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tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/__init__.py

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+from networkx.algorithms.assortativity import *
+from networkx.algorithms.asteroidal import *
+from networkx.algorithms.boundary import *
+from networkx.algorithms.bridges import *
+from networkx.algorithms.chains import *
+from networkx.algorithms.centrality import *
+from networkx.algorithms.chordal import *
+from networkx.algorithms.cluster import *
+from networkx.algorithms.clique import *
+from networkx.algorithms.communicability_alg import *
+from networkx.algorithms.components import *
+from networkx.algorithms.coloring import *
+from networkx.algorithms.core import *
+from networkx.algorithms.covering import *
+from networkx.algorithms.cycles import *
+from networkx.algorithms.cuts import *
+from networkx.algorithms.d_separation import *
+from networkx.algorithms.dag import *
+from networkx.algorithms.distance_measures import *
+from networkx.algorithms.distance_regular import *
+from networkx.algorithms.dominance import *
+from networkx.algorithms.dominating import *
+from networkx.algorithms.efficiency_measures import *
+from networkx.algorithms.euler import *
+from networkx.algorithms.graphical import *
+from networkx.algorithms.hierarchy import *
+from networkx.algorithms.hybrid import *
+from networkx.algorithms.link_analysis import *
+from networkx.algorithms.link_prediction import *
+from networkx.algorithms.lowest_common_ancestors import *
+from networkx.algorithms.isolate import *
+from networkx.algorithms.matching import *
+from networkx.algorithms.minors import *
+from networkx.algorithms.mis import *
+from networkx.algorithms.moral import *
+from networkx.algorithms.non_randomness import *
+from networkx.algorithms.operators import *
+from networkx.algorithms.planarity import *
+from networkx.algorithms.planar_drawing import *
+from networkx.algorithms.reciprocity import *
+from networkx.algorithms.regular import *
+from networkx.algorithms.richclub import *
+from networkx.algorithms.shortest_paths import *
+from networkx.algorithms.similarity import *
+from networkx.algorithms.graph_hashing import *
+from networkx.algorithms.simple_paths import *
+from networkx.algorithms.smallworld import *
+from networkx.algorithms.smetric import *
+from networkx.algorithms.structuralholes import *
+from networkx.algorithms.sparsifiers import *
+from networkx.algorithms.summarization import *
+from networkx.algorithms.swap import *
+from networkx.algorithms.time_dependent import *
+from networkx.algorithms.traversal import *
+from networkx.algorithms.triads import *
+from networkx.algorithms.vitality import *
+from networkx.algorithms.voronoi import *
+from networkx.algorithms.walks import *
+from networkx.algorithms.wiener import *
+from networkx.algorithms.polynomials import *
+
+# Make certain subpackages available to the user as direct imports from
+# the `networkx` namespace.
+from networkx.algorithms import approximation
+from networkx.algorithms import assortativity
+from networkx.algorithms import bipartite
+from networkx.algorithms import node_classification
+from networkx.algorithms import centrality
+from networkx.algorithms import chordal
+from networkx.algorithms import cluster
+from networkx.algorithms import clique
+from networkx.algorithms import components
+from networkx.algorithms import connectivity
+from networkx.algorithms import community
+from networkx.algorithms import coloring
+from networkx.algorithms import flow
+from networkx.algorithms import isomorphism
+from networkx.algorithms import link_analysis
+from networkx.algorithms import lowest_common_ancestors
+from networkx.algorithms import operators
+from networkx.algorithms import shortest_paths
+from networkx.algorithms import tournament
+from networkx.algorithms import traversal
+from networkx.algorithms import tree
+
+# Make certain functions from some of the previous subpackages available
+# to the user as direct imports from the `networkx` namespace.
+from networkx.algorithms.bipartite import complete_bipartite_graph
+from networkx.algorithms.bipartite import is_bipartite
+from networkx.algorithms.bipartite import projected_graph
+from networkx.algorithms.connectivity import all_pairs_node_connectivity
+from networkx.algorithms.connectivity import all_node_cuts
+from networkx.algorithms.connectivity import average_node_connectivity
+from networkx.algorithms.connectivity import edge_connectivity
+from networkx.algorithms.connectivity import edge_disjoint_paths
+from networkx.algorithms.connectivity import k_components
+from networkx.algorithms.connectivity import k_edge_components
+from networkx.algorithms.connectivity import k_edge_subgraphs
+from networkx.algorithms.connectivity import k_edge_augmentation
+from networkx.algorithms.connectivity import is_k_edge_connected
+from networkx.algorithms.connectivity import minimum_edge_cut
+from networkx.algorithms.connectivity import minimum_node_cut
+from networkx.algorithms.connectivity import node_connectivity
+from networkx.algorithms.connectivity import node_disjoint_paths
+from networkx.algorithms.connectivity import stoer_wagner
+from networkx.algorithms.flow import capacity_scaling
+from networkx.algorithms.flow import cost_of_flow
+from networkx.algorithms.flow import gomory_hu_tree
+from networkx.algorithms.flow import max_flow_min_cost
+from networkx.algorithms.flow import maximum_flow
+from networkx.algorithms.flow import maximum_flow_value
+from networkx.algorithms.flow import min_cost_flow
+from networkx.algorithms.flow import min_cost_flow_cost
+from networkx.algorithms.flow import minimum_cut
+from networkx.algorithms.flow import minimum_cut_value
+from networkx.algorithms.flow import network_simplex
+from networkx.algorithms.isomorphism import could_be_isomorphic
+from networkx.algorithms.isomorphism import fast_could_be_isomorphic
+from networkx.algorithms.isomorphism import faster_could_be_isomorphic
+from networkx.algorithms.isomorphism import is_isomorphic
+from networkx.algorithms.isomorphism.vf2pp import *
+from networkx.algorithms.tree.branchings import maximum_branching
+from networkx.algorithms.tree.branchings import maximum_spanning_arborescence
+from networkx.algorithms.tree.branchings import minimum_branching
+from networkx.algorithms.tree.branchings import minimum_spanning_arborescence
+from networkx.algorithms.tree.branchings import ArborescenceIterator
+from networkx.algorithms.tree.coding import *
+from networkx.algorithms.tree.decomposition import *
+from networkx.algorithms.tree.mst import *
+from networkx.algorithms.tree.operations import *
+from networkx.algorithms.tree.recognition import *
+from networkx.algorithms.tournament import is_tournament

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/__init__.py

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+"""Approximations of graph properties and Heuristic methods for optimization.
+
+The functions in this class are not imported into the top-level ``networkx``
+namespace so the easiest way to use them is with::
+
+    >>> from networkx.algorithms import approximation
+
+Another option is to import the specific function with
+``from networkx.algorithms.approximation import function_name``.
+
+"""
+from networkx.algorithms.approximation.clustering_coefficient import *
+from networkx.algorithms.approximation.clique import *
+from networkx.algorithms.approximation.connectivity import *
+from networkx.algorithms.approximation.distance_measures import *
+from networkx.algorithms.approximation.dominating_set import *
+from networkx.algorithms.approximation.kcomponents import *
+from networkx.algorithms.approximation.matching import *
+from networkx.algorithms.approximation.ramsey import *
+from networkx.algorithms.approximation.steinertree import *
+from networkx.algorithms.approximation.traveling_salesman import *
+from networkx.algorithms.approximation.treewidth import *
+from networkx.algorithms.approximation.vertex_cover import *
+from networkx.algorithms.approximation.maxcut import *

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/clustering_coefficient.py

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+import networkx as nx
+from networkx.utils import not_implemented_for, py_random_state
+
+__all__ = ["average_clustering"]
+
+
+@not_implemented_for("directed")
+@py_random_state(2)
+@nx._dispatch(name="approximate_average_clustering")
+def average_clustering(G, trials=1000, seed=None):
+    r"""Estimates the average clustering coefficient of G.
+
+    The local clustering of each node in `G` is the fraction of triangles
+    that actually exist over all possible triangles in its neighborhood.
+    The average clustering coefficient of a graph `G` is the mean of
+    local clusterings.
+
+    This function finds an approximate average clustering coefficient
+    for G by repeating `n` times (defined in `trials`) the following
+    experiment: choose a node at random, choose two of its neighbors
+    at random, and check if they are connected. The approximate
+    coefficient is the fraction of triangles found over the number
+    of trials [1]_.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    trials : integer
+        Number of trials to perform (default 1000).
+
+    seed : integer, random_state, or None (default)
+        Indicator of random number generation state.
+        See :ref:`Randomness<randomness>`.
+
+    Returns
+    -------
+    c : float
+        Approximated average clustering coefficient.
+
+    Examples
+    --------
+    >>> from networkx.algorithms import approximation
+    >>> G = nx.erdos_renyi_graph(10, 0.2, seed=10)
+    >>> approximation.average_clustering(G, trials=1000, seed=10)
+    0.214
+
+    References
+    ----------
+    .. [1] Schank, Thomas, and Dorothea Wagner. Approximating clustering
+       coefficient and transitivity. Universität Karlsruhe, Fakultät für
+       Informatik, 2004.
+       https://doi.org/10.5445/IR/1000001239
+
+    """
+    n = len(G)
+    triangles = 0
+    nodes = list(G)
+    for i in [int(seed.random() * n) for i in range(trials)]:
+        nbrs = list(G[nodes[i]])
+        if len(nbrs) < 2:
+            continue
+        u, v = seed.sample(nbrs, 2)
+        if u in G[v]:
+            triangles += 1
+    return triangles / trials

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/dominating_set.py

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+"""Functions for finding node and edge dominating sets.
+
+A `dominating set`_ for an undirected graph *G* with vertex set *V*
+and edge set *E* is a subset *D* of *V* such that every vertex not in
+*D* is adjacent to at least one member of *D*. An `edge dominating set`_
+is a subset *F* of *E* such that every edge not in *F* is
+incident to an endpoint of at least one edge in *F*.
+
+.. _dominating set: https://en.wikipedia.org/wiki/Dominating_set
+.. _edge dominating set: https://en.wikipedia.org/wiki/Edge_dominating_set
+
+"""
+import networkx as nx
+
+from ...utils import not_implemented_for
+from ..matching import maximal_matching
+
+__all__ = ["min_weighted_dominating_set", "min_edge_dominating_set"]
+
+
+# TODO Why doesn't this algorithm work for directed graphs?
+@not_implemented_for("directed")
+@nx._dispatch(node_attrs="weight")
+def min_weighted_dominating_set(G, weight=None):
+    r"""Returns a dominating set that approximates the minimum weight node
+    dominating set.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        Undirected graph.
+
+    weight : string
+        The node attribute storing the weight of an node. If provided,
+        the node attribute with this key must be a number for each
+        node. If not provided, each node is assumed to have weight one.
+
+    Returns
+    -------
+    min_weight_dominating_set : set
+        A set of nodes, the sum of whose weights is no more than `(\log
+        w(V)) w(V^*)`, where `w(V)` denotes the sum of the weights of
+        each node in the graph and `w(V^*)` denotes the sum of the
+        weights of each node in the minimum weight dominating set.
+
+    Notes
+    -----
+    This algorithm computes an approximate minimum weighted dominating
+    set for the graph `G`. The returned solution has weight `(\log
+    w(V)) w(V^*)`, where `w(V)` denotes the sum of the weights of each
+    node in the graph and `w(V^*)` denotes the sum of the weights of
+    each node in the minimum weight dominating set for the graph.
+
+    This implementation of the algorithm runs in $O(m)$ time, where $m$
+    is the number of edges in the graph.
+
+    References
+    ----------
+    .. [1] Vazirani, Vijay V.
+           *Approximation Algorithms*.
+           Springer Science & Business Media, 2001.
+
+    """
+    # The unique dominating set for the null graph is the empty set.
+    if len(G) == 0:
+        return set()
+
+    # This is the dominating set that will eventually be returned.
+    dom_set = set()
+
+    def _cost(node_and_neighborhood):
+        """Returns the cost-effectiveness of greedily choosing the given
+        node.
+
+        `node_and_neighborhood` is a two-tuple comprising a node and its
+        closed neighborhood.
+
+        """
+        v, neighborhood = node_and_neighborhood
+        return G.nodes[v].get(weight, 1) / len(neighborhood - dom_set)
+
+    # This is a set of all vertices not already covered by the
+    # dominating set.
+    vertices = set(G)
+    # This is a dictionary mapping each node to the closed neighborhood
+    # of that node.
+    neighborhoods = {v: {v} | set(G[v]) for v in G}
+
+    # Continue until all vertices are adjacent to some node in the
+    # dominating set.
+    while vertices:
+        # Find the most cost-effective node to add, along with its
+        # closed neighborhood.
+        dom_node, min_set = min(neighborhoods.items(), key=_cost)
+        # Add the node to the dominating set and reduce the remaining
+        # set of nodes to cover.
+        dom_set.add(dom_node)
+        del neighborhoods[dom_node]
+        vertices -= min_set
+
+    return dom_set
+
+
+@nx._dispatch
+def min_edge_dominating_set(G):
+    r"""Returns minimum cardinality edge dominating set.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+      Undirected graph
+
+    Returns
+    -------
+    min_edge_dominating_set : set
+      Returns a set of dominating edges whose size is no more than 2 * OPT.
+
+    Notes
+    -----
+    The algorithm computes an approximate solution to the edge dominating set
+    problem. The result is no more than 2 * OPT in terms of size of the set.
+    Runtime of the algorithm is $O(|E|)$.
+    """
+    if not G:
+        raise ValueError("Expected non-empty NetworkX graph!")
+    return maximal_matching(G)

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/ramsey.py

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+"""
+Ramsey numbers.
+"""
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+from ...utils import arbitrary_element
+
+__all__ = ["ramsey_R2"]
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatch
+def ramsey_R2(G):
+    r"""Compute the largest clique and largest independent set in `G`.
+
+    This can be used to estimate bounds for the 2-color
+    Ramsey number `R(2;s,t)` for `G`.
+
+    This is a recursive implementation which could run into trouble
+    for large recursions. Note that self-loop edges are ignored.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        Undirected graph
+
+    Returns
+    -------
+    max_pair : (set, set) tuple
+        Maximum clique, Maximum independent set.
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If the graph is directed or is a multigraph.
+    """
+    if not G:
+        return set(), set()
+
+    node = arbitrary_element(G)
+    nbrs = (nbr for nbr in nx.all_neighbors(G, node) if nbr != node)
+    nnbrs = nx.non_neighbors(G, node)
+    c_1, i_1 = ramsey_R2(G.subgraph(nbrs).copy())
+    c_2, i_2 = ramsey_R2(G.subgraph(nnbrs).copy())
+
+    c_1.add(node)
+    i_2.add(node)
+    # Choose the larger of the two cliques and the larger of the two
+    # independent sets, according to cardinality.
+    return max(c_1, c_2, key=len), max(i_1, i_2, key=len)

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_approx_clust_coeff.py

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+import networkx as nx
+from networkx.algorithms.approximation import average_clustering
+
+# This approximation has to be exact in regular graphs
+# with no triangles or with all possible triangles.
+
+
+def test_petersen():
+    # Actual coefficient is 0
+    G = nx.petersen_graph()
+    assert average_clustering(G, trials=len(G) // 2) == nx.average_clustering(G)
+
+
+def test_petersen_seed():
+    # Actual coefficient is 0
+    G = nx.petersen_graph()
+    assert average_clustering(G, trials=len(G) // 2, seed=1) == nx.average_clustering(G)
+
+
+def test_tetrahedral():
+    # Actual coefficient is 1
+    G = nx.tetrahedral_graph()
+    assert average_clustering(G, trials=len(G) // 2) == nx.average_clustering(G)
+
+
+def test_dodecahedral():
+    # Actual coefficient is 0
+    G = nx.dodecahedral_graph()
+    assert average_clustering(G, trials=len(G) // 2) == nx.average_clustering(G)
+
+
+def test_empty():
+    G = nx.empty_graph(5)
+    assert average_clustering(G, trials=len(G) // 2) == 0
+
+
+def test_complete():
+    G = nx.complete_graph(5)
+    assert average_clustering(G, trials=len(G) // 2) == 1
+    G = nx.complete_graph(7)
+    assert average_clustering(G, trials=len(G) // 2) == 1

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_clique.py

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+"""Unit tests for the :mod:`networkx.algorithms.approximation.clique` module."""
+
+
+import networkx as nx
+from networkx.algorithms.approximation import (
+    clique_removal,
+    large_clique_size,
+    max_clique,
+    maximum_independent_set,
+)
+
+
+def is_independent_set(G, nodes):
+    """Returns True if and only if `nodes` is a clique in `G`.
+
+    `G` is a NetworkX graph. `nodes` is an iterable of nodes in
+    `G`.
+
+    """
+    return G.subgraph(nodes).number_of_edges() == 0
+
+
+def is_clique(G, nodes):
+    """Returns True if and only if `nodes` is an independent set
+    in `G`.
+
+    `G` is an undirected simple graph. `nodes` is an iterable of
+    nodes in `G`.
+
+    """
+    H = G.subgraph(nodes)
+    n = len(H)
+    return H.number_of_edges() == n * (n - 1) // 2
+
+
+class TestCliqueRemoval:
+    """Unit tests for the
+    :func:`~networkx.algorithms.approximation.clique_removal` function.
+
+    """
+
+    def test_trivial_graph(self):
+        G = nx.trivial_graph()
+        independent_set, cliques = clique_removal(G)
+        assert is_independent_set(G, independent_set)
+        assert all(is_clique(G, clique) for clique in cliques)
+        # In fact, we should only have 1-cliques, that is, singleton nodes.
+        assert all(len(clique) == 1 for clique in cliques)
+
+    def test_complete_graph(self):
+        G = nx.complete_graph(10)
+        independent_set, cliques = clique_removal(G)
+        assert is_independent_set(G, independent_set)
+        assert all(is_clique(G, clique) for clique in cliques)
+
+    def test_barbell_graph(self):
+        G = nx.barbell_graph(10, 5)
+        independent_set, cliques = clique_removal(G)
+        assert is_independent_set(G, independent_set)
+        assert all(is_clique(G, clique) for clique in cliques)
+
+
+class TestMaxClique:
+    """Unit tests for the :func:`networkx.algorithms.approximation.max_clique`
+    function.
+
+    """
+
+    def test_null_graph(self):
+        G = nx.null_graph()
+        assert len(max_clique(G)) == 0
+
+    def test_complete_graph(self):
+        graph = nx.complete_graph(30)
+        # this should return the entire graph
+        mc = max_clique(graph)
+        assert 30 == len(mc)
+
+    def test_maximal_by_cardinality(self):
+        """Tests that the maximal clique is computed according to maximum
+        cardinality of the sets.
+
+        For more information, see pull request #1531.
+
+        """
+        G = nx.complete_graph(5)
+        G.add_edge(4, 5)
+        clique = max_clique(G)
+        assert len(clique) > 1
+
+        G = nx.lollipop_graph(30, 2)
+        clique = max_clique(G)
+        assert len(clique) > 2
+
+
+def test_large_clique_size():
+    G = nx.complete_graph(9)
+    nx.add_cycle(G, [9, 10, 11])
+    G.add_edge(8, 9)
+    G.add_edge(1, 12)
+    G.add_node(13)
+
+    assert large_clique_size(G) == 9
+    G.remove_node(5)
+    assert large_clique_size(G) == 8
+    G.remove_edge(2, 3)
+    assert large_clique_size(G) == 7
+
+
+def test_independent_set():
+    # smoke test
+    G = nx.Graph()
+    assert len(maximum_independent_set(G)) == 0

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_distance_measures.py

@@ -0,0 +1,60 @@
+"""Unit tests for the :mod:`networkx.algorithms.approximation.distance_measures` module.
+"""
+
+import pytest
+
+import networkx as nx
+from networkx.algorithms.approximation import diameter
+
+
+class TestDiameter:
+    """Unit tests for the approximate diameter function
+    :func:`~networkx.algorithms.approximation.distance_measures.diameter`.
+    """
+
+    def test_null_graph(self):
+        """Test empty graph."""
+        G = nx.null_graph()
+        with pytest.raises(
+            nx.NetworkXError, match="Expected non-empty NetworkX graph!"
+        ):
+            diameter(G)
+
+    def test_undirected_non_connected(self):
+        """Test an undirected disconnected graph."""
+        graph = nx.path_graph(10)
+        graph.remove_edge(3, 4)
+        with pytest.raises(nx.NetworkXError, match="Graph not connected."):
+            diameter(graph)
+
+    def test_directed_non_strongly_connected(self):
+        """Test a directed non strongly connected graph."""
+        graph = nx.path_graph(10, create_using=nx.DiGraph())
+        with pytest.raises(nx.NetworkXError, match="DiGraph not strongly connected."):
+            diameter(graph)
+
+    def test_complete_undirected_graph(self):
+        """Test a complete undirected graph."""
+        graph = nx.complete_graph(10)
+        assert diameter(graph) == 1
+
+    def test_complete_directed_graph(self):
+        """Test a complete directed graph."""
+        graph = nx.complete_graph(10, create_using=nx.DiGraph())
+        assert diameter(graph) == 1
+
+    def test_undirected_path_graph(self):
+        """Test an undirected path graph with 10 nodes."""
+        graph = nx.path_graph(10)
+        assert diameter(graph) == 9
+
+    def test_directed_path_graph(self):
+        """Test a directed path graph with 10 nodes."""
+        graph = nx.path_graph(10).to_directed()
+        assert diameter(graph) == 9
+
+    def test_single_node(self):
+        """Test a graph which contains just a node."""
+        graph = nx.Graph()
+        graph.add_node(1)
+        assert diameter(graph) == 0

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_maxcut.py

@@ -0,0 +1,82 @@
+import random
+
+import networkx as nx
+from networkx.algorithms.approximation import maxcut
+
+
+def _is_valid_cut(G, set1, set2):
+    union = set1.union(set2)
+    assert union == set(G.nodes)
+    assert len(set1) + len(set2) == G.number_of_nodes()
+
+
+def _cut_is_locally_optimal(G, cut_size, set1):
+    # test if cut can be locally improved
+    for i, node in enumerate(set1):
+        cut_size_without_node = nx.algorithms.cut_size(
+            G, set1 - {node}, weight="weight"
+        )
+        assert cut_size_without_node <= cut_size
+
+
+def test_random_partitioning():
+    G = nx.complete_graph(5)
+    _, (set1, set2) = maxcut.randomized_partitioning(G, seed=5)
+    _is_valid_cut(G, set1, set2)
+
+
+def test_random_partitioning_all_to_one():
+    G = nx.complete_graph(5)
+    _, (set1, set2) = maxcut.randomized_partitioning(G, p=1)
+    _is_valid_cut(G, set1, set2)
+    assert len(set1) == G.number_of_nodes()
+    assert len(set2) == 0
+
+
+def test_one_exchange_basic():
+    G = nx.complete_graph(5)
+    random.seed(5)
+    for u, v, w in G.edges(data=True):
+        w["weight"] = random.randrange(-100, 100, 1) / 10
+
+    initial_cut = set(random.sample(sorted(G.nodes()), k=5))
+    cut_size, (set1, set2) = maxcut.one_exchange(
+        G, initial_cut, weight="weight", seed=5
+    )
+
+    _is_valid_cut(G, set1, set2)
+    _cut_is_locally_optimal(G, cut_size, set1)
+
+
+def test_one_exchange_optimal():
+    # Greedy one exchange should find the optimal solution for this graph (14)
+    G = nx.Graph()
+    G.add_edge(1, 2, weight=3)
+    G.add_edge(1, 3, weight=3)
+    G.add_edge(1, 4, weight=3)
+    G.add_edge(1, 5, weight=3)
+    G.add_edge(2, 3, weight=5)
+
+    cut_size, (set1, set2) = maxcut.one_exchange(G, weight="weight", seed=5)
+
+    _is_valid_cut(G, set1, set2)
+    _cut_is_locally_optimal(G, cut_size, set1)
+    # check global optimality
+    assert cut_size == 14
+
+
+def test_negative_weights():
+    G = nx.complete_graph(5)
+    random.seed(5)
+    for u, v, w in G.edges(data=True):
+        w["weight"] = -1 * random.random()
+
+    initial_cut = set(random.sample(sorted(G.nodes()), k=5))
+    cut_size, (set1, set2) = maxcut.one_exchange(G, initial_cut, weight="weight")
+
+    # make sure it is a valid cut
+    _is_valid_cut(G, set1, set2)
+    # check local optimality
+    _cut_is_locally_optimal(G, cut_size, set1)
+    # test that all nodes are in the same partition
+    assert len(set1) == len(G.nodes) or len(set2) == len(G.nodes)

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/approximation/tests/test_vertex_cover.py

@@ -0,0 +1,68 @@
+import networkx as nx
+from networkx.algorithms.approximation import min_weighted_vertex_cover
+
+
+def is_cover(G, node_cover):
+    return all({u, v} & node_cover for u, v in G.edges())
+
+
+class TestMWVC:
+    """Unit tests for the approximate minimum weighted vertex cover
+    function,
+    :func:`~networkx.algorithms.approximation.vertex_cover.min_weighted_vertex_cover`.
+
+    """
+
+    def test_unweighted_directed(self):
+        # Create a star graph in which half the nodes are directed in
+        # and half are directed out.
+        G = nx.DiGraph()
+        G.add_edges_from((0, v) for v in range(1, 26))
+        G.add_edges_from((v, 0) for v in range(26, 51))
+        cover = min_weighted_vertex_cover(G)
+        assert 1 == len(cover)
+        assert is_cover(G, cover)
+
+    def test_unweighted_undirected(self):
+        # create a simple star graph
+        size = 50
+        sg = nx.star_graph(size)
+        cover = min_weighted_vertex_cover(sg)
+        assert 1 == len(cover)
+        assert is_cover(sg, cover)
+
+    def test_weighted(self):
+        wg = nx.Graph()
+        wg.add_node(0, weight=10)
+        wg.add_node(1, weight=1)
+        wg.add_node(2, weight=1)
+        wg.add_node(3, weight=1)
+        wg.add_node(4, weight=1)
+
+        wg.add_edge(0, 1)
+        wg.add_edge(0, 2)
+        wg.add_edge(0, 3)
+        wg.add_edge(0, 4)
+
+        wg.add_edge(1, 2)
+        wg.add_edge(2, 3)
+        wg.add_edge(3, 4)
+        wg.add_edge(4, 1)
+
+        cover = min_weighted_vertex_cover(wg, weight="weight")
+        csum = sum(wg.nodes[node]["weight"] for node in cover)
+        assert 4 == csum
+        assert is_cover(wg, cover)
+
+    def test_unweighted_self_loop(self):
+        slg = nx.Graph()
+        slg.add_node(0)
+        slg.add_node(1)
+        slg.add_node(2)
+
+        slg.add_edge(0, 1)
+        slg.add_edge(2, 2)
+
+        cover = min_weighted_vertex_cover(slg)
+        assert 2 == len(cover)
+        assert is_cover(slg, cover)

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/asteroidal.py

@@ -0,0 +1,170 @@
+"""
+Algorithms for asteroidal triples and asteroidal numbers in graphs.
+
+An asteroidal triple in a graph G is a set of three non-adjacent vertices
+u, v and w such that there exist a path between any two of them that avoids
+closed neighborhood of the third. More formally, v_j, v_k belongs to the same
+connected component of G - N[v_i], where N[v_i] denotes the closed neighborhood
+of v_i. A graph which does not contain any asteroidal triples is called
+an AT-free graph. The class of AT-free graphs is a graph class for which
+many NP-complete problems are solvable in polynomial time. Amongst them,
+independent set and coloring.
+"""
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+__all__ = ["is_at_free", "find_asteroidal_triple"]
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatch
+def find_asteroidal_triple(G):
+    r"""Find an asteroidal triple in the given graph.
+
+    An asteroidal triple is a triple of non-adjacent vertices such that
+    there exists a path between any two of them which avoids the closed
+    neighborhood of the third. It checks all independent triples of vertices
+    and whether they are an asteroidal triple or not. This is done with the
+    help of a data structure called a component structure.
+    A component structure encodes information about which vertices belongs to
+    the same connected component when the closed neighborhood of a given vertex
+    is removed from the graph. The algorithm used to check is the trivial
+    one, outlined in [1]_, which has a runtime of
+    :math:`O(|V||\overline{E} + |V||E|)`, where the second term is the
+    creation of the component structure.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+        The graph to check whether is AT-free or not
+
+    Returns
+    -------
+    list or None
+        An asteroidal triple is returned as a list of nodes. If no asteroidal
+        triple exists, i.e. the graph is AT-free, then None is returned.
+        The returned value depends on the certificate parameter. The default
+        option is a bool which is True if the graph is AT-free, i.e. the
+        given graph contains no asteroidal triples, and False otherwise, i.e.
+        if the graph contains at least one asteroidal triple.
+
+    Notes
+    -----
+    The component structure and the algorithm is described in [1]_. The current
+    implementation implements the trivial algorithm for simple graphs.
+
+    References
+    ----------
+    .. [1] Ekkehard Köhler,
+       "Recognizing Graphs without asteroidal triples",
+       Journal of Discrete Algorithms 2, pages 439-452, 2004.
+       https://www.sciencedirect.com/science/article/pii/S157086670400019X
+    """
+    V = set(G.nodes)
+
+    if len(V) < 6:
+        # An asteroidal triple cannot exist in a graph with 5 or less vertices.
+        return None
+
+    component_structure = create_component_structure(G)
+    E_complement = set(nx.complement(G).edges)
+
+    for e in E_complement:
+        u = e[0]
+        v = e[1]
+        u_neighborhood = set(G[u]).union([u])
+        v_neighborhood = set(G[v]).union([v])
+        union_of_neighborhoods = u_neighborhood.union(v_neighborhood)
+        for w in V - union_of_neighborhoods:
+            # Check for each pair of vertices whether they belong to the
+            # same connected component when the closed neighborhood of the
+            # third is removed.
+            if (
+                component_structure[u][v] == component_structure[u][w]
+                and component_structure[v][u] == component_structure[v][w]
+                and component_structure[w][u] == component_structure[w][v]
+            ):
+                return [u, v, w]
+    return None
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatch
+def is_at_free(G):
+    """Check if a graph is AT-free.
+
+    The method uses the `find_asteroidal_triple` method to recognize
+    an AT-free graph. If no asteroidal triple is found the graph is
+    AT-free and True is returned. If at least one asteroidal triple is
+    found the graph is not AT-free and False is returned.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+        The graph to check whether is AT-free or not.
+
+    Returns
+    -------
+    bool
+        True if G is AT-free and False otherwise.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(0, 1), (0, 2), (1, 2), (1, 3), (1, 4), (4, 5)])
+    >>> nx.is_at_free(G)
+    True
+
+    >>> G = nx.cycle_graph(6)
+    >>> nx.is_at_free(G)
+    False
+    """
+    return find_asteroidal_triple(G) is None
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatch
+def create_component_structure(G):
+    r"""Create component structure for G.
+
+    A *component structure* is an `nxn` array, denoted `c`, where `n` is
+    the number of vertices,  where each row and column corresponds to a vertex.
+
+    .. math::
+        c_{uv} = \begin{cases} 0, if v \in N[u] \\
+            k, if v \in component k of G \setminus N[u] \end{cases}
+
+    Where `k` is an arbitrary label for each component. The structure is used
+    to simplify the detection of asteroidal triples.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+        Undirected, simple graph.
+
+    Returns
+    -------
+    component_structure : dictionary
+        A dictionary of dictionaries, keyed by pairs of vertices.
+
+    """
+    V = set(G.nodes)
+    component_structure = {}
+    for v in V:
+        label = 0
+        closed_neighborhood = set(G[v]).union({v})
+        row_dict = {}
+        for u in closed_neighborhood:
+            row_dict[u] = 0
+
+        G_reduced = G.subgraph(set(G.nodes) - closed_neighborhood)
+        for cc in nx.connected_components(G_reduced):
+            label += 1
+            for u in cc:
+                row_dict[u] = label
+
+        component_structure[v] = row_dict
+
+    return component_structure

