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env-llmeval/lib/python3.10/site-packages/networkx/algorithms/asteroidal.py

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+"""
+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._dispatchable
+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._dispatchable
+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._dispatchable
+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

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/broadcasting.py

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+"""Routines to calculate the broadcast time of certain graphs.
+
+Broadcasting is an information dissemination problem in which a node in a graph,
+called the originator, must distribute a message to all other nodes by placing
+a series of calls along the edges of the graph. Once informed, other nodes aid
+the originator in distributing the message.
+
+The broadcasting must be completed as quickly as possible subject to the
+following constraints:
+- Each call requires one unit of time.
+- A node can only participate in one call per unit of time.
+- Each call only involves two adjacent nodes: a sender and a receiver.
+"""
+
+import networkx as nx
+from networkx import NetworkXError
+from networkx.utils import not_implemented_for
+
+__all__ = [
+    "tree_broadcast_center",
+    "tree_broadcast_time",
+]
+
+
+def _get_max_broadcast_value(G, U, v, values):
+    adj = sorted(set(G.neighbors(v)) & U, key=values.get, reverse=True)
+    return max(values[u] + i for i, u in enumerate(adj, start=1))
+
+
+def _get_broadcast_centers(G, v, values, target):
+    adj = sorted(G.neighbors(v), key=values.get, reverse=True)
+    j = next(i for i, u in enumerate(adj, start=1) if values[u] + i == target)
+    return set([v] + adj[:j])
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatchable
+def tree_broadcast_center(G):
+    """Return the Broadcast Center of the tree `G`.
+
+    The broadcast center of a graph G denotes the set of nodes having
+    minimum broadcast time [1]_. This is a linear algorithm for determining
+    the broadcast center of a tree with ``N`` nodes, as a by-product it also
+    determines the broadcast time from the broadcast center.
+
+    Parameters
+    ----------
+    G : undirected graph
+        The graph should be an undirected tree
+
+    Returns
+    -------
+    BC : (int, set) tuple
+        minimum broadcast number of the tree, set of broadcast centers
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If the graph is directed or is a multigraph.
+
+    References
+    ----------
+    .. [1] Slater, P.J., Cockayne, E.J., Hedetniemi, S.T,
+       Information dissemination in trees. SIAM J.Comput. 10(4), 692–701 (1981)
+    """
+    # Assert that the graph G is a tree
+    if not nx.is_tree(G):
+        NetworkXError("Input graph is not a tree")
+    # step 0
+    if G.number_of_nodes() == 2:
+        return 1, set(G.nodes())
+    if G.number_of_nodes() == 1:
+        return 0, set(G.nodes())
+
+    # step 1
+    U = {node for node, deg in G.degree if deg == 1}
+    values = {n: 0 for n in U}
+    T = G.copy()
+    T.remove_nodes_from(U)
+
+    # step 2
+    W = {node for node, deg in T.degree if deg == 1}
+    values.update((w, G.degree[w] - 1) for w in W)
+
+    # step 3
+    while T.number_of_nodes() >= 2:
+        # step 4
+        w = min(W, key=lambda n: values[n])
+        v = next(T.neighbors(w))
+
+        # step 5
+        U.add(w)
+        W.remove(w)
+        T.remove_node(w)
+
+        # step 6
+        if T.degree(v) == 1:
+            # update t(v)
+            values.update({v: _get_max_broadcast_value(G, U, v, values)})
+            W.add(v)
+
+    # step 7
+    v = nx.utils.arbitrary_element(T)
+    b_T = _get_max_broadcast_value(G, U, v, values)
+    return b_T, _get_broadcast_centers(G, v, values, b_T)
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatchable
+def tree_broadcast_time(G, node=None):
+    """Return the Broadcast Time of the tree `G`.
+
+    The minimum broadcast time of a node is defined as the minimum amount
+    of time required to complete broadcasting starting from the
+    originator. The broadcast time of a graph is the maximum over
+    all nodes of the minimum broadcast time from that node [1]_.
+    This function returns the minimum broadcast time of `node`.
+    If `node` is None the broadcast time for the graph is returned.
+
+    Parameters
+    ----------
+    G : undirected graph
+        The graph should be an undirected tree
+    node: int, optional
+        index of starting node. If `None`, the algorithm returns the broadcast
+        time of the tree.
+
+    Returns
+    -------
+    BT : int
+        Broadcast Time of a node in a tree
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If the graph is directed or is a multigraph.
+
+    References
+    ----------
+    .. [1] Harutyunyan, H. A. and Li, Z.
+        "A Simple Construction of Broadcast Graphs."
+        In Computing and Combinatorics. COCOON 2019
+        (Ed. D. Z. Du and C. Tian.) Springer, pp. 240-253, 2019.
+    """
+    b_T, b_C = tree_broadcast_center(G)
+    if node is not None:
+        return b_T + min(nx.shortest_path_length(G, node, u) for u in b_C)
+    dist_from_center = dict.fromkeys(G, len(G))
+    for u in b_C:
+        for v, dist in nx.shortest_path_length(G, u).items():
+            if dist < dist_from_center[v]:
+                dist_from_center[v] = dist
+    return b_T + max(dist_from_center.values())

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/chains.py

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+"""Functions for finding chains in a graph."""
+
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+__all__ = ["chain_decomposition"]
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatchable
+def chain_decomposition(G, root=None):
+    """Returns the chain decomposition of a graph.
+
+    The *chain decomposition* of a graph with respect a depth-first
+    search tree is a set of cycles or paths derived from the set of
+    fundamental cycles of the tree in the following manner. Consider
+    each fundamental cycle with respect to the given tree, represented
+    as a list of edges beginning with the nontree edge oriented away
+    from the root of the tree. For each fundamental cycle, if it
+    overlaps with any previous fundamental cycle, just take the initial
+    non-overlapping segment, which is a path instead of a cycle. Each
+    cycle or path is called a *chain*. For more information, see [1]_.
+
+    Parameters
+    ----------
+    G : undirected graph
+
+    root : node (optional)
+       A node in the graph `G`. If specified, only the chain
+       decomposition for the connected component containing this node
+       will be returned. This node indicates the root of the depth-first
+       search tree.
+
+    Yields
+    ------
+    chain : list
+       A list of edges representing a chain. There is no guarantee on
+       the orientation of the edges in each chain (for example, if a
+       chain includes the edge joining nodes 1 and 2, the chain may
+       include either (1, 2) or (2, 1)).
+
+    Raises
+    ------
+    NodeNotFound
+       If `root` is not in the graph `G`.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(0, 1), (1, 4), (3, 4), (3, 5), (4, 5)])
+    >>> list(nx.chain_decomposition(G))
+    [[(4, 5), (5, 3), (3, 4)]]
+
+    Notes
+    -----
+    The worst-case running time of this implementation is linear in the
+    number of nodes and number of edges [1]_.
+
+    References
+    ----------
+    .. [1] Jens M. Schmidt (2013). "A simple test on 2-vertex-
+       and 2-edge-connectivity." *Information Processing Letters*,
+       113, 241–244. Elsevier. <https://doi.org/10.1016/j.ipl.2013.01.016>
+
+    """
+
+    def _dfs_cycle_forest(G, root=None):
+        """Builds a directed graph composed of cycles from the given graph.
+
+        `G` is an undirected simple graph. `root` is a node in the graph
+        from which the depth-first search is started.
+
+        This function returns both the depth-first search cycle graph
+        (as a :class:`~networkx.DiGraph`) and the list of nodes in
+        depth-first preorder. The depth-first search cycle graph is a
+        directed graph whose edges are the edges of `G` oriented toward
+        the root if the edge is a tree edge and away from the root if
+        the edge is a non-tree edge. If `root` is not specified, this
+        performs a depth-first search on each connected component of `G`
+        and returns a directed forest instead.
+
+        If `root` is not in the graph, this raises :exc:`KeyError`.
+
+        """
+        # Create a directed graph from the depth-first search tree with
+        # root node `root` in which tree edges are directed toward the
+        # root and nontree edges are directed away from the root. For
+        # each node with an incident nontree edge, this creates a
+        # directed cycle starting with the nontree edge and returning to
+        # that node.
+        #
+        # The `parent` node attribute stores the parent of each node in
+        # the DFS tree. The `nontree` edge attribute indicates whether
+        # the edge is a tree edge or a nontree edge.
+        #
+        # We also store the order of the nodes found in the depth-first
+        # search in the `nodes` list.
+        H = nx.DiGraph()
+        nodes = []
+        for u, v, d in nx.dfs_labeled_edges(G, source=root):
+            if d == "forward":
+                # `dfs_labeled_edges()` yields (root, root, 'forward')
+                # if it is beginning the search on a new connected
+                # component.
+                if u == v:
+                    H.add_node(v, parent=None)
+                    nodes.append(v)
+                else:
+                    H.add_node(v, parent=u)
+                    H.add_edge(v, u, nontree=False)
+                    nodes.append(v)
+            # `dfs_labeled_edges` considers nontree edges in both
+            # orientations, so we need to not add the edge if it its
+            # other orientation has been added.
+            elif d == "nontree" and v not in H[u]:
+                H.add_edge(v, u, nontree=True)
+            else:
+                # Do nothing on 'reverse' edges; we only care about
+                # forward and nontree edges.
+                pass
+        return H, nodes
+
+    def _build_chain(G, u, v, visited):
+        """Generate the chain starting from the given nontree edge.
+
+        `G` is a DFS cycle graph as constructed by
+        :func:`_dfs_cycle_graph`. The edge (`u`, `v`) is a nontree edge
+        that begins a chain. `visited` is a set representing the nodes
+        in `G` that have already been visited.
+
+        This function yields the edges in an initial segment of the
+        fundamental cycle of `G` starting with the nontree edge (`u`,
+        `v`) that includes all the edges up until the first node that
+        appears in `visited`. The tree edges are given by the 'parent'
+        node attribute. The `visited` set is updated to add each node in
+        an edge yielded by this function.
+
+        """
+        while v not in visited:
+            yield u, v
+            visited.add(v)
+            u, v = v, G.nodes[v]["parent"]
+        yield u, v
+
+    # Check if the root is in the graph G. If not, raise NodeNotFound
+    if root is not None and root not in G:
+        raise nx.NodeNotFound(f"Root node {root} is not in graph")
+
+    # Create a directed version of H that has the DFS edges directed
+    # toward the root and the nontree edges directed away from the root
+    # (in each connected component).
+    H, nodes = _dfs_cycle_forest(G, root)
+
+    # Visit the nodes again in DFS order. For each node, and for each
+    # nontree edge leaving that node, compute the fundamental cycle for
+    # that nontree edge starting with that edge. If the fundamental
+    # cycle overlaps with any visited nodes, just take the prefix of the
+    # cycle up to the point of visited nodes.
+    #
+    # We repeat this process for each connected component (implicitly,
+    # since `nodes` already has a list of the nodes grouped by connected
+    # component).
+    visited = set()
+    for u in nodes:
+        visited.add(u)
+        # For each nontree edge going out of node u...
+        edges = ((u, v) for u, v, d in H.out_edges(u, data="nontree") if d)
+        for u, v in edges:
+            # Create the cycle or cycle prefix starting with the
+            # nontree edge.
+            chain = list(_build_chain(H, u, v, visited))
+            yield chain

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/cycles.py

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+"""
+========================
+Cycle finding algorithms
+========================
+"""
+
+from collections import Counter, defaultdict
+from itertools import combinations, product
+from math import inf
+
+import networkx as nx
+from networkx.utils import not_implemented_for, pairwise
+
+__all__ = [
+    "cycle_basis",
+    "simple_cycles",
+    "recursive_simple_cycles",
+    "find_cycle",
+    "minimum_cycle_basis",
+    "chordless_cycles",
+    "girth",
+]
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatchable
+def cycle_basis(G, root=None):
+    """Returns a list of cycles which form a basis for cycles of G.
+
+    A basis for cycles of a network is a minimal collection of
+    cycles such that any cycle in the network can be written
+    as a sum of cycles in the basis.  Here summation of cycles
+    is defined as "exclusive or" of the edges. Cycle bases are
+    useful, e.g. when deriving equations for electric circuits
+    using Kirchhoff's Laws.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+    root : node, optional
+       Specify starting node for basis.
+
+    Returns
+    -------
+    A list of cycle lists.  Each cycle list is a list of nodes
+    which forms a cycle (loop) in G.
+
+    Examples
+    --------
+    >>> G = nx.Graph()
+    >>> nx.add_cycle(G, [0, 1, 2, 3])
+    >>> nx.add_cycle(G, [0, 3, 4, 5])
+    >>> nx.cycle_basis(G, 0)
+    [[3, 4, 5, 0], [1, 2, 3, 0]]
+
+    Notes
+    -----
+    This is adapted from algorithm CACM 491 [1]_.
+
+    References
+    ----------
+    .. [1] Paton, K. An algorithm for finding a fundamental set of
+       cycles of a graph. Comm. ACM 12, 9 (Sept 1969), 514-518.
+
+    See Also
+    --------
+    simple_cycles
+    minimum_cycle_basis
+    """
+    gnodes = dict.fromkeys(G)  # set-like object that maintains node order
+    cycles = []
+    while gnodes:  # loop over connected components
+        if root is None:
+            root = gnodes.popitem()[0]
+        stack = [root]
+        pred = {root: root}
+        used = {root: set()}
+        while stack:  # walk the spanning tree finding cycles
+            z = stack.pop()  # use last-in so cycles easier to find
+            zused = used[z]
+            for nbr in G[z]:
+                if nbr not in used:  # new node
+                    pred[nbr] = z
+                    stack.append(nbr)
+                    used[nbr] = {z}
+                elif nbr == z:  # self loops
+                    cycles.append([z])
+                elif nbr not in zused:  # found a cycle
+                    pn = used[nbr]
+                    cycle = [nbr, z]
+                    p = pred[z]
+                    while p not in pn:
+                        cycle.append(p)
+                        p = pred[p]
+                    cycle.append(p)
+                    cycles.append(cycle)
+                    used[nbr].add(z)
+        for node in pred:
+            gnodes.pop(node, None)
+        root = None
+    return cycles
+
+
+@nx._dispatchable
+def simple_cycles(G, length_bound=None):
+    """Find simple cycles (elementary circuits) of a graph.
+
+    A `simple cycle`, or `elementary circuit`, is a closed path where
+    no node appears twice.  In a directed graph, two simple cycles are distinct
+    if they are not cyclic permutations of each other.  In an undirected graph,
+    two simple cycles are distinct if they are not cyclic permutations of each
+    other nor of the other's reversal.
+
+    Optionally, the cycles are bounded in length.  In the unbounded case, we use
+    a nonrecursive, iterator/generator version of Johnson's algorithm [1]_.  In
+    the bounded case, we use a version of the algorithm of Gupta and
+    Suzumura[2]_. There may be better algorithms for some cases [3]_ [4]_ [5]_.
+
+    The algorithms of Johnson, and Gupta and Suzumura, are enhanced by some
+    well-known preprocessing techniques.  When G is directed, we restrict our
+    attention to strongly connected components of G, generate all simple cycles
+    containing a certain node, remove that node, and further decompose the
+    remainder into strongly connected components.  When G is undirected, we
+    restrict our attention to biconnected components, generate all simple cycles
+    containing a particular edge, remove that edge, and further decompose the
+    remainder into biconnected components.
+
+    Note that multigraphs are supported by this function -- and in undirected
+    multigraphs, a pair of parallel edges is considered a cycle of length 2.
+    Likewise, self-loops are considered to be cycles of length 1.  We define
+    cycles as sequences of nodes; so the presence of loops and parallel edges
+    does not change the number of simple cycles in a graph.
+
+    Parameters
+    ----------
+    G : NetworkX DiGraph
+       A directed graph
+
+    length_bound : int or None, optional (default=None)
+       If length_bound is an int, generate all simple cycles of G with length at
+       most length_bound.  Otherwise, generate all simple cycles of G.
+
+    Yields
+    ------
+    list of nodes
+       Each cycle is represented by a list of nodes along the cycle.
+
+    Examples
+    --------
+    >>> edges = [(0, 0), (0, 1), (0, 2), (1, 2), (2, 0), (2, 1), (2, 2)]
+    >>> G = nx.DiGraph(edges)
+    >>> sorted(nx.simple_cycles(G))
+    [[0], [0, 1, 2], [0, 2], [1, 2], [2]]
+
+    To filter the cycles so that they don't include certain nodes or edges,
+    copy your graph and eliminate those nodes or edges before calling.
+    For example, to exclude self-loops from the above example:
+
+    >>> H = G.copy()
+    >>> H.remove_edges_from(nx.selfloop_edges(G))
+    >>> sorted(nx.simple_cycles(H))
+    [[0, 1, 2], [0, 2], [1, 2]]
+
+    Notes
+    -----
+    When length_bound is None, the time complexity is $O((n+e)(c+1))$ for $n$
+    nodes, $e$ edges and $c$ simple circuits.  Otherwise, when length_bound > 1,
+    the time complexity is $O((c+n)(k-1)d^k)$ where $d$ is the average degree of
+    the nodes of G and $k$ = length_bound.
+
+    Raises
+    ------
+    ValueError
+        when length_bound < 0.
+
+    References
+    ----------
+    .. [1] Finding all the elementary circuits of a directed graph.
+       D. B. Johnson, SIAM Journal on Computing 4, no. 1, 77-84, 1975.
+       https://doi.org/10.1137/0204007
+    .. [2] Finding All Bounded-Length Simple Cycles in a Directed Graph
+       A. Gupta and T. Suzumura https://arxiv.org/abs/2105.10094
+    .. [3] Enumerating the cycles of a digraph: a new preprocessing strategy.
+       G. Loizou and P. Thanish, Information Sciences, v. 27, 163-182, 1982.
+    .. [4] A search strategy for the elementary cycles of a directed graph.
+       J.L. Szwarcfiter and P.E. Lauer, BIT NUMERICAL MATHEMATICS,
+       v. 16, no. 2, 192-204, 1976.
+    .. [5] Optimal Listing of Cycles and st-Paths in Undirected Graphs
+        R. Ferreira and R. Grossi and A. Marino and N. Pisanti and R. Rizzi and
+        G. Sacomoto https://arxiv.org/abs/1205.2766
+
+    See Also
+    --------
+    cycle_basis
+    chordless_cycles
+    """
+
+    if length_bound is not None:
+        if length_bound == 0:
+            return
+        elif length_bound < 0:
+            raise ValueError("length bound must be non-negative")
+
+    directed = G.is_directed()
+    yield from ([v] for v, Gv in G.adj.items() if v in Gv)
+
+    if length_bound is not None and length_bound == 1:
+        return
+
+    if G.is_multigraph() and not directed:
+        visited = set()
+        for u, Gu in G.adj.items():
+            multiplicity = ((v, len(Guv)) for v, Guv in Gu.items() if v in visited)
+            yield from ([u, v] for v, m in multiplicity if m > 1)
+            visited.add(u)
+
+    # explicitly filter out loops; implicitly filter out parallel edges
+    if directed:
+        G = nx.DiGraph((u, v) for u, Gu in G.adj.items() for v in Gu if v != u)
+    else:
+        G = nx.Graph((u, v) for u, Gu in G.adj.items() for v in Gu if v != u)
+
+    # this case is not strictly necessary but improves performance
+    if length_bound is not None and length_bound == 2:
+        if directed:
+            visited = set()
+            for u, Gu in G.adj.items():
+                yield from (
+                    [v, u] for v in visited.intersection(Gu) if G.has_edge(v, u)
+                )
+                visited.add(u)
+        return
+
+    if directed:
+        yield from _directed_cycle_search(G, length_bound)
+    else:
+        yield from _undirected_cycle_search(G, length_bound)
+
+
+def _directed_cycle_search(G, length_bound):
+    """A dispatch function for `simple_cycles` for directed graphs.
+
+    We generate all cycles of G through binary partition.
+
+        1. Pick a node v in G which belongs to at least one cycle
+            a. Generate all cycles of G which contain the node v.
+            b. Recursively generate all cycles of G \\ v.
+
+    This is accomplished through the following:
+
+        1. Compute the strongly connected components SCC of G.
+        2. Select and remove a biconnected component C from BCC.  Select a
+           non-tree edge (u, v) of a depth-first search of G[C].
+        3. For each simple cycle P containing v in G[C], yield P.
+        4. Add the biconnected components of G[C \\ v] to BCC.
+
+    If the parameter length_bound is not None, then step 3 will be limited to
+    simple cycles of length at most length_bound.
+
+    Parameters
+    ----------
+    G : NetworkX DiGraph
+       A directed graph
+
+    length_bound : int or None
+       If length_bound is an int, generate all simple cycles of G with length at most length_bound.
+       Otherwise, generate all simple cycles of G.
+
+    Yields
+    ------
+    list of nodes
+       Each cycle is represented by a list of nodes along the cycle.
+    """
+
+    scc = nx.strongly_connected_components
+    components = [c for c in scc(G) if len(c) >= 2]
+    while components:
+        c = components.pop()
+        Gc = G.subgraph(c)
+        v = next(iter(c))
+        if length_bound is None:
+            yield from _johnson_cycle_search(Gc, [v])
+        else:
+            yield from _bounded_cycle_search(Gc, [v], length_bound)
+        # delete v after searching G, to make sure we can find v
+        G.remove_node(v)
+        components.extend(c for c in scc(Gc) if len(c) >= 2)
+
+
+def _undirected_cycle_search(G, length_bound):
+    """A dispatch function for `simple_cycles` for undirected graphs.
+
+    We generate all cycles of G through binary partition.
+
+        1. Pick an edge (u, v) in G which belongs to at least one cycle
+            a. Generate all cycles of G which contain the edge (u, v)
+            b. Recursively generate all cycles of G \\ (u, v)
+
+    This is accomplished through the following:
+
+        1. Compute the biconnected components BCC of G.
+        2. Select and remove a biconnected component C from BCC.  Select a
+           non-tree edge (u, v) of a depth-first search of G[C].
+        3. For each (v -> u) path P remaining in G[C] \\ (u, v), yield P.
+        4. Add the biconnected components of G[C] \\ (u, v) to BCC.
+
+    If the parameter length_bound is not None, then step 3 will be limited to simple paths
+    of length at most length_bound.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+       An undirected graph
+
+    length_bound : int or None
+       If length_bound is an int, generate all simple cycles of G with length at most length_bound.
+       Otherwise, generate all simple cycles of G.
+
+    Yields
+    ------
+    list of nodes
+       Each cycle is represented by a list of nodes along the cycle.
+    """
+
+    bcc = nx.biconnected_components
+    components = [c for c in bcc(G) if len(c) >= 3]
+    while components:
+        c = components.pop()
+        Gc = G.subgraph(c)
+        uv = list(next(iter(Gc.edges)))
+        G.remove_edge(*uv)
+        # delete (u, v) before searching G, to avoid fake 3-cycles [u, v, u]
+        if length_bound is None:
+            yield from _johnson_cycle_search(Gc, uv)
+        else:
+            yield from _bounded_cycle_search(Gc, uv, length_bound)
+        components.extend(c for c in bcc(Gc) if len(c) >= 3)
+
+
+class _NeighborhoodCache(dict):
+    """Very lightweight graph wrapper which caches neighborhoods as list.
+
+    This dict subclass uses the __missing__ functionality to query graphs for
+    their neighborhoods, and store the result as a list.  This is used to avoid
+    the performance penalty incurred by subgraph views.
+    """
+
+    def __init__(self, G):
+        self.G = G
+
+    def __missing__(self, v):
+        Gv = self[v] = list(self.G[v])
+        return Gv
+
+
+def _johnson_cycle_search(G, path):
+    """The main loop of the cycle-enumeration algorithm of Johnson.
+
+    Parameters
+    ----------
+    G : NetworkX Graph or DiGraph
+       A graph
+
+    path : list
+       A cycle prefix.  All cycles generated will begin with this prefix.
+
+    Yields
+    ------
+    list of nodes
+       Each cycle is represented by a list of nodes along the cycle.
+
+    References
+    ----------
+        .. [1] Finding all the elementary circuits of a directed graph.
+       D. B. Johnson, SIAM Journal on Computing 4, no. 1, 77-84, 1975.
+       https://doi.org/10.1137/0204007
+
+    """
+
+    G = _NeighborhoodCache(G)
+    blocked = set(path)
+    B = defaultdict(set)  # graph portions that yield no elementary circuit
+    start = path[0]
+    stack = [iter(G[path[-1]])]
+    closed = [False]
+    while stack:
+        nbrs = stack[-1]
+        for w in nbrs:
+            if w == start:
+                yield path[:]
+                closed[-1] = True
+            elif w not in blocked:
+                path.append(w)
+                closed.append(False)
+                stack.append(iter(G[w]))
+                blocked.add(w)
+                break
+        else:  # no more nbrs
+            stack.pop()
+            v = path.pop()
+            if closed.pop():
+                if closed:
+                    closed[-1] = True
+                unblock_stack = {v}
+                while unblock_stack:
+                    u = unblock_stack.pop()
+                    if u in blocked:
+                        blocked.remove(u)
+                        unblock_stack.update(B[u])
+                        B[u].clear()
+            else:
+                for w in G[v]:
+                    B[w].add(v)
+
+
+def _bounded_cycle_search(G, path, length_bound):
+    """The main loop of the cycle-enumeration algorithm of Gupta and Suzumura.
+
+    Parameters
+    ----------
+    G : NetworkX Graph or DiGraph
+       A graph
+
+    path : list
+       A cycle prefix.  All cycles generated will begin with this prefix.
+
+    length_bound: int
+        A length bound.  All cycles generated will have length at most length_bound.
+
+    Yields
+    ------
+    list of nodes
+       Each cycle is represented by a list of nodes along the cycle.
+
+    References
+    ----------
+    .. [1] Finding All Bounded-Length Simple Cycles in a Directed Graph
+       A. Gupta and T. Suzumura https://arxiv.org/abs/2105.10094
+
+    """
+    G = _NeighborhoodCache(G)
+    lock = {v: 0 for v in path}
+    B = defaultdict(set)
+    start = path[0]
+    stack = [iter(G[path[-1]])]
+    blen = [length_bound]
+    while stack:
+        nbrs = stack[-1]
+        for w in nbrs:
+            if w == start:
+                yield path[:]
+                blen[-1] = 1
+            elif len(path) < lock.get(w, length_bound):
+                path.append(w)
+                blen.append(length_bound)
+                lock[w] = len(path)
+                stack.append(iter(G[w]))
+                break
+        else:
+            stack.pop()
+            v = path.pop()
+            bl = blen.pop()
+            if blen:
+                blen[-1] = min(blen[-1], bl)
+            if bl < length_bound:
+                relax_stack = [(bl, v)]
+                while relax_stack:
+                    bl, u = relax_stack.pop()
+                    if lock.get(u, length_bound) < length_bound - bl + 1:
+                        lock[u] = length_bound - bl + 1
+                        relax_stack.extend((bl + 1, w) for w in B[u].difference(path))
+            else:
+                for w in G[v]:
+                    B[w].add(v)
+
+
+@nx._dispatchable
+def chordless_cycles(G, length_bound=None):
+    """Find simple chordless cycles of a graph.
+
+    A `simple cycle` is a closed path where no node appears twice.  In a simple
+    cycle, a `chord` is an additional edge between two nodes in the cycle.  A
+    `chordless cycle` is a simple cycle without chords.  Said differently, a
+    chordless cycle is a cycle C in a graph G where the number of edges in the
+    induced graph G[C] is equal to the length of `C`.
+
+    Note that some care must be taken in the case that G is not a simple graph
+    nor a simple digraph.  Some authors limit the definition of chordless cycles
+    to have a prescribed minimum length; we do not.
+
+        1. We interpret self-loops to be chordless cycles, except in multigraphs
+           with multiple loops in parallel.  Likewise, in a chordless cycle of
+           length greater than 1, there can be no nodes with self-loops.
+
+        2. We interpret directed two-cycles to be chordless cycles, except in
+           multi-digraphs when any edge in a two-cycle has a parallel copy.
+
+        3. We interpret parallel pairs of undirected edges as two-cycles, except
+           when a third (or more) parallel edge exists between the two nodes.
+
+        4. Generalizing the above, edges with parallel clones may not occur in
+           chordless cycles.
+
+    In a directed graph, two chordless cycles are distinct if they are not
+    cyclic permutations of each other.  In an undirected graph, two chordless
+    cycles are distinct if they are not cyclic permutations of each other nor of
+    the other's reversal.
+
+    Optionally, the cycles are bounded in length.
+
+    We use an algorithm strongly inspired by that of Dias et al [1]_.  It has
+    been modified in the following ways:
+
+        1. Recursion is avoided, per Python's limitations
+
+        2. The labeling function is not necessary, because the starting paths
+            are chosen (and deleted from the host graph) to prevent multiple
+            occurrences of the same path
+
+        3. The search is optionally bounded at a specified length
+
+        4. Support for directed graphs is provided by extending cycles along
+            forward edges, and blocking nodes along forward and reverse edges
+
+        5. Support for multigraphs is provided by omitting digons from the set
+            of forward edges
+
+    Parameters
+    ----------
+    G : NetworkX DiGraph
+       A directed graph
+
+    length_bound : int or None, optional (default=None)
+       If length_bound is an int, generate all simple cycles of G with length at
+       most length_bound.  Otherwise, generate all simple cycles of G.
+
+    Yields
+    ------
+    list of nodes
+       Each cycle is represented by a list of nodes along the cycle.
+
+    Examples
+    --------
+    >>> sorted(list(nx.chordless_cycles(nx.complete_graph(4))))
+    [[1, 0, 2], [1, 0, 3], [2, 0, 3], [2, 1, 3]]
+
+    Notes
+    -----
+    When length_bound is None, and the graph is simple, the time complexity is
+    $O((n+e)(c+1))$ for $n$ nodes, $e$ edges and $c$ chordless cycles.
+
+    Raises
+    ------
+    ValueError
+        when length_bound < 0.
+
+    References
+    ----------
+    .. [1] Efficient enumeration of chordless cycles
+       E. Dias and D. Castonguay and H. Longo and W.A.R. Jradi
+       https://arxiv.org/abs/1309.1051
+
+    See Also
+    --------
+    simple_cycles
+    """
+
+    if length_bound is not None:
+        if length_bound == 0:
+            return
+        elif length_bound < 0:
+            raise ValueError("length bound must be non-negative")
+
+    directed = G.is_directed()
+    multigraph = G.is_multigraph()
+
+    if multigraph:
+        yield from ([v] for v, Gv in G.adj.items() if len(Gv.get(v, ())) == 1)
+    else:
+        yield from ([v] for v, Gv in G.adj.items() if v in Gv)
+
+    if length_bound is not None and length_bound == 1:
+        return
+
+    # Nodes with loops cannot belong to longer cycles.  Let's delete them here.
+    # also, we implicitly reduce the multiplicity of edges down to 1 in the case
+    # of multiedges.
+    if directed:
+        F = nx.DiGraph((u, v) for u, Gu in G.adj.items() if u not in Gu for v in Gu)
+        B = F.to_undirected(as_view=False)
+    else:
+        F = nx.Graph((u, v) for u, Gu in G.adj.items() if u not in Gu for v in Gu)
+        B = None
+
+    # If we're given a multigraph, we have a few cases to consider with parallel
+    # edges.
+    #
+    # 1. If we have 2 or more edges in parallel between the nodes (u, v), we
+    #    must not construct longer cycles along (u, v).
+    # 2. If G is not directed, then a pair of parallel edges between (u, v) is a
+    #    chordless cycle unless there exists a third (or more) parallel edge.
+    # 3. If G is directed, then parallel edges do not form cycles, but do
+    #    preclude back-edges from forming cycles (handled in the next section),
+    #    Thus, if an edge (u, v) is duplicated and the reverse (v, u) is also
+    #    present, then we remove both from F.
+    #
+    # In directed graphs, we need to consider both directions that edges can
+    # take, so iterate over all edges (u, v) and possibly (v, u).  In undirected
+    # graphs, we need to be a little careful to only consider every edge once,
+    # so we use a "visited" set to emulate node-order comparisons.
+
+    if multigraph:
+        if not directed:
+            B = F.copy()
+            visited = set()
+        for u, Gu in G.adj.items():
+            if directed:
+                multiplicity = ((v, len(Guv)) for v, Guv in Gu.items())
+                for v, m in multiplicity:
+                    if m > 1:
+                        F.remove_edges_from(((u, v), (v, u)))
+            else:
+                multiplicity = ((v, len(Guv)) for v, Guv in Gu.items() if v in visited)
+                for v, m in multiplicity:
+                    if m == 2:
+                        yield [u, v]
+                    if m > 1:
+                        F.remove_edge(u, v)
+                visited.add(u)
+
+    # If we're given a directed graphs, we need to think about digons.  If we
+    # have two edges (u, v) and (v, u), then that's a two-cycle.  If either edge
+    # was duplicated above, then we removed both from F.  So, any digons we find
+    # here are chordless.  After finding digons, we remove their edges from F
+    # to avoid traversing them in the search for chordless cycles.
+    if directed:
+        for u, Fu in F.adj.items():
+            digons = [[u, v] for v in Fu if F.has_edge(v, u)]
+            yield from digons
+            F.remove_edges_from(digons)
+            F.remove_edges_from(e[::-1] for e in digons)
+
+    if length_bound is not None and length_bound == 2:
+        return
+
+    # Now, we prepare to search for cycles.  We have removed all cycles of
+    # lengths 1 and 2, so F is a simple graph or simple digraph.  We repeatedly
+    # separate digraphs into their strongly connected components, and undirected
+    # graphs into their biconnected components.  For each component, we pick a
+    # node v, search for chordless cycles based at each "stem" (u, v, w), and
+    # then remove v from that component before separating the graph again.
+    if directed:
+        separate = nx.strongly_connected_components
+
+        # Directed stems look like (u -> v -> w), so we use the product of
+        # predecessors of v with successors of v.
+        def stems(C, v):
+            for u, w in product(C.pred[v], C.succ[v]):
+                if not G.has_edge(u, w):  # omit stems with acyclic chords
+                    yield [u, v, w], F.has_edge(w, u)
+
+    else:
+        separate = nx.biconnected_components
+
+        # Undirected stems look like (u ~ v ~ w), but we must not also search
+        # (w ~ v ~ u), so we use combinations of v's neighbors of length 2.
+        def stems(C, v):
+            yield from (([u, v, w], F.has_edge(w, u)) for u, w in combinations(C[v], 2))
+
+    components = [c for c in separate(F) if len(c) > 2]
+    while components:
+        c = components.pop()
+        v = next(iter(c))
+        Fc = F.subgraph(c)
+        Fcc = Bcc = None
+        for S, is_triangle in stems(Fc, v):
+            if is_triangle:
+                yield S
+            else:
+                if Fcc is None:
+                    Fcc = _NeighborhoodCache(Fc)
+                    Bcc = Fcc if B is None else _NeighborhoodCache(B.subgraph(c))
+                yield from _chordless_cycle_search(Fcc, Bcc, S, length_bound)
+
+        components.extend(c for c in separate(F.subgraph(c - {v})) if len(c) > 2)
+
+
+def _chordless_cycle_search(F, B, path, length_bound):
+    """The main loop for chordless cycle enumeration.
+
+    This algorithm is strongly inspired by that of Dias et al [1]_.  It has been
+    modified in the following ways:
+
+        1. Recursion is avoided, per Python's limitations
+
+        2. The labeling function is not necessary, because the starting paths
+            are chosen (and deleted from the host graph) to prevent multiple
+            occurrences of the same path
+
+        3. The search is optionally bounded at a specified length
+
+        4. Support for directed graphs is provided by extending cycles along
+            forward edges, and blocking nodes along forward and reverse edges
+
+        5. Support for multigraphs is provided by omitting digons from the set
+            of forward edges
+
+    Parameters
+    ----------
+    F : _NeighborhoodCache
+       A graph of forward edges to follow in constructing cycles
+
+    B : _NeighborhoodCache
+       A graph of blocking edges to prevent the production of chordless cycles
+
+    path : list
+       A cycle prefix.  All cycles generated will begin with this prefix.
+
+    length_bound : int
+       A length bound.  All cycles generated will have length at most length_bound.
+
+
+    Yields
+    ------
+    list of nodes
+       Each cycle is represented by a list of nodes along the cycle.
+
+    References
+    ----------
+    .. [1] Efficient enumeration of chordless cycles
+       E. Dias and D. Castonguay and H. Longo and W.A.R. Jradi
+       https://arxiv.org/abs/1309.1051
+
+    """
+    blocked = defaultdict(int)
+    target = path[0]
+    blocked[path[1]] = 1
+    for w in path[1:]:
+        for v in B[w]:
+            blocked[v] += 1
+
+    stack = [iter(F[path[2]])]
+    while stack:
+        nbrs = stack[-1]
+        for w in nbrs:
+            if blocked[w] == 1 and (length_bound is None or len(path) < length_bound):
+                Fw = F[w]
+                if target in Fw:
+                    yield path + [w]
+                else:
+                    Bw = B[w]
+                    if target in Bw:
+                        continue
+                    for v in Bw:
+                        blocked[v] += 1
+                    path.append(w)
+                    stack.append(iter(Fw))
+                    break
+        else:
+            stack.pop()
+            for v in B[path.pop()]:
+                blocked[v] -= 1
+
+
+@not_implemented_for("undirected")
+@nx._dispatchable(mutates_input=True)
+def recursive_simple_cycles(G):
+    """Find simple cycles (elementary circuits) of a directed graph.
+
+    A `simple cycle`, or `elementary circuit`, is a closed path where
+    no node appears twice. Two elementary circuits are distinct if they
+    are not cyclic permutations of each other.
+
+    This version uses a recursive algorithm to build a list of cycles.
+    You should probably use the iterator version called simple_cycles().
+    Warning: This recursive version uses lots of RAM!
+    It appears in NetworkX for pedagogical value.
+
+    Parameters
+    ----------
+    G : NetworkX DiGraph
+       A directed graph
+
+    Returns
+    -------
+    A list of cycles, where each cycle is represented by a list of nodes
+    along the cycle.
+
+    Example:
+
+    >>> edges = [(0, 0), (0, 1), (0, 2), (1, 2), (2, 0), (2, 1), (2, 2)]
+    >>> G = nx.DiGraph(edges)
+    >>> nx.recursive_simple_cycles(G)
+    [[0], [2], [0, 1, 2], [0, 2], [1, 2]]
+
+    Notes
+    -----
+    The implementation follows pp. 79-80 in [1]_.
+
+    The time complexity is $O((n+e)(c+1))$ for $n$ nodes, $e$ edges and $c$
+    elementary circuits.
+
+    References
+    ----------
+    .. [1] Finding all the elementary circuits of a directed graph.
+       D. B. Johnson, SIAM Journal on Computing 4, no. 1, 77-84, 1975.
+       https://doi.org/10.1137/0204007
+
+    See Also
+    --------
+    simple_cycles, cycle_basis
+    """
+
+    # Jon Olav Vik, 2010-08-09
+    def _unblock(thisnode):
+        """Recursively unblock and remove nodes from B[thisnode]."""
+        if blocked[thisnode]:
+            blocked[thisnode] = False
+            while B[thisnode]:
+                _unblock(B[thisnode].pop())
+
+    def circuit(thisnode, startnode, component):
+        closed = False  # set to True if elementary path is closed
+        path.append(thisnode)
+        blocked[thisnode] = True
+        for nextnode in component[thisnode]:  # direct successors of thisnode
+            if nextnode == startnode:
+                result.append(path[:])
+                closed = True
+            elif not blocked[nextnode]:
+                if circuit(nextnode, startnode, component):
+                    closed = True
+        if closed:
+            _unblock(thisnode)
+        else:
+            for nextnode in component[thisnode]:
+                if thisnode not in B[nextnode]:  # TODO: use set for speedup?
+                    B[nextnode].append(thisnode)
+        path.pop()  # remove thisnode from path
+        return closed
+
+    path = []  # stack of nodes in current path
+    blocked = defaultdict(bool)  # vertex: blocked from search?
+    B = defaultdict(list)  # graph portions that yield no elementary circuit
+    result = []  # list to accumulate the circuits found
+
+    # Johnson's algorithm exclude self cycle edges like (v, v)
+    # To be backward compatible, we record those cycles in advance
+    # and then remove from subG
+    for v in G:
+        if G.has_edge(v, v):
+            result.append([v])
+            G.remove_edge(v, v)
+
+    # Johnson's algorithm requires some ordering of the nodes.
+    # They might not be sortable so we assign an arbitrary ordering.
+    ordering = dict(zip(G, range(len(G))))
+    for s in ordering:
+        # Build the subgraph induced by s and following nodes in the ordering
+        subgraph = G.subgraph(node for node in G if ordering[node] >= ordering[s])
+        # Find the strongly connected component in the subgraph
+        # that contains the least node according to the ordering
+        strongcomp = nx.strongly_connected_components(subgraph)
+        mincomp = min(strongcomp, key=lambda ns: min(ordering[n] for n in ns))
+        component = G.subgraph(mincomp)
+        if len(component) > 1:
+            # smallest node in the component according to the ordering
+            startnode = min(component, key=ordering.__getitem__)
+            for node in component:
+                blocked[node] = False
+                B[node][:] = []
+            dummy = circuit(startnode, startnode, component)
+    return result
+
+
+@nx._dispatchable
+def find_cycle(G, source=None, orientation=None):
+    """Returns a cycle found via depth-first traversal.
+
+    The cycle is a list of edges indicating the cyclic path.
+    Orientation of directed edges is controlled by `orientation`.
+
+    Parameters
+    ----------
+    G : graph
+        A directed/undirected graph/multigraph.
+
+    source : node, list of nodes
+        The node from which the traversal begins. If None, then a source
+        is chosen arbitrarily and repeatedly until all edges from each node in
+        the graph are searched.
+
+    orientation : None | 'original' | 'reverse' | 'ignore' (default: None)
+        For directed graphs and directed multigraphs, edge traversals need not
+        respect the original orientation of the edges.
+        When set to 'reverse' every edge is traversed in the reverse direction.
+        When set to 'ignore', every edge is treated as undirected.
+        When set to 'original', every edge is treated as directed.
+        In all three cases, the yielded edge tuples add a last entry to
+        indicate the direction in which that edge was traversed.
+        If orientation is None, the yielded edge has no direction indicated.
+        The direction is respected, but not reported.
+
+    Returns
+    -------
+    edges : directed edges
+        A list of directed edges indicating the path taken for the loop.
+        If no cycle is found, then an exception is raised.
+        For graphs, an edge is of the form `(u, v)` where `u` and `v`
+        are the tail and head of the edge as determined by the traversal.
+        For multigraphs, an edge is of the form `(u, v, key)`, where `key` is
+        the key of the edge. When the graph is directed, then `u` and `v`
+        are always in the order of the actual directed edge.
+        If orientation is not None then the edge tuple is extended to include
+        the direction of traversal ('forward' or 'reverse') on that edge.
+
+    Raises
+    ------
+    NetworkXNoCycle
+        If no cycle was found.
+
+    Examples
+    --------
+    In this example, we construct a DAG and find, in the first call, that there
+    are no directed cycles, and so an exception is raised. In the second call,
+    we ignore edge orientations and find that there is an undirected cycle.
+    Note that the second call finds a directed cycle while effectively
+    traversing an undirected graph, and so, we found an "undirected cycle".
+    This means that this DAG structure does not form a directed tree (which
+    is also known as a polytree).
+
+    >>> G = nx.DiGraph([(0, 1), (0, 2), (1, 2)])
+    >>> nx.find_cycle(G, orientation="original")
+    Traceback (most recent call last):
+        ...
+    networkx.exception.NetworkXNoCycle: No cycle found.
+    >>> list(nx.find_cycle(G, orientation="ignore"))
+    [(0, 1, 'forward'), (1, 2, 'forward'), (0, 2, 'reverse')]
+
+    See Also
+    --------
+    simple_cycles
+    """
+    if not G.is_directed() or orientation in (None, "original"):
+
+        def tailhead(edge):
+            return edge[:2]
+
+    elif orientation == "reverse":
+
+        def tailhead(edge):
+            return edge[1], edge[0]
+
+    elif orientation == "ignore":
+
+        def tailhead(edge):
+            if edge[-1] == "reverse":
+                return edge[1], edge[0]
+            return edge[:2]
+
+    explored = set()
+    cycle = []
+    final_node = None
+    for start_node in G.nbunch_iter(source):
+        if start_node in explored:
+            # No loop is possible.
+            continue
+
+        edges = []
+        # All nodes seen in this iteration of edge_dfs
+        seen = {start_node}
+        # Nodes in active path.
+        active_nodes = {start_node}
+        previous_head = None
+
+        for edge in nx.edge_dfs(G, start_node, orientation):
+            # Determine if this edge is a continuation of the active path.
+            tail, head = tailhead(edge)
+            if head in explored:
+                # Then we've already explored it. No loop is possible.
+                continue
+            if previous_head is not None and tail != previous_head:
+                # This edge results from backtracking.
+                # Pop until we get a node whose head equals the current tail.
+                # So for example, we might have:
+                #  (0, 1), (1, 2), (2, 3), (1, 4)
+                # which must become:
+                #  (0, 1), (1, 4)
+                while True:
+                    try:
+                        popped_edge = edges.pop()
+                    except IndexError:
+                        edges = []
+                        active_nodes = {tail}
+                        break
+                    else:
+                        popped_head = tailhead(popped_edge)[1]
+                        active_nodes.remove(popped_head)
+
+                    if edges:
+                        last_head = tailhead(edges[-1])[1]
+                        if tail == last_head:
+                            break
+            edges.append(edge)
+
+            if head in active_nodes:
+                # We have a loop!
+                cycle.extend(edges)
+                final_node = head
+                break
+            else:
+                seen.add(head)
+                active_nodes.add(head)
+                previous_head = head
+
+        if cycle:
+            break
+        else:
+            explored.update(seen)
+
+    else:
+        assert len(cycle) == 0
+        raise nx.exception.NetworkXNoCycle("No cycle found.")
+
+    # We now have a list of edges which ends on a cycle.
+    # So we need to remove from the beginning edges that are not relevant.
+
+    for i, edge in enumerate(cycle):
+        tail, head = tailhead(edge)
+        if tail == final_node:
+            break
+
+    return cycle[i:]
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatchable(edge_attrs="weight")
+def minimum_cycle_basis(G, weight=None):
+    """Returns a minimum weight cycle basis for G
+
+    Minimum weight means a cycle basis for which the total weight
+    (length for unweighted graphs) of all the cycles is minimum.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+    weight: string
+        name of the edge attribute to use for edge weights
+
+    Returns
+    -------
+    A list of cycle lists.  Each cycle list is a list of nodes
+    which forms a cycle (loop) in G. Note that the nodes are not
+    necessarily returned in a order by which they appear in the cycle
+
+    Examples
+    --------
+    >>> G = nx.Graph()
+    >>> nx.add_cycle(G, [0, 1, 2, 3])
+    >>> nx.add_cycle(G, [0, 3, 4, 5])
+    >>> nx.minimum_cycle_basis(G)
+    [[5, 4, 3, 0], [3, 2, 1, 0]]
+
+    References:
+        [1] Kavitha, Telikepalli, et al. "An O(m^2n) Algorithm for
+        Minimum Cycle Basis of Graphs."
+        http://link.springer.com/article/10.1007/s00453-007-9064-z
+        [2] de Pina, J. 1995. Applications of shortest path methods.
+        Ph.D. thesis, University of Amsterdam, Netherlands
+
+    See Also
+    --------
+    simple_cycles, cycle_basis
+    """
+    # We first split the graph in connected subgraphs
+    return sum(
+        (_min_cycle_basis(G.subgraph(c), weight) for c in nx.connected_components(G)),
+        [],
+    )
+
+
+def _min_cycle_basis(G, weight):
+    cb = []
+    # We  extract the edges not in a spanning tree. We do not really need a
+    # *minimum* spanning tree. That is why we call the next function with
+    # weight=None. Depending on implementation, it may be faster as well
+    tree_edges = list(nx.minimum_spanning_edges(G, weight=None, data=False))
+    chords = G.edges - tree_edges - {(v, u) for u, v in tree_edges}
+
+    # We maintain a set of vectors orthogonal to sofar found cycles
+    set_orth = [{edge} for edge in chords]
+    while set_orth:
+        base = set_orth.pop()
+        # kth cycle is "parallel" to kth vector in set_orth
+        cycle_edges = _min_cycle(G, base, weight)
+        cb.append([v for u, v in cycle_edges])
+
+        # now update set_orth so that k+1,k+2... th elements are
+        # orthogonal to the newly found cycle, as per [p. 336, 1]
+        set_orth = [
+            (
+                {e for e in orth if e not in base if e[::-1] not in base}
+                | {e for e in base if e not in orth if e[::-1] not in orth}
+            )
+            if sum((e in orth or e[::-1] in orth) for e in cycle_edges) % 2
+            else orth
+            for orth in set_orth
+        ]
+    return cb
+
+
+def _min_cycle(G, orth, weight):
+    """
+    Computes the minimum weight cycle in G,
+    orthogonal to the vector orth as per [p. 338, 1]
+    Use (u, 1) to indicate the lifted copy of u (denoted u' in paper).
+    """
+    Gi = nx.Graph()
+
+    # Add 2 copies of each edge in G to Gi.
+    # If edge is in orth, add cross edge; otherwise in-plane edge
+    for u, v, wt in G.edges(data=weight, default=1):
+        if (u, v) in orth or (v, u) in orth:
+            Gi.add_edges_from([(u, (v, 1)), ((u, 1), v)], Gi_weight=wt)
+        else:
+            Gi.add_edges_from([(u, v), ((u, 1), (v, 1))], Gi_weight=wt)
+
+    # find the shortest length in Gi between n and (n, 1) for each n
+    # Note: Use "Gi_weight" for name of weight attribute
+    spl = nx.shortest_path_length
+    lift = {n: spl(Gi, source=n, target=(n, 1), weight="Gi_weight") for n in G}
+
+    # Now compute that short path in Gi, which translates to a cycle in G
+    start = min(lift, key=lift.get)
+    end = (start, 1)
+    min_path_i = nx.shortest_path(Gi, source=start, target=end, weight="Gi_weight")
+
+    # Now we obtain the actual path, re-map nodes in Gi to those in G
+    min_path = [n if n in G else n[0] for n in min_path_i]
+
+    # Now remove the edges that occur two times
+    # two passes: flag which edges get kept, then build it
+    edgelist = list(pairwise(min_path))
+    edgeset = set()
+    for e in edgelist:
+        if e in edgeset:
+            edgeset.remove(e)
+        elif e[::-1] in edgeset:
+            edgeset.remove(e[::-1])
+        else:
+            edgeset.add(e)
+
+    min_edgelist = []
+    for e in edgelist:
+        if e in edgeset:
+            min_edgelist.append(e)
+            edgeset.remove(e)
+        elif e[::-1] in edgeset:
+            min_edgelist.append(e[::-1])
+            edgeset.remove(e[::-1])
+
+    return min_edgelist
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatchable
+def girth(G):
+    """Returns the girth of the graph.
+
+    The girth of a graph is the length of its shortest cycle, or infinity if
+    the graph is acyclic. The algorithm follows the description given on the
+    Wikipedia page [1]_, and runs in time O(mn) on a graph with m edges and n
+    nodes.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+
+    Returns
+    -------
+    int or math.inf
+
+    Examples
+    --------
+    All examples below (except P_5) can easily be checked using Wikipedia,
+    which has a page for each of these famous graphs.
+
+    >>> nx.girth(nx.chvatal_graph())
+    4
+    >>> nx.girth(nx.tutte_graph())
+    4
+    >>> nx.girth(nx.petersen_graph())
+    5
+    >>> nx.girth(nx.heawood_graph())
+    6
+    >>> nx.girth(nx.pappus_graph())
+    6
+    >>> nx.girth(nx.path_graph(5))
+    inf
+
+    References
+    ----------
+    .. [1] `Wikipedia: Girth <https://en.wikipedia.org/wiki/Girth_(graph_theory)>`_
+
+    """
+    girth = depth_limit = inf
+    tree_edge = nx.algorithms.traversal.breadth_first_search.TREE_EDGE
+    level_edge = nx.algorithms.traversal.breadth_first_search.LEVEL_EDGE
+    for n in G:
+        # run a BFS from source n, keeping track of distances; since we want
+        # the shortest cycle, no need to explore beyond the current minimum length
+        depth = {n: 0}
+        for u, v, label in nx.bfs_labeled_edges(G, n):
+            du = depth[u]
+            if du > depth_limit:
+                break
+            if label is tree_edge:
+                depth[v] = du + 1
+            else:
+                # if (u, v) is a level edge, the length is du + du + 1 (odd)
+                # otherwise, it's a forward edge; length is du + (du + 1) + 1 (even)
+                delta = label is level_edge
+                length = du + du + 2 - delta
+                if length < girth:
+                    girth = length
+                    depth_limit = du - delta
+
+    return girth

