COMPAT: pandas 3.0 compatibillity in Graph

.github/workflows/unittests.yml

@@ -69,7 +69,6 @@ jobs:
 
           geodatasets.fetch("nybb")
           geodatasets.fetch("geoda liquor_stores")
-          geodatasets.fetch("eea large_rivers")
           geodatasets.fetch("geoda groceries")
           geodatasets.fetch("geoda guerry")
           libpysal.examples.fetch_all()

libpysal/graph/_utils.py

@@ -143,7 +143,7 @@ def _neighbor_dict_to_edges(neighbors, weights=None):
                 FutureWarning,
             )
             idxs = idxs.fillna(pd.Series(idxs.index, index=idxs.index))  # self-loops
-    heads, tails = idxs.index.values, idxs.values
+    heads, tails = idxs.index.to_numpy(), idxs.to_numpy()
     tails = tails.astype(heads.dtype)
     if weights is not None:
         with warnings.catch_warnings():

libpysal/graph/base.py

@@ -1853,8 +1853,13 @@ def asymmetry(self, intrinsic=True):
                 zip(np.arange(self.unique_ids.shape[0]), self.unique_ids, strict=True)
             )
             focal, neighbor = np.nonzero(wd)
-            focal = focal.astype(self._adjacency.index.dtypes["focal"])
-            neighbor = neighbor.astype(self._adjacency.index.dtypes["focal"])
+            dtype = (
+                self._adjacency.index.dtypes["focal"]
+                if self._adjacency.index.dtypes["focal"] != "str"
+                else "object"
+            )
+            focal = focal.astype(dtype)
+            neighbor = neighbor.astype(dtype)
             for i in i2id:
                 focal[focal == i] = i2id[i]
                 neighbor[neighbor == i] = i2id[i]

libpysal/graph/tests/test_base.py

@@ -56,7 +56,8 @@ def setup_method(self):
             self.weight_dict_str_binary.values(),
             name="weight",
             index=pd.MultiIndex.from_arrays(
-                [self.index_str, self.neighbor_dict_str.values()],
+                # list() to allow pandas to coerce the data to its StringDtype
+                [list(self.index_str), self.neighbor_dict_str.values()],
                 names=["focal", "neighbor"],
             ),
         )
@@ -457,7 +458,8 @@ def test_from_dicts(self):
         pd.testing.assert_series_equal(
             g._adjacency,
             self.adjacency_str_binary,
-            check_dtype=False,
+            check_dtype=True,
+            check_index_type=False,
         )
 
     @pytest.mark.parametrize("y", [3, 5])
@@ -617,7 +619,6 @@ def test_cardinalities(self):
             [3, 3, 2, 3, 4, 3, 2, 3, 2, 0],
             index=pd.Index(
                 ["a", "b", "c", "d", "e", "f", "g", "h", "i", "j"],
-                dtype="object",
                 name="focal",
             ),
             name="cardinalities",

libpysal/graph/tests/test_contiguity.py

@@ -27,13 +27,14 @@
 
 @pytest.fixture(scope="session")
 def rivers():
-    numpy.random.seed(111211)
-    rivers = geopandas.read_file(geodatasets.get_path("eea large_rivers")).sample(
-        frac=1, replace=False
-    )
-    rivers["strID"] = rivers.NAME
-    rivers["intID"] = rivers.index.values + 2
-    return rivers
+    pytest.skip("eea large rivers not accessible")
+    # numpy.random.seed(111211)
+    # rivers = geopandas.read_file(geodatasets.get_path("eea large_rivers")).sample(
+    #     frac=1, replace=False
+    # )
+    # rivers["strID"] = rivers.NAME
+    # rivers["intID"] = rivers.index.values + 2
+    # return rivers
 
 
 @pytest.fixture(scope="session")

libpysal/graph/tests/test_utils.py

@@ -22,10 +22,11 @@ def guerry():
 
 @pytest.fixture(scope="session")
 def rivers():
-    rivers = geopandas.read_file(geodatasets.get_path("eea large_rivers"))
-    rivers["strID"] = rivers.NAME
-    rivers["intID"] = rivers.index.values + 1
-    return rivers
+    pytest.skip("eea large rivers not accessible")
+    # rivers = geopandas.read_file(geodatasets.get_path("eea large_rivers"))
+    # rivers["strID"] = rivers.NAME
+    # rivers["intID"] = rivers.index.values + 1
+    # return rivers
 
 
 @pytest.fixture(params=["guerry", "guerry centroids", "rivers"])