okstra 0.130.3 → 0.131.0

package/runtime/python/okstra_vendor/networkx/algorithms/approximation/kcomponents.py

@@ -1,369 +0,0 @@
-"""Fast approximation for k-component structure"""
-
-import itertools
-from collections import defaultdict
-from collections.abc import Mapping
-from functools import cached_property
-
-import networkx as nx
-from networkx.algorithms.approximation import local_node_connectivity
-from networkx.exception import NetworkXError
-from networkx.utils import not_implemented_for
-
-__all__ = ["k_components"]
-
-
-@not_implemented_for("directed")
-@nx._dispatchable(name="approximate_k_components")
-def k_components(G, min_density=0.95):
-    r"""Returns the approximate k-component structure of a graph G.
-
-    A `k`-component is a maximal subgraph of a graph G that has, at least,
-    node connectivity `k`: we need to remove at least `k` nodes to break it
-    into more components. `k`-components have an inherent hierarchical
-    structure because they are nested in terms of connectivity: a connected
-    graph can contain several 2-components, each of which can contain
-    one or more 3-components, and so forth.
-
-    This implementation is based on the fast heuristics to approximate
-    the `k`-component structure of a graph [1]_. Which, in turn, it is based on
-    a fast approximation algorithm for finding good lower bounds of the number
-    of node independent paths between two nodes [2]_.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-        Undirected graph
-
-    min_density : Float
-        Density relaxation threshold. Default value 0.95
-
-    Returns
-    -------
-    k_components : dict
-        Dictionary with connectivity level `k` as key and a list of
-        sets of nodes that form a k-component of level `k` as values.
-
-    Raises
-    ------
-    NetworkXNotImplemented
-        If G is directed.
-
-    Examples
-    --------
-    >>> # Petersen graph has 10 nodes and it is triconnected, thus all
-    >>> # nodes are in a single component on all three connectivity levels
-    >>> from networkx.algorithms import approximation as apxa
-    >>> G = nx.petersen_graph()
-    >>> k_components = apxa.k_components(G)
-
-    Notes
-    -----
-    The logic of the approximation algorithm for computing the `k`-component
-    structure [1]_ is based on repeatedly applying simple and fast algorithms
-    for `k`-cores and biconnected components in order to narrow down the
-    number of pairs of nodes over which we have to compute White and Newman's
-    approximation algorithm for finding node independent paths [2]_. More
-    formally, this algorithm is based on Whitney's theorem, which states
-    an inclusion relation among node connectivity, edge connectivity, and
-    minimum degree for any graph G. This theorem implies that every
-    `k`-component is nested inside a `k`-edge-component, which in turn,
-    is contained in a `k`-core. Thus, this algorithm computes node independent
-    paths among pairs of nodes in each biconnected part of each `k`-core,
-    and repeats this procedure for each `k` from 3 to the maximal core number
-    of a node in the input graph.
-
-    Because, in practice, many nodes of the core of level `k` inside a
-    bicomponent actually are part of a component of level k, the auxiliary
-    graph needed for the algorithm is likely to be very dense. Thus, we use
-    a complement graph data structure (see `AntiGraph`) to save memory.
-    AntiGraph only stores information of the edges that are *not* present
-    in the actual auxiliary graph. When applying algorithms to this
-    complement graph data structure, it behaves as if it were the dense
-    version.
-
-    See also
-    --------
-    k_components
-
-    References
-    ----------
-    .. [1]  Torrents, J. and F. Ferraro (2015) Structural Cohesion:
-            Visualization and Heuristics for Fast Computation.
-            https://arxiv.org/pdf/1503.04476v1
-
-    .. [2]  White, Douglas R., and Mark Newman (2001) A Fast Algorithm for
-            Node-Independent Paths. Santa Fe Institute Working Paper #01-07-035
-            https://www.santafe.edu/research/results/working-papers/fast-approximation-algorithms-for-finding-node-ind
-
-    .. [3]  Moody, J. and D. White (2003). Social cohesion and embeddedness:
-            A hierarchical conception of social groups.
-            American Sociological Review 68(1), 103--28.