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/bridges.py

@@ -0,0 +1,205 @@
+"""Bridge-finding algorithms."""
+from itertools import chain
+
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+__all__ = ["bridges", "has_bridges", "local_bridges"]
+
+
+@not_implemented_for("directed")
+@nx._dispatch
+def bridges(G, root=None):
+    """Generate all bridges in a graph.
+
+    A *bridge* in a graph is an edge whose removal causes the number of
+    connected components of the graph to increase.  Equivalently, a bridge is an
+    edge that does not belong to any cycle. Bridges are also known as cut-edges,
+    isthmuses, or cut arcs.
+
+    Parameters
+    ----------
+    G : undirected graph
+
+    root : node (optional)
+       A node in the graph `G`. If specified, only the bridges in the
+       connected component containing this node will be returned.
+
+    Yields
+    ------
+    e : edge
+       An edge in the graph whose removal disconnects the graph (or
+       causes the number of connected components to increase).
+
+    Raises
+    ------
+    NodeNotFound
+       If `root` is not in the graph `G`.
+
+    NetworkXNotImplemented
+        If `G` is a directed graph.
+
+    Examples
+    --------
+    The barbell graph with parameter zero has a single bridge:
+
+    >>> G = nx.barbell_graph(10, 0)
+    >>> list(nx.bridges(G))
+    [(9, 10)]
+
+    Notes
+    -----
+    This is an implementation of the algorithm described in [1]_.  An edge is a
+    bridge if and only if it is not contained in any chain. Chains are found
+    using the :func:`networkx.chain_decomposition` function.
+
+    The algorithm described in [1]_ requires a simple graph. If the provided
+    graph is a multigraph, we convert it to a simple graph and verify that any
+    bridges discovered by the chain decomposition algorithm are not multi-edges.
+
+    Ignoring polylogarithmic factors, the worst-case time complexity is the
+    same as the :func:`networkx.chain_decomposition` function,
+    $O(m + n)$, where $n$ is the number of nodes in the graph and $m$ is
+    the number of edges.
+
+    References
+    ----------
+    .. [1] https://en.wikipedia.org/wiki/Bridge_%28graph_theory%29#Bridge-Finding_with_Chain_Decompositions
+    """
+    multigraph = G.is_multigraph()
+    H = nx.Graph(G) if multigraph else G
+    chains = nx.chain_decomposition(H, root=root)
+    chain_edges = set(chain.from_iterable(chains))
+    H_copy = H.copy()
+    if root is not None:
+        H = H.subgraph(nx.node_connected_component(H, root)).copy()
+    for u, v in H.edges():
+        if (u, v) not in chain_edges and (v, u) not in chain_edges:
+            if multigraph and len(G[u][v]) > 1:
+                continue
+            yield u, v
+
+
+@not_implemented_for("directed")
+@nx._dispatch
+def has_bridges(G, root=None):
+    """Decide whether a graph has any bridges.
+
+    A *bridge* in a graph is an edge whose removal causes the number of
+    connected components of the graph to increase.
+
+    Parameters
+    ----------
+    G : undirected graph
+
+    root : node (optional)
+       A node in the graph `G`. If specified, only the bridges in the
+       connected component containing this node will be considered.
+
+    Returns
+    -------
+    bool
+       Whether the graph (or the connected component containing `root`)
+       has any bridges.
+
+    Raises
+    ------
+    NodeNotFound
+       If `root` is not in the graph `G`.
+
+    NetworkXNotImplemented
+        If `G` is a directed graph.
+
+    Examples
+    --------
+    The barbell graph with parameter zero has a single bridge::
+
+        >>> G = nx.barbell_graph(10, 0)
+        >>> nx.has_bridges(G)
+        True
+
+    On the other hand, the cycle graph has no bridges::
+
+        >>> G = nx.cycle_graph(5)
+        >>> nx.has_bridges(G)
+        False
+
+    Notes
+    -----
+    This implementation uses the :func:`networkx.bridges` function, so
+    it shares its worst-case time complexity, $O(m + n)$, ignoring
+    polylogarithmic factors, where $n$ is the number of nodes in the
+    graph and $m$ is the number of edges.
+
+    """
+    try:
+        next(bridges(G, root=root))
+    except StopIteration:
+        return False
+    else:
+        return True
+
+
+@not_implemented_for("multigraph")
+@not_implemented_for("directed")
+@nx._dispatch(edge_attrs="weight")
+def local_bridges(G, with_span=True, weight=None):
+    """Iterate over local bridges of `G` optionally computing the span
+
+    A *local bridge* is an edge whose endpoints have no common neighbors.
+    That is, the edge is not part of a triangle in the graph.
+
+    The *span* of a *local bridge* is the shortest path length between
+    the endpoints if the local bridge is removed.
+
+    Parameters
+    ----------
+    G : undirected graph
+
+    with_span : bool
+        If True, yield a 3-tuple `(u, v, span)`
+
+    weight : function, string or None (default: None)
+        If function, used to compute edge weights for the span.
+        If string, the edge data attribute used in calculating span.
+        If None, all edges have weight 1.
+
+    Yields
+    ------
+    e : edge
+        The local bridges as an edge 2-tuple of nodes `(u, v)` or
+        as a 3-tuple `(u, v, span)` when `with_span is True`.
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If `G` is a directed graph or multigraph.
+
+    Examples
+    --------
+    A cycle graph has every edge a local bridge with span N-1.
+
+       >>> G = nx.cycle_graph(9)
+       >>> (0, 8, 8) in set(nx.local_bridges(G))
+       True
+    """
+    if with_span is not True:
+        for u, v in G.edges:
+            if not (set(G[u]) & set(G[v])):
+                yield u, v
+    else:
+        wt = nx.weighted._weight_function(G, weight)
+        for u, v in G.edges:
+            if not (set(G[u]) & set(G[v])):
+                enodes = {u, v}
+
+                def hide_edge(n, nbr, d):
+                    if n not in enodes or nbr not in enodes:
+                        return wt(n, nbr, d)
+                    return None
+
+                try:
+                    span = nx.shortest_path_length(G, u, v, weight=hide_edge)
+                    yield u, v, span
+                except nx.NetworkXNoPath:
+                    yield u, v, float("inf")

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/chordal.py

@@ -0,0 +1,440 @@
+"""
+Algorithms for chordal graphs.
+
+A graph is chordal if every cycle of length at least 4 has a chord
+(an edge joining two nodes not adjacent in the cycle).
+https://en.wikipedia.org/wiki/Chordal_graph
+"""
+import sys
+
+import networkx as nx
+from networkx.algorithms.components import connected_components
+from networkx.utils import arbitrary_element, not_implemented_for
+
+__all__ = [
+    "is_chordal",
+    "find_induced_nodes",
+    "chordal_graph_cliques",
+    "chordal_graph_treewidth",
+    "NetworkXTreewidthBoundExceeded",
+    "complete_to_chordal_graph",
+]
+
+
+class NetworkXTreewidthBoundExceeded(nx.NetworkXException):
+    """Exception raised when a treewidth bound has been provided and it has
+    been exceeded"""
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatch
+def is_chordal(G):
+    """Checks whether G is a chordal graph.
+
+    A graph is chordal if every cycle of length at least 4 has a chord
+    (an edge joining two nodes not adjacent in the cycle).
+
+    Parameters
+    ----------
+    G : graph
+      A NetworkX graph.
+
+    Returns
+    -------
+    chordal : bool
+      True if G is a chordal graph and False otherwise.
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        The algorithm does not support DiGraph, MultiGraph and MultiDiGraph.
+
+    Examples
+    --------
+    >>> e = [
+    ...     (1, 2),
+    ...     (1, 3),
+    ...     (2, 3),
+    ...     (2, 4),
+    ...     (3, 4),
+    ...     (3, 5),
+    ...     (3, 6),
+    ...     (4, 5),
+    ...     (4, 6),
+    ...     (5, 6),
+    ... ]
+    >>> G = nx.Graph(e)
+    >>> nx.is_chordal(G)
+    True
+
+    Notes
+    -----
+    The routine tries to go through every node following maximum cardinality
+    search. It returns False when it finds that the separator for any node
+    is not a clique.  Based on the algorithms in [1]_.
+
+    Self loops are ignored.
+
+    References
+    ----------
+    .. [1] R. E. Tarjan and M. Yannakakis, Simple linear-time algorithms
+       to test chordality of graphs, test acyclicity of hypergraphs, and
+       selectively reduce acyclic hypergraphs, SIAM J. Comput., 13 (1984),
+       pp. 566–579.
+    """
+    if len(G.nodes) <= 3:
+        return True
+    return len(_find_chordality_breaker(G)) == 0
+
+
+@nx._dispatch
+def find_induced_nodes(G, s, t, treewidth_bound=sys.maxsize):
+    """Returns the set of induced nodes in the path from s to t.
+
+    Parameters
+    ----------
+    G : graph
+      A chordal NetworkX graph
+    s : node
+        Source node to look for induced nodes
+    t : node
+        Destination node to look for induced nodes
+    treewidth_bound: float
+        Maximum treewidth acceptable for the graph H. The search
+        for induced nodes will end as soon as the treewidth_bound is exceeded.
+
+    Returns
+    -------
+    induced_nodes : Set of nodes
+        The set of induced nodes in the path from s to t in G
+
+    Raises
+    ------
+    NetworkXError
+        The algorithm does not support DiGraph, MultiGraph and MultiDiGraph.
+        If the input graph is an instance of one of these classes, a
+        :exc:`NetworkXError` is raised.
+        The algorithm can only be applied to chordal graphs. If the input
+        graph is found to be non-chordal, a :exc:`NetworkXError` is raised.
+
+    Examples
+    --------
+    >>> G = nx.Graph()
+    >>> G = nx.generators.classic.path_graph(10)
+    >>> induced_nodes = nx.find_induced_nodes(G, 1, 9, 2)
+    >>> sorted(induced_nodes)
+    [1, 2, 3, 4, 5, 6, 7, 8, 9]
+
+    Notes
+    -----
+    G must be a chordal graph and (s,t) an edge that is not in G.
+
+    If a treewidth_bound is provided, the search for induced nodes will end
+    as soon as the treewidth_bound is exceeded.
+
+    The algorithm is inspired by Algorithm 4 in [1]_.
+    A formal definition of induced node can also be found on that reference.
+
+    Self Loops are ignored
+
+    References
+    ----------
+    .. [1] Learning Bounded Treewidth Bayesian Networks.
+       Gal Elidan, Stephen Gould; JMLR, 9(Dec):2699--2731, 2008.
+       http://jmlr.csail.mit.edu/papers/volume9/elidan08a/elidan08a.pdf
+    """
+    if not is_chordal(G):
+        raise nx.NetworkXError("Input graph is not chordal.")
+
+    H = nx.Graph(G)
+    H.add_edge(s, t)
+    induced_nodes = set()
+    triplet = _find_chordality_breaker(H, s, treewidth_bound)
+    while triplet:
+        (u, v, w) = triplet
+        induced_nodes.update(triplet)
+        for n in triplet:
+            if n != s:
+                H.add_edge(s, n)
+        triplet = _find_chordality_breaker(H, s, treewidth_bound)
+    if induced_nodes:
+        # Add t and the second node in the induced path from s to t.
+        induced_nodes.add(t)
+        for u in G[s]:
+            if len(induced_nodes & set(G[u])) == 2:
+                induced_nodes.add(u)
+                break
+    return induced_nodes
+
+
+@nx._dispatch
+def chordal_graph_cliques(G):
+    """Returns all maximal cliques of a chordal graph.
+
+    The algorithm breaks the graph in connected components and performs a
+    maximum cardinality search in each component to get the cliques.
+
+    Parameters
+    ----------
+    G : graph
+      A NetworkX graph
+
+    Yields
+    ------
+    frozenset of nodes
+        Maximal cliques, each of which is a frozenset of
+        nodes in `G`. The order of cliques is arbitrary.
+
+    Raises
+    ------
+    NetworkXError
+        The algorithm does not support DiGraph, MultiGraph and MultiDiGraph.
+        The algorithm can only be applied to chordal graphs. If the input
+        graph is found to be non-chordal, a :exc:`NetworkXError` is raised.
+
+    Examples
+    --------
+    >>> e = [
+    ...     (1, 2),
+    ...     (1, 3),
+    ...     (2, 3),
+    ...     (2, 4),
+    ...     (3, 4),
+    ...     (3, 5),
+    ...     (3, 6),
+    ...     (4, 5),
+    ...     (4, 6),
+    ...     (5, 6),
+    ...     (7, 8),
+    ... ]
+    >>> G = nx.Graph(e)
+    >>> G.add_node(9)
+    >>> cliques = [c for c in chordal_graph_cliques(G)]
+    >>> cliques[0]
+    frozenset({1, 2, 3})
+    """
+    for C in (G.subgraph(c).copy() for c in connected_components(G)):
+        if C.number_of_nodes() == 1:
+            if nx.number_of_selfloops(C) > 0:
+                raise nx.NetworkXError("Input graph is not chordal.")
+            yield frozenset(C.nodes())
+        else:
+            unnumbered = set(C.nodes())
+            v = arbitrary_element(C)
+            unnumbered.remove(v)
+            numbered = {v}
+            clique_wanna_be = {v}
+            while unnumbered:
+                v = _max_cardinality_node(C, unnumbered, numbered)
+                unnumbered.remove(v)
+                numbered.add(v)
+                new_clique_wanna_be = set(C.neighbors(v)) & numbered
+                sg = C.subgraph(clique_wanna_be)
+                if _is_complete_graph(sg):
+                    new_clique_wanna_be.add(v)
+                    if not new_clique_wanna_be >= clique_wanna_be:
+                        yield frozenset(clique_wanna_be)
+                    clique_wanna_be = new_clique_wanna_be
+                else:
+                    raise nx.NetworkXError("Input graph is not chordal.")
+            yield frozenset(clique_wanna_be)
+
+
+@nx._dispatch
+def chordal_graph_treewidth(G):
+    """Returns the treewidth of the chordal graph G.
+
+    Parameters
+    ----------
+    G : graph
+      A NetworkX graph
+
+    Returns
+    -------
+    treewidth : int
+        The size of the largest clique in the graph minus one.
+
+    Raises
+    ------
+    NetworkXError
+        The algorithm does not support DiGraph, MultiGraph and MultiDiGraph.
+        The algorithm can only be applied to chordal graphs. If the input
+        graph is found to be non-chordal, a :exc:`NetworkXError` is raised.
+
+    Examples
+    --------
+    >>> e = [
+    ...     (1, 2),
+    ...     (1, 3),
+    ...     (2, 3),
+    ...     (2, 4),
+    ...     (3, 4),
+    ...     (3, 5),
+    ...     (3, 6),
+    ...     (4, 5),
+    ...     (4, 6),
+    ...     (5, 6),
+    ...     (7, 8),
+    ... ]
+    >>> G = nx.Graph(e)
+    >>> G.add_node(9)
+    >>> nx.chordal_graph_treewidth(G)
+    3
+
+    References
+    ----------
+    .. [1] https://en.wikipedia.org/wiki/Tree_decomposition#Treewidth
+    """
+    if not is_chordal(G):
+        raise nx.NetworkXError("Input graph is not chordal.")
+
+    max_clique = -1
+    for clique in nx.chordal_graph_cliques(G):
+        max_clique = max(max_clique, len(clique))
+    return max_clique - 1
+
+
+def _is_complete_graph(G):
+    """Returns True if G is a complete graph."""
+    if nx.number_of_selfloops(G) > 0:
+        raise nx.NetworkXError("Self loop found in _is_complete_graph()")
+    n = G.number_of_nodes()
+    if n < 2:
+        return True
+    e = G.number_of_edges()
+    max_edges = (n * (n - 1)) / 2
+    return e == max_edges
+
+
+def _find_missing_edge(G):
+    """Given a non-complete graph G, returns a missing edge."""
+    nodes = set(G)
+    for u in G:
+        missing = nodes - set(list(G[u].keys()) + [u])
+        if missing:
+            return (u, missing.pop())
+
+
+def _max_cardinality_node(G, choices, wanna_connect):
+    """Returns a the node in choices that has more connections in G
+    to nodes in wanna_connect.
+    """
+    max_number = -1
+    for x in choices:
+        number = len([y for y in G[x] if y in wanna_connect])
+        if number > max_number:
+            max_number = number
+            max_cardinality_node = x
+    return max_cardinality_node
+
+
+def _find_chordality_breaker(G, s=None, treewidth_bound=sys.maxsize):
+    """Given a graph G, starts a max cardinality search
+    (starting from s if s is given and from an arbitrary node otherwise)
+    trying to find a non-chordal cycle.
+
+    If it does find one, it returns (u,v,w) where u,v,w are the three
+    nodes that together with s are involved in the cycle.
+
+    It ignores any self loops.
+    """
+    unnumbered = set(G)
+    if s is None:
+        s = arbitrary_element(G)
+    unnumbered.remove(s)
+    numbered = {s}
+    current_treewidth = -1
+    while unnumbered:  # and current_treewidth <= treewidth_bound:
+        v = _max_cardinality_node(G, unnumbered, numbered)
+        unnumbered.remove(v)
+        numbered.add(v)
+        clique_wanna_be = set(G[v]) & numbered
+        sg = G.subgraph(clique_wanna_be)
+        if _is_complete_graph(sg):
+            # The graph seems to be chordal by now. We update the treewidth
+            current_treewidth = max(current_treewidth, len(clique_wanna_be))
+            if current_treewidth > treewidth_bound:
+                raise nx.NetworkXTreewidthBoundExceeded(
+                    f"treewidth_bound exceeded: {current_treewidth}"
+                )
+        else:
+            # sg is not a clique,
+            # look for an edge that is not included in sg
+            (u, w) = _find_missing_edge(sg)
+            return (u, v, w)
+    return ()
+
+
+@not_implemented_for("directed")
+@nx._dispatch
+def complete_to_chordal_graph(G):
+    """Return a copy of G completed to a chordal graph
+
+    Adds edges to a copy of G to create a chordal graph. A graph G=(V,E) is
+    called chordal if for each cycle with length bigger than 3, there exist
+    two non-adjacent nodes connected by an edge (called a chord).
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        Undirected graph
+
+    Returns
+    -------
+    H : NetworkX graph
+        The chordal enhancement of G
+    alpha : Dictionary
+            The elimination ordering of nodes of G
+
+    Notes
+    -----
+    There are different approaches to calculate the chordal
+    enhancement of a graph. The algorithm used here is called
+    MCS-M and gives at least minimal (local) triangulation of graph. Note
+    that this triangulation is not necessarily a global minimum.
+
+    https://en.wikipedia.org/wiki/Chordal_graph
+
+    References
+    ----------
+    .. [1] Berry, Anne & Blair, Jean & Heggernes, Pinar & Peyton, Barry. (2004)
+           Maximum Cardinality Search for Computing Minimal Triangulations of
+           Graphs.  Algorithmica. 39. 287-298. 10.1007/s00453-004-1084-3.
+
+    Examples
+    --------
+    >>> from networkx.algorithms.chordal import complete_to_chordal_graph
+    >>> G = nx.wheel_graph(10)
+    >>> H, alpha = complete_to_chordal_graph(G)
+    """
+    H = G.copy()
+    alpha = {node: 0 for node in H}
+    if nx.is_chordal(H):
+        return H, alpha
+    chords = set()
+    weight = {node: 0 for node in H.nodes()}
+    unnumbered_nodes = list(H.nodes())
+    for i in range(len(H.nodes()), 0, -1):
+        # get the node in unnumbered_nodes with the maximum weight
+        z = max(unnumbered_nodes, key=lambda node: weight[node])
+        unnumbered_nodes.remove(z)
+        alpha[z] = i
+        update_nodes = []
+        for y in unnumbered_nodes:
+            if G.has_edge(y, z):
+                update_nodes.append(y)
+            else:
+                # y_weight will be bigger than node weights between y and z
+                y_weight = weight[y]
+                lower_nodes = [
+                    node for node in unnumbered_nodes if weight[node] < y_weight
+                ]
+                if nx.has_path(H.subgraph(lower_nodes + [z, y]), y, z):
+                    update_nodes.append(y)
+                    chords.add((z, y))
+        # during calculation of paths the weights should not be updated
+        for node in update_nodes:
+            weight[node] += 1
+    H.add_edges_from(chords)
+    return H, alpha

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/cluster.py

@@ -0,0 +1,605 @@
+"""Algorithms to characterize the number of triangles in a graph."""
+
+from collections import Counter
+from itertools import chain, combinations
+
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+__all__ = [
+    "triangles",
+    "average_clustering",
+    "clustering",
+    "transitivity",
+    "square_clustering",
+    "generalized_degree",
+]
+
+
+@not_implemented_for("directed")
+@nx._dispatch
+def triangles(G, nodes=None):
+    """Compute the number of triangles.
+
+    Finds the number of triangles that include a node as one vertex.
+
+    Parameters
+    ----------
+    G : graph
+       A networkx graph
+
+    nodes : node, iterable of nodes, or None (default=None)
+        If a singleton node, return the number of triangles for that node.
+        If an iterable, compute the number of triangles for each of those nodes.
+        If `None` (the default) compute the number of triangles for all nodes in `G`.
+
+    Returns
+    -------
+    out : dict or int
+       If `nodes` is a container of nodes, returns number of triangles keyed by node (dict).
+       If `nodes` is a specific node, returns number of triangles for the node (int).
+
+    Examples
+    --------
+    >>> G = nx.complete_graph(5)
+    >>> print(nx.triangles(G, 0))
+    6
+    >>> print(nx.triangles(G))
+    {0: 6, 1: 6, 2: 6, 3: 6, 4: 6}
+    >>> print(list(nx.triangles(G, [0, 1]).values()))
+    [6, 6]
+
+    Notes
+    -----
+    Self loops are ignored.
+
+    """
+    if nodes is not None:
+        # If `nodes` represents a single node, return only its number of triangles
+        if nodes in G:
+            return next(_triangles_and_degree_iter(G, nodes))[2] // 2
+
+        # if `nodes` is a container of nodes, then return a
+        # dictionary mapping node to number of triangles.
+        return {v: t // 2 for v, d, t, _ in _triangles_and_degree_iter(G, nodes)}
+
+    # if nodes is None, then compute triangles for the complete graph
+
+    # dict used to avoid visiting the same nodes twice
+    # this allows calculating/counting each triangle only once
+    later_neighbors = {}
+
+    # iterate over the nodes in a graph
+    for node, neighbors in G.adjacency():
+        later_neighbors[node] = {
+            n for n in neighbors if n not in later_neighbors and n != node
+        }
+
+    # instantiate Counter for each node to include isolated nodes
+    # add 1 to the count if a nodes neighbor's neighbor is also a neighbor
+    triangle_counts = Counter(dict.fromkeys(G, 0))
+    for node1, neighbors in later_neighbors.items():
+        for node2 in neighbors:
+            third_nodes = neighbors & later_neighbors[node2]
+            m = len(third_nodes)
+            triangle_counts[node1] += m
+            triangle_counts[node2] += m
+            triangle_counts.update(third_nodes)
+
+    return dict(triangle_counts)
+
+
+@not_implemented_for("multigraph")
+def _triangles_and_degree_iter(G, nodes=None):
+    """Return an iterator of (node, degree, triangles, generalized degree).
+
+    This double counts triangles so you may want to divide by 2.
+    See degree(), triangles() and generalized_degree() for definitions
+    and details.
+
+    """
+    if nodes is None:
+        nodes_nbrs = G.adj.items()
+    else:
+        nodes_nbrs = ((n, G[n]) for n in G.nbunch_iter(nodes))
+
+    for v, v_nbrs in nodes_nbrs:
+        vs = set(v_nbrs) - {v}
+        gen_degree = Counter(len(vs & (set(G[w]) - {w})) for w in vs)
+        ntriangles = sum(k * val for k, val in gen_degree.items())
+        yield (v, len(vs), ntriangles, gen_degree)
+
+
+@not_implemented_for("multigraph")
+def _weighted_triangles_and_degree_iter(G, nodes=None, weight="weight"):
+    """Return an iterator of (node, degree, weighted_triangles).
+
+    Used for weighted clustering.
+    Note: this returns the geometric average weight of edges in the triangle.
+    Also, each triangle is counted twice (each direction).
+    So you may want to divide by 2.
+
+    """
+    import numpy as np
+
+    if weight is None or G.number_of_edges() == 0:
+        max_weight = 1
+    else:
+        max_weight = max(d.get(weight, 1) for u, v, d in G.edges(data=True))
+    if nodes is None:
+        nodes_nbrs = G.adj.items()
+    else:
+        nodes_nbrs = ((n, G[n]) for n in G.nbunch_iter(nodes))
+
+    def wt(u, v):
+        return G[u][v].get(weight, 1) / max_weight
+
+    for i, nbrs in nodes_nbrs:
+        inbrs = set(nbrs) - {i}
+        weighted_triangles = 0
+        seen = set()
+        for j in inbrs:
+            seen.add(j)
+            # This avoids counting twice -- we double at the end.
+            jnbrs = set(G[j]) - seen
+            # Only compute the edge weight once, before the inner inner
+            # loop.
+            wij = wt(i, j)
+            weighted_triangles += sum(
+                np.cbrt([(wij * wt(j, k) * wt(k, i)) for k in inbrs & jnbrs])
+            )
+        yield (i, len(inbrs), 2 * weighted_triangles)
+
+
+@not_implemented_for("multigraph")
+def _directed_triangles_and_degree_iter(G, nodes=None):
+    """Return an iterator of
+    (node, total_degree, reciprocal_degree, directed_triangles).
+
+    Used for directed clustering.
+    Note that unlike `_triangles_and_degree_iter()`, this function counts
+    directed triangles so does not count triangles twice.
+
+    """
+    nodes_nbrs = ((n, G._pred[n], G._succ[n]) for n in G.nbunch_iter(nodes))
+
+    for i, preds, succs in nodes_nbrs:
+        ipreds = set(preds) - {i}
+        isuccs = set(succs) - {i}
+
+        directed_triangles = 0
+        for j in chain(ipreds, isuccs):
+            jpreds = set(G._pred[j]) - {j}
+            jsuccs = set(G._succ[j]) - {j}
+            directed_triangles += sum(
+                1
+                for k in chain(
+                    (ipreds & jpreds),
+                    (ipreds & jsuccs),
+                    (isuccs & jpreds),
+                    (isuccs & jsuccs),
+                )
+            )
+        dtotal = len(ipreds) + len(isuccs)
+        dbidirectional = len(ipreds & isuccs)
+        yield (i, dtotal, dbidirectional, directed_triangles)
+
+
+@not_implemented_for("multigraph")
+def _directed_weighted_triangles_and_degree_iter(G, nodes=None, weight="weight"):
+    """Return an iterator of
+    (node, total_degree, reciprocal_degree, directed_weighted_triangles).
+
+    Used for directed weighted clustering.
+    Note that unlike `_weighted_triangles_and_degree_iter()`, this function counts
+    directed triangles so does not count triangles twice.
+
+    """
+    import numpy as np
+
+    if weight is None or G.number_of_edges() == 0:
+        max_weight = 1
+    else:
+        max_weight = max(d.get(weight, 1) for u, v, d in G.edges(data=True))
+
+    nodes_nbrs = ((n, G._pred[n], G._succ[n]) for n in G.nbunch_iter(nodes))
+
+    def wt(u, v):
+        return G[u][v].get(weight, 1) / max_weight
+
+    for i, preds, succs in nodes_nbrs:
+        ipreds = set(preds) - {i}
+        isuccs = set(succs) - {i}
+
+        directed_triangles = 0
+        for j in ipreds:
+            jpreds = set(G._pred[j]) - {j}
+            jsuccs = set(G._succ[j]) - {j}
+            directed_triangles += sum(
+                np.cbrt([(wt(j, i) * wt(k, i) * wt(k, j)) for k in ipreds & jpreds])
+            )
+            directed_triangles += sum(
+                np.cbrt([(wt(j, i) * wt(k, i) * wt(j, k)) for k in ipreds & jsuccs])
+            )
+            directed_triangles += sum(
+                np.cbrt([(wt(j, i) * wt(i, k) * wt(k, j)) for k in isuccs & jpreds])
+            )
+            directed_triangles += sum(
+                np.cbrt([(wt(j, i) * wt(i, k) * wt(j, k)) for k in isuccs & jsuccs])
+            )
+
+        for j in isuccs:
+            jpreds = set(G._pred[j]) - {j}
+            jsuccs = set(G._succ[j]) - {j}
+            directed_triangles += sum(
+                np.cbrt([(wt(i, j) * wt(k, i) * wt(k, j)) for k in ipreds & jpreds])
+            )
+            directed_triangles += sum(
+                np.cbrt([(wt(i, j) * wt(k, i) * wt(j, k)) for k in ipreds & jsuccs])
+            )
+            directed_triangles += sum(
+                np.cbrt([(wt(i, j) * wt(i, k) * wt(k, j)) for k in isuccs & jpreds])
+            )
+            directed_triangles += sum(
+                np.cbrt([(wt(i, j) * wt(i, k) * wt(j, k)) for k in isuccs & jsuccs])
+            )
+
+        dtotal = len(ipreds) + len(isuccs)
+        dbidirectional = len(ipreds & isuccs)
+        yield (i, dtotal, dbidirectional, directed_triangles)
+
+
+@nx._dispatch(edge_attrs="weight")
+def average_clustering(G, nodes=None, weight=None, count_zeros=True):
+    r"""Compute the average clustering coefficient for the graph G.
+
+    The clustering coefficient for the graph is the average,
+
+    .. math::
+
+       C = \frac{1}{n}\sum_{v \in G} c_v,
+
+    where :math:`n` is the number of nodes in `G`.
+
+    Parameters
+    ----------
+    G : graph
+
+    nodes : container of nodes, optional (default=all nodes in G)
+       Compute average clustering for nodes in this container.
+
+    weight : string or None, optional (default=None)
+       The edge attribute that holds the numerical value used as a weight.
+       If None, then each edge has weight 1.
+
+    count_zeros : bool
+       If False include only the nodes with nonzero clustering in the average.
+
+    Returns
+    -------
+    avg : float
+       Average clustering
+
+    Examples
+    --------
+    >>> G = nx.complete_graph(5)
+    >>> print(nx.average_clustering(G))
+    1.0
+
+    Notes
+    -----
+    This is a space saving routine; it might be faster
+    to use the clustering function to get a list and then take the average.
+
+    Self loops are ignored.
+
+    References
+    ----------
+    .. [1] Generalizations of the clustering coefficient to weighted
+       complex networks by J. Saramäki, M. Kivelä, J.-P. Onnela,
+       K. Kaski, and J. Kertész, Physical Review E, 75 027105 (2007).
+       http://jponnela.com/web_documents/a9.pdf
+    .. [2] Marcus Kaiser,  Mean clustering coefficients: the role of isolated
+       nodes and leafs on clustering measures for small-world networks.
+       https://arxiv.org/abs/0802.2512
+    """
+    c = clustering(G, nodes, weight=weight).values()
+    if not count_zeros:
+        c = [v for v in c if abs(v) > 0]
+    return sum(c) / len(c)
+
+
+@nx._dispatch(edge_attrs="weight")
+def clustering(G, nodes=None, weight=None):
+    r"""Compute the clustering coefficient for nodes.
+
+    For unweighted graphs, the clustering of a node :math:`u`
+    is the fraction of possible triangles through that node that exist,
+
+    .. math::
+
+      c_u = \frac{2 T(u)}{deg(u)(deg(u)-1)},
+
+    where :math:`T(u)` is the number of triangles through node :math:`u` and
+    :math:`deg(u)` is the degree of :math:`u`.
+
+    For weighted graphs, there are several ways to define clustering [1]_.
+    the one used here is defined
+    as the geometric average of the subgraph edge weights [2]_,
+
+    .. math::
+
+       c_u = \frac{1}{deg(u)(deg(u)-1))}
+             \sum_{vw} (\hat{w}_{uv} \hat{w}_{uw} \hat{w}_{vw})^{1/3}.
+
+    The edge weights :math:`\hat{w}_{uv}` are normalized by the maximum weight
+    in the network :math:`\hat{w}_{uv} = w_{uv}/\max(w)`.
+
+    The value of :math:`c_u` is assigned to 0 if :math:`deg(u) < 2`.
+
+    Additionally, this weighted definition has been generalized to support negative edge weights [3]_.
+
+    For directed graphs, the clustering is similarly defined as the fraction
+    of all possible directed triangles or geometric average of the subgraph
+    edge weights for unweighted and weighted directed graph respectively [4]_.
+
+    .. math::
+
+       c_u = \frac{T(u)}{2(deg^{tot}(u)(deg^{tot}(u)-1) - 2deg^{\leftrightarrow}(u))},
+
+    where :math:`T(u)` is the number of directed triangles through node
+    :math:`u`, :math:`deg^{tot}(u)` is the sum of in degree and out degree of
+    :math:`u` and :math:`deg^{\leftrightarrow}(u)` is the reciprocal degree of
+    :math:`u`.
+
+
+    Parameters
+    ----------
+    G : graph
+
+    nodes : node, iterable of nodes, or None (default=None)
+        If a singleton node, return the number of triangles for that node.
+        If an iterable, compute the number of triangles for each of those nodes.
+        If `None` (the default) compute the number of triangles for all nodes in `G`.
+
+    weight : string or None, optional (default=None)
+       The edge attribute that holds the numerical value used as a weight.
+       If None, then each edge has weight 1.
+
+    Returns
+    -------
+    out : float, or dictionary
+       Clustering coefficient at specified nodes
+
+    Examples
+    --------
+    >>> G = nx.complete_graph(5)
+    >>> print(nx.clustering(G, 0))
+    1.0
+    >>> print(nx.clustering(G))
+    {0: 1.0, 1: 1.0, 2: 1.0, 3: 1.0, 4: 1.0}
+
+    Notes
+    -----
+    Self loops are ignored.
+
+    References
+    ----------
+    .. [1] Generalizations of the clustering coefficient to weighted
+       complex networks by J. Saramäki, M. Kivelä, J.-P. Onnela,
+       K. Kaski, and J. Kertész, Physical Review E, 75 027105 (2007).
+       http://jponnela.com/web_documents/a9.pdf
+    .. [2] Intensity and coherence of motifs in weighted complex
+       networks by J. P. Onnela, J. Saramäki, J. Kertész, and K. Kaski,
+       Physical Review E, 71(6), 065103 (2005).
+    .. [3] Generalization of Clustering Coefficients to Signed Correlation Networks
+       by G. Costantini and M. Perugini, PloS one, 9(2), e88669 (2014).
+    .. [4] Clustering in complex directed networks by G. Fagiolo,
+       Physical Review E, 76(2), 026107 (2007).
+    """
+    if G.is_directed():
+        if weight is not None:
+            td_iter = _directed_weighted_triangles_and_degree_iter(G, nodes, weight)
+            clusterc = {
+                v: 0 if t == 0 else t / ((dt * (dt - 1) - 2 * db) * 2)
+                for v, dt, db, t in td_iter
+            }
+        else:
+            td_iter = _directed_triangles_and_degree_iter(G, nodes)
+            clusterc = {
+                v: 0 if t == 0 else t / ((dt * (dt - 1) - 2 * db) * 2)
+                for v, dt, db, t in td_iter
+            }
+    else:
+        # The formula 2*T/(d*(d-1)) from docs is t/(d*(d-1)) here b/c t==2*T
+        if weight is not None:
+            td_iter = _weighted_triangles_and_degree_iter(G, nodes, weight)
+            clusterc = {v: 0 if t == 0 else t / (d * (d - 1)) for v, d, t in td_iter}
+        else:
+            td_iter = _triangles_and_degree_iter(G, nodes)
+            clusterc = {v: 0 if t == 0 else t / (d * (d - 1)) for v, d, t, _ in td_iter}
+    if nodes in G:
+        # Return the value of the sole entry in the dictionary.
+        return clusterc[nodes]
+    return clusterc
+
+
+@nx._dispatch
+def transitivity(G):
+    r"""Compute graph transitivity, the fraction of all possible triangles
+    present in G.
+
+    Possible triangles are identified by the number of "triads"
+    (two edges with a shared vertex).
+
+    The transitivity is
+
+    .. math::
+
+        T = 3\frac{\#triangles}{\#triads}.
+
+    Parameters
+    ----------
+    G : graph
+
+    Returns
+    -------
+    out : float
+       Transitivity
+
+    Examples
+    --------
+    >>> G = nx.complete_graph(5)
+    >>> print(nx.transitivity(G))
+    1.0
+    """
+    triangles_contri = [
+        (t, d * (d - 1)) for v, d, t, _ in _triangles_and_degree_iter(G)
+    ]
+    # If the graph is empty
+    if len(triangles_contri) == 0:
+        return 0
+    triangles, contri = map(sum, zip(*triangles_contri))
+    return 0 if triangles == 0 else triangles / contri
+
+
+@nx._dispatch
+def square_clustering(G, nodes=None):
+    r"""Compute the squares clustering coefficient for nodes.
+
+    For each node return the fraction of possible squares that exist at
+    the node [1]_
+
+    .. math::
+       C_4(v) = \frac{ \sum_{u=1}^{k_v}
+       \sum_{w=u+1}^{k_v} q_v(u,w) }{ \sum_{u=1}^{k_v}
+       \sum_{w=u+1}^{k_v} [a_v(u,w) + q_v(u,w)]},
+
+    where :math:`q_v(u,w)` are the number of common neighbors of :math:`u` and
+    :math:`w` other than :math:`v` (ie squares), and :math:`a_v(u,w) = (k_u -
+    (1+q_v(u,w)+\theta_{uv})) + (k_w - (1+q_v(u,w)+\theta_{uw}))`, where
+    :math:`\theta_{uw} = 1` if :math:`u` and :math:`w` are connected and 0
+    otherwise. [2]_
+
+    Parameters
+    ----------
+    G : graph
+
+    nodes : container of nodes, optional (default=all nodes in G)
+       Compute clustering for nodes in this container.
+
+    Returns
+    -------
+    c4 : dictionary
+       A dictionary keyed by node with the square clustering coefficient value.
+
+    Examples
+    --------
+    >>> G = nx.complete_graph(5)
+    >>> print(nx.square_clustering(G, 0))
+    1.0
+    >>> print(nx.square_clustering(G))
+    {0: 1.0, 1: 1.0, 2: 1.0, 3: 1.0, 4: 1.0}
+
+    Notes
+    -----
+    While :math:`C_3(v)` (triangle clustering) gives the probability that
+    two neighbors of node v are connected with each other, :math:`C_4(v)` is
+    the probability that two neighbors of node v share a common
+    neighbor different from v. This algorithm can be applied to both
+    bipartite and unipartite networks.
+
+    References
+    ----------
+    .. [1] Pedro G. Lind, Marta C. González, and Hans J. Herrmann. 2005
+        Cycles and clustering in bipartite networks.
+        Physical Review E (72) 056127.
+    .. [2] Zhang, Peng et al. Clustering Coefficient and Community Structure of
+        Bipartite Networks. Physica A: Statistical Mechanics and its Applications 387.27 (2008): 6869–6875.
+        https://arxiv.org/abs/0710.0117v1
+    """
+    if nodes is None:
+        node_iter = G
+    else:
+        node_iter = G.nbunch_iter(nodes)
+    clustering = {}
+    for v in node_iter:
+        clustering[v] = 0
+        potential = 0
+        for u, w in combinations(G[v], 2):
+            squares = len((set(G[u]) & set(G[w])) - {v})
+            clustering[v] += squares
+            degm = squares + 1
+            if w in G[u]:
+                degm += 1
+            potential += (len(G[u]) - degm) + (len(G[w]) - degm) + squares
+        if potential > 0:
+            clustering[v] /= potential
+    if nodes in G:
+        # Return the value of the sole entry in the dictionary.
+        return clustering[nodes]
+    return clustering
+
+
+@not_implemented_for("directed")
+@nx._dispatch
+def generalized_degree(G, nodes=None):
+    r"""Compute the generalized degree for nodes.
+
+    For each node, the generalized degree shows how many edges of given
+    triangle multiplicity the node is connected to. The triangle multiplicity
+    of an edge is the number of triangles an edge participates in. The
+    generalized degree of node :math:`i` can be written as a vector
+    :math:`\mathbf{k}_i=(k_i^{(0)}, \dotsc, k_i^{(N-2)})` where
+    :math:`k_i^{(j)}` is the number of edges attached to node :math:`i` that
+    participate in :math:`j` triangles.
+
+    Parameters
+    ----------
+    G : graph
+
+    nodes : container of nodes, optional (default=all nodes in G)
+       Compute the generalized degree for nodes in this container.
+
+    Returns
+    -------
+    out : Counter, or dictionary of Counters
+       Generalized degree of specified nodes. The Counter is keyed by edge
+       triangle multiplicity.
+
+    Examples
+    --------
+    >>> G = nx.complete_graph(5)
+    >>> print(nx.generalized_degree(G, 0))
+    Counter({3: 4})
+    >>> print(nx.generalized_degree(G))
+    {0: Counter({3: 4}), 1: Counter({3: 4}), 2: Counter({3: 4}), 3: Counter({3: 4}), 4: Counter({3: 4})}
+
+    To recover the number of triangles attached to a node:
+
+    >>> k1 = nx.generalized_degree(G, 0)
+    >>> sum([k * v for k, v in k1.items()]) / 2 == nx.triangles(G, 0)
+    True
+
+    Notes
+    -----
+    In a network of N nodes, the highest triangle multiplicity an edge can have
+    is N-2.
+
+    The return value does not include a `zero` entry if no edges of a
+    particular triangle multiplicity are present.
+
+    The number of triangles node :math:`i` is attached to can be recovered from
+    the generalized degree :math:`\mathbf{k}_i=(k_i^{(0)}, \dotsc,
+    k_i^{(N-2)})` by :math:`(k_i^{(1)}+2k_i^{(2)}+\dotsc +(N-2)k_i^{(N-2)})/2`.
+
+    References
+    ----------
+    .. [1] Networks with arbitrary edge multiplicities by V. Zlatić,
+        D. Garlaschelli and G. Caldarelli, EPL (Europhysics Letters),
+        Volume 97, Number 2 (2012).
+        https://iopscience.iop.org/article/10.1209/0295-5075/97/28005
+    """
+    if nodes in G:
+        return next(_triangles_and_degree_iter(G, nodes))[3]
+    return {v: gd for v, d, t, gd in _triangles_and_degree_iter(G, nodes)}

