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- .gitattributes +6 -0
- .venv/lib/python3.11/site-packages/PIL/__pycache__/TiffImagePlugin.cpython-311.pyc +3 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/__init__.py +25 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/__pycache__/__init__.cpython-311.pyc +0 -0
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- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/__pycache__/connectivity.cpython-311.pyc +0 -0
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- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/dominating_set.py +149 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/__init__.py +0 -0
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- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/__pycache__/test_traveling_salesman.cpython-311.pyc +0 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/__pycache__/test_treewidth.cpython-311.pyc +0 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/__pycache__/test_vertex_cover.cpython-311.pyc +0 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_approx_clust_coeff.py +41 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_clique.py +112 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_connectivity.py +199 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_distance_measures.py +59 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_dominating_set.py +78 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_kcomponents.py +303 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_matching.py +8 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_maxcut.py +94 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_ramsey.py +31 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_steinertree.py +265 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_traveling_salesman.py +977 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_treewidth.py +280 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_vertex_cover.py +68 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/treewidth.py +252 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/approximation/vertex_cover.py +83 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/community/__init__.py +26 -0
- .venv/lib/python3.11/site-packages/networkx/algorithms/community/__pycache__/centrality.cpython-311.pyc +0 -0
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"""Approximations of graph properties and Heuristic methods for optimization.
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The functions in this class are not imported into the top-level ``networkx``
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namespace so the easiest way to use them is with::
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>>> from networkx.algorithms import approximation
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Another option is to import the specific function with
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``from networkx.algorithms.approximation import function_name``.
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"""
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from networkx.algorithms.approximation.clustering_coefficient import *
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from networkx.algorithms.approximation.clique import *
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from networkx.algorithms.approximation.connectivity import *
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from networkx.algorithms.approximation.distance_measures import *
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from networkx.algorithms.approximation.dominating_set import *
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from networkx.algorithms.approximation.kcomponents import *
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from networkx.algorithms.approximation.matching import *
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from networkx.algorithms.approximation.ramsey import *
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from networkx.algorithms.approximation.steinertree import *
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from networkx.algorithms.approximation.traveling_salesman import *
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from networkx.algorithms.approximation.treewidth import *
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from networkx.algorithms.approximation.vertex_cover import *
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from networkx.algorithms.approximation.maxcut import *
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"""Functions for finding node and edge dominating sets.
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| 2 |
+
|
| 3 |
+
A `dominating set`_ for an undirected graph *G* with vertex set *V*
|
| 4 |
+
and edge set *E* is a subset *D* of *V* such that every vertex not in
|
| 5 |
+
*D* is adjacent to at least one member of *D*. An `edge dominating set`_
|
| 6 |
+
is a subset *F* of *E* such that every edge not in *F* is
|
| 7 |
+
incident to an endpoint of at least one edge in *F*.
|
| 8 |
+
|
| 9 |
+
.. _dominating set: https://en.wikipedia.org/wiki/Dominating_set
|
| 10 |
+
.. _edge dominating set: https://en.wikipedia.org/wiki/Edge_dominating_set
|
| 11 |
+
|
| 12 |
+
"""
|
| 13 |
+
|
| 14 |
+
import networkx as nx
|
| 15 |
+
|
| 16 |
+
from ...utils import not_implemented_for
|
| 17 |
+
from ..matching import maximal_matching
|
| 18 |
+
|
| 19 |
+
__all__ = ["min_weighted_dominating_set", "min_edge_dominating_set"]
|
| 20 |
+
|
| 21 |
+
|
| 22 |
+
# TODO Why doesn't this algorithm work for directed graphs?
|
| 23 |
+
@not_implemented_for("directed")
|
| 24 |
+
@nx._dispatchable(node_attrs="weight")
|
| 25 |
+
def min_weighted_dominating_set(G, weight=None):
|
| 26 |
+
r"""Returns a dominating set that approximates the minimum weight node
|
| 27 |
+
dominating set.
|
| 28 |
+
|
| 29 |
+
Parameters
|
| 30 |
+
----------
|
| 31 |
+
G : NetworkX graph
|
| 32 |
+
Undirected graph.
|
| 33 |
+
|
| 34 |
+
weight : string
|
| 35 |
+
The node attribute storing the weight of an node. If provided,
|
| 36 |
+
the node attribute with this key must be a number for each
|
| 37 |
+
node. If not provided, each node is assumed to have weight one.
|
| 38 |
+
|
| 39 |
+
Returns
|
| 40 |
+
-------
|
| 41 |
+
min_weight_dominating_set : set
|
| 42 |
+
A set of nodes, the sum of whose weights is no more than `(\log
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| 43 |
+
w(V)) w(V^*)`, where `w(V)` denotes the sum of the weights of
|
| 44 |
+
each node in the graph and `w(V^*)` denotes the sum of the
|
| 45 |
+
weights of each node in the minimum weight dominating set.
|
| 46 |
+
|
| 47 |
+
Examples
|
| 48 |
+
--------
|
| 49 |
+
>>> G = nx.Graph([(0, 1), (0, 4), (1, 4), (1, 2), (2, 3), (3, 4), (2, 5)])
|
| 50 |
+
>>> nx.approximation.min_weighted_dominating_set(G)
|
| 51 |
+
{1, 2, 4}
|
| 52 |
+
|
| 53 |
+
Raises
|
| 54 |
+
------
|
| 55 |
+
NetworkXNotImplemented
|
| 56 |
+
If G is directed.
|
| 57 |
+
|
| 58 |
+
Notes
|
| 59 |
+
-----
|
| 60 |
+
This algorithm computes an approximate minimum weighted dominating
|
| 61 |
+
set for the graph `G`. The returned solution has weight `(\log
|
| 62 |
+
w(V)) w(V^*)`, where `w(V)` denotes the sum of the weights of each
|
| 63 |
+
node in the graph and `w(V^*)` denotes the sum of the weights of
|
| 64 |
+
each node in the minimum weight dominating set for the graph.
|
| 65 |
+
|
| 66 |
+
This implementation of the algorithm runs in $O(m)$ time, where $m$
|
| 67 |
+
is the number of edges in the graph.
|
| 68 |
+
|
| 69 |
+
References
|
| 70 |
+
----------
|
| 71 |
+
.. [1] Vazirani, Vijay V.
|
| 72 |
+
*Approximation Algorithms*.
|
| 73 |
+
Springer Science & Business Media, 2001.
|
| 74 |
+
|
| 75 |
+
"""
|
| 76 |
+
# The unique dominating set for the null graph is the empty set.
|
| 77 |
+
if len(G) == 0:
|
| 78 |
+
return set()
|
| 79 |
+
|
| 80 |
+
# This is the dominating set that will eventually be returned.
|
| 81 |
+
dom_set = set()
|
| 82 |
+
|
| 83 |
+
def _cost(node_and_neighborhood):
|
| 84 |
+
"""Returns the cost-effectiveness of greedily choosing the given
|
| 85 |
+
node.
|
| 86 |
+
|
| 87 |
+
`node_and_neighborhood` is a two-tuple comprising a node and its
|
| 88 |
+
closed neighborhood.
|
| 89 |
+
|
| 90 |
+
"""
|
| 91 |
+
v, neighborhood = node_and_neighborhood
|
| 92 |
+
return G.nodes[v].get(weight, 1) / len(neighborhood - dom_set)
|
| 93 |
+
|
| 94 |
+
# This is a set of all vertices not already covered by the
|
| 95 |
+
# dominating set.
|
| 96 |
+
vertices = set(G)
|
| 97 |
+
# This is a dictionary mapping each node to the closed neighborhood
|
| 98 |
+
# of that node.
|
| 99 |
+
neighborhoods = {v: {v} | set(G[v]) for v in G}
|
| 100 |
+
|
| 101 |
+
# Continue until all vertices are adjacent to some node in the
|
| 102 |
+
# dominating set.
|
| 103 |
+
while vertices:
|
| 104 |
+
# Find the most cost-effective node to add, along with its
|
| 105 |
+
# closed neighborhood.
|
| 106 |
+
dom_node, min_set = min(neighborhoods.items(), key=_cost)
|
| 107 |
+
# Add the node to the dominating set and reduce the remaining
|
| 108 |
+
# set of nodes to cover.
|
| 109 |
+
dom_set.add(dom_node)
|
| 110 |
+
del neighborhoods[dom_node]
|
| 111 |
+
vertices -= min_set
|
| 112 |
+
|
| 113 |
+
return dom_set
|
| 114 |
+
|
| 115 |
+
|
| 116 |
+
@nx._dispatchable
|
| 117 |
+
def min_edge_dominating_set(G):
|
| 118 |
+
r"""Returns minimum cardinality edge dominating set.
|
| 119 |
+
|
| 120 |
+
Parameters
|
| 121 |
+
----------
|
| 122 |
+
G : NetworkX graph
|
| 123 |
+
Undirected graph
|
| 124 |
+
|
| 125 |
+
Returns
|
| 126 |
+
-------
|
| 127 |
+
min_edge_dominating_set : set
|
| 128 |
+
Returns a set of dominating edges whose size is no more than 2 * OPT.
|
| 129 |
+
|
| 130 |
+
Examples
|
| 131 |
+
--------
|
| 132 |
+
>>> G = nx.petersen_graph()
|
| 133 |
+
>>> nx.approximation.min_edge_dominating_set(G)
|
| 134 |
+
{(0, 1), (4, 9), (6, 8), (5, 7), (2, 3)}
|
| 135 |
+
|
| 136 |
+
Raises
|
| 137 |
+
------
|
| 138 |
+
ValueError
|
| 139 |
+
If the input graph `G` is empty.
|
| 140 |
+
|
| 141 |
+
Notes
|
| 142 |
+
-----
|
| 143 |
+
The algorithm computes an approximate solution to the edge dominating set
|
| 144 |
+
problem. The result is no more than 2 * OPT in terms of size of the set.
|
| 145 |
+
Runtime of the algorithm is $O(|E|)$.
|
| 146 |
+
"""
|
| 147 |
+
if not G:
|
| 148 |
+
raise ValueError("Expected non-empty NetworkX graph!")
|
| 149 |
+
return maximal_matching(G)
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/__init__.py
ADDED
|
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ADDED
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ADDED
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ADDED
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ADDED
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ADDED
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|
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ADDED
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|
|
|
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ADDED
|
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|
|
|
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ADDED
|
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|
|
|
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ADDED
|
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|
|
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/__pycache__/test_vertex_cover.cpython-311.pyc
ADDED
|
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|
|
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_approx_clust_coeff.py
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
| 1 |
+
import networkx as nx
|
| 2 |
+
from networkx.algorithms.approximation import average_clustering
|
| 3 |
+
|
| 4 |
+
# This approximation has to be exact in regular graphs
|
| 5 |
+
# with no triangles or with all possible triangles.
|
| 6 |
+
|
| 7 |
+
|
| 8 |
+
def test_petersen():
|
| 9 |
+
# Actual coefficient is 0
|
| 10 |
+
G = nx.petersen_graph()
|
| 11 |
+
assert average_clustering(G, trials=len(G) // 2) == nx.average_clustering(G)
|
| 12 |
+
|
| 13 |
+
|
| 14 |
+
def test_petersen_seed():
|
| 15 |
+
# Actual coefficient is 0
|
| 16 |
+
G = nx.petersen_graph()
|
| 17 |
+
assert average_clustering(G, trials=len(G) // 2, seed=1) == nx.average_clustering(G)
|
| 18 |
+
|
| 19 |
+
|
| 20 |
+
def test_tetrahedral():
|
| 21 |
+
# Actual coefficient is 1
|
| 22 |
+
G = nx.tetrahedral_graph()
|
| 23 |
+
assert average_clustering(G, trials=len(G) // 2) == nx.average_clustering(G)
|
| 24 |
+
|
| 25 |
+
|
| 26 |
+
def test_dodecahedral():
|
| 27 |
+
# Actual coefficient is 0
|
| 28 |
+
G = nx.dodecahedral_graph()
|
| 29 |
+
assert average_clustering(G, trials=len(G) // 2) == nx.average_clustering(G)
|
| 30 |
+
|
| 31 |
+
|
| 32 |
+
def test_empty():
|
| 33 |
+
G = nx.empty_graph(5)
|
| 34 |
+
assert average_clustering(G, trials=len(G) // 2) == 0
|
| 35 |
+
|
| 36 |
+
|
| 37 |
+
def test_complete():
|
| 38 |
+
G = nx.complete_graph(5)
|
| 39 |
+
assert average_clustering(G, trials=len(G) // 2) == 1
|
| 40 |
+
G = nx.complete_graph(7)
|
| 41 |
+
assert average_clustering(G, trials=len(G) // 2) == 1
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_clique.py
ADDED
|
@@ -0,0 +1,112 @@
|
|
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|
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|
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|
|
|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""Unit tests for the :mod:`networkx.algorithms.approximation.clique` module."""
|
| 2 |
+
|
| 3 |
+
import networkx as nx
|
| 4 |
+
from networkx.algorithms.approximation import (
|
| 5 |
+
clique_removal,
|
| 6 |
+
large_clique_size,
|
| 7 |
+
max_clique,
|
| 8 |
+
maximum_independent_set,
|
| 9 |
+
)
|
| 10 |
+
|
| 11 |
+
|
| 12 |
+
def is_independent_set(G, nodes):
|
| 13 |
+
"""Returns True if and only if `nodes` is a clique in `G`.
|
| 14 |
+
|
| 15 |
+
`G` is a NetworkX graph. `nodes` is an iterable of nodes in
|
| 16 |
+
`G`.
|
| 17 |
+
|
| 18 |
+
"""
|
| 19 |
+
return G.subgraph(nodes).number_of_edges() == 0
|
| 20 |
+
|
| 21 |
+
|
| 22 |
+
def is_clique(G, nodes):
|
| 23 |
+
"""Returns True if and only if `nodes` is an independent set
|
| 24 |
+
in `G`.
|
| 25 |
+
|
| 26 |
+
`G` is an undirected simple graph. `nodes` is an iterable of
|
| 27 |
+
nodes in `G`.
|
| 28 |
+
|
| 29 |
+
"""
|
| 30 |
+
H = G.subgraph(nodes)
|
| 31 |
+
n = len(H)
|
| 32 |
+
return H.number_of_edges() == n * (n - 1) // 2
|
| 33 |
+
|
| 34 |
+
|
| 35 |
+
class TestCliqueRemoval:
|
| 36 |
+
"""Unit tests for the
|
| 37 |
+
:func:`~networkx.algorithms.approximation.clique_removal` function.
|
| 38 |
+
|
| 39 |
+
"""
|
| 40 |
+
|
| 41 |
+
def test_trivial_graph(self):
|
| 42 |
+
G = nx.trivial_graph()
|
| 43 |
+
independent_set, cliques = clique_removal(G)
|
| 44 |
+
assert is_independent_set(G, independent_set)
|
| 45 |
+
assert all(is_clique(G, clique) for clique in cliques)
|
| 46 |
+
# In fact, we should only have 1-cliques, that is, singleton nodes.
|
| 47 |
+
assert all(len(clique) == 1 for clique in cliques)
|
| 48 |
+
|
| 49 |
+
def test_complete_graph(self):
|
| 50 |
+
G = nx.complete_graph(10)
|
| 51 |
+
independent_set, cliques = clique_removal(G)
|
| 52 |
+
assert is_independent_set(G, independent_set)
|
| 53 |
+
assert all(is_clique(G, clique) for clique in cliques)
|
| 54 |
+
|
| 55 |
+
def test_barbell_graph(self):
|
| 56 |
+
G = nx.barbell_graph(10, 5)
|
| 57 |
+
independent_set, cliques = clique_removal(G)
|
| 58 |
+
assert is_independent_set(G, independent_set)
|
| 59 |
+
assert all(is_clique(G, clique) for clique in cliques)
|
| 60 |
+
|
| 61 |
+
|
| 62 |
+
class TestMaxClique:
|
| 63 |
+
"""Unit tests for the :func:`networkx.algorithms.approximation.max_clique`
|
| 64 |
+
function.
|
| 65 |
+
|
| 66 |
+
"""
|
| 67 |
+
|
| 68 |
+
def test_null_graph(self):
|
| 69 |
+
G = nx.null_graph()
|
| 70 |
+
assert len(max_clique(G)) == 0
|
| 71 |
+
|
| 72 |
+
def test_complete_graph(self):
|
| 73 |
+
graph = nx.complete_graph(30)
|
| 74 |
+
# this should return the entire graph
|
| 75 |
+
mc = max_clique(graph)
|
| 76 |
+
assert 30 == len(mc)
|
| 77 |
+
|
| 78 |
+
def test_maximal_by_cardinality(self):
|
| 79 |
+
"""Tests that the maximal clique is computed according to maximum
|
| 80 |
+
cardinality of the sets.
|
| 81 |
+
|
| 82 |
+
For more information, see pull request #1531.
|
| 83 |
+
|
| 84 |
+
"""
|
| 85 |
+
G = nx.complete_graph(5)
|
| 86 |
+
G.add_edge(4, 5)
|
| 87 |
+
clique = max_clique(G)
|
| 88 |
+
assert len(clique) > 1
|
| 89 |
+
|
| 90 |
+
G = nx.lollipop_graph(30, 2)
|
| 91 |
+
clique = max_clique(G)
|
| 92 |
+
assert len(clique) > 2
|
| 93 |
+
|
| 94 |
+
|
| 95 |
+
def test_large_clique_size():
|
| 96 |
+
G = nx.complete_graph(9)
|
| 97 |
+
nx.add_cycle(G, [9, 10, 11])
|
| 98 |
+
G.add_edge(8, 9)
|
| 99 |
+
G.add_edge(1, 12)
|
| 100 |
+
G.add_node(13)
|
| 101 |
+
|
| 102 |
+
assert large_clique_size(G) == 9
|
| 103 |
+
G.remove_node(5)
|
| 104 |
+
assert large_clique_size(G) == 8
|
| 105 |
+
G.remove_edge(2, 3)
|
| 106 |
+
assert large_clique_size(G) == 7
|
| 107 |
+
|
| 108 |
+
|
| 109 |
+
def test_independent_set():
|
| 110 |
+
# smoke test
|
| 111 |
+
G = nx.Graph()
|
| 112 |
+
assert len(maximum_independent_set(G)) == 0
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_connectivity.py
ADDED
|
@@ -0,0 +1,199 @@
|
|
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|
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|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
|
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|
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|
|
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|
|
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|
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|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
|
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|
|
|
|
|
|
| 1 |
+
import pytest
|
| 2 |
+
|
| 3 |
+
import networkx as nx
|
| 4 |
+
from networkx.algorithms import approximation as approx
|
| 5 |
+
|
| 6 |
+
|
| 7 |
+
def test_global_node_connectivity():
|
| 8 |
+
# Figure 1 chapter on Connectivity
|
| 9 |
+
G = nx.Graph()
|
| 10 |
+
G.add_edges_from(
|
| 11 |
+
[
|
| 12 |
+
(1, 2),
|
| 13 |
+
(1, 3),
|
| 14 |
+
(1, 4),
|
| 15 |
+
(1, 5),
|
| 16 |
+
(2, 3),
|
| 17 |
+
(2, 6),
|
| 18 |
+
(3, 4),
|
| 19 |
+
(3, 6),
|
| 20 |
+
(4, 6),
|
| 21 |
+
(4, 7),
|
| 22 |
+
(5, 7),
|
| 23 |
+
(6, 8),
|
| 24 |
+
(6, 9),
|
| 25 |
+
(7, 8),
|
| 26 |
+
(7, 10),
|
| 27 |
+
(8, 11),
|
| 28 |
+
(9, 10),
|
| 29 |
+
(9, 11),
|
| 30 |
+
(10, 11),
|
| 31 |
+
]
|
| 32 |
+
)
|
| 33 |
+
assert 2 == approx.local_node_connectivity(G, 1, 11)
|
| 34 |
+
assert 2 == approx.node_connectivity(G)
|
| 35 |
+
assert 2 == approx.node_connectivity(G, 1, 11)
|
| 36 |
+
|
| 37 |
+
|
| 38 |
+
def test_white_harary1():
|
| 39 |
+
# Figure 1b white and harary (2001)
|
| 40 |
+
# A graph with high adhesion (edge connectivity) and low cohesion
|
| 41 |
+
# (node connectivity)
|
| 42 |
+
G = nx.disjoint_union(nx.complete_graph(4), nx.complete_graph(4))
|
| 43 |
+
G.remove_node(7)
|
| 44 |
+
for i in range(4, 7):
|
| 45 |
+
G.add_edge(0, i)
|
| 46 |
+
G = nx.disjoint_union(G, nx.complete_graph(4))
|
| 47 |
+
G.remove_node(G.order() - 1)
|
| 48 |
+
for i in range(7, 10):
|
| 49 |
+
G.add_edge(0, i)
|
| 50 |
+
assert 1 == approx.node_connectivity(G)
|
| 51 |
+
|
| 52 |
+
|
| 53 |
+
def test_complete_graphs():
|
| 54 |
+
for n in range(5, 25, 5):
|
| 55 |
+
G = nx.complete_graph(n)
|
| 56 |
+
assert n - 1 == approx.node_connectivity(G)
|
| 57 |
+
assert n - 1 == approx.node_connectivity(G, 0, 3)
|
| 58 |
+
|
| 59 |
+
|
| 60 |
+
def test_empty_graphs():
|
| 61 |
+
for k in range(5, 25, 5):
|
| 62 |
+
G = nx.empty_graph(k)
|
| 63 |
+
assert 0 == approx.node_connectivity(G)
|
| 64 |
+
assert 0 == approx.node_connectivity(G, 0, 3)
|
| 65 |
+
|
| 66 |
+
|
| 67 |
+
def test_petersen():
|
| 68 |
+
G = nx.petersen_graph()
|
| 69 |
+
assert 3 == approx.node_connectivity(G)
|
| 70 |
+
assert 3 == approx.node_connectivity(G, 0, 5)
|
| 71 |
+
|
| 72 |
+
|
| 73 |
+
# Approximation fails with tutte graph
|
| 74 |
+
# def test_tutte():
|
| 75 |
+
# G = nx.tutte_graph()
|
| 76 |
+
# assert_equal(3, approx.node_connectivity(G))
|
| 77 |
+
|
| 78 |
+
|
| 79 |
+
def test_dodecahedral():
|
| 80 |
+
G = nx.dodecahedral_graph()
|
| 81 |
+
assert 3 == approx.node_connectivity(G)
|
| 82 |
+
assert 3 == approx.node_connectivity(G, 0, 5)
|
| 83 |
+
|
| 84 |
+
|
| 85 |
+
def test_octahedral():
|
| 86 |
+
G = nx.octahedral_graph()
|
| 87 |
+
assert 4 == approx.node_connectivity(G)
|
| 88 |
+
assert 4 == approx.node_connectivity(G, 0, 5)
