okstra 0.130.4 → 0.131.1

package/runtime/python/okstra_vendor/networkx/algorithms/communicability_alg.py

@@ -1,163 +0,0 @@
-"""
-Communicability.
-"""
-
-import networkx as nx
-from networkx.utils import not_implemented_for
-
-__all__ = ["communicability", "communicability_exp"]
-
-
-@not_implemented_for("directed")
-@not_implemented_for("multigraph")
-@nx._dispatchable
-def communicability(G):
-    r"""Returns communicability between all pairs of nodes in G.
-
-    The communicability between pairs of nodes in G is the sum of
-    walks of different lengths starting at node u and ending at node v.
-
-    Parameters
-    ----------
-    G: graph
-
-    Returns
-    -------
-    comm: dictionary of dictionaries
-        Dictionary of dictionaries keyed by nodes with communicability
-        as the value.
-
-    Raises
-    ------
-    NetworkXError
-       If the graph is not undirected and simple.
-
-    See Also
-    --------
-    communicability_exp:
-       Communicability between all pairs of nodes in G  using spectral
-       decomposition.
-    communicability_betweenness_centrality:
-       Communicability betweenness centrality for each node in G.
-
-    Notes
-    -----
-    This algorithm uses a spectral decomposition of the adjacency matrix.
-    Let G=(V,E) be a simple undirected graph.  Using the connection between
-    the powers  of the adjacency matrix and the number of walks in the graph,
-    the communicability  between nodes `u` and `v` based on the graph spectrum
-    is [1]_
-
-    .. math::
-        C(u,v)=\sum_{j=1}^{n}\phi_{j}(u)\phi_{j}(v)e^{\lambda_{j}},
-
-    where `\phi_{j}(u)` is the `u\rm{th}` element of the `j\rm{th}` orthonormal
-    eigenvector of the adjacency matrix associated with the eigenvalue
-    `\lambda_{j}`.
-
-    References
-    ----------
-    .. [1] Ernesto Estrada, Naomichi Hatano,
-       "Communicability in complex networks",
-       Phys. Rev. E 77, 036111 (2008).
-       https://arxiv.org/abs/0707.0756
-
-    Examples
-    --------
-    >>> G = nx.Graph([(0, 1), (1, 2), (1, 5), (5, 4), (2, 4), (2, 3), (4, 3), (3, 6)])
-    >>> c = nx.communicability(G)
-    """
-    import numpy as np
-
-    nodelist = list(G)  # ordering of nodes in matrix
-    A = nx.to_numpy_array(G, nodelist)
-    # convert to 0-1 matrix
-    A[A != 0.0] = 1
-    w, vec = np.linalg.eigh(A)
-    expw = np.exp(w)
-    mapping = dict(zip(nodelist, range(len(nodelist))))
-    c = {}
-    # computing communicabilities
-    for u in G:
-        c[u] = {}
-        for v in G:
-            s = 0
-            p = mapping[u]
-            q = mapping[v]
-            for j in range(len(nodelist)):
-                s += vec[:, j][p] * vec[:, j][q] * expw[j]
-            c[u][v] = float(s)
-    return c
-
-
-@not_implemented_for("directed")
-@not_implemented_for("multigraph")
-@nx._dispatchable
-def communicability_exp(G):
-    r"""Returns communicability between all pairs of nodes in G.
-
-    Communicability between pair of node (u,v) of node in G is the sum of
-    walks of different lengths starting at node u and ending at node v.
-
-    Parameters
-    ----------
-    G: graph
-
-    Returns
-    -------
-    comm: dictionary of dictionaries
-        Dictionary of dictionaries keyed by nodes with communicability
-        as the value.
-
-    Raises
-    ------
-    NetworkXError
-        If the graph is not undirected and simple.
-
-    See Also
-    --------
-    communicability:
-       Communicability between pairs of nodes in G.
-    communicability_betweenness_centrality:
-       Communicability betweenness centrality for each node in G.
-
-    Notes
-    -----
-    This algorithm uses matrix exponentiation of the adjacency matrix.