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/community/centrality.py

@@ -0,0 +1,171 @@
+"""Functions for computing communities based on centrality notions."""
+
+import networkx as nx
+
+__all__ = ["girvan_newman"]
+
+
+@nx._dispatch(preserve_edge_attrs="most_valuable_edge")
+def girvan_newman(G, most_valuable_edge=None):
+    """Finds communities in a graph using the Girvan–Newman method.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    most_valuable_edge : function
+        Function that takes a graph as input and outputs an edge. The
+        edge returned by this function will be recomputed and removed at
+        each iteration of the algorithm.
+
+        If not specified, the edge with the highest
+        :func:`networkx.edge_betweenness_centrality` will be used.
+
+    Returns
+    -------
+    iterator
+        Iterator over tuples of sets of nodes in `G`. Each set of node
+        is a community, each tuple is a sequence of communities at a
+        particular level of the algorithm.
+
+    Examples
+    --------
+    To get the first pair of communities::
+
+        >>> G = nx.path_graph(10)
+        >>> comp = nx.community.girvan_newman(G)
+        >>> tuple(sorted(c) for c in next(comp))
+        ([0, 1, 2, 3, 4], [5, 6, 7, 8, 9])
+
+    To get only the first *k* tuples of communities, use
+    :func:`itertools.islice`::
+
+        >>> import itertools
+        >>> G = nx.path_graph(8)
+        >>> k = 2
+        >>> comp = nx.community.girvan_newman(G)
+        >>> for communities in itertools.islice(comp, k):
+        ...     print(tuple(sorted(c) for c in communities))
+        ...
+        ([0, 1, 2, 3], [4, 5, 6, 7])
+        ([0, 1], [2, 3], [4, 5, 6, 7])
+
+    To stop getting tuples of communities once the number of communities
+    is greater than *k*, use :func:`itertools.takewhile`::
+
+        >>> import itertools
+        >>> G = nx.path_graph(8)
+        >>> k = 4
+        >>> comp = nx.community.girvan_newman(G)
+        >>> limited = itertools.takewhile(lambda c: len(c) <= k, comp)
+        >>> for communities in limited:
+        ...     print(tuple(sorted(c) for c in communities))
+        ...
+        ([0, 1, 2, 3], [4, 5, 6, 7])
+        ([0, 1], [2, 3], [4, 5, 6, 7])
+        ([0, 1], [2, 3], [4, 5], [6, 7])
+
+    To just choose an edge to remove based on the weight::
+
+        >>> from operator import itemgetter
+        >>> G = nx.path_graph(10)
+        >>> edges = G.edges()
+        >>> nx.set_edge_attributes(G, {(u, v): v for u, v in edges}, "weight")
+        >>> def heaviest(G):
+        ...     u, v, w = max(G.edges(data="weight"), key=itemgetter(2))
+        ...     return (u, v)
+        ...
+        >>> comp = nx.community.girvan_newman(G, most_valuable_edge=heaviest)
+        >>> tuple(sorted(c) for c in next(comp))
+        ([0, 1, 2, 3, 4, 5, 6, 7, 8], [9])
+
+    To utilize edge weights when choosing an edge with, for example, the
+    highest betweenness centrality::
+
+        >>> from networkx import edge_betweenness_centrality as betweenness
+        >>> def most_central_edge(G):
+        ...     centrality = betweenness(G, weight="weight")
+        ...     return max(centrality, key=centrality.get)
+        ...
+        >>> G = nx.path_graph(10)
+        >>> comp = nx.community.girvan_newman(G, most_valuable_edge=most_central_edge)
+        >>> tuple(sorted(c) for c in next(comp))
+        ([0, 1, 2, 3, 4], [5, 6, 7, 8, 9])
+
+    To specify a different ranking algorithm for edges, use the
+    `most_valuable_edge` keyword argument::
+
+        >>> from networkx import edge_betweenness_centrality
+        >>> from random import random
+        >>> def most_central_edge(G):
+        ...     centrality = edge_betweenness_centrality(G)
+        ...     max_cent = max(centrality.values())
+        ...     # Scale the centrality values so they are between 0 and 1,
+        ...     # and add some random noise.
+        ...     centrality = {e: c / max_cent for e, c in centrality.items()}
+        ...     # Add some random noise.
+        ...     centrality = {e: c + random() for e, c in centrality.items()}
+        ...     return max(centrality, key=centrality.get)
+        ...
+        >>> G = nx.path_graph(10)
+        >>> comp = nx.community.girvan_newman(G, most_valuable_edge=most_central_edge)
+
+    Notes
+    -----
+    The Girvan–Newman algorithm detects communities by progressively
+    removing edges from the original graph. The algorithm removes the
+    "most valuable" edge, traditionally the edge with the highest
+    betweenness centrality, at each step. As the graph breaks down into
+    pieces, the tightly knit community structure is exposed and the
+    result can be depicted as a dendrogram.
+
+    """
+    # If the graph is already empty, simply return its connected
+    # components.
+    if G.number_of_edges() == 0:
+        yield tuple(nx.connected_components(G))
+        return
+    # If no function is provided for computing the most valuable edge,
+    # use the edge betweenness centrality.
+    if most_valuable_edge is None:
+
+        def most_valuable_edge(G):
+            """Returns the edge with the highest betweenness centrality
+            in the graph `G`.
+
+            """
+            # We have guaranteed that the graph is non-empty, so this
+            # dictionary will never be empty.
+            betweenness = nx.edge_betweenness_centrality(G)
+            return max(betweenness, key=betweenness.get)
+
+    # The copy of G here must include the edge weight data.
+    g = G.copy().to_undirected()
+    # Self-loops must be removed because their removal has no effect on
+    # the connected components of the graph.
+    g.remove_edges_from(nx.selfloop_edges(g))
+    while g.number_of_edges() > 0:
+        yield _without_most_central_edges(g, most_valuable_edge)
+
+
+def _without_most_central_edges(G, most_valuable_edge):
+    """Returns the connected components of the graph that results from
+    repeatedly removing the most "valuable" edge in the graph.
+
+    `G` must be a non-empty graph. This function modifies the graph `G`
+    in-place; that is, it removes edges on the graph `G`.
+
+    `most_valuable_edge` is a function that takes the graph `G` as input
+    (or a subgraph with one or more edges of `G` removed) and returns an
+    edge. That edge will be removed and this process will be repeated
+    until the number of connected components in the graph increases.
+
+    """
+    original_num_components = nx.number_connected_components(G)
+    num_new_components = original_num_components
+    while num_new_components <= original_num_components:
+        edge = most_valuable_edge(G)
+        G.remove_edge(*edge)
+        new_components = tuple(nx.connected_components(G))
+        num_new_components = len(new_components)
+    return new_components

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/community/louvain.py

@@ -0,0 +1,373 @@
+"""Function for detecting communities based on Louvain Community Detection
+Algorithm"""
+
+from collections import defaultdict, deque
+
+import networkx as nx
+from networkx.algorithms.community import modularity
+from networkx.utils import py_random_state
+
+__all__ = ["louvain_communities", "louvain_partitions"]
+
+
+@py_random_state("seed")
+@nx._dispatch(edge_attrs="weight")
+def louvain_communities(
+    G, weight="weight", resolution=1, threshold=0.0000001, seed=None
+):
+    r"""Find the best partition of a graph using the Louvain Community Detection
+    Algorithm.
+
+    Louvain Community Detection Algorithm is a simple method to extract the community
+    structure of a network. This is a heuristic method based on modularity optimization. [1]_
+
+    The algorithm works in 2 steps. On the first step it assigns every node to be
+    in its own community and then for each node it tries to find the maximum positive
+    modularity gain by moving each node to all of its neighbor communities. If no positive
+    gain is achieved the node remains in its original community.
+
+    The modularity gain obtained by moving an isolated node $i$ into a community $C$ can
+    easily be calculated by the following formula (combining [1]_ [2]_ and some algebra):
+
+    .. math::
+        \Delta Q = \frac{k_{i,in}}{2m} - \gamma\frac{ \Sigma_{tot} \cdot k_i}{2m^2}
+
+    where $m$ is the size of the graph, $k_{i,in}$ is the sum of the weights of the links
+    from $i$ to nodes in $C$, $k_i$ is the sum of the weights of the links incident to node $i$,
+    $\Sigma_{tot}$ is the sum of the weights of the links incident to nodes in $C$ and $\gamma$
+    is the resolution parameter.
+
+    For the directed case the modularity gain can be computed using this formula according to [3]_
+
+    .. math::
+        \Delta Q = \frac{k_{i,in}}{m}
+        - \gamma\frac{k_i^{out} \cdot\Sigma_{tot}^{in} + k_i^{in} \cdot \Sigma_{tot}^{out}}{m^2}
+
+    where $k_i^{out}$, $k_i^{in}$ are the outer and inner weighted degrees of node $i$ and
+    $\Sigma_{tot}^{in}$, $\Sigma_{tot}^{out}$ are the sum of in-going and out-going links incident
+    to nodes in $C$.
+
+    The first phase continues until no individual move can improve the modularity.
+
+    The second phase consists in building a new network whose nodes are now the communities
+    found in the first phase. To do so, the weights of the links between the new nodes are given by
+    the sum of the weight of the links between nodes in the corresponding two communities. Once this
+    phase is complete it is possible to reapply the first phase creating bigger communities with
+    increased modularity.
+
+    The above two phases are executed until no modularity gain is achieved (or is less than
+    the `threshold`).
+
+    Be careful with self-loops in the input graph. These are treated as
+    previously reduced communities -- as if the process had been started
+    in the middle of the algorithm. Large self-loop edge weights thus
+    represent strong communities and in practice may be hard to add
+    other nodes to.  If your input graph edge weights for self-loops
+    do not represent already reduced communities you may want to remove
+    the self-loops before inputting that graph.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+    weight : string or None, optional (default="weight")
+        The name of an edge attribute that holds the numerical value
+        used as a weight. If None then each edge has weight 1.
+    resolution : float, optional (default=1)
+        If resolution is less than 1, the algorithm favors larger communities.
+        Greater than 1 favors smaller communities
+    threshold : float, optional (default=0.0000001)
+        Modularity gain threshold for each level. If the gain of modularity
+        between 2 levels of the algorithm is less than the given threshold
+        then the algorithm stops and returns the resulting communities.
+    seed : integer, random_state, or None (default)
+        Indicator of random number generation state.
+        See :ref:`Randomness<randomness>`.
+
+    Returns
+    -------
+    list
+        A list of sets (partition of `G`). Each set represents one community and contains
+        all the nodes that constitute it.
+
+    Examples
+    --------
+    >>> import networkx as nx
+    >>> G = nx.petersen_graph()
+    >>> nx.community.louvain_communities(G, seed=123)
+    [{0, 4, 5, 7, 9}, {1, 2, 3, 6, 8}]
+
+    Notes
+    -----
+    The order in which the nodes are considered can affect the final output. In the algorithm
+    the ordering happens using a random shuffle.
+
+    References
+    ----------
+    .. [1] Blondel, V.D. et al. Fast unfolding of communities in
+       large networks. J. Stat. Mech 10008, 1-12(2008). https://doi.org/10.1088/1742-5468/2008/10/P10008
+    .. [2] Traag, V.A., Waltman, L. & van Eck, N.J. From Louvain to Leiden: guaranteeing
+       well-connected communities. Sci Rep 9, 5233 (2019). https://doi.org/10.1038/s41598-019-41695-z
+    .. [3] Nicolas Dugué, Anthony Perez. Directed Louvain : maximizing modularity in directed networks.
+        [Research Report] Université d’Orléans. 2015. hal-01231784. https://hal.archives-ouvertes.fr/hal-01231784
+
+    See Also
+    --------
+    louvain_partitions
+    """
+
+    d = louvain_partitions(G, weight, resolution, threshold, seed)
+    q = deque(d, maxlen=1)
+    return q.pop()
+
+
+@py_random_state("seed")
+@nx._dispatch(edge_attrs="weight")
+def louvain_partitions(
+    G, weight="weight", resolution=1, threshold=0.0000001, seed=None
+):
+    """Yields partitions for each level of the Louvain Community Detection Algorithm
+
+    Louvain Community Detection Algorithm is a simple method to extract the community
+    structure of a network. This is a heuristic method based on modularity optimization. [1]_
+
+    The partitions at each level (step of the algorithm) form a dendrogram of communities.
+    A dendrogram is a diagram representing a tree and each level represents
+    a partition of the G graph. The top level contains the smallest communities
+    and as you traverse to the bottom of the tree the communities get bigger
+    and the overall modularity increases making the partition better.
+
+    Each level is generated by executing the two phases of the Louvain Community
+    Detection Algorithm.
+
+    Be careful with self-loops in the input graph. These are treated as
+    previously reduced communities -- as if the process had been started
+    in the middle of the algorithm. Large self-loop edge weights thus
+    represent strong communities and in practice may be hard to add
+    other nodes to.  If your input graph edge weights for self-loops
+    do not represent already reduced communities you may want to remove
+    the self-loops before inputting that graph.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+    weight : string or None, optional (default="weight")
+     The name of an edge attribute that holds the numerical value
+     used as a weight. If None then each edge has weight 1.
+    resolution : float, optional (default=1)
+        If resolution is less than 1, the algorithm favors larger communities.
+        Greater than 1 favors smaller communities
+    threshold : float, optional (default=0.0000001)
+     Modularity gain threshold for each level. If the gain of modularity
+     between 2 levels of the algorithm is less than the given threshold
+     then the algorithm stops and returns the resulting communities.
+    seed : integer, random_state, or None (default)
+     Indicator of random number generation state.
+     See :ref:`Randomness<randomness>`.
+
+    Yields
+    ------
+    list
+        A list of sets (partition of `G`). Each set represents one community and contains
+        all the nodes that constitute it.
+
+    References
+    ----------
+    .. [1] Blondel, V.D. et al. Fast unfolding of communities in
+       large networks. J. Stat. Mech 10008, 1-12(2008)
+
+    See Also
+    --------
+    louvain_communities
+    """
+
+    partition = [{u} for u in G.nodes()]
+    if nx.is_empty(G):
+        yield partition
+        return
+    mod = modularity(G, partition, resolution=resolution, weight=weight)
+    is_directed = G.is_directed()
+    if G.is_multigraph():
+        graph = _convert_multigraph(G, weight, is_directed)
+    else:
+        graph = G.__class__()
+        graph.add_nodes_from(G)
+        graph.add_weighted_edges_from(G.edges(data=weight, default=1))
+
+    m = graph.size(weight="weight")
+    partition, inner_partition, improvement = _one_level(
+        graph, m, partition, resolution, is_directed, seed
+    )
+    improvement = True
+    while improvement:
+        # gh-5901 protect the sets in the yielded list from further manipulation here
+        yield [s.copy() for s in partition]
+        new_mod = modularity(
+            graph, inner_partition, resolution=resolution, weight="weight"
+        )
+        if new_mod - mod <= threshold:
+            return
+        mod = new_mod
+        graph = _gen_graph(graph, inner_partition)
+        partition, inner_partition, improvement = _one_level(
+            graph, m, partition, resolution, is_directed, seed
+        )
+
+
+def _one_level(G, m, partition, resolution=1, is_directed=False, seed=None):
+    """Calculate one level of the Louvain partitions tree
+
+    Parameters
+    ----------
+    G : NetworkX Graph/DiGraph
+        The graph from which to detect communities
+    m : number
+        The size of the graph `G`.
+    partition : list of sets of nodes
+        A valid partition of the graph `G`
+    resolution : positive number
+        The resolution parameter for computing the modularity of a partition
+    is_directed : bool
+        True if `G` is a directed graph.
+    seed : integer, random_state, or None (default)
+        Indicator of random number generation state.
+        See :ref:`Randomness<randomness>`.
+
+    """
+    node2com = {u: i for i, u in enumerate(G.nodes())}
+    inner_partition = [{u} for u in G.nodes()]
+    if is_directed:
+        in_degrees = dict(G.in_degree(weight="weight"))
+        out_degrees = dict(G.out_degree(weight="weight"))
+        Stot_in = list(in_degrees.values())
+        Stot_out = list(out_degrees.values())
+        # Calculate weights for both in and out neighbours without considering self-loops
+        nbrs = {}
+        for u in G:
+            nbrs[u] = defaultdict(float)
+            for _, n, wt in G.out_edges(u, data="weight"):
+                if u != n:
+                    nbrs[u][n] += wt
+            for n, _, wt in G.in_edges(u, data="weight"):
+                if u != n:
+                    nbrs[u][n] += wt
+    else:
+        degrees = dict(G.degree(weight="weight"))
+        Stot = list(degrees.values())
+        nbrs = {u: {v: data["weight"] for v, data in G[u].items() if v != u} for u in G}
+    rand_nodes = list(G.nodes)
+    seed.shuffle(rand_nodes)
+    nb_moves = 1
+    improvement = False
+    while nb_moves > 0:
+        nb_moves = 0
+        for u in rand_nodes:
+            best_mod = 0
+            best_com = node2com[u]
+            weights2com = _neighbor_weights(nbrs[u], node2com)
+            if is_directed:
+                in_degree = in_degrees[u]
+                out_degree = out_degrees[u]
+                Stot_in[best_com] -= in_degree
+                Stot_out[best_com] -= out_degree
+                remove_cost = (
+                    -weights2com[best_com] / m
+                    + resolution
+                    * (out_degree * Stot_in[best_com] + in_degree * Stot_out[best_com])
+                    / m**2
+                )
+            else:
+                degree = degrees[u]
+                Stot[best_com] -= degree
+                remove_cost = -weights2com[best_com] / m + resolution * (
+                    Stot[best_com] * degree
+                ) / (2 * m**2)
+            for nbr_com, wt in weights2com.items():
+                if is_directed:
+                    gain = (
+                        remove_cost
+                        + wt / m
+                        - resolution
+                        * (
+                            out_degree * Stot_in[nbr_com]
+                            + in_degree * Stot_out[nbr_com]
+                        )
+                        / m**2
+                    )
+                else:
+                    gain = (
+                        remove_cost
+                        + wt / m
+                        - resolution * (Stot[nbr_com] * degree) / (2 * m**2)
+                    )
+                if gain > best_mod:
+                    best_mod = gain
+                    best_com = nbr_com
+            if is_directed:
+                Stot_in[best_com] += in_degree
+                Stot_out[best_com] += out_degree
+            else:
+                Stot[best_com] += degree
+            if best_com != node2com[u]:
+                com = G.nodes[u].get("nodes", {u})
+                partition[node2com[u]].difference_update(com)
+                inner_partition[node2com[u]].remove(u)
+                partition[best_com].update(com)
+                inner_partition[best_com].add(u)
+                improvement = True
+                nb_moves += 1
+                node2com[u] = best_com
+    partition = list(filter(len, partition))
+    inner_partition = list(filter(len, inner_partition))
+    return partition, inner_partition, improvement
+
+
+def _neighbor_weights(nbrs, node2com):
+    """Calculate weights between node and its neighbor communities.
+
+    Parameters
+    ----------
+    nbrs : dictionary
+           Dictionary with nodes' neighbours as keys and their edge weight as value.
+    node2com : dictionary
+           Dictionary with all graph's nodes as keys and their community index as value.
+
+    """
+    weights = defaultdict(float)
+    for nbr, wt in nbrs.items():
+        weights[node2com[nbr]] += wt
+    return weights
+
+
+def _gen_graph(G, partition):
+    """Generate a new graph based on the partitions of a given graph"""
+    H = G.__class__()
+    node2com = {}
+    for i, part in enumerate(partition):
+        nodes = set()
+        for node in part:
+            node2com[node] = i
+            nodes.update(G.nodes[node].get("nodes", {node}))
+        H.add_node(i, nodes=nodes)
+
+    for node1, node2, wt in G.edges(data=True):
+        wt = wt["weight"]
+        com1 = node2com[node1]
+        com2 = node2com[node2]
+        temp = H.get_edge_data(com1, com2, {"weight": 0})["weight"]
+        H.add_edge(com1, com2, weight=wt + temp)
+    return H
+
+
+def _convert_multigraph(G, weight, is_directed):
+    """Convert a Multigraph to normal Graph"""
+    if is_directed:
+        H = nx.DiGraph()
+    else:
+        H = nx.Graph()
+    H.add_nodes_from(G)
+    for u, v, wt in G.edges(data=weight, default=1):
+        if H.has_edge(u, v):
+            H[u][v]["weight"] += wt
+        else:
+            H.add_edge(u, v, weight=wt)
+    return H

