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env-llmeval/lib/python3.10/site-packages/networkx/algorithms/centrality/tests/test_closeness_centrality.py

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+"""
+Tests for closeness centrality.
+"""
+import pytest
+
+import networkx as nx
+
+
+class TestClosenessCentrality:
+    @classmethod
+    def setup_class(cls):
+        cls.K = nx.krackhardt_kite_graph()
+        cls.P3 = nx.path_graph(3)
+        cls.P4 = nx.path_graph(4)
+        cls.K5 = nx.complete_graph(5)
+
+        cls.C4 = nx.cycle_graph(4)
+        cls.T = nx.balanced_tree(r=2, h=2)
+        cls.Gb = nx.Graph()
+        cls.Gb.add_edges_from([(0, 1), (0, 2), (1, 3), (2, 3), (2, 4), (4, 5), (3, 5)])
+
+        F = nx.florentine_families_graph()
+        cls.F = F
+
+        cls.LM = nx.les_miserables_graph()
+
+        # Create random undirected, unweighted graph for testing incremental version
+        cls.undirected_G = nx.fast_gnp_random_graph(n=100, p=0.6, seed=123)
+        cls.undirected_G_cc = nx.closeness_centrality(cls.undirected_G)
+
+    def test_wf_improved(self):
+        G = nx.union(self.P4, nx.path_graph([4, 5, 6]))
+        c = nx.closeness_centrality(G)
+        cwf = nx.closeness_centrality(G, wf_improved=False)
+        res = {0: 0.25, 1: 0.375, 2: 0.375, 3: 0.25, 4: 0.222, 5: 0.333, 6: 0.222}
+        wf_res = {0: 0.5, 1: 0.75, 2: 0.75, 3: 0.5, 4: 0.667, 5: 1.0, 6: 0.667}
+        for n in G:
+            assert c[n] == pytest.approx(res[n], abs=1e-3)
+            assert cwf[n] == pytest.approx(wf_res[n], abs=1e-3)
+
+    def test_digraph(self):
+        G = nx.path_graph(3, create_using=nx.DiGraph())
+        c = nx.closeness_centrality(G)
+        cr = nx.closeness_centrality(G.reverse())
+        d = {0: 0.0, 1: 0.500, 2: 0.667}
+        dr = {0: 0.667, 1: 0.500, 2: 0.0}
+        for n in sorted(self.P3):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+            assert cr[n] == pytest.approx(dr[n], abs=1e-3)
+
+    def test_k5_closeness(self):
+        c = nx.closeness_centrality(self.K5)
+        d = {0: 1.000, 1: 1.000, 2: 1.000, 3: 1.000, 4: 1.000}
+        for n in sorted(self.K5):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_p3_closeness(self):
+        c = nx.closeness_centrality(self.P3)
+        d = {0: 0.667, 1: 1.000, 2: 0.667}
+        for n in sorted(self.P3):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_krackhardt_closeness(self):
+        c = nx.closeness_centrality(self.K)
+        d = {
+            0: 0.529,
+            1: 0.529,
+            2: 0.500,
+            3: 0.600,
+            4: 0.500,
+            5: 0.643,
+            6: 0.643,
+            7: 0.600,
+            8: 0.429,
+            9: 0.310,
+        }
+        for n in sorted(self.K):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_florentine_families_closeness(self):
+        c = nx.closeness_centrality(self.F)
+        d = {
+            "Acciaiuoli": 0.368,
+            "Albizzi": 0.483,
+            "Barbadori": 0.4375,
+            "Bischeri": 0.400,
+            "Castellani": 0.389,
+            "Ginori": 0.333,
+            "Guadagni": 0.467,
+            "Lamberteschi": 0.326,
+            "Medici": 0.560,
+            "Pazzi": 0.286,
+            "Peruzzi": 0.368,
+            "Ridolfi": 0.500,
+            "Salviati": 0.389,
+            "Strozzi": 0.4375,
+            "Tornabuoni": 0.483,
+        }
+        for n in sorted(self.F):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_les_miserables_closeness(self):
+        c = nx.closeness_centrality(self.LM)
+        d = {
+            "Napoleon": 0.302,
+            "Myriel": 0.429,
+            "MlleBaptistine": 0.413,
+            "MmeMagloire": 0.413,
+            "CountessDeLo": 0.302,
+            "Geborand": 0.302,
+            "Champtercier": 0.302,
+            "Cravatte": 0.302,
+            "Count": 0.302,
+            "OldMan": 0.302,
+            "Valjean": 0.644,
+            "Labarre": 0.394,
+            "Marguerite": 0.413,
+            "MmeDeR": 0.394,
+            "Isabeau": 0.394,
+            "Gervais": 0.394,
+            "Listolier": 0.341,
+            "Tholomyes": 0.392,
+            "Fameuil": 0.341,
+            "Blacheville": 0.341,
+            "Favourite": 0.341,
+            "Dahlia": 0.341,
+            "Zephine": 0.341,
+            "Fantine": 0.461,
+            "MmeThenardier": 0.461,
+            "Thenardier": 0.517,
+            "Cosette": 0.478,
+            "Javert": 0.517,
+            "Fauchelevent": 0.402,
+            "Bamatabois": 0.427,
+            "Perpetue": 0.318,
+            "Simplice": 0.418,
+            "Scaufflaire": 0.394,
+            "Woman1": 0.396,
+            "Judge": 0.404,
+            "Champmathieu": 0.404,
+            "Brevet": 0.404,
+            "Chenildieu": 0.404,
+            "Cochepaille": 0.404,
+            "Pontmercy": 0.373,
+            "Boulatruelle": 0.342,
+            "Eponine": 0.396,
+            "Anzelma": 0.352,
+            "Woman2": 0.402,
+            "MotherInnocent": 0.398,
+            "Gribier": 0.288,
+            "MmeBurgon": 0.344,
+            "Jondrette": 0.257,
+            "Gavroche": 0.514,
+            "Gillenormand": 0.442,
+            "Magnon": 0.335,
+            "MlleGillenormand": 0.442,
+            "MmePontmercy": 0.315,
+            "MlleVaubois": 0.308,
+            "LtGillenormand": 0.365,
+            "Marius": 0.531,
+            "BaronessT": 0.352,
+            "Mabeuf": 0.396,
+            "Enjolras": 0.481,
+            "Combeferre": 0.392,
+            "Prouvaire": 0.357,
+            "Feuilly": 0.392,
+            "Courfeyrac": 0.400,
+            "Bahorel": 0.394,
+            "Bossuet": 0.475,
+            "Joly": 0.394,
+            "Grantaire": 0.358,
+            "MotherPlutarch": 0.285,
+            "Gueulemer": 0.463,
+            "Babet": 0.463,
+            "Claquesous": 0.452,
+            "Montparnasse": 0.458,
+            "Toussaint": 0.402,
+            "Child1": 0.342,
+            "Child2": 0.342,
+            "Brujon": 0.380,
+            "MmeHucheloup": 0.353,
+        }
+        for n in sorted(self.LM):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_weighted_closeness(self):
+        edges = [
+            ("s", "u", 10),
+            ("s", "x", 5),
+            ("u", "v", 1),
+            ("u", "x", 2),
+            ("v", "y", 1),
+            ("x", "u", 3),
+            ("x", "v", 5),
+            ("x", "y", 2),
+            ("y", "s", 7),
+            ("y", "v", 6),
+        ]
+        XG = nx.Graph()
+        XG.add_weighted_edges_from(edges)
+        c = nx.closeness_centrality(XG, distance="weight")
+        d = {"y": 0.200, "x": 0.286, "s": 0.138, "u": 0.235, "v": 0.200}
+        for n in sorted(XG):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    #
+    # Tests for incremental closeness centrality.
+    #
+    @staticmethod
+    def pick_add_edge(g):
+        u = nx.utils.arbitrary_element(g)
+        possible_nodes = set(g.nodes())
+        neighbors = list(g.neighbors(u)) + [u]
+        possible_nodes.difference_update(neighbors)
+        v = nx.utils.arbitrary_element(possible_nodes)
+        return (u, v)
+
+    @staticmethod
+    def pick_remove_edge(g):
+        u = nx.utils.arbitrary_element(g)
+        possible_nodes = list(g.neighbors(u))
+        v = nx.utils.arbitrary_element(possible_nodes)
+        return (u, v)
+
+    def test_directed_raises(self):
+        with pytest.raises(nx.NetworkXNotImplemented):
+            dir_G = nx.gn_graph(n=5)
+            prev_cc = None
+            edge = self.pick_add_edge(dir_G)
+            insert = True
+            nx.incremental_closeness_centrality(dir_G, edge, prev_cc, insert)
+
+    def test_wrong_size_prev_cc_raises(self):
+        with pytest.raises(nx.NetworkXError):
+            G = self.undirected_G.copy()
+            edge = self.pick_add_edge(G)
+            insert = True
+            prev_cc = self.undirected_G_cc.copy()
+            prev_cc.pop(0)
+            nx.incremental_closeness_centrality(G, edge, prev_cc, insert)
+
+    def test_wrong_nodes_prev_cc_raises(self):
+        with pytest.raises(nx.NetworkXError):
+            G = self.undirected_G.copy()
+            edge = self.pick_add_edge(G)
+            insert = True
+            prev_cc = self.undirected_G_cc.copy()
+            num_nodes = len(prev_cc)
+            prev_cc.pop(0)
+            prev_cc[num_nodes] = 0.5
+            nx.incremental_closeness_centrality(G, edge, prev_cc, insert)
+
+    def test_zero_centrality(self):
+        G = nx.path_graph(3)
+        prev_cc = nx.closeness_centrality(G)
+        edge = self.pick_remove_edge(G)
+        test_cc = nx.incremental_closeness_centrality(G, edge, prev_cc, insertion=False)
+        G.remove_edges_from([edge])
+        real_cc = nx.closeness_centrality(G)
+        shared_items = set(test_cc.items()) & set(real_cc.items())
+        assert len(shared_items) == len(real_cc)
+        assert 0 in test_cc.values()
+
+    def test_incremental(self):
+        # Check that incremental and regular give same output
+        G = self.undirected_G.copy()
+        prev_cc = None
+        for i in range(5):
+            if i % 2 == 0:
+                # Remove an edge
+                insert = False
+                edge = self.pick_remove_edge(G)
+            else:
+                # Add an edge
+                insert = True
+                edge = self.pick_add_edge(G)
+
+            # start = timeit.default_timer()
+            test_cc = nx.incremental_closeness_centrality(G, edge, prev_cc, insert)
+            # inc_elapsed = (timeit.default_timer() - start)
+            # print(f"incremental time: {inc_elapsed}")
+
+            if insert:
+                G.add_edges_from([edge])
+            else:
+                G.remove_edges_from([edge])
+
+            # start = timeit.default_timer()
+            real_cc = nx.closeness_centrality(G)
+            # reg_elapsed = (timeit.default_timer() - start)
+            # print(f"regular time: {reg_elapsed}")
+            # Example output:
+            # incremental time: 0.208
+            # regular time: 0.276
+            # incremental time: 0.00683
+            # regular time: 0.260
+            # incremental time: 0.0224
+            # regular time: 0.278
+            # incremental time: 0.00804
+            # regular time: 0.208
+            # incremental time: 0.00947
+            # regular time: 0.188
+
+            assert set(test_cc.items()) == set(real_cc.items())
+
+            prev_cc = test_cc

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/centrality/tests/test_current_flow_betweenness_centrality_subset.py

@@ -0,0 +1,147 @@
+import pytest
+
+pytest.importorskip("numpy")
+pytest.importorskip("scipy")
+
+import networkx as nx
+from networkx import edge_current_flow_betweenness_centrality as edge_current_flow
+from networkx import (
+    edge_current_flow_betweenness_centrality_subset as edge_current_flow_subset,
+)
+
+
+class TestFlowBetweennessCentrality:
+    def test_K4_normalized(self):
+        """Betweenness centrality: K4"""
+        G = nx.complete_graph(4)
+        b = nx.current_flow_betweenness_centrality_subset(
+            G, list(G), list(G), normalized=True
+        )
+        b_answer = nx.current_flow_betweenness_centrality(G, normalized=True)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+
+    def test_K4(self):
+        """Betweenness centrality: K4"""
+        G = nx.complete_graph(4)
+        b = nx.current_flow_betweenness_centrality_subset(
+            G, list(G), list(G), normalized=True
+        )
+        b_answer = nx.current_flow_betweenness_centrality(G, normalized=True)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+        # test weighted network
+        G.add_edge(0, 1, weight=0.5, other=0.3)
+        b = nx.current_flow_betweenness_centrality_subset(
+            G, list(G), list(G), normalized=True, weight=None
+        )
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+        b = nx.current_flow_betweenness_centrality_subset(
+            G, list(G), list(G), normalized=True
+        )
+        b_answer = nx.current_flow_betweenness_centrality(G, normalized=True)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+        b = nx.current_flow_betweenness_centrality_subset(
+            G, list(G), list(G), normalized=True, weight="other"
+        )
+        b_answer = nx.current_flow_betweenness_centrality(
+            G, normalized=True, weight="other"
+        )
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+
+    def test_P4_normalized(self):
+        """Betweenness centrality: P4 normalized"""
+        G = nx.path_graph(4)
+        b = nx.current_flow_betweenness_centrality_subset(
+            G, list(G), list(G), normalized=True
+        )
+        b_answer = nx.current_flow_betweenness_centrality(G, normalized=True)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+
+    def test_P4(self):
+        """Betweenness centrality: P4"""
+        G = nx.path_graph(4)
+        b = nx.current_flow_betweenness_centrality_subset(
+            G, list(G), list(G), normalized=True
+        )
+        b_answer = nx.current_flow_betweenness_centrality(G, normalized=True)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+
+    def test_star(self):
+        """Betweenness centrality: star"""
+        G = nx.Graph()
+        nx.add_star(G, ["a", "b", "c", "d"])
+        b = nx.current_flow_betweenness_centrality_subset(
+            G, list(G), list(G), normalized=True
+        )
+        b_answer = nx.current_flow_betweenness_centrality(G, normalized=True)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+
+
+# class TestWeightedFlowBetweennessCentrality():
+#     pass
+
+
+class TestEdgeFlowBetweennessCentrality:
+    def test_K4_normalized(self):
+        """Betweenness centrality: K4"""
+        G = nx.complete_graph(4)
+        b = edge_current_flow_subset(G, list(G), list(G), normalized=True)
+        b_answer = edge_current_flow(G, normalized=True)
+        for (s, t), v1 in b_answer.items():
+            v2 = b.get((s, t), b.get((t, s)))
+            assert v1 == pytest.approx(v2, abs=1e-7)
+
+    def test_K4(self):
+        """Betweenness centrality: K4"""
+        G = nx.complete_graph(4)
+        b = edge_current_flow_subset(G, list(G), list(G), normalized=False)
+        b_answer = edge_current_flow(G, normalized=False)
+        for (s, t), v1 in b_answer.items():
+            v2 = b.get((s, t), b.get((t, s)))
+            assert v1 == pytest.approx(v2, abs=1e-7)
+        # test weighted network
+        G.add_edge(0, 1, weight=0.5, other=0.3)
+        b = edge_current_flow_subset(G, list(G), list(G), normalized=False, weight=None)
+        # weight is None => same as unweighted network
+        for (s, t), v1 in b_answer.items():
+            v2 = b.get((s, t), b.get((t, s)))
+            assert v1 == pytest.approx(v2, abs=1e-7)
+
+        b = edge_current_flow_subset(G, list(G), list(G), normalized=False)
+        b_answer = edge_current_flow(G, normalized=False)
+        for (s, t), v1 in b_answer.items():
+            v2 = b.get((s, t), b.get((t, s)))
+            assert v1 == pytest.approx(v2, abs=1e-7)
+
+        b = edge_current_flow_subset(
+            G, list(G), list(G), normalized=False, weight="other"
+        )
+        b_answer = edge_current_flow(G, normalized=False, weight="other")
+        for (s, t), v1 in b_answer.items():
+            v2 = b.get((s, t), b.get((t, s)))
+            assert v1 == pytest.approx(v2, abs=1e-7)
+
+    def test_C4(self):
+        """Edge betweenness centrality: C4"""
+        G = nx.cycle_graph(4)
+        b = edge_current_flow_subset(G, list(G), list(G), normalized=True)
+        b_answer = edge_current_flow(G, normalized=True)
+        for (s, t), v1 in b_answer.items():
+            v2 = b.get((s, t), b.get((t, s)))
+            assert v1 == pytest.approx(v2, abs=1e-7)
+
+    def test_P4(self):
+        """Edge betweenness centrality: P4"""
+        G = nx.path_graph(4)
+        b = edge_current_flow_subset(G, list(G), list(G), normalized=True)
+        b_answer = edge_current_flow(G, normalized=True)
+        for (s, t), v1 in b_answer.items():
+            v2 = b.get((s, t), b.get((t, s)))
+            assert v1 == pytest.approx(v2, abs=1e-7)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/centrality/tests/test_harmonic_centrality.py

@@ -0,0 +1,115 @@
+"""
+Tests for degree centrality.
+"""
+import pytest
+
+import networkx as nx
+from networkx.algorithms.centrality import harmonic_centrality
+
+
+class TestClosenessCentrality:
+    @classmethod
+    def setup_class(cls):
+        cls.P3 = nx.path_graph(3)
+        cls.P4 = nx.path_graph(4)
+        cls.K5 = nx.complete_graph(5)
+
+        cls.C4 = nx.cycle_graph(4)
+        cls.C4_directed = nx.cycle_graph(4, create_using=nx.DiGraph)
+
+        cls.C5 = nx.cycle_graph(5)
+
+        cls.T = nx.balanced_tree(r=2, h=2)
+
+        cls.Gb = nx.DiGraph()
+        cls.Gb.add_edges_from([(0, 1), (0, 2), (0, 4), (2, 1), (2, 3), (4, 3)])
+
+    def test_p3_harmonic(self):
+        c = harmonic_centrality(self.P3)
+        d = {0: 1.5, 1: 2, 2: 1.5}
+        for n in sorted(self.P3):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_p4_harmonic(self):
+        c = harmonic_centrality(self.P4)
+        d = {0: 1.8333333, 1: 2.5, 2: 2.5, 3: 1.8333333}
+        for n in sorted(self.P4):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_clique_complete(self):
+        c = harmonic_centrality(self.K5)
+        d = {0: 4, 1: 4, 2: 4, 3: 4, 4: 4}
+        for n in sorted(self.P3):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_cycle_C4(self):
+        c = harmonic_centrality(self.C4)
+        d = {0: 2.5, 1: 2.5, 2: 2.5, 3: 2.5}
+        for n in sorted(self.C4):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_cycle_C5(self):
+        c = harmonic_centrality(self.C5)
+        d = {0: 3, 1: 3, 2: 3, 3: 3, 4: 3, 5: 4}
+        for n in sorted(self.C5):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_bal_tree(self):
+        c = harmonic_centrality(self.T)
+        d = {0: 4.0, 1: 4.1666, 2: 4.1666, 3: 2.8333, 4: 2.8333, 5: 2.8333, 6: 2.8333}
+        for n in sorted(self.T):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_exampleGraph(self):
+        c = harmonic_centrality(self.Gb)
+        d = {0: 0, 1: 2, 2: 1, 3: 2.5, 4: 1}
+        for n in sorted(self.Gb):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_weighted_harmonic(self):
+        XG = nx.DiGraph()
+        XG.add_weighted_edges_from(
+            [
+                ("a", "b", 10),
+                ("d", "c", 5),
+                ("a", "c", 1),
+                ("e", "f", 2),
+                ("f", "c", 1),
+                ("a", "f", 3),
+            ]
+        )
+        c = harmonic_centrality(XG, distance="weight")
+        d = {"a": 0, "b": 0.1, "c": 2.533, "d": 0, "e": 0, "f": 0.83333}
+        for n in sorted(XG):
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_empty(self):
+        G = nx.DiGraph()
+        c = harmonic_centrality(G, distance="weight")
+        d = {}
+        assert c == d
+
+    def test_singleton(self):
+        G = nx.DiGraph()
+        G.add_node(0)
+        c = harmonic_centrality(G, distance="weight")
+        d = {0: 0}
+        assert c == d
+
+    def test_cycle_c4_directed(self):
+        c = harmonic_centrality(self.C4_directed, nbunch=[0, 1], sources=[1, 2])
+        d = {0: 0.833, 1: 0.333}
+        for n in [0, 1]:
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_p3_harmonic_subset(self):
+        c = harmonic_centrality(self.P3, sources=[0, 1])
+        d = {0: 1, 1: 1, 2: 1.5}
+        for n in self.P3:
+            assert c[n] == pytest.approx(d[n], abs=1e-3)
+
+    def test_p4_harmonic_subset(self):
+        c = harmonic_centrality(self.P4, nbunch=[2, 3], sources=[0, 1])
+        d = {2: 1.5, 3: 0.8333333}
+        for n in [2, 3]:
+            assert c[n] == pytest.approx(d[n], abs=1e-3)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/centrality/tests/test_katz_centrality.py

