okstra 0.130.4 → 0.131.1

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

@@ -1,347 +0,0 @@
-"""Functions for measuring the quality of a partition (into
-communities).
-
-"""
-
-from itertools import combinations
-
-import networkx as nx
-from networkx import NetworkXError
-from networkx.algorithms.community.community_utils import is_partition
-from networkx.utils.decorators import argmap
-
-__all__ = ["modularity", "partition_quality"]
-
-
-class NotAPartition(NetworkXError):
-    """Raised if a given collection is not a partition."""
-
-    def __init__(self, G, collection):
-        msg = f"{collection} is not a valid partition of the graph {G}"
-        super().__init__(msg)
-
-
-def _require_partition(G, partition):
-    """Decorator to check that a valid partition is input to a function
-
-    Raises :exc:`networkx.NetworkXError` if the partition is not valid.
-
-    This decorator should be used on functions whose first two arguments
-    are a graph and a partition of the nodes of that graph (in that
-    order)::
-
-        >>> @require_partition
-        ... def foo(G, partition):
-        ...     print("partition is valid!")
-        ...
-        >>> G = nx.complete_graph(5)
-        >>> partition = [{0, 1}, {2, 3}, {4}]
-        >>> foo(G, partition)
-        partition is valid!
-        >>> partition = [{0}, {2, 3}, {4}]
-        >>> foo(G, partition)
-        Traceback (most recent call last):
-          ...
-        networkx.exception.NetworkXError: `partition` is not a valid partition of the nodes of G
-        >>> partition = [{0, 1}, {1, 2, 3}, {4}]
-        >>> foo(G, partition)
-        Traceback (most recent call last):
-          ...
-        networkx.exception.NetworkXError: `partition` is not a valid partition of the nodes of G
-
-    """
-    if is_partition(G, partition):
-        return G, partition
-    raise nx.NetworkXError("`partition` is not a valid partition of the nodes of G")
-
-
-require_partition = argmap(_require_partition, (0, 1))
-
-
-@nx._dispatchable
-def intra_community_edges(G, partition):
-    """Returns the number of intra-community edges for a partition of `G`.
-
-    Parameters
-    ----------
-    G : NetworkX graph.
-
-    partition : iterable of sets of nodes
-        This must be a partition of the nodes of `G`.
-
-    The "intra-community edges" are those edges joining a pair of nodes
-    in the same block of the partition.
-
-    """
-    return sum(G.subgraph(block).size() for block in partition)
-
-
-@nx._dispatchable
-def inter_community_edges(G, partition):
-    """Returns the number of inter-community edges for a partition of `G`.
-    according to the given
-    partition of the nodes of `G`.
-
-    Parameters
-    ----------
-    G : NetworkX graph.
-
-    partition : iterable of sets of nodes
-        This must be a partition of the nodes of `G`.
-
-    The *inter-community edges* are those edges joining a pair of nodes
-    in different blocks of the partition.
-
-    Implementation note: this function creates an intermediate graph
-    that may require the same amount of memory as that of `G`.
-
-    """
-    # Alternate implementation that does not require constructing a new
-    # graph object (but does require constructing an affiliation
-    # dictionary):
-    #
-    #     aff = dict(chain.from_iterable(((v, block) for v in block)
-    #                                    for block in partition))
-    #     return sum(1 for u, v in G.edges() if aff[u] != aff[v])
-    #
-    MG = nx.MultiDiGraph if G.is_directed() else nx.MultiGraph
-    return nx.quotient_graph(G, partition, create_using=MG).size()
-
-
-@nx._dispatchable
-def inter_community_non_edges(G, partition):
-    """Returns the number of inter-community non-edges according to the
-    given partition of the nodes of `G`.
-
-    Parameters
-    ----------
-    G : NetworkX graph.
-
-    partition : iterable of sets of nodes
-        This must be a partition of the nodes of `G`.
-
-    A *non-edge* is a pair of nodes (undirected if `G` is undirected)
-    that are not adjacent in `G`. The *inter-community non-edges* are
-    those non-edges on a pair of nodes in different blocks of the
-    partition.
-
-    Implementation note: this function creates two intermediate graphs,
-    which may require up to twice the amount of memory as required to
-    store `G`.
-
-    """
-    # Alternate implementation that does not require constructing two
-    # new graph objects (but does require constructing an affiliation
-    # dictionary):
-    #
-    #     aff = dict(chain.from_iterable(((v, block) for v in block)
-    #                                    for block in partition))
-    #     return sum(1 for u, v in nx.non_edges(G) if aff[u] != aff[v])
-    #
-    return inter_community_edges(nx.complement(G), partition)
-
-
-@nx._dispatchable(edge_attrs="weight")
-def modularity(G, communities, weight="weight", resolution=1):
-    r"""Returns the modularity of the given partition of the graph.
-
-    Modularity is defined in [1]_ as
-
-    .. math::
-        Q = \frac{1}{2m} \sum_{ij} \left( A_{ij} - \gamma\frac{k_ik_j}{2m}\right)
-            \delta(c_i,c_j)
-
-    where $m$ is the number of edges (or sum of all edge weights as in [5]_),
-    $A$ is the adjacency matrix of `G`, $k_i$ is the (weighted) degree of $i$,
-    $\gamma$ is the resolution parameter, and $\delta(c_i, c_j)$ is 1 if $i$ and
-    $j$ are in the same community else 0.
-
-    According to [2]_ (and verified by some algebra) this can be reduced to
-
-    .. math::
-       Q = \sum_{c=1}^{n}
-       \left[ \frac{L_c}{m} - \gamma\left( \frac{k_c}{2m} \right) ^2 \right]
-
-    where the sum iterates over all communities $c$, $m$ is the number of edges,
-    $L_c$ is the number of intra-community links for community $c$,
-    $k_c$ is the sum of degrees of the nodes in community $c$,
-    and $\gamma$ is the resolution parameter.
-
-    The resolution parameter sets an arbitrary tradeoff between intra-group
-    edges and inter-group edges. More complex grouping patterns can be
-    discovered by analyzing the same network with multiple values of gamma
