--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo/lib/python3.7/site-packages/networkx/linalg/algebraicconnectivity.py	Fri Jul 31 00:32:28 2020 -0400
@@ -0,0 +1,592 @@
+# -*- coding: utf-8 -*-
+# Copyright (C) 2014 ysitu <ysitu@users.noreply.github.com>
+# All rights reserved.
+# BSD license.
+#
+# Author: ysitu <ysitu@users.noreply.github.com>
+"""
+Algebraic connectivity and Fiedler vectors of undirected graphs.
+"""
+from functools import partial
+import networkx as nx
+from networkx.utils import not_implemented_for
+from networkx.utils import reverse_cuthill_mckee_ordering
+from networkx.utils import random_state
+
+try:
+    from numpy import array, asmatrix, asarray, dot, ndarray, ones, sqrt, zeros
+    from numpy.linalg import norm, qr
+    from numpy.random import normal
+    from scipy.linalg import eigh, inv
+    from scipy.sparse import csc_matrix, spdiags
+    from scipy.sparse.linalg import eigsh, lobpcg
+    __all__ = ['algebraic_connectivity', 'fiedler_vector', 'spectral_ordering']
+except ImportError:
+    __all__ = []
+
+try:
+    from scipy.linalg.blas import dasum, daxpy, ddot
+except ImportError:
+    if __all__:
+        # Make sure the imports succeeded.
+        # Use minimal replacements if BLAS is unavailable from SciPy.
+        dasum = partial(norm, ord=1)
+        ddot = dot
+
+        def daxpy(x, y, a):
+            y += a * x
+            return y
+
+
+class _PCGSolver(object):
+    """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 surragate for A
+
+    Warning: There is no limit on number of iterations.
+    """
+
+    def __init__(self, A, M):
+        self._A = A
+        self._M = M or (lambda x: x.copy())
+
+    def solve(self, B, tol):
+        B = asarray(B)
+        X = 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):
+        A = self._A
+        M = self._M
+        tol *= dasum(b)
+        # Initialize.
+        x = zeros(b.shape)
+        r = b.copy()
+        z = M(r)
+        rz = ddot(r, z)
+        p = z.copy()
+        # Iterate.
+        while True:
+            Ap = A(p)
+            alpha = rz / ddot(p, Ap)
+            x = daxpy(p, x, a=alpha)
+            r = daxpy(Ap, r, a=-alpha)
+            if dasum(r) < tol:
+                return x
+            z = M(r)
+            beta = ddot(r, z)
+            beta, rz = beta / rz, beta
+            p = daxpy(p, z, a=beta)
+
+
+class _CholeskySolver(object):
+    """Cholesky factorization.
+
+    To solve Ax = b:
+        solver = _CholeskySolver(A)
+        x = solver.solve(b)
+
+    optional argument `tol` on solve method is ignored but included
+    to match _PCGsolver API.
+    """
+
+    def __init__(self, A):
+        if not self._cholesky:
+            raise nx.NetworkXError('Cholesky solver unavailable.')
+        self._chol = self._cholesky(A)
+
+    def solve(self, B, tol=None):
+        return self._chol(B)
+
+    try:
+        from scikits.sparse.cholmod import cholesky
+        _cholesky = cholesky
+    except ImportError:
+        _cholesky = None
+
+
+class _LUSolver(object):
+    """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):
+        if not self._splu:
+            raise nx.NetworkXError('LU solver unavailable.')
+        self._LU = self._splu(A)
+
+    def solve(self, B, tol=None):
+        B = asarray(B)
+        X = ndarray(B.shape, order='F')
+        for j in range(B.shape[1]):
+            X[:, j] = self._LU.solve(B[:, j])
+        return X
+
+    try:
+        from scipy.sparse.linalg import splu
+        _splu = partial(splu, permc_spec='MMD_AT_PLUS_A', diag_pivot_thresh=0.,
+                        options={'Equil': True, 'SymmetricMode': True})
+    except ImportError:
+        _splu = None
+
+
+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.))
+                                   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.)))
+                 for u, v, e in G.edges(data=True) if u != v)
+    else:
+        edges = ((u, v, sum(abs(e.get(weight, 1.)) 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.
+    """
+    G = G.subgraph(nodelist)
+    order = reverse_cuthill_mckee_ordering(G)
+    n = len(nodelist)
+    index = dict(zip(nodelist, range(n)))
+    x = ndarray(n, dtype=float)
+    for i, u in enumerate(order):
+        x[index[u]] = i
+    x -= (n - 1) / 2.
+    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
+    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', 'tracemin_chol' 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.