@@ -0,0 +1,345 @@
+import math
+
+import pytest
+
+import networkx as nx
+
+
+class TestKatzCentrality:
+    def test_K5(self):
+        """Katz centrality: K5"""
+        G = nx.complete_graph(5)
+        alpha = 0.1
+        b = nx.katz_centrality(G, alpha)
+        v = math.sqrt(1 / 5.0)
+        b_answer = dict.fromkeys(G, v)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+        nstart = {n: 1 for n in G}
+        b = nx.katz_centrality(G, alpha, nstart=nstart)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+
+    def test_P3(self):
+        """Katz centrality: P3"""
+        alpha = 0.1
+        G = nx.path_graph(3)
+        b_answer = {0: 0.5598852584152165, 1: 0.6107839182711449, 2: 0.5598852584152162}
+        b = nx.katz_centrality(G, alpha)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-4)
+
+    def test_maxiter(self):
+        with pytest.raises(nx.PowerIterationFailedConvergence):
+            nx.katz_centrality(nx.path_graph(3), 0.1, max_iter=0)
+
+    def test_beta_as_scalar(self):
+        alpha = 0.1
+        beta = 0.1
+        b_answer = {0: 0.5598852584152165, 1: 0.6107839182711449, 2: 0.5598852584152162}
+        G = nx.path_graph(3)
+        b = nx.katz_centrality(G, alpha, beta)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-4)
+
+    def test_beta_as_dict(self):
+        alpha = 0.1
+        beta = {0: 1.0, 1: 1.0, 2: 1.0}
+        b_answer = {0: 0.5598852584152165, 1: 0.6107839182711449, 2: 0.5598852584152162}
+        G = nx.path_graph(3)
+        b = nx.katz_centrality(G, alpha, beta)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-4)
+
+    def test_multiple_alpha(self):
+        alpha_list = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6]
+        for alpha in alpha_list:
+            b_answer = {
+                0.1: {
+                    0: 0.5598852584152165,
+                    1: 0.6107839182711449,
+                    2: 0.5598852584152162,
+                },
+                0.2: {
+                    0: 0.5454545454545454,
+                    1: 0.6363636363636365,
+                    2: 0.5454545454545454,
+                },
+                0.3: {
+                    0: 0.5333964609104419,
+                    1: 0.6564879518897746,
+                    2: 0.5333964609104419,
+                },
+                0.4: {
+                    0: 0.5232045649263551,
+                    1: 0.6726915834767423,
+                    2: 0.5232045649263551,
+                },
+                0.5: {
+                    0: 0.5144957746691622,
+                    1: 0.6859943117075809,
+                    2: 0.5144957746691622,
+                },
+                0.6: {
+                    0: 0.5069794004195823,
+                    1: 0.6970966755769258,
+                    2: 0.5069794004195823,
+                },
+            }
+            G = nx.path_graph(3)
+            b = nx.katz_centrality(G, alpha)
+            for n in sorted(G):
+                assert b[n] == pytest.approx(b_answer[alpha][n], abs=1e-4)
+
+    def test_multigraph(self):
+        with pytest.raises(nx.NetworkXException):
+            nx.katz_centrality(nx.MultiGraph(), 0.1)
+
+    def test_empty(self):
+        e = nx.katz_centrality(nx.Graph(), 0.1)
+        assert e == {}
+
+    def test_bad_beta(self):
+        with pytest.raises(nx.NetworkXException):
+            G = nx.Graph([(0, 1)])
+            beta = {0: 77}
+            nx.katz_centrality(G, 0.1, beta=beta)
+
+    def test_bad_beta_number(self):
+        with pytest.raises(nx.NetworkXException):
+            G = nx.Graph([(0, 1)])
+            nx.katz_centrality(G, 0.1, beta="foo")
+
+
+class TestKatzCentralityNumpy:
+    @classmethod
+    def setup_class(cls):
+        global np
+        np = pytest.importorskip("numpy")
+        pytest.importorskip("scipy")
+
+    def test_K5(self):
+        """Katz centrality: K5"""
+        G = nx.complete_graph(5)
+        alpha = 0.1
+        b = nx.katz_centrality(G, alpha)
+        v = math.sqrt(1 / 5.0)
+        b_answer = dict.fromkeys(G, v)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+        b = nx.eigenvector_centrality_numpy(G)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-3)
+
+    def test_P3(self):
+        """Katz centrality: P3"""
+        alpha = 0.1
+        G = nx.path_graph(3)
+        b_answer = {0: 0.5598852584152165, 1: 0.6107839182711449, 2: 0.5598852584152162}
+        b = nx.katz_centrality_numpy(G, alpha)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-4)
+
+    def test_beta_as_scalar(self):
+        alpha = 0.1
+        beta = 0.1
+        b_answer = {0: 0.5598852584152165, 1: 0.6107839182711449, 2: 0.5598852584152162}
+        G = nx.path_graph(3)
+        b = nx.katz_centrality_numpy(G, alpha, beta)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-4)
+
+    def test_beta_as_dict(self):
+        alpha = 0.1
+        beta = {0: 1.0, 1: 1.0, 2: 1.0}
+        b_answer = {0: 0.5598852584152165, 1: 0.6107839182711449, 2: 0.5598852584152162}
+        G = nx.path_graph(3)
+        b = nx.katz_centrality_numpy(G, alpha, beta)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-4)
+
+    def test_multiple_alpha(self):
+        alpha_list = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6]
+        for alpha in alpha_list:
+            b_answer = {
+                0.1: {
+                    0: 0.5598852584152165,
+                    1: 0.6107839182711449,
+                    2: 0.5598852584152162,
+                },
+                0.2: {
+                    0: 0.5454545454545454,
+                    1: 0.6363636363636365,
+                    2: 0.5454545454545454,
+                },
+                0.3: {
+                    0: 0.5333964609104419,
+                    1: 0.6564879518897746,
+                    2: 0.5333964609104419,
+                },
+                0.4: {
+                    0: 0.5232045649263551,
+                    1: 0.6726915834767423,
+                    2: 0.5232045649263551,
+                },
+                0.5: {
+                    0: 0.5144957746691622,
+                    1: 0.6859943117075809,
+                    2: 0.5144957746691622,
+                },
+                0.6: {
+                    0: 0.5069794004195823,
+                    1: 0.6970966755769258,
+                    2: 0.5069794004195823,
+                },
+            }
+            G = nx.path_graph(3)
+            b = nx.katz_centrality_numpy(G, alpha)
+            for n in sorted(G):
+                assert b[n] == pytest.approx(b_answer[alpha][n], abs=1e-4)
+
+    def test_multigraph(self):
+        with pytest.raises(nx.NetworkXException):
+            nx.katz_centrality(nx.MultiGraph(), 0.1)
+
+    def test_empty(self):
+        e = nx.katz_centrality(nx.Graph(), 0.1)
+        assert e == {}
+
+    def test_bad_beta(self):
+        with pytest.raises(nx.NetworkXException):
+            G = nx.Graph([(0, 1)])
+            beta = {0: 77}
+            nx.katz_centrality_numpy(G, 0.1, beta=beta)
+
+    def test_bad_beta_numbe(self):
+        with pytest.raises(nx.NetworkXException):
+            G = nx.Graph([(0, 1)])
+            nx.katz_centrality_numpy(G, 0.1, beta="foo")
+
+    def test_K5_unweighted(self):
+        """Katz centrality: K5"""
+        G = nx.complete_graph(5)
+        alpha = 0.1
+        b = nx.katz_centrality(G, alpha, weight=None)
+        v = math.sqrt(1 / 5.0)
+        b_answer = dict.fromkeys(G, v)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-7)
+        b = nx.eigenvector_centrality_numpy(G, weight=None)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-3)
+
+    def test_P3_unweighted(self):
+        """Katz centrality: P3"""
+        alpha = 0.1
+        G = nx.path_graph(3)
+        b_answer = {0: 0.5598852584152165, 1: 0.6107839182711449, 2: 0.5598852584152162}
+        b = nx.katz_centrality_numpy(G, alpha, weight=None)
+        for n in sorted(G):
+            assert b[n] == pytest.approx(b_answer[n], abs=1e-4)
+
+
+class TestKatzCentralityDirected:
+    @classmethod
+    def setup_class(cls):
+        G = nx.DiGraph()
+        edges = [
+            (1, 2),
+            (1, 3),
+            (2, 4),
+            (3, 2),
+            (3, 5),
+            (4, 2),
+            (4, 5),
+            (4, 6),
+            (5, 6),
+            (5, 7),
+            (5, 8),
+            (6, 8),
+            (7, 1),
+            (7, 5),
+            (7, 8),
+            (8, 6),
+            (8, 7),
+        ]
+        G.add_edges_from(edges, weight=2.0)
+        cls.G = G.reverse()
+        cls.G.alpha = 0.1
+        cls.G.evc = [
+            0.3289589783189635,
+            0.2832077296243516,
+            0.3425906003685471,
+            0.3970420865198392,
+            0.41074871061646284,
+            0.272257430756461,
+            0.4201989685435462,
+            0.34229059218038554,
+        ]
+
+        H = nx.DiGraph(edges)
+        cls.H = G.reverse()
+        cls.H.alpha = 0.1
+        cls.H.evc = [
+            0.3289589783189635,
+            0.2832077296243516,
+            0.3425906003685471,
+            0.3970420865198392,
+            0.41074871061646284,
+            0.272257430756461,
+            0.4201989685435462,
+            0.34229059218038554,
+        ]
+
+    def test_katz_centrality_weighted(self):
+        G = self.G
+        alpha = self.G.alpha
+        p = nx.katz_centrality(G, alpha, weight="weight")
+        for a, b in zip(list(p.values()), self.G.evc):
+            assert a == pytest.approx(b, abs=1e-7)
+
+    def test_katz_centrality_unweighted(self):
+        H = self.H
+        alpha = self.H.alpha
+        p = nx.katz_centrality(H, alpha, weight="weight")
+        for a, b in zip(list(p.values()), self.H.evc):
+            assert a == pytest.approx(b, abs=1e-7)
+
+
+class TestKatzCentralityDirectedNumpy(TestKatzCentralityDirected):
+    @classmethod
+    def setup_class(cls):
+        global np
+        np = pytest.importorskip("numpy")
+        pytest.importorskip("scipy")
+        super().setup_class()
+
+    def test_katz_centrality_weighted(self):
+        G = self.G
+        alpha = self.G.alpha
+        p = nx.katz_centrality_numpy(G, alpha, weight="weight")
+        for a, b in zip(list(p.values()), self.G.evc):
+            assert a == pytest.approx(b, abs=1e-7)
+
+    def test_katz_centrality_unweighted(self):
+        H = self.H
+        alpha = self.H.alpha
+        p = nx.katz_centrality_numpy(H, alpha, weight="weight")
+        for a, b in zip(list(p.values()), self.H.evc):
+            assert a == pytest.approx(b, abs=1e-7)
+
+
+class TestKatzEigenvectorVKatz:
+    @classmethod
+    def setup_class(cls):
+        global np
+        np = pytest.importorskip("numpy")
+        pytest.importorskip("scipy")
+
+    def test_eigenvector_v_katz_random(self):
+        G = nx.gnp_random_graph(10, 0.5, seed=1234)
+        l = max(np.linalg.eigvals(nx.adjacency_matrix(G).todense()))
+        e = nx.eigenvector_centrality_numpy(G)
+        k = nx.katz_centrality_numpy(G, 1.0 / l)
+        for n in G:
+            assert e[n] == pytest.approx(k[n], abs=1e-7)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/centrality/tests/test_percolation_centrality.py

@@ -0,0 +1,87 @@
+import pytest
+
+import networkx as nx
+
+
+def example1a_G():
+    G = nx.Graph()
+    G.add_node(1, percolation=0.1)
+    G.add_node(2, percolation=0.2)
+    G.add_node(3, percolation=0.2)
+    G.add_node(4, percolation=0.2)
+    G.add_node(5, percolation=0.3)
+    G.add_node(6, percolation=0.2)
+    G.add_node(7, percolation=0.5)
+    G.add_node(8, percolation=0.5)
+    G.add_edges_from([(1, 4), (2, 4), (3, 4), (4, 5), (5, 6), (6, 7), (6, 8)])
+    return G
+
+
+def example1b_G():
+    G = nx.Graph()
+    G.add_node(1, percolation=0.3)
+    G.add_node(2, percolation=0.5)
+    G.add_node(3, percolation=0.5)
+    G.add_node(4, percolation=0.2)
+    G.add_node(5, percolation=0.3)
+    G.add_node(6, percolation=0.2)
+    G.add_node(7, percolation=0.1)
+    G.add_node(8, percolation=0.1)
+    G.add_edges_from([(1, 4), (2, 4), (3, 4), (4, 5), (5, 6), (6, 7), (6, 8)])
+    return G
+
+
+def test_percolation_example1a():
+    """percolation centrality: example 1a"""
+    G = example1a_G()
+    p = nx.percolation_centrality(G)
+    p_answer = {4: 0.625, 6: 0.667}
+    for n, k in p_answer.items():
+        assert p[n] == pytest.approx(k, abs=1e-3)
+
+
+def test_percolation_example1b():
+    """percolation centrality: example 1a"""
+    G = example1b_G()
+    p = nx.percolation_centrality(G)
+    p_answer = {4: 0.825, 6: 0.4}
+    for n, k in p_answer.items():
+        assert p[n] == pytest.approx(k, abs=1e-3)
+
+
+def test_converge_to_betweenness():
+    """percolation centrality: should converge to betweenness
+    centrality when all nodes are percolated the same"""
+    # taken from betweenness test test_florentine_families_graph
+    G = nx.florentine_families_graph()
+    b_answer = {
+        "Acciaiuoli": 0.000,
+        "Albizzi": 0.212,
+        "Barbadori": 0.093,
+        "Bischeri": 0.104,
+        "Castellani": 0.055,
+        "Ginori": 0.000,
+        "Guadagni": 0.255,
+        "Lamberteschi": 0.000,
+        "Medici": 0.522,
+        "Pazzi": 0.000,
+        "Peruzzi": 0.022,
+        "Ridolfi": 0.114,
+        "Salviati": 0.143,
+        "Strozzi": 0.103,
+        "Tornabuoni": 0.092,
+    }
+
+    # If no initial state is provided, state for
+    # every node defaults to 1
+    p_answer = nx.percolation_centrality(G)
+    assert p_answer == pytest.approx(b_answer, abs=1e-3)
+
+    p_states = {k: 0.3 for k, v in b_answer.items()}
+    p_answer = nx.percolation_centrality(G, states=p_states)
+    assert p_answer == pytest.approx(b_answer, abs=1e-3)
+
+
+def test_default_percolation():
+    G = nx.erdos_renyi_graph(42, 0.42, seed=42)
+    assert nx.percolation_centrality(G) == pytest.approx(nx.betweenness_centrality(G))

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/centrality/tests/test_trophic.py

@@ -0,0 +1,302 @@
+"""Test trophic levels, trophic differences and trophic coherence
+"""
+import pytest
+
+np = pytest.importorskip("numpy")
+pytest.importorskip("scipy")
+
+import networkx as nx
+
+
+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]
+    print("Calculated result: ", d)
+    print("Expected Result: ", expected_result)
+
+    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) 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_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)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_asteroidal.py

@@ -0,0 +1,23 @@
+import networkx as nx
+
+
+def test_is_at_free():
+    is_at_free = nx.asteroidal.is_at_free
+
+    cycle = nx.cycle_graph(6)
+    assert not is_at_free(cycle)
+
+    path = nx.path_graph(6)
+    assert is_at_free(path)
+
+    small_graph = nx.complete_graph(2)
+    assert is_at_free(small_graph)
+
+    petersen = nx.petersen_graph()
+    assert not is_at_free(petersen)
+
+    clique = nx.complete_graph(6)
+    assert is_at_free(clique)
+
+    line_clique = nx.line_graph(clique)
+    assert not is_at_free(line_clique)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_boundary.py

@@ -0,0 +1,154 @@
+"""Unit tests for the :mod:`networkx.algorithms.boundary` module."""
+
+from itertools import combinations
+
+import pytest
+
+import networkx as nx
+from networkx import convert_node_labels_to_integers as cnlti
+from networkx.utils import edges_equal
+
+
+class TestNodeBoundary:
+    """Unit tests for the :func:`~networkx.node_boundary` function."""
+
+    def test_null_graph(self):
+        """Tests that the null graph has empty node boundaries."""
+        null = nx.null_graph()
+        assert nx.node_boundary(null, []) == set()
+        assert nx.node_boundary(null, [], []) == set()
+        assert nx.node_boundary(null, [1, 2, 3]) == set()
+        assert nx.node_boundary(null, [1, 2, 3], [4, 5, 6]) == set()
+        assert nx.node_boundary(null, [1, 2, 3], [3, 4, 5]) == set()
+
+    def test_path_graph(self):
+        P10 = cnlti(nx.path_graph(10), first_label=1)
+        assert nx.node_boundary(P10, []) == set()
+        assert nx.node_boundary(P10, [], []) == set()
+        assert nx.node_boundary(P10, [1, 2, 3]) == {4}
+        assert nx.node_boundary(P10, [4, 5, 6]) == {3, 7}
+        assert nx.node_boundary(P10, [3, 4, 5, 6, 7]) == {2, 8}
+        assert nx.node_boundary(P10, [8, 9, 10]) == {7}
+        assert nx.node_boundary(P10, [4, 5, 6], [9, 10]) == set()
+
+    def test_complete_graph(self):
+        K10 = cnlti(nx.complete_graph(10), first_label=1)
+        assert nx.node_boundary(K10, []) == set()
+        assert nx.node_boundary(K10, [], []) == set()
+        assert nx.node_boundary(K10, [1, 2, 3]) == {4, 5, 6, 7, 8, 9, 10}
+        assert nx.node_boundary(K10, [4, 5, 6]) == {1, 2, 3, 7, 8, 9, 10}
+        assert nx.node_boundary(K10, [3, 4, 5, 6, 7]) == {1, 2, 8, 9, 10}
+        assert nx.node_boundary(K10, [4, 5, 6], []) == set()
+        assert nx.node_boundary(K10, K10) == set()
+        assert nx.node_boundary(K10, [1, 2, 3], [3, 4, 5]) == {4, 5}
+
+    def test_petersen(self):
+        """Check boundaries in the petersen graph
+
+        cheeger(G,k)=min(|bdy(S)|/|S| for |S|=k, 0<k<=|V(G)|/2)
+
+        """
+
+        def cheeger(G, k):
+            return min(len(nx.node_boundary(G, nn)) / k for nn in combinations(G, k))
+
+        P = nx.petersen_graph()
+        assert cheeger(P, 1) == pytest.approx(3.00, abs=1e-2)
+        assert cheeger(P, 2) == pytest.approx(2.00, abs=1e-2)
+        assert cheeger(P, 3) == pytest.approx(1.67, abs=1e-2)
+        assert cheeger(P, 4) == pytest.approx(1.00, abs=1e-2)
+        assert cheeger(P, 5) == pytest.approx(0.80, abs=1e-2)
+
+    def test_directed(self):
+        """Tests the node boundary of a directed graph."""
+        G = nx.DiGraph([(0, 1), (1, 2), (2, 3), (3, 4), (4, 0)])
+        S = {0, 1}
+        boundary = nx.node_boundary(G, S)
+        expected = {2}
+        assert boundary == expected
+
+    def test_multigraph(self):
+        """Tests the node boundary of a multigraph."""
+        G = nx.MultiGraph(list(nx.cycle_graph(5).edges()) * 2)
+        S = {0, 1}
+        boundary = nx.node_boundary(G, S)
+        expected = {2, 4}
+        assert boundary == expected
+
+    def test_multidigraph(self):
+        """Tests the edge boundary of a multidigraph."""
+        edges = [(0, 1), (1, 2), (2, 3), (3, 4), (4, 0)]
+        G = nx.MultiDiGraph(edges * 2)
+        S = {0, 1}
+        boundary = nx.node_boundary(G, S)
+        expected = {2}
+        assert boundary == expected
+
+
+class TestEdgeBoundary:
+    """Unit tests for the :func:`~networkx.edge_boundary` function."""
+
+    def test_null_graph(self):
+        null = nx.null_graph()
+        assert list(nx.edge_boundary(null, [])) == []
+        assert list(nx.edge_boundary(null, [], [])) == []
+        assert list(nx.edge_boundary(null, [1, 2, 3])) == []
+        assert list(nx.edge_boundary(null, [1, 2, 3], [4, 5, 6])) == []
+        assert list(nx.edge_boundary(null, [1, 2, 3], [3, 4, 5])) == []
+
+    def test_path_graph(self):
+        P10 = cnlti(nx.path_graph(10), first_label=1)
+        assert list(nx.edge_boundary(P10, [])) == []
+        assert list(nx.edge_boundary(P10, [], [])) == []
+        assert list(nx.edge_boundary(P10, [1, 2, 3])) == [(3, 4)]
+        assert sorted(nx.edge_boundary(P10, [4, 5, 6])) == [(4, 3), (6, 7)]
+        assert sorted(nx.edge_boundary(P10, [3, 4, 5, 6, 7])) == [(3, 2), (7, 8)]
+        assert list(nx.edge_boundary(P10, [8, 9, 10])) == [(8, 7)]
+        assert sorted(nx.edge_boundary(P10, [4, 5, 6], [9, 10])) == []
+        assert list(nx.edge_boundary(P10, [1, 2, 3], [3, 4, 5])) == [(2, 3), (3, 4)]
+
+    def test_complete_graph(self):
+        K10 = cnlti(nx.complete_graph(10), first_label=1)
+
+        def ilen(iterable):
+            return sum(1 for i in iterable)
+
+        assert list(nx.edge_boundary(K10, [])) == []
+        assert list(nx.edge_boundary(K10, [], [])) == []
+        assert ilen(nx.edge_boundary(K10, [1, 2, 3])) == 21
+        assert ilen(nx.edge_boundary(K10, [4, 5, 6, 7])) == 24
+        assert ilen(nx.edge_boundary(K10, [3, 4, 5, 6, 7])) == 25
+        assert ilen(nx.edge_boundary(K10, [8, 9, 10])) == 21
+        assert edges_equal(
+            nx.edge_boundary(K10, [4, 5, 6], [9, 10]),
+            [(4, 9), (4, 10), (5, 9), (5, 10), (6, 9), (6, 10)],
+        )
+        assert edges_equal(
+            nx.edge_boundary(K10, [1, 2, 3], [3, 4, 5]),
+            [(1, 3), (1, 4), (1, 5), (2, 3), (2, 4), (2, 5), (3, 4), (3, 5)],
+        )
+
+    def test_directed(self):
+        """Tests the edge boundary of a directed graph."""
+        G = nx.DiGraph([(0, 1), (1, 2), (2, 3), (3, 4), (4, 0)])
+        S = {0, 1}
+        boundary = list(nx.edge_boundary(G, S))
+        expected = [(1, 2)]
+        assert boundary == expected
+
+    def test_multigraph(self):
+        """Tests the edge boundary of a multigraph."""
+        G = nx.MultiGraph(list(nx.cycle_graph(5).edges()) * 2)
+        S = {0, 1}
+        boundary = list(nx.edge_boundary(G, S))
+        expected = [(0, 4), (0, 4), (1, 2), (1, 2)]
+        assert boundary == expected
+
+    def test_multidigraph(self):
+        """Tests the edge boundary of a multidigraph."""
+        edges = [(0, 1), (1, 2), (2, 3), (3, 4), (4, 0)]
+        G = nx.MultiDiGraph(edges * 2)
+        S = {0, 1}
+        boundary = list(nx.edge_boundary(G, S))
+        expected = [(1, 2), (1, 2)]
+        assert boundary == expected

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_bridges.py

@@ -0,0 +1,144 @@
+"""Unit tests for bridge-finding algorithms."""
+
+import pytest
+
+import networkx as nx
+
+
+class TestBridges:
+    """Unit tests for the bridge-finding function."""
+
+    def test_single_bridge(self):
+        edges = [
+            # DFS tree edges.
+            (1, 2),
+            (2, 3),
+            (3, 4),
+            (3, 5),
+            (5, 6),
+            (6, 7),
+            (7, 8),
+            (5, 9),
+            (9, 10),
+            # Nontree edges.
+            (1, 3),
+            (1, 4),
+            (2, 5),
+            (5, 10),
+            (6, 8),
+        ]
+        G = nx.Graph(edges)
+        source = 1
+        bridges = list(nx.bridges(G, source))
+        assert bridges == [(5, 6)]
+
+    def test_barbell_graph(self):
+        # The (3, 0) barbell graph has two triangles joined by a single edge.
+        G = nx.barbell_graph(3, 0)
+        source = 0
+        bridges = list(nx.bridges(G, source))
+        assert bridges == [(2, 3)]
+
+    def test_multiedge_bridge(self):
+        edges = [
+            (0, 1),
+            (0, 2),
+            (1, 2),
+            (1, 2),
+            (2, 3),
+            (3, 4),
+            (3, 4),
+        ]
+        G = nx.MultiGraph(edges)
+        assert list(nx.bridges(G)) == [(2, 3)]
+
+
+class TestHasBridges:
+    """Unit tests for the has bridges function."""
+
+    def test_single_bridge(self):
+        edges = [
+            # DFS tree edges.
+            (1, 2),
+            (2, 3),
+            (3, 4),
+            (3, 5),
+            (5, 6),  # The only bridge edge
+            (6, 7),
+            (7, 8),
+            (5, 9),
+            (9, 10),
+            # Nontree edges.
+            (1, 3),
+            (1, 4),
+            (2, 5),
+            (5, 10),
+            (6, 8),
+        ]
+        G = nx.Graph(edges)
+        assert nx.has_bridges(G)  # Default root
+        assert nx.has_bridges(G, root=1)  # arbitrary root in G
+
+    def test_has_bridges_raises_root_not_in_G(self):
+        G = nx.Graph()
+        G.add_nodes_from([1, 2, 3])
+        with pytest.raises(nx.NodeNotFound):
+            nx.has_bridges(G, root=6)
+
+    def test_multiedge_bridge(self):
+        edges = [
+            (0, 1),
+            (0, 2),
+            (1, 2),
+            (1, 2),
+            (2, 3),
+            (3, 4),
+            (3, 4),
+        ]
+        G = nx.MultiGraph(edges)
+        assert nx.has_bridges(G)
+        # Make every edge a multiedge
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        assert not nx.has_bridges(G)
+
+    def test_bridges_multiple_components(self):
+        G = nx.Graph()
+        nx.add_path(G, [0, 1, 2])  # One connected component
+        nx.add_path(G, [4, 5, 6])  # Another connected component
+        assert list(nx.bridges(G, root=4)) == [(4, 5), (5, 6)]
+
+
+class TestLocalBridges:
+    """Unit tests for the local_bridge function."""
+
+    @classmethod
+    def setup_class(cls):
+        cls.BB = nx.barbell_graph(4, 0)
+        cls.square = nx.cycle_graph(4)
+        cls.tri = nx.cycle_graph(3)
+
+    def test_nospan(self):
+        expected = {(3, 4), (4, 3)}
+        assert next(nx.local_bridges(self.BB, with_span=False)) in expected
+        assert set(nx.local_bridges(self.square, with_span=False)) == self.square.edges
+        assert list(nx.local_bridges(self.tri, with_span=False)) == []
+
+    def test_no_weight(self):
+        inf = float("inf")
+        expected = {(3, 4, inf), (4, 3, inf)}
+        assert next(nx.local_bridges(self.BB)) in expected
+        expected = {(u, v, 3) for u, v in self.square.edges}
+        assert set(nx.local_bridges(self.square)) == expected
+        assert list(nx.local_bridges(self.tri)) == []
+
+    def test_weight(self):
+        inf = float("inf")
+        G = self.square.copy()
+
+        G.edges[1, 2]["weight"] = 2
+        expected = {(u, v, 5 - wt) for u, v, wt in G.edges(data="weight", default=1)}
+        assert set(nx.local_bridges(G, weight="weight")) == expected
+
+        expected = {(u, v, 6) for u, v in G.edges}
+        lb = nx.local_bridges(G, weight=lambda u, v, d: 2)
+        assert set(lb) == expected