-    and then combining the results [3]_. That said, it is very common to
-    simply use gamma=1. More on the choice of gamma is in [4]_.
-
-    The second formula is the one actually used in calculation of the modularity.
-    For directed graphs the second formula replaces $k_c$ with $k^{in}_c k^{out}_c$.
-
-    Parameters
-    ----------
-    G : NetworkX Graph
-
-    communities : list or iterable of set of nodes
-        These node sets must represent a partition of G's nodes.
-
-    weight : string or None, optional (default="weight")
-        The edge attribute that holds the numerical value used
-        as a weight. If None or an edge does not have that attribute,
-        then that edge has weight 1.
-
-    resolution : float (default=1)
-        If resolution is less than 1, modularity favors larger communities.
-        Greater than 1 favors smaller communities.
-
-    Returns
-    -------
-    Q : float
-        The modularity of the partition.
-
-    Raises
-    ------
-    NotAPartition
-        If `communities` is not a partition of the nodes of `G`.
-
-    Examples
-    --------
-    >>> G = nx.barbell_graph(3, 0)
-    >>> nx.community.modularity(G, [{0, 1, 2}, {3, 4, 5}])
-    0.35714285714285715
-    >>> nx.community.modularity(G, nx.community.label_propagation_communities(G))
-    0.35714285714285715
-
-    References
-    ----------
-    .. [1] M. E. J. Newman "Networks: An Introduction", page 224.
-       Oxford University Press, 2011.
-    .. [2] Clauset, Aaron, Mark EJ Newman, and Cristopher Moore.
-       "Finding community structure in very large networks."
-       Phys. Rev. E 70.6 (2004). <https://arxiv.org/abs/cond-mat/0408187>
-    .. [3] Reichardt and Bornholdt "Statistical Mechanics of Community Detection"
-       Phys. Rev. E 74, 016110, 2006. https://doi.org/10.1103/PhysRevE.74.016110
-    .. [4] M. E. J. Newman, "Equivalence between modularity optimization and
-       maximum likelihood methods for community detection"
-       Phys. Rev. E 94, 052315, 2016. https://doi.org/10.1103/PhysRevE.94.052315
-    .. [5] Blondel, V.D. et al. "Fast unfolding of communities in large
-       networks" J. Stat. Mech 10008, 1-12 (2008).
-       https://doi.org/10.1088/1742-5468/2008/10/P10008
-    """
-    if not isinstance(communities, list):
-        communities = list(communities)
-    if not is_partition(G, communities):
-        raise NotAPartition(G, communities)
-
-    directed = G.is_directed()
-    if directed:
-        out_degree = dict(G.out_degree(weight=weight))
-        in_degree = dict(G.in_degree(weight=weight))
-        m = sum(out_degree.values())
-        norm = 1 / m**2
-    else:
-        out_degree = in_degree = dict(G.degree(weight=weight))
-        deg_sum = sum(out_degree.values())
-        m = deg_sum / 2
-        norm = 1 / deg_sum**2
-
-    def community_contribution(community):
-        comm = set(community)
-        L_c = sum(wt for u, v, wt in G.edges(comm, data=weight, default=1) if v in comm)
-
-        out_degree_sum = sum(out_degree[u] for u in comm)
-        in_degree_sum = sum(in_degree[u] for u in comm) if directed else out_degree_sum
-
-        return L_c / m - resolution * out_degree_sum * in_degree_sum * norm
-
-    return sum(map(community_contribution, communities))
-
-
-@require_partition
-@nx._dispatchable
-def partition_quality(G, partition):
-    """Returns the coverage and performance of a partition of G.
-
-    The *coverage* of a partition is the ratio of the number of
-    intra-community edges to the total number of edges in the graph.
-
-    The *performance* of a partition is the number of
-    intra-community edges plus inter-community non-edges divided by the total
-    number of potential edges.
-
-    This algorithm has complexity $O(C^2 + L)$ where C is the number of
-    communities and L is the number of links.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-
-    partition : sequence
-        Partition of the nodes of `G`, represented as a sequence of
-        sets of nodes (blocks). Each block of the partition represents a
-        community.
-
-    Returns
-    -------
-    (float, float)
-        The (coverage, performance) tuple of the partition, as defined above.
-
-    Raises
-    ------
-    NetworkXError
-        If `partition` is not a valid partition of the nodes of `G`.
-
-    Notes
-    -----
-    If `G` is a multigraph;
-        - for coverage, the multiplicity of edges is counted
-        - for performance, the result is -1 (total number of possible edges is not defined)
-
-    References
-    ----------
-    .. [1] Santo Fortunato.
-           "Community Detection in Graphs".
-           *Physical Reports*, Volume 486, Issue 3--5 pp. 75--174
-           <https://arxiv.org/abs/0906.0612>
-    """
-
-    node_community = {}
-    for i, community in enumerate(partition):
-        for node in community:
-            node_community[node] = i
-
-    # `performance` is not defined for multigraphs
-    if not G.is_multigraph():
-        # Iterate over the communities, quadratic, to calculate `possible_inter_community_edges`
-        possible_inter_community_edges = sum(
-            len(p1) * len(p2) for p1, p2 in combinations(partition, 2)
-        )
-
-        if G.is_directed():
-            possible_inter_community_edges *= 2
-    else:
-        possible_inter_community_edges = 0
-
-    # Compute the number of edges in the complete graph -- `n` nodes,
-    # directed or undirected, depending on `G`
-    n = len(G)
-    total_pairs = n * (n - 1)
-    if not G.is_directed():
-        total_pairs //= 2
-
-    intra_community_edges = 0
-    inter_community_non_edges = possible_inter_community_edges
-
-    # Iterate over the links to count `intra_community_edges` and `inter_community_non_edges`
-    for e in G.edges():
-        if node_community[e[0]] == node_community[e[1]]:
-            intra_community_edges += 1
-        else:
-            inter_community_non_edges -= 1
-
-    coverage = intra_community_edges / len(G.edges)
-
-    if G.is_multigraph():
-        performance = -1.0
-    else:
-        performance = (intra_community_edges + inter_community_non_edges) / total_pairs
-
-    return coverage, performance

