okstra 0.130.4 → 0.131.1

package/runtime/python/okstra_vendor/networkx/linalg/algebraicconnectivity.py

@@ -1,650 +0,0 @@
-"""
-Algebraic connectivity and Fiedler vectors of undirected graphs.
-"""
-
-import networkx as nx
-from networkx.utils import (
-    not_implemented_for,
-    np_random_state,
-    reverse_cuthill_mckee_ordering,
-)
-
-__all__ = [
-    "algebraic_connectivity",
-    "fiedler_vector",
-    "spectral_ordering",
-    "spectral_bisection",
-]
-
-
-class _PCGSolver:
-    """Preconditioned conjugate gradient method.
-
-    To solve Ax = b:
-        M = A.diagonal() # or some other preconditioner
-        solver = _PCGSolver(lambda x: A * x, lambda x: M * x)
-        x = solver.solve(b)
-
-    The inputs A and M are functions which compute
-    matrix multiplication on the argument.
-    A - multiply by the matrix A in Ax=b
-    M - multiply by M, the preconditioner surrogate for A
-
-    Warning: There is no limit on number of iterations.
-    """
-
-    def __init__(self, A, M):
-        self._A = A
-        self._M = M
-
-    def solve(self, B, tol):
-        import numpy as np
-
-        # Densifying step - can this be kept sparse?
-        B = np.asarray(B)
-        X = np.ndarray(B.shape, order="F")
-        for j in range(B.shape[1]):
-            X[:, j] = self._solve(B[:, j], tol)
-        return X
-
-    def _solve(self, b, tol):
-        import numpy as np
-        import scipy as sp
-
-        A = self._A
-        M = self._M
-        tol *= sp.linalg.blas.dasum(b)
-        # Initialize.
-        x = np.zeros(b.shape)
-        r = b.copy()
-        z = M(r)
-        rz = sp.linalg.blas.ddot(r, z)
-        p = z.copy()
-        # Iterate.
-        while True:
-            Ap = A(p)
-            alpha = rz / sp.linalg.blas.ddot(p, Ap)
-            x = sp.linalg.blas.daxpy(p, x, a=alpha)
-            r = sp.linalg.blas.daxpy(Ap, r, a=-alpha)
-            if sp.linalg.blas.dasum(r) < tol:
-                return x
-            z = M(r)
-            beta = sp.linalg.blas.ddot(r, z)
-            beta, rz = beta / rz, beta
-            p = sp.linalg.blas.daxpy(p, z, a=beta)
-
-
-class _LUSolver:
-    """LU factorization.
-
-    To solve Ax = b:
-        solver = _LUSolver(A)
-        x = solver.solve(b)
-
-    optional argument `tol` on solve method is ignored but included
-    to match _PCGsolver API.
-    """
-
-    def __init__(self, A):
-        import scipy as sp
-
-        self._LU = sp.sparse.linalg.splu(
-            A,
-            permc_spec="MMD_AT_PLUS_A",
-            diag_pivot_thresh=0.0,
-            options={"Equil": True, "SymmetricMode": True},
-        )
-
-    def solve(self, B, tol=None):
-        import numpy as np
-
-        B = np.asarray(B)
-        X = np.ndarray(B.shape, order="F")
-        for j in range(B.shape[1]):
-            X[:, j] = self._LU.solve(B[:, j])
-        return X
-
-
-def _preprocess_graph(G, weight):
-    """Compute edge weights and eliminate zero-weight edges."""
-    if G.is_directed():
-        H = nx.MultiGraph()
-        H.add_nodes_from(G)
-        H.add_weighted_edges_from(
-            ((u, v, e.get(weight, 1.0)) for u, v, e in G.edges(data=True) if u != v),
-            weight=weight,
-        )
-        G = H
-    if not G.is_multigraph():
-        edges = (
-            (u, v, abs(e.get(weight, 1.0))) for u, v, e in G.edges(data=True) if u != v
-        )
-    else:
-        edges = (
-            (u, v, sum(abs(e.get(weight, 1.0)) for e in G[u][v].values()))
-            for u, v in G.edges()
-            if u != v
-        )
-    H = nx.Graph()
-    H.add_nodes_from(G)
-    H.add_weighted_edges_from((u, v, e) for u, v, e in edges if e != 0)
-    return H
-
-
-def _rcm_estimate(G, nodelist):
-    """Estimate the Fiedler vector using the reverse Cuthill-McKee ordering."""
