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nx-cugraph: add ego_graph
#4395
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5c6dc05
Add `ego_graph`
eriknw 3030944
Merge branch 'branch-24.06' into add_ego_graph
eriknw ac11cb1
oops forgot `__all__`
eriknw 2e77df5
better docstring formatting (if a little awkward)
eriknw 0de940c
Update copyright years
eriknw 6ce039b
Merge branch 'branch-24.06' into add_ego_graph
eriknw dacc926
oops fix for Python 3.9 and nx 3.2
eriknw 71c98ad
Merge branch 'add_ego_graph' of github.com:eriknw/cugraph into add_eg…
eriknw 17baf34
Merge branch 'branch-24.06' into add_ego_graph
eriknw 3e3b7cb
Merge branch 'branch-24.06' into add_ego_graph
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,161 @@ | ||
| # Copyright (c) 2024, NVIDIA CORPORATION. | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
| import math | ||
|
|
||
| import cupy as cp | ||
| import networkx as nx | ||
| import numpy as np | ||
| import pylibcugraph as plc | ||
|
|
||
| import nx_cugraph as nxcg | ||
|
|
||
| from ..utils import _dtype_param, _get_float_dtype, index_dtype, networkx_algorithm | ||
|
|
||
| __all__ = ["ego_graph"] | ||
|
|
||
|
|
||
| @networkx_algorithm( | ||
| extra_params=_dtype_param, version_added="24.06", _plc={"bfs", "ego_graph", "sssp"} | ||
| ) | ||
| def ego_graph( | ||
| G, n, radius=1, center=True, undirected=False, distance=None, *, dtype=None | ||
| ): | ||
| """Weighted ego_graph with negative cycles is not yet supported. `NotImplementedError` will be raised if there are negative `distance` edge weights.""" # noqa: E501 | ||
| if isinstance(G, nx.Graph): | ||
| G = nxcg.from_networkx(G, preserve_all_attrs=True) | ||
| if n not in G: | ||
| if distance is None: | ||
| raise nx.NodeNotFound(f"Source {n} is not in G") | ||
| raise nx.NodeNotFound(f"Node {n} not found in graph") | ||
| src_index = n if G.key_to_id is None else G.key_to_id[n] | ||
| symmetrize = "union" if undirected and G.is_directed() else None | ||
| if distance is None or distance not in G.edge_values: | ||
| # Simple BFS to determine nodes | ||
| if radius is not None and radius <= 0: | ||
| if center: | ||
| node_ids = cp.array([src_index], dtype=index_dtype) | ||
| else: | ||
| node_ids = cp.empty(0, dtype=index_dtype) | ||
| node_mask = None | ||
| else: | ||
| if radius is None or np.isinf(radius): | ||
| radius = -1 | ||
| else: | ||
| radius = math.ceil(radius) | ||
| distances, unused_predecessors, node_ids = plc.bfs( | ||
| handle=plc.ResourceHandle(), | ||
| graph=G._get_plc_graph(symmetrize=symmetrize), | ||
| sources=cp.array([src_index], index_dtype), | ||
| direction_optimizing=False, # True for undirected only; what's best? | ||
| depth_limit=radius, | ||
| compute_predecessors=False, | ||
| do_expensive_check=False, | ||
| ) | ||
| node_mask = distances != np.iinfo(distances.dtype).max | ||
| else: | ||
| # SSSP to determine nodes | ||
| if callable(distance): | ||
| raise NotImplementedError("callable `distance` argument is not supported") | ||
| if symmetrize and G.is_multigraph(): | ||
| # G._get_plc_graph does not implement `symmetrize=True` w/ edge array | ||
| raise NotImplementedError( | ||
| "Weighted ego_graph with undirected=True not implemented" | ||
| ) | ||
| # Check for negative values since we don't support negative cycles | ||
| edge_vals = G.edge_values[distance] | ||
| if distance in G.edge_masks: | ||
| edge_vals = edge_vals[G.edge_masks[distance]] | ||