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/dag.py

@@ -0,0 +1,1258 @@
+"""Algorithms for directed acyclic graphs (DAGs).
+
+Note that most of these functions are only guaranteed to work for DAGs.
+In general, these functions do not check for acyclic-ness, so it is up
+to the user to check for that.
+"""
+
+import heapq
+from collections import deque
+from functools import partial
+from itertools import chain, combinations, product, starmap
+from math import gcd
+
+import networkx as nx
+from networkx.utils import arbitrary_element, not_implemented_for, pairwise
+
+__all__ = [
+    "descendants",
+    "ancestors",
+    "topological_sort",
+    "lexicographical_topological_sort",
+    "all_topological_sorts",
+    "topological_generations",
+    "is_directed_acyclic_graph",
+    "is_aperiodic",
+    "transitive_closure",
+    "transitive_closure_dag",
+    "transitive_reduction",
+    "antichains",
+    "dag_longest_path",
+    "dag_longest_path_length",
+    "dag_to_branching",
+    "compute_v_structures",
+]
+
+chaini = chain.from_iterable
+
+
+@nx._dispatch
+def descendants(G, source):
+    """Returns all nodes reachable from `source` in `G`.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+    source : node in `G`
+
+    Returns
+    -------
+    set()
+        The descendants of `source` in `G`
+
+    Raises
+    ------
+    NetworkXError
+        If node `source` is not in `G`.
+
+    Examples
+    --------
+    >>> DG = nx.path_graph(5, create_using=nx.DiGraph)
+    >>> sorted(nx.descendants(DG, 2))
+    [3, 4]
+
+    The `source` node is not a descendant of itself, but can be included manually:
+
+    >>> sorted(nx.descendants(DG, 2) | {2})
+    [2, 3, 4]
+
+    See also
+    --------
+    ancestors
+    """
+    return {child for parent, child in nx.bfs_edges(G, source)}
+
+
+@nx._dispatch
+def ancestors(G, source):
+    """Returns all nodes having a path to `source` in `G`.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+    source : node in `G`
+
+    Returns
+    -------
+    set()
+        The ancestors of `source` in `G`
+
+    Raises
+    ------
+    NetworkXError
+        If node `source` is not in `G`.
+
+    Examples
+    --------
+    >>> DG = nx.path_graph(5, create_using=nx.DiGraph)
+    >>> sorted(nx.ancestors(DG, 2))
+    [0, 1]
+
+    The `source` node is not an ancestor of itself, but can be included manually:
+
+    >>> sorted(nx.ancestors(DG, 2) | {2})
+    [0, 1, 2]
+
+    See also
+    --------
+    descendants
+    """
+    return {child for parent, child in nx.bfs_edges(G, source, reverse=True)}
+
+
+@nx._dispatch
+def has_cycle(G):
+    """Decides whether the directed graph has a cycle."""
+    try:
+        # Feed the entire iterator into a zero-length deque.
+        deque(topological_sort(G), maxlen=0)
+    except nx.NetworkXUnfeasible:
+        return True
+    else:
+        return False
+
+
+@nx._dispatch
+def is_directed_acyclic_graph(G):
+    """Returns True if the graph `G` is a directed acyclic graph (DAG) or
+    False if not.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    Returns
+    -------
+    bool
+        True if `G` is a DAG, False otherwise
+
+    Examples
+    --------
+    Undirected graph::
+
+        >>> G = nx.Graph([(1, 2), (2, 3)])
+        >>> nx.is_directed_acyclic_graph(G)
+        False
+
+    Directed graph with cycle::
+
+        >>> G = nx.DiGraph([(1, 2), (2, 3), (3, 1)])
+        >>> nx.is_directed_acyclic_graph(G)
+        False
+
+    Directed acyclic graph::
+
+        >>> G = nx.DiGraph([(1, 2), (2, 3)])
+        >>> nx.is_directed_acyclic_graph(G)
+        True
+
+    See also
+    --------
+    topological_sort
+    """
+    return G.is_directed() and not has_cycle(G)
+
+
+@nx._dispatch
+def topological_generations(G):
+    """Stratifies a DAG into generations.
+
+    A topological generation is node collection in which ancestors of a node in each
+    generation are guaranteed to be in a previous generation, and any descendants of
+    a node are guaranteed to be in a following generation. Nodes are guaranteed to
+    be in the earliest possible generation that they can belong to.
+
+    Parameters
+    ----------
+    G : NetworkX digraph
+        A directed acyclic graph (DAG)
+
+    Yields
+    ------
+    sets of nodes
+        Yields sets of nodes representing each generation.
+
+    Raises
+    ------
+    NetworkXError
+        Generations are defined for directed graphs only. If the graph
+        `G` is undirected, a :exc:`NetworkXError` is raised.
+
+    NetworkXUnfeasible
+        If `G` is not a directed acyclic graph (DAG) no topological generations
+        exist and a :exc:`NetworkXUnfeasible` exception is raised.  This can also
+        be raised if `G` is changed while the returned iterator is being processed
+
+    RuntimeError
+        If `G` is changed while the returned iterator is being processed.
+
+    Examples
+    --------
+    >>> DG = nx.DiGraph([(2, 1), (3, 1)])
+    >>> [sorted(generation) for generation in nx.topological_generations(DG)]
+    [[2, 3], [1]]
+
+    Notes
+    -----
+    The generation in which a node resides can also be determined by taking the
+    max-path-distance from the node to the farthest leaf node. That value can
+    be obtained with this function using `enumerate(topological_generations(G))`.
+
+    See also
+    --------
+    topological_sort
+    """
+    if not G.is_directed():
+        raise nx.NetworkXError("Topological sort not defined on undirected graphs.")
+
+    multigraph = G.is_multigraph()
+    indegree_map = {v: d for v, d in G.in_degree() if d > 0}
+    zero_indegree = [v for v, d in G.in_degree() if d == 0]
+
+    while zero_indegree:
+        this_generation = zero_indegree
+        zero_indegree = []
+        for node in this_generation:
+            if node not in G:
+                raise RuntimeError("Graph changed during iteration")
+            for child in G.neighbors(node):
+                try:
+                    indegree_map[child] -= len(G[node][child]) if multigraph else 1
+                except KeyError as err:
+                    raise RuntimeError("Graph changed during iteration") from err
+                if indegree_map[child] == 0:
+                    zero_indegree.append(child)
+                    del indegree_map[child]
+        yield this_generation
+
+    if indegree_map:
+        raise nx.NetworkXUnfeasible(
+            "Graph contains a cycle or graph changed during iteration"
+        )
+
+
+@nx._dispatch
+def topological_sort(G):
+    """Returns a generator of nodes in topologically sorted order.
+
+    A topological sort is a nonunique permutation of the nodes of a
+    directed graph such that an edge from u to v implies that u
+    appears before v in the topological sort order. This ordering is
+    valid only if the graph has no directed cycles.
+
+    Parameters
+    ----------
+    G : NetworkX digraph
+        A directed acyclic graph (DAG)
+
+    Yields
+    ------
+    nodes
+        Yields the nodes in topological sorted order.
+
+    Raises
+    ------
+    NetworkXError
+        Topological sort is defined for directed graphs only. If the graph `G`
+        is undirected, a :exc:`NetworkXError` is raised.
+
+    NetworkXUnfeasible
+        If `G` is not a directed acyclic graph (DAG) no topological sort exists
+        and a :exc:`NetworkXUnfeasible` exception is raised.  This can also be
+        raised if `G` is changed while the returned iterator is being processed
+
+    RuntimeError
+        If `G` is changed while the returned iterator is being processed.
+
+    Examples
+    --------
+    To get the reverse order of the topological sort:
+
+    >>> DG = nx.DiGraph([(1, 2), (2, 3)])
+    >>> list(reversed(list(nx.topological_sort(DG))))
+    [3, 2, 1]
+
+    If your DiGraph naturally has the edges representing tasks/inputs
+    and nodes representing people/processes that initiate tasks, then
+    topological_sort is not quite what you need. You will have to change
+    the tasks to nodes with dependence reflected by edges. The result is
+    a kind of topological sort of the edges. This can be done
+    with :func:`networkx.line_graph` as follows:
+
+    >>> list(nx.topological_sort(nx.line_graph(DG)))
+    [(1, 2), (2, 3)]
+
+    Notes
+    -----
+    This algorithm is based on a description and proof in
+    "Introduction to Algorithms: A Creative Approach" [1]_ .
+
+    See also
+    --------
+    is_directed_acyclic_graph, lexicographical_topological_sort
+
+    References
+    ----------
+    .. [1] Manber, U. (1989).
+       *Introduction to Algorithms - A Creative Approach.* Addison-Wesley.
+    """
+    for generation in nx.topological_generations(G):
+        yield from generation
+
+
+@nx._dispatch
+def lexicographical_topological_sort(G, key=None):
+    """Generate the nodes in the unique lexicographical topological sort order.
+
+    Generates a unique ordering of nodes by first sorting topologically (for which there are often
+    multiple valid orderings) and then additionally by sorting lexicographically.
+
+    A topological sort arranges the nodes of a directed graph so that the
+    upstream node of each directed edge precedes the downstream node.
+    It is always possible to find a solution for directed graphs that have no cycles.
+    There may be more than one valid solution.
+
+    Lexicographical sorting is just sorting alphabetically. It is used here to break ties in the
+    topological sort and to determine a single, unique ordering.  This can be useful in comparing
+    sort results.
+
+    The lexicographical order can be customized by providing a function to the `key=` parameter.
+    The definition of the key function is the same as used in python's built-in `sort()`.
+    The function takes a single argument and returns a key to use for sorting purposes.
+
+    Lexicographical sorting can fail if the node names are un-sortable. See the example below.
+    The solution is to provide a function to the `key=` argument that returns sortable keys.
+
+
+    Parameters
+    ----------
+    G : NetworkX digraph
+        A directed acyclic graph (DAG)
+
+    key : function, optional
+        A function of one argument that converts a node name to a comparison key.
+        It defines and resolves ambiguities in the sort order.  Defaults to the identity function.
+
+    Yields
+    ------
+    nodes
+        Yields the nodes of G in lexicographical topological sort order.
+
+    Raises
+    ------
+    NetworkXError
+        Topological sort is defined for directed graphs only. If the graph `G`
+        is undirected, a :exc:`NetworkXError` is raised.
+
+    NetworkXUnfeasible
+        If `G` is not a directed acyclic graph (DAG) no topological sort exists
+        and a :exc:`NetworkXUnfeasible` exception is raised.  This can also be
+        raised if `G` is changed while the returned iterator is being processed
+
+    RuntimeError
+        If `G` is changed while the returned iterator is being processed.
+
+    TypeError
+        Results from un-sortable node names.
+        Consider using `key=` parameter to resolve ambiguities in the sort order.
+
+    Examples
+    --------
+    >>> DG = nx.DiGraph([(2, 1), (2, 5), (1, 3), (1, 4), (5, 4)])
+    >>> list(nx.lexicographical_topological_sort(DG))
+    [2, 1, 3, 5, 4]
+    >>> list(nx.lexicographical_topological_sort(DG, key=lambda x: -x))
+    [2, 5, 1, 4, 3]
+
+    The sort will fail for any graph with integer and string nodes. Comparison of integer to strings
+    is not defined in python.  Is 3 greater or less than 'red'?
+
+    >>> DG = nx.DiGraph([(1, 'red'), (3, 'red'), (1, 'green'), (2, 'blue')])
+    >>> list(nx.lexicographical_topological_sort(DG))
+    Traceback (most recent call last):
+    ...
+    TypeError: '<' not supported between instances of 'str' and 'int'
+    ...
+
+    Incomparable nodes can be resolved using a `key` function. This example function
+    allows comparison of integers and strings by returning a tuple where the first
+    element is True for `str`, False otherwise. The second element is the node name.
+    This groups the strings and integers separately so they can be compared only among themselves.
+
+    >>> key = lambda node: (isinstance(node, str), node)
+    >>> list(nx.lexicographical_topological_sort(DG, key=key))
+    [1, 2, 3, 'blue', 'green', 'red']
+
+    Notes
+    -----
+    This algorithm is based on a description and proof in
+    "Introduction to Algorithms: A Creative Approach" [1]_ .
+
+    See also
+    --------
+    topological_sort
+
+    References
+    ----------
+    .. [1] Manber, U. (1989).
+       *Introduction to Algorithms - A Creative Approach.* Addison-Wesley.
+    """
+    if not G.is_directed():
+        msg = "Topological sort not defined on undirected graphs."
+        raise nx.NetworkXError(msg)
+
+    if key is None:
+
+        def key(node):
+            return node
+
+    nodeid_map = {n: i for i, n in enumerate(G)}
+
+    def create_tuple(node):
+        return key(node), nodeid_map[node], node
+
+    indegree_map = {v: d for v, d in G.in_degree() if d > 0}
+    # These nodes have zero indegree and ready to be returned.
+    zero_indegree = [create_tuple(v) for v, d in G.in_degree() if d == 0]
+    heapq.heapify(zero_indegree)
+
+    while zero_indegree:
+        _, _, node = heapq.heappop(zero_indegree)
+
+        if node not in G:
+            raise RuntimeError("Graph changed during iteration")
+        for _, child in G.edges(node):
+            try:
+                indegree_map[child] -= 1
+            except KeyError as err:
+                raise RuntimeError("Graph changed during iteration") from err
+            if indegree_map[child] == 0:
+                try:
+                    heapq.heappush(zero_indegree, create_tuple(child))
+                except TypeError as err:
+                    raise TypeError(
+                        f"{err}\nConsider using `key=` parameter to resolve ambiguities in the sort order."
+                    )
+                del indegree_map[child]
+
+        yield node
+
+    if indegree_map:
+        msg = "Graph contains a cycle or graph changed during iteration"
+        raise nx.NetworkXUnfeasible(msg)
+
+
+@not_implemented_for("undirected")
+@nx._dispatch
+def all_topological_sorts(G):
+    """Returns a generator of _all_ topological sorts of the directed graph G.
+
+    A topological sort is a nonunique permutation of the nodes such that an
+    edge from u to v implies that u appears before v in the topological sort
+    order.
+
+    Parameters
+    ----------
+    G : NetworkX DiGraph
+        A directed graph
+
+    Yields
+    ------
+    topological_sort_order : list
+        a list of nodes in `G`, representing one of the topological sort orders
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If `G` is not directed
+    NetworkXUnfeasible
+        If `G` is not acyclic
+
+    Examples
+    --------
+    To enumerate all topological sorts of directed graph:
+
+    >>> DG = nx.DiGraph([(1, 2), (2, 3), (2, 4)])
+    >>> list(nx.all_topological_sorts(DG))
+    [[1, 2, 4, 3], [1, 2, 3, 4]]
+
+    Notes
+    -----
+    Implements an iterative version of the algorithm given in [1].
+
+    References
+    ----------
+    .. [1] Knuth, Donald E., Szwarcfiter, Jayme L. (1974).
+       "A Structured Program to Generate All Topological Sorting Arrangements"
+       Information Processing Letters, Volume 2, Issue 6, 1974, Pages 153-157,
+       ISSN 0020-0190,
+       https://doi.org/10.1016/0020-0190(74)90001-5.
+       Elsevier (North-Holland), Amsterdam
+    """
+    if not G.is_directed():
+        raise nx.NetworkXError("Topological sort not defined on undirected graphs.")
+
+    # the names of count and D are chosen to match the global variables in [1]
+    # number of edges originating in a vertex v
+    count = dict(G.in_degree())
+    # vertices with indegree 0
+    D = deque([v for v, d in G.in_degree() if d == 0])
+    # stack of first value chosen at a position k in the topological sort
+    bases = []
+    current_sort = []
+
+    # do-while construct
+    while True:
+        assert all(count[v] == 0 for v in D)
+
+        if len(current_sort) == len(G):
+            yield list(current_sort)
+
+            # clean-up stack
+            while len(current_sort) > 0:
+                assert len(bases) == len(current_sort)
+                q = current_sort.pop()
+
+                # "restores" all edges (q, x)
+                # NOTE: it is important to iterate over edges instead
+                # of successors, so count is updated correctly in multigraphs
+                for _, j in G.out_edges(q):
+                    count[j] += 1
+                    assert count[j] >= 0
+                # remove entries from D
+                while len(D) > 0 and count[D[-1]] > 0:
+                    D.pop()
+
+                # corresponds to a circular shift of the values in D
+                # if the first value chosen (the base) is in the first
+                # position of D again, we are done and need to consider the
+                # previous condition
+                D.appendleft(q)
+                if D[-1] == bases[-1]:
+                    # all possible values have been chosen at current position
+                    # remove corresponding marker
+                    bases.pop()
+                else:
+                    # there are still elements that have not been fixed
+                    # at the current position in the topological sort
+                    # stop removing elements, escape inner loop
+                    break
+
+        else:
+            if len(D) == 0:
+                raise nx.NetworkXUnfeasible("Graph contains a cycle.")
+
+            # choose next node
+            q = D.pop()
+            # "erase" all edges (q, x)
+            # NOTE: it is important to iterate over edges instead
+            # of successors, so count is updated correctly in multigraphs
+            for _, j in G.out_edges(q):
+                count[j] -= 1
+                assert count[j] >= 0
+                if count[j] == 0:
+                    D.append(j)
+            current_sort.append(q)
+
+            # base for current position might _not_ be fixed yet
+            if len(bases) < len(current_sort):
+                bases.append(q)
+
+        if len(bases) == 0:
+            break
+
+
+@nx._dispatch
+def is_aperiodic(G):
+    """Returns True if `G` is aperiodic.
+
+    A directed graph is aperiodic if there is no integer k > 1 that
+    divides the length of every cycle in the graph.
+
+    Parameters
+    ----------
+    G : NetworkX DiGraph
+        A directed graph
+
+    Returns
+    -------
+    bool
+        True if the graph is aperiodic False otherwise
+
+    Raises
+    ------
+    NetworkXError
+        If `G` is not directed
+
+    Examples
+    --------
+    A graph consisting of one cycle, the length of which is 2. Therefore ``k = 2``
+    divides the length of every cycle in the graph and thus the graph
+    is *not aperiodic*::
+
+        >>> DG = nx.DiGraph([(1, 2), (2, 1)])
+        >>> nx.is_aperiodic(DG)
+        False
+
+    A graph consisting of two cycles: one of length 2 and the other of length 3.
+    The cycle lengths are coprime, so there is no single value of k where ``k > 1``
+    that divides each cycle length and therefore the graph is *aperiodic*::
+
+        >>> DG = nx.DiGraph([(1, 2), (2, 3), (3, 1), (1, 4), (4, 1)])
+        >>> nx.is_aperiodic(DG)
+        True
+
+    A graph consisting of two cycles: one of length 2 and the other of length 4.
+    The lengths of the cycles share a common factor ``k = 2``, and therefore
+    the graph is *not aperiodic*::
+
+        >>> DG = nx.DiGraph([(1, 2), (2, 1), (3, 4), (4, 5), (5, 6), (6, 3)])
+        >>> nx.is_aperiodic(DG)
+        False
+
+    An acyclic graph, therefore the graph is *not aperiodic*::
+
+        >>> DG = nx.DiGraph([(1, 2), (2, 3)])
+        >>> nx.is_aperiodic(DG)
+        False
+
+    Notes
+    -----
+    This uses the method outlined in [1]_, which runs in $O(m)$ time
+    given $m$ edges in `G`. Note that a graph is not aperiodic if it is
+    acyclic as every integer trivial divides length 0 cycles.
+
+    References
+    ----------
+    .. [1] Jarvis, J. P.; Shier, D. R. (1996),
+       "Graph-theoretic analysis of finite Markov chains,"
+       in Shier, D. R.; Wallenius, K. T., Applied Mathematical Modeling:
+       A Multidisciplinary Approach, CRC Press.
+    """
+    if not G.is_directed():
+        raise nx.NetworkXError("is_aperiodic not defined for undirected graphs")
+
+    s = arbitrary_element(G)
+    levels = {s: 0}
+    this_level = [s]
+    g = 0
+    lev = 1
+    while this_level:
+        next_level = []
+        for u in this_level:
+            for v in G[u]:
+                if v in levels:  # Non-Tree Edge
+                    g = gcd(g, levels[u] - levels[v] + 1)
+                else:  # Tree Edge
+                    next_level.append(v)
+                    levels[v] = lev
+        this_level = next_level
+        lev += 1
+    if len(levels) == len(G):  # All nodes in tree
+        return g == 1
+    else:
+        return g == 1 and nx.is_aperiodic(G.subgraph(set(G) - set(levels)))
+
+
+@nx._dispatch(preserve_all_attrs=True)
+def transitive_closure(G, reflexive=False):
+    """Returns transitive closure of a graph
+
+    The transitive closure of G = (V,E) is a graph G+ = (V,E+) such that
+    for all v, w in V there is an edge (v, w) in E+ if and only if there
+    is a path from v to w in G.
+
+    Handling of paths from v to v has some flexibility within this definition.
+    A reflexive transitive closure creates a self-loop for the path
+    from v to v of length 0. The usual transitive closure creates a
+    self-loop only if a cycle exists (a path from v to v with length > 0).
+    We also allow an option for no self-loops.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+        A directed/undirected graph/multigraph.
+    reflexive : Bool or None, optional (default: False)
+        Determines when cycles create self-loops in the Transitive Closure.
+        If True, trivial cycles (length 0) create self-loops. The result
+        is a reflexive transitive closure of G.
+        If False (the default) non-trivial cycles create self-loops.
+        If None, self-loops are not created.
+
+    Returns
+    -------
+    NetworkX graph
+        The transitive closure of `G`
+
+    Raises
+    ------
+    NetworkXError
+        If `reflexive` not in `{None, True, False}`
+
+    Examples
+    --------
+    The treatment of trivial (i.e. length 0) cycles is controlled by the
+    `reflexive` parameter.
+
+    Trivial (i.e. length 0) cycles do not create self-loops when
+    ``reflexive=False`` (the default)::
+
+        >>> DG = nx.DiGraph([(1, 2), (2, 3)])
+        >>> TC = nx.transitive_closure(DG, reflexive=False)
+        >>> TC.edges()
+        OutEdgeView([(1, 2), (1, 3), (2, 3)])
+
+    However, nontrivial (i.e. length greater than 0) cycles create self-loops
+    when ``reflexive=False`` (the default)::
+
+        >>> DG = nx.DiGraph([(1, 2), (2, 3), (3, 1)])
+        >>> TC = nx.transitive_closure(DG, reflexive=False)
+        >>> TC.edges()
+        OutEdgeView([(1, 2), (1, 3), (1, 1), (2, 3), (2, 1), (2, 2), (3, 1), (3, 2), (3, 3)])
+
+    Trivial cycles (length 0) create self-loops when ``reflexive=True``::
+
+        >>> DG = nx.DiGraph([(1, 2), (2, 3)])
+        >>> TC = nx.transitive_closure(DG, reflexive=True)
+        >>> TC.edges()
+        OutEdgeView([(1, 2), (1, 1), (1, 3), (2, 3), (2, 2), (3, 3)])
+
+    And the third option is not to create self-loops at all when ``reflexive=None``::
+
+        >>> DG = nx.DiGraph([(1, 2), (2, 3), (3, 1)])
+        >>> TC = nx.transitive_closure(DG, reflexive=None)
+        >>> TC.edges()
+        OutEdgeView([(1, 2), (1, 3), (2, 3), (2, 1), (3, 1), (3, 2)])
+
+    References
+    ----------
+    .. [1] https://www.ics.uci.edu/~eppstein/PADS/PartialOrder.py
+    """
+    TC = G.copy()
+
+    if reflexive not in {None, True, False}:
+        raise nx.NetworkXError("Incorrect value for the parameter `reflexive`")
+
+    for v in G:
+        if reflexive is None:
+            TC.add_edges_from((v, u) for u in nx.descendants(G, v) if u not in TC[v])
+        elif reflexive is True:
+            TC.add_edges_from(
+                (v, u) for u in nx.descendants(G, v) | {v} if u not in TC[v]
+            )
+        elif reflexive is False:
+            TC.add_edges_from((v, e[1]) for e in nx.edge_bfs(G, v) if e[1] not in TC[v])
+
+    return TC
+
+
+@not_implemented_for("undirected")
+@nx._dispatch(preserve_all_attrs=True)
+def transitive_closure_dag(G, topo_order=None):
+    """Returns the transitive closure of a directed acyclic graph.
+
+    This function is faster than the function `transitive_closure`, but fails
+    if the graph has a cycle.
+
+    The transitive closure of G = (V,E) is a graph G+ = (V,E+) such that
+    for all v, w in V there is an edge (v, w) in E+ if and only if there
+    is a non-null path from v to w in G.
+
+    Parameters
+    ----------
+    G : NetworkX DiGraph
+        A directed acyclic graph (DAG)
+
+    topo_order: list or tuple, optional
+        A topological order for G (if None, the function will compute one)
+
+    Returns
+    -------
+    NetworkX DiGraph
+        The transitive closure of `G`
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If `G` is not directed
+    NetworkXUnfeasible
+        If `G` has a cycle
+
+    Examples
+    --------
+    >>> DG = nx.DiGraph([(1, 2), (2, 3)])
+    >>> TC = nx.transitive_closure_dag(DG)
+    >>> TC.edges()
+    OutEdgeView([(1, 2), (1, 3), (2, 3)])
+
+    Notes
+    -----
+    This algorithm is probably simple enough to be well-known but I didn't find
+    a mention in the literature.
+    """
+    if topo_order is None:
+        topo_order = list(topological_sort(G))
+
+    TC = G.copy()
+
+    # idea: traverse vertices following a reverse topological order, connecting
+    # each vertex to its descendants at distance 2 as we go
+    for v in reversed(topo_order):
+        TC.add_edges_from((v, u) for u in nx.descendants_at_distance(TC, v, 2))
+
+    return TC
+
+
+@not_implemented_for("undirected")
+@nx._dispatch
+def transitive_reduction(G):
+    """Returns transitive reduction of a directed graph
+
+    The transitive reduction of G = (V,E) is a graph G- = (V,E-) such that
+    for all v,w in V there is an edge (v,w) in E- if and only if (v,w) is
+    in E and there is no path from v to w in G with length greater than 1.
+
+    Parameters
+    ----------
+    G : NetworkX DiGraph
+        A directed acyclic graph (DAG)
+
+    Returns
+    -------
+    NetworkX DiGraph
+        The transitive reduction of `G`
+
+    Raises
+    ------
+    NetworkXError
+        If `G` is not a directed acyclic graph (DAG) transitive reduction is
+        not uniquely defined and a :exc:`NetworkXError` exception is raised.
+
+    Examples
+    --------
+    To perform transitive reduction on a DiGraph:
+
+    >>> DG = nx.DiGraph([(1, 2), (2, 3), (1, 3)])
+    >>> TR = nx.transitive_reduction(DG)
+    >>> list(TR.edges)
+    [(1, 2), (2, 3)]
+
+    To avoid unnecessary data copies, this implementation does not return a
+    DiGraph with node/edge data.
+    To perform transitive reduction on a DiGraph and transfer node/edge data:
+
+    >>> DG = nx.DiGraph()
+    >>> DG.add_edges_from([(1, 2), (2, 3), (1, 3)], color='red')
+    >>> TR = nx.transitive_reduction(DG)
+    >>> TR.add_nodes_from(DG.nodes(data=True))
+    >>> TR.add_edges_from((u, v, DG.edges[u, v]) for u, v in TR.edges)
+    >>> list(TR.edges(data=True))
+    [(1, 2, {'color': 'red'}), (2, 3, {'color': 'red'})]
+
+    References
+    ----------
+    https://en.wikipedia.org/wiki/Transitive_reduction
+
+    """
+    if not is_directed_acyclic_graph(G):
+        msg = "Directed Acyclic Graph required for transitive_reduction"
+        raise nx.NetworkXError(msg)
+    TR = nx.DiGraph()
+    TR.add_nodes_from(G.nodes())
+    descendants = {}
+    # count before removing set stored in descendants
+    check_count = dict(G.in_degree)
+    for u in G:
+        u_nbrs = set(G[u])
+        for v in G[u]:
+            if v in u_nbrs:
+                if v not in descendants:
+                    descendants[v] = {y for x, y in nx.dfs_edges(G, v)}
+                u_nbrs -= descendants[v]
+            check_count[v] -= 1
+            if check_count[v] == 0:
+                del descendants[v]
+        TR.add_edges_from((u, v) for v in u_nbrs)
+    return TR
+
+
+@not_implemented_for("undirected")
+@nx._dispatch
+def antichains(G, topo_order=None):
+    """Generates antichains from a directed acyclic graph (DAG).
+
+    An antichain is a subset of a partially ordered set such that any
+    two elements in the subset are incomparable.
+
+    Parameters
+    ----------
+    G : NetworkX DiGraph
+        A directed acyclic graph (DAG)
+
+    topo_order: list or tuple, optional
+        A topological order for G (if None, the function will compute one)
+
+    Yields
+    ------
+    antichain : list
+        a list of nodes in `G` representing an antichain
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If `G` is not directed
+
+    NetworkXUnfeasible
+        If `G` contains a cycle
+
+    Examples
+    --------
+    >>> DG = nx.DiGraph([(1, 2), (1, 3)])
+    >>> list(nx.antichains(DG))
+    [[], [3], [2], [2, 3], [1]]
+
+    Notes
+    -----
+    This function was originally developed by Peter Jipsen and Franco Saliola
+    for the SAGE project. It's included in NetworkX with permission from the
+    authors. Original SAGE code at:
+
+    https://github.com/sagemath/sage/blob/master/src/sage/combinat/posets/hasse_diagram.py
+
+    References
+    ----------
+    .. [1] Free Lattices, by R. Freese, J. Jezek and J. B. Nation,
+       AMS, Vol 42, 1995, p. 226.
+    """
+    if topo_order is None:
+        topo_order = list(nx.topological_sort(G))
+
+    TC = nx.transitive_closure_dag(G, topo_order)
+    antichains_stacks = [([], list(reversed(topo_order)))]
+
+    while antichains_stacks:
+        (antichain, stack) = antichains_stacks.pop()
+        # Invariant:
+        #  - the elements of antichain are independent
+        #  - the elements of stack are independent from those of antichain
+        yield antichain
+        while stack:
+            x = stack.pop()
+            new_antichain = antichain + [x]
+            new_stack = [t for t in stack if not ((t in TC[x]) or (x in TC[t]))]
+            antichains_stacks.append((new_antichain, new_stack))
+
+
+@not_implemented_for("undirected")
+@nx._dispatch(edge_attrs={"weight": "default_weight"})
+def dag_longest_path(G, weight="weight", default_weight=1, topo_order=None):
+    """Returns the longest path in a directed acyclic graph (DAG).
+
+    If `G` has edges with `weight` attribute the edge data are used as
+    weight values.
+
+    Parameters
+    ----------
+    G : NetworkX DiGraph
+        A directed acyclic graph (DAG)
+
+    weight : str, optional
+        Edge data key to use for weight
+
+    default_weight : int, optional
+        The weight of edges that do not have a weight attribute
+
+    topo_order: list or tuple, optional
+        A topological order for `G` (if None, the function will compute one)
+
+    Returns
+    -------
+    list
+        Longest path
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If `G` is not directed
+
+    Examples
+    --------
+    >>> DG = nx.DiGraph([(0, 1, {'cost':1}), (1, 2, {'cost':1}), (0, 2, {'cost':42})])
+    >>> list(nx.all_simple_paths(DG, 0, 2))
+    [[0, 1, 2], [0, 2]]
+    >>> nx.dag_longest_path(DG)
+    [0, 1, 2]
+    >>> nx.dag_longest_path(DG, weight="cost")
+    [0, 2]
+
+    In the case where multiple valid topological orderings exist, `topo_order`
+    can be used to specify a specific ordering:
+
+    >>> DG = nx.DiGraph([(0, 1), (0, 2)])
+    >>> sorted(nx.all_topological_sorts(DG))  # Valid topological orderings
+    [[0, 1, 2], [0, 2, 1]]
+    >>> nx.dag_longest_path(DG, topo_order=[0, 1, 2])
+    [0, 1]
+    >>> nx.dag_longest_path(DG, topo_order=[0, 2, 1])
+    [0, 2]
+
+    See also
+    --------
+    dag_longest_path_length
+
+    """
+    if not G:
+        return []
+
+    if topo_order is None:
+        topo_order = nx.topological_sort(G)
+
+    dist = {}  # stores {v : (length, u)}
+    for v in topo_order:
+        us = [
+            (
+                dist[u][0]
+                + (
+                    max(data.values(), key=lambda x: x.get(weight, default_weight))
+                    if G.is_multigraph()
+                    else data
+                ).get(weight, default_weight),
+                u,
+            )
+            for u, data in G.pred[v].items()
+        ]
+
+        # Use the best predecessor if there is one and its distance is
+        # non-negative, otherwise terminate.
+        maxu = max(us, key=lambda x: x[0]) if us else (0, v)
+        dist[v] = maxu if maxu[0] >= 0 else (0, v)
+
+    u = None
+    v = max(dist, key=lambda x: dist[x][0])
+    path = []
+    while u != v:
+        path.append(v)
+        u = v
+        v = dist[v][1]
+
+    path.reverse()
+    return path
+
+
+@not_implemented_for("undirected")
+@nx._dispatch(edge_attrs={"weight": "default_weight"})
+def dag_longest_path_length(G, weight="weight", default_weight=1):
+    """Returns the longest path length in a DAG
+
+    Parameters
+    ----------
+    G : NetworkX DiGraph
+        A directed acyclic graph (DAG)
+
+    weight : string, optional
+        Edge data key to use for weight
+
+    default_weight : int, optional
+        The weight of edges that do not have a weight attribute
+
+    Returns
+    -------
+    int
+        Longest path length
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If `G` is not directed
+
+    Examples
+    --------
+    >>> DG = nx.DiGraph([(0, 1, {'cost':1}), (1, 2, {'cost':1}), (0, 2, {'cost':42})])
+    >>> list(nx.all_simple_paths(DG, 0, 2))
+    [[0, 1, 2], [0, 2]]
+    >>> nx.dag_longest_path_length(DG)
+    2
+    >>> nx.dag_longest_path_length(DG, weight="cost")
+    42
+
+    See also
+    --------
+    dag_longest_path
+    """
+    path = nx.dag_longest_path(G, weight, default_weight)
+    path_length = 0
+    if G.is_multigraph():
+        for u, v in pairwise(path):
+            i = max(G[u][v], key=lambda x: G[u][v][x].get(weight, default_weight))
+            path_length += G[u][v][i].get(weight, default_weight)
+    else:
+        for u, v in pairwise(path):
+            path_length += G[u][v].get(weight, default_weight)
+
+    return path_length
+
+
+@nx._dispatch
+def root_to_leaf_paths(G):
+    """Yields root-to-leaf paths in a directed acyclic graph.
+
+    `G` must be a directed acyclic graph. If not, the behavior of this
+    function is undefined. A "root" in this graph is a node of in-degree
+    zero and a "leaf" a node of out-degree zero.
+
+    When invoked, this function iterates over each path from any root to
+    any leaf. A path is a list of nodes.
+
+    """
+    roots = (v for v, d in G.in_degree() if d == 0)
+    leaves = (v for v, d in G.out_degree() if d == 0)
+    all_paths = partial(nx.all_simple_paths, G)
+    # TODO In Python 3, this would be better as `yield from ...`.
+    return chaini(starmap(all_paths, product(roots, leaves)))
+
+
+@not_implemented_for("multigraph")
+@not_implemented_for("undirected")
+@nx._dispatch
+def dag_to_branching(G):
+    """Returns a branching representing all (overlapping) paths from
+    root nodes to leaf nodes in the given directed acyclic graph.
+
+    As described in :mod:`networkx.algorithms.tree.recognition`, a
+    *branching* is a directed forest in which each node has at most one
+    parent. In other words, a branching is a disjoint union of
+    *arborescences*. For this function, each node of in-degree zero in
+    `G` becomes a root of one of the arborescences, and there will be
+    one leaf node for each distinct path from that root to a leaf node
+    in `G`.
+
+    Each node `v` in `G` with *k* parents becomes *k* distinct nodes in
+    the returned branching, one for each parent, and the sub-DAG rooted
+    at `v` is duplicated for each copy. The algorithm then recurses on
+    the children of each copy of `v`.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        A directed acyclic graph.
+
+    Returns
+    -------
+    DiGraph
+        The branching in which there is a bijection between root-to-leaf
+        paths in `G` (in which multiple paths may share the same leaf)
+        and root-to-leaf paths in the branching (in which there is a
+        unique path from a root to a leaf).
+
+        Each node has an attribute 'source' whose value is the original
+        node to which this node corresponds. No other graph, node, or
+        edge attributes are copied into this new graph.
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If `G` is not directed, or if `G` is a multigraph.
+
+    HasACycle
+        If `G` is not acyclic.
+
+    Examples
+    --------
+    To examine which nodes in the returned branching were produced by
+    which original node in the directed acyclic graph, we can collect
+    the mapping from source node to new nodes into a dictionary. For
+    example, consider the directed diamond graph::
+
+        >>> from collections import defaultdict
+        >>> from operator import itemgetter
+        >>>
+        >>> G = nx.DiGraph(nx.utils.pairwise("abd"))
+        >>> G.add_edges_from(nx.utils.pairwise("acd"))
+        >>> B = nx.dag_to_branching(G)
+        >>>
+        >>> sources = defaultdict(set)
+        >>> for v, source in B.nodes(data="source"):
+        ...     sources[source].add(v)
+        >>> len(sources["a"])
+        1
+        >>> len(sources["d"])
+        2
+
+    To copy node attributes from the original graph to the new graph,
+    you can use a dictionary like the one constructed in the above
+    example::
+
+        >>> for source, nodes in sources.items():
+        ...     for v in nodes:
+        ...         B.nodes[v].update(G.nodes[source])
+
+    Notes
+    -----
+    This function is not idempotent in the sense that the node labels in
+    the returned branching may be uniquely generated each time the
+    function is invoked. In fact, the node labels may not be integers;
+    in order to relabel the nodes to be more readable, you can use the
+    :func:`networkx.convert_node_labels_to_integers` function.
+
+    The current implementation of this function uses
+    :func:`networkx.prefix_tree`, so it is subject to the limitations of
+    that function.
+
+    """
+    if has_cycle(G):
+        msg = "dag_to_branching is only defined for acyclic graphs"
+        raise nx.HasACycle(msg)
+    paths = root_to_leaf_paths(G)
+    B = nx.prefix_tree(paths)
+    # Remove the synthetic `root`(0) and `NIL`(-1) nodes from the tree
+    B.remove_node(0)
+    B.remove_node(-1)
+    return B
+
+
+@not_implemented_for("undirected")
+@nx._dispatch
+def compute_v_structures(G):
+    """Iterate through the graph to compute all v-structures.
+
+    V-structures are triples in the directed graph where
+    two parent nodes point to the same child and the two parent nodes
+    are not adjacent.
+
+    Parameters
+    ----------
+    G : graph
+        A networkx DiGraph.
+
+    Returns
+    -------
+    vstructs : iterator of tuples
+        The v structures within the graph. Each v structure is a 3-tuple with the
+        parent, collider, and other parent.
+
+    Examples
+    --------
+    >>> G = nx.DiGraph()
+    >>> G.add_edges_from([(1, 2), (0, 5), (3, 1), (2, 4), (3, 1), (4, 5), (1, 5)])
+    >>> sorted(nx.compute_v_structures(G))
+    [(0, 5, 1), (0, 5, 4), (1, 5, 4)]
+
+    Notes
+    -----
+    https://en.wikipedia.org/wiki/Collider_(statistics)
+    """
+    for collider, preds in G.pred.items():
+        for common_parents in combinations(preds, r=2):
+            # ensure that the colliders are the same
+            common_parents = sorted(common_parents)
+            yield (common_parents[0], collider, common_parents[1])

