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

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/networkx/algorithms/tests/test_threshold.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,278 @@
+"""
+Threshold Graphs
+================
+"""
+
+import pytest
+
+import networkx as nx
+import networkx.algorithms.threshold as nxt
+from networkx.algorithms.isomorphism.isomorph import graph_could_be_isomorphic
+from networkx.testing import almost_equal
+
+cnlti = nx.convert_node_labels_to_integers
+
+
+class TestGeneratorThreshold:
+    def test_threshold_sequence_graph_test(self):
+        G = nx.star_graph(10)
+        assert nxt.is_threshold_graph(G)
+        assert nxt.is_threshold_sequence(list(d for n, d in G.degree()))
+
+        G = nx.complete_graph(10)
+        assert nxt.is_threshold_graph(G)
+        assert nxt.is_threshold_sequence(list(d for n, d in G.degree()))
+
+        deg = [3, 2, 2, 1, 1, 1]
+        assert not nxt.is_threshold_sequence(deg)
+
+        deg = [3, 2, 2, 1]
+        assert nxt.is_threshold_sequence(deg)
+
+        G = nx.generators.havel_hakimi_graph(deg)
+        assert nxt.is_threshold_graph(G)
+
+    def test_creation_sequences(self):
+        deg = [3, 2, 2, 1]
+        G = nx.generators.havel_hakimi_graph(deg)
+
+        with pytest.raises(ValueError):
+            nxt.creation_sequence(deg, with_labels=True, compact=True)
+
+        cs0 = nxt.creation_sequence(deg)
+        H0 = nxt.threshold_graph(cs0)
+        assert "".join(cs0) == "ddid"
+
+        cs1 = nxt.creation_sequence(deg, with_labels=True)
+        H1 = nxt.threshold_graph(cs1)
+        assert cs1 == [(1, "d"), (2, "d"), (3, "i"), (0, "d")]
+
+        cs2 = nxt.creation_sequence(deg, compact=True)
+        H2 = nxt.threshold_graph(cs2)
+        assert cs2 == [2, 1, 1]
+        assert "".join(nxt.uncompact(cs2)) == "ddid"
+        assert graph_could_be_isomorphic(H0, G)
+        assert graph_could_be_isomorphic(H0, H1)
+        assert graph_could_be_isomorphic(H0, H2)
+
+    def test_make_compact(self):
+        assert nxt.make_compact(["d", "d", "d", "i", "d", "d"]) == [3, 1, 2]
+        assert nxt.make_compact([3, 1, 2]) == [3, 1, 2]
+        assert pytest.raises(TypeError, nxt.make_compact, [3.0, 1.0, 2.0])
+
+    def test_uncompact(self):
+        assert nxt.uncompact([3, 1, 2]) == ["d", "d", "d", "i", "d", "d"]
+        assert nxt.uncompact(["d", "d", "i", "d"]) == ["d", "d", "i", "d"]
+        assert nxt.uncompact(
+            nxt.uncompact([(1, "d"), (2, "d"), (3, "i"), (0, "d")])
+        ) == nxt.uncompact([(1, "d"), (2, "d"), (3, "i"), (0, "d")])
+        assert pytest.raises(TypeError, nxt.uncompact, [3.0, 1.0, 2.0])
+
+    def test_creation_sequence_to_weights(self):
+        assert nxt.creation_sequence_to_weights([3, 1, 2]) == [
+            0.5,
+            0.5,
+            0.5,
+            0.25,
+            0.75,
+            0.75,
+        ]
+        assert pytest.raises(
+            TypeError, nxt.creation_sequence_to_weights, [3.0, 1.0, 2.0]
+        )
+
+    def test_weights_to_creation_sequence(self):
+        deg = [3, 2, 2, 1]
+        with pytest.raises(ValueError):
+            nxt.weights_to_creation_sequence(deg, with_labels=True, compact=True)
+        assert nxt.weights_to_creation_sequence(deg, with_labels=True) == [
+            (3, "d"),
+            (1, "d"),
+            (2, "d"),
+            (0, "d"),
+        ]
+        assert nxt.weights_to_creation_sequence(deg, compact=True) == [4]
+
+    def test_find_alternating_4_cycle(self):