|
| 89 |
+
|
| 90 |
+
|
| 91 |
+
# Approximation can fail with icosahedral graph depending
|
| 92 |
+
# on iteration order.
|
| 93 |
+
# def test_icosahedral():
|
| 94 |
+
# G=nx.icosahedral_graph()
|
| 95 |
+
# assert_equal(5, approx.node_connectivity(G))
|
| 96 |
+
# assert_equal(5, approx.node_connectivity(G, 0, 5))
|
| 97 |
+
|
| 98 |
+
|
| 99 |
+
def test_only_source():
|
| 100 |
+
G = nx.complete_graph(5)
|
| 101 |
+
pytest.raises(nx.NetworkXError, approx.node_connectivity, G, s=0)
|
| 102 |
+
|
| 103 |
+
|
| 104 |
+
def test_only_target():
|
| 105 |
+
G = nx.complete_graph(5)
|
| 106 |
+
pytest.raises(nx.NetworkXError, approx.node_connectivity, G, t=0)
|
| 107 |
+
|
| 108 |
+
|
| 109 |
+
def test_missing_source():
|
| 110 |
+
G = nx.path_graph(4)
|
| 111 |
+
pytest.raises(nx.NetworkXError, approx.node_connectivity, G, 10, 1)
|
| 112 |
+
|
| 113 |
+
|
| 114 |
+
def test_missing_target():
|
| 115 |
+
G = nx.path_graph(4)
|
| 116 |
+
pytest.raises(nx.NetworkXError, approx.node_connectivity, G, 1, 10)
|
| 117 |
+
|
| 118 |
+
|
| 119 |
+
def test_source_equals_target():
|
| 120 |
+
G = nx.complete_graph(5)
|
| 121 |
+
pytest.raises(nx.NetworkXError, approx.local_node_connectivity, G, 0, 0)
|
| 122 |
+
|
| 123 |
+
|
| 124 |
+
def test_directed_node_connectivity():
|
| 125 |
+
G = nx.cycle_graph(10, create_using=nx.DiGraph()) # only one direction
|
| 126 |
+
D = nx.cycle_graph(10).to_directed() # 2 reciprocal edges
|
| 127 |
+
assert 1 == approx.node_connectivity(G)
|
| 128 |
+
assert 1 == approx.node_connectivity(G, 1, 4)
|
| 129 |
+
assert 2 == approx.node_connectivity(D)
|
| 130 |
+
assert 2 == approx.node_connectivity(D, 1, 4)
|
| 131 |
+
|
| 132 |
+
|
| 133 |
+
class TestAllPairsNodeConnectivityApprox:
|
| 134 |
+
@classmethod
|
| 135 |
+
def setup_class(cls):
|
| 136 |
+
cls.path = nx.path_graph(7)
|
| 137 |
+
cls.directed_path = nx.path_graph(7, create_using=nx.DiGraph())
|
| 138 |
+
cls.cycle = nx.cycle_graph(7)
|
| 139 |
+
cls.directed_cycle = nx.cycle_graph(7, create_using=nx.DiGraph())
|
| 140 |
+
cls.gnp = nx.gnp_random_graph(30, 0.1)
|
| 141 |
+
cls.directed_gnp = nx.gnp_random_graph(30, 0.1, directed=True)
|
| 142 |
+
cls.K20 = nx.complete_graph(20)
|
| 143 |
+
cls.K10 = nx.complete_graph(10)
|
| 144 |
+
cls.K5 = nx.complete_graph(5)
|
| 145 |
+
cls.G_list = [
|
| 146 |
+
cls.path,
|
| 147 |
+
cls.directed_path,
|
| 148 |
+
cls.cycle,
|
| 149 |
+
cls.directed_cycle,
|
| 150 |
+
cls.gnp,
|
| 151 |
+
cls.directed_gnp,
|
| 152 |
+
cls.K10,
|
| 153 |
+
cls.K5,
|
| 154 |
+
cls.K20,
|
| 155 |
+
]
|
| 156 |
+
|
| 157 |
+
def test_cycles(self):
|
| 158 |
+
K_undir = approx.all_pairs_node_connectivity(self.cycle)
|
| 159 |
+
for source in K_undir:
|
| 160 |
+
for target, k in K_undir[source].items():
|
| 161 |
+
assert k == 2
|
| 162 |
+
K_dir = approx.all_pairs_node_connectivity(self.directed_cycle)
|
| 163 |
+
for source in K_dir:
|
| 164 |
+
for target, k in K_dir[source].items():
|
| 165 |
+
assert k == 1
|
| 166 |
+
|
| 167 |
+
def test_complete(self):
|
| 168 |
+
for G in [self.K10, self.K5, self.K20]:
|
| 169 |
+
K = approx.all_pairs_node_connectivity(G)
|
| 170 |
+
for source in K:
|
| 171 |
+
for target, k in K[source].items():
|
| 172 |
+
assert k == len(G) - 1
|
| 173 |
+
|
| 174 |
+
def test_paths(self):
|
| 175 |
+
K_undir = approx.all_pairs_node_connectivity(self.path)
|
| 176 |
+
for source in K_undir:
|
| 177 |
+
for target, k in K_undir[source].items():
|
| 178 |
+
assert k == 1
|
| 179 |
+
K_dir = approx.all_pairs_node_connectivity(self.directed_path)
|
| 180 |
+
for source in K_dir:
|
| 181 |
+
for target, k in K_dir[source].items():
|
| 182 |
+
if source < target:
|
| 183 |
+
assert k == 1
|
| 184 |
+
else:
|
| 185 |
+
assert k == 0
|
| 186 |
+
|
| 187 |
+
def test_cutoff(self):
|
| 188 |
+
for G in [self.K10, self.K5, self.K20]:
|
| 189 |
+
for mp in [2, 3, 4]:
|
| 190 |
+
paths = approx.all_pairs_node_connectivity(G, cutoff=mp)
|
| 191 |
+
for source in paths:
|
| 192 |
+
for target, K in paths[source].items():
|
| 193 |
+
assert K == mp
|
| 194 |
+
|
| 195 |
+
def test_all_pairs_connectivity_nbunch(self):
|
| 196 |
+
G = nx.complete_graph(5)
|
| 197 |
+
nbunch = [0, 2, 3]
|
| 198 |
+
C = approx.all_pairs_node_connectivity(G, nbunch=nbunch)
|
| 199 |
+
assert len(C) == len(nbunch)
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_distance_measures.py
ADDED
|
@@ -0,0 +1,59 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""Unit tests for the :mod:`networkx.algorithms.approximation.distance_measures` module."""
|
| 2 |
+
|
| 3 |
+
import pytest
|
| 4 |
+
|
| 5 |
+
import networkx as nx
|
| 6 |
+
from networkx.algorithms.approximation import diameter
|
| 7 |
+
|
| 8 |
+
|
| 9 |
+
class TestDiameter:
|
| 10 |
+
"""Unit tests for the approximate diameter function
|
| 11 |
+
:func:`~networkx.algorithms.approximation.distance_measures.diameter`.
|
| 12 |
+
"""
|
| 13 |
+
|
| 14 |
+
def test_null_graph(self):
|
| 15 |
+
"""Test empty graph."""
|
| 16 |
+
G = nx.null_graph()
|
| 17 |
+
with pytest.raises(
|
| 18 |
+
nx.NetworkXError, match="Expected non-empty NetworkX graph!"
|
| 19 |
+
):
|
| 20 |
+
diameter(G)
|
| 21 |
+
|
| 22 |
+
def test_undirected_non_connected(self):
|
| 23 |
+
"""Test an undirected disconnected graph."""
|
| 24 |
+
graph = nx.path_graph(10)
|
| 25 |
+
graph.remove_edge(3, 4)
|
| 26 |
+
with pytest.raises(nx.NetworkXError, match="Graph not connected."):
|
| 27 |
+
diameter(graph)
|
| 28 |
+
|
| 29 |
+
def test_directed_non_strongly_connected(self):
|
| 30 |
+
"""Test a directed non strongly connected graph."""
|
| 31 |
+
graph = nx.path_graph(10, create_using=nx.DiGraph())
|
| 32 |
+
with pytest.raises(nx.NetworkXError, match="DiGraph not strongly connected."):
|
| 33 |
+
diameter(graph)
|
| 34 |
+
|
| 35 |
+
def test_complete_undirected_graph(self):
|
| 36 |
+
"""Test a complete undirected graph."""
|
| 37 |
+
graph = nx.complete_graph(10)
|
| 38 |
+
assert diameter(graph) == 1
|
| 39 |
+
|
| 40 |
+
def test_complete_directed_graph(self):
|
| 41 |
+
"""Test a complete directed graph."""
|
| 42 |
+
graph = nx.complete_graph(10, create_using=nx.DiGraph())
|
| 43 |
+
assert diameter(graph) == 1
|
| 44 |
+
|
| 45 |
+
def test_undirected_path_graph(self):
|
| 46 |
+
"""Test an undirected path graph with 10 nodes."""
|
| 47 |
+
graph = nx.path_graph(10)
|
| 48 |
+
assert diameter(graph) == 9
|
| 49 |
+
|
| 50 |
+
def test_directed_path_graph(self):
|
| 51 |
+
"""Test a directed path graph with 10 nodes."""
|
| 52 |
+
graph = nx.path_graph(10).to_directed()
|
| 53 |
+
assert diameter(graph) == 9
|
| 54 |
+
|
| 55 |
+
def test_single_node(self):
|
| 56 |
+
"""Test a graph which contains just a node."""
|
| 57 |
+
graph = nx.Graph()
|
| 58 |
+
graph.add_node(1)
|
| 59 |
+
assert diameter(graph) == 0
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_dominating_set.py
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import pytest
|
| 2 |
+
|
| 3 |
+
import networkx as nx
|
| 4 |
+
from networkx.algorithms.approximation import (
|
| 5 |
+
min_edge_dominating_set,
|
| 6 |
+
min_weighted_dominating_set,
|
| 7 |
+
)
|
| 8 |
+
|
| 9 |
+
|
| 10 |
+
class TestMinWeightDominatingSet:
|
| 11 |
+
def test_min_weighted_dominating_set(self):
|
| 12 |
+
graph = nx.Graph()
|
| 13 |
+
graph.add_edge(1, 2)
|
| 14 |
+
graph.add_edge(1, 5)
|
| 15 |
+
graph.add_edge(2, 3)
|
| 16 |
+
graph.add_edge(2, 5)
|
| 17 |
+
graph.add_edge(3, 4)
|
| 18 |
+
graph.add_edge(3, 6)
|
| 19 |
+
graph.add_edge(5, 6)
|
| 20 |
+
|
| 21 |
+
vertices = {1, 2, 3, 4, 5, 6}
|
| 22 |
+
# due to ties, this might be hard to test tight bounds
|
| 23 |
+
dom_set = min_weighted_dominating_set(graph)
|
| 24 |
+
for vertex in vertices - dom_set:
|
| 25 |
+
neighbors = set(graph.neighbors(vertex))
|
| 26 |
+
assert len(neighbors & dom_set) > 0, "Non dominating set found!"
|
| 27 |
+
|
| 28 |
+
def test_star_graph(self):
|
| 29 |
+
"""Tests that an approximate dominating set for the star graph,
|
| 30 |
+
even when the center node does not have the smallest integer
|
| 31 |
+
label, gives just the center node.
|
| 32 |
+
|
| 33 |
+
For more information, see #1527.
|
| 34 |
+
|
| 35 |
+
"""
|
| 36 |
+
# Create a star graph in which the center node has the highest
|
| 37 |
+
# label instead of the lowest.
|
| 38 |
+
G = nx.star_graph(10)
|
| 39 |
+
G = nx.relabel_nodes(G, {0: 9, 9: 0})
|
| 40 |
+
assert min_weighted_dominating_set(G) == {9}
|
| 41 |
+
|
| 42 |
+
def test_null_graph(self):
|
| 43 |
+
"""Tests that the unique dominating set for the null graph is an empty set"""
|
| 44 |
+
G = nx.Graph()
|
| 45 |
+
assert min_weighted_dominating_set(G) == set()
|
| 46 |
+
|
| 47 |
+
def test_min_edge_dominating_set(self):
|
| 48 |
+
graph = nx.path_graph(5)
|
| 49 |
+
dom_set = min_edge_dominating_set(graph)
|
| 50 |
+
|
| 51 |
+
# this is a crappy way to test, but good enough for now.
|
| 52 |
+
for edge in graph.edges():
|
| 53 |
+
if edge in dom_set:
|
| 54 |
+
continue
|
| 55 |
+
else:
|
| 56 |
+
u, v = edge
|
| 57 |
+
found = False
|
| 58 |
+
for dom_edge in dom_set:
|
| 59 |
+
found |= u == dom_edge[0] or u == dom_edge[1]
|
| 60 |
+
assert found, "Non adjacent edge found!"
|
| 61 |
+
|
| 62 |
+
graph = nx.complete_graph(10)
|
| 63 |
+
dom_set = min_edge_dominating_set(graph)
|
| 64 |
+
|
| 65 |
+
# this is a crappy way to test, but good enough for now.
|
| 66 |
+
for edge in graph.edges():
|
| 67 |
+
if edge in dom_set:
|
| 68 |
+
continue
|
| 69 |
+
else:
|
| 70 |
+
u, v = edge
|
| 71 |
+
found = False
|
| 72 |
+
for dom_edge in dom_set:
|
| 73 |
+
found |= u == dom_edge[0] or u == dom_edge[1]
|
| 74 |
+
assert found, "Non adjacent edge found!"
|
| 75 |
+
|
| 76 |
+
graph = nx.Graph() # empty Networkx graph
|
| 77 |
+
with pytest.raises(ValueError, match="Expected non-empty NetworkX graph!"):
|
| 78 |
+
min_edge_dominating_set(graph)
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_kcomponents.py
ADDED
|
@@ -0,0 +1,303 @@
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|
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|
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|
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|
|
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|
|
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|
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|
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|
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|
|
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|
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|
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|
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# Test for approximation to k-components algorithm
|
| 2 |
+
import pytest
|
| 3 |
+
|
| 4 |
+
import networkx as nx
|
| 5 |
+
from networkx.algorithms.approximation import k_components
|
| 6 |
+
from networkx.algorithms.approximation.kcomponents import _AntiGraph, _same
|
| 7 |
+
|
| 8 |
+
|
| 9 |
+
def build_k_number_dict(k_components):
|
| 10 |
+
k_num = {}
|
| 11 |
+
for k, comps in sorted(k_components.items()):
|
| 12 |
+
for comp in comps:
|
| 13 |
+
for node in comp:
|
| 14 |
+
k_num[node] = k
|
| 15 |
+
return k_num
|
| 16 |
+
|
| 17 |
+
|
| 18 |
+
##
|
| 19 |
+
# Some nice synthetic graphs
|
| 20 |
+
##
|
| 21 |
+
|
| 22 |
+
|
| 23 |
+
def graph_example_1():
|
| 24 |
+
G = nx.convert_node_labels_to_integers(
|
| 25 |
+
nx.grid_graph([5, 5]), label_attribute="labels"
|
| 26 |
+
)
|
| 27 |
+
rlabels = nx.get_node_attributes(G, "labels")
|
| 28 |
+
labels = {v: k for k, v in rlabels.items()}
|
| 29 |
+
|
| 30 |
+
for nodes in [
|
| 31 |
+
(labels[(0, 0)], labels[(1, 0)]),
|
| 32 |
+
(labels[(0, 4)], labels[(1, 4)]),
|
| 33 |
+
(labels[(3, 0)], labels[(4, 0)]),
|
| 34 |
+
(labels[(3, 4)], labels[(4, 4)]),
|
| 35 |
+
]:
|
| 36 |
+
new_node = G.order() + 1
|
| 37 |
+
# Petersen graph is triconnected
|
| 38 |
+
P = nx.petersen_graph()
|
| 39 |
+
G = nx.disjoint_union(G, P)
|
| 40 |
+
# Add two edges between the grid and P
|
| 41 |
+
G.add_edge(new_node + 1, nodes[0])
|
| 42 |
+
G.add_edge(new_node, nodes[1])
|
| 43 |
+
# K5 is 4-connected
|
| 44 |
+
K = nx.complete_graph(5)
|
| 45 |
+
G = nx.disjoint_union(G, K)
|
| 46 |
+
# Add three edges between P and K5
|
| 47 |
+
G.add_edge(new_node + 2, new_node + 11)
|
| 48 |
+
G.add_edge(new_node + 3, new_node + 12)
|
| 49 |
+
G.add_edge(new_node + 4, new_node + 13)
|
| 50 |
+
# Add another K5 sharing a node
|
| 51 |
+
G = nx.disjoint_union(G, K)
|
| 52 |
+
nbrs = G[new_node + 10]
|
| 53 |
+
G.remove_node(new_node + 10)
|
| 54 |
+
for nbr in nbrs:
|
| 55 |
+
G.add_edge(new_node + 17, nbr)
|
| 56 |
+
G.add_edge(new_node + 16, new_node + 5)
|
| 57 |
+
return G
|
| 58 |
+
|
| 59 |
+
|
| 60 |
+
def torrents_and_ferraro_graph():
|
| 61 |
+
G = nx.convert_node_labels_to_integers(
|
| 62 |
+
nx.grid_graph([5, 5]), label_attribute="labels"
|
| 63 |
+
)
|
| 64 |
+
rlabels = nx.get_node_attributes(G, "labels")
|
| 65 |
+
labels = {v: k for k, v in rlabels.items()}
|
| 66 |
+
|
| 67 |
+
for nodes in [(labels[(0, 4)], labels[(1, 4)]), (labels[(3, 4)], labels[(4, 4)])]:
|
| 68 |
+
new_node = G.order() + 1
|
| 69 |
+
# Petersen graph is triconnected
|
| 70 |
+
P = nx.petersen_graph()
|
| 71 |
+
G = nx.disjoint_union(G, P)
|
| 72 |
+
# Add two edges between the grid and P
|
| 73 |
+
G.add_edge(new_node + 1, nodes[0])
|
| 74 |
+
G.add_edge(new_node, nodes[1])
|
| 75 |
+
# K5 is 4-connected
|
| 76 |
+
K = nx.complete_graph(5)
|
| 77 |
+
G = nx.disjoint_union(G, K)
|
| 78 |
+
# Add three edges between P and K5
|
| 79 |
+
G.add_edge(new_node + 2, new_node + 11)
|
| 80 |
+
G.add_edge(new_node + 3, new_node + 12)
|
| 81 |
+
G.add_edge(new_node + 4, new_node + 13)
|
| 82 |
+
# Add another K5 sharing a node
|
| 83 |
+
G = nx.disjoint_union(G, K)
|
| 84 |
+
nbrs = G[new_node + 10]
|
| 85 |
+
G.remove_node(new_node + 10)
|
| 86 |
+
for nbr in nbrs:
|
| 87 |
+
G.add_edge(new_node + 17, nbr)
