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)