+        G = nx.Graph()
+        G.add_edge(1, 2)
+        assert not nxt.find_alternating_4_cycle(G)
+
+    def test_shortest_path(self):
+        deg = [3, 2, 2, 1]
+        G = nx.generators.havel_hakimi_graph(deg)
+        cs1 = nxt.creation_sequence(deg, with_labels=True)
+        for n, m in [(3, 0), (0, 3), (0, 2), (0, 1), (1, 3), (3, 1), (1, 2), (2, 3)]:
+            assert nxt.shortest_path(cs1, n, m) == nx.shortest_path(G, n, m)
+
+        spl = nxt.shortest_path_length(cs1, 3)
+        spl2 = nxt.shortest_path_length([t for v, t in cs1], 2)
+        assert spl == spl2
+
+        spld = {}
+        for j, pl in enumerate(spl):
+            n = cs1[j][0]
+            spld[n] = pl
+        assert spld == nx.single_source_shortest_path_length(G, 3)
+
+        assert nxt.shortest_path(["d", "d", "d", "i", "d", "d"], 1, 2) == [1, 2]
+        assert nxt.shortest_path([3, 1, 2], 1, 2) == [1, 2]
+        assert pytest.raises(TypeError, nxt.shortest_path, [3.0, 1.0, 2.0], 1, 2)
+        assert pytest.raises(ValueError, nxt.shortest_path, [3, 1, 2], "a", 2)
+        assert pytest.raises(ValueError, nxt.shortest_path, [3, 1, 2], 1, "b")
+        assert nxt.shortest_path([3, 1, 2], 1, 1) == [1]
+
+    def test_shortest_path_length(self):
+        assert nxt.shortest_path_length([3, 1, 2], 1) == [1, 0, 1, 2, 1, 1]
+        assert nxt.shortest_path_length(["d", "d", "d", "i", "d", "d"], 1) == [
+            1,
+            0,
+            1,
+            2,
+            1,
+            1,
+        ]
+        assert nxt.shortest_path_length(("d", "d", "d", "i", "d", "d"), 1) == [
+            1,
+            0,
+            1,
+            2,
+            1,
+            1,
+        ]
+        assert pytest.raises(TypeError, nxt.shortest_path, [3.0, 1.0, 2.0], 1)
+
+    def random_threshold_sequence(self):
+        assert len(nxt.random_threshold_sequence(10, 0.5)) == 10
+        assert nxt.random_threshold_sequence(10, 0.5, seed=42) == [
+            "d",
+            "i",
+            "d",
+            "d",
+            "d",
+            "i",
+            "i",
+            "i",
+            "d",
+            "d",
+        ]
+        assert pytest.raises(ValueError, nxt.random_threshold_sequence, 10, 1.5)
+
+    def test_right_d_threshold_sequence(self):
+        assert nxt.right_d_threshold_sequence(3, 2) == ["d", "i", "d"]
+        assert pytest.raises(ValueError, nxt.right_d_threshold_sequence, 2, 3)
+
+    def test_left_d_threshold_sequence(self):
+        assert nxt.left_d_threshold_sequence(3, 2) == ["d", "i", "d"]
+        assert pytest.raises(ValueError, nxt.left_d_threshold_sequence, 2, 3)
+
+    def test_weights_thresholds(self):
+        wseq = [3, 4, 3, 3, 5, 6, 5, 4, 5, 6]
+        cs = nxt.weights_to_creation_sequence(wseq, threshold=10)
+        wseq = nxt.creation_sequence_to_weights(cs)
+        cs2 = nxt.weights_to_creation_sequence(wseq)
+        assert cs == cs2
+
+        wseq = nxt.creation_sequence_to_weights(nxt.uncompact([3, 1, 2, 3, 3, 2, 3]))
+        assert wseq == [
+            s * 0.125 for s in [4, 4, 4, 3, 5, 5, 2, 2, 2, 6, 6, 6, 1, 1, 7, 7, 7]
+        ]
+
+        wseq = nxt.creation_sequence_to_weights([3, 1, 2, 3, 3, 2, 3])
+        assert wseq == [
+            s * 0.125 for s in [4, 4, 4, 3, 5, 5, 2, 2, 2, 6, 6, 6, 1, 1, 7, 7, 7]
+        ]
+
+        wseq = nxt.creation_sequence_to_weights(list(enumerate("ddidiiidididi")))
+        assert wseq == [s * 0.1 for s in [5, 5, 4, 6, 3, 3, 3, 7, 2, 8, 1, 9, 0]]
+