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/d_separation.py

@@ -0,0 +1,722 @@
+"""
+Algorithm for testing d-separation in DAGs.
+
+*d-separation* is a test for conditional independence in probability
+distributions that can be factorized using DAGs.  It is a purely
+graphical test that uses the underlying graph and makes no reference
+to the actual distribution parameters.  See [1]_ for a formal
+definition.
+
+The implementation is based on the conceptually simple linear time
+algorithm presented in [2]_.  Refer to [3]_, [4]_ for a couple of
+alternative algorithms.
+
+The functional interface in NetworkX consists of three functions:
+
+- `find_minimal_d_separator` returns a minimal d-separator set ``z``.
+  That is, removing any node or nodes from it makes it no longer a d-separator.
+- `is_d_separator` checks if a given set is a d-separator.
+- `is_minimal_d_separator` checks if a given set is a minimal d-separator.
+
+D-separators
+------------
+
+Here, we provide a brief overview of d-separation and related concepts that
+are relevant for understanding it:
+
+The ideas of d-separation and d-connection relate to paths being open or blocked.
+
+- A "path" is a sequence of nodes connected in order by edges. Unlike for most
+  graph theory analysis, the direction of the edges is ignored. Thus the path
+  can be thought of as a traditional path on the undirected version of the graph.
+- A "candidate d-separator" ``z`` is a set of nodes being considered as
+  possibly blocking all paths between two prescribed sets ``x`` and ``y`` of nodes.
+  We refer to each node in the candidate d-separator as "known".
+- A "collider" node on a path is a node that is a successor of its two neighbor
+  nodes on the path. That is, ``c`` is a collider if the edge directions
+  along the path look like ``... u -> c <- v ...``.
+- If a collider node or any of its descendants are "known", the collider
+  is called an "open collider". Otherwise it is a "blocking collider".
+- Any path can be "blocked" in two ways. If the path contains a "known" node
+  that is not a collider, the path is blocked. Also, if the path contains a
+  collider that is not a "known" node, the path is blocked.
+- A path is "open" if it is not blocked. That is, it is open if every node is
+  either an open collider or not a "known". Said another way, every
+  "known" in the path is a collider and every collider is open (has a
+  "known" as a inclusive descendant). The concept of "open path" is meant to
+  demonstrate a probabilistic conditional dependence between two nodes given
+  prescribed knowledge ("known" nodes).
+- Two sets ``x`` and ``y`` of nodes are "d-separated" by a set of nodes ``z``
+  if all paths between nodes in ``x`` and nodes in ``y`` are blocked. That is,
+  if there are no open paths from any node in ``x`` to any node in ``y``.
+  Such a set ``z`` is a "d-separator" of ``x`` and ``y``.
+- A "minimal d-separator" is a d-separator ``z`` for which no node or subset
+  of nodes can be removed with it still being a d-separator.
+
+The d-separator blocks some paths between ``x`` and ``y`` but opens others.
+Nodes in the d-separator block paths if the nodes are not colliders.
+But if a collider or its descendant nodes are in the d-separation set, the
+colliders are open, allowing a path through that collider.
+
+Illustration of D-separation with examples
+------------------------------------------
+
+A pair of two nodes, ``u`` and ``v``, are d-connected if there is a path
+from ``u`` to ``v`` that is not blocked. That means, there is an open
+path from ``u`` to ``v``.
+
+For example, if the d-separating set is the empty set, then the following paths are
+open between ``u`` and ``v``:
+
+- u <- n -> v
+- u -> w -> ... -> n -> v
+
+If  on the other hand, ``n`` is in the d-separating set, then ``n`` blocks
+those paths between ``u`` and ``v``.
+
+Colliders block a path if they and their descendants are not included
+in the d-separating set. An example of a path that is blocked when the
+d-separating set is empty is:
+
+- u -> w -> ... -> n <- v
+
+The node ``n`` is a collider in this path and is not in the d-separating set.
+So ``n`` blocks this path. However, if ``n`` or a descendant of ``n`` is
+included in the d-separating set, then the path through the collider
+at ``n`` (... -> n <- ...) is "open".
+
+D-separation is concerned with blocking all paths between nodes from ``x`` to ``y``.
+A d-separating set between ``x`` and ``y`` is one where all paths are blocked.
+
+D-separation and its applications in probability
+------------------------------------------------
+
+D-separation is commonly used in probabilistic causal-graph models. D-separation
+connects the idea of probabilistic "dependence" with separation in a graph. If
+one assumes the causal Markov condition [5]_, (every node is conditionally
+independent of its non-descendants, given its parents) then d-separation implies
+conditional independence in probability distributions.
+Symmetrically, d-connection implies dependence.
+
+The intuition is as follows. The edges on a causal graph indicate which nodes
+influence the outcome of other nodes directly. An edge from u to v
+implies that the outcome of event ``u`` influences the probabilities for
+the outcome of event ``v``. Certainly knowing ``u`` changes predictions for ``v``.
+But also knowing ``v`` changes predictions for ``u``. The outcomes are dependent.
+Furthermore, an edge from ``v`` to ``w`` would mean that ``w`` and ``v`` are dependent
+and thus that ``u`` could indirectly influence ``w``.
+
+Without any knowledge about the system (candidate d-separating set is empty)
+a causal graph ``u -> v -> w`` allows all three nodes to be dependent. But
+if we know the outcome of ``v``, the conditional probabilities of outcomes for
+``u`` and ``w`` are independent of each other. That is, once we know the outcome
+for ```v`, the probabilities for ``w`` do not depend on the outcome for ``u``.
+This is the idea behind ``v`` blocking the path if it is "known" (in the candidate
+d-separating set).
+
+The same argument works whether the direction of the edges are both
+left-going and when both arrows head out from the middle. Having a "known"
+node on a path blocks the collider-free path because those relationships
+make the conditional probabilities independent.
+
+The direction of the causal edges does impact dependence precisely in the
+case of a collider e.g. ``u -> v <- w``. In that situation, both ``u`` and ``w``
+influence ``v```. But they do not directly influence each other. So without any
+knowledge of any outcomes, ``u`` and ``w`` are independent. That is the idea behind
+colliders blocking the path. But, if ``v`` is known, the conditional probabilities
+of ``u`` and ``w`` can be dependent. This is the heart of Berkson's Paradox [6]_.
+For example, suppose ``u`` and ``w`` are boolean events (they either happen or do not)
+and ``v`` represents the outcome "at least one of ``u`` and ``w`` occur". Then knowing
+``v`` is true makes the conditional probabilities of ``u`` and ``w`` dependent.
+Essentially, knowing that at least one of them is true raises the probability of
+each. But further knowledge that ``w`` is true (or false) change the conditional
+probability of ``u`` to either the original value or 1. So the conditional
+probability of ``u`` depends on the outcome of ``w`` even though there is no
+causal relationship between them. When a collider is known, dependence can
+occur across paths through that collider. This is the reason open colliders
+do not block paths.
+
+Furthermore, even if ``v`` is not "known", if one of its descendants is "known"
+we can use that information to know more about ``v`` which again makes
+``u`` and ``w`` potentially dependent. Suppose the chance of ``n`` occurring
+is much higher when ``v`` occurs ("at least one of ``u`` and ``w`` occur").
+Then if we know ``n`` occurred, it is more likely that ``v`` occurred and that
+makes the chance of ``u`` and ``w`` dependent. This is the idea behind why
+a collider does no block a path if any descendant of the collider is "known".
+
+When two sets of nodes ``x`` and ``y`` are d-separated by a set ``z``,
+it means that given the outcomes of the nodes in ``z``, the probabilities
+of outcomes of the nodes in ``x`` are independent of the outcomes of the
+nodes in ``y`` and vice versa.
+
+Examples
+--------
+A Hidden Markov Model with 5 observed states and 5 hidden states
+where the hidden states have causal relationships resulting in
+a path results in the following causal network. We check that
+early states along the path are separated from late state in
+the path by the d-separator of the middle hidden state.
+Thus if we condition on the middle hidden state, the early
+state probabilities are independent of the late state outcomes.
+
+>>> G = nx.DiGraph()
+>>> G.add_edges_from(
+...     [
+...         ("H1", "H2"),
+...         ("H2", "H3"),
+...         ("H3", "H4"),
+...         ("H4", "H5"),
+...         ("H1", "O1"),
+...         ("H2", "O2"),
+...         ("H3", "O3"),
+...         ("H4", "O4"),
+...         ("H5", "O5"),
+...     ]
+... )
+>>> x, y, z = ({"H1", "O1"}, {"H5", "O5"}, {"H3"})
+>>> nx.is_d_separator(G, x, y, z)
+True
+>>> nx.is_minimal_d_separator(G, x, y, z)
+True
+>>> nx.is_minimal_d_separator(G, x, y, z | {"O3"})
+False
+>>> z = nx.find_minimal_d_separator(G, x | y, {"O2", "O3", "O4"})
+>>> z == {"H2", "H4"}
+True
+
+If no minimal_d_separator exists, `None` is returned
+
+>>> other_z = nx.find_minimal_d_separator(G, x | y, {"H2", "H3"})
+>>> other_z is None
+True
+
+
+References
+----------
+
+.. [1] Pearl, J.  (2009).  Causality.  Cambridge: Cambridge University Press.
+
+.. [2] Darwiche, A.  (2009).  Modeling and reasoning with Bayesian networks.
+   Cambridge: Cambridge University Press.
+
+.. [3] Shachter, Ross D. "Bayes-ball: The rational pastime (for
+   determining irrelevance and requisite information in belief networks
+   and influence diagrams)." In Proceedings of the Fourteenth Conference
+   on Uncertainty in Artificial Intelligence (UAI), (pp. 480–487). 1998.
+
+.. [4] Koller, D., & Friedman, N. (2009).
+   Probabilistic graphical models: principles and techniques. The MIT Press.
+
+.. [5] https://en.wikipedia.org/wiki/Causal_Markov_condition
+
+.. [6] https://en.wikipedia.org/wiki/Berkson%27s_paradox
+
+"""
+
+from collections import deque
+from itertools import chain
+
+import networkx as nx
+from networkx.utils import UnionFind, not_implemented_for
+
+__all__ = [
+    "is_d_separator",
+    "is_minimal_d_separator",
+    "find_minimal_d_separator",
+    "d_separated",
+    "minimal_d_separator",
+]
+
+
+@not_implemented_for("undirected")
+@nx._dispatchable
+def is_d_separator(G, x, y, z):
+    """Return whether node sets `x` and `y` are d-separated by `z`.
+
+    Parameters
+    ----------
+    G : nx.DiGraph
+        A NetworkX DAG.
+
+    x : node or set of nodes
+        First node or set of nodes in `G`.
+
+    y : node or set of nodes
+        Second node or set of nodes in `G`.
+
+    z : node or set of nodes
+        Potential separator (set of conditioning nodes in `G`). Can be empty set.
+
+    Returns
+    -------
+    b : bool
+        A boolean that is true if `x` is d-separated from `y` given `z` in `G`.
+
+    Raises
+    ------
+    NetworkXError
+        The *d-separation* test is commonly used on disjoint sets of
+        nodes in acyclic directed graphs.  Accordingly, the algorithm
+        raises a :exc:`NetworkXError` if the node sets are not
+        disjoint or if the input graph is not a DAG.
+
+    NodeNotFound
+        If any of the input nodes are not found in the graph,
+        a :exc:`NodeNotFound` exception is raised
+
+    Notes
+    -----
+    A d-separating set in a DAG is a set of nodes that
+    blocks all paths between the two sets. Nodes in `z`
+    block a path if they are part of the path and are not a collider,
+    or a descendant of a collider. Also colliders that are not in `z`
+    block a path. A collider structure along a path
+    is ``... -> c <- ...`` where ``c`` is the collider node.
+
+    https://en.wikipedia.org/wiki/Bayesian_network#d-separation
+    """
+    try:
+        x = {x} if x in G else x
+        y = {y} if y in G else y
+        z = {z} if z in G else z
+
+        intersection = x & y or x & z or y & z
+        if intersection:
+            raise nx.NetworkXError(
+                f"The sets are not disjoint, with intersection {intersection}"
+            )
+
+        set_v = x | y | z
+        if set_v - G.nodes:
+            raise nx.NodeNotFound(f"The node(s) {set_v - G.nodes} are not found in G")
+    except TypeError:
+        raise nx.NodeNotFound("One of x, y, or z is not a node or a set of nodes in G")
+
+    if not nx.is_directed_acyclic_graph(G):
+        raise nx.NetworkXError("graph should be directed acyclic")
+
+    # contains -> and <-> edges from starting node T
+    forward_deque = deque([])
+    forward_visited = set()
+
+    # contains <- and - edges from starting node T
+    backward_deque = deque(x)
+    backward_visited = set()
+
+    ancestors_or_z = set().union(*[nx.ancestors(G, node) for node in x]) | z | x
+
+    while forward_deque or backward_deque:
+        if backward_deque:
+            node = backward_deque.popleft()
+            backward_visited.add(node)
+            if node in y:
+                return False
+            if node in z:
+                continue
+
+            # add <- edges to backward deque
+            backward_deque.extend(G.pred[node].keys() - backward_visited)
+            # add -> edges to forward deque
+            forward_deque.extend(G.succ[node].keys() - forward_visited)
+
+        if forward_deque:
+            node = forward_deque.popleft()
+            forward_visited.add(node)
+            if node in y:
+                return False
+
+            # Consider if -> node <- is opened due to ancestor of node in z
+            if node in ancestors_or_z:
+                # add <- edges to backward deque
+                backward_deque.extend(G.pred[node].keys() - backward_visited)
+            if node not in z:
+                # add -> edges to forward deque
+                forward_deque.extend(G.succ[node].keys() - forward_visited)
+
+    return True
+
+
+@not_implemented_for("undirected")
+@nx._dispatchable
+def find_minimal_d_separator(G, x, y, *, included=None, restricted=None):
+    """Returns a minimal d-separating set between `x` and `y` if possible
+
+    A d-separating set in a DAG is a set of nodes that blocks all
+    paths between the two sets of nodes, `x` and `y`. This function
+    constructs a d-separating set that is "minimal", meaning no nodes can
+    be removed without it losing the d-separating property for `x` and `y`.
+    If no d-separating sets exist for `x` and `y`, this returns `None`.
+
+    In a DAG there may be more than one minimal d-separator between two
+    sets of nodes. Minimal d-separators are not always unique. This function
+    returns one minimal d-separator, or `None` if no d-separator exists.
+
+    Uses the algorithm presented in [1]_. The complexity of the algorithm
+    is :math:`O(m)`, where :math:`m` stands for the number of edges in
+    the subgraph of G consisting of only the ancestors of `x` and `y`.
+    For full details, see [1]_.
+
+    Parameters
+    ----------
+    G : graph
+        A networkx DAG.
+    x : set | node
+        A node or set of nodes in the graph.
+    y : set | node
+        A node or set of nodes in the graph.
+    included : set | node | None
+        A node or set of nodes which must be included in the found separating set,
+        default is None, which means the empty set.
+    restricted : set | node | None
+        Restricted node or set of nodes to consider. Only these nodes can be in
+        the found separating set, default is None meaning all nodes in ``G``.
+
+    Returns
+    -------
+    z : set | None
+        The minimal d-separating set, if at least one d-separating set exists,
+        otherwise None.
+
+    Raises
+    ------
+    NetworkXError
+        Raises a :exc:`NetworkXError` if the input graph is not a DAG
+        or if node sets `x`, `y`, and `included` are not disjoint.
+
+    NodeNotFound
+        If any of the input nodes are not found in the graph,
+        a :exc:`NodeNotFound` exception is raised.
+
+    References
+    ----------
+    .. [1] van der Zander, Benito, and Maciej Liśkiewicz. "Finding
+        minimal d-separators in linear time and applications." In
+        Uncertainty in Artificial Intelligence, pp. 637-647. PMLR, 2020.
+    """
+    if not nx.is_directed_acyclic_graph(G):
+        raise nx.NetworkXError("graph should be directed acyclic")
+
+    try:
+        x = {x} if x in G else x
+        y = {y} if y in G else y
+
+        if included is None:
+            included = set()
+        elif included in G:
+            included = {included}
+
+        if restricted is None:
+            restricted = set(G)
+        elif restricted in G:
+            restricted = {restricted}
+
+        set_y = x | y | included | restricted
+        if set_y - G.nodes:
+            raise nx.NodeNotFound(f"The node(s) {set_y - G.nodes} are not found in G")
+    except TypeError:
+        raise nx.NodeNotFound(
+            "One of x, y, included or restricted is not a node or set of nodes in G"
+        )
+
+    if not included <= restricted:
+        raise nx.NetworkXError(
+            f"Included nodes {included} must be in restricted nodes {restricted}"
+        )
+
+    intersection = x & y or x & included or y & included
+    if intersection:
+        raise nx.NetworkXError(
+            f"The sets x, y, included are not disjoint. Overlap: {intersection}"
+        )
+
+    nodeset = x | y | included
+    ancestors_x_y_included = nodeset.union(*[nx.ancestors(G, node) for node in nodeset])
+
+    z_init = restricted & (ancestors_x_y_included - (x | y))
+
+    x_closure = _reachable(G, x, ancestors_x_y_included, z_init)
+    if x_closure & y:
+        return None
+
+    z_updated = z_init & (x_closure | included)
+    y_closure = _reachable(G, y, ancestors_x_y_included, z_updated)
+    return z_updated & (y_closure | included)
+
+
+@not_implemented_for("undirected")
+@nx._dispatchable
+def is_minimal_d_separator(G, x, y, z, *, included=None, restricted=None):
+    """Determine if `z` is a minimal d-separator for `x` and `y`.
+
+    A d-separator, `z`, in a DAG is a set of nodes that blocks
+    all paths from nodes in set `x` to nodes in set `y`.
+    A minimal d-separator is a d-separator `z` such that removing
+    any subset of nodes makes it no longer a d-separator.
+
+    Note: This function checks whether `z` is a d-separator AND is
+    minimal. One can use the function `is_d_separator` to only check if
+    `z` is a d-separator. See examples below.
+
+    Parameters
+    ----------
+    G : nx.DiGraph
+        A NetworkX DAG.
+    x : node | set
+        A node or set of nodes in the graph.
+    y : node | set
+        A node or set of nodes in the graph.
+    z : node | set
+        The node or set of nodes to check if it is a minimal d-separating set.
+        The function :func:`is_d_separator` is called inside this function
+        to verify that `z` is in fact a d-separator.
+    included : set | node | None
+        A node or set of nodes which must be included in the found separating set,
+        default is ``None``, which means the empty set.
+    restricted : set | node | None
+        Restricted node or set of nodes to consider. Only these nodes can be in
+        the found separating set, default is ``None`` meaning all nodes in ``G``.
+
+    Returns
+    -------
+    bool
+        Whether or not the set `z` is a minimal d-separator subject to
+        `restricted` nodes and `included` node constraints.
+
+    Examples
+    --------
+    >>> G = nx.path_graph([0, 1, 2, 3], create_using=nx.DiGraph)
+    >>> G.add_node(4)
+    >>> nx.is_minimal_d_separator(G, 0, 2, {1})
+    True
+    >>> # since {1} is the minimal d-separator, {1, 3, 4} is not minimal
+    >>> nx.is_minimal_d_separator(G, 0, 2, {1, 3, 4})
+    False
+    >>> # alternatively, if we only want to check that {1, 3, 4} is a d-separator
+    >>> nx.is_d_separator(G, 0, 2, {1, 3, 4})
+    True
+
+    Raises
+    ------
+    NetworkXError
+        Raises a :exc:`NetworkXError` if the input graph is not a DAG.
+
+    NodeNotFound
+        If any of the input nodes are not found in the graph,
+        a :exc:`NodeNotFound` exception is raised.
+
+    References
+    ----------
+    .. [1] van der Zander, Benito, and Maciej Liśkiewicz. "Finding
+        minimal d-separators in linear time and applications." In
+        Uncertainty in Artificial Intelligence, pp. 637-647. PMLR, 2020.
+
+    Notes
+    -----
+    This function works on verifying that a set is minimal and
+    d-separating between two nodes. Uses criterion (a), (b), (c) on
+    page 4 of [1]_. a) closure(`x`) and `y` are disjoint. b) `z` contains
+    all nodes from `included` and is contained in the `restricted`
+    nodes and in the union of ancestors of `x`, `y`, and `included`.
+    c) the nodes in `z` not in `included` are contained in both
+    closure(x) and closure(y). The closure of a set is the set of nodes
+    connected to the set by a directed path in G.
+
+    The complexity is :math:`O(m)`, where :math:`m` stands for the
+    number of edges in the subgraph of G consisting of only the
+    ancestors of `x` and `y`.
+
+    For full details, see [1]_.
+    """
+    if not nx.is_directed_acyclic_graph(G):
+        raise nx.NetworkXError("graph should be directed acyclic")
+
+    try:
+        x = {x} if x in G else x
+        y = {y} if y in G else y
+        z = {z} if z in G else z
+
+        if included is None:
+            included = set()
+        elif included in G:
+            included = {included}
+
+        if restricted is None:
+            restricted = set(G)
+        elif restricted in G:
+            restricted = {restricted}
+
+        set_y = x | y | included | restricted
+        if set_y - G.nodes:
+            raise nx.NodeNotFound(f"The node(s) {set_y - G.nodes} are not found in G")
+    except TypeError:
+        raise nx.NodeNotFound(
+            "One of x, y, z, included or restricted is not a node or set of nodes in G"
+        )
+
+    if not included <= z:
+        raise nx.NetworkXError(
+            f"Included nodes {included} must be in proposed separating set z {x}"
+        )
+    if not z <= restricted:
+        raise nx.NetworkXError(
+            f"Separating set {z} must be contained in restricted set {restricted}"
+        )
+
+    intersection = x.intersection(y) or x.intersection(z) or y.intersection(z)
+    if intersection:
+        raise nx.NetworkXError(
+            f"The sets are not disjoint, with intersection {intersection}"
+        )
+
+    nodeset = x | y | included
+    ancestors_x_y_included = nodeset.union(*[nx.ancestors(G, n) for n in nodeset])
+
+    # criterion (a) -- check that z is actually a separator
+    x_closure = _reachable(G, x, ancestors_x_y_included, z)
+    if x_closure & y:
+        return False
+
+    # criterion (b) -- basic constraint; included and restricted already checked above
+    if not (z <= ancestors_x_y_included):
+        return False
+
+    # criterion (c) -- check that z is minimal
+    y_closure = _reachable(G, y, ancestors_x_y_included, z)
+    if not ((z - included) <= (x_closure & y_closure)):
+        return False
+    return True
+
+
+@not_implemented_for("undirected")
+def _reachable(G, x, a, z):
+    """Modified Bayes-Ball algorithm for finding d-connected nodes.
+
+    Find all nodes in `a` that are d-connected to those in `x` by
+    those in `z`. This is an implementation of the function
+    `REACHABLE` in [1]_ (which is itself a modification of the
+    Bayes-Ball algorithm [2]_) when restricted to DAGs.
+
+    Parameters
+    ----------
+    G : nx.DiGraph
+        A NetworkX DAG.
+    x : node | set
+        A node in the DAG, or a set of nodes.
+    a : node | set
+        A (set of) node(s) in the DAG containing the ancestors of `x`.
+    z : node | set
+        The node or set of nodes conditioned on when checking d-connectedness.
+
+    Returns
+    -------
+    w : set
+        The closure of `x` in `a` with respect to d-connectedness
+        given `z`.
+
+    References
+    ----------
+    .. [1] van der Zander, Benito, and Maciej Liśkiewicz. "Finding
+        minimal d-separators in linear time and applications." In
+        Uncertainty in Artificial Intelligence, pp. 637-647. PMLR, 2020.
+
+    .. [2] Shachter, Ross D. "Bayes-ball: The rational pastime
+       (for determining irrelevance and requisite information in
+       belief networks and influence diagrams)." In Proceedings of the
+       Fourteenth Conference on Uncertainty in Artificial Intelligence
+       (UAI), (pp. 480–487). 1998.
+    """
+
+    def _pass(e, v, f, n):
+        """Whether a ball entering node `v` along edge `e` passes to `n` along `f`.
+
+        Boolean function defined on page 6 of [1]_.
+
+        Parameters
+        ----------
+        e : bool
+            Directed edge by which the ball got to node `v`; `True` iff directed into `v`.
+        v : node
+            Node where the ball is.
+        f : bool
+            Directed edge connecting nodes `v` and `n`; `True` iff directed `n`.
+        n : node
+            Checking whether the ball passes to this node.
+
+        Returns
+        -------
+        b : bool
+            Whether the ball passes or not.
+
+        References
+        ----------
+        .. [1] van der Zander, Benito, and Maciej Liśkiewicz. "Finding
+           minimal d-separators in linear time and applications." In
+           Uncertainty in Artificial Intelligence, pp. 637-647. PMLR, 2020.
+        """
+        is_element_of_A = n in a
+        # almost_definite_status = True  # always true for DAGs; not so for RCGs
+        collider_if_in_Z = v not in z or (e and not f)
+        return is_element_of_A and collider_if_in_Z  # and almost_definite_status
+
+    queue = deque([])
+    for node in x:
+        if bool(G.pred[node]):
+            queue.append((True, node))
+        if bool(G.succ[node]):
+            queue.append((False, node))
+    processed = queue.copy()
+
+    while any(queue):
+        e, v = queue.popleft()
+        preds = ((False, n) for n in G.pred[v])
+        succs = ((True, n) for n in G.succ[v])
+        f_n_pairs = chain(preds, succs)
+        for f, n in f_n_pairs:
+            if (f, n) not in processed and _pass(e, v, f, n):
+                queue.append((f, n))
+                processed.append((f, n))
+
+    return {w for (_, w) in processed}
+
+
+# Deprecated functions:
+def d_separated(G, x, y, z):
+    """Return whether nodes sets ``x`` and ``y`` are d-separated by ``z``.
+
+    .. deprecated:: 3.3
+
+        This function is deprecated and will be removed in NetworkX v3.5.
+        Please use `is_d_separator(G, x, y, z)`.
+
+    """
+    import warnings
+
+    warnings.warn(
+        "d_separated is deprecated and will be removed in NetworkX v3.5."
+        "Please use `is_d_separator(G, x, y, z)`.",
+        category=DeprecationWarning,
+        stacklevel=2,
+    )
+    return nx.is_d_separator(G, x, y, z)
+
+
+def minimal_d_separator(G, u, v):
+    """Returns a minimal_d-separating set between `x` and `y` if possible
+
+    .. deprecated:: 3.3
+
+        minimal_d_separator is deprecated and will be removed in NetworkX v3.5.
+        Please use `find_minimal_d_separator(G, x, y)`.
+
+    """
+    import warnings
+
+    warnings.warn(
+        (
+            "This function is deprecated and will be removed in NetworkX v3.5."
+            "Please use `is_d_separator(G, x, y)`."
+        ),
+        category=DeprecationWarning,
+        stacklevel=2,
+    )
+    return nx.find_minimal_d_separator(G, u, v)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/distance_measures.py

@@ -0,0 +1,951 @@
+"""Graph diameter, radius, eccentricity and other properties."""
+
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+__all__ = [
+    "eccentricity",
+    "diameter",
+    "radius",
+    "periphery",
+    "center",
+    "barycenter",
+    "resistance_distance",
+    "kemeny_constant",
+    "effective_graph_resistance",
+]
+
+
+def _extrema_bounding(G, compute="diameter", weight=None):
+    """Compute requested extreme distance metric of undirected graph G
+
+    Computation is based on smart lower and upper bounds, and in practice
+    linear in the number of nodes, rather than quadratic (except for some
+    border cases such as complete graphs or circle shaped graphs).
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       An undirected graph
+
+    compute : string denoting the requesting metric
+       "diameter" for the maximal eccentricity value,
+       "radius" for the minimal eccentricity value,
+       "periphery" for the set of nodes with eccentricity equal to the diameter,
+       "center" for the set of nodes with eccentricity equal to the radius,
+       "eccentricities" for the maximum distance from each node to all other nodes in G
+
+    weight : string, function, or None
+        If this is a string, then edge weights will be accessed via the
+        edge attribute with this key (that is, the weight of the edge
+        joining `u` to `v` will be ``G.edges[u, v][weight]``). If no
+        such edge attribute exists, the weight of the edge is assumed to
+        be one.
+
+        If this is a function, the weight of an edge is the value
+        returned by the function. The function must accept exactly three
+        positional arguments: the two endpoints of an edge and the
+        dictionary of edge attributes for that edge. The function must
+        return a number.
+
+        If this is None, every edge has weight/distance/cost 1.
+
+        Weights stored as floating point values can lead to small round-off
+        errors in distances. Use integer weights to avoid this.
+
+        Weights should be positive, since they are distances.
+
+    Returns
+    -------
+    value : value of the requested metric
+       int for "diameter" and "radius" or
+       list of nodes for "center" and "periphery" or
+       dictionary of eccentricity values keyed by node for "eccentricities"
+
+    Raises
+    ------
+    NetworkXError
+        If the graph consists of multiple components
+    ValueError
+        If `compute` is not one of "diameter", "radius", "periphery", "center", or "eccentricities".
+
+    Notes
+    -----
+    This algorithm was proposed in [1]_ and discussed further in [2]_ and [3]_.
+
+    References
+    ----------
+    .. [1] F. W. Takes, W. A. Kosters,
+       "Determining the diameter of small world networks."
+       Proceedings of the 20th ACM international conference on Information and knowledge management, 2011
+       https://dl.acm.org/doi/abs/10.1145/2063576.2063748
+    .. [2] F. W. Takes, W. A. Kosters,
+       "Computing the Eccentricity Distribution of Large Graphs."
+       Algorithms, 2013
+       https://www.mdpi.com/1999-4893/6/1/100
+    .. [3] M. Borassi, P. Crescenzi, M. Habib, W. A. Kosters, A. Marino, F. W. Takes,
+       "Fast diameter and radius BFS-based computation in (weakly connected) real-world graphs: With an application to the six degrees of separation games. "
+       Theoretical Computer Science, 2015
+       https://www.sciencedirect.com/science/article/pii/S0304397515001644
+    """
+    # init variables
+    degrees = dict(G.degree())  # start with the highest degree node
+    minlowernode = max(degrees, key=degrees.get)
+    N = len(degrees)  # number of nodes
+    # alternate between smallest lower and largest upper bound
+    high = False
+    # status variables
+    ecc_lower = dict.fromkeys(G, 0)
+    ecc_upper = dict.fromkeys(G, N)
+    candidates = set(G)
+
+    # (re)set bound extremes
+    minlower = N
+    maxlower = 0
+    minupper = N
+    maxupper = 0
+
+    # repeat the following until there are no more candidates
+    while candidates:
+        if high:
+            current = maxuppernode  # select node with largest upper bound
+        else:
+            current = minlowernode  # select node with smallest lower bound
+        high = not high
+
+        # get distances from/to current node and derive eccentricity
+        dist = nx.shortest_path_length(G, source=current, weight=weight)
+
+        if len(dist) != N:
+            msg = "Cannot compute metric because graph is not connected."
+            raise nx.NetworkXError(msg)
+        current_ecc = max(dist.values())
+
+        # print status update
+        #        print ("ecc of " + str(current) + " (" + str(ecc_lower[current]) + "/"
+        #        + str(ecc_upper[current]) + ", deg: " + str(dist[current]) + ") is "
+        #        + str(current_ecc))
+        #        print(ecc_upper)
+
+        # (re)set bound extremes
+        maxuppernode = None
+        minlowernode = None
+
+        # update node bounds
+        for i in candidates:
+            # update eccentricity bounds
+            d = dist[i]
+            ecc_lower[i] = low = max(ecc_lower[i], max(d, (current_ecc - d)))
+            ecc_upper[i] = upp = min(ecc_upper[i], current_ecc + d)
+
+            # update min/max values of lower and upper bounds
+            minlower = min(ecc_lower[i], minlower)
+            maxlower = max(ecc_lower[i], maxlower)
+            minupper = min(ecc_upper[i], minupper)
+            maxupper = max(ecc_upper[i], maxupper)
+
+        # update candidate set
+        if compute == "diameter":
+            ruled_out = {
+                i
+                for i in candidates
+                if ecc_upper[i] <= maxlower and 2 * ecc_lower[i] >= maxupper
+            }
+        elif compute == "radius":
+            ruled_out = {
+                i
+                for i in candidates
+                if ecc_lower[i] >= minupper and ecc_upper[i] + 1 <= 2 * minlower
+            }
+        elif compute == "periphery":
+            ruled_out = {
+                i
+                for i in candidates
+                if ecc_upper[i] < maxlower
+                and (maxlower == maxupper or ecc_lower[i] > maxupper)
+            }
+        elif compute == "center":
+            ruled_out = {
+                i
+                for i in candidates
+                if ecc_lower[i] > minupper
+                and (minlower == minupper or ecc_upper[i] + 1 < 2 * minlower)
+            }
+        elif compute == "eccentricities":
+            ruled_out = set()
+        else:
+            msg = "compute must be one of 'diameter', 'radius', 'periphery', 'center', 'eccentricities'"
+            raise ValueError(msg)
+
+        ruled_out.update(i for i in candidates if ecc_lower[i] == ecc_upper[i])
+        candidates -= ruled_out
+
+        #        for i in ruled_out:
+        #            print("removing %g: ecc_u: %g maxl: %g ecc_l: %g maxu: %g"%
+        #                    (i,ecc_upper[i],maxlower,ecc_lower[i],maxupper))
+        #        print("node %g: ecc_u: %g maxl: %g ecc_l: %g maxu: %g"%
+        #                    (4,ecc_upper[4],maxlower,ecc_lower[4],maxupper))
+        #        print("NODE 4: %g"%(ecc_upper[4] <= maxlower))
+        #        print("NODE 4: %g"%(2 * ecc_lower[4] >= maxupper))
+        #        print("NODE 4: %g"%(ecc_upper[4] <= maxlower
+        #                            and 2 * ecc_lower[4] >= maxupper))
+
+        # updating maxuppernode and minlowernode for selection in next round
+        for i in candidates:
+            if (
+                minlowernode is None
+                or (
+                    ecc_lower[i] == ecc_lower[minlowernode]
+                    and degrees[i] > degrees[minlowernode]
+                )
+                or (ecc_lower[i] < ecc_lower[minlowernode])
+            ):
+                minlowernode = i
+
+            if (
+                maxuppernode is None
+                or (
+                    ecc_upper[i] == ecc_upper[maxuppernode]
+                    and degrees[i] > degrees[maxuppernode]
+                )
+                or (ecc_upper[i] > ecc_upper[maxuppernode])
+            ):
+                maxuppernode = i
+
+        # print status update
+    #        print (" min=" + str(minlower) + "/" + str(minupper) +
+    #        " max=" + str(maxlower) + "/" + str(maxupper) +
+    #        " candidates: " + str(len(candidates)))
+    #        print("cand:",candidates)
+    #        print("ecc_l",ecc_lower)
+    #        print("ecc_u",ecc_upper)
+    #        wait = input("press Enter to continue")
+
+    # return the correct value of the requested metric
+    if compute == "diameter":
+        return maxlower
+    if compute == "radius":
+        return minupper
+    if compute == "periphery":
+        p = [v for v in G if ecc_lower[v] == maxlower]
+        return p
+    if compute == "center":
+        c = [v for v in G if ecc_upper[v] == minupper]
+        return c
+    if compute == "eccentricities":
+        return ecc_lower
+    return None
+
+
+@nx._dispatchable(edge_attrs="weight")
+def eccentricity(G, v=None, sp=None, weight=None):
+    """Returns the eccentricity of nodes in G.
+
+    The eccentricity of a node v is the maximum distance from v to
+    all other nodes in G.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       A graph
+
+    v : node, optional
+       Return value of specified node
+
+    sp : dict of dicts, optional
+       All pairs shortest path lengths as a dictionary of dictionaries
+
+    weight : string, function, or None (default=None)
+        If this is a string, then edge weights will be accessed via the
+        edge attribute with this key (that is, the weight of the edge
+        joining `u` to `v` will be ``G.edges[u, v][weight]``). If no
+        such edge attribute exists, the weight of the edge is assumed to
+        be one.
+
+        If this is a function, the weight of an edge is the value
+        returned by the function. The function must accept exactly three
+        positional arguments: the two endpoints of an edge and the
+        dictionary of edge attributes for that edge. The function must
+        return a number.
+
+        If this is None, every edge has weight/distance/cost 1.
+
+        Weights stored as floating point values can lead to small round-off
+        errors in distances. Use integer weights to avoid this.
+
+        Weights should be positive, since they are distances.
+
+    Returns
+    -------
+    ecc : dictionary
+       A dictionary of eccentricity values keyed by node.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(1, 2), (1, 3), (1, 4), (3, 4), (3, 5), (4, 5)])
+    >>> dict(nx.eccentricity(G))
+    {1: 2, 2: 3, 3: 2, 4: 2, 5: 3}
+
+    >>> dict(nx.eccentricity(G, v=[1, 5]))  # This returns the eccentricity of node 1 & 5
+    {1: 2, 5: 3}
+
+    """
+    #    if v is None:                # none, use entire graph
+    #        nodes=G.nodes()
+    #    elif v in G:               # is v a single node
+    #        nodes=[v]
+    #    else:                      # assume v is a container of nodes
+    #        nodes=v
+    order = G.order()
+    e = {}
+    for n in G.nbunch_iter(v):
+        if sp is None:
+            length = nx.shortest_path_length(G, source=n, weight=weight)
+
+            L = len(length)
+        else:
+            try:
+                length = sp[n]
+                L = len(length)
+            except TypeError as err:
+                raise nx.NetworkXError('Format of "sp" is invalid.') from err
+        if L != order:
+            if G.is_directed():
+                msg = (
+                    "Found infinite path length because the digraph is not"
+                    " strongly connected"
+                )
+            else:
+                msg = "Found infinite path length because the graph is not" " connected"
+            raise nx.NetworkXError(msg)
+
+        e[n] = max(length.values())
+
+    if v in G:
+        return e[v]  # return single value
+    return e
+
+
+@nx._dispatchable(edge_attrs="weight")
+def diameter(G, e=None, usebounds=False, weight=None):
+    """Returns the diameter of the graph G.
+
+    The diameter is the maximum eccentricity.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       A graph
+
+    e : eccentricity dictionary, optional
+      A precomputed dictionary of eccentricities.
+
+    weight : string, function, or None
+        If this is a string, then edge weights will be accessed via the
+        edge attribute with this key (that is, the weight of the edge
+        joining `u` to `v` will be ``G.edges[u, v][weight]``). If no
+        such edge attribute exists, the weight of the edge is assumed to
+        be one.
+
+        If this is a function, the weight of an edge is the value
+        returned by the function. The function must accept exactly three
+        positional arguments: the two endpoints of an edge and the
+        dictionary of edge attributes for that edge. The function must
+        return a number.
+
+        If this is None, every edge has weight/distance/cost 1.
+
+        Weights stored as floating point values can lead to small round-off
+        errors in distances. Use integer weights to avoid this.
+
+        Weights should be positive, since they are distances.
+
+    Returns
+    -------
+    d : integer
+       Diameter of graph
+
+    Examples
+    --------
+    >>> G = nx.Graph([(1, 2), (1, 3), (1, 4), (3, 4), (3, 5), (4, 5)])
+    >>> nx.diameter(G)
+    3
+
+    See Also
+    --------
+    eccentricity
+    """
+    if usebounds is True and e is None and not G.is_directed():
+        return _extrema_bounding(G, compute="diameter", weight=weight)
+    if e is None:
+        e = eccentricity(G, weight=weight)
+    return max(e.values())
+
+
+@nx._dispatchable(edge_attrs="weight")
+def periphery(G, e=None, usebounds=False, weight=None):
+    """Returns the periphery of the graph G.
+
+    The periphery is the set of nodes with eccentricity equal to the diameter.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       A graph
+
+    e : eccentricity dictionary, optional
+      A precomputed dictionary of eccentricities.
+
+    weight : string, function, or None
+        If this is a string, then edge weights will be accessed via the
+        edge attribute with this key (that is, the weight of the edge
+        joining `u` to `v` will be ``G.edges[u, v][weight]``). If no
+        such edge attribute exists, the weight of the edge is assumed to
+        be one.
+
+        If this is a function, the weight of an edge is the value
+        returned by the function. The function must accept exactly three
+        positional arguments: the two endpoints of an edge and the
+        dictionary of edge attributes for that edge. The function must
+        return a number.
+
+        If this is None, every edge has weight/distance/cost 1.
+
+        Weights stored as floating point values can lead to small round-off
+        errors in distances. Use integer weights to avoid this.
+
+        Weights should be positive, since they are distances.
+
+    Returns
+    -------
+    p : list
+       List of nodes in periphery
+
+    Examples
+    --------
+    >>> G = nx.Graph([(1, 2), (1, 3), (1, 4), (3, 4), (3, 5), (4, 5)])
+    >>> nx.periphery(G)
+    [2, 5]
+
+    See Also
+    --------
+    barycenter
+    center
+    """
+    if usebounds is True and e is None and not G.is_directed():
+        return _extrema_bounding(G, compute="periphery", weight=weight)
+    if e is None:
+        e = eccentricity(G, weight=weight)
+    diameter = max(e.values())
+    p = [v for v in e if e[v] == diameter]
+    return p
+
+
+@nx._dispatchable(edge_attrs="weight")
+def radius(G, e=None, usebounds=False, weight=None):
+    """Returns the radius of the graph G.
+
+    The radius is the minimum eccentricity.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       A graph
+
+    e : eccentricity dictionary, optional
+      A precomputed dictionary of eccentricities.
+
+    weight : string, function, or None
+        If this is a string, then edge weights will be accessed via the
+        edge attribute with this key (that is, the weight of the edge
+        joining `u` to `v` will be ``G.edges[u, v][weight]``). If no
+        such edge attribute exists, the weight of the edge is assumed to
+        be one.
+
+        If this is a function, the weight of an edge is the value
+        returned by the function. The function must accept exactly three
+        positional arguments: the two endpoints of an edge and the
+        dictionary of edge attributes for that edge. The function must
+        return a number.
+
+        If this is None, every edge has weight/distance/cost 1.
+
+        Weights stored as floating point values can lead to small round-off
+        errors in distances. Use integer weights to avoid this.
+
+        Weights should be positive, since they are distances.
+
+    Returns
+    -------
+    r : integer
+       Radius of graph
+
+    Examples
+    --------
+    >>> G = nx.Graph([(1, 2), (1, 3), (1, 4), (3, 4), (3, 5), (4, 5)])
+    >>> nx.radius(G)
+    2
+
+    """
+    if usebounds is True and e is None and not G.is_directed():
+        return _extrema_bounding(G, compute="radius", weight=weight)
+    if e is None:
+        e = eccentricity(G, weight=weight)
+    return min(e.values())
+
+
+@nx._dispatchable(edge_attrs="weight")
+def center(G, e=None, usebounds=False, weight=None):
+    """Returns the center of the graph G.
+
+    The center is the set of nodes with eccentricity equal to radius.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       A graph
+
+    e : eccentricity dictionary, optional
+      A precomputed dictionary of eccentricities.
+
+    weight : string, function, or None
+        If this is a string, then edge weights will be accessed via the
+        edge attribute with this key (that is, the weight of the edge
+        joining `u` to `v` will be ``G.edges[u, v][weight]``). If no
+        such edge attribute exists, the weight of the edge is assumed to
+        be one.
+
+        If this is a function, the weight of an edge is the value
+        returned by the function. The function must accept exactly three
+        positional arguments: the two endpoints of an edge and the
+        dictionary of edge attributes for that edge. The function must
+        return a number.
+
+        If this is None, every edge has weight/distance/cost 1.
+
+        Weights stored as floating point values can lead to small round-off
+        errors in distances. Use integer weights to avoid this.
+
+        Weights should be positive, since they are distances.
+
+    Returns
+    -------
+    c : list
+       List of nodes in center
+
+    Examples
+    --------
+    >>> G = nx.Graph([(1, 2), (1, 3), (1, 4), (3, 4), (3, 5), (4, 5)])
+    >>> list(nx.center(G))
+    [1, 3, 4]
+
+    See Also
+    --------
+    barycenter
+    periphery
+    """
+    if usebounds is True and e is None and not G.is_directed():
+        return _extrema_bounding(G, compute="center", weight=weight)
+    if e is None:
+        e = eccentricity(G, weight=weight)
+    radius = min(e.values())
+    p = [v for v in e if e[v] == radius]
+    return p
+
+
+@nx._dispatchable(edge_attrs="weight", mutates_input={"attr": 2})
+def barycenter(G, weight=None, attr=None, sp=None):
+    r"""Calculate barycenter of a connected graph, optionally with edge weights.
+
+    The :dfn:`barycenter` a
+    :func:`connected <networkx.algorithms.components.is_connected>` graph
+    :math:`G` is the subgraph induced by the set of its nodes :math:`v`
+    minimizing the objective function
+
+    .. math::
+
+        \sum_{u \in V(G)} d_G(u, v),
+
+    where :math:`d_G` is the (possibly weighted) :func:`path length
+    <networkx.algorithms.shortest_paths.generic.shortest_path_length>`.
+    The barycenter is also called the :dfn:`median`. See [West01]_, p. 78.
+
+    Parameters
+    ----------
+    G : :class:`networkx.Graph`
+        The connected graph :math:`G`.
+    weight : :class:`str`, optional
+        Passed through to
+        :func:`~networkx.algorithms.shortest_paths.generic.shortest_path_length`.
+    attr : :class:`str`, optional
+        If given, write the value of the objective function to each node's
+        `attr` attribute. Otherwise do not store the value.
+    sp : dict of dicts, optional
+       All pairs shortest path lengths as a dictionary of dictionaries
+
+    Returns
+    -------
+    list
+        Nodes of `G` that induce the barycenter of `G`.
+
+    Raises
+    ------
+    NetworkXNoPath
+        If `G` is disconnected. `G` may appear disconnected to
+        :func:`barycenter` if `sp` is given but is missing shortest path
+        lengths for any pairs.
+    ValueError
+        If `sp` and `weight` are both given.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(1, 2), (1, 3), (1, 4), (3, 4), (3, 5), (4, 5)])
+    >>> nx.barycenter(G)
+    [1, 3, 4]
+
+    See Also
+    --------
+    center
+    periphery
+    """
+    if sp is None:
+        sp = nx.shortest_path_length(G, weight=weight)
+    else:
+        sp = sp.items()
+        if weight is not None:
+            raise ValueError("Cannot use both sp, weight arguments together")
+    smallest, barycenter_vertices, n = float("inf"), [], len(G)
+    for v, dists in sp:
+        if len(dists) < n:
+            raise nx.NetworkXNoPath(
+                f"Input graph {G} is disconnected, so every induced subgraph "
+                "has infinite barycentricity."
+            )
+        barycentricity = sum(dists.values())
+        if attr is not None:
+            G.nodes[v][attr] = barycentricity
+        if barycentricity < smallest:
+            smallest = barycentricity
+            barycenter_vertices = [v]
+        elif barycentricity == smallest:
+            barycenter_vertices.append(v)
+    if attr is not None:
+        nx._clear_cache(G)
+    return barycenter_vertices
+
+
+@not_implemented_for("directed")
+@nx._dispatchable(edge_attrs="weight")
+def resistance_distance(G, nodeA=None, nodeB=None, weight=None, invert_weight=True):
+    """Returns the resistance distance between pairs of nodes in graph G.
+
+    The resistance distance between two nodes of a graph is akin to treating
+    the graph as a grid of resistors with a resistance equal to the provided
+    weight [1]_, [2]_.
+
+    If weight is not provided, then a weight of 1 is used for all edges.
+
+    If two nodes are the same, the resistance distance is zero.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       A graph
+
+    nodeA : node or None, optional (default=None)
+      A node within graph G.
+      If None, compute resistance distance using all nodes as source nodes.
+
+    nodeB : node or None, optional (default=None)
+      A node within graph G.
+      If None, compute resistance distance using all nodes as target nodes.
+
+    weight : string or None, optional (default=None)
+       The edge data key used to compute the resistance distance.
+       If None, then each edge has weight 1.
+
+    invert_weight : boolean (default=True)
+        Proper calculation of resistance distance requires building the
+        Laplacian matrix with the reciprocal of the weight. Not required
+        if the weight is already inverted. Weight cannot be zero.
+
+    Returns
+    -------
+    rd : dict or float
+       If `nodeA` and `nodeB` are given, resistance distance between `nodeA`
+       and `nodeB`. If `nodeA` or `nodeB` is unspecified (the default), a
+       dictionary of nodes with resistance distances as the value.
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If `G` is a directed graph.
+
+    NetworkXError
+        If `G` is not connected, or contains no nodes,
+        or `nodeA` is not in `G` or `nodeB` is not in `G`.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(1, 2), (1, 3), (1, 4), (3, 4), (3, 5), (4, 5)])
+    >>> round(nx.resistance_distance(G, 1, 3), 10)
+    0.625
+
+    Notes
+    -----
+    The implementation is based on Theorem A in [2]_. Self-loops are ignored.
+    Multi-edges are contracted in one edge with weight equal to the harmonic sum of the weights.
+
+    References
+    ----------
+    .. [1] Wikipedia
+       "Resistance distance."
+       https://en.wikipedia.org/wiki/Resistance_distance
+    .. [2] D. J. Klein and M. Randic.
+        Resistance distance.
+        J. of Math. Chem. 12:81-95, 1993.
+    """
+    import numpy as np
+
+    if len(G) == 0:
+        raise nx.NetworkXError("Graph G must contain at least one node.")
+    if not nx.is_connected(G):
+        raise nx.NetworkXError("Graph G must be strongly connected.")
+    if nodeA is not None and nodeA not in G:
+        raise nx.NetworkXError("Node A is not in graph G.")
+    if nodeB is not None and nodeB not in G:
+        raise nx.NetworkXError("Node B is not in graph G.")
+
+    G = G.copy()
+    node_list = list(G)
+
+    # Invert weights
+    if invert_weight and weight is not None:
+        if G.is_multigraph():
+            for u, v, k, d in G.edges(keys=True, data=True):
+                d[weight] = 1 / d[weight]
+        else:
+            for u, v, d in G.edges(data=True):
+                d[weight] = 1 / d[weight]
+
+    # Compute resistance distance using the Pseudo-inverse of the Laplacian
+    # Self-loops are ignored
+    L = nx.laplacian_matrix(G, weight=weight).todense()
+    Linv = np.linalg.pinv(L, hermitian=True)
+
+    # Return relevant distances
+    if nodeA is not None and nodeB is not None:
+        i = node_list.index(nodeA)
+        j = node_list.index(nodeB)
+        return Linv.item(i, i) + Linv.item(j, j) - Linv.item(i, j) - Linv.item(j, i)
+
+    elif nodeA is not None:
+        i = node_list.index(nodeA)
+        d = {}
+        for n in G:
+            j = node_list.index(n)
+            d[n] = Linv.item(i, i) + Linv.item(j, j) - Linv.item(i, j) - Linv.item(j, i)
+        return d
+
+    elif nodeB is not None:
+        j = node_list.index(nodeB)
+        d = {}
+        for n in G:
+            i = node_list.index(n)
+            d[n] = Linv.item(i, i) + Linv.item(j, j) - Linv.item(i, j) - Linv.item(j, i)
+        return d
+
+    else:
+        d = {}
+        for n in G:
+            i = node_list.index(n)
+            d[n] = {}
+            for n2 in G:
+                j = node_list.index(n2)
+                d[n][n2] = (
+                    Linv.item(i, i)
+                    + Linv.item(j, j)
+                    - Linv.item(i, j)
+                    - Linv.item(j, i)
+                )
+        return d
+
+
+@not_implemented_for("directed")
+@nx._dispatchable(edge_attrs="weight")
+def effective_graph_resistance(G, weight=None, invert_weight=True):
+    """Returns the Effective graph resistance of G.
+
+    Also known as the Kirchhoff index.
+
+    The effective graph resistance is defined as the sum
+    of the resistance distance of every node pair in G [1]_.
+
+    If weight is not provided, then a weight of 1 is used for all edges.
+
+    The effective graph resistance of a disconnected graph is infinite.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       A graph
+
+    weight : string or None, optional (default=None)
+       The edge data key used to compute the effective graph resistance.
+       If None, then each edge has weight 1.
+
+    invert_weight : boolean (default=True)
+        Proper calculation of resistance distance requires building the
+        Laplacian matrix with the reciprocal of the weight. Not required
+        if the weight is already inverted. Weight cannot be zero.
+
+    Returns
+    -------
+    RG : float
+        The effective graph resistance of `G`.
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If `G` is a directed graph.
+
+    NetworkXError
+        If `G` does not contain any nodes.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(1, 2), (1, 3), (1, 4), (3, 4), (3, 5), (4, 5)])
+    >>> round(nx.effective_graph_resistance(G), 10)
+    10.25
+
+    Notes
+    -----
+    The implementation is based on Theorem 2.2 in [2]_. Self-loops are ignored.
+    Multi-edges are contracted in one edge with weight equal to the harmonic sum of the weights.
+
+    References
+    ----------
+    .. [1] Wolfram
+       "Kirchhoff Index."
+       https://mathworld.wolfram.com/KirchhoffIndex.html
+    .. [2] W. Ellens, F. M. Spieksma, P. Van Mieghem, A. Jamakovic, R. E. Kooij.
+        Effective graph resistance.
+        Lin. Alg. Appl. 435:2491-2506, 2011.
+    """
+    import numpy as np
+
+    if len(G) == 0:
+        raise nx.NetworkXError("Graph G must contain at least one node.")
+
+    # Disconnected graphs have infinite Effective graph resistance
+    if not nx.is_connected(G):
+        return float("inf")
+
+    # Invert weights
+    G = G.copy()
+    if invert_weight and weight is not None:
+        if G.is_multigraph():
+            for u, v, k, d in G.edges(keys=True, data=True):
+                d[weight] = 1 / d[weight]
+        else:
+            for u, v, d in G.edges(data=True):
+                d[weight] = 1 / d[weight]
+
+    # Get Laplacian eigenvalues
+    mu = np.sort(nx.laplacian_spectrum(G, weight=weight))
+
+    # Compute Effective graph resistance based on spectrum of the Laplacian
+    # Self-loops are ignored
+    return float(np.sum(1 / mu[1:]) * G.number_of_nodes())
+
+
+@nx.utils.not_implemented_for("directed")
+@nx._dispatchable(edge_attrs="weight")
+def kemeny_constant(G, *, weight=None):
+    """Returns the Kemeny constant of the given graph.
+
+    The *Kemeny constant* (or Kemeny's constant) of a graph `G`
+    can be computed by regarding the graph as a Markov chain.
+    The Kemeny constant is then the expected number of time steps
+    to transition from a starting state i to a random destination state
+    sampled from the Markov chain's stationary distribution.
+    The Kemeny constant is independent of the chosen initial state [1]_.
+
+    The Kemeny constant measures the time needed for spreading
+    across a graph. Low values indicate a closely connected graph
+    whereas high values indicate a spread-out graph.
+
+    If weight is not provided, then a weight of 1 is used for all edges.
+
+    Since `G` represents a Markov chain, the weights must be positive.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    weight : string or None, optional (default=None)
+       The edge data key used to compute the Kemeny constant.
+       If None, then each edge has weight 1.
+
+    Returns
+    -------
+    float
+        The Kemeny constant of the graph `G`.
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        If the graph `G` is directed.
+
+    NetworkXError
+        If the graph `G` is not connected, or contains no nodes,
+        or has edges with negative weights.
+
+    Examples
+    --------
+    >>> G = nx.complete_graph(5)
+    >>> round(nx.kemeny_constant(G), 10)
+    3.2
+
+    Notes
+    -----
+    The implementation is based on equation (3.3) in [2]_.
+    Self-loops are allowed and indicate a Markov chain where
+    the state can remain the same. Multi-edges are contracted
+    in one edge with weight equal to the sum of the weights.
+
+    References
+    ----------
+    .. [1] Wikipedia
+       "Kemeny's constant."
+       https://en.wikipedia.org/wiki/Kemeny%27s_constant
+    .. [2] Lovász L.
+        Random walks on graphs: A survey.
+        Paul Erdös is Eighty, vol. 2, Bolyai Society,
+        Mathematical Studies, Keszthely, Hungary (1993), pp. 1-46
+    """
+    import numpy as np
+    import scipy as sp
+
+    if len(G) == 0:
+        raise nx.NetworkXError("Graph G must contain at least one node.")
+    if not nx.is_connected(G):
+        raise nx.NetworkXError("Graph G must be connected.")
+    if nx.is_negatively_weighted(G, weight=weight):
+        raise nx.NetworkXError("The weights of graph G must be nonnegative.")
+
+    # Compute matrix H = D^-1/2 A D^-1/2
+    A = nx.adjacency_matrix(G, weight=weight)
+    n, m = A.shape
+    diags = A.sum(axis=1)
+    with np.errstate(divide="ignore"):
+        diags_sqrt = 1.0 / np.sqrt(diags)
+    diags_sqrt[np.isinf(diags_sqrt)] = 0
+    DH = sp.sparse.csr_array(sp.sparse.spdiags(diags_sqrt, 0, m, n, format="csr"))
+    H = DH @ (A @ DH)
+
+    # Compute eigenvalues of H
+    eig = np.sort(sp.linalg.eigvalsh(H.todense()))
+
+    # Compute the Kemeny constant
+    return float(np.sum(1 / (1 - eig[:-1])))

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/distance_regular.py

@@ -0,0 +1,238 @@
+"""
+=======================
+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._dispatchable
+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")
+@not_implemented_for("multigraph")
+@nx._dispatchable
+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)
+    if len(G) == 0:
+        raise nx.NetworkXPointlessConcept("Graph has no nodes.")
+    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")
+@not_implemented_for("multigraph")
+@nx._dispatchable
+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