|
| 88 |
+
# Commenting this makes the graph not biconnected !!
|
| 89 |
+
# This stupid mistake make one reviewer very angry :P
|
| 90 |
+
G.add_edge(new_node + 16, new_node + 8)
|
| 91 |
+
|
| 92 |
+
for nodes in [(labels[(0, 0)], labels[(1, 0)]), (labels[(3, 0)], labels[(4, 0)])]:
|
| 93 |
+
new_node = G.order() + 1
|
| 94 |
+
# Petersen graph is triconnected
|
| 95 |
+
P = nx.petersen_graph()
|
| 96 |
+
G = nx.disjoint_union(G, P)
|
| 97 |
+
# Add two edges between the grid and P
|
| 98 |
+
G.add_edge(new_node + 1, nodes[0])
|
| 99 |
+
G.add_edge(new_node, nodes[1])
|
| 100 |
+
# K5 is 4-connected
|
| 101 |
+
K = nx.complete_graph(5)
|
| 102 |
+
G = nx.disjoint_union(G, K)
|
| 103 |
+
# Add three edges between P and K5
|
| 104 |
+
G.add_edge(new_node + 2, new_node + 11)
|
| 105 |
+
G.add_edge(new_node + 3, new_node + 12)
|
| 106 |
+
G.add_edge(new_node + 4, new_node + 13)
|
| 107 |
+
# Add another K5 sharing two nodes
|
| 108 |
+
G = nx.disjoint_union(G, K)
|
| 109 |
+
nbrs = G[new_node + 10]
|
| 110 |
+
G.remove_node(new_node + 10)
|
| 111 |
+
for nbr in nbrs:
|
| 112 |
+
G.add_edge(new_node + 17, nbr)
|
| 113 |
+
nbrs2 = G[new_node + 9]
|
| 114 |
+
G.remove_node(new_node + 9)
|
| 115 |
+
for nbr in nbrs2:
|
| 116 |
+
G.add_edge(new_node + 18, nbr)
|
| 117 |
+
return G
|
| 118 |
+
|
| 119 |
+
|
| 120 |
+
# Helper function
|
| 121 |
+
|
| 122 |
+
|
| 123 |
+
def _check_connectivity(G):
|
| 124 |
+
result = k_components(G)
|
| 125 |
+
for k, components in result.items():
|
| 126 |
+
if k < 3:
|
| 127 |
+
continue
|
| 128 |
+
for component in components:
|
| 129 |
+
C = G.subgraph(component)
|
| 130 |
+
K = nx.node_connectivity(C)
|
| 131 |
+
assert K >= k
|
| 132 |
+
|
| 133 |
+
|
| 134 |
+
def test_torrents_and_ferraro_graph():
|
| 135 |
+
G = torrents_and_ferraro_graph()
|
| 136 |
+
_check_connectivity(G)
|
| 137 |
+
|
| 138 |
+
|
| 139 |
+
def test_example_1():
|
| 140 |
+
G = graph_example_1()
|
| 141 |
+
_check_connectivity(G)
|
| 142 |
+
|
| 143 |
+
|
| 144 |
+
def test_karate_0():
|
| 145 |
+
G = nx.karate_club_graph()
|
| 146 |
+
_check_connectivity(G)
|
| 147 |
+
|
| 148 |
+
|
| 149 |
+
def test_karate_1():
|
| 150 |
+
karate_k_num = {
|
| 151 |
+
0: 4,
|
| 152 |
+
1: 4,
|
| 153 |
+
2: 4,
|
| 154 |
+
3: 4,
|
| 155 |
+
4: 3,
|
| 156 |
+
5: 3,
|
| 157 |
+
6: 3,
|
| 158 |
+
7: 4,
|
| 159 |
+
8: 4,
|
| 160 |
+
9: 2,
|
| 161 |
+
10: 3,
|
| 162 |
+
11: 1,
|
| 163 |
+
12: 2,
|
| 164 |
+
13: 4,
|
| 165 |
+
14: 2,
|
| 166 |
+
15: 2,
|
| 167 |
+
16: 2,
|
| 168 |
+
17: 2,
|
| 169 |
+
18: 2,
|
| 170 |
+
19: 3,
|
| 171 |
+
20: 2,
|
| 172 |
+
21: 2,
|
| 173 |
+
22: 2,
|
| 174 |
+
23: 3,
|
| 175 |
+
24: 3,
|
| 176 |
+
25: 3,
|
| 177 |
+
26: 2,
|
| 178 |
+
27: 3,
|
| 179 |
+
28: 3,
|
| 180 |
+
29: 3,
|
| 181 |
+
30: 4,
|
| 182 |
+
31: 3,
|
| 183 |
+
32: 4,
|
| 184 |
+
33: 4,
|
| 185 |
+
}
|
| 186 |
+
approx_karate_k_num = karate_k_num.copy()
|
| 187 |
+
approx_karate_k_num[24] = 2
|
| 188 |
+
approx_karate_k_num[25] = 2
|
| 189 |
+
G = nx.karate_club_graph()
|
| 190 |
+
k_comps = k_components(G)
|
| 191 |
+
k_num = build_k_number_dict(k_comps)
|
| 192 |
+
assert k_num in (karate_k_num, approx_karate_k_num)
|
| 193 |
+
|
| 194 |
+
|
| 195 |
+
def test_example_1_detail_3_and_4():
|
| 196 |
+
G = graph_example_1()
|
| 197 |
+
result = k_components(G)
|
| 198 |
+
# In this example graph there are 8 3-components, 4 with 15 nodes
|
| 199 |
+
# and 4 with 5 nodes.
|
| 200 |
+
assert len(result[3]) == 8
|
| 201 |
+
assert len([c for c in result[3] if len(c) == 15]) == 4
|
| 202 |
+
assert len([c for c in result[3] if len(c) == 5]) == 4
|
| 203 |
+
# There are also 8 4-components all with 5 nodes.
|
| 204 |
+
assert len(result[4]) == 8
|
| 205 |
+
assert all(len(c) == 5 for c in result[4])
|
| 206 |
+
# Finally check that the k-components detected have actually node
|
| 207 |
+
# connectivity >= k.
|
| 208 |
+
for k, components in result.items():
|
| 209 |
+
if k < 3:
|
| 210 |
+
continue
|
| 211 |
+
for component in components:
|
| 212 |
+
K = nx.node_connectivity(G.subgraph(component))
|
| 213 |
+
assert K >= k
|
| 214 |
+
|
| 215 |
+
|
| 216 |
+
def test_directed():
|
| 217 |
+
with pytest.raises(nx.NetworkXNotImplemented):
|
| 218 |
+
G = nx.gnp_random_graph(10, 0.4, directed=True)
|
| 219 |
+
kc = k_components(G)
|
| 220 |
+
|
| 221 |
+
|
| 222 |
+
def test_same():
|
| 223 |
+
equal = {"A": 2, "B": 2, "C": 2}
|
| 224 |
+
slightly_different = {"A": 2, "B": 1, "C": 2}
|
| 225 |
+
different = {"A": 2, "B": 8, "C": 18}
|
| 226 |
+
assert _same(equal)
|
| 227 |
+
assert not _same(slightly_different)
|
| 228 |
+
assert _same(slightly_different, tol=1)
|
| 229 |
+
assert not _same(different)
|
| 230 |
+
assert not _same(different, tol=4)
|
| 231 |
+
|
| 232 |
+
|
| 233 |
+
class TestAntiGraph:
|
| 234 |
+
@classmethod
|
| 235 |
+
def setup_class(cls):
|
| 236 |
+
cls.Gnp = nx.gnp_random_graph(20, 0.8, seed=42)
|
| 237 |
+
cls.Anp = _AntiGraph(nx.complement(cls.Gnp))
|
| 238 |
+
cls.Gd = nx.davis_southern_women_graph()
|
| 239 |
+
cls.Ad = _AntiGraph(nx.complement(cls.Gd))
|
| 240 |
+
cls.Gk = nx.karate_club_graph()
|
| 241 |
+
cls.Ak = _AntiGraph(nx.complement(cls.Gk))
|
| 242 |
+
cls.GA = [(cls.Gnp, cls.Anp), (cls.Gd, cls.Ad), (cls.Gk, cls.Ak)]
|
| 243 |
+
|
| 244 |
+
def test_size(self):
|
| 245 |
+
for G, A in self.GA:
|
| 246 |
+
n = G.order()
|
| 247 |
+
s = len(list(G.edges())) + len(list(A.edges()))
|
| 248 |
+
assert s == (n * (n - 1)) / 2
|
| 249 |
+
|
| 250 |
+
def test_degree(self):
|
| 251 |
+
for G, A in self.GA:
|
| 252 |
+
assert sorted(G.degree()) == sorted(A.degree())
|
| 253 |
+
|
| 254 |
+
def test_core_number(self):
|
| 255 |
+
for G, A in self.GA:
|
| 256 |
+
assert nx.core_number(G) == nx.core_number(A)
|
| 257 |
+
|
| 258 |
+
def test_connected_components(self):
|
| 259 |
+
# ccs are same unless isolated nodes or any node has degree=len(G)-1
|
| 260 |
+
# graphs in self.GA avoid this problem
|
| 261 |
+
for G, A in self.GA:
|
| 262 |
+
gc = [set(c) for c in nx.connected_components(G)]
|
| 263 |
+
ac = [set(c) for c in nx.connected_components(A)]
|
| 264 |
+
for comp in ac:
|
| 265 |
+
assert comp in gc
|
| 266 |
+
|
| 267 |
+
def test_adj(self):
|
| 268 |
+
for G, A in self.GA:
|
| 269 |
+
for n, nbrs in G.adj.items():
|
| 270 |
+
a_adj = sorted((n, sorted(ad)) for n, ad in A.adj.items())
|
| 271 |
+
g_adj = sorted((n, sorted(ad)) for n, ad in G.adj.items())
|
| 272 |
+
assert a_adj == g_adj
|
| 273 |
+
|
| 274 |
+
def test_adjacency(self):
|
| 275 |
+
for G, A in self.GA:
|
| 276 |
+
a_adj = list(A.adjacency())
|
| 277 |
+
for n, nbrs in G.adjacency():
|
| 278 |
+
assert (n, set(nbrs)) in a_adj
|
| 279 |
+
|
| 280 |
+
def test_neighbors(self):
|
| 281 |
+
for G, A in self.GA:
|
| 282 |
+
node = list(G.nodes())[0]
|
| 283 |
+
assert set(G.neighbors(node)) == set(A.neighbors(node))
|
| 284 |
+
|
| 285 |
+
def test_node_not_in_graph(self):
|
| 286 |
+
for G, A in self.GA:
|
| 287 |
+
node = "non_existent_node"
|
| 288 |
+
pytest.raises(nx.NetworkXError, A.neighbors, node)
|
| 289 |
+
pytest.raises(nx.NetworkXError, G.neighbors, node)
|
| 290 |
+
|
| 291 |
+
def test_degree_thingraph(self):
|
| 292 |
+
for G, A in self.GA:
|
| 293 |
+
node = list(G.nodes())[0]
|
| 294 |
+
nodes = list(G.nodes())[1:4]
|
| 295 |
+
assert G.degree(node) == A.degree(node)
|
| 296 |
+
assert sum(d for n, d in G.degree()) == sum(d for n, d in A.degree())
|
| 297 |
+
# AntiGraph is a ThinGraph, so all the weights are 1
|
| 298 |
+
assert sum(d for n, d in A.degree()) == sum(
|
| 299 |
+
d for n, d in A.degree(weight="weight")
|
| 300 |
+
)
|
| 301 |
+
assert sum(d for n, d in G.degree(nodes)) == sum(
|
| 302 |
+
d for n, d in A.degree(nodes)
|
| 303 |
+
)
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_matching.py
ADDED
|
@@ -0,0 +1,8 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import networkx as nx
|
| 2 |
+
import networkx.algorithms.approximation as a
|
| 3 |
+
|
| 4 |
+
|
| 5 |
+
def test_min_maximal_matching():
|
| 6 |
+
# smoke test
|
| 7 |
+
G = nx.Graph()
|
| 8 |
+
assert len(a.min_maximal_matching(G)) == 0
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_maxcut.py
ADDED
|
@@ -0,0 +1,94 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import random
|
| 2 |
+
|
| 3 |
+
import pytest
|
| 4 |
+
|
| 5 |
+
import networkx as nx
|
| 6 |
+
from networkx.algorithms.approximation import maxcut
|
| 7 |
+
|
| 8 |
+
|
| 9 |
+
@pytest.mark.parametrize(
|
| 10 |
+
"f", (nx.approximation.randomized_partitioning, nx.approximation.one_exchange)
|
| 11 |
+
)
|
| 12 |
+
@pytest.mark.parametrize("graph_constructor", (nx.DiGraph, nx.MultiGraph))
|
| 13 |
+
def test_raises_on_directed_and_multigraphs(f, graph_constructor):
|
| 14 |
+
G = graph_constructor([(0, 1), (1, 2)])
|
| 15 |
+
with pytest.raises(nx.NetworkXNotImplemented):
|
| 16 |
+
f(G)
|
| 17 |
+
|
| 18 |
+
|
| 19 |
+
def _is_valid_cut(G, set1, set2):
|
| 20 |
+
union = set1.union(set2)
|
| 21 |
+
assert union == set(G.nodes)
|
| 22 |
+
assert len(set1) + len(set2) == G.number_of_nodes()
|
| 23 |
+
|
| 24 |
+
|
| 25 |
+
def _cut_is_locally_optimal(G, cut_size, set1):
|
| 26 |
+
# test if cut can be locally improved
|
| 27 |
+
for i, node in enumerate(set1):
|
| 28 |
+
cut_size_without_node = nx.algorithms.cut_size(
|
| 29 |
+
G, set1 - {node}, weight="weight"
|
| 30 |
+
)
|
| 31 |
+
assert cut_size_without_node <= cut_size
|
| 32 |
+
|
| 33 |
+
|
| 34 |
+
def test_random_partitioning():
|
| 35 |
+
G = nx.complete_graph(5)
|
| 36 |
+
_, (set1, set2) = maxcut.randomized_partitioning(G, seed=5)
|
| 37 |
+
_is_valid_cut(G, set1, set2)
|
| 38 |
+
|
| 39 |
+
|
| 40 |
+
def test_random_partitioning_all_to_one():
|
| 41 |
+
G = nx.complete_graph(5)
|
| 42 |
+
_, (set1, set2) = maxcut.randomized_partitioning(G, p=1)
|
| 43 |
+
_is_valid_cut(G, set1, set2)
|
| 44 |
+
assert len(set1) == G.number_of_nodes()
|
| 45 |
+
assert len(set2) == 0
|
| 46 |
+
|
| 47 |
+
|
| 48 |
+
def test_one_exchange_basic():
|
| 49 |
+
G = nx.complete_graph(5)
|
| 50 |
+
random.seed(5)
|
| 51 |
+
for u, v, w in G.edges(data=True):
|
| 52 |
+
w["weight"] = random.randrange(-100, 100, 1) / 10
|
| 53 |
+
|
| 54 |
+
initial_cut = set(random.sample(sorted(G.nodes()), k=5))
|
| 55 |
+
cut_size, (set1, set2) = maxcut.one_exchange(
|
| 56 |
+
G, initial_cut, weight="weight", seed=5
|
| 57 |
+
)
|
| 58 |
+
|
| 59 |
+
_is_valid_cut(G, set1, set2)
|
| 60 |
+
_cut_is_locally_optimal(G, cut_size, set1)
|
| 61 |
+
|
| 62 |
+
|
| 63 |
+
def test_one_exchange_optimal():
|
| 64 |
+
# Greedy one exchange should find the optimal solution for this graph (14)
|
| 65 |
+
G = nx.Graph()
|
| 66 |
+
G.add_edge(1, 2, weight=3)
|
| 67 |
+
G.add_edge(1, 3, weight=3)
|
| 68 |
+
G.add_edge(1, 4, weight=3)
|
| 69 |
+
G.add_edge(1, 5, weight=3)
|
| 70 |
+
G.add_edge(2, 3, weight=5)
|
| 71 |
+
|
| 72 |
+
cut_size, (set1, set2) = maxcut.one_exchange(G, weight="weight", seed=5)
|
| 73 |
+
|
| 74 |
+
_is_valid_cut(G, set1, set2)
|
| 75 |
+
_cut_is_locally_optimal(G, cut_size, set1)
|
| 76 |
+
# check global optimality
|
| 77 |
+
assert cut_size == 14
|
| 78 |
+
|
| 79 |
+
|
| 80 |
+
def test_negative_weights():
|
| 81 |
+
G = nx.complete_graph(5)
|
| 82 |
+
random.seed(5)
|
| 83 |
+
for u, v, w in G.edges(data=True):
|
| 84 |
+
w["weight"] = -1 * random.random()
|
| 85 |
+
|
| 86 |
+
initial_cut = set(random.sample(sorted(G.nodes()), k=5))
|
| 87 |
+
cut_size, (set1, set2) = maxcut.one_exchange(G, initial_cut, weight="weight")
|
| 88 |
+
|
| 89 |
+
# make sure it is a valid cut
|
| 90 |
+
_is_valid_cut(G, set1, set2)
|
| 91 |
+
# check local optimality
|
| 92 |
+
_cut_is_locally_optimal(G, cut_size, set1)
|
| 93 |
+
# test that all nodes are in the same partition
|
| 94 |
+
assert len(set1) == len(G.nodes) or len(set2) == len(G.nodes)
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_ramsey.py
ADDED
|
@@ -0,0 +1,31 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import networkx as nx
|
| 2 |
+
import networkx.algorithms.approximation as apxa
|
| 3 |
+
|
| 4 |
+
|
| 5 |
+
def test_ramsey():
|
| 6 |
+
# this should only find the complete graph
|
| 7 |
+
graph = nx.complete_graph(10)
|
| 8 |
+
c, i = apxa.ramsey_R2(graph)
|
| 9 |
+
cdens = nx.density(graph.subgraph(c))
|
| 10 |
+
assert cdens == 1.0, "clique not correctly found by ramsey!"
|
| 11 |
+
idens = nx.density(graph.subgraph(i))
|
| 12 |
+
assert idens == 0.0, "i-set not correctly found by ramsey!"
|
| 13 |
+
|
| 14 |
+
# this trivial graph has no cliques. should just find i-sets
|
| 15 |
+
graph = nx.trivial_graph()
|
| 16 |
+
c, i = apxa.ramsey_R2(graph)
|
| 17 |
+
assert c == {0}, "clique not correctly found by ramsey!"
|
| 18 |
+
assert i == {0}, "i-set not correctly found by ramsey!"
|
| 19 |
+
|
| 20 |
+
graph = nx.barbell_graph(10, 5, nx.Graph())
|
| 21 |
+
c, i = apxa.ramsey_R2(graph)
|
| 22 |
+
cdens = nx.density(graph.subgraph(c))
|
| 23 |
+
assert cdens == 1.0, "clique not correctly found by ramsey!"
|
| 24 |
+
idens = nx.density(graph.subgraph(i))
|
| 25 |
+
assert idens == 0.0, "i-set not correctly found by ramsey!"