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

@@ -1,6 +0,0 @@
-from .connected import *
-from .strongly_connected import *
-from .weakly_connected import *
-from .attracting import *
-from .biconnected import *
-from .semiconnected import *

package/runtime/python/okstra_vendor/networkx/algorithms/components/attracting.py

@@ -1,115 +0,0 @@
-"""Attracting components."""
-
-import networkx as nx
-from networkx.utils.decorators import not_implemented_for
-
-__all__ = [
-    "number_attracting_components",
-    "attracting_components",
-    "is_attracting_component",
-]
-
-
-@not_implemented_for("undirected")
-@nx._dispatchable
-def attracting_components(G):
-    """Generates the attracting components in `G`.
-
-    An attracting component in a directed graph `G` is a strongly connected
-    component with the property that a random walker on the graph will never
-    leave the component, once it enters the component.
-
-    The nodes in attracting components can also be thought of as recurrent
-    nodes.  If a random walker enters the attractor containing the node, then
-    the node will be visited infinitely often.
-
-    To obtain induced subgraphs on each component use:
-    ``(G.subgraph(c).copy() for c in attracting_components(G))``
-
-    Parameters
-    ----------
-    G : DiGraph, MultiDiGraph
-        The graph to be analyzed.
-
-    Returns
-    -------
-    attractors : generator of sets
-        A generator of sets of nodes, one for each attracting component of G.
-
-    Raises
-    ------
-    NetworkXNotImplemented
-        If the input graph is undirected.
-
-    See Also
-    --------
-    number_attracting_components
-    is_attracting_component
-
-    """
-    scc = list(nx.strongly_connected_components(G))
-    cG = nx.condensation(G, scc)
-    for n in cG:
-        if cG.out_degree(n) == 0:
-            yield scc[n]
-
-
-@not_implemented_for("undirected")
-@nx._dispatchable
-def number_attracting_components(G):
-    """Returns the number of attracting components in `G`.
-
-    Parameters
-    ----------
-    G : DiGraph, MultiDiGraph
-        The graph to be analyzed.
-
-    Returns
-    -------
-    n : int
-        The number of attracting components in G.
-
-    Raises
-    ------
-    NetworkXNotImplemented
-        If the input graph is undirected.
-
-    See Also
-    --------
-    attracting_components
-    is_attracting_component
-
-    """
-    return sum(1 for ac in attracting_components(G))
-
-
-@not_implemented_for("undirected")
-@nx._dispatchable
-def is_attracting_component(G):
-    """Returns True if `G` consists of a single attracting component.
-
-    Parameters
-    ----------
-    G : DiGraph, MultiDiGraph
-        The graph to be analyzed.
-
-    Returns
-    -------
-    attracting : bool
-        True if `G` has a single attracting component. Otherwise, False.
-
-    Raises
-    ------
-    NetworkXNotImplemented
-        If the input graph is undirected.
-
-    See Also
-    --------
-    attracting_components
-    number_attracting_components
-
-    """
-    ac = list(attracting_components(G))
-    if len(ac) == 1:
-        return len(ac[0]) == len(G)
-    return False