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/euler.py

@@ -0,0 +1,469 @@
+"""
+Eulerian circuits and graphs.
+"""
+from itertools import combinations
+
+import networkx as nx
+
+from ..utils import arbitrary_element, not_implemented_for
+
+__all__ = [
+    "is_eulerian",
+    "eulerian_circuit",
+    "eulerize",
+    "is_semieulerian",
+    "has_eulerian_path",
+    "eulerian_path",
+]
+
+
+@nx._dispatchable
+def is_eulerian(G):
+    """Returns True if and only if `G` is Eulerian.
+
+    A graph is *Eulerian* if it has an Eulerian circuit. An *Eulerian
+    circuit* is a closed walk that includes each edge of a graph exactly
+    once.
+
+    Graphs with isolated vertices (i.e. vertices with zero degree) are not
+    considered to have Eulerian circuits. Therefore, if the graph is not
+    connected (or not strongly connected, for directed graphs), this function
+    returns False.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       A graph, either directed or undirected.
+
+    Examples
+    --------
+    >>> nx.is_eulerian(nx.DiGraph({0: [3], 1: [2], 2: [3], 3: [0, 1]}))
+    True
+    >>> nx.is_eulerian(nx.complete_graph(5))
+    True
+    >>> nx.is_eulerian(nx.petersen_graph())
+    False
+
+    If you prefer to allow graphs with isolated vertices to have Eulerian circuits,
+    you can first remove such vertices and then call `is_eulerian` as below example shows.
+
+    >>> G = nx.Graph([(0, 1), (1, 2), (0, 2)])
+    >>> G.add_node(3)
+    >>> nx.is_eulerian(G)
+    False
+
+    >>> G.remove_nodes_from(list(nx.isolates(G)))
+    >>> nx.is_eulerian(G)
+    True
+
+
+    """
+    if G.is_directed():
+        # Every node must have equal in degree and out degree and the
+        # graph must be strongly connected
+        return all(
+            G.in_degree(n) == G.out_degree(n) for n in G
+        ) and nx.is_strongly_connected(G)
+    # An undirected Eulerian graph has no vertices of odd degree and
+    # must be connected.
+    return all(d % 2 == 0 for v, d in G.degree()) and nx.is_connected(G)
+
+
+@nx._dispatchable
+def is_semieulerian(G):
+    """Return True iff `G` is semi-Eulerian.
+
+    G is semi-Eulerian if it has an Eulerian path but no Eulerian circuit.
+
+    See Also
+    --------
+    has_eulerian_path
+    is_eulerian
+    """
+    return has_eulerian_path(G) and not is_eulerian(G)
+
+
+def _find_path_start(G):
+    """Return a suitable starting vertex for an Eulerian path.
+
+    If no path exists, return None.
+    """
+    if not has_eulerian_path(G):
+        return None
+
+    if is_eulerian(G):
+        return arbitrary_element(G)
+
+    if G.is_directed():
+        v1, v2 = (v for v in G if G.in_degree(v) != G.out_degree(v))
+        # Determines which is the 'start' node (as opposed to the 'end')
+        if G.out_degree(v1) > G.in_degree(v1):
+            return v1
+        else:
+            return v2
+
+    else:
+        # In an undirected graph randomly choose one of the possibilities
+        start = [v for v in G if G.degree(v) % 2 != 0][0]
+        return start
+
+
+def _simplegraph_eulerian_circuit(G, source):
+    if G.is_directed():
+        degree = G.out_degree
+        edges = G.out_edges
+    else:
+        degree = G.degree
+        edges = G.edges
+    vertex_stack = [source]
+    last_vertex = None
+    while vertex_stack:
+        current_vertex = vertex_stack[-1]
+        if degree(current_vertex) == 0:
+            if last_vertex is not None:
+                yield (last_vertex, current_vertex)
+            last_vertex = current_vertex
+            vertex_stack.pop()
+        else:
+            _, next_vertex = arbitrary_element(edges(current_vertex))
+            vertex_stack.append(next_vertex)
+            G.remove_edge(current_vertex, next_vertex)
+
+
+def _multigraph_eulerian_circuit(G, source):
+    if G.is_directed():
+        degree = G.out_degree
+        edges = G.out_edges
+    else:
+        degree = G.degree
+        edges = G.edges
+    vertex_stack = [(source, None)]
+    last_vertex = None
+    last_key = None
+    while vertex_stack:
+        current_vertex, current_key = vertex_stack[-1]
+        if degree(current_vertex) == 0:
+            if last_vertex is not None:
+                yield (last_vertex, current_vertex, last_key)
+            last_vertex, last_key = current_vertex, current_key
+            vertex_stack.pop()
+        else:
+            triple = arbitrary_element(edges(current_vertex, keys=True))
+            _, next_vertex, next_key = triple
+            vertex_stack.append((next_vertex, next_key))
+            G.remove_edge(current_vertex, next_vertex, next_key)
+
+
+@nx._dispatchable
+def eulerian_circuit(G, source=None, keys=False):
+    """Returns an iterator over the edges of an Eulerian circuit in `G`.
+
+    An *Eulerian circuit* is a closed walk that includes each edge of a
+    graph exactly once.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       A graph, either directed or undirected.
+
+    source : node, optional
+       Starting node for circuit.
+
+    keys : bool
+       If False, edges generated by this function will be of the form
+       ``(u, v)``. Otherwise, edges will be of the form ``(u, v, k)``.
+       This option is ignored unless `G` is a multigraph.
+
+    Returns
+    -------
+    edges : iterator
+       An iterator over edges in the Eulerian circuit.
+
+    Raises
+    ------
+    NetworkXError
+       If the graph is not Eulerian.
+
+    See Also
+    --------
+    is_eulerian
+
+    Notes
+    -----
+    This is a linear time implementation of an algorithm adapted from [1]_.
+
+    For general information about Euler tours, see [2]_.
+
+    References
+    ----------
+    .. [1] J. Edmonds, E. L. Johnson.
+       Matching, Euler tours and the Chinese postman.
+       Mathematical programming, Volume 5, Issue 1 (1973), 111-114.
+    .. [2] https://en.wikipedia.org/wiki/Eulerian_path
+
+    Examples
+    --------
+    To get an Eulerian circuit in an undirected graph::
+
+        >>> G = nx.complete_graph(3)
+        >>> list(nx.eulerian_circuit(G))
+        [(0, 2), (2, 1), (1, 0)]
+        >>> list(nx.eulerian_circuit(G, source=1))
+        [(1, 2), (2, 0), (0, 1)]
+
+    To get the sequence of vertices in an Eulerian circuit::
+
+        >>> [u for u, v in nx.eulerian_circuit(G)]
+        [0, 2, 1]
+
+    """
+    if not is_eulerian(G):
+        raise nx.NetworkXError("G is not Eulerian.")
+    if G.is_directed():
+        G = G.reverse()
+    else:
+        G = G.copy()
+    if source is None:
+        source = arbitrary_element(G)
+    if G.is_multigraph():
+        for u, v, k in _multigraph_eulerian_circuit(G, source):
+            if keys:
+                yield u, v, k
+            else:
+                yield u, v
+    else:
+        yield from _simplegraph_eulerian_circuit(G, source)
+
+
+@nx._dispatchable
+def has_eulerian_path(G, source=None):
+    """Return True iff `G` has an Eulerian path.
+
+    An Eulerian path is a path in a graph which uses each edge of a graph
+    exactly once. If `source` is specified, then this function checks
+    whether an Eulerian path that starts at node `source` exists.
+
+    A directed graph has an Eulerian path iff:
+        - at most one vertex has out_degree - in_degree = 1,
+        - at most one vertex has in_degree - out_degree = 1,
+        - every other vertex has equal in_degree and out_degree,
+        - and all of its vertices belong to a single connected
+          component of the underlying undirected graph.
+
+    If `source` is not None, an Eulerian path starting at `source` exists if no
+    other node has out_degree - in_degree = 1. This is equivalent to either
+    there exists an Eulerian circuit or `source` has out_degree - in_degree = 1
+    and the conditions above hold.
+
+    An undirected graph has an Eulerian path iff:
+        - exactly zero or two vertices have odd degree,
+        - and all of its vertices belong to a single connected component.
+
+    If `source` is not None, an Eulerian path starting at `source` exists if
+    either there exists an Eulerian circuit or `source` has an odd degree and the
+    conditions above hold.
+
+    Graphs with isolated vertices (i.e. vertices with zero degree) are not considered
+    to have an Eulerian path. Therefore, if the graph is not connected (or not strongly
+    connected, for directed graphs), this function returns False.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+        The graph to find an euler path in.
+
+    source : node, optional
+        Starting node for path.
+
+    Returns
+    -------
+    Bool : True if G has an Eulerian path.
+
+    Examples
+    --------
+    If you prefer to allow graphs with isolated vertices to have Eulerian path,
+    you can first remove such vertices and then call `has_eulerian_path` as below example shows.
+
+    >>> G = nx.Graph([(0, 1), (1, 2), (0, 2)])
+    >>> G.add_node(3)
+    >>> nx.has_eulerian_path(G)
+    False
+
+    >>> G.remove_nodes_from(list(nx.isolates(G)))
+    >>> nx.has_eulerian_path(G)
+    True
+
+    See Also
+    --------
+    is_eulerian
+    eulerian_path
+    """
+    if nx.is_eulerian(G):
+        return True
+
+    if G.is_directed():
+        ins = G.in_degree
+        outs = G.out_degree
+        # Since we know it is not eulerian, outs - ins must be 1 for source
+        if source is not None and outs[source] - ins[source] != 1:
+            return False
+
+        unbalanced_ins = 0
+        unbalanced_outs = 0
+        for v in G:
+            if ins[v] - outs[v] == 1:
+                unbalanced_ins += 1
+            elif outs[v] - ins[v] == 1:
+                unbalanced_outs += 1
+            elif ins[v] != outs[v]:
+                return False
+
+        return (
+            unbalanced_ins <= 1 and unbalanced_outs <= 1 and nx.is_weakly_connected(G)
+        )
+    else:
+        # We know it is not eulerian, so degree of source must be odd.
+        if source is not None and G.degree[source] % 2 != 1:
+            return False
+
+        # Sum is 2 since we know it is not eulerian (which implies sum is 0)
+        return sum(d % 2 == 1 for v, d in G.degree()) == 2 and nx.is_connected(G)
+
+
+@nx._dispatchable
+def eulerian_path(G, source=None, keys=False):
+    """Return an iterator over the edges of an Eulerian path in `G`.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+        The graph in which to look for an eulerian path.
+    source : node or None (default: None)
+        The node at which to start the search. None means search over all
+        starting nodes.
+    keys : Bool (default: False)
+        Indicates whether to yield edge 3-tuples (u, v, edge_key).
+        The default yields edge 2-tuples
+
+    Yields
+    ------
+    Edge tuples along the eulerian path.
+
+    Warning: If `source` provided is not the start node of an Euler path
+    will raise error even if an Euler Path exists.
+    """
+    if not has_eulerian_path(G, source):
+        raise nx.NetworkXError("Graph has no Eulerian paths.")
+    if G.is_directed():
+        G = G.reverse()
+        if source is None or nx.is_eulerian(G) is False:
+            source = _find_path_start(G)
+        if G.is_multigraph():
+            for u, v, k in _multigraph_eulerian_circuit(G, source):
+                if keys:
+                    yield u, v, k
+                else:
+                    yield u, v
+        else:
+            yield from _simplegraph_eulerian_circuit(G, source)
+    else:
+        G = G.copy()
+        if source is None:
+            source = _find_path_start(G)
+        if G.is_multigraph():
+            if keys:
+                yield from reversed(
+                    [(v, u, k) for u, v, k in _multigraph_eulerian_circuit(G, source)]
+                )
+            else:
+                yield from reversed(
+                    [(v, u) for u, v, k in _multigraph_eulerian_circuit(G, source)]
+                )
+        else:
+            yield from reversed(
+                [(v, u) for u, v in _simplegraph_eulerian_circuit(G, source)]
+            )
+
+
+@not_implemented_for("directed")
+@nx._dispatchable(returns_graph=True)
+def eulerize(G):
+    """Transforms a graph into an Eulerian graph.
+
+    If `G` is Eulerian the result is `G` as a MultiGraph, otherwise the result is a smallest
+    (in terms of the number of edges) multigraph whose underlying simple graph is `G`.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       An undirected graph
+
+    Returns
+    -------
+    G : NetworkX multigraph
+
+    Raises
+    ------
+    NetworkXError
+       If the graph is not connected.
+
+    See Also
+    --------
+    is_eulerian
+    eulerian_circuit
+
+    References
+    ----------
+    .. [1] J. Edmonds, E. L. Johnson.
+       Matching, Euler tours and the Chinese postman.
+       Mathematical programming, Volume 5, Issue 1 (1973), 111-114.
+    .. [2] https://en.wikipedia.org/wiki/Eulerian_path
+    .. [3] http://web.math.princeton.edu/math_alive/5/Notes1.pdf
+
+    Examples
+    --------
+        >>> G = nx.complete_graph(10)
+        >>> H = nx.eulerize(G)
+        >>> nx.is_eulerian(H)
+        True
+
+    """
+    if G.order() == 0:
+        raise nx.NetworkXPointlessConcept("Cannot Eulerize null graph")
+    if not nx.is_connected(G):
+        raise nx.NetworkXError("G is not connected")
+    odd_degree_nodes = [n for n, d in G.degree() if d % 2 == 1]
+    G = nx.MultiGraph(G)
+    if len(odd_degree_nodes) == 0:
+        return G
+
+    # get all shortest paths between vertices of odd degree
+    odd_deg_pairs_paths = [
+        (m, {n: nx.shortest_path(G, source=m, target=n)})
+        for m, n in combinations(odd_degree_nodes, 2)
+    ]
+
+    # use the number of vertices in a graph + 1 as an upper bound on
+    # the maximum length of a path in G
+    upper_bound_on_max_path_length = len(G) + 1
+
+    # use "len(G) + 1 - len(P)",
+    # where P is a shortest path between vertices n and m,
+    # as edge-weights in a new graph
+    # store the paths in the graph for easy indexing later
+    Gp = nx.Graph()
+    for n, Ps in odd_deg_pairs_paths:
+        for m, P in Ps.items():
+            if n != m:
+                Gp.add_edge(
+                    m, n, weight=upper_bound_on_max_path_length - len(P), path=P
+                )
+
+    # find the minimum weight matching of edges in the weighted graph
+    best_matching = nx.Graph(list(nx.max_weight_matching(Gp)))
+
+    # duplicate each edge along each path in the set of paths in Gp
+    for m, n in best_matching.edges():
+        path = Gp[m][n]["path"]
+        G.add_edges_from(nx.utils.pairwise(path))
+    return G

env-llmeval/lib/python3.10/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

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/boykovkolmogorov.py

@@ -0,0 +1,369 @@
+"""
+Boykov-Kolmogorov algorithm for maximum flow problems.
+"""
+from collections import deque
+from operator import itemgetter
+
+import networkx as nx
+from networkx.algorithms.flow.utils import build_residual_network
+
+__all__ = ["boykov_kolmogorov"]
+
+
+@nx._dispatchable(edge_attrs={"capacity": float("inf")}, returns_graph=True)
+def boykov_kolmogorov(
+    G, s, t, capacity="capacity", residual=None, value_only=False, cutoff=None
+):
+    r"""Find a maximum single-commodity flow using Boykov-Kolmogorov 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 worse case complexity $O(n^2 m |C|)$ for $n$ nodes, $m$
+    edges, and $|C|$ the cost of the minimum cut [1]_. This implementation
+    uses the marking heuristic defined in [2]_ which improves its running
+    time in many practical problems.
+
+    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 boykov_kolmogorov
+
+    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 = boykov_kolmogorov(G, "x", "y")
+    >>> flow_value = nx.maximum_flow_value(G, "x", "y")
+    >>> flow_value
+    3.0
+    >>> flow_value == R.graph["flow_value"]
+    True
+
+    A nice feature of the Boykov-Kolmogorov algorithm is that a partition
+    of the nodes that defines a minimum cut can be easily computed based
+    on the search trees used during the algorithm. These trees are stored
+    in the graph attribute `trees` of the residual network.
+
+    >>> source_tree, target_tree = R.graph["trees"]
+    >>> partition = (set(source_tree), set(G) - set(source_tree))
+
+    Or equivalently:
+
+    >>> partition = (set(G) - set(target_tree), set(target_tree))
+
+    References
+    ----------
+    .. [1] Boykov, Y., & Kolmogorov, V. (2004). An experimental comparison
+           of min-cut/max-flow algorithms for energy minimization in vision.
+           Pattern Analysis and Machine Intelligence, IEEE Transactions on,
+           26(9), 1124-1137.
+           https://doi.org/10.1109/TPAMI.2004.60
+
+    .. [2] Vladimir Kolmogorov. Graph-based Algorithms for Multi-camera
+           Reconstruction Problem. PhD thesis, Cornell University, CS Department,
+           2003. pp. 109-114.
+           https://web.archive.org/web/20170809091249/https://pub.ist.ac.at/~vnk/papers/thesis.pdf
+
+    """
+    R = boykov_kolmogorov_impl(G, s, t, capacity, residual, cutoff)
+    R.graph["algorithm"] = "boykov_kolmogorov"
+    nx._clear_cache(R)
+    return R
+
+
+def boykov_kolmogorov_impl(G, s, t, capacity, residual, cutoff):
+    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.
+    # This is way too slow
+    # nx.set_edge_attributes(R, 0, 'flow')
+    for u in R:
+        for e in R[u].values():
+            e["flow"] = 0
+
+    # Use an arbitrary high value as infinite. It is computed
+    # when building the residual network.
+    INF = R.graph["inf"]
+
+    if cutoff is None:
+        cutoff = INF
+
+    R_succ = R.succ
+    R_pred = R.pred
+
+    def grow():
+        """Bidirectional breadth-first search for the growth stage.
+
+        Returns a connecting edge, that is and edge that connects
+        a node from the source search tree with a node from the
+        target search tree.
+        The first node in the connecting edge is always from the
+        source tree and the last node from the target tree.
+        """
+        while active:
+            u = active[0]
+            if u in source_tree:
+                this_tree = source_tree
+                other_tree = target_tree
+                neighbors = R_succ
+            else:
+                this_tree = target_tree
+                other_tree = source_tree
+                neighbors = R_pred
+            for v, attr in neighbors[u].items():
+                if attr["capacity"] - attr["flow"] > 0:
+                    if v not in this_tree:
+                        if v in other_tree:
+                            return (u, v) if this_tree is source_tree else (v, u)
+                        this_tree[v] = u
+                        dist[v] = dist[u] + 1
+                        timestamp[v] = timestamp[u]
+                        active.append(v)
+                    elif v in this_tree and _is_closer(u, v):
+                        this_tree[v] = u
+                        dist[v] = dist[u] + 1
+                        timestamp[v] = timestamp[u]
+            _ = active.popleft()
+        return None, None
+
+    def augment(u, v):
+        """Augmentation stage.
+
+        Reconstruct path and determine its residual capacity.
+        We start from a connecting edge, which links a node
+        from the source tree to a node from the target tree.
+        The connecting edge is the output of the grow function
+        and the input of this function.
+        """
+        attr = R_succ[u][v]
+        flow = min(INF, attr["capacity"] - attr["flow"])
+        path = [u]
+        # Trace a path from u to s in source_tree.
+        w = u
+        while w != s:
+            n = w
+            w = source_tree[n]
+            attr = R_pred[n][w]
+            flow = min(flow, attr["capacity"] - attr["flow"])
+            path.append(w)
+        path.reverse()
+        # Trace a path from v to t in target_tree.
+        path.append(v)
+        w = v
+        while w != t:
+            n = w
+            w = target_tree[n]
+            attr = R_succ[n][w]
+            flow = min(flow, attr["capacity"] - attr["flow"])
+            path.append(w)
+        # Augment flow along the path and check for saturated edges.
+        it = iter(path)
+        u = next(it)
+        these_orphans = []
+        for v in it:
+            R_succ[u][v]["flow"] += flow
+            R_succ[v][u]["flow"] -= flow
+            if R_succ[u][v]["flow"] == R_succ[u][v]["capacity"]:
+                if v in source_tree:
+                    source_tree[v] = None
+                    these_orphans.append(v)
+                if u in target_tree:
+                    target_tree[u] = None
+                    these_orphans.append(u)
+            u = v
+        orphans.extend(sorted(these_orphans, key=dist.get))
+        return flow
+
+    def adopt():
+        """Adoption stage.
+
+        Reconstruct search trees by adopting or discarding orphans.
+        During augmentation stage some edges got saturated and thus
+        the source and target search trees broke down to forests, with
+        orphans as roots of some of its trees. We have to reconstruct
+        the search trees rooted to source and target before we can grow
+        them again.
+        """
+        while orphans:
+            u = orphans.popleft()
+            if u in source_tree:
+                tree = source_tree
+                neighbors = R_pred
+            else:
+                tree = target_tree
+                neighbors = R_succ
+            nbrs = ((n, attr, dist[n]) for n, attr in neighbors[u].items() if n in tree)
+            for v, attr, d in sorted(nbrs, key=itemgetter(2)):
+                if attr["capacity"] - attr["flow"] > 0:
+                    if _has_valid_root(v, tree):
+                        tree[u] = v
+                        dist[u] = dist[v] + 1
+                        timestamp[u] = time
+                        break
+            else:
+                nbrs = (
+                    (n, attr, dist[n]) for n, attr in neighbors[u].items() if n in tree
+                )
+                for v, attr, d in sorted(nbrs, key=itemgetter(2)):
+                    if attr["capacity"] - attr["flow"] > 0:
+                        if v not in active:
+                            active.append(v)
+                    if tree[v] == u:
+                        tree[v] = None
+                        orphans.appendleft(v)
+                if u in active:
+                    active.remove(u)
+                del tree[u]
+
+    def _has_valid_root(n, tree):
+        path = []
+        v = n
+        while v is not None:
+            path.append(v)
+            if v in (s, t):
+                base_dist = 0
+                break
+            elif timestamp[v] == time:
+                base_dist = dist[v]
+                break
+            v = tree[v]
+        else:
+            return False
+        length = len(path)
+        for i, u in enumerate(path, 1):
+            dist[u] = base_dist + length - i
+            timestamp[u] = time
+        return True
+
+    def _is_closer(u, v):
+        return timestamp[v] <= timestamp[u] and dist[v] > dist[u] + 1
+
+    source_tree = {s: None}
+    target_tree = {t: None}
+    active = deque([s, t])
+    orphans = deque()
+    flow_value = 0
+    # data structures for the marking heuristic
+    time = 1
+    timestamp = {s: time, t: time}
+    dist = {s: 0, t: 0}
+    while flow_value < cutoff:
+        # Growth stage
+        u, v = grow()
+        if u is None:
+            break
+        time += 1
+        # Augmentation stage
+        flow_value += augment(u, v)
+        # Adoption stage
+        adopt()
+
+    if flow_value * 2 > INF:
+        raise nx.NetworkXUnbounded("Infinite capacity path, flow unbounded above.")
+
+    # Add source and target tree in a graph attribute.
+    # A partition that defines a minimum cut can be directly
+    # computed from the search trees as explained in the docstrings.
+    R.graph["trees"] = (source_tree, target_tree)
+    # Add the standard flow_value graph attribute.
+    R.graph["flow_value"] = flow_value
+    return R

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/capacityscaling.py

@@ -0,0 +1,407 @@
+"""
+Capacity scaling minimum cost flow algorithm.
+"""
+
+__all__ = ["capacity_scaling"]
+
+from itertools import chain
+from math import log
+
+import networkx as nx
+
+from ...utils import BinaryHeap, arbitrary_element, not_implemented_for
+
+
+def _detect_unboundedness(R):
+    """Detect infinite-capacity negative cycles."""
+    G = nx.DiGraph()
+    G.add_nodes_from(R)
+
+    # Value simulating infinity.
+    inf = R.graph["inf"]
+    # True infinity.
+    f_inf = float("inf")
+    for u in R:
+        for v, e in R[u].items():
+            # Compute the minimum weight of infinite-capacity (u, v) edges.
+            w = f_inf
+            for k, e in e.items():
+                if e["capacity"] == inf:
+                    w = min(w, e["weight"])
+            if w != f_inf:
+                G.add_edge(u, v, weight=w)
+
+    if nx.negative_edge_cycle(G):
+        raise nx.NetworkXUnbounded(
+            "Negative cost cycle of infinite capacity found. "
+            "Min cost flow may be unbounded below."
+        )
+
+
+@not_implemented_for("undirected")
+def _build_residual_network(G, demand, capacity, weight):
+    """Build a residual network and initialize a zero flow."""
+    if sum(G.nodes[u].get(demand, 0) for u in G) != 0:
+        raise nx.NetworkXUnfeasible("Sum of the demands should be 0.")
+
+    R = nx.MultiDiGraph()
+    R.add_nodes_from(
+        (u, {"excess": -G.nodes[u].get(demand, 0), "potential": 0}) for u in G
+    )
+
+    inf = float("inf")
+    # Detect selfloops with infinite capacities and negative weights.
+    for u, v, e in nx.selfloop_edges(G, data=True):
+        if e.get(weight, 0) < 0 and e.get(capacity, inf) == inf:
+            raise nx.NetworkXUnbounded(
+                "Negative cost cycle of infinite capacity found. "
+                "Min cost flow may be unbounded below."
+            )
+
+    # Extract edges with positive capacities. Self loops excluded.
+    if G.is_multigraph():
+        edge_list = [
+            (u, v, k, e)
+            for u, v, k, e in G.edges(data=True, keys=True)
+            if u != v and e.get(capacity, inf) > 0
+        ]
+    else:
+        edge_list = [
+            (u, v, 0, e)
+            for u, v, e in G.edges(data=True)
+            if u != v and e.get(capacity, inf) > 0
+        ]
+    # Simulate infinity with the larger of the sum of absolute node imbalances
+    # the sum of finite edge capacities or any positive value if both sums are
+    # zero. This allows the infinite-capacity edges to be distinguished for
+    # unboundedness detection and directly participate in residual capacity
+    # calculation.
+    inf = (
+        max(
+            sum(abs(R.nodes[u]["excess"]) for u in R),
+            2
+            * sum(
+                e[capacity]
+                for u, v, k, e in edge_list
+                if capacity in e and e[capacity] != inf
+            ),
+        )
+        or 1
+    )
+    for u, v, k, e in edge_list:
+        r = min(e.get(capacity, inf), inf)
+        w = e.get(weight, 0)
+        # Add both (u, v) and (v, u) into the residual network marked with the
+        # original key. (key[1] == True) indicates the (u, v) is in the
+        # original network.
+        R.add_edge(u, v, key=(k, True), capacity=r, weight=w, flow=0)
+        R.add_edge(v, u, key=(k, False), capacity=0, weight=-w, flow=0)
+
+    # Record the value simulating infinity.
+    R.graph["inf"] = inf
+
+    _detect_unboundedness(R)
+
+    return R
+
+
+def _build_flow_dict(G, R, capacity, weight):
+    """Build a flow dictionary from a residual network."""
+    inf = float("inf")
+    flow_dict = {}
+    if G.is_multigraph():
+        for u in G:
+            flow_dict[u] = {}
+            for v, es in G[u].items():
+                flow_dict[u][v] = {
+                    # Always saturate negative selfloops.
+                    k: (
+                        0
+                        if (
+                            u != v or e.get(capacity, inf) <= 0 or e.get(weight, 0) >= 0
+                        )
+                        else e[capacity]
+                    )
+                    for k, e in es.items()
+                }
+            for v, es in R[u].items():
+                if v in flow_dict[u]:
+                    flow_dict[u][v].update(
+                        (k[0], e["flow"]) for k, e in es.items() if e["flow"] > 0
+                    )
+    else:
+        for u in G:
+            flow_dict[u] = {
+                # Always saturate negative selfloops.
+                v: (
+                    0
+                    if (u != v or e.get(capacity, inf) <= 0 or e.get(weight, 0) >= 0)
+                    else e[capacity]
+                )
+                for v, e in G[u].items()
+            }
+            flow_dict[u].update(
+                (v, e["flow"])
+                for v, es in R[u].items()
+                for e in es.values()
+                if e["flow"] > 0
+            )
+    return flow_dict
+
+
+@nx._dispatchable(
+    node_attrs="demand", edge_attrs={"capacity": float("inf"), "weight": 0}
+)
+def capacity_scaling(
+    G, demand="demand", capacity="capacity", weight="weight", heap=BinaryHeap
+):
+    r"""Find a minimum cost flow satisfying all demands in digraph G.
+
+    This is a capacity scaling successive shortest augmenting path algorithm.
+
+    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 or MultiDiGraph 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'.
+
+    heap : class
+        Type of heap to be used in the algorithm. It should be a subclass of
+        :class:`MinHeap` or implement a compatible interface.
+
+        If a stock heap implementation is to be used, :class:`BinaryHeap` is
+        recommended over :class:`PairingHeap` for Python implementations without
+        optimized attribute accesses (e.g., CPython) despite a slower
+        asymptotic running time. For Python implementations with optimized
+        attribute accesses (e.g., PyPy), :class:`PairingHeap` provides better
+        performance. Default value: :class:`BinaryHeap`.
+
+    Returns
+    -------
+    flowCost : integer
+        Cost of a minimum cost flow satisfying all demands.
+
+    flowDict : dictionary
+        If G is a digraph, a dict-of-dicts keyed by nodes such that
+        flowDict[u][v] is the flow on edge (u, v).
+        If G is a MultiDiGraph, a dict-of-dicts-of-dicts keyed by nodes
+        so that flowDict[u][v][key] is the flow on edge (u, v, key).
+
+    Raises
+    ------
+    NetworkXError
+        This exception is raised if the input graph is not directed,
+        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.
+
+    Notes
+    -----
+    This algorithm does not work if edge weights are floating-point numbers.
+
+    See also
+    --------
+    :meth:`network_simplex`
+
+    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, flowDict = nx.capacity_scaling(G)
+    >>> flowCost
+    24
+    >>> flowDict
+    {'a': {'b': 4, 'c': 1}, 'd': {}, 'b': {'d': 4}, 'c': {'d': 1}}
+
+    It is possible to change the name of the attributes used for the
+    algorithm.
+
+    >>> G = nx.DiGraph()
+    >>> G.add_node("p", spam=-4)
+    >>> G.add_node("q", spam=2)
+    >>> G.add_node("a", spam=-2)
+    >>> G.add_node("d", spam=-1)
+    >>> G.add_node("t", spam=2)
+    >>> G.add_node("w", spam=3)
+    >>> G.add_edge("p", "q", cost=7, vacancies=5)
+    >>> G.add_edge("p", "a", cost=1, vacancies=4)
+    >>> G.add_edge("q", "d", cost=2, vacancies=3)
+    >>> G.add_edge("t", "q", cost=1, vacancies=2)
+    >>> G.add_edge("a", "t", cost=2, vacancies=4)
+    >>> G.add_edge("d", "w", cost=3, vacancies=4)
+    >>> G.add_edge("t", "w", cost=4, vacancies=1)
+    >>> flowCost, flowDict = nx.capacity_scaling(
+    ...     G, demand="spam", capacity="vacancies", weight="cost"
+    ... )
+    >>> flowCost
+    37
+    >>> flowDict
+    {'p': {'q': 2, 'a': 2}, 'q': {'d': 1}, 'a': {'t': 4}, 'd': {'w': 2}, 't': {'q': 1, 'w': 1}, 'w': {}}
+    """
+    R = _build_residual_network(G, demand, capacity, weight)
+
+    inf = float("inf")
+    # Account cost of negative selfloops.
+    flow_cost = sum(
+        0
+        if e.get(capacity, inf) <= 0 or e.get(weight, 0) >= 0
+        else e[capacity] * e[weight]
+        for u, v, e in nx.selfloop_edges(G, data=True)
+    )
+
+    # Determine the maximum edge capacity.
+    wmax = max(chain([-inf], (e["capacity"] for u, v, e in R.edges(data=True))))
+    if wmax == -inf:
+        # Residual network has no edges.
+        return flow_cost, _build_flow_dict(G, R, capacity, weight)
+
+    R_nodes = R.nodes
+    R_succ = R.succ
+
+    delta = 2 ** int(log(wmax, 2))
+    while delta >= 1:
+        # Saturate Δ-residual edges with negative reduced costs to achieve
+        # Δ-optimality.
+        for u in R:
+            p_u = R_nodes[u]["potential"]
+            for v, es in R_succ[u].items():
+                for k, e in es.items():
+                    flow = e["capacity"] - e["flow"]
+                    if e["weight"] - p_u + R_nodes[v]["potential"] < 0:
+                        flow = e["capacity"] - e["flow"]
+                        if flow >= delta:
+                            e["flow"] += flow
+                            R_succ[v][u][(k[0], not k[1])]["flow"] -= flow
+                            R_nodes[u]["excess"] -= flow
+                            R_nodes[v]["excess"] += flow
+        # Determine the Δ-active nodes.
+        S = set()
+        T = set()
+        S_add = S.add
+        S_remove = S.remove
+        T_add = T.add
+        T_remove = T.remove
+        for u in R:
+            excess = R_nodes[u]["excess"]
+            if excess >= delta:
+                S_add(u)
+            elif excess <= -delta:
+                T_add(u)
+        # Repeatedly augment flow from S to T along shortest paths until
+        # Δ-feasibility is achieved.
+        while S and T:
+            s = arbitrary_element(S)
+            t = None
+            # Search for a shortest path in terms of reduce costs from s to
+            # any t in T in the Δ-residual network.
+            d = {}
+            pred = {s: None}
+            h = heap()
+            h_insert = h.insert
+            h_get = h.get
+            h_insert(s, 0)
+            while h:
+                u, d_u = h.pop()
+                d[u] = d_u
+                if u in T:
+                    # Path found.
+                    t = u
+                    break
+                p_u = R_nodes[u]["potential"]
+                for v, es in R_succ[u].items():
+                    if v in d:
+                        continue
+                    wmin = inf
+                    # Find the minimum-weighted (u, v) Δ-residual edge.
+                    for k, e in es.items():
+                        if e["capacity"] - e["flow"] >= delta:
+                            w = e["weight"]
+                            if w < wmin:
+                                wmin = w
+                                kmin = k
+                                emin = e
+                    if wmin == inf:
+                        continue
+                    # Update the distance label of v.
+                    d_v = d_u + wmin - p_u + R_nodes[v]["potential"]
+                    if h_insert(v, d_v):
+                        pred[v] = (u, kmin, emin)
+            if t is not None:
+                # Augment Δ units of flow from s to t.
+                while u != s:
+                    v = u
+                    u, k, e = pred[v]
+                    e["flow"] += delta
+                    R_succ[v][u][(k[0], not k[1])]["flow"] -= delta
+                # Account node excess and deficit.
+                R_nodes[s]["excess"] -= delta
+                R_nodes[t]["excess"] += delta
+                if R_nodes[s]["excess"] < delta:
+                    S_remove(s)
+                if R_nodes[t]["excess"] > -delta:
+                    T_remove(t)
+                # Update node potentials.
+                d_t = d[t]
+                for u, d_u in d.items():
+                    R_nodes[u]["potential"] -= d_u - d_t
+            else:
+                # Path not found.
+                S_remove(s)
+        delta //= 2
+
+    if any(R.nodes[u]["excess"] != 0 for u in R):
+        raise nx.NetworkXUnfeasible("No flow satisfying all demands.")
+
+    # Calculate the flow cost.
+    for u in R:
+        for v, es in R_succ[u].items():
+            for e in es.values():
+                flow = e["flow"]
+                if flow > 0:
+                    flow_cost += flow * e["weight"]
+
+    return flow_cost, _build_flow_dict(G, R, capacity, weight)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/dinitz_alg.py

@@ -0,0 +1,237 @@
+"""
+Dinitz' algorithm for maximum flow problems.
+"""
+from collections import deque
+
+import networkx as nx
+from networkx.algorithms.flow.utils import build_residual_network
+from networkx.utils import pairwise
+
+__all__ = ["dinitz"]
+
+
+@nx._dispatchable(edge_attrs={"capacity": float("inf")}, returns_graph=True)
+def dinitz(G, s, t, capacity="capacity", residual=None, value_only=False, cutoff=None):
+    """Find a maximum single-commodity flow using Dinitz' 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 [1]_.
+
+
+    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 dinitz
+
+    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 = dinitz(G, "x", "y")
+    >>> flow_value = nx.maximum_flow_value(G, "x", "y")
+    >>> flow_value
+    3.0
+    >>> flow_value == R.graph["flow_value"]
+    True
+
+    References
+    ----------
+    .. [1] Dinitz' Algorithm: The Original Version and Even's Version.
+           2006. Yefim Dinitz. In Theoretical Computer Science. Lecture
+           Notes in Computer Science. Volume 3895. pp 218-240.
+           https://doi.org/10.1007/11685654_10
+
+    """
+    R = dinitz_impl(G, s, t, capacity, residual, cutoff)
+    R.graph["algorithm"] = "dinitz"
+    nx._clear_cache(R)
+    return R
+
+
+def dinitz_impl(G, s, t, capacity, residual, cutoff):
+    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
+
+    # Use an arbitrary high value as infinite. It is computed
+    # when building the residual network.
+    INF = R.graph["inf"]
+
+    if cutoff is None:
+        cutoff = INF
+
+    R_succ = R.succ
+    R_pred = R.pred
+
+    def breath_first_search():
+        parents = {}
+        vertex_dist = {s: 0}
+        queue = deque([(s, 0)])
+        # Record all the potential edges of shortest augmenting paths
+        while queue:
+            if t in parents:
+                break
+            u, dist = queue.popleft()
+            for v, attr in R_succ[u].items():
+                if attr["capacity"] - attr["flow"] > 0:
+                    if v in parents:
+                        if vertex_dist[v] == dist + 1:
+                            parents[v].append(u)
+                    else:
+                        parents[v] = deque([u])
+                        vertex_dist[v] = dist + 1
+                        queue.append((v, dist + 1))
+        return parents
+
+    def depth_first_search(parents):
+        # DFS to find all the shortest augmenting paths
+        """Build a path using DFS starting from the sink"""
+        total_flow = 0
+        u = t
+        # path also functions as a stack
+        path = [u]
+        # The loop ends with no augmenting path left in the layered graph
+        while True:
+            if len(parents[u]) > 0:
+                v = parents[u][0]
+                path.append(v)
+            else:
+                path.pop()
+                if len(path) == 0:
+                    break
+                v = path[-1]
+                parents[v].popleft()
+            # Augment the flow along the path found
+            if v == s:
+                flow = INF
+                for u, v in pairwise(path):
+                    flow = min(flow, R_pred[u][v]["capacity"] - R_pred[u][v]["flow"])
+                for u, v in pairwise(reversed(path)):
+                    R_pred[v][u]["flow"] += flow
+                    R_pred[u][v]["flow"] -= flow
+                    # Find the proper node to continue the search
+                    if R_pred[v][u]["capacity"] - R_pred[v][u]["flow"] == 0:
+                        parents[v].popleft()
+                        while path[-1] != v:
+                            path.pop()
+                total_flow += flow
+                v = path[-1]
+            u = v
+        return total_flow
+
+    flow_value = 0
+    while flow_value < cutoff:
+        parents = breath_first_search()
+        if t not in parents:
+            break
+        this_flow = depth_first_search(parents)
+        if this_flow * 2 > INF:
+            raise nx.NetworkXUnbounded("Infinite capacity path, flow unbounded above.")
+        flow_value += this_flow
+
+    R.graph["flow_value"] = flow_value
+    return R

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/edmondskarp.py

@@ -0,0 +1,241 @@
+"""
+Edmonds-Karp algorithm for maximum flow problems.
+"""
+
+import networkx as nx
+from networkx.algorithms.flow.utils import build_residual_network
+
+__all__ = ["edmonds_karp"]
+
+
+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._dispatchable(edge_attrs={"capacity": float("inf")}, returns_graph=True)
+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"
+    nx._clear_cache(R)
+    return R

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/gomory_hu.py

@@ -0,0 +1,177 @@
+"""
+Gomory-Hu tree of undirected Graphs.
+"""
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+from .edmondskarp import edmonds_karp
+from .utils import build_residual_network
+
+default_flow_func = edmonds_karp
+
+__all__ = ["gomory_hu_tree"]
+
+
+@not_implemented_for("directed")
+@nx._dispatchable(edge_attrs={"capacity": float("inf")}, returns_graph=True)
+def gomory_hu_tree(G, capacity="capacity", flow_func=None):
+    r"""Returns the Gomory-Hu tree of an undirected graph G.
+
+    A Gomory-Hu tree of an undirected graph with capacities is a
+    weighted tree that represents the minimum s-t cuts for all s-t
+    pairs in the graph.
+
+    It only requires `n-1` minimum cut computations instead of the
+    obvious `n(n-1)/2`. The tree represents all s-t cuts as the
+    minimum cut value among any pair of nodes is the minimum edge
+    weight in the shortest path between the two nodes in the
+    Gomory-Hu tree.
+
+    The Gomory-Hu tree also has the property that removing the
+    edge with the minimum weight in the shortest path between
+    any two nodes leaves two connected components that form
+    a partition of the nodes in G that defines the minimum s-t
+    cut.
+
+    See Examples section below for details.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        Undirected graph
+
+    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'.
+
+    flow_func : function
+        Function to perform the underlying flow computations. Default value
+        :func:`edmonds_karp`. This function performs better in sparse graphs
+        with right tailed degree distributions.
+        :func:`shortest_augmenting_path` will perform better in denser
+        graphs.
+
+    Returns
+    -------
+    Tree : NetworkX graph
+        A NetworkX graph representing the Gomory-Hu tree of the input graph.
+
+    Raises
+    ------
+    NetworkXNotImplemented
+        Raised if the input graph is directed.
+
+    NetworkXError
+        Raised if the input graph is an empty Graph.
+
+    Examples
+    --------
+    >>> G = nx.karate_club_graph()
+    >>> nx.set_edge_attributes(G, 1, "capacity")
+    >>> T = nx.gomory_hu_tree(G)
+    >>> # The value of the minimum cut between any pair
+    ... # of nodes in G is the minimum edge weight in the
+    ... # shortest path between the two nodes in the
+    ... # Gomory-Hu tree.
+    ... def minimum_edge_weight_in_shortest_path(T, u, v):
+    ...     path = nx.shortest_path(T, u, v, weight="weight")
+    ...     return min((T[u][v]["weight"], (u, v)) for (u, v) in zip(path, path[1:]))
+    >>> u, v = 0, 33
+    >>> cut_value, edge = minimum_edge_weight_in_shortest_path(T, u, v)
+    >>> cut_value
+    10
+    >>> nx.minimum_cut_value(G, u, v)
+    10
+    >>> # The Gomory-Hu tree also has the property that removing the
+    ... # edge with the minimum weight in the shortest path between
+    ... # any two nodes leaves two connected components that form
+    ... # a partition of the nodes in G that defines the minimum s-t
+    ... # cut.
+    ... cut_value, edge = minimum_edge_weight_in_shortest_path(T, u, v)
+    >>> T.remove_edge(*edge)
+    >>> U, V = list(nx.connected_components(T))
+    >>> # Thus U and V form a partition that defines a minimum cut
+    ... # between u and v in G. You can compute the edge cut set,
+    ... # that is, the set of edges that if removed from G will
+    ... # disconnect u from v in G, with this information:
+    ... cutset = set()
+    >>> for x, nbrs in ((n, G[n]) for n in U):
+    ...     cutset.update((x, y) for y in nbrs if y in V)
+    >>> # Because we have set the capacities of all edges to 1
+    ... # the cutset contains ten edges
+    ... len(cutset)
+    10
+    >>> # You can use any maximum flow algorithm for the underlying
+    ... # flow computations using the argument flow_func
+    ... from networkx.algorithms import flow
+    >>> T = nx.gomory_hu_tree(G, flow_func=flow.boykov_kolmogorov)
+    >>> cut_value, edge = minimum_edge_weight_in_shortest_path(T, u, v)
+    >>> cut_value
+    10
+    >>> nx.minimum_cut_value(G, u, v, flow_func=flow.boykov_kolmogorov)
+    10
+
+    Notes
+    -----
+    This implementation is based on Gusfield approach [1]_ to compute
+    Gomory-Hu trees, which does not require node contractions and has
+    the same computational complexity than the original method.
+
+    See also
+    --------
+    :func:`minimum_cut`
+    :func:`maximum_flow`
+
+    References
+    ----------
+    .. [1] Gusfield D: Very simple methods for all pairs network flow analysis.
+           SIAM J Comput 19(1):143-155, 1990.
+
+    """
+    if flow_func is None:
+        flow_func = default_flow_func
+
+    if len(G) == 0:  # empty graph
+        msg = "Empty Graph does not have a Gomory-Hu tree representation"
+        raise nx.NetworkXError(msg)
+
+    # Start the tree as a star graph with an arbitrary node at the center
+    tree = {}
+    labels = {}
+    iter_nodes = iter(G)
+    root = next(iter_nodes)
+    for n in iter_nodes:
+        tree[n] = root
+
+    # Reuse residual network
+    R = build_residual_network(G, capacity)
+
+    # For all the leaves in the star graph tree (that is n-1 nodes).
+    for source in tree:
+        # Find neighbor in the tree
+        target = tree[source]
+        # compute minimum cut
+        cut_value, partition = nx.minimum_cut(
+            G, source, target, capacity=capacity, flow_func=flow_func, residual=R
+        )
+        labels[(source, target)] = cut_value
+        # Update the tree
+        # Source will always be in partition[0] and target in partition[1]
+        for node in partition[0]:
+            if node != source and node in tree and tree[node] == target:
+                tree[node] = source
+                labels[node, source] = labels.get((node, target), cut_value)
+        #
+        if target != root and tree[target] in partition[0]:
+            labels[source, tree[target]] = labels[target, tree[target]]
+            labels[target, source] = cut_value
+            tree[source] = tree[target]
+            tree[target] = source
+
+    # Build the tree
+    T = nx.Graph()
+    T.add_nodes_from(G)
+    T.add_weighted_edges_from(((u, v, labels[u, v]) for u, v in tree.items()))
+    return T

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/maxflow.py

@@ -0,0 +1,601 @@
+"""
+Maximum flow (and minimum cut) algorithms on capacitated graphs.
+"""
+import networkx as nx
+
+from .boykovkolmogorov import boykov_kolmogorov
+from .dinitz_alg import dinitz
+from .edmondskarp import edmonds_karp
+from .preflowpush import preflow_push
+from .shortestaugmentingpath import shortest_augmenting_path
+from .utils import build_flow_dict
+
+# Define the default flow function for computing maximum flow.
+default_flow_func = preflow_push
+
+__all__ = ["maximum_flow", "maximum_flow_value", "minimum_cut", "minimum_cut_value"]
+
+
+@nx._dispatchable(graphs="flowG", edge_attrs={"capacity": float("inf")})
+def maximum_flow(flowG, _s, _t, capacity="capacity", flow_func=None, **kwargs):
+    """Find a maximum single-commodity flow.
+
+    Parameters
+    ----------
+    flowG : 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'.
+
+    flow_func : function
+        A function for computing the maximum flow among a pair of nodes
+        in a capacitated graph. The function has to accept at least three
+        parameters: a Graph or Digraph, a source node, and a target node.
+        And return a residual network that follows NetworkX conventions
+        (see Notes). If flow_func is None, the default maximum
+        flow function (:meth:`preflow_push`) is used. See below for
+        alternative algorithms. The choice of the default function may change
+        from version to version and should not be relied on. Default value:
+        None.
+
+    kwargs : Any other keyword parameter is passed to the function that
+        computes the maximum flow.
+
+    Returns
+    -------
+    flow_value : integer, float
+        Value of the maximum flow, i.e., net outflow from the source.
+
+    flow_dict : dict
+        A dictionary containing the value of the flow that went through
+        each edge.
+
+    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_value`
+    :meth:`minimum_cut`
+    :meth:`minimum_cut_value`
+    :meth:`edmonds_karp`
+    :meth:`preflow_push`
+    :meth:`shortest_augmenting_path`
+
+    Notes
+    -----
+    The function used in the flow_func parameter has to return a residual
+    network that follows NetworkX conventions:
+
+    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']`. 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.
+
+    Specific algorithms may store extra data in :samp:`R`.
+
+    The function should supports an optional boolean parameter value_only. When
+    True, it can optionally terminate the algorithm as soon as the maximum flow
+    value and the minimum cut can be determined.
+
+    Examples
+    --------
+    >>> 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)
+
+    maximum_flow returns both the value of the maximum flow and a
+    dictionary with all flows.
+
+    >>> flow_value, flow_dict = nx.maximum_flow(G, "x", "y")
+    >>> flow_value
+    3.0
+    >>> print(flow_dict["x"]["b"])
+    1.0
+
+    You can also use alternative algorithms for computing the
+    maximum flow by using the flow_func parameter.
+
+    >>> from networkx.algorithms.flow import shortest_augmenting_path
+    >>> flow_value == nx.maximum_flow(G, "x", "y", flow_func=shortest_augmenting_path)[0]
+    True
+
+    """
+    if flow_func is None:
+        if kwargs:
+            raise nx.NetworkXError(
+                "You have to explicitly set a flow_func if"
+                " you need to pass parameters via kwargs."
+            )
+        flow_func = default_flow_func
+
+    if not callable(flow_func):
+        raise nx.NetworkXError("flow_func has to be callable.")
+
+    R = flow_func(flowG, _s, _t, capacity=capacity, value_only=False, **kwargs)
+    flow_dict = build_flow_dict(flowG, R)
+
+    return (R.graph["flow_value"], flow_dict)
+
+
+@nx._dispatchable(graphs="flowG", edge_attrs={"capacity": float("inf")})
+def maximum_flow_value(flowG, _s, _t, capacity="capacity", flow_func=None, **kwargs):
+    """Find the value of maximum single-commodity flow.
+
+    Parameters
+    ----------
+    flowG : 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'.
+
+    flow_func : function
+        A function for computing the maximum flow among a pair of nodes
+        in a capacitated graph. The function has to accept at least three
+        parameters: a Graph or Digraph, a source node, and a target node.
+        And return a residual network that follows NetworkX conventions
+        (see Notes). If flow_func is None, the default maximum
+        flow function (:meth:`preflow_push`) is used. See below for
+        alternative algorithms. The choice of the default function may change
+        from version to version and should not be relied on. Default value:
+        None.
+
+    kwargs : Any other keyword parameter is passed to the function that
+        computes the maximum flow.
+
+    Returns
+    -------
+    flow_value : integer, float
+        Value of the maximum flow, i.e., net outflow from the source.
+
+    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:`minimum_cut_value`
+    :meth:`edmonds_karp`
+    :meth:`preflow_push`
+    :meth:`shortest_augmenting_path`
+
+    Notes
+    -----
+    The function used in the flow_func parameter has to return a residual
+    network that follows NetworkX conventions:
+
+    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']`. 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.
+
+    Specific algorithms may store extra data in :samp:`R`.
+
+    The function should supports an optional boolean parameter value_only. When
+    True, it can optionally terminate the algorithm as soon as the maximum flow
+    value and the minimum cut can be determined.
+
+    Examples
+    --------
+    >>> 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)
+
+    maximum_flow_value computes only the value of the
+    maximum flow:
+
+    >>> flow_value = nx.maximum_flow_value(G, "x", "y")
+    >>> flow_value
+    3.0
+
+    You can also use alternative algorithms for computing the
+    maximum flow by using the flow_func parameter.
+
+    >>> from networkx.algorithms.flow import shortest_augmenting_path
+    >>> flow_value == nx.maximum_flow_value(G, "x", "y", flow_func=shortest_augmenting_path)
+    True
+
+    """
+    if flow_func is None:
+        if kwargs:
+            raise nx.NetworkXError(
+                "You have to explicitly set a flow_func if"
+                " you need to pass parameters via kwargs."
+            )
+        flow_func = default_flow_func
+
+    if not callable(flow_func):
+        raise nx.NetworkXError("flow_func has to be callable.")
+
+    R = flow_func(flowG, _s, _t, capacity=capacity, value_only=True, **kwargs)
+
+    return R.graph["flow_value"]
+
+
+@nx._dispatchable(graphs="flowG", edge_attrs={"capacity": float("inf")})
+def minimum_cut(flowG, _s, _t, capacity="capacity", flow_func=None, **kwargs):
+    """Compute the value and the node partition of a minimum (s, t)-cut.
+
+    Use the max-flow min-cut theorem, i.e., the capacity of a minimum
+    capacity cut is equal to the flow value of a maximum flow.
+
+    Parameters
+    ----------
+    flowG : 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'.
+
+    flow_func : function
+        A function for computing the maximum flow among a pair of nodes
+        in a capacitated graph. The function has to accept at least three
+        parameters: a Graph or Digraph, a source node, and a target node.
+        And return a residual network that follows NetworkX conventions
+        (see Notes). If flow_func is None, the default maximum
+        flow function (:meth:`preflow_push`) is used. See below for
+        alternative algorithms. The choice of the default function may change
+        from version to version and should not be relied on. Default value:
+        None.
+
+    kwargs : Any other keyword parameter is passed to the function that
+        computes the maximum flow.
+
+    Returns
+    -------
+    cut_value : integer, float
+        Value of the minimum cut.
+
+    partition : pair of node sets
+        A partitioning of the nodes that defines a minimum cut.
+
+    Raises
+    ------
+    NetworkXUnbounded
+        If the graph has a path of infinite capacity, all cuts have
+        infinite capacity and the function raises a NetworkXError.
+
+    See also
+    --------
+    :meth:`maximum_flow`
+    :meth:`maximum_flow_value`
+    :meth:`minimum_cut_value`
+    :meth:`edmonds_karp`
+    :meth:`preflow_push`
+    :meth:`shortest_augmenting_path`
+
+    Notes
+    -----
+    The function used in the flow_func parameter has to return a residual
+    network that follows NetworkX conventions:
+
+    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']`. 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.
+
+    Specific algorithms may store extra data in :samp:`R`.
+
+    The function should supports an optional boolean parameter value_only. When
+    True, it can optionally terminate the algorithm as soon as the maximum flow
+    value and the minimum cut can be determined.
+
+    Examples
+    --------
+    >>> 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)
+
+    minimum_cut computes both the value of the
+    minimum cut and the node partition:
+
+    >>> cut_value, partition = nx.minimum_cut(G, "x", "y")
+    >>> reachable, non_reachable = partition
+
+    'partition' here is a tuple with the two sets of nodes that define
+    the minimum cut. You can compute the cut set of edges that induce
+    the minimum cut as follows:
+
+    >>> cutset = set()
+    >>> for u, nbrs in ((n, G[n]) for n in reachable):
+    ...     cutset.update((u, v) for v in nbrs if v in non_reachable)
+    >>> print(sorted(cutset))
+    [('c', 'y'), ('x', 'b')]
+    >>> cut_value == sum(G.edges[u, v]["capacity"] for (u, v) in cutset)
+    True
+
+    You can also use alternative algorithms for computing the
+    minimum cut by using the flow_func parameter.
+
+    >>> from networkx.algorithms.flow import shortest_augmenting_path
+    >>> cut_value == nx.minimum_cut(G, "x", "y", flow_func=shortest_augmenting_path)[0]
+    True
+
+    """
+    if flow_func is None:
+        if kwargs:
+            raise nx.NetworkXError(
+                "You have to explicitly set a flow_func if"
+                " you need to pass parameters via kwargs."
+            )
+        flow_func = default_flow_func
+
+    if not callable(flow_func):
+        raise nx.NetworkXError("flow_func has to be callable.")
+
+    if kwargs.get("cutoff") is not None and flow_func is preflow_push:
+        raise nx.NetworkXError("cutoff should not be specified.")
+
+    R = flow_func(flowG, _s, _t, capacity=capacity, value_only=True, **kwargs)
+    # Remove saturated edges from the residual network
+    cutset = [(u, v, d) for u, v, d in R.edges(data=True) if d["flow"] == d["capacity"]]
+    R.remove_edges_from(cutset)
+
+    # Then, reachable and non reachable nodes from source in the
+    # residual network form the node partition that defines
+    # the minimum cut.
+    non_reachable = set(dict(nx.shortest_path_length(R, target=_t)))
+    partition = (set(flowG) - non_reachable, non_reachable)
+    # Finally add again cutset edges to the residual network to make
+    # sure that it is reusable.
+    if cutset is not None:
+        R.add_edges_from(cutset)
+    return (R.graph["flow_value"], partition)
+
+
+@nx._dispatchable(graphs="flowG", edge_attrs={"capacity": float("inf")})
+def minimum_cut_value(flowG, _s, _t, capacity="capacity", flow_func=None, **kwargs):
+    """Compute the value of a minimum (s, t)-cut.
+
+    Use the max-flow min-cut theorem, i.e., the capacity of a minimum
+    capacity cut is equal to the flow value of a maximum flow.
+
+    Parameters
+    ----------
+    flowG : 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'.
+
+    flow_func : function
+        A function for computing the maximum flow among a pair of nodes
+        in a capacitated graph. The function has to accept at least three
+        parameters: a Graph or Digraph, a source node, and a target node.
+        And return a residual network that follows NetworkX conventions
+        (see Notes). If flow_func is None, the default maximum
+        flow function (:meth:`preflow_push`) is used. See below for
+        alternative algorithms. The choice of the default function may change
+        from version to version and should not be relied on. Default value:
+        None.
+
+    kwargs : Any other keyword parameter is passed to the function that
+        computes the maximum flow.
+
+    Returns
+    -------
+    cut_value : integer, float
+        Value of the minimum cut.
+
+    Raises
+    ------
+    NetworkXUnbounded
+        If the graph has a path of infinite capacity, all cuts have
+        infinite capacity and the function raises a NetworkXError.
+
+    See also
+    --------
+    :meth:`maximum_flow`
+    :meth:`maximum_flow_value`
+    :meth:`minimum_cut`
+    :meth:`edmonds_karp`
+    :meth:`preflow_push`
+    :meth:`shortest_augmenting_path`
+
+    Notes
+    -----
+    The function used in the flow_func parameter has to return a residual
+    network that follows NetworkX conventions:
+
+    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']`. 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.
+
+    Specific algorithms may store extra data in :samp:`R`.
+
+    The function should supports an optional boolean parameter value_only. When
+    True, it can optionally terminate the algorithm as soon as the maximum flow
+    value and the minimum cut can be determined.
+
+    Examples
+    --------
+    >>> 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)
+
+    minimum_cut_value computes only the value of the
+    minimum cut:
+
+    >>> cut_value = nx.minimum_cut_value(G, "x", "y")
+    >>> cut_value
+    3.0
+
+    You can also use alternative algorithms for computing the
+    minimum cut by using the flow_func parameter.
+
+    >>> from networkx.algorithms.flow import shortest_augmenting_path
+    >>> cut_value == nx.minimum_cut_value(G, "x", "y", flow_func=shortest_augmenting_path)
+    True
+
+    """
+    if flow_func is None:
+        if kwargs:
+            raise nx.NetworkXError(
+                "You have to explicitly set a flow_func if"
+                " you need to pass parameters via kwargs."
+            )
+        flow_func = default_flow_func
+
+    if not callable(flow_func):
+        raise nx.NetworkXError("flow_func has to be callable.")
+
+    if kwargs.get("cutoff") is not None and flow_func is preflow_push:
+        raise nx.NetworkXError("cutoff should not be specified.")
+
+    R = flow_func(flowG, _s, _t, capacity=capacity, value_only=True, **kwargs)
+
+    return R.graph["flow_value"]