|
| 26 |
+
|
| 27 |
+
# add self-loops and test again
|
| 28 |
+
graph.add_edges_from([(n, n) for n in range(0, len(graph), 2)])
|
| 29 |
+
cc, ii = apxa.ramsey_R2(graph)
|
| 30 |
+
assert cc == c
|
| 31 |
+
assert ii == i
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_steinertree.py
ADDED
|
@@ -0,0 +1,265 @@
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
| 1 |
+
import pytest
|
| 2 |
+
|
| 3 |
+
import networkx as nx
|
| 4 |
+
from networkx.algorithms.approximation.steinertree import (
|
| 5 |
+
_remove_nonterminal_leaves,
|
| 6 |
+
metric_closure,
|
| 7 |
+
steiner_tree,
|
| 8 |
+
)
|
| 9 |
+
from networkx.utils import edges_equal
|
| 10 |
+
|
| 11 |
+
|
| 12 |
+
class TestSteinerTree:
|
| 13 |
+
@classmethod
|
| 14 |
+
def setup_class(cls):
|
| 15 |
+
G1 = nx.Graph()
|
| 16 |
+
G1.add_edge(1, 2, weight=10)
|
| 17 |
+
G1.add_edge(2, 3, weight=10)
|
| 18 |
+
G1.add_edge(3, 4, weight=10)
|
| 19 |
+
G1.add_edge(4, 5, weight=10)
|
| 20 |
+
G1.add_edge(5, 6, weight=10)
|
| 21 |
+
G1.add_edge(2, 7, weight=1)
|
| 22 |
+
G1.add_edge(7, 5, weight=1)
|
| 23 |
+
|
| 24 |
+
G2 = nx.Graph()
|
| 25 |
+
G2.add_edge(0, 5, weight=6)
|
| 26 |
+
G2.add_edge(1, 2, weight=2)
|
| 27 |
+
G2.add_edge(1, 5, weight=3)
|
| 28 |
+
G2.add_edge(2, 4, weight=4)
|
| 29 |
+
G2.add_edge(3, 5, weight=5)
|
| 30 |
+
G2.add_edge(4, 5, weight=1)
|
| 31 |
+
|
| 32 |
+
G3 = nx.Graph()
|
| 33 |
+
G3.add_edge(1, 2, weight=8)
|
| 34 |
+
G3.add_edge(1, 9, weight=3)
|
| 35 |
+
G3.add_edge(1, 8, weight=6)
|
| 36 |
+
G3.add_edge(1, 10, weight=2)
|
| 37 |
+
G3.add_edge(1, 14, weight=3)
|
| 38 |
+
G3.add_edge(2, 3, weight=6)
|
| 39 |
+
G3.add_edge(3, 4, weight=3)
|
| 40 |
+
G3.add_edge(3, 10, weight=2)
|
| 41 |
+
G3.add_edge(3, 11, weight=1)
|
| 42 |
+
G3.add_edge(4, 5, weight=1)
|
| 43 |
+
G3.add_edge(4, 11, weight=1)
|
| 44 |
+
G3.add_edge(5, 6, weight=4)
|
| 45 |
+
G3.add_edge(5, 11, weight=2)
|
| 46 |
+
G3.add_edge(5, 12, weight=1)
|
| 47 |
+
G3.add_edge(5, 13, weight=3)
|
| 48 |
+
G3.add_edge(6, 7, weight=2)
|
| 49 |
+
G3.add_edge(6, 12, weight=3)
|
| 50 |
+
G3.add_edge(6, 13, weight=1)
|
| 51 |
+
G3.add_edge(7, 8, weight=3)
|
| 52 |
+
G3.add_edge(7, 9, weight=3)
|
| 53 |
+
G3.add_edge(7, 11, weight=5)
|
| 54 |
+
G3.add_edge(7, 13, weight=2)
|
| 55 |
+
G3.add_edge(7, 14, weight=4)
|
| 56 |
+
G3.add_edge(8, 9, weight=2)
|
| 57 |
+
G3.add_edge(9, 14, weight=1)
|
| 58 |
+
G3.add_edge(10, 11, weight=2)
|
| 59 |
+
G3.add_edge(10, 14, weight=1)
|
| 60 |
+
G3.add_edge(11, 12, weight=1)
|
| 61 |
+
G3.add_edge(11, 14, weight=7)
|
| 62 |
+
G3.add_edge(12, 14, weight=3)
|
| 63 |
+
G3.add_edge(12, 15, weight=1)
|
| 64 |
+
G3.add_edge(13, 14, weight=4)
|
| 65 |
+
G3.add_edge(13, 15, weight=1)
|
| 66 |
+
G3.add_edge(14, 15, weight=2)
|
| 67 |
+
|
| 68 |
+
cls.G1 = G1
|
| 69 |
+
cls.G2 = G2
|
| 70 |
+
cls.G3 = G3
|
| 71 |
+
cls.G1_term_nodes = [1, 2, 3, 4, 5]
|
| 72 |
+
cls.G2_term_nodes = [0, 2, 3]
|
| 73 |
+
cls.G3_term_nodes = [1, 3, 5, 6, 8, 10, 11, 12, 13]
|
| 74 |
+
|
| 75 |
+
cls.methods = ["kou", "mehlhorn"]
|
| 76 |
+
|
| 77 |
+
def test_connected_metric_closure(self):
|
| 78 |
+
G = self.G1.copy()
|
| 79 |
+
G.add_node(100)
|
| 80 |
+
pytest.raises(nx.NetworkXError, metric_closure, G)
|
| 81 |
+
|
| 82 |
+
def test_metric_closure(self):
|
| 83 |
+
M = metric_closure(self.G1)
|
| 84 |
+
mc = [
|
| 85 |
+
(1, 2, {"distance": 10, "path": [1, 2]}),
|
| 86 |
+
(1, 3, {"distance": 20, "path": [1, 2, 3]}),
|
| 87 |
+
(1, 4, {"distance": 22, "path": [1, 2, 7, 5, 4]}),
|
| 88 |
+
(1, 5, {"distance": 12, "path": [1, 2, 7, 5]}),
|
| 89 |
+
(1, 6, {"distance": 22, "path": [1, 2, 7, 5, 6]}),
|
| 90 |
+
(1, 7, {"distance": 11, "path": [1, 2, 7]}),
|
| 91 |
+
(2, 3, {"distance": 10, "path": [2, 3]}),
|
| 92 |
+
(2, 4, {"distance": 12, "path": [2, 7, 5, 4]}),
|
| 93 |
+
(2, 5, {"distance": 2, "path": [2, 7, 5]}),
|
| 94 |
+
(2, 6, {"distance": 12, "path": [2, 7, 5, 6]}),
|
| 95 |
+
(2, 7, {"distance": 1, "path": [2, 7]}),
|
| 96 |
+
(3, 4, {"distance": 10, "path": [3, 4]}),
|
| 97 |
+
(3, 5, {"distance": 12, "path": [3, 2, 7, 5]}),
|
| 98 |
+
(3, 6, {"distance": 22, "path": [3, 2, 7, 5, 6]}),
|
| 99 |
+
(3, 7, {"distance": 11, "path": [3, 2, 7]}),
|
| 100 |
+
(4, 5, {"distance": 10, "path": [4, 5]}),
|
| 101 |
+
(4, 6, {"distance": 20, "path": [4, 5, 6]}),
|
| 102 |
+
(4, 7, {"distance": 11, "path": [4, 5, 7]}),
|
| 103 |
+
(5, 6, {"distance": 10, "path": [5, 6]}),
|
| 104 |
+
(5, 7, {"distance": 1, "path": [5, 7]}),
|
| 105 |
+
(6, 7, {"distance": 11, "path": [6, 5, 7]}),
|
| 106 |
+
]
|
| 107 |
+
assert edges_equal(list(M.edges(data=True)), mc)
|
| 108 |
+
|
| 109 |
+
def test_steiner_tree(self):
|
| 110 |
+
valid_steiner_trees = [
|
| 111 |
+
[
|
| 112 |
+
[
|
| 113 |
+
(1, 2, {"weight": 10}),
|
| 114 |
+
(2, 3, {"weight": 10}),
|
| 115 |
+
(2, 7, {"weight": 1}),
|
| 116 |
+
(3, 4, {"weight": 10}),
|
| 117 |
+
(5, 7, {"weight": 1}),
|
| 118 |
+
],
|
| 119 |
+
[
|
| 120 |
+
(1, 2, {"weight": 10}),
|
| 121 |
+
(2, 7, {"weight": 1}),
|
| 122 |
+
(3, 4, {"weight": 10}),
|
| 123 |
+
(4, 5, {"weight": 10}),
|
| 124 |
+
(5, 7, {"weight": 1}),
|
| 125 |
+
],
|
| 126 |
+
[
|
| 127 |
+
(1, 2, {"weight": 10}),
|
| 128 |
+
(2, 3, {"weight": 10}),
|
| 129 |
+
(2, 7, {"weight": 1}),
|
| 130 |
+
(4, 5, {"weight": 10}),
|
| 131 |
+
(5, 7, {"weight": 1}),
|
| 132 |
+
],
|
| 133 |
+
],
|
| 134 |
+
[
|
| 135 |
+
[
|
| 136 |
+
(0, 5, {"weight": 6}),
|
| 137 |
+
(1, 2, {"weight": 2}),
|
| 138 |
+
(1, 5, {"weight": 3}),
|
| 139 |
+
(3, 5, {"weight": 5}),
|
| 140 |
+
],
|
| 141 |
+
[
|
| 142 |
+
(0, 5, {"weight": 6}),
|
| 143 |
+
(4, 2, {"weight": 4}),
|
| 144 |
+
(4, 5, {"weight": 1}),
|
| 145 |
+
(3, 5, {"weight": 5}),
|
| 146 |
+
],
|
| 147 |
+
],
|
| 148 |
+
[
|
| 149 |
+
[
|
| 150 |
+
(1, 10, {"weight": 2}),
|
| 151 |
+
(3, 10, {"weight": 2}),
|
| 152 |
+
(3, 11, {"weight": 1}),
|
| 153 |
+
(5, 12, {"weight": 1}),
|
| 154 |
+
(6, 13, {"weight": 1}),
|
| 155 |
+
(8, 9, {"weight": 2}),
|
| 156 |
+
(9, 14, {"weight": 1}),
|
| 157 |
+
(10, 14, {"weight": 1}),
|
| 158 |
+
(11, 12, {"weight": 1}),
|
| 159 |
+
(12, 15, {"weight": 1}),
|
| 160 |
+
(13, 15, {"weight": 1}),
|
| 161 |
+
]
|
| 162 |
+
],
|
| 163 |
+
]
|
| 164 |
+
for method in self.methods:
|
| 165 |
+
for G, term_nodes, valid_trees in zip(
|
| 166 |
+
[self.G1, self.G2, self.G3],
|
| 167 |
+
[self.G1_term_nodes, self.G2_term_nodes, self.G3_term_nodes],
|
| 168 |
+
valid_steiner_trees,
|
| 169 |
+
):
|
| 170 |
+
S = steiner_tree(G, term_nodes, method=method)
|
| 171 |
+
assert any(
|
| 172 |
+
edges_equal(list(S.edges(data=True)), valid_tree)
|
| 173 |
+
for valid_tree in valid_trees
|
| 174 |
+
)
|
| 175 |
+
|
| 176 |
+
def test_multigraph_steiner_tree(self):
|
| 177 |
+
G = nx.MultiGraph()
|
| 178 |
+
G.add_edges_from(
|
| 179 |
+
[
|
| 180 |
+
(1, 2, 0, {"weight": 1}),
|
| 181 |
+
(2, 3, 0, {"weight": 999}),
|
| 182 |
+
(2, 3, 1, {"weight": 1}),
|
| 183 |
+
(3, 4, 0, {"weight": 1}),
|
| 184 |
+
(3, 5, 0, {"weight": 1}),
|
| 185 |
+
]
|
| 186 |
+
)
|
| 187 |
+
terminal_nodes = [2, 4, 5]
|
| 188 |
+
expected_edges = [
|
| 189 |
+
(2, 3, 1, {"weight": 1}), # edge with key 1 has lower weight
|
| 190 |
+
(3, 4, 0, {"weight": 1}),
|
| 191 |
+
(3, 5, 0, {"weight": 1}),
|
| 192 |
+
]
|
| 193 |
+
for method in self.methods:
|
| 194 |
+
S = steiner_tree(G, terminal_nodes, method=method)
|
| 195 |
+
assert edges_equal(S.edges(data=True, keys=True), expected_edges)
|
| 196 |
+
|
| 197 |
+
def test_remove_nonterminal_leaves(self):
|
| 198 |
+
G = nx.path_graph(10)
|
| 199 |
+
_remove_nonterminal_leaves(G, [4, 5, 6])
|
| 200 |
+
|
| 201 |
+
assert list(G) == [4, 5, 6] # only the terminal nodes are left
|
| 202 |
+
|
| 203 |
+
|
| 204 |
+
@pytest.mark.parametrize("method", ("kou", "mehlhorn"))
|
| 205 |
+
def test_steiner_tree_weight_attribute(method):
|
| 206 |
+
G = nx.star_graph(4)
|
| 207 |
+
# Add an edge attribute that is named something other than "weight"
|
| 208 |
+
nx.set_edge_attributes(G, {e: 10 for e in G.edges}, name="distance")
|
| 209 |
+
H = nx.approximation.steiner_tree(G, [1, 3], method=method, weight="distance")
|
| 210 |
+
assert nx.utils.edges_equal(H.edges, [(0, 1), (0, 3)])
|
| 211 |
+
|
| 212 |
+
|
| 213 |
+
@pytest.mark.parametrize("method", ("kou", "mehlhorn"))
|
| 214 |
+
def test_steiner_tree_multigraph_weight_attribute(method):
|
| 215 |
+
G = nx.cycle_graph(3, create_using=nx.MultiGraph)
|
| 216 |
+
nx.set_edge_attributes(G, {e: 10 for e in G.edges}, name="distance")
|
| 217 |
+
G.add_edge(2, 0, distance=5)
|
| 218 |
+
H = nx.approximation.steiner_tree(G, list(G), method=method, weight="distance")
|
| 219 |
+
assert len(H.edges) == 2 and H.has_edge(2, 0, key=1)
|
| 220 |
+
assert sum(dist for *_, dist in H.edges(data="distance")) == 15
|
| 221 |
+
|
| 222 |
+
|
| 223 |
+
@pytest.mark.parametrize("method", (None, "mehlhorn", "kou"))
|
| 224 |
+
def test_steiner_tree_methods(method):
|
| 225 |
+
G = nx.star_graph(4)
|
| 226 |
+
expected = nx.Graph([(0, 1), (0, 3)])
|
| 227 |
+
st = nx.approximation.steiner_tree(G, [1, 3], method=method)
|
| 228 |
+
assert nx.utils.edges_equal(st.edges, expected.edges)
|
| 229 |
+
|
| 230 |
+
|
| 231 |
+
def test_steiner_tree_method_invalid():
|
| 232 |
+
G = nx.star_graph(4)
|
| 233 |
+
with pytest.raises(
|
| 234 |
+
ValueError, match="invalid_method is not a valid choice for an algorithm."
|
| 235 |
+
):
|
| 236 |
+
nx.approximation.steiner_tree(G, terminal_nodes=[1, 3], method="invalid_method")
|
| 237 |
+
|
| 238 |
+
|
| 239 |
+
def test_steiner_tree_remove_non_terminal_leaves_self_loop_edges():
|
| 240 |
+
# To verify that the last step of the steiner tree approximation
|
| 241 |
+
# behaves in the case where a non-terminal leaf has a self loop edge
|
| 242 |
+
G = nx.path_graph(10)
|
| 243 |
+
|
| 244 |
+
# Add self loops to the terminal nodes
|
| 245 |
+
G.add_edges_from([(2, 2), (3, 3), (4, 4), (7, 7), (8, 8)])
|
| 246 |
+
|
| 247 |
+
# Remove non-terminal leaves
|
| 248 |
+
_remove_nonterminal_leaves(G, [4, 5, 6, 7])
|
| 249 |
+
|
| 250 |
+
# The terminal nodes should be left
|
| 251 |
+
assert list(G) == [4, 5, 6, 7] # only the terminal nodes are left
|
| 252 |
+
|
| 253 |
+
|
| 254 |
+
def test_steiner_tree_non_terminal_leaves_multigraph_self_loop_edges():
|
| 255 |
+
# To verify that the last step of the steiner tree approximation
|
| 256 |
+
# behaves in the case where a non-terminal leaf has a self loop edge
|
| 257 |
+
G = nx.MultiGraph()
|
| 258 |
+
G.add_edges_from([(i, i + 1) for i in range(10)])
|
| 259 |
+
G.add_edges_from([(2, 2), (3, 3), (4, 4), (4, 4), (7, 7)])
|
| 260 |
+
|
| 261 |
+
# Remove non-terminal leaves
|
| 262 |
+
_remove_nonterminal_leaves(G, [4, 5, 6, 7])
|
| 263 |
+
|
| 264 |
+
# Only the terminal nodes should be left
|
| 265 |
+
assert list(G) == [4, 5, 6, 7]
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_traveling_salesman.py
ADDED
|
@@ -0,0 +1,977 @@
|
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"""Unit tests for the traveling_salesman module."""
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import random
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import pytest
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import networkx as nx
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import networkx.algorithms.approximation as nx_app
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pairwise = nx.utils.pairwise
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def test_christofides_hamiltonian():
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random.seed(42)
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G = nx.complete_graph(20)
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for u, v in G.edges():
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G[u][v]["weight"] = random.randint(0, 10)
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H = nx.Graph()
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H.add_edges_from(pairwise(nx_app.christofides(G)))
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H.remove_edges_from(nx.find_cycle(H))
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assert len(H.edges) == 0
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tree = nx.minimum_spanning_tree(G, weight="weight")
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H = nx.Graph()
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H.add_edges_from(pairwise(nx_app.christofides(G, tree)))
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H.remove_edges_from(nx.find_cycle(H))
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assert len(H.edges) == 0
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def test_christofides_incomplete_graph():
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G = nx.complete_graph(10)
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G.remove_edge(0, 1)
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pytest.raises(nx.NetworkXError, nx_app.christofides, G)
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def test_christofides_ignore_selfloops():
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G = nx.complete_graph(5)
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G.add_edge(3, 3)
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cycle = nx_app.christofides(G)
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assert len(cycle) - 1 == len(G) == len(set(cycle))
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| 43 |
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| 44 |
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# set up graphs for other tests
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class TestBase:
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@classmethod
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def setup_class(cls):
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| 48 |
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cls.DG = nx.DiGraph()
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cls.DG.add_weighted_edges_from(
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{
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("A", "B", 3),
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("A", "C", 17),
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("A", "D", 14),
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("B", "A", 3),
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("B", "C", 12),
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("B", "D", 16),
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| 57 |
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("C", "A", 13),
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("C", "B", 12),
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("C", "D", 4),
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("D", "A", 14),
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("D", "B", 15),
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("D", "C", 2),
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}
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)
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cls.DG_cycle = ["D", "C", "B", "A", "D"]
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cls.DG_cost = 31.0
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cls.DG2 = nx.DiGraph()
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cls.DG2.add_weighted_edges_from(
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{
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("A", "B", 3),
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("A", "C", 17),
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("A", "D", 14),
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("B", "A", 30),
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("B", "C", 2),
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("B", "D", 16),
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("C", "A", 33),
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("C", "B", 32),
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("C", "D", 34),
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| 80 |
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("D", "A", 14),
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("D", "B", 15),
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("D", "C", 2),
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}
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)
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cls.DG2_cycle = ["D", "A", "B", "C", "D"]
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cls.DG2_cost = 53.0
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cls.unweightedUG = nx.complete_graph(5, nx.Graph())
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cls.unweightedDG = nx.complete_graph(5, nx.DiGraph())
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cls.incompleteUG = nx.Graph()
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cls.incompleteUG.add_weighted_edges_from({(0, 1, 1), (1, 2, 3)})
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cls.incompleteDG = nx.DiGraph()
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cls.incompleteDG.add_weighted_edges_from({(0, 1, 1), (1, 2, 3)})
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cls.UG = nx.Graph()
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cls.UG.add_weighted_edges_from(
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{
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("A", "B", 3),
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("A", "C", 17),
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("A", "D", 14),
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("B", "C", 12),
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("B", "D", 16),
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("C", "D", 4),
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}
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)
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cls.UG_cycle = ["D", "C", "B", "A", "D"]
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cls.UG_cost = 33.0
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cls.UG2 = nx.Graph()
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cls.UG2.add_weighted_edges_from(
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{
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("A", "B", 1),
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("A", "C", 15),
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("A", "D", 5),
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("B", "C", 16),
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("B", "D", 8),
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("C", "D", 3),
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}
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)
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cls.UG2_cycle = ["D", "C", "B", "A", "D"]
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cls.UG2_cost = 25.0
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def validate_solution(soln, cost, exp_soln, exp_cost):
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assert soln == exp_soln
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assert cost == exp_cost
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| 129 |
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def validate_symmetric_solution(soln, cost, exp_soln, exp_cost):
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assert soln == exp_soln or soln == exp_soln[::-1]
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| 132 |
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assert cost == exp_cost
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| 133 |
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| 134 |
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class TestGreedyTSP(TestBase):
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def test_greedy(self):
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cycle = nx_app.greedy_tsp(self.DG, source="D")
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cost = sum(self.DG[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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validate_solution(cycle, cost, ["D", "C", "B", "A", "D"], 31.0)
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cycle = nx_app.greedy_tsp(self.DG2, source="D")
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cost = sum(self.DG2[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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validate_solution(cycle, cost, ["D", "C", "B", "A", "D"], 78.0)
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cycle = nx_app.greedy_tsp(self.UG, source="D")
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cost = sum(self.UG[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 147 |
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validate_solution(cycle, cost, ["D", "C", "B", "A", "D"], 33.0)
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| 148 |
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| 149 |
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cycle = nx_app.greedy_tsp(self.UG2, source="D")
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| 150 |
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cost = sum(self.UG2[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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validate_solution(cycle, cost, ["D", "C", "A", "B", "D"], 27.0)
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| 152 |
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| 153 |
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def test_not_complete_graph(self):
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pytest.raises(nx.NetworkXError, nx_app.greedy_tsp, self.incompleteUG)
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| 155 |
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pytest.raises(nx.NetworkXError, nx_app.greedy_tsp, self.incompleteDG)
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| 156 |
+
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| 157 |
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def test_not_weighted_graph(self):
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nx_app.greedy_tsp(self.unweightedUG)
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nx_app.greedy_tsp(self.unweightedDG)
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| 160 |
+
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| 161 |
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def test_two_nodes(self):
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| 162 |
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G = nx.Graph()
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G.add_weighted_edges_from({(1, 2, 1)})
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cycle = nx_app.greedy_tsp(G)
