okstra 0.130.3 → 0.131.0

package/runtime/python/okstra_vendor/networkx/algorithms/centrality/betweenness_subset.py

@@ -1,236 +0,0 @@
-"""Betweenness centrality measures for subsets of nodes."""
-
-import networkx as nx
-from networkx.algorithms.centrality.betweenness import (
-    _add_edge_keys,
-    _rescale,
-)
-from networkx.algorithms.centrality.betweenness import (
-    _single_source_dijkstra_path_basic as dijkstra,
-)
-from networkx.algorithms.centrality.betweenness import (
-    _single_source_shortest_path_basic as shortest_path,
-)
-
-__all__ = [
-    "betweenness_centrality_subset",
-    "edge_betweenness_centrality_subset",
-]
-
-
-@nx._dispatchable(edge_attrs="weight")
-def betweenness_centrality_subset(G, sources, targets, normalized=False, weight=None):
-    r"""Compute betweenness centrality for a subset of nodes.
-
-    .. math::
-
-       c_B(v) = \sum_{s \in S, t \in T} \frac{\sigma(s, t | v)}{\sigma(s, t)}
-
-    where $S$ is the set of sources, $T$ is the set of targets,
-    $\sigma(s, t)$ is the number of shortest $(s, t)$-paths,
-    and $\sigma(s, t | v)$ is the number of those paths
-    passing through some node $v$ other than $s$ and $t$.
-    If $s = t$, $\sigma(s, t) = 1$,
-    and if $v \in \{s, t\}$, $\sigma(s, t | v) = 0$ [2]_.
-    The denominator $\sigma(s, t)$ is a normalization factor that can be
-    turned off to get the raw path counts.
-
-    Parameters
-    ----------
-    G : graph
-        A NetworkX graph.
-
-    sources: list of nodes
-        Nodes to use as sources for shortest paths in betweenness.
-
-    targets: list of nodes
-        Nodes to use as targets for shortest paths in betweenness.
-
-    normalized : bool, optional (default=False)
-        If `True`, the betweenness values are rescaled by dividing by the number of
-        possible $(s, t)$-pairs in the graph.
-
-    weight : None or string, optional (default=None)
-        If `None`, all edge weights are 1.
-        Otherwise holds the name of the edge attribute used as weight.
-        Weights are used to calculate weighted shortest paths, so they are
-        interpreted as distances.
-
-    Returns
-    -------
-    nodes : dict
-        Dictionary of nodes with betweenness centrality as the value.
-
-    See Also
-    --------
-    betweenness_centrality
-    edge_betweenness_centrality
-    edge_betweenness_centrality_subset
-    load_centrality
-
-    Notes
-    -----
-    The basic algorithm is from [1]_.
-
-    For weighted graphs the edge weights must be greater than zero.
-    Zero edge weights can produce an infinite number of equal length
-    paths between pairs of nodes.
-
-    The normalization might seem a little strange but it is
-    designed to make betweenness_centrality(G) be the same as
-    betweenness_centrality_subset(G,sources=G.nodes(),targets=G.nodes()).
-
-    The total number of paths between source and target is counted
-    differently for directed and undirected graphs. Directed paths
-    are easy to count. Undirected paths are tricky: should a path
-    from ``u`` to ``v`` count as 1 undirected path or as 2 directed paths?
-    We are only counting the paths in one direction. They are
-    undirected paths but we are counting them in a directed way.
-    To count them as undirected paths, each should count as half a path.
-
-    References
-    ----------
-    .. [1] Ulrik Brandes, A Faster Algorithm for Betweenness Centrality.
-       Journal of Mathematical Sociology 25(2):163-177, 2001.
-       https://doi.org/10.1080/0022250X.2001.9990249
-    .. [2] Ulrik Brandes: On Variants of Shortest-Path Betweenness
-       Centrality and their Generic Computation.
-       Social Networks 30(2):136-145, 2008.
