Default to CF standard axes for accessing dimension names

.github/workflows/continuous-integration.yml

@@ -25,7 +25,7 @@ jobs:
         run: python -m pip install .[dev]
 
       - name: Run tests
-        run: pytest -v
+        run: pytest tests -v
 
       - name: Lint
         run: pre-commit run --all-files

pyproject.toml

@@ -8,6 +8,7 @@ author = "Tom Augspurger"
 author-email = "taugspurger@microsoft.com"
 classifiers = [ "License :: OSI Approved :: MIT License",]
 requires = [
+    "cf_xarray",
     "xarray",
     "numpy",
     "pystac>=1.0.0b3",

test_xstac.py → tests/conftest.py

@@ -1,13 +1,8 @@
-from xstac import xarray_to_stac, fix_attrs
-from xstac._xstac import _bbox_to_geometry
-import xarray as xr
+import pytest
 import numpy as np
 import pandas as pd
-import pytest
-import pystac
-
-import xstac
-
+import xarray as xr
+from xstac import fix_attrs
 
 data = np.empty((40, 584, 284), dtype="float32")
 x = xr.DataArray(
@@ -117,7 +112,23 @@ def ds():
     return fix_attrs(ds)
 
 
-def test_xarray_to_stac(ds):
+@pytest.fixture
+def ds_without_spatial_dims():
+    ds = xr.Dataset(
+        {
+            "data": xr.DataArray(
+                [1, 2],
+                dims=("time",),
+                coords={"time": pd.to_datetime(["2021-01-01", "2021-01-02"])},
+            )
+        }
+    )
+    ds.time.attrs["long_name"] = "time"
+    return ds
+
+
+@pytest.fixture
+def collection_template():
     template = {
         "id": "id",
         "type": "Collection",
@@ -126,19 +137,25 @@ def test_xarray_to_stac(ds):
         "license": "license",
         "stac_version": "1.0.0",
     }
-    result = xarray_to_stac(
-        ds,
-        template=template,
-        temporal_dimension="time",
-        x_dimension="x",
-        y_dimension="y",
-    )
-    assert result.id == "id"
-    assert isinstance(result, pystac.Collection)
-    assert result.description == "description"
-    assert result.license == "license"
+    return template
+
 
-    dimensions = result.extra_fields["cube:dimensions"]
+@pytest.fixture
+def item_template():
+    template = {
+        "id": "id",
+        "type": "Feature",
+        "links": [],
+        "geometry": None,
+        "stac_version": "1.0.0",
+        "properties": {"datetime": "2021-01-01T00:00:00Z"},
+        "assets": {},
+    }
+    return template
+
+
+@pytest.fixture
+def collection_expected_dims():
     expected = {
         "time": {
             "type": "temporal",
@@ -352,7 +369,11 @@ def test_xarray_to_stac(ds):
             },
         },
     }
-    assert dimensions == expected
+    return expected
+
+
+@pytest.fixture
+def collection_expected_vars():
     expected = {
         "lat": {
             "type": "auxiliary",
@@ -419,65 +440,11 @@ def test_xarray_to_stac(ds):
             },
         },
     }
-    assert result.extra_fields["cube:variables"] == expected
+    return expected
 
 
-def test_validation_with_none():
-    # https://github.com/TomAugspurger/xstac/issues/9
-    template = {
-        "type": "Collection",
-        "id": "cesm2-lens",
-        "stac_version": "1.0.0",
-        "description": "desc",
-        "stac_extensions": [
-            "https://stac-extensions.github.io/datacube/v2.0.0/schema.json"
-        ],
-        "extent": {
-            "spatial": {"bbox": [[-180, -90, 180, 90]]},
-            "temporal": {
-                "interval": [["1851-01-01T00:00:00Z", "1851-01-01T00:00:00Z"]]
-            },
-        },
-        "providers": [],
-        "license": "CC0-1.0",
-        "links": [],
-    }
-    ds = xr.Dataset(
-        {
-            "data": xr.DataArray(
-                [1, 2],
-                dims=("time",),
-                coords={"time": pd.to_datetime(["2021-01-01", "2021-01-02"])},
-            )
-        }
-    )
-    ds.time.attrs["long_name"] = "time"
-    c = xarray_to_stac(ds, template, temporal_dimension="time")
-    c.normalize_hrefs("/")
-    c.validate()
-
-
-def test_xarray_to_stac_item(ds):
-    template = {
-        "id": "id",
-        "type": "Feature",
-        "links": [],
-        "geometry": None,
-        "stac_version": "1.0.0",
-        "properties": {"datetime": "2021-01-01T00:00:00Z"},
-        "assets": {},
-    }
-    result = xarray_to_stac(
-        ds,
-        template=template,
-        temporal_dimension="time",
-        x_dimension="x",
-        y_dimension="y",
-    )
-    assert result.id == "id"
-    assert isinstance(result, pystac.Item)
-
-    dimensions = result.properties["cube:dimensions"]
+@pytest.fixture
+def item_expected_dims():
     expected = {
         "time": {
             "type": "temporal",
@@ -691,7 +658,11 @@ def test_xarray_to_stac_item(ds):
             },
         },
     }
-    assert dimensions == expected
+    return expected
+
+
+@pytest.fixture
+def item_expected_vars():
     expected = {
         "lat": {
             "type": "auxiliary",
@@ -758,21 +729,4 @@ def test_xarray_to_stac_item(ds):
             },
         },
     }
-    assert result.properties["cube:variables"] == expected
-
-    assert result.properties["start_datetime"] == "1980-07-31T00:00:00Z"
-    assert result.properties["end_datetime"] == "2019-07-31T00:00:00Z"
-
-
-def test_bbox_to_geometry():
-    import shapely.geometry
-
-    bbox = [
-        -160.2988400944475,
-        17.960033949329812,
-        -154.7780670634169,
-        23.51232608231902,
-    ]
-    result = shapely.geometry.mapping(shapely.geometry.shape(_bbox_to_geometry(bbox)))
-    expected = shapely.geometry.mapping(shapely.geometry.box(*bbox))
-    assert result == expected
+    return expected