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| 165 |
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cost = sum(G[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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validate_solution(cycle, cost, [1, 2, 1], 2)
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| 167 |
+
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| 168 |
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def test_ignore_selfloops(self):
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G = nx.complete_graph(5)
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| 170 |
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G.add_edge(3, 3)
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cycle = nx_app.greedy_tsp(G)
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| 172 |
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assert len(cycle) - 1 == len(G) == len(set(cycle))
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| 173 |
+
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| 174 |
+
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| 175 |
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class TestSimulatedAnnealingTSP(TestBase):
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| 176 |
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tsp = staticmethod(nx_app.simulated_annealing_tsp)
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| 177 |
+
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| 178 |
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def test_simulated_annealing_directed(self):
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| 179 |
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cycle = self.tsp(self.DG, "greedy", source="D", seed=42)
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| 180 |
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cost = sum(self.DG[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 181 |
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validate_solution(cycle, cost, self.DG_cycle, self.DG_cost)
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| 182 |
+
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| 183 |
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initial_sol = ["D", "B", "A", "C", "D"]
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| 184 |
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cycle = self.tsp(self.DG, initial_sol, source="D", seed=42)
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| 185 |
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cost = sum(self.DG[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 186 |
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validate_solution(cycle, cost, self.DG_cycle, self.DG_cost)
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| 187 |
+
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| 188 |
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initial_sol = ["D", "A", "C", "B", "D"]
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| 189 |
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cycle = self.tsp(self.DG, initial_sol, move="1-0", source="D", seed=42)
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| 190 |
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cost = sum(self.DG[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 191 |
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validate_solution(cycle, cost, self.DG_cycle, self.DG_cost)
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| 192 |
+
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| 193 |
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cycle = self.tsp(self.DG2, "greedy", source="D", seed=42)
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| 194 |
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cost = sum(self.DG2[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 195 |
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validate_solution(cycle, cost, self.DG2_cycle, self.DG2_cost)
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| 196 |
+
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| 197 |
+
cycle = self.tsp(self.DG2, "greedy", move="1-0", source="D", seed=42)
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| 198 |
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cost = sum(self.DG2[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 199 |
+
validate_solution(cycle, cost, self.DG2_cycle, self.DG2_cost)
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| 200 |
+
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| 201 |
+
def test_simulated_annealing_undirected(self):
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| 202 |
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cycle = self.tsp(self.UG, "greedy", source="D", seed=42)
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| 203 |
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cost = sum(self.UG[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 204 |
+
validate_solution(cycle, cost, self.UG_cycle, self.UG_cost)
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| 205 |
+
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| 206 |
+
cycle = self.tsp(self.UG2, "greedy", source="D", seed=42)
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| 207 |
+
cost = sum(self.UG2[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 208 |
+
validate_symmetric_solution(cycle, cost, self.UG2_cycle, self.UG2_cost)
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| 209 |
+
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| 210 |
+
cycle = self.tsp(self.UG2, "greedy", move="1-0", source="D", seed=42)
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| 211 |
+
cost = sum(self.UG2[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 212 |
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validate_symmetric_solution(cycle, cost, self.UG2_cycle, self.UG2_cost)
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| 213 |
+
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| 214 |
+
def test_error_on_input_order_mistake(self):
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| 215 |
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# see issue #4846 https://github.com/networkx/networkx/issues/4846
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| 216 |
+
pytest.raises(TypeError, self.tsp, self.UG, weight="weight")
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| 217 |
+
pytest.raises(nx.NetworkXError, self.tsp, self.UG, "weight")
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| 218 |
+
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| 219 |
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def test_not_complete_graph(self):
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| 220 |
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pytest.raises(nx.NetworkXError, self.tsp, self.incompleteUG, "greedy", source=0)
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| 221 |
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pytest.raises(nx.NetworkXError, self.tsp, self.incompleteDG, "greedy", source=0)
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| 222 |
+
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| 223 |
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def test_ignore_selfloops(self):
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| 224 |
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G = nx.complete_graph(5)
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| 225 |
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G.add_edge(3, 3)
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| 226 |
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cycle = self.tsp(G, "greedy")
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| 227 |
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assert len(cycle) - 1 == len(G) == len(set(cycle))
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| 228 |
+
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| 229 |
+
def test_not_weighted_graph(self):
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| 230 |
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self.tsp(self.unweightedUG, "greedy")
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| 231 |
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self.tsp(self.unweightedDG, "greedy")
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| 232 |
+
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| 233 |
+
def test_two_nodes(self):
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| 234 |
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G = nx.Graph()
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| 235 |
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G.add_weighted_edges_from({(1, 2, 1)})
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| 236 |
+
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| 237 |
+
cycle = self.tsp(G, "greedy", source=1, seed=42)
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| 238 |
+
cost = sum(G[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 239 |
+
validate_solution(cycle, cost, [1, 2, 1], 2)
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| 240 |
+
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| 241 |
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cycle = self.tsp(G, [1, 2, 1], source=1, seed=42)
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| 242 |
+
cost = sum(G[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 243 |
+
validate_solution(cycle, cost, [1, 2, 1], 2)
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| 244 |
+
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| 245 |
+
def test_failure_of_costs_too_high_when_iterations_low(self):
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| 246 |
+
# Simulated Annealing Version:
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| 247 |
+
# set number of moves low and alpha high
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| 248 |
+
cycle = self.tsp(
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| 249 |
+
self.DG2, "greedy", source="D", move="1-0", alpha=1, N_inner=1, seed=42
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| 250 |
+
)
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| 251 |
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cost = sum(self.DG2[n][nbr]["weight"] for n, nbr in pairwise(cycle))
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| 252 |
+
print(cycle, cost)
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| 253 |
+
assert cost > self.DG2_cost
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| 254 |
+
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| 255 |
+
# Try with an incorrect initial guess
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| 256 |
+
initial_sol = ["D", "A", "B", "C", "D"]
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| 257 |
+
cycle = self.tsp(
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| 258 |
+
self.DG,
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| 259 |
+
initial_sol,
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| 260 |
+
source="D",
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| 261 |
+
move="1-0",
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| 262 |
+
alpha=0.1,
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| 263 |
+
N_inner=1,
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| 264 |
+
max_iterations=1,
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| 265 |
+
seed=42,
|
| 266 |
+
)
|
| 267 |
+
cost = sum(self.DG[n][nbr]["weight"] for n, nbr in pairwise(cycle))
|
| 268 |
+
print(cycle, cost)
|
| 269 |
+
assert cost > self.DG_cost
|
| 270 |
+
|
| 271 |
+
|
| 272 |
+
class TestThresholdAcceptingTSP(TestSimulatedAnnealingTSP):
|
| 273 |
+
tsp = staticmethod(nx_app.threshold_accepting_tsp)
|
| 274 |
+
|
| 275 |
+
def test_failure_of_costs_too_high_when_iterations_low(self):
|
| 276 |
+
# Threshold Version:
|
| 277 |
+
# set number of moves low and number of iterations low
|
| 278 |
+
cycle = self.tsp(
|
| 279 |
+
self.DG2,
|
| 280 |
+
"greedy",
|
| 281 |
+
source="D",
|
| 282 |
+
move="1-0",
|
| 283 |
+
N_inner=1,
|
| 284 |
+
max_iterations=1,
|
| 285 |
+
seed=4,
|
| 286 |
+
)
|
| 287 |
+
cost = sum(self.DG2[n][nbr]["weight"] for n, nbr in pairwise(cycle))
|
| 288 |
+
assert cost > self.DG2_cost
|
| 289 |
+
|
| 290 |
+
# set threshold too low
|
| 291 |
+
initial_sol = ["D", "A", "B", "C", "D"]
|
| 292 |
+
cycle = self.tsp(
|
| 293 |
+
self.DG, initial_sol, source="D", move="1-0", threshold=-3, seed=42
|
| 294 |
+
)
|
| 295 |
+
cost = sum(self.DG[n][nbr]["weight"] for n, nbr in pairwise(cycle))
|
| 296 |
+
assert cost > self.DG_cost
|
| 297 |
+
|
| 298 |
+
|
| 299 |
+
# Tests for function traveling_salesman_problem
|
| 300 |
+
def test_TSP_method():
|
| 301 |
+
G = nx.cycle_graph(9)
|
| 302 |
+
G[4][5]["weight"] = 10
|
| 303 |
+
|
| 304 |
+
# Test using the old currying method
|
| 305 |
+
sa_tsp = lambda G, weight: nx_app.simulated_annealing_tsp(
|
| 306 |
+
G, "greedy", weight, source=4, seed=1
|
| 307 |
+
)
|
| 308 |
+
|
| 309 |
+
path = nx_app.traveling_salesman_problem(
|
| 310 |
+
G,
|
| 311 |
+
method=sa_tsp,
|
| 312 |
+
cycle=False,
|
| 313 |
+
)
|
| 314 |
+
print(path)
|
| 315 |
+
assert path == [4, 3, 2, 1, 0, 8, 7, 6, 5]
|
| 316 |
+
|
| 317 |
+
|
| 318 |
+
def test_TSP_unweighted():
|
| 319 |
+
G = nx.cycle_graph(9)
|
| 320 |
+
path = nx_app.traveling_salesman_problem(G, nodes=[3, 6], cycle=False)
|
| 321 |
+
assert path in ([3, 4, 5, 6], [6, 5, 4, 3])
|
| 322 |
+
|
| 323 |
+
cycle = nx_app.traveling_salesman_problem(G, nodes=[3, 6])
|
| 324 |
+
assert cycle in ([3, 4, 5, 6, 5, 4, 3], [6, 5, 4, 3, 4, 5, 6])
|
| 325 |
+
|
| 326 |
+
|
| 327 |
+
def test_TSP_weighted():
|
| 328 |
+
G = nx.cycle_graph(9)
|
| 329 |
+
G[0][1]["weight"] = 2
|
| 330 |
+
G[1][2]["weight"] = 2
|
| 331 |
+
G[2][3]["weight"] = 2
|
| 332 |
+
G[3][4]["weight"] = 4
|
| 333 |
+
G[4][5]["weight"] = 5
|
| 334 |
+
G[5][6]["weight"] = 4
|
| 335 |
+
G[6][7]["weight"] = 2
|
| 336 |
+
G[7][8]["weight"] = 2
|
| 337 |
+
G[8][0]["weight"] = 2
|
| 338 |
+
tsp = nx_app.traveling_salesman_problem
|
| 339 |
+
|
| 340 |
+
# path between 3 and 6
|
| 341 |
+
expected_paths = ([3, 2, 1, 0, 8, 7, 6], [6, 7, 8, 0, 1, 2, 3])
|
| 342 |
+
# cycle between 3 and 6
|
| 343 |
+
expected_cycles = (
|
| 344 |
+
[3, 2, 1, 0, 8, 7, 6, 7, 8, 0, 1, 2, 3],
|
| 345 |
+
[6, 7, 8, 0, 1, 2, 3, 2, 1, 0, 8, 7, 6],
|
| 346 |
+
)
|
| 347 |
+
# path through all nodes
|
| 348 |
+
expected_tourpaths = ([5, 6, 7, 8, 0, 1, 2, 3, 4], [4, 3, 2, 1, 0, 8, 7, 6, 5])
|
| 349 |
+
|
| 350 |
+
# Check default method
|
| 351 |
+
cycle = tsp(G, nodes=[3, 6], weight="weight")
|
| 352 |
+
assert cycle in expected_cycles
|
| 353 |
+
|
| 354 |
+
path = tsp(G, nodes=[3, 6], weight="weight", cycle=False)
|
| 355 |
+
assert path in expected_paths
|
| 356 |
+
|
| 357 |
+
tourpath = tsp(G, weight="weight", cycle=False)
|
| 358 |
+
assert tourpath in expected_tourpaths
|
| 359 |
+
|
| 360 |
+
# Check all methods
|
| 361 |
+
methods = [
|
| 362 |
+
(nx_app.christofides, {}),
|
| 363 |
+
(nx_app.greedy_tsp, {}),
|
| 364 |
+
(
|
| 365 |
+
nx_app.simulated_annealing_tsp,
|
| 366 |
+
{"init_cycle": "greedy"},
|
| 367 |
+
),
|
| 368 |
+
(
|
| 369 |
+
nx_app.threshold_accepting_tsp,
|
| 370 |
+
{"init_cycle": "greedy"},
|
| 371 |
+
),
|
| 372 |
+
]
|
| 373 |
+
for method, kwargs in methods:
|
| 374 |
+
cycle = tsp(G, nodes=[3, 6], weight="weight", method=method, **kwargs)
|
| 375 |
+
assert cycle in expected_cycles
|
| 376 |
+
|
| 377 |
+
path = tsp(
|
| 378 |
+
G, nodes=[3, 6], weight="weight", method=method, cycle=False, **kwargs
|
| 379 |
+
)
|
| 380 |
+
assert path in expected_paths
|
| 381 |
+
|
| 382 |
+
tourpath = tsp(G, weight="weight", method=method, cycle=False, **kwargs)
|
| 383 |
+
assert tourpath in expected_tourpaths
|
| 384 |
+
|
| 385 |
+
|
| 386 |
+
def test_TSP_incomplete_graph_short_path():
|
| 387 |
+
G = nx.cycle_graph(9)
|
| 388 |
+
G.add_edges_from([(4, 9), (9, 10), (10, 11), (11, 0)])
|
| 389 |
+
G[4][5]["weight"] = 5
|
| 390 |
+
|
| 391 |
+
cycle = nx_app.traveling_salesman_problem(G)
|
| 392 |
+
print(cycle)
|
| 393 |
+
assert len(cycle) == 17 and len(set(cycle)) == 12
|
| 394 |
+
|
| 395 |
+
# make sure that cutting one edge out of complete graph formulation
|
| 396 |
+
# cuts out many edges out of the path of the TSP
|
| 397 |
+
path = nx_app.traveling_salesman_problem(G, cycle=False)
|
| 398 |
+
print(path)
|
| 399 |
+
assert len(path) == 13 and len(set(path)) == 12
|
| 400 |
+
|
| 401 |
+
|
| 402 |
+
def test_held_karp_ascent():
|
| 403 |
+
"""
|
| 404 |
+
Test the Held-Karp relaxation with the ascent method
|
| 405 |
+
"""
|
| 406 |
+
import networkx.algorithms.approximation.traveling_salesman as tsp
|
| 407 |
+
|
| 408 |
+
np = pytest.importorskip("numpy")
|
| 409 |
+
pytest.importorskip("scipy")
|
| 410 |
+
|
| 411 |
+
# Adjacency matrix from page 1153 of the 1970 Held and Karp paper
|
| 412 |
+
# which have been edited to be directional, but also symmetric
|
| 413 |
+
G_array = np.array(
|
| 414 |
+
[
|
| 415 |
+
[0, 97, 60, 73, 17, 52],
|
| 416 |
+
[97, 0, 41, 52, 90, 30],
|
| 417 |
+
[60, 41, 0, 21, 35, 41],
|
| 418 |
+
[73, 52, 21, 0, 95, 46],
|
| 419 |
+
[17, 90, 35, 95, 0, 81],
|
| 420 |
+
[52, 30, 41, 46, 81, 0],
|
| 421 |
+
]
|
| 422 |
+
)
|
| 423 |
+
|
| 424 |
+
solution_edges = [(1, 3), (2, 4), (3, 2), (4, 0), (5, 1), (0, 5)]
|
| 425 |
+
|
| 426 |
+
G = nx.from_numpy_array(G_array, create_using=nx.DiGraph)
|
| 427 |
+
opt_hk, z_star = tsp.held_karp_ascent(G)
|
| 428 |
+
|
| 429 |
+
# Check that the optimal weights are the same
|
| 430 |
+
assert round(opt_hk, 2) == 207.00
|
| 431 |
+
# Check that the z_stars are the same
|
| 432 |
+
solution = nx.DiGraph()
|
| 433 |
+
solution.add_edges_from(solution_edges)
|
| 434 |
+
assert nx.utils.edges_equal(z_star.edges, solution.edges)
|
| 435 |
+
|
| 436 |
+
|
| 437 |
+
def test_ascent_fractional_solution():
|
| 438 |
+
"""
|
| 439 |
+
Test the ascent method using a modified version of Figure 2 on page 1140
|
| 440 |
+
in 'The Traveling Salesman Problem and Minimum Spanning Trees' by Held and
|
| 441 |
+
Karp
|
| 442 |
+
"""
|
| 443 |
+
import networkx.algorithms.approximation.traveling_salesman as tsp
|
| 444 |
+
|
| 445 |
+
np = pytest.importorskip("numpy")
|
| 446 |
+
pytest.importorskip("scipy")
|
| 447 |
+
|
| 448 |
+
# This version of Figure 2 has all of the edge weights multiplied by 100
|
| 449 |
+
# and is a complete directed graph with infinite edge weights for the
|
| 450 |
+
# edges not listed in the original graph
|
| 451 |
+
G_array = np.array(
|
| 452 |
+
[
|
| 453 |
+
[0, 100, 100, 100000, 100000, 1],
|
| 454 |
+
[100, 0, 100, 100000, 1, 100000],
|
| 455 |
+
[100, 100, 0, 1, 100000, 100000],
|
| 456 |
+
[100000, 100000, 1, 0, 100, 100],
|
| 457 |
+
[100000, 1, 100000, 100, 0, 100],
|
| 458 |
+
[1, 100000, 100000, 100, 100, 0],
|
| 459 |
+
]
|
| 460 |
+
)
|
| 461 |
+
|
| 462 |
+
solution_z_star = {
|
| 463 |
+
(0, 1): 5 / 12,
|
| 464 |
+
(0, 2): 5 / 12,
|
| 465 |
+
(0, 5): 5 / 6,
|
| 466 |
+
(1, 0): 5 / 12,
|
| 467 |
+
(1, 2): 1 / 3,
|
| 468 |
+
(1, 4): 5 / 6,
|
| 469 |
+
(2, 0): 5 / 12,
|
| 470 |
+
(2, 1): 1 / 3,
|
| 471 |
+
(2, 3): 5 / 6,
|
| 472 |
+
(3, 2): 5 / 6,
|
| 473 |
+
(3, 4): 1 / 3,
|
| 474 |
+
(3, 5): 1 / 2,
|
| 475 |
+
(4, 1): 5 / 6,
|
| 476 |
+
(4, 3): 1 / 3,
|
| 477 |
+
(4, 5): 1 / 2,
|
| 478 |
+
(5, 0): 5 / 6,
|
| 479 |
+
(5, 3): 1 / 2,
|
| 480 |
+
(5, 4): 1 / 2,
|
| 481 |
+
}
|
| 482 |
+
|
| 483 |
+
G = nx.from_numpy_array(G_array, create_using=nx.DiGraph)
|
| 484 |
+
opt_hk, z_star = tsp.held_karp_ascent(G)
|
| 485 |
+
|
| 486 |
+
# Check that the optimal weights are the same
|
| 487 |
+
assert round(opt_hk, 2) == 303.00
|
| 488 |
+
# Check that the z_stars are the same
|
| 489 |
+
assert {key: round(z_star[key], 4) for key in z_star} == {
|
| 490 |
+
key: round(solution_z_star[key], 4) for key in solution_z_star
|
| 491 |
+
}
|
| 492 |
+
|
| 493 |
+
|
| 494 |
+
def test_ascent_method_asymmetric():
|
| 495 |
+
"""
|
| 496 |
+
Tests the ascent method using a truly asymmetric graph for which the
|
| 497 |
+
solution has been brute forced
|
| 498 |
+
"""
|
| 499 |
+
import networkx.algorithms.approximation.traveling_salesman as tsp
|
| 500 |
+
|
| 501 |
+
np = pytest.importorskip("numpy")
|
| 502 |
+
pytest.importorskip("scipy")
|
| 503 |
+
|
| 504 |
+
G_array = np.array(
|
| 505 |
+
[
|
| 506 |
+
[0, 26, 63, 59, 69, 31, 41],
|
| 507 |
+
[62, 0, 91, 53, 75, 87, 47],
|
| 508 |
+
[47, 82, 0, 90, 15, 9, 18],
|
| 509 |
+
[68, 19, 5, 0, 58, 34, 93],
|
| 510 |
+
[11, 58, 53, 55, 0, 61, 79],
|
| 511 |
+
[88, 75, 13, 76, 98, 0, 40],
|
| 512 |
+
[41, 61, 55, 88, 46, 45, 0],
|
| 513 |
+
]
|
| 514 |
+
)
|
| 515 |
+
|
| 516 |
+
solution_edges = [(0, 1), (1, 3), (3, 2), (2, 5), (5, 6), (4, 0), (6, 4)]
|
| 517 |
+
|
| 518 |
+
G = nx.from_numpy_array(G_array, create_using=nx.DiGraph)
|
| 519 |
+
opt_hk, z_star = tsp.held_karp_ascent(G)
|
| 520 |
+
|
| 521 |
+
# Check that the optimal weights are the same
|
| 522 |
+
assert round(opt_hk, 2) == 190.00
|
| 523 |
+
# Check that the z_stars match.
|
| 524 |
+
solution = nx.DiGraph()
|
| 525 |
+
solution.add_edges_from(solution_edges)
|
| 526 |
+
assert nx.utils.edges_equal(z_star.edges, solution.edges)
|
| 527 |
+
|
| 528 |
+
|
| 529 |
+
def test_ascent_method_asymmetric_2():
|
| 530 |
+
"""
|
| 531 |
+
Tests the ascent method using a truly asymmetric graph for which the
|
| 532 |
+
solution has been brute forced
|
| 533 |
+
"""
|
| 534 |
+
import networkx.algorithms.approximation.traveling_salesman as tsp
|
| 535 |
+
|
| 536 |
+
np = pytest.importorskip("numpy")
|
| 537 |
+
pytest.importorskip("scipy")
|
| 538 |
+
|
| 539 |
+
G_array = np.array(
|
| 540 |
+
[
|
| 541 |
+
[0, 45, 39, 92, 29, 31],
|
| 542 |
+
[72, 0, 4, 12, 21, 60],
|
| 543 |
+
[81, 6, 0, 98, 70, 53],
|
| 544 |
+
[49, 71, 59, 0, 98, 94],
|
| 545 |
+
[74, 95, 24, 43, 0, 47],
|
| 546 |
+
[56, 43, 3, 65, 22, 0],
|
| 547 |
+
]
|
| 548 |
+
)
|
| 549 |
+
|
| 550 |
+
solution_edges = [(0, 5), (5, 4), (1, 3), (3, 0), (2, 1), (4, 2)]
|
| 551 |
+
|
| 552 |
+
G = nx.from_numpy_array(G_array, create_using=nx.DiGraph)
|
| 553 |
+
opt_hk, z_star = tsp.held_karp_ascent(G)
|
| 554 |
+
|
| 555 |
+
# Check that the optimal weights are the same
|
| 556 |
+
assert round(opt_hk, 2) == 144.00
|
| 557 |
+
# Check that the z_stars match.
|
| 558 |
+
solution = nx.DiGraph()
|
| 559 |
+
solution.add_edges_from(solution_edges)
|
| 560 |
+
assert nx.utils.edges_equal(z_star.edges, solution.edges)
|
| 561 |
+
|
| 562 |
+
|
| 563 |
+
def test_held_karp_ascent_asymmetric_3():
|
| 564 |
+
"""
|
| 565 |
+
Tests the ascent method using a truly asymmetric graph with a fractional
|
| 566 |
+
solution for which the solution has been brute forced.
