okstra 0.114.0 → 0.116.0

package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_subgraph.py

@@ -1,110 +0,0 @@
-import pytest
-
-pytest.importorskip("numpy")
-pytest.importorskip("scipy")
-
-import networkx as nx
-from networkx.algorithms.centrality.subgraph_alg import (
-    communicability_betweenness_centrality,
-    estrada_index,
-    subgraph_centrality,
-    subgraph_centrality_exp,
-)
-
-
-class TestSubgraph:
-    def test_subgraph_centrality(self):
-        answer = {0: 1.5430806348152433, 1: 1.5430806348152433}
-        result = subgraph_centrality(nx.path_graph(2))
-        for k, v in result.items():
-            assert answer[k] == pytest.approx(v, abs=1e-7)
-
-        answer1 = {
-            "1": 1.6445956054135658,
-            "Albert": 2.4368257358712189,
-            "Aric": 2.4368257358712193,
-            "Dan": 3.1306328496328168,
-            "Franck": 2.3876142275231915,
-        }
-        G1 = nx.Graph(
-            [
-                ("Franck", "Aric"),
-                ("Aric", "Dan"),
-                ("Dan", "Albert"),
-                ("Albert", "Franck"),
-                ("Dan", "1"),
-                ("Franck", "Albert"),
-            ]
-        )
-        result1 = subgraph_centrality(G1)
-        for k, v in result1.items():
-            assert answer1[k] == pytest.approx(v, abs=1e-7)
-        result1 = subgraph_centrality_exp(G1)
-        for k, v in result1.items():
-            assert answer1[k] == pytest.approx(v, abs=1e-7)
-
-    def test_subgraph_centrality_big_graph(self):
-        g199 = nx.complete_graph(199)
-        g200 = nx.complete_graph(200)
-
-        comm199 = nx.subgraph_centrality(g199)
-        comm199_exp = nx.subgraph_centrality_exp(g199)
-
-        comm200 = nx.subgraph_centrality(g200)
-        comm200_exp = nx.subgraph_centrality_exp(g200)
-
-    def test_communicability_betweenness_centrality_small(self):
-        result = communicability_betweenness_centrality(nx.path_graph(2))
-        assert result == {0: 0, 1: 0}
-
-        result = communicability_betweenness_centrality(nx.path_graph(1))
-        assert result == {0: 0}
-
-        result = communicability_betweenness_centrality(nx.path_graph(0))
-        assert result == {}
-
-        answer = {0: 0.1411224421177313, 1: 1.0, 2: 0.1411224421177313}
-        result = communicability_betweenness_centrality(nx.path_graph(3))
-        for k, v in result.items():
-            assert answer[k] == pytest.approx(v, abs=1e-7)
-
-        result = communicability_betweenness_centrality(nx.complete_graph(3))
-        for k, v in result.items():
-            assert 0.49786143366223296 == pytest.approx(v, abs=1e-7)
-
-    def test_communicability_betweenness_centrality(self):
-        answer = {
-            0: 0.07017447951484615,
-            1: 0.71565598701107991,
-            2: 0.71565598701107991,
-            3: 0.07017447951484615,
-        }
-        result = communicability_betweenness_centrality(nx.path_graph(4))
-        for k, v in result.items():
-            assert answer[k] == pytest.approx(v, abs=1e-7)
-
-        answer1 = {
-            "1": 0.060039074193949521,
-            "Albert": 0.315470761661372,
-            "Aric": 0.31547076166137211,
-            "Dan": 0.68297778678316201,
-            "Franck": 0.21977926617449497,
-        }
-        G1 = nx.Graph(
-            [
-                ("Franck", "Aric"),
-                ("Aric", "Dan"),
-                ("Dan", "Albert"),
-                ("Albert", "Franck"),
-                ("Dan", "1"),
-                ("Franck", "Albert"),
-            ]
-        )
-        result1 = communicability_betweenness_centrality(G1)
-        for k, v in result1.items():
-            assert answer1[k] == pytest.approx(v, abs=1e-7)
-
-    def test_estrada_index(self):
-        answer = 1041.2470334195475
-        result = estrada_index(nx.karate_club_graph())
-        assert answer == pytest.approx(result, abs=1e-7)

package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_trophic.py

@@ -1,302 +0,0 @@
-"""Test trophic levels, trophic differences and trophic coherence"""
-
-import pytest
-
-import networkx as nx
-
-np = pytest.importorskip("numpy")