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/distance_regular.py

@@ -0,0 +1,234 @@
+"""
+=======================
+Distance-regular graphs
+=======================
+"""
+
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+from .distance_measures import diameter
+
+__all__ = [
+    "is_distance_regular",
+    "is_strongly_regular",
+    "intersection_array",
+    "global_parameters",
+]
+
+
+@nx._dispatch
+def is_distance_regular(G):
+    """Returns True if the graph is distance regular, False otherwise.
+
+    A connected graph G is distance-regular if for any nodes x,y
+    and any integers i,j=0,1,...,d (where d is the graph
+    diameter), the number of vertices at distance i from x and
+    distance j from y depends only on i,j and the graph distance
+    between x and y, independently of the choice of x and y.
+
+    Parameters
+    ----------
+    G: Networkx graph (undirected)
+
+    Returns
+    -------
+    bool
+      True if the graph is Distance Regular, False otherwise
+
+    Examples
+    --------
+    >>> G = nx.hypercube_graph(6)
+    >>> nx.is_distance_regular(G)
+    True
+
+    See Also
+    --------
+    intersection_array, global_parameters
+
+    Notes
+    -----
+    For undirected and simple graphs only
+
+    References
+    ----------
+    .. [1] Brouwer, A. E.; Cohen, A. M.; and Neumaier, A.
+        Distance-Regular Graphs. New York: Springer-Verlag, 1989.
+    .. [2] Weisstein, Eric W. "Distance-Regular Graph."
+        http://mathworld.wolfram.com/Distance-RegularGraph.html
+
+    """
+    try:
+        intersection_array(G)
+        return True
+    except nx.NetworkXError:
+        return False
+
+
+def global_parameters(b, c):
+    """Returns global parameters for a given intersection array.
+
+    Given a distance-regular graph G with integers b_i, c_i,i = 0,....,d
+    such that for any 2 vertices x,y in G at a distance i=d(x,y), there
+    are exactly c_i neighbors of y at a distance of i-1 from x and b_i
+    neighbors of y at a distance of i+1 from x.
+
+    Thus, a distance regular graph has the global parameters,
+    [[c_0,a_0,b_0],[c_1,a_1,b_1],......,[c_d,a_d,b_d]] for the
+    intersection array  [b_0,b_1,.....b_{d-1};c_1,c_2,.....c_d]
+    where a_i+b_i+c_i=k , k= degree of every vertex.
+
+    Parameters
+    ----------
+    b : list
+
+    c : list
+
+    Returns
+    -------
+    iterable
+       An iterable over three tuples.
+
+    Examples
+    --------
+    >>> G = nx.dodecahedral_graph()
+    >>> b, c = nx.intersection_array(G)
+    >>> list(nx.global_parameters(b, c))
+    [(0, 0, 3), (1, 0, 2), (1, 1, 1), (1, 1, 1), (2, 0, 1), (3, 0, 0)]
+
+    References
+    ----------
+    .. [1] Weisstein, Eric W. "Global Parameters."
+       From MathWorld--A Wolfram Web Resource.
+       http://mathworld.wolfram.com/GlobalParameters.html
+
+    See Also
+    --------
+    intersection_array
+    """
+    return ((y, b[0] - x - y, x) for x, y in zip(b + [0], [0] + c))
+
+
+@not_implemented_for("directed", "multigraph")
+@nx._dispatch
+def intersection_array(G):
+    """Returns the intersection array of a distance-regular graph.
+
+    Given a distance-regular graph G with integers b_i, c_i,i = 0,....,d
+    such that for any 2 vertices x,y in G at a distance i=d(x,y), there
+    are exactly c_i neighbors of y at a distance of i-1 from x and b_i
+    neighbors of y at a distance of i+1 from x.
+
+    A distance regular graph's intersection array is given by,
+    [b_0,b_1,.....b_{d-1};c_1,c_2,.....c_d]
+
+    Parameters
+    ----------
+    G: Networkx graph (undirected)
+
+    Returns
+    -------
+    b,c: tuple of lists
+
+    Examples
+    --------
+    >>> G = nx.icosahedral_graph()
+    >>> nx.intersection_array(G)
+    ([5, 2, 1], [1, 2, 5])
+
+    References
+    ----------
+    .. [1] Weisstein, Eric W. "Intersection Array."
+       From MathWorld--A Wolfram Web Resource.
+       http://mathworld.wolfram.com/IntersectionArray.html
+
+    See Also
+    --------
+    global_parameters
+    """
+    # test for regular graph (all degrees must be equal)
+    degree = iter(G.degree())
+    (_, k) = next(degree)
+    for _, knext in degree:
+        if knext != k:
+            raise nx.NetworkXError("Graph is not distance regular.")
+        k = knext
+    path_length = dict(nx.all_pairs_shortest_path_length(G))
+    diameter = max(max(path_length[n].values()) for n in path_length)
+    bint = {}  # 'b' intersection array
+    cint = {}  # 'c' intersection array
+    for u in G:
+        for v in G:
+            try:
+                i = path_length[u][v]
+            except KeyError as err:  # graph must be connected
+                raise nx.NetworkXError("Graph is not distance regular.") from err
+            # number of neighbors of v at a distance of i-1 from u
+            c = len([n for n in G[v] if path_length[n][u] == i - 1])
+            # number of neighbors of v at a distance of i+1 from u
+            b = len([n for n in G[v] if path_length[n][u] == i + 1])
+            # b,c are independent of u and v
+            if cint.get(i, c) != c or bint.get(i, b) != b:
+                raise nx.NetworkXError("Graph is not distance regular")
+            bint[i] = b
+            cint[i] = c
+    return (
+        [bint.get(j, 0) for j in range(diameter)],
+        [cint.get(j + 1, 0) for j in range(diameter)],
+    )
+
+
+# TODO There is a definition for directed strongly regular graphs.
+@not_implemented_for("directed", "multigraph")
+@nx._dispatch
+def is_strongly_regular(G):
+    """Returns True if and only if the given graph is strongly
+    regular.
+
+    An undirected graph is *strongly regular* if
+
+    * it is regular,
+    * each pair of adjacent vertices has the same number of neighbors in
+      common,
+    * each pair of nonadjacent vertices has the same number of neighbors
+      in common.
+
+    Each strongly regular graph is a distance-regular graph.
+    Conversely, if a distance-regular graph has diameter two, then it is
+    a strongly regular graph. For more information on distance-regular
+    graphs, see :func:`is_distance_regular`.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        An undirected graph.
+
+    Returns
+    -------
+    bool
+        Whether `G` is strongly regular.
+
+    Examples
+    --------
+
+    The cycle graph on five vertices is strongly regular. It is
+    two-regular, each pair of adjacent vertices has no shared neighbors,
+    and each pair of nonadjacent vertices has one shared neighbor::
+
+        >>> G = nx.cycle_graph(5)
+        >>> nx.is_strongly_regular(G)
+        True
+
+    """
+    # Here is an alternate implementation based directly on the
+    # definition of strongly regular graphs:
+    #
+    #     return (all_equal(G.degree().values())
+    #             and all_equal(len(common_neighbors(G, u, v))
+    #                           for u, v in G.edges())
+    #             and all_equal(len(common_neighbors(G, u, v))
+    #                           for u, v in non_edges(G)))
+    #
+    # We instead use the fact that a distance-regular graph of diameter
+    # two is strongly regular.
+    return is_distance_regular(G) and diameter(G) == 2

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/flow/__init__.py

@@ -0,0 +1,11 @@
+from .maxflow import *
+from .mincost import *
+from .boykovkolmogorov import *
+from .dinitz_alg import *
+from .edmondskarp import *
+from .gomory_hu import *
+from .preflowpush import *
+from .shortestaugmentingpath import *
+from .capacityscaling import *
+from .networksimplex import *
+from .utils import build_flow_dict, build_residual_network

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/flow/edmondskarp.py

@@ -0,0 +1,250 @@
+"""
+Edmonds-Karp algorithm for maximum flow problems.
+"""
+
+import networkx as nx
+from networkx.algorithms.flow.utils import build_residual_network
+
+__all__ = ["edmonds_karp"]
+
+
+@nx._dispatch(
+    graphs="R",
+    preserve_edge_attrs={"R": {"capacity": float("inf"), "flow": 0}},
+    preserve_graph_attrs=True,
+)
+def edmonds_karp_core(R, s, t, cutoff):
+    """Implementation of the Edmonds-Karp algorithm."""
+    R_nodes = R.nodes
+    R_pred = R.pred
+    R_succ = R.succ
+
+    inf = R.graph["inf"]
+
+    def augment(path):
+        """Augment flow along a path from s to t."""
+        # Determine the path residual capacity.
+        flow = inf
+        it = iter(path)
+        u = next(it)
+        for v in it:
+            attr = R_succ[u][v]
+            flow = min(flow, attr["capacity"] - attr["flow"])
+            u = v
+        if flow * 2 > inf:
+            raise nx.NetworkXUnbounded("Infinite capacity path, flow unbounded above.")
+        # Augment flow along the path.
+        it = iter(path)
+        u = next(it)
+        for v in it:
+            R_succ[u][v]["flow"] += flow
+            R_succ[v][u]["flow"] -= flow
+            u = v
+        return flow
+
+    def bidirectional_bfs():
+        """Bidirectional breadth-first search for an augmenting path."""
+        pred = {s: None}
+        q_s = [s]
+        succ = {t: None}
+        q_t = [t]
+        while True:
+            q = []
+            if len(q_s) <= len(q_t):
+                for u in q_s:
+                    for v, attr in R_succ[u].items():
+                        if v not in pred and attr["flow"] < attr["capacity"]:
+                            pred[v] = u
+                            if v in succ:
+                                return v, pred, succ
+                            q.append(v)
+                if not q:
+                    return None, None, None
+                q_s = q
+            else:
+                for u in q_t:
+                    for v, attr in R_pred[u].items():
+                        if v not in succ and attr["flow"] < attr["capacity"]:
+                            succ[v] = u
+                            if v in pred:
+                                return v, pred, succ
+                            q.append(v)
+                if not q:
+                    return None, None, None
+                q_t = q
+
+    # Look for shortest augmenting paths using breadth-first search.
+    flow_value = 0
+    while flow_value < cutoff:
+        v, pred, succ = bidirectional_bfs()
+        if pred is None:
+            break
+        path = [v]
+        # Trace a path from s to v.
+        u = v
+        while u != s:
+            u = pred[u]
+            path.append(u)
+        path.reverse()
+        # Trace a path from v to t.
+        u = v
+        while u != t:
+            u = succ[u]
+            path.append(u)
+        flow_value += augment(path)
+
+    return flow_value
+
+
+def edmonds_karp_impl(G, s, t, capacity, residual, cutoff):
+    """Implementation of the Edmonds-Karp algorithm."""
+    if s not in G:
+        raise nx.NetworkXError(f"node {str(s)} not in graph")
+    if t not in G:
+        raise nx.NetworkXError(f"node {str(t)} not in graph")
+    if s == t:
+        raise nx.NetworkXError("source and sink are the same node")
+
+    if residual is None:
+        R = build_residual_network(G, capacity)
+    else:
+        R = residual
+
+    # Initialize/reset the residual network.
+    for u in R:
+        for e in R[u].values():
+            e["flow"] = 0
+
+    if cutoff is None:
+        cutoff = float("inf")
+    R.graph["flow_value"] = edmonds_karp_core(R, s, t, cutoff)
+
+    return R
+
+
+@nx._dispatch(
+    graphs={"G": 0, "residual?": 4},
+    edge_attrs={"capacity": float("inf")},
+    preserve_edge_attrs={"residual": {"capacity": float("inf")}},
+    preserve_graph_attrs={"residual"},
+)
+def edmonds_karp(
+    G, s, t, capacity="capacity", residual=None, value_only=False, cutoff=None
+):
+    """Find a maximum single-commodity flow using the Edmonds-Karp algorithm.
+
+    This function returns the residual network resulting after computing
+    the maximum flow. See below for details about the conventions
+    NetworkX uses for defining residual networks.
+
+    This algorithm has a running time of $O(n m^2)$ for $n$ nodes and $m$
+    edges.
+
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        Edges of the graph are expected to have an attribute called
+        'capacity'. If this attribute is not present, the edge is
+        considered to have infinite capacity.
+
+    s : node
+        Source node for the flow.
+
+    t : node
+        Sink node for the flow.
+
+    capacity : string
+        Edges of the graph G are expected to have an attribute capacity
+        that indicates how much flow the edge can support. If this
+        attribute is not present, the edge is considered to have
+        infinite capacity. Default value: 'capacity'.
+
+    residual : NetworkX graph
+        Residual network on which the algorithm is to be executed. If None, a
+        new residual network is created. Default value: None.
+
+    value_only : bool
+        If True compute only the value of the maximum flow. This parameter
+        will be ignored by this algorithm because it is not applicable.
+
+    cutoff : integer, float
+        If specified, the algorithm will terminate when the flow value reaches
+        or exceeds the cutoff. In this case, it may be unable to immediately
+        determine a minimum cut. Default value: None.
+
+    Returns
+    -------
+    R : NetworkX DiGraph
+        Residual network after computing the maximum flow.
+
+    Raises
+    ------
+    NetworkXError
+        The algorithm does not support MultiGraph and MultiDiGraph. If
+        the input graph is an instance of one of these two classes, a
+        NetworkXError is raised.
+
+    NetworkXUnbounded
+        If the graph has a path of infinite capacity, the value of a
+        feasible flow on the graph is unbounded above and the function
+        raises a NetworkXUnbounded.
+
+    See also
+    --------
+    :meth:`maximum_flow`
+    :meth:`minimum_cut`
+    :meth:`preflow_push`
+    :meth:`shortest_augmenting_path`
+
+    Notes
+    -----
+    The residual network :samp:`R` from an input graph :samp:`G` has the
+    same nodes as :samp:`G`. :samp:`R` is a DiGraph that contains a pair
+    of edges :samp:`(u, v)` and :samp:`(v, u)` iff :samp:`(u, v)` is not a
+    self-loop, and at least one of :samp:`(u, v)` and :samp:`(v, u)` exists
+    in :samp:`G`.
+
+    For each edge :samp:`(u, v)` in :samp:`R`, :samp:`R[u][v]['capacity']`
+    is equal to the capacity of :samp:`(u, v)` in :samp:`G` if it exists
+    in :samp:`G` or zero otherwise. If the capacity is infinite,
+    :samp:`R[u][v]['capacity']` will have a high arbitrary finite value
+    that does not affect the solution of the problem. This value is stored in
+    :samp:`R.graph['inf']`. For each edge :samp:`(u, v)` in :samp:`R`,
+    :samp:`R[u][v]['flow']` represents the flow function of :samp:`(u, v)` and
+    satisfies :samp:`R[u][v]['flow'] == -R[v][u]['flow']`.
+
+    The flow value, defined as the total flow into :samp:`t`, the sink, is
+    stored in :samp:`R.graph['flow_value']`. If :samp:`cutoff` is not
+    specified, reachability to :samp:`t` using only edges :samp:`(u, v)` such
+    that :samp:`R[u][v]['flow'] < R[u][v]['capacity']` induces a minimum
+    :samp:`s`-:samp:`t` cut.
+
+    Examples
+    --------
+    >>> from networkx.algorithms.flow import edmonds_karp
+
+    The functions that implement flow algorithms and output a residual
+    network, such as this one, are not imported to the base NetworkX
+    namespace, so you have to explicitly import them from the flow package.
+
+    >>> G = nx.DiGraph()
+    >>> G.add_edge("x", "a", capacity=3.0)
+    >>> G.add_edge("x", "b", capacity=1.0)
+    >>> G.add_edge("a", "c", capacity=3.0)
+    >>> G.add_edge("b", "c", capacity=5.0)
+    >>> G.add_edge("b", "d", capacity=4.0)
+    >>> G.add_edge("d", "e", capacity=2.0)
+    >>> G.add_edge("c", "y", capacity=2.0)
+    >>> G.add_edge("e", "y", capacity=3.0)
+    >>> R = edmonds_karp(G, "x", "y")
+    >>> flow_value = nx.maximum_flow_value(G, "x", "y")
+    >>> flow_value
+    3.0
+    >>> flow_value == R.graph["flow_value"]
+    True
+
+    """
+    R = edmonds_karp_impl(G, s, t, capacity, residual, cutoff)
+    R.graph["algorithm"] = "edmonds_karp"
+    return R

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/flow/mincost.py

@@ -0,0 +1,335 @@
+"""
+Minimum cost flow algorithms on directed connected graphs.
+"""
+
+__all__ = ["min_cost_flow_cost", "min_cost_flow", "cost_of_flow", "max_flow_min_cost"]
+
+import networkx as nx
+
+
+@nx._dispatch(node_attrs="demand", edge_attrs={"capacity": float("inf"), "weight": 0})
+def min_cost_flow_cost(G, demand="demand", capacity="capacity", weight="weight"):
+    r"""Find the cost of a minimum cost flow satisfying all demands in digraph G.
+
+    G is a digraph with edge costs and capacities and in which nodes
+    have demand, i.e., they want to send or receive some amount of
+    flow. A negative demand means that the node wants to send flow, a
+    positive demand means that the node want to receive flow. A flow on
+    the digraph G satisfies all demand if the net flow into each node
+    is equal to the demand of that node.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        DiGraph on which a minimum cost flow satisfying all demands is
+        to be found.
+
+    demand : string
+        Nodes of the graph G are expected to have an attribute demand
+        that indicates how much flow a node wants to send (negative
+        demand) or receive (positive demand). Note that the sum of the
+        demands should be 0 otherwise the problem in not feasible. If
+        this attribute is not present, a node is considered to have 0
+        demand. Default value: 'demand'.
+
+    capacity : string
+        Edges of the graph G are expected to have an attribute capacity
+        that indicates how much flow the edge can support. If this
+        attribute is not present, the edge is considered to have
+        infinite capacity. Default value: 'capacity'.
+
+    weight : string
+        Edges of the graph G are expected to have an attribute weight
+        that indicates the cost incurred by sending one unit of flow on
+        that edge. If not present, the weight is considered to be 0.
+        Default value: 'weight'.
+
+    Returns
+    -------
+    flowCost : integer, float
+        Cost of a minimum cost flow satisfying all demands.
+
+    Raises
+    ------
+    NetworkXError
+        This exception is raised if the input graph is not directed or
+        not connected.
+
+    NetworkXUnfeasible
+        This exception is raised in the following situations:
+
+            * The sum of the demands is not zero. Then, there is no
+              flow satisfying all demands.
+            * There is no flow satisfying all demand.
+
+    NetworkXUnbounded
+        This exception is raised if the digraph G has a cycle of
+        negative cost and infinite capacity. Then, the cost of a flow
+        satisfying all demands is unbounded below.
+
+    See also
+    --------
+    cost_of_flow, max_flow_min_cost, min_cost_flow, network_simplex
+
+    Notes
+    -----
+    This algorithm is not guaranteed to work if edge weights or demands
+    are floating point numbers (overflows and roundoff errors can
+    cause problems). As a workaround you can use integer numbers by
+    multiplying the relevant edge attributes by a convenient
+    constant factor (eg 100).
+
+    Examples
+    --------
+    A simple example of a min cost flow problem.
+
+    >>> G = nx.DiGraph()
+    >>> G.add_node("a", demand=-5)
+    >>> G.add_node("d", demand=5)
+    >>> G.add_edge("a", "b", weight=3, capacity=4)
+    >>> G.add_edge("a", "c", weight=6, capacity=10)
+    >>> G.add_edge("b", "d", weight=1, capacity=9)
+    >>> G.add_edge("c", "d", weight=2, capacity=5)
+    >>> flowCost = nx.min_cost_flow_cost(G)
+    >>> flowCost
+    24
+    """
+    return nx.network_simplex(G, demand=demand, capacity=capacity, weight=weight)[0]
+
+
+@nx._dispatch(node_attrs="demand", edge_attrs={"capacity": float("inf"), "weight": 0})
+def min_cost_flow(G, demand="demand", capacity="capacity", weight="weight"):
+    r"""Returns a minimum cost flow satisfying all demands in digraph G.
+
+    G is a digraph with edge costs and capacities and in which nodes
+    have demand, i.e., they want to send or receive some amount of
+    flow. A negative demand means that the node wants to send flow, a
+    positive demand means that the node want to receive flow. A flow on
+    the digraph G satisfies all demand if the net flow into each node
+    is equal to the demand of that node.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        DiGraph on which a minimum cost flow satisfying all demands is
+        to be found.
+
+    demand : string
+        Nodes of the graph G are expected to have an attribute demand
+        that indicates how much flow a node wants to send (negative
+        demand) or receive (positive demand). Note that the sum of the
+        demands should be 0 otherwise the problem in not feasible. If
+        this attribute is not present, a node is considered to have 0
+        demand. Default value: 'demand'.
+
+    capacity : string
+        Edges of the graph G are expected to have an attribute capacity
+        that indicates how much flow the edge can support. If this
+        attribute is not present, the edge is considered to have
+        infinite capacity. Default value: 'capacity'.
+
+    weight : string
+        Edges of the graph G are expected to have an attribute weight
+        that indicates the cost incurred by sending one unit of flow on
+        that edge. If not present, the weight is considered to be 0.
+        Default value: 'weight'.
+
+    Returns
+    -------
+    flowDict : dictionary
+        Dictionary of dictionaries keyed by nodes such that
+        flowDict[u][v] is the flow edge (u, v).
+
+    Raises
+    ------
+    NetworkXError
+        This exception is raised if the input graph is not directed or
+        not connected.
+
+    NetworkXUnfeasible
+        This exception is raised in the following situations:
+
+            * The sum of the demands is not zero. Then, there is no
+              flow satisfying all demands.
+            * There is no flow satisfying all demand.
+
+    NetworkXUnbounded
+        This exception is raised if the digraph G has a cycle of
+        negative cost and infinite capacity. Then, the cost of a flow
+        satisfying all demands is unbounded below.
+
+    See also
+    --------
+    cost_of_flow, max_flow_min_cost, min_cost_flow_cost, network_simplex
+
+    Notes
+    -----
+    This algorithm is not guaranteed to work if edge weights or demands
+    are floating point numbers (overflows and roundoff errors can
+    cause problems). As a workaround you can use integer numbers by
+    multiplying the relevant edge attributes by a convenient
+    constant factor (eg 100).
+
+    Examples
+    --------
+    A simple example of a min cost flow problem.
+
+    >>> G = nx.DiGraph()
+    >>> G.add_node("a", demand=-5)
+    >>> G.add_node("d", demand=5)
+    >>> G.add_edge("a", "b", weight=3, capacity=4)
+    >>> G.add_edge("a", "c", weight=6, capacity=10)
+    >>> G.add_edge("b", "d", weight=1, capacity=9)
+    >>> G.add_edge("c", "d", weight=2, capacity=5)
+    >>> flowDict = nx.min_cost_flow(G)
+    """
+    return nx.network_simplex(G, demand=demand, capacity=capacity, weight=weight)[1]
+
+
+@nx._dispatch(edge_attrs={"weight": 0})
+def cost_of_flow(G, flowDict, weight="weight"):
+    """Compute the cost of the flow given by flowDict on graph G.
+
+    Note that this function does not check for the validity of the
+    flow flowDict. This function will fail if the graph G and the
+    flow don't have the same edge set.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        DiGraph on which a minimum cost flow satisfying all demands is
+        to be found.
+
+    weight : string
+        Edges of the graph G are expected to have an attribute weight
+        that indicates the cost incurred by sending one unit of flow on
+        that edge. If not present, the weight is considered to be 0.
+        Default value: 'weight'.
+
+    flowDict : dictionary
+        Dictionary of dictionaries keyed by nodes such that
+        flowDict[u][v] is the flow edge (u, v).
+
+    Returns
+    -------
+    cost : Integer, float
+        The total cost of the flow. This is given by the sum over all
+        edges of the product of the edge's flow and the edge's weight.
+
+    See also
+    --------
+    max_flow_min_cost, min_cost_flow, min_cost_flow_cost, network_simplex
+
+    Notes
+    -----
+    This algorithm is not guaranteed to work if edge weights or demands
+    are floating point numbers (overflows and roundoff errors can
+    cause problems). As a workaround you can use integer numbers by
+    multiplying the relevant edge attributes by a convenient
+    constant factor (eg 100).
+    """
+    return sum((flowDict[u][v] * d.get(weight, 0) for u, v, d in G.edges(data=True)))
+
+
+@nx._dispatch(edge_attrs={"capacity": float("inf"), "weight": 0})
+def max_flow_min_cost(G, s, t, capacity="capacity", weight="weight"):
+    """Returns a maximum (s, t)-flow of minimum cost.
+
+    G is a digraph with edge costs and capacities. There is a source
+    node s and a sink node t. This function finds a maximum flow from
+    s to t whose total cost is minimized.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        DiGraph on which a minimum cost flow satisfying all demands is
+        to be found.
+
+    s: node label
+        Source of the flow.
+
+    t: node label
+        Destination of the flow.
+
+    capacity: string
+        Edges of the graph G are expected to have an attribute capacity
+        that indicates how much flow the edge can support. If this
+        attribute is not present, the edge is considered to have
+        infinite capacity. Default value: 'capacity'.
+
+    weight: string
+        Edges of the graph G are expected to have an attribute weight
+        that indicates the cost incurred by sending one unit of flow on
+        that edge. If not present, the weight is considered to be 0.
+        Default value: 'weight'.
+
+    Returns
+    -------
+    flowDict: dictionary
+        Dictionary of dictionaries keyed by nodes such that
+        flowDict[u][v] is the flow edge (u, v).
+
+    Raises
+    ------
+    NetworkXError
+        This exception is raised if the input graph is not directed or
+        not connected.
+
+    NetworkXUnbounded
+        This exception is raised if there is an infinite capacity path
+        from s to t in G. In this case there is no maximum flow. This
+        exception is also raised if the digraph G has a cycle of
+        negative cost and infinite capacity. Then, the cost of a flow
+        is unbounded below.
+
+    See also
+    --------
+    cost_of_flow, min_cost_flow, min_cost_flow_cost, network_simplex
+
+    Notes
+    -----
+    This algorithm is not guaranteed to work if edge weights or demands
+    are floating point numbers (overflows and roundoff errors can
+    cause problems). As a workaround you can use integer numbers by
+    multiplying the relevant edge attributes by a convenient
+    constant factor (eg 100).
+
+    Examples
+    --------
+    >>> G = nx.DiGraph()
+    >>> G.add_edges_from(
+    ...     [
+    ...         (1, 2, {"capacity": 12, "weight": 4}),
+    ...         (1, 3, {"capacity": 20, "weight": 6}),
+    ...         (2, 3, {"capacity": 6, "weight": -3}),
+    ...         (2, 6, {"capacity": 14, "weight": 1}),
+    ...         (3, 4, {"weight": 9}),
+    ...         (3, 5, {"capacity": 10, "weight": 5}),
+    ...         (4, 2, {"capacity": 19, "weight": 13}),
+    ...         (4, 5, {"capacity": 4, "weight": 0}),
+    ...         (5, 7, {"capacity": 28, "weight": 2}),
+    ...         (6, 5, {"capacity": 11, "weight": 1}),
+    ...         (6, 7, {"weight": 8}),
+    ...         (7, 4, {"capacity": 6, "weight": 6}),
+    ...     ]
+    ... )
+    >>> mincostFlow = nx.max_flow_min_cost(G, 1, 7)
+    >>> mincost = nx.cost_of_flow(G, mincostFlow)
+    >>> mincost
+    373
+    >>> from networkx.algorithms.flow import maximum_flow
+    >>> maxFlow = maximum_flow(G, 1, 7)[1]
+    >>> nx.cost_of_flow(G, maxFlow) >= mincost
+    True
+    >>> mincostFlowValue = sum((mincostFlow[u][7] for u in G.predecessors(7))) - sum(
+    ...     (mincostFlow[7][v] for v in G.successors(7))
+    ... )
+    >>> mincostFlowValue == nx.maximum_flow_value(G, 1, 7)
+    True
+
+    """
+    maxFlow = nx.maximum_flow_value(G, s, t, capacity=capacity)
+    H = nx.DiGraph(G)
+    H.add_node(s, demand=-maxFlow)
+    H.add_node(t, demand=maxFlow)
+    return min_cost_flow(H, capacity=capacity, weight=weight)

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/flow/shortestaugmentingpath.py

@@ -0,0 +1,304 @@
+"""
+Shortest augmenting path algorithm for maximum flow problems.
+"""
+
+from collections import deque
+
+import networkx as nx
+
+from .edmondskarp import edmonds_karp_core
+from .utils import CurrentEdge, build_residual_network
+
+__all__ = ["shortest_augmenting_path"]
+
+
+def shortest_augmenting_path_impl(G, s, t, capacity, residual, two_phase, cutoff):
+    """Implementation of the shortest augmenting path algorithm."""
+    if s not in G:
+        raise nx.NetworkXError(f"node {str(s)} not in graph")
+    if t not in G:
+        raise nx.NetworkXError(f"node {str(t)} not in graph")
+    if s == t:
+        raise nx.NetworkXError("source and sink are the same node")
+
+    if residual is None:
+        R = build_residual_network(G, capacity)
+    else:
+        R = residual
+
+    R_nodes = R.nodes
+    R_pred = R.pred
+    R_succ = R.succ
+
+    # Initialize/reset the residual network.
+    for u in R:
+        for e in R_succ[u].values():
+            e["flow"] = 0
+
+    # Initialize heights of the nodes.
+    heights = {t: 0}
+    q = deque([(t, 0)])
+    while q:
+        u, height = q.popleft()
+        height += 1
+        for v, attr in R_pred[u].items():
+            if v not in heights and attr["flow"] < attr["capacity"]:
+                heights[v] = height
+                q.append((v, height))
+
+    if s not in heights:
+        # t is not reachable from s in the residual network. The maximum flow
+        # must be zero.
+        R.graph["flow_value"] = 0
+        return R
+
+    n = len(G)
+    m = R.size() / 2
+
+    # Initialize heights and 'current edge' data structures of the nodes.
+    for u in R:
+        R_nodes[u]["height"] = heights[u] if u in heights else n
+        R_nodes[u]["curr_edge"] = CurrentEdge(R_succ[u])
+
+    # Initialize counts of nodes in each level.
+    counts = [0] * (2 * n - 1)
+    for u in R:
+        counts[R_nodes[u]["height"]] += 1
+
+    inf = R.graph["inf"]
+
+    def augment(path):
+        """Augment flow along a path from s to t."""
+        # Determine the path residual capacity.
+        flow = inf
+        it = iter(path)
+        u = next(it)
+        for v in it:
+            attr = R_succ[u][v]
+            flow = min(flow, attr["capacity"] - attr["flow"])
+            u = v
+        if flow * 2 > inf:
+            raise nx.NetworkXUnbounded("Infinite capacity path, flow unbounded above.")
+        # Augment flow along the path.
+        it = iter(path)
+        u = next(it)
+        for v in it:
+            R_succ[u][v]["flow"] += flow
+            R_succ[v][u]["flow"] -= flow
+            u = v
+        return flow
+
+    def relabel(u):
+        """Relabel a node to create an admissible edge."""
+        height = n - 1
+        for v, attr in R_succ[u].items():
+            if attr["flow"] < attr["capacity"]:
+                height = min(height, R_nodes[v]["height"])
+        return height + 1
+
+    if cutoff is None:
+        cutoff = float("inf")
+
+    # Phase 1: Look for shortest augmenting paths using depth-first search.
+
+    flow_value = 0
+    path = [s]
+    u = s
+    d = n if not two_phase else int(min(m**0.5, 2 * n ** (2.0 / 3)))
+    done = R_nodes[s]["height"] >= d
+    while not done:
+        height = R_nodes[u]["height"]
+        curr_edge = R_nodes[u]["curr_edge"]
+        # Depth-first search for the next node on the path to t.
+        while True:
+            v, attr = curr_edge.get()
+            if height == R_nodes[v]["height"] + 1 and attr["flow"] < attr["capacity"]:
+                # Advance to the next node following an admissible edge.
+                path.append(v)
+                u = v
+                break
+            try:
+                curr_edge.move_to_next()
+            except StopIteration:
+                counts[height] -= 1
+                if counts[height] == 0:
+                    # Gap heuristic: If relabeling causes a level to become
+                    # empty, a minimum cut has been identified. The algorithm
+                    # can now be terminated.
+                    R.graph["flow_value"] = flow_value
+                    return R
+                height = relabel(u)
+                if u == s and height >= d:
+                    if not two_phase:
+                        # t is disconnected from s in the residual network. No
+                        # more augmenting paths exist.
+                        R.graph["flow_value"] = flow_value
+                        return R
+                    else:
+                        # t is at least d steps away from s. End of phase 1.
+                        done = True
+                        break
+                counts[height] += 1
+                R_nodes[u]["height"] = height
+                if u != s:
+                    # After relabeling, the last edge on the path is no longer
+                    # admissible. Retreat one step to look for an alternative.
+                    path.pop()
+                    u = path[-1]
+                    break
+        if u == t:
+            # t is reached. Augment flow along the path and reset it for a new
+            # depth-first search.
+            flow_value += augment(path)
+            if flow_value >= cutoff:
+                R.graph["flow_value"] = flow_value
+                return R
+            path = [s]
+            u = s
+
+    # Phase 2: Look for shortest augmenting paths using breadth-first search.
+    flow_value += edmonds_karp_core(R, s, t, cutoff - flow_value)
+
+    R.graph["flow_value"] = flow_value
+    return R
+
+
+@nx._dispatch(
+    graphs={"G": 0, "residual?": 4},
+    edge_attrs={"capacity": float("inf")},
+    preserve_edge_attrs={"residual": {"capacity": float("inf")}},
+    preserve_graph_attrs={"residual"},
+)
+def shortest_augmenting_path(
+    G,
+    s,
+    t,
+    capacity="capacity",
+    residual=None,
+    value_only=False,
+    two_phase=False,
+    cutoff=None,
+):
+    r"""Find a maximum single-commodity flow using the shortest augmenting path
+    algorithm.
+
+    This function returns the residual network resulting after computing
+    the maximum flow. See below for details about the conventions
+    NetworkX uses for defining residual networks.
+
+    This algorithm has a running time of $O(n^2 m)$ for $n$ nodes and $m$
+    edges.
+
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        Edges of the graph are expected to have an attribute called
+        'capacity'. If this attribute is not present, the edge is
+        considered to have infinite capacity.
+
+    s : node
+        Source node for the flow.
+
+    t : node
+        Sink node for the flow.
+
+    capacity : string
+        Edges of the graph G are expected to have an attribute capacity
+        that indicates how much flow the edge can support. If this
+        attribute is not present, the edge is considered to have
+        infinite capacity. Default value: 'capacity'.
+
+    residual : NetworkX graph
+        Residual network on which the algorithm is to be executed. If None, a
+        new residual network is created. Default value: None.
+
+    value_only : bool
+        If True compute only the value of the maximum flow. This parameter
+        will be ignored by this algorithm because it is not applicable.
+
+    two_phase : bool
+        If True, a two-phase variant is used. The two-phase variant improves
+        the running time on unit-capacity networks from $O(nm)$ to
+        $O(\min(n^{2/3}, m^{1/2}) m)$. Default value: False.
+
+    cutoff : integer, float
+        If specified, the algorithm will terminate when the flow value reaches
+        or exceeds the cutoff. In this case, it may be unable to immediately
+        determine a minimum cut. Default value: None.
+
+    Returns
+    -------
+    R : NetworkX DiGraph
+        Residual network after computing the maximum flow.
+
+    Raises
+    ------
+    NetworkXError
+        The algorithm does not support MultiGraph and MultiDiGraph. If
+        the input graph is an instance of one of these two classes, a
+        NetworkXError is raised.
+
+    NetworkXUnbounded
+        If the graph has a path of infinite capacity, the value of a
+        feasible flow on the graph is unbounded above and the function
+        raises a NetworkXUnbounded.
+
+    See also
+    --------
+    :meth:`maximum_flow`
+    :meth:`minimum_cut`
+    :meth:`edmonds_karp`
+    :meth:`preflow_push`
+
+    Notes
+    -----
+    The residual network :samp:`R` from an input graph :samp:`G` has the
+    same nodes as :samp:`G`. :samp:`R` is a DiGraph that contains a pair
+    of edges :samp:`(u, v)` and :samp:`(v, u)` iff :samp:`(u, v)` is not a
+    self-loop, and at least one of :samp:`(u, v)` and :samp:`(v, u)` exists
+    in :samp:`G`.
+
+    For each edge :samp:`(u, v)` in :samp:`R`, :samp:`R[u][v]['capacity']`
+    is equal to the capacity of :samp:`(u, v)` in :samp:`G` if it exists
+    in :samp:`G` or zero otherwise. If the capacity is infinite,
+    :samp:`R[u][v]['capacity']` will have a high arbitrary finite value
+    that does not affect the solution of the problem. This value is stored in
+    :samp:`R.graph['inf']`. For each edge :samp:`(u, v)` in :samp:`R`,
+    :samp:`R[u][v]['flow']` represents the flow function of :samp:`(u, v)` and
+    satisfies :samp:`R[u][v]['flow'] == -R[v][u]['flow']`.
+
+    The flow value, defined as the total flow into :samp:`t`, the sink, is
+    stored in :samp:`R.graph['flow_value']`. If :samp:`cutoff` is not
+    specified, reachability to :samp:`t` using only edges :samp:`(u, v)` such
+    that :samp:`R[u][v]['flow'] < R[u][v]['capacity']` induces a minimum
+    :samp:`s`-:samp:`t` cut.
+
+    Examples
+    --------
+    >>> from networkx.algorithms.flow import shortest_augmenting_path
+
+    The functions that implement flow algorithms and output a residual
+    network, such as this one, are not imported to the base NetworkX
+    namespace, so you have to explicitly import them from the flow package.
+
+    >>> G = nx.DiGraph()
+    >>> G.add_edge("x", "a", capacity=3.0)
+    >>> G.add_edge("x", "b", capacity=1.0)
+    >>> G.add_edge("a", "c", capacity=3.0)
+    >>> G.add_edge("b", "c", capacity=5.0)
+    >>> G.add_edge("b", "d", capacity=4.0)
+    >>> G.add_edge("d", "e", capacity=2.0)
+    >>> G.add_edge("c", "y", capacity=2.0)
+    >>> G.add_edge("e", "y", capacity=3.0)
+    >>> R = shortest_augmenting_path(G, "x", "y")
+    >>> flow_value = nx.maximum_flow_value(G, "x", "y")
+    >>> flow_value
+    3.0
+    >>> flow_value == R.graph["flow_value"]
+    True
+
+    """
+    R = shortest_augmenting_path_impl(G, s, t, capacity, residual, two_phase, cutoff)
+    R.graph["algorithm"] = "shortest_augmenting_path"
+    return R

