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nx-cugraph: adds ancestors, descendants, and BFS algos #4029

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merged 10 commits into from
Dec 21, 2023
5 changes: 5 additions & 0 deletions ci/test_python.sh
Original file line number Diff line number Diff line change
Expand Up @@ -111,6 +111,11 @@ popd
rapids-logger "pytest networkx using nx-cugraph backend"
pushd python/nx-cugraph
./run_nx_tests.sh
# Individually run tests that are skipped above b/c they may run out of memory
PYTEST_NO_SKIP=True ./run_nx_tests.sh --cov-append -k "TestDAG and test_antichains"
PYTEST_NO_SKIP=True ./run_nx_tests.sh --cov-append -k "TestMultiDiGraph_DAGLCA and test_all_pairs_lca_pairs_without_lca"
PYTEST_NO_SKIP=True ./run_nx_tests.sh --cov-append -k "TestDAGLCA and test_all_pairs_lca_pairs_without_lca"
PYTEST_NO_SKIP=True ./run_nx_tests.sh --cov-append -k "TestEfficiency and test_using_ego_graph"
Comment on lines +114 to +118
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We can leave this in place in order to get this PR merged, but I think this is masking a bug (likely in pylibcugraph/libcugraph, not in nx-cugraph).

I filed this issue and I'll open a PR to remove these lines and the skipped tests separately, which will be merged when the bug is fixed.

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The PR to eventually fix the bug is #4068

# run_nx_tests.sh outputs coverage data, so check that total coverage is >0.0%
# in case nx-cugraph failed to load but fallback mode allowed the run to pass.
_coverage=$(coverage report|grep "^TOTAL")
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14 changes: 14 additions & 0 deletions python/nx-cugraph/_nx_cugraph/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -29,8 +29,14 @@
# "description": "TODO",
"functions": {
# BEGIN: functions
"ancestors",
"barbell_graph",
"betweenness_centrality",
"bfs_edges",
"bfs_layers",
"bfs_predecessors",
"bfs_successors",
"bfs_tree",
"bull_graph",
"caveman_graph",
"chvatal_graph",
Expand All @@ -44,6 +50,8 @@
"davis_southern_women_graph",
"degree_centrality",
"desargues_graph",
"descendants",
"descendants_at_distance",
"diamond_graph",
"dodecahedral_graph",
"edge_betweenness_centrality",
Expand All @@ -53,6 +61,7 @@
"from_pandas_edgelist",
"from_scipy_sparse_array",
"frucht_graph",
"generic_bfs_edges",
"heawood_graph",
"hits",
"house_graph",
Expand Down Expand Up @@ -99,9 +108,14 @@
"extra_docstrings": {
# BEGIN: extra_docstrings
"betweenness_centrality": "`weight` parameter is not yet supported.",
"bfs_edges": "`sort_neighbors` parameter is not yet supported.",
"bfs_predecessors": "`sort_neighbors` parameter is not yet supported.",
"bfs_successors": "`sort_neighbors` parameter is not yet supported.",
"bfs_tree": "`sort_neighbors` parameter is not yet supported.",
"edge_betweenness_centrality": "`weight` parameter is not yet supported.",
"eigenvector_centrality": "`nstart` parameter is not used, but it is checked for validity.",
"from_pandas_edgelist": "cudf.DataFrame inputs also supported.",
"generic_bfs_edges": "`neighbors` and `sort_neighbors` parameters are not yet supported.",
"k_truss": (
"Currently raises `NotImplementedError` for graphs with more than one connected\n"
"component when k >= 3. We expect to fix this soon."
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3 changes: 3 additions & 0 deletions python/nx-cugraph/nx_cugraph/algorithms/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@
components,
link_analysis,
shortest_paths,
traversal,
)
from .bipartite import complete_bipartite_graph
from .centrality import *
from .components import *
from .core import *
from .dag import *
from .isolate import *
from .link_analysis import *
from .shortest_paths import *
from .traversal import *
13 changes: 8 additions & 5 deletions python/nx-cugraph/nx_cugraph/algorithms/core.py
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,12 @@
import pylibcugraph as plc

import nx_cugraph as nxcg
from nx_cugraph.utils import _get_int_dtype, networkx_algorithm, not_implemented_for
from nx_cugraph.utils import (
_get_int_dtype,
index_dtype,
networkx_algorithm,
not_implemented_for,
)

__all__ = ["k_truss"]

Expand Down Expand Up @@ -81,10 +86,8 @@ def k_truss(G, k):
edge_values = {key: val[edge_indices] for key, val in G.edge_values.items()}
edge_masks = {key: val[edge_indices] for key, val in G.edge_masks.items()}
# Renumber step 2: edge indices
mapper = cp.zeros(len(G), src_indices.dtype)
mapper[node_indices] = cp.arange(node_indices.size, dtype=mapper.dtype)
src_indices = mapper[src_indices]
dst_indices = mapper[dst_indices]
src_indices = cp.searchsorted(node_indices, src_indices).astype(index_dtype)
dst_indices = cp.searchsorted(node_indices, dst_indices).astype(index_dtype)
# Renumber step 3: node values
node_values = {key: val[node_indices] for key, val in G.node_values.items()}
node_masks = {key: val[node_indices] for key, val in G.node_masks.items()}
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55 changes: 55 additions & 0 deletions python/nx-cugraph/nx_cugraph/algorithms/dag.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,55 @@
# Copyright (c) 2023, 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 cupy as cp
import networkx as nx
import numpy as np
import pylibcugraph as plc

from nx_cugraph.convert import _to_graph
from nx_cugraph.utils import index_dtype, networkx_algorithm

__all__ = [
"descendants",
"ancestors",
]


def _ancestors_and_descendants(G, source, *, is_ancestors):
G = _to_graph(G)
if source not in G:
hash(source) # To raise TypeError if appropriate
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raise nx.NetworkXError(
f"The node {source} is not in the {G.__class__.__name__.lower()}."
)
src_index = source if G.key_to_id is None else G.key_to_id[source]
distances, predecessors, node_ids = plc.bfs(
handle=plc.ResourceHandle(),
graph=G._get_plc_graph(switch_indices=is_ancestors),
sources=cp.array([src_index], dtype=index_dtype),
direction_optimizing=False,
depth_limit=-1,
compute_predecessors=False,
do_expensive_check=False,
)
mask = (distances != np.iinfo(distances.dtype).max) & (distances != 0)
return G._nodearray_to_set(node_ids[mask])


@networkx_algorithm
def descendants(G, source):
return _ancestors_and_descendants(G, source, is_ancestors=False)


@networkx_algorithm
def ancestors(G, source):
return _ancestors_and_descendants(G, source, is_ancestors=True)
13 changes: 13 additions & 0 deletions python/nx-cugraph/nx_cugraph/algorithms/traversal/__init__.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
# Copyright (c) 2023, 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.
from .breadth_first_search import *
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