Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/networkx/tests/test_convert_scipy.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
---|---|
date | Mon, 22 Mar 2021 18:12:50 +0000 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/networkx/tests/test_convert_scipy.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,258 @@ +import pytest + +import networkx as nx +from networkx.testing import assert_graphs_equal +from networkx.generators.classic import barbell_graph, cycle_graph, path_graph + + +class TestConvertNumpy: + @classmethod + def setup_class(cls): + global np, sp, sparse, np_assert_equal + np = pytest.importorskip("numpy") + sp = pytest.importorskip("scipy") + sparse = sp.sparse + np_assert_equal = np.testing.assert_equal + + def setup_method(self): + self.G1 = barbell_graph(10, 3) + self.G2 = cycle_graph(10, create_using=nx.DiGraph) + + self.G3 = self.create_weighted(nx.Graph()) + self.G4 = self.create_weighted(nx.DiGraph()) + + def test_exceptions(self): + class G: + format = None + + pytest.raises(nx.NetworkXError, nx.to_networkx_graph, G) + + def create_weighted(self, G): + g = cycle_graph(4) + e = list(g.edges()) + source = [u for u, v in e] + dest = [v for u, v in e] + weight = [s + 10 for s in source] + ex = zip(source, dest, weight) + G.add_weighted_edges_from(ex) + return G + + def assert_isomorphic(self, G1, G2): + assert nx.is_isomorphic(G1, G2) + + def identity_conversion(self, G, A, create_using): + GG = nx.from_scipy_sparse_matrix(A, create_using=create_using) + self.assert_isomorphic(G, GG) + + GW = nx.to_networkx_graph(A, create_using=create_using) + self.assert_isomorphic(G, GW) + + GI = nx.empty_graph(0, create_using).__class__(A) + self.assert_isomorphic(G, GI) + + ACSR = A.tocsr() + GI = nx.empty_graph(0, create_using).__class__(ACSR) + self.assert_isomorphic(G, GI) + + ACOO = A.tocoo() + GI = nx.empty_graph(0, create_using).__class__(ACOO) + self.assert_isomorphic(G, GI) + + ACSC = A.tocsc() + GI = nx.empty_graph(0, create_using).__class__(ACSC) + self.assert_isomorphic(G, GI) + + AD = A.todense() + GI = nx.empty_graph(0, create_using).__class__(AD) + self.assert_isomorphic(G, GI) + + AA = A.toarray() + GI = nx.empty_graph(0, create_using).__class__(AA) + self.assert_isomorphic(G, GI) + + def test_shape(self): + "Conversion from non-square sparse array." + A = sp.sparse.lil_matrix([[1, 2, 3], [4, 5, 6]]) + pytest.raises(nx.NetworkXError, nx.from_scipy_sparse_matrix, A) + + def test_identity_graph_matrix(self): + "Conversion from graph to sparse matrix to graph." + A = nx.to_scipy_sparse_matrix(self.G1) + self.identity_conversion(self.G1, A, nx.Graph()) + + def test_identity_digraph_matrix(self): + "Conversion from digraph to sparse matrix to digraph." + A = nx.to_scipy_sparse_matrix(self.G2) + self.identity_conversion(self.G2, A, nx.DiGraph()) + + def test_identity_weighted_graph_matrix(self): + """Conversion from weighted graph to sparse matrix to weighted graph.""" + A = nx.to_scipy_sparse_matrix(self.G3) + self.identity_conversion(self.G3, A, nx.Graph()) + + def test_identity_weighted_digraph_matrix(self): + """Conversion from weighted digraph to sparse matrix to weighted digraph.""" + A = nx.to_scipy_sparse_matrix(self.G4) + self.identity_conversion(self.G4, A, nx.DiGraph()) + + def test_nodelist(self): + """Conversion from graph to sparse matrix to graph with nodelist.""" + P4 = path_graph(4) + P3 = path_graph(3) + nodelist = list(P3.nodes()) + A = nx.to_scipy_sparse_matrix(P4, nodelist=nodelist) + GA = nx.Graph(A) + self.assert_isomorphic(GA, P3) + + # Make nodelist ambiguous by containing duplicates. + nodelist += [nodelist[0]] + pytest.raises(nx.NetworkXError, nx.to_numpy_matrix, P3, nodelist=nodelist) + + def test_weight_keyword(self): + WP4 = nx.Graph() + WP4.add_edges_from((n, n + 1, dict(weight=0.5, other=0.3)) for n in range(3)) + P4 = path_graph(4) + A = nx.to_scipy_sparse_matrix(P4) + np_assert_equal( + A.todense(), nx.to_scipy_sparse_matrix(WP4, weight=None).todense() + ) + np_assert_equal(0.5 * A.todense(), nx.to_scipy_sparse_matrix(WP4).todense()) + np_assert_equal( + 0.3 * A.todense(), nx.to_scipy_sparse_matrix(WP4, weight="other").todense() + ) + + def test_format_keyword(self): + WP4 = nx.Graph() + WP4.add_edges_from((n, n + 1, dict(weight=0.5, other=0.3)) for n in range(3)) + P4 = path_graph(4) + A = nx.to_scipy_sparse_matrix(P4, format="csr") + np_assert_equal( + A.todense(), nx.to_scipy_sparse_matrix(WP4, weight=None).todense() + ) + + A = nx.to_scipy_sparse_matrix(P4, format="csc") + np_assert_equal( + A.todense(), nx.to_scipy_sparse_matrix(WP4, weight=None).todense() + ) + + A = nx.to_scipy_sparse_matrix(P4, format="coo") + np_assert_equal( + A.todense(), nx.to_scipy_sparse_matrix(WP4, weight=None).todense() + ) + + A = nx.to_scipy_sparse_matrix(P4, format="bsr") + np_assert_equal( + A.todense(), nx.to_scipy_sparse_matrix(WP4, weight=None).todense() + ) + + A = nx.to_scipy_sparse_matrix(P4, format="lil") + np_assert_equal( + A.todense(), nx.to_scipy_sparse_matrix(WP4, weight=None).todense() + ) + + A = nx.to_scipy_sparse_matrix(P4, format="dia") + np_assert_equal( + A.todense(), nx.to_scipy_sparse_matrix(WP4, weight=None).todense() + ) + + A = nx.to_scipy_sparse_matrix(P4, format="dok") + np_assert_equal( + A.todense(), nx.to_scipy_sparse_matrix(WP4, weight=None).todense() + ) + + def test_format_keyword_raise(self): + with pytest.raises(nx.NetworkXError): + WP4 = nx.Graph() + WP4.add_edges_from( + (n, n + 1, dict(weight=0.5, other=0.3)) for n in range(3) + ) + P4 = path_graph(4) + nx.to_scipy_sparse_matrix(P4, format="any_other") + + def test_null_raise(self): + with pytest.raises(nx.NetworkXError): + nx.to_scipy_sparse_matrix(nx.Graph()) + + def test_empty(self): + G = nx.Graph() + G.add_node(1) + M = nx.to_scipy_sparse_matrix(G) + np_assert_equal(M.todense(), np.matrix([[0]])) + + def test_ordering(self): + G = nx.DiGraph() + G.add_edge(1, 2) + G.add_edge(2, 3) + G.add_edge(3, 1) + M = nx.to_scipy_sparse_matrix(G, nodelist=[3, 2, 1]) + np_assert_equal(M.todense(), np.matrix([[0, 0, 1], [1, 0, 0], [0, 1, 0]])) + + def test_selfloop_graph(self): + G = nx.Graph([(1, 1)]) + M = nx.to_scipy_sparse_matrix(G) + np_assert_equal(M.todense(), np.matrix([[1]])) + + G.add_edges_from([(2, 3), (3, 4)]) + M = nx.to_scipy_sparse_matrix(G, nodelist=[2, 3, 4]) + np_assert_equal(M.todense(), np.matrix([[0, 1, 0], [1, 0, 1], [0, 1, 0]])) + + def test_selfloop_digraph(self): + G = nx.DiGraph([(1, 1)]) + M = nx.to_scipy_sparse_matrix(G) + np_assert_equal(M.todense(), np.matrix([[1]])) + + G.add_edges_from([(2, 3), (3, 4)]) + M = nx.to_scipy_sparse_matrix(G, nodelist=[2, 3, 4]) + np_assert_equal(M.todense(), np.matrix([[0, 1, 0], [0, 0, 1], [0, 0, 0]])) + + def test_from_scipy_sparse_matrix_parallel_edges(self): + """Tests that the :func:`networkx.from_scipy_sparse_matrix` function + interprets integer weights as the number of parallel edges when + creating a multigraph. + + """ + A = sparse.csr_matrix([[1, 1], [1, 2]]) + # First, with a simple graph, each integer entry in the adjacency + # matrix is interpreted as the weight of a single edge in the graph. + expected = nx.DiGraph() + edges = [(0, 0), (0, 1), (1, 0)] + expected.add_weighted_edges_from([(u, v, 1) for (u, v) in edges]) + expected.add_edge(1, 1, weight=2) + actual = nx.from_scipy_sparse_matrix( + A, parallel_edges=True, create_using=nx.DiGraph + ) + assert_graphs_equal(actual, expected) + actual = nx.from_scipy_sparse_matrix( + A, parallel_edges=False, create_using=nx.DiGraph + ) + assert_graphs_equal(actual, expected) + # Now each integer entry in the adjacency matrix is interpreted as the + # number of parallel edges in the graph if the appropriate keyword + # argument is specified. + edges = [(0, 0), (0, 1), (1, 0), (1, 1), (1, 1)] + expected = nx.MultiDiGraph() + expected.add_weighted_edges_from([(u, v, 1) for (u, v) in edges]) + actual = nx.from_scipy_sparse_matrix( + A, parallel_edges=True, create_using=nx.MultiDiGraph + ) + assert_graphs_equal(actual, expected) + expected = nx.MultiDiGraph() + expected.add_edges_from(set(edges), weight=1) + # The sole self-loop (edge 0) on vertex 1 should have weight 2. + expected[1][1][0]["weight"] = 2 + actual = nx.from_scipy_sparse_matrix( + A, parallel_edges=False, create_using=nx.MultiDiGraph + ) + assert_graphs_equal(actual, expected) + + def test_symmetric(self): + """Tests that a symmetric matrix has edges added only once to an + undirected multigraph when using + :func:`networkx.from_scipy_sparse_matrix`. + + """ + A = sparse.csr_matrix([[0, 1], [1, 0]]) + G = nx.from_scipy_sparse_matrix(A, create_using=nx.MultiGraph) + expected = nx.MultiGraph() + expected.add_edge(0, 1, weight=1) + assert_graphs_equal(G, expected)