okstra 0.130.3 → 0.131.0

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

@@ -1,500 +0,0 @@
-# See https://github.com/networkx/networkx/pull/1474
-# Copyright 2011 Reya Group <http://www.reyagroup.com>
-# Copyright 2011 Alex Levenson <alex@isnotinvain.com>
-# Copyright 2011 Diederik van Liere <diederik.vanliere@rotman.utoronto.ca>
-"""Functions for analyzing triads of a graph."""
-
-from collections import defaultdict
-from itertools import combinations, permutations
-
-import networkx as nx
-from networkx.utils import not_implemented_for, py_random_state
-
-__all__ = [
-    "triadic_census",
-    "is_triad",
-    "all_triads",
-    "triads_by_type",
-    "triad_type",
-]
-
-#: The integer codes representing each type of triad.
-#:
-#: Triads that are the same up to symmetry have the same code.
-TRICODES = (
-    1,
-    2,
-    2,
-    3,
-    2,
-    4,
-    6,
-    8,
-    2,
-    6,
-    5,
-    7,
-    3,
-    8,
-    7,
-    11,
-    2,
-    6,
-    4,
-    8,
-    5,
-    9,
-    9,
-    13,
-    6,
-    10,
-    9,
-    14,
-    7,
-    14,
-    12,
-    15,
-    2,
-    5,
-    6,
-    7,
-    6,
-    9,
-    10,
-    14,
-    4,
-    9,
-    9,
-    12,
-    8,
-    13,
-    14,
-    15,
-    3,
-    7,
-    8,
-    11,
-    7,
-    12,
-    14,
-    15,
-    8,
-    14,
-    13,
-    15,
-    11,
-    15,
-    15,
-    16,
-)
-
-#: The names of each type of triad. The order of the elements is
-#: important: it corresponds to the tricodes given in :data:`TRICODES`.
-TRIAD_NAMES = (
-    "003",
-    "012",
-    "102",
-    "021D",
-    "021U",
-    "021C",
-    "111D",
-    "111U",
-    "030T",
-    "030C",
-    "201",
-    "120D",
-    "120U",
-    "120C",
-    "210",
-    "300",
-)
-
-
-#: A dictionary mapping triad code to triad name.
-TRICODE_TO_NAME = {i: TRIAD_NAMES[code - 1] for i, code in enumerate(TRICODES)}
-
-
-def _tricode(G, v, u, w):
-    """Returns the integer code of the given triad.
-
-    This is some fancy magic that comes from Batagelj and Mrvar's paper. It
-    treats each edge joining a pair of `v`, `u`, and `w` as a bit in
-    the binary representation of an integer.
-
-    """
-    combos = ((v, u, 1), (u, v, 2), (v, w, 4), (w, v, 8), (u, w, 16), (w, u, 32))
-    return sum(x for u, v, x in combos if v in G[u])
-
-
-@not_implemented_for("undirected")
-@nx._dispatchable
-def triadic_census(G, nodelist=None):
-    """Determines the triadic census of a directed graph.
-
-    The triadic census is a count of how many of the 16 possible types of
-    triads are present in a directed graph. If a list of nodes is passed, then
-    only those triads are taken into account which have elements of nodelist in them.
-
-    Parameters
-    ----------
-    G : digraph
-       A NetworkX DiGraph
-    nodelist : list
-        List of nodes for which you want to calculate triadic census
-
-    Returns
-    -------
-    census : dict
-       Dictionary with triad type as keys and number of occurrences as values.
-
-    Examples
-    --------
-    >>> G = nx.DiGraph([(1, 2), (2, 3), (3, 1), (3, 4), (4, 1), (4, 2)])
-    >>> triadic_census = nx.triadic_census(G)
-    >>> for key, value in triadic_census.items():
-    ...     print(f"{key}: {value}")
-    003: 0
-    012: 0
-    102: 0
-    021D: 0
-    021U: 0
-    021C: 0
-    111D: 0
-    111U: 0
-    030T: 2
-    030C: 2
-    201: 0
-    120D: 0
-    120U: 0
-    120C: 0
-    210: 0
-    300: 0
-
-    Notes
-    -----
-    This algorithm has complexity $O(m)$ where $m$ is the number of edges in
-    the graph.
-
-    For undirected graphs, the triadic census can be computed by first converting
-    the graph into a directed graph using the ``G.to_directed()`` method.
-    After this conversion, only the triad types 003, 102, 201 and 300 will be
-    present in the undirected scenario.
-
-    Raises
-    ------
-    ValueError
-        If `nodelist` contains duplicate nodes or nodes not in `G`.