-            https://doi.org/10.2307/3088904
-
-    """
-    # Dictionary with connectivity level (k) as keys and a list of
-    # sets of nodes that form a k-component as values
-    k_components = defaultdict(list)
-    # make a few functions local for speed
-    node_connectivity = local_node_connectivity
-    k_core = nx.k_core
-    core_number = nx.core_number
-    biconnected_components = nx.biconnected_components
-    combinations = itertools.combinations
-    # Exact solution for k = {1,2}
-    # There is a linear time algorithm for triconnectivity, if we had an
-    # implementation available we could start from k = 4.
-    for component in nx.connected_components(G):
-        # isolated nodes have connectivity 0
-        comp = set(component)
-        if len(comp) > 1:
-            k_components[1].append(comp)
-    for bicomponent in nx.biconnected_components(G):
-        # avoid considering dyads as bicomponents
-        bicomp = set(bicomponent)
-        if len(bicomp) > 2:
-            k_components[2].append(bicomp)
-    # There is no k-component of k > maximum core number
-    # \kappa(G) <= \lambda(G) <= \delta(G)
-    g_cnumber = core_number(G)
-    max_core = max(g_cnumber.values())
-    for k in range(3, max_core + 1):
-        C = k_core(G, k, core_number=g_cnumber)
-        for nodes in biconnected_components(C):
-            # Build a subgraph SG induced by the nodes that are part of
-            # each biconnected component of the k-core subgraph C.
-            if len(nodes) < k:
-                continue
-            SG = G.subgraph(nodes)
-            # Build auxiliary graph
-            H = _AntiGraph()
-            H.add_nodes_from(SG.nodes())
-            for u, v in combinations(SG, 2):
-                K = node_connectivity(SG, u, v, cutoff=k)
-                if k > K:
-                    H.add_edge(u, v)
-            for h_nodes in biconnected_components(H):
-                if len(h_nodes) <= k:
-                    continue
-                SH = H.subgraph(h_nodes)
-                for Gc in _cliques_heuristic(SG, SH, k, min_density):
-                    for k_nodes in biconnected_components(Gc):
-                        Gk = nx.k_core(SG.subgraph(k_nodes), k)
-                        if len(Gk) <= k:
-                            continue
-                        k_components[k].append(set(Gk))
-    return k_components
-
-
-def _cliques_heuristic(G, H, k, min_density):
-    h_cnumber = nx.core_number(H)
-    for i, c_value in enumerate(sorted(set(h_cnumber.values()), reverse=True)):
-        cands = {n for n, c in h_cnumber.items() if c == c_value}
-        # Skip checking for overlap for the highest core value
-        if i == 0:
-            overlap = False
-        else:
-            overlap = set.intersection(
-                *[{x for x in H[n] if x not in cands} for n in cands]
-            )
-        if overlap and len(overlap) < k:
-            SH = H.subgraph(cands | overlap)
-        else:
-            SH = H.subgraph(cands)
-        sh_cnumber = nx.core_number(SH)
-        SG = nx.k_core(G.subgraph(SH), k)
-        while not (_same(sh_cnumber) and nx.density(SH) >= min_density):
-            # This subgraph must be writable => .copy()
-            SH = H.subgraph(SG).copy()
-            if len(SH) <= k:
-                break
-            sh_cnumber = nx.core_number(SH)
-            sh_deg = dict(SH.degree())
-            min_deg = min(sh_deg.values())
-            SH.remove_nodes_from(n for n, d in sh_deg.items() if d == min_deg)
-            SG = nx.k_core(G.subgraph(SH), k)
-        else:
-            yield SG
-
-
-def _same(measure, tol=0):
-    vals = set(measure.values())
-    if (max(vals) - min(vals)) <= tol:
-        return True
-    return False
-
-
-class _AntiGraph(nx.Graph):
-    """
-    Class for complement graphs.
-
-    The main goal is to be able to work with big and dense graphs with
-    a low memory footprint.
-
-    In this class you add the edges that *do not exist* in the dense graph,
-    the report methods of the class return the neighbors, the edges and
-    the degree as if it was the dense graph. Thus it's possible to use
-    an instance of this class with some of NetworkX functions. In this
-    case we only use k-core, connected_components, and biconnected_components.
