import math import random from itertools import combinations import pytest import networkx as nx def l1dist(x, y): return sum(abs(a - b) for a, b in zip(x, y)) class TestRandomGeometricGraph: """Unit tests for :func:`~networkx.random_geometric_graph`""" def test_number_of_nodes(self): G = nx.random_geometric_graph(50, 0.25, seed=42) assert len(G) == 50 G = nx.random_geometric_graph(range(50), 0.25, seed=42) assert len(G) == 50 def test_distances(self): """Tests that pairs of vertices adjacent if and only if they are within the prescribed radius. """ # Use the Euclidean metric, the default according to the # documentation. G = nx.random_geometric_graph(50, 0.25) for u, v in combinations(G, 2): # Adjacent vertices must be within the given distance. if v in G[u]: assert math.dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 # Nonadjacent vertices must be at greater distance. else: assert not math.dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 def test_p(self): """Tests for providing an alternate distance metric to the generator.""" # Use the L1 metric. G = nx.random_geometric_graph(50, 0.25, p=1) for u, v in combinations(G, 2): # Adjacent vertices must be within the given distance. if v in G[u]: assert l1dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 # Nonadjacent vertices must be at greater distance. else: assert not l1dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 def test_node_names(self): """Tests using values other than sequential numbers as node IDs.""" import string nodes = list(string.ascii_lowercase) G = nx.random_geometric_graph(nodes, 0.25) assert len(G) == len(nodes) for u, v in combinations(G, 2): # Adjacent vertices must be within the given distance. if v in G[u]: assert math.dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 # Nonadjacent vertices must be at greater distance. else: assert not math.dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 def test_pos_name(self): G = nx.random_geometric_graph(50, 0.25, seed=42, pos_name="coords") assert all(len(d["coords"]) == 2 for n, d in G.nodes.items()) class TestSoftRandomGeometricGraph: """Unit tests for :func:`~networkx.soft_random_geometric_graph`""" def test_number_of_nodes(self): G = nx.soft_random_geometric_graph(50, 0.25, seed=42) assert len(G) == 50 G = nx.soft_random_geometric_graph(range(50), 0.25, seed=42) assert len(G) == 50 def test_distances(self): """Tests that pairs of vertices adjacent if and only if they are within the prescribed radius. """ # Use the Euclidean metric, the default according to the # documentation. G = nx.soft_random_geometric_graph(50, 0.25) for u, v in combinations(G, 2): # Adjacent vertices must be within the given distance. if v in G[u]: assert math.dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 def test_p(self): """Tests for providing an alternate distance metric to the generator.""" # Use the L1 metric. def dist(x, y): return sum(abs(a - b) for a, b in zip(x, y)) G = nx.soft_random_geometric_graph(50, 0.25, p=1) for u, v in combinations(G, 2): # Adjacent vertices must be within the given distance. if v in G[u]: assert dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 def test_node_names(self): """Tests using values other than sequential numbers as node IDs.""" import string nodes = list(string.ascii_lowercase) G = nx.soft_random_geometric_graph(nodes, 0.25) assert len(G) == len(nodes) for u, v in combinations(G, 2): # Adjacent vertices must be within the given distance. if v in G[u]: assert math.dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 def test_p_dist_default(self): """Tests default p_dict = 0.5 returns graph with edge count <= RGG with same n, radius, dim and positions """ nodes = 50 dim = 2 pos = {v: [random.random() for i in range(dim)] for v in range(nodes)} RGG = nx.random_geometric_graph(50, 