-        If you want to ignore this you can preprocess with `set(nodelist) & G.nodes`
-
-    See also
-    --------
-    triad_graph
-
-    References
-    ----------
-    .. [1] Vladimir Batagelj and Andrej Mrvar, A subquadratic triad census
-        algorithm for large sparse networks with small maximum degree,
-        University of Ljubljana,
-        http://vlado.fmf.uni-lj.si/pub/networks/doc/triads/triads.pdf
-
-    """
-    nodeset = set(G.nbunch_iter(nodelist))
-    if nodelist is not None and len(nodelist) != len(nodeset):
-        raise ValueError("nodelist includes duplicate nodes or nodes not in G")
-
-    N = len(G)
-    Nnot = N - len(nodeset)  # can signal special counting for subset of nodes
-
-    # create an ordering of nodes with nodeset nodes first
-    m = {n: i for i, n in enumerate(nodeset)}
-    if Nnot:
-        # add non-nodeset nodes later in the ordering
-        not_nodeset = G.nodes - nodeset
-        m.update((n, i + N) for i, n in enumerate(not_nodeset))
-
-    # build all_neighbor dicts for easy counting
-    # After Python 3.8 can leave off these keys(). Speedup also using G._pred
-    # nbrs = {n: G._pred[n].keys() | G._succ[n].keys() for n in G}
-    nbrs = {n: G.pred[n].keys() | G.succ[n].keys() for n in G}
-    dbl_nbrs = {n: G.pred[n].keys() & G.succ[n].keys() for n in G}
-
-    if Nnot:
-        sgl_nbrs = {n: G.pred[n].keys() ^ G.succ[n].keys() for n in not_nodeset}
-        # find number of edges not incident to nodes in nodeset
-        sgl = sum(1 for n in not_nodeset for nbr in sgl_nbrs[n] if nbr not in nodeset)
-        sgl_edges_outside = sgl // 2
-        dbl = sum(1 for n in not_nodeset for nbr in dbl_nbrs[n] if nbr not in nodeset)
-        dbl_edges_outside = dbl // 2
-
-    # Initialize the count for each triad to be zero.
-    census = {name: 0 for name in TRIAD_NAMES}
-    # Main loop over nodes
-    for v in nodeset:
-        vnbrs = nbrs[v]
-        dbl_vnbrs = dbl_nbrs[v]
-        if Nnot:
-            # set up counts of edges attached to v.
-            sgl_unbrs_bdy = sgl_unbrs_out = dbl_unbrs_bdy = dbl_unbrs_out = 0
-        for u in vnbrs:
-            if m[u] <= m[v]:
-                continue
-            unbrs = nbrs[u]
-            neighbors = (vnbrs | unbrs) - {u, v}
-            # Count connected triads.
-            for w in neighbors:
-                if m[u] < m[w] or (m[v] < m[w] < m[u] and v not in nbrs[w]):
-                    code = _tricode(G, v, u, w)
-                    census[TRICODE_TO_NAME[code]] += 1
-
-            # Use a formula for dyadic triads with edge incident to v
-            if u in dbl_vnbrs:
-                census["102"] += N - len(neighbors) - 2
-            else:
-                census["012"] += N - len(neighbors) - 2
-
-            # Count edges attached to v. Subtract later to get triads with v isolated
-            # _out are (u,unbr) for unbrs outside boundary of nodeset
-            # _bdy are (u,unbr) for unbrs on boundary of nodeset (get double counted)
-            if Nnot and u not in nodeset:
-                sgl_unbrs = sgl_nbrs[u]
-                sgl_unbrs_bdy += len(sgl_unbrs & vnbrs - nodeset)
-                sgl_unbrs_out += len(sgl_unbrs - vnbrs - nodeset)
-                dbl_unbrs = dbl_nbrs[u]
-                dbl_unbrs_bdy += len(dbl_unbrs & vnbrs - nodeset)
-                dbl_unbrs_out += len(dbl_unbrs - vnbrs - nodeset)
-        # if nodeset == G.nodes, skip this b/c we will find the edge later.
-        if Nnot:
-            # Count edges outside nodeset not connected with v (v isolated triads)
-            census["012"] += sgl_edges_outside - (sgl_unbrs_out + sgl_unbrs_bdy // 2)
-            census["102"] += dbl_edges_outside - (dbl_unbrs_out + dbl_unbrs_bdy // 2)
-
-    # calculate null triads: "003"
-    # null triads = total number of possible triads - all found triads
-    total_triangles = (N * (N - 1) * (N - 2)) // 6
-    triangles_without_nodeset = (Nnot * (Nnot - 1) * (Nnot - 2)) // 6
-    total_census = total_triangles - triangles_without_nodeset
-    census["003"] = total_census - sum(census.values())
-
-    return census
-
-
-@nx._dispatchable
-def is_triad(G):
-    """Returns True if the graph G is a triad, else False.
