Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/networkx/algorithms/approximation/tests/test_kcomponents.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/networkx/algorithms/approximation/tests/test_kcomponents.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,300 @@ +# Test for approximation to k-components algorithm +import pytest +import networkx as nx +from networkx.algorithms.approximation import k_components +from networkx.algorithms.approximation.kcomponents import _AntiGraph, _same + + +def build_k_number_dict(k_components): + k_num = {} + for k, comps in sorted(k_components.items()): + for comp in comps: + for node in comp: + k_num[node] = k + return k_num + + +## +# Some nice synthetic graphs +## + + +def graph_example_1(): + G = nx.convert_node_labels_to_integers( + nx.grid_graph([5, 5]), label_attribute="labels" + ) + rlabels = nx.get_node_attributes(G, "labels") + labels = {v: k for k, v in rlabels.items()} + + for nodes in [ + (labels[(0, 0)], labels[(1, 0)]), + (labels[(0, 4)], labels[(1, 4)]), + (labels[(3, 0)], labels[(4, 0)]), + (labels[(3, 4)], labels[(4, 4)]), + ]: + new_node = G.order() + 1 + # Petersen graph is triconnected + P = nx.petersen_graph() + G = nx.disjoint_union(G, P) + # Add two edges between the grid and P + G.add_edge(new_node + 1, nodes[0]) + G.add_edge(new_node, nodes[1]) + # K5 is 4-connected + K = nx.complete_graph(5) + G = nx.disjoint_union(G, K) + # Add three edges between P and K5 + G.add_edge(new_node + 2, new_node + 11) + G.add_edge(new_node + 3, new_node + 12) + G.add_edge(new_node + 4, new_node + 13) + # Add another K5 sharing a node + G = nx.disjoint_union(G, K) + nbrs = G[new_node + 10] + G.remove_node(new_node + 10) + for nbr in nbrs: + G.add_edge(new_node + 17, nbr) + G.add_edge(new_node + 16, new_node + 5) + return G + + +def torrents_and_ferraro_graph(): + G = nx.convert_node_labels_to_integers( + nx.grid_graph([5, 5]), label_attribute="labels" + ) + rlabels = nx.get_node_attributes(G, "labels") + labels = {v: k for k, v in rlabels.items()} + + for nodes in [(labels[(0, 4)], labels[(1, 4)]), (labels[(3, 4)], labels[(4, 4)])]: + new_node = G.order() + 1 + # Petersen graph is triconnected + P = nx.petersen_graph() + G = nx.disjoint_union(G, P) + # Add two edges between the grid and P + G.add_edge(new_node + 1, nodes[0]) + G.add_edge(new_node, nodes[1]) + # K5 is 4-connected + K = nx.complete_graph(5) + G = nx.disjoint_union(G, K) + # Add three edges between P and K5 + G.add_edge(new_node + 2, new_node + 11) + G.add_edge(new_node + 3, new_node + 12) + G.add_edge(new_node + 4, new_node + 13) + # Add another K5 sharing a node + G = nx.disjoint_union(G, K) + nbrs = G[new_node + 10] + G.remove_node(new_node + 10) + for nbr in nbrs: + G.add_edge(new_node + 17, nbr) + # Commenting this makes the graph not biconnected !! + # This stupid mistake make one reviewer very angry :P + G.add_edge(new_node + 16, new_node + 8) + + for nodes in [(labels[(0, 0)], labels[(1, 0)]), (labels[(3, 0)], labels[(4, 0)])]: + new_node = G.order() + 1 + # Petersen graph is triconnected + P = nx.petersen_graph() + G = nx.disjoint_union(G, P) + # Add two edges between the grid and P + G.add_edge(new_node + 1, nodes[0]) + G.add_edge(new_node, nodes[1]) + # K5 is 4-connected + K = nx.complete_graph(5) + G = nx.disjoint_union(G, K) + # Add three edges between P and K5 + G.add_edge(new_node + 2, new_node + 11) + G.add_edge(new_node + 3, new_node + 12) + G.add_edge(new_node + 4, new_node + 13) + # Add another K5 sharing two nodes + G = nx.disjoint_union(G, K) + nbrs = G[new_node + 10] + G.remove_node(new_node + 10) + for nbr in nbrs: + G.add_edge(new_node + 17, nbr) + nbrs2 = G[new_node + 9] + G.remove_node(new_node + 9) + for nbr in nbrs2: + G.add_edge(new_node + 18, nbr) + return G + + +# Helper function + + +def _check_connectivity(G): + result = k_components(G) + for k, components in result.items(): + if k < 3: + continue + for component in components: + C = G.subgraph(component) + K = nx.node_connectivity(C) + assert K >= k + + +def test_torrents_and_ferraro_graph(): + G = torrents_and_ferraro_graph() + _check_connectivity(G) + + +def test_example_1(): + G = graph_example_1() + _check_connectivity(G) + + +def test_karate_0(): + G = nx.karate_club_graph() + _check_connectivity(G) + + +def test_karate_1(): + karate_k_num = { + 0: 4, + 1: 4, + 2: 4, + 3: 4, + 4: 3, + 5: 3, + 6: 3, + 7: 4, + 8: 4, + 9: 2, + 10: 3, + 11: 1, + 12: 2, + 13: 4, + 14: 2, + 15: 2, + 16: 2, + 17: 2, + 18: 2, + 19: 3, + 20: 2, + 21: 2, + 22: 2, + 23: 3, + 24: 3, + 25: 3, + 26: 2, + 27: 3, + 28: 3, + 29: 3, + 30: 4, + 31: 3, + 32: 4, + 33: 4, + } + approx_karate_k_num = karate_k_num.copy() + approx_karate_k_num[24] = 2 + approx_karate_k_num[25] = 2 + G = nx.karate_club_graph() + k_comps = k_components(G) + k_num = build_k_number_dict(k_comps) + assert k_num in (karate_k_num, approx_karate_k_num) + + +def test_example_1_detail_3_and_4(): + G = graph_example_1() + result = k_components(G) + # In this example graph there are 8 3-components, 4 with 15 nodes + # and 4 with 5 nodes. + assert len(result[3]) == 8 + assert len([c for c in result[3] if len(c) == 15]) == 4 + assert len([c for c in result[3] if len(c) == 5]) == 4 + # There are also 8 4-components all with 5 nodes. + assert len(result[4]) == 8 + assert all(len(c) == 5 for c in result[4]) + # Finally check that the k-components detected have actually node + # connectivity >= k. + for k, components in result.items(): + if k < 3: + continue + for component in components: + K = nx.node_connectivity(G.subgraph(component)) + assert K >= k + + +def test_directed(): + with pytest.raises(nx.NetworkXNotImplemented): + G = nx.gnp_random_graph(10, 0.4, directed=True) + kc = k_components(G) + + +def test_same(): + equal = {"A": 2, "B": 2, "C": 2} + slightly_different = {"A": 2, "B": 1, "C": 2} + different = {"A": 2, "B": 8, "C": 18} + assert _same(equal) + assert not _same(slightly_different) + assert _same(slightly_different, tol=1) + assert not _same(different) + assert not _same(different, tol=4) + + +class TestAntiGraph: + @classmethod + def setup_class(cls): + cls.Gnp = nx.gnp_random_graph(20, 0.8) + cls.Anp = _AntiGraph(nx.complement(cls.Gnp)) + cls.Gd = nx.davis_southern_women_graph() + cls.Ad = _AntiGraph(nx.complement(cls.Gd)) + cls.Gk = nx.karate_club_graph() + cls.Ak = _AntiGraph(nx.complement(cls.Gk)) + cls.GA = [(cls.Gnp, cls.Anp), (cls.Gd, cls.Ad), (cls.Gk, cls.Ak)] + + def test_size(self): + for G, A in self.GA: + n = G.order() + s = len(list(G.edges())) + len(list(A.edges())) + assert s == (n * (n - 1)) / 2 + + def test_degree(self): + for G, A in self.GA: + assert sorted(G.degree()) == sorted(A.degree()) + + def test_core_number(self): + for G, A in self.GA: + assert nx.core_number(G) == nx.core_number(A) + + def test_connected_components(self): + for G, A in self.GA: + gc = [set(c) for c in nx.connected_components(G)] + ac = [set(c) for c in nx.connected_components(A)] + for comp in ac: + assert comp in gc + + def test_adj(self): + for G, A in self.GA: + for n, nbrs in G.adj.items(): + a_adj = sorted((n, sorted(ad)) for n, ad in A.adj.items()) + g_adj = sorted((n, sorted(ad)) for n, ad in G.adj.items()) + assert a_adj == g_adj + + def test_adjacency(self): + for G, A in self.GA: + a_adj = list(A.adjacency()) + for n, nbrs in G.adjacency(): + assert (n, set(nbrs)) in a_adj + + def test_neighbors(self): + for G, A in self.GA: + node = list(G.nodes())[0] + assert set(G.neighbors(node)) == set(A.neighbors(node)) + + def test_node_not_in_graph(self): + for G, A in self.GA: + node = "non_existent_node" + pytest.raises(nx.NetworkXError, A.neighbors, node) + pytest.raises(nx.NetworkXError, G.neighbors, node) + + def test_degree_thingraph(self): + for G, A in self.GA: + node = list(G.nodes())[0] + nodes = list(G.nodes())[1:4] + assert G.degree(node) == A.degree(node) + assert sum(d for n, d in G.degree()) == sum(d for n, d in A.degree()) + # AntiGraph is a ThinGraph, so all the weights are 1 + assert sum(d for n, d in A.degree()) == sum( + d for n, d in A.degree(weight="weight") + ) + assert sum(d for n, d in G.degree(nodes)) == sum( + d for n, d in A.degree(nodes) + )