from math import sqrt import pytest numpy = pytest.importorskip('numpy') numpy.linalg = pytest.importorskip('numpy.linalg') scipy = pytest.importorskip('scipy') scipy.sparse = pytest.importorskip('scipy.sparse') import networkx as nx from networkx.testing import almost_equal try: from scikits.sparse.cholmod import cholesky _cholesky = cholesky except ImportError: _cholesky = None if _cholesky is None: methods = ('tracemin_pcg', 'tracemin_lu', 'lanczos', 'lobpcg') else: methods = ('tracemin_pcg', 'tracemin_chol', 'tracemin_lu', 'lanczos', 'lobpcg') def check_eigenvector(A, l, x): nx = numpy.linalg.norm(x) # Check zeroness. assert not almost_equal(nx, 0) y = A * x ny = numpy.linalg.norm(y) # Check collinearity. assert almost_equal(numpy.dot(x, y), nx * ny) # Check eigenvalue. assert almost_equal(ny, l * nx) class TestAlgebraicConnectivity(object): def test_directed(self): G = nx.DiGraph() for method in self._methods: pytest.raises(nx.NetworkXNotImplemented, nx.algebraic_connectivity, G, method=method) pytest.raises(nx.NetworkXNotImplemented, nx.fiedler_vector, G, method=method) def test_null_and_singleton(self): G = nx.Graph() for method in self._methods: pytest.raises(nx.NetworkXError, nx.algebraic_connectivity, G, method=method) pytest.raises(nx.NetworkXError, nx.fiedler_vector, G, method=method) G.add_edge(0, 0) for method in self._methods: pytest.raises(nx.NetworkXError, nx.algebraic_connectivity, G, method=method) pytest.raises(nx.NetworkXError, nx.fiedler_vector, G, method=method) def test_disconnected(self): G = nx.Graph() G.add_nodes_from(range(2)) for method in self._methods: assert nx.algebraic_connectivity(G) == 0 pytest.raises(nx.NetworkXError, nx.fiedler_vector, G, method=method) G.add_edge(0, 1, weight=0) for method in self._methods: assert nx.algebraic_connectivity(G) == 0 pytest.raises(nx.NetworkXError, nx.fiedler_vector, G, method=method) def test_unrecognized_method(self): G = nx.path_graph(4) pytest.raises(nx.NetworkXError, nx.algebraic_connectivity, G, method='unknown') pytest.raises(nx.NetworkXError, nx.fiedler_vector, G, method='unknown') def test_two_nodes(self): G = nx.Graph() G.add_edge(0, 1, weight=1) A = nx.laplacian_matrix(G) for method in self._methods: assert almost_equal(nx.algebraic_connectivity( G, tol=1e-12, method=method), 2) x = nx.fiedler_vector(G, tol=1e-12, method=method) check_eigenvector(A, 2, x) G = nx.MultiGraph() G.add_edge(0, 0, spam=1e8) G.add_edge(0, 1, spam=1) G.add_edge(0, 1, spam=-2) A = -3 * nx.laplacian_matrix(G, weight='spam') for method in self._methods: assert almost_equal(nx.algebraic_connectivity( G, weight='spam', tol=1e-12, method=method), 6) x = nx.fiedler_vector(G, weight='spam', tol=1e-12, method=method) check_eigenvector(A, 6, x) def test_abbreviation_of_method(self): G = nx.path_graph(8) A = nx.laplacian_matrix(G) sigma = 2 - sqrt(2 + sqrt(2)) ac = nx.algebraic_connectivity(G, tol=1e-12, method='tracemin') assert almost_equal(ac, sigma) x = nx.fiedler_vector(G, tol=1e-12, method='tracemin') check_eigenvector(A, sigma, x) def test_path(self): G = nx.path_graph(8) A = nx.laplacian_matrix(G) sigma = 2 - sqrt(2 + sqrt(2)) for method in self._methods: ac = nx.algebraic_connectivity(G, tol=1e-12, method=method) assert almost_equal(ac, sigma) x = nx.fiedler_vector(G, tol=1e-12, method=method) check_eigenvector(A, sigma, x) def test_problematic_graph_issue_2381(self): G = nx.path_graph(4) G.add_edges_from([(4, 2), (5, 1)]) A = nx.laplacian_matrix(G) sigma = 0.438447187191 for method in self._methods: ac = nx.algebraic_connectivity(G, tol=1e-12, method=method) assert almost_equal(ac, sigma) x = nx.fiedler_vector(G, tol=1e-12, method=method) check_eigenvector(A, sigma, x) def test_cycle(self): G = nx.cycle_graph(8) A = nx.laplacian_matrix(G) sigma = 2 - sqrt(2) for method in self._methods: ac = nx.algebraic_connectivity(G, tol=1e-12, method=method) assert almost_equal(ac, sigma) x = nx.fiedler_vector(G, tol=1e-12, method=method) check_eigenvector(A, sigma, x) def test_seed_argument(self): G = nx.cycle_graph(8) A = nx.laplacian_matrix(G) sigma = 2 - sqrt(2) for method in self._methods: ac = nx.algebraic_connectivity(G, tol=1e-12, method=method, seed=1) assert almost_equal(ac, sigma) x = nx.fiedler_vector(G, tol=1e-12, method=method, seed=1) check_eigenvector(A, sigma, x) def