diff env/lib/python3.9/site-packages/networkx/generators/joint_degree_seq.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/networkx/generators/joint_degree_seq.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,670 @@
+"""Generate graphs with a given joint degree and directed joint degree"""
+
+import networkx as nx
+from networkx.utils import py_random_state
+
+__all__ = [
+    "is_valid_joint_degree",
+    "is_valid_directed_joint_degree",
+    "joint_degree_graph",
+    "directed_joint_degree_graph",
+]
+
+
+def is_valid_joint_degree(joint_degrees):
+    """ Checks whether the given joint degree dictionary is realizable.
+
+    A *joint degree dictionary* is a dictionary of dictionaries, in
+    which entry ``joint_degrees[k][l]`` is an integer representing the
+    number of edges joining nodes of degree *k* with nodes of degree
+    *l*. Such a dictionary is realizable as a simple graph if and only
+    if the following conditions are satisfied.
+
+    - each entry must be an integer,
+    - the total number of nodes of degree *k*, computed by
+      ``sum(joint_degrees[k].values()) / k``, must be an integer,
+    - the total number of edges joining nodes of degree *k* with
+      nodes of degree *l* cannot exceed the total number of possible edges,
+    - each diagonal entry ``joint_degrees[k][k]`` must be even (this is
+      a convention assumed by the :func:`joint_degree_graph` function).
+
+
+    Parameters
+    ----------
+    joint_degrees :  dictionary of dictionary of integers
+        A joint degree dictionary in which entry ``joint_degrees[k][l]``
+        is the number of edges joining nodes of degree *k* with nodes of
+        degree *l*.
+
+    Returns
+    -------
+    bool
+        Whether the given joint degree dictionary is realizable as a
+        simple graph.
+
+    References
+    ----------
+    .. [1] M. Gjoka, M. Kurant, A. Markopoulou, "2.5K Graphs: from Sampling
+       to Generation", IEEE Infocom, 2013.
+    .. [2] I. Stanton, A. Pinar, "Constructing and sampling graphs with a
+       prescribed joint degree distribution", Journal of Experimental
+       Algorithmics, 2012.
+    """
+
+    degree_count = {}
+    for k in joint_degrees:
+        if k > 0:
+            k_size = sum(joint_degrees[k].values()) / k
+            if not k_size.is_integer():
+                return False
+            degree_count[k] = k_size
+
+    for k in joint_degrees:
+        for l in joint_degrees[k]:
+            if not float(joint_degrees[k][l]).is_integer():
+                return False
+
+            if (k != l) and (joint_degrees[k][l] > degree_count[k] * degree_count[l]):
+                return False
+            elif k == l:
+                if joint_degrees[k][k] > degree_count[k] * (degree_count[k] - 1):
+                    return False
+                if joint_degrees[k][k] % 2 != 0:
+                    return False
+
+    # if all above conditions have been satisfied then the input
+    # joint degree is realizable as a simple graph.
+    return True
+
+
+def _neighbor_switch(G, w, unsat, h_node_residual, avoid_node_id=None):
+    """ Releases one free stub for ``w``, while preserving joint degree in G.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        Graph in which the neighbor switch will take place.
+    w : integer
+        Node id for which we will execute this neighbor switch.
+    unsat : set of integers
+        Set of unsaturated node ids that have the same degree as w.
+    h_node_residual: dictionary of integers
+        Keeps track of the remaining stubs  for a given node.
+    avoid_node_id: integer
+        Node id to avoid when selecting w_prime.
+
+    Notes
+    -----
+    First, it selects *w_prime*, an  unsaturated node that has the same degree
+    as ``w``. Second, it selects *switch_node*, a neighbor node of ``w`` that
+    is not  connected to *w_prime*. Then it executes an edge swap i.e. removes
+    (``w``,*switch_node*) and adds (*w_prime*,*switch_node*). Gjoka et. al. [1]
+    prove that such an edge swap is always possible.
