view env/lib/python3.9/site-packages/networkx/tests/test_convert_numpy.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

import pytest

np = pytest.importorskip("numpy")
np_assert_equal = np.testing.assert_equal

import networkx as nx
from networkx.generators.classic import barbell_graph, cycle_graph, path_graph
from networkx.testing.utils import assert_graphs_equal


class TestConvertNumpy:
    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):
        G = np.array("a")
        pytest.raises(nx.NetworkXError, nx.to_networkx_graph, G)

    def create_weighted(self, G):
        g = cycle_graph(4)
        G.add_nodes_from(g)
        G.add_weighted_edges_from((u, v, 10 + u) for u, v in g.edges())
        return G

    def assert_equal(self, G1, G2):
        assert sorted(G1.nodes()) == sorted(G2.nodes())
        assert sorted(G1.edges()) == sorted(G2.edges())

    def identity_conversion(self, G, A, create_using):
        assert A.sum() > 0
        GG = nx.from_numpy_matrix(A, create_using=create_using)
        self.assert_equal(G, GG)
        GW = nx.to_networkx_graph(A, create_using=create_using)
        self.assert_equal(G, GW)
        GI = nx.empty_graph(0, create_using).__class__(A)
        self.assert_equal(G, GI)

    def test_shape(self):
        "Conversion from non-square array."
        A = np.array([[1, 2, 3], [4, 5, 6]])
        pytest.raises(nx.NetworkXError, nx.from_numpy_matrix, A)

    def test_identity_graph_matrix(self):
        "Conversion from graph to matrix to graph."
        A = nx.to_numpy_matrix(self.G1)
        self.identity_conversion(self.G1, A, nx.Graph())

    def test_identity_graph_array(self):
        "Conversion from graph to array to graph."
        A = nx.to_numpy_matrix(self.G1)
        A = np.asarray(A)
        self.identity_conversion(self.G1, A, nx.Graph())

    def test_identity_digraph_matrix(self):
        """Conversion from digraph to matrix to digraph."""
        A = nx.to_numpy_matrix(self.G2)
        self.identity_conversion(self.G2, A, nx.DiGraph())

    def test_identity_digraph_array(self):
        """Conversion from digraph to array to digraph."""
        A = nx.to_numpy_matrix(self.G2)
        A = np.asarray(A)
        self.identity_conversion(self.G2, A, nx.DiGraph())

    def test_identity_weighted_graph_matrix(self):
        """Conversion from weighted graph to matrix to weighted graph."""
        A = nx.to_numpy_matrix(self.G3)
        self.identity_conversion(self.G3, A, nx.Graph())

    def test_identity_weighted_graph_array(self):
        """Conversion from weighted graph to array to weighted graph."""
        A = nx.to_numpy_matrix(self.G3)
        A = np.asarray(A)
        self.identity_conversion(self.G3, A, nx.Graph())

    def test_identity_weighted_digraph_matrix(self):
        """Conversion from weighted digraph to matrix to weighted digraph."""
        A = nx.to_numpy_matrix(self.G4)
        self.identity_conversion(self.G4, A, nx.DiGraph())

    def test_identity_weighted_digraph_array(self):
        """Conversion from weighted digraph to array to weighted digraph."""
        A = nx.to_numpy_matrix(self.G4)
        A = np.asarray(A)
        self.identity_conversion(self.G4, A, nx.DiGraph())

    def test_nodelist(self):
        """Conversion from graph to matrix to graph with nodelist."""
        P4 = path_graph(4)
        P3 = path_graph(3)
        nodelist = list(P3)
        A = nx.to_numpy_matrix(P4, nodelist=nodelist)
        GA = nx.Graph(A)
        self.assert_equal(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_numpy_matrix(P4)
        np_assert_equal(A, nx.to_numpy_matrix(WP4, weight=None))
        np_assert_equal(0.5 * A, nx.to_numpy_matrix(WP4))
        np_assert_equal(0.3 * A, nx.to_numpy_matrix(WP4, weight="other"))

    def test_from_numpy_matrix_type(self):
        A = np.matrix([[1]])
        G = nx.from_numpy_matrix(A)
        assert type(G[0][0]["weight"]) == int

        A = np.matrix([[1]]).astype(np.float)
        G = nx.from_numpy_matrix(A)
        assert type(G[0][0]["weight"]) == float

        A = np.matrix([[1]]).astype(np.str)
        G = nx.from_numpy_matrix(A)
        assert type(G[0][0]["weight"]) == str

        A = np.matrix([[1]]).astype(np.bool)
        G = nx.from_numpy_matrix(A)
        assert type(G[0][0]["weight"]) == bool

        A = np.matrix([[1]]).astype(np.complex)
        G = nx.from_numpy_matrix(A)
        assert type(G[0][0]["weight"]) == complex