-pytest.importorskip("scipy")
-
-
-def test_trophic_levels():
-    """Trivial example"""
-    G = nx.DiGraph()
-    G.add_edge("a", "b")
-    G.add_edge("b", "c")
-
-    d = nx.trophic_levels(G)
-    assert d == {"a": 1, "b": 2, "c": 3}
-
-
-def test_trophic_levels_levine():
-    """Example from Figure 5 in Stephen Levine (1980) J. theor. Biol. 83,
-    195-207
-    """
-    S = nx.DiGraph()
-    S.add_edge(1, 2, weight=1.0)
-    S.add_edge(1, 3, weight=0.2)
-    S.add_edge(1, 4, weight=0.8)
-    S.add_edge(2, 3, weight=0.2)
-    S.add_edge(2, 5, weight=0.3)
-    S.add_edge(4, 3, weight=0.6)
-    S.add_edge(4, 5, weight=0.7)
-    S.add_edge(5, 4, weight=0.2)
-
-    # save copy for later, test intermediate implementation details first
-    S2 = S.copy()
-
-    # drop nodes of in-degree zero
-    z = [nid for nid, d in S.in_degree if d == 0]
-    for nid in z:
-        S.remove_node(nid)
-
-    # find adjacency matrix
-    q = nx.linalg.graphmatrix.adjacency_matrix(S).T
-
-    # fmt: off
-    expected_q = np.array([
-        [0, 0, 0., 0],
-        [0.2, 0, 0.6, 0],
-        [0, 0, 0, 0.2],
-        [0.3, 0, 0.7, 0]
-    ])
-    # fmt: on
-    assert np.array_equal(q.todense(), expected_q)
-
-    # must be square, size of number of nodes
-    assert len(q.shape) == 2
-    assert q.shape[0] == q.shape[1]
-    assert q.shape[0] == len(S)
-
-    nn = q.shape[0]
-
-    i = np.eye(nn)
-    n = np.linalg.inv(i - q)
-    y = np.asarray(n) @ np.ones(nn)
-
-    expected_y = np.array([1, 2.07906977, 1.46511628, 2.3255814])
-    assert np.allclose(y, expected_y)
-
-    expected_d = {1: 1, 2: 2, 3: 3.07906977, 4: 2.46511628, 5: 3.3255814}
-
-    d = nx.trophic_levels(S2)
-
-    for nid, level in d.items():
-        expected_level = expected_d[nid]
-        assert expected_level == pytest.approx(level, abs=1e-7)
-
-
-def test_trophic_levels_simple():
-    matrix_a = np.array([[0, 0], [1, 0]])
-    G = nx.from_numpy_array(matrix_a, create_using=nx.DiGraph)
-    d = nx.trophic_levels(G)
-    assert d[0] == pytest.approx(2, abs=1e-7)
-    assert d[1] == pytest.approx(1, abs=1e-7)
-
-
-def test_trophic_levels_more_complex():
-    # fmt: off
-    matrix = np.array([
-        [0, 1, 0, 0],
-        [0, 0, 1, 0],
-        [0, 0, 0, 1],
-        [0, 0, 0, 0]
-    ])
-    # fmt: on
-    G = nx.from_numpy_array(matrix, create_using=nx.DiGraph)
-    d = nx.trophic_levels(G)
-    expected_result = [1, 2, 3, 4]
-    for ind in range(4):
-        assert d[ind] == pytest.approx(expected_result[ind], abs=1e-7)
-
-    # fmt: off
-    matrix = np.array([
-        [0, 1, 1, 0],
-        [0, 0, 1, 1],
-        [0, 0, 0, 1],
-        [0, 0, 0, 0]
-    ])
-    # fmt: on
-    G = nx.from_numpy_array(matrix, create_using=nx.DiGraph)
-    d = nx.trophic_levels(G)
-
-    expected_result = [1, 2, 2.5, 3.25]
-    for ind in range(4):
-        assert d[ind] == pytest.approx(expected_result[ind], abs=1e-7)
-
-
-def test_trophic_levels_even_more_complex():
-    # fmt: off
-    # Another, bigger matrix
-    matrix = np.array([
-        [0, 0, 0, 0, 0],
-        [0, 1, 0, 1, 0],
-        [1, 0, 0, 0, 0],
-        [0, 1, 0, 0, 0],
-        [0, 0, 0, 1, 0]
-    ])
-    # Generated this linear system using pen and paper:
-    K = np.array([
-        [1, 0, -1, 0, 0],
-        [0, 0.5, 0, -0.5, 0],
-        [0, 0, 1, 0, 0],
-        [0, -0.5, 0, 1, -0.5],
-        [0, 0, 0, 0, 1],
-    ])
-    # fmt: on
-    result_1 = np.ravel(np.linalg.inv(K) @ np.ones(5))
-    G = nx.from_numpy_array(matrix, create_using=nx.DiGraph)
-    result_2 = nx.trophic_levels(G)
-
-    for ind in range(5):
-        assert result_1[ind] == pytest.approx(result_2[ind], abs=1e-7)
-
-
-def test_trophic_levels_singular_matrix():
-    """Should raise an error with graphs with only non-basal nodes"""
-    matrix = np.identity(4)
-    G = nx.from_numpy_array(matrix, create_using=nx.DiGraph)
-    with pytest.raises(nx.NetworkXError, match="no basal nodes"):
-        nx.trophic_levels(G)
-
-
-def test_trophic_levels_singular_with_basal():
-    """Should fail to compute if there are any parts of the graph which are not
-    reachable from any basal node (with in-degree zero).