-       https://doi.org/10.1016/j.socnet.2007.11.001
-    """
-    b = dict.fromkeys(G, 0.0)  # b[v]=0 for v in G
-    for s in sources:
-        # single source shortest paths
-        if weight is None:  # use BFS
-            S, P, sigma, _ = shortest_path(G, s)
-        else:  # use Dijkstra's algorithm
-            S, P, sigma, _ = dijkstra(G, s, weight)
-        b = _accumulate_subset(b, S, P, sigma, s, targets)
-    b = _rescale(
-        b, len(G), normalized=normalized, directed=G.is_directed(), endpoints=False
-    )
-    return b
-
-
-@nx._dispatchable(edge_attrs="weight")
-def edge_betweenness_centrality_subset(
-    G, sources, targets, normalized=False, weight=None
-):
-    r"""Compute betweenness centrality for edges for a subset of nodes.
-
-    .. math::
-
-       c_B(e) = \sum_{s \in S, t \in T} \frac{\sigma(s, t | e)}{\sigma(s, t)}
-
-    where $S$ is the set of sources, $T$ is the set of targets,
-    $\sigma(s, t)$ is the number of shortest $(s, t)$-paths,
-    and $\sigma(s, t | e)$ is the number of those paths
-    passing through edge $e$ [1]_.
-    The denominator $\sigma(s, t)$ is a normalization factor that can be
-    turned off to get the raw path counts.
-
-    Parameters
-    ----------
-    G : graph
-        A networkx graph.
-
-    sources: list of nodes
-        Nodes to use as sources for shortest paths in betweenness.
-
-    targets: list of nodes
-        Nodes to use as targets for shortest paths in betweenness.
-
-    normalized : bool, optional (default=False)
-        If `True`, the betweenness values are rescaled by dividing by the number of
-        possible $(s, t)$-pairs in the graph.
-
-    weight : None or string, optional (default=None)
-        If `None`, all edge weights are 1.
-        Otherwise holds the name of the edge attribute used as weight.
-        Weights are used to calculate weighted shortest paths, so they are
-        interpreted as distances.
-
-    Returns
-    -------
-    edges : dict
-        Dictionary of edges with betweenness centrality as the value.
-
-    See Also
-    --------
-    betweenness_centrality
-    betweenness_centrality_subset
-    edge_betweenness_centrality
-    edge_load
-
-    Notes
-    -----
-    The basic algorithm is from [1]_.
-
-    For weighted graphs the edge weights must be greater than zero.
-    Zero edge weights can produce an infinite number of equal length
-    paths between pairs of nodes.
-
-    The normalization might seem a little strange but it is the same
-    as in edge_betweenness_centrality() and is designed to make
-    edge_betweenness_centrality(G) be the same as
-    edge_betweenness_centrality_subset(G,sources=G.nodes(),targets=G.nodes()).
-
-    References
-    ----------
-    .. [1] Ulrik Brandes: On Variants of Shortest-Path Betweenness
-       Centrality and their Generic Computation.
-       Social Networks 30(2):136-145, 2008.
-       https://doi.org/10.1016/j.socnet.2007.11.001
-    """
-    b = dict.fromkeys(G, 0.0)  # b[v]=0 for v in G
-    b.update(dict.fromkeys(G.edges(), 0.0))  # b[e] for e in G.edges()
-    for s in sources:
-        # single source shortest paths
-        if weight is None:  # use BFS
-            S, P, sigma, _ = shortest_path(G, s)
-        else:  # use Dijkstra's algorithm
-            S, P, sigma, _ = dijkstra(G, s, weight)
-        b = _accumulate_edges_subset(b, S, P, sigma, s, targets)
-    for n in G:  # remove nodes to only return edges
-        del b[n]
-    b = _rescale(b, len(G), normalized=normalized, directed=G.is_directed())
-    if G.is_multigraph():
-        b = _add_edge_keys(G, b, weight=weight)
-    return b
-
-
-def _accumulate_subset(betweenness, S, P, sigma, s, targets):
-    delta = dict.fromkeys(S, 0.0)
-    target_set = set(targets) - {s}
-    while S:
-        w = S.pop()
-        if w in target_set:
-            coeff = (delta[w] + 1.0) / sigma[w]
-        else:
-            coeff = delta[w] / sigma[w]
-        for v in P[w]:
-            delta[v] += sigma[v] * coeff
-        if w != s:
-            betweenness[w] += delta[w]
-    return betweenness
-
-
-def _accumulate_edges_subset(betweenness, S, P, sigma, s, targets):
-    """edge_betweenness_centrality_subset helper."""