-    import numpy as np
-
-    G = G.subgraph(nodelist)
-    order = reverse_cuthill_mckee_ordering(G)
-    n = len(nodelist)
-    index = dict(zip(nodelist, range(n)))
-    x = np.ndarray(n, dtype=float)
-    for i, u in enumerate(order):
-        x[index[u]] = i
-    x -= (n - 1) / 2.0
-    return x
-
-
-def _tracemin_fiedler(L, X, normalized, tol, method):
-    """Compute the Fiedler vector of L using the TraceMIN-Fiedler algorithm.
-
-    The Fiedler vector of a connected undirected graph is the eigenvector
-    corresponding to the second smallest eigenvalue of the Laplacian matrix
-    of the graph. This function starts with the Laplacian L, not the Graph.
-
-    Parameters
-    ----------
-    L : Laplacian of a possibly weighted or normalized, but undirected graph
-
-    X : Initial guess for a solution. Usually a matrix of random numbers.
-        This function allows more than one column in X to identify more than
-        one eigenvector if desired.
-
-    normalized : bool
-        Whether the normalized Laplacian matrix is used.
-
-    tol : float
-        Tolerance of relative residual in eigenvalue computation.
-        Warning: There is no limit on number of iterations.
-
-    method : string
-        Should be 'tracemin_pcg' or 'tracemin_lu'.
-        Otherwise exception is raised.
-
-    Returns
-    -------
-    sigma, X : Two NumPy arrays of floats.
-        The lowest eigenvalues and corresponding eigenvectors of L.
-        The size of input X determines the size of these outputs.
-        As this is for Fiedler vectors, the zero eigenvalue (and
-        constant eigenvector) are avoided.
-    """
-    import numpy as np
-    import scipy as sp
-
-    n = X.shape[0]
-
-    if normalized:
-        # Form the normalized Laplacian matrix and determine the eigenvector of
-        # its nullspace.
-        e = np.sqrt(L.diagonal())
-        D = sp.sparse.dia_array((1 / e, 0), shape=(n, n)).tocsr()
-        L = D @ L @ D
-        e *= 1.0 / np.linalg.norm(e, 2)
-
-    if normalized:
-
-        def project(X):
-            """Make X orthogonal to the nullspace of L."""
-            X = np.asarray(X)
-            for j in range(X.shape[1]):
-                X[:, j] -= (X[:, j] @ e) * e
-
-    else:
-
-        def project(X):
-            """Make X orthogonal to the nullspace of L."""
-            X = np.asarray(X)
-            for j in range(X.shape[1]):
-                X[:, j] -= X[:, j].sum() / n
-
-    if method == "tracemin_pcg":
-        D = L.diagonal().astype(float)
-        solver = _PCGSolver(lambda x: L @ x, lambda x: D * x)
-    elif method == "tracemin_lu":
-        # Convert A to CSC to suppress SparseEfficiencyWarning.
-        A = sp.sparse.csc_array(L, dtype=float, copy=True)
-        # Force A to be nonsingular. Since A is the Laplacian matrix of a
-        # connected graph, its rank deficiency is one, and thus one diagonal
-        # element needs to modified. Changing to infinity forces a zero in the
-        # corresponding element in the solution.
-        i = (A.indptr[1:] - A.indptr[:-1]).argmax()
-        A[i, i] = np.inf
-        solver = _LUSolver(A)
-    else:
-        raise nx.NetworkXError(f"Unknown linear system solver: {method}")
-
-    # Initialize.
-    Lnorm = abs(L).sum(axis=1).flatten().max()
-    project(X)
-    W = np.ndarray(X.shape, order="F")
-
-    while True:
-        # Orthonormalize X.
-        X = np.linalg.qr(X)[0]
-        # Compute iteration matrix H.
-        W[:, :] = L @ X
-        H = X.T @ W
-        sigma, Y = sp.linalg.eigh(H, overwrite_a=True)
-        # Compute the Ritz vectors.
-        X = X @ Y
-        # Test for convergence exploiting the fact that L * X == W * Y.
-        res = sp.linalg.blas.dasum(W @ Y[:, 0] - sigma[0] * X[:, 0]) / Lnorm
-        if res < tol:
-            break
-        # Compute X = L \ X / (X' * (L \ X)).
-        # L \ X can have an arbitrary projection on the nullspace of L,
-        # which will be eliminated.
-        W[:, :] = solver.solve(X, tol)
-        X = (sp.linalg.inv(W.T @ X) @ W.T).T  # Preserves Fortran storage order.