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_broadcasting.py

@@ -0,0 +1,81 @@
+"""Unit tests for the broadcasting module."""
+import math
+
+import networkx as nx
+
+
+def test_example_tree_broadcast():
+    """
+    Test the BROADCAST algorithm on the example in the paper titled: "Information Dissemination in Trees"
+    """
+    edge_list = [
+        (0, 1),
+        (1, 2),
+        (2, 7),
+        (3, 4),
+        (5, 4),
+        (4, 7),
+        (6, 7),
+        (7, 9),
+        (8, 9),
+        (9, 13),
+        (13, 14),
+        (14, 15),
+        (14, 16),
+        (14, 17),
+        (13, 11),
+        (11, 10),
+        (11, 12),
+        (13, 18),
+        (18, 19),
+        (18, 20),
+    ]
+    G = nx.Graph(edge_list)
+    b_T, b_C = nx.tree_broadcast_center(G)
+    assert b_T == 6
+    assert b_C == {13, 9}
+    # test broadcast time from specific vertex
+    assert nx.tree_broadcast_time(G, 17) == 8
+    assert nx.tree_broadcast_time(G, 3) == 9
+    # test broadcast time of entire tree
+    assert nx.tree_broadcast_time(G) == 10
+
+
+def test_path_broadcast():
+    for i in range(2, 12):
+        G = nx.path_graph(i)
+        b_T, b_C = nx.tree_broadcast_center(G)
+        assert b_T == math.ceil(i / 2)
+        assert b_C == {
+            math.ceil(i / 2),
+            math.floor(i / 2),
+            math.ceil(i / 2 - 1),
+            math.floor(i / 2 - 1),
+        }
+        assert nx.tree_broadcast_time(G) == i - 1
+
+
+def test_empty_graph_broadcast():
+    H = nx.empty_graph(1)
+    b_T, b_C = nx.tree_broadcast_center(H)
+    assert b_T == 0
+    assert b_C == {0}
+    assert nx.tree_broadcast_time(H) == 0
+
+
+def test_star_broadcast():
+    for i in range(4, 12):
+        G = nx.star_graph(i)
+        b_T, b_C = nx.tree_broadcast_center(G)
+        assert b_T == i
+        assert b_C == set(G.nodes())
+        assert nx.tree_broadcast_time(G) == b_T
+
+
+def test_binomial_tree_broadcast():
+    for i in range(2, 8):
+        G = nx.binomial_tree(i)
+        b_T, b_C = nx.tree_broadcast_center(G)
+        assert b_T == i
+        assert b_C == {0, 2 ** (i - 1)}
+        assert nx.tree_broadcast_time(G) == 2 * i - 1

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_chains.py

@@ -0,0 +1,140 @@
+"""Unit tests for the chain decomposition functions."""
+from itertools import cycle, islice
+
+import pytest
+
+import networkx as nx
+
+
+def cycles(seq):
+    """Yields cyclic permutations of the given sequence.
+
+    For example::
+
+        >>> list(cycles("abc"))
+        [('a', 'b', 'c'), ('b', 'c', 'a'), ('c', 'a', 'b')]
+
+    """
+    n = len(seq)
+    cycled_seq = cycle(seq)
+    for x in seq:
+        yield tuple(islice(cycled_seq, n))
+        next(cycled_seq)
+
+
+def cyclic_equals(seq1, seq2):
+    """Decide whether two sequences are equal up to cyclic permutations.
+
+    For example::
+
+        >>> cyclic_equals("xyz", "zxy")
+        True
+        >>> cyclic_equals("xyz", "zyx")
+        False
+
+    """
+    # Cast seq2 to a tuple since `cycles()` yields tuples.
+    seq2 = tuple(seq2)
+    return any(x == tuple(seq2) for x in cycles(seq1))
+
+
+class TestChainDecomposition:
+    """Unit tests for the chain decomposition function."""
+
+    def assertContainsChain(self, chain, expected):
+        # A cycle could be expressed in two different orientations, one
+        # forward and one backward, so we need to check for cyclic
+        # equality in both orientations.
+        reversed_chain = list(reversed([tuple(reversed(e)) for e in chain]))
+        for candidate in expected:
+            if cyclic_equals(chain, candidate):
+                break
+            if cyclic_equals(reversed_chain, candidate):
+                break
+        else:
+            self.fail("chain not found")
+
+    def test_decomposition(self):
+        edges = [
+            # DFS tree edges.
+            (1, 2),
+            (2, 3),
+            (3, 4),
+            (3, 5),
+            (5, 6),
+            (6, 7),
+            (7, 8),
+            (5, 9),
+            (9, 10),
+            # Nontree edges.
+            (1, 3),
+            (1, 4),
+            (2, 5),
+            (5, 10),
+            (6, 8),
+        ]
+        G = nx.Graph(edges)
+        expected = [
+            [(1, 3), (3, 2), (2, 1)],
+            [(1, 4), (4, 3)],
+            [(2, 5), (5, 3)],
+            [(5, 10), (10, 9), (9, 5)],
+            [(6, 8), (8, 7), (7, 6)],
+        ]
+        chains = list(nx.chain_decomposition(G, root=1))
+        assert len(chains) == len(expected)
+
+    # This chain decomposition isn't unique
+    #        for chain in chains:
+    #            print(chain)
+    #            self.assertContainsChain(chain, expected)
+
+    def test_barbell_graph(self):
+        # The (3, 0) barbell graph has two triangles joined by a single edge.
+        G = nx.barbell_graph(3, 0)
+        chains = list(nx.chain_decomposition(G, root=0))
+        expected = [[(0, 1), (1, 2), (2, 0)], [(3, 4), (4, 5), (5, 3)]]
+        assert len(chains) == len(expected)
+        for chain in chains:
+            self.assertContainsChain(chain, expected)
+
+    def test_disconnected_graph(self):
+        """Test for a graph with multiple connected components."""
+        G = nx.barbell_graph(3, 0)
+        H = nx.barbell_graph(3, 0)
+        mapping = dict(zip(range(6), "abcdef"))
+        nx.relabel_nodes(H, mapping, copy=False)
+        G = nx.union(G, H)
+        chains = list(nx.chain_decomposition(G))
+        expected = [
+            [(0, 1), (1, 2), (2, 0)],
+            [(3, 4), (4, 5), (5, 3)],
+            [("a", "b"), ("b", "c"), ("c", "a")],
+            [("d", "e"), ("e", "f"), ("f", "d")],
+        ]
+        assert len(chains) == len(expected)
+        for chain in chains:
+            self.assertContainsChain(chain, expected)
+
+    def test_disconnected_graph_root_node(self):
+        """Test for a single component of a disconnected graph."""
+        G = nx.barbell_graph(3, 0)
+        H = nx.barbell_graph(3, 0)
+        mapping = dict(zip(range(6), "abcdef"))
+        nx.relabel_nodes(H, mapping, copy=False)
+        G = nx.union(G, H)
+        chains = list(nx.chain_decomposition(G, root="a"))
+        expected = [
+            [("a", "b"), ("b", "c"), ("c", "a")],
+            [("d", "e"), ("e", "f"), ("f", "d")],
+        ]
+        assert len(chains) == len(expected)
+        for chain in chains:
+            self.assertContainsChain(chain, expected)
+
+    def test_chain_decomposition_root_not_in_G(self):
+        """Test chain decomposition when root is not in graph"""
+        G = nx.Graph()
+        G.add_nodes_from([1, 2, 3])
+        with pytest.raises(nx.NodeNotFound):
+            nx.has_bridges(G, root=6)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_chordal.py

@@ -0,0 +1,129 @@
+import pytest
+
+import networkx as nx
+
+
+class TestMCS:
+    @classmethod
+    def setup_class(cls):
+        # simple graph
+        connected_chordal_G = nx.Graph()
+        connected_chordal_G.add_edges_from(
+            [
+                (1, 2),
+                (1, 3),
+                (2, 3),
+                (2, 4),
+                (3, 4),
+                (3, 5),
+                (3, 6),
+                (4, 5),
+                (4, 6),
+                (5, 6),
+            ]
+        )
+        cls.connected_chordal_G = connected_chordal_G
+
+        chordal_G = nx.Graph()
+        chordal_G.add_edges_from(
+            [
+                (1, 2),
+                (1, 3),
+                (2, 3),
+                (2, 4),
+                (3, 4),
+                (3, 5),
+                (3, 6),
+                (4, 5),
+                (4, 6),
+                (5, 6),
+                (7, 8),
+            ]
+        )
+        chordal_G.add_node(9)
+        cls.chordal_G = chordal_G
+
+        non_chordal_G = nx.Graph()
+        non_chordal_G.add_edges_from([(1, 2), (1, 3), (2, 4), (2, 5), (3, 4), (3, 5)])
+        cls.non_chordal_G = non_chordal_G
+
+        self_loop_G = nx.Graph()
+        self_loop_G.add_edges_from([(1, 1)])
+        cls.self_loop_G = self_loop_G
+
+    @pytest.mark.parametrize("G", (nx.DiGraph(), nx.MultiGraph(), nx.MultiDiGraph()))
+    def test_is_chordal_not_implemented(self, G):
+        with pytest.raises(nx.NetworkXNotImplemented):
+            nx.is_chordal(G)
+
+    def test_is_chordal(self):
+        assert not nx.is_chordal(self.non_chordal_G)
+        assert nx.is_chordal(self.chordal_G)
+        assert nx.is_chordal(self.connected_chordal_G)
+        assert nx.is_chordal(nx.Graph())
+        assert nx.is_chordal(nx.complete_graph(3))
+        assert nx.is_chordal(nx.cycle_graph(3))
+        assert not nx.is_chordal(nx.cycle_graph(5))
+        assert nx.is_chordal(self.self_loop_G)
+
+    def test_induced_nodes(self):
+        G = nx.generators.classic.path_graph(10)
+        Induced_nodes = nx.find_induced_nodes(G, 1, 9, 2)
+        assert Induced_nodes == {1, 2, 3, 4, 5, 6, 7, 8, 9}
+        pytest.raises(
+            nx.NetworkXTreewidthBoundExceeded, nx.find_induced_nodes, G, 1, 9, 1
+        )
+        Induced_nodes = nx.find_induced_nodes(self.chordal_G, 1, 6)
+        assert Induced_nodes == {1, 2, 4, 6}
+        pytest.raises(nx.NetworkXError, nx.find_induced_nodes, self.non_chordal_G, 1, 5)
+
+    def test_graph_treewidth(self):
+        with pytest.raises(nx.NetworkXError, match="Input graph is not chordal"):
+            nx.chordal_graph_treewidth(self.non_chordal_G)
+
+    def test_chordal_find_cliques(self):
+        cliques = {
+            frozenset([9]),
+            frozenset([7, 8]),
+            frozenset([1, 2, 3]),
+            frozenset([2, 3, 4]),
+            frozenset([3, 4, 5, 6]),
+        }
+        assert set(nx.chordal_graph_cliques(self.chordal_G)) == cliques
+        with pytest.raises(nx.NetworkXError, match="Input graph is not chordal"):
+            set(nx.chordal_graph_cliques(self.non_chordal_G))
+        with pytest.raises(nx.NetworkXError, match="Input graph is not chordal"):
+            set(nx.chordal_graph_cliques(self.self_loop_G))
+
+    def test_chordal_find_cliques_path(self):
+        G = nx.path_graph(10)
+        cliqueset = nx.chordal_graph_cliques(G)
+        for u, v in G.edges():
+            assert frozenset([u, v]) in cliqueset or frozenset([v, u]) in cliqueset
+
+    def test_chordal_find_cliquesCC(self):
+        cliques = {frozenset([1, 2, 3]), frozenset([2, 3, 4]), frozenset([3, 4, 5, 6])}
+        cgc = nx.chordal_graph_cliques
+        assert set(cgc(self.connected_chordal_G)) == cliques
+
+    def test_complete_to_chordal_graph(self):
+        fgrg = nx.fast_gnp_random_graph
+        test_graphs = [
+            nx.barbell_graph(6, 2),
+            nx.cycle_graph(15),
+            nx.wheel_graph(20),
+            nx.grid_graph([10, 4]),
+            nx.ladder_graph(15),
+            nx.star_graph(5),
+            nx.bull_graph(),
+            fgrg(20, 0.3, seed=1),
+        ]
+        for G in test_graphs:
+            H, a = nx.complete_to_chordal_graph(G)
+            assert nx.is_chordal(H)
+            assert len(a) == H.number_of_nodes()
+            if nx.is_chordal(G):
+                assert G.number_of_edges() == H.number_of_edges()
+                assert set(a.values()) == {0}
+            else:
+                assert len(set(a.values())) == H.number_of_nodes()

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_communicability.py

@@ -0,0 +1,80 @@
+from collections import defaultdict
+
+import pytest
+
+pytest.importorskip("numpy")
+pytest.importorskip("scipy")
+
+import networkx as nx
+from networkx.algorithms.communicability_alg import communicability, communicability_exp
+
+
+class TestCommunicability:
+    def test_communicability(self):
+        answer = {
+            0: {0: 1.5430806348152435, 1: 1.1752011936438012},
+            1: {0: 1.1752011936438012, 1: 1.5430806348152435},
+        }
+        #        answer={(0, 0): 1.5430806348152435,
+        #                (0, 1): 1.1752011936438012,
+        #                (1, 0): 1.1752011936438012,
+        #                (1, 1): 1.5430806348152435}
+
+        result = communicability(nx.path_graph(2))
+        for k1, val in result.items():
+            for k2 in val:
+                assert answer[k1][k2] == pytest.approx(result[k1][k2], abs=1e-7)
+
+    def test_communicability2(self):
+        answer_orig = {
+            ("1", "1"): 1.6445956054135658,
+            ("1", "Albert"): 0.7430186221096251,
+            ("1", "Aric"): 0.7430186221096251,
+            ("1", "Dan"): 1.6208126320442937,
+            ("1", "Franck"): 0.42639707170035257,
+            ("Albert", "1"): 0.7430186221096251,
+            ("Albert", "Albert"): 2.4368257358712189,
+            ("Albert", "Aric"): 1.4368257358712191,
+            ("Albert", "Dan"): 2.0472097037446453,
+            ("Albert", "Franck"): 1.8340111678944691,
+            ("Aric", "1"): 0.7430186221096251,
+            ("Aric", "Albert"): 1.4368257358712191,
+            ("Aric", "Aric"): 2.4368257358712193,
+            ("Aric", "Dan"): 2.0472097037446457,
+            ("Aric", "Franck"): 1.8340111678944691,
+            ("Dan", "1"): 1.6208126320442937,
+            ("Dan", "Albert"): 2.0472097037446453,
+            ("Dan", "Aric"): 2.0472097037446457,
+            ("Dan", "Dan"): 3.1306328496328168,
+            ("Dan", "Franck"): 1.4860372442192515,
+            ("Franck", "1"): 0.42639707170035257,
+            ("Franck", "Albert"): 1.8340111678944691,
+            ("Franck", "Aric"): 1.8340111678944691,
+            ("Franck", "Dan"): 1.4860372442192515,
+            ("Franck", "Franck"): 2.3876142275231915,
+        }
+
+        answer = defaultdict(dict)
+        for (k1, k2), v in answer_orig.items():
+            answer[k1][k2] = v
+
+        G1 = nx.Graph(
+            [
+                ("Franck", "Aric"),
+                ("Aric", "Dan"),
+                ("Dan", "Albert"),
+                ("Albert", "Franck"),
+                ("Dan", "1"),
+                ("Franck", "Albert"),
+            ]
+        )
+
+        result = communicability(G1)
+        for k1, val in result.items():
+            for k2 in val:
+                assert answer[k1][k2] == pytest.approx(result[k1][k2], abs=1e-7)
+
+        result = communicability_exp(G1)
+        for k1, val in result.items():
+            for k2 in val:
+                assert answer[k1][k2] == pytest.approx(result[k1][k2], abs=1e-7)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_core.py

@@ -0,0 +1,266 @@
+import pytest
+
+import networkx as nx
+from networkx.utils import nodes_equal
+
+
+class TestCore:
+    @classmethod
+    def setup_class(cls):
+        # G is the example graph in Figure 1 from Batagelj and
+        # Zaversnik's paper titled An O(m) Algorithm for Cores
+        # Decomposition of Networks, 2003,
+        # http://arXiv.org/abs/cs/0310049.  With nodes labeled as
+        # shown, the 3-core is given by nodes 1-8, the 2-core by nodes
+        # 9-16, the 1-core by nodes 17-20 and node 21 is in the
+        # 0-core.
+        t1 = nx.convert_node_labels_to_integers(nx.tetrahedral_graph(), 1)
+        t2 = nx.convert_node_labels_to_integers(t1, 5)
+        G = nx.union(t1, t2)
+        G.add_edges_from(
+            [
+                (3, 7),
+                (2, 11),
+                (11, 5),
+                (11, 12),
+                (5, 12),
+                (12, 19),
+                (12, 18),
+                (3, 9),
+                (7, 9),
+                (7, 10),
+                (9, 10),
+                (9, 20),
+                (17, 13),
+                (13, 14),
+                (14, 15),
+                (15, 16),
+                (16, 13),
+            ]
+        )
+        G.add_node(21)
+        cls.G = G
+
+        # Create the graph H resulting from the degree sequence
+        # [0, 1, 2, 2, 2, 2, 3] when using the Havel-Hakimi algorithm.
+
+        degseq = [0, 1, 2, 2, 2, 2, 3]
+        H = nx.havel_hakimi_graph(degseq)
+        mapping = {6: 0, 0: 1, 4: 3, 5: 6, 3: 4, 1: 2, 2: 5}
+        cls.H = nx.relabel_nodes(H, mapping)
+
+    def test_trivial(self):
+        """Empty graph"""
+        G = nx.Graph()
+        assert nx.core_number(G) == {}
+
+    def test_core_number(self):
+        core = nx.core_number(self.G)
+        nodes_by_core = [sorted(n for n in core if core[n] == val) for val in range(4)]
+        assert nodes_equal(nodes_by_core[0], [21])
+        assert nodes_equal(nodes_by_core[1], [17, 18, 19, 20])
+        assert nodes_equal(nodes_by_core[2], [9, 10, 11, 12, 13, 14, 15, 16])
+        assert nodes_equal(nodes_by_core[3], [1, 2, 3, 4, 5, 6, 7, 8])
+
+    def test_core_number2(self):
+        core = nx.core_number(self.H)
+        nodes_by_core = [sorted(n for n in core if core[n] == val) for val in range(3)]
+        assert nodes_equal(nodes_by_core[0], [0])
+        assert nodes_equal(nodes_by_core[1], [1, 3])
+        assert nodes_equal(nodes_by_core[2], [2, 4, 5, 6])
+
+    def test_core_number_multigraph(self):
+        G = nx.complete_graph(3)
+        G = nx.MultiGraph(G)
+        G.add_edge(1, 2)
+        with pytest.raises(
+            nx.NetworkXNotImplemented, match="not implemented for multigraph type"
+        ):
+            nx.core_number(G)
+
+    def test_core_number_self_loop(self):
+        G = nx.cycle_graph(3)
+        G.add_edge(0, 0)
+        with pytest.raises(
+            nx.NetworkXNotImplemented, match="Input graph has self loops"
+        ):
+            nx.core_number(G)
+
+    def test_directed_core_number(self):
+        """core number had a bug for directed graphs found in issue #1959"""
+        # small example where too timid edge removal can make cn[2] = 3
+        G = nx.DiGraph()
+        edges = [(1, 2), (2, 1), (2, 3), (2, 4), (3, 4), (4, 3)]
+        G.add_edges_from(edges)
+        assert nx.core_number(G) == {1: 2, 2: 2, 3: 2, 4: 2}
+        # small example where too aggressive edge removal can make cn[2] = 2
+        more_edges = [(1, 5), (3, 5), (4, 5), (3, 6), (4, 6), (5, 6)]
+        G.add_edges_from(more_edges)
+        assert nx.core_number(G) == {1: 3, 2: 3, 3: 3, 4: 3, 5: 3, 6: 3}
+
+    def test_main_core(self):
+        main_core_subgraph = nx.k_core(self.H)
+        assert sorted(main_core_subgraph.nodes()) == [2, 4, 5, 6]
+
+    def test_k_core(self):
+        # k=0
+        k_core_subgraph = nx.k_core(self.H, k=0)
+        assert sorted(k_core_subgraph.nodes()) == sorted(self.H.nodes())
+        # k=1
+        k_core_subgraph = nx.k_core(self.H, k=1)
+        assert sorted(k_core_subgraph.nodes()) == [1, 2, 3, 4, 5, 6]
+        # k = 2
+        k_core_subgraph = nx.k_core(self.H, k=2)
+        assert sorted(k_core_subgraph.nodes()) == [2, 4, 5, 6]
+
+    def test_k_core_multigraph(self):
+        core_number = nx.core_number(self.H)
+        H = nx.MultiGraph(self.H)
+        with pytest.deprecated_call():
+            nx.k_core(H, k=0, core_number=core_number)
+
+    def test_main_crust(self):
+        main_crust_subgraph = nx.k_crust(self.H)
+        assert sorted(main_crust_subgraph.nodes()) == [0, 1, 3]
+
+    def test_k_crust(self):
+        # k = 0
+        k_crust_subgraph = nx.k_crust(self.H, k=2)
+        assert sorted(k_crust_subgraph.nodes()) == sorted(self.H.nodes())
+        # k=1
+        k_crust_subgraph = nx.k_crust(self.H, k=1)
+        assert sorted(k_crust_subgraph.nodes()) == [0, 1, 3]
+        # k=2
+        k_crust_subgraph = nx.k_crust(self.H, k=0)
+        assert sorted(k_crust_subgraph.nodes()) == [0]
+
+    def test_k_crust_multigraph(self):
+        core_number = nx.core_number(self.H)
+        H = nx.MultiGraph(self.H)
+        with pytest.deprecated_call():
+            nx.k_crust(H, k=0, core_number=core_number)
+
+    def test_main_shell(self):
+        main_shell_subgraph = nx.k_shell(self.H)
+        assert sorted(main_shell_subgraph.nodes()) == [2, 4, 5, 6]
+
+    def test_k_shell(self):
+        # k=0
+        k_shell_subgraph = nx.k_shell(self.H, k=2)
+        assert sorted(k_shell_subgraph.nodes()) == [2, 4, 5, 6]
+        # k=1
+        k_shell_subgraph = nx.k_shell(self.H, k=1)
+        assert sorted(k_shell_subgraph.nodes()) == [1, 3]
+        # k=2
+        k_shell_subgraph = nx.k_shell(self.H, k=0)
+        assert sorted(k_shell_subgraph.nodes()) == [0]
+
+    def test_k_shell_multigraph(self):
+        core_number = nx.core_number(self.H)
+        H = nx.MultiGraph(self.H)
+        with pytest.deprecated_call():
+            nx.k_shell(H, k=0, core_number=core_number)
+
+    def test_k_corona(self):
+        # k=0
+        k_corona_subgraph = nx.k_corona(self.H, k=2)
+        assert sorted(k_corona_subgraph.nodes()) == [2, 4, 5, 6]
+        # k=1
+        k_corona_subgraph = nx.k_corona(self.H, k=1)
+        assert sorted(k_corona_subgraph.nodes()) == [1]
+        # k=2
+        k_corona_subgraph = nx.k_corona(self.H, k=0)
+        assert sorted(k_corona_subgraph.nodes()) == [0]
+
+    def test_k_corona_multigraph(self):
+        core_number = nx.core_number(self.H)
+        H = nx.MultiGraph(self.H)
+        with pytest.deprecated_call():
+            nx.k_corona(H, k=0, core_number=core_number)
+
+    def test_k_truss(self):
+        # k=-1
+        k_truss_subgraph = nx.k_truss(self.G, -1)
+        assert sorted(k_truss_subgraph.nodes()) == list(range(1, 21))
+        # k=0
+        k_truss_subgraph = nx.k_truss(self.G, 0)
+        assert sorted(k_truss_subgraph.nodes()) == list(range(1, 21))
+        # k=1
+        k_truss_subgraph = nx.k_truss(self.G, 1)
+        assert sorted(k_truss_subgraph.nodes()) == list(range(1, 21))
+        # k=2
+        k_truss_subgraph = nx.k_truss(self.G, 2)
+        assert sorted(k_truss_subgraph.nodes()) == list(range(1, 21))
+        # k=3
+        k_truss_subgraph = nx.k_truss(self.G, 3)
+        assert sorted(k_truss_subgraph.nodes()) == list(range(1, 13))
+
+        k_truss_subgraph = nx.k_truss(self.G, 4)
+        assert sorted(k_truss_subgraph.nodes()) == list(range(1, 9))
+
+        k_truss_subgraph = nx.k_truss(self.G, 5)
+        assert sorted(k_truss_subgraph.nodes()) == []
+
+    def test_k_truss_digraph(self):
+        G = nx.complete_graph(3)
+        G = nx.DiGraph(G)
+        G.add_edge(2, 1)
+        with pytest.raises(
+            nx.NetworkXNotImplemented, match="not implemented for directed type"
+        ):
+            nx.k_truss(G, k=1)
+
+    def test_k_truss_multigraph(self):
+        G = nx.complete_graph(3)
+        G = nx.MultiGraph(G)
+        G.add_edge(1, 2)
+        with pytest.raises(
+            nx.NetworkXNotImplemented, match="not implemented for multigraph type"
+        ):
+            nx.k_truss(G, k=1)
+
+    def test_k_truss_self_loop(self):
+        G = nx.cycle_graph(3)
+        G.add_edge(0, 0)
+        with pytest.raises(
+            nx.NetworkXNotImplemented, match="Input graph has self loops"
+        ):
+            nx.k_truss(G, k=1)
+
+    def test_onion_layers(self):
+        layers = nx.onion_layers(self.G)
+        nodes_by_layer = [
+            sorted(n for n in layers if layers[n] == val) for val in range(1, 7)
+        ]
+        assert nodes_equal(nodes_by_layer[0], [21])
+        assert nodes_equal(nodes_by_layer[1], [17, 18, 19, 20])
+        assert nodes_equal(nodes_by_layer[2], [10, 12, 13, 14, 15, 16])
+        assert nodes_equal(nodes_by_layer[3], [9, 11])
+        assert nodes_equal(nodes_by_layer[4], [1, 2, 4, 5, 6, 8])
+        assert nodes_equal(nodes_by_layer[5], [3, 7])
+
+    def test_onion_digraph(self):
+        G = nx.complete_graph(3)
+        G = nx.DiGraph(G)
+        G.add_edge(2, 1)
+        with pytest.raises(
+            nx.NetworkXNotImplemented, match="not implemented for directed type"
+        ):
+            nx.onion_layers(G)
+
+    def test_onion_multigraph(self):
+        G = nx.complete_graph(3)
+        G = nx.MultiGraph(G)
+        G.add_edge(1, 2)
+        with pytest.raises(
+            nx.NetworkXNotImplemented, match="not implemented for multigraph type"
+        ):
+            nx.onion_layers(G)
+
+    def test_onion_self_loop(self):
+        G = nx.cycle_graph(3)
+        G.add_edge(0, 0)
+        with pytest.raises(
+            nx.NetworkXNotImplemented, match="Input graph contains self loops"
+        ):
+            nx.onion_layers(G)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_covering.py