+
+    References
+    ----------
+    .. [1] M. Gjoka, B. Tillman, A. Markopoulou, "Construction of Simple
+       Graphs with a Target Joint Degree Matrix and Beyond", IEEE Infocom, '15
+    """
+
+    if (avoid_node_id is None) or (h_node_residual[avoid_node_id] > 1):
+        # select unsatured node w_prime that has the same degree as w
+        w_prime = next(iter(unsat))
+    else:
+        # assume that the node pair (v,w) has been selected for connection. if
+        # - neighbor_switch is called for node w,
+        # - nodes v and w have the same degree,
+        # - node v=avoid_node_id has only one stub left,
+        # then prevent v=avoid_node_id from being selected as w_prime.
+
+        iter_var = iter(unsat)
+        while True:
+            w_prime = next(iter_var)
+            if w_prime != avoid_node_id:
+                break
+
+    # select switch_node, a neighbor of w, that is not connected to w_prime
+    w_prime_neighbs = G[w_prime]  # slightly faster declaring this variable
+    for v in G[w]:
+        if (v not in w_prime_neighbs) and (v != w_prime):
+            switch_node = v
+            break
+
+    # remove edge (w,switch_node), add edge (w_prime,switch_node) and update
+    # data structures
+    G.remove_edge(w, switch_node)
+    G.add_edge(w_prime, switch_node)
+    h_node_residual[w] += 1
+    h_node_residual[w_prime] -= 1
+    if h_node_residual[w_prime] == 0:
+        unsat.remove(w_prime)
+
+
+@py_random_state(1)
+def joint_degree_graph(joint_degrees, seed=None):
+    """ Generates a random simple graph with the given joint degree dictionary.
+
+    Parameters
+    ----------
+    joint_degrees :  dictionary of dictionary of integers
+        A joint degree dictionary in which entry ``joint_degrees[k][l]`` is the
+        number of edges joining nodes of degree *k* with nodes of degree *l*.
+    seed : integer, random_state, or None (default)
+        Indicator of random number generation state.
+        See :ref:`Randomness<randomness>`.
+
+    Returns
+    -------
+    G : Graph
+        A graph with the specified joint degree dictionary.
+
+    Raises
+    ------
+    NetworkXError
+        If *joint_degrees* dictionary is not realizable.
+
+    Notes
+    -----
+    In each iteration of the "while loop" the algorithm picks two disconnected
+    nodes *v* and *w*, of degree *k* and *l* correspondingly,  for which
+    ``joint_degrees[k][l]`` has not reached its target yet. It then adds
+    edge (*v*, *w*) and increases the number of edges in graph G by one.
+
+    The intelligence of the algorithm lies in the fact that  it is always
+    possible to add an edge between such disconnected nodes *v* and *w*,
+    even if one or both nodes do not have free stubs. That is made possible by
+    executing a "neighbor switch", an edge rewiring move that releases
+    a free stub while keeping the joint degree of G the same.
+
+    The algorithm continues for E (number of edges) iterations of
+    the "while loop", at the which point all entries of the given
+    ``joint_degrees[k][l]`` have reached their target values and the
+    construction is complete.
+
+    References
+    ----------
+    ..  [1] M. Gjoka, B. Tillman, A. Markopoulou, "Construction of Simple
+        Graphs with a Target Joint Degree Matrix and Beyond", IEEE Infocom, '15
+
+    Examples
+    --------
+    >>> joint_degrees = {
+    ...     1: {4: 1},
+    ...     2: {2: 2, 3: 2, 4: 2},
+    ...     3: {2: 2, 4: 1},
+    ...     4: {1: 1, 2: 2, 3: 1},
+    ... }
+    >>> G = nx.joint_degree_graph(joint_degrees)
+    >>>
+    """
+
+    if not is_valid_joint_degree(joint_degrees):
+        msg = "Input joint degree dict not realizable as a simple graph"
+        raise nx.NetworkXError(msg)
+
+    # compute degree count from joint_degrees
+    degree_count = {k: sum(l.values()) // k for k, l in joint_degrees.items() if k > 0}
+
+    # start with empty N-node graph
+    N = sum(degree_count.values())
+    G = nx.empty_graph(N)
+
+    # for a given degree group, keep the list of all node ids
+    h_degree_nodelist = {}
+
+    # for a given node, keep track of the remaining stubs
+    h_node_residual = {}
+
+    # populate h_degree_nodelist and h_node_residual
+    nodeid = 0
+    for degree, num_nodes in degree_count.items():
