MAINT: avoid most of the warnings coming from dev CI

libpysal/cg/alpha_shapes.py

@@ -12,6 +12,7 @@
 import numpy as np
 import scipy.spatial as spat
 from scipy import sparse
+from packaging.version import Version
 
 from ..common import requires, jit, HAS_JIT
 
@@ -24,7 +25,6 @@
 
 try:
     import shapely
-    from packaging.version import Version
 
     assert Version(shapely.__version__) >= Version("2")
 
@@ -715,13 +715,18 @@ def _filter_holes(geoms, points):
     """
     Filter hole polygons using a computational geometry solution
     """
+    import geopandas
     if (geoms.interiors.apply(len) > 0).any():
         from shapely.geometry import Polygon
 
         # Extract the "shell", or outer ring of the polygon.
         shells = geoms.exterior.apply(Polygon)
         # Compute which original geometries are within each shell, self-inclusive
-        inside, outside = shells.sindex.query_bulk(geoms, predicate="within")
+        if Version(geopandas.__version__) >= Version("0.13"):
+            inside, outside = shells.sindex.query(geoms, predicate="within")
+        else:
+            inside, outside = shells.sindex.query_bulk(geoms, predicate="within")
+
         # Now, create the sparse matrix relating the inner geom (rows)
         # to the outer shell (cols) and take the sum.
         # A z-order of 1 means the polygon is only inside if its own exterior. This means it's not a hole.

libpysal/cg/tests/test_ashapes.py

@@ -3,12 +3,14 @@
 from ..alpha_shapes import alpha_shape, alpha_shape_auto
 import numpy as np
 import os
+from packaging.version import Version
 
 try:
     import geopandas
     from shapely import geometry
 
     GEOPANDAS_EXTINCT = False
+    GPD_013 = Version(geopandas.__version__) >= Version("0.13")
 except ImportError:
     GEOPANDAS_EXTINCT = True
 
@@ -98,20 +100,29 @@ def test_circles(self):
         ashape, radius, centers = alpha_shape_auto(self.vertices, return_circles=True)
         np.testing.assert_allclose(radius, self.circle_radii)
         np.testing.assert_allclose(centers, self.circle_verts)
-    
+
     def test_holes(self):
         np.random.seed(seed=100)
-        points = np.random.rand(1000, 2)*100
+        points = np.random.rand(1000, 2) * 100
         inv_alpha = 3.5
-        geoms = alpha_shape(points, 1/inv_alpha)
+        geoms = alpha_shape(points, 1 / inv_alpha)
         assert len(geoms) == 1
         holes = geopandas.GeoSeries(geoms.interiors.explode()).reset_index(drop=True)
         assert len(holes) == 30
         # No holes are within the shape (shape has holes already)
-        result = geoms.sindex.query_bulk(holes.centroid, predicate='within')
-        assert result.shape == (2,0)
+        if GPD_013:
+            result = geoms.sindex.query(holes.centroid, predicate="within")
+        else:
+            result = geoms.sindex.query_bulk(holes.centroid, predicate="within")
+
+        assert result.shape == (2, 0)
         # All holes are within the exterior
         shell = geopandas.GeoSeries(geoms.exterior.apply(geometry.Polygon))
-        within, outside = shell.sindex.query_bulk(holes.centroid, predicate='within')
+        if GPD_013:
+            within, outside = shell.sindex.query(holes.centroid, predicate="within")
+        else:
+            within, outside = shell.sindex.query_bulk(
+                holes.centroid, predicate="within"
+            )
         assert (outside == 0).all()
-        np.testing.assert_array_equal(within, np.arange(30))
+        np.testing.assert_array_equal(within, np.arange(30))

libpysal/graph/_utils.py

@@ -1,3 +1,5 @@
+import warnings
+
 import geopandas
 import numpy as np
 import pandas as pd
@@ -106,11 +108,23 @@ def _neighbor_dict_to_edges(neighbors, weights=None):
     that the any self-loops have a weight of zero.
     """
     idxs = pd.Series(neighbors).explode()
-    idxs = idxs.fillna(pd.Series(idxs.index, index=idxs.index))  # self-loops
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore",
+            "Downcasting object dtype arrays on .fillna, .ffill, .bfill ",
+            FutureWarning,
+        )
+        idxs = idxs.fillna(pd.Series(idxs.index, index=idxs.index))  # self-loops
     heads, tails = idxs.index.values, idxs.values
     tails = tails.astype(heads.dtype)
     if weights is not None:
-        data_array = pd.Series(weights).explode().fillna(0).values
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                "ignore",
+                "Downcasting object dtype arrays on .fillna, .ffill, .bfill ",
+                FutureWarning,
+            )
+            data_array = pd.Series(weights).explode().fillna(0).values
         if not pd.api.types.is_numeric_dtype(data_array):
             data_array = pd.to_numeric(data_array)
     else:

libpysal/graph/base.py

@@ -1007,7 +1007,7 @@ def nonzero(self):
         return (self._adjacency.drop(self.isolates) > 0).sum()
 
     def asymmetry(self, intrinsic=True):
-        """Asymmetry check.
+        r"""Asymmetry check.
 
         Parameters
         ----------

libpysal/io/iohandlers/pyDbfIO.py

@@ -14,14 +14,14 @@
 class DBF(tables.DataTable):
     """PySAL DBF Reader/Writer. This DBF handler implements the PySAL DataTable
     interface and initializes an instance of the PySAL's DBF handler.
-    
+
     Parameters
     -----------
     dataPath : str
         Path to file, including file name and extension.
     mode : str
         Mode for file interaction; either ``'r'`` or ``'w'``.
-    
+
     Attributes
     ----------
     header : list
@@ -41,7 +41,7 @@ class DBF(tables.DataTable):
     >>> dbf = libpysal.io.open(libpysal.examples.get_path('juvenile.dbf'), 'r')
     >>> dbf.header
     ['ID', 'X', 'Y']
-    
+
     >>> dbf.field_spec
     [('N', 9, 0), ('N', 9, 0), ('N', 9, 0)]
 
@@ -51,7 +51,6 @@ class DBF(tables.DataTable):
     MODES = ["r", "w"]
 
     def __init__(self, *args, **kwargs):
-
         tables.DataTable.__init__(self, *args, **kwargs)
 
         if self.mode == "r":
@@ -115,12 +114,12 @@ def __init__(self, *args, **kwargs):
 
     def __len__(self) -> int:
         """
-        
+
         Raises
         ------
         IOError
             Raised when a file is open ``'w'`` mode.
-        
+
         """
 
         if self.mode != "r":
@@ -135,12 +134,12 @@ def seek(self, i):
 
     def _get_col(self, key: str) -> list:
         """Return the column vector.
-        
+
         Raises
         ------
         AttributeError
             Raised when a field does not exist in the header.
-        
+
         """
 
         if key not in self._col_index:
@@ -196,7 +195,6 @@ def _get_col(self, key: str) -> list:
         return col
 
     def read_record(self, i: int) -> list:
-
         self.seek(i)
 
         rec = list(struct.unpack(self.record_fmt, self.f.read(self.record_size)))
@@ -246,12 +244,12 @@ def read_record(self, i: int) -> list:
 
     def _read(self) -> Union[list, None]:
         """
-        
+
         Raises
         ------
         IOError
             Raised when a file is open ``'w'`` mode.
-        
+
         """
 
         if self.mode != "r":
@@ -267,14 +265,14 @@ def _read(self) -> Union[list, None]:
 
     def write(self, obj: list):
         """
-        
+
         Raises
         ------
         IOError
             Raised when a file is open ``'r'`` mode.
         TypeError
             Raised when a row length and header length are not equivalent.
-        
+
         """
 
         self._complain_ifclosed(self.closed)
@@ -326,7 +324,6 @@ def flush(self):
         self.f.flush()
 
     def close(self):
-
         if self.mode == "w":
             self.flush()
             # End of file
@@ -337,14 +334,14 @@ def close(self):
 
     def _firstWrite(self):
         """
-        
+
         Raises
         ------
         IOError
             Raised when there is no specified header.
         IOError
             Raised when there is no field specification.
-        
+
         """
 
         if not self.header:

libpysal/io/iohandlers/tests/test_gwt.py

@@ -4,6 +4,7 @@
 from .... import examples as pysal_examples
 import tempfile
 import os
+import pytest
 import warnings
 