-    """
-
-    all_edge_dict = {"weight": 1}
-
-    def single_edge_dict(self):
-        return self.all_edge_dict
-
-    edge_attr_dict_factory = single_edge_dict  # type: ignore[assignment]
-
-    def __getitem__(self, n):
-        """Returns a dict of neighbors of node n in the dense graph.
-
-        Parameters
-        ----------
-        n : node
-           A node in the graph.
-
-        Returns
-        -------
-        adj_dict : dictionary
-           The adjacency dictionary for nodes connected to n.
-
-        """
-        all_edge_dict = self.all_edge_dict
-        return {
-            node: all_edge_dict for node in set(self._adj) - set(self._adj[n]) - {n}
-        }
-
-    def neighbors(self, n):
-        """Returns an iterator over all neighbors of node n in the
-        dense graph.
-        """
-        try:
-            return iter(set(self._adj) - set(self._adj[n]) - {n})
-        except KeyError as err:
-            raise NetworkXError(f"The node {n} is not in the graph.") from err
-
-    class AntiAtlasView(Mapping):
-        """An adjacency inner dict for AntiGraph"""
-
-        def __init__(self, graph, node):
-            self._graph = graph
-            self._atlas = graph._adj[node]
-            self._node = node
-
-        def __len__(self):
-            return len(self._graph) - len(self._atlas) - 1
-
-        def __iter__(self):
-            return (n for n in self._graph if n not in self._atlas and n != self._node)
-
-        def __getitem__(self, nbr):
-            nbrs = set(self._graph._adj) - set(self._atlas) - {self._node}
-            if nbr in nbrs:
-                return self._graph.all_edge_dict
-            raise KeyError(nbr)
-
-    class AntiAdjacencyView(AntiAtlasView):
-        """An adjacency outer dict for AntiGraph"""
-
-        def __init__(self, graph):
-            self._graph = graph
-            self._atlas = graph._adj
-
-        def __len__(self):
-            return len(self._atlas)
-
-        def __iter__(self):
-            return iter(self._graph)
-
-        def __getitem__(self, node):
-            if node not in self._graph:
-                raise KeyError(node)
-            return self._graph.AntiAtlasView(self._graph, node)
-
-    @cached_property
-    def adj(self):
-        return self.AntiAdjacencyView(self)
-
-    def subgraph(self, nodes):
-        """This subgraph method returns a full AntiGraph. Not a View"""
-        nodes = set(nodes)
-        G = _AntiGraph()
-        G.add_nodes_from(nodes)
-        for n in G:
-            Gnbrs = G.adjlist_inner_dict_factory()
-            G._adj[n] = Gnbrs
-            for nbr, d in self._adj[n].items():
-                if nbr in G._adj:
-                    Gnbrs[nbr] = d
-                    G._adj[nbr][n] = d
-        G.graph = self.graph
-        return G
-
-    class AntiDegreeView(nx.reportviews.DegreeView):
-        def __iter__(self):
-            all_nodes = set(self._succ)
-            for n in self._nodes:
-                nbrs = all_nodes - set(self._succ[n]) - {n}
-                yield (n, len(nbrs))
-
-        def __getitem__(self, n):
-            nbrs = set(self._succ) - set(self._succ[n]) - {n}
-            # AntiGraph is a ThinGraph so all edges have weight 1
-            return len(nbrs) + (n in nbrs)
-
-    @cached_property
-    def degree(self):
-        """Returns an iterator for (node, degree) and degree for single node.
-
-        The node degree is the number of edges adjacent to the node.
-
-        Parameters
-        ----------
-        nbunch : iterable container, optional (default=all nodes)
-            A container of nodes.  The container will be iterated
-            through once.
-
-        weight : string or None, optional (default=None)
-           The edge attribute that holds the numerical value used
-           as a weight.  If None, then each edge has weight 1.
-           The degree is the sum of the edge weights adjacent to the node.
-
-        Returns
-        -------
-        deg:
-            Degree of the node, if a single node is passed as argument.
-        nd_iter : an iterator
-            The iterator returns two-tuples of (node, degree).