+        h_degree_nodelist[degree] = range(nodeid, nodeid + num_nodes)
+        for v in h_degree_nodelist[degree]:
+            h_node_residual[v] = degree
+        nodeid += int(num_nodes)
+
+    # iterate over every degree pair (k,l) and add the number of edges given
+    # for each pair
+    for k in joint_degrees:
+        for l in joint_degrees[k]:
+
+            # n_edges_add is the number of edges to add for the
+            # degree pair (k,l)
+            n_edges_add = joint_degrees[k][l]
+
+            if (n_edges_add > 0) and (k >= l):
+
+                # number of nodes with degree k and l
+                k_size = degree_count[k]
+                l_size = degree_count[l]
+
+                # k_nodes and l_nodes consist of all nodes of degree k and l
+                k_nodes = h_degree_nodelist[k]
+                l_nodes = h_degree_nodelist[l]
+
+                # k_unsat and l_unsat consist of nodes of degree k and l that
+                # are unsaturated (nodes that have at least 1 available stub)
+                k_unsat = {v for v in k_nodes if h_node_residual[v] > 0}
+
+                if k != l:
+                    l_unsat = {w for w in l_nodes if h_node_residual[w] > 0}
+                else:
+                    l_unsat = k_unsat
+                    n_edges_add = joint_degrees[k][l] // 2
+
+                while n_edges_add > 0:
+
+                    # randomly pick nodes v and w that have degrees k and l
+                    v = k_nodes[seed.randrange(k_size)]
+                    w = l_nodes[seed.randrange(l_size)]
+
+                    # if nodes v and w are disconnected then attempt to connect
+                    if not G.has_edge(v, w) and (v != w):
+
+                        # if node v has no free stubs then do neighbor switch
+                        if h_node_residual[v] == 0:
+                            _neighbor_switch(G, v, k_unsat, h_node_residual)
+
+                        # if node w has no free stubs then do neighbor switch
+                        if h_node_residual[w] == 0:
+                            if k != l:
+                                _neighbor_switch(G, w, l_unsat, h_node_residual)
+                            else:
+                                _neighbor_switch(
+                                    G, w, l_unsat, h_node_residual, avoid_node_id=v
+                                )
+
+                        # add edge (v, w) and update data structures
+                        G.add_edge(v, w)
+                        h_node_residual[v] -= 1
+                        h_node_residual[w] -= 1
+                        n_edges_add -= 1
+
+                        if h_node_residual[v] == 0:
+                            k_unsat.discard(v)
+                        if h_node_residual[w] == 0:
+                            l_unsat.discard(w)
+    return G
+
+
+def is_valid_directed_joint_degree(in_degrees, out_degrees, nkk):
+    """ Checks whether the given directed joint degree input is realizable
+
+    Parameters
+    ----------
+    in_degrees :  list of integers
+        in degree sequence contains the in degrees of nodes.
+    out_degrees : list of integers
+        out degree sequence contains the out degrees of nodes.
+    nkk  :  dictionary of dictionary of integers
+        directed joint degree dictionary. for nodes of out degree k (first
+        level of dict) and nodes of in degree l (seconnd level of dict)
+        describes the number of edges.
+
+    Returns
+    -------
+    boolean
+        returns true if given input is realizable, else returns false.
+
+    Notes
+    -----
+    Here is the list of conditions that the inputs (in/out degree sequences,
+    nkk) need to satisfy for simple directed graph realizability:
+
+    - Condition 0: in_degrees and out_degrees have the same length
+    - Condition 1: nkk[k][l]  is integer for all k,l
+    - Condition 2: sum(nkk[k])/k = number of nodes with partition id k, is an
+                   integer and matching degree sequence
+    - Condition 3: number of edges and non-chords between k and l cannot exceed
+                   maximum possible number of edges
+
+
+    References
+    ----------
+    [1] B. Tillman, A. Markopoulou, C. T. Butts & M. Gjoka,
+        "Construction of Directed 2K Graphs". In Proc. of KDD 2017.
+    """
+    V = {}  # number of nodes with in/out degree.