-        project(X)
-
-    return sigma, np.asarray(X)
-
-
-def _get_fiedler_func(method):
-    """Returns a function that solves the Fiedler eigenvalue problem."""
-    import numpy as np
-
-    if method == "tracemin":  # old style keyword <v2.1
-        method = "tracemin_pcg"
-    if method in ("tracemin_pcg", "tracemin_lu"):
-
-        def find_fiedler(L, x, normalized, tol, seed):
-            q = 1 if method == "tracemin_pcg" else min(4, L.shape[0] - 1)
-            X = np.asarray(seed.normal(size=(q, L.shape[0]))).T
-            sigma, X = _tracemin_fiedler(L, X, normalized, tol, method)
-            return sigma[0], X[:, 0]
-
-    elif method == "lanczos" or method == "lobpcg":
-
-        def find_fiedler(L, x, normalized, tol, seed):
-            import scipy as sp
-
-            L = sp.sparse.csc_array(L, dtype=float)
-            n = L.shape[0]
-            if normalized:
-                D = sp.sparse.dia_array(
-                    (1.0 / np.sqrt(L.diagonal()), 0), shape=(n, n)
-                ).tocsc()
-                L = D @ L @ D
-            if method == "lanczos" or n < 10:
-                # Avoid LOBPCG when n < 10 due to
-                # https://github.com/scipy/scipy/issues/3592
-                # https://github.com/scipy/scipy/pull/3594
-                sigma, X = sp.sparse.linalg.eigsh(
-                    L, 2, which="SM", tol=tol, return_eigenvectors=True
-                )
-                return sigma[1], X[:, 1]
-            else:
-                X = np.asarray(np.atleast_2d(x).T)
-                M = sp.sparse.dia_array((1.0 / L.diagonal(), 0), shape=(n, n)).tocsr()
-                Y = np.ones(n)
-                if normalized:
-                    Y /= D.diagonal()
-                sigma, X = sp.sparse.linalg.lobpcg(
-                    L, X, M=M, Y=np.atleast_2d(Y).T, tol=tol, maxiter=n, largest=False
-                )
-                return sigma[0], X[:, 0]
-
-    else:
-        raise nx.NetworkXError(f"unknown method {method!r}.")
-
-    return find_fiedler
-
-
-@not_implemented_for("directed")
-@np_random_state(5)
-@nx._dispatchable(edge_attrs="weight")
-def algebraic_connectivity(
-    G, weight="weight", normalized=False, tol=1e-8, method="tracemin_pcg", seed=None
-):
-    r"""Returns the algebraic connectivity of an undirected graph.
-
-    The algebraic connectivity of a connected undirected graph is the second
-    smallest eigenvalue of its Laplacian matrix.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-        An undirected graph.
-
-    weight : object, optional (default: None)
-        The data key used to determine the weight of each edge. If None, then
-        each edge has unit weight.
-
-    normalized : bool, optional (default: False)
-        Whether the normalized Laplacian matrix is used.
-
-    tol : float, optional (default: 1e-8)
-        Tolerance of relative residual in eigenvalue computation.
-
-    method : string, optional (default: 'tracemin_pcg')
-        Method of eigenvalue computation. It must be one of the tracemin
-        options shown below (TraceMIN), 'lanczos' (Lanczos iteration)
-        or 'lobpcg' (LOBPCG).
-
-        The TraceMIN algorithm uses a linear system solver. The following
-        values allow specifying the solver to be used.
-
-        =============== ========================================
-        Value           Solver
-        =============== ========================================
-        'tracemin_pcg'  Preconditioned conjugate gradient method
-        'tracemin_lu'   LU factorization
-        =============== ========================================
-
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state.
-        See :ref:`Randomness<randomness>`.
-
-    Returns
-    -------
-    algebraic_connectivity : float
-        Algebraic connectivity.
-
-    Raises
-    ------
-    NetworkXNotImplemented
-        If G is directed.
-
-    NetworkXError
-        If G has less than two nodes.
-
-    Notes
-    -----
-    Edge weights are interpreted by their absolute values. For MultiGraph's,
-    weights of parallel edges are summed. Zero-weighted edges are ignored.
-
-    See Also
-    --------
-    laplacian_matrix
-
-    Examples
-    --------
-    For undirected graphs algebraic connectivity can tell us if a graph is connected or not
-    `G` is connected iff  ``algebraic_connectivity(G) > 0``:
-
-    >>> G = nx.complete_graph(5)
-    >>> nx.algebraic_connectivity(G) > 0
-    True
-    >>> G.add_node(10)  # G is no longer connected
-    >>> nx.algebraic_connectivity(G) > 0
-    False
-
-    """
-    if len(G) < 2:
-        raise nx.NetworkXError("graph has less than two nodes.")
