okstra 0.108.0 → 0.110.0

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

@@ -0,0 +1,369 @@
+"""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

@@ -0,0 +1,44 @@
+"""
+**************
+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

@@ -0,0 +1,143 @@
+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

@@ -0,0 +1,53 @@
+"""
+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)