test_buckminsterfullerene(self): G = nx.Graph( [(1, 10), (1, 41), (1, 59), (2, 12), (2, 42), (2, 60), (3, 6), (3, 43), (3, 57), (4, 8), (4, 44), (4, 58), (5, 13), (5, 56), (5, 57), (6, 10), (6, 31), (7, 14), (7, 56), (7, 58), (8, 12), (8, 32), (9, 23), (9, 53), (9, 59), (10, 15), (11, 24), (11, 53), (11, 60), (12, 16), (13, 14), (13, 25), (14, 26), (15, 27), (15, 49), (16, 28), (16, 50), (17, 18), (17, 19), (17, 54), (18, 20), (18, 55), (19, 23), (19, 41), (20, 24), (20, 42), (21, 31), (21, 33), (21, 57), (22, 32), (22, 34), (22, 58), (23, 24), (25, 35), (25, 43), (26, 36), (26, 44), (27, 51), (27, 59), (28, 52), (28, 60), (29, 33), (29, 34), (29, 56), (30, 51), (30, 52), (30, 53), (31, 47), (32, 48), (33, 45), (34, 46), (35, 36), (35, 37), (36, 38), (37, 39), (37, 49), (38, 40), (38, 50), (39, 40), (39, 51), (40, 52), (41, 47), (42, 48), (43, 49), (44, 50), (45, 46), (45, 54), (46, 55), (47, 54), (48, 55)]) for normalized in (False, True): if not normalized: A = nx.laplacian_matrix(G) sigma = 0.2434017461399311 else: A = nx.normalized_laplacian_matrix(G) sigma = 0.08113391537997749 for method in methods: try: assert almost_equal(nx.algebraic_connectivity( G, normalized=normalized, tol=1e-12, method=method), sigma) x = nx.fiedler_vector(G, normalized=normalized, tol=1e-12, method=method) check_eigenvector(A, sigma, x) except nx.NetworkXError as e: if e.args not in (('Cholesky solver unavailable.',), ('LU solver unavailable.',)): raise _methods = methods class TestSpectralOrdering(object): def test_nullgraph(self): for graph in (nx.Graph, nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph): G = graph() pytest.raises(nx.NetworkXError, nx.spectral_ordering, G) def test_singleton(self): for graph in (nx.Graph, nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph): G = graph() G.add_node('x') assert nx.spectral_ordering(G) == ['x'] G.add_edge('x', 'x', weight=33) G.add_edge('x', 'x', weight=33) assert nx.spectral_ordering(G) == ['x'] def test_unrecognized_method(self): G = nx.path_graph(4) pytest.raises(nx.NetworkXError, nx.spectral_ordering, G, method='unknown') def test_three_nodes(self): G = nx.Graph() G.add_weighted_edges_from([(1, 2, 1), (1, 3, 2), (2, 3, 1)], weight='spam') for method in self._methods: order = nx.spectral_ordering(G, weight='spam', method=method) assert set(order) == set(G) assert set([1, 3]) in (set(order[:-1]), set(order[1:])) G = nx.MultiDiGraph() G.add_weighted_edges_from([(1, 2, 1), (1, 3, 2), (2, 3, 1), (2, 3, 2)]) for method in self._methods: order = nx.spectral_ordering(G, method=method) assert set(order) == set(G) assert set([2, 3]) in (set(order[:-1]), set(order[1:])) def test_path(self): # based on setup_class numpy is installed if we get here from numpy.random import shuffle path = list(range(10)) shuffle(path) G = nx.Graph() nx.add_path(G, path) for method in self._methods: order = nx.spectral_ordering(G, method=method) assert order in [path, list(reversed(path))] def test_seed_argument(self): # based on setup_class numpy is installed if we get here from numpy.random import shuffle path = list(range(10)) shuffle(path) G = nx.Graph() nx.add_path(G, path) for method in self._methods: order = nx.spectral_ordering(G, method=method, seed=1) assert order in [path, list(reversed(path))] def test_disconnected(self): G = nx.Graph() nx.add_path(G, range(0, 10, 2)) nx.add_path(G, range(1, 10, 2)) for method in self._methods: order = nx.spectral_ordering(G, method=method) assert set(order) == set(G) seqs = [list(range(0, 10, 2)), list(range(8, -1, -2)), list(range(1, 10, 2)), list(range(9, -1, -2))] assert order[:5] in seqs assert order[5:] in seqs def test_cycle(self): path = list(range(10)) G = nx.Graph() nx.add_path(G, path, weight=5) G.add_edge(path[-1], path[0], weight=1) A = nx.laplacian_matrix(G).todense() for normalized in (False, True): for method in methods: try: order = nx.spectral_ordering(G, normalized=normalized, method=method) except nx.NetworkXError as e: if e.args not in (('Cholesky solver unavailable.',), ('LU solver unavailable.',)): raise else: if not normalized: assert order in [[1, 2, 0, 3, 4, 5, 6, 9, 7, 8], [8, 7, 9, 6, 5, 4, 3, 0, 2, 1]] else: assert order in [[1, 2, 3, 0, 4, 5, 9, 6, 7, 8], [8, 7, 6, 9, 5, 4, 0, 3, 2, 1]] _methods = methods