-
-    Parameters
-    ----------
-    G : graph
-       A NetworkX Graph
-
-    Returns
-    -------
-    istriad : boolean
-       Whether G is a valid triad
-
-    Examples
-    --------
-    >>> G = nx.DiGraph([(1, 2), (2, 3), (3, 1)])
-    >>> nx.is_triad(G)
-    True
-    >>> G.add_edge(0, 1)
-    >>> nx.is_triad(G)
-    False
-    """
-    if isinstance(G, nx.Graph):
-        if G.order() == 3 and nx.is_directed(G):
-            if not any((n, n) in G.edges() for n in G.nodes()):
-                return True
-    return False
-
-
-@not_implemented_for("undirected")
-@nx._dispatchable(returns_graph=True)
-def all_triads(G):
-    """A generator of all possible triads in G.
-
-    Parameters
-    ----------
-    G : digraph
-       A NetworkX DiGraph
-
-    Returns
-    -------
-    all_triads : generator of DiGraphs
-       Generator of triads (order-3 DiGraphs)
-
-    Examples
-    --------
-    >>> G = nx.DiGraph([(1, 2), (2, 3), (3, 1), (3, 4), (4, 1), (4, 2)])
-    >>> for triad in nx.all_triads(G):
-    ...     print(triad.edges)
-    [(1, 2), (2, 3), (3, 1)]
-    [(1, 2), (4, 1), (4, 2)]
-    [(3, 1), (3, 4), (4, 1)]
-    [(2, 3), (3, 4), (4, 2)]
-
-    """
-    triplets = combinations(G.nodes(), 3)
-    for triplet in triplets:
-        yield G.subgraph(triplet).copy()
-
-
-@not_implemented_for("undirected")
-@nx._dispatchable
-def triads_by_type(G):
-    """Returns a list of all triads for each triad type in a directed graph.
-    There are exactly 16 different types of triads possible. Suppose 1, 2, 3 are three
-    nodes, they will be classified as a particular triad type if their connections
-    are as follows:
-
-    - 003: 1, 2, 3
-    - 012: 1 -> 2, 3
-    - 102: 1 <-> 2, 3
-    - 021D: 1 <- 2 -> 3
-    - 021U: 1 -> 2 <- 3
-    - 021C: 1 -> 2 -> 3
-    - 111D: 1 <-> 2 <- 3
-    - 111U: 1 <-> 2 -> 3
-    - 030T: 1 -> 2 -> 3, 1 -> 3
-    - 030C: 1 <- 2 <- 3, 1 -> 3
-    - 201: 1 <-> 2 <-> 3
-    - 120D: 1 <- 2 -> 3, 1 <-> 3
-    - 120U: 1 -> 2 <- 3, 1 <-> 3
-    - 120C: 1 -> 2 -> 3, 1 <-> 3
-    - 210: 1 -> 2 <-> 3, 1 <-> 3
-    - 300: 1 <-> 2 <-> 3, 1 <-> 3
-
-    Refer to the :doc:`example gallery </auto_examples/graph/plot_triad_types>`
-    for visual examples of the triad types.
-
-    Parameters
-    ----------
-    G : digraph
-       A NetworkX DiGraph
-
-    Returns
-    -------
-    tri_by_type : dict
-       Dictionary with triad types as keys and lists of triads as values.
-
-    Examples
-    --------
-    >>> G = nx.DiGraph([(1, 2), (1, 3), (2, 3), (3, 1), (5, 6), (5, 4), (6, 7)])
-    >>> dict = nx.triads_by_type(G)
-    >>> dict["120C"][0].edges()
-    OutEdgeView([(1, 2), (1, 3), (2, 3), (3, 1)])
-    >>> dict["012"][0].edges()
-    OutEdgeView([(1, 2)])
-
-    References
-    ----------
-    .. [1] Snijders, T. (2012). "Transitivity and triads." University of
-        Oxford.
-        https://web.archive.org/web/20170830032057/http://www.stats.ox.ac.uk/~snijders/Trans_Triads_ha.pdf
-    """
-    # num_triads = o * (o - 1) * (o - 2) // 6
-    # if num_triads > TRIAD_LIMIT: print(WARNING)
-    all_tri = all_triads(G)
-    tri_by_type = defaultdict(list)
-    for triad in all_tri:
-        name = triad_type(triad)
-        tri_by_type[name].append(triad)
-    return tri_by_type
-
-
-@not_implemented_for("undirected")
-@nx._dispatchable
-def triad_type(G):
-    """Returns the sociological triad type for a triad.