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/mincost.py

@@ -0,0 +1,356 @@
+"""
+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._dispatchable(
+    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._dispatchable(
+    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)
+    >>> flowDict
+    {'a': {'b': 4, 'c': 1}, 'd': {}, 'b': {'d': 4}, 'c': {'d': 1}}
+    """
+    return nx.network_simplex(G, demand=demand, capacity=capacity, weight=weight)[1]
+
+
+@nx._dispatchable(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).
+
+    Examples
+    --------
+    >>> 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)
+    >>> flowDict
+    {'a': {'b': 4, 'c': 1}, 'd': {}, 'b': {'d': 4}, 'c': {'d': 1}}
+    >>> nx.cost_of_flow(G, flowDict)
+    24
+    """
+    return sum((flowDict[u][v] * d.get(weight, 0) for u, v, d in G.edges(data=True)))
+
+
+@nx._dispatchable(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)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/networksimplex.py

@@ -0,0 +1,666 @@
+"""
+Minimum cost flow algorithms on directed connected graphs.
+"""
+
+__all__ = ["network_simplex"]
+
+from itertools import chain, islice, repeat
+from math import ceil, sqrt
+
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+
+class _DataEssentialsAndFunctions:
+    def __init__(
+        self, G, multigraph, demand="demand", capacity="capacity", weight="weight"
+    ):
+        # Number all nodes and edges and hereafter reference them using ONLY their numbers
+        self.node_list = list(G)  # nodes
+        self.node_indices = {u: i for i, u in enumerate(self.node_list)}  # node indices
+        self.node_demands = [
+            G.nodes[u].get(demand, 0) for u in self.node_list
+        ]  # node demands
+
+        self.edge_sources = []  # edge sources
+        self.edge_targets = []  # edge targets
+        if multigraph:
+            self.edge_keys = []  # edge keys
+        self.edge_indices = {}  # edge indices
+        self.edge_capacities = []  # edge capacities
+        self.edge_weights = []  # edge weights
+
+        if not multigraph:
+            edges = G.edges(data=True)
+        else:
+            edges = G.edges(data=True, keys=True)
+
+        inf = float("inf")
+        edges = (e for e in edges if e[0] != e[1] and e[-1].get(capacity, inf) != 0)
+        for i, e in enumerate(edges):
+            self.edge_sources.append(self.node_indices[e[0]])
+            self.edge_targets.append(self.node_indices[e[1]])
+            if multigraph:
+                self.edge_keys.append(e[2])
+            self.edge_indices[e[:-1]] = i
+            self.edge_capacities.append(e[-1].get(capacity, inf))
+            self.edge_weights.append(e[-1].get(weight, 0))
+
+        # spanning tree specific data to be initialized
+
+        self.edge_count = None  # number of edges
+        self.edge_flow = None  # edge flows
+        self.node_potentials = None  # node potentials
+        self.parent = None  # parent nodes
+        self.parent_edge = None  # edges to parents
+        self.subtree_size = None  # subtree sizes
+        self.next_node_dft = None  # next nodes in depth-first thread
+        self.prev_node_dft = None  # previous nodes in depth-first thread
+        self.last_descendent_dft = None  # last descendants in depth-first thread
+        self._spanning_tree_initialized = (
+            False  # False until initialize_spanning_tree() is called
+        )
+
+    def initialize_spanning_tree(self, n, faux_inf):
+        self.edge_count = len(self.edge_indices)  # number of edges
+        self.edge_flow = list(
+            chain(repeat(0, self.edge_count), (abs(d) for d in self.node_demands))
+        )  # edge flows
+        self.node_potentials = [
+            faux_inf if d <= 0 else -faux_inf for d in self.node_demands
+        ]  # node potentials
+        self.parent = list(chain(repeat(-1, n), [None]))  # parent nodes
+        self.parent_edge = list(
+            range(self.edge_count, self.edge_count + n)
+        )  # edges to parents
+        self.subtree_size = list(chain(repeat(1, n), [n + 1]))  # subtree sizes
+        self.next_node_dft = list(
+            chain(range(1, n), [-1, 0])
+        )  # next nodes in depth-first thread
+        self.prev_node_dft = list(range(-1, n))  # previous nodes in depth-first thread
+        self.last_descendent_dft = list(
+            chain(range(n), [n - 1])
+        )  # last descendants in depth-first thread
+        self._spanning_tree_initialized = True  # True only if all the assignments pass
+
+    def find_apex(self, p, q):
+        """
+        Find the lowest common ancestor of nodes p and q in the spanning tree.
+        """
+        size_p = self.subtree_size[p]
+        size_q = self.subtree_size[q]
+        while True:
+            while size_p < size_q:
+                p = self.parent[p]
+                size_p = self.subtree_size[p]
+            while size_p > size_q:
+                q = self.parent[q]
+                size_q = self.subtree_size[q]
+            if size_p == size_q:
+                if p != q:
+                    p = self.parent[p]
+                    size_p = self.subtree_size[p]
+                    q = self.parent[q]
+                    size_q = self.subtree_size[q]
+                else:
+                    return p
+
+    def trace_path(self, p, w):
+        """
+        Returns the nodes and edges on the path from node p to its ancestor w.
+        """
+        Wn = [p]
+        We = []
+        while p != w:
+            We.append(self.parent_edge[p])
+            p = self.parent[p]
+            Wn.append(p)
+        return Wn, We
+
+    def find_cycle(self, i, p, q):
+        """
+        Returns the nodes and edges on the cycle containing edge i == (p, q)
+        when the latter is added to the spanning tree.
+
+        The cycle is oriented in the direction from p to q.
+        """
+        w = self.find_apex(p, q)
+        Wn, We = self.trace_path(p, w)
+        Wn.reverse()
+        We.reverse()
+        if We != [i]:
+            We.append(i)
+        WnR, WeR = self.trace_path(q, w)
+        del WnR[-1]
+        Wn += WnR
+        We += WeR
+        return Wn, We
+
+    def augment_flow(self, Wn, We, f):
+        """
+        Augment f units of flow along a cycle represented by Wn and We.
+        """
+        for i, p in zip(We, Wn):
+            if self.edge_sources[i] == p:
+                self.edge_flow[i] += f
+            else:
+                self.edge_flow[i] -= f
+
+    def trace_subtree(self, p):
+        """
+        Yield the nodes in the subtree rooted at a node p.
+        """
+        yield p
+        l = self.last_descendent_dft[p]
+        while p != l:
+            p = self.next_node_dft[p]
+            yield p
+
+    def remove_edge(self, s, t):
+        """
+        Remove an edge (s, t) where parent[t] == s from the spanning tree.
+        """
+        size_t = self.subtree_size[t]
+        prev_t = self.prev_node_dft[t]
+        last_t = self.last_descendent_dft[t]
+        next_last_t = self.next_node_dft[last_t]
+        # Remove (s, t).
+        self.parent[t] = None
+        self.parent_edge[t] = None
+        # Remove the subtree rooted at t from the depth-first thread.
+        self.next_node_dft[prev_t] = next_last_t
+        self.prev_node_dft[next_last_t] = prev_t
+        self.next_node_dft[last_t] = t
+        self.prev_node_dft[t] = last_t
+        # Update the subtree sizes and last descendants of the (old) ancestors
+        # of t.
+        while s is not None:
+            self.subtree_size[s] -= size_t
+            if self.last_descendent_dft[s] == last_t:
+                self.last_descendent_dft[s] = prev_t
+            s = self.parent[s]
+
+    def make_root(self, q):
+        """
+        Make a node q the root of its containing subtree.
+        """
+        ancestors = []
+        while q is not None:
+            ancestors.append(q)
+            q = self.parent[q]
+        ancestors.reverse()
+        for p, q in zip(ancestors, islice(ancestors, 1, None)):
+            size_p = self.subtree_size[p]
+            last_p = self.last_descendent_dft[p]
+            prev_q = self.prev_node_dft[q]
+            last_q = self.last_descendent_dft[q]
+            next_last_q = self.next_node_dft[last_q]
+            # Make p a child of q.
+            self.parent[p] = q
+            self.parent[q] = None
+            self.parent_edge[p] = self.parent_edge[q]
+            self.parent_edge[q] = None
+            self.subtree_size[p] = size_p - self.subtree_size[q]
+            self.subtree_size[q] = size_p
+            # Remove the subtree rooted at q from the depth-first thread.
+            self.next_node_dft[prev_q] = next_last_q
+            self.prev_node_dft[next_last_q] = prev_q
+            self.next_node_dft[last_q] = q
+            self.prev_node_dft[q] = last_q
+            if last_p == last_q:
+                self.last_descendent_dft[p] = prev_q
+                last_p = prev_q
+            # Add the remaining parts of the subtree rooted at p as a subtree
+            # of q in the depth-first thread.
+            self.prev_node_dft[p] = last_q
+            self.next_node_dft[last_q] = p
+            self.next_node_dft[last_p] = q
+            self.prev_node_dft[q] = last_p
+            self.last_descendent_dft[q] = last_p
+
+    def add_edge(self, i, p, q):
+        """
+        Add an edge (p, q) to the spanning tree where q is the root of a subtree.
+        """
+        last_p = self.last_descendent_dft[p]
+        next_last_p = self.next_node_dft[last_p]
+        size_q = self.subtree_size[q]
+        last_q = self.last_descendent_dft[q]
+        # Make q a child of p.
+        self.parent[q] = p
+        self.parent_edge[q] = i
+        # Insert the subtree rooted at q into the depth-first thread.
+        self.next_node_dft[last_p] = q
+        self.prev_node_dft[q] = last_p
+        self.prev_node_dft[next_last_p] = last_q
+        self.next_node_dft[last_q] = next_last_p
+        # Update the subtree sizes and last descendants of the (new) ancestors
+        # of q.
+        while p is not None:
+            self.subtree_size[p] += size_q
+            if self.last_descendent_dft[p] == last_p:
+                self.last_descendent_dft[p] = last_q
+            p = self.parent[p]
+
+    def update_potentials(self, i, p, q):
+        """
+        Update the potentials of the nodes in the subtree rooted at a node
+        q connected to its parent p by an edge i.
+        """
+        if q == self.edge_targets[i]:
+            d = self.node_potentials[p] - self.edge_weights[i] - self.node_potentials[q]
+        else:
+            d = self.node_potentials[p] + self.edge_weights[i] - self.node_potentials[q]
+        for q in self.trace_subtree(q):
+            self.node_potentials[q] += d
+
+    def reduced_cost(self, i):
+        """Returns the reduced cost of an edge i."""
+        c = (
+            self.edge_weights[i]
+            - self.node_potentials[self.edge_sources[i]]
+            + self.node_potentials[self.edge_targets[i]]
+        )
+        return c if self.edge_flow[i] == 0 else -c
+
+    def find_entering_edges(self):
+        """Yield entering edges until none can be found."""
+        if self.edge_count == 0:
+            return
+
+        # Entering edges are found by combining Dantzig's rule and Bland's
+        # rule. The edges are cyclically grouped into blocks of size B. Within
+        # each block, Dantzig's rule is applied to find an entering edge. The
+        # blocks to search is determined following Bland's rule.
+        B = int(ceil(sqrt(self.edge_count)))  # pivot block size
+        M = (self.edge_count + B - 1) // B  # number of blocks needed to cover all edges
+        m = 0  # number of consecutive blocks without eligible
+        # entering edges
+        f = 0  # first edge in block
+        while m < M:
+            # Determine the next block of edges.
+            l = f + B
+            if l <= self.edge_count:
+                edges = range(f, l)
+            else:
+                l -= self.edge_count
+                edges = chain(range(f, self.edge_count), range(l))
+            f = l
+            # Find the first edge with the lowest reduced cost.
+            i = min(edges, key=self.reduced_cost)
+            c = self.reduced_cost(i)
+            if c >= 0:
+                # No entering edge found in the current block.
+                m += 1
+            else:
+                # Entering edge found.
+                if self.edge_flow[i] == 0:
+                    p = self.edge_sources[i]
+                    q = self.edge_targets[i]
+                else:
+                    p = self.edge_targets[i]
+                    q = self.edge_sources[i]
+                yield i, p, q
+                m = 0
+        # All edges have nonnegative reduced costs. The current flow is
+        # optimal.
+
+    def residual_capacity(self, i, p):
+        """Returns the residual capacity of an edge i in the direction away
+        from its endpoint p.
+        """
+        return (
+            self.edge_capacities[i] - self.edge_flow[i]
+            if self.edge_sources[i] == p
+            else self.edge_flow[i]
+        )
+
+    def find_leaving_edge(self, Wn, We):
+        """Returns the leaving edge in a cycle represented by Wn and We."""
+        j, s = min(
+            zip(reversed(We), reversed(Wn)),
+            key=lambda i_p: self.residual_capacity(*i_p),
+        )
+        t = self.edge_targets[j] if self.edge_sources[j] == s else self.edge_sources[j]
+        return j, s, t
+
+
+@not_implemented_for("undirected")
+@nx._dispatchable(
+    node_attrs="demand", edge_attrs={"capacity": float("inf"), "weight": 0}
+)
+def network_simplex(G, demand="demand", capacity="capacity", weight="weight"):
+    r"""Find a minimum cost flow satisfying all demands in digraph G.
+
+    This is a primal network simplex algorithm that uses the leaving
+    arc rule to prevent cycling.
+
+    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.
+
+    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.
+
+    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).
+
+    See also
+    --------
+    cost_of_flow, max_flow_min_cost, min_cost_flow, min_cost_flow_cost
+
+    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, flowDict = nx.network_simplex(G)
+    >>> flowCost
+    24
+    >>> flowDict
+    {'a': {'b': 4, 'c': 1}, 'd': {}, 'b': {'d': 4}, 'c': {'d': 1}}
+
+    The mincost flow algorithm can also be used to solve shortest path
+    problems. To find the shortest path between two nodes u and v,
+    give all edges an infinite capacity, give node u a demand of -1 and
+    node v a demand a 1. Then run the network simplex. The value of a
+    min cost flow will be the distance between u and v and edges
+    carrying positive flow will indicate the path.
+
+    >>> G = nx.DiGraph()
+    >>> G.add_weighted_edges_from(
+    ...     [
+    ...         ("s", "u", 10),
+    ...         ("s", "x", 5),
+    ...         ("u", "v", 1),
+    ...         ("u", "x", 2),
+    ...         ("v", "y", 1),
+    ...         ("x", "u", 3),
+    ...         ("x", "v", 5),
+    ...         ("x", "y", 2),
+    ...         ("y", "s", 7),
+    ...         ("y", "v", 6),
+    ...     ]
+    ... )
+    >>> G.add_node("s", demand=-1)
+    >>> G.add_node("v", demand=1)
+    >>> flowCost, flowDict = nx.network_simplex(G)
+    >>> flowCost == nx.shortest_path_length(G, "s", "v", weight="weight")
+    True
+    >>> sorted([(u, v) for u in flowDict for v in flowDict[u] if flowDict[u][v] > 0])
+    [('s', 'x'), ('u', 'v'), ('x', 'u')]
+    >>> nx.shortest_path(G, "s", "v", weight="weight")
+    ['s', 'x', 'u', 'v']
+
+    It is possible to change the name of the attributes used for the
+    algorithm.
+
+    >>> G = nx.DiGraph()
+    >>> G.add_node("p", spam=-4)
+    >>> G.add_node("q", spam=2)
+    >>> G.add_node("a", spam=-2)
+    >>> G.add_node("d", spam=-1)
+    >>> G.add_node("t", spam=2)
+    >>> G.add_node("w", spam=3)
+    >>> G.add_edge("p", "q", cost=7, vacancies=5)
+    >>> G.add_edge("p", "a", cost=1, vacancies=4)
+    >>> G.add_edge("q", "d", cost=2, vacancies=3)
+    >>> G.add_edge("t", "q", cost=1, vacancies=2)
+    >>> G.add_edge("a", "t", cost=2, vacancies=4)
+    >>> G.add_edge("d", "w", cost=3, vacancies=4)
+    >>> G.add_edge("t", "w", cost=4, vacancies=1)
+    >>> flowCost, flowDict = nx.network_simplex(
+    ...     G, demand="spam", capacity="vacancies", weight="cost"
+    ... )
+    >>> flowCost
+    37
+    >>> flowDict
+    {'p': {'q': 2, 'a': 2}, 'q': {'d': 1}, 'a': {'t': 4}, 'd': {'w': 2}, 't': {'q': 1, 'w': 1}, 'w': {}}
+
+    References
+    ----------
+    .. [1] Z. Kiraly, P. Kovacs.
+           Efficient implementation of minimum-cost flow algorithms.
+           Acta Universitatis Sapientiae, Informatica 4(1):67--118. 2012.
+    .. [2] R. Barr, F. Glover, D. Klingman.
+           Enhancement of spanning tree labeling procedures for network
+           optimization.
+           INFOR 17(1):16--34. 1979.
+    """
+    ###########################################################################
+    # Problem essentials extraction and sanity check
+    ###########################################################################
+
+    if len(G) == 0:
+        raise nx.NetworkXError("graph has no nodes")
+
+    multigraph = G.is_multigraph()
+
+    # extracting data essential to problem
+    DEAF = _DataEssentialsAndFunctions(
+        G, multigraph, demand=demand, capacity=capacity, weight=weight
+    )
+
+    ###########################################################################
+    # Quick Error Detection
+    ###########################################################################
+
+    inf = float("inf")
+    for u, d in zip(DEAF.node_list, DEAF.node_demands):
+        if abs(d) == inf:
+            raise nx.NetworkXError(f"node {u!r} has infinite demand")
+    for e, w in zip(DEAF.edge_indices, DEAF.edge_weights):
+        if abs(w) == inf:
+            raise nx.NetworkXError(f"edge {e!r} has infinite weight")
+    if not multigraph:
+        edges = nx.selfloop_edges(G, data=True)
+    else:
+        edges = nx.selfloop_edges(G, data=True, keys=True)
+    for e in edges:
+        if abs(e[-1].get(weight, 0)) == inf:
+            raise nx.NetworkXError(f"edge {e[:-1]!r} has infinite weight")
+
+    ###########################################################################
+    # Quick Infeasibility Detection
+    ###########################################################################
+
+    if sum(DEAF.node_demands) != 0:
+        raise nx.NetworkXUnfeasible("total node demand is not zero")
+    for e, c in zip(DEAF.edge_indices, DEAF.edge_capacities):
+        if c < 0:
+            raise nx.NetworkXUnfeasible(f"edge {e!r} has negative capacity")
+    if not multigraph:
+        edges = nx.selfloop_edges(G, data=True)
+    else:
+        edges = nx.selfloop_edges(G, data=True, keys=True)
+    for e in edges:
+        if e[-1].get(capacity, inf) < 0:
+            raise nx.NetworkXUnfeasible(f"edge {e[:-1]!r} has negative capacity")
+
+    ###########################################################################
+    # Initialization
+    ###########################################################################
+
+    # Add a dummy node -1 and connect all existing nodes to it with infinite-
+    # capacity dummy edges. Node -1 will serve as the root of the
+    # spanning tree of the network simplex method. The new edges will used to
+    # trivially satisfy the node demands and create an initial strongly
+    # feasible spanning tree.
+    for i, d in enumerate(DEAF.node_demands):
+        # Must be greater-than here. Zero-demand nodes must have
+        # edges pointing towards the root to ensure strong feasibility.
+        if d > 0:
+            DEAF.edge_sources.append(-1)
+            DEAF.edge_targets.append(i)
+        else:
+            DEAF.edge_sources.append(i)
+            DEAF.edge_targets.append(-1)
+    faux_inf = (
+        3
+        * max(
+            chain(
+                [
+                    sum(c for c in DEAF.edge_capacities if c < inf),
+                    sum(abs(w) for w in DEAF.edge_weights),
+                ],
+                (abs(d) for d in DEAF.node_demands),
+            )
+        )
+        or 1
+    )
+
+    n = len(DEAF.node_list)  # number of nodes
+    DEAF.edge_weights.extend(repeat(faux_inf, n))
+    DEAF.edge_capacities.extend(repeat(faux_inf, n))
+
+    # Construct the initial spanning tree.
+    DEAF.initialize_spanning_tree(n, faux_inf)
+
+    ###########################################################################
+    # Pivot loop
+    ###########################################################################
+
+    for i, p, q in DEAF.find_entering_edges():
+        Wn, We = DEAF.find_cycle(i, p, q)
+        j, s, t = DEAF.find_leaving_edge(Wn, We)
+        DEAF.augment_flow(Wn, We, DEAF.residual_capacity(j, s))
+        # Do nothing more if the entering edge is the same as the leaving edge.
+        if i != j:
+            if DEAF.parent[t] != s:
+                # Ensure that s is the parent of t.
+                s, t = t, s
+            if We.index(i) > We.index(j):
+                # Ensure that q is in the subtree rooted at t.
+                p, q = q, p
+            DEAF.remove_edge(s, t)
+            DEAF.make_root(q)
+            DEAF.add_edge(i, p, q)
+            DEAF.update_potentials(i, p, q)
+
+    ###########################################################################
+    # Infeasibility and unboundedness detection
+    ###########################################################################
+
+    if any(DEAF.edge_flow[i] != 0 for i in range(-n, 0)):
+        raise nx.NetworkXUnfeasible("no flow satisfies all node demands")
+
+    if any(DEAF.edge_flow[i] * 2 >= faux_inf for i in range(DEAF.edge_count)) or any(
+        e[-1].get(capacity, inf) == inf and e[-1].get(weight, 0) < 0
+        for e in nx.selfloop_edges(G, data=True)
+    ):
+        raise nx.NetworkXUnbounded("negative cycle with infinite capacity found")
+
+    ###########################################################################
+    # Flow cost calculation and flow dict construction
+    ###########################################################################
+
+    del DEAF.edge_flow[DEAF.edge_count :]
+    flow_cost = sum(w * x for w, x in zip(DEAF.edge_weights, DEAF.edge_flow))
+    flow_dict = {n: {} for n in DEAF.node_list}
+
+    def add_entry(e):
+        """Add a flow dict entry."""
+        d = flow_dict[e[0]]
+        for k in e[1:-2]:
+            try:
+                d = d[k]
+            except KeyError:
+                t = {}
+                d[k] = t
+                d = t
+        d[e[-2]] = e[-1]
+
+    DEAF.edge_sources = (
+        DEAF.node_list[s] for s in DEAF.edge_sources
+    )  # Use original nodes.
+    DEAF.edge_targets = (
+        DEAF.node_list[t] for t in DEAF.edge_targets
+    )  # Use original nodes.
+    if not multigraph:
+        for e in zip(DEAF.edge_sources, DEAF.edge_targets, DEAF.edge_flow):
+            add_entry(e)
+        edges = G.edges(data=True)
+    else:
+        for e in zip(
+            DEAF.edge_sources, DEAF.edge_targets, DEAF.edge_keys, DEAF.edge_flow
+        ):
+            add_entry(e)
+        edges = G.edges(data=True, keys=True)
+    for e in edges:
+        if e[0] != e[1]:
+            if e[-1].get(capacity, inf) == 0:
+                add_entry(e[:-1] + (0,))
+        else:
+            w = e[-1].get(weight, 0)
+            if w >= 0:
+                add_entry(e[:-1] + (0,))
+            else:
+                c = e[-1][capacity]
+                flow_cost += w * c
+                add_entry(e[:-1] + (c,))
+
+    return flow_cost, flow_dict

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/preflowpush.py

@@ -0,0 +1,425 @@
+"""
+Highest-label preflow-push algorithm for maximum flow problems.
+"""
+
+from collections import deque
+from itertools import islice
+
+import networkx as nx
+
+from ...utils import arbitrary_element
+from .utils import (
+    CurrentEdge,
+    GlobalRelabelThreshold,
+    Level,
+    build_residual_network,
+    detect_unboundedness,
+)
+
+__all__ = ["preflow_push"]
+
+
+def preflow_push_impl(G, s, t, capacity, residual, global_relabel_freq, value_only):
+    """Implementation of the highest-label preflow-push 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 global_relabel_freq is None:
+        global_relabel_freq = 0
+    if global_relabel_freq < 0:
+        raise nx.NetworkXError("global_relabel_freq must be nonnegative.")
+
+    if residual is None:
+        R = build_residual_network(G, capacity)
+    else:
+        R = residual
+
+    detect_unboundedness(R, s, t)
+
+    R_nodes = R.nodes
+    R_pred = R.pred
+    R_succ = R.succ
+
+    # Initialize/reset the residual network.
+    for u in R:
+        R_nodes[u]["excess"] = 0
+        for e in R_succ[u].values():
+            e["flow"] = 0
+
+    def reverse_bfs(src):
+        """Perform a reverse breadth-first search from src in the residual
+        network.
+        """
+        heights = {src: 0}
+        q = deque([(src, 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))
+        return heights
+
+    # Initialize heights of the nodes.
+    heights = reverse_bfs(t)
+
+    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(R)
+    # max_height represents the height of the highest level below level n with
+    # at least one active node.
+    max_height = max(heights[u] for u in heights if u != s)
+    heights[s] = n
+
+    grt = GlobalRelabelThreshold(n, R.size(), global_relabel_freq)
+
+    # 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 + 1
+        R_nodes[u]["curr_edge"] = CurrentEdge(R_succ[u])
+
+    def push(u, v, flow):
+        """Push flow units of flow from u to v."""
+        R_succ[u][v]["flow"] += flow
+        R_succ[v][u]["flow"] -= flow
+        R_nodes[u]["excess"] -= flow
+        R_nodes[v]["excess"] += flow
+
+    # The maximum flow must be nonzero now. Initialize the preflow by
+    # saturating all edges emanating from s.
+    for u, attr in R_succ[s].items():
+        flow = attr["capacity"]
+        if flow > 0:
+            push(s, u, flow)
+
+    # Partition nodes into levels.
+    levels = [Level() for i in range(2 * n)]
+    for u in R:
+        if u != s and u != t:
+            level = levels[R_nodes[u]["height"]]
+            if R_nodes[u]["excess"] > 0:
+                level.active.add(u)
+            else:
+                level.inactive.add(u)
+
+    def activate(v):
+        """Move a node from the inactive set to the active set of its level."""
+        if v != s and v != t:
+            level = levels[R_nodes[v]["height"]]
+            if v in level.inactive:
+                level.inactive.remove(v)
+                level.active.add(v)
+
+    def relabel(u):
+        """Relabel a node to create an admissible edge."""
+        grt.add_work(len(R_succ[u]))
+        return (
+            min(
+                R_nodes[v]["height"]
+                for v, attr in R_succ[u].items()
+                if attr["flow"] < attr["capacity"]
+            )
+            + 1
+        )
+
+    def discharge(u, is_phase1):
+        """Discharge a node until it becomes inactive or, during phase 1 (see
+        below), its height reaches at least n. The node is known to have the
+        largest height among active nodes.
+        """
+        height = R_nodes[u]["height"]
+        curr_edge = R_nodes[u]["curr_edge"]
+        # next_height represents the next height to examine after discharging
+        # the current node. During phase 1, it is capped to below n.
+        next_height = height
+        levels[height].active.remove(u)
+        while True:
+            v, attr = curr_edge.get()
+            if height == R_nodes[v]["height"] + 1 and attr["flow"] < attr["capacity"]:
+                flow = min(R_nodes[u]["excess"], attr["capacity"] - attr["flow"])
+                push(u, v, flow)
+                activate(v)
+                if R_nodes[u]["excess"] == 0:
+                    # The node has become inactive.
+                    levels[height].inactive.add(u)
+                    break
+            try:
+                curr_edge.move_to_next()
+            except StopIteration:
+                # We have run off the end of the adjacency list, and there can
+                # be no more admissible edges. Relabel the node to create one.
+                height = relabel(u)
+                if is_phase1 and height >= n - 1:
+                    # Although the node is still active, with a height at least
+                    # n - 1, it is now known to be on the s side of the minimum
+                    # s-t cut. Stop processing it until phase 2.
+                    levels[height].active.add(u)
+                    break
+                # The first relabel operation after global relabeling may not
+                # increase the height of the node since the 'current edge' data
+                # structure is not rewound. Use height instead of (height - 1)
+                # in case other active nodes at the same level are missed.
+                next_height = height
+        R_nodes[u]["height"] = height
+        return next_height
+
+    def gap_heuristic(height):
+        """Apply the gap heuristic."""
+        # Move all nodes at levels (height + 1) to max_height to level n + 1.
+        for level in islice(levels, height + 1, max_height + 1):
+            for u in level.active:
+                R_nodes[u]["height"] = n + 1
+            for u in level.inactive:
+                R_nodes[u]["height"] = n + 1
+            levels[n + 1].active.update(level.active)
+            level.active.clear()
+            levels[n + 1].inactive.update(level.inactive)
+            level.inactive.clear()
+
+    def global_relabel(from_sink):
+        """Apply the global relabeling heuristic."""
+        src = t if from_sink else s
+        heights = reverse_bfs(src)
+        if not from_sink:
+            # s must be reachable from t. Remove t explicitly.
+            del heights[t]
+        max_height = max(heights.values())
+        if from_sink:
+            # Also mark nodes from which t is unreachable for relabeling. This
+            # serves the same purpose as the gap heuristic.
+            for u in R:
+                if u not in heights and R_nodes[u]["height"] < n:
+                    heights[u] = n + 1
+        else:
+            # Shift the computed heights because the height of s is n.
+            for u in heights:
+                heights[u] += n
+            max_height += n
+        del heights[src]
+        for u, new_height in heights.items():
+            old_height = R_nodes[u]["height"]
+            if new_height != old_height:
+                if u in levels[old_height].active:
+                    levels[old_height].active.remove(u)
+                    levels[new_height].active.add(u)
+                else:
+                    levels[old_height].inactive.remove(u)
+                    levels[new_height].inactive.add(u)
+                R_nodes[u]["height"] = new_height
+        return max_height
+
+    # Phase 1: Find the maximum preflow by pushing as much flow as possible to
+    # t.
+
+    height = max_height
+    while height > 0:
+        # Discharge active nodes in the current level.
+        while True:
+            level = levels[height]
+            if not level.active:
+                # All active nodes in the current level have been discharged.
+                # Move to the next lower level.
+                height -= 1
+                break
+            # Record the old height and level for the gap heuristic.
+            old_height = height
+            old_level = level
+            u = arbitrary_element(level.active)
+            height = discharge(u, True)
+            if grt.is_reached():
+                # Global relabeling heuristic: Recompute the exact heights of
+                # all nodes.
+                height = global_relabel(True)
+                max_height = height
+                grt.clear_work()
+            elif not old_level.active and not old_level.inactive:
+                # Gap heuristic: If the level at old_height is empty (a 'gap'),
+                # a minimum cut has been identified. All nodes with heights
+                # above old_height can have their heights set to n + 1 and not
+                # be further processed before a maximum preflow is found.
+                gap_heuristic(old_height)
+                height = old_height - 1
+                max_height = height
+            else:
+                # Update the height of the highest level with at least one
+                # active node.
+                max_height = max(max_height, height)
+
+    # A maximum preflow has been found. The excess at t is the maximum flow
+    # value.
+    if value_only:
+        R.graph["flow_value"] = R_nodes[t]["excess"]
+        return R
+
+    # Phase 2: Convert the maximum preflow into a maximum flow by returning the
+    # excess to s.
+
+    # Relabel all nodes so that they have accurate heights.
+    height = global_relabel(False)
+    grt.clear_work()
+
+    # Continue to discharge the active nodes.
+    while height > n:
+        # Discharge active nodes in the current level.
+        while True:
+            level = levels[height]
+            if not level.active:
+                # All active nodes in the current level have been discharged.
+                # Move to the next lower level.
+                height -= 1
+                break
+            u = arbitrary_element(level.active)
+            height = discharge(u, False)
+            if grt.is_reached():
+                # Global relabeling heuristic.
+                height = global_relabel(False)
+                grt.clear_work()
+
+    R.graph["flow_value"] = R_nodes[t]["excess"]
+    return R
+
+
+@nx._dispatchable(edge_attrs={"capacity": float("inf")}, returns_graph=True)
+def preflow_push(
+    G, s, t, capacity="capacity", residual=None, global_relabel_freq=1, value_only=False
+):
+    r"""Find a maximum single-commodity flow using the highest-label
+    preflow-push 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 $O(n^2 \sqrt{m})$ 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.
+
+    global_relabel_freq : integer, float
+        Relative frequency of applying the global relabeling heuristic to speed
+        up the algorithm. If it is None, the heuristic is disabled. Default
+        value: 1.
+
+    value_only : bool
+        If False, compute a maximum flow; otherwise, compute a maximum preflow
+        which is enough for computing the maximum flow value. Default value:
+        False.
+
+    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:`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 node :samp:`u` in :samp:`R`,
+    :samp:`R.nodes[u]['excess']` represents the difference between flow into
+    :samp:`u` and flow out of :samp:`u`.
+
+    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']`. 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 preflow_push
+
+    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 = preflow_push(G, "x", "y")
+    >>> flow_value = nx.maximum_flow_value(G, "x", "y")
+    >>> flow_value == R.graph["flow_value"]
+    True
+    >>> # preflow_push also stores the maximum flow value
+    >>> # in the excess attribute of the sink node t
+    >>> flow_value == R.nodes["y"]["excess"]
+    True
+    >>> # For some problems, you might only want to compute a
+    >>> # maximum preflow.
+    >>> R = preflow_push(G, "x", "y", value_only=True)
+    >>> flow_value == R.graph["flow_value"]
+    True
+    >>> flow_value == R.nodes["y"]["excess"]
+    True
+
+    """
+    R = preflow_push_impl(G, s, t, capacity, residual, global_relabel_freq, value_only)
+    R.graph["algorithm"] = "preflow_push"
+    nx._clear_cache(R)
+    return R

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/shortestaugmentingpath.py

@@ -0,0 +1,300 @@
+"""
+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._dispatchable(edge_attrs={"capacity": float("inf")}, returns_graph=True)
+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"
+    nx._clear_cache(R)
+    return R

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/tests/test_gomory_hu.py

@@ -0,0 +1,128 @@
+from itertools import combinations
+
+import pytest
+
+import networkx as nx
+from networkx.algorithms.flow import (
+    boykov_kolmogorov,
+    dinitz,
+    edmonds_karp,
+    preflow_push,
+    shortest_augmenting_path,
+)
+
+flow_funcs = [
+    boykov_kolmogorov,
+    dinitz,
+    edmonds_karp,
+    preflow_push,
+    shortest_augmenting_path,
+]
+
+
+class TestGomoryHuTree:
+    def minimum_edge_weight(self, T, u, v):
+        path = nx.shortest_path(T, u, v, weight="weight")
+        return min((T[u][v]["weight"], (u, v)) for (u, v) in zip(path, path[1:]))
+
+    def compute_cutset(self, G, T_orig, edge):
+        T = T_orig.copy()
+        T.remove_edge(*edge)
+        U, V = list(nx.connected_components(T))
+        cutset = set()
+        for x, nbrs in ((n, G[n]) for n in U):
+            cutset.update((x, y) for y in nbrs if y in V)
+        return cutset
+
+    def test_default_flow_function_karate_club_graph(self):
+        G = nx.karate_club_graph()
+        nx.set_edge_attributes(G, 1, "capacity")
+        T = nx.gomory_hu_tree(G)
+        assert nx.is_tree(T)
+        for u, v in combinations(G, 2):
+            cut_value, edge = self.minimum_edge_weight(T, u, v)
+            assert nx.minimum_cut_value(G, u, v) == cut_value
+
+    def test_karate_club_graph(self):
+        G = nx.karate_club_graph()
+        nx.set_edge_attributes(G, 1, "capacity")
+        for flow_func in flow_funcs:
+            T = nx.gomory_hu_tree(G, flow_func=flow_func)
+            assert nx.is_tree(T)
+            for u, v in combinations(G, 2):
+                cut_value, edge = self.minimum_edge_weight(T, u, v)
+                assert nx.minimum_cut_value(G, u, v) == cut_value
+
+    def test_davis_southern_women_graph(self):
+        G = nx.davis_southern_women_graph()
+        nx.set_edge_attributes(G, 1, "capacity")
+        for flow_func in flow_funcs:
+            T = nx.gomory_hu_tree(G, flow_func=flow_func)
+            assert nx.is_tree(T)
+            for u, v in combinations(G, 2):
+                cut_value, edge = self.minimum_edge_weight(T, u, v)
+                assert nx.minimum_cut_value(G, u, v) == cut_value
+
+    def test_florentine_families_graph(self):
+        G = nx.florentine_families_graph()
+        nx.set_edge_attributes(G, 1, "capacity")
+        for flow_func in flow_funcs:
+            T = nx.gomory_hu_tree(G, flow_func=flow_func)
+            assert nx.is_tree(T)
+            for u, v in combinations(G, 2):
+                cut_value, edge = self.minimum_edge_weight(T, u, v)
+                assert nx.minimum_cut_value(G, u, v) == cut_value
+
+    @pytest.mark.slow
+    def test_les_miserables_graph_cutset(self):
+        G = nx.les_miserables_graph()
+        nx.set_edge_attributes(G, 1, "capacity")
+        for flow_func in flow_funcs:
+            T = nx.gomory_hu_tree(G, flow_func=flow_func)
+            assert nx.is_tree(T)
+            for u, v in combinations(G, 2):
+                cut_value, edge = self.minimum_edge_weight(T, u, v)
+                assert nx.minimum_cut_value(G, u, v) == cut_value
+
+    def test_karate_club_graph_cutset(self):
+        G = nx.karate_club_graph()
+        nx.set_edge_attributes(G, 1, "capacity")
+        T = nx.gomory_hu_tree(G)
+        assert nx.is_tree(T)
+        u, v = 0, 33
+        cut_value, edge = self.minimum_edge_weight(T, u, v)
+        cutset = self.compute_cutset(G, T, edge)
+        assert cut_value == len(cutset)
+
+    def test_wikipedia_example(self):
+        # Example from https://en.wikipedia.org/wiki/Gomory%E2%80%93Hu_tree
+        G = nx.Graph()
+        G.add_weighted_edges_from(
+            (
+                (0, 1, 1),
+                (0, 2, 7),
+                (1, 2, 1),
+                (1, 3, 3),
+                (1, 4, 2),
+                (2, 4, 4),
+                (3, 4, 1),
+                (3, 5, 6),
+                (4, 5, 2),
+            )
+        )
+        for flow_func in flow_funcs:
+            T = nx.gomory_hu_tree(G, capacity="weight", flow_func=flow_func)
+            assert nx.is_tree(T)
+            for u, v in combinations(G, 2):
+                cut_value, edge = self.minimum_edge_weight(T, u, v)
+                assert nx.minimum_cut_value(G, u, v, capacity="weight") == cut_value
+
+    def test_directed_raises(self):
+        with pytest.raises(nx.NetworkXNotImplemented):
+            G = nx.DiGraph()
+            T = nx.gomory_hu_tree(G)
+
+    def test_empty_raises(self):
+        with pytest.raises(nx.NetworkXError):
+            G = nx.empty_graph()
+            T = nx.gomory_hu_tree(G)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/tests/test_maxflow.py

@@ -0,0 +1,560 @@
+"""Maximum flow algorithms test suite.
+"""
+import pytest
+
+import networkx as nx
+from networkx.algorithms.flow import (
+    boykov_kolmogorov,
+    build_flow_dict,
+    build_residual_network,
+    dinitz,
+    edmonds_karp,
+    preflow_push,
+    shortest_augmenting_path,
+)
+
+flow_funcs = {
+    boykov_kolmogorov,
+    dinitz,
+    edmonds_karp,
+    preflow_push,
+    shortest_augmenting_path,
+}
+
+max_min_funcs = {nx.maximum_flow, nx.minimum_cut}
+flow_value_funcs = {nx.maximum_flow_value, nx.minimum_cut_value}
+interface_funcs = max_min_funcs & flow_value_funcs
+all_funcs = flow_funcs & interface_funcs
+
+
+def compute_cutset(G, partition):
+    reachable, non_reachable = partition
+    cutset = set()
+    for u, nbrs in ((n, G[n]) for n in reachable):
+        cutset.update((u, v) for v in nbrs if v in non_reachable)
+    return cutset
+
+
+def validate_flows(G, s, t, flowDict, solnValue, capacity, flow_func):
+    errmsg = f"Assertion failed in function: {flow_func.__name__}"
+    assert set(G) == set(flowDict), errmsg
+    for u in G:
+        assert set(G[u]) == set(flowDict[u]), errmsg
+    excess = {u: 0 for u in flowDict}
+    for u in flowDict:
+        for v, flow in flowDict[u].items():
+            if capacity in G[u][v]:
+                assert flow <= G[u][v][capacity]
+            assert flow >= 0, errmsg
+            excess[u] -= flow
+            excess[v] += flow
+    for u, exc in excess.items():
+        if u == s:
+            assert exc == -solnValue, errmsg
+        elif u == t:
+            assert exc == solnValue, errmsg
+        else:
+            assert exc == 0, errmsg
+
+
+def validate_cuts(G, s, t, solnValue, partition, capacity, flow_func):
+    errmsg = f"Assertion failed in function: {flow_func.__name__}"
+    assert all(n in G for n in partition[0]), errmsg
+    assert all(n in G for n in partition[1]), errmsg
+    cutset = compute_cutset(G, partition)
+    assert all(G.has_edge(u, v) for (u, v) in cutset), errmsg
+    assert solnValue == sum(G[u][v][capacity] for (u, v) in cutset), errmsg
+    H = G.copy()
+    H.remove_edges_from(cutset)
+    if not G.is_directed():
+        assert not nx.is_connected(H), errmsg
+    else:
+        assert not nx.is_strongly_connected(H), errmsg
+
+
+def compare_flows_and_cuts(G, s, t, solnFlows, solnValue, capacity="capacity"):
+    for flow_func in flow_funcs:
+        errmsg = f"Assertion failed in function: {flow_func.__name__}"
+        R = flow_func(G, s, t, capacity)
+        # Test both legacy and new implementations.
+        flow_value = R.graph["flow_value"]
+        flow_dict = build_flow_dict(G, R)
+        assert flow_value == solnValue, errmsg
+        validate_flows(G, s, t, flow_dict, solnValue, capacity, flow_func)
+        # Minimum cut
+        cut_value, partition = nx.minimum_cut(
+            G, s, t, capacity=capacity, flow_func=flow_func
+        )
+        validate_cuts(G, s, t, solnValue, partition, capacity, flow_func)
+
+
+class TestMaxflowMinCutCommon:
+    def test_graph1(self):
+        # Trivial undirected graph
+        G = nx.Graph()
+        G.add_edge(1, 2, capacity=1.0)
+
+        solnFlows = {1: {2: 1.0}, 2: {1: 1.0}}
+
+        compare_flows_and_cuts(G, 1, 2, solnFlows, 1.0)
+
+    def test_graph2(self):
+        # A more complex undirected graph
+        # adapted from https://web.archive.org/web/20220815055650/https://www.topcoder.com/thrive/articles/Maximum%20Flow:%20Part%20One
+        G = nx.Graph()
+        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)
+
+        H = {
+            "x": {"a": 3, "b": 1},
+            "a": {"c": 3, "x": 3},
+            "b": {"c": 1, "d": 2, "x": 1},
+            "c": {"a": 3, "b": 1, "y": 2},
+            "d": {"b": 2, "e": 2},
+            "e": {"d": 2, "y": 2},
+            "y": {"c": 2, "e": 2},
+        }
+
+        compare_flows_and_cuts(G, "x", "y", H, 4.0)
+
+    def test_digraph1(self):
+        # The classic directed graph example
+        G = nx.DiGraph()
+        G.add_edge("a", "b", capacity=1000.0)
+        G.add_edge("a", "c", capacity=1000.0)
+        G.add_edge("b", "c", capacity=1.0)
+        G.add_edge("b", "d", capacity=1000.0)
+        G.add_edge("c", "d", capacity=1000.0)
+
+        H = {
+            "a": {"b": 1000.0, "c": 1000.0},
+            "b": {"c": 0, "d": 1000.0},
+            "c": {"d": 1000.0},
+            "d": {},
+        }
+
+        compare_flows_and_cuts(G, "a", "d", H, 2000.0)
+
+    def test_digraph2(self):
+        # An example in which some edges end up with zero flow.
+        G = nx.DiGraph()
+        G.add_edge("s", "b", capacity=2)
+        G.add_edge("s", "c", capacity=1)
+        G.add_edge("c", "d", capacity=1)
+        G.add_edge("d", "a", capacity=1)
+        G.add_edge("b", "a", capacity=2)
+        G.add_edge("a", "t", capacity=2)
+
+        H = {
+            "s": {"b": 2, "c": 0},
+            "c": {"d": 0},
+            "d": {"a": 0},
+            "b": {"a": 2},
+            "a": {"t": 2},
+            "t": {},
+        }
+
+        compare_flows_and_cuts(G, "s", "t", H, 2)
+
+    def test_digraph3(self):
+        # A directed graph example from Cormen et al.
+        G = nx.DiGraph()
+        G.add_edge("s", "v1", capacity=16.0)
+        G.add_edge("s", "v2", capacity=13.0)
+        G.add_edge("v1", "v2", capacity=10.0)
+        G.add_edge("v2", "v1", capacity=4.0)
+        G.add_edge("v1", "v3", capacity=12.0)
+        G.add_edge("v3", "v2", capacity=9.0)
+        G.add_edge("v2", "v4", capacity=14.0)
+        G.add_edge("v4", "v3", capacity=7.0)
+        G.add_edge("v3", "t", capacity=20.0)
+        G.add_edge("v4", "t", capacity=4.0)
+
+        H = {
+            "s": {"v1": 12.0, "v2": 11.0},
+            "v2": {"v1": 0, "v4": 11.0},
+            "v1": {"v2": 0, "v3": 12.0},
+            "v3": {"v2": 0, "t": 19.0},
+            "v4": {"v3": 7.0, "t": 4.0},
+            "t": {},
+        }
+
+        compare_flows_and_cuts(G, "s", "t", H, 23.0)
+
+    def test_digraph4(self):
+        # A more complex directed graph
+        # from https://web.archive.org/web/20220815055650/https://www.topcoder.com/thrive/articles/Maximum%20Flow:%20Part%20One
+        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)
+
+        H = {
+            "x": {"a": 2.0, "b": 1.0},
+            "a": {"c": 2.0},
+            "b": {"c": 0, "d": 1.0},
+            "c": {"y": 2.0},
+            "d": {"e": 1.0},
+            "e": {"y": 1.0},
+            "y": {},
+        }
+
+        compare_flows_and_cuts(G, "x", "y", H, 3.0)
+
+    def test_wikipedia_dinitz_example(self):
+        # Nice example from https://en.wikipedia.org/wiki/Dinic's_algorithm
+        G = nx.DiGraph()
+        G.add_edge("s", 1, capacity=10)
+        G.add_edge("s", 2, capacity=10)
+        G.add_edge(1, 3, capacity=4)
+        G.add_edge(1, 4, capacity=8)
+        G.add_edge(1, 2, capacity=2)
+        G.add_edge(2, 4, capacity=9)
+        G.add_edge(3, "t", capacity=10)
+        G.add_edge(4, 3, capacity=6)
+        G.add_edge(4, "t", capacity=10)
+
+        solnFlows = {
+            1: {2: 0, 3: 4, 4: 6},
+            2: {4: 9},
+            3: {"t": 9},
+            4: {3: 5, "t": 10},
+            "s": {1: 10, 2: 9},
+            "t": {},
+        }
+
+        compare_flows_and_cuts(G, "s", "t", solnFlows, 19)
+
+    def test_optional_capacity(self):
+        # Test optional capacity parameter.
+        G = nx.DiGraph()
+        G.add_edge("x", "a", spam=3.0)
+        G.add_edge("x", "b", spam=1.0)
+        G.add_edge("a", "c", spam=3.0)
+        G.add_edge("b", "c", spam=5.0)
+        G.add_edge("b", "d", spam=4.0)
+        G.add_edge("d", "e", spam=2.0)
+        G.add_edge("c", "y", spam=2.0)
+        G.add_edge("e", "y", spam=3.0)
+
+        solnFlows = {
+            "x": {"a": 2.0, "b": 1.0},
+            "a": {"c": 2.0},
+            "b": {"c": 0, "d": 1.0},
+            "c": {"y": 2.0},
+            "d": {"e": 1.0},
+            "e": {"y": 1.0},
+            "y": {},
+        }
+        solnValue = 3.0
+        s = "x"
+        t = "y"
+
+        compare_flows_and_cuts(G, s, t, solnFlows, solnValue, capacity="spam")
+
+    def test_digraph_infcap_edges(self):
+        # DiGraph with infinite capacity edges
+        G = nx.DiGraph()
+        G.add_edge("s", "a")
+        G.add_edge("s", "b", capacity=30)
+        G.add_edge("a", "c", capacity=25)
+        G.add_edge("b", "c", capacity=12)
+        G.add_edge("a", "t", capacity=60)
+        G.add_edge("c", "t")
+
+        H = {
+            "s": {"a": 85, "b": 12},
+            "a": {"c": 25, "t": 60},
+            "b": {"c": 12},
+            "c": {"t": 37},
+            "t": {},
+        }
+
+        compare_flows_and_cuts(G, "s", "t", H, 97)
+
+        # DiGraph with infinite capacity digon
+        G = nx.DiGraph()
+        G.add_edge("s", "a", capacity=85)
+        G.add_edge("s", "b", capacity=30)
+        G.add_edge("a", "c")
+        G.add_edge("c", "a")
+        G.add_edge("b", "c", capacity=12)
+        G.add_edge("a", "t", capacity=60)
+        G.add_edge("c", "t", capacity=37)
+
+        H = {
+            "s": {"a": 85, "b": 12},
+            "a": {"c": 25, "t": 60},
+            "c": {"a": 0, "t": 37},
+            "b": {"c": 12},
+            "t": {},
+        }
+
+        compare_flows_and_cuts(G, "s", "t", H, 97)
+
+    def test_digraph_infcap_path(self):
+        # Graph with infinite capacity (s, t)-path
+        G = nx.DiGraph()
+        G.add_edge("s", "a")
+        G.add_edge("s", "b", capacity=30)
+        G.add_edge("a", "c")
+        G.add_edge("b", "c", capacity=12)
+        G.add_edge("a", "t", capacity=60)
+        G.add_edge("c", "t")
+
+        for flow_func in all_funcs:
+            pytest.raises(nx.NetworkXUnbounded, flow_func, G, "s", "t")
+
+    def test_graph_infcap_edges(self):
+        # Undirected graph with infinite capacity edges
+        G = nx.Graph()
+        G.add_edge("s", "a")
+        G.add_edge("s", "b", capacity=30)
+        G.add_edge("a", "c", capacity=25)
+        G.add_edge("b", "c", capacity=12)
+        G.add_edge("a", "t", capacity=60)
+        G.add_edge("c", "t")
+
+        H = {
+            "s": {"a": 85, "b": 12},
+            "a": {"c": 25, "s": 85, "t": 60},
+            "b": {"c": 12, "s": 12},
+            "c": {"a": 25, "b": 12, "t": 37},
+            "t": {"a": 60, "c": 37},
+        }
+
+        compare_flows_and_cuts(G, "s", "t", H, 97)
+
+    def test_digraph5(self):
+        # From ticket #429 by mfrasca.
+        G = nx.DiGraph()
+        G.add_edge("s", "a", capacity=2)
+        G.add_edge("s", "b", capacity=2)
+        G.add_edge("a", "b", capacity=5)
+        G.add_edge("a", "t", capacity=1)
+        G.add_edge("b", "a", capacity=1)
+        G.add_edge("b", "t", capacity=3)
+        flowSoln = {
+            "a": {"b": 1, "t": 1},
+            "b": {"a": 0, "t": 3},
+            "s": {"a": 2, "b": 2},
+            "t": {},
+        }
+        compare_flows_and_cuts(G, "s", "t", flowSoln, 4)
+
+    def test_disconnected(self):
+        G = nx.Graph()
+        G.add_weighted_edges_from([(0, 1, 1), (1, 2, 1), (2, 3, 1)], weight="capacity")
+        G.remove_node(1)
+        assert nx.maximum_flow_value(G, 0, 3) == 0
+        flowSoln = {0: {}, 2: {3: 0}, 3: {2: 0}}
+        compare_flows_and_cuts(G, 0, 3, flowSoln, 0)
+
+    def test_source_target_not_in_graph(self):
+        G = nx.Graph()
+        G.add_weighted_edges_from([(0, 1, 1), (1, 2, 1), (2, 3, 1)], weight="capacity")
+        G.remove_node(0)
+        for flow_func in all_funcs:
+            pytest.raises(nx.NetworkXError, flow_func, G, 0, 3)
+        G.add_weighted_edges_from([(0, 1, 1), (1, 2, 1), (2, 3, 1)], weight="capacity")
+        G.remove_node(3)
+        for flow_func in all_funcs:
+            pytest.raises(nx.NetworkXError, flow_func, G, 0, 3)
+
+    def test_source_target_coincide(self):
+        G = nx.Graph()
+        G.add_node(0)
+        for flow_func in all_funcs:
+            pytest.raises(nx.NetworkXError, flow_func, G, 0, 0)
+
+    def test_multigraphs_raise(self):
+        G = nx.MultiGraph()
+        M = nx.MultiDiGraph()
+        G.add_edges_from([(0, 1), (1, 0)], capacity=True)
+        for flow_func in all_funcs:
+            pytest.raises(nx.NetworkXError, flow_func, G, 0, 0)
+
+
+class TestMaxFlowMinCutInterface:
+    def setup_method(self):
+        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)
+        self.G = G
+        H = nx.DiGraph()
+        H.add_edge(0, 1, capacity=1.0)
+        H.add_edge(1, 2, capacity=1.0)
+        self.H = H
+
+    def test_flow_func_not_callable(self):
+        elements = ["this_should_be_callable", 10, {1, 2, 3}]
+        G = nx.Graph()
+        G.add_weighted_edges_from([(0, 1, 1), (1, 2, 1), (2, 3, 1)], weight="capacity")
+        for flow_func in interface_funcs:
+            for element in elements:
+                pytest.raises(nx.NetworkXError, flow_func, G, 0, 1, flow_func=element)
+                pytest.raises(nx.NetworkXError, flow_func, G, 0, 1, flow_func=element)
+
+    def test_flow_func_parameters(self):
+        G = self.G
+        fv = 3.0
+        for interface_func in interface_funcs:
+            for flow_func in flow_funcs:
+                errmsg = (
+                    f"Assertion failed in function: {flow_func.__name__} "
+                    f"in interface {interface_func.__name__}"
+                )
+                result = interface_func(G, "x", "y", flow_func=flow_func)
+                if interface_func in max_min_funcs:
+                    result = result[0]
+                assert fv == result, errmsg
+
+    def test_minimum_cut_no_cutoff(self):
+        G = self.G
+        pytest.raises(
+            nx.NetworkXError,
+            nx.minimum_cut,
+            G,
+            "x",
+            "y",
+            flow_func=preflow_push,
+            cutoff=1.0,
+        )
+        pytest.raises(
+            nx.NetworkXError,
+            nx.minimum_cut_value,
+            G,
+            "x",
+            "y",
+            flow_func=preflow_push,
+            cutoff=1.0,
+        )
+
+    def test_kwargs(self):
+        G = self.H
+        fv = 1.0
+        to_test = (
+            (shortest_augmenting_path, {"two_phase": True}),
+            (preflow_push, {"global_relabel_freq": 5}),
+        )
+        for interface_func in interface_funcs:
+            for flow_func, kwargs in to_test:
+                errmsg = (
+                    f"Assertion failed in function: {flow_func.__name__} "
+                    f"in interface {interface_func.__name__}"
+                )
+                result = interface_func(G, 0, 2, flow_func=flow_func, **kwargs)
+                if interface_func in max_min_funcs:
+                    result = result[0]
+                assert fv == result, errmsg
+
+    def test_kwargs_default_flow_func(self):
+        G = self.H
+        for interface_func in interface_funcs:
+            pytest.raises(
+                nx.NetworkXError, interface_func, G, 0, 1, global_relabel_freq=2
+            )
+
+    def test_reusing_residual(self):
+        G = self.G
+        fv = 3.0
+        s, t = "x", "y"
+        R = build_residual_network(G, "capacity")
+        for interface_func in interface_funcs:
+            for flow_func in flow_funcs:
+                errmsg = (
+                    f"Assertion failed in function: {flow_func.__name__} "
+                    f"in interface {interface_func.__name__}"
+                )
+                for i in range(3):
+                    result = interface_func(
+                        G, "x", "y", flow_func=flow_func, residual=R
+                    )
+                    if interface_func in max_min_funcs:
+                        result = result[0]
+                    assert fv == result, errmsg
+
+
+# Tests specific to one algorithm
+def test_preflow_push_global_relabel_freq():
+    G = nx.DiGraph()
+    G.add_edge(1, 2, capacity=1)
+    R = preflow_push(G, 1, 2, global_relabel_freq=None)
+    assert R.graph["flow_value"] == 1
+    pytest.raises(nx.NetworkXError, preflow_push, G, 1, 2, global_relabel_freq=-1)
+
+
+def test_preflow_push_makes_enough_space():
+    # From ticket #1542
+    G = nx.DiGraph()
+    nx.add_path(G, [0, 1, 3], capacity=1)
+    nx.add_path(G, [1, 2, 3], capacity=1)
+    R = preflow_push(G, 0, 3, value_only=False)
+    assert R.graph["flow_value"] == 1
+
+
+def test_shortest_augmenting_path_two_phase():
+    k = 5
+    p = 1000
+    G = nx.DiGraph()
+    for i in range(k):
+        G.add_edge("s", (i, 0), capacity=1)
+        nx.add_path(G, ((i, j) for j in range(p)), capacity=1)
+        G.add_edge((i, p - 1), "t", capacity=1)
+    R = shortest_augmenting_path(G, "s", "t", two_phase=True)
+    assert R.graph["flow_value"] == k
+    R = shortest_augmenting_path(G, "s", "t", two_phase=False)
+    assert R.graph["flow_value"] == k
+
+
+class TestCutoff:
+    def test_cutoff(self):
+        k = 5
+        p = 1000
+        G = nx.DiGraph()
+        for i in range(k):
+            G.add_edge("s", (i, 0), capacity=2)
+            nx.add_path(G, ((i, j) for j in range(p)), capacity=2)
+            G.add_edge((i, p - 1), "t", capacity=2)
+        R = shortest_augmenting_path(G, "s", "t", two_phase=True, cutoff=k)
+        assert k <= R.graph["flow_value"] <= (2 * k)
+        R = shortest_augmenting_path(G, "s", "t", two_phase=False, cutoff=k)
+        assert k <= R.graph["flow_value"] <= (2 * k)
+        R = edmonds_karp(G, "s", "t", cutoff=k)
+        assert k <= R.graph["flow_value"] <= (2 * k)
+        R = dinitz(G, "s", "t", cutoff=k)
+        assert k <= R.graph["flow_value"] <= (2 * k)
+        R = boykov_kolmogorov(G, "s", "t", cutoff=k)
+        assert k <= R.graph["flow_value"] <= (2 * k)
+
+    def test_complete_graph_cutoff(self):
+        G = nx.complete_graph(5)
+        nx.set_edge_attributes(G, {(u, v): 1 for u, v in G.edges()}, "capacity")
+        for flow_func in [
+            shortest_augmenting_path,
+            edmonds_karp,
+            dinitz,
+            boykov_kolmogorov,
+        ]:
+            for cutoff in [3, 2, 1]:
+                result = nx.maximum_flow_value(
+                    G, 0, 4, flow_func=flow_func, cutoff=cutoff
+                )
+                assert cutoff == result, f"cutoff error in {flow_func.__name__}"