-
-    Let G=(V,E) be a simple undirected graph.  Using the connection between
-    the powers  of the adjacency matrix and the number of walks in the graph,
-    the communicability between nodes u and v is [1]_,
-
-    .. math::
-        C(u,v) = (e^A)_{uv},
-
-    where `A` is the adjacency matrix of G.
-
-    References
-    ----------
-    .. [1] Ernesto Estrada, Naomichi Hatano,
-       "Communicability in complex networks",
-       Phys. Rev. E 77, 036111 (2008).
-       https://arxiv.org/abs/0707.0756
-
-    Examples
-    --------
-    >>> G = nx.Graph([(0, 1), (1, 2), (1, 5), (5, 4), (2, 4), (2, 3), (4, 3), (3, 6)])
-    >>> c = nx.communicability_exp(G)
-    """
-    import scipy as sp
-
-    nodelist = list(G)  # ordering of nodes in matrix
-    A = nx.to_numpy_array(G, nodelist)
-    # convert to 0-1 matrix
-    A[A != 0.0] = 1
-    # communicability matrix
-    expA = sp.linalg.expm(A)
-    mapping = dict(zip(nodelist, range(len(nodelist))))
-    c = {}
-    for u in G:
-        c[u] = {}
-        for v in G:
-            c[u][v] = float(expA[mapping[u], mapping[v]])
-    return c

package/runtime/python/okstra_vendor/networkx/algorithms/community/__init__.py

@@ -1,28 +0,0 @@
-"""Functions for computing and measuring community structure.
-
-The ``community`` subpackage can be accessed by using :mod:`networkx.community`, then accessing the
-functions as attributes of ``community``. For example::
-
-    >>> import networkx as nx
-    >>> G = nx.barbell_graph(5, 1)
-    >>> communities_generator = nx.community.girvan_newman(G)
-    >>> top_level_communities = next(communities_generator)
-    >>> next_level_communities = next(communities_generator)
-    >>> sorted(map(sorted, next_level_communities))
-    [[0, 1, 2, 3, 4], [5], [6, 7, 8, 9, 10]]
-
-"""
-
-from networkx.algorithms.community.asyn_fluid import *
-from networkx.algorithms.community.bipartitions import *
-from networkx.algorithms.community.centrality import *
-from networkx.algorithms.community.divisive import *
-from networkx.algorithms.community.kclique import *
-from networkx.algorithms.community.label_propagation import *
-from networkx.algorithms.community.lukes import *
-from networkx.algorithms.community.modularity_max import *
-from networkx.algorithms.community.quality import *
-from networkx.algorithms.community.community_utils import *
-from networkx.algorithms.community.louvain import *
-from networkx.algorithms.community.leiden import *
-from networkx.algorithms.community.local import *

package/runtime/python/okstra_vendor/networkx/algorithms/community/asyn_fluid.py

@@ -1,153 +0,0 @@
-"""Asynchronous Fluid Communities algorithm for community detection."""
-
-from collections import Counter
-
-import networkx as nx
-from networkx.algorithms.components import is_connected
-from networkx.exception import NetworkXError
-from networkx.utils import groups, not_implemented_for, py_random_state
-
-__all__ = ["asyn_fluidc"]
-
-
-@not_implemented_for("directed")
-@not_implemented_for("multigraph")
-@py_random_state(3)
-@nx._dispatchable
-def asyn_fluidc(G, k, max_iter=100, seed=None):
-    """Returns communities in `G` as detected by Fluid Communities algorithm.
-
-    The asynchronous fluid communities algorithm is described in
-    [1]_. The algorithm is based on the simple idea of fluids interacting
-    in an environment, expanding and pushing each other. Its initialization is
-    random, so found communities may vary on different executions.
-
-    The algorithm proceeds as follows. First each of the initial k communities
-    is initialized in a random vertex in the graph. Then the algorithm iterates
-    over all vertices in a random order, updating the community of each vertex
-    based on its own community and the communities of its neighbors. This
-    process is performed several times until convergence.