-
-        See Also
-        --------
-        degree
-
-        Examples
-        --------
-        >>> G = nx.path_graph(4)
-        >>> G.degree(0)  # node 0 with degree 1
-        1
-        >>> list(G.degree([0, 1]))
-        [(0, 1), (1, 2)]
-
-        """
-        return self.AntiDegreeView(self)
-
-    def adjacency(self):
-        """Returns an iterator of (node, adjacency set) tuples for all nodes
-           in the dense graph.
-
-        This is the fastest way to look at every edge.
-        For directed graphs, only outgoing adjacencies are included.
-
-        Returns
-        -------
-        adj_iter : iterator
-           An iterator of (node, adjacency set) for all nodes in
-           the graph.
-
-        """
-        for n in self._adj:
-            yield (n, set(self._adj) - set(self._adj[n]) - {n})

package/runtime/python/okstra_vendor/networkx/algorithms/approximation/matching.py

@@ -1,44 +0,0 @@
-"""
-**************
-Graph Matching
-**************
-
-Given a graph G = (V,E), a matching M in G is a set of pairwise non-adjacent
-edges; that is, no two edges share a common vertex.
-
-`Wikipedia: Matching <https://en.wikipedia.org/wiki/Matching_(graph_theory)>`_
-"""
-
-import networkx as nx
-
-__all__ = ["min_maximal_matching"]
-
-
-@nx._dispatchable
-def min_maximal_matching(G):
-    r"""Returns the minimum maximal matching of G. That is, out of all maximal
-    matchings of the graph G, the smallest is returned.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-      Undirected graph
-
-    Returns
-    -------
-    min_maximal_matching : set
-      Returns a set of edges such that no two edges share a common endpoint
-      and every edge not in the set shares some common endpoint in the set.
-      Cardinality will be 2*OPT in the worst case.
-
-    Notes
-    -----
-    The algorithm computes an approximate solution for the minimum maximal
-    cardinality matching problem. The solution is no more than 2 * OPT in size.
-    Runtime is $O(|E|)$.
-
-    References
-    ----------
-    .. [1] Vazirani, Vijay Approximation Algorithms (2001)
-    """
-    return nx.maximal_matching(G)

package/runtime/python/okstra_vendor/networkx/algorithms/approximation/maxcut.py

@@ -1,143 +0,0 @@
-import networkx as nx
-from networkx.utils.decorators import not_implemented_for, py_random_state
-
-__all__ = ["randomized_partitioning", "one_exchange"]
-
-
-@not_implemented_for("directed")
-@not_implemented_for("multigraph")
-@py_random_state(1)
-@nx._dispatchable(edge_attrs="weight")
-def randomized_partitioning(G, seed=None, p=0.5, weight=None):
-    """Compute a random partitioning of the graph nodes and its cut value.
-
-    A partitioning is calculated by observing each node
-    and deciding to add it to the partition with probability `p`,
-    returning a random cut and its corresponding value (the
-    sum of weights of edges connecting different partitions).
-
-    Parameters
-    ----------
-    G : NetworkX graph
-
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state.
-        See :ref:`Randomness<randomness>`.
-
-    p : scalar
-        Probability for each node to be part of the first partition.
-        Should be in [0,1]
-
-    weight : object
-        Edge attribute key to use as weight. If not specified, edges
-        have weight one.
-
-    Returns
-    -------
-    cut_size : scalar
-        Value of the minimum cut.
-
-    partition : pair of node sets
-        A partitioning of the nodes that defines a minimum cut.
-
-    Examples
-    --------
-    >>> G = nx.complete_graph(5)
-    >>> cut_size, partition = nx.approximation.randomized_partitioning(G, seed=1)
-    >>> cut_size
-    6
-    >>> partition
-    ({0, 3, 4}, {1, 2})
-
-    Raises
-    ------
-    NetworkXNotImplemented
-        If the graph is directed or is a multigraph.
-    """
-    cut = {node for node in G.nodes() if seed.random() < p}
-    cut_size = nx.algorithms.cut_size(G, cut, weight=weight)
-    partition = (cut, G.nodes - cut)
-    return cut_size, partition
-
-
-def _swap_node_partition(cut, node):
-    return cut - {node} if node in cut else cut.union({node})
-
-
-@not_implemented_for("directed")
-@not_implemented_for("multigraph")
-@py_random_state(2)
-@nx._dispatchable(edge_attrs="weight")
-def one_exchange(G, initial_cut=None, seed=None, weight=None):
-    """Compute a partitioning of the graphs nodes and the corresponding cut value.
