okstra 0.130.4 → 0.131.1

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

@@ -1,338 +0,0 @@
-"""
-Label propagation community detection algorithms.
-"""
-
-from collections import Counter, defaultdict, deque
-
-import networkx as nx
-from networkx.utils import groups, not_implemented_for, py_random_state
-
-__all__ = [
-    "label_propagation_communities",
-    "asyn_lpa_communities",
-    "fast_label_propagation_communities",
-]
-
-
-@py_random_state("seed")
-@nx._dispatchable(edge_attrs="weight")
-def fast_label_propagation_communities(G, *, weight=None, seed=None):
-    """Returns communities in `G` as detected by fast label propagation.
-
-    The fast label propagation algorithm is described in [1]_. The algorithm is
-    probabilistic and the found communities may vary in different executions.
-
-    The algorithm operates as follows. First, the community label of each node is
-    set to a unique label. The algorithm then repeatedly updates the labels of
-    the nodes to the most frequent label in their neighborhood. In case of ties,
-    a random label is chosen from the most frequent labels.
-
-    The algorithm maintains a queue of nodes that still need to be processed.
-    Initially, all nodes are added to the queue in a random order. Then the nodes
-    are removed from the queue one by one and processed. If a node updates its label,
-    all its neighbors that have a different label are added to the queue (if not
-    already in the queue). The algorithm stops when the queue is empty.
-
-    Parameters
-    ----------
-    G : Graph, DiGraph, MultiGraph, or MultiDiGraph
-        Any NetworkX graph.
-
-    weight : string, or None (default)
-        The edge attribute representing a non-negative weight of an edge. If None,
-        each edge is assumed to have weight one. The weight of an edge is used in
-        determining the frequency with which a label appears among the neighbors of
-        a node (edge with weight `w` is equivalent to `w` unweighted edges).
-
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state. See :ref:`Randomness<randomness>`.
-
-    Returns
-    -------
-    communities : iterable
-        Iterable of communities given as sets of nodes.
-
-    Notes
-    -----
-    Edge directions are ignored for directed graphs.
-    Edge weights must be non-negative numbers.
-
-    References
-    ----------
-    .. [1] Vincent A. Traag & Lovro Šubelj. "Large network community detection by
-       fast label propagation." Scientific Reports 13 (2023): 2701.
-       https://doi.org/10.1038/s41598-023-29610-z
-    """
-
-    # Queue of nodes to be processed.
-    nodes_queue = deque(G)
-    seed.shuffle(nodes_queue)
-
-    # Set of nodes in the queue.
-    nodes_set = set(G)
-
-    # Assign unique label to each node.
-    comms = {node: i for i, node in enumerate(G)}
-
-    while nodes_queue:
-        # Remove next node from the queue to process.
-        node = nodes_queue.popleft()
-        nodes_set.remove(node)
-
-        # Isolated nodes retain their initial label.
-        if G.degree(node) > 0:
-            # Compute frequency of labels in node's neighborhood.
-            label_freqs = _fast_label_count(G, comms, node, weight)
-            max_freq = max(label_freqs.values())
-
-            # Always sample new label from most frequent labels.
-            comm = seed.choice(
-                [comm for comm in label_freqs if label_freqs[comm] == max_freq]
-            )
-
-            if comms[node] != comm:
-                comms[node] = comm
-
-                # Add neighbors that have different label to the queue.
-                for nbr in nx.all_neighbors(G, node):
-                    if comms[nbr] != comm and nbr not in nodes_set:
-                        nodes_queue.append(nbr)
-                        nodes_set.add(nbr)
-
-    yield from groups(comms).values()
-
-
-def _fast_label_count(G, comms, node, weight=None):
-    """Computes the frequency of labels in the neighborhood of a node.
-
-    Returns a dictionary keyed by label to the frequency of that label.
-    """
-
-    if weight is None:
-        # Unweighted (un)directed simple graph.
-        if not G.is_multigraph():
-            label_freqs = Counter(map(comms.get, nx.all_neighbors(G, node)))
-
-        # Unweighted (un)directed multigraph.
-        else:
-            label_freqs = defaultdict(int)
-            for nbr in G[node]:
-                label_freqs[comms[nbr]] += len(G[node][nbr])
-
-            if G.is_directed():
-                for nbr in G.pred[node]:
-                    label_freqs[comms[nbr]] += len(G.pred[node][nbr])
-
-    else:
-        # Weighted undirected simple/multigraph.