-    G = _preprocess_graph(G, weight)
-    if not nx.is_connected(G):
-        return 0.0
-
-    L = nx.laplacian_matrix(G)
-    if L.shape[0] == 2:
-        return 2.0 * float(L[0, 0]) if not normalized else 2.0
-
-    find_fiedler = _get_fiedler_func(method)
-    x = None if method != "lobpcg" else _rcm_estimate(G, G)
-    sigma, fiedler = find_fiedler(L, x, normalized, tol, seed)
-    return float(sigma)
-
-
-@not_implemented_for("directed")
-@np_random_state(5)
-@nx._dispatchable(edge_attrs="weight")
-def fiedler_vector(
-    G, weight="weight", normalized=False, tol=1e-8, method="tracemin_pcg", seed=None
-):
-    """Returns the Fiedler vector of a connected undirected graph.
-
-    The Fiedler vector of a connected undirected graph is the eigenvector
-    corresponding to the second smallest eigenvalue of the Laplacian matrix
-    of the graph.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-        An undirected graph.
-
-    weight : object, optional (default: None)
-        The data key used to determine the weight of each edge. If None, then
-        each edge has unit weight.
-
-    normalized : bool, optional (default: False)
-        Whether the normalized Laplacian matrix is used.
-
-    tol : float, optional (default: 1e-8)
-        Tolerance of relative residual in eigenvalue computation.
-
-    method : string, optional (default: 'tracemin_pcg')
-        Method of eigenvalue computation. It must be one of the tracemin
-        options shown below (TraceMIN), 'lanczos' (Lanczos iteration)
-        or 'lobpcg' (LOBPCG).
-
-        The TraceMIN algorithm uses a linear system solver. The following
-        values allow specifying the solver to be used.
-
-        =============== ========================================
-        Value           Solver
-        =============== ========================================
-        'tracemin_pcg'  Preconditioned conjugate gradient method
-        'tracemin_lu'   LU factorization
-        =============== ========================================
-
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state.
-        See :ref:`Randomness<randomness>`.
-
-    Returns
-    -------
-    fiedler_vector : NumPy array of floats.
-        Fiedler vector.
-
-    Raises
-    ------
-    NetworkXNotImplemented
-        If G is directed.
-
-    NetworkXError
-        If G has less than two nodes or is not connected.
-
-    Notes
-    -----
-    Edge weights are interpreted by their absolute values. For MultiGraph's,
-    weights of parallel edges are summed. Zero-weighted edges are ignored.
-
-    See Also
-    --------
-    laplacian_matrix
-
-    Examples
-    --------
-    Given a connected graph the signs of the values in the Fiedler vector can be
-    used to partition the graph into two components.
-
-    >>> G = nx.barbell_graph(5, 0)
-    >>> nx.fiedler_vector(G, normalized=True, seed=1)
-    array([-0.32864129, -0.32864129, -0.32864129, -0.32864129, -0.26072899,
-            0.26072899,  0.32864129,  0.32864129,  0.32864129,  0.32864129])
-
-    The connected components are the two 5-node cliques of the barbell graph.
-    """
-    import numpy as np
-
-    if len(G) < 2:
-        raise nx.NetworkXError("graph has less than two nodes.")
-    G = _preprocess_graph(G, weight)
-    if not nx.is_connected(G):
-        raise nx.NetworkXError("graph is not connected.")
-
-    if len(G) == 2:
-        return np.array([1.0, -1.0])
-
-    find_fiedler = _get_fiedler_func(method)
-    L = nx.laplacian_matrix(G)
-    x = None if method != "lobpcg" else _rcm_estimate(G, G)
-    sigma, fiedler = find_fiedler(L, x, normalized, tol, seed)
-    return fiedler
-
-
-@np_random_state(5)
-@nx._dispatchable(edge_attrs="weight")
-def spectral_ordering(
-    G, weight="weight", normalized=False, tol=1e-8, method="tracemin_pcg", seed=None
-):
-    """Compute the spectral_ordering of a graph.
-
-    The spectral ordering of a graph is an ordering of its nodes where nodes
-    in the same weakly connected components appear contiguous and ordered by
-    their corresponding elements in the Fiedler vector of the component.
