask()
-    assert B8_da.shape == (1, 15601, 15281)
-    with pytest.raises(ValueError, match='B8 has different ground sampling'):
-        items.stack_bands(list_of_bands)
-
-
 def test_stac_entry_constructor():
     key = 'B1'
     item = {

setup.cfg

@@ -11,7 +11,7 @@ select = B,C,E,F,W,T4,B9
 
 [isort]
 known_first_party=intake_stac
-known_third_party=intake,pkg_resources,pytest,satstac,setuptools,yaml
+known_third_party=intake,pkg_resources,pytest,satstac,setuptools
 multi_line_output=3
 include_trailing_comma=True
 force_grid_wrap=0