Fixed database typo and removed unnecessary class identifier.
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5098 changed files with 952558 additions and 85 deletions
293
venv/Lib/site-packages/networkx/linalg/tests/test_graphmatrix.py
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293
venv/Lib/site-packages/networkx/linalg/tests/test_graphmatrix.py
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import pytest
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np = pytest.importorskip("numpy")
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npt = pytest.importorskip("numpy.testing")
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scipy = pytest.importorskip("scipy")
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import networkx as nx
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from networkx.generators.degree_seq import havel_hakimi_graph
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from networkx.exception import NetworkXError
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def test_incidence_matrix_simple():
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deg = [3, 2, 2, 1, 0]
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G = havel_hakimi_graph(deg)
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deg = [(1, 0), (1, 0), (1, 0), (2, 0), (1, 0), (2, 1), (0, 1), (0, 1)]
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MG = nx.random_clustered_graph(deg, seed=42)
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I = nx.incidence_matrix(G).todense().astype(int)
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# fmt: off
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expected = np.array(
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[[1, 1, 1, 0],
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[0, 1, 0, 1],
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[1, 0, 0, 1],
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[0, 0, 1, 0],
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[0, 0, 0, 0]]
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)
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# fmt: on
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npt.assert_equal(I, expected)
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I = nx.incidence_matrix(MG).todense().astype(int)
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# fmt: off
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expected = np.array(
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[[1, 0, 0, 0, 0, 0, 0],
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[1, 0, 0, 0, 0, 0, 0],
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[0, 1, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0, 0],
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[0, 1, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 1, 1, 0],
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[0, 0, 0, 0, 0, 1, 1],
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[0, 0, 0, 0, 1, 0, 1]]
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)
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# fmt: on
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npt.assert_equal(I, expected)
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with pytest.raises(NetworkXError):
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nx.incidence_matrix(G, nodelist=[0, 1])
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class TestGraphMatrix:
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@classmethod
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def setup_class(cls):
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deg = [3, 2, 2, 1, 0]
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cls.G = havel_hakimi_graph(deg)
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# fmt: off
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cls.OI = np.array(
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[[-1, -1, -1, 0],
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[1, 0, 0, -1],
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[0, 1, 0, 1],
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[0, 0, 1, 0],
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[0, 0, 0, 0]]
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)
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cls.A = np.array(
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[[0, 1, 1, 1, 0],
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[1, 0, 1, 0, 0],
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[1, 1, 0, 0, 0],
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[1, 0, 0, 0, 0],
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[0, 0, 0, 0, 0]]
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)
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# fmt: on
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cls.WG = havel_hakimi_graph(deg)
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cls.WG.add_edges_from(
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(u, v, {"weight": 0.5, "other": 0.3}) for (u, v) in cls.G.edges()
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)
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# fmt: off
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cls.WA = np.array(
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[[0, 0.5, 0.5, 0.5, 0],
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[0.5, 0, 0.5, 0, 0],
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[0.5, 0.5, 0, 0, 0],
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[0.5, 0, 0, 0, 0],
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[0, 0, 0, 0, 0]]
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)
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# fmt: on
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cls.MG = nx.MultiGraph(cls.G)
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cls.MG2 = cls.MG.copy()
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cls.MG2.add_edge(0, 1)
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# fmt: off
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cls.MG2A = np.array(
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[[0, 2, 1, 1, 0],
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[2, 0, 1, 0, 0],
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[1, 1, 0, 0, 0],
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[1, 0, 0, 0, 0],
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[0, 0, 0, 0, 0]]
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)
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cls.MGOI = np.array(
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[[-1, -1, -1, -1, 0],
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[1, 1, 0, 0, -1],
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[0, 0, 1, 0, 1],
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[0, 0, 0, 1, 0],
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[0, 0, 0, 0, 0]]
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)
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# fmt: on
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cls.no_edges_G = nx.Graph([(1, 2), (3, 2, {"weight": 8})])
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cls.no_edges_A = np.array([[0, 0], [0, 0]])
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def test_incidence_matrix(self):
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"Conversion to incidence matrix"
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I = (
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nx.incidence_matrix(
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self.G,
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nodelist=sorted(self.G),
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edgelist=sorted(self.G.edges()),
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oriented=True,
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)
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.todense()
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.astype(int)
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)
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npt.assert_equal(I, self.OI)
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I = (
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nx.incidence_matrix(
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self.G,
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nodelist=sorted(self.G),
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edgelist=sorted(self.G.edges()),
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oriented=False,
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)
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.todense()
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.astype(int)
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)
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npt.assert_equal(I, np.abs(self.OI))
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I = (
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nx.incidence_matrix(
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self.MG,
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nodelist=sorted(self.MG),
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edgelist=sorted(self.MG.edges()),
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oriented=True,
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)
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.todense()
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.astype(int)
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)
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npt.assert_equal(I, self.OI)
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I = (
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nx.incidence_matrix(
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self.MG,
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nodelist=sorted(self.MG),
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edgelist=sorted(self.MG.edges()),
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oriented=False,
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)