+    forbidden = {}
+    if len(in_degrees) != len(out_degrees):
+        return False
+
+    for idx in range(0, len(in_degrees)):
+        i = in_degrees[idx]
+        o = out_degrees[idx]
+        V[(i, 0)] = V.get((i, 0), 0) + 1
+        V[(o, 1)] = V.get((o, 1), 0) + 1
+
+        forbidden[(o, i)] = forbidden.get((o, i), 0) + 1
+
+    S = {}  # number of edges going from in/out degree nodes.
+    for k in nkk:
+        for l in nkk[k]:
+            val = nkk[k][l]
+            if not float(val).is_integer():  # condition 1
+                return False
+
+            if val > 0:
+                S[(k, 1)] = S.get((k, 1), 0) + val
+                S[(l, 0)] = S.get((l, 0), 0) + val
+                # condition 3
+                if val + forbidden.get((k, l), 0) > V[(k, 1)] * V[(l, 0)]:
+                    return False
+
+    for s in S:
+        if not float(S[s]) / s[0] == V[s]:  # condition 2
+            return False
+
+    # if all conditions abive have been satisfied then the input nkk is
+    # realizable as a simple graph.
+    return True
+
+
+def _directed_neighbor_switch(
+    G, w, unsat, h_node_residual_out, chords, h_partition_in, partition
+):
+    """ Releases one free stub for node w, while preserving joint degree in G.
+
+    Parameters
+    ----------
+    G : networkx directed graph
+        graph within which the edge swap will take place.
+    w : integer
+        node id for which we need to perform a neighbor switch.
+    unsat: set of integers
+        set of node ids that have the same degree as w and are unsaturated.
+    h_node_residual_out: dict of integers
+        for a given node, keeps track of the remaining stubs to be added.
+    chords: set of tuples
+        keeps track of available positions to add edges.
+    h_partition_in: dict of integers
+        for a given node, keeps track of its partition id (in degree).
+    partition: integer
+        partition id to check if chords have to be updated.
+
+    Notes
+    -----
+    First, it selects node w_prime that (1) has the same degree as w and
+    (2) is unsaturated. Then, it selects node v, a neighbor of w, that is
+    not connected to w_prime and does an edge swap i.e. removes (w,v) and
+    adds (w_prime,v). If neighbor switch is not possible for w using
+    w_prime and v, then return w_prime; in [1] it's proven that
+    such unsaturated nodes can be used.
+
+    References
+    ----------
+    [1] B. Tillman, A. Markopoulou, C. T. Butts & M. Gjoka,
+        "Construction of Directed 2K Graphs". In Proc. of KDD 2017.
+    """
+    w_prime = unsat.pop()
+    unsat.add(w_prime)
+    # select node t, a neighbor of w, that is not connected to w_prime
+    w_neighbs = list(G.successors(w))
+    # slightly faster declaring this variable
+    w_prime_neighbs = list(G.successors(w_prime))
+
+    for v in w_neighbs:
+        if (v not in w_prime_neighbs) and w_prime != v:
+            # removes (w,v), add (w_prime,v)  and update data structures
+            G.remove_edge(w, v)
+            G.add_edge(w_prime, v)
+
+            if h_partition_in[v] == partition:
+                chords.add((w, v))
+                chords.discard((w_prime, v))
+
+            h_node_residual_out[w] += 1
+            h_node_residual_out[w_prime] -= 1
+            if h_node_residual_out[w_prime] == 0:
+                unsat.remove(w_prime)
+            return None
+
+    # If neighbor switch didn't work, use unsaturated node
+    return w_prime
+
+
+def _directed_neighbor_switch_rev(
+    G, w, unsat, h_node_residual_in, chords, h_partition_out, partition
+):
+    """ The reverse of directed_neighbor_switch.
+
+    Parameters
+    ----------
+    G : networkx directed graph
+        graph within which the edge swap will take place.
+    w : integer
+        node id for which we need to perform a neighbor switch.
+    unsat: set of integers
+        set of node ids that have the same degree as w and are unsaturated.
+    h_node_residual_in: dict of integers
+        for a given node, keeps track of the remaining stubs to be added.
+    chords: set of tuples
+        keeps track of available positions to add edges.
+    h_partition_out: dict of integers
+        for a given node, keeps track of its partition id (out degree).