-        label_freqs = defaultdict(float)
-        for _, nbr, w in G.edges(node, data=weight, default=1):
-            label_freqs[comms[nbr]] += w
-
-        # Weighted directed simple/multigraph.
-        if G.is_directed():
-            for nbr, _, w in G.in_edges(node, data=weight, default=1):
-                label_freqs[comms[nbr]] += w
-
-    return label_freqs
-
-
-@py_random_state(2)
-@nx._dispatchable(edge_attrs="weight")
-def asyn_lpa_communities(G, weight=None, seed=None):
-    """Returns communities in `G` as detected by asynchronous label
-    propagation.
-
-    The asynchronous label propagation algorithm is described in
-    [1]_. The algorithm is probabilistic and the found communities may
-    vary on different executions.
-
-    The algorithm proceeds as follows. After initializing each node with
-    a unique label, the algorithm repeatedly sets the label of a node to
-    be the label that appears most frequently among that nodes
-    neighbors. The algorithm halts when each node has the label that
-    appears most frequently among its neighbors. The algorithm is
-    asynchronous because each node is updated without waiting for
-    updates on the remaining nodes.
-
-    This generalized version of the algorithm in [1]_ accepts edge
-    weights.
-
-    Parameters
-    ----------
-    G : Graph
-
-    weight : string
-        The edge attribute representing the weight of an edge.
-        If None, each edge is assumed to have weight one. In this
-        algorithm, the weight of an edge is used in determining the
-        frequency with which a label appears among the neighbors of a
-        node: a higher weight means the label appears more often.
-
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state.
-        See :ref:`Randomness<randomness>`.
-
-    Returns
-    -------
-    communities : iterable
-        Iterable of communities given as sets of nodes.
-
-    Notes
-    -----
-    Edge weight attributes must be numerical.
-
-    References
-    ----------
-    .. [1] Raghavan, Usha Nandini, Réka Albert, and Soundar Kumara. "Near
-           linear time algorithm to detect community structures in large-scale
-           networks." Physical Review E 76.3 (2007): 036106.
-    """
-
-    labels = {n: i for i, n in enumerate(G)}
-    cont = True
-
-    while cont:
-        cont = False
-        nodes = list(G)
-        seed.shuffle(nodes)
-
-        for node in nodes:
-            if not G[node]:
-                continue
-
-            # Get label frequencies among adjacent nodes.
-            # Depending on the order they are processed in,
-            # some nodes will be in iteration t and others in t-1,
-            # making the algorithm asynchronous.
-            if weight is None:
-                # initialising a Counter from an iterator of labels is
-                # faster for getting unweighted label frequencies
-                label_freq = Counter(map(labels.get, G[node]))
-            else:
-                # updating a defaultdict is substantially faster
-                # for getting weighted label frequencies
-                label_freq = defaultdict(float)
-                for _, v, wt in G.edges(node, data=weight, default=1):
-                    label_freq[labels[v]] += wt
-
-            # Get the labels that appear with maximum frequency.
-            max_freq = max(label_freq.values())
-            best_labels = [
-                label for label, freq in label_freq.items() if freq == max_freq
-            ]
-
-            # If the node does not have one of the maximum frequency labels,
-            # randomly choose one of them and update the node's label.
-            # Continue the iteration as long as at least one node
-            # doesn't have a maximum frequency label.
-            if labels[node] not in best_labels:
-                labels[node] = seed.choice(best_labels)
-                cont = True
-
-    yield from groups(labels).values()
-
-
-@not_implemented_for("directed")
-@nx._dispatchable
-def label_propagation_communities(G):
-    """Generates community sets determined by label propagation
-
-    Finds communities in `G` using a semi-synchronous label propagation
-    method [1]_. This method combines the advantages of both the synchronous
-    and asynchronous models. Not implemented for directed graphs.
-
-    Parameters
-    ----------
-    G : graph
-        An undirected NetworkX graph.
-
-    Returns
-    -------
-    communities : iterable
-        A dict_values object that contains a set of nodes for each community.
-
-    Raises
-    ------
-    NetworkXNotImplemented
-       If the graph is directed
-
-    References
-    ----------
-    .. [1] Cordasco, G., & Gargano, L. (2010, December). Community detection
-       via semi-synchronous label propagation algorithms. In Business
-       Applications of Social Network Analysis (BASNA), 2010 IEEE International
-       Workshop on (pp. 1-8). IEEE.