 
@@ -35,20 +36,21 @@ def test_seek(self):
     # see issue #153.
     # Added back by CRS,
     def test_write(self):
-        w = self.obj.read()
-        f = tempfile.NamedTemporaryFile(suffix=".gwt")
-        fname = f.name
-        f.close()
-        o = psopen(fname, "w")
-        # copy the shapefile and ID variable names from the old gwt.
-        # this is only available after the read() method has been called.
-        # o.shpName = self.obj.shpName
-        # o.varName = self.obj.varName
-        o.write(w)
-        o.close()
-        wnew = psopen(fname, "r").read()
-        self.assertEqual(wnew.pct_nonzero, w.pct_nonzero)
-        os.remove(fname)
+        with pytest.warns(RuntimeWarning, match="DBF relating to GWT was not found"):
+            w = self.obj.read()
+            f = tempfile.NamedTemporaryFile(suffix=".gwt")
+            fname = f.name
+            f.close()
+            o = psopen(fname, "w")
+            # copy the shapefile and ID variable names from the old gwt.
+            # this is only available after the read() method has been called.
+            # o.shpName = self.obj.shpName
+            # o.varName = self.obj.varName
+            o.write(w)
+            o.close()
+            wnew = psopen(fname, "r").read()
+            self.assertEqual(wnew.pct_nonzero, w.pct_nonzero)
+            os.remove(fname)
 
 
 if __name__ == "__main__":

libpysal/weights/tests/test_util.py

@@ -201,7 +201,7 @@ def test_full2W(self):
         for i in range(len(a)):
             for j in range(len(a[i])):
                 if i != j:
-                    a[i, j] = np.random.random(1)
+                    a[i, j] = np.random.random(1)[0]
         w = util.full2W(a)
         np.testing.assert_array_equal(w.full()[0], a)
         ids = ["myID0", "myID1", "myID2", "myID3"]

libpysal/weights/util.py

@@ -18,7 +18,7 @@
 try:
     import geopandas as gpd
 
-    GPD_08 = Version(gpd.__version__) >= Version("0.8.0")
+    GPD_013 = Version(gpd.__version__) >= Version("0.13.0")
 except ImportError:
     warn("geopandas not available. Some functionality will be disabled.")
 
@@ -1653,28 +1653,20 @@ def fuzzy_contiguity(
         gdf.set_geometry("_buffer", inplace=True)
 
     neighbors = {}
-    if GPD_08:
+    if GPD_013:
         # query tree based on set predicate
-        inp, res = gdf.sindex.query_bulk(gdf.geometry, predicate=predicate)
-        # remove self hits
-        itself = inp == res
-        inp = inp[~itself]
-        res = res[~itself]
-
-        # extract index values of neighbors
-        for i, ix in enumerate(gdf.index):
-            ids = gdf.index[res[inp == i]].tolist()
-            neighbors[ix] = ids
+        inp, res = gdf.sindex.query(gdf.geometry, predicate=predicate)
     else:
-        if predicate != "intersects":
-            raise ValueError(f"Predicate `{predicate}` requires geopandas >= 0.8.0.")
-        tree = gdf.sindex
-        for i, (ix, geom) in enumerate(gdf.geometry.iteritems()):
-            hits = list(tree.intersection(geom.bounds))
-            hits.remove(i)
-            possible = gdf.iloc[hits]
-            ids = possible[possible.intersects(geom)].index.tolist()
-            neighbors[ix] = ids
+        inp, res = gdf.sindex.query_bulk(gdf.geometry, predicate=predicate)
+    # remove self hits
+    itself = inp == res
+    inp = inp[~itself]
+    res = res[~itself]
+
+    # extract index values of neighbors
+    for i, ix in enumerate(gdf.index):
+        ids = gdf.index[res[inp == i]].tolist()
+        neighbors[ix] = ids
 
     if buffering:
         gdf.set_geometry(old_geometry_name, inplace=True)

pyproject.toml

@@ -114,3 +114,21 @@ exclude_lines = [
 ]
 ignore_errors = true
 omit = ["libpysal/tests/*", "docs/conf.py"]
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "ignore:The numba package is used",
+    "ignore:numba cannot be imported",
+    "ignore:Numba not imported",
+    "ignore:The weights matrix is not fully connected",
+    "ignore:You are trying to build a full W object from",
+    "ignore:Multiple layers detected. Using first layer as default",
+    "ignore:Geometry is in a geographic CRS",
+    "ignore:`use_index` defaults to False",
+    "ignore:Objects based on the `Geometry` class will deprecated",
+    "ignore:PolygonLocator is deprecated",
+    "ignore:SegmentGrid is deprecated",
+    "ignore:In the next version of libpysal, observations with no neighbors",
+    "ignore:divide by zero encountered",
+    "ignore:invalid value encountered",
+]