-
-    Use a greedy one exchange strategy to find a locally maximal cut
-    and its value, it works by finding the best node (one that gives
-    the highest gain to the cut value) to add to the current cut
-    and repeats this process until no improvement can be made.
-
-    Parameters
-    ----------
-    G : networkx Graph
-        Graph to find a maximum cut for.
-
-    initial_cut : set
-        Cut to use as a starting point. If not supplied the algorithm
-        starts with an empty cut.
-
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state.
-        See :ref:`Randomness<randomness>`.
-
-    weight : object
-        Edge attribute key to use as weight. If not specified, edges
-        have weight one.
-
-    Returns
-    -------
-    cut_value : scalar
-        Value of the maximum cut.
-
-    partition : pair of node sets
-        A partitioning of the nodes that defines a maximum cut.
-
-    Examples
-    --------
-    >>> G = nx.complete_graph(5)
-    >>> curr_cut_size, partition = nx.approximation.one_exchange(G, seed=1)
-    >>> curr_cut_size
-    6
-    >>> partition
-    ({0, 2}, {1, 3, 4})
-
-    Raises
-    ------
-    NetworkXNotImplemented
-        If the graph is directed or is a multigraph.
-    """
-    if initial_cut is None:
-        initial_cut = set()
-    cut = set(initial_cut)
-    current_cut_size = nx.algorithms.cut_size(G, cut, weight=weight)
-    while True:
-        nodes = list(G.nodes())
-        # Shuffling the nodes ensures random tie-breaks in the following call to max
-        seed.shuffle(nodes)
-        best_node_to_swap = max(
-            nodes,
-            key=lambda v: nx.algorithms.cut_size(
-                G, _swap_node_partition(cut, v), weight=weight
-            ),
-            default=None,
-        )
-        potential_cut = _swap_node_partition(cut, best_node_to_swap)
-        potential_cut_size = nx.algorithms.cut_size(G, potential_cut, weight=weight)
-
-        if potential_cut_size > current_cut_size:
-            cut = potential_cut
-            current_cut_size = potential_cut_size
-        else:
-            break
-
-    partition = (cut, G.nodes - cut)
-    return current_cut_size, partition

package/runtime/python/okstra_vendor/networkx/algorithms/approximation/ramsey.py

@@ -1,53 +0,0 @@
-"""
-Ramsey numbers.
-"""
-
-import networkx as nx
-from networkx.utils import not_implemented_for
-
-from ...utils import arbitrary_element
-
-__all__ = ["ramsey_R2"]
-
-
-@not_implemented_for("directed")
-@not_implemented_for("multigraph")
-@nx._dispatchable
-def ramsey_R2(G):
-    r"""Compute the largest clique and largest independent set in `G`.
-
-    This can be used to estimate bounds for the 2-color
-    Ramsey number `R(2;s,t)` for `G`.
-
-    This is a recursive implementation which could run into trouble
-    for large recursions. Note that self-loop edges are ignored.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-        Undirected graph
-
-    Returns
-    -------
-    max_pair : (set, set) tuple
-        Maximum clique, Maximum independent set.
-
-    Raises
-    ------
-    NetworkXNotImplemented
-        If the graph is directed or is a multigraph.
-    """
-    if not G:
-        return set(), set()
-
-    node = arbitrary_element(G)
-    nbrs = (nbr for nbr in nx.all_neighbors(G, node) if nbr != node)
-    nnbrs = nx.non_neighbors(G, node)
-    c_1, i_1 = ramsey_R2(G.subgraph(nbrs).copy())
-    c_2, i_2 = ramsey_R2(G.subgraph(nnbrs).copy())
-
-    c_1.add(node)
-    i_2.add(node)
-    # Choose the larger of the two cliques and the larger of the two
-    # independent sets, according to cardinality.
-    return max(c_1, c_2, key=len), max(i_1, i_2, key=len)