-    """
-    coloring = _color_network(G)
-    # Create a unique label for each node in the graph
-    labeling = {v: k for k, v in enumerate(G)}
-    while not _labeling_complete(labeling, G):
-        # Update the labels of every node with the same color.
-        for color, nodes in coloring.items():
-            for n in nodes:
-                _update_label(n, labeling, G)
-
-    clusters = defaultdict(set)
-    for node, label in labeling.items():
-        clusters[label].add(node)
-    return clusters.values()
-
-
-def _color_network(G):
-    """Colors the network so that neighboring nodes all have distinct colors.
-
-    Returns a dict keyed by color to a set of nodes with that color.
-    """
-    coloring = {}  # color => set(node)
-    colors = nx.coloring.greedy_color(G)
-    for node, color in colors.items():
-        if color in coloring:
-            coloring[color].add(node)
-        else:
-            coloring[color] = {node}
-    return coloring
-
-
-def _labeling_complete(labeling, G):
-    """Determines whether or not LPA is done.
-
-    Label propagation is complete when all nodes have a label that is
-    in the set of highest frequency labels amongst its neighbors.
-
-    Nodes with no neighbors are considered complete.
-    """
-    return all(
-        labeling[v] in _most_frequent_labels(v, labeling, G) for v in G if len(G[v]) > 0
-    )
-
-
-def _most_frequent_labels(node, labeling, G):
-    """Returns a set of all labels with maximum frequency in `labeling`.
-
-    Input `labeling` should be a dict keyed by node to labels.
-    """
-    if not G[node]:
-        # Nodes with no neighbors are themselves a community and are labeled
-        # accordingly, hence the immediate if statement.
-        return {labeling[node]}
-
-    # Compute the frequencies of all neighbors of node
-    freqs = Counter(labeling[q] for q in G[node])
-    max_freq = max(freqs.values())
-    return {label for label, freq in freqs.items() if freq == max_freq}
-
-
-def _update_label(node, labeling, G):
-    """Updates the label of a node using the Prec-Max tie breaking algorithm
-
-    The algorithm is explained in: 'Community Detection via Semi-Synchronous
-    Label Propagation Algorithms' Cordasco and Gargano, 2011
-    """
-    high_labels = _most_frequent_labels(node, labeling, G)
-    if len(high_labels) == 1:
-        labeling[node] = high_labels.pop()
-    elif len(high_labels) > 1:
-        # Prec-Max
-        if labeling[node] not in high_labels:
-            labeling[node] = max(high_labels)

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

@@ -1,162 +0,0 @@
-"""Functions for detecting communities based on Leiden Community Detection
-algorithm.
-
-These functions do not have NetworkX implementations.
-They may only be run with an installable :doc:`backend </backends>`
-that supports them.
-"""
-
-import itertools
-from collections import deque
-
-import networkx as nx
-from networkx.utils import not_implemented_for, py_random_state
-
-__all__ = ["leiden_communities", "leiden_partitions"]
-
-
-@not_implemented_for("directed")
-@py_random_state("seed")
-@nx._dispatchable(edge_attrs="weight", implemented_by_nx=False)
-def leiden_communities(G, weight="weight", resolution=1, max_level=None, seed=None):
-    r"""Find a best partition of `G` using Leiden Community Detection (backend required)
-
-    Leiden Community Detection is an algorithm to extract the community structure
-    of a network based on modularity optimization. It is an improvement upon the
-    Louvain Community Detection algorithm. See :any:`louvain_communities`.
-
-    Unlike the Louvain algorithm, it guarantees that communities are well connected in addition
-    to being faster and uncovering better partitions. [1]_
-
-    The algorithm works in 3 phases. On the first phase, it adds the nodes to a queue randomly
-    and assigns every node to be in its own community. For each node it tries to find the
-    maximum positive modularity gain by moving each node to all of its neighbor communities.
-    If a node is moved from its community, it adds to the rear of the queue all neighbors of
-    the node that do not belong to the node’s new community and that are not in the queue.
-
-    The first phase continues until the queue is empty.
-
-    The second phase consists in refining the partition $P$ obtained from the first phase. It starts
-    with a singleton partition $P_{refined}$. Then it merges nodes locally in $P_{refined}$ within
-    each community of the partition $P$. Nodes are merged with a community in $P_{refined}$ only if
-    both are sufficiently well connected to their community in $P$. This means that after the
-    refinement phase is concluded, communities in $P$ sometimes will have been split into multiple
-    communities.