-
-    Parameters
-    ----------
-    G : digraph
-       A NetworkX DiGraph with 3 nodes
-
-    Returns
-    -------
-    triad_type : str
-       A string identifying the triad type
-
-    Examples
-    --------
-    >>> G = nx.DiGraph([(1, 2), (2, 3), (3, 1)])
-    >>> nx.triad_type(G)
-    '030C'
-    >>> G.add_edge(1, 3)
-    >>> nx.triad_type(G)
-    '120C'
-
-    Notes
-    -----
-    There can be 6 unique edges in a triad (order-3 DiGraph) (so 2^^6=64 unique
-    triads given 3 nodes). These 64 triads each display exactly 1 of 16
-    topologies of triads (topologies can be permuted). These topologies are
-    identified by the following notation:
-
-    {m}{a}{n}{type} (for example: 111D, 210, 102)
-
-    Here:
-
-    {m}     = number of mutual ties (takes 0, 1, 2, 3); a mutual tie is (0,1)
-              AND (1,0)
-    {a}     = number of asymmetric ties (takes 0, 1, 2, 3); an asymmetric tie
-              is (0,1) BUT NOT (1,0) or vice versa
-    {n}     = number of null ties (takes 0, 1, 2, 3); a null tie is NEITHER
-              (0,1) NOR (1,0)
-    {type}  = a letter (takes U, D, C, T) corresponding to up, down, cyclical
-              and transitive. This is only used for topologies that can have
-              more than one form (eg: 021D and 021U).
-
-    References
-    ----------
-    .. [1] Snijders, T. (2012). "Transitivity and triads." University of
-        Oxford.
-        https://web.archive.org/web/20170830032057/http://www.stats.ox.ac.uk/~snijders/Trans_Triads_ha.pdf
-    """
-    if not is_triad(G):
-        raise nx.NetworkXAlgorithmError("G is not a triad (order-3 DiGraph)")
-    num_edges = len(G.edges())
-    if num_edges == 0:
-        return "003"
-    elif num_edges == 1:
-        return "012"
-    elif num_edges == 2:
-        e1, e2 = G.edges()
-        if set(e1) == set(e2):
-            return "102"
-        elif e1[0] == e2[0]:
-            return "021D"
-        elif e1[1] == e2[1]:
-            return "021U"
-        elif e1[1] == e2[0] or e2[1] == e1[0]:
-            return "021C"
-    elif num_edges == 3:
-        for e1, e2, e3 in permutations(G.edges(), 3):
-            if set(e1) == set(e2):
-                if e3[0] in e1:
-                    return "111U"
-                # e3[1] in e1:
-                return "111D"
-            elif set(e1).symmetric_difference(set(e2)) == set(e3):
-                if {e1[0], e2[0], e3[0]} == {e1[0], e2[0], e3[0]} == set(G.nodes()):
-                    return "030C"
-                # e3 == (e1[0], e2[1]) and e2 == (e1[1], e3[1]):
-                return "030T"
-    elif num_edges == 4:
-        for e1, e2, e3, e4 in permutations(G.edges(), 4):
-            if set(e1) == set(e2):
-                # identify pair of symmetric edges (which necessarily exists)
-                if set(e3) == set(e4):
-                    return "201"
-                if {e3[0]} == {e4[0]} == set(e3).intersection(set(e4)):
-                    return "120D"
-                if {e3[1]} == {e4[1]} == set(e3).intersection(set(e4)):
-                    return "120U"
-                if e3[1] == e4[0]:
-                    return "120C"
-    elif num_edges == 5:
-        return "210"
-    elif num_edges == 6:
-        return "300"

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

@@ -1,76 +0,0 @@
-"""
-Vitality measures.
-"""
-
-from functools import partial
-
-import networkx as nx
-
-__all__ = ["closeness_vitality"]
-
-
-@nx._dispatchable(edge_attrs="weight")
-def closeness_vitality(G, node=None, weight=None, wiener_index=None):
-    """Returns the closeness vitality for nodes in the graph.
-
-    The *closeness vitality* of a node, defined in Section 3.6.2 of [1],
-    is the change in the sum of distances between all node pairs when
-    excluding that node.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-        A strongly-connected graph.
-
-    weight : string
-        The name of the edge attribute used as weight. This is passed
-        directly to the :func:`~networkx.wiener_index` function.
-
-    node : object
-        If specified, only the closeness vitality for this node will be
-        returned. Otherwise, a dictionary mapping each node to its
-        closeness vitality will be returned.