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/flow/tests/test_mincost.py

@@ -0,0 +1,476 @@
+import bz2
+import importlib.resources
+import os
+import pickle
+
+import pytest
+
+import networkx as nx
+
+
+class TestMinCostFlow:
+    def test_simple_digraph(self):
+        G = nx.DiGraph()
+        G.add_node("a", demand=-5)
+        G.add_node("d", demand=5)
+        G.add_edge("a", "b", weight=3, capacity=4)
+        G.add_edge("a", "c", weight=6, capacity=10)
+        G.add_edge("b", "d", weight=1, capacity=9)
+        G.add_edge("c", "d", weight=2, capacity=5)
+        flowCost, H = nx.network_simplex(G)
+        soln = {"a": {"b": 4, "c": 1}, "b": {"d": 4}, "c": {"d": 1}, "d": {}}
+        assert flowCost == 24
+        assert nx.min_cost_flow_cost(G) == 24
+        assert H == soln
+        assert nx.min_cost_flow(G) == soln
+        assert nx.cost_of_flow(G, H) == 24
+
+        flowCost, H = nx.capacity_scaling(G)
+        assert flowCost == 24
+        assert nx.cost_of_flow(G, H) == 24
+        assert H == soln
+
+    def test_negcycle_infcap(self):
+        G = nx.DiGraph()
+        G.add_node("s", demand=-5)
+        G.add_node("t", demand=5)
+        G.add_edge("s", "a", weight=1, capacity=3)
+        G.add_edge("a", "b", weight=3)
+        G.add_edge("c", "a", weight=-6)
+        G.add_edge("b", "d", weight=1)
+        G.add_edge("d", "c", weight=-2)
+        G.add_edge("d", "t", weight=1, capacity=3)
+        pytest.raises(nx.NetworkXUnfeasible, nx.network_simplex, G)
+        pytest.raises(nx.NetworkXUnbounded, nx.capacity_scaling, G)
+
+    def test_sum_demands_not_zero(self):
+        G = nx.DiGraph()
+        G.add_node("s", demand=-5)
+        G.add_node("t", demand=4)
+        G.add_edge("s", "a", weight=1, capacity=3)
+        G.add_edge("a", "b", weight=3)
+        G.add_edge("a", "c", weight=-6)
+        G.add_edge("b", "d", weight=1)
+        G.add_edge("c", "d", weight=-2)
+        G.add_edge("d", "t", weight=1, capacity=3)
+        pytest.raises(nx.NetworkXUnfeasible, nx.network_simplex, G)
+        pytest.raises(nx.NetworkXUnfeasible, nx.capacity_scaling, G)
+
+    def test_no_flow_satisfying_demands(self):
+        G = nx.DiGraph()
+        G.add_node("s", demand=-5)
+        G.add_node("t", demand=5)
+        G.add_edge("s", "a", weight=1, capacity=3)
+        G.add_edge("a", "b", weight=3)
+        G.add_edge("a", "c", weight=-6)
+        G.add_edge("b", "d", weight=1)
+        G.add_edge("c", "d", weight=-2)
+        G.add_edge("d", "t", weight=1, capacity=3)
+        pytest.raises(nx.NetworkXUnfeasible, nx.network_simplex, G)
+        pytest.raises(nx.NetworkXUnfeasible, nx.capacity_scaling, G)
+
+    def test_transshipment(self):
+        G = nx.DiGraph()
+        G.add_node("a", demand=1)
+        G.add_node("b", demand=-2)
+        G.add_node("c", demand=-2)
+        G.add_node("d", demand=3)
+        G.add_node("e", demand=-4)
+        G.add_node("f", demand=-4)
+        G.add_node("g", demand=3)
+        G.add_node("h", demand=2)
+        G.add_node("r", demand=3)
+        G.add_edge("a", "c", weight=3)
+        G.add_edge("r", "a", weight=2)
+        G.add_edge("b", "a", weight=9)
+        G.add_edge("r", "c", weight=0)
+        G.add_edge("b", "r", weight=-6)
+        G.add_edge("c", "d", weight=5)
+        G.add_edge("e", "r", weight=4)
+        G.add_edge("e", "f", weight=3)
+        G.add_edge("h", "b", weight=4)
+        G.add_edge("f", "d", weight=7)
+        G.add_edge("f", "h", weight=12)
+        G.add_edge("g", "d", weight=12)
+        G.add_edge("f", "g", weight=-1)
+        G.add_edge("h", "g", weight=-10)
+        flowCost, H = nx.network_simplex(G)
+        soln = {
+            "a": {"c": 0},
+            "b": {"a": 0, "r": 2},
+            "c": {"d": 3},
+            "d": {},
+            "e": {"r": 3, "f": 1},
+            "f": {"d": 0, "g": 3, "h": 2},
+            "g": {"d": 0},
+            "h": {"b": 0, "g": 0},
+            "r": {"a": 1, "c": 1},
+        }
+        assert flowCost == 41
+        assert nx.min_cost_flow_cost(G) == 41
+        assert H == soln
+        assert nx.min_cost_flow(G) == soln
+        assert nx.cost_of_flow(G, H) == 41
+
+        flowCost, H = nx.capacity_scaling(G)
+        assert flowCost == 41
+        assert nx.cost_of_flow(G, H) == 41
+        assert H == soln
+
+    def test_max_flow_min_cost(self):
+        G = nx.DiGraph()
+        G.add_edge("s", "a", bandwidth=6)
+        G.add_edge("s", "c", bandwidth=10, cost=10)
+        G.add_edge("a", "b", cost=6)
+        G.add_edge("b", "d", bandwidth=8, cost=7)
+        G.add_edge("c", "d", cost=10)
+        G.add_edge("d", "t", bandwidth=5, cost=5)
+        soln = {
+            "s": {"a": 5, "c": 0},
+            "a": {"b": 5},
+            "b": {"d": 5},
+            "c": {"d": 0},
+            "d": {"t": 5},
+            "t": {},
+        }
+        flow = nx.max_flow_min_cost(G, "s", "t", capacity="bandwidth", weight="cost")
+        assert flow == soln
+        assert nx.cost_of_flow(G, flow, weight="cost") == 90
+
+        G.add_edge("t", "s", cost=-100)
+        flowCost, flow = nx.capacity_scaling(G, capacity="bandwidth", weight="cost")
+        G.remove_edge("t", "s")
+        assert flowCost == -410
+        assert flow["t"]["s"] == 5
+        del flow["t"]["s"]
+        assert flow == soln
+        assert nx.cost_of_flow(G, flow, weight="cost") == 90
+
+    def test_digraph1(self):
+        # From Bradley, S. P., Hax, A. C. and Magnanti, T. L. Applied
+        # Mathematical Programming. Addison-Wesley, 1977.
+        G = nx.DiGraph()
+        G.add_node(1, demand=-20)
+        G.add_node(4, demand=5)
+        G.add_node(5, demand=15)
+        G.add_edges_from(
+            [
+                (1, 2, {"capacity": 15, "weight": 4}),
+                (1, 3, {"capacity": 8, "weight": 4}),
+                (2, 3, {"weight": 2}),
+                (2, 4, {"capacity": 4, "weight": 2}),
+                (2, 5, {"capacity": 10, "weight": 6}),
+                (3, 4, {"capacity": 15, "weight": 1}),
+                (3, 5, {"capacity": 5, "weight": 3}),
+                (4, 5, {"weight": 2}),
+                (5, 3, {"capacity": 4, "weight": 1}),
+            ]
+        )
+        flowCost, H = nx.network_simplex(G)
+        soln = {
+            1: {2: 12, 3: 8},
+            2: {3: 8, 4: 4, 5: 0},
+            3: {4: 11, 5: 5},
+            4: {5: 10},
+            5: {3: 0},
+        }
+        assert flowCost == 150
+        assert nx.min_cost_flow_cost(G) == 150
+        assert H == soln
+        assert nx.min_cost_flow(G) == soln
+        assert nx.cost_of_flow(G, H) == 150
+
+        flowCost, H = nx.capacity_scaling(G)
+        assert flowCost == 150
+        assert H == soln
+        assert nx.cost_of_flow(G, H) == 150
+
+    def test_digraph2(self):
+        # Example from ticket #430 from mfrasca. Original source:
+        # http://www.cs.princeton.edu/courses/archive/spr03/cs226/lectures/mincost.4up.pdf, slide 11.
+        G = nx.DiGraph()
+        G.add_edge("s", 1, capacity=12)
+        G.add_edge("s", 2, capacity=6)
+        G.add_edge("s", 3, capacity=14)
+        G.add_edge(1, 2, capacity=11, weight=4)
+        G.add_edge(2, 3, capacity=9, weight=6)
+        G.add_edge(1, 4, capacity=5, weight=5)
+        G.add_edge(1, 5, capacity=2, weight=12)
+        G.add_edge(2, 5, capacity=4, weight=4)
+        G.add_edge(2, 6, capacity=2, weight=6)
+        G.add_edge(3, 6, capacity=31, weight=3)
+        G.add_edge(4, 5, capacity=18, weight=4)
+        G.add_edge(5, 6, capacity=9, weight=5)
+        G.add_edge(4, "t", capacity=3)
+        G.add_edge(5, "t", capacity=7)
+        G.add_edge(6, "t", capacity=22)
+        flow = nx.max_flow_min_cost(G, "s", "t")
+        soln = {
+            1: {2: 6, 4: 5, 5: 1},
+            2: {3: 6, 5: 4, 6: 2},
+            3: {6: 20},
+            4: {5: 2, "t": 3},
+            5: {6: 0, "t": 7},
+            6: {"t": 22},
+            "s": {1: 12, 2: 6, 3: 14},
+            "t": {},
+        }
+        assert flow == soln
+
+        G.add_edge("t", "s", weight=-100)
+        flowCost, flow = nx.capacity_scaling(G)
+        G.remove_edge("t", "s")
+        assert flow["t"]["s"] == 32
+        assert flowCost == -3007
+        del flow["t"]["s"]
+        assert flow == soln
+        assert nx.cost_of_flow(G, flow) == 193
+
+    def test_digraph3(self):
+        """Combinatorial Optimization: Algorithms and Complexity,
+        Papadimitriou Steiglitz at page 140 has an example, 7.1, but that
+        admits multiple solutions, so I alter it a bit. From ticket #430
+        by mfrasca."""
+
+        G = nx.DiGraph()
+        G.add_edge("s", "a")
+        G["s"]["a"].update({0: 2, 1: 4})
+        G.add_edge("s", "b")
+        G["s"]["b"].update({0: 2, 1: 1})
+        G.add_edge("a", "b")
+        G["a"]["b"].update({0: 5, 1: 2})
+        G.add_edge("a", "t")
+        G["a"]["t"].update({0: 1, 1: 5})
+        G.add_edge("b", "a")
+        G["b"]["a"].update({0: 1, 1: 3})
+        G.add_edge("b", "t")
+        G["b"]["t"].update({0: 3, 1: 2})
+
+        "PS.ex.7.1: testing main function"
+        sol = nx.max_flow_min_cost(G, "s", "t", capacity=0, weight=1)
+        flow = sum(v for v in sol["s"].values())
+        assert 4 == flow
+        assert 23 == nx.cost_of_flow(G, sol, weight=1)
+        assert sol["s"] == {"a": 2, "b": 2}
+        assert sol["a"] == {"b": 1, "t": 1}
+        assert sol["b"] == {"a": 0, "t": 3}
+        assert sol["t"] == {}
+
+        G.add_edge("t", "s")
+        G["t"]["s"].update({1: -100})
+        flowCost, sol = nx.capacity_scaling(G, capacity=0, weight=1)
+        G.remove_edge("t", "s")
+        flow = sum(v for v in sol["s"].values())
+        assert 4 == flow
+        assert sol["t"]["s"] == 4
+        assert flowCost == -377
+        del sol["t"]["s"]
+        assert sol["s"] == {"a": 2, "b": 2}
+        assert sol["a"] == {"b": 1, "t": 1}
+        assert sol["b"] == {"a": 0, "t": 3}
+        assert sol["t"] == {}
+        assert nx.cost_of_flow(G, sol, weight=1) == 23
+
+    def test_zero_capacity_edges(self):
+        """Address issue raised in ticket #617 by arv."""
+        G = nx.DiGraph()
+        G.add_edges_from(
+            [
+                (1, 2, {"capacity": 1, "weight": 1}),
+                (1, 5, {"capacity": 1, "weight": 1}),
+                (2, 3, {"capacity": 0, "weight": 1}),
+                (2, 5, {"capacity": 1, "weight": 1}),
+                (5, 3, {"capacity": 2, "weight": 1}),
+                (5, 4, {"capacity": 0, "weight": 1}),
+                (3, 4, {"capacity": 2, "weight": 1}),
+            ]
+        )
+        G.nodes[1]["demand"] = -1
+        G.nodes[2]["demand"] = -1
+        G.nodes[4]["demand"] = 2
+
+        flowCost, H = nx.network_simplex(G)
+        soln = {1: {2: 0, 5: 1}, 2: {3: 0, 5: 1}, 3: {4: 2}, 4: {}, 5: {3: 2, 4: 0}}
+        assert flowCost == 6
+        assert nx.min_cost_flow_cost(G) == 6
+        assert H == soln
+        assert nx.min_cost_flow(G) == soln
+        assert nx.cost_of_flow(G, H) == 6
+
+        flowCost, H = nx.capacity_scaling(G)
+        assert flowCost == 6
+        assert H == soln
+        assert nx.cost_of_flow(G, H) == 6
+
+    def test_digon(self):
+        """Check if digons are handled properly. Taken from ticket
+        #618 by arv."""
+        nodes = [(1, {}), (2, {"demand": -4}), (3, {"demand": 4})]
+        edges = [
+            (1, 2, {"capacity": 3, "weight": 600000}),
+            (2, 1, {"capacity": 2, "weight": 0}),
+            (2, 3, {"capacity": 5, "weight": 714285}),
+            (3, 2, {"capacity": 2, "weight": 0}),
+        ]
+        G = nx.DiGraph(edges)
+        G.add_nodes_from(nodes)
+        flowCost, H = nx.network_simplex(G)
+        soln = {1: {2: 0}, 2: {1: 0, 3: 4}, 3: {2: 0}}
+        assert flowCost == 2857140
+        assert nx.min_cost_flow_cost(G) == 2857140
+        assert H == soln
+        assert nx.min_cost_flow(G) == soln
+        assert nx.cost_of_flow(G, H) == 2857140
+
+        flowCost, H = nx.capacity_scaling(G)
+        assert flowCost == 2857140
+        assert H == soln
+        assert nx.cost_of_flow(G, H) == 2857140
+
+    def test_deadend(self):
+        """Check if one-node cycles are handled properly. Taken from ticket
+        #2906 from @sshraven."""
+        G = nx.DiGraph()
+
+        G.add_nodes_from(range(5), demand=0)
+        G.nodes[4]["demand"] = -13
+        G.nodes[3]["demand"] = 13
+
+        G.add_edges_from([(0, 2), (0, 3), (2, 1)], capacity=20, weight=0.1)
+        pytest.raises(nx.NetworkXUnfeasible, nx.min_cost_flow, G)
+
+    def test_infinite_capacity_neg_digon(self):
+        """An infinite capacity negative cost digon results in an unbounded
+        instance."""
+        nodes = [(1, {}), (2, {"demand": -4}), (3, {"demand": 4})]
+        edges = [
+            (1, 2, {"weight": -600}),
+            (2, 1, {"weight": 0}),
+            (2, 3, {"capacity": 5, "weight": 714285}),
+            (3, 2, {"capacity": 2, "weight": 0}),
+        ]
+        G = nx.DiGraph(edges)
+        G.add_nodes_from(nodes)
+        pytest.raises(nx.NetworkXUnbounded, nx.network_simplex, G)
+        pytest.raises(nx.NetworkXUnbounded, nx.capacity_scaling, G)
+
+    def test_finite_capacity_neg_digon(self):
+        """The digon should receive the maximum amount of flow it can handle.
+        Taken from ticket #749 by @chuongdo."""
+        G = nx.DiGraph()
+        G.add_edge("a", "b", capacity=1, weight=-1)
+        G.add_edge("b", "a", capacity=1, weight=-1)
+        min_cost = -2
+        assert nx.min_cost_flow_cost(G) == min_cost
+
+        flowCost, H = nx.capacity_scaling(G)
+        assert flowCost == -2
+        assert H == {"a": {"b": 1}, "b": {"a": 1}}
+        assert nx.cost_of_flow(G, H) == -2
+
+    def test_multidigraph(self):
+        """Multidigraphs are acceptable."""
+        G = nx.MultiDiGraph()
+        G.add_weighted_edges_from([(1, 2, 1), (2, 3, 2)], weight="capacity")
+        flowCost, H = nx.network_simplex(G)
+        assert flowCost == 0
+        assert H == {1: {2: {0: 0}}, 2: {3: {0: 0}}, 3: {}}
+
+        flowCost, H = nx.capacity_scaling(G)
+        assert flowCost == 0
+        assert H == {1: {2: {0: 0}}, 2: {3: {0: 0}}, 3: {}}
+
+    def test_negative_selfloops(self):
+        """Negative selfloops should cause an exception if uncapacitated and
+        always be saturated otherwise.
+        """
+        G = nx.DiGraph()
+        G.add_edge(1, 1, weight=-1)
+        pytest.raises(nx.NetworkXUnbounded, nx.network_simplex, G)
+        pytest.raises(nx.NetworkXUnbounded, nx.capacity_scaling, G)
+        G[1][1]["capacity"] = 2
+        flowCost, H = nx.network_simplex(G)
+        assert flowCost == -2
+        assert H == {1: {1: 2}}
+        flowCost, H = nx.capacity_scaling(G)
+        assert flowCost == -2
+        assert H == {1: {1: 2}}
+
+        G = nx.MultiDiGraph()
+        G.add_edge(1, 1, "x", weight=-1)
+        G.add_edge(1, 1, "y", weight=1)
+        pytest.raises(nx.NetworkXUnbounded, nx.network_simplex, G)
+        pytest.raises(nx.NetworkXUnbounded, nx.capacity_scaling, G)
+        G[1][1]["x"]["capacity"] = 2
+        flowCost, H = nx.network_simplex(G)
+        assert flowCost == -2
+        assert H == {1: {1: {"x": 2, "y": 0}}}
+        flowCost, H = nx.capacity_scaling(G)
+        assert flowCost == -2
+        assert H == {1: {1: {"x": 2, "y": 0}}}
+
+    def test_bone_shaped(self):
+        # From #1283
+        G = nx.DiGraph()
+        G.add_node(0, demand=-4)
+        G.add_node(1, demand=2)
+        G.add_node(2, demand=2)
+        G.add_node(3, demand=4)
+        G.add_node(4, demand=-2)
+        G.add_node(5, demand=-2)
+        G.add_edge(0, 1, capacity=4)
+        G.add_edge(0, 2, capacity=4)
+        G.add_edge(4, 3, capacity=4)
+        G.add_edge(5, 3, capacity=4)
+        G.add_edge(0, 3, capacity=0)
+        flowCost, H = nx.network_simplex(G)
+        assert flowCost == 0
+        assert H == {0: {1: 2, 2: 2, 3: 0}, 1: {}, 2: {}, 3: {}, 4: {3: 2}, 5: {3: 2}}
+        flowCost, H = nx.capacity_scaling(G)
+        assert flowCost == 0
+        assert H == {0: {1: 2, 2: 2, 3: 0}, 1: {}, 2: {}, 3: {}, 4: {3: 2}, 5: {3: 2}}
+
+    def test_exceptions(self):
+        G = nx.Graph()
+        pytest.raises(nx.NetworkXNotImplemented, nx.network_simplex, G)
+        pytest.raises(nx.NetworkXNotImplemented, nx.capacity_scaling, G)
+        G = nx.MultiGraph()
+        pytest.raises(nx.NetworkXNotImplemented, nx.network_simplex, G)
+        pytest.raises(nx.NetworkXNotImplemented, nx.capacity_scaling, G)
+        G = nx.DiGraph()
+        pytest.raises(nx.NetworkXError, nx.network_simplex, G)
+        # pytest.raises(nx.NetworkXError, nx.capacity_scaling, G)
+        G.add_node(0, demand=float("inf"))
+        pytest.raises(nx.NetworkXError, nx.network_simplex, G)
+        pytest.raises(nx.NetworkXUnfeasible, nx.capacity_scaling, G)
+        G.nodes[0]["demand"] = 0
+        G.add_node(1, demand=0)
+        G.add_edge(0, 1, weight=-float("inf"))
+        pytest.raises(nx.NetworkXError, nx.network_simplex, G)
+        pytest.raises(nx.NetworkXUnfeasible, nx.capacity_scaling, G)
+        G[0][1]["weight"] = 0
+        G.add_edge(0, 0, weight=float("inf"))
+        pytest.raises(nx.NetworkXError, nx.network_simplex, G)
+        # pytest.raises(nx.NetworkXError, nx.capacity_scaling, G)
+        G[0][0]["weight"] = 0
+        G[0][1]["capacity"] = -1
+        pytest.raises(nx.NetworkXUnfeasible, nx.network_simplex, G)
+        # pytest.raises(nx.NetworkXUnfeasible, nx.capacity_scaling, G)
+        G[0][1]["capacity"] = 0
+        G[0][0]["capacity"] = -1
+        pytest.raises(nx.NetworkXUnfeasible, nx.network_simplex, G)
+        # pytest.raises(nx.NetworkXUnfeasible, nx.capacity_scaling, G)
+
+    def test_large(self):
+        fname = (
+            importlib.resources.files("networkx.algorithms.flow.tests")
+            / "netgen-2.gpickle.bz2"
+        )
+        with bz2.BZ2File(fname, "rb") as f:
+            G = pickle.load(f)
+        flowCost, flowDict = nx.network_simplex(G)
+        assert 6749969302 == flowCost
+        assert 6749969302 == nx.cost_of_flow(G, flowDict)
+        flowCost, flowDict = nx.capacity_scaling(G)
+        assert 6749969302 == flowCost
+        assert 6749969302 == nx.cost_of_flow(G, flowDict)

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/graph_hashing.py

@@ -0,0 +1,313 @@
+"""
+Functions for hashing graphs to strings.
+Isomorphic graphs should be assigned identical hashes.
+For now, only Weisfeiler-Lehman hashing is implemented.
+"""
+
+from collections import Counter, defaultdict
+from hashlib import blake2b
+
+import networkx as nx
+
+__all__ = ["weisfeiler_lehman_graph_hash", "weisfeiler_lehman_subgraph_hashes"]
+
+
+def _hash_label(label, digest_size):
+    return blake2b(label.encode("ascii"), digest_size=digest_size).hexdigest()
+
+
+def _init_node_labels(G, edge_attr, node_attr):
+    if node_attr:
+        return {u: str(dd[node_attr]) for u, dd in G.nodes(data=True)}
+    elif edge_attr:
+        return {u: "" for u in G}
+    else:
+        return {u: str(deg) for u, deg in G.degree()}
+
+
+def _neighborhood_aggregate(G, node, node_labels, edge_attr=None):
+    """
+    Compute new labels for given node by aggregating
+    the labels of each node's neighbors.
+    """
+    label_list = []
+    for nbr in G.neighbors(node):
+        prefix = "" if edge_attr is None else str(G[node][nbr][edge_attr])
+        label_list.append(prefix + node_labels[nbr])
+    return node_labels[node] + "".join(sorted(label_list))
+
+
+@nx._dispatch(edge_attrs={"edge_attr": None}, node_attrs="node_attr")
+def weisfeiler_lehman_graph_hash(
+    G, edge_attr=None, node_attr=None, iterations=3, digest_size=16
+):
+    """Return Weisfeiler Lehman (WL) graph hash.
+
+    The function iteratively aggregates and hashes neighbourhoods of each node.
+    After each node's neighbors are hashed to obtain updated node labels,
+    a hashed histogram of resulting labels is returned as the final hash.
+
+    Hashes are identical for isomorphic graphs and strong guarantees that
+    non-isomorphic graphs will get different hashes. See [1]_ for details.
+
+    If no node or edge attributes are provided, the degree of each node
+    is used as its initial label.
+    Otherwise, node and/or edge labels are used to compute the hash.
+
+    Parameters
+    ----------
+    G: graph
+        The graph to be hashed.
+        Can have node and/or edge attributes. Can also have no attributes.
+    edge_attr: string, default=None
+        The key in edge attribute dictionary to be used for hashing.
+        If None, edge labels are ignored.
+    node_attr: string, default=None
+        The key in node attribute dictionary to be used for hashing.
+        If None, and no edge_attr given, use the degrees of the nodes as labels.
+    iterations: int, default=3
+        Number of neighbor aggregations to perform.
+        Should be larger for larger graphs.
+    digest_size: int, default=16
+        Size (in bits) of blake2b hash digest to use for hashing node labels.
+
+    Returns
+    -------
+    h : string
+        Hexadecimal string corresponding to hash of the input graph.
+
+    Examples
+    --------
+    Two graphs with edge attributes that are isomorphic, except for
+    differences in the edge labels.
+
+    >>> G1 = nx.Graph()
+    >>> G1.add_edges_from(
+    ...     [
+    ...         (1, 2, {"label": "A"}),
+    ...         (2, 3, {"label": "A"}),
+    ...         (3, 1, {"label": "A"}),
+    ...         (1, 4, {"label": "B"}),
+    ...     ]
+    ... )
+    >>> G2 = nx.Graph()
+    >>> G2.add_edges_from(
+    ...     [
+    ...         (5, 6, {"label": "B"}),
+    ...         (6, 7, {"label": "A"}),
+    ...         (7, 5, {"label": "A"}),
+    ...         (7, 8, {"label": "A"}),
+    ...     ]
+    ... )
+
+    Omitting the `edge_attr` option, results in identical hashes.
+
+    >>> nx.weisfeiler_lehman_graph_hash(G1)
+    '7bc4dde9a09d0b94c5097b219891d81a'
+    >>> nx.weisfeiler_lehman_graph_hash(G2)
+    '7bc4dde9a09d0b94c5097b219891d81a'
+
+    With edge labels, the graphs are no longer assigned
+    the same hash digest.
+
+    >>> nx.weisfeiler_lehman_graph_hash(G1, edge_attr="label")
+    'c653d85538bcf041d88c011f4f905f10'
+    >>> nx.weisfeiler_lehman_graph_hash(G2, edge_attr="label")
+    '3dcd84af1ca855d0eff3c978d88e7ec7'
+
+    Notes
+    -----
+    To return the WL hashes of each subgraph of a graph, use
+    `weisfeiler_lehman_subgraph_hashes`
+
+    Similarity between hashes does not imply similarity between graphs.
+
+    References
+    ----------
+    .. [1] Shervashidze, Nino, Pascal Schweitzer, Erik Jan Van Leeuwen,
+       Kurt Mehlhorn, and Karsten M. Borgwardt. Weisfeiler Lehman
+       Graph Kernels. Journal of Machine Learning Research. 2011.
+       http://www.jmlr.org/papers/volume12/shervashidze11a/shervashidze11a.pdf
+
+    See also
+    --------
+    weisfeiler_lehman_subgraph_hashes
+    """
+
+    def weisfeiler_lehman_step(G, labels, edge_attr=None):
+        """
+        Apply neighborhood aggregation to each node
+        in the graph.
+        Computes a dictionary with labels for each node.
+        """
+        new_labels = {}
+        for node in G.nodes():
+            label = _neighborhood_aggregate(G, node, labels, edge_attr=edge_attr)
+            new_labels[node] = _hash_label(label, digest_size)
+        return new_labels
+
+    # set initial node labels
+    node_labels = _init_node_labels(G, edge_attr, node_attr)
+
+    subgraph_hash_counts = []
+    for _ in range(iterations):
+        node_labels = weisfeiler_lehman_step(G, node_labels, edge_attr=edge_attr)
+        counter = Counter(node_labels.values())
+        # sort the counter, extend total counts
+        subgraph_hash_counts.extend(sorted(counter.items(), key=lambda x: x[0]))
+
+    # hash the final counter
+    return _hash_label(str(tuple(subgraph_hash_counts)), digest_size)
+
+
+@nx._dispatch(edge_attrs={"edge_attr": None}, node_attrs="node_attr")
+def weisfeiler_lehman_subgraph_hashes(
+    G, edge_attr=None, node_attr=None, iterations=3, digest_size=16
+):
+    """
+    Return a dictionary of subgraph hashes by node.
+
+    Dictionary keys are nodes in `G`, and values are a list of hashes.
+    Each hash corresponds to a subgraph rooted at a given node u in `G`.
+    Lists of subgraph hashes are sorted in increasing order of depth from
+    their root node, with the hash at index i corresponding to a subgraph
+    of nodes at most i edges distance from u. Thus, each list will contain
+    ``iterations + 1`` elements - a hash for a subgraph at each depth, and
+    additionally a hash of the initial node label (or equivalently a
+    subgraph of depth 0)
+
+    The function iteratively aggregates and hashes neighbourhoods of each node.
+    This is achieved for each step by replacing for each node its label from
+    the previous iteration with its hashed 1-hop neighborhood aggregate.
+    The new node label is then appended to a list of node labels for each
+    node.
+
+    To aggregate neighborhoods at each step for a node $n$, all labels of
+    nodes adjacent to $n$ are concatenated. If the `edge_attr` parameter is set,
+    labels for each neighboring node are prefixed with the value of this attribute
+    along the connecting edge from this neighbor to node $n$. The resulting string
+    is then hashed to compress this information into a fixed digest size.
+
+    Thus, at the $i$-th iteration, nodes within $i$ hops influence any given
+    hashed node label. We can therefore say that at depth $i$ for node $n$
+    we have a hash for a subgraph induced by the $2i$-hop neighborhood of $n$.
+
+    The output can be used to to create general Weisfeiler-Lehman graph kernels,
+    or generate features for graphs or nodes - for example to generate 'words' in
+    a graph as seen in the 'graph2vec' algorithm.
+    See [1]_ & [2]_ respectively for details.
+
+    Hashes are identical for isomorphic subgraphs and there exist strong
+    guarantees that non-isomorphic graphs will get different hashes.
+    See [1]_ for details.
+
+    If no node or edge attributes are provided, the degree of each node
+    is used as its initial label.
+    Otherwise, node and/or edge labels are used to compute the hash.
+
+    Parameters
+    ----------
+    G: graph
+        The graph to be hashed.
+        Can have node and/or edge attributes. Can also have no attributes.
+    edge_attr: string, default=None
+        The key in edge attribute dictionary to be used for hashing.
+        If None, edge labels are ignored.
+    node_attr: string, default=None
+        The key in node attribute dictionary to be used for hashing.
+        If None, and no edge_attr given, use the degrees of the nodes as labels.
+    iterations: int, default=3
+        Number of neighbor aggregations to perform.
+        Should be larger for larger graphs.
+    digest_size: int, default=16
+        Size (in bits) of blake2b hash digest to use for hashing node labels.
+        The default size is 16 bits
+
+    Returns
+    -------
+    node_subgraph_hashes : dict
+        A dictionary with each key given by a node in G, and each value given
+        by the subgraph hashes in order of depth from the key node.
+
+    Examples
+    --------
+    Finding similar nodes in different graphs:
+
+    >>> G1 = nx.Graph()
+    >>> G1.add_edges_from([
+    ...     (1, 2), (2, 3), (2, 4), (3, 5), (4, 6), (5, 7), (6, 7)
+    ... ])
+    >>> G2 = nx.Graph()
+    >>> G2.add_edges_from([
+    ...     (1, 3), (2, 3), (1, 6), (1, 5), (4, 6)
+    ... ])
+    >>> g1_hashes = nx.weisfeiler_lehman_subgraph_hashes(G1, iterations=3, digest_size=8)
+    >>> g2_hashes = nx.weisfeiler_lehman_subgraph_hashes(G2, iterations=3, digest_size=8)
+
+    Even though G1 and G2 are not isomorphic (they have different numbers of edges),
+    the hash sequence of depth 3 for node 1 in G1 and node 5 in G2 are similar:
+
+    >>> g1_hashes[1]
+    ['a93b64973cfc8897', 'db1b43ae35a1878f', '57872a7d2059c1c0']
+    >>> g2_hashes[5]
+    ['a93b64973cfc8897', 'db1b43ae35a1878f', '1716d2a4012fa4bc']
+
+    The first 2 WL subgraph hashes match. From this we can conclude that it's very
+    likely the neighborhood of 4 hops around these nodes are isomorphic: each
+    iteration aggregates 1-hop neighbourhoods meaning hashes at depth $n$ are influenced
+    by every node within $2n$ hops.
+
+    However the neighborhood of 6 hops is no longer isomorphic since their 3rd hash does
+    not match.
+
+    These nodes may be candidates to be classified together since their local topology
+    is similar.
+
+    Notes
+    -----
+    To hash the full graph when subgraph hashes are not needed, use
+    `weisfeiler_lehman_graph_hash` for efficiency.
+
+    Similarity between hashes does not imply similarity between graphs.
+
+    References
+    ----------
+    .. [1] Shervashidze, Nino, Pascal Schweitzer, Erik Jan Van Leeuwen,
+       Kurt Mehlhorn, and Karsten M. Borgwardt. Weisfeiler Lehman
+       Graph Kernels. Journal of Machine Learning Research. 2011.
+       http://www.jmlr.org/papers/volume12/shervashidze11a/shervashidze11a.pdf
+    .. [2] Annamalai Narayanan, Mahinthan Chandramohan, Rajasekar Venkatesan,
+       Lihui Chen, Yang Liu and Shantanu Jaiswa. graph2vec: Learning
+       Distributed Representations of Graphs. arXiv. 2017
+       https://arxiv.org/pdf/1707.05005.pdf
+
+    See also
+    --------
+    weisfeiler_lehman_graph_hash
+    """
+
+    def weisfeiler_lehman_step(G, labels, node_subgraph_hashes, edge_attr=None):
+        """
+        Apply neighborhood aggregation to each node
+        in the graph.
+        Computes a dictionary with labels for each node.
+        Appends the new hashed label to the dictionary of subgraph hashes
+        originating from and indexed by each node in G
+        """
+        new_labels = {}
+        for node in G.nodes():
+            label = _neighborhood_aggregate(G, node, labels, edge_attr=edge_attr)
+            hashed_label = _hash_label(label, digest_size)
+            new_labels[node] = hashed_label
+            node_subgraph_hashes[node].append(hashed_label)
+        return new_labels
+
+    node_labels = _init_node_labels(G, edge_attr, node_attr)
+
+    node_subgraph_hashes = defaultdict(list)
+    for _ in range(iterations):
+        node_labels = weisfeiler_lehman_step(
+            G, node_labels, node_subgraph_hashes, edge_attr
+        )
+
+    return dict(node_subgraph_hashes)