| if (edge_vals < 0).any(): | ||
| raise NotImplementedError( | ||
| "Negative edge weights not yet supported by ego_graph" | ||
| ) | ||
| # PERF: we could use BFS if all edges are equal | ||
| if radius is None: | ||
| radius = np.inf | ||
| dtype = _get_float_dtype(dtype, graph=G, weight=distance) | ||
| node_ids, distances, unused_predecessors = plc.sssp( | ||
| resource_handle=plc.ResourceHandle(), | ||
| graph=(G.to_undirected() if symmetrize else G)._get_plc_graph( | ||
| distance, 1, dtype | ||
| ), | ||
| source=src_index, | ||
| cutoff=np.nextafter(radius, np.inf, dtype=np.float64), | ||
| compute_predecessors=True, # TODO: False is not yet supported | ||
| do_expensive_check=False, | ||
| ) | ||
| node_mask = distances != np.finfo(distances.dtype).max | ||
|
|
||
| if node_mask is not None: | ||
| if not center: | ||
| node_mask &= node_ids != src_index | ||
| node_ids = node_ids[node_mask] | ||
| if node_ids.size == G._N: | ||
| return G.copy() | ||
| # TODO: create renumbering helper function(s) | ||
| node_ids.sort() # TODO: is this ever necessary? Keep for safety | ||
| node_values = {key: val[node_ids] for key, val in G.node_values.items()} | ||
| node_masks = {key: val[node_ids] for key, val in G.node_masks.items()} | ||
|
|
||
| G._sort_edge_indices() # TODO: is this ever necessary? Keep for safety | ||
| edge_mask = cp.isin(G.src_indices, node_ids) & cp.isin(G.dst_indices, node_ids) | ||
| src_indices = cp.searchsorted(node_ids, G.src_indices[edge_mask]).astype( | ||
| index_dtype | ||
| ) | ||
| dst_indices = cp.searchsorted(node_ids, G.dst_indices[edge_mask]).astype( | ||
| index_dtype | ||
| ) | ||
| edge_values = {key: val[edge_mask] for key, val in G.edge_values.items()} | ||
| edge_masks = {key: val[edge_mask] for key, val in G.edge_masks.items()} | ||
|
|
||
| # Renumber nodes | ||
| if (id_to_key := G.id_to_key) is not None: | ||
| key_to_id = { | ||
| id_to_key[old_index]: new_index | ||
| for new_index, old_index in enumerate(node_ids.tolist()) | ||
| } | ||
| else: | ||
| key_to_id = { | ||
| old_index: new_index | ||
| for new_index, old_index in enumerate(node_ids.tolist()) | ||
| } | ||
| kwargs = { | ||
| "N": node_ids.size, | ||
| "src_indices": src_indices, | ||
| "dst_indices": dst_indices, | ||
| "edge_values": edge_values, | ||
| "edge_masks": edge_masks, | ||
| "node_values": node_values, | ||
| "node_masks": node_masks, | ||
| "key_to_id": key_to_id, | ||
| } | ||
| if G.is_multigraph(): | ||
| if G.edge_keys is not None: | ||
| kwargs["edge_keys"] = [ | ||
| x for x, m in zip(G.edge_keys, edge_mask.tolist()) if m | ||
| ] | ||
| if G.edge_indices is not None: | ||
| kwargs["edge_indices"] = G.edge_indices[edge_mask] | ||
| rv = G.__class__.from_coo(**kwargs) | ||
| rv.graph.update(G.graph) | ||
| return rv | ||
|
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||
|
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||
| @ego_graph._can_run | ||
| def _(G, n, radius=1, center=True, undirected=False, distance=None, *, dtype=None): | ||
| if distance is not None and undirected and G.is_directed() and G.is_multigraph(): | ||
| return "Weighted ego_graph with undirected=True not implemented" | ||
| if distance is not None and nx.is_negatively_weighted(G, weight=distance): | ||
| return "Weighted ego_graph with negative cycles not yet supported" | ||
| if callable(distance): | ||
| return "callable `distance` argument is not supported" | ||