|
| 567 |
+
|
| 568 |
+
In this graph their are two different optimal, integral solutions (which
|
| 569 |
+
are also the overall atsp solutions) to the Held Karp relaxation. However,
|
| 570 |
+
this particular graph has two different tours of optimal value and the
|
| 571 |
+
possible solutions in the held_karp_ascent function are not stored in an
|
| 572 |
+
ordered data structure.
|
| 573 |
+
"""
|
| 574 |
+
import networkx.algorithms.approximation.traveling_salesman as tsp
|
| 575 |
+
|
| 576 |
+
np = pytest.importorskip("numpy")
|
| 577 |
+
pytest.importorskip("scipy")
|
| 578 |
+
|
| 579 |
+
G_array = np.array(
|
| 580 |
+
[
|
| 581 |
+
[0, 1, 5, 2, 7, 4],
|
| 582 |
+
[7, 0, 7, 7, 1, 4],
|
| 583 |
+
[4, 7, 0, 9, 2, 1],
|
| 584 |
+
[7, 2, 7, 0, 4, 4],
|
| 585 |
+
[5, 5, 4, 4, 0, 3],
|
| 586 |
+
[3, 9, 1, 3, 4, 0],
|
| 587 |
+
]
|
| 588 |
+
)
|
| 589 |
+
|
| 590 |
+
solution1_edges = [(0, 3), (1, 4), (2, 5), (3, 1), (4, 2), (5, 0)]
|
| 591 |
+
|
| 592 |
+
solution2_edges = [(0, 3), (3, 1), (1, 4), (4, 5), (2, 0), (5, 2)]
|
| 593 |
+
|
| 594 |
+
G = nx.from_numpy_array(G_array, create_using=nx.DiGraph)
|
| 595 |
+
opt_hk, z_star = tsp.held_karp_ascent(G)
|
| 596 |
+
|
| 597 |
+
assert round(opt_hk, 2) == 13.00
|
| 598 |
+
# Check that the z_stars are the same
|
| 599 |
+
solution1 = nx.DiGraph()
|
| 600 |
+
solution1.add_edges_from(solution1_edges)
|
| 601 |
+
solution2 = nx.DiGraph()
|
| 602 |
+
solution2.add_edges_from(solution2_edges)
|
| 603 |
+
assert nx.utils.edges_equal(z_star.edges, solution1.edges) or nx.utils.edges_equal(
|
| 604 |
+
z_star.edges, solution2.edges
|
| 605 |
+
)
|
| 606 |
+
|
| 607 |
+
|
| 608 |
+
def test_held_karp_ascent_fractional_asymmetric():
|
| 609 |
+
"""
|
| 610 |
+
Tests the ascent method using a truly asymmetric graph with a fractional
|
| 611 |
+
solution for which the solution has been brute forced
|
| 612 |
+
"""
|
| 613 |
+
import networkx.algorithms.approximation.traveling_salesman as tsp
|
| 614 |
+
|
| 615 |
+
np = pytest.importorskip("numpy")
|
| 616 |
+
pytest.importorskip("scipy")
|
| 617 |
+
|
| 618 |
+
G_array = np.array(
|
| 619 |
+
[
|
| 620 |
+
[0, 100, 150, 100000, 100000, 1],
|
| 621 |
+
[150, 0, 100, 100000, 1, 100000],
|
| 622 |
+
[100, 150, 0, 1, 100000, 100000],
|
| 623 |
+
[100000, 100000, 1, 0, 150, 100],
|
| 624 |
+
[100000, 2, 100000, 100, 0, 150],
|
| 625 |
+
[2, 100000, 100000, 150, 100, 0],
|
| 626 |
+
]
|
| 627 |
+
)
|
| 628 |
+
|
| 629 |
+
solution_z_star = {
|
| 630 |
+
(0, 1): 5 / 12,
|
| 631 |
+
(0, 2): 5 / 12,
|
| 632 |
+
(0, 5): 5 / 6,
|
| 633 |
+
(1, 0): 5 / 12,
|
| 634 |
+
(1, 2): 5 / 12,
|
| 635 |
+
(1, 4): 5 / 6,
|
| 636 |
+
(2, 0): 5 / 12,
|
| 637 |
+
(2, 1): 5 / 12,
|
| 638 |
+
(2, 3): 5 / 6,
|
| 639 |
+
(3, 2): 5 / 6,
|
| 640 |
+
(3, 4): 5 / 12,
|
| 641 |
+
(3, 5): 5 / 12,
|
| 642 |
+
(4, 1): 5 / 6,
|
| 643 |
+
(4, 3): 5 / 12,
|
| 644 |
+
(4, 5): 5 / 12,
|
| 645 |
+
(5, 0): 5 / 6,
|
| 646 |
+
(5, 3): 5 / 12,
|
| 647 |
+
(5, 4): 5 / 12,
|
| 648 |
+
}
|
| 649 |
+
|
| 650 |
+
G = nx.from_numpy_array(G_array, create_using=nx.DiGraph)
|
| 651 |
+
opt_hk, z_star = tsp.held_karp_ascent(G)
|
| 652 |
+
|
| 653 |
+
# Check that the optimal weights are the same
|
| 654 |
+
assert round(opt_hk, 2) == 304.00
|
| 655 |
+
# Check that the z_stars are the same
|
| 656 |
+
assert {key: round(z_star[key], 4) for key in z_star} == {
|
| 657 |
+
key: round(solution_z_star[key], 4) for key in solution_z_star
|
| 658 |
+
}
|
| 659 |
+
|
| 660 |
+
|
| 661 |
+
def test_spanning_tree_distribution():
|
| 662 |
+
"""
|
| 663 |
+
Test that we can create an exponential distribution of spanning trees such
|
| 664 |
+
that the probability of each tree is proportional to the product of edge
|
| 665 |
+
weights.
|
| 666 |
+
|
| 667 |
+
Results of this test have been confirmed with hypothesis testing from the
|
| 668 |
+
created distribution.
|
| 669 |
+
|
| 670 |
+
This test uses the symmetric, fractional Held Karp solution.
|
| 671 |
+
"""
|
| 672 |
+
import networkx.algorithms.approximation.traveling_salesman as tsp
|
| 673 |
+
|
| 674 |
+
pytest.importorskip("numpy")
|
| 675 |
+
pytest.importorskip("scipy")
|
| 676 |
+
|
| 677 |
+
z_star = {
|
| 678 |
+
(0, 1): 5 / 12,
|
| 679 |
+
(0, 2): 5 / 12,
|
| 680 |
+
(0, 5): 5 / 6,
|
| 681 |
+
(1, 0): 5 / 12,
|
| 682 |
+
(1, 2): 1 / 3,
|
| 683 |
+
(1, 4): 5 / 6,
|
| 684 |
+
(2, 0): 5 / 12,
|
| 685 |
+
(2, 1): 1 / 3,
|
| 686 |
+
(2, 3): 5 / 6,
|
| 687 |
+
(3, 2): 5 / 6,
|
| 688 |
+
(3, 4): 1 / 3,
|
| 689 |
+
(3, 5): 1 / 2,
|
| 690 |
+
(4, 1): 5 / 6,
|
| 691 |
+
(4, 3): 1 / 3,
|
| 692 |
+
(4, 5): 1 / 2,
|
| 693 |
+
(5, 0): 5 / 6,
|
| 694 |
+
(5, 3): 1 / 2,
|
| 695 |
+
(5, 4): 1 / 2,
|
| 696 |
+
}
|
| 697 |
+
|
| 698 |
+
solution_gamma = {
|
| 699 |
+
(0, 1): -0.6383,
|
| 700 |
+
(0, 2): -0.6827,
|
| 701 |
+
(0, 5): 0,
|
| 702 |
+
(1, 2): -1.0781,
|
| 703 |
+
(1, 4): 0,
|
| 704 |
+
(2, 3): 0,
|
| 705 |
+
(5, 3): -0.2820,
|
| 706 |
+
(5, 4): -0.3327,
|
| 707 |
+
(4, 3): -0.9927,
|
| 708 |
+
}
|
| 709 |
+
|
| 710 |
+
# The undirected support of z_star
|
| 711 |
+
G = nx.MultiGraph()
|
| 712 |
+
for u, v in z_star:
|
| 713 |
+
if (u, v) in G.edges or (v, u) in G.edges:
|
| 714 |
+
continue
|
| 715 |
+
G.add_edge(u, v)
|
| 716 |
+
|
| 717 |
+
gamma = tsp.spanning_tree_distribution(G, z_star)
|
| 718 |
+
|
| 719 |
+
assert {key: round(gamma[key], 4) for key in gamma} == solution_gamma
|
| 720 |
+
|
| 721 |
+
|
| 722 |
+
def test_asadpour_tsp():
|
| 723 |
+
"""
|
| 724 |
+
Test the complete asadpour tsp algorithm with the fractional, symmetric
|
| 725 |
+
Held Karp solution. This test also uses an incomplete graph as input.
|
| 726 |
+
"""
|
| 727 |
+
# This version of Figure 2 has all of the edge weights multiplied by 100
|
| 728 |
+
# and the 0 weight edges have a weight of 1.
|
| 729 |
+
pytest.importorskip("numpy")
|
| 730 |
+
pytest.importorskip("scipy")
|
| 731 |
+
|
| 732 |
+
edge_list = [
|
| 733 |
+
(0, 1, 100),
|
| 734 |
+
(0, 2, 100),
|
| 735 |
+
(0, 5, 1),
|
| 736 |
+
(1, 2, 100),
|
| 737 |
+
(1, 4, 1),
|
| 738 |
+
(2, 3, 1),
|
| 739 |
+
(3, 4, 100),
|
| 740 |
+
(3, 5, 100),
|
| 741 |
+
(4, 5, 100),
|
| 742 |
+
(1, 0, 100),
|
| 743 |
+
(2, 0, 100),
|
| 744 |
+
(5, 0, 1),
|
| 745 |
+
(2, 1, 100),
|
| 746 |
+
(4, 1, 1),
|
| 747 |
+
(3, 2, 1),
|
| 748 |
+
(4, 3, 100),
|
| 749 |
+
(5, 3, 100),
|
| 750 |
+
(5, 4, 100),
|
| 751 |
+
]
|
| 752 |
+
|
| 753 |
+
G = nx.DiGraph()
|
| 754 |
+
G.add_weighted_edges_from(edge_list)
|
| 755 |
+
|
| 756 |
+
tour = nx_app.traveling_salesman_problem(
|
| 757 |
+
G, weight="weight", method=nx_app.asadpour_atsp, seed=19
|
| 758 |
+
)
|
| 759 |
+
|
| 760 |
+
# Check that the returned list is a valid tour. Because this is an
|
| 761 |
+
# incomplete graph, the conditions are not as strict. We need the tour to
|
| 762 |
+
#
|
| 763 |
+
# Start and end at the same node
|
| 764 |
+
# Pass through every vertex at least once
|
| 765 |
+
# Have a total cost at most ln(6) / ln(ln(6)) = 3.0723 times the optimal
|
| 766 |
+
#
|
| 767 |
+
# For the second condition it is possible to have the tour pass through the
|
| 768 |
+
# same vertex more then. Imagine that the tour on the complete version takes
|
| 769 |
+
# an edge not in the original graph. In the output this is substituted with
|
| 770 |
+
# the shortest path between those vertices, allowing vertices to appear more
|
| 771 |
+
# than once.
|
| 772 |
+
#
|
| 773 |
+
# Even though we are using a fixed seed, multiple tours have been known to
|
| 774 |
+
# be returned. The first two are from the original development of this test,
|
| 775 |
+
# and the third one from issue #5913 on GitHub. If other tours are returned,
|
| 776 |
+
# add it on the list of expected tours.
|
| 777 |
+
expected_tours = [
|
| 778 |
+
[1, 4, 5, 0, 2, 3, 2, 1],
|
| 779 |
+
[3, 2, 0, 1, 4, 5, 3],
|
| 780 |
+
[3, 2, 1, 0, 5, 4, 3],
|
| 781 |
+
]
|
| 782 |
+
|
| 783 |
+
assert tour in expected_tours
|
| 784 |
+
|
| 785 |
+
|
| 786 |
+
def test_asadpour_real_world():
|
| 787 |
+
"""
|
| 788 |
+
This test uses airline prices between the six largest cities in the US.
|
| 789 |
+
|
| 790 |
+
* New York City -> JFK
|
| 791 |
+
* Los Angeles -> LAX
|
| 792 |
+
* Chicago -> ORD
|
| 793 |
+
* Houston -> IAH
|
| 794 |
+
* Phoenix -> PHX
|
| 795 |
+
* Philadelphia -> PHL
|
| 796 |
+
|
| 797 |
+
Flight prices from August 2021 using Delta or American airlines to get
|
| 798 |
+
nonstop flight. The brute force solution found the optimal tour to cost $872
|
| 799 |
+
|
| 800 |
+
This test also uses the `source` keyword argument to ensure that the tour
|
| 801 |
+
always starts at city 0.
|
| 802 |
+
"""
|
| 803 |
+
np = pytest.importorskip("numpy")
|
| 804 |
+
pytest.importorskip("scipy")
|
| 805 |
+
|
| 806 |
+
G_array = np.array(
|
| 807 |
+
[
|
| 808 |
+
# JFK LAX ORD IAH PHX PHL
|
| 809 |
+
[0, 243, 199, 208, 169, 183], # JFK
|
| 810 |
+
[277, 0, 217, 123, 127, 252], # LAX
|
| 811 |
+
[297, 197, 0, 197, 123, 177], # ORD
|
| 812 |
+
[303, 169, 197, 0, 117, 117], # IAH
|
| 813 |
+
[257, 127, 160, 117, 0, 319], # PHX
|
| 814 |
+
[183, 332, 217, 117, 319, 0], # PHL
|
| 815 |
+
]
|
| 816 |
+
)
|
| 817 |
+
|
| 818 |
+
node_list = ["JFK", "LAX", "ORD", "IAH", "PHX", "PHL"]
|
| 819 |
+
|
| 820 |
+
expected_tours = [
|
| 821 |
+
["JFK", "LAX", "PHX", "ORD", "IAH", "PHL", "JFK"],
|
| 822 |
+
["JFK", "ORD", "PHX", "LAX", "IAH", "PHL", "JFK"],
|
| 823 |
+
]
|
| 824 |
+
|
| 825 |
+
G = nx.from_numpy_array(G_array, nodelist=node_list, create_using=nx.DiGraph)
|
| 826 |
+
|
| 827 |
+
tour = nx_app.traveling_salesman_problem(
|
| 828 |
+
G, weight="weight", method=nx_app.asadpour_atsp, seed=37, source="JFK"
|
| 829 |
+
)
|
| 830 |
+
|
| 831 |
+
assert tour in expected_tours
|
| 832 |
+
|
| 833 |
+
|
| 834 |
+
def test_asadpour_real_world_path():
|
| 835 |
+
"""
|
| 836 |
+
This test uses airline prices between the six largest cities in the US. This
|
| 837 |
+
time using a path, not a cycle.
|
| 838 |
+
|
| 839 |
+
* New York City -> JFK
|
| 840 |
+
* Los Angeles -> LAX
|
| 841 |
+
* Chicago -> ORD
|
| 842 |
+
* Houston -> IAH
|
| 843 |
+
* Phoenix -> PHX
|
| 844 |
+
* Philadelphia -> PHL
|
| 845 |
+
|
| 846 |
+
Flight prices from August 2021 using Delta or American airlines to get
|
| 847 |
+
nonstop flight. The brute force solution found the optimal tour to cost $872
|
| 848 |
+
"""
|
| 849 |
+
np = pytest.importorskip("numpy")
|
| 850 |
+
pytest.importorskip("scipy")
|
| 851 |
+
|
| 852 |
+
G_array = np.array(
|
| 853 |
+
[
|
| 854 |
+
# JFK LAX ORD IAH PHX PHL
|
| 855 |
+
[0, 243, 199, 208, 169, 183], # JFK
|
| 856 |
+
[277, 0, 217, 123, 127, 252], # LAX
|
| 857 |
+
[297, 197, 0, 197, 123, 177], # ORD
|
| 858 |
+
[303, 169, 197, 0, 117, 117], # IAH
|
| 859 |
+
[257, 127, 160, 117, 0, 319], # PHX
|
| 860 |
+
[183, 332, 217, 117, 319, 0], # PHL
|
| 861 |
+
]
|
| 862 |
+
)
|
| 863 |
+
|
| 864 |
+
node_list = ["JFK", "LAX", "ORD", "IAH", "PHX", "PHL"]
|
| 865 |
+
|
| 866 |
+
expected_paths = [
|
| 867 |
+
["ORD", "PHX", "LAX", "IAH", "PHL", "JFK"],
|
| 868 |
+
["JFK", "PHL", "IAH", "ORD", "PHX", "LAX"],
|
| 869 |
+
]
|
| 870 |
+
|
| 871 |
+
G = nx.from_numpy_array(G_array, nodelist=node_list, create_using=nx.DiGraph)
|
| 872 |
+
|
| 873 |
+
path = nx_app.traveling_salesman_problem(
|
| 874 |
+
G, weight="weight", cycle=False, method=nx_app.asadpour_atsp, seed=56
|
| 875 |
+
)
|
| 876 |
+
|
| 877 |
+
assert path in expected_paths
|
| 878 |
+
|
| 879 |
+
|
| 880 |
+
def test_asadpour_disconnected_graph():
|
| 881 |
+
"""
|
| 882 |
+
Test that the proper exception is raised when asadpour_atsp is given an
|
| 883 |
+
disconnected graph.
|
| 884 |
+
"""
|
| 885 |
+
|
| 886 |
+
G = nx.complete_graph(4, create_using=nx.DiGraph)
|
| 887 |
+
# have to set edge weights so that if the exception is not raised, the
|
| 888 |
+
# function will complete and we will fail the test
|
| 889 |
+
nx.set_edge_attributes(G, 1, "weight")
|
| 890 |
+
G.add_node(5)
|
| 891 |
+
|
| 892 |
+
pytest.raises(nx.NetworkXError, nx_app.asadpour_atsp, G)
|
| 893 |
+
|
| 894 |
+
|
| 895 |
+
def test_asadpour_incomplete_graph():
|
| 896 |
+
"""
|
| 897 |
+
Test that the proper exception is raised when asadpour_atsp is given an
|
| 898 |
+
incomplete graph
|
| 899 |
+
"""
|
| 900 |
+
|
| 901 |
+
G = nx.complete_graph(4, create_using=nx.DiGraph)
|
| 902 |
+
# have to set edge weights so that if the exception is not raised, the
|
| 903 |
+
# function will complete and we will fail the test
|
| 904 |
+
nx.set_edge_attributes(G, 1, "weight")
|
| 905 |
+
G.remove_edge(0, 1)
|
| 906 |
+
|
| 907 |
+
pytest.raises(nx.NetworkXError, nx_app.asadpour_atsp, G)
|
| 908 |
+
|
| 909 |
+
|
| 910 |
+
def test_asadpour_empty_graph():
|
| 911 |
+
"""
|
| 912 |
+
Test the asadpour_atsp function with an empty graph
|
| 913 |
+
"""
|
| 914 |
+
G = nx.DiGraph()
|
| 915 |
+
|
| 916 |
+
pytest.raises(nx.NetworkXError, nx_app.asadpour_atsp, G)
|
| 917 |
+
|
| 918 |
+
|
| 919 |
+
@pytest.mark.slow
|
| 920 |
+
def test_asadpour_integral_held_karp():
|
| 921 |
+
"""
|
| 922 |
+
This test uses an integral held karp solution and the held karp function
|
| 923 |
+
will return a graph rather than a dict, bypassing most of the asadpour
|
| 924 |
+
algorithm.