-    At all times, each community has a total density of 1, which is equally
-    distributed among the vertices it contains. If a vertex changes of
-    community, vertex densities of affected communities are adjusted
-    immediately. When a complete iteration over all vertices is done, such that
-    no vertex changes the community it belongs to, the algorithm has converged
-    and returns.
-
-    This is the original version of the algorithm described in [1]_.
-    Unfortunately, it does not support weighted graphs yet.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-        Graph must be simple and undirected.
-
-    k : integer
-        The number of communities to be found.
-
-    max_iter : integer
-        The number of maximum iterations allowed. By default 100.
-
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state.
-        See :ref:`Randomness<randomness>`.
-
-    Returns
-    -------
-    communities : iterable
-        Iterable of communities given as sets of nodes.
-
-    Notes
-    -----
-    k variable is not an optional argument.
-
-    References
-    ----------
-    .. [1] Parés F., Garcia-Gasulla D. et al. "Fluid Communities: A
-       Competitive and Highly Scalable Community Detection Algorithm".
-       [https://arxiv.org/pdf/1703.09307.pdf].
-    """
-    # Initial checks
-    if not isinstance(k, int):
-        raise NetworkXError("k must be an integer.")
-    if not k > 0:
-        raise NetworkXError("k must be greater than 0.")
-    if not is_connected(G):
-        raise NetworkXError("Fluid Communities require connected Graphs.")
-    if len(G) < k:
-        raise NetworkXError("k cannot be bigger than the number of nodes.")
-    if max_iter <= 0:
-        msg = f"{max_iter=} must be greater than 0"
-        raise ValueError(msg)
-    # Initialization
-    max_density = 1.0
-    vertices = list(G)
-    seed.shuffle(vertices)
-    communities = {n: i for i, n in enumerate(vertices[:k])}
-    density = {}
-    com_to_numvertices = {}
-    for vertex in communities:
-        com_to_numvertices[communities[vertex]] = 1
-        density[communities[vertex]] = max_density
-    # Set up control variables and start iterating
-    iter_count = 0
-    cont = True
-    while cont and iter_count < max_iter:
-        cont = False
-        iter_count += 1
-        # Loop over all vertices in graph in a random order
-        vertices = list(G)
-        seed.shuffle(vertices)
-        for vertex in vertices:
-            # Updating rule
-            com_counter = Counter()
-            # Take into account self vertex community
-            try:
-                com_counter.update({communities[vertex]: density[communities[vertex]]})
-            except KeyError:
-                pass
-            # Gather neighbor vertex communities
-            for v in G[vertex]:
-                try:
-                    com_counter.update({communities[v]: density[communities[v]]})
-                except KeyError:
-                    continue
-            # Check which is the community with highest density
-            new_com = -1
-            if len(com_counter.keys()) > 0:
-                max_freq = max(com_counter.values())
-                best_communities = [
-                    com
-                    for com, freq in com_counter.items()
-                    if (max_freq - freq) < 0.0001
-                ]
-                # If actual vertex com in best communities, it is preserved
-                try:
-                    if communities[vertex] in best_communities:
-                        new_com = communities[vertex]
-                except KeyError:
-                    pass
-
-                # If vertex community changes...
-                if new_com == -1:
-                    # Set flag of non-convergence
-                    cont = True
-                    # Randomly chose a new community from candidates
-                    new_com = seed.choice(best_communities)
-                    # Update previous community status
-                    try:
-                        com_to_numvertices[communities[vertex]] -= 1
-                        density[communities[vertex]] = (
-                            max_density / com_to_numvertices[communities[vertex]]
-                        )
-                    except KeyError:
-                        pass
-                    # Update new community status
-                    communities[vertex] = new_com
-                    com_to_numvertices[communities[vertex]] += 1
-                    density[communities[vertex]] = (
-                        max_density / com_to_numvertices[communities[vertex]]
-                    )
-    # If maximum iterations reached --> output actual results
-    # Return results by grouping communities as list of vertices
-    return iter(groups(communities).values())

package/runtime/python/okstra_vendor/networkx/algorithms/community/bipartitions.py

@@ -1,354 +0,0 @@
-"""Functions for splitting a network into two communities (finding a bipartition)."""