@@ -0,0 +1,85 @@
+import pytest
+
+import networkx as nx
+
+
+class TestMinEdgeCover:
+    """Tests for :func:`networkx.algorithms.min_edge_cover`"""
+
+    def test_empty_graph(self):
+        G = nx.Graph()
+        assert nx.min_edge_cover(G) == set()
+
+    def test_graph_with_loop(self):
+        G = nx.Graph()
+        G.add_edge(0, 0)
+        assert nx.min_edge_cover(G) == {(0, 0)}
+
+    def test_graph_with_isolated_v(self):
+        G = nx.Graph()
+        G.add_node(1)
+        with pytest.raises(
+            nx.NetworkXException,
+            match="Graph has a node with no edge incident on it, so no edge cover exists.",
+        ):
+            nx.min_edge_cover(G)
+
+    def test_graph_single_edge(self):
+        G = nx.Graph([(0, 1)])
+        assert nx.min_edge_cover(G) in ({(0, 1)}, {(1, 0)})
+
+    def test_graph_two_edge_path(self):
+        G = nx.path_graph(3)
+        min_cover = nx.min_edge_cover(G)
+        assert len(min_cover) == 2
+        for u, v in G.edges:
+            assert (u, v) in min_cover or (v, u) in min_cover
+
+    def test_bipartite_explicit(self):
+        G = nx.Graph()
+        G.add_nodes_from([1, 2, 3, 4], bipartite=0)
+        G.add_nodes_from(["a", "b", "c"], bipartite=1)
+        G.add_edges_from([(1, "a"), (1, "b"), (2, "b"), (2, "c"), (3, "c"), (4, "a")])
+        # Use bipartite method by prescribing the algorithm
+        min_cover = nx.min_edge_cover(
+            G, nx.algorithms.bipartite.matching.eppstein_matching
+        )
+        assert nx.is_edge_cover(G, min_cover)
+        assert len(min_cover) == 8
+        # Use the default method which is not specialized for bipartite
+        min_cover2 = nx.min_edge_cover(G)
+        assert nx.is_edge_cover(G, min_cover2)
+        assert len(min_cover2) == 4
+
+    def test_complete_graph_even(self):
+        G = nx.complete_graph(10)
+        min_cover = nx.min_edge_cover(G)
+        assert nx.is_edge_cover(G, min_cover)
+        assert len(min_cover) == 5
+
+    def test_complete_graph_odd(self):
+        G = nx.complete_graph(11)
+        min_cover = nx.min_edge_cover(G)
+        assert nx.is_edge_cover(G, min_cover)
+        assert len(min_cover) == 6
+
+
+class TestIsEdgeCover:
+    """Tests for :func:`networkx.algorithms.is_edge_cover`"""
+
+    def test_empty_graph(self):
+        G = nx.Graph()
+        assert nx.is_edge_cover(G, set())
+
+    def test_graph_with_loop(self):
+        G = nx.Graph()
+        G.add_edge(1, 1)
+        assert nx.is_edge_cover(G, {(1, 1)})
+
+    def test_graph_single_edge(self):
+        G = nx.Graph()
+        G.add_edge(0, 1)
+        assert nx.is_edge_cover(G, {(0, 0), (1, 1)})
+        assert nx.is_edge_cover(G, {(0, 1), (1, 0)})
+        assert nx.is_edge_cover(G, {(0, 1)})
+        assert not nx.is_edge_cover(G, {(0, 0)})

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_cuts.py

@@ -0,0 +1,172 @@
+"""Unit tests for the :mod:`networkx.algorithms.cuts` module."""
+
+
+import networkx as nx
+
+
+class TestCutSize:
+    """Unit tests for the :func:`~networkx.cut_size` function."""
+
+    def test_symmetric(self):
+        """Tests that the cut size is symmetric."""
+        G = nx.barbell_graph(3, 0)
+        S = {0, 1, 4}
+        T = {2, 3, 5}
+        assert nx.cut_size(G, S, T) == 4
+        assert nx.cut_size(G, T, S) == 4
+
+    def test_single_edge(self):
+        """Tests for a cut of a single edge."""
+        G = nx.barbell_graph(3, 0)
+        S = {0, 1, 2}
+        T = {3, 4, 5}
+        assert nx.cut_size(G, S, T) == 1
+        assert nx.cut_size(G, T, S) == 1
+
+    def test_directed(self):
+        """Tests that each directed edge is counted once in the cut."""
+        G = nx.barbell_graph(3, 0).to_directed()
+        S = {0, 1, 2}
+        T = {3, 4, 5}
+        assert nx.cut_size(G, S, T) == 2
+        assert nx.cut_size(G, T, S) == 2
+
+    def test_directed_symmetric(self):
+        """Tests that a cut in a directed graph is symmetric."""
+        G = nx.barbell_graph(3, 0).to_directed()
+        S = {0, 1, 4}
+        T = {2, 3, 5}
+        assert nx.cut_size(G, S, T) == 8
+        assert nx.cut_size(G, T, S) == 8
+
+    def test_multigraph(self):
+        """Tests that parallel edges are each counted for a cut."""
+        G = nx.MultiGraph(["ab", "ab"])
+        assert nx.cut_size(G, {"a"}, {"b"}) == 2
+
+
+class TestVolume:
+    """Unit tests for the :func:`~networkx.volume` function."""
+
+    def test_graph(self):
+        G = nx.cycle_graph(4)
+        assert nx.volume(G, {0, 1}) == 4
+
+    def test_digraph(self):
+        G = nx.DiGraph([(0, 1), (1, 2), (2, 3), (3, 0)])
+        assert nx.volume(G, {0, 1}) == 2
+
+    def test_multigraph(self):
+        edges = list(nx.cycle_graph(4).edges())
+        G = nx.MultiGraph(edges * 2)
+        assert nx.volume(G, {0, 1}) == 8
+
+    def test_multidigraph(self):
+        edges = [(0, 1), (1, 2), (2, 3), (3, 0)]
+        G = nx.MultiDiGraph(edges * 2)
+        assert nx.volume(G, {0, 1}) == 4
+
+    def test_barbell(self):
+        G = nx.barbell_graph(3, 0)
+        assert nx.volume(G, {0, 1, 2}) == 7
+        assert nx.volume(G, {3, 4, 5}) == 7
+
+
+class TestNormalizedCutSize:
+    """Unit tests for the :func:`~networkx.normalized_cut_size` function."""
+
+    def test_graph(self):
+        G = nx.path_graph(4)
+        S = {1, 2}
+        T = set(G) - S
+        size = nx.normalized_cut_size(G, S, T)
+        # The cut looks like this: o-{-o--o-}-o
+        expected = 2 * ((1 / 4) + (1 / 2))
+        assert expected == size
+        # Test with no input T
+        assert expected == nx.normalized_cut_size(G, S)
+
+    def test_directed(self):
+        G = nx.DiGraph([(0, 1), (1, 2), (2, 3)])
+        S = {1, 2}
+        T = set(G) - S
+        size = nx.normalized_cut_size(G, S, T)
+        # The cut looks like this: o-{->o-->o-}->o
+        expected = 2 * ((1 / 2) + (1 / 1))
+        assert expected == size
+        # Test with no input T
+        assert expected == nx.normalized_cut_size(G, S)
+
+
+class TestConductance:
+    """Unit tests for the :func:`~networkx.conductance` function."""
+
+    def test_graph(self):
+        G = nx.barbell_graph(5, 0)
+        # Consider the singleton sets containing the "bridge" nodes.
+        # There is only one cut edge, and each set has volume five.
+        S = {4}
+        T = {5}
+        conductance = nx.conductance(G, S, T)
+        expected = 1 / 5
+        assert expected == conductance
+        # Test with no input T
+        G2 = nx.barbell_graph(3, 0)
+        # There is only one cut edge, and each set has volume seven.
+        S2 = {0, 1, 2}
+        assert nx.conductance(G2, S2) == 1 / 7
+
+
+class TestEdgeExpansion:
+    """Unit tests for the :func:`~networkx.edge_expansion` function."""
+
+    def test_graph(self):
+        G = nx.barbell_graph(5, 0)
+        S = set(range(5))
+        T = set(G) - S
+        expansion = nx.edge_expansion(G, S, T)
+        expected = 1 / 5
+        assert expected == expansion
+        # Test with no input T
+        assert expected == nx.edge_expansion(G, S)
+
+
+class TestNodeExpansion:
+    """Unit tests for the :func:`~networkx.node_expansion` function."""
+
+    def test_graph(self):
+        G = nx.path_graph(8)
+        S = {3, 4, 5}
+        expansion = nx.node_expansion(G, S)
+        # The neighborhood of S has cardinality five, and S has
+        # cardinality three.
+        expected = 5 / 3
+        assert expected == expansion
+
+
+class TestBoundaryExpansion:
+    """Unit tests for the :func:`~networkx.boundary_expansion` function."""
+
+    def test_graph(self):
+        G = nx.complete_graph(10)
+        S = set(range(4))
+        expansion = nx.boundary_expansion(G, S)
+        # The node boundary of S has cardinality six, and S has
+        # cardinality three.
+        expected = 6 / 4
+        assert expected == expansion
+
+
+class TestMixingExpansion:
+    """Unit tests for the :func:`~networkx.mixing_expansion` function."""
+
+    def test_graph(self):
+        G = nx.barbell_graph(5, 0)
+        S = set(range(5))
+        T = set(G) - S
+        expansion = nx.mixing_expansion(G, S, T)
+        # There is one cut edge, and the total number of edges in the
+        # graph is twice the total number of edges in a clique of size
+        # five, plus one more for the bridge.
+        expected = 1 / (2 * (5 * 4 + 1))
+        assert expected == expansion