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/tests/test_maxflow_large_graph.py

@@ -0,0 +1,157 @@
+"""Maximum flow algorithms test suite on large graphs.
+"""
+
+import bz2
+import importlib.resources
+import os
+import pickle
+
+import pytest
+
+import networkx as nx
+from networkx.algorithms.flow import (
+    boykov_kolmogorov,
+    build_flow_dict,
+    build_residual_network,
+    dinitz,
+    edmonds_karp,
+    preflow_push,
+    shortest_augmenting_path,
+)
+
+flow_funcs = [
+    boykov_kolmogorov,
+    dinitz,
+    edmonds_karp,
+    preflow_push,
+    shortest_augmenting_path,
+]
+
+
+def gen_pyramid(N):
+    # This graph admits a flow of value 1 for which every arc is at
+    # capacity (except the arcs incident to the sink which have
+    # infinite capacity).
+    G = nx.DiGraph()
+
+    for i in range(N - 1):
+        cap = 1.0 / (i + 2)
+        for j in range(i + 1):
+            G.add_edge((i, j), (i + 1, j), capacity=cap)
+            cap = 1.0 / (i + 1) - cap
+            G.add_edge((i, j), (i + 1, j + 1), capacity=cap)
+            cap = 1.0 / (i + 2) - cap
+
+    for j in range(N):
+        G.add_edge((N - 1, j), "t")
+
+    return G
+
+
+def read_graph(name):
+    fname = (
+        importlib.resources.files("networkx.algorithms.flow.tests")
+        / f"{name}.gpickle.bz2"
+    )
+
+    with bz2.BZ2File(fname, "rb") as f:
+        G = pickle.load(f)
+    return G
+
+
+def validate_flows(G, s, t, soln_value, R, flow_func):
+    flow_value = R.graph["flow_value"]
+    flow_dict = build_flow_dict(G, R)
+    errmsg = f"Assertion failed in function: {flow_func.__name__}"
+    assert soln_value == flow_value, errmsg
+    assert set(G) == set(flow_dict), errmsg
+    for u in G:
+        assert set(G[u]) == set(flow_dict[u]), errmsg
+    excess = {u: 0 for u in flow_dict}
+    for u in flow_dict:
+        for v, flow in flow_dict[u].items():
+            assert flow <= G[u][v].get("capacity", float("inf")), errmsg
+            assert flow >= 0, errmsg
+            excess[u] -= flow
+            excess[v] += flow
+    for u, exc in excess.items():
+        if u == s:
+            assert exc == -soln_value, errmsg
+        elif u == t:
+            assert exc == soln_value, errmsg
+        else:
+            assert exc == 0, errmsg
+
+
+class TestMaxflowLargeGraph:
+    def test_complete_graph(self):
+        N = 50
+        G = nx.complete_graph(N)
+        nx.set_edge_attributes(G, 5, "capacity")
+        R = build_residual_network(G, "capacity")
+        kwargs = {"residual": R}
+
+        for flow_func in flow_funcs:
+            kwargs["flow_func"] = flow_func
+            errmsg = f"Assertion failed in function: {flow_func.__name__}"
+            flow_value = nx.maximum_flow_value(G, 1, 2, **kwargs)
+            assert flow_value == 5 * (N - 1), errmsg
+
+    def test_pyramid(self):
+        N = 10
+        # N = 100 # this gives a graph with 5051 nodes
+        G = gen_pyramid(N)
+        R = build_residual_network(G, "capacity")
+        kwargs = {"residual": R}
+
+        for flow_func in flow_funcs:
+            kwargs["flow_func"] = flow_func
+            errmsg = f"Assertion failed in function: {flow_func.__name__}"
+            flow_value = nx.maximum_flow_value(G, (0, 0), "t", **kwargs)
+            assert flow_value == pytest.approx(1.0, abs=1e-7)
+
+    def test_gl1(self):
+        G = read_graph("gl1")
+        s = 1
+        t = len(G)
+        R = build_residual_network(G, "capacity")
+        kwargs = {"residual": R}
+
+        # do one flow_func to save time
+        flow_func = flow_funcs[0]
+        validate_flows(G, s, t, 156545, flow_func(G, s, t, **kwargs), flow_func)
+
+    #        for flow_func in flow_funcs:
+    #            validate_flows(G, s, t, 156545, flow_func(G, s, t, **kwargs),
+    #                           flow_func)
+
+    @pytest.mark.slow
+    def test_gw1(self):
+        G = read_graph("gw1")
+        s = 1
+        t = len(G)
+        R = build_residual_network(G, "capacity")
+        kwargs = {"residual": R}
+
+        for flow_func in flow_funcs:
+            validate_flows(G, s, t, 1202018, flow_func(G, s, t, **kwargs), flow_func)
+
+    def test_wlm3(self):
+        G = read_graph("wlm3")
+        s = 1
+        t = len(G)
+        R = build_residual_network(G, "capacity")
+        kwargs = {"residual": R}
+
+        # do one flow_func to save time
+        flow_func = flow_funcs[0]
+        validate_flows(G, s, t, 11875108, flow_func(G, s, t, **kwargs), flow_func)
+
+    #        for flow_func in flow_funcs:
+    #            validate_flows(G, s, t, 11875108, flow_func(G, s, t, **kwargs),
+    #                           flow_func)
+
+    def test_preflow_push_global_relabel(self):
+        G = read_graph("gw1")
+        R = preflow_push(G, 1, len(G), global_relabel_freq=50)
+        assert R.graph["flow_value"] == 1202018

env-llmeval/lib/python3.10/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)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/tests/test_networksimplex.py

@@ -0,0 +1,387 @@
+import bz2
+import importlib.resources
+import os
+import pickle
+
+import pytest
+
+import networkx as nx
+
+
+@pytest.fixture
+def simple_flow_graph():
+    G = nx.DiGraph()
+    G.add_node("a", demand=0)
+    G.add_node("b", demand=-5)
+    G.add_node("c", demand=50000000)
+    G.add_node("d", demand=-49999995)
+    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)
+    return G
+
+
+@pytest.fixture
+def simple_no_flow_graph():
+    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)
+    return G
+
+
+def get_flowcost_from_flowdict(G, flowDict):
+    """Returns flow cost calculated from flow dictionary"""
+    flowCost = 0
+    for u in flowDict:
+        for v in flowDict[u]:
+            flowCost += flowDict[u][v] * G[u][v]["weight"]
+    return flowCost
+
+
+def test_infinite_demand_raise(simple_flow_graph):
+    G = simple_flow_graph
+    inf = float("inf")
+    nx.set_node_attributes(G, {"a": {"demand": inf}})
+    pytest.raises(nx.NetworkXError, nx.network_simplex, G)
+
+
+def test_neg_infinite_demand_raise(simple_flow_graph):
+    G = simple_flow_graph
+    inf = float("inf")
+    nx.set_node_attributes(G, {"a": {"demand": -inf}})
+    pytest.raises(nx.NetworkXError, nx.network_simplex, G)
+
+
+def test_infinite_weight_raise(simple_flow_graph):
+    G = simple_flow_graph
+    inf = float("inf")
+    nx.set_edge_attributes(
+        G, {("a", "b"): {"weight": inf}, ("b", "d"): {"weight": inf}}
+    )
+    pytest.raises(nx.NetworkXError, nx.network_simplex, G)
+
+
+def test_nonzero_net_demand_raise(simple_flow_graph):
+    G = simple_flow_graph
+    nx.set_node_attributes(G, {"b": {"demand": -4}})
+    pytest.raises(nx.NetworkXUnfeasible, nx.network_simplex, G)
+
+
+def test_negative_capacity_raise(simple_flow_graph):
+    G = simple_flow_graph
+    nx.set_edge_attributes(G, {("a", "b"): {"weight": 1}, ("b", "d"): {"capacity": -9}})
+    pytest.raises(nx.NetworkXUnfeasible, nx.network_simplex, G)
+
+
+def test_no_flow_satisfying_demands(simple_no_flow_graph):
+    G = simple_no_flow_graph
+    pytest.raises(nx.NetworkXUnfeasible, nx.network_simplex, G)
+
+
+def test_sum_demands_not_zero(simple_no_flow_graph):
+    G = simple_no_flow_graph
+    nx.set_node_attributes(G, {"t": {"demand": 4}})
+    pytest.raises(nx.NetworkXUnfeasible, nx.network_simplex, G)
+
+
+def test_google_or_tools_example():
+    """
+    https://developers.google.com/optimization/flow/mincostflow
+    """
+    G = nx.DiGraph()
+    start_nodes = [0, 0, 1, 1, 1, 2, 2, 3, 4]
+    end_nodes = [1, 2, 2, 3, 4, 3, 4, 4, 2]
+    capacities = [15, 8, 20, 4, 10, 15, 4, 20, 5]
+    unit_costs = [4, 4, 2, 2, 6, 1, 3, 2, 3]
+    supplies = [20, 0, 0, -5, -15]
+    answer = 150
+
+    for i in range(len(supplies)):
+        G.add_node(i, demand=(-1) * supplies[i])  # supplies are negative of demand
+
+    for i in range(len(start_nodes)):
+        G.add_edge(
+            start_nodes[i], end_nodes[i], weight=unit_costs[i], capacity=capacities[i]
+        )
+
+    flowCost, flowDict = nx.network_simplex(G)
+    assert flowCost == answer
+    assert flowCost == get_flowcost_from_flowdict(G, flowDict)
+
+
+def test_google_or_tools_example2():
+    """
+    https://developers.google.com/optimization/flow/mincostflow
+    """
+    G = nx.DiGraph()
+    start_nodes = [0, 0, 1, 1, 1, 2, 2, 3, 4, 3]
+    end_nodes = [1, 2, 2, 3, 4, 3, 4, 4, 2, 5]
+    capacities = [15, 8, 20, 4, 10, 15, 4, 20, 5, 10]
+    unit_costs = [4, 4, 2, 2, 6, 1, 3, 2, 3, 4]
+    supplies = [23, 0, 0, -5, -15, -3]
+    answer = 183
+
+    for i in range(len(supplies)):
+        G.add_node(i, demand=(-1) * supplies[i])  # supplies are negative of demand
+
+    for i in range(len(start_nodes)):
+        G.add_edge(
+            start_nodes[i], end_nodes[i], weight=unit_costs[i], capacity=capacities[i]
+        )
+
+    flowCost, flowDict = nx.network_simplex(G)
+    assert flowCost == answer
+    assert flowCost == get_flowcost_from_flowdict(G, flowDict)
+
+
+def test_large():
+    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)
+
+
+def test_simple_digraph():
+    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
+
+
+def test_negcycle_infcap():
+    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)
+
+
+def test_transshipment():
+    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 H == soln
+
+
+def test_digraph1():
+    # 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
+
+
+def test_zero_capacity_edges():
+    """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
+
+
+def test_digon():
+    """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
+
+
+def test_deadend():
+    """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.network_simplex, G)
+
+
+def test_infinite_capacity_neg_digon():
+    """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)
+
+
+def test_multidigraph():
+    """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: {}}
+
+
+def test_negative_selfloops():
+    """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)
+
+    G[1][1]["capacity"] = 2
+    flowCost, H = nx.network_simplex(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)
+
+    G[1][1]["x"]["capacity"] = 2
+    flowCost, H = nx.network_simplex(G)
+    assert flowCost == -2
+    assert H == {1: {1: {"x": 2, "y": 0}}}
+
+
+def test_bone_shaped():
+    # 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}}
+
+
+def test_graphs_type_exceptions():
+    G = nx.Graph()
+    pytest.raises(nx.NetworkXNotImplemented, nx.network_simplex, G)
+    G = nx.MultiGraph()
+    pytest.raises(nx.NetworkXNotImplemented, nx.network_simplex, G)
+    G = nx.DiGraph()
+    pytest.raises(nx.NetworkXError, nx.network_simplex, G)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/flow/utils.py

@@ -0,0 +1,189 @@
+"""
+Utility classes and functions for network flow algorithms.
+"""
+
+from collections import deque
+
+import networkx as nx
+
+__all__ = [
+    "CurrentEdge",
+    "Level",
+    "GlobalRelabelThreshold",
+    "build_residual_network",
+    "detect_unboundedness",
+    "build_flow_dict",
+]
+
+
+class CurrentEdge:
+    """Mechanism for iterating over out-edges incident to a node in a circular
+    manner. StopIteration exception is raised when wraparound occurs.
+    """
+
+    __slots__ = ("_edges", "_it", "_curr")
+
+    def __init__(self, edges):
+        self._edges = edges
+        if self._edges:
+            self._rewind()
+
+    def get(self):
+        return self._curr
+
+    def move_to_next(self):
+        try:
+            self._curr = next(self._it)
+        except StopIteration:
+            self._rewind()
+            raise
+
+    def _rewind(self):
+        self._it = iter(self._edges.items())
+        self._curr = next(self._it)
+
+
+class Level:
+    """Active and inactive nodes in a level."""
+
+    __slots__ = ("active", "inactive")
+
+    def __init__(self):
+        self.active = set()
+        self.inactive = set()
+
+
+class GlobalRelabelThreshold:
+    """Measurement of work before the global relabeling heuristic should be
+    applied.
+    """
+
+    def __init__(self, n, m, freq):
+        self._threshold = (n + m) / freq if freq else float("inf")
+        self._work = 0
+
+    def add_work(self, work):
+        self._work += work
+
+    def is_reached(self):
+        return self._work >= self._threshold
+
+    def clear_work(self):
+        self._work = 0
+
+
+@nx._dispatchable(edge_attrs={"capacity": float("inf")}, returns_graph=True)
+def build_residual_network(G, capacity):
+    """Build a residual network and initialize a zero flow.
+
+    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.
+
+    """
+    if G.is_multigraph():
+        raise nx.NetworkXError("MultiGraph and MultiDiGraph not supported (yet).")
+
+    R = nx.DiGraph()
+    R.__networkx_cache__ = None  # Disable caching
+    R.add_nodes_from(G)
+
+    inf = float("inf")
+    # Extract edges with positive capacities. Self loops excluded.
+    edge_list = [
+        (u, v, attr)
+        for u, v, attr in G.edges(data=True)
+        if u != v and attr.get(capacity, inf) > 0
+    ]
+    # Simulate infinity with three times the sum of the finite edge capacities
+    # or any positive value if the sum is zero. This allows the
+    # infinite-capacity edges to be distinguished for unboundedness detection
+    # and directly participate in residual capacity calculation. If the maximum
+    # flow is finite, these edges cannot appear in the minimum cut and thus
+    # guarantee correctness. Since the residual capacity of an
+    # infinite-capacity edge is always at least 2/3 of inf, while that of an
+    # finite-capacity edge is at most 1/3 of inf, if an operation moves more
+    # than 1/3 of inf units of flow to t, there must be an infinite-capacity
+    # s-t path in G.
+    inf = (
+        3
+        * sum(
+            attr[capacity]
+            for u, v, attr in edge_list
+            if capacity in attr and attr[capacity] != inf
+        )
+        or 1
+    )
+    if G.is_directed():
+        for u, v, attr in edge_list:
+            r = min(attr.get(capacity, inf), inf)
+            if not R.has_edge(u, v):
+                # Both (u, v) and (v, u) must be present in the residual
+                # network.
+                R.add_edge(u, v, capacity=r)
+                R.add_edge(v, u, capacity=0)
+            else:
+                # The edge (u, v) was added when (v, u) was visited.
+                R[u][v]["capacity"] = r
+    else:
+        for u, v, attr in edge_list:
+            # Add a pair of edges with equal residual capacities.
+            r = min(attr.get(capacity, inf), inf)
+            R.add_edge(u, v, capacity=r)
+            R.add_edge(v, u, capacity=r)
+
+    # Record the value simulating infinity.
+    R.graph["inf"] = inf
+
+    return R
+
+
+@nx._dispatchable(
+    graphs="R",
+    preserve_edge_attrs={"R": {"capacity": float("inf")}},
+    preserve_graph_attrs=True,
+)
+def detect_unboundedness(R, s, t):
+    """Detect an infinite-capacity s-t path in R."""
+    q = deque([s])
+    seen = {s}
+    inf = R.graph["inf"]
+    while q:
+        u = q.popleft()
+        for v, attr in R[u].items():
+            if attr["capacity"] == inf and v not in seen:
+                if v == t:
+                    raise nx.NetworkXUnbounded(
+                        "Infinite capacity path, flow unbounded above."
+                    )
+                seen.add(v)
+                q.append(v)
+
+
+@nx._dispatchable(graphs={"G": 0, "R": 1}, preserve_edge_attrs={"R": {"flow": None}})
+def build_flow_dict(G, R):
+    """Build a flow dictionary from a residual network."""
+    flow_dict = {}
+    for u in G:
+        flow_dict[u] = {v: 0 for v in G[u]}
+        flow_dict[u].update(
+            (v, attr["flow"]) for v, attr in R[u].items() if attr["flow"] > 0
+        )
+    return flow_dict

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/graph_hashing.py

@@ -0,0 +1,322 @@
+"""
+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._dispatchable(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 neighborhoods 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, optional (default=None)
+        The key in edge attribute dictionary to be used for hashing.
+        If None, edge labels are ignored.
+    node_attr: string, optional (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, optional (default=3)
+        Number of neighbor aggregations to perform.
+        Should be larger for larger graphs.
+    digest_size: int, optional (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._dispatchable(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,
+    include_initial_labels=False,
+):
+    """
+    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` elements - a hash for a subgraph at each depth. If
+    `include_initial_labels` is set to `True`, each list will additionally
+    have contain a hash of the initial node label (or equivalently a
+    subgraph of depth 0) prepended, totalling ``iterations + 1`` elements.
+
+    The function iteratively aggregates and hashes neighborhoods 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 for a node $u$ at each step, all labels of
+    nodes adjacent to $u$ 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 $u$. 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 $u$
+    we have a hash for a subgraph induced by the $i$-hop neighborhood of $u$.
+
+    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, optional (default=None)
+        The key in edge attribute dictionary to be used for hashing.
+        If None, edge labels are ignored.
+    node_attr : string, optional (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.
+        If None, and edge_attr is given, each node starts with an identical label.
+    iterations : int, optional (default=3)
+        Number of neighbor aggregations to perform.
+        Should be larger for larger graphs.
+    digest_size : int, optional (default=16)
+        Size (in bits) of blake2b hash digest to use for hashing node labels.
+        The default size is 16 bits.
+    include_initial_labels : bool, optional (default=False)
+        If True, include the hashed initial node label as the first subgraph
+        hash for each node.
+
+    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 2 hops around these nodes are isomorphic.
+
+    However the 3-hop neighborhoods of ``G1`` and ``G2`` are not isomorphic since the
+    3rd hashes in the lists above are not equal.
+
+    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)
+    if include_initial_labels:
+        node_subgraph_hashes = {
+            k: [_hash_label(v, digest_size)] for k, v in node_labels.items()
+        }
+    else:
+        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)

env-llmeval/lib/python3.10/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._dispatchable(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._dispatchable(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._dispatchable(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._dispatchable(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._dispatchable(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._dispatchable(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

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/hybrid.py

@@ -0,0 +1,195 @@
+"""
+Provides functions for finding and testing for locally `(k, l)`-connected
+graphs.
+
+"""
+import copy
+
+import networkx as nx
+
+__all__ = ["kl_connected_subgraph", "is_kl_connected"]
+
+
+@nx._dispatchable(returns_graph=True)
+def kl_connected_subgraph(G, k, l, low_memory=False, same_as_graph=False):
+    """Returns the maximum locally `(k, l)`-connected subgraph of `G`.
+
+    A graph is locally `(k, l)`-connected if for each edge `(u, v)` in the
+    graph there are at least `l` edge-disjoint paths of length at most `k`
+    joining `u` to `v`.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        The graph in which to find a maximum locally `(k, l)`-connected
+        subgraph.
+
+    k : integer
+        The maximum length of paths to consider. A higher number means a looser
+        connectivity requirement.
+
+    l : integer
+        The number of edge-disjoint paths. A higher number means a stricter
+        connectivity requirement.
+
+    low_memory : bool
+        If this is True, this function uses an algorithm that uses slightly
+        more time but less memory.
+
+    same_as_graph : bool
+        If True then return a tuple of the form `(H, is_same)`,
+        where `H` is the maximum locally `(k, l)`-connected subgraph and
+        `is_same` is a Boolean representing whether `G` is locally `(k,
+        l)`-connected (and hence, whether `H` is simply a copy of the input
+        graph `G`).
+
+    Returns
+    -------
+    NetworkX graph or two-tuple
+        If `same_as_graph` is True, then this function returns a
+        two-tuple as described above. Otherwise, it returns only the maximum
+        locally `(k, l)`-connected subgraph.
+
+    See also
+    --------
+    is_kl_connected
+
+    References
+    ----------
+    .. [1] Chung, Fan and Linyuan Lu. "The Small World Phenomenon in Hybrid
+           Power Law Graphs." *Complex Networks*. Springer Berlin Heidelberg,
+           2004. 89--104.
+
+    """
+    H = copy.deepcopy(G)  # subgraph we construct by removing from G
+
+    graphOK = True
+    deleted_some = True  # hack to start off the while loop
+    while deleted_some:
+        deleted_some = False
+        # We use `for edge in list(H.edges()):` instead of
+        # `for edge in H.edges():` because we edit the graph `H` in
+        # the loop. Hence using an iterator will result in
+        # `RuntimeError: dictionary changed size during iteration`
+        for edge in list(H.edges()):
+            (u, v) = edge
+            # Get copy of graph needed for this search
+            if low_memory:
+                verts = {u, v}
+                for i in range(k):
+                    for w in verts.copy():
+                        verts.update(G[w])
+                G2 = G.subgraph(verts).copy()
+            else:
+                G2 = copy.deepcopy(G)
+            ###
+            path = [u, v]
+            cnt = 0
+            accept = 0
+            while path:
+                cnt += 1  # Found a path
+                if cnt >= l:
+                    accept = 1
+                    break
+                # record edges along this graph
+                prev = u
+                for w in path:
+                    if prev != w:
+                        G2.remove_edge(prev, w)
+                        prev = w
+                #                path = shortest_path(G2, u, v, k) # ??? should "Cutoff" be k+1?
+                try:
+                    path = nx.shortest_path(G2, u, v)  # ??? should "Cutoff" be k+1?
+                except nx.NetworkXNoPath:
+                    path = False
+            # No Other Paths
+            if accept == 0:
+                H.remove_edge(u, v)
+                deleted_some = True
+                if graphOK:
+                    graphOK = False
+    # We looked through all edges and removed none of them.
+    # So, H is the maximal (k,l)-connected subgraph of G
+    if same_as_graph:
+        return (H, graphOK)
+    return H
+
+
+@nx._dispatchable
+def is_kl_connected(G, k, l, low_memory=False):
+    """Returns True if and only if `G` is locally `(k, l)`-connected.
+
+    A graph is locally `(k, l)`-connected if for each edge `(u, v)` in the
+    graph there are at least `l` edge-disjoint paths of length at most `k`
+    joining `u` to `v`.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        The graph to test for local `(k, l)`-connectedness.
+
+    k : integer
+        The maximum length of paths to consider. A higher number means a looser
+        connectivity requirement.
+
+    l : integer
+        The number of edge-disjoint paths. A higher number means a stricter
+        connectivity requirement.
+
+    low_memory : bool
+        If this is True, this function uses an algorithm that uses slightly
+        more time but less memory.
+
+    Returns
+    -------
+    bool
+        Whether the graph is locally `(k, l)`-connected subgraph.
+
+    See also
+    --------
+    kl_connected_subgraph
+
+    References
+    ----------
+    .. [1] Chung, Fan and Linyuan Lu. "The Small World Phenomenon in Hybrid
+           Power Law Graphs." *Complex Networks*. Springer Berlin Heidelberg,
+           2004. 89--104.
+
+    """
+    graphOK = True
+    for edge in G.edges():
+        (u, v) = edge
+        # Get copy of graph needed for this search
+        if low_memory:
+            verts = {u, v}
+            for i in range(k):
+                [verts.update(G.neighbors(w)) for w in verts.copy()]
+            G2 = G.subgraph(verts)
+        else:
+            G2 = copy.deepcopy(G)
+        ###
+        path = [u, v]
+        cnt = 0
+        accept = 0
+        while path:
+            cnt += 1  # Found a path
+            if cnt >= l:
+                accept = 1
+                break
+            # record edges along this graph
+            prev = u
+            for w in path:
+                if w != prev:
+                    G2.remove_edge(prev, w)
+                    prev = w
+            #            path = shortest_path(G2, u, v, k) # ??? should "Cutoff" be k+1?
+            try:
+                path = nx.shortest_path(G2, u, v)  # ??? should "Cutoff" be k+1?
+            except nx.NetworkXNoPath:
+                path = False
+        # No Other Paths
+        if accept == 0:
+            graphOK = False
+            break
+    # return status
+    return graphOK

env-llmeval/lib/python3.10/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._dispatchable(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._dispatchable(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)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/planarity.py

@@ -0,0 +1,1402 @@
+from collections import defaultdict
+
+import networkx as nx
+
+__all__ = ["check_planarity", "is_planar", "PlanarEmbedding"]
+
+
+@nx._dispatchable
+def is_planar(G):
+    """Returns True if and only if `G` is planar.
+
+    A graph is *planar* iff it can be drawn in a plane without
+    any edge intersections.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    Returns
+    -------
+    bool
+       Whether the graph is planar.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(0, 1), (0, 2)])
+    >>> nx.is_planar(G)
+    True
+    >>> nx.is_planar(nx.complete_graph(5))
+    False
+
+    See Also
+    --------
+    check_planarity :
+        Check if graph is planar *and* return a `PlanarEmbedding` instance if True.
+    """
+
+    return check_planarity(G, counterexample=False)[0]
+
+
+@nx._dispatchable(returns_graph=True)
+def check_planarity(G, counterexample=False):
+    """Check if a graph is planar and return a counterexample or an embedding.
+
+    A graph is planar iff it can be drawn in a plane without
+    any edge intersections.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+    counterexample : bool
+        A Kuratowski subgraph (to proof non planarity) is only returned if set
+        to true.
+
+    Returns
+    -------
+    (is_planar, certificate) : (bool, NetworkX graph) tuple
+        is_planar is true if the graph is planar.
+        If the graph is planar `certificate` is a PlanarEmbedding
+        otherwise it is a Kuratowski subgraph.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(0, 1), (0, 2)])
+    >>> is_planar, P = nx.check_planarity(G)
+    >>> print(is_planar)
+    True
+
+    When `G` is planar, a `PlanarEmbedding` instance is returned:
+
+    >>> P.get_data()
+    {0: [1, 2], 1: [0], 2: [0]}
+
+    Notes
+    -----
+    A (combinatorial) embedding consists of cyclic orderings of the incident
+    edges at each vertex. Given such an embedding there are multiple approaches
+    discussed in literature to drawing the graph (subject to various
+    constraints, e.g. integer coordinates), see e.g. [2].
+
+    The planarity check algorithm and extraction of the combinatorial embedding
+    is based on the Left-Right Planarity Test [1].
+
+    A counterexample is only generated if the corresponding parameter is set,
+    because the complexity of the counterexample generation is higher.
+
+    See also
+    --------
+    is_planar :
+        Check for planarity without creating a `PlanarEmbedding` or counterexample.
+
+    References
+    ----------
+    .. [1] Ulrik Brandes:
+        The Left-Right Planarity Test
+        2009
+        http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.217.9208
+    .. [2] Takao Nishizeki, Md Saidur Rahman:
+        Planar graph drawing
+        Lecture Notes Series on Computing: Volume 12
+        2004
+    """
+
+    planarity_state = LRPlanarity(G)
+    embedding = planarity_state.lr_planarity()
+    if embedding is None:
+        # graph is not planar
+        if counterexample:
+            return False, get_counterexample(G)
+        else:
+            return False, None
+    else:
+        # graph is planar
+        return True, embedding
+
+
+@nx._dispatchable(returns_graph=True)
+def check_planarity_recursive(G, counterexample=False):
+    """Recursive version of :meth:`check_planarity`."""
+    planarity_state = LRPlanarity(G)
+    embedding = planarity_state.lr_planarity_recursive()
+    if embedding is None:
+        # graph is not planar
+        if counterexample:
+            return False, get_counterexample_recursive(G)
+        else:
+            return False, None
+    else:
+        # graph is planar
+        return True, embedding
+
+
+@nx._dispatchable(returns_graph=True)
+def get_counterexample(G):
+    """Obtains a Kuratowski subgraph.
+
+    Raises nx.NetworkXException if G is planar.
+
+    The function removes edges such that the graph is still not planar.
+    At some point the removal of any edge would make the graph planar.
+    This subgraph must be a Kuratowski subgraph.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    Returns
+    -------
+    subgraph : NetworkX graph
+        A Kuratowski subgraph that proves that G is not planar.
+
+    """
+    # copy graph
+    G = nx.Graph(G)
+
+    if check_planarity(G)[0]:
+        raise nx.NetworkXException("G is planar - no counter example.")
+
+    # find Kuratowski subgraph
+    subgraph = nx.Graph()
+    for u in G:
+        nbrs = list(G[u])
+        for v in nbrs:
+            G.remove_edge(u, v)
+            if check_planarity(G)[0]:
+                G.add_edge(u, v)
+                subgraph.add_edge(u, v)
+
+    return subgraph
+
+
+@nx._dispatchable(returns_graph=True)
+def get_counterexample_recursive(G):
+    """Recursive version of :meth:`get_counterexample`."""
+
+    # copy graph
+    G = nx.Graph(G)
+
+    if check_planarity_recursive(G)[0]:
+        raise nx.NetworkXException("G is planar - no counter example.")
+
+    # find Kuratowski subgraph
+    subgraph = nx.Graph()
+    for u in G:
+        nbrs = list(G[u])
+        for v in nbrs:
+            G.remove_edge(u, v)
+            if check_planarity_recursive(G)[0]:
+                G.add_edge(u, v)
+                subgraph.add_edge(u, v)
+
+    return subgraph
+
+
+class Interval:
+    """Represents a set of return edges.
+
+    All return edges in an interval induce a same constraint on the contained
+    edges, which means that all edges must either have a left orientation or
+    all edges must have a right orientation.
+    """
+
+    def __init__(self, low=None, high=None):
+        self.low = low
+        self.high = high
+
+    def empty(self):
+        """Check if the interval is empty"""
+        return self.low is None and self.high is None
+
+    def copy(self):
+        """Returns a copy of this interval"""
+        return Interval(self.low, self.high)
+
+    def conflicting(self, b, planarity_state):
+        """Returns True if interval I conflicts with edge b"""
+        return (
+            not self.empty()
+            and planarity_state.lowpt[self.high] > planarity_state.lowpt[b]
+        )
+
+
+class ConflictPair:
+    """Represents a different constraint between two intervals.
+
+    The edges in the left interval must have a different orientation than
+    the one in the right interval.
+    """
+
+    def __init__(self, left=Interval(), right=Interval()):
+        self.left = left
+        self.right = right
+
+    def swap(self):
+        """Swap left and right intervals"""
+        temp = self.left
+        self.left = self.right
+        self.right = temp
+
+    def lowest(self, planarity_state):
+        """Returns the lowest lowpoint of a conflict pair"""
+        if self.left.empty():
+            return planarity_state.lowpt[self.right.low]
+        if self.right.empty():
+            return planarity_state.lowpt[self.left.low]
+        return min(
+            planarity_state.lowpt[self.left.low], planarity_state.lowpt[self.right.low]
+        )
+
+
+def top_of_stack(l):
+    """Returns the element on top of the stack."""
+    if not l:
+        return None
+    return l[-1]
+
+
+class LRPlanarity:
+    """A class to maintain the state during planarity check."""
+
+    __slots__ = [
+        "G",
+        "roots",
+        "height",
+        "lowpt",
+        "lowpt2",
+        "nesting_depth",
+        "parent_edge",
+        "DG",
+        "adjs",
+        "ordered_adjs",
+        "ref",
+        "side",
+        "S",
+        "stack_bottom",
+        "lowpt_edge",
+        "left_ref",
+        "right_ref",
+        "embedding",
+    ]
+
+    def __init__(self, G):
+        # copy G without adding self-loops
+        self.G = nx.Graph()
+        self.G.add_nodes_from(G.nodes)
+        for e in G.edges:
+            if e[0] != e[1]:
+                self.G.add_edge(e[0], e[1])
+
+        self.roots = []
+
+        # distance from tree root
+        self.height = defaultdict(lambda: None)
+
+        self.lowpt = {}  # height of lowest return point of an edge
+        self.lowpt2 = {}  # height of second lowest return point
+        self.nesting_depth = {}  # for nesting order
+
+        # None -> missing edge
+        self.parent_edge = defaultdict(lambda: None)
+
+        # oriented DFS graph
+        self.DG = nx.DiGraph()
+        self.DG.add_nodes_from(G.nodes)
+
+        self.adjs = {}
+        self.ordered_adjs = {}
+
+        self.ref = defaultdict(lambda: None)
+        self.side = defaultdict(lambda: 1)
+
+        # stack of conflict pairs
+        self.S = []
+        self.stack_bottom = {}
+        self.lowpt_edge = {}
+
+        self.left_ref = {}
+        self.right_ref = {}
+
+        self.embedding = PlanarEmbedding()
+
+    def lr_planarity(self):
+        """Execute the LR planarity test.
+
+        Returns
+        -------
+        embedding : dict
+            If the graph is planar an embedding is returned. Otherwise None.
+        """
+        if self.G.order() > 2 and self.G.size() > 3 * self.G.order() - 6:
+            # graph is not planar
+            return None
+
+        # make adjacency lists for dfs
+        for v in self.G:
+            self.adjs[v] = list(self.G[v])
+
+        # orientation of the graph by depth first search traversal
+        for v in self.G:
+            if self.height[v] is None:
+                self.height[v] = 0
+                self.roots.append(v)
+                self.dfs_orientation(v)
+
+        # Free no longer used variables
+        self.G = None
+        self.lowpt2 = None
+        self.adjs = None
+
+        # testing
+        for v in self.DG:  # sort the adjacency lists by nesting depth
+            # note: this sorting leads to non linear time
+            self.ordered_adjs[v] = sorted(
+                self.DG[v], key=lambda x: self.nesting_depth[(v, x)]
+            )
+        for v in self.roots:
+            if not self.dfs_testing(v):
+                return None
+
+        # Free no longer used variables
+        self.height = None
+        self.lowpt = None
+        self.S = None
+        self.stack_bottom = None
+        self.lowpt_edge = None
+
+        for e in self.DG.edges:
+            self.nesting_depth[e] = self.sign(e) * self.nesting_depth[e]
+
+        self.embedding.add_nodes_from(self.DG.nodes)
+        for v in self.DG:
+            # sort the adjacency lists again
+            self.ordered_adjs[v] = sorted(
+                self.DG[v], key=lambda x: self.nesting_depth[(v, x)]
+            )
+            # initialize the embedding
+            previous_node = None
+            for w in self.ordered_adjs[v]:
+                self.embedding.add_half_edge(v, w, ccw=previous_node)
+                previous_node = w
+
+        # Free no longer used variables
+        self.DG = None
+        self.nesting_depth = None
+        self.ref = None
+
+        # compute the complete embedding
+        for v in self.roots:
+            self.dfs_embedding(v)
+
+        # Free no longer used variables
+        self.roots = None
+        self.parent_edge = None
+        self.ordered_adjs = None
+        self.left_ref = None
+        self.right_ref = None
+        self.side = None
+
+        return self.embedding
+
+    def lr_planarity_recursive(self):
+        """Recursive version of :meth:`lr_planarity`."""
+        if self.G.order() > 2 and self.G.size() > 3 * self.G.order() - 6:
+            # graph is not planar
+            return None
+
+        # orientation of the graph by depth first search traversal
+        for v in self.G:
+            if self.height[v] is None:
+                self.height[v] = 0
+                self.roots.append(v)
+                self.dfs_orientation_recursive(v)
+
+        # Free no longer used variable
+        self.G = None
+
+        # testing
+        for v in self.DG:  # sort the adjacency lists by nesting depth
+            # note: this sorting leads to non linear time
+            self.ordered_adjs[v] = sorted(
+                self.DG[v], key=lambda x: self.nesting_depth[(v, x)]
+            )
+        for v in self.roots:
+            if not self.dfs_testing_recursive(v):
+                return None
+
+        for e in self.DG.edges:
+            self.nesting_depth[e] = self.sign_recursive(e) * self.nesting_depth[e]
+
+        self.embedding.add_nodes_from(self.DG.nodes)
+        for v in self.DG:
+            # sort the adjacency lists again
+            self.ordered_adjs[v] = sorted(
+                self.DG[v], key=lambda x: self.nesting_depth[(v, x)]
+            )
+            # initialize the embedding
+            previous_node = None
+            for w in self.ordered_adjs[v]:
+                self.embedding.add_half_edge(v, w, ccw=previous_node)
+                previous_node = w
+
+        # compute the complete embedding
+        for v in self.roots:
+            self.dfs_embedding_recursive(v)
+
+        return self.embedding
+
+    def dfs_orientation(self, v):
+        """Orient the graph by DFS, compute lowpoints and nesting order."""
+        # the recursion stack
+        dfs_stack = [v]
+        # index of next edge to handle in adjacency list of each node
+        ind = defaultdict(lambda: 0)
+        # boolean to indicate whether to skip the initial work for an edge
+        skip_init = defaultdict(lambda: False)
+
+        while dfs_stack:
+            v = dfs_stack.pop()
+            e = self.parent_edge[v]
+
+            for w in self.adjs[v][ind[v] :]:
+                vw = (v, w)
+
+                if not skip_init[vw]:
+                    if (v, w) in self.DG.edges or (w, v) in self.DG.edges:
+                        ind[v] += 1
+                        continue  # the edge was already oriented
+
+                    self.DG.add_edge(v, w)  # orient the edge
+
+                    self.lowpt[vw] = self.height[v]
+                    self.lowpt2[vw] = self.height[v]
+                    if self.height[w] is None:  # (v, w) is a tree edge
+                        self.parent_edge[w] = vw
+                        self.height[w] = self.height[v] + 1
+
+                        dfs_stack.append(v)  # revisit v after finishing w
+                        dfs_stack.append(w)  # visit w next
+                        skip_init[vw] = True  # don't redo this block
+                        break  # handle next node in dfs_stack (i.e. w)
+                    else:  # (v, w) is a back edge
+                        self.lowpt[vw] = self.height[w]
+
+                # determine nesting graph
+                self.nesting_depth[vw] = 2 * self.lowpt[vw]
+                if self.lowpt2[vw] < self.height[v]:  # chordal
+                    self.nesting_depth[vw] += 1
+
+                # update lowpoints of parent edge e
+                if e is not None:
+                    if self.lowpt[vw] < self.lowpt[e]:
+                        self.lowpt2[e] = min(self.lowpt[e], self.lowpt2[vw])
+                        self.lowpt[e] = self.lowpt[vw]
+                    elif self.lowpt[vw] > self.lowpt[e]:
+                        self.lowpt2[e] = min(self.lowpt2[e], self.lowpt[vw])
+                    else:
+                        self.lowpt2[e] = min(self.lowpt2[e], self.lowpt2[vw])
+
+                ind[v] += 1
+
+    def dfs_orientation_recursive(self, v):
+        """Recursive version of :meth:`dfs_orientation`."""
+        e = self.parent_edge[v]
+        for w in self.G[v]:
+            if (v, w) in self.DG.edges or (w, v) in self.DG.edges:
+                continue  # the edge was already oriented
+            vw = (v, w)
+            self.DG.add_edge(v, w)  # orient the edge
+
+            self.lowpt[vw] = self.height[v]
+            self.lowpt2[vw] = self.height[v]
+            if self.height[w] is None:  # (v, w) is a tree edge
+                self.parent_edge[w] = vw
+                self.height[w] = self.height[v] + 1
+                self.dfs_orientation_recursive(w)
+            else:  # (v, w) is a back edge
+                self.lowpt[vw] = self.height[w]
+
+            # determine nesting graph
+            self.nesting_depth[vw] = 2 * self.lowpt[vw]
+            if self.lowpt2[vw] < self.height[v]:  # chordal
+                self.nesting_depth[vw] += 1
+
+            # update lowpoints of parent edge e
+            if e is not None:
+                if self.lowpt[vw] < self.lowpt[e]:
+                    self.lowpt2[e] = min(self.lowpt[e], self.lowpt2[vw])
+                    self.lowpt[e] = self.lowpt[vw]
+                elif self.lowpt[vw] > self.lowpt[e]:
+                    self.lowpt2[e] = min(self.lowpt2[e], self.lowpt[vw])
+                else:
+                    self.lowpt2[e] = min(self.lowpt2[e], self.lowpt2[vw])
+
+    def dfs_testing(self, v):
+        """Test for LR partition."""
+        # the recursion stack
+        dfs_stack = [v]
+        # index of next edge to handle in adjacency list of each node
+        ind = defaultdict(lambda: 0)
+        # boolean to indicate whether to skip the initial work for an edge
+        skip_init = defaultdict(lambda: False)
+
+        while dfs_stack:
+            v = dfs_stack.pop()
+            e = self.parent_edge[v]
+            # to indicate whether to skip the final block after the for loop
+            skip_final = False
+
+            for w in self.ordered_adjs[v][ind[v] :]:
+                ei = (v, w)
+
+                if not skip_init[ei]:
+                    self.stack_bottom[ei] = top_of_stack(self.S)
+
+                    if ei == self.parent_edge[w]:  # tree edge
+                        dfs_stack.append(v)  # revisit v after finishing w
+                        dfs_stack.append(w)  # visit w next
+                        skip_init[ei] = True  # don't redo this block
+                        skip_final = True  # skip final work after breaking
+                        break  # handle next node in dfs_stack (i.e. w)
+                    else:  # back edge
+                        self.lowpt_edge[ei] = ei
+                        self.S.append(ConflictPair(right=Interval(ei, ei)))
+
+                # integrate new return edges
+                if self.lowpt[ei] < self.height[v]:
+                    if w == self.ordered_adjs[v][0]:  # e_i has return edge
+                        self.lowpt_edge[e] = self.lowpt_edge[ei]
+                    else:  # add constraints of e_i
+                        if not self.add_constraints(ei, e):
+                            # graph is not planar
+                            return False
+
+                ind[v] += 1
+
+            if not skip_final:
+                # remove back edges returning to parent
+                if e is not None:  # v isn't root
+                    self.remove_back_edges(e)
+
+        return True
+
+    def dfs_testing_recursive(self, v):
+        """Recursive version of :meth:`dfs_testing`."""
+        e = self.parent_edge[v]
+        for w in self.ordered_adjs[v]:
+            ei = (v, w)
+            self.stack_bottom[ei] = top_of_stack(self.S)
+            if ei == self.parent_edge[w]:  # tree edge
+                if not self.dfs_testing_recursive(w):
+                    return False
+            else:  # back edge
+                self.lowpt_edge[ei] = ei
+                self.S.append(ConflictPair(right=Interval(ei, ei)))
+
+            # integrate new return edges
+            if self.lowpt[ei] < self.height[v]:
+                if w == self.ordered_adjs[v][0]:  # e_i has return edge
+                    self.lowpt_edge[e] = self.lowpt_edge[ei]
+                else:  # add constraints of e_i
+                    if not self.add_constraints(ei, e):
+                        # graph is not planar
+                        return False
+
+        # remove back edges returning to parent
+        if e is not None:  # v isn't root
+            self.remove_back_edges(e)
+        return True
+
+    def add_constraints(self, ei, e):
+        P = ConflictPair()
+        # merge return edges of e_i into P.right
+        while True:
+            Q = self.S.pop()
+            if not Q.left.empty():
+                Q.swap()
+            if not Q.left.empty():  # not planar
+                return False
+            if self.lowpt[Q.right.low] > self.lowpt[e]:
+                # merge intervals
+                if P.right.empty():  # topmost interval
+                    P.right = Q.right.copy()
+                else:
+                    self.ref[P.right.low] = Q.right.high
+                P.right.low = Q.right.low
+            else:  # align
+                self.ref[Q.right.low] = self.lowpt_edge[e]
+            if top_of_stack(self.S) == self.stack_bottom[ei]:
+                break
+        # merge conflicting return edges of e_1,...,e_i-1 into P.L
+        while top_of_stack(self.S).left.conflicting(ei, self) or top_of_stack(
+            self.S
+        ).right.conflicting(ei, self):
+            Q = self.S.pop()
+            if Q.right.conflicting(ei, self):
+                Q.swap()
+            if Q.right.conflicting(ei, self):  # not planar
+                return False
+            # merge interval below lowpt(e_i) into P.R
+            self.ref[P.right.low] = Q.right.high
+            if Q.right.low is not None:
+                P.right.low = Q.right.low
+
+            if P.left.empty():  # topmost interval
+                P.left = Q.left.copy()
+            else:
+                self.ref[P.left.low] = Q.left.high
+            P.left.low = Q.left.low
+
+        if not (P.left.empty() and P.right.empty()):
+            self.S.append(P)
+        return True
+
+    def remove_back_edges(self, e):
+        u = e[0]
+        # trim back edges ending at parent u
+        # drop entire conflict pairs
+        while self.S and top_of_stack(self.S).lowest(self) == self.height[u]:
+            P = self.S.pop()
+            if P.left.low is not None:
+                self.side[P.left.low] = -1
+
+        if self.S:  # one more conflict pair to consider
+            P = self.S.pop()
+            # trim left interval
+            while P.left.high is not None and P.left.high[1] == u:
+                P.left.high = self.ref[P.left.high]
+            if P.left.high is None and P.left.low is not None:
+                # just emptied
+                self.ref[P.left.low] = P.right.low
+                self.side[P.left.low] = -1
+                P.left.low = None
+            # trim right interval
+            while P.right.high is not None and P.right.high[1] == u:
+                P.right.high = self.ref[P.right.high]
+            if P.right.high is None and P.right.low is not None:
+                # just emptied
+                self.ref[P.right.low] = P.left.low
+                self.side[P.right.low] = -1
+                P.right.low = None
+            self.S.append(P)
+
+        # side of e is side of a highest return edge
+        if self.lowpt[e] < self.height[u]:  # e has return edge
+            hl = top_of_stack(self.S).left.high
+            hr = top_of_stack(self.S).right.high
+
+            if hl is not None and (hr is None or self.lowpt[hl] > self.lowpt[hr]):
+                self.ref[e] = hl
+            else:
+                self.ref[e] = hr
+
+    def dfs_embedding(self, v):
+        """Completes the embedding."""
+        # the recursion stack
+        dfs_stack = [v]
+        # index of next edge to handle in adjacency list of each node
+        ind = defaultdict(lambda: 0)
+
+        while dfs_stack:
+            v = dfs_stack.pop()
+
+            for w in self.ordered_adjs[v][ind[v] :]:
+                ind[v] += 1
+                ei = (v, w)
+
+                if ei == self.parent_edge[w]:  # tree edge
+                    self.embedding.add_half_edge_first(w, v)
+                    self.left_ref[v] = w
+                    self.right_ref[v] = w
+
+                    dfs_stack.append(v)  # revisit v after finishing w
+                    dfs_stack.append(w)  # visit w next
+                    break  # handle next node in dfs_stack (i.e. w)
+                else:  # back edge
+                    if self.side[ei] == 1:
+                        self.embedding.add_half_edge(w, v, ccw=self.right_ref[w])
+                    else:
+                        self.embedding.add_half_edge(w, v, cw=self.left_ref[w])
+                        self.left_ref[w] = v
+
+    def dfs_embedding_recursive(self, v):
+        """Recursive version of :meth:`dfs_embedding`."""
+        for w in self.ordered_adjs[v]:
+            ei = (v, w)
+            if ei == self.parent_edge[w]:  # tree edge
+                self.embedding.add_half_edge_first(w, v)
+                self.left_ref[v] = w
+                self.right_ref[v] = w
+                self.dfs_embedding_recursive(w)
+            else:  # back edge
+                if self.side[ei] == 1:
+                    # place v directly after right_ref[w] in embed. list of w
+                    self.embedding.add_half_edge(w, v, ccw=self.right_ref[w])
+                else:
+                    # place v directly before left_ref[w] in embed. list of w
+                    self.embedding.add_half_edge(w, v, cw=self.left_ref[w])
+                    self.left_ref[w] = v
+
+    def sign(self, e):
+        """Resolve the relative side of an edge to the absolute side."""
+        # the recursion stack
+        dfs_stack = [e]
+        # dict to remember reference edges
+        old_ref = defaultdict(lambda: None)
+
+        while dfs_stack:
+            e = dfs_stack.pop()
+
+            if self.ref[e] is not None:
+                dfs_stack.append(e)  # revisit e after finishing self.ref[e]
+                dfs_stack.append(self.ref[e])  # visit self.ref[e] next
+                old_ref[e] = self.ref[e]  # remember value of self.ref[e]
+                self.ref[e] = None
+            else:
+                self.side[e] *= self.side[old_ref[e]]
+
+        return self.side[e]
+
+    def sign_recursive(self, e):
+        """Recursive version of :meth:`sign`."""
+        if self.ref[e] is not None:
+            self.side[e] = self.side[e] * self.sign_recursive(self.ref[e])
+            self.ref[e] = None
+        return self.side[e]
+
+
+class PlanarEmbedding(nx.DiGraph):
+    """Represents a planar graph with its planar embedding.
+
+    The planar embedding is given by a `combinatorial embedding
+    <https://en.wikipedia.org/wiki/Graph_embedding#Combinatorial_embedding>`_.
+
+    .. note:: `check_planarity` is the preferred way to check if a graph is planar.
+
+    **Neighbor ordering:**
+
+    In comparison to a usual graph structure, the embedding also stores the
+    order of all neighbors for every vertex.
+    The order of the neighbors can be given in clockwise (cw) direction or
+    counterclockwise (ccw) direction. This order is stored as edge attributes
+    in the underlying directed graph. For the edge (u, v) the edge attribute
+    'cw' is set to the neighbor of u that follows immediately after v in
+    clockwise direction.
+
+    In order for a PlanarEmbedding to be valid it must fulfill multiple
+    conditions. It is possible to check if these conditions are fulfilled with
+    the method :meth:`check_structure`.
+    The conditions are:
+
+    * Edges must go in both directions (because the edge attributes differ)
+    * Every edge must have a 'cw' and 'ccw' attribute which corresponds to a
+      correct planar embedding.
+
+    As long as a PlanarEmbedding is invalid only the following methods should
+    be called:
+
+    * :meth:`add_half_edge`
+    * :meth:`connect_components`
+
+    Even though the graph is a subclass of nx.DiGraph, it can still be used
+    for algorithms that require undirected graphs, because the method
+    :meth:`is_directed` is overridden. This is possible, because a valid
+    PlanarGraph must have edges in both directions.
+
+    **Half edges:**
+
+    In methods like `add_half_edge` the term "half-edge" is used, which is
+    a term that is used in `doubly connected edge lists
+    <https://en.wikipedia.org/wiki/Doubly_connected_edge_list>`_. It is used
+    to emphasize that the edge is only in one direction and there exists
+    another half-edge in the opposite direction.
+    While conventional edges always have two faces (including outer face) next
+    to them, it is possible to assign each half-edge *exactly one* face.
+    For a half-edge (u, v) that is oriented such that u is below v then the
+    face that belongs to (u, v) is to the right of this half-edge.
+
+    See Also
+    --------
+    is_planar :
+        Preferred way to check if an existing graph is planar.
+
+    check_planarity :
+        A convenient way to create a `PlanarEmbedding`. If not planar,
+        it returns a subgraph that shows this.
+
+    Examples
+    --------
+
+    Create an embedding of a star graph (compare `nx.star_graph(3)`):
+
+    >>> G = nx.PlanarEmbedding()
+    >>> G.add_half_edge(0, 1)
+    >>> G.add_half_edge(0, 2, ccw=1)
+    >>> G.add_half_edge(0, 3, ccw=2)
+    >>> G.add_half_edge(1, 0)
+    >>> G.add_half_edge(2, 0)
+    >>> G.add_half_edge(3, 0)
+
+    Alternatively the same embedding can also be defined in counterclockwise
+    orientation. The following results in exactly the same PlanarEmbedding:
+
+    >>> G = nx.PlanarEmbedding()
+    >>> G.add_half_edge(0, 1)
+    >>> G.add_half_edge(0, 3, cw=1)
+    >>> G.add_half_edge(0, 2, cw=3)
+    >>> G.add_half_edge(1, 0)
+    >>> G.add_half_edge(2, 0)
+    >>> G.add_half_edge(3, 0)
+
+    After creating a graph, it is possible to validate that the PlanarEmbedding
+    object is correct:
+
+    >>> G.check_structure()
+
+    """
+
+    def __init__(self, incoming_graph_data=None, **attr):
+        super().__init__(incoming_graph_data=incoming_graph_data, **attr)
+        self.add_edge = self.__forbidden
+        self.add_edges_from = self.__forbidden
+        self.add_weighted_edges_from = self.__forbidden
+
+    def __forbidden(self, *args, **kwargs):
+        """Forbidden operation
+
+        Any edge additions to a PlanarEmbedding should be done using
+        method `add_half_edge`.
+        """
+        raise NotImplementedError(
+            "Use `add_half_edge` method to add edges to a PlanarEmbedding."
+        )
+
+    def get_data(self):
+        """Converts the adjacency structure into a better readable structure.
+
+        Returns
+        -------
+        embedding : dict
+            A dict mapping all nodes to a list of neighbors sorted in
+            clockwise order.
+
+        See Also
+        --------
+        set_data
+
+        """
+        embedding = {}
+        for v in self:
+            embedding[v] = list(self.neighbors_cw_order(v))
+        return embedding
+
+    def set_data(self, data):
+        """Inserts edges according to given sorted neighbor list.
+
+        The input format is the same as the output format of get_data().
+
+        Parameters
+        ----------
+        data : dict
+            A dict mapping all nodes to a list of neighbors sorted in
+            clockwise order.
+
+        See Also
+        --------
+        get_data
+
+        """
+        for v in data:
+            ref = None
+            for w in reversed(data[v]):
+                self.add_half_edge(v, w, cw=ref)
+                ref = w
+
+    def remove_node(self, n):
+        """Remove node n.
+
+        Removes the node n and all adjacent edges, updating the
+        PlanarEmbedding to account for any resulting edge removal.
+        Attempting to remove a non-existent node will raise an exception.
+
+        Parameters
+        ----------
+        n : node
+           A node in the graph
+
+        Raises
+        ------
+        NetworkXError
+           If n is not in the graph.
+
+        See Also
+        --------
+        remove_nodes_from
+
+        """
+        try:
+            for u in self._pred[n]:
+                succs_u = self._succ[u]
+                un_cw = succs_u[n]["cw"]
+                un_ccw = succs_u[n]["ccw"]
+                del succs_u[n]
+                del self._pred[u][n]
+                if n != un_cw:
+                    succs_u[un_cw]["ccw"] = un_ccw
+                    succs_u[un_ccw]["cw"] = un_cw
+            del self._node[n]
+            del self._succ[n]
+            del self._pred[n]
+        except KeyError as err:  # NetworkXError if n not in self
+            raise nx.NetworkXError(
+                f"The node {n} is not in the planar embedding."
+            ) from err
+        nx._clear_cache(self)
+
+    def remove_nodes_from(self, nodes):
+        """Remove multiple nodes.
+
+        Parameters
+        ----------
+        nodes : iterable container
+            A container of nodes (list, dict, set, etc.).  If a node
+            in the container is not in the graph it is silently ignored.
+
+        See Also
+        --------
+        remove_node
+
+        Notes
+        -----
+        When removing nodes from an iterator over the graph you are changing,
+        a `RuntimeError` will be raised with message:
+        `RuntimeError: dictionary changed size during iteration`. This
+        happens when the graph's underlying dictionary is modified during
+        iteration. To avoid this error, evaluate the iterator into a separate
+        object, e.g. by using `list(iterator_of_nodes)`, and pass this
+        object to `G.remove_nodes_from`.
+
+        """
+        for n in nodes:
+            if n in self._node:
+                self.remove_node(n)
+            # silently skip non-existing nodes
+
+    def neighbors_cw_order(self, v):
+        """Generator for the neighbors of v in clockwise order.
+
+        Parameters
+        ----------
+        v : node
+
+        Yields
+        ------
+        node
+
+        """
+        succs = self._succ[v]
+        if not succs:
+            # v has no neighbors
+            return
+        start_node = next(reversed(succs))
+        yield start_node
+        current_node = succs[start_node]["cw"]
+        while start_node != current_node:
+            yield current_node
+            current_node = succs[current_node]["cw"]
+
+    def add_half_edge(self, start_node, end_node, *, cw=None, ccw=None):
+        """Adds a half-edge from `start_node` to `end_node`.
+
+        If the half-edge is not the first one out of `start_node`, a reference
+        node must be provided either in the clockwise (parameter `cw`) or in
+        the counterclockwise (parameter `ccw`) direction. Only one of `cw`/`ccw`
+        can be specified (or neither in the case of the first edge).
+        Note that specifying a reference in the clockwise (`cw`) direction means
+        inserting the new edge in the first counterclockwise position with
+        respect to the reference (and vice-versa).
+
+        Parameters
+        ----------
+        start_node : node
+            Start node of inserted edge.
+        end_node : node
+            End node of inserted edge.
+        cw, ccw: node
+            End node of reference edge.
+            Omit or pass `None` if adding the first out-half-edge of `start_node`.
+
+
+        Raises
+        ------
+        NetworkXException
+            If the `cw` or `ccw` node is not a successor of `start_node`.
+            If `start_node` has successors, but neither `cw` or `ccw` is provided.
+            If both `cw` and `ccw` are specified.
+
+        See Also
+        --------
+        connect_components
+        """
+
+        succs = self._succ.get(start_node)
+        if succs:
+            # there is already some edge out of start_node
+            leftmost_nbr = next(reversed(self._succ[start_node]))
+            if cw is not None:
+                if cw not in succs:
+                    raise nx.NetworkXError("Invalid clockwise reference node.")
+                if ccw is not None:
+                    raise nx.NetworkXError("Only one of cw/ccw can be specified.")
+                ref_ccw = succs[cw]["ccw"]
+                super().add_edge(start_node, end_node, cw=cw, ccw=ref_ccw)
+                succs[ref_ccw]["cw"] = end_node
+                succs[cw]["ccw"] = end_node
+                # when (cw == leftmost_nbr), the newly added neighbor is
+                # already at the end of dict self._succ[start_node] and
+                # takes the place of the former leftmost_nbr
+                move_leftmost_nbr_to_end = cw != leftmost_nbr
+            elif ccw is not None:
+                if ccw not in succs:
+                    raise nx.NetworkXError("Invalid counterclockwise reference node.")
+                ref_cw = succs[ccw]["cw"]
+                super().add_edge(start_node, end_node, cw=ref_cw, ccw=ccw)
+                succs[ref_cw]["ccw"] = end_node
+                succs[ccw]["cw"] = end_node
+                move_leftmost_nbr_to_end = True
+            else:
+                raise nx.NetworkXError(
+                    "Node already has out-half-edge(s), either cw or ccw reference node required."
+                )
+            if move_leftmost_nbr_to_end:
+                # LRPlanarity (via self.add_half_edge_first()) requires that
+                # we keep track of the leftmost neighbor, which we accomplish
+                # by keeping it as the last key in dict self._succ[start_node]
+                succs[leftmost_nbr] = succs.pop(leftmost_nbr)
+
+        else:
+            if cw is not None or ccw is not None:
+                raise nx.NetworkXError("Invalid reference node.")
+            # adding the first edge out of start_node
+            super().add_edge(start_node, end_node, ccw=end_node, cw=end_node)
+
+    def check_structure(self):
+        """Runs without exceptions if this object is valid.
+
+        Checks that the following properties are fulfilled:
+
+        * Edges go in both directions (because the edge attributes differ).
+        * Every edge has a 'cw' and 'ccw' attribute which corresponds to a
+          correct planar embedding.
+
+        Running this method verifies that the underlying Graph must be planar.
+
+        Raises
+        ------
+        NetworkXException
+            This exception is raised with a short explanation if the
+            PlanarEmbedding is invalid.
+        """
+        # Check fundamental structure
+        for v in self:
+            try:
+                sorted_nbrs = set(self.neighbors_cw_order(v))
+            except KeyError as err:
+                msg = f"Bad embedding. Missing orientation for a neighbor of {v}"
+                raise nx.NetworkXException(msg) from err
+
+            unsorted_nbrs = set(self[v])
+            if sorted_nbrs != unsorted_nbrs:
+                msg = "Bad embedding. Edge orientations not set correctly."
+                raise nx.NetworkXException(msg)
+            for w in self[v]:
+                # Check if opposite half-edge exists
+                if not self.has_edge(w, v):
+                    msg = "Bad embedding. Opposite half-edge is missing."
+                    raise nx.NetworkXException(msg)
+
+        # Check planarity
+        counted_half_edges = set()
+        for component in nx.connected_components(self):
+            if len(component) == 1:
+                # Don't need to check single node component
+                continue
+            num_nodes = len(component)
+            num_half_edges = 0
+            num_faces = 0
+            for v in component:
+                for w in self.neighbors_cw_order(v):
+                    num_half_edges += 1
+                    if (v, w) not in counted_half_edges:
+                        # We encountered a new face
+                        num_faces += 1
+                        # Mark all half-edges belonging to this face
+                        self.traverse_face(v, w, counted_half_edges)
+            num_edges = num_half_edges // 2  # num_half_edges is even
+            if num_nodes - num_edges + num_faces != 2:
+                # The result does not match Euler's formula
+                msg = "Bad embedding. The graph does not match Euler's formula"
+                raise nx.NetworkXException(msg)
+
+    def add_half_edge_ccw(self, start_node, end_node, reference_neighbor):
+        """Adds a half-edge from start_node to end_node.
+
+        The half-edge is added counter clockwise next to the existing half-edge
+        (start_node, reference_neighbor).
+
+        Parameters
+        ----------
+        start_node : node
+            Start node of inserted edge.
+        end_node : node
+            End node of inserted edge.
+        reference_neighbor: node
+            End node of reference edge.
+
+        Raises
+        ------
+        NetworkXException
+            If the reference_neighbor does not exist.
+
+        See Also
+        --------
+        add_half_edge
+        add_half_edge_cw
+        connect_components
+
+        """
+        self.add_half_edge(start_node, end_node, cw=reference_neighbor)
+
+    def add_half_edge_cw(self, start_node, end_node, reference_neighbor):
+        """Adds a half-edge from start_node to end_node.
+
+        The half-edge is added clockwise next to the existing half-edge
+        (start_node, reference_neighbor).
+
+        Parameters
+        ----------
+        start_node : node
+            Start node of inserted edge.
+        end_node : node
+            End node of inserted edge.
+        reference_neighbor: node
+            End node of reference edge.
+
+        Raises
+        ------
+        NetworkXException
+            If the reference_neighbor does not exist.
+
+        See Also
+        --------
+        add_half_edge
+        add_half_edge_ccw
+        connect_components
+        """
+        self.add_half_edge(start_node, end_node, ccw=reference_neighbor)
+
+    def remove_edge(self, u, v):
+        """Remove the edge between u and v.
+
+        Parameters
+        ----------
+        u, v : nodes
+        Remove the half-edges (u, v) and (v, u) and update the
+        edge ordering around the removed edge.
+
+        Raises
+        ------
+        NetworkXError
+        If there is not an edge between u and v.
+
+        See Also
+        --------
+        remove_edges_from : remove a collection of edges
+        """
+        try:
+            succs_u = self._succ[u]
+            succs_v = self._succ[v]
+            uv_cw = succs_u[v]["cw"]
+            uv_ccw = succs_u[v]["ccw"]
+            vu_cw = succs_v[u]["cw"]
+            vu_ccw = succs_v[u]["ccw"]
+            del succs_u[v]
+            del self._pred[v][u]
+            del succs_v[u]
+            del self._pred[u][v]
+            if v != uv_cw:
+                succs_u[uv_cw]["ccw"] = uv_ccw
+                succs_u[uv_ccw]["cw"] = uv_cw
+            if u != vu_cw:
+                succs_v[vu_cw]["ccw"] = vu_ccw
+                succs_v[vu_ccw]["cw"] = vu_cw
+        except KeyError as err:
+            raise nx.NetworkXError(
+                f"The edge {u}-{v} is not in the planar embedding."
+            ) from err
+        nx._clear_cache(self)
+
+    def remove_edges_from(self, ebunch):
+        """Remove all edges specified in ebunch.
+
+        Parameters
+        ----------
+        ebunch: list or container of edge tuples
+            Each pair of half-edges between the nodes given in the tuples
+            will be removed from the graph. The nodes can be passed as:
+
+                - 2-tuples (u, v) half-edges (u, v) and (v, u).
+                - 3-tuples (u, v, k) where k is ignored.
+
+        See Also
+        --------
+        remove_edge : remove a single edge
+
+        Notes
+        -----
+        Will fail silently if an edge in ebunch is not in the graph.
+
+        Examples
+        --------
+        >>> G = nx.path_graph(4)  # or DiGraph, MultiGraph, MultiDiGraph, etc
+        >>> ebunch = [(1, 2), (2, 3)]
+        >>> G.remove_edges_from(ebunch)
+        """
+        for e in ebunch:
+            u, v = e[:2]  # ignore edge data
+            # assuming that the PlanarEmbedding is valid, if the half_edge
+            # (u, v) is in the graph, then so is half_edge (v, u)
+            if u in self._succ and v in self._succ[u]:
+                self.remove_edge(u, v)
+
+    def connect_components(self, v, w):
+        """Adds half-edges for (v, w) and (w, v) at some position.
+
+        This method should only be called if v and w are in different
+        components, or it might break the embedding.
+        This especially means that if `connect_components(v, w)`
+        is called it is not allowed to call `connect_components(w, v)`
+        afterwards. The neighbor orientations in both directions are
+        all set correctly after the first call.
+
+        Parameters
+        ----------
+        v : node
+        w : node
+
+        See Also
+        --------
+        add_half_edge
+        """
+        if v in self._succ and self._succ[v]:
+            ref = next(reversed(self._succ[v]))
+        else:
+            ref = None
+        self.add_half_edge(v, w, cw=ref)
+        if w in self._succ and self._succ[w]:
+            ref = next(reversed(self._succ[w]))
+        else:
+            ref = None
+        self.add_half_edge(w, v, cw=ref)
+
+    def add_half_edge_first(self, start_node, end_node):
+        """Add a half-edge and set end_node as start_node's leftmost neighbor.
+
+        The new edge is inserted counterclockwise with respect to the current
+        leftmost neighbor, if there is one.
+
+        Parameters
+        ----------
+        start_node : node
+        end_node : node
+
+        See Also
+        --------
+        add_half_edge
+        connect_components
+        """
+        succs = self._succ.get(start_node)
+        # the leftmost neighbor is the last entry in the
+        # self._succ[start_node] dict
+        leftmost_nbr = next(reversed(succs)) if succs else None
+        self.add_half_edge(start_node, end_node, cw=leftmost_nbr)
+
+    def next_face_half_edge(self, v, w):
+        """Returns the following half-edge left of a face.
+
+        Parameters
+        ----------
+        v : node
+        w : node
+
+        Returns
+        -------
+        half-edge : tuple
+        """
+        new_node = self[w][v]["ccw"]
+        return w, new_node
+
+    def traverse_face(self, v, w, mark_half_edges=None):
+        """Returns nodes on the face that belong to the half-edge (v, w).
+
+        The face that is traversed lies to the right of the half-edge (in an
+        orientation where v is below w).
+
+        Optionally it is possible to pass a set to which all encountered half
+        edges are added. Before calling this method, this set must not include
+        any half-edges that belong to the face.
+
+        Parameters
+        ----------
+        v : node
+            Start node of half-edge.
+        w : node
+            End node of half-edge.
+        mark_half_edges: set, optional
+            Set to which all encountered half-edges are added.
+
+        Returns
+        -------
+        face : list
+            A list of nodes that lie on this face.
+        """
+        if mark_half_edges is None:
+            mark_half_edges = set()
+
+        face_nodes = [v]
+        mark_half_edges.add((v, w))
+        prev_node = v
+        cur_node = w
+        # Last half-edge is (incoming_node, v)
+        incoming_node = self[v][w]["cw"]
+
+        while cur_node != v or prev_node != incoming_node:
+            face_nodes.append(cur_node)
+            prev_node, cur_node = self.next_face_half_edge(prev_node, cur_node)
+            if (prev_node, cur_node) in mark_half_edges:
+                raise nx.NetworkXException("Bad planar embedding. Impossible face.")
+            mark_half_edges.add((prev_node, cur_node))
+
+        return face_nodes
+
+    def is_directed(self):
+        """A valid PlanarEmbedding is undirected.
+
+        All reverse edges are contained, i.e. for every existing
+        half-edge (v, w) the half-edge in the opposite direction (w, v) is also
+        contained.
+        """
+        return False
+
+    def copy(self, as_view=False):
+        if as_view is True:
+            return nx.graphviews.generic_graph_view(self)
+        G = self.__class__()
+        G.graph.update(self.graph)
+        G.add_nodes_from((n, d.copy()) for n, d in self._node.items())
+        super(self.__class__, G).add_edges_from(
+            (u, v, datadict.copy())
+            for u, nbrs in self._adj.items()
+            for v, datadict in nbrs.items()
+        )
+        return G