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/graphical.py

@@ -0,0 +1,483 @@
+"""Test sequences for graphiness.
+"""
+import heapq
+
+import networkx as nx
+
+__all__ = [
+    "is_graphical",
+    "is_multigraphical",
+    "is_pseudographical",
+    "is_digraphical",
+    "is_valid_degree_sequence_erdos_gallai",
+    "is_valid_degree_sequence_havel_hakimi",
+]
+
+
+@nx._dispatch(graphs=None)
+def is_graphical(sequence, method="eg"):
+    """Returns True if sequence is a valid degree sequence.
+
+    A degree sequence is valid if some graph can realize it.
+
+    Parameters
+    ----------
+    sequence : list or iterable container
+        A sequence of integer node degrees
+
+    method : "eg" | "hh"  (default: 'eg')
+        The method used to validate the degree sequence.
+        "eg" corresponds to the Erdős-Gallai algorithm
+        [EG1960]_, [choudum1986]_, and
+        "hh" to the Havel-Hakimi algorithm
+        [havel1955]_, [hakimi1962]_, [CL1996]_.
+
+    Returns
+    -------
+    valid : bool
+        True if the sequence is a valid degree sequence and False if not.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> sequence = (d for n, d in G.degree())
+    >>> nx.is_graphical(sequence)
+    True
+
+    To test a non-graphical sequence:
+    >>> sequence_list = [d for n, d in G.degree()]
+    >>> sequence_list[-1] += 1
+    >>> nx.is_graphical(sequence_list)
+    False
+
+    References
+    ----------
+    .. [EG1960] Erdős and Gallai, Mat. Lapok 11 264, 1960.
+    .. [choudum1986] S.A. Choudum. "A simple proof of the Erdős-Gallai theorem on
+       graph sequences." Bulletin of the Australian Mathematical Society, 33,
+       pp 67-70, 1986. https://doi.org/10.1017/S0004972700002872
+    .. [havel1955] Havel, V. "A Remark on the Existence of Finite Graphs"
+       Casopis Pest. Mat. 80, 477-480, 1955.
+    .. [hakimi1962] Hakimi, S. "On the Realizability of a Set of Integers as
+       Degrees of the Vertices of a Graph." SIAM J. Appl. Math. 10, 496-506, 1962.
+    .. [CL1996] G. Chartrand and L. Lesniak, "Graphs and Digraphs",
+       Chapman and Hall/CRC, 1996.
+    """
+    if method == "eg":
+        valid = is_valid_degree_sequence_erdos_gallai(list(sequence))
+    elif method == "hh":
+        valid = is_valid_degree_sequence_havel_hakimi(list(sequence))
+    else:
+        msg = "`method` must be 'eg' or 'hh'"
+        raise nx.NetworkXException(msg)
+    return valid
+
+
+def _basic_graphical_tests(deg_sequence):
+    # Sort and perform some simple tests on the sequence
+    deg_sequence = nx.utils.make_list_of_ints(deg_sequence)
+    p = len(deg_sequence)
+    num_degs = [0] * p
+    dmax, dmin, dsum, n = 0, p, 0, 0
+    for d in deg_sequence:
+        # Reject if degree is negative or larger than the sequence length
+        if d < 0 or d >= p:
+            raise nx.NetworkXUnfeasible
+        # Process only the non-zero integers
+        elif d > 0:
+            dmax, dmin, dsum, n = max(dmax, d), min(dmin, d), dsum + d, n + 1
+            num_degs[d] += 1
+    # Reject sequence if it has odd sum or is oversaturated
+    if dsum % 2 or dsum > n * (n - 1):
+        raise nx.NetworkXUnfeasible
+    return dmax, dmin, dsum, n, num_degs
+
+
+@nx._dispatch(graphs=None)
+def is_valid_degree_sequence_havel_hakimi(deg_sequence):
+    r"""Returns True if deg_sequence can be realized by a simple graph.
+
+    The validation proceeds using the Havel-Hakimi theorem
+    [havel1955]_, [hakimi1962]_, [CL1996]_.
+    Worst-case run time is $O(s)$ where $s$ is the sum of the sequence.
+
+    Parameters
+    ----------
+    deg_sequence : list
+        A list of integers where each element specifies the degree of a node
+        in a graph.
+
+    Returns
+    -------
+    valid : bool
+        True if deg_sequence is graphical and False if not.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(1, 2), (1, 3), (2, 3), (3, 4), (4, 2), (5, 1), (5, 4)])
+    >>> sequence = (d for _, d in G.degree())
+    >>> nx.is_valid_degree_sequence_havel_hakimi(sequence)
+    True
+
+    To test a non-valid sequence:
+    >>> sequence_list = [d for _, d in G.degree()]
+    >>> sequence_list[-1] += 1
+    >>> nx.is_valid_degree_sequence_havel_hakimi(sequence_list)
+    False
+
+    Notes
+    -----
+    The ZZ condition says that for the sequence d if
+
+    .. math::
+        |d| >= \frac{(\max(d) + \min(d) + 1)^2}{4*\min(d)}
+
+    then d is graphical.  This was shown in Theorem 6 in [1]_.
+
+    References
+    ----------
+    .. [1] I.E. Zverovich and V.E. Zverovich. "Contributions to the theory
+       of graphic sequences", Discrete Mathematics, 105, pp. 292-303 (1992).
+    .. [havel1955] Havel, V. "A Remark on the Existence of Finite Graphs"
+       Casopis Pest. Mat. 80, 477-480, 1955.
+    .. [hakimi1962] Hakimi, S. "On the Realizability of a Set of Integers as
+       Degrees of the Vertices of a Graph." SIAM J. Appl. Math. 10, 496-506, 1962.
+    .. [CL1996] G. Chartrand and L. Lesniak, "Graphs and Digraphs",
+       Chapman and Hall/CRC, 1996.
+    """
+    try:
+        dmax, dmin, dsum, n, num_degs = _basic_graphical_tests(deg_sequence)
+    except nx.NetworkXUnfeasible:
+        return False
+    # Accept if sequence has no non-zero degrees or passes the ZZ condition
+    if n == 0 or 4 * dmin * n >= (dmax + dmin + 1) * (dmax + dmin + 1):
+        return True
+
+    modstubs = [0] * (dmax + 1)
+    # Successively reduce degree sequence by removing the maximum degree
+    while n > 0:
+        # Retrieve the maximum degree in the sequence
+        while num_degs[dmax] == 0:
+            dmax -= 1
+        # If there are not enough stubs to connect to, then the sequence is
+        # not graphical
+        if dmax > n - 1:
+            return False
+
+        # Remove largest stub in list
+        num_degs[dmax], n = num_degs[dmax] - 1, n - 1
+        # Reduce the next dmax largest stubs
+        mslen = 0
+        k = dmax
+        for i in range(dmax):
+            while num_degs[k] == 0:
+                k -= 1
+            num_degs[k], n = num_degs[k] - 1, n - 1
+            if k > 1:
+                modstubs[mslen] = k - 1
+                mslen += 1
+        # Add back to the list any non-zero stubs that were removed
+        for i in range(mslen):
+            stub = modstubs[i]
+            num_degs[stub], n = num_degs[stub] + 1, n + 1
+    return True
+
+
+@nx._dispatch(graphs=None)
+def is_valid_degree_sequence_erdos_gallai(deg_sequence):
+    r"""Returns True if deg_sequence can be realized by a simple graph.
+
+    The validation is done using the Erdős-Gallai theorem [EG1960]_.
+
+    Parameters
+    ----------
+    deg_sequence : list
+        A list of integers
+
+    Returns
+    -------
+    valid : bool
+        True if deg_sequence is graphical and False if not.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(1, 2), (1, 3), (2, 3), (3, 4), (4, 2), (5, 1), (5, 4)])
+    >>> sequence = (d for _, d in G.degree())
+    >>> nx.is_valid_degree_sequence_erdos_gallai(sequence)
+    True
+
+    To test a non-valid sequence:
+    >>> sequence_list = [d for _, d in G.degree()]
+    >>> sequence_list[-1] += 1
+    >>> nx.is_valid_degree_sequence_erdos_gallai(sequence_list)
+    False
+
+    Notes
+    -----
+
+    This implementation uses an equivalent form of the Erdős-Gallai criterion.
+    Worst-case run time is $O(n)$ where $n$ is the length of the sequence.
+
+    Specifically, a sequence d is graphical if and only if the
+    sum of the sequence is even and for all strong indices k in the sequence,
+
+     .. math::
+
+       \sum_{i=1}^{k} d_i \leq k(k-1) + \sum_{j=k+1}^{n} \min(d_i,k)
+             = k(n-1) - ( k \sum_{j=0}^{k-1} n_j - \sum_{j=0}^{k-1} j n_j )
+
+    A strong index k is any index where d_k >= k and the value n_j is the
+    number of occurrences of j in d.  The maximal strong index is called the
+    Durfee index.
+
+    This particular rearrangement comes from the proof of Theorem 3 in [2]_.
+
+    The ZZ condition says that for the sequence d if
+
+    .. math::
+        |d| >= \frac{(\max(d) + \min(d) + 1)^2}{4*\min(d)}
+
+    then d is graphical.  This was shown in Theorem 6 in [2]_.
+
+    References
+    ----------
+    .. [1] A. Tripathi and S. Vijay. "A note on a theorem of Erdős & Gallai",
+       Discrete Mathematics, 265, pp. 417-420 (2003).
+    .. [2] I.E. Zverovich and V.E. Zverovich. "Contributions to the theory
+       of graphic sequences", Discrete Mathematics, 105, pp. 292-303 (1992).
+    .. [EG1960] Erdős and Gallai, Mat. Lapok 11 264, 1960.
+    """
+    try:
+        dmax, dmin, dsum, n, num_degs = _basic_graphical_tests(deg_sequence)
+    except nx.NetworkXUnfeasible:
+        return False
+    # Accept if sequence has no non-zero degrees or passes the ZZ condition
+    if n == 0 or 4 * dmin * n >= (dmax + dmin + 1) * (dmax + dmin + 1):
+        return True
+
+    # Perform the EG checks using the reformulation of Zverovich and Zverovich
+    k, sum_deg, sum_nj, sum_jnj = 0, 0, 0, 0
+    for dk in range(dmax, dmin - 1, -1):
+        if dk < k + 1:  # Check if already past Durfee index
+            return True
+        if num_degs[dk] > 0:
+            run_size = num_degs[dk]  # Process a run of identical-valued degrees
+            if dk < k + run_size:  # Check if end of run is past Durfee index
+                run_size = dk - k  # Adjust back to Durfee index
+            sum_deg += run_size * dk
+            for v in range(run_size):
+                sum_nj += num_degs[k + v]
+                sum_jnj += (k + v) * num_degs[k + v]
+            k += run_size
+            if sum_deg > k * (n - 1) - k * sum_nj + sum_jnj:
+                return False
+    return True
+
+
+@nx._dispatch(graphs=None)
+def is_multigraphical(sequence):
+    """Returns True if some multigraph can realize the sequence.
+
+    Parameters
+    ----------
+    sequence : list
+        A list of integers
+
+    Returns
+    -------
+    valid : bool
+        True if deg_sequence is a multigraphic degree sequence and False if not.
+
+    Examples
+    --------
+    >>> G = nx.MultiGraph([(1, 2), (1, 3), (2, 3), (3, 4), (4, 2), (5, 1), (5, 4)])
+    >>> sequence = (d for _, d in G.degree())
+    >>> nx.is_multigraphical(sequence)
+    True
+
+    To test a non-multigraphical sequence:
+    >>> sequence_list = [d for _, d in G.degree()]
+    >>> sequence_list[-1] += 1
+    >>> nx.is_multigraphical(sequence_list)
+    False
+
+    Notes
+    -----
+    The worst-case run time is $O(n)$ where $n$ is the length of the sequence.
+
+    References
+    ----------
+    .. [1] S. L. Hakimi. "On the realizability of a set of integers as
+       degrees of the vertices of a linear graph", J. SIAM, 10, pp. 496-506
+       (1962).
+    """
+    try:
+        deg_sequence = nx.utils.make_list_of_ints(sequence)
+    except nx.NetworkXError:
+        return False
+    dsum, dmax = 0, 0
+    for d in deg_sequence:
+        if d < 0:
+            return False
+        dsum, dmax = dsum + d, max(dmax, d)
+    if dsum % 2 or dsum < 2 * dmax:
+        return False
+    return True
+
+
+@nx._dispatch(graphs=None)
+def is_pseudographical(sequence):
+    """Returns True if some pseudograph can realize the sequence.
+
+    Every nonnegative integer sequence with an even sum is pseudographical
+    (see [1]_).
+
+    Parameters
+    ----------
+    sequence : list or iterable container
+        A sequence of integer node degrees
+
+    Returns
+    -------
+    valid : bool
+      True if the sequence is a pseudographic degree sequence and False if not.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(1, 2), (1, 3), (2, 3), (3, 4), (4, 2), (5, 1), (5, 4)])
+    >>> sequence = (d for _, d in G.degree())
+    >>> nx.is_pseudographical(sequence)
+    True
+
+    To test a non-pseudographical sequence:
+    >>> sequence_list = [d for _, d in G.degree()]
+    >>> sequence_list[-1] += 1
+    >>> nx.is_pseudographical(sequence_list)
+    False
+
+    Notes
+    -----
+    The worst-case run time is $O(n)$ where n is the length of the sequence.
+
+    References
+    ----------
+    .. [1] F. Boesch and F. Harary. "Line removal algorithms for graphs
+       and their degree lists", IEEE Trans. Circuits and Systems, CAS-23(12),
+       pp. 778-782 (1976).
+    """
+    try:
+        deg_sequence = nx.utils.make_list_of_ints(sequence)
+    except nx.NetworkXError:
+        return False
+    return sum(deg_sequence) % 2 == 0 and min(deg_sequence) >= 0
+
+
+@nx._dispatch(graphs=None)
+def is_digraphical(in_sequence, out_sequence):
+    r"""Returns True if some directed graph can realize the in- and out-degree
+    sequences.
+
+    Parameters
+    ----------
+    in_sequence : list or iterable container
+        A sequence of integer node in-degrees
+
+    out_sequence : list or iterable container
+        A sequence of integer node out-degrees
+
+    Returns
+    -------
+    valid : bool
+      True if in and out-sequences are digraphic False if not.
+
+    Examples
+    --------
+    >>> G = nx.DiGraph([(1, 2), (1, 3), (2, 3), (3, 4), (4, 2), (5, 1), (5, 4)])
+    >>> in_seq = (d for n, d in G.in_degree())
+    >>> out_seq = (d for n, d in G.out_degree())
+    >>> nx.is_digraphical(in_seq, out_seq)
+    True
+
+    To test a non-digraphical scenario:
+    >>> in_seq_list = [d for n, d in G.in_degree()]
+    >>> in_seq_list[-1] += 1
+    >>> nx.is_digraphical(in_seq_list, out_seq)
+    False
+
+    Notes
+    -----
+    This algorithm is from Kleitman and Wang [1]_.
+    The worst case runtime is $O(s \times \log n)$ where $s$ and $n$ are the
+    sum and length of the sequences respectively.
+
+    References
+    ----------
+    .. [1] D.J. Kleitman and D.L. Wang
+       Algorithms for Constructing Graphs and Digraphs with Given Valences
+       and Factors, Discrete Mathematics, 6(1), pp. 79-88 (1973)
+    """
+    try:
+        in_deg_sequence = nx.utils.make_list_of_ints(in_sequence)
+        out_deg_sequence = nx.utils.make_list_of_ints(out_sequence)
+    except nx.NetworkXError:
+        return False
+    # Process the sequences and form two heaps to store degree pairs with
+    # either zero or non-zero out degrees
+    sumin, sumout, nin, nout = 0, 0, len(in_deg_sequence), len(out_deg_sequence)
+    maxn = max(nin, nout)
+    maxin = 0
+    if maxn == 0:
+        return True
+    stubheap, zeroheap = [], []
+    for n in range(maxn):
+        in_deg, out_deg = 0, 0
+        if n < nout:
+            out_deg = out_deg_sequence[n]
+        if n < nin:
+            in_deg = in_deg_sequence[n]
+        if in_deg < 0 or out_deg < 0:
+            return False
+        sumin, sumout, maxin = sumin + in_deg, sumout + out_deg, max(maxin, in_deg)
+        if in_deg > 0:
+            stubheap.append((-1 * out_deg, -1 * in_deg))
+        elif out_deg > 0:
+            zeroheap.append(-1 * out_deg)
+    if sumin != sumout:
+        return False
+    heapq.heapify(stubheap)
+    heapq.heapify(zeroheap)
+
+    modstubs = [(0, 0)] * (maxin + 1)
+    # Successively reduce degree sequence by removing the maximum out degree
+    while stubheap:
+        # Take the first value in the sequence with non-zero in degree
+        (freeout, freein) = heapq.heappop(stubheap)
+        freein *= -1
+        if freein > len(stubheap) + len(zeroheap):
+            return False
+
+        # Attach out stubs to the nodes with the most in stubs
+        mslen = 0
+        for i in range(freein):
+            if zeroheap and (not stubheap or stubheap[0][0] > zeroheap[0]):
+                stubout = heapq.heappop(zeroheap)
+                stubin = 0
+            else:
+                (stubout, stubin) = heapq.heappop(stubheap)
+            if stubout == 0:
+                return False
+            # Check if target is now totally connected
+            if stubout + 1 < 0 or stubin < 0:
+                modstubs[mslen] = (stubout + 1, stubin)
+                mslen += 1
+
+        # Add back the nodes to the heap that still have available stubs
+        for i in range(mslen):
+            stub = modstubs[i]
+            if stub[1] < 0:
+                heapq.heappush(stubheap, stub)
+            else:
+                heapq.heappush(zeroheap, stub[0])
+        if freeout < 0:
+            heapq.heappush(zeroheap, freeout)
+    return True

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/hierarchy.py

@@ -0,0 +1,48 @@
+"""
+Flow Hierarchy.
+"""
+import networkx as nx
+
+__all__ = ["flow_hierarchy"]
+
+
+@nx._dispatch(edge_attrs="weight")
+def flow_hierarchy(G, weight=None):
+    """Returns the flow hierarchy of a directed network.
+
+    Flow hierarchy is defined as the fraction of edges not participating
+    in cycles in a directed graph [1]_.
+
+    Parameters
+    ----------
+    G : DiGraph or MultiDiGraph
+       A directed graph
+
+    weight : string, optional (default=None)
+       Attribute to use for edge weights. If None the weight defaults to 1.
+
+    Returns
+    -------
+    h : float
+       Flow hierarchy value
+
+    Notes
+    -----
+    The algorithm described in [1]_ computes the flow hierarchy through
+    exponentiation of the adjacency matrix.  This function implements an
+    alternative approach that finds strongly connected components.
+    An edge is in a cycle if and only if it is in a strongly connected
+    component, which can be found in $O(m)$ time using Tarjan's algorithm.
+
+    References
+    ----------
+    .. [1] Luo, J.; Magee, C.L. (2011),
+       Detecting evolving patterns of self-organizing networks by flow
+       hierarchy measurement, Complexity, Volume 16 Issue 6 53-61.
+       DOI: 10.1002/cplx.20368
+       http://web.mit.edu/~cmagee/www/documents/28-DetectingEvolvingPatterns_FlowHierarchy.pdf
+    """
+    if not G.is_directed():
+        raise nx.NetworkXError("G must be a digraph in flow_hierarchy")
+    scc = nx.strongly_connected_components(G)
+    return 1 - sum(G.subgraph(c).size(weight) for c in scc) / G.size(weight)

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/isolate.py

@@ -0,0 +1,107 @@
+"""
+Functions for identifying isolate (degree zero) nodes.
+"""
+import networkx as nx
+
+__all__ = ["is_isolate", "isolates", "number_of_isolates"]
+
+
+@nx._dispatch
+def is_isolate(G, n):
+    """Determines whether a node is an isolate.
+
+    An *isolate* is a node with no neighbors (that is, with degree
+    zero). For directed graphs, this means no in-neighbors and no
+    out-neighbors.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    n : node
+        A node in `G`.
+
+    Returns
+    -------
+    is_isolate : bool
+       True if and only if `n` has no neighbors.
+
+    Examples
+    --------
+    >>> G = nx.Graph()
+    >>> G.add_edge(1, 2)
+    >>> G.add_node(3)
+    >>> nx.is_isolate(G, 2)
+    False
+    >>> nx.is_isolate(G, 3)
+    True
+    """
+    return G.degree(n) == 0
+
+
+@nx._dispatch
+def isolates(G):
+    """Iterator over isolates in the graph.
+
+    An *isolate* is a node with no neighbors (that is, with degree
+    zero). For directed graphs, this means no in-neighbors and no
+    out-neighbors.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    Returns
+    -------
+    iterator
+        An iterator over the isolates of `G`.
+
+    Examples
+    --------
+    To get a list of all isolates of a graph, use the :class:`list`
+    constructor::
+
+        >>> G = nx.Graph()
+        >>> G.add_edge(1, 2)
+        >>> G.add_node(3)
+        >>> list(nx.isolates(G))
+        [3]
+
+    To remove all isolates in the graph, first create a list of the
+    isolates, then use :meth:`Graph.remove_nodes_from`::
+
+        >>> G.remove_nodes_from(list(nx.isolates(G)))
+        >>> list(G)
+        [1, 2]
+
+    For digraphs, isolates have zero in-degree and zero out_degre::
+
+        >>> G = nx.DiGraph([(0, 1), (1, 2)])
+        >>> G.add_node(3)
+        >>> list(nx.isolates(G))
+        [3]
+
+    """
+    return (n for n, d in G.degree() if d == 0)
+
+
+@nx._dispatch
+def number_of_isolates(G):
+    """Returns the number of isolates in the graph.
+
+    An *isolate* is a node with no neighbors (that is, with degree
+    zero). For directed graphs, this means no in-neighbors and no
+    out-neighbors.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    Returns
+    -------
+    int
+        The number of degree zero nodes in the graph `G`.
+
+    """
+    # TODO This can be parallelized.
+    return sum(1 for v in isolates(G))

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/link_analysis/tests/test_hits.py

@@ -0,0 +1,78 @@
+import pytest
+
+import networkx as nx
+
+np = pytest.importorskip("numpy")
+sp = pytest.importorskip("scipy")
+
+from networkx.algorithms.link_analysis.hits_alg import (
+    _hits_numpy,
+    _hits_python,
+    _hits_scipy,
+)
+
+# Example from
+# A. Langville and C. Meyer, "A survey of eigenvector methods of web
+# information retrieval."  http://citeseer.ist.psu.edu/713792.html
+
+
+class TestHITS:
+    @classmethod
+    def setup_class(cls):
+        G = nx.DiGraph()
+
+        edges = [(1, 3), (1, 5), (2, 1), (3, 5), (5, 4), (5, 3), (6, 5)]
+
+        G.add_edges_from(edges, weight=1)
+        cls.G = G
+        cls.G.a = dict(
+            zip(sorted(G), [0.000000, 0.000000, 0.366025, 0.133975, 0.500000, 0.000000])
+        )
+        cls.G.h = dict(
+            zip(sorted(G), [0.366025, 0.000000, 0.211325, 0.000000, 0.211325, 0.211325])
+        )
+
+    def test_hits_numpy(self):
+        G = self.G
+        h, a = _hits_numpy(G)
+        for n in G:
+            assert h[n] == pytest.approx(G.h[n], abs=1e-4)
+        for n in G:
+            assert a[n] == pytest.approx(G.a[n], abs=1e-4)
+
+    @pytest.mark.parametrize("hits_alg", (nx.hits, _hits_python, _hits_scipy))
+    def test_hits(self, hits_alg):
+        G = self.G
+        h, a = hits_alg(G, tol=1.0e-08)
+        for n in G:
+            assert h[n] == pytest.approx(G.h[n], abs=1e-4)
+        for n in G:
+            assert a[n] == pytest.approx(G.a[n], abs=1e-4)
+        nstart = {i: 1.0 / 2 for i in G}
+        h, a = hits_alg(G, nstart=nstart)
+        for n in G:
+            assert h[n] == pytest.approx(G.h[n], abs=1e-4)
+        for n in G:
+            assert a[n] == pytest.approx(G.a[n], abs=1e-4)
+
+    def test_empty(self):
+        G = nx.Graph()
+        assert nx.hits(G) == ({}, {})
+        assert _hits_numpy(G) == ({}, {})
+        assert _hits_python(G) == ({}, {})
+        assert _hits_scipy(G) == ({}, {})
+
+    def test_hits_not_convergent(self):
+        G = nx.path_graph(50)
+        with pytest.raises(nx.PowerIterationFailedConvergence):
+            _hits_scipy(G, max_iter=1)
+        with pytest.raises(nx.PowerIterationFailedConvergence):
+            _hits_python(G, max_iter=1)
+        with pytest.raises(nx.PowerIterationFailedConvergence):
+            _hits_scipy(G, max_iter=0)
+        with pytest.raises(nx.PowerIterationFailedConvergence):
+            _hits_python(G, max_iter=0)
+        with pytest.raises(ValueError):
+            nx.hits(G, max_iter=0)
+        with pytest.raises(sp.sparse.linalg.ArpackNoConvergence):
+            nx.hits(G, max_iter=1)

