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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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"""Algorithms to calculate reciprocity in a directed graph."""
from networkx import NetworkXError
from ..utils import not_implemented_for

__all__ = ["reciprocity", "overall_reciprocity"]

@not_implemented_for("undirected", "multigraph")
def reciprocity(G, nodes=None):
    r"""Compute the reciprocity in a directed graph.

    The reciprocity of a directed graph is defined as the ratio
    of the number of edges pointing in both directions to the total
    number of edges in the graph.
    Formally, $r = |{(u,v) \in G|(v,u) \in G}| / |{(u,v) \in G}|$.

    The reciprocity of a single node u is defined similarly,
    it is the ratio of the number of edges in both directions to
    the total number of edges attached to node u.

    G : graph
       A networkx directed graph
    nodes : container of nodes, optional (default=whole graph)
       Compute reciprocity for nodes in this container.

    out : dictionary
       Reciprocity keyed by node label.

    The reciprocity is not defined for isolated nodes.
    In such cases this function will return None.

    # If `nodes` is not specified, calculate the reciprocity of the graph.
    if nodes is None:
        return overall_reciprocity(G)

    # If `nodes` represents a single node in the graph, return only its
    # reciprocity.
    if nodes in G:
        reciprocity = next(_reciprocity_iter(G, nodes))[1]
        if reciprocity is None:
            raise NetworkXError("Not defined for isolated nodes.")
            return reciprocity

    # Otherwise, `nodes` represents an iterable of nodes, so return a
    # dictionary mapping node to its reciprocity.
    return dict(_reciprocity_iter(G, nodes))

def _reciprocity_iter(G, nodes):
    """ Return an iterator of (node, reciprocity).
    n = G.nbunch_iter(nodes)
    for node in n:
        pred = set(G.predecessors(node))
        succ = set(G.successors(node))
        overlap = pred & succ
        n_total = len(pred) + len(succ)

        # Reciprocity is not defined for isolated nodes.
        # Return None.
        if n_total == 0:
            yield (node, None)
            reciprocity = 2.0 * float(len(overlap)) / float(n_total)
            yield (node, reciprocity)

@not_implemented_for("undirected", "multigraph")
def overall_reciprocity(G):
    """Compute the reciprocity for the whole graph.

    See the doc of reciprocity for the definition.

    G : graph
       A networkx graph

    n_all_edge = G.number_of_edges()
    n_overlap_edge = (n_all_edge - G.to_undirected().number_of_edges()) * 2

    if n_all_edge == 0:
        raise NetworkXError("Not defined for empty graphs")

    return float(n_overlap_edge) / float(n_all_edge)