-
-    Other parameters
-    ----------------
-    wiener_index : number
-        If you have already computed the Wiener index of the graph
-        `G`, you can provide that value here. Otherwise, it will be
-        computed for you.
-
-    Returns
-    -------
-    dictionary or float
-        If `node` is None, this function returns a dictionary
-        with nodes as keys and closeness vitality as the
-        value. Otherwise, it returns only the closeness vitality for the
-        specified `node`.
-
-        The closeness vitality of a node may be negative infinity if
-        removing that node would disconnect the graph.
-
-    Examples
-    --------
-    >>> G = nx.cycle_graph(3)
-    >>> nx.closeness_vitality(G)
-    {0: 2.0, 1: 2.0, 2: 2.0}
-
-    See Also
-    --------
-    closeness_centrality
-
-    References
-    ----------
-    .. [1] Ulrik Brandes, Thomas Erlebach (eds.).
-           *Network Analysis: Methodological Foundations*.
-           Springer, 2005.
-           <http://books.google.com/books?id=TTNhSm7HYrIC>
-
-    """
-    if wiener_index is None:
-        wiener_index = nx.wiener_index(G, weight=weight)
-    if node is not None:
-        after = nx.wiener_index(G.subgraph(set(G) - {node}), weight=weight)
-        return wiener_index - after
-    vitality = partial(closeness_vitality, G, weight=weight, wiener_index=wiener_index)
-    return {v: vitality(node=v) for v in G}

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

@@ -1,86 +0,0 @@
-"""Functions for computing the Voronoi cells of a graph."""
-
-import networkx as nx
-from networkx.utils import groups
-
-__all__ = ["voronoi_cells"]
-
-
-@nx._dispatchable(edge_attrs="weight")
-def voronoi_cells(G, center_nodes, weight="weight"):
-    """Returns the Voronoi cells centered at `center_nodes` with respect
-    to the shortest-path distance metric.
-
-    If $C$ is a set of nodes in the graph and $c$ is an element of $C$,
-    the *Voronoi cell* centered at a node $c$ is the set of all nodes
-    $v$ that are closer to $c$ than to any other center node in $C$ with
-    respect to the shortest-path distance metric. [1]_
-
-    For directed graphs, this will compute the "outward" Voronoi cells,
-    as defined in [1]_, in which distance is measured from the center
-    nodes to the target node. For the "inward" Voronoi cells, use the
-    :meth:`DiGraph.reverse` method to reverse the orientation of the
-    edges before invoking this function on the directed graph.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-
-    center_nodes : set
-        A nonempty set of nodes in the graph `G` that represent the
-        center of the Voronoi cells.
-
-    weight : string or function
-        The edge attribute (or an arbitrary function) representing the
-        weight of an edge. This keyword argument is as described in the
-        documentation for :func:`~networkx.multi_source_dijkstra_path`,
-        for example.
-
-    Returns
-    -------
-    dictionary
-        A mapping from center node to set of all nodes in the graph
-        closer to that center node than to any other center node. The
-        keys of the dictionary are the element of `center_nodes`, and
-        the values of the dictionary form a partition of the nodes of
-        `G`.
-
-    Examples
-    --------
-    To get only the partition of the graph induced by the Voronoi cells,
-    take the collection of all values in the returned dictionary::
-
-        >>> G = nx.path_graph(6)
-        >>> center_nodes = {0, 3}
-        >>> cells = nx.voronoi_cells(G, center_nodes)
-        >>> partition = set(map(frozenset, cells.values()))
-        >>> sorted(map(sorted, partition))
-        [[0, 1], [2, 3, 4, 5]]
-
-    Raises
-    ------
-    ValueError
-        If `center_nodes` is empty.
-
-    References
-    ----------
-    .. [1] Erwig, Martin. (2000),"The graph Voronoi diagram with applications."
-        *Networks*, 36: 156--163.
-        https://doi.org/10.1002/1097-0037(200010)36:3<156::AID-NET2>3.0.CO;2-L
-
-    """
-    # Determine the shortest paths from any one of the center nodes to
-    # every node in the graph.
-    #
-    # This raises `ValueError` if `center_nodes` is an empty set.
-    paths = nx.multi_source_dijkstra_path(G, center_nodes, weight=weight)
-    # Determine the center node from which the shortest path originates.
-    nearest = {v: p[0] for v, p in paths.items()}
-    # Get the mapping from center node to all nodes closer to it than to
-    # any other center node.
-    cells = groups(nearest)
-    # We collect all unreachable nodes under a special key, if there are any.
-    unreachable = set(G) - set(nearest)
-    if unreachable:
-        cells["unreachable"] = unreachable
-    return cells