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_cycles.py

@@ -0,0 +1,974 @@
+from itertools import chain, islice, tee
+from math import inf
+from random import shuffle
+
+import pytest
+
+import networkx as nx
+from networkx.algorithms.traversal.edgedfs import FORWARD, REVERSE
+
+
+def check_independent(basis):
+    if len(basis) == 0:
+        return
+
+    np = pytest.importorskip("numpy")
+    sp = pytest.importorskip("scipy")  # Required by incidence_matrix
+
+    H = nx.Graph()
+    for b in basis:
+        nx.add_cycle(H, b)
+    inc = nx.incidence_matrix(H, oriented=True)
+    rank = np.linalg.matrix_rank(inc.toarray(), tol=None, hermitian=False)
+    assert inc.shape[1] - rank == len(basis)
+
+
+class TestCycles:
+    @classmethod
+    def setup_class(cls):
+        G = nx.Graph()
+        nx.add_cycle(G, [0, 1, 2, 3])
+        nx.add_cycle(G, [0, 3, 4, 5])
+        nx.add_cycle(G, [0, 1, 6, 7, 8])
+        G.add_edge(8, 9)
+        cls.G = G
+
+    def is_cyclic_permutation(self, a, b):
+        n = len(a)
+        if len(b) != n:
+            return False
+        l = a + a
+        return any(l[i : i + n] == b for i in range(n))
+
+    def test_cycle_basis(self):
+        G = self.G
+        cy = nx.cycle_basis(G, 0)
+        sort_cy = sorted(sorted(c) for c in cy)
+        assert sort_cy == [[0, 1, 2, 3], [0, 1, 6, 7, 8], [0, 3, 4, 5]]
+        cy = nx.cycle_basis(G, 1)
+        sort_cy = sorted(sorted(c) for c in cy)
+        assert sort_cy == [[0, 1, 2, 3], [0, 1, 6, 7, 8], [0, 3, 4, 5]]
+        cy = nx.cycle_basis(G, 9)
+        sort_cy = sorted(sorted(c) for c in cy)
+        assert sort_cy == [[0, 1, 2, 3], [0, 1, 6, 7, 8], [0, 3, 4, 5]]
+        # test disconnected graphs
+        nx.add_cycle(G, "ABC")
+        cy = nx.cycle_basis(G, 9)
+        sort_cy = sorted(sorted(c) for c in cy[:-1]) + [sorted(cy[-1])]
+        assert sort_cy == [[0, 1, 2, 3], [0, 1, 6, 7, 8], [0, 3, 4, 5], ["A", "B", "C"]]
+
+    def test_cycle_basis2(self):
+        with pytest.raises(nx.NetworkXNotImplemented):
+            G = nx.DiGraph()
+            cy = nx.cycle_basis(G, 0)
+
+    def test_cycle_basis3(self):
+        with pytest.raises(nx.NetworkXNotImplemented):
+            G = nx.MultiGraph()
+            cy = nx.cycle_basis(G, 0)
+
+    def test_cycle_basis_ordered(self):
+        # see gh-6654 replace sets with (ordered) dicts
+        G = nx.cycle_graph(5)
+        G.update(nx.cycle_graph(range(3, 8)))
+        cbG = nx.cycle_basis(G)
+
+        perm = {1: 0, 0: 1}  # switch 0 and 1
+        H = nx.relabel_nodes(G, perm)
+        cbH = [[perm.get(n, n) for n in cyc] for cyc in nx.cycle_basis(H)]
+        assert cbG == cbH
+
+    def test_cycle_basis_self_loop(self):
+        """Tests the function for graphs with self loops"""
+        G = nx.Graph()
+        nx.add_cycle(G, [0, 1, 2, 3])
+        nx.add_cycle(G, [0, 0, 6, 2])
+        cy = nx.cycle_basis(G)
+        sort_cy = sorted(sorted(c) for c in cy)
+        assert sort_cy == [[0], [0, 1, 2], [0, 2, 3], [0, 2, 6]]
+
+    def test_simple_cycles(self):
+        edges = [(0, 0), (0, 1), (0, 2), (1, 2), (2, 0), (2, 1), (2, 2)]
+        G = nx.DiGraph(edges)
+        cc = sorted(nx.simple_cycles(G))
+        ca = [[0], [0, 1, 2], [0, 2], [1, 2], [2]]
+        assert len(cc) == len(ca)
+        for c in cc:
+            assert any(self.is_cyclic_permutation(c, rc) for rc in ca)
+
+    def test_simple_cycles_singleton(self):
+        G = nx.Graph([(0, 0)])  # self-loop
+        assert list(nx.simple_cycles(G)) == [[0]]
+
+    def test_unsortable(self):
+        # this test ensures that graphs whose nodes without an intrinsic
+        # ordering do not cause issues
+        G = nx.DiGraph()
+        nx.add_cycle(G, ["a", 1])
+        c = list(nx.simple_cycles(G))
+        assert len(c) == 1
+
+    def test_simple_cycles_small(self):
+        G = nx.DiGraph()
+        nx.add_cycle(G, [1, 2, 3])
+        c = sorted(nx.simple_cycles(G))
+        assert len(c) == 1
+        assert self.is_cyclic_permutation(c[0], [1, 2, 3])
+        nx.add_cycle(G, [10, 20, 30])
+        cc = sorted(nx.simple_cycles(G))
+        assert len(cc) == 2
+        ca = [[1, 2, 3], [10, 20, 30]]
+        for c in cc:
+            assert any(self.is_cyclic_permutation(c, rc) for rc in ca)
+
+    def test_simple_cycles_empty(self):
+        G = nx.DiGraph()
+        assert list(nx.simple_cycles(G)) == []
+
+    def worst_case_graph(self, k):
+        # see figure 1 in Johnson's paper
+        # this graph has exactly 3k simple cycles
+        G = nx.DiGraph()
+        for n in range(2, k + 2):
+            G.add_edge(1, n)
+            G.add_edge(n, k + 2)
+        G.add_edge(2 * k + 1, 1)
+        for n in range(k + 2, 2 * k + 2):
+            G.add_edge(n, 2 * k + 2)
+            G.add_edge(n, n + 1)
+        G.add_edge(2 * k + 3, k + 2)
+        for n in range(2 * k + 3, 3 * k + 3):
+            G.add_edge(2 * k + 2, n)
+            G.add_edge(n, 3 * k + 3)
+        G.add_edge(3 * k + 3, 2 * k + 2)
+        return G
+
+    def test_worst_case_graph(self):
+        # see figure 1 in Johnson's paper
+        for k in range(3, 10):
+            G = self.worst_case_graph(k)
+            l = len(list(nx.simple_cycles(G)))
+            assert l == 3 * k
+
+    def test_recursive_simple_and_not(self):
+        for k in range(2, 10):
+            G = self.worst_case_graph(k)
+            cc = sorted(nx.simple_cycles(G))
+            rcc = sorted(nx.recursive_simple_cycles(G))
+            assert len(cc) == len(rcc)
+            for c in cc:
+                assert any(self.is_cyclic_permutation(c, r) for r in rcc)
+            for rc in rcc:
+                assert any(self.is_cyclic_permutation(rc, c) for c in cc)
+
+    def test_simple_graph_with_reported_bug(self):
+        G = nx.DiGraph()
+        edges = [
+            (0, 2),
+            (0, 3),
+            (1, 0),
+            (1, 3),
+            (2, 1),
+            (2, 4),
+            (3, 2),
+            (3, 4),
+            (4, 0),
+            (4, 1),
+            (4, 5),
+            (5, 0),
+            (5, 1),
+            (5, 2),
+            (5, 3),
+        ]
+        G.add_edges_from(edges)
+        cc = sorted(nx.simple_cycles(G))
+        assert len(cc) == 26
+        rcc = sorted(nx.recursive_simple_cycles(G))
+        assert len(cc) == len(rcc)
+        for c in cc:
+            assert any(self.is_cyclic_permutation(c, rc) for rc in rcc)
+        for rc in rcc:
+            assert any(self.is_cyclic_permutation(rc, c) for c in cc)
+
+
+def pairwise(iterable):
+    a, b = tee(iterable)
+    next(b, None)
+    return zip(a, b)
+
+
+def cycle_edges(c):
+    return pairwise(chain(c, islice(c, 1)))
+
+
+def directed_cycle_edgeset(c):
+    return frozenset(cycle_edges(c))
+
+
+def undirected_cycle_edgeset(c):
+    if len(c) == 1:
+        return frozenset(cycle_edges(c))
+    return frozenset(map(frozenset, cycle_edges(c)))
+
+
+def multigraph_cycle_edgeset(c):
+    if len(c) <= 2:
+        return frozenset(cycle_edges(c))
+    else:
+        return frozenset(map(frozenset, cycle_edges(c)))
+
+
+class TestCycleEnumeration:
+    @staticmethod
+    def K(n):
+        return nx.complete_graph(n)
+
+    @staticmethod
+    def D(n):
+        return nx.complete_graph(n).to_directed()
+
+    @staticmethod
+    def edgeset_function(g):
+        if g.is_directed():
+            return directed_cycle_edgeset
+        elif g.is_multigraph():
+            return multigraph_cycle_edgeset
+        else:
+            return undirected_cycle_edgeset
+
+    def check_cycle(self, g, c, es, cache, source, original_c, length_bound, chordless):
+        if length_bound is not None and len(c) > length_bound:
+            raise RuntimeError(
+                f"computed cycle {original_c} exceeds length bound {length_bound}"
+            )
+        if source == "computed":
+            if es in cache:
+                raise RuntimeError(
+                    f"computed cycle {original_c} has already been found!"
+                )
+            else:
+                cache[es] = tuple(original_c)
+        else:
+            if es in cache:
+                cache.pop(es)
+            else:
+                raise RuntimeError(f"expected cycle {original_c} was not computed")
+
+        if not all(g.has_edge(*e) for e in es):
+            raise RuntimeError(
+                f"{source} claimed cycle {original_c} is not a cycle of g"
+            )
+        if chordless and len(g.subgraph(c).edges) > len(c):
+            raise RuntimeError(f"{source} cycle {original_c} is not chordless")
+
+    def check_cycle_algorithm(
+        self,
+        g,
+        expected_cycles,
+        length_bound=None,
+        chordless=False,
+        algorithm=None,
+    ):
+        if algorithm is None:
+            algorithm = nx.chordless_cycles if chordless else nx.simple_cycles
+
+        # note: we shuffle the labels of g to rule out accidentally-correct
+        # behavior which occurred during the development of chordless cycle
+        # enumeration algorithms
+
+        relabel = list(range(len(g)))
+        shuffle(relabel)
+        label = dict(zip(g, relabel))
+        unlabel = dict(zip(relabel, g))
+        h = nx.relabel_nodes(g, label, copy=True)
+
+        edgeset = self.edgeset_function(h)
+
+        params = {}
+        if length_bound is not None:
+            params["length_bound"] = length_bound
+
+        cycle_cache = {}
+        for c in algorithm(h, **params):
+            original_c = [unlabel[x] for x in c]
+            es = edgeset(c)
+            self.check_cycle(
+                h, c, es, cycle_cache, "computed", original_c, length_bound, chordless
+            )
+
+        if isinstance(expected_cycles, int):
+            if len(cycle_cache) != expected_cycles:
+                raise RuntimeError(
+                    f"expected {expected_cycles} cycles, got {len(cycle_cache)}"
+                )
+            return
+        for original_c in expected_cycles:
+            c = [label[x] for x in original_c]
+            es = edgeset(c)
+            self.check_cycle(
+                h, c, es, cycle_cache, "expected", original_c, length_bound, chordless
+            )
+
+        if len(cycle_cache):
+            for c in cycle_cache.values():
+                raise RuntimeError(
+                    f"computed cycle {c} is valid but not in the expected cycle set!"
+                )
+
+    def check_cycle_enumeration_integer_sequence(
+        self,
+        g_family,
+        cycle_counts,
+        length_bound=None,
+        chordless=False,
+        algorithm=None,
+    ):
+        for g, num_cycles in zip(g_family, cycle_counts):
+            self.check_cycle_algorithm(
+                g,
+                num_cycles,
+                length_bound=length_bound,
+                chordless=chordless,
+                algorithm=algorithm,
+            )
+
+    def test_directed_chordless_cycle_digons(self):
+        g = nx.DiGraph()
+        nx.add_cycle(g, range(5))
+        nx.add_cycle(g, range(5)[::-1])
+        g.add_edge(0, 0)
+        expected_cycles = [(0,), (1, 2), (2, 3), (3, 4)]
+        self.check_cycle_algorithm(g, expected_cycles, chordless=True)
+
+        self.check_cycle_algorithm(g, expected_cycles, chordless=True, length_bound=2)
+
+        expected_cycles = [c for c in expected_cycles if len(c) < 2]
+        self.check_cycle_algorithm(g, expected_cycles, chordless=True, length_bound=1)
+
+    def test_directed_chordless_cycle_undirected(self):
+        g = nx.DiGraph([(1, 2), (2, 3), (3, 4), (4, 5), (5, 0), (5, 1), (0, 2)])
+        expected_cycles = [(0, 2, 3, 4, 5), (1, 2, 3, 4, 5)]
+        self.check_cycle_algorithm(g, expected_cycles, chordless=True)
+
+        g = nx.DiGraph()
+        nx.add_cycle(g, range(5))
+        nx.add_cycle(g, range(4, 9))
+        g.add_edge(7, 3)
+        expected_cycles = [(0, 1, 2, 3, 4), (3, 4, 5, 6, 7), (4, 5, 6, 7, 8)]
+        self.check_cycle_algorithm(g, expected_cycles, chordless=True)
+
+        g.add_edge(3, 7)
+        expected_cycles = [(0, 1, 2, 3, 4), (3, 7), (4, 5, 6, 7, 8)]
+        self.check_cycle_algorithm(g, expected_cycles, chordless=True)
+
+        expected_cycles = [(3, 7)]
+        self.check_cycle_algorithm(g, expected_cycles, chordless=True, length_bound=4)
+
+        g.remove_edge(7, 3)
+        expected_cycles = [(0, 1, 2, 3, 4), (4, 5, 6, 7, 8)]
+        self.check_cycle_algorithm(g, expected_cycles, chordless=True)
+
+        g = nx.DiGraph((i, j) for i in range(10) for j in range(i))
+        expected_cycles = []
+        self.check_cycle_algorithm(g, expected_cycles, chordless=True)
+
+    def test_chordless_cycles_directed(self):
+        G = nx.DiGraph()
+        nx.add_cycle(G, range(5))
+        nx.add_cycle(G, range(4, 12))
+        expected = [[*range(5)], [*range(4, 12)]]
+        self.check_cycle_algorithm(G, expected, chordless=True)
+        self.check_cycle_algorithm(
+            G, [c for c in expected if len(c) <= 5], length_bound=5, chordless=True
+        )
+
+        G.add_edge(7, 3)
+        expected.append([*range(3, 8)])
+        self.check_cycle_algorithm(G, expected, chordless=True)
+        self.check_cycle_algorithm(
+            G, [c for c in expected if len(c) <= 5], length_bound=5, chordless=True
+        )
+
+        G.add_edge(3, 7)
+        expected[-1] = [7, 3]
+        self.check_cycle_algorithm(G, expected, chordless=True)
+        self.check_cycle_algorithm(
+            G, [c for c in expected if len(c) <= 5], length_bound=5, chordless=True
+        )
+
+        expected.pop()
+        G.remove_edge(7, 3)
+        self.check_cycle_algorithm(G, expected, chordless=True)
+        self.check_cycle_algorithm(
+            G, [c for c in expected if len(c) <= 5], length_bound=5, chordless=True
+        )
+
+    def test_directed_chordless_cycle_diclique(self):
+        g_family = [self.D(n) for n in range(10)]
+        expected_cycles = [(n * n - n) // 2 for n in range(10)]
+        self.check_cycle_enumeration_integer_sequence(
+            g_family, expected_cycles, chordless=True
+        )
+
+        expected_cycles = [(n * n - n) // 2 for n in range(10)]
+        self.check_cycle_enumeration_integer_sequence(
+            g_family, expected_cycles, length_bound=2
+        )
+
+    def test_directed_chordless_loop_blockade(self):
+        g = nx.DiGraph((i, i) for i in range(10))
+        nx.add_cycle(g, range(10))
+        expected_cycles = [(i,) for i in range(10)]
+        self.check_cycle_algorithm(g, expected_cycles, chordless=True)
+
+        self.check_cycle_algorithm(g, expected_cycles, length_bound=1)
+
+        g = nx.MultiDiGraph(g)
+        g.add_edges_from((i, i) for i in range(0, 10, 2))
+        expected_cycles = [(i,) for i in range(1, 10, 2)]
+        self.check_cycle_algorithm(g, expected_cycles, chordless=True)
+
+    def test_simple_cycles_notable_clique_sequences(self):
+        # A000292: Number of labeled graphs on n+3 nodes that are triangles.
+        g_family = [self.K(n) for n in range(2, 12)]
+        expected = [0, 1, 4, 10, 20, 35, 56, 84, 120, 165, 220]
+        self.check_cycle_enumeration_integer_sequence(
+            g_family, expected, length_bound=3
+        )
+
+        def triangles(g, **kwargs):
+            yield from (c for c in nx.simple_cycles(g, **kwargs) if len(c) == 3)
+
+        # directed complete graphs have twice as many triangles thanks to reversal
+        g_family = [self.D(n) for n in range(2, 12)]
+        expected = [2 * e for e in expected]
+        self.check_cycle_enumeration_integer_sequence(
+            g_family, expected, length_bound=3, algorithm=triangles
+        )
+
+        def four_cycles(g, **kwargs):
+            yield from (c for c in nx.simple_cycles(g, **kwargs) if len(c) == 4)
+
+        # A050534: the number of 4-cycles in the complete graph K_{n+1}
+        expected = [0, 0, 0, 3, 15, 45, 105, 210, 378, 630, 990]
+        g_family = [self.K(n) for n in range(1, 12)]
+        self.check_cycle_enumeration_integer_sequence(
+            g_family, expected, length_bound=4, algorithm=four_cycles
+        )
+
+        # directed complete graphs have twice as many 4-cycles thanks to reversal
+        expected = [2 * e for e in expected]
+        g_family = [self.D(n) for n in range(1, 15)]
+        self.check_cycle_enumeration_integer_sequence(
+            g_family, expected, length_bound=4, algorithm=four_cycles
+        )
+
+        # A006231: the number of elementary circuits in a complete directed graph with n nodes
+        expected = [0, 1, 5, 20, 84, 409, 2365]
+        g_family = [self.D(n) for n in range(1, 8)]
+        self.check_cycle_enumeration_integer_sequence(g_family, expected)
+
+        # A002807: Number of cycles in the complete graph on n nodes K_{n}.
+        expected = [0, 0, 0, 1, 7, 37, 197, 1172]
+        g_family = [self.K(n) for n in range(8)]
+        self.check_cycle_enumeration_integer_sequence(g_family, expected)
+
+    def test_directed_chordless_cycle_parallel_multiedges(self):
+        g = nx.MultiGraph()
+
+        nx.add_cycle(g, range(5))
+        expected = [[*range(5)]]
+        self.check_cycle_algorithm(g, expected, chordless=True)
+
+        nx.add_cycle(g, range(5))
+        expected = [*cycle_edges(range(5))]
+        self.check_cycle_algorithm(g, expected, chordless=True)
+
+        nx.add_cycle(g, range(5))
+        expected = []
+        self.check_cycle_algorithm(g, expected, chordless=True)
+
+        g = nx.MultiDiGraph()
+
+        nx.add_cycle(g, range(5))
+        expected = [[*range(5)]]
+        self.check_cycle_algorithm(g, expected, chordless=True)
+
+        nx.add_cycle(g, range(5))
+        self.check_cycle_algorithm(g, [], chordless=True)
+
+        nx.add_cycle(g, range(5))
+        self.check_cycle_algorithm(g, [], chordless=True)
+
+        g = nx.MultiDiGraph()
+
+        nx.add_cycle(g, range(5))
+        nx.add_cycle(g, range(5)[::-1])
+        expected = [*cycle_edges(range(5))]
+        self.check_cycle_algorithm(g, expected, chordless=True)
+
+        nx.add_cycle(g, range(5))
+        self.check_cycle_algorithm(g, [], chordless=True)
+
+    def test_chordless_cycles_graph(self):
+        G = nx.Graph()
+        nx.add_cycle(G, range(5))
+        nx.add_cycle(G, range(4, 12))
+        expected = [[*range(5)], [*range(4, 12)]]
+        self.check_cycle_algorithm(G, expected, chordless=True)
+        self.check_cycle_algorithm(
+            G, [c for c in expected if len(c) <= 5], length_bound=5, chordless=True
+        )
+
+        G.add_edge(7, 3)
+        expected.append([*range(3, 8)])
+        expected.append([4, 3, 7, 8, 9, 10, 11])
+        self.check_cycle_algorithm(G, expected, chordless=True)
+        self.check_cycle_algorithm(
+            G, [c for c in expected if len(c) <= 5], length_bound=5, chordless=True
+        )
+
+    def test_chordless_cycles_giant_hamiltonian(self):
+        # ... o - e - o - e - o ... # o = odd, e = even
+        # ... ---/ \-----/ \--- ... # <-- "long" edges
+        #
+        # each long edge belongs to exactly one triangle, and one giant cycle
+        # of length n/2.  The remaining edges each belong to a triangle
+
+        n = 1000
+        assert n % 2 == 0
+        G = nx.Graph()
+        for v in range(n):
+            if not v % 2:
+                G.add_edge(v, (v + 2) % n)
+            G.add_edge(v, (v + 1) % n)
+
+        expected = [[*range(0, n, 2)]] + [
+            [x % n for x in range(i, i + 3)] for i in range(0, n, 2)
+        ]
+        self.check_cycle_algorithm(G, expected, chordless=True)
+        self.check_cycle_algorithm(
+            G, [c for c in expected if len(c) <= 3], length_bound=3, chordless=True
+        )
+
+        # ... o -> e -> o -> e -> o ... # o = odd, e = even
+        # ... <---/ \---<---/ \---< ... # <-- "long" edges
+        #
+        # this time, we orient the short and long edges in opposition
+        # the cycle structure of this graph is the same, but we need to reverse
+        # the long one in our representation.  Also, we need to drop the size
+        # because our partitioning algorithm uses strongly connected components
+        # instead of separating graphs by their strong articulation points
+
+        n = 100
+        assert n % 2 == 0
+        G = nx.DiGraph()
+        for v in range(n):
+            G.add_edge(v, (v + 1) % n)
+            if not v % 2:
+                G.add_edge((v + 2) % n, v)
+
+        expected = [[*range(n - 2, -2, -2)]] + [
+            [x % n for x in range(i, i + 3)] for i in range(0, n, 2)
+        ]
+        self.check_cycle_algorithm(G, expected, chordless=True)
+        self.check_cycle_algorithm(
+            G, [c for c in expected if len(c) <= 3], length_bound=3, chordless=True
+        )
+
+    def test_simple_cycles_acyclic_tournament(self):
+        n = 10
+        G = nx.DiGraph((x, y) for x in range(n) for y in range(x))
+        self.check_cycle_algorithm(G, [])
+        self.check_cycle_algorithm(G, [], chordless=True)
+
+        for k in range(n + 1):
+            self.check_cycle_algorithm(G, [], length_bound=k)
+            self.check_cycle_algorithm(G, [], length_bound=k, chordless=True)
+
+    def test_simple_cycles_graph(self):
+        testG = nx.cycle_graph(8)
+        cyc1 = tuple(range(8))
+        self.check_cycle_algorithm(testG, [cyc1])
+
+        testG.add_edge(4, -1)
+        nx.add_path(testG, [3, -2, -3, -4])
+        self.check_cycle_algorithm(testG, [cyc1])
+
+        testG.update(nx.cycle_graph(range(8, 16)))
+        cyc2 = tuple(range(8, 16))
+        self.check_cycle_algorithm(testG, [cyc1, cyc2])
+
+        testG.update(nx.cycle_graph(range(4, 12)))
+        cyc3 = tuple(range(4, 12))
+        expected = {
+            (0, 1, 2, 3, 4, 5, 6, 7),  # cyc1
+            (8, 9, 10, 11, 12, 13, 14, 15),  # cyc2
+            (4, 5, 6, 7, 8, 9, 10, 11),  # cyc3
+            (4, 5, 6, 7, 8, 15, 14, 13, 12, 11),  # cyc2 + cyc3
+            (0, 1, 2, 3, 4, 11, 10, 9, 8, 7),  # cyc1 + cyc3
+            (0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 8, 7),  # cyc1 + cyc2 + cyc3
+        }
+        self.check_cycle_algorithm(testG, expected)
+        assert len(expected) == (2**3 - 1) - 1  # 1 disjoint comb: cyc1 + cyc2
+
+        # Basis size = 5 (2 loops overlapping gives 5 small loops
+        #        E
+        #       / \         Note: A-F = 10-15
+        #    1-2-3-4-5
+        #    / |   |  \   cyc1=012DAB -- left
+        #   0  D   F  6   cyc2=234E   -- top
+        #   \  |   |  /   cyc3=45678F -- right
+        #    B-A-9-8-7    cyc4=89AC   -- bottom
+        #       \ /       cyc5=234F89AD -- middle
+        #        C
+        #
+        # combinations of 5 basis elements: 2^5 - 1  (one includes no cycles)
+        #
+        # disjoint combs: (11 total) not simple cycles
+        #   Any pair not including cyc5 => choose(4, 2) = 6
+        #   Any triple not including cyc5 => choose(4, 3) = 4
+        #   Any quad not including cyc5 => choose(4, 4) = 1
+        #
+        # we expect 31 - 11 = 20 simple cycles
+        #
+        testG = nx.cycle_graph(12)
+        testG.update(nx.cycle_graph([12, 10, 13, 2, 14, 4, 15, 8]).edges)
+        expected = (2**5 - 1) - 11  # 11 disjoint combinations
+        self.check_cycle_algorithm(testG, expected)
+
+    def test_simple_cycles_bounded(self):
+        # iteratively construct a cluster of nested cycles running in the same direction
+        # there should be one cycle of every length
+        d = nx.DiGraph()
+        expected = []
+        for n in range(10):
+            nx.add_cycle(d, range(n))
+            expected.append(n)
+            for k, e in enumerate(expected):
+                self.check_cycle_algorithm(d, e, length_bound=k)
+
+        # iteratively construct a path of undirected cycles, connected at articulation
+        # points.  there should be one cycle of every length except 2: no digons
+        g = nx.Graph()
+        top = 0
+        expected = []
+        for n in range(10):
+            expected.append(n if n < 2 else n - 1)
+            if n == 2:
+                # no digons in undirected graphs
+                continue
+            nx.add_cycle(g, range(top, top + n))
+            top += n
+            for k, e in enumerate(expected):
+                self.check_cycle_algorithm(g, e, length_bound=k)
+
+    def test_simple_cycles_bound_corner_cases(self):
+        G = nx.cycle_graph(4)
+        DG = nx.cycle_graph(4, create_using=nx.DiGraph)
+        assert list(nx.simple_cycles(G, length_bound=0)) == []
+        assert list(nx.simple_cycles(DG, length_bound=0)) == []
+        assert list(nx.chordless_cycles(G, length_bound=0)) == []
+        assert list(nx.chordless_cycles(DG, length_bound=0)) == []
+
+    def test_simple_cycles_bound_error(self):
+        with pytest.raises(ValueError):
+            G = nx.DiGraph()
+            for c in nx.simple_cycles(G, -1):
+                assert False
+
+        with pytest.raises(ValueError):
+            G = nx.Graph()
+            for c in nx.simple_cycles(G, -1):
+                assert False
+
+        with pytest.raises(ValueError):
+            G = nx.Graph()
+            for c in nx.chordless_cycles(G, -1):
+                assert False
+
+        with pytest.raises(ValueError):
+            G = nx.DiGraph()
+            for c in nx.chordless_cycles(G, -1):
+                assert False
+
+    def test_chordless_cycles_clique(self):
+        g_family = [self.K(n) for n in range(2, 15)]
+        expected = [0, 1, 4, 10, 20, 35, 56, 84, 120, 165, 220, 286, 364]
+        self.check_cycle_enumeration_integer_sequence(
+            g_family, expected, chordless=True
+        )
+
+        # directed cliques have as many digons as undirected graphs have edges
+        expected = [(n * n - n) // 2 for n in range(15)]
+        g_family = [self.D(n) for n in range(15)]
+        self.check_cycle_enumeration_integer_sequence(
+            g_family, expected, chordless=True
+        )
+
+
+# These tests might fail with hash randomization since they depend on
+# edge_dfs. For more information, see the comments in:
+#    networkx/algorithms/traversal/tests/test_edgedfs.py
+
+
+class TestFindCycle:
+    @classmethod
+    def setup_class(cls):
+        cls.nodes = [0, 1, 2, 3]
+        cls.edges = [(-1, 0), (0, 1), (1, 0), (1, 0), (2, 1), (3, 1)]
+
+    def test_graph_nocycle(self):
+        G = nx.Graph(self.edges)
+        pytest.raises(nx.exception.NetworkXNoCycle, nx.find_cycle, G, self.nodes)
+
+    def test_graph_cycle(self):
+        G = nx.Graph(self.edges)
+        G.add_edge(2, 0)
+        x = list(nx.find_cycle(G, self.nodes))
+        x_ = [(0, 1), (1, 2), (2, 0)]
+        assert x == x_
+
+    def test_graph_orientation_none(self):
+        G = nx.Graph(self.edges)
+        G.add_edge(2, 0)
+        x = list(nx.find_cycle(G, self.nodes, orientation=None))
+        x_ = [(0, 1), (1, 2), (2, 0)]
+        assert x == x_
+
+    def test_graph_orientation_original(self):
+        G = nx.Graph(self.edges)
+        G.add_edge(2, 0)
+        x = list(nx.find_cycle(G, self.nodes, orientation="original"))
+        x_ = [(0, 1, FORWARD), (1, 2, FORWARD), (2, 0, FORWARD)]
+        assert x == x_
+
+    def test_digraph(self):
+        G = nx.DiGraph(self.edges)
+        x = list(nx.find_cycle(G, self.nodes))
+        x_ = [(0, 1), (1, 0)]
+        assert x == x_
+
+    def test_digraph_orientation_none(self):
+        G = nx.DiGraph(self.edges)
+        x = list(nx.find_cycle(G, self.nodes, orientation=None))
+        x_ = [(0, 1), (1, 0)]
+        assert x == x_
+
+    def test_digraph_orientation_original(self):
+        G = nx.DiGraph(self.edges)
+        x = list(nx.find_cycle(G, self.nodes, orientation="original"))
+        x_ = [(0, 1, FORWARD), (1, 0, FORWARD)]
+        assert x == x_
+
+    def test_multigraph(self):
+        G = nx.MultiGraph(self.edges)
+        x = list(nx.find_cycle(G, self.nodes))
+        x_ = [(0, 1, 0), (1, 0, 1)]  # or (1, 0, 2)
+        # Hash randomization...could be any edge.
+        assert x[0] == x_[0]
+        assert x[1][:2] == x_[1][:2]
+
+    def test_multidigraph(self):
+        G = nx.MultiDiGraph(self.edges)
+        x = list(nx.find_cycle(G, self.nodes))
+        x_ = [(0, 1, 0), (1, 0, 0)]  # (1, 0, 1)
+        assert x[0] == x_[0]
+        assert x[1][:2] == x_[1][:2]
+
+    def test_digraph_ignore(self):
+        G = nx.DiGraph(self.edges)
+        x = list(nx.find_cycle(G, self.nodes, orientation="ignore"))
+        x_ = [(0, 1, FORWARD), (1, 0, FORWARD)]
+        assert x == x_
+
+    def test_digraph_reverse(self):
+        G = nx.DiGraph(self.edges)
+        x = list(nx.find_cycle(G, self.nodes, orientation="reverse"))
+        x_ = [(1, 0, REVERSE), (0, 1, REVERSE)]
+        assert x == x_
+
+    def test_multidigraph_ignore(self):
+        G = nx.MultiDiGraph(self.edges)
+        x = list(nx.find_cycle(G, self.nodes, orientation="ignore"))
+        x_ = [(0, 1, 0, FORWARD), (1, 0, 0, FORWARD)]  # or (1, 0, 1, 1)
+        assert x[0] == x_[0]
+        assert x[1][:2] == x_[1][:2]
+        assert x[1][3] == x_[1][3]
+
+    def test_multidigraph_ignore2(self):
+        # Loop traversed an edge while ignoring its orientation.
+        G = nx.MultiDiGraph([(0, 1), (1, 2), (1, 2)])
+        x = list(nx.find_cycle(G, [0, 1, 2], orientation="ignore"))
+        x_ = [(1, 2, 0, FORWARD), (1, 2, 1, REVERSE)]
+        assert x == x_
+
+    def test_multidigraph_original(self):
+        # Node 2 doesn't need to be searched again from visited from 4.
+        # The goal here is to cover the case when 2 to be researched from 4,
+        # when 4 is visited from the first time (so we must make sure that 4
+        # is not visited from 2, and hence, we respect the edge orientation).
+        G = nx.MultiDiGraph([(0, 1), (1, 2), (2, 3), (4, 2)])
+        pytest.raises(
+            nx.exception.NetworkXNoCycle,
+            nx.find_cycle,
+            G,
+            [0, 1, 2, 3, 4],
+            orientation="original",
+        )
+
+    def test_dag(self):
+        G = nx.DiGraph([(0, 1), (0, 2), (1, 2)])
+        pytest.raises(
+            nx.exception.NetworkXNoCycle, nx.find_cycle, G, orientation="original"
+        )
+        x = list(nx.find_cycle(G, orientation="ignore"))
+        assert x == [(0, 1, FORWARD), (1, 2, FORWARD), (0, 2, REVERSE)]
+
+    def test_prev_explored(self):
+        # https://github.com/networkx/networkx/issues/2323
+
+        G = nx.DiGraph()
+        G.add_edges_from([(1, 0), (2, 0), (1, 2), (2, 1)])
+        pytest.raises(nx.NetworkXNoCycle, nx.find_cycle, G, source=0)
+        x = list(nx.find_cycle(G, 1))
+        x_ = [(1, 2), (2, 1)]
+        assert x == x_
+
+        x = list(nx.find_cycle(G, 2))
+        x_ = [(2, 1), (1, 2)]
+        assert x == x_
+
+        x = list(nx.find_cycle(G))
+        x_ = [(1, 2), (2, 1)]
+        assert x == x_
+
+    def test_no_cycle(self):
+        # https://github.com/networkx/networkx/issues/2439
+
+        G = nx.DiGraph()
+        G.add_edges_from([(1, 2), (2, 0), (3, 1), (3, 2)])
+        pytest.raises(nx.NetworkXNoCycle, nx.find_cycle, G, source=0)
+        pytest.raises(nx.NetworkXNoCycle, nx.find_cycle, G)
+
+
+def assert_basis_equal(a, b):
+    assert sorted(a) == sorted(b)
+
+
+class TestMinimumCycleBasis:
+    @classmethod
+    def setup_class(cls):
+        T = nx.Graph()
+        nx.add_cycle(T, [1, 2, 3, 4], weight=1)
+        T.add_edge(2, 4, weight=5)
+        cls.diamond_graph = T
+
+    def test_unweighted_diamond(self):
+        mcb = nx.minimum_cycle_basis(self.diamond_graph)
+        assert_basis_equal(mcb, [[2, 4, 1], [3, 4, 2]])
+
+    def test_weighted_diamond(self):
+        mcb = nx.minimum_cycle_basis(self.diamond_graph, weight="weight")
+        assert_basis_equal(mcb, [[2, 4, 1], [4, 3, 2, 1]])
+
+    def test_dimensionality(self):
+        # checks |MCB|=|E|-|V|+|NC|
+        ntrial = 10
+        for seed in range(1234, 1234 + ntrial):
+            rg = nx.erdos_renyi_graph(10, 0.3, seed=seed)
+            nnodes = rg.number_of_nodes()
+            nedges = rg.number_of_edges()
+            ncomp = nx.number_connected_components(rg)
+
+            mcb = nx.minimum_cycle_basis(rg)
+            assert len(mcb) == nedges - nnodes + ncomp
+            check_independent(mcb)
+
+    def test_complete_graph(self):
+        cg = nx.complete_graph(5)
+        mcb = nx.minimum_cycle_basis(cg)
+        assert all(len(cycle) == 3 for cycle in mcb)
+        check_independent(mcb)
+
+    def test_tree_graph(self):
+        tg = nx.balanced_tree(3, 3)
+        assert not nx.minimum_cycle_basis(tg)
+
+    def test_petersen_graph(self):
+        G = nx.petersen_graph()
+        mcb = list(nx.minimum_cycle_basis(G))
+        expected = [
+            [4, 9, 7, 5, 0],
+            [1, 2, 3, 4, 0],
+            [1, 6, 8, 5, 0],
+            [4, 3, 8, 5, 0],
+            [1, 6, 9, 4, 0],
+            [1, 2, 7, 5, 0],
+        ]
+        assert len(mcb) == len(expected)
+        assert all(c in expected for c in mcb)
+
+        # check that order of the nodes is a path
+        for c in mcb:
+            assert all(G.has_edge(u, v) for u, v in nx.utils.pairwise(c, cyclic=True))
+        # check independence of the basis
+        check_independent(mcb)
+
+    def test_gh6787_variable_weighted_complete_graph(self):
+        N = 8
+        cg = nx.complete_graph(N)
+        cg.add_weighted_edges_from([(u, v, 9) for u, v in cg.edges])
+        cg.add_weighted_edges_from([(u, v, 1) for u, v in nx.cycle_graph(N).edges])
+        mcb = nx.minimum_cycle_basis(cg, weight="weight")
+        check_independent(mcb)
+
+    def test_gh6787_and_edge_attribute_names(self):
+        G = nx.cycle_graph(4)
+        G.add_weighted_edges_from([(0, 2, 10), (1, 3, 10)], weight="dist")
+        expected = [[1, 3, 0], [3, 2, 1, 0], [1, 2, 0]]
+        mcb = list(nx.minimum_cycle_basis(G, weight="dist"))
+        assert len(mcb) == len(expected)
+        assert all(c in expected for c in mcb)
+
+        # test not using a weight with weight attributes
+        expected = [[1, 3, 0], [1, 2, 0], [3, 2, 0]]
+        mcb = list(nx.minimum_cycle_basis(G))
+        assert len(mcb) == len(expected)
+        assert all(c in expected for c in mcb)
+
+
+class TestGirth:
+    @pytest.mark.parametrize(
+        ("G", "expected"),
+        (
+            (nx.chvatal_graph(), 4),
+            (nx.tutte_graph(), 4),
+            (nx.petersen_graph(), 5),
+            (nx.heawood_graph(), 6),
+            (nx.pappus_graph(), 6),
+            (nx.random_tree(10, seed=42), inf),
+            (nx.empty_graph(10), inf),
+            (nx.Graph(chain(cycle_edges(range(5)), cycle_edges(range(6, 10)))), 4),
+            (
+                nx.Graph(
+                    [
+                        (0, 6),
+                        (0, 8),
+                        (0, 9),
+                        (1, 8),
+                        (2, 8),
+                        (2, 9),
+                        (4, 9),
+                        (5, 9),
+                        (6, 8),
+                        (6, 9),
+                        (7, 8),
+                    ]
+                ),
+                3,
+            ),
+        ),
+    )
+    def test_girth(self, G, expected):
+        assert nx.girth(G) == expected