tests/test_xstac.py

@@ -0,0 +1,95 @@
+from xstac import xarray_to_stac
+from xstac._xstac import _bbox_to_geometry
+import xarray as xr
+import pytest
+import pystac
+
+import xstac
+
+
+# def test_no_time_dimension(ds, collection_template):
+#    _ = xarray_to_stac(ds, template=collection_template, temporal_dimension=False)
+
+
+@pytest.mark.parametrize("explicit_dims", [False, True])
+def test_xarray_to_stac(
+    ds,
+    collection_template,
+    collection_expected_dims,
+    collection_expected_vars,
+    explicit_dims,
+):
+    kw = (
+        dict()
+        if not explicit_dims
+        else dict(temporal_dimension="time", x_dimension="x", y_dimension="y")
+    )
+    result = xarray_to_stac(ds, template=collection_template, **kw)
+    assert result.id == "id"
+    assert isinstance(result, pystac.Collection)
+    assert result.description == "description"
+    assert result.license == "license"
+
+    dimensions = result.extra_fields["cube:dimensions"]
+    assert dimensions == collection_expected_dims
+    assert result.extra_fields["cube:variables"] == collection_expected_vars
+
+
+def test_validation_with_none(ds_without_spatial_dims):
+    # https://github.com/TomAugspurger/xstac/issues/9
+    template = {
+        "type": "Collection",
+        "id": "cesm2-lens",
+        "stac_version": "1.0.0",
+        "description": "desc",
+        "stac_extensions": [
+            "https://stac-extensions.github.io/datacube/v2.0.0/schema.json"
+        ],
+        "extent": {
+            "spatial": {"bbox": [[-180, -90, 180, 90]]},
+            "temporal": {
+                "interval": [["1851-01-01T00:00:00Z", "1851-01-01T00:00:00Z"]]
+            },
+        },
+        "providers": [],
+        "license": "CC0-1.0",
+        "links": [],
+    }
+    c = xarray_to_stac(
+        ds_without_spatial_dims, template, x_dimension=False, y_dimension=False
+    )
+    c.normalize_hrefs("/")
+    c.validate()
+
+
+def test_xarray_to_stac_item(ds, item_template, item_expected_dims, item_expected_vars):
+
+    result = xarray_to_stac(ds, template=item_template)
+    assert result.id == "id"
+    assert isinstance(result, pystac.Item)
+
+    dimensions = result.properties["cube:dimensions"]
+    assert dimensions == item_expected_dims
+    assert result.properties["cube:variables"] == item_expected_vars
+
+    assert result.properties["start_datetime"] == "1980-07-31T00:00:00Z"
+    assert result.properties["end_datetime"] == "2019-07-31T00:00:00Z"
+
+
+def test_bbox_to_geometry():
+    import shapely.geometry
+
+    bbox = [
+        -160.2988400944475,
+        17.960033949329812,
+        -154.7780670634169,
+        23.51232608231902,
+    ]
+    result = shapely.geometry.mapping(shapely.geometry.shape(_bbox_to_geometry(bbox)))
+    expected = shapely.geometry.mapping(shapely.geometry.box(*bbox))
+    assert result == expected
+
+
+def test_missing_dims_error(ds_without_spatial_dims, collection_template):
+    with pytest.raises(KeyError):
+        _ = xarray_to_stac(ds_without_spatial_dims, collection_template)

xstac/_generate.py

@@ -8,6 +8,7 @@
 import argparse
 import json
 import fsspec
+import cf_xarray
 import xarray as xr
 
 import xstac
@@ -40,16 +41,10 @@ def parse_args(args=None):
 
     parser.add_argument("--reference-system", default=None)
     parser.add_argument(
-        "--temporal_dimension",
-        default="time",
-        help="Coordinate name for the 'time' dimension",
-    )
-    parser.add_argument(
-        "--x-dimension", default="x", help="Coordinate name for the 'x' dimension"
-    )
-    parser.add_argument(
-        "--y-dimension", default="y", help="Coordinate name for the 'y' dimension"
+        "--temporal_dimension", help="Coordinate name for the 'time' dimension"
     )
+    parser.add_argument("--x-dimension", help="Coordinate name for the 'x' dimension")
+    parser.add_argument("--y-dimension", help="Coordinate name for the 'y' dimension")
     parser.add_argument(
         "--no-validate",
         action="store_false",
@@ -62,9 +57,9 @@ def parse_args(args=None):
 def generate(
     template,
     asset_key,
-    x_dimension="x",
-    y_dimension="y",
-    temporal_dimension="time",
+    x_dimension=None,
+    y_dimension=None,
+    temporal_dimension=None,
     reference_system=None,
     validate: bool = True,
 ):