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/polynomials.py

@@ -0,0 +1,305 @@
+"""Provides algorithms supporting the computation of graph polynomials.
+
+Graph polynomials are polynomial-valued graph invariants that encode a wide
+variety of structural information. Examples include the Tutte polynomial,
+chromatic polynomial, characteristic polynomial, and matching polynomial. An
+extensive treatment is provided in [1]_.
+
+For a simple example, the `~sympy.matrices.matrices.MatrixDeterminant.charpoly`
+method can be used to compute the characteristic polynomial from the adjacency
+matrix of a graph. Consider the complete graph ``K_4``:
+
+>>> import sympy
+>>> x = sympy.Symbol("x")
+>>> G = nx.complete_graph(4)
+>>> A = nx.adjacency_matrix(G)
+>>> M = sympy.SparseMatrix(A.todense())
+>>> M.charpoly(x).as_expr()
+x**4 - 6*x**2 - 8*x - 3
+
+
+.. [1] Y. Shi, M. Dehmer, X. Li, I. Gutman,
+   "Graph Polynomials"
+"""
+from collections import deque
+
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+__all__ = ["tutte_polynomial", "chromatic_polynomial"]
+
+
+@not_implemented_for("directed")
+@nx._dispatchable
+def tutte_polynomial(G):
+    r"""Returns the Tutte polynomial of `G`
+
+    This function computes the Tutte polynomial via an iterative version of
+    the deletion-contraction algorithm.
+
+    The Tutte polynomial `T_G(x, y)` is a fundamental graph polynomial invariant in
+    two variables. It encodes a wide array of information related to the
+    edge-connectivity of a graph; "Many problems about graphs can be reduced to
+    problems of finding and evaluating the Tutte polynomial at certain values" [1]_.
+    In fact, every deletion-contraction-expressible feature of a graph is a
+    specialization of the Tutte polynomial [2]_ (see Notes for examples).
+
+    There are several equivalent definitions; here are three:
+
+    Def 1 (rank-nullity expansion): For `G` an undirected graph, `n(G)` the
+    number of vertices of `G`, `E` the edge set of `G`, `V` the vertex set of
+    `G`, and `c(A)` the number of connected components of the graph with vertex
+    set `V` and edge set `A` [3]_:
+
+    .. math::
+
+        T_G(x, y) = \sum_{A \in E} (x-1)^{c(A) - c(E)} (y-1)^{c(A) + |A| - n(G)}
+
+    Def 2 (spanning tree expansion): Let `G` be an undirected graph, `T` a spanning
+    tree of `G`, and `E` the edge set of `G`. Let `E` have an arbitrary strict
+    linear order `L`. Let `B_e` be the unique minimal nonempty edge cut of
+    $E \setminus T \cup {e}$. An edge `e` is internally active with respect to
+    `T` and `L` if `e` is the least edge in `B_e` according to the linear order
+    `L`. The internal activity of `T` (denoted `i(T)`) is the number of edges
+    in $E \setminus T$ that are internally active with respect to `T` and `L`.
+    Let `P_e` be the unique path in $T \cup {e}$ whose source and target vertex
+    are the same. An edge `e` is externally active with respect to `T` and `L`
+    if `e` is the least edge in `P_e` according to the linear order `L`. The
+    external activity of `T` (denoted `e(T)`) is the number of edges in
+    $E \setminus T$ that are externally active with respect to `T` and `L`.
+    Then [4]_ [5]_:
+
+    .. math::
+
+        T_G(x, y) = \sum_{T \text{ a spanning tree of } G} x^{i(T)} y^{e(T)}
+
+    Def 3 (deletion-contraction recurrence): For `G` an undirected graph, `G-e`
+    the graph obtained from `G` by deleting edge `e`, `G/e` the graph obtained
+    from `G` by contracting edge `e`, `k(G)` the number of cut-edges of `G`,
+    and `l(G)` the number of self-loops of `G`:
+
+    .. math::
+        T_G(x, y) = \begin{cases}
+    	   x^{k(G)} y^{l(G)}, & \text{if all edges are cut-edges or self-loops} \\
+           T_{G-e}(x, y) + T_{G/e}(x, y), & \text{otherwise, for an arbitrary edge $e$ not a cut-edge or loop}
+        \end{cases}
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    Returns
+    -------
+    instance of `sympy.core.add.Add`
+        A Sympy expression representing the Tutte polynomial for `G`.
+
+    Examples
+    --------
+    >>> C = nx.cycle_graph(5)
+    >>> nx.tutte_polynomial(C)
+    x**4 + x**3 + x**2 + x + y
+
+    >>> D = nx.diamond_graph()
+    >>> nx.tutte_polynomial(D)
+    x**3 + 2*x**2 + 2*x*y + x + y**2 + y
+
+    Notes
+    -----
+    Some specializations of the Tutte polynomial:
+
+    - `T_G(1, 1)` counts the number of spanning trees of `G`
+    - `T_G(1, 2)` counts the number of connected spanning subgraphs of `G`
+    - `T_G(2, 1)` counts the number of spanning forests in `G`
+    - `T_G(0, 2)` counts the number of strong orientations of `G`
+    - `T_G(2, 0)` counts the number of acyclic orientations of `G`
+
+    Edge contraction is defined and deletion-contraction is introduced in [6]_.
+    Combinatorial meaning of the coefficients is introduced in [7]_.
+    Universality, properties, and applications are discussed in [8]_.
+
+    Practically, up-front computation of the Tutte polynomial may be useful when
+    users wish to repeatedly calculate edge-connectivity-related information
+    about one or more graphs.
+
+    References
+    ----------
+    .. [1] M. Brandt,
+       "The Tutte Polynomial."
+       Talking About Combinatorial Objects Seminar, 2015
+       https://math.berkeley.edu/~brandtm/talks/tutte.pdf
+    .. [2] A. Björklund, T. Husfeldt, P. Kaski, M. Koivisto,
+       "Computing the Tutte polynomial in vertex-exponential time"
+       49th Annual IEEE Symposium on Foundations of Computer Science, 2008
+       https://ieeexplore.ieee.org/abstract/document/4691000
+    .. [3] Y. Shi, M. Dehmer, X. Li, I. Gutman,
+       "Graph Polynomials," p. 14
+    .. [4] Y. Shi, M. Dehmer, X. Li, I. Gutman,
+       "Graph Polynomials," p. 46
+    .. [5] A. Nešetril, J. Goodall,
+       "Graph invariants, homomorphisms, and the Tutte polynomial"
+       https://iuuk.mff.cuni.cz/~andrew/Tutte.pdf
+    .. [6] D. B. West,
+       "Introduction to Graph Theory," p. 84
+    .. [7] G. Coutinho,
+       "A brief introduction to the Tutte polynomial"
+       Structural Analysis of Complex Networks, 2011
+       https://homepages.dcc.ufmg.br/~gabriel/seminars/coutinho_tuttepolynomial_seminar.pdf
+    .. [8] J. A. Ellis-Monaghan, C. Merino,
+       "Graph polynomials and their applications I: The Tutte polynomial"
+       Structural Analysis of Complex Networks, 2011
+       https://arxiv.org/pdf/0803.3079.pdf
+    """
+    import sympy
+
+    x = sympy.Symbol("x")
+    y = sympy.Symbol("y")
+    stack = deque()
+    stack.append(nx.MultiGraph(G))
+
+    polynomial = 0
+    while stack:
+        G = stack.pop()
+        bridges = set(nx.bridges(G))
+
+        e = None
+        for i in G.edges:
+            if (i[0], i[1]) not in bridges and i[0] != i[1]:
+                e = i
+                break
+        if not e:
+            loops = list(nx.selfloop_edges(G, keys=True))
+            polynomial += x ** len(bridges) * y ** len(loops)
+        else:
+            # deletion-contraction
+            C = nx.contracted_edge(G, e, self_loops=True)
+            C.remove_edge(e[0], e[0])
+            G.remove_edge(*e)
+            stack.append(G)
+            stack.append(C)
+    return sympy.simplify(polynomial)
+
+
+@not_implemented_for("directed")
+@nx._dispatchable
+def chromatic_polynomial(G):
+    r"""Returns the chromatic polynomial of `G`
+
+    This function computes the chromatic polynomial via an iterative version of
+    the deletion-contraction algorithm.
+
+    The chromatic polynomial `X_G(x)` is a fundamental graph polynomial
+    invariant in one variable. Evaluating `X_G(k)` for an natural number `k`
+    enumerates the proper k-colorings of `G`.
+
+    There are several equivalent definitions; here are three:
+
+    Def 1 (explicit formula):
+    For `G` an undirected graph, `c(G)` the number of connected components of
+    `G`, `E` the edge set of `G`, and `G(S)` the spanning subgraph of `G` with
+    edge set `S` [1]_:
+
+    .. math::
+
+        X_G(x) = \sum_{S \subseteq E} (-1)^{|S|} x^{c(G(S))}
+
+
+    Def 2 (interpolating polynomial):
+    For `G` an undirected graph, `n(G)` the number of vertices of `G`, `k_0 = 0`,
+    and `k_i` the number of distinct ways to color the vertices of `G` with `i`
+    unique colors (for `i` a natural number at most `n(G)`), `X_G(x)` is the
+    unique Lagrange interpolating polynomial of degree `n(G)` through the points
+    `(0, k_0), (1, k_1), \dots, (n(G), k_{n(G)})` [2]_.
+
+
+    Def 3 (chromatic recurrence):
+    For `G` an undirected graph, `G-e` the graph obtained from `G` by deleting
+    edge `e`, `G/e` the graph obtained from `G` by contracting edge `e`, `n(G)`
+    the number of vertices of `G`, and `e(G)` the number of edges of `G` [3]_:
+
+    .. math::
+        X_G(x) = \begin{cases}
+    	   x^{n(G)}, & \text{if $e(G)=0$} \\
+           X_{G-e}(x) - X_{G/e}(x), & \text{otherwise, for an arbitrary edge $e$}
+        \end{cases}
+
+    This formulation is also known as the Fundamental Reduction Theorem [4]_.
+
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    Returns
+    -------
+    instance of `sympy.core.add.Add`
+        A Sympy expression representing the chromatic polynomial for `G`.
+
+    Examples
+    --------
+    >>> C = nx.cycle_graph(5)
+    >>> nx.chromatic_polynomial(C)
+    x**5 - 5*x**4 + 10*x**3 - 10*x**2 + 4*x
+
+    >>> G = nx.complete_graph(4)
+    >>> nx.chromatic_polynomial(G)
+    x**4 - 6*x**3 + 11*x**2 - 6*x
+
+    Notes
+    -----
+    Interpretation of the coefficients is discussed in [5]_. Several special
+    cases are listed in [2]_.
+
+    The chromatic polynomial is a specialization of the Tutte polynomial; in
+    particular, ``X_G(x) = T_G(x, 0)`` [6]_.
+
+    The chromatic polynomial may take negative arguments, though evaluations
+    may not have chromatic interpretations. For instance, ``X_G(-1)`` enumerates
+    the acyclic orientations of `G` [7]_.
+
+    References
+    ----------
+    .. [1] D. B. West,
+       "Introduction to Graph Theory," p. 222
+    .. [2] E. W. Weisstein
+       "Chromatic Polynomial"
+       MathWorld--A Wolfram Web Resource
+       https://mathworld.wolfram.com/ChromaticPolynomial.html
+    .. [3] D. B. West,
+       "Introduction to Graph Theory," p. 221
+    .. [4] J. Zhang, J. Goodall,
+       "An Introduction to Chromatic Polynomials"
+       https://math.mit.edu/~apost/courses/18.204_2018/Julie_Zhang_paper.pdf
+    .. [5] R. C. Read,
+       "An Introduction to Chromatic Polynomials"
+       Journal of Combinatorial Theory, 1968
+       https://math.berkeley.edu/~mrklug/ReadChromatic.pdf
+    .. [6] W. T. Tutte,
+       "Graph-polynomials"
+       Advances in Applied Mathematics, 2004
+       https://www.sciencedirect.com/science/article/pii/S0196885803000411
+    .. [7] R. P. Stanley,
+       "Acyclic orientations of graphs"
+       Discrete Mathematics, 2006
+       https://math.mit.edu/~rstan/pubs/pubfiles/18.pdf
+    """
+    import sympy
+
+    x = sympy.Symbol("x")
+    stack = deque()
+    stack.append(nx.MultiGraph(G, contraction_idx=0))
+
+    polynomial = 0
+    while stack:
+        G = stack.pop()
+        edges = list(G.edges)
+        if not edges:
+            polynomial += (-1) ** G.graph["contraction_idx"] * x ** len(G)
+        else:
+            e = edges[0]
+            C = nx.contracted_edge(G, e, self_loops=True)
+            C.graph["contraction_idx"] = G.graph["contraction_idx"] + 1
+            C.remove_edge(e[0], e[0])
+            G.remove_edge(*e)
+            stack.append(G)
+            stack.append(C)
+    return polynomial

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/richclub.py

@@ -0,0 +1,138 @@
+"""Functions for computing rich-club coefficients."""
+
+from itertools import accumulate
+
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+__all__ = ["rich_club_coefficient"]
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatchable
+def rich_club_coefficient(G, normalized=True, Q=100, seed=None):
+    r"""Returns the rich-club coefficient of the graph `G`.
+
+    For each degree *k*, the *rich-club coefficient* is the ratio of the
+    number of actual to the number of potential edges for nodes with
+    degree greater than *k*:
+
+    .. math::
+
+        \phi(k) = \frac{2 E_k}{N_k (N_k - 1)}
+
+    where `N_k` is the number of nodes with degree larger than *k*, and
+    `E_k` is the number of edges among those nodes.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        Undirected graph with neither parallel edges nor self-loops.
+    normalized : bool (optional)
+        Normalize using randomized network as in [1]_
+    Q : float (optional, default=100)
+        If `normalized` is True, perform `Q * m` double-edge
+        swaps, where `m` is the number of edges in `G`, to use as a
+        null-model for normalization.
+    seed : integer, random_state, or None (default)
+        Indicator of random number generation state.
+        See :ref:`Randomness<randomness>`.
+
+    Returns
+    -------
+    rc : dictionary
+       A dictionary, keyed by degree, with rich-club coefficient values.
+
+    Raises
+    ------
+    NetworkXError
+        If `G` has fewer than four nodes and ``normalized=True``.
+        A randomly sampled graph for normalization cannot be generated in this case.
+
+    Examples
+    --------
+    >>> G = nx.Graph([(0, 1), (0, 2), (1, 2), (1, 3), (1, 4), (4, 5)])
+    >>> rc = nx.rich_club_coefficient(G, normalized=False, seed=42)
+    >>> rc[0]
+    0.4
+
+    Notes
+    -----
+    The rich club definition and algorithm are found in [1]_.  This
+    algorithm ignores any edge weights and is not defined for directed
+    graphs or graphs with parallel edges or self loops.
+
+    Normalization is done by computing the rich club coefficient for a randomly
+    sampled graph with the same degree distribution as `G` by
+    repeatedly swapping the endpoints of existing edges. For graphs with fewer than 4
+    nodes, it is not possible to generate a random graph with a prescribed
+    degree distribution, as the degree distribution fully determines the graph
+    (hence making the coefficients trivially normalized to 1).
+    This function raises an exception in this case.
+
+    Estimates for appropriate values of `Q` are found in [2]_.
+
+    References
+    ----------
+    .. [1] Julian J. McAuley, Luciano da Fontoura Costa,
+       and Tibério S. Caetano,
+       "The rich-club phenomenon across complex network hierarchies",
+       Applied Physics Letters Vol 91 Issue 8, August 2007.
+       https://arxiv.org/abs/physics/0701290
+    .. [2] R. Milo, N. Kashtan, S. Itzkovitz, M. E. J. Newman, U. Alon,
+       "Uniform generation of random graphs with arbitrary degree
+       sequences", 2006. https://arxiv.org/abs/cond-mat/0312028
+    """
+    if nx.number_of_selfloops(G) > 0:
+        raise Exception(
+            "rich_club_coefficient is not implemented for graphs with self loops."
+        )
+    rc = _compute_rc(G)
+    if normalized:
+        # make R a copy of G, randomize with Q*|E| double edge swaps
+        # and use rich_club coefficient of R to normalize
+        R = G.copy()
+        E = R.number_of_edges()
+        nx.double_edge_swap(R, Q * E, max_tries=Q * E * 10, seed=seed)
+        rcran = _compute_rc(R)
+        rc = {k: v / rcran[k] for k, v in rc.items()}
+    return rc
+
+
+def _compute_rc(G):
+    """Returns the rich-club coefficient for each degree in the graph
+    `G`.
+
+    `G` is an undirected graph without multiedges.
+
+    Returns a dictionary mapping degree to rich-club coefficient for
+    that degree.
+
+    """
+    deghist = nx.degree_histogram(G)
+    total = sum(deghist)
+    # Compute the number of nodes with degree greater than `k`, for each
+    # degree `k` (omitting the last entry, which is zero).
+    nks = (total - cs for cs in accumulate(deghist) if total - cs > 1)
+    # Create a sorted list of pairs of edge endpoint degrees.
+    #
+    # The list is sorted in reverse order so that we can pop from the
+    # right side of the list later, instead of popping from the left
+    # side of the list, which would have a linear time cost.
+    edge_degrees = sorted((sorted(map(G.degree, e)) for e in G.edges()), reverse=True)
+    ek = G.number_of_edges()
+    if ek == 0:
+        return {}
+
+    k1, k2 = edge_degrees.pop()
+    rc = {}
+    for d, nk in enumerate(nks):
+        while k1 <= d:
+            if len(edge_degrees) == 0:
+                ek = 0
+                break
+            k1, k2 = edge_degrees.pop()
+            ek -= 1
+        rc[d] = 2 * ek / (nk * (nk - 1))
+    return rc