+    """
+    n = X.shape[0]
+
+    if normalized:
+        # Form the normalized Laplacian matrix and determine the eigenvector of
+        # its nullspace.
+        e = sqrt(L.diagonal())
+        D = spdiags(1. / e, [0], n, n, format='csr')
+        L = D * L * D
+        e *= 1. / norm(e, 2)
+
+    if normalized:
+        def project(X):
+            """Make X orthogonal to the nullspace of L.
+            """
+            X = asarray(X)
+            for j in range(X.shape[1]):
+                X[:, j] -= dot(X[:, j], e) * e
+    else:
+        def project(X):
+            """Make X orthogonal to the nullspace of L.
+            """
+            X = 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_chol' or method == 'tracemin_lu':
+        # Convert A to CSC to suppress SparseEfficiencyWarning.
+        A = csc_matrix(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] = float('inf')
+        if method == 'tracemin_chol':
+            solver = _CholeskySolver(A)
+        else:
+            solver = _LUSolver(A)
+    else:
+        raise nx.NetworkXError('Unknown linear system solver: ' + method)
+
+    # Initialize.
+    Lnorm = abs(L).sum(axis=1).flatten().max()
+    project(X)
+    W = asmatrix(ndarray(X.shape, order='F'))
+
+    while True:
+        # Orthonormalize X.
+        X = qr(X)[0]
+        # Compute iteration matrix H.
+        W[:, :] = L * X
+        H = X.T * W
+        sigma, Y = eigh(H, overwrite_a=True)
+        # Compute the Ritz vectors.
+        X *= Y
+        # Test for convergence exploiting the fact that L * X == W * Y.
+        res = dasum(W * asmatrix(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 = (inv(W.T * X) * W.T).T  # Preserves Fortran storage order.
+        project(X)
+
+    return sigma, asarray(X)
+
+
+def _get_fiedler_func(method):
+    """Returns a function that solves the Fiedler eigenvalue problem.
+    """
+    if method == "tracemin":  # old style keyword <v2.1
+        method = "tracemin_pcg"
+    if method in ("tracemin_pcg", "tracemin_chol", "tracemin_lu"):
+        def find_fiedler(L, x, normalized, tol, seed):
+            q = 1 if method == 'tracemin_pcg' else min(4, L.shape[0] - 1)
+            X = asmatrix(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):
+            L = csc_matrix(L, dtype=float)
+            n = L.shape[0]
+            if normalized:
+                D = spdiags(1. / sqrt(L.diagonal()), [0], n, n, format='csc')
+                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 = eigsh(L, 2, which='SM', tol=tol,
+                                 return_eigenvectors=True)
+                return sigma[1], X[:, 1]
+            else:
+                X = asarray(asmatrix(x).T)
+                M = spdiags(1. / L.diagonal(), [0], n, n)
+                Y = ones(n)
+                if normalized:
+                    Y /= D.diagonal()
+                sigma, X = lobpcg(L, X, M=M, Y=asmatrix(Y).T, tol=tol,
+                                  maxiter=n, largest=False)
+                return sigma[0], X[:, 0]
+    else:
+        raise nx.NetworkXError("unknown method '%s'." % method)
+
+    return find_fiedler
+
+
+@random_state(5)
+@not_implemented_for('directed')
+def algebraic_connectivity(G, weight='weight', normalized=False, tol=1e-8,
+                           method='tracemin_pcg', seed=None):
+    """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_chol' Cholesky factorization
+        '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.
+
+    To use Cholesky factorization in the TraceMIN algorithm, the
+    :samp:`scikits.sparse` package must be installed.
+
+    See Also
+    --------
+    laplacian_matrix
+    """
+    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.
+
+    L = nx.laplacian_matrix(G)
+    if L.shape[0] == 2:
+        return 2. * L[0, 0] if not normalized else 2.
+
+    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 sigma
+
+
+@random_state(5)
+@not_implemented_for('directed')
+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
+    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_chol' Cholesky factorization
+        '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.
+
+    To use Cholesky factorization in the TraceMIN algorithm, the
+    :samp:`scikits.sparse` package must be installed.
+
+    See Also
+    --------
+    laplacian_matrix
+    """
+    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 array([1., -1.])
+
+    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
+
+
+@random_state(5)
+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_chol' Cholesky factorization
+        '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.
+
+    To use Cholesky factorization in the TraceMIN algorithm, the
+    :samp:`scikits.sparse` package must be installed.
+
+    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
+
+
+# fixture for pytest
+def setup_module(module):
+    import pytest
+    numpy = pytest.importorskip('numpy')
+    scipy.sparse = pytest.importorskip('scipy.sparse')