0.25, pos=pos) SRGG = nx.soft_random_geometric_graph(50, 0.25, pos=pos) assert len(SRGG.edges()) <= len(RGG.edges()) def test_p_dist_zero(self): """Tests if p_dict = 0 returns disconnected graph with 0 edges""" def p_dist(dist): return 0 G = nx.soft_random_geometric_graph(50, 0.25, p_dist=p_dist) assert len(G.edges) == 0 def test_pos_name(self): G = nx.soft_random_geometric_graph(50, 0.25, seed=42, pos_name="coords") assert all(len(d["coords"]) == 2 for n, d in G.nodes.items()) def join(G, u, v, theta, alpha, metric): """Returns ``True`` if and only if the nodes whose attributes are ``du`` and ``dv`` should be joined, according to the threshold condition for geographical threshold graphs. ``G`` is an undirected NetworkX graph, and ``u`` and ``v`` are nodes in that graph. The nodes must have node attributes ``'pos'`` and ``'weight'``. ``metric`` is a distance metric. """ du, dv = G.nodes[u], G.nodes[v] u_pos, v_pos = du["pos"], dv["pos"] u_weight, v_weight = du["weight"], dv["weight"] return (u_weight + v_weight) * metric(u_pos, v_pos) ** alpha >= theta class TestGeographicalThresholdGraph: """Unit tests for :func:`~networkx.geographical_threshold_graph`""" def test_number_of_nodes(self): G = nx.geographical_threshold_graph(50, 100, seed=42) assert len(G) == 50 G = nx.geographical_threshold_graph(range(50), 100, seed=42) assert len(G) == 50 def test_distances(self): """Tests that pairs of vertices adjacent if and only if their distances meet the given threshold. """ # Use the Euclidean metric and alpha = -2 # the default according to the documentation. G = nx.geographical_threshold_graph(50, 10) for u, v in combinations(G, 2): # Adjacent vertices must exceed the threshold. if v in G[u]: assert join(G, u, v, 10, -2, math.dist) # Nonadjacent vertices must not exceed the threshold. else: assert not join(G, u, v, 10, -2, math.dist) def test_metric(self): """Tests for providing an alternate distance metric to the generator.""" # Use the L1 metric. G = nx.geographical_threshold_graph(50, 10, metric=l1dist) for u, v in combinations(G, 2): # Adjacent vertices must exceed the threshold. if v in G[u]: assert join(G, u, v, 10, -2, l1dist) # Nonadjacent vertices must not exceed the threshold. else: assert not join(G, u, v, 10, -2, l1dist) def test_p_dist_zero(self): """Tests if p_dict = 0 returns disconnected graph with 0 edges""" def p_dist(dist): return 0 G = nx.geographical_threshold_graph(50, 1, p_dist=p_dist) assert len(G.edges) == 0 def test_pos_weight_name(self): gtg = nx.geographical_threshold_graph G = gtg(50, 100, seed=42, pos_name="coords", weight_name="wt") assert all(len(d["coords"]) == 2 for n, d in G.nodes.items()) assert all(d["wt"] > 0 for n, d in G.nodes.items()) class TestWaxmanGraph: """Unit tests for the :func:`~networkx.waxman_graph` function.""" def test_number_of_nodes_1(self): G = nx.waxman_graph(50, 0.5, 0.1, seed=42) assert len(G) == 50 G = nx.waxman_graph(range(50), 0.5, 0.1, seed=42) assert len(G) == 50 def test_number_of_nodes_2(self): G = nx.waxman_graph(50, 0.5, 0.1, L=1) assert len(G) == 50 G = nx.waxman_graph(range(50), 0.5, 0.1, L=1) assert len(G) == 50 def test_metric(self): """Tests for providing an alternate distance metric to the generator.""" # Use the L1 metric. G = nx.waxman_graph(50, 0.5, 0.1, metric=l1dist) assert len(G) == 50 def test_pos_name(self): G = nx.waxman_graph(50, 0.5, 0.1, seed=42, pos_name="coords") assert all(len(d["coords"]) == 2 for n, d in G.nodes.items()) class TestNavigableSmallWorldGraph: def test_navigable_small_world(self): G = nx.navigable_small_world_graph(5, p=1, q=0, seed=42) gg = nx.grid_2d_graph(5, 5).to_directed() assert nx.is_isomorphic(G, gg) G = nx.navigable_small_world_graph(5, p=1, q=0, dim=3) gg = nx.grid_graph([5, 5, 5]).to_directed() assert nx.is_isomorphic(G, gg) G = nx.navigable_small_world_graph(5, p=1, q=0, dim=1) gg = nx.grid_graph([5]).to_directed() assert nx.is_isomorphic(G, gg) def test_invalid_diameter_value(self): with pytest.raises(nx.NetworkXException, match=".