-
-import random
-from copy import deepcopy
-from itertools import count
-
-import networkx as nx
-
-__all__ = [
-    "kernighan_lin_bisection",
-    "spectral_modularity_bipartition",
-    "greedy_node_swap_bipartition",
-]
-
-
-def _kernighan_lin_sweep(edge_info, side):
-    """
-    This is a modified form of Kernighan-Lin, which moves single nodes at a
-    time, alternating between sides to keep the bisection balanced.  We keep
-    two min-heaps of swap costs to make optimal-next-move selection fast.
-    """
-    heap0, heap1 = cost_heaps = nx.utils.BinaryHeap(), nx.utils.BinaryHeap()
-    # we use heap methods insert, pop, and get
-    for u, nbrs in edge_info.items():
-        cost_u = sum(wt if side[v] else -wt for v, wt in nbrs.items())
-        if side[u]:
-            heap1.insert(u, cost_u)
-        else:
-            heap0.insert(u, -cost_u)
-
-    def _update_heap_values(node):
-        side_node = side[node]
-        for nbr, wt in edge_info[node].items():
-            side_nbr = side[nbr]
-            if side_nbr == side_node:
-                wt = -wt
-            heap_nbr = cost_heaps[side_nbr]
-            if nbr in heap_nbr:
-                cost_nbr = heap_nbr.get(nbr) + 2 * wt
-                # allow_increase lets us update a value already on the heap
-                heap_nbr.insert(nbr, cost_nbr, allow_increase=True)
-
-    i = 0
-    totcost = 0
-    while heap0 and heap1:
-        u, cost_u = heap0.pop()
-        _update_heap_values(u)
-        v, cost_v = heap1.pop()
-        _update_heap_values(v)
-        totcost += cost_u + cost_v
-        i += 1
-        yield totcost, i, (u, v)
-
-
-@nx.utils.not_implemented_for("directed")
-@nx.utils.py_random_state(4)
-@nx._dispatchable(edge_attrs="weight")
-def kernighan_lin_bisection(G, partition=None, max_iter=10, weight="weight", seed=None):
-    """Partition a graph into two blocks using the Kernighan–Lin algorithm.
-
-    This algorithm partitions a network into two sets by iteratively
-    swapping pairs of nodes to reduce the edge cut between the two sets.  The
-    pairs are chosen according to a modified form of Kernighan-Lin [1]_, which
-    moves nodes individually, alternating between sides to keep the bisection
-    balanced.
-
-    Kernighan-Lin is an approximate algorithm for maximal modularity bisection.
-    In [2]_ they suggest that fine-tuned improvements can be made using
-    greedy node swapping, (see `greedy_node_swap_bipartition`).
-    The improvements are typically only a few percent of the modularity value.
-    But they claim that can make a difference between a good and excellent method.
-    This function does not perform any improvements. But you can do that yourself.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-        Graph must be undirected.
-
-    partition : tuple
-        Pair of iterables containing an initial partition. If not
-        specified, a random balanced partition is used.
-
-    max_iter : int
-        Maximum number of times to attempt swaps to find an
-        improvement before giving up.
-
-    weight : string or function (default: "weight")
-        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 or None to indicate a hidden edge.
-
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state.
-        See :ref:`Randomness<randomness>`.
-        Only used if partition is None
-
-    Returns
-    -------
-    partition : tuple
-        A pair of sets of nodes representing the bipartition.
-
-    Raises
-    ------
-    NetworkXError
-        If `partition` is not a valid partition of the nodes of the graph.
-
-    References
-    ----------
-    .. [1] Kernighan, B. W.; Lin, Shen (1970).
-       "An efficient heuristic procedure for partitioning graphs."
-       *Bell Systems Technical Journal* 49: 291--307.
-       Oxford University Press 2011.