-    """
-    G = nx.DiGraph()
-    # a has in-degree zero
-    G.add_edge("a", "b")
-
-    # b is one level above a, c and d
-    G.add_edge("c", "b")
-    G.add_edge("d", "b")
-
-    # c and d form a loop, neither are reachable from a
-    G.add_edge("c", "d")
-    G.add_edge("d", "c")
-
-    with pytest.raises(nx.NetworkXError) as e:
-        nx.trophic_levels(G)
-    msg = (
-        "Trophic levels are only defined for graphs where every node "
-        + "has a path from a basal node (basal nodes are nodes with no "
-        + "incoming edges)."
-    )
-    assert msg in str(e.value)
-
-    # if self-loops are allowed, smaller example:
-    G = nx.DiGraph()
-    G.add_edge("a", "b")  # a has in-degree zero
-    G.add_edge("c", "b")  # b is one level above a and c
-    G.add_edge("c", "c")  # c has a self-loop
-    with pytest.raises(nx.NetworkXError) as e:
-        nx.trophic_levels(G)
-    msg = (
-        "Trophic levels are only defined for graphs where every node "
-        + "has a path from a basal node (basal nodes are nodes with no "
-        + "incoming edges)."
-    )
-    assert msg in str(e.value)
-
-
-def test_trophic_differences():
-    matrix_a = np.array([[0, 1], [0, 0]])
-    G = nx.from_numpy_array(matrix_a, create_using=nx.DiGraph)
-    diffs = nx.trophic_differences(G)
-    assert diffs[(0, 1)] == pytest.approx(1, abs=1e-7)
-
-    # fmt: off
-    matrix_b = np.array([
-        [0, 1, 1, 0],
-        [0, 0, 1, 1],
-        [0, 0, 0, 1],
-        [0, 0, 0, 0]
-    ])
-    # fmt: on
-    G = nx.from_numpy_array(matrix_b, create_using=nx.DiGraph)
-    diffs = nx.trophic_differences(G)
-
-    assert diffs[(0, 1)] == pytest.approx(1, abs=1e-7)
-    assert diffs[(0, 2)] == pytest.approx(1.5, abs=1e-7)
-    assert diffs[(1, 2)] == pytest.approx(0.5, abs=1e-7)
-    assert diffs[(1, 3)] == pytest.approx(1.25, abs=1e-7)
-    assert diffs[(2, 3)] == pytest.approx(0.75, abs=1e-7)
-
-
-def test_trophic_incoherence_parameter_no_cannibalism():
-    matrix_a = np.array([[0, 1], [0, 0]])
-    G = nx.from_numpy_array(matrix_a, create_using=nx.DiGraph)
-    q = nx.trophic_incoherence_parameter(G, cannibalism=False)
-    assert q == pytest.approx(0, abs=1e-7)
-
-    # fmt: off
-    matrix_b = np.array([
-        [0, 1, 1, 0],
-        [0, 0, 1, 1],
-        [0, 0, 0, 1],
-        [0, 0, 0, 0]
-    ])
-    # fmt: on
-    G = nx.from_numpy_array(matrix_b, create_using=nx.DiGraph)
-    q = nx.trophic_incoherence_parameter(G, cannibalism=False)
-    assert q == pytest.approx(np.std([1, 1.5, 0.5, 0.75, 1.25]), abs=1e-7)
-
-    # fmt: off
-    matrix_c = np.array([
-        [0, 1, 1, 0],
-        [0, 1, 1, 1],
-        [0, 0, 0, 1],
-        [0, 0, 0, 1]
-    ])
-    # fmt: on
-    G = nx.from_numpy_array(matrix_c, create_using=nx.DiGraph)
-    q = nx.trophic_incoherence_parameter(G, cannibalism=False)
-    # Ignore the -link
-    assert q == pytest.approx(np.std([1, 1.5, 0.5, 0.75, 1.25]), abs=1e-7)
-
-    # no self-loops case
-    # fmt: off
-    matrix_d = np.array([
-        [0, 1, 1, 0],
-        [0, 0, 1, 1],
-        [0, 0, 0, 1],
-        [0, 0, 0, 0]
-    ])
-    # fmt: on
-    G = nx.from_numpy_array(matrix_d, create_using=nx.DiGraph)
-    q = nx.trophic_incoherence_parameter(G, cannibalism=False)
-    # Ignore the -link