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_d_separation.py

@@ -0,0 +1,348 @@
+from itertools import combinations
+
+import pytest
+
+import networkx as nx
+
+
+def path_graph():
+    """Return a path graph of length three."""
+    G = nx.path_graph(3, create_using=nx.DiGraph)
+    G.graph["name"] = "path"
+    nx.freeze(G)
+    return G
+
+
+def fork_graph():
+    """Return a three node fork graph."""
+    G = nx.DiGraph(name="fork")
+    G.add_edges_from([(0, 1), (0, 2)])
+    nx.freeze(G)
+    return G
+
+
+def collider_graph():
+    """Return a collider/v-structure graph with three nodes."""
+    G = nx.DiGraph(name="collider")
+    G.add_edges_from([(0, 2), (1, 2)])
+    nx.freeze(G)
+    return G
+
+
+def naive_bayes_graph():
+    """Return a simply Naive Bayes PGM graph."""
+    G = nx.DiGraph(name="naive_bayes")
+    G.add_edges_from([(0, 1), (0, 2), (0, 3), (0, 4)])
+    nx.freeze(G)
+    return G
+
+
+def asia_graph():
+    """Return the 'Asia' PGM graph."""
+    G = nx.DiGraph(name="asia")
+    G.add_edges_from(
+        [
+            ("asia", "tuberculosis"),
+            ("smoking", "cancer"),
+            ("smoking", "bronchitis"),
+            ("tuberculosis", "either"),
+            ("cancer", "either"),
+            ("either", "xray"),
+            ("either", "dyspnea"),
+            ("bronchitis", "dyspnea"),
+        ]
+    )
+    nx.freeze(G)
+    return G
+
+
+@pytest.fixture(name="path_graph")
+def path_graph_fixture():
+    return path_graph()
+
+
+@pytest.fixture(name="fork_graph")
+def fork_graph_fixture():
+    return fork_graph()
+
+
+@pytest.fixture(name="collider_graph")
+def collider_graph_fixture():
+    return collider_graph()
+
+
+@pytest.fixture(name="naive_bayes_graph")
+def naive_bayes_graph_fixture():
+    return naive_bayes_graph()
+
+
+@pytest.fixture(name="asia_graph")
+def asia_graph_fixture():
+    return asia_graph()
+
+
+@pytest.fixture()
+def large_collider_graph():
+    edge_list = [("A", "B"), ("C", "B"), ("B", "D"), ("D", "E"), ("B", "F"), ("G", "E")]
+    G = nx.DiGraph(edge_list)
+    return G
+
+
+@pytest.fixture()
+def chain_and_fork_graph():
+    edge_list = [("A", "B"), ("B", "C"), ("B", "D"), ("D", "C")]
+    G = nx.DiGraph(edge_list)
+    return G
+
+
+@pytest.fixture()
+def no_separating_set_graph():
+    edge_list = [("A", "B")]
+    G = nx.DiGraph(edge_list)
+    return G
+
+
+@pytest.fixture()
+def large_no_separating_set_graph():
+    edge_list = [("A", "B"), ("C", "A"), ("C", "B")]
+    G = nx.DiGraph(edge_list)
+    return G
+
+
+@pytest.fixture()
+def collider_trek_graph():
+    edge_list = [("A", "B"), ("C", "B"), ("C", "D")]
+    G = nx.DiGraph(edge_list)
+    return G
+
+
+@pytest.mark.parametrize(
+    "graph",
+    [path_graph(), fork_graph(), collider_graph(), naive_bayes_graph(), asia_graph()],
+)
+def test_markov_condition(graph):
+    """Test that the Markov condition holds for each PGM graph."""
+    for node in graph.nodes:
+        parents = set(graph.predecessors(node))
+        non_descendants = graph.nodes - nx.descendants(graph, node) - {node} - parents
+        assert nx.is_d_separator(graph, {node}, non_descendants, parents)
+
+
+def test_path_graph_dsep(path_graph):
+    """Example-based test of d-separation for path_graph."""
+    assert nx.is_d_separator(path_graph, {0}, {2}, {1})
+    assert not nx.is_d_separator(path_graph, {0}, {2}, set())
+
+
+def test_fork_graph_dsep(fork_graph):
+    """Example-based test of d-separation for fork_graph."""
+    assert nx.is_d_separator(fork_graph, {1}, {2}, {0})
+    assert not nx.is_d_separator(fork_graph, {1}, {2}, set())
+
+
+def test_collider_graph_dsep(collider_graph):
+    """Example-based test of d-separation for collider_graph."""
+    assert nx.is_d_separator(collider_graph, {0}, {1}, set())
+    assert not nx.is_d_separator(collider_graph, {0}, {1}, {2})
+
+
+def test_naive_bayes_dsep(naive_bayes_graph):
+    """Example-based test of d-separation for naive_bayes_graph."""
+    for u, v in combinations(range(1, 5), 2):
+        assert nx.is_d_separator(naive_bayes_graph, {u}, {v}, {0})
+        assert not nx.is_d_separator(naive_bayes_graph, {u}, {v}, set())
+
+
+def test_asia_graph_dsep(asia_graph):
+    """Example-based test of d-separation for asia_graph."""
+    assert nx.is_d_separator(
+        asia_graph, {"asia", "smoking"}, {"dyspnea", "xray"}, {"bronchitis", "either"}
+    )
+    assert nx.is_d_separator(
+        asia_graph, {"tuberculosis", "cancer"}, {"bronchitis"}, {"smoking", "xray"}
+    )
+
+
+def test_undirected_graphs_are_not_supported():
+    """
+    Test that undirected graphs are not supported.
+
+    d-separation and its related algorithms do not apply in
+    the case of undirected graphs.
+    """
+    g = nx.path_graph(3, nx.Graph)
+    with pytest.raises(nx.NetworkXNotImplemented):
+        nx.is_d_separator(g, {0}, {1}, {2})
+    with pytest.raises(nx.NetworkXNotImplemented):
+        nx.is_minimal_d_separator(g, {0}, {1}, {2})
+    with pytest.raises(nx.NetworkXNotImplemented):
+        nx.find_minimal_d_separator(g, {0}, {1})
+
+
+def test_cyclic_graphs_raise_error():
+    """
+    Test that cycle graphs should cause erroring.
+
+    This is because PGMs assume a directed acyclic graph.
+    """
+    g = nx.cycle_graph(3, nx.DiGraph)
+    with pytest.raises(nx.NetworkXError):
+        nx.is_d_separator(g, {0}, {1}, {2})
+    with pytest.raises(nx.NetworkXError):
+        nx.find_minimal_d_separator(g, {0}, {1})
+    with pytest.raises(nx.NetworkXError):
+        nx.is_minimal_d_separator(g, {0}, {1}, {2})
+
+
+def test_invalid_nodes_raise_error(asia_graph):
+    """
+    Test that graphs that have invalid nodes passed in raise errors.
+    """
+    # Check both set and node arguments
+    with pytest.raises(nx.NodeNotFound):
+        nx.is_d_separator(asia_graph, {0}, {1}, {2})
+    with pytest.raises(nx.NodeNotFound):
+        nx.is_d_separator(asia_graph, 0, 1, 2)
+    with pytest.raises(nx.NodeNotFound):
+        nx.is_minimal_d_separator(asia_graph, {0}, {1}, {2})
+    with pytest.raises(nx.NodeNotFound):
+        nx.is_minimal_d_separator(asia_graph, 0, 1, 2)
+    with pytest.raises(nx.NodeNotFound):
+        nx.find_minimal_d_separator(asia_graph, {0}, {1})
+    with pytest.raises(nx.NodeNotFound):
+        nx.find_minimal_d_separator(asia_graph, 0, 1)
+
+
+def test_nondisjoint_node_sets_raise_error(collider_graph):
+    """
+    Test that error is raised when node sets aren't disjoint.
+    """
+    with pytest.raises(nx.NetworkXError):
+        nx.is_d_separator(collider_graph, 0, 1, 0)
+    with pytest.raises(nx.NetworkXError):
+        nx.is_d_separator(collider_graph, 0, 2, 0)
+    with pytest.raises(nx.NetworkXError):
+        nx.is_d_separator(collider_graph, 0, 0, 1)
+    with pytest.raises(nx.NetworkXError):
+        nx.is_d_separator(collider_graph, 1, 0, 0)
+    with pytest.raises(nx.NetworkXError):
+        nx.find_minimal_d_separator(collider_graph, 0, 0)
+    with pytest.raises(nx.NetworkXError):
+        nx.find_minimal_d_separator(collider_graph, 0, 1, included=0)
+    with pytest.raises(nx.NetworkXError):
+        nx.find_minimal_d_separator(collider_graph, 1, 0, included=0)
+    with pytest.raises(nx.NetworkXError):
+        nx.is_minimal_d_separator(collider_graph, 0, 0, set())
+    with pytest.raises(nx.NetworkXError):
+        nx.is_minimal_d_separator(collider_graph, 0, 1, set(), included=0)
+    with pytest.raises(nx.NetworkXError):
+        nx.is_minimal_d_separator(collider_graph, 1, 0, set(), included=0)
+
+
+def test_is_minimal_d_separator(
+    large_collider_graph,
+    chain_and_fork_graph,
+    no_separating_set_graph,
+    large_no_separating_set_graph,
+    collider_trek_graph,
+):
+    # Case 1:
+    # create a graph A -> B <- C
+    # B -> D -> E;
+    # B -> F;
+    # G -> E;
+    assert not nx.is_d_separator(large_collider_graph, {"B"}, {"E"}, set())
+
+    # minimal set of the corresponding graph
+    # for B and E should be (D,)
+    Zmin = nx.find_minimal_d_separator(large_collider_graph, "B", "E")
+    # check that the minimal d-separator is a d-separating set
+    assert nx.is_d_separator(large_collider_graph, "B", "E", Zmin)
+    # the minimal separating set should also pass the test for minimality
+    assert nx.is_minimal_d_separator(large_collider_graph, "B", "E", Zmin)
+    # function should also work with set arguments
+    assert nx.is_minimal_d_separator(large_collider_graph, {"A", "B"}, {"G", "E"}, Zmin)
+    assert Zmin == {"D"}
+
+    # Case 2:
+    # create a graph A -> B -> C
+    # B -> D -> C;
+    assert not nx.is_d_separator(chain_and_fork_graph, {"A"}, {"C"}, set())
+    Zmin = nx.find_minimal_d_separator(chain_and_fork_graph, "A", "C")
+
+    # the minimal separating set should pass the test for minimality
+    assert nx.is_minimal_d_separator(chain_and_fork_graph, "A", "C", Zmin)
+    assert Zmin == {"B"}
+    Znotmin = Zmin.union({"D"})
+    assert not nx.is_minimal_d_separator(chain_and_fork_graph, "A", "C", Znotmin)
+
+    # Case 3:
+    # create a graph A -> B
+
+    # there is no m-separating set between A and B at all, so
+    # no minimal m-separating set can exist
+    assert not nx.is_d_separator(no_separating_set_graph, {"A"}, {"B"}, set())
+    assert nx.find_minimal_d_separator(no_separating_set_graph, "A", "B") is None
+
+    # Case 4:
+    # create a graph A -> B with A <- C -> B
+
+    # there is no m-separating set between A and B at all, so
+    # no minimal m-separating set can exist
+    # however, the algorithm will initially propose C as a
+    # minimal (but invalid) separating set
+    assert not nx.is_d_separator(large_no_separating_set_graph, {"A"}, {"B"}, {"C"})
+    assert nx.find_minimal_d_separator(large_no_separating_set_graph, "A", "B") is None
+
+    # Test `included` and `excluded` args
+    # create graph A -> B <- C -> D
+    assert nx.find_minimal_d_separator(collider_trek_graph, "A", "D", included="B") == {
+        "B",
+        "C",
+    }
+    assert (
+        nx.find_minimal_d_separator(
+            collider_trek_graph, "A", "D", included="B", restricted="B"
+        )
+        is None
+    )
+
+
+def test_is_minimal_d_separator_checks_dsep():
+    """Test that is_minimal_d_separator checks for d-separation as well."""
+    g = nx.DiGraph()
+    g.add_edges_from(
+        [
+            ("A", "B"),
+            ("A", "E"),
+            ("B", "C"),
+            ("B", "D"),
+            ("D", "C"),
+            ("D", "F"),
+            ("E", "D"),
+            ("E", "F"),
+        ]
+    )
+
+    assert not nx.is_d_separator(g, {"C"}, {"F"}, {"D"})
+
+    # since {'D'} and {} are not d-separators, we return false
+    assert not nx.is_minimal_d_separator(g, "C", "F", {"D"})
+    assert not nx.is_minimal_d_separator(g, "C", "F", set())
+
+
+def test__reachable(large_collider_graph):
+    reachable = nx.algorithms.d_separation._reachable
+    g = large_collider_graph
+    x = {"F", "D"}
+    ancestors = {"A", "B", "C", "D", "F"}
+    assert reachable(g, x, ancestors, {"B"}) == {"B", "F", "D"}
+    assert reachable(g, x, ancestors, set()) == ancestors
+
+
+def test_deprecations():
+    G = nx.DiGraph([(0, 1), (1, 2)])
+    with pytest.deprecated_call():
+        nx.d_separated(G, 0, 2, {1})
+    with pytest.deprecated_call():
+        z = nx.minimal_d_separator(G, 0, 2)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_dag.py