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.todense()
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.astype(int)
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)
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npt.assert_equal(I, np.abs(self.OI))
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I = (
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nx.incidence_matrix(
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self.MG2,
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nodelist=sorted(self.MG2),
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edgelist=sorted(self.MG2.edges()),
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oriented=True,
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)
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.todense()
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.astype(int)
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)
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npt.assert_equal(I, self.MGOI)
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I = (
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nx.incidence_matrix(
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self.MG2,
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nodelist=sorted(self.MG),
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edgelist=sorted(self.MG2.edges()),
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oriented=False,
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)
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.todense()
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.astype(int)
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)
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npt.assert_equal(I, np.abs(self.MGOI))
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def test_weighted_incidence_matrix(self):
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I = (
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nx.incidence_matrix(
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self.WG,
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nodelist=sorted(self.WG),
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edgelist=sorted(self.WG.edges()),
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oriented=True,
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)
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.todense()
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.astype(int)
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)
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npt.assert_equal(I, self.OI)
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I = (
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nx.incidence_matrix(
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self.WG,
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nodelist=sorted(self.WG),
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edgelist=sorted(self.WG.edges()),
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oriented=False,
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)
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.todense()
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.astype(int)
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)
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npt.assert_equal(I, np.abs(self.OI))
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# npt.assert_equal(nx.incidence_matrix(self.WG,oriented=True,
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# weight='weight').todense(),0.5*self.OI)
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# npt.assert_equal(nx.incidence_matrix(self.WG,weight='weight').todense(),
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# np.abs(0.5*self.OI))
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# npt.assert_equal(nx.incidence_matrix(self.WG,oriented=True,weight='other').todense(),
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# 0.3*self.OI)
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I = nx.incidence_matrix(
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self.WG,
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nodelist=sorted(self.WG),
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edgelist=sorted(self.WG.edges()),
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oriented=True,
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weight="weight",
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).todense()
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npt.assert_equal(I, 0.5 * self.OI)
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I = nx.incidence_matrix(
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self.WG,
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nodelist=sorted(self.WG),
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edgelist=sorted(self.WG.edges()),
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oriented=False,
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weight="weight",
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).todense()
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npt.assert_equal(I, np.abs(0.5 * self.OI))
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I = nx.incidence_matrix(
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self.WG,
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nodelist=sorted(self.WG),
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edgelist=sorted(self.WG.edges()),
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oriented=True,
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weight="other",
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).todense()
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npt.assert_equal(I, 0.3 * self.OI)
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# WMG=nx.MultiGraph(self.WG)
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# WMG.add_edge(0,1,weight=0.5,other=0.3)
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# npt.assert_equal(nx.incidence_matrix(WMG,weight='weight').todense(),
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# np.abs(0.5*self.MGOI))
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# npt.assert_equal(nx.incidence_matrix(WMG,weight='weight',oriented=True).todense(),
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# 0.5*self.MGOI)
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# npt.assert_equal(nx.incidence_matrix(WMG,weight='other',oriented=True).todense(),
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# 0.3*self.MGOI)
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WMG = nx.MultiGraph(self.WG)
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WMG.add_edge(0, 1, weight=0.5, other=0.3)
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I = nx.incidence_matrix(
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WMG,
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nodelist=sorted(WMG),
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edgelist=sorted(WMG.edges(keys=True)),
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oriented=True,
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weight="weight",
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).todense()
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npt.assert_equal(I, 0.5 * self.MGOI)
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I = nx.incidence_matrix(
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WMG,
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nodelist=sorted(WMG),
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edgelist=sorted(WMG.edges(keys=True)),
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oriented=False,
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weight="weight",
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).todense()
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npt.assert_equal(I, np.abs(0.5 * self.MGOI))
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I = nx.incidence_matrix(
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WMG,
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nodelist=sorted(WMG),
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edgelist=sorted(WMG.edges(keys=True)),
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oriented=True,
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weight="other",
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).todense()
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npt.assert_equal(I, 0.3 * self.MGOI)
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def test_adjacency_matrix(self):
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"Conversion to adjacency matrix"
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npt.assert_equal(nx.adj_matrix(self.G).todense(), self.A)
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npt.assert_equal(nx.adj_matrix(self.MG).todense(), self.A)
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npt.assert_equal(nx.adj_matrix(self.MG2).todense(), self.MG2A)
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npt.assert_equal(
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nx.adj_matrix(self.G, nodelist=[0, 1]).todense(), self.A[:2, :2]
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)
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npt.assert_equal(nx.adj_matrix(self.WG).todense(), self.WA)
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npt.assert_equal(nx.adj_matrix(self.WG, weight=None).todense(), self.A)
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npt.assert_equal(nx.adj_matrix(self.MG2, weight=None).todense(), self.MG2A)
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npt.assert_equal(
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nx.adj_matrix(self.WG, weight="other").todense(), 0.6 * self.WA
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)
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npt.assert_equal(
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nx.adj_matrix(self.no_edges_G, nodelist=[1, 3]).todense(), self.no_edges_A
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)
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