-    delta = dict.fromkeys(S, 0)
-    target_set = set(targets)
-    while S:
-        w = S.pop()
-        for v in P[w]:
-            if w in target_set:
-                c = (sigma[v] / sigma[w]) * (1.0 + delta[w])
-            else:
-                c = delta[w] / len(P[w])
-            if (v, w) not in betweenness:
-                betweenness[(w, v)] += c
-            else:
-                betweenness[(v, w)] += c
-            delta[v] += c
-        if w != s:
-            betweenness[w] += delta[w]
-    return betweenness

package/runtime/python/okstra_vendor/networkx/algorithms/centrality/closeness.py

@@ -1,282 +0,0 @@
-"""
-Closeness centrality measures.
-"""
-
-import functools
-
-import networkx as nx
-from networkx.exception import NetworkXError
-from networkx.utils.decorators import not_implemented_for
-
-__all__ = ["closeness_centrality", "incremental_closeness_centrality"]
-
-
-@nx._dispatchable(edge_attrs="distance")
-def closeness_centrality(G, u=None, distance=None, wf_improved=True):
-    r"""Compute closeness centrality for nodes.
-
-    Closeness centrality [1]_ of a node `u` is the reciprocal of the
-    average shortest path distance to `u` over all `n-1` reachable nodes.
-
-    .. math::
-
-        C(u) = \frac{n - 1}{\sum_{v=1}^{n-1} d(v, u)},
-
-    where `d(v, u)` is the shortest-path distance between `v` and `u`,
-    and `n-1` is the number of nodes reachable from `u`. Notice that the
-    closeness distance function computes the incoming distance to `u`
-    for directed graphs. To use outward distance, act on `G.reverse()`.
-
-    Notice that higher values of closeness indicate higher centrality.
-
-    Wasserman and Faust propose an improved formula for graphs with
-    more than one connected component. The result is "a ratio of the
-    fraction of actors in the group who are reachable, to the average
-    distance" from the reachable actors [2]_. You might think this
-    scale factor is inverted but it is not. As is, nodes from small
-    components receive a smaller closeness value. Letting `N` denote
-    the number of nodes in the graph,
-
-    .. math::
-
-        C_{WF}(u) = \frac{n-1}{N-1} \frac{n - 1}{\sum_{v=1}^{n-1} d(v, u)},
-
-    Parameters
-    ----------
-    G : graph
-      A NetworkX graph
-
-    u : node, optional
-      Return only the value for node u
-
-    distance : edge attribute key, optional (default=None)
-      Use the specified edge attribute as the edge distance in shortest
-      path calculations.  If `None` (the default) all edges have a distance of 1.
-      Absent edge attributes are assigned a distance of 1. Note that no check
-      is performed to ensure that edges have the provided attribute.
-
-    wf_improved : bool, optional (default=True)
-      If True, scale by the fraction of nodes reachable. This gives the
-      Wasserman and Faust improved formula. For single component graphs
-      it is the same as the original formula.
-
-    Returns
-    -------
-    nodes : dictionary
-      Dictionary of nodes with closeness centrality as the value.
-
-    Examples
-    --------
-    >>> G = nx.Graph([(0, 1), (0, 2), (0, 3), (1, 2), (1, 3)])
-    >>> nx.closeness_centrality(G)
-    {0: 1.0, 1: 1.0, 2: 0.75, 3: 0.75}
-
-    See Also
-    --------
-    betweenness_centrality, load_centrality, eigenvector_centrality,
-    degree_centrality, incremental_closeness_centrality
-
-    Notes
-    -----
-    The closeness centrality is normalized to `(n-1)/(|G|-1)` where
-    `n` is the number of nodes in the connected part of graph
-    containing the node.  If the graph is not completely connected,
-    this algorithm computes the closeness centrality for each
-    connected part separately scaled by that parts size.