|
| 925 |
+
|
| 926 |
+
At first glance, this test probably doesn't look like it ensures that we
|
| 927 |
+
skip the rest of the asadpour algorithm, but it does. We are not fixing a
|
| 928 |
+
see for the random number generator, so if we sample any spanning trees
|
| 929 |
+
the approximation would be different basically every time this test is
|
| 930 |
+
executed but it is not since held karp is deterministic and we do not
|
| 931 |
+
reach the portion of the code with the dependence on random numbers.
|
| 932 |
+
"""
|
| 933 |
+
np = pytest.importorskip("numpy")
|
| 934 |
+
|
| 935 |
+
G_array = np.array(
|
| 936 |
+
[
|
| 937 |
+
[0, 26, 63, 59, 69, 31, 41],
|
| 938 |
+
[62, 0, 91, 53, 75, 87, 47],
|
| 939 |
+
[47, 82, 0, 90, 15, 9, 18],
|
| 940 |
+
[68, 19, 5, 0, 58, 34, 93],
|
| 941 |
+
[11, 58, 53, 55, 0, 61, 79],
|
| 942 |
+
[88, 75, 13, 76, 98, 0, 40],
|
| 943 |
+
[41, 61, 55, 88, 46, 45, 0],
|
| 944 |
+
]
|
| 945 |
+
)
|
| 946 |
+
|
| 947 |
+
G = nx.from_numpy_array(G_array, create_using=nx.DiGraph)
|
| 948 |
+
|
| 949 |
+
for _ in range(2):
|
| 950 |
+
tour = nx_app.traveling_salesman_problem(G, method=nx_app.asadpour_atsp)
|
| 951 |
+
|
| 952 |
+
assert [1, 3, 2, 5, 2, 6, 4, 0, 1] == tour
|
| 953 |
+
|
| 954 |
+
|
| 955 |
+
def test_directed_tsp_impossible():
|
| 956 |
+
"""
|
| 957 |
+
Test the asadpour algorithm with a graph without a hamiltonian circuit
|
| 958 |
+
"""
|
| 959 |
+
pytest.importorskip("numpy")
|
| 960 |
+
|
| 961 |
+
# In this graph, once we leave node 0 we cannot return
|
| 962 |
+
edges = [
|
| 963 |
+
(0, 1, 10),
|
| 964 |
+
(0, 2, 11),
|
| 965 |
+
(0, 3, 12),
|
| 966 |
+
(1, 2, 4),
|
| 967 |
+
(1, 3, 6),
|
| 968 |
+
(2, 1, 3),
|
| 969 |
+
(2, 3, 2),
|
| 970 |
+
(3, 1, 5),
|
| 971 |
+
(3, 2, 1),
|
| 972 |
+
]
|
| 973 |
+
|
| 974 |
+
G = nx.DiGraph()
|
| 975 |
+
G.add_weighted_edges_from(edges)
|
| 976 |
+
|
| 977 |
+
pytest.raises(nx.NetworkXError, nx_app.traveling_salesman_problem, G)
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_treewidth.py
ADDED
|
@@ -0,0 +1,280 @@
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|
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|
|
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|
|
|
| 1 |
+
import itertools
|
| 2 |
+
|
| 3 |
+
import networkx as nx
|
| 4 |
+
from networkx.algorithms.approximation import (
|
| 5 |
+
treewidth_min_degree,
|
| 6 |
+
treewidth_min_fill_in,
|
| 7 |
+
)
|
| 8 |
+
from networkx.algorithms.approximation.treewidth import (
|
| 9 |
+
MinDegreeHeuristic,
|
| 10 |
+
min_fill_in_heuristic,
|
| 11 |
+
)
|
| 12 |
+
|
| 13 |
+
|
| 14 |
+
def is_tree_decomp(graph, decomp):
|
| 15 |
+
"""Check if the given tree decomposition is valid."""
|
| 16 |
+
for x in graph.nodes():
|
| 17 |
+
appear_once = False
|
| 18 |
+
for bag in decomp.nodes():
|
| 19 |
+
if x in bag:
|
| 20 |
+
appear_once = True
|
| 21 |
+
break
|
| 22 |
+
assert appear_once
|
| 23 |
+
|
| 24 |
+
# Check if each connected pair of nodes are at least once together in a bag
|
| 25 |
+
for x, y in graph.edges():
|
| 26 |
+
appear_together = False
|
| 27 |
+
for bag in decomp.nodes():
|
| 28 |
+
if x in bag and y in bag:
|
| 29 |
+
appear_together = True
|
| 30 |
+
break
|
| 31 |
+
assert appear_together
|
| 32 |
+
|
| 33 |
+
# Check if the nodes associated with vertex v form a connected subset of T
|
| 34 |
+
for v in graph.nodes():
|
| 35 |
+
subset = []
|
| 36 |
+
for bag in decomp.nodes():
|
| 37 |
+
if v in bag:
|
| 38 |
+
subset.append(bag)
|
| 39 |
+
sub_graph = decomp.subgraph(subset)
|
| 40 |
+
assert nx.is_connected(sub_graph)
|
| 41 |
+
|
| 42 |
+
|
| 43 |
+
class TestTreewidthMinDegree:
|
| 44 |
+
"""Unit tests for the min_degree function"""
|
| 45 |
+
|
| 46 |
+
@classmethod
|
| 47 |
+
def setup_class(cls):
|
| 48 |
+
"""Setup for different kinds of trees"""
|
| 49 |
+
cls.complete = nx.Graph()
|
| 50 |
+
cls.complete.add_edge(1, 2)
|
| 51 |
+
cls.complete.add_edge(2, 3)
|
| 52 |
+
cls.complete.add_edge(1, 3)
|
| 53 |
+
|
| 54 |
+
cls.small_tree = nx.Graph()
|
| 55 |
+
cls.small_tree.add_edge(1, 3)
|
| 56 |
+
cls.small_tree.add_edge(4, 3)
|
| 57 |
+
cls.small_tree.add_edge(2, 3)
|
| 58 |
+
cls.small_tree.add_edge(3, 5)
|
| 59 |
+
cls.small_tree.add_edge(5, 6)
|
| 60 |
+
cls.small_tree.add_edge(5, 7)
|
| 61 |
+
cls.small_tree.add_edge(6, 7)
|
| 62 |
+
|
| 63 |
+
cls.deterministic_graph = nx.Graph()
|
| 64 |
+
cls.deterministic_graph.add_edge(0, 1) # deg(0) = 1
|
| 65 |
+
|
| 66 |
+
cls.deterministic_graph.add_edge(1, 2) # deg(1) = 2
|
| 67 |
+
|
| 68 |
+
cls.deterministic_graph.add_edge(2, 3)
|
| 69 |
+
cls.deterministic_graph.add_edge(2, 4) # deg(2) = 3
|
| 70 |
+
|
| 71 |
+
cls.deterministic_graph.add_edge(3, 4)
|
| 72 |
+
cls.deterministic_graph.add_edge(3, 5)
|
| 73 |
+
cls.deterministic_graph.add_edge(3, 6) # deg(3) = 4
|
| 74 |
+
|
| 75 |
+
cls.deterministic_graph.add_edge(4, 5)
|
| 76 |
+
cls.deterministic_graph.add_edge(4, 6)
|
| 77 |
+
cls.deterministic_graph.add_edge(4, 7) # deg(4) = 5
|
| 78 |
+
|
| 79 |
+
cls.deterministic_graph.add_edge(5, 6)
|
| 80 |
+
cls.deterministic_graph.add_edge(5, 7)
|
| 81 |
+
cls.deterministic_graph.add_edge(5, 8)
|
| 82 |
+
cls.deterministic_graph.add_edge(5, 9) # deg(5) = 6
|
| 83 |
+
|
| 84 |
+
cls.deterministic_graph.add_edge(6, 7)
|
| 85 |
+
cls.deterministic_graph.add_edge(6, 8)
|
| 86 |
+
cls.deterministic_graph.add_edge(6, 9) # deg(6) = 6
|
| 87 |
+
|
| 88 |
+
cls.deterministic_graph.add_edge(7, 8)
|
| 89 |
+
cls.deterministic_graph.add_edge(7, 9) # deg(7) = 5
|
| 90 |
+
|
| 91 |
+
cls.deterministic_graph.add_edge(8, 9) # deg(8) = 4
|
| 92 |
+
|
| 93 |
+
def test_petersen_graph(self):
|
| 94 |
+
"""Test Petersen graph tree decomposition result"""
|
| 95 |
+
G = nx.petersen_graph()
|
| 96 |
+
_, decomp = treewidth_min_degree(G)
|
| 97 |
+
is_tree_decomp(G, decomp)
|
| 98 |
+
|
| 99 |
+
def test_small_tree_treewidth(self):
|
| 100 |
+
"""Test small tree
|
| 101 |
+
|
| 102 |
+
Test if the computed treewidth of the known self.small_tree is 2.
|
| 103 |
+
As we know which value we can expect from our heuristic, values other
|
| 104 |
+
than two are regressions
|
| 105 |
+
"""
|
| 106 |
+
G = self.small_tree
|
| 107 |
+
# the order of removal should be [1,2,4]3[5,6,7]
|
| 108 |
+
# (with [] denoting any order of the containing nodes)
|
| 109 |
+
# resulting in treewidth 2 for the heuristic
|
| 110 |
+
treewidth, _ = treewidth_min_fill_in(G)
|
| 111 |
+
assert treewidth == 2
|
| 112 |
+
|
| 113 |
+
def test_heuristic_abort(self):
|
| 114 |
+
"""Test heuristic abort condition for fully connected graph"""
|
| 115 |
+
graph = {}
|
| 116 |
+
for u in self.complete:
|
| 117 |
+
graph[u] = set()
|
| 118 |
+
for v in self.complete[u]:
|
| 119 |
+
if u != v: # ignore self-loop
|
| 120 |
+
graph[u].add(v)
|
| 121 |
+
|
| 122 |
+
deg_heuristic = MinDegreeHeuristic(graph)
|
| 123 |
+
node = deg_heuristic.best_node(graph)
|
| 124 |
+
if node is None:
|
| 125 |
+
pass
|
| 126 |
+
else:
|
| 127 |
+
assert False
|
| 128 |
+
|
| 129 |
+
def test_empty_graph(self):
|
| 130 |
+
"""Test empty graph"""
|
| 131 |
+
G = nx.Graph()
|
| 132 |
+
_, _ = treewidth_min_degree(G)
|
| 133 |
+
|
| 134 |
+
def test_two_component_graph(self):
|
| 135 |
+
G = nx.Graph()
|
| 136 |
+
G.add_node(1)
|
| 137 |
+
G.add_node(2)
|
| 138 |
+
treewidth, _ = treewidth_min_degree(G)
|
| 139 |
+
assert treewidth == 0
|
| 140 |
+
|
| 141 |
+
def test_not_sortable_nodes(self):
|
| 142 |
+
G = nx.Graph([(0, "a")])
|
| 143 |
+
treewidth_min_degree(G)
|
| 144 |
+
|
| 145 |
+
def test_heuristic_first_steps(self):
|
| 146 |
+
"""Test first steps of min_degree heuristic"""
|
| 147 |
+
graph = {
|
| 148 |
+
n: set(self.deterministic_graph[n]) - {n} for n in self.deterministic_graph
|
| 149 |
+
}
|
| 150 |
+
deg_heuristic = MinDegreeHeuristic(graph)
|
| 151 |
+
elim_node = deg_heuristic.best_node(graph)
|
| 152 |
+
print(f"Graph {graph}:")
|
| 153 |
+
steps = []
|
| 154 |
+
|
| 155 |
+
while elim_node is not None:
|
| 156 |
+
print(f"Removing {elim_node}:")
|
| 157 |
+
steps.append(elim_node)
|
| 158 |
+
nbrs = graph[elim_node]
|
| 159 |
+
|
| 160 |
+
for u, v in itertools.permutations(nbrs, 2):
|
| 161 |
+
if v not in graph[u]:
|
| 162 |
+
graph[u].add(v)
|
| 163 |
+
|
| 164 |
+
for u in graph:
|
| 165 |
+
if elim_node in graph[u]:
|
| 166 |
+
graph[u].remove(elim_node)
|
| 167 |
+
|
| 168 |
+
del graph[elim_node]
|
| 169 |
+
print(f"Graph {graph}:")
|
| 170 |
+
elim_node = deg_heuristic.best_node(graph)
|
| 171 |
+
|
| 172 |
+
# check only the first 5 elements for equality
|
| 173 |
+
assert steps[:5] == [0, 1, 2, 3, 4]
|
| 174 |
+
|
| 175 |
+
|
| 176 |
+
class TestTreewidthMinFillIn:
|
| 177 |
+
"""Unit tests for the treewidth_min_fill_in function."""
|
| 178 |
+
|
| 179 |
+
@classmethod
|
| 180 |
+
def setup_class(cls):
|
| 181 |
+
"""Setup for different kinds of trees"""
|
| 182 |
+
cls.complete = nx.Graph()
|
| 183 |
+
cls.complete.add_edge(1, 2)
|
| 184 |
+
cls.complete.add_edge(2, 3)
|
| 185 |
+
cls.complete.add_edge(1, 3)
|
| 186 |
+
|
| 187 |
+
cls.small_tree = nx.Graph()
|
| 188 |
+
cls.small_tree.add_edge(1, 2)
|
| 189 |
+
cls.small_tree.add_edge(2, 3)
|
| 190 |
+
cls.small_tree.add_edge(3, 4)
|
| 191 |
+
cls.small_tree.add_edge(1, 4)
|
| 192 |
+
cls.small_tree.add_edge(2, 4)
|
| 193 |
+
cls.small_tree.add_edge(4, 5)
|
| 194 |
+
cls.small_tree.add_edge(5, 6)
|
| 195 |
+
cls.small_tree.add_edge(5, 7)
|
| 196 |
+
cls.small_tree.add_edge(6, 7)
|
| 197 |
+
|
| 198 |
+
cls.deterministic_graph = nx.Graph()
|
| 199 |
+
cls.deterministic_graph.add_edge(1, 2)
|
| 200 |
+
cls.deterministic_graph.add_edge(1, 3)
|
| 201 |
+
cls.deterministic_graph.add_edge(3, 4)
|
| 202 |
+
cls.deterministic_graph.add_edge(2, 4)
|
| 203 |
+
cls.deterministic_graph.add_edge(3, 5)
|
| 204 |
+
cls.deterministic_graph.add_edge(4, 5)
|
| 205 |
+
cls.deterministic_graph.add_edge(3, 6)
|
| 206 |
+
cls.deterministic_graph.add_edge(5, 6)
|
| 207 |
+
|
| 208 |
+
def test_petersen_graph(self):
|
| 209 |
+
"""Test Petersen graph tree decomposition result"""
|
| 210 |
+
G = nx.petersen_graph()
|
| 211 |
+
_, decomp = treewidth_min_fill_in(G)
|
| 212 |
+
is_tree_decomp(G, decomp)
|
| 213 |
+
|
| 214 |
+
def test_small_tree_treewidth(self):
|
| 215 |
+
"""Test if the computed treewidth of the known self.small_tree is 2"""
|
| 216 |
+
G = self.small_tree
|
| 217 |
+
# the order of removal should be [1,2,4]3[5,6,7]
|
| 218 |
+
# (with [] denoting any order of the containing nodes)
|
| 219 |
+
# resulting in treewidth 2 for the heuristic
|
| 220 |
+
treewidth, _ = treewidth_min_fill_in(G)
|
| 221 |
+
assert treewidth == 2
|
| 222 |
+
|
| 223 |
+
def test_heuristic_abort(self):
|
| 224 |
+
"""Test if min_fill_in returns None for fully connected graph"""
|
| 225 |
+
graph = {}
|
| 226 |
+
for u in self.complete:
|
| 227 |
+
graph[u] = set()
|
| 228 |
+
for v in self.complete[u]:
|
| 229 |
+
if u != v: # ignore self-loop
|
| 230 |
+
graph[u].add(v)
|
| 231 |
+
next_node = min_fill_in_heuristic(graph)
|
| 232 |
+
if next_node is None:
|
| 233 |
+
pass
|
| 234 |
+
else:
|
| 235 |
+
assert False
|
| 236 |
+
|
| 237 |
+
def test_empty_graph(self):
|
| 238 |
+
"""Test empty graph"""
|
| 239 |
+
G = nx.Graph()
|
| 240 |
+
_, _ = treewidth_min_fill_in(G)
|
| 241 |
+
|
| 242 |
+
def test_two_component_graph(self):
|
| 243 |
+
G = nx.Graph()
|
| 244 |
+
G.add_node(1)
|
| 245 |
+
G.add_node(2)
|
| 246 |
+
treewidth, _ = treewidth_min_fill_in(G)
|
| 247 |
+
assert treewidth == 0
|
| 248 |
+
|
| 249 |
+
def test_not_sortable_nodes(self):
|
| 250 |
+
G = nx.Graph([(0, "a")])
|
| 251 |
+
treewidth_min_fill_in(G)
|
| 252 |
+
|
| 253 |
+
def test_heuristic_first_steps(self):
|
| 254 |
+
"""Test first steps of min_fill_in heuristic"""
|
| 255 |
+
graph = {
|
| 256 |
+
n: set(self.deterministic_graph[n]) - {n} for n in self.deterministic_graph
|
| 257 |
+
}
|
| 258 |
+
print(f"Graph {graph}:")
|
| 259 |
+
elim_node = min_fill_in_heuristic(graph)
|
| 260 |
+
steps = []
|
| 261 |
+
|
| 262 |
+
while elim_node is not None:
|
| 263 |
+
print(f"Removing {elim_node}:")
|
| 264 |
+
steps.append(elim_node)
|
| 265 |
+
nbrs = graph[elim_node]
|
| 266 |
+
|
| 267 |
+
for u, v in itertools.permutations(nbrs, 2):
|
| 268 |
+
if v not in graph[u]:
|
| 269 |
+
graph[u].add(v)
|
| 270 |
+
|
| 271 |
+
for u in graph:
|
| 272 |
+
if elim_node in graph[u]:
|
| 273 |
+
graph[u].remove(elim_node)
|
| 274 |
+
|
| 275 |
+
del graph[elim_node]
|
| 276 |
+
print(f"Graph {graph}:")
|
| 277 |
+
elim_node = min_fill_in_heuristic(graph)
|
| 278 |
+
|
| 279 |
+
# check only the first 2 elements for equality
|
| 280 |
+
assert steps[:2] == [6, 5]
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_vertex_cover.py
ADDED
|
@@ -0,0 +1,68 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import networkx as nx
|
| 2 |
+
from networkx.algorithms.approximation import min_weighted_vertex_cover
|
| 3 |
+
|
| 4 |
+
|
| 5 |
+
def is_cover(G, node_cover):
|
| 6 |
+
return all({u, v} & node_cover for u, v in G.edges())
|
| 7 |
+
|
| 8 |
+
|
| 9 |
+
class TestMWVC:
|
| 10 |
+
"""Unit tests for the approximate minimum weighted vertex cover
|
| 11 |
+
function,
|
| 12 |
+
:func:`~networkx.algorithms.approximation.vertex_cover.min_weighted_vertex_cover`.
|
| 13 |
+
|
| 14 |
+
"""
|
| 15 |
+
|
| 16 |
+
def test_unweighted_directed(self):
|
| 17 |
+
# Create a star graph in which half the nodes are directed in
|
| 18 |
+
# and half are directed out.
|
| 19 |
+
G = nx.DiGraph()
|
| 20 |
+
G.add_edges_from((0, v) for v in range(1, 26))
|
| 21 |
+
G.add_edges_from((v, 0) for v in range(26, 51))
|
| 22 |
+
cover = min_weighted_vertex_cover(G)
|
| 23 |
+
assert 1 == len(cover)
|
| 24 |
+
assert is_cover(G, cover)
|
| 25 |
+
|
| 26 |
+
def test_unweighted_undirected(self):
|
| 27 |
+
# create a simple star graph
|
| 28 |
+
size = 50
|
| 29 |
+
sg = nx.star_graph(size)
|
| 30 |
+
cover = min_weighted_vertex_cover(sg)
|
| 31 |
+
assert 1 == len(cover)
|
| 32 |
+
assert is_cover(sg, cover)
|
| 33 |
+
|
| 34 |
+
def test_weighted(self):
|
| 35 |
+
wg = nx.Graph()
|
| 36 |
+
wg.add_node(0, weight=10)
|
| 37 |
+
wg.add_node(1, weight=1)
|
| 38 |
+
wg.add_node(2, weight=1)
|
| 39 |
+
wg.add_node(3, weight=1)
|
| 40 |
+
wg.add_node(4, weight=1)
|
| 41 |
+
|
| 42 |
+
wg.add_edge(0, 1)
|
| 43 |
+
wg.add_edge(0, 2)
|
| 44 |
+
wg.add_edge(0, 3)
|
| 45 |
+
wg.add_edge(0, 4)
|
| 46 |
+
|
| 47 |
+
wg.add_edge(1, 2)
|
| 48 |
+
wg.add_edge(2, 3)
|
| 49 |
+
wg.add_edge(3, 4)
|
| 50 |
+
wg.add_edge(4, 1)
|
| 51 |
+
|
| 52 |
+
cover = min_weighted_vertex_cover(wg, weight="weight")
|
| 53 |
+
csum = sum(wg.nodes[node]["weight"] for node in cover)
|
| 54 |
+
assert 4 == csum
|
| 55 |
+
assert is_cover(wg, cover)
|
| 56 |
+
|
| 57 |
+
def test_unweighted_self_loop(self):
|
| 58 |
+
slg = nx.Graph()
|
| 59 |
+
slg.add_node(0)
|
| 60 |
+
slg.add_node(1)
|
| 61 |
+
slg.add_node(2)
|
| 62 |
+
|
| 63 |
+
slg.add_edge(0, 1)
|
| 64 |
+
slg.add_edge(2, 2)
|
| 65 |
+
|
| 66 |
+
cover = min_weighted_vertex_cover(slg)
|
| 67 |
+
assert 2 == len(cover)
|
| 68 |
+
assert is_cover(slg, cover)
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/treewidth.py
ADDED
|
@@ -0,0 +1,252 @@
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
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|
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|
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|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""Functions for computing treewidth decomposition.