-    .. [2] M. E. J. Newman,
-       "Modularity and community structure in networks",
-       PNAS, 103 (23), p. 8577-8582,
-       https://doi.org/10.1073/pnas.0601602103
-
-    """
-    nodes = list(G)
-
-    if partition is None:
-        seed.shuffle(nodes)
-        mid = len(nodes) // 2
-        A, B = nodes[:mid], nodes[mid:]
-    else:
-        try:
-            A, B = partition
-        except (TypeError, ValueError) as err:
-            raise nx.NetworkXError("partition must be two sets") from err
-        if not nx.community.is_partition(G, [A, B]):
-            raise nx.NetworkXError("partition invalid")
-
-    side = {node: (node in A) for node in nodes}
-
-    # ruff: noqa: E731   skips check for no lambda functions
-    # Using shortest_paths _weight_function with sum instead of min on multiedges
-    if callable(weight):
-        sum_weight = weight
-    elif G.is_multigraph():
-        sum_weight = lambda u, v, d: sum(dd.get(weight, 1) for dd in d.values())
-    else:
-        sum_weight = lambda u, v, d: d.get(weight, 1)
-
-    edge_info = {
-        u: {v: wt for v, d in nbrs.items() if (wt := sum_weight(u, v, d)) is not None}
-        for u, nbrs in G._adj.items()
-    }
-
-    for i in range(max_iter):
-        costs = list(_kernighan_lin_sweep(edge_info, side))
-        # find out how many edges to update: min_i
-        min_cost, min_i, _ = min(costs)
-        if min_cost >= 0:
-            break
-
-        for _, _, (u, v) in costs[:min_i]:
-            side[u] = 1
-            side[v] = 0
-
-    part1 = {u for u, s in side.items() if s == 0}
-    part2 = {u for u, s in side.items() if s == 1}
-    return part1, part2
-
-
-@nx.utils.not_implemented_for("directed")
-@nx.utils.not_implemented_for("multigraph")
-def spectral_modularity_bipartition(G):
-    r"""Return a bipartition of the nodes based on the spectrum of the
-    modularity matrix of the graph.
-
-    This method calculates the eigenvector associated with the second
-    largest eigenvalue of the modularity matrix, where the modularity
-    matrix *B* is defined by
-
-    ..math::
-
-        B_{i j} = A_{i j} - \frac{k_i k_j}{2 m},
-
-    where *A* is the adjacency matrix, `k_i` is the degree of node *i*,
-    and *m* is the number of edges in the graph. Nodes whose
-    corresponding values in the eigenvector are negative are placed in
-    one block, nodes whose values are nonnegative are placed in another
-    block.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-
-    Returns
-    -------
-    C : tuple
-        Pair of communities as two sets of nodes of ``G``, partitioned
-        according to second largest eigenvalue of the modularity matrix.
-
-    Examples
-    --------
-    >>> G = nx.karate_club_graph()
-    >>> MrHi, Officer = nx.community.spectral_modularity_bipartition(G)
-    >>> MrHi, Officer = sorted([sorted(MrHi), sorted(Officer)])
-    >>> MrHi
-    [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 16, 17, 19, 21]
-    >>> Officer
-    [8, 9, 14, 15, 18, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]
-
-    References
-    ----------
-    .. [1] M. E. J. Newman *Networks: An Introduction*, pages 373--378
-       Oxford University Press 2011.
-    .. [2] M. E. J. Newman,
-       "Modularity and community structure in networks",
-       PNAS, 103 (23), p. 8577-8582,
-       https://doi.org/10.1073/pnas.0601602103
-
-    """
-    import numpy as np
-
-    B = nx.linalg.modularity_matrix(G)
-    eigenvalues, eigenvectors = np.linalg.eig(B)
-    index = np.argsort(eigenvalues)[-1]
-    v2 = zip(np.real(eigenvectors[:, index]), G)
-    left, right = set(), set()
-    for u, n in v2:
-        if u < 0:
-            left.add(n)
-        else:
-            right.add(n)
-    return left, right
-
-
-@nx.utils.not_implemented_for("multigraph")
-def greedy_node_swap_bipartition(G, *, init_split=None, max_iter=10):
-    """Split the nodes into two communities based on greedy
-    modularity maximization.