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/lowest_common_ancestors.py

@@ -0,0 +1,268 @@
+"""Algorithms for finding the lowest common ancestor of trees and DAGs."""
+from collections import defaultdict
+from collections.abc import Mapping, Set
+from itertools import combinations_with_replacement
+
+import networkx as nx
+from networkx.utils import UnionFind, arbitrary_element, not_implemented_for
+
+__all__ = [
+    "all_pairs_lowest_common_ancestor",
+    "tree_all_pairs_lowest_common_ancestor",
+    "lowest_common_ancestor",
+]
+
+
+@not_implemented_for("undirected")
+@nx._dispatch
+def all_pairs_lowest_common_ancestor(G, pairs=None):
+    """Return the lowest common ancestor of all pairs or the provided pairs
+
+    Parameters
+    ----------
+    G : NetworkX directed graph
+
+    pairs : iterable of pairs of nodes, optional (default: all pairs)
+        The pairs of nodes of interest.
+        If None, will find the LCA of all pairs of nodes.
+
+    Yields
+    ------
+    ((node1, node2), lca) : 2-tuple
+        Where lca is least common ancestor of node1 and node2.
+        Note that for the default case, the order of the node pair is not considered,
+        e.g. you will not get both ``(a, b)`` and ``(b, a)``
+
+    Raises
+    ------
+    NetworkXPointlessConcept
+        If `G` is null.
+    NetworkXError
+        If `G` is not a DAG.
+
+    Examples
+    --------
+    The default behavior is to yield the lowest common ancestor for all
+    possible combinations of nodes in `G`, including self-pairings:
+
+    >>> G = nx.DiGraph([(0, 1), (0, 3), (1, 2)])
+    >>> dict(nx.all_pairs_lowest_common_ancestor(G))
+    {(0, 0): 0, (0, 1): 0, (0, 3): 0, (0, 2): 0, (1, 1): 1, (1, 3): 0, (1, 2): 1, (3, 3): 3, (3, 2): 0, (2, 2): 2}
+
+    The pairs argument can be used to limit the output to only the
+    specified node pairings:
+
+    >>> dict(nx.all_pairs_lowest_common_ancestor(G, pairs=[(1, 2), (2, 3)]))
+    {(1, 2): 1, (2, 3): 0}
+
+    Notes
+    -----
+    Only defined on non-null directed acyclic graphs.
+
+    See Also
+    --------
+    lowest_common_ancestor
+    """
+    if not nx.is_directed_acyclic_graph(G):
+        raise nx.NetworkXError("LCA only defined on directed acyclic graphs.")
+    if len(G) == 0:
+        raise nx.NetworkXPointlessConcept("LCA meaningless on null graphs.")
+
+    if pairs is None:
+        pairs = combinations_with_replacement(G, 2)
+    else:
+        # Convert iterator to iterable, if necessary. Trim duplicates.
+        pairs = dict.fromkeys(pairs)
+        # Verify that each of the nodes in the provided pairs is in G
+        nodeset = set(G)
+        for pair in pairs:
+            if set(pair) - nodeset:
+                raise nx.NodeNotFound(
+                    f"Node(s) {set(pair) - nodeset} from pair {pair} not in G."
+                )
+
+    # Once input validation is done, construct the generator
+    def generate_lca_from_pairs(G, pairs):
+        ancestor_cache = {}
+
+        for v, w in pairs:
+            if v not in ancestor_cache:
+                ancestor_cache[v] = nx.ancestors(G, v)
+                ancestor_cache[v].add(v)
+            if w not in ancestor_cache:
+                ancestor_cache[w] = nx.ancestors(G, w)
+                ancestor_cache[w].add(w)
+
+            common_ancestors = ancestor_cache[v] & ancestor_cache[w]
+
+            if common_ancestors:
+                common_ancestor = next(iter(common_ancestors))
+                while True:
+                    successor = None
+                    for lower_ancestor in G.successors(common_ancestor):
+                        if lower_ancestor in common_ancestors:
+                            successor = lower_ancestor
+                            break
+                    if successor is None:
+                        break
+                    common_ancestor = successor
+                yield ((v, w), common_ancestor)
+
+    return generate_lca_from_pairs(G, pairs)
+
+
+@not_implemented_for("undirected")
+@nx._dispatch
+def lowest_common_ancestor(G, node1, node2, default=None):
+    """Compute the lowest common ancestor of the given pair of nodes.
+
+    Parameters
+    ----------
+    G : NetworkX directed graph
+
+    node1, node2 : nodes in the graph.
+
+    default : object
+        Returned if no common ancestor between `node1` and `node2`
+
+    Returns
+    -------
+    The lowest common ancestor of node1 and node2,
+    or default if they have no common ancestors.
+
+    Examples
+    --------
+    >>> G = nx.DiGraph()
+    >>> nx.add_path(G, (0, 1, 2, 3))
+    >>> nx.add_path(G, (0, 4, 3))
+    >>> nx.lowest_common_ancestor(G, 2, 4)
+    0
+
+    See Also
+    --------
+    all_pairs_lowest_common_ancestor"""
+
+    ans = list(all_pairs_lowest_common_ancestor(G, pairs=[(node1, node2)]))
+    if ans:
+        assert len(ans) == 1
+        return ans[0][1]
+    return default
+
+
+@not_implemented_for("undirected")
+@nx._dispatch
+def tree_all_pairs_lowest_common_ancestor(G, root=None, pairs=None):
+    r"""Yield the lowest common ancestor for sets of pairs in a tree.
+
+    Parameters
+    ----------
+    G : NetworkX directed graph (must be a tree)
+
+    root : node, optional (default: None)
+        The root of the subtree to operate on.
+        If None, assume the entire graph has exactly one source and use that.
+
+    pairs : iterable or iterator of pairs of nodes, optional (default: None)
+        The pairs of interest. If None, Defaults to all pairs of nodes
+        under `root` that have a lowest common ancestor.
+
+    Returns
+    -------
+    lcas : generator of tuples `((u, v), lca)` where `u` and `v` are nodes
+        in `pairs` and `lca` is their lowest common ancestor.
+
+    Examples
+    --------
+    >>> import pprint
+    >>> G = nx.DiGraph([(1, 3), (2, 4), (1, 2)])
+    >>> pprint.pprint(dict(nx.tree_all_pairs_lowest_common_ancestor(G)))
+    {(1, 1): 1,
+     (2, 1): 1,
+     (2, 2): 2,
+     (3, 1): 1,
+     (3, 2): 1,
+     (3, 3): 3,
+     (3, 4): 1,
+     (4, 1): 1,
+     (4, 2): 2,
+     (4, 4): 4}
+
+    We can also use `pairs` argument to specify the pairs of nodes for which we
+    want to compute lowest common ancestors. Here is an example:
+
+    >>> dict(nx.tree_all_pairs_lowest_common_ancestor(G, pairs=[(1, 4), (2, 3)]))
+    {(2, 3): 1, (1, 4): 1}
+
+    Notes
+    -----
+    Only defined on non-null trees represented with directed edges from
+    parents to children. Uses Tarjan's off-line lowest-common-ancestors
+    algorithm. Runs in time $O(4 \times (V + E + P))$ time, where 4 is the largest
+    value of the inverse Ackermann function likely to ever come up in actual
+    use, and $P$ is the number of pairs requested (or $V^2$ if all are needed).
+
+    Tarjan, R. E. (1979), "Applications of path compression on balanced trees",
+    Journal of the ACM 26 (4): 690-715, doi:10.1145/322154.322161.
+
+    See Also
+    --------
+    all_pairs_lowest_common_ancestor: similar routine for general DAGs
+    lowest_common_ancestor: just a single pair for general DAGs
+    """
+    if len(G) == 0:
+        raise nx.NetworkXPointlessConcept("LCA meaningless on null graphs.")
+
+    # Index pairs of interest for efficient lookup from either side.
+    if pairs is not None:
+        pair_dict = defaultdict(set)
+        # See note on all_pairs_lowest_common_ancestor.
+        if not isinstance(pairs, (Mapping, Set)):
+            pairs = set(pairs)
+        for u, v in pairs:
+            for n in (u, v):
+                if n not in G:
+                    msg = f"The node {str(n)} is not in the digraph."
+                    raise nx.NodeNotFound(msg)
+            pair_dict[u].add(v)
+            pair_dict[v].add(u)
+
+    # If root is not specified, find the exactly one node with in degree 0 and
+    # use it. Raise an error if none are found, or more than one is. Also check
+    # for any nodes with in degree larger than 1, which would imply G is not a
+    # tree.
+    if root is None:
+        for n, deg in G.in_degree:
+            if deg == 0:
+                if root is not None:
+                    msg = "No root specified and tree has multiple sources."
+                    raise nx.NetworkXError(msg)
+                root = n
+            # checking deg>1 is not sufficient for MultiDiGraphs
+            elif deg > 1 and len(G.pred[n]) > 1:
+                msg = "Tree LCA only defined on trees; use DAG routine."
+                raise nx.NetworkXError(msg)
+    if root is None:
+        raise nx.NetworkXError("Graph contains a cycle.")
+
+    # Iterative implementation of Tarjan's offline lca algorithm
+    # as described in CLRS on page 521 (2nd edition)/page 584 (3rd edition)
+    uf = UnionFind()
+    ancestors = {}
+    for node in G:
+        ancestors[node] = uf[node]
+
+    colors = defaultdict(bool)
+    for node in nx.dfs_postorder_nodes(G, root):
+        colors[node] = True
+        for v in pair_dict[node] if pairs is not None else G:
+            if colors[v]:
+                # If the user requested both directions of a pair, give it.
+                # Otherwise, just give one.
+                if pairs is not None and (node, v) in pairs:
+                    yield (node, v), ancestors[uf[v]]
+                if pairs is None or (v, node) in pairs:
+                    yield (v, node), ancestors[uf[v]]
+        if node != root:
+            parent = arbitrary_element(G.pred[node])
+            uf.union(parent, node)
+            ancestors[uf[parent]] = parent

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/minors/tests/test_contraction.py

@@ -0,0 +1,445 @@
+"""Unit tests for the :mod:`networkx.algorithms.minors.contraction` module."""
+import pytest
+
+import networkx as nx
+from networkx.utils import arbitrary_element, edges_equal, nodes_equal
+
+
+def test_quotient_graph_complete_multipartite():
+    """Tests that the quotient graph of the complete *n*-partite graph
+    under the "same neighbors" node relation is the complete graph on *n*
+    nodes.
+
+    """
+    G = nx.complete_multipartite_graph(2, 3, 4)
+    # Two nodes are equivalent if they are not adjacent but have the same
+    # neighbor set.
+
+    def same_neighbors(u, v):
+        return u not in G[v] and v not in G[u] and G[u] == G[v]
+
+    expected = nx.complete_graph(3)
+    actual = nx.quotient_graph(G, same_neighbors)
+    # It won't take too long to run a graph isomorphism algorithm on such
+    # small graphs.
+    assert nx.is_isomorphic(expected, actual)
+
+
+def test_quotient_graph_complete_bipartite():
+    """Tests that the quotient graph of the complete bipartite graph under
+    the "same neighbors" node relation is `K_2`.
+
+    """
+    G = nx.complete_bipartite_graph(2, 3)
+    # Two nodes are equivalent if they are not adjacent but have the same
+    # neighbor set.
+
+    def same_neighbors(u, v):
+        return u not in G[v] and v not in G[u] and G[u] == G[v]
+
+    expected = nx.complete_graph(2)
+    actual = nx.quotient_graph(G, same_neighbors)
+    # It won't take too long to run a graph isomorphism algorithm on such
+    # small graphs.
+    assert nx.is_isomorphic(expected, actual)
+
+
+def test_quotient_graph_edge_relation():
+    """Tests for specifying an alternate edge relation for the quotient
+    graph.
+
+    """
+    G = nx.path_graph(5)
+
+    def identity(u, v):
+        return u == v
+
+    def same_parity(b, c):
+        return arbitrary_element(b) % 2 == arbitrary_element(c) % 2
+
+    actual = nx.quotient_graph(G, identity, same_parity)
+    expected = nx.Graph()
+    expected.add_edges_from([(0, 2), (0, 4), (2, 4)])
+    expected.add_edge(1, 3)
+    assert nx.is_isomorphic(actual, expected)
+
+
+def test_condensation_as_quotient():
+    """This tests that the condensation of a graph can be viewed as the
+    quotient graph under the "in the same connected component" equivalence
+    relation.
+
+    """
+    # This example graph comes from the file `test_strongly_connected.py`.
+    G = nx.DiGraph()
+    G.add_edges_from(
+        [
+            (1, 2),
+            (2, 3),
+            (2, 11),
+            (2, 12),
+            (3, 4),
+            (4, 3),
+            (4, 5),
+            (5, 6),
+            (6, 5),
+            (6, 7),
+            (7, 8),
+            (7, 9),
+            (7, 10),
+            (8, 9),
+            (9, 7),
+            (10, 6),
+            (11, 2),
+            (11, 4),
+            (11, 6),
+            (12, 6),
+            (12, 11),
+        ]
+    )
+    scc = list(nx.strongly_connected_components(G))
+    C = nx.condensation(G, scc)
+    component_of = C.graph["mapping"]
+    # Two nodes are equivalent if they are in the same connected component.
+
+    def same_component(u, v):
+        return component_of[u] == component_of[v]
+
+    Q = nx.quotient_graph(G, same_component)
+    assert nx.is_isomorphic(C, Q)
+
+
+def test_path():
+    G = nx.path_graph(6)
+    partition = [{0, 1}, {2, 3}, {4, 5}]
+    M = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(M, [0, 1, 2])
+    assert edges_equal(M.edges(), [(0, 1), (1, 2)])
+    for n in M:
+        assert M.nodes[n]["nedges"] == 1
+        assert M.nodes[n]["nnodes"] == 2
+        assert M.nodes[n]["density"] == 1
+
+
+def test_path__partition_provided_as_dict_of_lists():
+    G = nx.path_graph(6)
+    partition = {0: [0, 1], 2: [2, 3], 4: [4, 5]}
+    M = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(M, [0, 1, 2])
+    assert edges_equal(M.edges(), [(0, 1), (1, 2)])
+    for n in M:
+        assert M.nodes[n]["nedges"] == 1
+        assert M.nodes[n]["nnodes"] == 2
+        assert M.nodes[n]["density"] == 1
+
+
+def test_path__partition_provided_as_dict_of_tuples():
+    G = nx.path_graph(6)
+    partition = {0: (0, 1), 2: (2, 3), 4: (4, 5)}
+    M = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(M, [0, 1, 2])
+    assert edges_equal(M.edges(), [(0, 1), (1, 2)])
+    for n in M:
+        assert M.nodes[n]["nedges"] == 1
+        assert M.nodes[n]["nnodes"] == 2
+        assert M.nodes[n]["density"] == 1
+
+
+def test_path__partition_provided_as_dict_of_sets():
+    G = nx.path_graph(6)
+    partition = {0: {0, 1}, 2: {2, 3}, 4: {4, 5}}
+    M = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(M, [0, 1, 2])
+    assert edges_equal(M.edges(), [(0, 1), (1, 2)])
+    for n in M:
+        assert M.nodes[n]["nedges"] == 1
+        assert M.nodes[n]["nnodes"] == 2
+        assert M.nodes[n]["density"] == 1
+
+
+def test_multigraph_path():
+    G = nx.MultiGraph(nx.path_graph(6))
+    partition = [{0, 1}, {2, 3}, {4, 5}]
+    M = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(M, [0, 1, 2])
+    assert edges_equal(M.edges(), [(0, 1), (1, 2)])
+    for n in M:
+        assert M.nodes[n]["nedges"] == 1
+        assert M.nodes[n]["nnodes"] == 2
+        assert M.nodes[n]["density"] == 1
+
+
+def test_directed_path():
+    G = nx.DiGraph()
+    nx.add_path(G, range(6))
+    partition = [{0, 1}, {2, 3}, {4, 5}]
+    M = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(M, [0, 1, 2])
+    assert edges_equal(M.edges(), [(0, 1), (1, 2)])
+    for n in M:
+        assert M.nodes[n]["nedges"] == 1
+        assert M.nodes[n]["nnodes"] == 2
+        assert M.nodes[n]["density"] == 0.5
+
+
+def test_directed_multigraph_path():
+    G = nx.MultiDiGraph()
+    nx.add_path(G, range(6))
+    partition = [{0, 1}, {2, 3}, {4, 5}]
+    M = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(M, [0, 1, 2])
+    assert edges_equal(M.edges(), [(0, 1), (1, 2)])
+    for n in M:
+        assert M.nodes[n]["nedges"] == 1
+        assert M.nodes[n]["nnodes"] == 2
+        assert M.nodes[n]["density"] == 0.5
+
+
+def test_overlapping_blocks():
+    with pytest.raises(nx.NetworkXException):
+        G = nx.path_graph(6)
+        partition = [{0, 1, 2}, {2, 3}, {4, 5}]
+        nx.quotient_graph(G, partition)
+
+
+def test_weighted_path():
+    G = nx.path_graph(6)
+    for i in range(5):
+        G[i][i + 1]["w"] = i + 1
+    partition = [{0, 1}, {2, 3}, {4, 5}]
+    M = nx.quotient_graph(G, partition, weight="w", relabel=True)
+    assert nodes_equal(M, [0, 1, 2])
+    assert edges_equal(M.edges(), [(0, 1), (1, 2)])
+    assert M[0][1]["weight"] == 2
+    assert M[1][2]["weight"] == 4
+    for n in M:
+        assert M.nodes[n]["nedges"] == 1
+        assert M.nodes[n]["nnodes"] == 2
+        assert M.nodes[n]["density"] == 1
+
+
+def test_barbell():
+    G = nx.barbell_graph(3, 0)
+    partition = [{0, 1, 2}, {3, 4, 5}]
+    M = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(M, [0, 1])
+    assert edges_equal(M.edges(), [(0, 1)])
+    for n in M:
+        assert M.nodes[n]["nedges"] == 3
+        assert M.nodes[n]["nnodes"] == 3
+        assert M.nodes[n]["density"] == 1
+
+
+def test_barbell_plus():
+    G = nx.barbell_graph(3, 0)
+    # Add an extra edge joining the bells.
+    G.add_edge(0, 5)
+    partition = [{0, 1, 2}, {3, 4, 5}]
+    M = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(M, [0, 1])
+    assert edges_equal(M.edges(), [(0, 1)])
+    assert M[0][1]["weight"] == 2
+    for n in M:
+        assert M.nodes[n]["nedges"] == 3
+        assert M.nodes[n]["nnodes"] == 3
+        assert M.nodes[n]["density"] == 1
+
+
+def test_blockmodel():
+    G = nx.path_graph(6)
+    partition = [[0, 1], [2, 3], [4, 5]]
+    M = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(M.nodes(), [0, 1, 2])
+    assert edges_equal(M.edges(), [(0, 1), (1, 2)])
+    for n in M.nodes():
+        assert M.nodes[n]["nedges"] == 1
+        assert M.nodes[n]["nnodes"] == 2
+        assert M.nodes[n]["density"] == 1.0
+
+
+def test_multigraph_blockmodel():
+    G = nx.MultiGraph(nx.path_graph(6))
+    partition = [[0, 1], [2, 3], [4, 5]]
+    M = nx.quotient_graph(G, partition, create_using=nx.MultiGraph(), relabel=True)
+    assert nodes_equal(M.nodes(), [0, 1, 2])
+    assert edges_equal(M.edges(), [(0, 1), (1, 2)])
+    for n in M.nodes():
+        assert M.nodes[n]["nedges"] == 1
+        assert M.nodes[n]["nnodes"] == 2
+        assert M.nodes[n]["density"] == 1.0
+
+
+def test_quotient_graph_incomplete_partition():
+    G = nx.path_graph(6)
+    partition = []
+    H = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(H.nodes(), [])
+    assert edges_equal(H.edges(), [])
+
+    partition = [[0, 1], [2, 3], [5]]
+    H = nx.quotient_graph(G, partition, relabel=True)
+    assert nodes_equal(H.nodes(), [0, 1, 2])
+    assert edges_equal(H.edges(), [(0, 1)])
+
+
+def test_undirected_node_contraction():
+    """Tests for node contraction in an undirected graph."""
+    G = nx.cycle_graph(4)
+    actual = nx.contracted_nodes(G, 0, 1)
+    expected = nx.cycle_graph(3)
+    expected.add_edge(0, 0)
+    assert nx.is_isomorphic(actual, expected)
+
+
+def test_directed_node_contraction():
+    """Tests for node contraction in a directed graph."""
+    G = nx.DiGraph(nx.cycle_graph(4))
+    actual = nx.contracted_nodes(G, 0, 1)
+    expected = nx.DiGraph(nx.cycle_graph(3))
+    expected.add_edge(0, 0)
+    expected.add_edge(0, 0)
+    assert nx.is_isomorphic(actual, expected)
+
+
+def test_undirected_node_contraction_no_copy():
+    """Tests for node contraction in an undirected graph
+    by making changes in place."""
+    G = nx.cycle_graph(4)
+    actual = nx.contracted_nodes(G, 0, 1, copy=False)
+    expected = nx.cycle_graph(3)
+    expected.add_edge(0, 0)
+    assert nx.is_isomorphic(actual, G)
+    assert nx.is_isomorphic(actual, expected)
+
+
+def test_directed_node_contraction_no_copy():
+    """Tests for node contraction in a directed graph
+    by making changes in place."""
+    G = nx.DiGraph(nx.cycle_graph(4))
+    actual = nx.contracted_nodes(G, 0, 1, copy=False)
+    expected = nx.DiGraph(nx.cycle_graph(3))
+    expected.add_edge(0, 0)
+    expected.add_edge(0, 0)
+    assert nx.is_isomorphic(actual, G)
+    assert nx.is_isomorphic(actual, expected)
+
+
+def test_create_multigraph():
+    """Tests that using a MultiGraph creates multiple edges."""
+    G = nx.path_graph(3, create_using=nx.MultiGraph())
+    G.add_edge(0, 1)
+    G.add_edge(0, 0)
+    G.add_edge(0, 2)
+    actual = nx.contracted_nodes(G, 0, 2)
+    expected = nx.MultiGraph()
+    expected.add_edge(0, 1)
+    expected.add_edge(0, 1)
+    expected.add_edge(0, 1)
+    expected.add_edge(0, 0)
+    expected.add_edge(0, 0)
+    assert edges_equal(actual.edges, expected.edges)
+
+
+def test_multigraph_keys():
+    """Tests that multiedge keys are reset in new graph."""
+    G = nx.path_graph(3, create_using=nx.MultiGraph())
+    G.add_edge(0, 1, 5)
+    G.add_edge(0, 0, 0)
+    G.add_edge(0, 2, 5)
+    actual = nx.contracted_nodes(G, 0, 2)
+    expected = nx.MultiGraph()
+    expected.add_edge(0, 1, 0)
+    expected.add_edge(0, 1, 5)
+    expected.add_edge(0, 1, 2)  # keyed as 2 b/c 2 edges already in G
+    expected.add_edge(0, 0, 0)
+    expected.add_edge(0, 0, 1)  # this comes from (0, 2, 5)
+    assert edges_equal(actual.edges, expected.edges)
+
+
+def test_node_attributes():
+    """Tests that node contraction preserves node attributes."""
+    G = nx.cycle_graph(4)
+    # Add some data to the two nodes being contracted.
+    G.nodes[0]["foo"] = "bar"
+    G.nodes[1]["baz"] = "xyzzy"
+    actual = nx.contracted_nodes(G, 0, 1)
+    # We expect that contracting the nodes 0 and 1 in C_4 yields K_3, but
+    # with nodes labeled 0, 2, and 3, and with a -loop on 0.
+    expected = nx.complete_graph(3)
+    expected = nx.relabel_nodes(expected, {1: 2, 2: 3})
+    expected.add_edge(0, 0)
+    cdict = {1: {"baz": "xyzzy"}}
+    expected.nodes[0].update({"foo": "bar", "contraction": cdict})
+    assert nx.is_isomorphic(actual, expected)
+    assert actual.nodes == expected.nodes
+
+
+def test_edge_attributes():
+    """Tests that node contraction preserves edge attributes."""
+    # Shape: src1 --> dest <-- src2
+    G = nx.DiGraph([("src1", "dest"), ("src2", "dest")])
+    G["src1"]["dest"]["value"] = "src1-->dest"
+    G["src2"]["dest"]["value"] = "src2-->dest"
+    H = nx.MultiDiGraph(G)
+
+    G = nx.contracted_nodes(G, "src1", "src2")  # New Shape: src1 --> dest
+    assert G.edges[("src1", "dest")]["value"] == "src1-->dest"
+    assert (
+        G.edges[("src1", "dest")]["contraction"][("src2", "dest")]["value"]
+        == "src2-->dest"
+    )
+
+    H = nx.contracted_nodes(H, "src1", "src2")  # New Shape: src1 -(x2)-> dest
+    assert len(H.edges(("src1", "dest"))) == 2
+
+
+def test_without_self_loops():
+    """Tests for node contraction without preserving -loops."""
+    G = nx.cycle_graph(4)
+    actual = nx.contracted_nodes(G, 0, 1, self_loops=False)
+    expected = nx.complete_graph(3)
+    assert nx.is_isomorphic(actual, expected)
+
+
+def test_contract_loop_graph():
+    """Tests for node contraction when nodes have loops."""
+    G = nx.cycle_graph(4)
+    G.add_edge(0, 0)
+    actual = nx.contracted_nodes(G, 0, 1)
+    expected = nx.complete_graph([0, 2, 3])
+    expected.add_edge(0, 0)
+    expected.add_edge(0, 0)
+    assert edges_equal(actual.edges, expected.edges)
+    actual = nx.contracted_nodes(G, 1, 0)
+    expected = nx.complete_graph([1, 2, 3])
+    expected.add_edge(1, 1)
+    expected.add_edge(1, 1)
+    assert edges_equal(actual.edges, expected.edges)
+
+
+def test_undirected_edge_contraction():
+    """Tests for edge contraction in an undirected graph."""
+    G = nx.cycle_graph(4)
+    actual = nx.contracted_edge(G, (0, 1))
+    expected = nx.complete_graph(3)
+    expected.add_edge(0, 0)
+    assert nx.is_isomorphic(actual, expected)
+
+
+def test_multigraph_edge_contraction():
+    """Tests for edge contraction in a multigraph"""
+    G = nx.cycle_graph(4)
+    actual = nx.contracted_edge(G, (0, 1, 0))
+    expected = nx.complete_graph(3)
+    expected.add_edge(0, 0)
+    assert nx.is_isomorphic(actual, expected)
+
+
+def test_nonexistent_edge():
+    """Tests that attempting to contract a nonexistent edge raises an
+    exception.
+
+    """
+    with pytest.raises(ValueError):
+        G = nx.cycle_graph(4)
+        nx.contracted_edge(G, (0, 2))

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/mis.py

@@ -0,0 +1,77 @@
+"""
+Algorithm to find a maximal (not maximum) independent set.
+
+"""
+import networkx as nx
+from networkx.utils import not_implemented_for, py_random_state
+
+__all__ = ["maximal_independent_set"]
+
+
+@not_implemented_for("directed")
+@py_random_state(2)
+@nx._dispatch
+def maximal_independent_set(G, nodes=None, seed=None):
+    """Returns a random maximal independent set guaranteed to contain
+    a given set of nodes.
+
+    An independent set is a set of nodes such that the subgraph
+    of G induced by these nodes contains no edges. A maximal
+    independent set is an independent set such that it is not possible
+    to add a new node and still get an independent set.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    nodes : list or iterable
+       Nodes that must be part of the independent set. This set of nodes
+       must be independent.
+
+    seed : integer, random_state, or None (default)
+        Indicator of random number generation state.
+        See :ref:`Randomness<randomness>`.
+
+    Returns
+    -------
+    indep_nodes : list
+       List of nodes that are part of a maximal independent set.
+
+    Raises
+    ------
+    NetworkXUnfeasible
+       If the nodes in the provided list are not part of the graph or
+       do not form an independent set, an exception is raised.
+
+    NetworkXNotImplemented
+        If `G` is directed.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(5)
+    >>> nx.maximal_independent_set(G)  # doctest: +SKIP
+    [4, 0, 2]
+    >>> nx.maximal_independent_set(G, [1])  # doctest: +SKIP
+    [1, 3]
+
+    Notes
+    -----
+    This algorithm does not solve the maximum independent set problem.
+
+    """
+    if not nodes:
+        nodes = {seed.choice(list(G))}
+    else:
+        nodes = set(nodes)
+    if not nodes.issubset(G):
+        raise nx.NetworkXUnfeasible(f"{nodes} is not a subset of the nodes of G")
+    neighbors = set.union(*[set(G.adj[v]) for v in nodes])
+    if set.intersection(neighbors, nodes):
+        raise nx.NetworkXUnfeasible(f"{nodes} is not an independent set of G")
+    indep_nodes = list(nodes)
+    available_nodes = set(G.nodes()).difference(neighbors.union(nodes))
+    while available_nodes:
+        node = seed.choice(list(available_nodes))
+        indep_nodes.append(node)
+        available_nodes.difference_update(list(G.adj[node]) + [node])
+    return indep_nodes

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/moral.py

@@ -0,0 +1,59 @@
+r"""Function for computing the moral graph of a directed graph."""
+
+import itertools
+
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+__all__ = ["moral_graph"]
+
+
+@not_implemented_for("undirected")
+@nx._dispatch
+def moral_graph(G):
+    r"""Return the Moral Graph
+
+    Returns the moralized graph of a given directed graph.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        Directed graph
+
+    Returns
+    -------
+    H : NetworkX graph
+        The undirected moralized graph of G
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If `G` is undirected.
+
+    Examples
+    --------
+    >>> G = nx.DiGraph([(1, 2), (2, 3), (2, 5), (3, 4), (4, 3)])
+    >>> G_moral = nx.moral_graph(G)
+    >>> G_moral.edges()
+    EdgeView([(1, 2), (2, 3), (2, 5), (2, 4), (3, 4)])
+
+    Notes
+    -----
+    A moral graph is an undirected graph H = (V, E) generated from a
+    directed Graph, where if a node has more than one parent node, edges
+    between these parent nodes are inserted and all directed edges become
+    undirected.
+
+    https://en.wikipedia.org/wiki/Moral_graph
+
+    References
+    ----------
+    .. [1] Wray L. Buntine. 1995. Chain graphs for learning.
+           In Proceedings of the Eleventh conference on Uncertainty
+           in artificial intelligence (UAI'95)
+    """
+    H = G.to_undirected()
+    for preds in G.pred.values():
+        predecessors_combinations = itertools.combinations(preds, r=2)
+        H.add_edges_from(predecessors_combinations)
+    return H

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/algorithms/node_classification.py

@@ -0,0 +1,218 @@
+""" This module provides the functions for node classification problem.
+
+The functions in this module are not imported
+into the top level `networkx` namespace.
+You can access these functions by importing
+the `networkx.algorithms.node_classification` modules,
+then accessing the functions as attributes of `node_classification`.
+For example:
+
+  >>> from networkx.algorithms import node_classification
+  >>> G = nx.path_graph(4)
+  >>> G.edges()
+  EdgeView([(0, 1), (1, 2), (2, 3)])
+  >>> G.nodes[0]["label"] = "A"
+  >>> G.nodes[3]["label"] = "B"
+  >>> node_classification.harmonic_function(G)
+  ['A', 'A', 'B', 'B']
+
+References
+----------
+Zhu, X., Ghahramani, Z., & Lafferty, J. (2003, August).
+Semi-supervised learning using gaussian fields and harmonic functions.
+In ICML (Vol. 3, pp. 912-919).
+"""
+import networkx as nx
+
+__all__ = ["harmonic_function", "local_and_global_consistency"]
+
+
+@nx.utils.not_implemented_for("directed")
+@nx._dispatch(node_attrs="label_name")
+def harmonic_function(G, max_iter=30, label_name="label"):
+    """Node classification by Harmonic function
+
+    Function for computing Harmonic function algorithm by Zhu et al.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+    max_iter : int
+        maximum number of iterations allowed
+    label_name : string
+        name of target labels to predict
+
+    Returns
+    -------
+    predicted : list
+        List of length ``len(G)`` with the predicted labels for each node.
+
+    Raises
+    ------
+    NetworkXError
+        If no nodes in `G` have attribute `label_name`.
+
+    Examples
+    --------
+    >>> from networkx.algorithms import node_classification
+    >>> G = nx.path_graph(4)
+    >>> G.nodes[0]["label"] = "A"
+    >>> G.nodes[3]["label"] = "B"
+    >>> G.nodes(data=True)
+    NodeDataView({0: {'label': 'A'}, 1: {}, 2: {}, 3: {'label': 'B'}})
+    >>> G.edges()
+    EdgeView([(0, 1), (1, 2), (2, 3)])
+    >>> predicted = node_classification.harmonic_function(G)
+    >>> predicted
+    ['A', 'A', 'B', 'B']
+
+    References
+    ----------
+    Zhu, X., Ghahramani, Z., & Lafferty, J. (2003, August).
+    Semi-supervised learning using gaussian fields and harmonic functions.
+    In ICML (Vol. 3, pp. 912-919).
+    """
+    import numpy as np
+    import scipy as sp
+
+    X = nx.to_scipy_sparse_array(G)  # adjacency matrix
+    labels, label_dict = _get_label_info(G, label_name)
+
+    if labels.shape[0] == 0:
+        raise nx.NetworkXError(
+            f"No node on the input graph is labeled by '{label_name}'."
+        )
+
+    n_samples = X.shape[0]
+    n_classes = label_dict.shape[0]
+    F = np.zeros((n_samples, n_classes))
+
+    # Build propagation matrix
+    degrees = X.sum(axis=0)
+    degrees[degrees == 0] = 1  # Avoid division by 0
+    # TODO: csr_array
+    D = sp.sparse.csr_array(sp.sparse.diags((1.0 / degrees), offsets=0))
+    P = (D @ X).tolil()
+    P[labels[:, 0]] = 0  # labels[:, 0] indicates IDs of labeled nodes
+    # Build base matrix
+    B = np.zeros((n_samples, n_classes))
+    B[labels[:, 0], labels[:, 1]] = 1
+
+    for _ in range(max_iter):
+        F = (P @ F) + B
+
+    return label_dict[np.argmax(F, axis=1)].tolist()
+
+
+@nx.utils.not_implemented_for("directed")
+@nx._dispatch(node_attrs="label_name")
+def local_and_global_consistency(G, alpha=0.99, max_iter=30, label_name="label"):
+    """Node classification by Local and Global Consistency
+
+    Function for computing Local and global consistency algorithm by Zhou et al.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+    alpha : float
+        Clamping factor
+    max_iter : int
+        Maximum number of iterations allowed
+    label_name : string
+        Name of target labels to predict
+
+    Returns
+    -------
+    predicted : list
+        List of length ``len(G)`` with the predicted labels for each node.
+
+    Raises
+    ------
+    NetworkXError
+        If no nodes in `G` have attribute `label_name`.
+
+    Examples
+    --------
+    >>> from networkx.algorithms import node_classification
+    >>> G = nx.path_graph(4)
+    >>> G.nodes[0]["label"] = "A"
+    >>> G.nodes[3]["label"] = "B"
+    >>> G.nodes(data=True)
+    NodeDataView({0: {'label': 'A'}, 1: {}, 2: {}, 3: {'label': 'B'}})
+    >>> G.edges()
+    EdgeView([(0, 1), (1, 2), (2, 3)])
+    >>> predicted = node_classification.local_and_global_consistency(G)
+    >>> predicted
+    ['A', 'A', 'B', 'B']
+
+    References
+    ----------
+    Zhou, D., Bousquet, O., Lal, T. N., Weston, J., & Schölkopf, B. (2004).
+    Learning with local and global consistency.
+    Advances in neural information processing systems, 16(16), 321-328.
+    """
+    import numpy as np
+    import scipy as sp
+
+    X = nx.to_scipy_sparse_array(G)  # adjacency matrix
+    labels, label_dict = _get_label_info(G, label_name)
+
+    if labels.shape[0] == 0:
+        raise nx.NetworkXError(
+            f"No node on the input graph is labeled by '{label_name}'."
+        )
+
+    n_samples = X.shape[0]
+    n_classes = label_dict.shape[0]
+    F = np.zeros((n_samples, n_classes))
+
+    # Build propagation matrix
+    degrees = X.sum(axis=0)
+    degrees[degrees == 0] = 1  # Avoid division by 0
+    # TODO: csr_array
+    D2 = np.sqrt(sp.sparse.csr_array(sp.sparse.diags((1.0 / degrees), offsets=0)))
+    P = alpha * ((D2 @ X) @ D2)
+    # Build base matrix
+    B = np.zeros((n_samples, n_classes))
+    B[labels[:, 0], labels[:, 1]] = 1 - alpha
+
+    for _ in range(max_iter):
+        F = (P @ F) + B
+
+    return label_dict[np.argmax(F, axis=1)].tolist()
+
+
+def _get_label_info(G, label_name):
+    """Get and return information of labels from the input graph
+
+    Parameters
+    ----------
+    G : Network X graph
+    label_name : string
+        Name of the target label
+
+    Returns
+    -------
+    labels : numpy array, shape = [n_labeled_samples, 2]
+        Array of pairs of labeled node ID and label ID
+    label_dict : numpy array, shape = [n_classes]
+        Array of labels
+        i-th element contains the label corresponding label ID `i`
+    """
+    import numpy as np
+
+    labels = []
+    label_to_id = {}
+    lid = 0
+    for i, n in enumerate(G.nodes(data=True)):
+        if label_name in n[1]:
+            label = n[1][label_name]
+            if label not in label_to_id:
+                label_to_id[label] = lid
+                lid += 1
+            labels.append([i, label_to_id[label]])
+    labels = np.array(labels)
+    label_dict = np.array(
+        [label for label, _ in sorted(label_to_id.items(), key=lambda x: x[1])]
+    )
+    return (labels, label_dict)