-    assert q == pytest.approx(np.std([1, 1.5, 0.5, 0.75, 1.25]), abs=1e-7)
-
-
-def test_trophic_incoherence_parameter_cannibalism():
-    matrix_a = np.array([[0, 1], [0, 0]])
-    G = nx.from_numpy_array(matrix_a, create_using=nx.DiGraph)
-    q = nx.trophic_incoherence_parameter(G, cannibalism=True)
-    assert q == pytest.approx(0, abs=1e-7)
-
-    # fmt: off
-    matrix_b = np.array([
-        [0, 0, 0, 0, 0],
-        [0, 1, 0, 1, 0],
-        [1, 0, 0, 0, 0],
-        [0, 1, 0, 0, 0],
-        [0, 0, 0, 1, 0]
-    ])
-    # fmt: on
-    G = nx.from_numpy_array(matrix_b, create_using=nx.DiGraph)
-    q = nx.trophic_incoherence_parameter(G, cannibalism=True)
-    assert q == pytest.approx(2, abs=1e-7)
-
-    # fmt: off
-    matrix_c = np.array([
-        [0, 1, 1, 0],
-        [0, 0, 1, 1],
-        [0, 0, 0, 1],
-        [0, 0, 0, 0]
-    ])
-    # fmt: on
-    G = nx.from_numpy_array(matrix_c, create_using=nx.DiGraph)
-    q = nx.trophic_incoherence_parameter(G, cannibalism=True)
-    # Ignore the -link
-    assert q == pytest.approx(np.std([1, 1.5, 0.5, 0.75, 1.25]), abs=1e-7)
-
-
-def test_no_basal_node():
-    G = nx.DiGraph([(1, 2), (2, 3), (3, 1)])  # No basal node, should raise an error
-    with pytest.raises(nx.NetworkXError, match="no basal node"):
-        nx.trophic_levels(G)
-    G.add_node(4)  # add basal node, but not connected
-    with pytest.raises(nx.NetworkXError, match="every node .* path from a basal node"):
-        nx.trophic_levels(G)

package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_voterank.py

@@ -1,64 +0,0 @@
-"""
-Unit tests for VoteRank.
-"""
-
-import networkx as nx
-
-
-class TestVoteRankCentrality:
-    # Example Graph present in reference paper
-    def test_voterank_centrality_1(self):
-        G = nx.Graph()
-        G.add_edges_from(
-            [
-                (7, 8),
-                (7, 5),
-                (7, 9),
-                (5, 0),
-                (0, 1),
-                (0, 2),
-                (0, 3),
-                (0, 4),
-                (1, 6),
-                (2, 6),
-                (3, 6),
-                (4, 6),
-            ]
-        )
-        assert [0, 7, 6] == nx.voterank(G)
-
-    def test_voterank_emptygraph(self):
-        G = nx.Graph()
-        assert [] == nx.voterank(G)
-
-    # Graph unit test
-    def test_voterank_centrality_2(self):
-        G = nx.florentine_families_graph()
-        d = nx.voterank(G, 4)
-        exact = ["Medici", "Strozzi", "Guadagni", "Castellani"]
-        assert exact == d
-
-    # DiGraph unit test
-    def test_voterank_centrality_3(self):
-        G = nx.gnc_graph(10, seed=7)
-        d = nx.voterank(G, 4)
-        exact = [3, 6, 8]
-        assert exact == d
-
-    # MultiGraph unit test
-    def test_voterank_centrality_4(self):
-        G = nx.MultiGraph()
-        G.add_edges_from(
-            [(0, 1), (0, 1), (1, 2), (2, 5), (2, 5), (5, 6), (5, 6), (2, 4), (4, 3)]
-        )
-        exact = [2, 1, 5, 4]
-        assert exact == nx.voterank(G)
-
-    # MultiDiGraph unit test
-    def test_voterank_centrality_5(self):
-        G = nx.MultiDiGraph()
-        G.add_edges_from(
-            [(0, 1), (0, 1), (1, 2), (2, 5), (2, 5), (5, 6), (5, 6), (2, 4), (4, 3)]
-        )
-        exact = [2, 0, 5, 4]
-        assert exact == nx.voterank(G)