        A = np.matrix([[1]]).astype(np.object)
        pytest.raises(TypeError, nx.from_numpy_matrix, A)

        G = nx.cycle_graph(3)
        A = nx.adj_matrix(G).todense()
        H = nx.from_numpy_matrix(A)
        assert all(type(m) == int and type(n) == int for m, n in H.edges())
        H = nx.from_numpy_array(A)
        assert all(type(m) == int and type(n) == int for m, n in H.edges())

    def test_from_numpy_matrix_dtype(self):
        dt = [("weight", float), ("cost", int)]
        A = np.matrix([[(1.0, 2)]], dtype=dt)
        G = nx.from_numpy_matrix(A)
        assert type(G[0][0]["weight"]) == float
        assert type(G[0][0]["cost"]) == int
        assert G[0][0]["cost"] == 2
        assert G[0][0]["weight"] == 1.0

    def test_to_numpy_recarray(self):
        G = nx.Graph()
        G.add_edge(1, 2, weight=7.0, cost=5)
        A = nx.to_numpy_recarray(G, dtype=[("weight", float), ("cost", int)])
        assert sorted(A.dtype.names) == ["cost", "weight"]
        assert A.weight[0, 1] == 7.0
        assert A.weight[0, 0] == 0.0
        assert A.cost[0, 1] == 5
        assert A.cost[0, 0] == 0

    def test_numpy_multigraph(self):
        G = nx.MultiGraph()
        G.add_edge(1, 2, weight=7)
        G.add_edge(1, 2, weight=70)
        A = nx.to_numpy_matrix(G)
        assert A[1, 0] == 77
        A = nx.to_numpy_matrix(G, multigraph_weight=min)
        assert A[1, 0] == 7
        A = nx.to_numpy_matrix(G, multigraph_weight=max)
        assert A[1, 0] == 70

    def test_from_numpy_matrix_parallel_edges(self):
        """Tests that the :func:`networkx.from_numpy_matrix` function
        interprets integer weights as the number of parallel edges when
        creating a multigraph.

        """
        A = np.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_numpy_matrix(A, parallel_edges=True, create_using=nx.DiGraph)
        assert_graphs_equal(actual, expected)
        actual = nx.from_numpy_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_numpy_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_numpy_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_numpy_matrix`.

        """
        A = np.matrix([[0, 1], [1, 0]])
        G = nx.from_numpy_matrix(A, create_using=nx.MultiGraph)
        expected = nx.MultiGraph()
        expected.add_edge(0, 1, weight=1)
        assert_graphs_equal(G, expected)

    def test_dtype_int_graph(self):
        """Test that setting dtype int actually gives an integer matrix.

        For more information, see GitHub pull request #1363.

        """
        G = nx.complete_graph(3)
        A = nx.to_numpy_matrix(G, dtype=int)
        assert A.dtype == int

    def test_dtype_int_multigraph(self):
        """Test that setting dtype int actually gives an integer matrix.

        For more information, see GitHub pull request #1363.

        """
        G = nx.MultiGraph(nx.complete_graph(3))
        A = nx.to_numpy_matrix(G, dtype=int)
        assert A.dtype == int


class TestConvertNumpyArray:
    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 create_weighted(self, G):
        g = cycle_graph(4)
        G.add_nodes_from(g)
        G.add_weighted_edges_from((u, v, 10 + u) for u, v in g.edges())
        return G

    def assert_equal(self, G1, G2):
        assert sorted(G1.nodes()) == sorted(G2.nodes())
        assert sorted(G1.edges()) == sorted(G2.edges())

    def identity_conversion(self, G, A, create_using):
        assert A.sum() > 0
        GG = nx.from_numpy_array(A, create_using=create_using)
        self.assert_equal(G, GG)
        GW = nx.to_networkx_graph(A, create_using=create_using)
        self.assert_equal(G, GW)
        GI = nx.empty_graph(0, create_using).__class__(A)
        self.assert_equal(G, GI)

    def test_shape(self):
        "Conversion from non-square array."
        A = np.array([[1, 2, 3], [4, 5, 6]])
        pytest.raises(nx.NetworkXError, nx.from_numpy_array, A)

    def test_identity_graph_array(self):
        "Conversion from graph to array to graph."
        A = nx.to_numpy_array(self.G1)
        self.identity_conversion(self.G1, A, nx.Graph())

    def test_identity_digraph_array(self):
        """Conversion from digraph to array to digraph."""
        A = nx.to_numpy_array(self.G2)
        self.identity_conversion(self.G2, A, nx.DiGraph())

    def test_identity_weighted_graph_array(self):
        """Conversion from weighted graph to array to weighted graph."""
        A = nx.to_numpy_array(self.G3)
        self.identity_conversion(self.G3, A, nx.Graph())

    def test_identity_weighted_digraph_array(self):
        """Conversion from weighted digraph to array to weighted digraph."""
        A = nx.to_numpy_array(self.G4)
        self.identity_conversion(self.G4, A, nx.DiGraph())

    def test_nodelist(self):
        """Conversion from graph to array to graph with nodelist."""
        P4 = path_graph(4)
        P3 = path_graph(3)
        nodelist = list(P3)
        A = nx.to_numpy_array(P4, nodelist=nodelist)
        GA = nx.Graph(A)
        self.assert_equal(GA, P3)