+    partition: integer
+        partition id to check if chords have to be updated.
+
+    Notes
+    -----
+    Same operation as directed_neighbor_switch except it handles this operation
+    for incoming edges instead of outgoing.
+    """
+    w_prime = unsat.pop()
+    unsat.add(w_prime)
+    # slightly faster declaring these as variables.
+    w_neighbs = list(G.predecessors(w))
+    w_prime_neighbs = list(G.predecessors(w_prime))
+    # select node v, a neighbor of w, that is not connected to w_prime.
+    for v in w_neighbs:
+        if (v not in w_prime_neighbs) and w_prime != v:
+            # removes (v,w), add (v,w_prime) and update data structures.
+            G.remove_edge(v, w)
+            G.add_edge(v, w_prime)
+            if h_partition_out[v] == partition:
+                chords.add((v, w))
+                chords.discard((v, w_prime))
+
+            h_node_residual_in[w] += 1
+            h_node_residual_in[w_prime] -= 1
+            if h_node_residual_in[w_prime] == 0:
+                unsat.remove(w_prime)
+            return None
+
+    # If neighbor switch didn't work, use the unsaturated node.
+    return w_prime
+
+
+@py_random_state(3)
+def directed_joint_degree_graph(in_degrees, out_degrees, nkk, seed=None):
+    """ Generates a random simple directed graph with the joint degree.
+
+    Parameters
+    ----------
+    degree_seq :  list of tuples (of size 3)
+        degree sequence contains tuples of nodes with node id, in degree and
+        out degree.
+    nkk  :  dictionary of dictionary of integers
+        directed joint degree dictionary, for nodes of out degree k (first
+        level of dict) and nodes of in degree l (second level of dict)
+        describes the number of edges.
+    seed : hashable object, optional
+        Seed for random number generator.
+
+    Returns
+    -------
+    G : Graph
+        A directed graph with the specified inputs.
+
+    Raises
+    ------
+    NetworkXError
+        If degree_seq and nkk are not realizable as a simple directed graph.
+
+
+    Notes
+    -----
+    Similarly to the undirected version:
+    In each iteration of the "while loop" the algorithm picks two disconnected
+    nodes v and w, of degree k and l correspondingly,  for which nkk[k][l] has
+    not reached its target yet i.e. (for given k,l): n_edges_add < nkk[k][l].
+    It then adds edge (v,w) and always increases the number of edges in graph G
+    by one.
+
+    The intelligence of the algorithm lies in the fact that  it is always
+    possible to add an edge between disconnected nodes v and w, for which
+    nkk[degree(v)][degree(w)] has not reached its target, even if one or both
+    nodes do not have free stubs. If either node v or w does not have a free
+    stub, we perform a "neighbor switch", an edge rewiring move that releases a
+    free stub while keeping nkk the same.
+
+    The difference for the directed version lies in the fact that neighbor
+    switches might not be able to rewire, but in these cases unsaturated nodes
+    can be reassigned to use instead, see [1] for detailed description and
+    proofs.
+
+    The algorithm continues for E (number of edges in the graph) iterations of
+    the "while loop", at which point all entries of the given nkk[k][l] have
+    reached their target values and the construction is complete.
+
+    References
+    ----------
+    [1] B. Tillman, A. Markopoulou, C. T. Butts & M. Gjoka,
+        "Construction of Directed 2K Graphs". In Proc. of KDD 2017.
+
+    Examples
+    --------
+    >>> in_degrees = [0, 1, 1, 2]
+    >>> out_degrees = [1, 1, 1, 1]
+    >>> nkk = {1: {1: 2, 2: 2}}
+    >>> G = nx.directed_joint_degree_graph(in_degrees, out_degrees, nkk)
+    >>>
+    """
+    if not is_valid_directed_joint_degree(in_degrees, out_degrees, nkk):
+        msg = "Input is not realizable as a simple graph"
+        raise nx.NetworkXError(msg)
+
+    # start with an empty directed graph.
+    G = nx.DiGraph()
+
+    # for a given group, keep the list of all node ids.
+    h_degree_nodelist_in = {}
+    h_degree_nodelist_out = {}
+    # for a given group, keep the list of all unsaturated node ids.