-
-    The algorithm works by selecting a node to change communities which
-    will maximize the modularity. The swap is made and the community
-    structure with the highest modularity is kept.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-
-    init_split : 2-tuple of sets of nodes
-        Pair of sets of nodes in ``G`` providing an initial bipartition
-        for the algorithm. If not specified, a random balanced partition
-        is used. If this pair of sets is not a partition of the nodes of `G`,
-        :exc:`NetworkXException` is raised.
-
-    max_iter : int
-      Maximum number of iterations of attempting swaps to find an improvement.
-
-    Returns
-    -------
-    max_split : 2-tuple of sets of nodes
-        Pair of sets of nodes of ``G``, partitioned according to a
-        node swap greedy modularity maximization algorithm.
-
-    Raises
-    ------
-    NetworkXError
-      if init_split is not a valid partition of the
-      graph into two communities or if G is a MultiGraph
-
-    Examples
-    --------
-    >>> G = nx.barbell_graph(3, 0)
-    >>> left, right = nx.community.greedy_node_swap_bipartition(G)
-    >>> # Sort the communities so the nodes appear in increasing order.
-    >>> left, right = sorted([sorted(left), sorted(right)])
-    >>> sorted(left)
-    [0, 1, 2]
-    >>> sorted(right)
-    [3, 4, 5]
-
-    Notes
-    -----
-    This function is not implemented for multigraphs.
-
-    References
-    ----------
-    .. [1] M. E. J. Newman "Networks: An Introduction", pages 373--375.
-       Oxford University Press 2011.
-
-    """
-    if init_split is None:
-        m1 = len(G) // 2
-        m2 = len(G) - m1
-        some_nodes = set(random.sample(list(G), m1))
-        other_nodes = {n for n in G if n not in some_nodes}
-        best_split_so_far = (some_nodes, other_nodes)
-    else:
-        if not nx.community.is_partition(G, init_split):
-            raise nx.NetworkXError("init_split is not a partition of G")
-        if not len(init_split) == 2:
-            raise nx.NetworkXError("init_split must be a bipartition")
-        best_split_so_far = deepcopy(init_split)
-
-    best_mod = nx.community.modularity(G, best_split_so_far)
-
-    max_split, max_mod = best_split_so_far, best_mod
-    its = 0
-    m = G.number_of_edges()
-    G_degree = dict(G.degree)
-
-    while max_mod >= best_mod and its < max_iter:
-        best_split_so_far = max_split
-        best_mod = max_mod
-        next_split = deepcopy(max_split)
-        next_mod = max_mod
-        nodes = set(G)
-        while nodes:
-            max_swap = -1
-            max_node = None
-            max_node_comm = None
-            left, right = next_split
-            leftd = sum(G_degree[n] for n in left)
-            rightd = sum(G_degree[n] for n in right)
-            for n in nodes:
-                if n in left:
-                    in_comm, out_comm = left, right
-                    in_deg, out_deg = leftd, rightd
-                else:
-                    in_comm, out_comm = right, left
-                    in_deg, out_deg = rightd, leftd
-
-                d_eii = -len(G[n].keys() & in_comm) / m
-                d_ejj = len(G[n].keys() & out_comm) / m
-                deg = G_degree[n]
-                d_sum_ai = (deg / (2 * m**2)) * (in_deg - out_deg - deg)
-                swap_change = d_eii + d_ejj + d_sum_ai
-
-                if swap_change > max_swap:
-                    max_swap = swap_change
-                    max_node = n
-                    max_node_comm = in_comm
-                    non_max_node_comm = out_comm
-            # swap the node from one comm to the other
-            max_node_comm.remove(max_node)
-            non_max_node_comm.add(max_node)
-            next_mod += max_swap
-            # deepcopy next_split each time it reaches a high (might go lower later)
-            if next_mod > max_mod:
-                max_split, max_mod = deepcopy(next_split), next_mod
-            nodes.remove(max_node)
-        its += 1
-    return best_split_so_far