|
| 2 |
+
|
| 3 |
+
Treewidth of an undirected graph is a number associated with the graph.
|
| 4 |
+
It can be defined as the size of the largest vertex set (bag) in a tree
|
| 5 |
+
decomposition of the graph minus one.
|
| 6 |
+
|
| 7 |
+
`Wikipedia: Treewidth <https://en.wikipedia.org/wiki/Treewidth>`_
|
| 8 |
+
|
| 9 |
+
The notions of treewidth and tree decomposition have gained their
|
| 10 |
+
attractiveness partly because many graph and network problems that are
|
| 11 |
+
intractable (e.g., NP-hard) on arbitrary graphs become efficiently
|
| 12 |
+
solvable (e.g., with a linear time algorithm) when the treewidth of the
|
| 13 |
+
input graphs is bounded by a constant [1]_ [2]_.
|
| 14 |
+
|
| 15 |
+
There are two different functions for computing a tree decomposition:
|
| 16 |
+
:func:`treewidth_min_degree` and :func:`treewidth_min_fill_in`.
|
| 17 |
+
|
| 18 |
+
.. [1] Hans L. Bodlaender and Arie M. C. A. Koster. 2010. "Treewidth
|
| 19 |
+
computations I.Upper bounds". Inf. Comput. 208, 3 (March 2010),259-275.
|
| 20 |
+
http://dx.doi.org/10.1016/j.ic.2009.03.008
|
| 21 |
+
|
| 22 |
+
.. [2] Hans L. Bodlaender. "Discovering Treewidth". Institute of Information
|
| 23 |
+
and Computing Sciences, Utrecht University.
|
| 24 |
+
Technical Report UU-CS-2005-018.
|
| 25 |
+
http://www.cs.uu.nl
|
| 26 |
+
|
| 27 |
+
.. [3] K. Wang, Z. Lu, and J. Hicks *Treewidth*.
|
| 28 |
+
https://web.archive.org/web/20210507025929/http://web.eecs.utk.edu/~cphill25/cs594_spring2015_projects/treewidth.pdf
|
| 29 |
+
|
| 30 |
+
"""
|
| 31 |
+
|
| 32 |
+
import itertools
|
| 33 |
+
import sys
|
| 34 |
+
from heapq import heapify, heappop, heappush
|
| 35 |
+
|
| 36 |
+
import networkx as nx
|
| 37 |
+
from networkx.utils import not_implemented_for
|
| 38 |
+
|
| 39 |
+
__all__ = ["treewidth_min_degree", "treewidth_min_fill_in"]
|
| 40 |
+
|
| 41 |
+
|
| 42 |
+
@not_implemented_for("directed")
|
| 43 |
+
@not_implemented_for("multigraph")
|
| 44 |
+
@nx._dispatchable(returns_graph=True)
|
| 45 |
+
def treewidth_min_degree(G):
|
| 46 |
+
"""Returns a treewidth decomposition using the Minimum Degree heuristic.
|
| 47 |
+
|
| 48 |
+
The heuristic chooses the nodes according to their degree, i.e., first
|
| 49 |
+
the node with the lowest degree is chosen, then the graph is updated
|
| 50 |
+
and the corresponding node is removed. Next, a new node with the lowest
|
| 51 |
+
degree is chosen, and so on.
|
| 52 |
+
|
| 53 |
+
Parameters
|
| 54 |
+
----------
|
| 55 |
+
G : NetworkX graph
|
| 56 |
+
|
| 57 |
+
Returns
|
| 58 |
+
-------
|
| 59 |
+
Treewidth decomposition : (int, Graph) tuple
|
| 60 |
+
2-tuple with treewidth and the corresponding decomposed tree.
|
| 61 |
+
"""
|
| 62 |
+
deg_heuristic = MinDegreeHeuristic(G)
|
| 63 |
+
return treewidth_decomp(G, lambda graph: deg_heuristic.best_node(graph))
|
| 64 |
+
|
| 65 |
+
|
| 66 |
+
@not_implemented_for("directed")
|
| 67 |
+
@not_implemented_for("multigraph")
|
| 68 |
+
@nx._dispatchable(returns_graph=True)
|
| 69 |
+
def treewidth_min_fill_in(G):
|
| 70 |
+
"""Returns a treewidth decomposition using the Minimum Fill-in heuristic.
|
| 71 |
+
|
| 72 |
+
The heuristic chooses a node from the graph, where the number of edges
|
| 73 |
+
added turning the neighborhood of the chosen node into clique is as
|
| 74 |
+
small as possible.
|
| 75 |
+
|
| 76 |
+
Parameters
|
| 77 |
+
----------
|
| 78 |
+
G : NetworkX graph
|
| 79 |
+
|
| 80 |
+
Returns
|
| 81 |
+
-------
|
| 82 |
+
Treewidth decomposition : (int, Graph) tuple
|
| 83 |
+
2-tuple with treewidth and the corresponding decomposed tree.
|
| 84 |
+
"""
|
| 85 |
+
return treewidth_decomp(G, min_fill_in_heuristic)
|
| 86 |
+
|
| 87 |
+
|
| 88 |
+
class MinDegreeHeuristic:
|
| 89 |
+
"""Implements the Minimum Degree heuristic.
|
| 90 |
+
|
| 91 |
+
The heuristic chooses the nodes according to their degree
|
| 92 |
+
(number of neighbors), i.e., first the node with the lowest degree is
|
| 93 |
+
chosen, then the graph is updated and the corresponding node is
|
| 94 |
+
removed. Next, a new node with the lowest degree is chosen, and so on.
|
| 95 |
+
"""
|
| 96 |
+
|
| 97 |
+
def __init__(self, graph):
|
| 98 |
+
self._graph = graph
|
| 99 |
+
|
| 100 |
+
# nodes that have to be updated in the heap before each iteration
|
| 101 |
+
self._update_nodes = []
|
| 102 |
+
|
| 103 |
+
self._degreeq = [] # a heapq with 3-tuples (degree,unique_id,node)
|
| 104 |
+
self.count = itertools.count()
|
| 105 |
+
|
| 106 |
+
# build heap with initial degrees
|
| 107 |
+
for n in graph:
|
| 108 |
+
self._degreeq.append((len(graph[n]), next(self.count), n))
|
| 109 |
+
heapify(self._degreeq)
|
| 110 |
+
|
| 111 |
+
def best_node(self, graph):
|
| 112 |
+
# update nodes in self._update_nodes
|
| 113 |
+
for n in self._update_nodes:
|
| 114 |
+
# insert changed degrees into degreeq
|
| 115 |
+
heappush(self._degreeq, (len(graph[n]), next(self.count), n))
|
| 116 |
+
|
| 117 |
+
# get the next valid (minimum degree) node
|
| 118 |
+
while self._degreeq:
|
| 119 |
+
(min_degree, _, elim_node) = heappop(self._degreeq)
|
| 120 |
+
if elim_node not in graph or len(graph[elim_node]) != min_degree:
|
| 121 |
+
# outdated entry in degreeq
|
| 122 |
+
continue
|
| 123 |
+
elif min_degree == len(graph) - 1:
|
| 124 |
+
# fully connected: abort condition
|
| 125 |
+
return None
|
| 126 |
+
|
| 127 |
+
# remember to update nodes in the heap before getting the next node
|
| 128 |
+
self._update_nodes = graph[elim_node]
|
| 129 |
+
return elim_node
|
| 130 |
+
|
| 131 |
+
# the heap is empty: abort
|
| 132 |
+
return None
|
| 133 |
+
|
| 134 |
+
|
| 135 |
+
def min_fill_in_heuristic(graph):
|
| 136 |
+
"""Implements the Minimum Degree heuristic.
|
| 137 |
+
|
| 138 |
+
Returns the node from the graph, where the number of edges added when
|
| 139 |
+
turning the neighborhood of the chosen node into clique is as small as
|
| 140 |
+
possible. This algorithm chooses the nodes using the Minimum Fill-In
|
| 141 |
+
heuristic. The running time of the algorithm is :math:`O(V^3)` and it uses
|
| 142 |
+
additional constant memory."""
|
| 143 |
+
|
| 144 |
+
if len(graph) == 0:
|
| 145 |
+
return None
|
| 146 |
+
|
| 147 |
+
min_fill_in_node = None
|
| 148 |
+
|
| 149 |
+
min_fill_in = sys.maxsize
|
| 150 |
+
|
| 151 |
+
# sort nodes by degree
|
| 152 |
+
nodes_by_degree = sorted(graph, key=lambda x: len(graph[x]))
|
| 153 |
+
min_degree = len(graph[nodes_by_degree[0]])
|
| 154 |
+
|
| 155 |
+
# abort condition (handle complete graph)
|
| 156 |
+
if min_degree == len(graph) - 1:
|
| 157 |
+
return None
|
| 158 |
+
|
| 159 |
+
for node in nodes_by_degree:
|
| 160 |
+
num_fill_in = 0
|
| 161 |
+
nbrs = graph[node]
|
| 162 |
+
for nbr in nbrs:
|
| 163 |
+
# count how many nodes in nbrs current nbr is not connected to
|
| 164 |
+
# subtract 1 for the node itself
|
| 165 |
+
num_fill_in += len(nbrs - graph[nbr]) - 1
|
| 166 |
+
if num_fill_in >= 2 * min_fill_in:
|
| 167 |
+
break
|
| 168 |
+
|
| 169 |
+
num_fill_in /= 2 # divide by 2 because of double counting
|
| 170 |
+
|
| 171 |
+
if num_fill_in < min_fill_in: # update min-fill-in node
|
| 172 |
+
if num_fill_in == 0:
|
| 173 |
+
return node
|
| 174 |
+
min_fill_in = num_fill_in
|
| 175 |
+
min_fill_in_node = node
|
| 176 |
+
|
| 177 |
+
return min_fill_in_node
|
| 178 |
+
|
| 179 |
+
|
| 180 |
+
@nx._dispatchable(returns_graph=True)
|
| 181 |
+
def treewidth_decomp(G, heuristic=min_fill_in_heuristic):
|
| 182 |
+
"""Returns a treewidth decomposition using the passed heuristic.
|
| 183 |
+
|
| 184 |
+
Parameters
|
| 185 |
+
----------
|
| 186 |
+
G : NetworkX graph
|
| 187 |
+
heuristic : heuristic function
|
| 188 |
+
|
| 189 |
+
Returns
|
| 190 |
+
-------
|
| 191 |
+
Treewidth decomposition : (int, Graph) tuple
|
| 192 |
+
2-tuple with treewidth and the corresponding decomposed tree.
|
| 193 |
+
"""
|
| 194 |
+
|
| 195 |
+
# make dict-of-sets structure
|
| 196 |
+
graph = {n: set(G[n]) - {n} for n in G}
|
| 197 |
+
|
| 198 |
+
# stack containing nodes and neighbors in the order from the heuristic
|
| 199 |
+
node_stack = []
|
| 200 |
+
|
| 201 |
+
# get first node from heuristic
|
| 202 |
+
elim_node = heuristic(graph)
|
| 203 |
+
while elim_node is not None:
|
| 204 |
+
# connect all neighbors with each other
|
| 205 |
+
nbrs = graph[elim_node]
|
| 206 |
+
for u, v in itertools.permutations(nbrs, 2):
|
| 207 |
+
if v not in graph[u]:
|
| 208 |
+
graph[u].add(v)
|
| 209 |
+
|
| 210 |
+
# push node and its current neighbors on stack
|
| 211 |
+
node_stack.append((elim_node, nbrs))
|
| 212 |
+
|
| 213 |
+
# remove node from graph
|
| 214 |
+
for u in graph[elim_node]:
|
| 215 |
+
graph[u].remove(elim_node)
|
| 216 |
+
|
| 217 |
+
del graph[elim_node]
|
| 218 |
+
elim_node = heuristic(graph)
|
| 219 |
+
|
| 220 |
+
# the abort condition is met; put all remaining nodes into one bag
|
| 221 |
+
decomp = nx.Graph()
|
| 222 |
+
first_bag = frozenset(graph.keys())
|
| 223 |
+
decomp.add_node(first_bag)
|
| 224 |
+
|
| 225 |
+
treewidth = len(first_bag) - 1
|
| 226 |
+
|
| 227 |
+
while node_stack:
|
| 228 |
+
# get node and its neighbors from the stack
|
| 229 |
+
(curr_node, nbrs) = node_stack.pop()
|
| 230 |
+
|
| 231 |
+
# find a bag all neighbors are in
|
| 232 |
+
old_bag = None
|
| 233 |
+
for bag in decomp.nodes:
|
| 234 |
+
if nbrs <= bag:
|
| 235 |
+
old_bag = bag
|
| 236 |
+
break
|
| 237 |
+
|
| 238 |
+
if old_bag is None:
|
| 239 |
+
# no old_bag was found: just connect to the first_bag
|
| 240 |
+
old_bag = first_bag
|
| 241 |
+
|
| 242 |
+
# create new node for decomposition
|
| 243 |
+
nbrs.add(curr_node)
|
| 244 |
+
new_bag = frozenset(nbrs)
|
| 245 |
+
|
| 246 |
+
# update treewidth
|
| 247 |
+
treewidth = max(treewidth, len(new_bag) - 1)
|
| 248 |
+
|
| 249 |
+
# add edge to decomposition (implicitly also adds the new node)
|
| 250 |
+
decomp.add_edge(old_bag, new_bag)
|
| 251 |
+
|
| 252 |
+
return treewidth, decomp
|
.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/vertex_cover.py
ADDED
|
@@ -0,0 +1,83 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
| 1 |
+
"""Functions for computing an approximate minimum weight vertex cover.
|
| 2 |
+
|
| 3 |
+
A |vertex cover|_ is a subset of nodes such that each edge in the graph
|
| 4 |
+
is incident to at least one node in the subset.
|
| 5 |
+
|
| 6 |
+
.. _vertex cover: https://en.wikipedia.org/wiki/Vertex_cover
|
| 7 |
+
.. |vertex cover| replace:: *vertex cover*
|
| 8 |
+
|
| 9 |
+
"""
|
| 10 |
+
|
| 11 |
+
import networkx as nx
|
| 12 |
+
|
| 13 |
+
__all__ = ["min_weighted_vertex_cover"]
|
| 14 |
+
|
| 15 |
+
|
| 16 |
+
@nx._dispatchable(node_attrs="weight")
|
| 17 |
+
def min_weighted_vertex_cover(G, weight=None):
|
| 18 |
+
r"""Returns an approximate minimum weighted vertex cover.
|
| 19 |
+
|
| 20 |
+
The set of nodes returned by this function is guaranteed to be a
|
| 21 |
+
vertex cover, and the total weight of the set is guaranteed to be at
|
| 22 |
+
most twice the total weight of the minimum weight vertex cover. In
|
| 23 |
+
other words,
|
| 24 |
+
|
| 25 |
+
.. math::
|
| 26 |
+
|
| 27 |
+
w(S) \leq 2 * w(S^*),
|
| 28 |
+
|
| 29 |
+
where $S$ is the vertex cover returned by this function,
|
| 30 |
+
$S^*$ is the vertex cover of minimum weight out of all vertex
|
| 31 |
+
covers of the graph, and $w$ is the function that computes the
|
| 32 |
+
sum of the weights of each node in that given set.
|
| 33 |
+
|
| 34 |
+
Parameters
|
| 35 |
+
----------
|
| 36 |
+
G : NetworkX graph
|
| 37 |
+
|
| 38 |
+
weight : string, optional (default = None)
|
| 39 |
+
If None, every node has weight 1. If a string, use this node
|
| 40 |
+
attribute as the node weight. A node without this attribute is
|
| 41 |
+
assumed to have weight 1.
|
| 42 |
+
|
| 43 |
+
Returns
|
| 44 |
+
-------
|
| 45 |
+
min_weighted_cover : set
|
| 46 |
+
Returns a set of nodes whose weight sum is no more than twice
|
| 47 |
+
the weight sum of the minimum weight vertex cover.
|
| 48 |
+
|
| 49 |
+
Notes
|
| 50 |
+
-----
|
| 51 |
+
For a directed graph, a vertex cover has the same definition: a set
|
| 52 |
+
of nodes such that each edge in the graph is incident to at least
|
| 53 |
+
one node in the set. Whether the node is the head or tail of the
|
| 54 |
+
directed edge is ignored.
|
| 55 |
+
|
| 56 |
+
This is the local-ratio algorithm for computing an approximate
|
| 57 |
+
vertex cover. The algorithm greedily reduces the costs over edges,
|
| 58 |
+
iteratively building a cover. The worst-case runtime of this
|
| 59 |
+
implementation is $O(m \log n)$, where $n$ is the number
|
| 60 |
+
of nodes and $m$ the number of edges in the graph.
|
| 61 |
+
|
| 62 |
+
References
|
| 63 |
+
----------
|
| 64 |
+
.. [1] Bar-Yehuda, R., and Even, S. (1985). "A local-ratio theorem for
|
| 65 |
+
approximating the weighted vertex cover problem."
|
| 66 |
+
*Annals of Discrete Mathematics*, 25, 27–46
|
| 67 |
+
<http://www.cs.technion.ac.il/~reuven/PDF/vc_lr.pdf>
|
| 68 |
+
|
| 69 |
+
"""
|
| 70 |
+
cost = dict(G.nodes(data=weight, default=1))
|
| 71 |
+
# While there are uncovered edges, choose an uncovered and update
|
| 72 |
+
# the cost of the remaining edges.
|
| 73 |
+
cover = set()
|
| 74 |
+
for u, v in G.edges():
|
| 75 |
+
if u in cover or v in cover:
|
| 76 |
+
continue
|
| 77 |
+
if cost[u] <= cost[v]:
|
| 78 |
+
cover.add(u)
|
| 79 |
+
cost[v] -= cost[u]
|
| 80 |
+
else:
|
| 81 |
+
cover.add(v)
|
| 82 |
+
cost[u] -= cost[v]
|
| 83 |
+
return cover
|
.venv/lib/python3.11/site-packages/networkx/algorithms/community/__init__.py
ADDED
|
@@ -0,0 +1,26 @@
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|
|
|
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|
|
|
|
|
|
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|
|
|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""Functions for computing and measuring community structure.
|
| 2 |
+
|
| 3 |
+
The ``community`` subpackage can be accessed by using :mod:`networkx.community`, then accessing the
|
| 4 |
+
functions as attributes of ``community``. For example::
|
| 5 |
+
|
| 6 |
+
>>> import networkx as nx
|
| 7 |
+
>>> G = nx.barbell_graph(5, 1)
|
| 8 |
+
>>> communities_generator = nx.community.girvan_newman(G)
|
| 9 |
+
>>> top_level_communities = next(communities_generator)
|
| 10 |
+
>>> next_level_communities = next(communities_generator)
|
| 11 |
+
>>> sorted(map(sorted, next_level_communities))
|
| 12 |
+
[[0, 1, 2, 3, 4], [5], [6, 7, 8, 9, 10]]
|
| 13 |
+
|
| 14 |
+
"""
|
| 15 |
+
|
| 16 |
+
from networkx.algorithms.community.asyn_fluid import *
|
| 17 |
+
from networkx.algorithms.community.centrality import *
|
| 18 |
+
from networkx.algorithms.community.divisive import *
|
| 19 |
+
from networkx.algorithms.community.kclique import *
|
| 20 |
+
from networkx.algorithms.community.kernighan_lin import *
|
| 21 |
+
from networkx.algorithms.community.label_propagation import *
|
| 22 |
+
from networkx.algorithms.community.lukes import *
|
| 23 |
+
from networkx.algorithms.community.modularity_max import *
|
| 24 |
+
from networkx.algorithms.community.quality import *
|
| 25 |
+
from networkx.algorithms.community.community_utils import *
|
| 26 |
+
from networkx.algorithms.community.louvain import *
|
.venv/lib/python3.11/site-packages/networkx/algorithms/community/__pycache__/centrality.cpython-311.pyc
ADDED
|
Binary file (7.3 kB). View file
|
|
|