        # Make nodelist ambiguous by containing duplicates.
        nodelist += [nodelist[0]]
        pytest.raises(nx.NetworkXError, nx.to_numpy_array, 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_numpy_array(P4)
        np_assert_equal(A, nx.to_numpy_array(WP4, weight=None))
        np_assert_equal(0.5 * A, nx.to_numpy_array(WP4))
        np_assert_equal(0.3 * A, nx.to_numpy_array(WP4, weight="other"))

    def test_from_numpy_array_type(self):
        A = np.array([[1]])
        G = nx.from_numpy_array(A)
        assert type(G[0][0]["weight"]) == int

        A = np.array([[1]]).astype(np.float)
        G = nx.from_numpy_array(A)
        assert type(G[0][0]["weight"]) == float

        A = np.array([[1]]).astype(np.str)
        G = nx.from_numpy_array(A)
        assert type(G[0][0]["weight"]) == str

        A = np.array([[1]]).astype(np.bool)
        G = nx.from_numpy_array(A)
        assert type(G[0][0]["weight"]) == bool

        A = np.array([[1]]).astype(np.complex)
        G = nx.from_numpy_array(A)
        assert type(G[0][0]["weight"]) == complex

        A = np.array([[1]]).astype(np.object)
        pytest.raises(TypeError, nx.from_numpy_array, A)

    def test_from_numpy_array_dtype(self):
        dt = [("weight", float), ("cost", int)]
        A = np.array([[(1.0, 2)]], dtype=dt)
        G = nx.from_numpy_array(A)
        assert type(G[0][0]["weight"]) == float
        assert type(G[0][0]["cost"]) == int
        assert G[0][0]["cost"] == 2
        assert G[0][0]["weight"] == 1.0

    def test_to_numpy_recarray(self):
        G = nx.Graph()
        G.add_edge(1, 2, weight=7.0, cost=5)
        A = nx.to_numpy_recarray(G, dtype=[("weight", float), ("cost", int)])
        assert sorted(A.dtype.names) == ["cost", "weight"]
        assert A.weight[0, 1] == 7.0
        assert A.weight[0, 0] == 0.0
        assert A.cost[0, 1] == 5
        assert A.cost[0, 0] == 0

    def test_numpy_multigraph(self):
        G = nx.MultiGraph()
        G.add_edge(1, 2, weight=7)
        G.add_edge(1, 2, weight=70)
        A = nx.to_numpy_array(G)
        assert A[1, 0] == 77
        A = nx.to_numpy_array(G, multigraph_weight=min)
        assert A[1, 0] == 7
        A = nx.to_numpy_array(G, multigraph_weight=max)
        assert A[1, 0] == 70

    def test_from_numpy_array_parallel_edges(self):
        """Tests that the :func:`networkx.from_numpy_array` function
        interprets integer weights as the number of parallel edges when
        creating a multigraph.

        """
        A = np.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_numpy_array(A, parallel_edges=True, create_using=nx.DiGraph)
        assert_graphs_equal(actual, expected)
        actual = nx.from_numpy_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_numpy_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_numpy_array(
            A, parallel_edges=False, create_using=nx.MultiDiGraph
        )
        assert_graphs_equal(actual, expected)

    def test_symmetric(self):
        """Tests that a symmetric array has edges added only once to an
        undirected multigraph when using :func:`networkx.from_numpy_array`.

        """
        A = np.array([[0, 1], [1, 0]])
        G = nx.from_numpy_array(A, create_using=nx.MultiGraph)
        expected = nx.MultiGraph()
        expected.add_edge(0, 1, weight=1)
        assert_graphs_equal(G, expected)

    def test_dtype_int_graph(self):
        """Test that setting dtype int actually gives an integer array.

        For more information, see GitHub pull request #1363.

        """
        G = nx.complete_graph(3)
        A = nx.to_numpy_array(G, dtype=int)
        assert A.dtype == int

    def test_dtype_int_multigraph(self):
        """Test that setting dtype int actually gives an integer array.

        For more information, see GitHub pull request #1363.

        """
        G = nx.MultiGraph(nx.complete_graph(3))
        A = nx.to_numpy_array(G, dtype=int)
        assert A.dtype == int