-
-    If the 'distance' keyword is set to an edge attribute key then the
-    shortest-path length will be computed using Dijkstra's algorithm with
-    that edge attribute as the edge weight.
-
-    The closeness centrality uses *inward* distance to a node, not outward.
-    If you want to use outword distances apply the function to `G.reverse()`
-
-    In NetworkX 2.2 and earlier a bug caused Dijkstra's algorithm to use the
-    outward distance rather than the inward distance. If you use a 'distance'
-    keyword and a DiGraph, your results will change between v2.2 and v2.3.
-
-    References
-    ----------
-    .. [1] Linton C. Freeman: Centrality in networks: I.
-       Conceptual clarification. Social Networks 1:215-239, 1979.
-       https://doi.org/10.1016/0378-8733(78)90021-7
-    .. [2] pg. 201 of Wasserman, S. and Faust, K.,
-       Social Network Analysis: Methods and Applications, 1994,
-       Cambridge University Press.
-    """
-    if G.is_directed():
-        G = G.reverse()  # create a reversed graph view
-
-    if distance is not None:
-        # use Dijkstra's algorithm with specified attribute as edge weight
-        path_length = functools.partial(
-            nx.single_source_dijkstra_path_length, weight=distance
-        )
-    else:
-        path_length = nx.single_source_shortest_path_length
-
-    if u is None:
-        nodes = G.nodes
-    else:
-        nodes = [u]
-    closeness_dict = {}
-    for n in nodes:
-        sp = path_length(G, n)
-        totsp = sum(sp.values())
-        len_G = len(G)
-        _closeness_centrality = 0.0
-        if totsp > 0.0 and len_G > 1:
-            _closeness_centrality = (len(sp) - 1.0) / totsp
-            # normalize to number of nodes-1 in connected part
-            if wf_improved:
-                s = (len(sp) - 1.0) / (len_G - 1)
-                _closeness_centrality *= s
-        closeness_dict[n] = _closeness_centrality
-    if u is not None:
-        return closeness_dict[u]
-    return closeness_dict
-
-
-@not_implemented_for("directed")
-@nx._dispatchable(mutates_input=True)
-def incremental_closeness_centrality(
-    G, edge, prev_cc=None, insertion=True, wf_improved=True
-):
-    r"""Incremental closeness centrality for nodes.
-
-    Compute closeness centrality for nodes using level-based work filtering
-    as described in Incremental Algorithms for Closeness Centrality by Sariyuce et al.
-
-    Level-based work filtering detects unnecessary updates to the closeness
-    centrality and filters them out.
-
-    ---
-    From "Incremental Algorithms for Closeness Centrality":
-
-    Theorem 1: Let :math:`G = (V, E)` be a graph and u and v be two vertices in V
-    such that there is no edge (u, v) in E. Let :math:`G' = (V, E \cup uv)`
-    Then :math:`cc[s] = cc'[s]` if and only if :math:`\left|dG(s, u) - dG(s, v)\right| \leq 1`.
-
-    Where :math:`dG(u, v)` denotes the length of the shortest path between
-    two vertices u, v in a graph G, cc[s] is the closeness centrality for a
-    vertex s in V, and cc'[s] is the closeness centrality for a
-    vertex s in V, with the (u, v) edge added.
-    ---
-
-    We use Theorem 1 to filter out updates when adding or removing an edge.
-    When adding an edge (u, v), we compute the shortest path lengths from all
-    other nodes to u and to v before the node is added. When removing an edge,
-    we compute the shortest path lengths after the edge is removed. Then we
-    apply Theorem 1 to use previously computed closeness centrality for nodes
-    where :math:`\left|dG(s, u) - dG(s, v)\right| \leq 1`. This works only for
-    undirected, unweighted graphs; the distance argument is not supported.