+        wseq = nxt.creation_sequence_to_weights("ddidiiidididi")
+        assert wseq == [s * 0.1 for s in [5, 5, 4, 6, 3, 3, 3, 7, 2, 8, 1, 9, 0]]
+
+        wseq = nxt.creation_sequence_to_weights("ddidiiidididid")
+        ws = [s / float(12) for s in [6, 6, 5, 7, 4, 4, 4, 8, 3, 9, 2, 10, 1, 11]]
+        assert sum([abs(c - d) for c, d in zip(wseq, ws)]) < 1e-14
+
+    def test_finding_routines(self):
+        G = nx.Graph({1: [2], 2: [3], 3: [4], 4: [5], 5: [6]})
+        G.add_edge(2, 4)
+        G.add_edge(2, 5)
+        G.add_edge(2, 7)
+        G.add_edge(3, 6)
+        G.add_edge(4, 6)
+
+        # Alternating 4 cycle
+        assert nxt.find_alternating_4_cycle(G) == [1, 2, 3, 6]
+
+        # Threshold graph
+        TG = nxt.find_threshold_graph(G)
+        assert nxt.is_threshold_graph(TG)
+        assert sorted(TG.nodes()) == [1, 2, 3, 4, 5, 7]
+
+        cs = nxt.creation_sequence(dict(TG.degree()), with_labels=True)
+        assert nxt.find_creation_sequence(G) == cs
+
+    def test_fast_versions_properties_threshold_graphs(self):
+        cs = "ddiiddid"
+        G = nxt.threshold_graph(cs)
+        assert nxt.density("ddiiddid") == nx.density(G)
+        assert sorted(nxt.degree_sequence(cs)) == sorted(d for n, d in G.degree())
+
+        ts = nxt.triangle_sequence(cs)
+        assert ts == list(nx.triangles(G).values())
+        assert sum(ts) // 3 == nxt.triangles(cs)
+
+        c1 = nxt.cluster_sequence(cs)
+        c2 = list(nx.clustering(G).values())
+        assert almost_equal(sum([abs(c - d) for c, d in zip(c1, c2)]), 0)
+
+        b1 = nx.betweenness_centrality(G).values()
+        b2 = nxt.betweenness_sequence(cs)
+        assert sum([abs(c - d) for c, d in zip(b1, b2)]) < 1e-14
+
+        assert nxt.eigenvalues(cs) == [0, 1, 3, 3, 5, 7, 7, 8]
+
+        # Degree Correlation
+        assert abs(nxt.degree_correlation(cs) + 0.593038821954) < 1e-12
+        assert nxt.degree_correlation("diiiddi") == -0.8
+        assert nxt.degree_correlation("did") == -1.0
+        assert nxt.degree_correlation("ddd") == 1.0
+        assert nxt.eigenvalues("dddiii") == [0, 0, 0, 0, 3, 3]
+        assert nxt.eigenvalues("dddiiid") == [0, 1, 1, 1, 4, 4, 7]
+
+    def test_tg_creation_routines(self):
+        s = nxt.left_d_threshold_sequence(5, 7)
+        s = nxt.right_d_threshold_sequence(5, 7)
+        s1 = nxt.swap_d(s, 1.0, 1.0)
+        s1 = nxt.swap_d(s, 1.0, 1.0, seed=1)
+
+    def test_eigenvectors(self):
+        np = pytest.importorskip("numpy")
+        eigenval = np.linalg.eigvals
+        scipy = pytest.importorskip("scipy")
+
+        cs = "ddiiddid"
+        G = nxt.threshold_graph(cs)
+        (tgeval, tgevec) = nxt.eigenvectors(cs)
+        dot = np.dot
+        assert [abs(dot(lv, lv) - 1.0) < 1e-9 for lv in tgevec] == [True] * 8
+        lapl = nx.laplacian_matrix(G)
+
+    #        tgev=[ dot(lv,dot(lapl,lv)) for lv in tgevec ]
+    #        assert_true(sum([abs(c-d) for c,d in zip(tgev,tgeval)]) < 1e-9)
+    #        tgev.sort()
+    #        lev=list(eigenval(lapl))
+    #        lev.sort()
+    #        assert_true(sum([abs(c-d) for c,d in zip(tgev,lev)]) < 1e-9)
+
+    def test_create_using(self):
+        cs = "ddiiddid"
+        G = nxt.threshold_graph(cs)
+        assert pytest.raises(
+            nx.exception.NetworkXError,
+            nxt.threshold_graph,
+            cs,
+            create_using=nx.DiGraph(),
+        )
+        MG = nxt.threshold_graph(cs, create_using=nx.MultiGraph())
+        assert sorted(MG.edges()) == sorted(G.edges())