| return True |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| # Copyright (c) 2024, NVIDIA CORPORATION. | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
| import networkx as nx | ||
| import pytest | ||
| from packaging.version import parse | ||
|
|
||
| import nx_cugraph as nxcg | ||
|
|
||
| from .testing_utils import assert_graphs_equal | ||
|
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||
| nxver = parse(nx.__version__) | ||
|
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||
|
|
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| if nxver.major == 3 and nxver.minor < 2: | ||
| pytest.skip("Need NetworkX >=3.2 to test ego_graph", allow_module_level=True) | ||
|
|
||
|
|
||
| @pytest.mark.parametrize( | ||
| "create_using", [nx.Graph, nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph] | ||
| ) | ||
| @pytest.mark.parametrize("radius", [-1, 0, 1, 1.5, 2, float("inf"), None]) | ||
| @pytest.mark.parametrize("center", [True, False]) | ||
| @pytest.mark.parametrize("undirected", [False, True]) | ||
| @pytest.mark.parametrize("multiple_edges", [False, True]) | ||
| @pytest.mark.parametrize("n", [0, 3]) | ||
| def test_ego_graph_cycle_graph( | ||
| create_using, radius, center, undirected, multiple_edges, n | ||
| ): | ||
| Gnx = nx.cycle_graph(7, create_using=create_using) | ||
| if multiple_edges: | ||
| # Test multigraph with multiple edges | ||
| if not Gnx.is_multigraph(): | ||
| return | ||
| Gnx.add_edges_from(nx.cycle_graph(7, create_using=nx.DiGraph).edges) | ||
| Gnx.add_edge(0, 1, 10) | ||
| Gcg = nxcg.from_networkx(Gnx, preserve_all_attrs=True) | ||
| assert_graphs_equal(Gnx, Gcg) # Sanity check | ||
|
|
||
| kwargs = {"radius": radius, "center": center, "undirected": undirected} | ||
| Hnx = nx.ego_graph(Gnx, n, **kwargs) | ||
| Hcg = nx.ego_graph(Gnx, n, **kwargs, backend="cugraph") | ||
| assert_graphs_equal(Hnx, Hcg) | ||
| with pytest.raises(nx.NodeNotFound, match="not in G"): | ||
| nx.ego_graph(Gnx, -1, **kwargs) | ||
| with pytest.raises(nx.NodeNotFound, match="not in G"): | ||
| nx.ego_graph(Gnx, -1, **kwargs, backend="cugraph") | ||
| # Using sssp with default weight of 1 should give same answer as bfs | ||
| nx.set_edge_attributes(Gnx, 1, name="weight") | ||
| Gcg = nxcg.from_networkx(Gnx, preserve_all_attrs=True) | ||
| assert_graphs_equal(Gnx, Gcg) # Sanity check | ||
|
|
||
| kwargs["distance"] = "weight" | ||
| H2nx = nx.ego_graph(Gnx, n, **kwargs) | ||
| is_nx32 = nxver.major == 3 and nxver.minor == 2 | ||
| if undirected and Gnx.is_directed() and Gnx.is_multigraph(): | ||
| if is_nx32: | ||
| # `should_run` was added in nx 3.3 | ||
| match = "Weighted ego_graph with undirected=True not implemented" | ||
| else: | ||
| match = "not implemented by cugraph" | ||
| with pytest.raises(RuntimeError, match=match): | ||
| nx.ego_graph(Gnx, n, **kwargs, backend="cugraph") | ||
| with pytest.raises(NotImplementedError, match="ego_graph"): | ||
| nx.ego_graph(Gcg, n, **kwargs) | ||
| else: | ||
| H2cg = nx.ego_graph(Gnx, n, **kwargs, backend="cugraph") | ||
| assert_graphs_equal(H2nx, H2cg) | ||
| with pytest.raises(nx.NodeNotFound, match="not found in graph"): | ||
| nx.ego_graph(Gnx, -1, **kwargs) | ||
| with pytest.raises(nx.NodeNotFound, match="not found in graph"): | ||
| nx.ego_graph(Gnx, -1, **kwargs, backend="cugraph") |
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Excellent, thanks!