@@ -0,0 +1,777 @@
+from collections import deque
+from itertools import combinations, permutations
+
+import pytest
+
+import networkx as nx
+from networkx.utils import edges_equal, pairwise
+
+
+# Recipe from the itertools documentation.
+def _consume(iterator):
+    "Consume the iterator entirely."
+    # Feed the entire iterator into a zero-length deque.
+    deque(iterator, maxlen=0)
+
+
+class TestDagLongestPath:
+    """Unit tests computing the longest path in a directed acyclic graph."""
+
+    def test_empty(self):
+        G = nx.DiGraph()
+        assert nx.dag_longest_path(G) == []
+
+    def test_unweighted1(self):
+        edges = [(1, 2), (2, 3), (2, 4), (3, 5), (5, 6), (3, 7)]
+        G = nx.DiGraph(edges)
+        assert nx.dag_longest_path(G) == [1, 2, 3, 5, 6]
+
+    def test_unweighted2(self):
+        edges = [(1, 2), (2, 3), (3, 4), (4, 5), (1, 3), (1, 5), (3, 5)]
+        G = nx.DiGraph(edges)
+        assert nx.dag_longest_path(G) == [1, 2, 3, 4, 5]
+
+    def test_weighted(self):
+        G = nx.DiGraph()
+        edges = [(1, 2, -5), (2, 3, 1), (3, 4, 1), (4, 5, 0), (3, 5, 4), (1, 6, 2)]
+        G.add_weighted_edges_from(edges)
+        assert nx.dag_longest_path(G) == [2, 3, 5]
+
+    def test_undirected_not_implemented(self):
+        G = nx.Graph()
+        pytest.raises(nx.NetworkXNotImplemented, nx.dag_longest_path, G)
+
+    def test_unorderable_nodes(self):
+        """Tests that computing the longest path does not depend on
+        nodes being orderable.
+
+        For more information, see issue #1989.
+
+        """
+        # Create the directed path graph on four nodes in a diamond shape,
+        # with nodes represented as (unorderable) Python objects.
+        nodes = [object() for n in range(4)]
+        G = nx.DiGraph()
+        G.add_edge(nodes[0], nodes[1])
+        G.add_edge(nodes[0], nodes[2])
+        G.add_edge(nodes[2], nodes[3])
+        G.add_edge(nodes[1], nodes[3])
+
+        # this will raise NotImplementedError when nodes need to be ordered
+        nx.dag_longest_path(G)
+
+    def test_multigraph_unweighted(self):
+        edges = [(1, 2), (2, 3), (2, 3), (3, 4), (4, 5), (1, 3), (1, 5), (3, 5)]
+        G = nx.MultiDiGraph(edges)
+        assert nx.dag_longest_path(G) == [1, 2, 3, 4, 5]
+
+    def test_multigraph_weighted(self):
+        G = nx.MultiDiGraph()
+        edges = [
+            (1, 2, 2),
+            (2, 3, 2),
+            (1, 3, 1),
+            (1, 3, 5),
+            (1, 3, 2),
+        ]
+        G.add_weighted_edges_from(edges)
+        assert nx.dag_longest_path(G) == [1, 3]
+
+    def test_multigraph_weighted_default_weight(self):
+        G = nx.MultiDiGraph([(1, 2), (2, 3)])  # Unweighted edges
+        G.add_weighted_edges_from([(1, 3, 1), (1, 3, 5), (1, 3, 2)])
+
+        # Default value for default weight is 1
+        assert nx.dag_longest_path(G) == [1, 3]
+        assert nx.dag_longest_path(G, default_weight=3) == [1, 2, 3]
+
+
+class TestDagLongestPathLength:
+    """Unit tests for computing the length of a longest path in a
+    directed acyclic graph.
+
+    """
+
+    def test_unweighted(self):
+        edges = [(1, 2), (2, 3), (2, 4), (3, 5), (5, 6), (5, 7)]
+        G = nx.DiGraph(edges)
+        assert nx.dag_longest_path_length(G) == 4
+
+        edges = [(1, 2), (2, 3), (3, 4), (4, 5), (1, 3), (1, 5), (3, 5)]
+        G = nx.DiGraph(edges)
+        assert nx.dag_longest_path_length(G) == 4
+
+        # test degenerate graphs
+        G = nx.DiGraph()
+        G.add_node(1)
+        assert nx.dag_longest_path_length(G) == 0
+
+    def test_undirected_not_implemented(self):
+        G = nx.Graph()
+        pytest.raises(nx.NetworkXNotImplemented, nx.dag_longest_path_length, G)
+
+    def test_weighted(self):
+        edges = [(1, 2, -5), (2, 3, 1), (3, 4, 1), (4, 5, 0), (3, 5, 4), (1, 6, 2)]
+        G = nx.DiGraph()
+        G.add_weighted_edges_from(edges)
+        assert nx.dag_longest_path_length(G) == 5
+
+    def test_multigraph_unweighted(self):
+        edges = [(1, 2), (2, 3), (2, 3), (3, 4), (4, 5), (1, 3), (1, 5), (3, 5)]
+        G = nx.MultiDiGraph(edges)
+        assert nx.dag_longest_path_length(G) == 4
+
+    def test_multigraph_weighted(self):
+        G = nx.MultiDiGraph()
+        edges = [
+            (1, 2, 2),
+            (2, 3, 2),
+            (1, 3, 1),
+            (1, 3, 5),
+            (1, 3, 2),
+        ]
+        G.add_weighted_edges_from(edges)
+        assert nx.dag_longest_path_length(G) == 5
+
+
+class TestDAG:
+    @classmethod
+    def setup_class(cls):
+        pass
+
+    def test_topological_sort1(self):
+        DG = nx.DiGraph([(1, 2), (1, 3), (2, 3)])
+
+        for algorithm in [nx.topological_sort, nx.lexicographical_topological_sort]:
+            assert tuple(algorithm(DG)) == (1, 2, 3)
+
+        DG.add_edge(3, 2)
+
+        for algorithm in [nx.topological_sort, nx.lexicographical_topological_sort]:
+            pytest.raises(nx.NetworkXUnfeasible, _consume, algorithm(DG))
+
+        DG.remove_edge(2, 3)
+
+        for algorithm in [nx.topological_sort, nx.lexicographical_topological_sort]:
+            assert tuple(algorithm(DG)) == (1, 3, 2)
+
+        DG.remove_edge(3, 2)
+
+        assert tuple(nx.topological_sort(DG)) in {(1, 2, 3), (1, 3, 2)}
+        assert tuple(nx.lexicographical_topological_sort(DG)) == (1, 2, 3)
+
+    def test_is_directed_acyclic_graph(self):
+        G = nx.generators.complete_graph(2)
+        assert not nx.is_directed_acyclic_graph(G)
+        assert not nx.is_directed_acyclic_graph(G.to_directed())
+        assert not nx.is_directed_acyclic_graph(nx.Graph([(3, 4), (4, 5)]))
+        assert nx.is_directed_acyclic_graph(nx.DiGraph([(3, 4), (4, 5)]))
+
+    def test_topological_sort2(self):
+        DG = nx.DiGraph(
+            {
+                1: [2],
+                2: [3],
+                3: [4],
+                4: [5],
+                5: [1],
+                11: [12],
+                12: [13],
+                13: [14],
+                14: [15],
+            }
+        )
+        pytest.raises(nx.NetworkXUnfeasible, _consume, nx.topological_sort(DG))
+
+        assert not nx.is_directed_acyclic_graph(DG)
+
+        DG.remove_edge(1, 2)
+        _consume(nx.topological_sort(DG))
+        assert nx.is_directed_acyclic_graph(DG)
+
+    def test_topological_sort3(self):
+        DG = nx.DiGraph()
+        DG.add_edges_from([(1, i) for i in range(2, 5)])
+        DG.add_edges_from([(2, i) for i in range(5, 9)])
+        DG.add_edges_from([(6, i) for i in range(9, 12)])
+        DG.add_edges_from([(4, i) for i in range(12, 15)])
+
+        def validate(order):
+            assert isinstance(order, list)
+            assert set(order) == set(DG)
+            for u, v in combinations(order, 2):
+                assert not nx.has_path(DG, v, u)
+
+        validate(list(nx.topological_sort(DG)))
+
+        DG.add_edge(14, 1)
+        pytest.raises(nx.NetworkXUnfeasible, _consume, nx.topological_sort(DG))
+
+    def test_topological_sort4(self):
+        G = nx.Graph()
+        G.add_edge(1, 2)
+        # Only directed graphs can be topologically sorted.
+        pytest.raises(nx.NetworkXError, _consume, nx.topological_sort(G))
+
+    def test_topological_sort5(self):
+        G = nx.DiGraph()
+        G.add_edge(0, 1)
+        assert list(nx.topological_sort(G)) == [0, 1]
+
+    def test_topological_sort6(self):
+        for algorithm in [nx.topological_sort, nx.lexicographical_topological_sort]:
+
+            def runtime_error():
+                DG = nx.DiGraph([(1, 2), (2, 3), (3, 4)])
+                first = True
+                for x in algorithm(DG):
+                    if first:
+                        first = False
+                        DG.add_edge(5 - x, 5)
+
+            def unfeasible_error():
+                DG = nx.DiGraph([(1, 2), (2, 3), (3, 4)])
+                first = True
+                for x in algorithm(DG):
+                    if first:
+                        first = False
+                        DG.remove_node(4)
+
+            def runtime_error2():
+                DG = nx.DiGraph([(1, 2), (2, 3), (3, 4)])
+                first = True
+                for x in algorithm(DG):
+                    if first:
+                        first = False
+                        DG.remove_node(2)
+
+            pytest.raises(RuntimeError, runtime_error)
+            pytest.raises(RuntimeError, runtime_error2)
+            pytest.raises(nx.NetworkXUnfeasible, unfeasible_error)
+
+    def test_all_topological_sorts_1(self):
+        DG = nx.DiGraph([(1, 2), (2, 3), (3, 4), (4, 5)])
+        assert list(nx.all_topological_sorts(DG)) == [[1, 2, 3, 4, 5]]
+
+    def test_all_topological_sorts_2(self):
+        DG = nx.DiGraph([(1, 3), (2, 1), (2, 4), (4, 3), (4, 5)])
+        assert sorted(nx.all_topological_sorts(DG)) == [
+            [2, 1, 4, 3, 5],
+            [2, 1, 4, 5, 3],
+            [2, 4, 1, 3, 5],
+            [2, 4, 1, 5, 3],
+            [2, 4, 5, 1, 3],
+        ]
+
+    def test_all_topological_sorts_3(self):
+        def unfeasible():
+            DG = nx.DiGraph([(1, 2), (2, 3), (3, 4), (4, 2), (4, 5)])
+            # convert to list to execute generator
+            list(nx.all_topological_sorts(DG))
+
+        def not_implemented():
+            G = nx.Graph([(1, 2), (2, 3)])
+            # convert to list to execute generator
+            list(nx.all_topological_sorts(G))
+
+        def not_implemented_2():
+            G = nx.MultiGraph([(1, 2), (1, 2), (2, 3)])
+            list(nx.all_topological_sorts(G))
+
+        pytest.raises(nx.NetworkXUnfeasible, unfeasible)
+        pytest.raises(nx.NetworkXNotImplemented, not_implemented)
+        pytest.raises(nx.NetworkXNotImplemented, not_implemented_2)
+
+    def test_all_topological_sorts_4(self):
+        DG = nx.DiGraph()
+        for i in range(7):
+            DG.add_node(i)
+        assert sorted(map(list, permutations(DG.nodes))) == sorted(
+            nx.all_topological_sorts(DG)
+        )
+
+    def test_all_topological_sorts_multigraph_1(self):
+        DG = nx.MultiDiGraph([(1, 2), (1, 2), (2, 3), (3, 4), (3, 5), (3, 5), (3, 5)])
+        assert sorted(nx.all_topological_sorts(DG)) == sorted(
+            [[1, 2, 3, 4, 5], [1, 2, 3, 5, 4]]
+        )
+
+    def test_all_topological_sorts_multigraph_2(self):
+        N = 9
+        edges = []
+        for i in range(1, N):
+            edges.extend([(i, i + 1)] * i)
+        DG = nx.MultiDiGraph(edges)
+        assert list(nx.all_topological_sorts(DG)) == [list(range(1, N + 1))]
+
+    def test_ancestors(self):
+        G = nx.DiGraph()
+        ancestors = nx.algorithms.dag.ancestors
+        G.add_edges_from([(1, 2), (1, 3), (4, 2), (4, 3), (4, 5), (2, 6), (5, 6)])
+        assert ancestors(G, 6) == {1, 2, 4, 5}
+        assert ancestors(G, 3) == {1, 4}
+        assert ancestors(G, 1) == set()
+        pytest.raises(nx.NetworkXError, ancestors, G, 8)
+
+    def test_descendants(self):
+        G = nx.DiGraph()
+        descendants = nx.algorithms.dag.descendants
+        G.add_edges_from([(1, 2), (1, 3), (4, 2), (4, 3), (4, 5), (2, 6), (5, 6)])
+        assert descendants(G, 1) == {2, 3, 6}
+        assert descendants(G, 4) == {2, 3, 5, 6}
+        assert descendants(G, 3) == set()
+        pytest.raises(nx.NetworkXError, descendants, G, 8)
+
+    def test_transitive_closure(self):
+        G = nx.DiGraph([(1, 2), (2, 3), (3, 4)])
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4), (3, 4)]
+        assert edges_equal(nx.transitive_closure(G).edges(), solution)
+        G = nx.DiGraph([(1, 2), (2, 3), (2, 4)])
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4)]
+        assert edges_equal(nx.transitive_closure(G).edges(), solution)
+        G = nx.DiGraph([(1, 2), (2, 3), (3, 1)])
+        solution = [(1, 2), (2, 1), (2, 3), (3, 2), (1, 3), (3, 1)]
+        soln = sorted(solution + [(n, n) for n in G])
+        assert edges_equal(sorted(nx.transitive_closure(G).edges()), soln)
+
+        G = nx.Graph([(1, 2), (2, 3), (3, 4)])
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4), (3, 4)]
+        assert edges_equal(sorted(nx.transitive_closure(G).edges()), solution)
+
+        G = nx.MultiGraph([(1, 2), (2, 3), (3, 4)])
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4), (3, 4)]
+        assert edges_equal(sorted(nx.transitive_closure(G).edges()), solution)
+
+        G = nx.MultiDiGraph([(1, 2), (2, 3), (3, 4)])
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4), (3, 4)]
+        assert edges_equal(sorted(nx.transitive_closure(G).edges()), solution)
+
+        # test if edge data is copied
+        G = nx.DiGraph([(1, 2, {"a": 3}), (2, 3, {"b": 0}), (3, 4)])
+        H = nx.transitive_closure(G)
+        for u, v in G.edges():
+            assert G.get_edge_data(u, v) == H.get_edge_data(u, v)
+
+        k = 10
+        G = nx.DiGraph((i, i + 1, {"f": "b", "weight": i}) for i in range(k))
+        H = nx.transitive_closure(G)
+        for u, v in G.edges():
+            assert G.get_edge_data(u, v) == H.get_edge_data(u, v)
+
+        G = nx.Graph()
+        with pytest.raises(nx.NetworkXError):
+            nx.transitive_closure(G, reflexive="wrong input")
+
+    def test_reflexive_transitive_closure(self):
+        G = nx.DiGraph([(1, 2), (2, 3), (3, 4)])
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4), (3, 4)]
+        soln = sorted(solution + [(n, n) for n in G])
+        assert edges_equal(nx.transitive_closure(G).edges(), solution)
+        assert edges_equal(nx.transitive_closure(G, False).edges(), solution)
+        assert edges_equal(nx.transitive_closure(G, True).edges(), soln)
+        assert edges_equal(nx.transitive_closure(G, None).edges(), solution)
+
+        G = nx.DiGraph([(1, 2), (2, 3), (2, 4)])
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4)]
+        soln = sorted(solution + [(n, n) for n in G])
+        assert edges_equal(nx.transitive_closure(G).edges(), solution)
+        assert edges_equal(nx.transitive_closure(G, False).edges(), solution)
+        assert edges_equal(nx.transitive_closure(G, True).edges(), soln)
+        assert edges_equal(nx.transitive_closure(G, None).edges(), solution)
+
+        G = nx.DiGraph([(1, 2), (2, 3), (3, 1)])
+        solution = sorted([(1, 2), (2, 1), (2, 3), (3, 2), (1, 3), (3, 1)])
+        soln = sorted(solution + [(n, n) for n in G])
+        assert edges_equal(sorted(nx.transitive_closure(G).edges()), soln)
+        assert edges_equal(sorted(nx.transitive_closure(G, False).edges()), soln)
+        assert edges_equal(sorted(nx.transitive_closure(G, None).edges()), solution)
+        assert edges_equal(sorted(nx.transitive_closure(G, True).edges()), soln)
+
+        G = nx.Graph([(1, 2), (2, 3), (3, 4)])
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4), (3, 4)]
+        soln = sorted(solution + [(n, n) for n in G])
+        assert edges_equal(nx.transitive_closure(G).edges(), solution)
+        assert edges_equal(nx.transitive_closure(G, False).edges(), solution)
+        assert edges_equal(nx.transitive_closure(G, True).edges(), soln)
+        assert edges_equal(nx.transitive_closure(G, None).edges(), solution)
+
+        G = nx.MultiGraph([(1, 2), (2, 3), (3, 4)])
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4), (3, 4)]
+        soln = sorted(solution + [(n, n) for n in G])
+        assert edges_equal(nx.transitive_closure(G).edges(), solution)
+        assert edges_equal(nx.transitive_closure(G, False).edges(), solution)
+        assert edges_equal(nx.transitive_closure(G, True).edges(), soln)
+        assert edges_equal(nx.transitive_closure(G, None).edges(), solution)
+
+        G = nx.MultiDiGraph([(1, 2), (2, 3), (3, 4)])
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4), (3, 4)]
+        soln = sorted(solution + [(n, n) for n in G])
+        assert edges_equal(nx.transitive_closure(G).edges(), solution)
+        assert edges_equal(nx.transitive_closure(G, False).edges(), solution)
+        assert edges_equal(nx.transitive_closure(G, True).edges(), soln)
+        assert edges_equal(nx.transitive_closure(G, None).edges(), solution)
+
+    def test_transitive_closure_dag(self):
+        G = nx.DiGraph([(1, 2), (2, 3), (3, 4)])
+        transitive_closure = nx.algorithms.dag.transitive_closure_dag
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4), (3, 4)]
+        assert edges_equal(transitive_closure(G).edges(), solution)
+        G = nx.DiGraph([(1, 2), (2, 3), (2, 4)])
+        solution = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 4)]
+        assert edges_equal(transitive_closure(G).edges(), solution)
+        G = nx.Graph([(1, 2), (2, 3), (3, 4)])
+        pytest.raises(nx.NetworkXNotImplemented, transitive_closure, G)
+
+        # test if edge data is copied
+        G = nx.DiGraph([(1, 2, {"a": 3}), (2, 3, {"b": 0}), (3, 4)])
+        H = transitive_closure(G)
+        for u, v in G.edges():
+            assert G.get_edge_data(u, v) == H.get_edge_data(u, v)
+
+        k = 10
+        G = nx.DiGraph((i, i + 1, {"foo": "bar", "weight": i}) for i in range(k))
+        H = transitive_closure(G)
+        for u, v in G.edges():
+            assert G.get_edge_data(u, v) == H.get_edge_data(u, v)
+
+    def test_transitive_reduction(self):
+        G = nx.DiGraph([(1, 2), (1, 3), (1, 4), (2, 3), (2, 4), (3, 4)])
+        transitive_reduction = nx.algorithms.dag.transitive_reduction
+        solution = [(1, 2), (2, 3), (3, 4)]
+        assert edges_equal(transitive_reduction(G).edges(), solution)
+        G = nx.DiGraph([(1, 2), (1, 3), (1, 4), (2, 3), (2, 4)])
+        transitive_reduction = nx.algorithms.dag.transitive_reduction
+        solution = [(1, 2), (2, 3), (2, 4)]
+        assert edges_equal(transitive_reduction(G).edges(), solution)
+        G = nx.Graph([(1, 2), (2, 3), (3, 4)])
+        pytest.raises(nx.NetworkXNotImplemented, transitive_reduction, G)
+
+    def _check_antichains(self, solution, result):
+        sol = [frozenset(a) for a in solution]
+        res = [frozenset(a) for a in result]
+        assert set(sol) == set(res)
+
+    def test_antichains(self):
+        antichains = nx.algorithms.dag.antichains
+        G = nx.DiGraph([(1, 2), (2, 3), (3, 4)])
+        solution = [[], [4], [3], [2], [1]]
+        self._check_antichains(list(antichains(G)), solution)
+        G = nx.DiGraph([(1, 2), (2, 3), (2, 4), (3, 5), (5, 6), (5, 7)])
+        solution = [
+            [],
+            [4],
+            [7],
+            [7, 4],
+            [6],
+            [6, 4],
+            [6, 7],
+            [6, 7, 4],
+            [5],
+            [5, 4],
+            [3],
+            [3, 4],
+            [2],
+            [1],
+        ]
+        self._check_antichains(list(antichains(G)), solution)
+        G = nx.DiGraph([(1, 2), (1, 3), (3, 4), (3, 5), (5, 6)])
+        solution = [
+            [],
+            [6],
+            [5],
+            [4],
+            [4, 6],
+            [4, 5],
+            [3],
+            [2],
+            [2, 6],
+            [2, 5],
+            [2, 4],
+            [2, 4, 6],
+            [2, 4, 5],
+            [2, 3],
+            [1],
+        ]
+        self._check_antichains(list(antichains(G)), solution)
+        G = nx.DiGraph({0: [1, 2], 1: [4], 2: [3], 3: [4]})
+        solution = [[], [4], [3], [2], [1], [1, 3], [1, 2], [0]]
+        self._check_antichains(list(antichains(G)), solution)
+        G = nx.DiGraph()
+        self._check_antichains(list(antichains(G)), [[]])
+        G = nx.DiGraph()
+        G.add_nodes_from([0, 1, 2])
+        solution = [[], [0], [1], [1, 0], [2], [2, 0], [2, 1], [2, 1, 0]]
+        self._check_antichains(list(antichains(G)), solution)
+
+        def f(x):
+            return list(antichains(x))
+
+        G = nx.Graph([(1, 2), (2, 3), (3, 4)])
+        pytest.raises(nx.NetworkXNotImplemented, f, G)
+        G = nx.DiGraph([(1, 2), (2, 3), (3, 1)])
+        pytest.raises(nx.NetworkXUnfeasible, f, G)
+
+    def test_lexicographical_topological_sort(self):
+        G = nx.DiGraph([(1, 2), (2, 3), (1, 4), (1, 5), (2, 6)])
+        assert list(nx.lexicographical_topological_sort(G)) == [1, 2, 3, 4, 5, 6]
+        assert list(nx.lexicographical_topological_sort(G, key=lambda x: x)) == [
+            1,
+            2,
+            3,
+            4,
+            5,
+            6,
+        ]
+        assert list(nx.lexicographical_topological_sort(G, key=lambda x: -x)) == [
+            1,
+            5,
+            4,
+            2,
+            6,
+            3,
+        ]
+
+    def test_lexicographical_topological_sort2(self):
+        """
+        Check the case of two or more nodes with same key value.
+        Want to avoid exception raised due to comparing nodes directly.
+        See Issue #3493
+        """
+
+        class Test_Node:
+            def __init__(self, n):
+                self.label = n
+                self.priority = 1
+
+            def __repr__(self):
+                return f"Node({self.label})"
+
+        def sorting_key(node):
+            return node.priority
+
+        test_nodes = [Test_Node(n) for n in range(4)]
+        G = nx.DiGraph()
+        edges = [(0, 1), (0, 2), (0, 3), (2, 3)]
+        G.add_edges_from((test_nodes[a], test_nodes[b]) for a, b in edges)
+
+        sorting = list(nx.lexicographical_topological_sort(G, key=sorting_key))
+        assert sorting == test_nodes
+
+
+def test_topological_generations():
+    G = nx.DiGraph(
+        {1: [2, 3], 2: [4, 5], 3: [7], 4: [], 5: [6, 7], 6: [], 7: []}
+    ).reverse()
+    # order within each generation is inconsequential
+    generations = [sorted(gen) for gen in nx.topological_generations(G)]
+    expected = [[4, 6, 7], [3, 5], [2], [1]]
+    assert generations == expected
+
+    MG = nx.MultiDiGraph(G.edges)
+    MG.add_edge(2, 1)
+    generations = [sorted(gen) for gen in nx.topological_generations(MG)]
+    assert generations == expected
+
+
+def test_topological_generations_empty():
+    G = nx.DiGraph()
+    assert list(nx.topological_generations(G)) == []
+
+
+def test_topological_generations_cycle():
+    G = nx.DiGraph([[2, 1], [3, 1], [1, 2]])
+    with pytest.raises(nx.NetworkXUnfeasible):
+        list(nx.topological_generations(G))
+
+
+def test_is_aperiodic_cycle():
+    G = nx.DiGraph()
+    nx.add_cycle(G, [1, 2, 3, 4])
+    assert not nx.is_aperiodic(G)
+
+
+def test_is_aperiodic_cycle2():
+    G = nx.DiGraph()
+    nx.add_cycle(G, [1, 2, 3, 4])
+    nx.add_cycle(G, [3, 4, 5, 6, 7])
+    assert nx.is_aperiodic(G)
+
+
+def test_is_aperiodic_cycle3():
+    G = nx.DiGraph()
+    nx.add_cycle(G, [1, 2, 3, 4])
+    nx.add_cycle(G, [3, 4, 5, 6])
+    assert not nx.is_aperiodic(G)
+
+
+def test_is_aperiodic_cycle4():
+    G = nx.DiGraph()
+    nx.add_cycle(G, [1, 2, 3, 4])
+    G.add_edge(1, 3)
+    assert nx.is_aperiodic(G)
+
+
+def test_is_aperiodic_selfloop():
+    G = nx.DiGraph()
+    nx.add_cycle(G, [1, 2, 3, 4])
+    G.add_edge(1, 1)
+    assert nx.is_aperiodic(G)
+
+
+def test_is_aperiodic_undirected_raises():
+    G = nx.Graph()
+    pytest.raises(nx.NetworkXError, nx.is_aperiodic, G)
+
+
+def test_is_aperiodic_empty_graph():
+    G = nx.empty_graph(create_using=nx.DiGraph)
+    with pytest.raises(nx.NetworkXPointlessConcept, match="Graph has no nodes."):
+        nx.is_aperiodic(G)
+
+
+def test_is_aperiodic_bipartite():
+    # Bipartite graph
+    G = nx.DiGraph(nx.davis_southern_women_graph())
+    assert not nx.is_aperiodic(G)
+
+
+def test_is_aperiodic_rary_tree():
+    G = nx.full_rary_tree(3, 27, create_using=nx.DiGraph())
+    assert not nx.is_aperiodic(G)
+
+
+def test_is_aperiodic_disconnected():
+    # disconnected graph
+    G = nx.DiGraph()
+    nx.add_cycle(G, [1, 2, 3, 4])
+    nx.add_cycle(G, [5, 6, 7, 8])
+    assert not nx.is_aperiodic(G)
+    G.add_edge(1, 3)
+    G.add_edge(5, 7)
+    assert nx.is_aperiodic(G)
+
+
+def test_is_aperiodic_disconnected2():
+    G = nx.DiGraph()
+    nx.add_cycle(G, [0, 1, 2])
+    G.add_edge(3, 3)
+    assert not nx.is_aperiodic(G)
+
+
+class TestDagToBranching:
+    """Unit tests for the :func:`networkx.dag_to_branching` function."""
+
+    def test_single_root(self):
+        """Tests that a directed acyclic graph with a single degree
+        zero node produces an arborescence.
+
+        """
+        G = nx.DiGraph([(0, 1), (0, 2), (1, 3), (2, 3)])
+        B = nx.dag_to_branching(G)
+        expected = nx.DiGraph([(0, 1), (1, 3), (0, 2), (2, 4)])
+        assert nx.is_arborescence(B)
+        assert nx.is_isomorphic(B, expected)
+
+    def test_multiple_roots(self):
+        """Tests that a directed acyclic graph with multiple degree zero
+        nodes creates an arborescence with multiple (weakly) connected
+        components.
+
+        """
+        G = nx.DiGraph([(0, 1), (0, 2), (1, 3), (2, 3), (5, 2)])
+        B = nx.dag_to_branching(G)
+        expected = nx.DiGraph([(0, 1), (1, 3), (0, 2), (2, 4), (5, 6), (6, 7)])
+        assert nx.is_branching(B)
+        assert not nx.is_arborescence(B)
+        assert nx.is_isomorphic(B, expected)
+
+    # # Attributes are not copied by this function. If they were, this would
+    # # be a good test to uncomment.
+    # def test_copy_attributes(self):
+    #     """Tests that node attributes are copied in the branching."""
+    #     G = nx.DiGraph([(0, 1), (0, 2), (1, 3), (2, 3)])
+    #     for v in G:
+    #         G.node[v]['label'] = str(v)
+    #     B = nx.dag_to_branching(G)
+    #     # Determine the root node of the branching.
+    #     root = next(v for v, d in B.in_degree() if d == 0)
+    #     assert_equal(B.node[root]['label'], '0')
+    #     children = B[root]
+    #     # Get the left and right children, nodes 1 and 2, respectively.
+    #     left, right = sorted(children, key=lambda v: B.node[v]['label'])
+    #     assert_equal(B.node[left]['label'], '1')
+    #     assert_equal(B.node[right]['label'], '2')
+    #     # Get the left grandchild.
+    #     children = B[left]
+    #     assert_equal(len(children), 1)
+    #     left_grandchild = arbitrary_element(children)
+    #     assert_equal(B.node[left_grandchild]['label'], '3')
+    #     # Get the right grandchild.
+    #     children = B[right]
+    #     assert_equal(len(children), 1)
+    #     right_grandchild = arbitrary_element(children)
+    #     assert_equal(B.node[right_grandchild]['label'], '3')
+
+    def test_already_arborescence(self):
+        """Tests that a directed acyclic graph that is already an
+        arborescence produces an isomorphic arborescence as output.
+
+        """
+        A = nx.balanced_tree(2, 2, create_using=nx.DiGraph())
+        B = nx.dag_to_branching(A)
+        assert nx.is_isomorphic(A, B)
+
+    def test_already_branching(self):
+        """Tests that a directed acyclic graph that is already a
+        branching produces an isomorphic branching as output.
+
+        """
+        T1 = nx.balanced_tree(2, 2, create_using=nx.DiGraph())
+        T2 = nx.balanced_tree(2, 2, create_using=nx.DiGraph())
+        G = nx.disjoint_union(T1, T2)
+        B = nx.dag_to_branching(G)
+        assert nx.is_isomorphic(G, B)
+
+    def test_not_acyclic(self):
+        """Tests that a non-acyclic graph causes an exception."""
+        with pytest.raises(nx.HasACycle):
+            G = nx.DiGraph(pairwise("abc", cyclic=True))
+            nx.dag_to_branching(G)
+
+    def test_undirected(self):
+        with pytest.raises(nx.NetworkXNotImplemented):
+            nx.dag_to_branching(nx.Graph())
+
+    def test_multigraph(self):
+        with pytest.raises(nx.NetworkXNotImplemented):
+            nx.dag_to_branching(nx.MultiGraph())
+
+    def test_multidigraph(self):
+        with pytest.raises(nx.NetworkXNotImplemented):
+            nx.dag_to_branching(nx.MultiDiGraph())
+
+
+def test_ancestors_descendants_undirected():
+    """Regression test to ensure ancestors and descendants work as expected on
+    undirected graphs."""
+    G = nx.path_graph(5)
+    nx.ancestors(G, 2) == nx.descendants(G, 2) == {0, 1, 3, 4}
+
+
+def test_compute_v_structures_raise():
+    G = nx.Graph()
+    pytest.raises(nx.NetworkXNotImplemented, nx.compute_v_structures, G)
+
+
+def test_compute_v_structures():
+    edges = [(0, 1), (0, 2), (3, 2)]
+    G = nx.DiGraph(edges)
+
+    v_structs = set(nx.compute_v_structures(G))
+    assert len(v_structs) == 1
+    assert (0, 2, 3) in v_structs
+
+    edges = [("A", "B"), ("C", "B"), ("B", "D"), ("D", "E"), ("G", "E")]
+    G = nx.DiGraph(edges)
+    v_structs = set(nx.compute_v_structures(G))
+    assert len(v_structs) == 2