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/similarity.py

@@ -0,0 +1,1777 @@
+""" Functions measuring similarity using graph edit distance.
+
+The graph edit distance is the number of edge/node changes needed
+to make two graphs isomorphic.
+
+The default algorithm/implementation is sub-optimal for some graphs.
+The problem of finding the exact Graph Edit Distance (GED) is NP-hard
+so it is often slow. If the simple interface `graph_edit_distance`
+takes too long for your graph, try `optimize_graph_edit_distance`
+and/or `optimize_edit_paths`.
+
+At the same time, I encourage capable people to investigate
+alternative GED algorithms, in order to improve the choices available.
+"""
+
+import math
+import time
+import warnings
+from dataclasses import dataclass
+from itertools import product
+
+import networkx as nx
+from networkx.utils import np_random_state
+
+__all__ = [
+    "graph_edit_distance",
+    "optimal_edit_paths",
+    "optimize_graph_edit_distance",
+    "optimize_edit_paths",
+    "simrank_similarity",
+    "panther_similarity",
+    "generate_random_paths",
+]
+
+
+def debug_print(*args, **kwargs):
+    print(*args, **kwargs)
+
+
+@nx._dispatchable(
+    graphs={"G1": 0, "G2": 1}, preserve_edge_attrs=True, preserve_node_attrs=True
+)
+def graph_edit_distance(
+    G1,
+    G2,
+    node_match=None,
+    edge_match=None,
+    node_subst_cost=None,
+    node_del_cost=None,
+    node_ins_cost=None,
+    edge_subst_cost=None,
+    edge_del_cost=None,
+    edge_ins_cost=None,
+    roots=None,
+    upper_bound=None,
+    timeout=None,
+):
+    """Returns GED (graph edit distance) between graphs G1 and G2.
+
+    Graph edit distance is a graph similarity measure analogous to
+    Levenshtein distance for strings.  It is defined as minimum cost
+    of edit path (sequence of node and edge edit operations)
+    transforming graph G1 to graph isomorphic to G2.
+
+    Parameters
+    ----------
+    G1, G2: graphs
+        The two graphs G1 and G2 must be of the same type.
+
+    node_match : callable
+        A function that returns True if node n1 in G1 and n2 in G2
+        should be considered equal during matching.
+
+        The function will be called like
+
+           node_match(G1.nodes[n1], G2.nodes[n2]).
+
+        That is, the function will receive the node attribute
+        dictionaries for n1 and n2 as inputs.
+
+        Ignored if node_subst_cost is specified.  If neither
+        node_match nor node_subst_cost are specified then node
+        attributes are not considered.
+
+    edge_match : callable
+        A function that returns True if the edge attribute dictionaries
+        for the pair of nodes (u1, v1) in G1 and (u2, v2) in G2 should
+        be considered equal during matching.
+
+        The function will be called like
+
+           edge_match(G1[u1][v1], G2[u2][v2]).
+
+        That is, the function will receive the edge attribute
+        dictionaries of the edges under consideration.
+
+        Ignored if edge_subst_cost is specified.  If neither
+        edge_match nor edge_subst_cost are specified then edge
+        attributes are not considered.
+
+    node_subst_cost, node_del_cost, node_ins_cost : callable
+        Functions that return the costs of node substitution, node
+        deletion, and node insertion, respectively.
+
+        The functions will be called like
+
+           node_subst_cost(G1.nodes[n1], G2.nodes[n2]),
+           node_del_cost(G1.nodes[n1]),
+           node_ins_cost(G2.nodes[n2]).
+
+        That is, the functions will receive the node attribute
+        dictionaries as inputs.  The functions are expected to return
+        positive numeric values.
+
+        Function node_subst_cost overrides node_match if specified.
+        If neither node_match nor node_subst_cost are specified then
+        default node substitution cost of 0 is used (node attributes
+        are not considered during matching).
+
+        If node_del_cost is not specified then default node deletion
+        cost of 1 is used.  If node_ins_cost is not specified then
+        default node insertion cost of 1 is used.
+
+    edge_subst_cost, edge_del_cost, edge_ins_cost : callable
+        Functions that return the costs of edge substitution, edge
+        deletion, and edge insertion, respectively.
+
+        The functions will be called like
+
+           edge_subst_cost(G1[u1][v1], G2[u2][v2]),
+           edge_del_cost(G1[u1][v1]),
+           edge_ins_cost(G2[u2][v2]).
+
+        That is, the functions will receive the edge attribute
+        dictionaries as inputs.  The functions are expected to return
+        positive numeric values.
+
+        Function edge_subst_cost overrides edge_match if specified.
+        If neither edge_match nor edge_subst_cost are specified then
+        default edge substitution cost of 0 is used (edge attributes
+        are not considered during matching).
+
+        If edge_del_cost is not specified then default edge deletion
+        cost of 1 is used.  If edge_ins_cost is not specified then
+        default edge insertion cost of 1 is used.
+
+    roots : 2-tuple
+        Tuple where first element is a node in G1 and the second
+        is a node in G2.
+        These nodes are forced to be matched in the comparison to
+        allow comparison between rooted graphs.
+
+    upper_bound : numeric
+        Maximum edit distance to consider.  Return None if no edit
+        distance under or equal to upper_bound exists.
+
+    timeout : numeric
+        Maximum number of seconds to execute.
+        After timeout is met, the current best GED is returned.
+
+    Examples
+    --------
+    >>> G1 = nx.cycle_graph(6)
+    >>> G2 = nx.wheel_graph(7)
+    >>> nx.graph_edit_distance(G1, G2)
+    7.0
+
+    >>> G1 = nx.star_graph(5)
+    >>> G2 = nx.star_graph(5)
+    >>> nx.graph_edit_distance(G1, G2, roots=(0, 0))
+    0.0
+    >>> nx.graph_edit_distance(G1, G2, roots=(1, 0))
+    8.0
+
+    See Also
+    --------
+    optimal_edit_paths, optimize_graph_edit_distance,
+
+    is_isomorphic: test for graph edit distance of 0
+
+    References
+    ----------
+    .. [1] Zeina Abu-Aisheh, Romain Raveaux, Jean-Yves Ramel, Patrick
+       Martineau. An Exact Graph Edit Distance Algorithm for Solving
+       Pattern Recognition Problems. 4th International Conference on
+       Pattern Recognition Applications and Methods 2015, Jan 2015,
+       Lisbon, Portugal. 2015,
+       <10.5220/0005209202710278>. <hal-01168816>
+       https://hal.archives-ouvertes.fr/hal-01168816
+
+    """
+    bestcost = None
+    for _, _, cost in optimize_edit_paths(
+        G1,
+        G2,
+        node_match,
+        edge_match,
+        node_subst_cost,
+        node_del_cost,
+        node_ins_cost,
+        edge_subst_cost,
+        edge_del_cost,
+        edge_ins_cost,
+        upper_bound,
+        True,
+        roots,
+        timeout,
+    ):
+        # assert bestcost is None or cost < bestcost
+        bestcost = cost
+    return bestcost
+
+
+@nx._dispatchable(graphs={"G1": 0, "G2": 1})
+def optimal_edit_paths(
+    G1,
+    G2,
+    node_match=None,
+    edge_match=None,
+    node_subst_cost=None,
+    node_del_cost=None,
+    node_ins_cost=None,
+    edge_subst_cost=None,
+    edge_del_cost=None,
+    edge_ins_cost=None,
+    upper_bound=None,
+):
+    """Returns all minimum-cost edit paths transforming G1 to G2.
+
+    Graph edit path is a sequence of node and edge edit operations
+    transforming graph G1 to graph isomorphic to G2.  Edit operations
+    include substitutions, deletions, and insertions.
+
+    Parameters
+    ----------
+    G1, G2: graphs
+        The two graphs G1 and G2 must be of the same type.
+
+    node_match : callable
+        A function that returns True if node n1 in G1 and n2 in G2
+        should be considered equal during matching.
+
+        The function will be called like
+
+           node_match(G1.nodes[n1], G2.nodes[n2]).
+
+        That is, the function will receive the node attribute
+        dictionaries for n1 and n2 as inputs.
+
+        Ignored if node_subst_cost is specified.  If neither
+        node_match nor node_subst_cost are specified then node
+        attributes are not considered.
+
+    edge_match : callable
+        A function that returns True if the edge attribute dictionaries
+        for the pair of nodes (u1, v1) in G1 and (u2, v2) in G2 should
+        be considered equal during matching.
+
+        The function will be called like
+
+           edge_match(G1[u1][v1], G2[u2][v2]).
+
+        That is, the function will receive the edge attribute
+        dictionaries of the edges under consideration.
+
+        Ignored if edge_subst_cost is specified.  If neither
+        edge_match nor edge_subst_cost are specified then edge
+        attributes are not considered.
+
+    node_subst_cost, node_del_cost, node_ins_cost : callable
+        Functions that return the costs of node substitution, node
+        deletion, and node insertion, respectively.
+
+        The functions will be called like
+
+           node_subst_cost(G1.nodes[n1], G2.nodes[n2]),
+           node_del_cost(G1.nodes[n1]),
+           node_ins_cost(G2.nodes[n2]).
+
+        That is, the functions will receive the node attribute
+        dictionaries as inputs.  The functions are expected to return
+        positive numeric values.
+
+        Function node_subst_cost overrides node_match if specified.
+        If neither node_match nor node_subst_cost are specified then
+        default node substitution cost of 0 is used (node attributes
+        are not considered during matching).
+
+        If node_del_cost is not specified then default node deletion
+        cost of 1 is used.  If node_ins_cost is not specified then
+        default node insertion cost of 1 is used.
+
+    edge_subst_cost, edge_del_cost, edge_ins_cost : callable
+        Functions that return the costs of edge substitution, edge
+        deletion, and edge insertion, respectively.
+
+        The functions will be called like
+
+           edge_subst_cost(G1[u1][v1], G2[u2][v2]),
+           edge_del_cost(G1[u1][v1]),
+           edge_ins_cost(G2[u2][v2]).
+
+        That is, the functions will receive the edge attribute
+        dictionaries as inputs.  The functions are expected to return
+        positive numeric values.
+
+        Function edge_subst_cost overrides edge_match if specified.
+        If neither edge_match nor edge_subst_cost are specified then
+        default edge substitution cost of 0 is used (edge attributes
+        are not considered during matching).
+
+        If edge_del_cost is not specified then default edge deletion
+        cost of 1 is used.  If edge_ins_cost is not specified then
+        default edge insertion cost of 1 is used.
+
+    upper_bound : numeric
+        Maximum edit distance to consider.
+
+    Returns
+    -------
+    edit_paths : list of tuples (node_edit_path, edge_edit_path)
+        node_edit_path : list of tuples (u, v)
+        edge_edit_path : list of tuples ((u1, v1), (u2, v2))
+
+    cost : numeric
+        Optimal edit path cost (graph edit distance). When the cost
+        is zero, it indicates that `G1` and `G2` are isomorphic.
+
+    Examples
+    --------
+    >>> G1 = nx.cycle_graph(4)
+    >>> G2 = nx.wheel_graph(5)
+    >>> paths, cost = nx.optimal_edit_paths(G1, G2)
+    >>> len(paths)
+    40
+    >>> cost
+    5.0
+
+    Notes
+    -----
+    To transform `G1` into a graph isomorphic to `G2`, apply the node
+    and edge edits in the returned ``edit_paths``.
+    In the case of isomorphic graphs, the cost is zero, and the paths
+    represent different isomorphic mappings (isomorphisms). That is, the
+    edits involve renaming nodes and edges to match the structure of `G2`.
+
+    See Also
+    --------
+    graph_edit_distance, optimize_edit_paths
+
+    References
+    ----------
+    .. [1] Zeina Abu-Aisheh, Romain Raveaux, Jean-Yves Ramel, Patrick
+       Martineau. An Exact Graph Edit Distance Algorithm for Solving
+       Pattern Recognition Problems. 4th International Conference on
+       Pattern Recognition Applications and Methods 2015, Jan 2015,
+       Lisbon, Portugal. 2015,
+       <10.5220/0005209202710278>. <hal-01168816>
+       https://hal.archives-ouvertes.fr/hal-01168816
+
+    """
+    paths = []
+    bestcost = None
+    for vertex_path, edge_path, cost in optimize_edit_paths(
+        G1,
+        G2,
+        node_match,
+        edge_match,
+        node_subst_cost,
+        node_del_cost,
+        node_ins_cost,
+        edge_subst_cost,
+        edge_del_cost,
+        edge_ins_cost,
+        upper_bound,
+        False,
+    ):
+        # assert bestcost is None or cost <= bestcost
+        if bestcost is not None and cost < bestcost:
+            paths = []
+        paths.append((vertex_path, edge_path))
+        bestcost = cost
+    return paths, bestcost
+
+
+@nx._dispatchable(graphs={"G1": 0, "G2": 1})
+def optimize_graph_edit_distance(
+    G1,
+    G2,
+    node_match=None,
+    edge_match=None,
+    node_subst_cost=None,
+    node_del_cost=None,
+    node_ins_cost=None,
+    edge_subst_cost=None,
+    edge_del_cost=None,
+    edge_ins_cost=None,
+    upper_bound=None,
+):
+    """Returns consecutive approximations of GED (graph edit distance)
+    between graphs G1 and G2.
+
+    Graph edit distance is a graph similarity measure analogous to
+    Levenshtein distance for strings.  It is defined as minimum cost
+    of edit path (sequence of node and edge edit operations)
+    transforming graph G1 to graph isomorphic to G2.
+
+    Parameters
+    ----------
+    G1, G2: graphs
+        The two graphs G1 and G2 must be of the same type.
+
+    node_match : callable
+        A function that returns True if node n1 in G1 and n2 in G2
+        should be considered equal during matching.
+
+        The function will be called like
+
+           node_match(G1.nodes[n1], G2.nodes[n2]).
+
+        That is, the function will receive the node attribute
+        dictionaries for n1 and n2 as inputs.
+
+        Ignored if node_subst_cost is specified.  If neither
+        node_match nor node_subst_cost are specified then node
+        attributes are not considered.
+
+    edge_match : callable
+        A function that returns True if the edge attribute dictionaries
+        for the pair of nodes (u1, v1) in G1 and (u2, v2) in G2 should
+        be considered equal during matching.
+
+        The function will be called like
+
+           edge_match(G1[u1][v1], G2[u2][v2]).
+
+        That is, the function will receive the edge attribute
+        dictionaries of the edges under consideration.
+
+        Ignored if edge_subst_cost is specified.  If neither
+        edge_match nor edge_subst_cost are specified then edge
+        attributes are not considered.
+
+    node_subst_cost, node_del_cost, node_ins_cost : callable
+        Functions that return the costs of node substitution, node
+        deletion, and node insertion, respectively.
+
+        The functions will be called like
+
+           node_subst_cost(G1.nodes[n1], G2.nodes[n2]),
+           node_del_cost(G1.nodes[n1]),
+           node_ins_cost(G2.nodes[n2]).
+
+        That is, the functions will receive the node attribute
+        dictionaries as inputs.  The functions are expected to return
+        positive numeric values.
+
+        Function node_subst_cost overrides node_match if specified.
+        If neither node_match nor node_subst_cost are specified then
+        default node substitution cost of 0 is used (node attributes
+        are not considered during matching).
+
+        If node_del_cost is not specified then default node deletion
+        cost of 1 is used.  If node_ins_cost is not specified then
+        default node insertion cost of 1 is used.
+
+    edge_subst_cost, edge_del_cost, edge_ins_cost : callable
+        Functions that return the costs of edge substitution, edge
+        deletion, and edge insertion, respectively.
+
+        The functions will be called like
+
+           edge_subst_cost(G1[u1][v1], G2[u2][v2]),
+           edge_del_cost(G1[u1][v1]),
+           edge_ins_cost(G2[u2][v2]).
+
+        That is, the functions will receive the edge attribute
+        dictionaries as inputs.  The functions are expected to return
+        positive numeric values.
+
+        Function edge_subst_cost overrides edge_match if specified.
+        If neither edge_match nor edge_subst_cost are specified then
+        default edge substitution cost of 0 is used (edge attributes
+        are not considered during matching).
+
+        If edge_del_cost is not specified then default edge deletion
+        cost of 1 is used.  If edge_ins_cost is not specified then
+        default edge insertion cost of 1 is used.
+
+    upper_bound : numeric
+        Maximum edit distance to consider.
+
+    Returns
+    -------
+    Generator of consecutive approximations of graph edit distance.
+
+    Examples
+    --------
+    >>> G1 = nx.cycle_graph(6)
+    >>> G2 = nx.wheel_graph(7)
+    >>> for v in nx.optimize_graph_edit_distance(G1, G2):
+    ...     minv = v
+    >>> minv
+    7.0
+
+    See Also
+    --------
+    graph_edit_distance, optimize_edit_paths
+
+    References
+    ----------
+    .. [1] Zeina Abu-Aisheh, Romain Raveaux, Jean-Yves Ramel, Patrick
+       Martineau. An Exact Graph Edit Distance Algorithm for Solving
+       Pattern Recognition Problems. 4th International Conference on
+       Pattern Recognition Applications and Methods 2015, Jan 2015,
+       Lisbon, Portugal. 2015,
+       <10.5220/0005209202710278>. <hal-01168816>
+       https://hal.archives-ouvertes.fr/hal-01168816
+    """
+    for _, _, cost in optimize_edit_paths(
+        G1,
+        G2,
+        node_match,
+        edge_match,
+        node_subst_cost,
+        node_del_cost,
+        node_ins_cost,
+        edge_subst_cost,
+        edge_del_cost,
+        edge_ins_cost,
+        upper_bound,
+        True,
+    ):
+        yield cost
+
+
+@nx._dispatchable(
+    graphs={"G1": 0, "G2": 1}, preserve_edge_attrs=True, preserve_node_attrs=True
+)
+def optimize_edit_paths(
+    G1,
+    G2,
+    node_match=None,
+    edge_match=None,
+    node_subst_cost=None,
+    node_del_cost=None,
+    node_ins_cost=None,
+    edge_subst_cost=None,
+    edge_del_cost=None,
+    edge_ins_cost=None,
+    upper_bound=None,
+    strictly_decreasing=True,
+    roots=None,
+    timeout=None,
+):
+    """GED (graph edit distance) calculation: advanced interface.
+
+    Graph edit path is a sequence of node and edge edit operations
+    transforming graph G1 to graph isomorphic to G2.  Edit operations
+    include substitutions, deletions, and insertions.
+
+    Graph edit distance is defined as minimum cost of edit path.
+
+    Parameters
+    ----------
+    G1, G2: graphs
+        The two graphs G1 and G2 must be of the same type.
+
+    node_match : callable
+        A function that returns True if node n1 in G1 and n2 in G2
+        should be considered equal during matching.
+
+        The function will be called like
+
+           node_match(G1.nodes[n1], G2.nodes[n2]).
+
+        That is, the function will receive the node attribute
+        dictionaries for n1 and n2 as inputs.
+
+        Ignored if node_subst_cost is specified.  If neither
+        node_match nor node_subst_cost are specified then node
+        attributes are not considered.
+
+    edge_match : callable
+        A function that returns True if the edge attribute dictionaries
+        for the pair of nodes (u1, v1) in G1 and (u2, v2) in G2 should
+        be considered equal during matching.
+
+        The function will be called like
+
+           edge_match(G1[u1][v1], G2[u2][v2]).
+
+        That is, the function will receive the edge attribute
+        dictionaries of the edges under consideration.
+
+        Ignored if edge_subst_cost is specified.  If neither
+        edge_match nor edge_subst_cost are specified then edge
+        attributes are not considered.
+
+    node_subst_cost, node_del_cost, node_ins_cost : callable
+        Functions that return the costs of node substitution, node
+        deletion, and node insertion, respectively.
+
+        The functions will be called like
+
+           node_subst_cost(G1.nodes[n1], G2.nodes[n2]),
+           node_del_cost(G1.nodes[n1]),
+           node_ins_cost(G2.nodes[n2]).
+
+        That is, the functions will receive the node attribute
+        dictionaries as inputs.  The functions are expected to return
+        positive numeric values.
+
+        Function node_subst_cost overrides node_match if specified.
+        If neither node_match nor node_subst_cost are specified then
+        default node substitution cost of 0 is used (node attributes
+        are not considered during matching).
+
+        If node_del_cost is not specified then default node deletion
+        cost of 1 is used.  If node_ins_cost is not specified then
+        default node insertion cost of 1 is used.
+
+    edge_subst_cost, edge_del_cost, edge_ins_cost : callable
+        Functions that return the costs of edge substitution, edge
+        deletion, and edge insertion, respectively.
+
+        The functions will be called like
+
+           edge_subst_cost(G1[u1][v1], G2[u2][v2]),
+           edge_del_cost(G1[u1][v1]),
+           edge_ins_cost(G2[u2][v2]).
+
+        That is, the functions will receive the edge attribute
+        dictionaries as inputs.  The functions are expected to return
+        positive numeric values.
+
+        Function edge_subst_cost overrides edge_match if specified.
+        If neither edge_match nor edge_subst_cost are specified then
+        default edge substitution cost of 0 is used (edge attributes
+        are not considered during matching).
+
+        If edge_del_cost is not specified then default edge deletion
+        cost of 1 is used.  If edge_ins_cost is not specified then
+        default edge insertion cost of 1 is used.
+
+    upper_bound : numeric
+        Maximum edit distance to consider.
+
+    strictly_decreasing : bool
+        If True, return consecutive approximations of strictly
+        decreasing cost.  Otherwise, return all edit paths of cost
+        less than or equal to the previous minimum cost.
+
+    roots : 2-tuple
+        Tuple where first element is a node in G1 and the second
+        is a node in G2.
+        These nodes are forced to be matched in the comparison to
+        allow comparison between rooted graphs.
+
+    timeout : numeric
+        Maximum number of seconds to execute.
+        After timeout is met, the current best GED is returned.
+
+    Returns
+    -------
+    Generator of tuples (node_edit_path, edge_edit_path, cost)
+        node_edit_path : list of tuples (u, v)
+        edge_edit_path : list of tuples ((u1, v1), (u2, v2))
+        cost : numeric
+
+    See Also
+    --------
+    graph_edit_distance, optimize_graph_edit_distance, optimal_edit_paths
+
+    References
+    ----------
+    .. [1] Zeina Abu-Aisheh, Romain Raveaux, Jean-Yves Ramel, Patrick
+       Martineau. An Exact Graph Edit Distance Algorithm for Solving
+       Pattern Recognition Problems. 4th International Conference on
+       Pattern Recognition Applications and Methods 2015, Jan 2015,
+       Lisbon, Portugal. 2015,
+       <10.5220/0005209202710278>. <hal-01168816>
+       https://hal.archives-ouvertes.fr/hal-01168816
+
+    """
+    # TODO: support DiGraph
+
+    import numpy as np
+    import scipy as sp
+
+    @dataclass
+    class CostMatrix:
+        C: ...
+        lsa_row_ind: ...
+        lsa_col_ind: ...
+        ls: ...
+
+    def make_CostMatrix(C, m, n):
+        # assert(C.shape == (m + n, m + n))
+        lsa_row_ind, lsa_col_ind = sp.optimize.linear_sum_assignment(C)
+
+        # Fixup dummy assignments:
+        # each substitution i<->j should have dummy assignment m+j<->n+i
+        # NOTE: fast reduce of Cv relies on it
+        # assert len(lsa_row_ind) == len(lsa_col_ind)
+        indexes = zip(range(len(lsa_row_ind)), lsa_row_ind, lsa_col_ind)
+        subst_ind = [k for k, i, j in indexes if i < m and j < n]
+        indexes = zip(range(len(lsa_row_ind)), lsa_row_ind, lsa_col_ind)
+        dummy_ind = [k for k, i, j in indexes if i >= m and j >= n]
+        # assert len(subst_ind) == len(dummy_ind)
+        lsa_row_ind[dummy_ind] = lsa_col_ind[subst_ind] + m
+        lsa_col_ind[dummy_ind] = lsa_row_ind[subst_ind] + n
+
+        return CostMatrix(
+            C, lsa_row_ind, lsa_col_ind, C[lsa_row_ind, lsa_col_ind].sum()
+        )
+
+    def extract_C(C, i, j, m, n):
+        # assert(C.shape == (m + n, m + n))
+        row_ind = [k in i or k - m in j for k in range(m + n)]
+        col_ind = [k in j or k - n in i for k in range(m + n)]
+        return C[row_ind, :][:, col_ind]
+
+    def reduce_C(C, i, j, m, n):
+        # assert(C.shape == (m + n, m + n))
+        row_ind = [k not in i and k - m not in j for k in range(m + n)]
+        col_ind = [k not in j and k - n not in i for k in range(m + n)]
+        return C[row_ind, :][:, col_ind]
+
+    def reduce_ind(ind, i):
+        # assert set(ind) == set(range(len(ind)))
+        rind = ind[[k not in i for k in ind]]
+        for k in set(i):
+            rind[rind >= k] -= 1
+        return rind
+
+    def match_edges(u, v, pending_g, pending_h, Ce, matched_uv=None):
+        """
+        Parameters:
+            u, v: matched vertices, u=None or v=None for
+               deletion/insertion
+            pending_g, pending_h: lists of edges not yet mapped
+            Ce: CostMatrix of pending edge mappings
+            matched_uv: partial vertex edit path
+                list of tuples (u, v) of previously matched vertex
+                    mappings u<->v, u=None or v=None for
+                    deletion/insertion
+
+        Returns:
+            list of (i, j): indices of edge mappings g<->h
+            localCe: local CostMatrix of edge mappings
+                (basically submatrix of Ce at cross of rows i, cols j)
+        """
+        M = len(pending_g)
+        N = len(pending_h)
+        # assert Ce.C.shape == (M + N, M + N)
+
+        # only attempt to match edges after one node match has been made
+        # this will stop self-edges on the first node being automatically deleted
+        # even when a substitution is the better option
+        if matched_uv is None or len(matched_uv) == 0:
+            g_ind = []
+            h_ind = []
+        else:
+            g_ind = [
+                i
+                for i in range(M)
+                if pending_g[i][:2] == (u, u)
+                or any(
+                    pending_g[i][:2] in ((p, u), (u, p), (p, p)) for p, q in matched_uv
+                )
+            ]
+            h_ind = [
+                j
+                for j in range(N)
+                if pending_h[j][:2] == (v, v)
+                or any(
+                    pending_h[j][:2] in ((q, v), (v, q), (q, q)) for p, q in matched_uv
+                )
+            ]
+
+        m = len(g_ind)
+        n = len(h_ind)
+
+        if m or n:
+            C = extract_C(Ce.C, g_ind, h_ind, M, N)
+            # assert C.shape == (m + n, m + n)
+
+            # Forbid structurally invalid matches
+            # NOTE: inf remembered from Ce construction
+            for k, i in enumerate(g_ind):
+                g = pending_g[i][:2]
+                for l, j in enumerate(h_ind):
+                    h = pending_h[j][:2]
+                    if nx.is_directed(G1) or nx.is_directed(G2):
+                        if any(
+                            g == (p, u) and h == (q, v) or g == (u, p) and h == (v, q)
+                            for p, q in matched_uv
+                        ):
+                            continue
+                    else:
+                        if any(
+                            g in ((p, u), (u, p)) and h in ((q, v), (v, q))
+                            for p, q in matched_uv
+                        ):
+                            continue
+                    if g == (u, u) or any(g == (p, p) for p, q in matched_uv):
+                        continue
+                    if h == (v, v) or any(h == (q, q) for p, q in matched_uv):
+                        continue
+                    C[k, l] = inf
+
+            localCe = make_CostMatrix(C, m, n)
+            ij = [
+                (
+                    g_ind[k] if k < m else M + h_ind[l],
+                    h_ind[l] if l < n else N + g_ind[k],
+                )
+                for k, l in zip(localCe.lsa_row_ind, localCe.lsa_col_ind)
+                if k < m or l < n
+            ]
+
+        else:
+            ij = []
+            localCe = CostMatrix(np.empty((0, 0)), [], [], 0)
+
+        return ij, localCe
+
+    def reduce_Ce(Ce, ij, m, n):
+        if len(ij):
+            i, j = zip(*ij)
+            m_i = m - sum(1 for t in i if t < m)
+            n_j = n - sum(1 for t in j if t < n)
+            return make_CostMatrix(reduce_C(Ce.C, i, j, m, n), m_i, n_j)
+        return Ce
+
+    def get_edit_ops(
+        matched_uv, pending_u, pending_v, Cv, pending_g, pending_h, Ce, matched_cost
+    ):
+        """
+        Parameters:
+            matched_uv: partial vertex edit path
+                list of tuples (u, v) of vertex mappings u<->v,
+                u=None or v=None for deletion/insertion
+            pending_u, pending_v: lists of vertices not yet mapped
+            Cv: CostMatrix of pending vertex mappings
+            pending_g, pending_h: lists of edges not yet mapped
+            Ce: CostMatrix of pending edge mappings
+            matched_cost: cost of partial edit path
+
+        Returns:
+            sequence of
+                (i, j): indices of vertex mapping u<->v
+                Cv_ij: reduced CostMatrix of pending vertex mappings
+                    (basically Cv with row i, col j removed)
+                list of (x, y): indices of edge mappings g<->h
+                Ce_xy: reduced CostMatrix of pending edge mappings
+                    (basically Ce with rows x, cols y removed)
+                cost: total cost of edit operation
+            NOTE: most promising ops first
+        """
+        m = len(pending_u)
+        n = len(pending_v)
+        # assert Cv.C.shape == (m + n, m + n)
+
+        # 1) a vertex mapping from optimal linear sum assignment
+        i, j = min(
+            (k, l) for k, l in zip(Cv.lsa_row_ind, Cv.lsa_col_ind) if k < m or l < n
+        )
+        xy, localCe = match_edges(
+            pending_u[i] if i < m else None,
+            pending_v[j] if j < n else None,
+            pending_g,
+            pending_h,
+            Ce,
+            matched_uv,
+        )
+        Ce_xy = reduce_Ce(Ce, xy, len(pending_g), len(pending_h))
+        # assert Ce.ls <= localCe.ls + Ce_xy.ls
+        if prune(matched_cost + Cv.ls + localCe.ls + Ce_xy.ls):
+            pass
+        else:
+            # get reduced Cv efficiently
+            Cv_ij = CostMatrix(
+                reduce_C(Cv.C, (i,), (j,), m, n),
+                reduce_ind(Cv.lsa_row_ind, (i, m + j)),
+                reduce_ind(Cv.lsa_col_ind, (j, n + i)),
+                Cv.ls - Cv.C[i, j],
+            )
+            yield (i, j), Cv_ij, xy, Ce_xy, Cv.C[i, j] + localCe.ls
+
+        # 2) other candidates, sorted by lower-bound cost estimate
+        other = []
+        fixed_i, fixed_j = i, j
+        if m <= n:
+            candidates = (
+                (t, fixed_j)
+                for t in range(m + n)
+                if t != fixed_i and (t < m or t == m + fixed_j)
+            )
+        else:
+            candidates = (
+                (fixed_i, t)
+                for t in range(m + n)
+                if t != fixed_j and (t < n or t == n + fixed_i)
+            )
+        for i, j in candidates:
+            if prune(matched_cost + Cv.C[i, j] + Ce.ls):
+                continue
+            Cv_ij = make_CostMatrix(
+                reduce_C(Cv.C, (i,), (j,), m, n),
+                m - 1 if i < m else m,
+                n - 1 if j < n else n,
+            )
+            # assert Cv.ls <= Cv.C[i, j] + Cv_ij.ls
+            if prune(matched_cost + Cv.C[i, j] + Cv_ij.ls + Ce.ls):
+                continue
+            xy, localCe = match_edges(
+                pending_u[i] if i < m else None,
+                pending_v[j] if j < n else None,
+                pending_g,
+                pending_h,
+                Ce,
+                matched_uv,
+            )
+            if prune(matched_cost + Cv.C[i, j] + Cv_ij.ls + localCe.ls):
+                continue
+            Ce_xy = reduce_Ce(Ce, xy, len(pending_g), len(pending_h))
+            # assert Ce.ls <= localCe.ls + Ce_xy.ls
+            if prune(matched_cost + Cv.C[i, j] + Cv_ij.ls + localCe.ls + Ce_xy.ls):
+                continue
+            other.append(((i, j), Cv_ij, xy, Ce_xy, Cv.C[i, j] + localCe.ls))
+
+        yield from sorted(other, key=lambda t: t[4] + t[1].ls + t[3].ls)
+
+    def get_edit_paths(
+        matched_uv,
+        pending_u,
+        pending_v,
+        Cv,
+        matched_gh,
+        pending_g,
+        pending_h,
+        Ce,
+        matched_cost,
+    ):
+        """
+        Parameters:
+            matched_uv: partial vertex edit path
+                list of tuples (u, v) of vertex mappings u<->v,
+                u=None or v=None for deletion/insertion
+            pending_u, pending_v: lists of vertices not yet mapped
+            Cv: CostMatrix of pending vertex mappings
+            matched_gh: partial edge edit path
+                list of tuples (g, h) of edge mappings g<->h,
+                g=None or h=None for deletion/insertion
+            pending_g, pending_h: lists of edges not yet mapped
+            Ce: CostMatrix of pending edge mappings
+            matched_cost: cost of partial edit path
+
+        Returns:
+            sequence of (vertex_path, edge_path, cost)
+                vertex_path: complete vertex edit path
+                    list of tuples (u, v) of vertex mappings u<->v,
+                    u=None or v=None for deletion/insertion
+                edge_path: complete edge edit path
+                    list of tuples (g, h) of edge mappings g<->h,
+                    g=None or h=None for deletion/insertion
+                cost: total cost of edit path
+            NOTE: path costs are non-increasing
+        """
+        # debug_print('matched-uv:', matched_uv)
+        # debug_print('matched-gh:', matched_gh)
+        # debug_print('matched-cost:', matched_cost)
+        # debug_print('pending-u:', pending_u)
+        # debug_print('pending-v:', pending_v)
+        # debug_print(Cv.C)
+        # assert list(sorted(G1.nodes)) == list(sorted(list(u for u, v in matched_uv if u is not None) + pending_u))
+        # assert list(sorted(G2.nodes)) == list(sorted(list(v for u, v in matched_uv if v is not None) + pending_v))
+        # debug_print('pending-g:', pending_g)
+        # debug_print('pending-h:', pending_h)
+        # debug_print(Ce.C)
+        # assert list(sorted(G1.edges)) == list(sorted(list(g for g, h in matched_gh if g is not None) + pending_g))
+        # assert list(sorted(G2.edges)) == list(sorted(list(h for g, h in matched_gh if h is not None) + pending_h))
+        # debug_print()
+
+        if prune(matched_cost + Cv.ls + Ce.ls):
+            return
+
+        if not max(len(pending_u), len(pending_v)):
+            # assert not len(pending_g)
+            # assert not len(pending_h)
+            # path completed!
+            # assert matched_cost <= maxcost_value
+            nonlocal maxcost_value
+            maxcost_value = min(maxcost_value, matched_cost)
+            yield matched_uv, matched_gh, matched_cost
+
+        else:
+            edit_ops = get_edit_ops(
+                matched_uv,
+                pending_u,
+                pending_v,
+                Cv,
+                pending_g,
+                pending_h,
+                Ce,
+                matched_cost,
+            )
+            for ij, Cv_ij, xy, Ce_xy, edit_cost in edit_ops:
+                i, j = ij
+                # assert Cv.C[i, j] + sum(Ce.C[t] for t in xy) == edit_cost
+                if prune(matched_cost + edit_cost + Cv_ij.ls + Ce_xy.ls):
+                    continue
+
+                # dive deeper
+                u = pending_u.pop(i) if i < len(pending_u) else None
+                v = pending_v.pop(j) if j < len(pending_v) else None
+                matched_uv.append((u, v))
+                for x, y in xy:
+                    len_g = len(pending_g)
+                    len_h = len(pending_h)
+                    matched_gh.append(
+                        (
+                            pending_g[x] if x < len_g else None,
+                            pending_h[y] if y < len_h else None,
+                        )
+                    )
+                sortedx = sorted(x for x, y in xy)
+                sortedy = sorted(y for x, y in xy)
+                G = [
+                    (pending_g.pop(x) if x < len(pending_g) else None)
+                    for x in reversed(sortedx)
+                ]
+                H = [
+                    (pending_h.pop(y) if y < len(pending_h) else None)
+                    for y in reversed(sortedy)
+                ]
+
+                yield from get_edit_paths(
+                    matched_uv,
+                    pending_u,
+                    pending_v,
+                    Cv_ij,
+                    matched_gh,
+                    pending_g,
+                    pending_h,
+                    Ce_xy,
+                    matched_cost + edit_cost,
+                )
+
+                # backtrack
+                if u is not None:
+                    pending_u.insert(i, u)
+                if v is not None:
+                    pending_v.insert(j, v)
+                matched_uv.pop()
+                for x, g in zip(sortedx, reversed(G)):
+                    if g is not None:
+                        pending_g.insert(x, g)
+                for y, h in zip(sortedy, reversed(H)):
+                    if h is not None:
+                        pending_h.insert(y, h)
+                for _ in xy:
+                    matched_gh.pop()
+
+    # Initialization
+
+    pending_u = list(G1.nodes)
+    pending_v = list(G2.nodes)
+
+    initial_cost = 0
+    if roots:
+        root_u, root_v = roots
+        if root_u not in pending_u or root_v not in pending_v:
+            raise nx.NodeNotFound("Root node not in graph.")
+
+        # remove roots from pending
+        pending_u.remove(root_u)
+        pending_v.remove(root_v)
+
+    # cost matrix of vertex mappings
+    m = len(pending_u)
+    n = len(pending_v)
+    C = np.zeros((m + n, m + n))
+    if node_subst_cost:
+        C[0:m, 0:n] = np.array(
+            [
+                node_subst_cost(G1.nodes[u], G2.nodes[v])
+                for u in pending_u
+                for v in pending_v
+            ]
+        ).reshape(m, n)
+        if roots:
+            initial_cost = node_subst_cost(G1.nodes[root_u], G2.nodes[root_v])
+    elif node_match:
+        C[0:m, 0:n] = np.array(
+            [
+                1 - int(node_match(G1.nodes[u], G2.nodes[v]))
+                for u in pending_u
+                for v in pending_v
+            ]
+        ).reshape(m, n)
+        if roots:
+            initial_cost = 1 - node_match(G1.nodes[root_u], G2.nodes[root_v])
+    else:
+        # all zeroes
+        pass
+    # assert not min(m, n) or C[0:m, 0:n].min() >= 0
+    if node_del_cost:
+        del_costs = [node_del_cost(G1.nodes[u]) for u in pending_u]
+    else:
+        del_costs = [1] * len(pending_u)
+    # assert not m or min(del_costs) >= 0
+    if node_ins_cost:
+        ins_costs = [node_ins_cost(G2.nodes[v]) for v in pending_v]
+    else:
+        ins_costs = [1] * len(pending_v)
+    # assert not n or min(ins_costs) >= 0
+    inf = C[0:m, 0:n].sum() + sum(del_costs) + sum(ins_costs) + 1
+    C[0:m, n : n + m] = np.array(
+        [del_costs[i] if i == j else inf for i in range(m) for j in range(m)]
+    ).reshape(m, m)
+    C[m : m + n, 0:n] = np.array(
+        [ins_costs[i] if i == j else inf for i in range(n) for j in range(n)]
+    ).reshape(n, n)
+    Cv = make_CostMatrix(C, m, n)
+    # debug_print(f"Cv: {m} x {n}")
+    # debug_print(Cv.C)
+
+    pending_g = list(G1.edges)
+    pending_h = list(G2.edges)
+
+    # cost matrix of edge mappings
+    m = len(pending_g)
+    n = len(pending_h)
+    C = np.zeros((m + n, m + n))
+    if edge_subst_cost:
+        C[0:m, 0:n] = np.array(
+            [
+                edge_subst_cost(G1.edges[g], G2.edges[h])
+                for g in pending_g
+                for h in pending_h
+            ]
+        ).reshape(m, n)
+    elif edge_match:
+        C[0:m, 0:n] = np.array(
+            [
+                1 - int(edge_match(G1.edges[g], G2.edges[h]))
+                for g in pending_g
+                for h in pending_h
+            ]
+        ).reshape(m, n)
+    else:
+        # all zeroes
+        pass
+    # assert not min(m, n) or C[0:m, 0:n].min() >= 0
+    if edge_del_cost:
+        del_costs = [edge_del_cost(G1.edges[g]) for g in pending_g]
+    else:
+        del_costs = [1] * len(pending_g)
+    # assert not m or min(del_costs) >= 0
+    if edge_ins_cost:
+        ins_costs = [edge_ins_cost(G2.edges[h]) for h in pending_h]
+    else:
+        ins_costs = [1] * len(pending_h)
+    # assert not n or min(ins_costs) >= 0
+    inf = C[0:m, 0:n].sum() + sum(del_costs) + sum(ins_costs) + 1
+    C[0:m, n : n + m] = np.array(
+        [del_costs[i] if i == j else inf for i in range(m) for j in range(m)]
+    ).reshape(m, m)
+    C[m : m + n, 0:n] = np.array(
+        [ins_costs[i] if i == j else inf for i in range(n) for j in range(n)]
+    ).reshape(n, n)
+    Ce = make_CostMatrix(C, m, n)
+    # debug_print(f'Ce: {m} x {n}')
+    # debug_print(Ce.C)
+    # debug_print()
+
+    maxcost_value = Cv.C.sum() + Ce.C.sum() + 1
+
+    if timeout is not None:
+        if timeout <= 0:
+            raise nx.NetworkXError("Timeout value must be greater than 0")
+        start = time.perf_counter()
+
+    def prune(cost):
+        if timeout is not None:
+            if time.perf_counter() - start > timeout:
+                return True
+        if upper_bound is not None:
+            if cost > upper_bound:
+                return True
+        if cost > maxcost_value:
+            return True
+        if strictly_decreasing and cost >= maxcost_value:
+            return True
+        return False
+
+    # Now go!
+
+    done_uv = [] if roots is None else [roots]
+
+    for vertex_path, edge_path, cost in get_edit_paths(
+        done_uv, pending_u, pending_v, Cv, [], pending_g, pending_h, Ce, initial_cost
+    ):
+        # assert sorted(G1.nodes) == sorted(u for u, v in vertex_path if u is not None)
+        # assert sorted(G2.nodes) == sorted(v for u, v in vertex_path if v is not None)
+        # assert sorted(G1.edges) == sorted(g for g, h in edge_path if g is not None)
+        # assert sorted(G2.edges) == sorted(h for g, h in edge_path if h is not None)
+        # print(vertex_path, edge_path, cost, file = sys.stderr)
+        # assert cost == maxcost_value
+        yield list(vertex_path), list(edge_path), float(cost)
+
+
+@nx._dispatchable
+def simrank_similarity(
+    G,
+    source=None,
+    target=None,
+    importance_factor=0.9,
+    max_iterations=1000,
+    tolerance=1e-4,
+):
+    """Returns the SimRank similarity of nodes in the graph ``G``.
+
+    SimRank is a similarity metric that says "two objects are considered
+    to be similar if they are referenced by similar objects." [1]_.
+
+    The pseudo-code definition from the paper is::
+
+        def simrank(G, u, v):
+            in_neighbors_u = G.predecessors(u)
+            in_neighbors_v = G.predecessors(v)
+            scale = C / (len(in_neighbors_u) * len(in_neighbors_v))
+            return scale * sum(
+                simrank(G, w, x) for w, x in product(in_neighbors_u, in_neighbors_v)
+            )
+
+    where ``G`` is the graph, ``u`` is the source, ``v`` is the target,
+    and ``C`` is a float decay or importance factor between 0 and 1.
+
+    The SimRank algorithm for determining node similarity is defined in
+    [2]_.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        A NetworkX graph
+
+    source : node
+        If this is specified, the returned dictionary maps each node
+        ``v`` in the graph to the similarity between ``source`` and
+        ``v``.
+
+    target : node
+        If both ``source`` and ``target`` are specified, the similarity
+        value between ``source`` and ``target`` is returned. If
+        ``target`` is specified but ``source`` is not, this argument is
+        ignored.
+
+    importance_factor : float
+        The relative importance of indirect neighbors with respect to
+        direct neighbors.
+
+    max_iterations : integer
+        Maximum number of iterations.
+
+    tolerance : float
+        Error tolerance used to check convergence. When an iteration of
+        the algorithm finds that no similarity value changes more than
+        this amount, the algorithm halts.
+
+    Returns
+    -------
+    similarity : dictionary or float
+        If ``source`` and ``target`` are both ``None``, this returns a
+        dictionary of dictionaries, where keys are node pairs and value
+        are similarity of the pair of nodes.
+
+        If ``source`` is not ``None`` but ``target`` is, this returns a
+        dictionary mapping node to the similarity of ``source`` and that
+        node.
+
+        If neither ``source`` nor ``target`` is ``None``, this returns
+        the similarity value for the given pair of nodes.
+
+    Raises
+    ------
+    ExceededMaxIterations
+        If the algorithm does not converge within ``max_iterations``.
+
+    NodeNotFound
+        If either ``source`` or ``target`` is not in `G`.
+
+    Examples
+    --------
+    >>> G = nx.cycle_graph(2)
+    >>> nx.simrank_similarity(G)
+    {0: {0: 1.0, 1: 0.0}, 1: {0: 0.0, 1: 1.0}}
+    >>> nx.simrank_similarity(G, source=0)
+    {0: 1.0, 1: 0.0}
+    >>> nx.simrank_similarity(G, source=0, target=0)
+    1.0
+
+    The result of this function can be converted to a numpy array
+    representing the SimRank matrix by using the node order of the
+    graph to determine which row and column represent each node.
+    Other ordering of nodes is also possible.
+
+    >>> import numpy as np
+    >>> sim = nx.simrank_similarity(G)
+    >>> np.array([[sim[u][v] for v in G] for u in G])
+    array([[1., 0.],
+           [0., 1.]])
+    >>> sim_1d = nx.simrank_similarity(G, source=0)
+    >>> np.array([sim[0][v] for v in G])
+    array([1., 0.])
+
+    References
+    ----------
+    .. [1] https://en.wikipedia.org/wiki/SimRank
+    .. [2] G. Jeh and J. Widom.
+           "SimRank: a measure of structural-context similarity",
+           In KDD'02: Proceedings of the Eighth ACM SIGKDD
+           International Conference on Knowledge Discovery and Data Mining,
+           pp. 538--543. ACM Press, 2002.
+    """
+    import numpy as np
+
+    nodelist = list(G)
+    if source is not None:
+        if source not in nodelist:
+            raise nx.NodeNotFound(f"Source node {source} not in G")
+        else:
+            s_indx = nodelist.index(source)
+    else:
+        s_indx = None
+
+    if target is not None:
+        if target not in nodelist:
+            raise nx.NodeNotFound(f"Target node {target} not in G")
+        else:
+            t_indx = nodelist.index(target)
+    else:
+        t_indx = None
+
+    x = _simrank_similarity_numpy(
+        G, s_indx, t_indx, importance_factor, max_iterations, tolerance
+    )
+
+    if isinstance(x, np.ndarray):
+        if x.ndim == 1:
+            return dict(zip(G, x.tolist()))
+        # else x.ndim == 2
+        return {u: dict(zip(G, row)) for u, row in zip(G, x.tolist())}
+    return float(x)
+
+
+def _simrank_similarity_python(
+    G,
+    source=None,
+    target=None,
+    importance_factor=0.9,
+    max_iterations=1000,
+    tolerance=1e-4,
+):
+    """Returns the SimRank similarity of nodes in the graph ``G``.
+
+    This pure Python version is provided for pedagogical purposes.
+
+    Examples
+    --------
+    >>> G = nx.cycle_graph(2)
+    >>> nx.similarity._simrank_similarity_python(G)
+    {0: {0: 1, 1: 0.0}, 1: {0: 0.0, 1: 1}}
+    >>> nx.similarity._simrank_similarity_python(G, source=0)
+    {0: 1, 1: 0.0}
+    >>> nx.similarity._simrank_similarity_python(G, source=0, target=0)
+    1
+    """
+    # build up our similarity adjacency dictionary output
+    newsim = {u: {v: 1 if u == v else 0 for v in G} for u in G}
+
+    # These functions compute the update to the similarity value of the nodes
+    # `u` and `v` with respect to the previous similarity values.
+    def avg_sim(s):
+        return sum(newsim[w][x] for (w, x) in s) / len(s) if s else 0.0
+
+    Gadj = G.pred if G.is_directed() else G.adj
+
+    def sim(u, v):
+        return importance_factor * avg_sim(list(product(Gadj[u], Gadj[v])))
+
+    for its in range(max_iterations):
+        oldsim = newsim
+        newsim = {u: {v: sim(u, v) if u != v else 1 for v in G} for u in G}
+        is_close = all(
+            all(
+                abs(newsim[u][v] - old) <= tolerance * (1 + abs(old))
+                for v, old in nbrs.items()
+            )
+            for u, nbrs in oldsim.items()
+        )
+        if is_close:
+            break
+
+    if its + 1 == max_iterations:
+        raise nx.ExceededMaxIterations(
+            f"simrank did not converge after {max_iterations} iterations."
+        )
+
+    if source is not None and target is not None:
+        return newsim[source][target]
+    if source is not None:
+        return newsim[source]
+    return newsim
+
+
+def _simrank_similarity_numpy(
+    G,
+    source=None,
+    target=None,
+    importance_factor=0.9,
+    max_iterations=1000,
+    tolerance=1e-4,
+):
+    """Calculate SimRank of nodes in ``G`` using matrices with ``numpy``.
+
+    The SimRank algorithm for determining node similarity is defined in
+    [1]_.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        A NetworkX graph
+
+    source : node
+        If this is specified, the returned dictionary maps each node
+        ``v`` in the graph to the similarity between ``source`` and
+        ``v``.
+
+    target : node
+        If both ``source`` and ``target`` are specified, the similarity
+        value between ``source`` and ``target`` is returned. If
+        ``target`` is specified but ``source`` is not, this argument is
+        ignored.
+
+    importance_factor : float
+        The relative importance of indirect neighbors with respect to
+        direct neighbors.
+
+    max_iterations : integer
+        Maximum number of iterations.
+
+    tolerance : float
+        Error tolerance used to check convergence. When an iteration of
+        the algorithm finds that no similarity value changes more than
+        this amount, the algorithm halts.
+
+    Returns
+    -------
+    similarity : numpy array or float
+        If ``source`` and ``target`` are both ``None``, this returns a
+        2D array containing SimRank scores of the nodes.
+
+        If ``source`` is not ``None`` but ``target`` is, this returns an
+        1D array containing SimRank scores of ``source`` and that
+        node.
+
+        If neither ``source`` nor ``target`` is ``None``, this returns
+        the similarity value for the given pair of nodes.
+
+    Examples
+    --------
+    >>> G = nx.cycle_graph(2)
+    >>> nx.similarity._simrank_similarity_numpy(G)
+    array([[1., 0.],
+           [0., 1.]])
+    >>> nx.similarity._simrank_similarity_numpy(G, source=0)
+    array([1., 0.])
+    >>> nx.similarity._simrank_similarity_numpy(G, source=0, target=0)
+    1.0
+
+    References
+    ----------
+    .. [1] G. Jeh and J. Widom.
+           "SimRank: a measure of structural-context similarity",
+           In KDD'02: Proceedings of the Eighth ACM SIGKDD
+           International Conference on Knowledge Discovery and Data Mining,
+           pp. 538--543. ACM Press, 2002.
+    """
+    # This algorithm follows roughly
+    #
+    #     S = max{C * (A.T * S * A), I}
+    #
+    # where C is the importance factor, A is the column normalized
+    # adjacency matrix, and I is the identity matrix.
+    import numpy as np
+
+    adjacency_matrix = nx.to_numpy_array(G)
+
+    # column-normalize the ``adjacency_matrix``
+    s = np.array(adjacency_matrix.sum(axis=0))
+    s[s == 0] = 1
+    adjacency_matrix /= s  # adjacency_matrix.sum(axis=0)
+
+    newsim = np.eye(len(G), dtype=np.float64)
+    for its in range(max_iterations):
+        prevsim = newsim.copy()
+        newsim = importance_factor * ((adjacency_matrix.T @ prevsim) @ adjacency_matrix)
+        np.fill_diagonal(newsim, 1.0)
+
+        if np.allclose(prevsim, newsim, atol=tolerance):
+            break
+
+    if its + 1 == max_iterations:
+        raise nx.ExceededMaxIterations(
+            f"simrank did not converge after {max_iterations} iterations."
+        )
+
+    if source is not None and target is not None:
+        return float(newsim[source, target])
+    if source is not None:
+        return newsim[source]
+    return newsim
+
+
+@nx._dispatchable(edge_attrs="weight")
+def panther_similarity(
+    G, source, k=5, path_length=5, c=0.5, delta=0.1, eps=None, weight="weight"
+):
+    r"""Returns the Panther similarity of nodes in the graph `G` to node ``v``.
+
+    Panther is a similarity metric that says "two objects are considered
+    to be similar if they frequently appear on the same paths." [1]_.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        A NetworkX graph
+    source : node
+        Source node for which to find the top `k` similar other nodes
+    k : int (default = 5)
+        The number of most similar nodes to return.
+    path_length : int (default = 5)
+        How long the randomly generated paths should be (``T`` in [1]_)
+    c : float (default = 0.5)
+        A universal positive constant used to scale the number
+        of sample random paths to generate.
+    delta : float (default = 0.1)
+        The probability that the similarity $S$ is not an epsilon-approximation to (R, phi),
+        where $R$ is the number of random paths and $\phi$ is the probability
+        that an element sampled from a set $A \subseteq D$, where $D$ is the domain.
+    eps : float or None (default = None)
+        The error bound. Per [1]_, a good value is ``sqrt(1/|E|)``. Therefore,
+        if no value is provided, the recommended computed value will be used.
+    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.
+
+    Returns
+    -------
+    similarity : dictionary
+        Dictionary of nodes to similarity scores (as floats). Note:
+        the self-similarity (i.e., ``v``) will not be included in
+        the returned dictionary. So, for ``k = 5``, a dictionary of
+        top 4 nodes and their similarity scores will be returned.
+
+    Raises
+    ------
+    NetworkXUnfeasible
+        If `source` is an isolated node.
+
+    NodeNotFound
+        If `source` is not in `G`.
+
+    Notes
+    -----
+        The isolated nodes in `G` are ignored.
+
+    Examples
+    --------
+    >>> G = nx.star_graph(10)
+    >>> sim = nx.panther_similarity(G, 0)
+
+    References
+    ----------
+    .. [1] Zhang, J., Tang, J., Ma, C., Tong, H., Jing, Y., & Li, J.
+           Panther: Fast top-k similarity search on large networks.
+           In Proceedings of the ACM SIGKDD International Conference
+           on Knowledge Discovery and Data Mining (Vol. 2015-August, pp. 1445–1454).
+           Association for Computing Machinery. https://doi.org/10.1145/2783258.2783267.
+    """
+    import numpy as np
+
+    if source not in G:
+        raise nx.NodeNotFound(f"Source node {source} not in G")
+
+    isolates = set(nx.isolates(G))
+
+    if source in isolates:
+        raise nx.NetworkXUnfeasible(
+            f"Panther similarity is not defined for the isolated source node {source}."
+        )
+
+    G = G.subgraph([node for node in G.nodes if node not in isolates]).copy()
+
+    num_nodes = G.number_of_nodes()
+    if num_nodes < k:
+        warnings.warn(
+            f"Number of nodes is {num_nodes}, but requested k is {k}. "
+            "Setting k to number of nodes."
+        )
+        k = num_nodes
+    # According to [1], they empirically determined
+    # a good value for ``eps`` to be sqrt( 1 / |E| )
+    if eps is None:
+        eps = np.sqrt(1.0 / G.number_of_edges())
+
+    inv_node_map = {name: index for index, name in enumerate(G.nodes)}
+    node_map = np.array(G)
+
+    # Calculate the sample size ``R`` for how many paths
+    # to randomly generate
+    t_choose_2 = math.comb(path_length, 2)
+    sample_size = int((c / eps**2) * (np.log2(t_choose_2) + 1 + np.log(1 / delta)))
+    index_map = {}
+    _ = list(
+        generate_random_paths(
+            G, sample_size, path_length=path_length, index_map=index_map, weight=weight
+        )
+    )
+    S = np.zeros(num_nodes)
+
+    inv_sample_size = 1 / sample_size
+
+    source_paths = set(index_map[source])
+
+    # Calculate the path similarities
+    # between ``source`` (v) and ``node`` (v_j)
+    # using our inverted index mapping of
+    # vertices to paths
+    for node, paths in index_map.items():
+        # Only consider paths where both
+        # ``node`` and ``source`` are present
+        common_paths = source_paths.intersection(paths)
+        S[inv_node_map[node]] = len(common_paths) * inv_sample_size
+
+    # Retrieve top ``k`` similar
+    # Note: the below performed anywhere from 4-10x faster
+    # (depending on input sizes) vs the equivalent ``np.argsort(S)[::-1]``
+    top_k_unsorted = np.argpartition(S, -k)[-k:]
+    top_k_sorted = top_k_unsorted[np.argsort(S[top_k_unsorted])][::-1]
+
+    # Add back the similarity scores
+    top_k_with_val = dict(
+        zip(node_map[top_k_sorted].tolist(), S[top_k_sorted].tolist())
+    )
+
+    # Remove the self-similarity
+    top_k_with_val.pop(source, None)
+    return top_k_with_val
+
+
+@np_random_state(5)
+@nx._dispatchable(edge_attrs="weight")
+def generate_random_paths(
+    G, sample_size, path_length=5, index_map=None, weight="weight", seed=None
+):
+    """Randomly generate `sample_size` paths of length `path_length`.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        A NetworkX graph
+    sample_size : integer
+        The number of paths to generate. This is ``R`` in [1]_.
+    path_length : integer (default = 5)
+        The maximum size of the path to randomly generate.
+        This is ``T`` in [1]_. According to the paper, ``T >= 5`` is
+        recommended.
+    index_map : dictionary, optional
+        If provided, this will be populated with the inverted
+        index of nodes mapped to the set of generated random path
+        indices within ``paths``.
+    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.
+    seed : integer, random_state, or None (default)
+        Indicator of random number generation state.
+        See :ref:`Randomness<randomness>`.
+
+    Returns
+    -------
+    paths : generator of lists
+        Generator of `sample_size` paths each with length `path_length`.
+
+    Examples
+    --------
+    Note that the return value is the list of paths:
+
+    >>> G = nx.star_graph(3)
+    >>> random_path = nx.generate_random_paths(G, 2)
+
+    By passing a dictionary into `index_map`, it will build an
+    inverted index mapping of nodes to the paths in which that node is present:
+
+    >>> G = nx.star_graph(3)
+    >>> index_map = {}
+    >>> random_path = nx.generate_random_paths(G, 3, index_map=index_map)
+    >>> paths_containing_node_0 = [
+    ...     random_path[path_idx] for path_idx in index_map.get(0, [])
+    ... ]
+
+    References
+    ----------
+    .. [1] Zhang, J., Tang, J., Ma, C., Tong, H., Jing, Y., & Li, J.
+           Panther: Fast top-k similarity search on large networks.
+           In Proceedings of the ACM SIGKDD International Conference
+           on Knowledge Discovery and Data Mining (Vol. 2015-August, pp. 1445–1454).
+           Association for Computing Machinery. https://doi.org/10.1145/2783258.2783267.
+    """
+    import numpy as np
+
+    randint_fn = (
+        seed.integers if isinstance(seed, np.random.Generator) else seed.randint
+    )
+
+    # Calculate transition probabilities between
+    # every pair of vertices according to Eq. (3)
+    adj_mat = nx.to_numpy_array(G, weight=weight)
+    inv_row_sums = np.reciprocal(adj_mat.sum(axis=1)).reshape(-1, 1)
+    transition_probabilities = adj_mat * inv_row_sums
+
+    node_map = list(G)
+    num_nodes = G.number_of_nodes()
+
+    for path_index in range(sample_size):
+        # Sample current vertex v = v_i uniformly at random
+        node_index = randint_fn(num_nodes)
+        node = node_map[node_index]
+
+        # Add v into p_r and add p_r into the path set
+        # of v, i.e., P_v
+        path = [node]
+
+        # Build the inverted index (P_v) of vertices to paths
+        if index_map is not None:
+            if node in index_map:
+                index_map[node].add(path_index)
+            else:
+                index_map[node] = {path_index}
+
+        starting_index = node_index
+        for _ in range(path_length):
+            # Randomly sample a neighbor (v_j) according
+            # to transition probabilities from ``node`` (v) to its neighbors
+            nbr_index = seed.choice(
+                num_nodes, p=transition_probabilities[starting_index]
+            )
+
+            # Set current vertex (v = v_j)
+            starting_index = nbr_index
+
+            # Add v into p_r
+            nbr_node = node_map[nbr_index]
+            path.append(nbr_node)
+
+            # Add p_r into P_v
+            if index_map is not None:
+                if nbr_node in index_map:
+                    index_map[nbr_node].add(path_index)
+                else:
+                    index_map[nbr_node] = {path_index}
+
+        yield path

