import pytest np = pytest.importorskip("numpy") sp = pytest.importorskip("scipy") import networkx as nx from networkx.generators.classic import barbell_graph, cycle_graph, path_graph from networkx.utils import graphs_equal class TestConvertScipy: 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 identity_conversion(self, G, A, create_using): GG = nx.from_scipy_sparse_array(A, create_using=create_using) assert nx.is_isomorphic(G, GG) GW = nx.to_networkx_graph(A, create_using=create_using) assert nx.is_isomorphic(G, GW) GI = nx.empty_graph(0, create_using).__class__(A) assert nx.is_isomorphic(G, GI) ACSR = A.tocsr() GI = nx.empty_graph(0, create_using).__class__(ACSR) assert nx.is_isomorphic(G, GI) ACOO = A.tocoo() GI = nx.empty_graph(0, create_using).__class__(ACOO) assert nx.is_isomorphic(G, GI) ACSC = A.tocsc() GI = nx.empty_graph(0, create_using).__class__(ACSC) assert nx.is_isomorphic(G, GI) AD = A.todense() GI = nx.empty_graph(0, create_using).__class__(AD) assert nx.is_isomorphic(G, GI) AA = A.toarray() GI = nx.empty_graph(0, create_using).__class__(AA) assert nx.is_isomorphic(G, GI) def test_shape(self): "Conversion from non-square sparse array." A = sp.sparse.lil_array([[1, 2, 3], [4, 5, 6]]) pytest.raises(nx.NetworkXError, nx.from_scipy_sparse_array, A) def test_identity_graph_matrix(self): "Conversion from graph to sparse matrix to graph." A = nx.to_scipy_sparse_array(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_array(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_array(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_array(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_array(P4, nodelist=nodelist) GA = nx.Graph(A) assert nx.is_isomorphic(GA, P3) pytest.raises(nx.NetworkXError, nx.to_scipy_sparse_array, P3, nodelist=[]) # Test nodelist duplicates. long_nl = nodelist + [0] pytest.raises(nx.NetworkXError, nx.to_scipy_sparse_array, P3, nodelist=long_nl) # Test nodelist contains non-nodes non_nl = [-1, 0, 1, 2] pytest.raises(nx.NetworkXError, nx.to_scipy_sparse_array, P3, nodelist=non_nl) def test_weight_keyword(self): WP4 = nx.Graph() WP4.add_edges_from((n, n + 1, {"weight": 0.5, "other": 0.3}) for n in range(3)) P4 = path_graph(4) A = nx.to_scipy_sparse_array(P4) np.testing.assert_equal( A.todense(), nx.to_scipy_sparse_array(WP4, weight=None).todense() ) np.testing.assert_equal( 0.5 * A.todense(), nx.to_scipy_sparse_array(WP4).todense() ) np.testing.assert_equal( 0.3 * A.todense(), nx.to_scipy_sparse_array(WP4, weight="other").todense() ) def test_format_keyword(self): WP4 = nx.Graph() WP4.add_edges_from((n, n + 1, {"weight": 0.5, "other": 0.3}) for n in range(3)) P4 = path_graph(4) A = nx.to_scipy_sparse_array(P4, format="csr") np.testing.assert_equal( A.todense(), nx.to_scipy_sparse_array(WP4, weight=None).todense() ) A = nx.to_scipy_sparse_array(P4, format="csc") np.testing.assert_equal( A.todense(), nx.to_scipy_sparse_array(WP4, weight=None).todense() ) A = nx.to_scipy_sparse_array(P4, format="coo") np.testing.assert_equal( A.todense(), nx.to_scipy_sparse_array(WP4, weight=None).todense() ) A = nx.to_scipy_sparse_array(P4, format="bsr") np.testing.assert_equal( A.todense(), nx.to_scipy_sparse_array(WP4, weight=None).todense() ) A = nx.to_scipy_sparse_array(P4, format="lil") np.testing.assert_equal( A.todense(), nx.to_scipy_sparse_array(WP4, weight=None).todense() ) A = nx.to_scipy_sparse_array(P4, format="dia") np.testing.assert_equal( A.todense(), nx.to_scipy_sparse_array(WP4, weight=None).todense() ) A = nx.to_scipy_sparse_array(P4, format="dok") np.testing.assert_equal( A.todense(), nx.to_scipy_sparse_array(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, {"weight": 0.5, "other": 0.3}) for n in range(3) ) P4 = path_graph(4) nx.to_scipy_sparse_array(P4, format="any_other") def test_null_raise(self): with pytest.raises(nx.NetworkXError): nx.to_scipy_sparse_array(nx.Graph()) def test_empty(self): G = nx.Graph() G.add_node(1) M = nx.to_scipy_sparse_array(G) np.testing.assert_equal(M.toarray(), np.array([[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_array(G, nodelist=[3, 2, 1]) np.testing.assert_equal( M.toarray(), np.array([[0, 0, 1], [1, 0, 0], [0, 1, 0]]) ) def test_selfloop_graph(self): G = nx.Graph([(1, 1)]) M = nx.to_scipy_sparse_array(G) np.testing.assert_equal(M.toarray(), np.array([[1]])) G.add_edges_from([(2, 3), (3, 4)]) M = nx.to_scipy_sparse_array(G, nodelist=[2, 3, 4]) np.testing.assert_equal( M.toarray(), np.array([[0, 1, 0], [1, 0, 1], [0, 1, 0]]) ) def test_selfloop_digraph(self): G = nx.DiGraph([(1, 1)]) M = nx.to_scipy_sparse_array(G) np.testing.assert_equal(M.toarray(), np.array([[1]])) G.add_edges_from([(2, 3), (3, 4)]) M = nx.to_scipy_sparse_array(G, nodelist=[2, 3, 4]) np.testing.assert_equal( M.toarray(), np.array([[0, 1, 0], [0, 0, 1], [0, 0, 0]]) ) def test_from_scipy_sparse_array_parallel_edges(self): """Tests that the :func:`networkx.from_scipy_sparse_array` function interprets integer weights as the number of parallel edges when creating a multigraph. """ A = sp.sparse.csr_array([[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_array( A, parallel_edges=True, create_using=nx.DiGraph ) assert graphs_equal(actual, expected) actual = nx.from_scipy_sparse_array( 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_array( 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_array( 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_array`. """ A = sp.sparse.csr_array([[0, 1], [1, 0]]) G = nx.from_scipy_sparse_array(A, create_using=nx.MultiGraph) expected = nx.MultiGraph() expected.add_edge(0, 1, weight=1) assert graphs_equal(G, expected) @pytest.mark.parametrize("sparse_format", ("csr", "csc", "dok")) def test_from_scipy_sparse_array_formats(sparse_format): """Test all formats supported by _generate_weighted_edges.""" # trinode complete graph with non-uniform edge weights expected = nx.Graph() expected.add_edges_from( [ (0, 1, {"weight": 3}), (0, 2, {"weight": 2}), (1, 0, {"weight": 3}), (1, 2, {"weight": 1}), (2, 0, {"weight": 2}), (2, 1, {"weight": 1}), ] ) A = sp.sparse.coo_array([[0, 3, 2], [3, 0, 1], [2, 1, 0]]).asformat(sparse_format) assert graphs_equal(expected, nx.from_scipy_sparse_array(A))