-
-    Closeness centrality [1]_ of a node `u` is the reciprocal of the
-    sum of the shortest path distances from `u` to all `n-1` other nodes.
-    Since the sum of distances depends on the number of nodes in the
-    graph, closeness is normalized by the sum of minimum possible
-    distances `n-1`.
-
-    .. math::
-
-        C(u) = \frac{n - 1}{\sum_{v=1}^{n-1} d(v, u)},
-
-    where `d(v, u)` is the shortest-path distance between `v` and `u`,
-    and `n` is the number of nodes in the graph.
-
-    Notice that higher values of closeness indicate higher centrality.
-
-    Parameters
-    ----------
-    G : graph
-      A NetworkX graph
-
-    edge : tuple
-      The modified edge (u, v) in the graph.
-
-    prev_cc : dictionary
-      The previous closeness centrality for all nodes in the graph.
-
-    insertion : bool, optional
-      If True (default) the edge was inserted, otherwise it was deleted from the graph.
-
-    wf_improved : bool, optional (default=True)
-      If True, scale by the fraction of nodes reachable. This gives the
-      Wasserman and Faust improved formula. For single component graphs
-      it is the same as the original formula.
-
-    Returns
-    -------
-    nodes : dictionary
-      Dictionary of nodes with closeness centrality as the value.
-
-    See Also
-    --------
-    betweenness_centrality, load_centrality, eigenvector_centrality,
-    degree_centrality, closeness_centrality
-
-    Notes
-    -----
-    The closeness centrality is normalized to `(n-1)/(|G|-1)` where
-    `n` is the number of nodes in the connected part of graph
-    containing the node.  If the graph is not completely connected,
-    this algorithm computes the closeness centrality for each
-    connected part separately.
-
-    References
-    ----------
-    .. [1] Freeman, L.C., 1979. Centrality in networks: I.
-       Conceptual clarification.  Social Networks 1, 215--239.
-       https://doi.org/10.1016/0378-8733(78)90021-7
-    .. [2] Sariyuce, A.E. ; Kaya, K. ; Saule, E. ; Catalyiirek, U.V. Incremental
-       Algorithms for Closeness Centrality. 2013 IEEE International Conference on Big Data
-       http://sariyuce.com/papers/bigdata13.pdf
-    """
-    if prev_cc is not None and set(prev_cc.keys()) != set(G.nodes()):
-        raise NetworkXError("prev_cc and G do not have the same nodes")
-
-    # Unpack edge
-    (u, v) = edge
-    path_length = nx.single_source_shortest_path_length
-
-    if insertion:
-        # For edge insertion, we want shortest paths before the edge is inserted
-        du = path_length(G, u)
-        dv = path_length(G, v)
-
-        G.add_edge(u, v)
-    else:
-        G.remove_edge(u, v)
-
-        # For edge removal, we want shortest paths after the edge is removed
-        du = path_length(G, u)
-        dv = path_length(G, v)
-
-    if prev_cc is None:
-        return nx.closeness_centrality(G)
-
-    nodes = G.nodes()
-    closeness_dict = {}
-    for n in nodes:
-        if n in du and n in dv and abs(du[n] - dv[n]) <= 1:
-            closeness_dict[n] = prev_cc[n]
-        else:
-            sp = path_length(G, n)
-            totsp = sum(sp.values())
-            len_G = len(G)
-            _closeness_centrality = 0.0
-            if totsp > 0.0 and len_G > 1:
-                _closeness_centrality = (len(sp) - 1.0) / totsp
-                # normalize to number of nodes-1 in connected part
-                if wf_improved:
-                    s = (len(sp) - 1.0) / (len_G - 1)
-                    _closeness_centrality *= s
-            closeness_dict[n] = _closeness_centrality
-
-    # Leave the graph as we found it
-    if insertion:
-        G.remove_edge(u, v)
-    else:
-        G.add_edge(u, v)
-
-    return closeness_dict