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/simple_paths.py

@@ -0,0 +1,937 @@
+from heapq import heappop, heappush
+from itertools import count
+
+import networkx as nx
+from networkx.algorithms.shortest_paths.weighted import _weight_function
+from networkx.utils import not_implemented_for, pairwise
+
+__all__ = [
+    "all_simple_paths",
+    "is_simple_path",
+    "shortest_simple_paths",
+    "all_simple_edge_paths",
+]
+
+
+@nx._dispatchable
+def is_simple_path(G, nodes):
+    """Returns True if and only if `nodes` form a simple path in `G`.
+
+    A *simple path* in a graph is a nonempty sequence of nodes in which
+    no node appears more than once in the sequence, and each adjacent
+    pair of nodes in the sequence is adjacent in the graph.
+
+    Parameters
+    ----------
+    G : graph
+        A NetworkX graph.
+    nodes : list
+        A list of one or more nodes in the graph `G`.
+
+    Returns
+    -------
+    bool
+        Whether the given list of nodes represents a simple path in `G`.
+
+    Notes
+    -----
+    An empty list of nodes is not a path but a list of one node is a
+    path. Here's an explanation why.
+
+    This function operates on *node paths*. One could also consider
+    *edge paths*. There is a bijection between node paths and edge
+    paths.
+
+    The *length of a path* is the number of edges in the path, so a list
+    of nodes of length *n* corresponds to a path of length *n* - 1.
+    Thus the smallest edge path would be a list of zero edges, the empty
+    path. This corresponds to a list of one node.
+
+    To convert between a node path and an edge path, you can use code
+    like the following::
+
+        >>> from networkx.utils import pairwise
+        >>> nodes = [0, 1, 2, 3]
+        >>> edges = list(pairwise(nodes))
+        >>> edges
+        [(0, 1), (1, 2), (2, 3)]
+        >>> nodes = [edges[0][0]] + [v for u, v in edges]
+        >>> nodes
+        [0, 1, 2, 3]
+
+    Examples
+    --------
+    >>> G = nx.cycle_graph(4)
+    >>> nx.is_simple_path(G, [2, 3, 0])
+    True
+    >>> nx.is_simple_path(G, [0, 2])
+    False
+
+    """
+    # The empty list is not a valid path. Could also return
+    # NetworkXPointlessConcept here.
+    if len(nodes) == 0:
+        return False
+
+    # If the list is a single node, just check that the node is actually
+    # in the graph.
+    if len(nodes) == 1:
+        return nodes[0] in G
+
+    # check that all nodes in the list are in the graph, if at least one
+    # is not in the graph, then this is not a simple path
+    if not all(n in G for n in nodes):
+        return False
+
+    # If the list contains repeated nodes, then it's not a simple path
+    if len(set(nodes)) != len(nodes):
+        return False
+
+    # Test that each adjacent pair of nodes is adjacent.
+    return all(v in G[u] for u, v in pairwise(nodes))
+
+
+@nx._dispatchable
+def all_simple_paths(G, source, target, cutoff=None):
+    """Generate all simple paths in the graph G from source to target.
+
+    A simple path is a path with no repeated nodes.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    source : node
+       Starting node for path
+
+    target : nodes
+       Single node or iterable of nodes at which to end path
+
+    cutoff : integer, optional
+        Depth to stop the search. Only paths of length <= cutoff are returned.
+
+    Returns
+    -------
+    path_generator: generator
+       A generator that produces lists of simple paths.  If there are no paths
+       between the source and target within the given cutoff the generator
+       produces no output. If it is possible to traverse the same sequence of
+       nodes in multiple ways, namely through parallel edges, then it will be
+       returned multiple times (once for each viable edge combination).
+
+    Examples
+    --------
+    This iterator generates lists of nodes::
+
+        >>> G = nx.complete_graph(4)
+        >>> for path in nx.all_simple_paths(G, source=0, target=3):
+        ...     print(path)
+        ...
+        [0, 1, 2, 3]
+        [0, 1, 3]
+        [0, 2, 1, 3]
+        [0, 2, 3]
+        [0, 3]
+
+    You can generate only those paths that are shorter than a certain
+    length by using the `cutoff` keyword argument::
+
+        >>> paths = nx.all_simple_paths(G, source=0, target=3, cutoff=2)
+        >>> print(list(paths))
+        [[0, 1, 3], [0, 2, 3], [0, 3]]
+
+    To get each path as the corresponding list of edges, you can use the
+    :func:`networkx.utils.pairwise` helper function::
+
+        >>> paths = nx.all_simple_paths(G, source=0, target=3)
+        >>> for path in map(nx.utils.pairwise, paths):
+        ...     print(list(path))
+        [(0, 1), (1, 2), (2, 3)]
+        [(0, 1), (1, 3)]
+        [(0, 2), (2, 1), (1, 3)]
+        [(0, 2), (2, 3)]
+        [(0, 3)]
+
+    Pass an iterable of nodes as target to generate all paths ending in any of several nodes::
+
+        >>> G = nx.complete_graph(4)
+        >>> for path in nx.all_simple_paths(G, source=0, target=[3, 2]):
+        ...     print(path)
+        ...
+        [0, 1, 2]
+        [0, 1, 2, 3]
+        [0, 1, 3]
+        [0, 1, 3, 2]
+        [0, 2]
+        [0, 2, 1, 3]
+        [0, 2, 3]
+        [0, 3]
+        [0, 3, 1, 2]
+        [0, 3, 2]
+
+    The singleton path from ``source`` to itself is considered a simple path and is
+    included in the results:
+
+        >>> G = nx.empty_graph(5)
+        >>> list(nx.all_simple_paths(G, source=0, target=0))
+        [[0]]
+
+        >>> G = nx.path_graph(3)
+        >>> list(nx.all_simple_paths(G, source=0, target={0, 1, 2}))
+        [[0], [0, 1], [0, 1, 2]]
+
+    Iterate over each path from the root nodes to the leaf nodes in a
+    directed acyclic graph using a functional programming approach::
+
+        >>> from itertools import chain
+        >>> from itertools import product
+        >>> from itertools import starmap
+        >>> from functools import partial
+        >>>
+        >>> chaini = chain.from_iterable
+        >>>
+        >>> G = nx.DiGraph([(0, 1), (1, 2), (0, 3), (3, 2)])
+        >>> 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)
+        >>> list(chaini(starmap(all_paths, product(roots, leaves))))
+        [[0, 1, 2], [0, 3, 2]]
+
+    The same list computed using an iterative approach::
+
+        >>> G = nx.DiGraph([(0, 1), (1, 2), (0, 3), (3, 2)])
+        >>> 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 = []
+        >>> for root in roots:
+        ...     for leaf in leaves:
+        ...         paths = nx.all_simple_paths(G, root, leaf)
+        ...         all_paths.extend(paths)
+        >>> all_paths
+        [[0, 1, 2], [0, 3, 2]]
+
+    Iterate over each path from the root nodes to the leaf nodes in a
+    directed acyclic graph passing all leaves together to avoid unnecessary
+    compute::
+
+        >>> G = nx.DiGraph([(0, 1), (2, 1), (1, 3), (1, 4)])
+        >>> 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 = []
+        >>> for root in roots:
+        ...     paths = nx.all_simple_paths(G, root, leaves)
+        ...     all_paths.extend(paths)
+        >>> all_paths
+        [[0, 1, 3], [0, 1, 4], [2, 1, 3], [2, 1, 4]]
+
+    If parallel edges offer multiple ways to traverse a given sequence of
+    nodes, this sequence of nodes will be returned multiple times:
+
+        >>> G = nx.MultiDiGraph([(0, 1), (0, 1), (1, 2)])
+        >>> list(nx.all_simple_paths(G, 0, 2))
+        [[0, 1, 2], [0, 1, 2]]
+
+    Notes
+    -----
+    This algorithm uses a modified depth-first search to generate the
+    paths [1]_.  A single path can be found in $O(V+E)$ time but the
+    number of simple paths in a graph can be very large, e.g. $O(n!)$ in
+    the complete graph of order $n$.
+
+    This function does not check that a path exists between `source` and
+    `target`. For large graphs, this may result in very long runtimes.
+    Consider using `has_path` to check that a path exists between `source` and
+    `target` before calling this function on large graphs.
+
+    References
+    ----------
+    .. [1] R. Sedgewick, "Algorithms in C, Part 5: Graph Algorithms",
+       Addison Wesley Professional, 3rd ed., 2001.
+
+    See Also
+    --------
+    all_shortest_paths, shortest_path, has_path
+
+    """
+    for edge_path in all_simple_edge_paths(G, source, target, cutoff):
+        yield [source] + [edge[1] for edge in edge_path]
+
+
+@nx._dispatchable
+def all_simple_edge_paths(G, source, target, cutoff=None):
+    """Generate lists of edges for all simple paths in G from source to target.
+
+    A simple path is a path with no repeated nodes.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    source : node
+       Starting node for path
+
+    target : nodes
+       Single node or iterable of nodes at which to end path
+
+    cutoff : integer, optional
+        Depth to stop the search. Only paths of length <= cutoff are returned.
+
+    Returns
+    -------
+    path_generator: generator
+       A generator that produces lists of simple paths.  If there are no paths
+       between the source and target within the given cutoff the generator
+       produces no output.
+       For multigraphs, the list of edges have elements of the form `(u,v,k)`.
+       Where `k` corresponds to the edge key.
+
+    Examples
+    --------
+
+    Print the simple path edges of a Graph::
+
+        >>> g = nx.Graph([(1, 2), (2, 4), (1, 3), (3, 4)])
+        >>> for path in sorted(nx.all_simple_edge_paths(g, 1, 4)):
+        ...     print(path)
+        [(1, 2), (2, 4)]
+        [(1, 3), (3, 4)]
+
+    Print the simple path edges of a MultiGraph. Returned edges come with
+    their associated keys::
+
+        >>> mg = nx.MultiGraph()
+        >>> mg.add_edge(1, 2, key="k0")
+        'k0'
+        >>> mg.add_edge(1, 2, key="k1")
+        'k1'
+        >>> mg.add_edge(2, 3, key="k0")
+        'k0'
+        >>> for path in sorted(nx.all_simple_edge_paths(mg, 1, 3)):
+        ...     print(path)
+        [(1, 2, 'k0'), (2, 3, 'k0')]
+        [(1, 2, 'k1'), (2, 3, 'k0')]
+
+    When ``source`` is one of the targets, the empty path starting and ending at
+    ``source`` without traversing any edge is considered a valid simple edge path
+    and is included in the results:
+
+        >>> G = nx.Graph()
+        >>> G.add_node(0)
+        >>> paths = list(nx.all_simple_edge_paths(G, 0, 0))
+        >>> for path in paths:
+        ...     print(path)
+        []
+        >>> len(paths)
+        1
+
+
+    Notes
+    -----
+    This algorithm uses a modified depth-first search to generate the
+    paths [1]_.  A single path can be found in $O(V+E)$ time but the
+    number of simple paths in a graph can be very large, e.g. $O(n!)$ in
+    the complete graph of order $n$.
+
+    References
+    ----------
+    .. [1] R. Sedgewick, "Algorithms in C, Part 5: Graph Algorithms",
+       Addison Wesley Professional, 3rd ed., 2001.
+
+    See Also
+    --------
+    all_shortest_paths, shortest_path, all_simple_paths
+
+    """
+    if source not in G:
+        raise nx.NodeNotFound(f"source node {source} not in graph")
+
+    if target in G:
+        targets = {target}
+    else:
+        try:
+            targets = set(target)
+        except TypeError as err:
+            raise nx.NodeNotFound(f"target node {target} not in graph") from err
+
+    cutoff = cutoff if cutoff is not None else len(G) - 1
+
+    if cutoff >= 0 and targets:
+        yield from _all_simple_edge_paths(G, source, targets, cutoff)
+
+
+def _all_simple_edge_paths(G, source, targets, cutoff):
+    # We simulate recursion with a stack, keeping the current path being explored
+    # and the outgoing edge iterators at each point in the stack.
+    # To avoid unnecessary checks, the loop is structured in a way such that a path
+    # is considered for yielding only after a new node/edge is added.
+    # We bootstrap the search by adding a dummy iterator to the stack that only yields
+    # a dummy edge to source (so that the trivial path has a chance of being included).
+
+    get_edges = (
+        (lambda node: G.edges(node, keys=True))
+        if G.is_multigraph()
+        else (lambda node: G.edges(node))
+    )
+
+    # The current_path is a dictionary that maps nodes in the path to the edge that was
+    # used to enter that node (instead of a list of edges) because we want both a fast
+    # membership test for nodes in the path and the preservation of insertion order.
+    current_path = {None: None}
+    stack = [iter([(None, source)])]
+
+    while stack:
+        # 1. Try to extend the current path.
+        next_edge = next((e for e in stack[-1] if e[1] not in current_path), None)
+        if next_edge is None:
+            # All edges of the last node in the current path have been explored.
+            stack.pop()
+            current_path.popitem()
+            continue
+        previous_node, next_node, *_ = next_edge
+
+        # 2. Check if we've reached a target.
+        if next_node in targets:
+            yield (list(current_path.values()) + [next_edge])[2:]  # remove dummy edge
+
+        # 3. Only expand the search through the next node if it makes sense.
+        if len(current_path) - 1 < cutoff and (
+            targets - current_path.keys() - {next_node}
+        ):
+            current_path[next_node] = next_edge
+            stack.append(iter(get_edges(next_node)))
+
+
+@not_implemented_for("multigraph")
+@nx._dispatchable(edge_attrs="weight")
+def shortest_simple_paths(G, source, target, weight=None):
+    """Generate all simple paths in the graph G from source to target,
+       starting from shortest ones.
+
+    A simple path is a path with no repeated nodes.
+
+    If a weighted shortest path search is to be used, no negative weights
+    are allowed.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    source : node
+       Starting node for path
+
+    target : node
+       Ending node for path
+
+    weight : string or function
+        If it is a string, it is the name of the edge attribute to be
+        used as a weight.
+
+        If it is a function, the weight of an edge is the value returned
+        by the function. The function must accept exactly three positional
+        arguments: the two endpoints of an edge and the dictionary of edge
+        attributes for that edge. The function must return a number.
+
+        If None all edges are considered to have unit weight. Default
+        value None.
+
+    Returns
+    -------
+    path_generator: generator
+       A generator that produces lists of simple paths, in order from
+       shortest to longest.
+
+    Raises
+    ------
+    NetworkXNoPath
+       If no path exists between source and target.
+
+    NetworkXError
+       If source or target nodes are not in the input graph.
+
+    NetworkXNotImplemented
+       If the input graph is a Multi[Di]Graph.
+
+    Examples
+    --------
+
+    >>> G = nx.cycle_graph(7)
+    >>> paths = list(nx.shortest_simple_paths(G, 0, 3))
+    >>> print(paths)
+    [[0, 1, 2, 3], [0, 6, 5, 4, 3]]
+
+    You can use this function to efficiently compute the k shortest/best
+    paths between two nodes.
+
+    >>> from itertools import islice
+    >>> def k_shortest_paths(G, source, target, k, weight=None):
+    ...     return list(
+    ...         islice(nx.shortest_simple_paths(G, source, target, weight=weight), k)
+    ...     )
+    >>> for path in k_shortest_paths(G, 0, 3, 2):
+    ...     print(path)
+    [0, 1, 2, 3]
+    [0, 6, 5, 4, 3]
+
+    Notes
+    -----
+    This procedure is based on algorithm by Jin Y. Yen [1]_.  Finding
+    the first $K$ paths requires $O(KN^3)$ operations.
+
+    See Also
+    --------
+    all_shortest_paths
+    shortest_path
+    all_simple_paths
+
+    References
+    ----------
+    .. [1] Jin Y. Yen, "Finding the K Shortest Loopless Paths in a
+       Network", Management Science, Vol. 17, No. 11, Theory Series
+       (Jul., 1971), pp. 712-716.
+
+    """
+    if source not in G:
+        raise nx.NodeNotFound(f"source node {source} not in graph")
+
+    if target not in G:
+        raise nx.NodeNotFound(f"target node {target} not in graph")
+
+    if weight is None:
+        length_func = len
+        shortest_path_func = _bidirectional_shortest_path
+    else:
+        wt = _weight_function(G, weight)
+
+        def length_func(path):
+            return sum(
+                wt(u, v, G.get_edge_data(u, v)) for (u, v) in zip(path, path[1:])
+            )
+
+        shortest_path_func = _bidirectional_dijkstra
+
+    listA = []
+    listB = PathBuffer()
+    prev_path = None
+    while True:
+        if not prev_path:
+            length, path = shortest_path_func(G, source, target, weight=weight)
+            listB.push(length, path)
+        else:
+            ignore_nodes = set()
+            ignore_edges = set()
+            for i in range(1, len(prev_path)):
+                root = prev_path[:i]
+                root_length = length_func(root)
+                for path in listA:
+                    if path[:i] == root:
+                        ignore_edges.add((path[i - 1], path[i]))
+                try:
+                    length, spur = shortest_path_func(
+                        G,
+                        root[-1],
+                        target,
+                        ignore_nodes=ignore_nodes,
+                        ignore_edges=ignore_edges,
+                        weight=weight,
+                    )
+                    path = root[:-1] + spur
+                    listB.push(root_length + length, path)
+                except nx.NetworkXNoPath:
+                    pass
+                ignore_nodes.add(root[-1])
+
+        if listB:
+            path = listB.pop()
+            yield path
+            listA.append(path)
+            prev_path = path
+        else:
+            break
+
+
+class PathBuffer:
+    def __init__(self):
+        self.paths = set()
+        self.sortedpaths = []
+        self.counter = count()
+
+    def __len__(self):
+        return len(self.sortedpaths)
+
+    def push(self, cost, path):
+        hashable_path = tuple(path)
+        if hashable_path not in self.paths:
+            heappush(self.sortedpaths, (cost, next(self.counter), path))
+            self.paths.add(hashable_path)
+
+    def pop(self):
+        (cost, num, path) = heappop(self.sortedpaths)
+        hashable_path = tuple(path)
+        self.paths.remove(hashable_path)
+        return path
+
+
+def _bidirectional_shortest_path(
+    G, source, target, ignore_nodes=None, ignore_edges=None, weight=None
+):
+    """Returns the shortest path between source and target ignoring
+       nodes and edges in the containers ignore_nodes and ignore_edges.
+
+    This is a custom modification of the standard bidirectional shortest
+    path implementation at networkx.algorithms.unweighted
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    source : node
+       starting node for path
+
+    target : node
+       ending node for path
+
+    ignore_nodes : container of nodes
+       nodes to ignore, optional
+
+    ignore_edges : container of edges
+       edges to ignore, optional
+
+    weight : None
+       This function accepts a weight argument for convenience of
+       shortest_simple_paths function. It will be ignored.
+
+    Returns
+    -------
+    path: list
+       List of nodes in a path from source to target.
+
+    Raises
+    ------
+    NetworkXNoPath
+       If no path exists between source and target.
+
+    See Also
+    --------
+    shortest_path
+
+    """
+    # call helper to do the real work
+    results = _bidirectional_pred_succ(G, source, target, ignore_nodes, ignore_edges)
+    pred, succ, w = results
+
+    # build path from pred+w+succ
+    path = []
+    # from w to target
+    while w is not None:
+        path.append(w)
+        w = succ[w]
+    # from source to w
+    w = pred[path[0]]
+    while w is not None:
+        path.insert(0, w)
+        w = pred[w]
+
+    return len(path), path
+
+
+def _bidirectional_pred_succ(G, source, target, ignore_nodes=None, ignore_edges=None):
+    """Bidirectional shortest path helper.
+    Returns (pred,succ,w) where
+    pred is a dictionary of predecessors from w to the source, and
+    succ is a dictionary of successors from w to the target.
+    """
+    # does BFS from both source and target and meets in the middle
+    if ignore_nodes and (source in ignore_nodes or target in ignore_nodes):
+        raise nx.NetworkXNoPath(f"No path between {source} and {target}.")
+    if target == source:
+        return ({target: None}, {source: None}, source)
+
+    # handle either directed or undirected
+    if G.is_directed():
+        Gpred = G.predecessors
+        Gsucc = G.successors
+    else:
+        Gpred = G.neighbors
+        Gsucc = G.neighbors
+
+    # support optional nodes filter
+    if ignore_nodes:
+
+        def filter_iter(nodes):
+            def iterate(v):
+                for w in nodes(v):
+                    if w not in ignore_nodes:
+                        yield w
+
+            return iterate
+
+        Gpred = filter_iter(Gpred)
+        Gsucc = filter_iter(Gsucc)
+
+    # support optional edges filter
+    if ignore_edges:
+        if G.is_directed():
+
+            def filter_pred_iter(pred_iter):
+                def iterate(v):
+                    for w in pred_iter(v):
+                        if (w, v) not in ignore_edges:
+                            yield w
+
+                return iterate
+
+            def filter_succ_iter(succ_iter):
+                def iterate(v):
+                    for w in succ_iter(v):
+                        if (v, w) not in ignore_edges:
+                            yield w
+
+                return iterate
+
+            Gpred = filter_pred_iter(Gpred)
+            Gsucc = filter_succ_iter(Gsucc)
+
+        else:
+
+            def filter_iter(nodes):
+                def iterate(v):
+                    for w in nodes(v):
+                        if (v, w) not in ignore_edges and (w, v) not in ignore_edges:
+                            yield w
+
+                return iterate
+
+            Gpred = filter_iter(Gpred)
+            Gsucc = filter_iter(Gsucc)
+
+    # predecessor and successors in search
+    pred = {source: None}
+    succ = {target: None}
+
+    # initialize fringes, start with forward
+    forward_fringe = [source]
+    reverse_fringe = [target]
+
+    while forward_fringe and reverse_fringe:
+        if len(forward_fringe) <= len(reverse_fringe):
+            this_level = forward_fringe
+            forward_fringe = []
+            for v in this_level:
+                for w in Gsucc(v):
+                    if w not in pred:
+                        forward_fringe.append(w)
+                        pred[w] = v
+                    if w in succ:
+                        # found path
+                        return pred, succ, w
+        else:
+            this_level = reverse_fringe
+            reverse_fringe = []
+            for v in this_level:
+                for w in Gpred(v):
+                    if w not in succ:
+                        succ[w] = v
+                        reverse_fringe.append(w)
+                    if w in pred:
+                        # found path
+                        return pred, succ, w
+
+    raise nx.NetworkXNoPath(f"No path between {source} and {target}.")
+
+
+def _bidirectional_dijkstra(
+    G, source, target, weight="weight", ignore_nodes=None, ignore_edges=None
+):
+    """Dijkstra's algorithm for shortest paths using bidirectional search.
+
+    This function returns the shortest path between source and target
+    ignoring nodes and edges in the containers ignore_nodes and
+    ignore_edges.
+
+    This is a custom modification of the standard Dijkstra bidirectional
+    shortest path implementation at networkx.algorithms.weighted
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    source : node
+       Starting node.
+
+    target : node
+       Ending node.
+
+    weight: string, function, optional (default='weight')
+       Edge data key or weight function corresponding to the edge weight
+
+    ignore_nodes : container of nodes
+       nodes to ignore, optional
+
+    ignore_edges : container of edges
+       edges to ignore, optional
+
+    Returns
+    -------
+    length : number
+        Shortest path length.
+
+    Returns a tuple of two dictionaries keyed by node.
+    The first dictionary stores distance from the source.
+    The second stores the path from the source to that node.
+
+    Raises
+    ------
+    NetworkXNoPath
+        If no path exists between source and target.
+
+    Notes
+    -----
+    Edge weight attributes must be numerical.
+    Distances are calculated as sums of weighted edges traversed.
+
+    In practice  bidirectional Dijkstra is much more than twice as fast as
+    ordinary Dijkstra.
+
+    Ordinary Dijkstra expands nodes in a sphere-like manner from the
+    source. The radius of this sphere will eventually be the length
+    of the shortest path. Bidirectional Dijkstra will expand nodes
+    from both the source and the target, making two spheres of half
+    this radius. Volume of the first sphere is pi*r*r while the
+    others are 2*pi*r/2*r/2, making up half the volume.
+
+    This algorithm is not guaranteed to work if edge weights
+    are negative or are floating point numbers
+    (overflows and roundoff errors can cause problems).
+
+    See Also
+    --------
+    shortest_path
+    shortest_path_length
+    """
+    if ignore_nodes and (source in ignore_nodes or target in ignore_nodes):
+        raise nx.NetworkXNoPath(f"No path between {source} and {target}.")
+    if source == target:
+        if source not in G:
+            raise nx.NodeNotFound(f"Node {source} not in graph")
+        return (0, [source])
+
+    # handle either directed or undirected
+    if G.is_directed():
+        Gpred = G.predecessors
+        Gsucc = G.successors
+    else:
+        Gpred = G.neighbors
+        Gsucc = G.neighbors
+
+    # support optional nodes filter
+    if ignore_nodes:
+
+        def filter_iter(nodes):
+            def iterate(v):
+                for w in nodes(v):
+                    if w not in ignore_nodes:
+                        yield w
+
+            return iterate
+
+        Gpred = filter_iter(Gpred)
+        Gsucc = filter_iter(Gsucc)
+
+    # support optional edges filter
+    if ignore_edges:
+        if G.is_directed():
+
+            def filter_pred_iter(pred_iter):
+                def iterate(v):
+                    for w in pred_iter(v):
+                        if (w, v) not in ignore_edges:
+                            yield w
+
+                return iterate
+
+            def filter_succ_iter(succ_iter):
+                def iterate(v):
+                    for w in succ_iter(v):
+                        if (v, w) not in ignore_edges:
+                            yield w
+
+                return iterate
+
+            Gpred = filter_pred_iter(Gpred)
+            Gsucc = filter_succ_iter(Gsucc)
+
+        else:
+
+            def filter_iter(nodes):
+                def iterate(v):
+                    for w in nodes(v):
+                        if (v, w) not in ignore_edges and (w, v) not in ignore_edges:
+                            yield w
+
+                return iterate
+
+            Gpred = filter_iter(Gpred)
+            Gsucc = filter_iter(Gsucc)
+
+    push = heappush
+    pop = heappop
+    # Init:   Forward             Backward
+    dists = [{}, {}]  # dictionary of final distances
+    paths = [{source: [source]}, {target: [target]}]  # dictionary of paths
+    fringe = [[], []]  # heap of (distance, node) tuples for
+    # extracting next node to expand
+    seen = [{source: 0}, {target: 0}]  # dictionary of distances to
+    # nodes seen
+    c = count()
+    # initialize fringe heap
+    push(fringe[0], (0, next(c), source))
+    push(fringe[1], (0, next(c), target))
+    # neighs for extracting correct neighbor information
+    neighs = [Gsucc, Gpred]
+    # variables to hold shortest discovered path
+    # finaldist = 1e30000
+    finalpath = []
+    dir = 1
+    while fringe[0] and fringe[1]:
+        # choose direction
+        # dir == 0 is forward direction and dir == 1 is back
+        dir = 1 - dir
+        # extract closest to expand
+        (dist, _, v) = pop(fringe[dir])
+        if v in dists[dir]:
+            # Shortest path to v has already been found
+            continue
+        # update distance
+        dists[dir][v] = dist  # equal to seen[dir][v]
+        if v in dists[1 - dir]:
+            # if we have scanned v in both directions we are done
+            # we have now discovered the shortest path
+            return (finaldist, finalpath)
+
+        wt = _weight_function(G, weight)
+        for w in neighs[dir](v):
+            if dir == 0:  # forward
+                minweight = wt(v, w, G.get_edge_data(v, w))
+                vwLength = dists[dir][v] + minweight
+            else:  # back, must remember to change v,w->w,v
+                minweight = wt(w, v, G.get_edge_data(w, v))
+                vwLength = dists[dir][v] + minweight
+
+            if w in dists[dir]:
+                if vwLength < dists[dir][w]:
+                    raise ValueError("Contradictory paths found: negative weights?")
+            elif w not in seen[dir] or vwLength < seen[dir][w]:
+                # relaxing
+                seen[dir][w] = vwLength
+                push(fringe[dir], (vwLength, next(c), w))
+                paths[dir][w] = paths[dir][v] + [w]
+                if w in seen[0] and w in seen[1]:
+                    # see if this path is better than the already
+                    # discovered shortest path
+                    totaldist = seen[0][w] + seen[1][w]
+                    if finalpath == [] or finaldist > totaldist:
+                        finaldist = totaldist
+                        revpath = paths[1][w][:]
+                        revpath.reverse()
+                        finalpath = paths[0][w] + revpath[1:]
+    raise nx.NetworkXNoPath(f"No path between {source} and {target}.")

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/structuralholes.py

@@ -0,0 +1,283 @@
+"""Functions for computing measures of structural holes."""
+
+import networkx as nx
+
+__all__ = ["constraint", "local_constraint", "effective_size"]
+
+
+@nx._dispatchable(edge_attrs="weight")
+def mutual_weight(G, u, v, weight=None):
+    """Returns the sum of the weights of the edge from `u` to `v` and
+    the edge from `v` to `u` in `G`.
+
+    `weight` is the edge data key that represents the edge weight. If
+    the specified key is `None` or is not in the edge data for an edge,
+    that edge is assumed to have weight 1.
+
+    Pre-conditions: `u` and `v` must both be in `G`.
+
+    """
+    try:
+        a_uv = G[u][v].get(weight, 1)
+    except KeyError:
+        a_uv = 0
+    try:
+        a_vu = G[v][u].get(weight, 1)
+    except KeyError:
+        a_vu = 0
+    return a_uv + a_vu
+
+
+@nx._dispatchable(edge_attrs="weight")
+def normalized_mutual_weight(G, u, v, norm=sum, weight=None):
+    """Returns normalized mutual weight of the edges from `u` to `v`
+    with respect to the mutual weights of the neighbors of `u` in `G`.
+
+    `norm` specifies how the normalization factor is computed. It must
+    be a function that takes a single argument and returns a number.
+    The argument will be an iterable of mutual weights
+    of pairs ``(u, w)``, where ``w`` ranges over each (in- and
+    out-)neighbor of ``u``. Commons values for `normalization` are
+    ``sum`` and ``max``.
+
+    `weight` can be ``None`` or a string, if None, all edge weights
+    are considered equal. Otherwise holds the name of the edge
+    attribute used as weight.
+
+    """
+    scale = norm(mutual_weight(G, u, w, weight) for w in set(nx.all_neighbors(G, u)))
+    return 0 if scale == 0 else mutual_weight(G, u, v, weight) / scale
+
+
+@nx._dispatchable(edge_attrs="weight")
+def effective_size(G, nodes=None, weight=None):
+    r"""Returns the effective size of all nodes in the graph ``G``.
+
+    The *effective size* of a node's ego network is based on the concept
+    of redundancy. A person's ego network has redundancy to the extent
+    that her contacts are connected to each other as well. The
+    nonredundant part of a person's relationships is the effective
+    size of her ego network [1]_.  Formally, the effective size of a
+    node $u$, denoted $e(u)$, is defined by
+
+    .. math::
+
+       e(u) = \sum_{v \in N(u) \setminus \{u\}}
+       \left(1 - \sum_{w \in N(v)} p_{uw} m_{vw}\right)
+
+    where $N(u)$ is the set of neighbors of $u$ and $p_{uw}$ is the
+    normalized mutual weight of the (directed or undirected) edges
+    joining $u$ and $v$, for each vertex $u$ and $v$ [1]_. And $m_{vw}$
+    is the mutual weight of $v$ and $w$ divided by $v$ highest mutual
+    weight with any of its neighbors. The *mutual weight* of $u$ and $v$
+    is the sum of the weights of edges joining them (edge weights are
+    assumed to be one if the graph is unweighted).
+
+    For the case of unweighted and undirected graphs, Borgatti proposed
+    a simplified formula to compute effective size [2]_
+
+    .. math::
+
+       e(u) = n - \frac{2t}{n}
+
+    where `t` is the number of ties in the ego network (not including
+    ties to ego) and `n` is the number of nodes (excluding ego).
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        The graph containing ``v``. Directed graphs are treated like
+        undirected graphs when computing neighbors of ``v``.
+
+    nodes : container, optional
+        Container of nodes in the graph ``G`` to compute the effective size.
+        If None, the effective size of every node is computed.
+
+    weight : None or string, optional
+      If None, all edge weights are considered equal.
+      Otherwise holds the name of the edge attribute used as weight.
+
+    Returns
+    -------
+    dict
+        Dictionary with nodes as keys and the effective size of the node as values.
+
+    Notes
+    -----
+    Burt also defined the related concept of *efficiency* of a node's ego
+    network, which is its effective size divided by the degree of that
+    node [1]_. So you can easily compute efficiency:
+
+    >>> G = nx.DiGraph()
+    >>> G.add_edges_from([(0, 1), (0, 2), (1, 0), (2, 1)])
+    >>> esize = nx.effective_size(G)
+    >>> efficiency = {n: v / G.degree(n) for n, v in esize.items()}
+
+    See also
+    --------
+    constraint
+
+    References
+    ----------
+    .. [1] Burt, Ronald S.
+           *Structural Holes: The Social Structure of Competition.*
+           Cambridge: Harvard University Press, 1995.
+
+    .. [2] Borgatti, S.
+           "Structural Holes: Unpacking Burt's Redundancy Measures"
+           CONNECTIONS 20(1):35-38.
+           http://www.analytictech.com/connections/v20(1)/holes.htm
+
+    """
+
+    def redundancy(G, u, v, weight=None):
+        nmw = normalized_mutual_weight
+        r = sum(
+            nmw(G, u, w, weight=weight) * nmw(G, v, w, norm=max, weight=weight)
+            for w in set(nx.all_neighbors(G, u))
+        )
+        return 1 - r
+
+    effective_size = {}
+    if nodes is None:
+        nodes = G
+    # Use Borgatti's simplified formula for unweighted and undirected graphs
+    if not G.is_directed() and weight is None:
+        for v in nodes:
+            # Effective size is not defined for isolated nodes
+            if len(G[v]) == 0:
+                effective_size[v] = float("nan")
+                continue
+            E = nx.ego_graph(G, v, center=False, undirected=True)
+            effective_size[v] = len(E) - (2 * E.size()) / len(E)
+    else:
+        for v in nodes:
+            # Effective size is not defined for isolated nodes
+            if len(G[v]) == 0:
+                effective_size[v] = float("nan")
+                continue
+            effective_size[v] = sum(
+                redundancy(G, v, u, weight) for u in set(nx.all_neighbors(G, v))
+            )
+    return effective_size
+
+
+@nx._dispatchable(edge_attrs="weight")
+def constraint(G, nodes=None, weight=None):
+    r"""Returns the constraint on all nodes in the graph ``G``.
+
+    The *constraint* is a measure of the extent to which a node *v* is
+    invested in those nodes that are themselves invested in the
+    neighbors of *v*. Formally, the *constraint on v*, denoted `c(v)`,
+    is defined by
+
+    .. math::
+
+       c(v) = \sum_{w \in N(v) \setminus \{v\}} \ell(v, w)
+
+    where $N(v)$ is the subset of the neighbors of `v` that are either
+    predecessors or successors of `v` and $\ell(v, w)$ is the local
+    constraint on `v` with respect to `w` [1]_. For the definition of local
+    constraint, see :func:`local_constraint`.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        The graph containing ``v``. This can be either directed or undirected.
+
+    nodes : container, optional
+        Container of nodes in the graph ``G`` to compute the constraint. If
+        None, the constraint of every node is computed.
+
+    weight : None or string, optional
+      If None, all edge weights are considered equal.
+      Otherwise holds the name of the edge attribute used as weight.
+
+    Returns
+    -------
+    dict
+        Dictionary with nodes as keys and the constraint on the node as values.
+
+    See also
+    --------
+    local_constraint
+
+    References
+    ----------
+    .. [1] Burt, Ronald S.
+           "Structural holes and good ideas".
+           American Journal of Sociology (110): 349–399.
+
+    """
+    if nodes is None:
+        nodes = G
+    constraint = {}
+    for v in nodes:
+        # Constraint is not defined for isolated nodes
+        if len(G[v]) == 0:
+            constraint[v] = float("nan")
+            continue
+        constraint[v] = sum(
+            local_constraint(G, v, n, weight) for n in set(nx.all_neighbors(G, v))
+        )
+    return constraint
+
+
+@nx._dispatchable(edge_attrs="weight")
+def local_constraint(G, u, v, weight=None):
+    r"""Returns the local constraint on the node ``u`` with respect to
+    the node ``v`` in the graph ``G``.
+
+    Formally, the *local constraint on u with respect to v*, denoted
+    $\ell(u, v)$, is defined by
+
+    .. math::
+
+       \ell(u, v) = \left(p_{uv} + \sum_{w \in N(v)} p_{uw} p_{wv}\right)^2,
+
+    where $N(v)$ is the set of neighbors of $v$ and $p_{uv}$ is the
+    normalized mutual weight of the (directed or undirected) edges
+    joining $u$ and $v$, for each vertex $u$ and $v$ [1]_. The *mutual
+    weight* of $u$ and $v$ is the sum of the weights of edges joining
+    them (edge weights are assumed to be one if the graph is
+    unweighted).
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        The graph containing ``u`` and ``v``. This can be either
+        directed or undirected.
+
+    u : node
+        A node in the graph ``G``.
+
+    v : node
+        A node in the graph ``G``.
+
+    weight : None or string, optional
+      If None, all edge weights are considered equal.
+      Otherwise holds the name of the edge attribute used as weight.
+
+    Returns
+    -------
+    float
+        The constraint of the node ``v`` in the graph ``G``.
+
+    See also
+    --------
+    constraint
+
+    References
+    ----------
+    .. [1] Burt, Ronald S.
+           "Structural holes and good ideas".
+           American Journal of Sociology (110): 349–399.
+
+    """
+    nmw = normalized_mutual_weight
+    direct = nmw(G, u, v, weight=weight)
+    indirect = sum(
+        nmw(G, u, w, weight=weight) * nmw(G, w, v, weight=weight)
+        for w in set(nx.all_neighbors(G, u))
+    )
+    return (direct + indirect) ** 2

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/threshold.py

@@ -0,0 +1,979 @@
+"""
+Threshold Graphs - Creation, manipulation and identification.
+"""
+from math import sqrt
+
+import networkx as nx
+from networkx.utils import py_random_state
+
+__all__ = ["is_threshold_graph", "find_threshold_graph"]
+
+
+@nx._dispatchable
+def is_threshold_graph(G):
+    """
+    Returns `True` if `G` is a threshold graph.
+
+    Parameters
+    ----------
+    G : NetworkX graph instance
+        An instance of `Graph`, `DiGraph`, `MultiGraph` or `MultiDiGraph`
+
+    Returns
+    -------
+    bool
+        `True` if `G` is a threshold graph, `False` otherwise.
+
+    Examples
+    --------
+    >>> from networkx.algorithms.threshold import is_threshold_graph
+    >>> G = nx.path_graph(3)
+    >>> is_threshold_graph(G)
+    True
+    >>> G = nx.barbell_graph(3, 3)
+    >>> is_threshold_graph(G)
+    False
+
+    References
+    ----------
+    .. [1] Threshold graphs: https://en.wikipedia.org/wiki/Threshold_graph
+    """
+    return is_threshold_sequence([d for n, d in G.degree()])
+
+
+def is_threshold_sequence(degree_sequence):
+    """
+    Returns True if the sequence is a threshold degree sequence.
+
+    Uses the property that a threshold graph must be constructed by
+    adding either dominating or isolated nodes. Thus, it can be
+    deconstructed iteratively by removing a node of degree zero or a
+    node that connects to the remaining nodes.  If this deconstruction
+    fails then the sequence is not a threshold sequence.
+    """
+    ds = degree_sequence[:]  # get a copy so we don't destroy original
+    ds.sort()
+    while ds:
+        if ds[0] == 0:  # if isolated node
+            ds.pop(0)  # remove it
+            continue
+        if ds[-1] != len(ds) - 1:  # is the largest degree node dominating?
+            return False  # no, not a threshold degree sequence
+        ds.pop()  # yes, largest is the dominating node
+        ds = [d - 1 for d in ds]  # remove it and decrement all degrees
+    return True
+
+
+def creation_sequence(degree_sequence, with_labels=False, compact=False):
+    """
+    Determines the creation sequence for the given threshold degree sequence.
+
+    The creation sequence is a list of single characters 'd'
+    or 'i': 'd' for dominating or 'i' for isolated vertices.
+    Dominating vertices are connected to all vertices present when it
+    is added.  The first node added is by convention 'd'.
+    This list can be converted to a string if desired using "".join(cs)
+
+    If with_labels==True:
+    Returns a list of 2-tuples containing the vertex number
+    and a character 'd' or 'i' which describes the type of vertex.
+
+    If compact==True:
+    Returns the creation sequence in a compact form that is the number
+    of 'i's and 'd's alternating.
+    Examples:
+    [1,2,2,3] represents d,i,i,d,d,i,i,i
+    [3,1,2] represents d,d,d,i,d,d
+
+    Notice that the first number is the first vertex to be used for
+    construction and so is always 'd'.
+
+    with_labels and compact cannot both be True.
+
+    Returns None if the sequence is not a threshold sequence
+    """
+    if with_labels and compact:
+        raise ValueError("compact sequences cannot be labeled")
+
+    # make an indexed copy
+    if isinstance(degree_sequence, dict):  # labeled degree sequence
+        ds = [[degree, label] for (label, degree) in degree_sequence.items()]
+    else:
+        ds = [[d, i] for i, d in enumerate(degree_sequence)]
+    ds.sort()
+    cs = []  # creation sequence
+    while ds:
+        if ds[0][0] == 0:  # isolated node
+            (d, v) = ds.pop(0)
+            if len(ds) > 0:  # make sure we start with a d
+                cs.insert(0, (v, "i"))
+            else:
+                cs.insert(0, (v, "d"))
+            continue
+        if ds[-1][0] != len(ds) - 1:  # Not dominating node
+            return None  # not a threshold degree sequence
+        (d, v) = ds.pop()
+        cs.insert(0, (v, "d"))
+        ds = [[d[0] - 1, d[1]] for d in ds]  # decrement due to removing node
+
+    if with_labels:
+        return cs
+    if compact:
+        return make_compact(cs)
+    return [v[1] for v in cs]  # not labeled
+
+
+def make_compact(creation_sequence):
+    """
+    Returns the creation sequence in a compact form
+    that is the number of 'i's and 'd's alternating.
+
+    Examples
+    --------
+    >>> from networkx.algorithms.threshold import make_compact
+    >>> make_compact(["d", "i", "i", "d", "d", "i", "i", "i"])
+    [1, 2, 2, 3]
+    >>> make_compact(["d", "d", "d", "i", "d", "d"])
+    [3, 1, 2]
+
+    Notice that the first number is the first vertex
+    to be used for construction and so is always 'd'.
+
+    Labeled creation sequences lose their labels in the
+    compact representation.
+
+    >>> make_compact([3, 1, 2])
+    [3, 1, 2]
+    """
+    first = creation_sequence[0]
+    if isinstance(first, str):  # creation sequence
+        cs = creation_sequence[:]
+    elif isinstance(first, tuple):  # labeled creation sequence
+        cs = [s[1] for s in creation_sequence]
+    elif isinstance(first, int):  # compact creation sequence
+        return creation_sequence
+    else:
+        raise TypeError("Not a valid creation sequence type")
+
+    ccs = []
+    count = 1  # count the run lengths of d's or i's.
+    for i in range(1, len(cs)):
+        if cs[i] == cs[i - 1]:
+            count += 1
+        else:
+            ccs.append(count)
+            count = 1
+    ccs.append(count)  # don't forget the last one
+    return ccs
+
+
+def uncompact(creation_sequence):
+    """
+    Converts a compact creation sequence for a threshold
+    graph to a standard creation sequence (unlabeled).
+    If the creation_sequence is already standard, return it.
+    See creation_sequence.
+    """
+    first = creation_sequence[0]
+    if isinstance(first, str):  # creation sequence
+        return creation_sequence
+    elif isinstance(first, tuple):  # labeled creation sequence
+        return creation_sequence
+    elif isinstance(first, int):  # compact creation sequence
+        ccscopy = creation_sequence[:]
+    else:
+        raise TypeError("Not a valid creation sequence type")
+    cs = []
+    while ccscopy:
+        cs.extend(ccscopy.pop(0) * ["d"])
+        if ccscopy:
+            cs.extend(ccscopy.pop(0) * ["i"])
+    return cs
+
+
+def creation_sequence_to_weights(creation_sequence):
+    """
+    Returns a list of node weights which create the threshold
+    graph designated by the creation sequence.  The weights
+    are scaled so that the threshold is 1.0.  The order of the
+    nodes is the same as that in the creation sequence.
+    """
+    # Turn input sequence into a labeled creation sequence
+    first = creation_sequence[0]
+    if isinstance(first, str):  # creation sequence
+        if isinstance(creation_sequence, list):
+            wseq = creation_sequence[:]
+        else:
+            wseq = list(creation_sequence)  # string like 'ddidid'
+    elif isinstance(first, tuple):  # labeled creation sequence
+        wseq = [v[1] for v in creation_sequence]
+    elif isinstance(first, int):  # compact creation sequence
+        wseq = uncompact(creation_sequence)
+    else:
+        raise TypeError("Not a valid creation sequence type")
+    # pass through twice--first backwards
+    wseq.reverse()
+    w = 0
+    prev = "i"
+    for j, s in enumerate(wseq):
+        if s == "i":
+            wseq[j] = w
+            prev = s
+        elif prev == "i":
+            prev = s
+            w += 1
+    wseq.reverse()  # now pass through forwards
+    for j, s in enumerate(wseq):
+        if s == "d":
+            wseq[j] = w
+            prev = s
+        elif prev == "d":
+            prev = s
+            w += 1
+    # Now scale weights
+    if prev == "d":
+        w += 1
+    wscale = 1 / w
+    return [ww * wscale for ww in wseq]
+    # return wseq
+
+
+def weights_to_creation_sequence(
+    weights, threshold=1, with_labels=False, compact=False
+):
+    """
+    Returns a creation sequence for a threshold graph
+    determined by the weights and threshold given as input.
+    If the sum of two node weights is greater than the
+    threshold value, an edge is created between these nodes.
+
+    The creation sequence is a list of single characters 'd'
+    or 'i': 'd' for dominating or 'i' for isolated vertices.
+    Dominating vertices are connected to all vertices present
+    when it is added.  The first node added is by convention 'd'.
+
+    If with_labels==True:
+    Returns a list of 2-tuples containing the vertex number
+    and a character 'd' or 'i' which describes the type of vertex.
+
+    If compact==True:
+    Returns the creation sequence in a compact form that is the number
+    of 'i's and 'd's alternating.
+    Examples:
+    [1,2,2,3] represents d,i,i,d,d,i,i,i
+    [3,1,2] represents d,d,d,i,d,d
+
+    Notice that the first number is the first vertex to be used for
+    construction and so is always 'd'.
+
+    with_labels and compact cannot both be True.
+    """
+    if with_labels and compact:
+        raise ValueError("compact sequences cannot be labeled")
+
+    # make an indexed copy
+    if isinstance(weights, dict):  # labeled weights
+        wseq = [[w, label] for (label, w) in weights.items()]
+    else:
+        wseq = [[w, i] for i, w in enumerate(weights)]
+    wseq.sort()
+    cs = []  # creation sequence
+    cutoff = threshold - wseq[-1][0]
+    while wseq:
+        if wseq[0][0] < cutoff:  # isolated node
+            (w, label) = wseq.pop(0)
+            cs.append((label, "i"))
+        else:
+            (w, label) = wseq.pop()
+            cs.append((label, "d"))
+            cutoff = threshold - wseq[-1][0]
+        if len(wseq) == 1:  # make sure we start with a d
+            (w, label) = wseq.pop()
+            cs.append((label, "d"))
+    # put in correct order
+    cs.reverse()
+
+    if with_labels:
+        return cs
+    if compact:
+        return make_compact(cs)
+    return [v[1] for v in cs]  # not labeled
+
+
+# Manipulating NetworkX.Graphs in context of threshold graphs
+@nx._dispatchable(graphs=None, returns_graph=True)
+def threshold_graph(creation_sequence, create_using=None):
+    """
+    Create a threshold graph from the creation sequence or compact
+    creation_sequence.
+
+    The input sequence can be a
+
+    creation sequence (e.g. ['d','i','d','d','d','i'])
+    labeled creation sequence (e.g. [(0,'d'),(2,'d'),(1,'i')])
+    compact creation sequence (e.g. [2,1,1,2,0])
+
+    Use cs=creation_sequence(degree_sequence,labeled=True)
+    to convert a degree sequence to a creation sequence.
+
+    Returns None if the sequence is not valid
+    """
+    # Turn input sequence into a labeled creation sequence
+    first = creation_sequence[0]
+    if isinstance(first, str):  # creation sequence
+        ci = list(enumerate(creation_sequence))
+    elif isinstance(first, tuple):  # labeled creation sequence
+        ci = creation_sequence[:]
+    elif isinstance(first, int):  # compact creation sequence
+        cs = uncompact(creation_sequence)
+        ci = list(enumerate(cs))
+    else:
+        print("not a valid creation sequence type")
+        return None
+
+    G = nx.empty_graph(0, create_using)
+    if G.is_directed():
+        raise nx.NetworkXError("Directed Graph not supported")
+
+    G.name = "Threshold Graph"
+
+    # add nodes and edges
+    # if type is 'i' just add nodea
+    # if type is a d connect to everything previous
+    while ci:
+        (v, node_type) = ci.pop(0)
+        if node_type == "d":  # dominating type, connect to all existing nodes
+            # We use `for u in list(G):` instead of
+            # `for u in G:` because we edit the graph `G` in
+            # the loop. Hence using an iterator will result in
+            # `RuntimeError: dictionary changed size during iteration`
+            for u in list(G):
+                G.add_edge(v, u)
+        G.add_node(v)
+    return G
+
+
+@nx._dispatchable
+def find_alternating_4_cycle(G):
+    """
+    Returns False if there aren't any alternating 4 cycles.
+    Otherwise returns the cycle as [a,b,c,d] where (a,b)
+    and (c,d) are edges and (a,c) and (b,d) are not.
+    """
+    for u, v in G.edges():
+        for w in G.nodes():
+            if not G.has_edge(u, w) and u != w:
+                for x in G.neighbors(w):
+                    if not G.has_edge(v, x) and v != x:
+                        return [u, v, w, x]
+    return False
+
+
+@nx._dispatchable(returns_graph=True)
+def find_threshold_graph(G, create_using=None):
+    """
+    Returns a threshold subgraph that is close to largest in `G`.
+
+    The threshold graph will contain the largest degree node in G.
+
+    Parameters
+    ----------
+    G : NetworkX graph instance
+        An instance of `Graph`, or `MultiDiGraph`
+    create_using : NetworkX graph class or `None` (default), optional
+        Type of graph to use when constructing the threshold graph.
+        If `None`, infer the appropriate graph type from the input.
+
+    Returns
+    -------
+    graph :
+        A graph instance representing the threshold graph
+
+    Examples
+    --------
+    >>> from networkx.algorithms.threshold import find_threshold_graph
+    >>> G = nx.barbell_graph(3, 3)
+    >>> T = find_threshold_graph(G)
+    >>> T.nodes  # may vary
+    NodeView((7, 8, 5, 6))
+
+    References
+    ----------
+    .. [1] Threshold graphs: https://en.wikipedia.org/wiki/Threshold_graph
+    """
+    return threshold_graph(find_creation_sequence(G), create_using)
+
+
+@nx._dispatchable
+def find_creation_sequence(G):
+    """
+    Find a threshold subgraph that is close to largest in G.
+    Returns the labeled creation sequence of that threshold graph.
+    """
+    cs = []
+    # get a local pointer to the working part of the graph
+    H = G
+    while H.order() > 0:
+        # get new degree sequence on subgraph
+        dsdict = dict(H.degree())
+        ds = [(d, v) for v, d in dsdict.items()]
+        ds.sort()
+        # Update threshold graph nodes
+        if ds[-1][0] == 0:  # all are isolated
+            cs.extend(zip(dsdict, ["i"] * (len(ds) - 1) + ["d"]))
+            break  # Done!
+        # pull off isolated nodes
+        while ds[0][0] == 0:
+            (d, iso) = ds.pop(0)
+            cs.append((iso, "i"))
+        # find new biggest node
+        (d, bigv) = ds.pop()
+        # add edges of star to t_g
+        cs.append((bigv, "d"))
+        # form subgraph of neighbors of big node
+        H = H.subgraph(H.neighbors(bigv))
+    cs.reverse()
+    return cs
+
+
+# Properties of Threshold Graphs
+def triangles(creation_sequence):
+    """
+    Compute number of triangles in the threshold graph with the
+    given creation sequence.
+    """
+    # shortcut algorithm that doesn't require computing number
+    # of triangles at each node.
+    cs = creation_sequence  # alias
+    dr = cs.count("d")  # number of d's in sequence
+    ntri = dr * (dr - 1) * (dr - 2) / 6  # number of triangles in clique of nd d's
+    # now add dr choose 2 triangles for every 'i' in sequence where
+    # dr is the number of d's to the right of the current i
+    for i, typ in enumerate(cs):
+        if typ == "i":
+            ntri += dr * (dr - 1) / 2
+        else:
+            dr -= 1
+    return ntri
+
+
+def triangle_sequence(creation_sequence):
+    """
+    Return triangle sequence for the given threshold graph creation sequence.
+
+    """
+    cs = creation_sequence
+    seq = []
+    dr = cs.count("d")  # number of d's to the right of the current pos
+    dcur = (dr - 1) * (dr - 2) // 2  # number of triangles through a node of clique dr
+    irun = 0  # number of i's in the last run
+    drun = 0  # number of d's in the last run
+    for i, sym in enumerate(cs):
+        if sym == "d":
+            drun += 1
+            tri = dcur + (dr - 1) * irun  # new triangles at this d
+        else:  # cs[i]="i":
+            if prevsym == "d":  # new string of i's
+                dcur += (dr - 1) * irun  # accumulate shared shortest paths
+                irun = 0  # reset i run counter
+                dr -= drun  # reduce number of d's to right
+                drun = 0  # reset d run counter
+            irun += 1
+            tri = dr * (dr - 1) // 2  # new triangles at this i
+        seq.append(tri)
+        prevsym = sym
+    return seq
+
+
+def cluster_sequence(creation_sequence):
+    """
+    Return cluster sequence for the given threshold graph creation sequence.
+    """
+    triseq = triangle_sequence(creation_sequence)
+    degseq = degree_sequence(creation_sequence)
+    cseq = []
+    for i, deg in enumerate(degseq):
+        tri = triseq[i]
+        if deg <= 1:  # isolated vertex or single pair gets cc 0
+            cseq.append(0)
+            continue
+        max_size = (deg * (deg - 1)) // 2
+        cseq.append(tri / max_size)
+    return cseq
+
+
+def degree_sequence(creation_sequence):
+    """
+    Return degree sequence for the threshold graph with the given
+    creation sequence
+    """
+    cs = creation_sequence  # alias
+    seq = []
+    rd = cs.count("d")  # number of d to the right
+    for i, sym in enumerate(cs):
+        if sym == "d":
+            rd -= 1
+            seq.append(rd + i)
+        else:
+            seq.append(rd)
+    return seq
+
+
+def density(creation_sequence):
+    """
+    Return the density of the graph with this creation_sequence.
+    The density is the fraction of possible edges present.
+    """
+    N = len(creation_sequence)
+    two_size = sum(degree_sequence(creation_sequence))
+    two_possible = N * (N - 1)
+    den = two_size / two_possible
+    return den
+
+
+def degree_correlation(creation_sequence):
+    """
+    Return the degree-degree correlation over all edges.
+    """
+    cs = creation_sequence
+    s1 = 0  # deg_i*deg_j
+    s2 = 0  # deg_i^2+deg_j^2
+    s3 = 0  # deg_i+deg_j
+    m = 0  # number of edges
+    rd = cs.count("d")  # number of d nodes to the right
+    rdi = [i for i, sym in enumerate(cs) if sym == "d"]  # index of "d"s
+    ds = degree_sequence(cs)
+    for i, sym in enumerate(cs):
+        if sym == "d":
+            if i != rdi[0]:
+                print("Logic error in degree_correlation", i, rdi)
+                raise ValueError
+            rdi.pop(0)
+        degi = ds[i]
+        for dj in rdi:
+            degj = ds[dj]
+            s1 += degj * degi
+            s2 += degi**2 + degj**2
+            s3 += degi + degj
+            m += 1
+    denom = 2 * m * s2 - s3 * s3
+    numer = 4 * m * s1 - s3 * s3
+    if denom == 0:
+        if numer == 0:
+            return 1
+        raise ValueError(f"Zero Denominator but Numerator is {numer}")
+    return numer / denom
+
+
+def shortest_path(creation_sequence, u, v):
+    """
+    Find the shortest path between u and v in a
+    threshold graph G with the given creation_sequence.
+
+    For an unlabeled creation_sequence, the vertices
+    u and v must be integers in (0,len(sequence)) referring
+    to the position of the desired vertices in the sequence.
+
+    For a labeled creation_sequence, u and v are labels of vertices.
+
+    Use cs=creation_sequence(degree_sequence,with_labels=True)
+    to convert a degree sequence to a creation sequence.
+
+    Returns a list of vertices from u to v.
+    Example: if they are neighbors, it returns [u,v]
+    """
+    # Turn input sequence into a labeled creation sequence
+    first = creation_sequence[0]
+    if isinstance(first, str):  # creation sequence
+        cs = [(i, creation_sequence[i]) for i in range(len(creation_sequence))]
+    elif isinstance(first, tuple):  # labeled creation sequence
+        cs = creation_sequence[:]
+    elif isinstance(first, int):  # compact creation sequence
+        ci = uncompact(creation_sequence)
+        cs = [(i, ci[i]) for i in range(len(ci))]
+    else:
+        raise TypeError("Not a valid creation sequence type")
+
+    verts = [s[0] for s in cs]
+    if v not in verts:
+        raise ValueError(f"Vertex {v} not in graph from creation_sequence")
+    if u not in verts:
+        raise ValueError(f"Vertex {u} not in graph from creation_sequence")
+    # Done checking
+    if u == v:
+        return [u]
+
+    uindex = verts.index(u)
+    vindex = verts.index(v)
+    bigind = max(uindex, vindex)
+    if cs[bigind][1] == "d":
+        return [u, v]
+    # must be that cs[bigind][1]=='i'
+    cs = cs[bigind:]
+    while cs:
+        vert = cs.pop()
+        if vert[1] == "d":
+            return [u, vert[0], v]
+    # All after u are type 'i' so no connection
+    return -1
+
+
+def shortest_path_length(creation_sequence, i):
+    """
+    Return the shortest path length from indicated node to
+    every other node for the threshold graph with the given
+    creation sequence.
+    Node is indicated by index i in creation_sequence unless
+    creation_sequence is labeled in which case, i is taken to
+    be the label of the node.
+
+    Paths lengths in threshold graphs are at most 2.
+    Length to unreachable nodes is set to -1.
+    """
+    # Turn input sequence into a labeled creation sequence
+    first = creation_sequence[0]
+    if isinstance(first, str):  # creation sequence
+        if isinstance(creation_sequence, list):
+            cs = creation_sequence[:]
+        else:
+            cs = list(creation_sequence)
+    elif isinstance(first, tuple):  # labeled creation sequence
+        cs = [v[1] for v in creation_sequence]
+        i = [v[0] for v in creation_sequence].index(i)
+    elif isinstance(first, int):  # compact creation sequence
+        cs = uncompact(creation_sequence)
+    else:
+        raise TypeError("Not a valid creation sequence type")
+
+    # Compute
+    N = len(cs)
+    spl = [2] * N  # length 2 to every node
+    spl[i] = 0  # except self which is 0
+    # 1 for all d's to the right
+    for j in range(i + 1, N):
+        if cs[j] == "d":
+            spl[j] = 1
+    if cs[i] == "d":  # 1 for all nodes to the left
+        for j in range(i):
+            spl[j] = 1
+    # and -1 for any trailing i to indicate unreachable
+    for j in range(N - 1, 0, -1):
+        if cs[j] == "d":
+            break
+        spl[j] = -1
+    return spl
+
+
+def betweenness_sequence(creation_sequence, normalized=True):
+    """
+    Return betweenness for the threshold graph with the given creation
+    sequence.  The result is unscaled.  To scale the values
+    to the interval [0,1] divide by (n-1)*(n-2).
+    """
+    cs = creation_sequence
+    seq = []  # betweenness
+    lastchar = "d"  # first node is always a 'd'
+    dr = float(cs.count("d"))  # number of d's to the right of current pos
+    irun = 0  # number of i's in the last run
+    drun = 0  # number of d's in the last run
+    dlast = 0.0  # betweenness of last d
+    for i, c in enumerate(cs):
+        if c == "d":  # cs[i]=="d":
+            # betweenness = amt shared with earlier d's and i's
+            #             + new isolated nodes covered
+            #             + new paths to all previous nodes
+            b = dlast + (irun - 1) * irun / dr + 2 * irun * (i - drun - irun) / dr
+            drun += 1  # update counter
+        else:  # cs[i]="i":
+            if lastchar == "d":  # if this is a new run of i's
+                dlast = b  # accumulate betweenness
+                dr -= drun  # update number of d's to the right
+                drun = 0  # reset d counter
+                irun = 0  # reset i counter
+            b = 0  # isolated nodes have zero betweenness
+            irun += 1  # add another i to the run
+        seq.append(float(b))
+        lastchar = c
+
+    # normalize by the number of possible shortest paths
+    if normalized:
+        order = len(cs)
+        scale = 1.0 / ((order - 1) * (order - 2))
+        seq = [s * scale for s in seq]
+
+    return seq
+
+
+def eigenvectors(creation_sequence):
+    """
+    Return a 2-tuple of Laplacian eigenvalues and eigenvectors
+    for the threshold network with creation_sequence.
+    The first value is a list of eigenvalues.
+    The second value is a list of eigenvectors.
+    The lists are in the same order so corresponding eigenvectors
+    and eigenvalues are in the same position in the two lists.
+
+    Notice that the order of the eigenvalues returned by eigenvalues(cs)
+    may not correspond to the order of these eigenvectors.
+    """
+    ccs = make_compact(creation_sequence)
+    N = sum(ccs)
+    vec = [0] * N
+    val = vec[:]
+    # get number of type d nodes to the right (all for first node)
+    dr = sum(ccs[::2])
+
+    nn = ccs[0]
+    vec[0] = [1.0 / sqrt(N)] * N
+    val[0] = 0
+    e = dr
+    dr -= nn
+    type_d = True
+    i = 1
+    dd = 1
+    while dd < nn:
+        scale = 1.0 / sqrt(dd * dd + i)
+        vec[i] = i * [-scale] + [dd * scale] + [0] * (N - i - 1)
+        val[i] = e
+        i += 1
+        dd += 1
+    if len(ccs) == 1:
+        return (val, vec)
+    for nn in ccs[1:]:
+        scale = 1.0 / sqrt(nn * i * (i + nn))
+        vec[i] = i * [-nn * scale] + nn * [i * scale] + [0] * (N - i - nn)
+        # find eigenvalue
+        type_d = not type_d
+        if type_d:
+            e = i + dr
+            dr -= nn
+        else:
+            e = dr
+        val[i] = e
+        st = i
+        i += 1
+        dd = 1
+        while dd < nn:
+            scale = 1.0 / sqrt(i - st + dd * dd)
+            vec[i] = [0] * st + (i - st) * [-scale] + [dd * scale] + [0] * (N - i - 1)
+            val[i] = e
+            i += 1
+            dd += 1
+    return (val, vec)
+
+
+def spectral_projection(u, eigenpairs):
+    """
+    Returns the coefficients of each eigenvector
+    in a projection of the vector u onto the normalized
+    eigenvectors which are contained in eigenpairs.
+
+    eigenpairs should be a list of two objects.  The
+    first is a list of eigenvalues and the second a list
+    of eigenvectors.  The eigenvectors should be lists.
+
+    There's not a lot of error checking on lengths of
+    arrays, etc. so be careful.
+    """
+    coeff = []
+    evect = eigenpairs[1]
+    for ev in evect:
+        c = sum(evv * uv for (evv, uv) in zip(ev, u))
+        coeff.append(c)
+    return coeff
+
+
+def eigenvalues(creation_sequence):
+    """
+    Return sequence of eigenvalues of the Laplacian of the threshold
+    graph for the given creation_sequence.
+
+    Based on the Ferrer's diagram method.  The spectrum is integral
+    and is the conjugate of the degree sequence.
+
+    See::
+
+      @Article{degree-merris-1994,
+       author = {Russel Merris},
+       title = {Degree maximal graphs are Laplacian integral},
+       journal = {Linear Algebra Appl.},
+       year = {1994},
+       volume = {199},
+       pages = {381--389},
+      }
+
+    """
+    degseq = degree_sequence(creation_sequence)
+    degseq.sort()
+    eiglist = []  # zero is always one eigenvalue
+    eig = 0
+    row = len(degseq)
+    bigdeg = degseq.pop()
+    while row:
+        if bigdeg < row:
+            eiglist.append(eig)
+            row -= 1
+        else:
+            eig += 1
+            if degseq:
+                bigdeg = degseq.pop()
+            else:
+                bigdeg = 0
+    return eiglist
+
+
+# Threshold graph creation routines
+
+
+@py_random_state(2)
+def random_threshold_sequence(n, p, seed=None):
+    """
+    Create a random threshold sequence of size n.
+    A creation sequence is built by randomly choosing d's with
+    probability p and i's with probability 1-p.
+
+    s=nx.random_threshold_sequence(10,0.5)
+
+    returns a threshold sequence of length 10 with equal
+    probably of an i or a d at each position.
+
+    A "random" threshold graph can be built with
+
+    G=nx.threshold_graph(s)
+
+    seed : integer, random_state, or None (default)
+        Indicator of random number generation state.
+        See :ref:`Randomness<randomness>`.
+    """
+    if not (0 <= p <= 1):
+        raise ValueError("p must be in [0,1]")
+
+    cs = ["d"]  # threshold sequences always start with a d
+    for i in range(1, n):
+        if seed.random() < p:
+            cs.append("d")
+        else:
+            cs.append("i")
+    return cs
+
+
+# maybe *_d_threshold_sequence routines should
+# be (or be called from) a single routine with a more descriptive name
+# and a keyword parameter?
+def right_d_threshold_sequence(n, m):
+    """
+    Create a skewed threshold graph with a given number
+    of vertices (n) and a given number of edges (m).
+
+    The routine returns an unlabeled creation sequence
+    for the threshold graph.
+
+    FIXME: describe algorithm
+
+    """
+    cs = ["d"] + ["i"] * (n - 1)  # create sequence with n insolated nodes
+
+    #  m <n : not enough edges, make disconnected
+    if m < n:
+        cs[m] = "d"
+        return cs
+
+    # too many edges
+    if m > n * (n - 1) / 2:
+        raise ValueError("Too many edges for this many nodes.")
+
+    # connected case m >n-1
+    ind = n - 1
+    sum = n - 1
+    while sum < m:
+        cs[ind] = "d"
+        ind -= 1
+        sum += ind
+    ind = m - (sum - ind)
+    cs[ind] = "d"
+    return cs
+
+
+def left_d_threshold_sequence(n, m):
+    """
+    Create a skewed threshold graph with a given number
+    of vertices (n) and a given number of edges (m).
+
+    The routine returns an unlabeled creation sequence
+    for the threshold graph.
+
+    FIXME: describe algorithm
+
+    """
+    cs = ["d"] + ["i"] * (n - 1)  # create sequence with n insolated nodes
+
+    #  m <n : not enough edges, make disconnected
+    if m < n:
+        cs[m] = "d"
+        return cs
+
+    # too many edges
+    if m > n * (n - 1) / 2:
+        raise ValueError("Too many edges for this many nodes.")
+
+    # Connected case when M>N-1
+    cs[n - 1] = "d"
+    sum = n - 1
+    ind = 1
+    while sum < m:
+        cs[ind] = "d"
+        sum += ind
+        ind += 1
+    if sum > m:  # be sure not to change the first vertex
+        cs[sum - m] = "i"
+    return cs
+
+
+@py_random_state(3)
+def swap_d(cs, p_split=1.0, p_combine=1.0, seed=None):
+    """
+    Perform a "swap" operation on a threshold sequence.
+
+    The swap preserves the number of nodes and edges
+    in the graph for the given sequence.
+    The resulting sequence is still a threshold sequence.
+
+    Perform one split and one combine operation on the
+    'd's of a creation sequence for a threshold graph.
+    This operation maintains the number of nodes and edges
+    in the graph, but shifts the edges from node to node
+    maintaining the threshold quality of the graph.
+
+    seed : integer, random_state, or None (default)
+        Indicator of random number generation state.
+        See :ref:`Randomness<randomness>`.
+    """
+    # preprocess the creation sequence
+    dlist = [i for (i, node_type) in enumerate(cs[1:-1]) if node_type == "d"]
+    # split
+    if seed.random() < p_split:
+        choice = seed.choice(dlist)
+        split_to = seed.choice(range(choice))
+        flip_side = choice - split_to
+        if split_to != flip_side and cs[split_to] == "i" and cs[flip_side] == "i":
+            cs[choice] = "i"
+            cs[split_to] = "d"
+            cs[flip_side] = "d"
+            dlist.remove(choice)
+            # don't add or combine may reverse this action
+            # dlist.extend([split_to,flip_side])
+    #            print >>sys.stderr,"split at %s to %s and %s"%(choice,split_to,flip_side)
+    # combine
+    if seed.random() < p_combine and dlist:
+        first_choice = seed.choice(dlist)
+        second_choice = seed.choice(dlist)
+        target = first_choice + second_choice
+        if target >= len(cs) or cs[target] == "d" or first_choice == second_choice:
+            return cs
+        # OK to combine
+        cs[first_choice] = "i"
+        cs[second_choice] = "i"
+        cs[target] = "d"
+    #        print >>sys.stderr,"combine %s and %s to make %s."%(first_choice,second_choice,target)
+
+    return cs