*p must be >= 1"): nx.navigable_small_world_graph(5, p=0, q=0, dim=1) def test_invalid_long_range_connections_value(self): with pytest.raises(nx.NetworkXException, match=".*q must be >= 0"): nx.navigable_small_world_graph(5, p=1, q=-1, dim=1) def test_invalid_exponent_for_decaying_probability_value(self): with pytest.raises(nx.NetworkXException, match=".*r must be >= 0"): nx.navigable_small_world_graph(5, p=1, q=0, r=-1, dim=1) def test_r_between_0_and_1(self): """Smoke test for radius in range [0, 1]""" # q=0 means no long-range connections G = nx.navigable_small_world_graph(3, p=1, q=0, r=0.5, dim=2, seed=42) expected = nx.grid_2d_graph(3, 3, create_using=nx.DiGraph) assert nx.utils.graphs_equal(G, expected) @pytest.mark.parametrize("seed", range(2478, 2578, 10)) def test_r_general_scaling(self, seed): """The probability of adding a long-range edge scales with `1 / dist**r`, so a navigable_small_world graph created with r < 1 should generally result in more edges than a navigable_small_world graph with r >= 1 (for 0 < q << n). N.B. this is probabilistic, so this test may not hold for all seeds.""" G1 = nx.navigable_small_world_graph(7, q=3, r=0.5, seed=seed) G2 = nx.navigable_small_world_graph(7, q=3, r=1, seed=seed) G3 = nx.navigable_small_world_graph(7, q=3, r=2, seed=seed) assert G1.number_of_edges() > G2.number_of_edges() assert G2.number_of_edges() > G3.number_of_edges() class TestThresholdedRandomGeometricGraph: """Unit tests for :func:`~networkx.thresholded_random_geometric_graph`""" def test_number_of_nodes(self): G = nx.thresholded_random_geometric_graph(50, 0.2, 0.1, seed=42) assert len(G) == 50 G = nx.thresholded_random_geometric_graph(range(50), 0.2, 0.1, seed=42) assert len(G) == 50 def test_distances(self): """Tests that pairs of vertices adjacent if and only if they are within the prescribed radius. """ # Use the Euclidean metric, the default according to the # documentation. G = nx.thresholded_random_geometric_graph(50, 0.25, 0.1, seed=42) for u, v in combinations(G, 2): # Adjacent vertices must be within the given distance. if v in G[u]: assert math.dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 def test_p(self): """Tests for providing an alternate distance metric to the generator.""" # Use the L1 metric. def dist(x, y): return sum(abs(a - b) for a, b in zip(x, y)) G = nx.thresholded_random_geometric_graph(50, 0.25, 0.1, p=1, seed=42) for u, v in combinations(G, 2): # Adjacent vertices must be within the given distance. if v in G[u]: assert dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 def test_node_names(self): """Tests using values other than sequential numbers as node IDs.""" import string nodes = list(string.ascii_lowercase) G = nx.thresholded_random_geometric_graph(nodes, 0.25, 0.1, seed=42) assert len(G) == len(nodes) for u, v in combinations(G, 2): # Adjacent vertices must be within the given distance. if v in G[u]: assert math.dist(G.nodes[u]["pos"], G.nodes[v]["pos"]) <= 0.25 def test_theta(self): """Tests that pairs of vertices adjacent if and only if their sum weights exceeds the threshold parameter theta. """ G = nx.thresholded_random_geometric_graph(50, 0.25, 0.1, seed=42) for u, v in combinations(G, 2): # Adjacent vertices must be within the given distance. if v in G[u]: assert (G.nodes[u]["weight"] + G.nodes[v]["weight"]) >= 0.1 def test_pos_name(self): trgg = nx.thresholded_random_geometric_graph G = trgg(50, 0.25, 0.1, seed=42, pos_name="p", weight_name="wt") assert all(len(d["p"]) == 2 for n, d in G.nodes.items()) assert all(d["wt"] > 0 for n, d in G.nodes.items()) def