from shapely import Point
import geopandas as gpd
from libpysal.graph import Graph
Graph.build_kernel(gpd.GeoSeries(
[
Point(0, 0),
Point(0, 0),
Point(1, 0),
Point(2, 0),
Point(3, 0),
Point(4, 0),
]
), k=2, coplanar="clique")
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[5], line 1
----> 1 Graph.build_kernel(gpd.GeoSeries(
2 [
3 Point(0, 0),
4 Point(0, 0),
5 Point(1, 0),
6 Point(2, 0),
7 Point(3, 0),
8 Point(4, 0),
9 ]
10 ), k=2, coplanar="clique")
File ~/dev/pysal/gwlearn/.pixi/envs/default/lib/python3.13/site-packages/libpysal/graph/base.py:1120, in Graph.build_kernel(cls, data, kernel, k, bandwidth, metric, p, coplanar, taper, decay)
1058 """Generate Graph from geometry data based on a kernel function
1059
1060 Parameters
(...) 1116 libpysal.graph.Graph encoding kernel weights
1117 """
1118 ids = _evaluate_index(data)
-> 1120 head, tail, weight = _kernel(
1121 data,
1122 bandwidth=bandwidth,
1123 metric=metric,
1124 kernel=kernel,
1125 k=k,
1126 p=p,
1127 ids=ids,
1128 coplanar=coplanar,
1129 decay=decay,
1130 taper=taper,
1131 )
1133 return cls.from_arrays(head, tail, weight)
File ~/dev/pysal/gwlearn/.pixi/envs/default/lib/python3.13/site-packages/libpysal/graph/_kernel.py:127, in _kernel(coordinates, bandwidth, metric, kernel, k, ids, p, taper, decay, coplanar, resolve_isolates, exclude_self_weights)
125 if k is not None:
126 if metric != "precomputed":
--> 127 d = _knn(coordinates, k=k, metric=metric, p=p, coplanar=coplanar)
128 else:
129 d = coordinates * (coordinates.argsort(axis=1, kind="stable") < (k + 1))
File ~/dev/pysal/gwlearn/.pixi/envs/default/lib/python3.13/site-packages/libpysal/graph/_kernel.py:249, in _knn(coordinates, metric, k, p, coplanar)
247 adjtable["focal"] = ids[adjtable.focal]
248 adjtable["neighbor"] = ids[adjtable.neighbor]
--> 249 adjtable = _reorder_adjtable_by_ids(adjtable, ids)
250 sparse_out = sparse.csr_array(
251 (
252 adjtable.weight.values,
(...) 255 shape=(n_samples, n_samples),
256 )
257 sparse_out.data[sparse_out.data < 0] = 0
File ~/dev/pysal/gwlearn/.pixi/envs/default/lib/python3.13/site-packages/libpysal/graph/_utils.py:283, in _reorder_adjtable_by_ids(adjtable, ids)
280 def _reorder_adjtable_by_ids(adjtable, ids):
281 return (
282 adjtable.set_index(["focal", "neighbor"])
--> 283 .reindex(ids, level=0)
284 .reindex(ids, level=1)
285 .reset_index()
286 )
File ~/dev/pysal/gwlearn/.pixi/envs/default/lib/python3.13/site-packages/pandas/core/frame.py:5400, in DataFrame.reindex(self, labels, index, columns, axis, method, copy, level, fill_value, limit, tolerance)
5381 @doc(
5382 NDFrame.reindex,
5383 klass=_shared_doc_kwargs["klass"],
(...) 5398 tolerance=None,
5399 ) -> DataFrame:
-> 5400 return super().reindex(
5401 labels=labels,
5402 index=index,
5403 columns=columns,
5404 axis=axis,
5405 method=method,
5406 copy=copy,
5407 level=level,
5408 fill_value=fill_value,
5409 limit=limit,
5410 tolerance=tolerance,
5411 )
File ~/dev/pysal/gwlearn/.pixi/envs/default/lib/python3.13/site-packages/pandas/core/generic.py:5632, in NDFrame.reindex(self, labels, index, columns, axis, method, copy, level, fill_value, limit, tolerance)
5629 return self._reindex_multi(axes, copy, fill_value)
5631 # perform the reindex on the axes
-> 5632 return self._reindex_axes(
5633 axes, level, limit, tolerance, method, fill_value, copy
5634 ).__finalize__(self, method="reindex")
File ~/dev/pysal/gwlearn/.pixi/envs/default/lib/python3.13/site-packages/pandas/core/generic.py:5660, in NDFrame._reindex_axes(self, axes, level, limit, tolerance, method, fill_value, copy)
5655 new_index, indexer = ax.reindex(
5656 labels, level=level, limit=limit, tolerance=tolerance, method=method
5657 )
5659 axis = self._get_axis_number(a)
-> 5660 obj = obj._reindex_with_indexers(
5661 {axis: [new_index, indexer]},
...
4326 # trying to reindex on an axis with duplicates
4327 if not self._index_as_unique and len(indexer):
-> 4328 raise ValueError("cannot reindex on an axis with duplicate labels")
ValueError: cannot reindex on an axis with duplicate labels