-
-    Parameters
-    ----------
-    G : NetworkX graph
-        A graph.
-
-    weight : object, optional (default: None)
-        The data key used to determine the weight of each edge. If None, then
-        each edge has unit weight.
-
-    normalized : bool, optional (default: False)
-        Whether the normalized Laplacian matrix is used.
-
-    tol : float, optional (default: 1e-8)
-        Tolerance of relative residual in eigenvalue computation.
-
-    method : string, optional (default: 'tracemin_pcg')
-        Method of eigenvalue computation. It must be one of the tracemin
-        options shown below (TraceMIN), 'lanczos' (Lanczos iteration)
-        or 'lobpcg' (LOBPCG).
-
-        The TraceMIN algorithm uses a linear system solver. The following
-        values allow specifying the solver to be used.
-
-        =============== ========================================
-        Value           Solver
-        =============== ========================================
-        'tracemin_pcg'  Preconditioned conjugate gradient method
-        'tracemin_lu'   LU factorization
-        =============== ========================================
-
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state.
-        See :ref:`Randomness<randomness>`.
-
-    Returns
-    -------
-    spectral_ordering : NumPy array of floats.
-        Spectral ordering of nodes.
-
-    Raises
-    ------
-    NetworkXError
-        If G is empty.
-
-    Notes
-    -----
-    Edge weights are interpreted by their absolute values. For MultiGraph's,
-    weights of parallel edges are summed. Zero-weighted edges are ignored.
-
-    See Also
-    --------
-    laplacian_matrix
-    """
-    if len(G) == 0:
-        raise nx.NetworkXError("graph is empty.")
-    G = _preprocess_graph(G, weight)
-
-    find_fiedler = _get_fiedler_func(method)
-    order = []
-    for component in nx.connected_components(G):
-        size = len(component)
-        if size > 2:
-            L = nx.laplacian_matrix(G, component)
-            x = None if method != "lobpcg" else _rcm_estimate(G, component)
-            sigma, fiedler = find_fiedler(L, x, normalized, tol, seed)
-            sort_info = zip(fiedler, range(size), component)
-            order.extend(u for x, c, u in sorted(sort_info))
-        else:
-            order.extend(component)
-
-    return order
-
-
-@nx._dispatchable(edge_attrs="weight")
-def spectral_bisection(
-    G, weight="weight", normalized=False, tol=1e-8, method="tracemin_pcg", seed=None
-):
-    """Bisect the graph using the Fiedler vector.
-
-    This method uses the Fiedler vector to bisect a graph.
-    The partition is defined by the nodes which are associated with
-    either positive or negative values in the vector.
-
-    Parameters
-    ----------
-    G : NetworkX Graph
-
-    weight : str, optional (default: weight)
-        The data key used to determine the weight of each edge. If None, then
-        each edge has unit weight.
-
-    normalized : bool, optional (default: False)
-        Whether the normalized Laplacian matrix is used.
-
-    tol : float, optional (default: 1e-8)
-        Tolerance of relative residual in eigenvalue computation.
-
-    method : string, optional (default: 'tracemin_pcg')
-        Method of eigenvalue computation. It must be one of the tracemin
-        options shown below (TraceMIN), 'lanczos' (Lanczos iteration)
-        or 'lobpcg' (LOBPCG).
-
-        The TraceMIN algorithm uses a linear system solver. The following
-        values allow specifying the solver to be used.
-
-        =============== ========================================
-        Value           Solver
-        =============== ========================================
-        'tracemin_pcg'  Preconditioned conjugate gradient method
-        'tracemin_lu'   LU factorization
-        =============== ========================================
-
-    seed : integer, random_state, or None (default)
-        Indicator of random number generation state.
-        See :ref:`Randomness<randomness>`.
-
-    Returns
-    -------
-    bisection : tuple of sets
-        Sets with the bisection of nodes
-
-    Examples
-    --------
-    >>> G = nx.barbell_graph(3, 0)
-    >>> nx.spectral_bisection(G)
-    ({0, 1, 2}, {3, 4, 5})
-
-    References
-    ----------
-    .. [1] M. E. J Newman 'Networks: An Introduction', pages 364-370
-       Oxford University Press 2011.
-    """
-    import numpy as np
-
-    v = nx.fiedler_vector(G, weight, normalized, tol, method, seed)
-    nodes = np.array(list(G))
-    pos_vals = v >= 0
-
-    return set(nodes[~pos_vals].tolist()), set(nodes[pos_vals].tolist())