-
-    The third phase consists of aggregating the network by building a new network whose nodes are
-    now the communities found in the second phase. However, the non-refined partition is used to create
-    an initial partition for the aggregate network.
-
-    Once this phase is complete it is possible to reapply the first and second phases creating bigger
-    communities with increased modularity.
-
-    The above three phases are executed until no modularity gain is achieved or `max_level` number
-    of iterations have been performed.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-    weight : string or None, optional (default="weight")
-        The name of an edge attribute that holds the numerical value
-        used as a weight. If None then each edge has weight 1.
-    resolution : float, optional (default=1)
-        If resolution is less than 1, the algorithm favors larger communities.
-        Greater than 1 favors smaller communities.
-    max_level : int or None, optional (default=None)
-        The maximum number of levels (steps of the algorithm) to compute.
-        Must be a positive integer or None. If None, then there is no max
-        level and the algorithm will run until converged.
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state.
-        See :ref:`Randomness<randomness>`.
-
-    Returns
-    -------
-    list
-        A list of disjoint sets (partition of `G`). Each set represents one community.
-        All communities together contain all the nodes in `G`.
-
-    Examples
-    --------
-    >>> import networkx as nx
-    >>> G = nx.petersen_graph()
-    >>> nx.community.leiden_communities(G, backend="example_backend")  # doctest: +SKIP
-    [{2, 3, 5, 7, 8}, {0, 1, 4, 6, 9}]
-
-    Notes
-    -----
-    The order in which the nodes are considered can affect the final output. In the algorithm
-    the ordering happens using a random shuffle.
-
-    References
-    ----------
-    .. [1] Traag, V.A., Waltman, L. & van Eck, N.J. From Louvain to Leiden: guaranteeing
-       well-connected communities. Sci Rep 9, 5233 (2019). https://doi.org/10.1038/s41598-019-41695-z
-
-    See Also
-    --------
-    leiden_partitions
-    :any:`louvain_communities`
-    """
-    partitions = leiden_partitions(G, weight, resolution, seed)
-    if max_level is not None:
-        if max_level <= 0:
-            raise ValueError("max_level argument must be a positive integer or None")
-        partitions = itertools.islice(partitions, max_level)
-    final_partition = deque(partitions, maxlen=1)
-    return final_partition.pop()
-
-
-@not_implemented_for("directed")
-@py_random_state("seed")
-@nx._dispatchable(edge_attrs="weight", implemented_by_nx=False)
-def leiden_partitions(G, weight="weight", resolution=1, seed=None):
-    """Yield partitions for each level of Leiden Community Detection (backend required)
-
-    Leiden Community Detection is an algorithm to extract the community
-    structure of a network based on modularity optimization.
-
-    The partitions across levels (steps of the algorithm) form a dendrogram
-    of communities. A dendrogram is a diagram representing a tree and each
-    level represents a partition of the G graph. The top level contains the
-    smallest communities and as you traverse to the bottom of the tree the
-    communities get bigger and the overall modularity increases making
-    the partition better.
-
-    Each level is generated by executing the three phases of the Leiden Community
-    Detection algorithm. See :any:`leiden_communities`.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-    weight : string or None, optional (default="weight")
-        The name of an edge attribute that holds the numerical value
-        used as a weight. If None then each edge has weight 1.
-    resolution : float, optional (default=1)
-        If resolution is less than 1, the algorithm favors larger communities.
-        Greater than 1 favors smaller communities.
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state.
-        See :ref:`Randomness<randomness>`.
-
-    Yields
-    ------
-    list
-        A list of disjoint sets (partition of `G`). Each set represents one community.
-        All communities together contain all the nodes in `G`. The yielded partitions
-        increase modularity with each iteration.
-
-    References
-    ----------
-    .. [1] Traag, V.A., Waltman, L. & van Eck, N.J. From Louvain to Leiden: guaranteeing
-       well-connected communities. Sci Rep 9, 5233 (2019). https://doi.org/10.1038/s41598-019-41695-z
-
-    See Also
-    --------
-    leiden_communities
-    :any:`louvain_partitions`
-    """
-    raise NotImplementedError(
-        "'leiden_partitions' is not implemented by networkx. "
-        "Please try a different backend."
-    )