test_geometric_edges_pos_attribute(): G = nx.Graph() G.add_nodes_from( [ (0, {"position": (0, 0)}), (1, {"position": (0, 1)}), (2, {"position": (1, 0)}), ] ) expected_edges = [(0, 1), (0, 2)] assert expected_edges == nx.geometric_edges(G, radius=1, pos_name="position") def test_geometric_edges_raises_no_pos(): G = nx.path_graph(3) msg = "all nodes. must have a '" with pytest.raises(nx.NetworkXError, match=msg): nx.geometric_edges(G, radius=1) def test_number_of_nodes_S1(): G = nx.geometric_soft_configuration_graph( beta=1.5, n=100, gamma=2.7, mean_degree=10, seed=42 ) assert len(G) == 100 def test_set_attributes_S1(): G = nx.geometric_soft_configuration_graph( beta=1.5, n=100, gamma=2.7, mean_degree=10, seed=42 ) kappas = nx.get_node_attributes(G, "kappa") assert len(kappas) == 100 thetas = nx.get_node_attributes(G, "theta") assert len(thetas) == 100 radii = nx.get_node_attributes(G, "radius") assert len(radii) == 100 def test_mean_kappas_mean_degree_S1(): G = nx.geometric_soft_configuration_graph( beta=2.5, n=50, gamma=2.7, mean_degree=10, seed=8023 ) kappas = nx.get_node_attributes(G, "kappa") mean_kappas = sum(kappas.values()) / len(kappas) assert math.fabs(mean_kappas - 10) < 0.5 degrees = dict(G.degree()) mean_degree = sum(degrees.values()) / len(degrees) assert math.fabs(mean_degree - 10) < 1 def test_dict_kappas_S1(): kappas = {i: 10 for i in range(1000)} G = nx.geometric_soft_configuration_graph(beta=1, kappas=kappas) assert len(G) == 1000 kappas = nx.get_node_attributes(G, "kappa") assert all(kappa == 10 for kappa in kappas.values()) def test_beta_clustering_S1(): G1 = nx.geometric_soft_configuration_graph( beta=1.5, n=100, gamma=3.5, mean_degree=10, seed=42 ) G2 = nx.geometric_soft_configuration_graph( beta=3.0, n=100, gamma=3.5, mean_degree=10, seed=42 ) assert nx.average_clustering(G1) < nx.average_clustering(G2) def test_wrong_parameters_S1(): with pytest.raises( nx.NetworkXError, match="Please provide either kappas, or all 3 of: n, gamma and mean_degree.", ): G = nx.geometric_soft_configuration_graph( beta=1.5, gamma=3.5, mean_degree=10, seed=42 ) with pytest.raises( nx.NetworkXError, match="When kappas is input, n, gamma and mean_degree must not be.", ): kappas = {i: 10 for i in range(1000)} G = nx.geometric_soft_configuration_graph( beta=1.5, kappas=kappas, gamma=2.3, seed=42 ) with pytest.raises( nx.NetworkXError, match="Please provide either kappas, or all 3 of: n, gamma and mean_degree.", ): G = nx.geometric_soft_configuration_graph(beta=1.5, seed=42) def test_negative_beta_S1(): with pytest.raises( nx.NetworkXError, match="The parameter beta cannot be smaller or equal to 0." ): G = nx.geometric_soft_configuration_graph( beta=-1, n=100, gamma=2.3, mean_degree=10, seed=42 ) def test_non_zero_clustering_beta_lower_one_S1(): G = nx.geometric_soft_configuration_graph( beta=0.5, n=100, gamma=3.5, mean_degree=10, seed=42 ) assert nx.average_clustering(G) > 0 def test_mean_degree_influence_on_connectivity_S1(): low_mean_degree = 2 high_mean_degree = 20 G_low = nx.geometric_soft_configuration_graph( beta=1.2, n=100, gamma=2.7, mean_degree=low_mean_degree, seed=42 ) G_high = nx.geometric_soft_configuration_graph( beta=1.2, n=100, gamma=2.7, mean_degree=high_mean_degree, seed=42 ) assert nx.number_connected_components(G_low) > nx.number_connected_components( G_high ) def test_compare_mean_kappas_different_gammas_S1(): G1 = nx.geometric_soft_configuration_graph( beta=1.5, n=20, gamma=2.7, mean_degree=5, seed=42 ) G2 = nx.geometric_soft_configuration_graph( beta=1.5, n=20, gamma=3.5, mean_degree=5, seed=42 ) kappas1 = nx.get_node_attributes(G1, "kappa") mean_kappas1 = sum(kappas1.values()) / len(kappas1) kappas2 = nx.get_node_attributes(G2, "kappa") mean_kappas2 = sum(kappas2.values()) / len(kappas2) assert math.fabs(mean_kappas1 - mean_kappas2) < 1