test configs and minor bugs introed from doc cleanup

bento/io/_index.py

@@ -98,7 +98,7 @@ def _sjoin_shapes(sdata: SpatialData, instance_key: str, shape_keys: List[str]):
     if len(shape_keys) == 0:
         return sdata
 
-    parent_shape = gpd.GeoDataFrame(geometry=sdata.shapes[instance_key])
+    parent_shape = gpd.GeoDataFrame(geometry=sdata.shapes[instance_key].geometry)
 
     # sjoin shapes to instance_key shape
     for shape_key in shape_keys:
@@ -118,10 +118,14 @@ def _sjoin_shapes(sdata: SpatialData, instance_key: str, shape_keys: List[str]):
                 ]
                 .fillna("")
                 .astype("category")
-                .cat.add_categories([""])
             )
             .rename(columns={"index_right": shape_key})
         )
+
+        # Add empty category to shape_key if not already present
+        if "" not in parent_shape[shape_key].cat.categories:
+            parent_shape[shape_key] = parent_shape[shape_key].cat.add_categories([""])
+
         parent_shape[shape_key] = parent_shape[shape_key].fillna("")
 
         # Save shape index as column in instance_key shape

bento/tools/_point_features.py

@@ -245,7 +245,7 @@ def extract(self, df: pd.DataFrame) -> Dict[str, float]:
         Dict[str, float]
             Computed feature values
         """
-        return df.to_dict("list")
+        return df
 
 
 class ShapeProximity(PointFeature):
@@ -914,7 +914,7 @@ def _second_moment(centroid: np.ndarray, pts: np.ndarray) -> float:
     float
         Second moment value
     """
-    if type(centroid) is np.ndarray:
+    if type(centroid) is not np.ndarray:
         centroid = centroid.coords
     centroid = np.array(centroid).reshape(1, 2)
     radii = distance.cdist(centroid, pts)

tests/__init__.py

@@ -0,0 +1,5 @@
+import os
+import sys
+
+# Add the parent directory to the Python path
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))

tests/test_flux.py

@@ -2,7 +2,7 @@
 
 
 import bento as bt
-from . import conftest
+from tests import conftest
 
 
 @pytest.fixture(scope="module")

tests/test_io.py

@@ -1,5 +1,5 @@
 
-from . import conftest
+from tests import conftest
 
 
 def test_points_indexing(small_data):

tests/test_lp.py

@@ -3,7 +3,7 @@
 
 import bento as bt
 
-from . import conftest
+from tests import conftest
 
 
 @pytest.fixture(scope="module")

tests/test_point_features.py

@@ -1,7 +1,7 @@
 import pytest
 import bento as bt
 
-from . import conftest
+from tests import conftest
 
 
 @pytest.fixture(scope="module")

tests/test_shape_features.py

@@ -1,7 +1,7 @@
 import pytest
 import bento as bt
 
-from . import conftest
+from tests import conftest
 
 
 @pytest.fixture(scope="module")