+    h_degree_nodelist_in_unsat = {}
+    h_degree_nodelist_out_unsat = {}
+    # for a given node, keep track of the remaining stubs to be added.
+    h_node_residual_out = {}
+    h_node_residual_in = {}
+    # for a given node, keep track of the partition id.
+    h_partition_out = {}
+    h_partition_in = {}
+    # keep track of non-chords between pairs of partition ids.
+    non_chords = {}
+
+    # populate data structures
+    for idx, i in enumerate(in_degrees):
+        idx = int(idx)
+        if i > 0:
+            h_degree_nodelist_in.setdefault(i, [])
+            h_degree_nodelist_in_unsat.setdefault(i, set())
+            h_degree_nodelist_in[i].append(idx)
+            h_degree_nodelist_in_unsat[i].add(idx)
+            h_node_residual_in[idx] = i
+            h_partition_in[idx] = i
+
+    for idx, o in enumerate(out_degrees):
+        o = out_degrees[idx]
+        non_chords[(o, in_degrees[idx])] = non_chords.get((o, in_degrees[idx]), 0) + 1
+        idx = int(idx)
+        if o > 0:
+            h_degree_nodelist_out.setdefault(o, [])
+            h_degree_nodelist_out_unsat.setdefault(o, set())
+            h_degree_nodelist_out[o].append(idx)
+            h_degree_nodelist_out_unsat[o].add(idx)
+            h_node_residual_out[idx] = o
+            h_partition_out[idx] = o
+
+        G.add_node(idx)
+
+    nk_in = {}
+    nk_out = {}
+    for p in h_degree_nodelist_in:
+        nk_in[p] = len(h_degree_nodelist_in[p])
+    for p in h_degree_nodelist_out:
+        nk_out[p] = len(h_degree_nodelist_out[p])
+
+    # iterate over every degree pair (k,l) and add the number of edges given
+    # for each pair.
+    for k in nkk:
+        for l in nkk[k]:
+            n_edges_add = nkk[k][l]
+
+            if n_edges_add > 0:
+                # chords contains a random set of potential edges.
+                chords = set()
+
+                k_len = nk_out[k]
+                l_len = nk_in[l]
+                chords_sample = seed.sample(
+                    range(k_len * l_len), n_edges_add + non_chords.get((k, l), 0)
+                )
+
+                num = 0
+                while len(chords) < n_edges_add:
+                    i = h_degree_nodelist_out[k][chords_sample[num] % k_len]
+                    j = h_degree_nodelist_in[l][chords_sample[num] // k_len]
+                    num += 1
+                    if i != j:
+                        chords.add((i, j))
+
+                # k_unsat and l_unsat consist of nodes of in/out degree k and l
+                # that are unsaturated i.e. those nodes that have at least one
+                # available stub
+                k_unsat = h_degree_nodelist_out_unsat[k]
+                l_unsat = h_degree_nodelist_in_unsat[l]
+
+                while n_edges_add > 0:
+                    v, w = chords.pop()
+                    chords.add((v, w))
+
+                    # if node v has no free stubs then do neighbor switch.
+                    if h_node_residual_out[v] == 0:
+                        _v = _directed_neighbor_switch(
+                            G,
+                            v,
+                            k_unsat,
+                            h_node_residual_out,
+                            chords,
+                            h_partition_in,
+                            l,
+                        )
+                        if _v is not None:
+                            v = _v
+
+                    # if node w has no free stubs then do neighbor switch.
+                    if h_node_residual_in[w] == 0:
+                        _w = _directed_neighbor_switch_rev(
+                            G,
+                            w,
+                            l_unsat,
+                            h_node_residual_in,
+                            chords,
+                            h_partition_out,
+                            k,
+                        )
+                        if _w is not None:
+                            w = _w
+
+                    # add edge (v,w) and update data structures.
+                    G.add_edge(v, w)
+                    h_node_residual_out[v] -= 1
+                    h_node_residual_in[w] -= 1
+                    n_edges_add -= 1
+                    chords.discard((v, w))
+
+                    if h_node_residual_out[v] == 0:
+                        k_unsat.discard(v)
+                    if h_node_residual_in[w] == 0:
+                        l_unsat.discard(w)
+    return G