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_distance_measures.py

@@ -0,0 +1,756 @@
+from random import Random
+
+import pytest
+
+import networkx as nx
+from networkx import convert_node_labels_to_integers as cnlti
+from networkx.algorithms.distance_measures import _extrema_bounding
+
+
+def test__extrema_bounding_invalid_compute_kwarg():
+    G = nx.path_graph(3)
+    with pytest.raises(ValueError, match="compute must be one of"):
+        _extrema_bounding(G, compute="spam")
+
+
+class TestDistance:
+    def setup_method(self):
+        G = cnlti(nx.grid_2d_graph(4, 4), first_label=1, ordering="sorted")
+        self.G = G
+
+    def test_eccentricity(self):
+        assert nx.eccentricity(self.G, 1) == 6
+        e = nx.eccentricity(self.G)
+        assert e[1] == 6
+
+        sp = dict(nx.shortest_path_length(self.G))
+        e = nx.eccentricity(self.G, sp=sp)
+        assert e[1] == 6
+
+        e = nx.eccentricity(self.G, v=1)
+        assert e == 6
+
+        # This behavior changed in version 1.8 (ticket #739)
+        e = nx.eccentricity(self.G, v=[1, 1])
+        assert e[1] == 6
+        e = nx.eccentricity(self.G, v=[1, 2])
+        assert e[1] == 6
+
+        # test against graph with one node
+        G = nx.path_graph(1)
+        e = nx.eccentricity(G)
+        assert e[0] == 0
+        e = nx.eccentricity(G, v=0)
+        assert e == 0
+        pytest.raises(nx.NetworkXError, nx.eccentricity, G, 1)
+
+        # test against empty graph
+        G = nx.empty_graph()
+        e = nx.eccentricity(G)
+        assert e == {}
+
+    def test_diameter(self):
+        assert nx.diameter(self.G) == 6
+
+    def test_radius(self):
+        assert nx.radius(self.G) == 4
+
+    def test_periphery(self):
+        assert set(nx.periphery(self.G)) == {1, 4, 13, 16}
+
+    def test_center(self):
+        assert set(nx.center(self.G)) == {6, 7, 10, 11}
+
+    def test_bound_diameter(self):
+        assert nx.diameter(self.G, usebounds=True) == 6
+
+    def test_bound_radius(self):
+        assert nx.radius(self.G, usebounds=True) == 4
+
+    def test_bound_periphery(self):
+        result = {1, 4, 13, 16}
+        assert set(nx.periphery(self.G, usebounds=True)) == result
+
+    def test_bound_center(self):
+        result = {6, 7, 10, 11}
+        assert set(nx.center(self.G, usebounds=True)) == result
+
+    def test_radius_exception(self):
+        G = nx.Graph()
+        G.add_edge(1, 2)
+        G.add_edge(3, 4)
+        pytest.raises(nx.NetworkXError, nx.diameter, G)
+
+    def test_eccentricity_infinite(self):
+        with pytest.raises(nx.NetworkXError):
+            G = nx.Graph([(1, 2), (3, 4)])
+            e = nx.eccentricity(G)
+
+    def test_eccentricity_undirected_not_connected(self):
+        with pytest.raises(nx.NetworkXError):
+            G = nx.Graph([(1, 2), (3, 4)])
+            e = nx.eccentricity(G, sp=1)
+
+    def test_eccentricity_directed_weakly_connected(self):
+        with pytest.raises(nx.NetworkXError):
+            DG = nx.DiGraph([(1, 2), (1, 3)])
+            nx.eccentricity(DG)
+
+
+class TestWeightedDistance:
+    def setup_method(self):
+        G = nx.Graph()
+        G.add_edge(0, 1, weight=0.6, cost=0.6, high_cost=6)
+        G.add_edge(0, 2, weight=0.2, cost=0.2, high_cost=2)
+        G.add_edge(2, 3, weight=0.1, cost=0.1, high_cost=1)
+        G.add_edge(2, 4, weight=0.7, cost=0.7, high_cost=7)
+        G.add_edge(2, 5, weight=0.9, cost=0.9, high_cost=9)
+        G.add_edge(1, 5, weight=0.3, cost=0.3, high_cost=3)
+        self.G = G
+        self.weight_fn = lambda v, u, e: 2
+
+    def test_eccentricity_weight_None(self):
+        assert nx.eccentricity(self.G, 1, weight=None) == 3
+        e = nx.eccentricity(self.G, weight=None)
+        assert e[1] == 3
+
+        e = nx.eccentricity(self.G, v=1, weight=None)
+        assert e == 3
+
+        # This behavior changed in version 1.8 (ticket #739)
+        e = nx.eccentricity(self.G, v=[1, 1], weight=None)
+        assert e[1] == 3
+        e = nx.eccentricity(self.G, v=[1, 2], weight=None)
+        assert e[1] == 3
+
+    def test_eccentricity_weight_attr(self):
+        assert nx.eccentricity(self.G, 1, weight="weight") == 1.5
+        e = nx.eccentricity(self.G, weight="weight")
+        assert (
+            e
+            == nx.eccentricity(self.G, weight="cost")
+            != nx.eccentricity(self.G, weight="high_cost")
+        )
+        assert e[1] == 1.5
+
+        e = nx.eccentricity(self.G, v=1, weight="weight")
+        assert e == 1.5
+
+        # This behavior changed in version 1.8 (ticket #739)
+        e = nx.eccentricity(self.G, v=[1, 1], weight="weight")
+        assert e[1] == 1.5
+        e = nx.eccentricity(self.G, v=[1, 2], weight="weight")
+        assert e[1] == 1.5
+
+    def test_eccentricity_weight_fn(self):
+        assert nx.eccentricity(self.G, 1, weight=self.weight_fn) == 6
+        e = nx.eccentricity(self.G, weight=self.weight_fn)
+        assert e[1] == 6
+
+        e = nx.eccentricity(self.G, v=1, weight=self.weight_fn)
+        assert e == 6
+
+        # This behavior changed in version 1.8 (ticket #739)
+        e = nx.eccentricity(self.G, v=[1, 1], weight=self.weight_fn)
+        assert e[1] == 6
+        e = nx.eccentricity(self.G, v=[1, 2], weight=self.weight_fn)
+        assert e[1] == 6
+
+    def test_diameter_weight_None(self):
+        assert nx.diameter(self.G, weight=None) == 3
+
+    def test_diameter_weight_attr(self):
+        assert (
+            nx.diameter(self.G, weight="weight")
+            == nx.diameter(self.G, weight="cost")
+            == 1.6
+            != nx.diameter(self.G, weight="high_cost")
+        )
+
+    def test_diameter_weight_fn(self):
+        assert nx.diameter(self.G, weight=self.weight_fn) == 6
+
+    def test_radius_weight_None(self):
+        assert pytest.approx(nx.radius(self.G, weight=None)) == 2
+
+    def test_radius_weight_attr(self):
+        assert (
+            pytest.approx(nx.radius(self.G, weight="weight"))
+            == pytest.approx(nx.radius(self.G, weight="cost"))
+            == 0.9
+            != nx.radius(self.G, weight="high_cost")
+        )
+
+    def test_radius_weight_fn(self):
+        assert nx.radius(self.G, weight=self.weight_fn) == 4
+
+    def test_periphery_weight_None(self):
+        for v in set(nx.periphery(self.G, weight=None)):
+            assert nx.eccentricity(self.G, v, weight=None) == nx.diameter(
+                self.G, weight=None
+            )
+
+    def test_periphery_weight_attr(self):
+        periphery = set(nx.periphery(self.G, weight="weight"))
+        assert (
+            periphery
+            == set(nx.periphery(self.G, weight="cost"))
+            == set(nx.periphery(self.G, weight="high_cost"))
+        )
+        for v in periphery:
+            assert (
+                nx.eccentricity(self.G, v, weight="high_cost")
+                != nx.eccentricity(self.G, v, weight="weight")
+                == nx.eccentricity(self.G, v, weight="cost")
+                == nx.diameter(self.G, weight="weight")
+                == nx.diameter(self.G, weight="cost")
+                != nx.diameter(self.G, weight="high_cost")
+            )
+            assert nx.eccentricity(self.G, v, weight="high_cost") == nx.diameter(
+                self.G, weight="high_cost"
+            )
+
+    def test_periphery_weight_fn(self):
+        for v in set(nx.periphery(self.G, weight=self.weight_fn)):
+            assert nx.eccentricity(self.G, v, weight=self.weight_fn) == nx.diameter(
+                self.G, weight=self.weight_fn
+            )
+
+    def test_center_weight_None(self):
+        for v in set(nx.center(self.G, weight=None)):
+            assert pytest.approx(nx.eccentricity(self.G, v, weight=None)) == nx.radius(
+                self.G, weight=None
+            )
+
+    def test_center_weight_attr(self):
+        center = set(nx.center(self.G, weight="weight"))
+        assert (
+            center
+            == set(nx.center(self.G, weight="cost"))
+            != set(nx.center(self.G, weight="high_cost"))
+        )
+        for v in center:
+            assert (
+                nx.eccentricity(self.G, v, weight="high_cost")
+                != pytest.approx(nx.eccentricity(self.G, v, weight="weight"))
+                == pytest.approx(nx.eccentricity(self.G, v, weight="cost"))
+                == nx.radius(self.G, weight="weight")
+                == nx.radius(self.G, weight="cost")
+                != nx.radius(self.G, weight="high_cost")
+            )
+            assert nx.eccentricity(self.G, v, weight="high_cost") == nx.radius(
+                self.G, weight="high_cost"
+            )
+
+    def test_center_weight_fn(self):
+        for v in set(nx.center(self.G, weight=self.weight_fn)):
+            assert nx.eccentricity(self.G, v, weight=self.weight_fn) == nx.radius(
+                self.G, weight=self.weight_fn
+            )
+
+    def test_bound_diameter_weight_None(self):
+        assert nx.diameter(self.G, usebounds=True, weight=None) == 3
+
+    def test_bound_diameter_weight_attr(self):
+        assert (
+            nx.diameter(self.G, usebounds=True, weight="high_cost")
+            != nx.diameter(self.G, usebounds=True, weight="weight")
+            == nx.diameter(self.G, usebounds=True, weight="cost")
+            == 1.6
+            != nx.diameter(self.G, usebounds=True, weight="high_cost")
+        )
+        assert nx.diameter(self.G, usebounds=True, weight="high_cost") == nx.diameter(
+            self.G, usebounds=True, weight="high_cost"
+        )
+
+    def test_bound_diameter_weight_fn(self):
+        assert nx.diameter(self.G, usebounds=True, weight=self.weight_fn) == 6
+
+    def test_bound_radius_weight_None(self):
+        assert pytest.approx(nx.radius(self.G, usebounds=True, weight=None)) == 2
+
+    def test_bound_radius_weight_attr(self):
+        assert (
+            nx.radius(self.G, usebounds=True, weight="high_cost")
+            != pytest.approx(nx.radius(self.G, usebounds=True, weight="weight"))
+            == pytest.approx(nx.radius(self.G, usebounds=True, weight="cost"))
+            == 0.9
+            != nx.radius(self.G, usebounds=True, weight="high_cost")
+        )
+        assert nx.radius(self.G, usebounds=True, weight="high_cost") == nx.radius(
+            self.G, usebounds=True, weight="high_cost"
+        )
+
+    def test_bound_radius_weight_fn(self):
+        assert nx.radius(self.G, usebounds=True, weight=self.weight_fn) == 4
+
+    def test_bound_periphery_weight_None(self):
+        result = {1, 3, 4}
+        assert set(nx.periphery(self.G, usebounds=True, weight=None)) == result
+
+    def test_bound_periphery_weight_attr(self):
+        result = {4, 5}
+        assert (
+            set(nx.periphery(self.G, usebounds=True, weight="weight"))
+            == set(nx.periphery(self.G, usebounds=True, weight="cost"))
+            == result
+        )
+
+    def test_bound_periphery_weight_fn(self):
+        result = {1, 3, 4}
+        assert (
+            set(nx.periphery(self.G, usebounds=True, weight=self.weight_fn)) == result
+        )
+
+    def test_bound_center_weight_None(self):
+        result = {0, 2, 5}
+        assert set(nx.center(self.G, usebounds=True, weight=None)) == result
+
+    def test_bound_center_weight_attr(self):
+        result = {0}
+        assert (
+            set(nx.center(self.G, usebounds=True, weight="weight"))
+            == set(nx.center(self.G, usebounds=True, weight="cost"))
+            == result
+        )
+
+    def test_bound_center_weight_fn(self):
+        result = {0, 2, 5}
+        assert set(nx.center(self.G, usebounds=True, weight=self.weight_fn)) == result
+
+
+class TestResistanceDistance:
+    @classmethod
+    def setup_class(cls):
+        global np
+        np = pytest.importorskip("numpy")
+        sp = pytest.importorskip("scipy")
+
+    def setup_method(self):
+        G = nx.Graph()
+        G.add_edge(1, 2, weight=2)
+        G.add_edge(2, 3, weight=4)
+        G.add_edge(3, 4, weight=1)
+        G.add_edge(1, 4, weight=3)
+        self.G = G
+
+    def test_resistance_distance_directed_graph(self):
+        G = nx.DiGraph()
+        with pytest.raises(nx.NetworkXNotImplemented):
+            nx.resistance_distance(G)
+
+    def test_resistance_distance_empty(self):
+        G = nx.Graph()
+        with pytest.raises(nx.NetworkXError):
+            nx.resistance_distance(G)
+
+    def test_resistance_distance_not_connected(self):
+        with pytest.raises(nx.NetworkXError):
+            self.G.add_node(5)
+            nx.resistance_distance(self.G, 1, 5)
+
+    def test_resistance_distance_nodeA_not_in_graph(self):
+        with pytest.raises(nx.NetworkXError):
+            nx.resistance_distance(self.G, 9, 1)
+
+    def test_resistance_distance_nodeB_not_in_graph(self):
+        with pytest.raises(nx.NetworkXError):
+            nx.resistance_distance(self.G, 1, 9)
+
+    def test_resistance_distance(self):
+        rd = nx.resistance_distance(self.G, 1, 3, "weight", True)
+        test_data = 1 / (1 / (2 + 4) + 1 / (1 + 3))
+        assert round(rd, 5) == round(test_data, 5)
+
+    def test_resistance_distance_noinv(self):
+        rd = nx.resistance_distance(self.G, 1, 3, "weight", False)
+        test_data = 1 / (1 / (1 / 2 + 1 / 4) + 1 / (1 / 1 + 1 / 3))
+        assert round(rd, 5) == round(test_data, 5)
+
+    def test_resistance_distance_no_weight(self):
+        rd = nx.resistance_distance(self.G, 1, 3)
+        assert round(rd, 5) == 1
+
+    def test_resistance_distance_neg_weight(self):
+        self.G[2][3]["weight"] = -4
+        rd = nx.resistance_distance(self.G, 1, 3, "weight", True)
+        test_data = 1 / (1 / (2 + -4) + 1 / (1 + 3))
+        assert round(rd, 5) == round(test_data, 5)
+
+    def test_multigraph(self):
+        G = nx.MultiGraph()
+        G.add_edge(1, 2, weight=2)
+        G.add_edge(2, 3, weight=4)
+        G.add_edge(3, 4, weight=1)
+        G.add_edge(1, 4, weight=3)
+        rd = nx.resistance_distance(G, 1, 3, "weight", True)
+        assert np.isclose(rd, 1 / (1 / (2 + 4) + 1 / (1 + 3)))
+
+    def test_resistance_distance_div0(self):
+        with pytest.raises(ZeroDivisionError):
+            self.G[1][2]["weight"] = 0
+            nx.resistance_distance(self.G, 1, 3, "weight")
+
+    def test_resistance_distance_same_node(self):
+        assert nx.resistance_distance(self.G, 1, 1) == 0
+
+    def test_resistance_distance_only_nodeA(self):
+        rd = nx.resistance_distance(self.G, nodeA=1)
+        test_data = {}
+        test_data[1] = 0
+        test_data[2] = 0.75
+        test_data[3] = 1
+        test_data[4] = 0.75
+        assert type(rd) == dict
+        assert sorted(rd.keys()) == sorted(test_data.keys())
+        for key in rd:
+            assert np.isclose(rd[key], test_data[key])
+
+    def test_resistance_distance_only_nodeB(self):
+        rd = nx.resistance_distance(self.G, nodeB=1)
+        test_data = {}
+        test_data[1] = 0
+        test_data[2] = 0.75
+        test_data[3] = 1
+        test_data[4] = 0.75
+        assert type(rd) == dict
+        assert sorted(rd.keys()) == sorted(test_data.keys())
+        for key in rd:
+            assert np.isclose(rd[key], test_data[key])
+
+    def test_resistance_distance_all(self):
+        rd = nx.resistance_distance(self.G)
+        assert type(rd) == dict
+        assert round(rd[1][3], 5) == 1
+
+
+class TestEffectiveGraphResistance:
+    @classmethod
+    def setup_class(cls):
+        global np
+        np = pytest.importorskip("numpy")
+        sp = pytest.importorskip("scipy")
+
+    def setup_method(self):
+        G = nx.Graph()
+        G.add_edge(1, 2, weight=2)
+        G.add_edge(1, 3, weight=1)
+        G.add_edge(2, 3, weight=4)
+        self.G = G
+
+    def test_effective_graph_resistance_directed_graph(self):
+        G = nx.DiGraph()
+        with pytest.raises(nx.NetworkXNotImplemented):
+            nx.effective_graph_resistance(G)
+
+    def test_effective_graph_resistance_empty(self):
+        G = nx.Graph()
+        with pytest.raises(nx.NetworkXError):
+            nx.effective_graph_resistance(G)
+
+    def test_effective_graph_resistance_not_connected(self):
+        G = nx.Graph([(1, 2), (3, 4)])
+        RG = nx.effective_graph_resistance(G)
+        assert np.isinf(RG)
+
+    def test_effective_graph_resistance(self):
+        RG = nx.effective_graph_resistance(self.G, "weight", True)
+        rd12 = 1 / (1 / (1 + 4) + 1 / 2)
+        rd13 = 1 / (1 / (1 + 2) + 1 / 4)
+        rd23 = 1 / (1 / (2 + 4) + 1 / 1)
+        assert np.isclose(RG, rd12 + rd13 + rd23)
+
+    def test_effective_graph_resistance_noinv(self):
+        RG = nx.effective_graph_resistance(self.G, "weight", False)
+        rd12 = 1 / (1 / (1 / 1 + 1 / 4) + 1 / (1 / 2))
+        rd13 = 1 / (1 / (1 / 1 + 1 / 2) + 1 / (1 / 4))
+        rd23 = 1 / (1 / (1 / 2 + 1 / 4) + 1 / (1 / 1))
+        assert np.isclose(RG, rd12 + rd13 + rd23)
+
+    def test_effective_graph_resistance_no_weight(self):
+        RG = nx.effective_graph_resistance(self.G)
+        assert np.isclose(RG, 2)
+
+    def test_effective_graph_resistance_neg_weight(self):
+        self.G[2][3]["weight"] = -4
+        RG = nx.effective_graph_resistance(self.G, "weight", True)
+        rd12 = 1 / (1 / (1 + -4) + 1 / 2)
+        rd13 = 1 / (1 / (1 + 2) + 1 / (-4))
+        rd23 = 1 / (1 / (2 + -4) + 1 / 1)
+        assert np.isclose(RG, rd12 + rd13 + rd23)
+
+    def test_effective_graph_resistance_multigraph(self):
+        G = nx.MultiGraph()
+        G.add_edge(1, 2, weight=2)
+        G.add_edge(1, 3, weight=1)
+        G.add_edge(2, 3, weight=1)
+        G.add_edge(2, 3, weight=3)
+        RG = nx.effective_graph_resistance(G, "weight", True)
+        edge23 = 1 / (1 / 1 + 1 / 3)
+        rd12 = 1 / (1 / (1 + edge23) + 1 / 2)
+        rd13 = 1 / (1 / (1 + 2) + 1 / edge23)
+        rd23 = 1 / (1 / (2 + edge23) + 1 / 1)
+        assert np.isclose(RG, rd12 + rd13 + rd23)
+
+    def test_effective_graph_resistance_div0(self):
+        with pytest.raises(ZeroDivisionError):
+            self.G[1][2]["weight"] = 0
+            nx.effective_graph_resistance(self.G, "weight")
+
+    def test_effective_graph_resistance_complete_graph(self):
+        N = 10
+        G = nx.complete_graph(N)
+        RG = nx.effective_graph_resistance(G)
+        assert np.isclose(RG, N - 1)
+
+    def test_effective_graph_resistance_path_graph(self):
+        N = 10
+        G = nx.path_graph(N)
+        RG = nx.effective_graph_resistance(G)
+        assert np.isclose(RG, (N - 1) * N * (N + 1) // 6)
+
+
+class TestBarycenter:
+    """Test :func:`networkx.algorithms.distance_measures.barycenter`."""
+
+    def barycenter_as_subgraph(self, g, **kwargs):
+        """Return the subgraph induced on the barycenter of g"""
+        b = nx.barycenter(g, **kwargs)
+        assert isinstance(b, list)
+        assert set(b) <= set(g)
+        return g.subgraph(b)
+
+    def test_must_be_connected(self):
+        pytest.raises(nx.NetworkXNoPath, nx.barycenter, nx.empty_graph(5))
+
+    def test_sp_kwarg(self):
+        # Complete graph K_5. Normally it works...
+        K_5 = nx.complete_graph(5)
+        sp = dict(nx.shortest_path_length(K_5))
+        assert nx.barycenter(K_5, sp=sp) == list(K_5)
+
+        # ...but not with the weight argument
+        for u, v, data in K_5.edges.data():
+            data["weight"] = 1
+        pytest.raises(ValueError, nx.barycenter, K_5, sp=sp, weight="weight")
+
+        # ...and a corrupted sp can make it seem like K_5 is disconnected
+        del sp[0][1]
+        pytest.raises(nx.NetworkXNoPath, nx.barycenter, K_5, sp=sp)
+
+    def test_trees(self):
+        """The barycenter of a tree is a single vertex or an edge.
+
+        See [West01]_, p. 78.
+        """
+        prng = Random(0xDEADBEEF)
+        for i in range(50):
+            RT = nx.random_labeled_tree(prng.randint(1, 75), seed=prng)
+            b = self.barycenter_as_subgraph(RT)
+            if len(b) == 2:
+                assert b.size() == 1
+            else:
+                assert len(b) == 1
+                assert b.size() == 0
+
+    def test_this_one_specific_tree(self):
+        """Test the tree pictured at the bottom of [West01]_, p. 78."""
+        g = nx.Graph(
+            {
+                "a": ["b"],
+                "b": ["a", "x"],
+                "x": ["b", "y"],
+                "y": ["x", "z"],
+                "z": ["y", 0, 1, 2, 3, 4],
+                0: ["z"],
+                1: ["z"],
+                2: ["z"],
+                3: ["z"],
+                4: ["z"],
+            }
+        )
+        b = self.barycenter_as_subgraph(g, attr="barycentricity")
+        assert list(b) == ["z"]
+        assert not b.edges
+        expected_barycentricity = {
+            0: 23,
+            1: 23,
+            2: 23,
+            3: 23,
+            4: 23,
+            "a": 35,
+            "b": 27,
+            "x": 21,
+            "y": 17,
+            "z": 15,
+        }
+        for node, barycentricity in expected_barycentricity.items():
+            assert g.nodes[node]["barycentricity"] == barycentricity
+
+        # Doubling weights should do nothing but double the barycentricities
+        for edge in g.edges:
+            g.edges[edge]["weight"] = 2
+        b = self.barycenter_as_subgraph(g, weight="weight", attr="barycentricity2")
+        assert list(b) == ["z"]
+        assert not b.edges
+        for node, barycentricity in expected_barycentricity.items():
+            assert g.nodes[node]["barycentricity2"] == barycentricity * 2
+
+
+class TestKemenyConstant:
+    @classmethod
+    def setup_class(cls):
+        global np
+        np = pytest.importorskip("numpy")
+        sp = pytest.importorskip("scipy")
+
+    def setup_method(self):
+        G = nx.Graph()
+        w12 = 2
+        w13 = 3
+        w23 = 4
+        G.add_edge(1, 2, weight=w12)
+        G.add_edge(1, 3, weight=w13)
+        G.add_edge(2, 3, weight=w23)
+        self.G = G
+
+    def test_kemeny_constant_directed(self):
+        G = nx.DiGraph()
+        G.add_edge(1, 2)
+        G.add_edge(1, 3)
+        G.add_edge(2, 3)
+        with pytest.raises(nx.NetworkXNotImplemented):
+            nx.kemeny_constant(G)
+
+    def test_kemeny_constant_not_connected(self):
+        self.G.add_node(5)
+        with pytest.raises(nx.NetworkXError):
+            nx.kemeny_constant(self.G)
+
+    def test_kemeny_constant_no_nodes(self):
+        G = nx.Graph()
+        with pytest.raises(nx.NetworkXError):
+            nx.kemeny_constant(G)
+
+    def test_kemeny_constant_negative_weight(self):
+        G = nx.Graph()
+        w12 = 2
+        w13 = 3
+        w23 = -10
+        G.add_edge(1, 2, weight=w12)
+        G.add_edge(1, 3, weight=w13)
+        G.add_edge(2, 3, weight=w23)
+        with pytest.raises(nx.NetworkXError):
+            nx.kemeny_constant(G, weight="weight")
+
+    def test_kemeny_constant(self):
+        K = nx.kemeny_constant(self.G, weight="weight")
+        w12 = 2
+        w13 = 3
+        w23 = 4
+        test_data = (
+            3
+            / 2
+            * (w12 + w13)
+            * (w12 + w23)
+            * (w13 + w23)
+            / (
+                w12**2 * (w13 + w23)
+                + w13**2 * (w12 + w23)
+                + w23**2 * (w12 + w13)
+                + 3 * w12 * w13 * w23
+            )
+        )
+        assert np.isclose(K, test_data)
+
+    def test_kemeny_constant_no_weight(self):
+        K = nx.kemeny_constant(self.G)
+        assert np.isclose(K, 4 / 3)
+
+    def test_kemeny_constant_multigraph(self):
+        G = nx.MultiGraph()
+        w12_1 = 2
+        w12_2 = 1
+        w13 = 3
+        w23 = 4
+        G.add_edge(1, 2, weight=w12_1)
+        G.add_edge(1, 2, weight=w12_2)
+        G.add_edge(1, 3, weight=w13)
+        G.add_edge(2, 3, weight=w23)
+        K = nx.kemeny_constant(G, weight="weight")
+        w12 = w12_1 + w12_2
+        test_data = (
+            3
+            / 2
+            * (w12 + w13)
+            * (w12 + w23)
+            * (w13 + w23)
+            / (
+                w12**2 * (w13 + w23)
+                + w13**2 * (w12 + w23)
+                + w23**2 * (w12 + w13)
+                + 3 * w12 * w13 * w23
+            )
+        )
+        assert np.isclose(K, test_data)
+
+    def test_kemeny_constant_weight0(self):
+        G = nx.Graph()
+        w12 = 0
+        w13 = 3
+        w23 = 4
+        G.add_edge(1, 2, weight=w12)
+        G.add_edge(1, 3, weight=w13)
+        G.add_edge(2, 3, weight=w23)
+        K = nx.kemeny_constant(G, weight="weight")
+        test_data = (
+            3
+            / 2
+            * (w12 + w13)
+            * (w12 + w23)
+            * (w13 + w23)
+            / (
+                w12**2 * (w13 + w23)
+                + w13**2 * (w12 + w23)
+                + w23**2 * (w12 + w13)
+                + 3 * w12 * w13 * w23
+            )
+        )
+        assert np.isclose(K, test_data)
+
+    def test_kemeny_constant_selfloop(self):
+        G = nx.Graph()
+        w11 = 1
+        w12 = 2
+        w13 = 3
+        w23 = 4
+        G.add_edge(1, 1, weight=w11)
+        G.add_edge(1, 2, weight=w12)
+        G.add_edge(1, 3, weight=w13)
+        G.add_edge(2, 3, weight=w23)
+        K = nx.kemeny_constant(G, weight="weight")
+        test_data = (
+            (2 * w11 + 3 * w12 + 3 * w13)
+            * (w12 + w23)
+            * (w13 + w23)
+            / (
+                (w12 * w13 + w12 * w23 + w13 * w23)
+                * (w11 + 2 * w12 + 2 * w13 + 2 * w23)
+            )
+        )
+        assert np.isclose(K, test_data)
+
+    def test_kemeny_constant_complete_bipartite_graph(self):
+        # Theorem 1 in https://www.sciencedirect.com/science/article/pii/S0166218X20302912
+        n1 = 5
+        n2 = 4
+        G = nx.complete_bipartite_graph(n1, n2)
+        K = nx.kemeny_constant(G)
+        assert np.isclose(K, n1 + n2 - 3 / 2)
+
+    def test_kemeny_constant_path_graph(self):
+        # Theorem 2 in https://www.sciencedirect.com/science/article/pii/S0166218X20302912
+        n = 10
+        G = nx.path_graph(n)
+        K = nx.kemeny_constant(G)
+        assert np.isclose(K, n**2 / 3 - 2 * n / 3 + 1 / 2)

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_dominance.py

@@ -0,0 +1,285 @@
+import pytest
+
+import networkx as nx
+
+
+class TestImmediateDominators:
+    def test_exceptions(self):
+        G = nx.Graph()
+        G.add_node(0)
+        pytest.raises(nx.NetworkXNotImplemented, nx.immediate_dominators, G, 0)
+        G = nx.MultiGraph(G)
+        pytest.raises(nx.NetworkXNotImplemented, nx.immediate_dominators, G, 0)
+        G = nx.DiGraph([[0, 0]])
+        pytest.raises(nx.NetworkXError, nx.immediate_dominators, G, 1)
+
+    def test_singleton(self):
+        G = nx.DiGraph()
+        G.add_node(0)
+        assert nx.immediate_dominators(G, 0) == {0: 0}
+        G.add_edge(0, 0)
+        assert nx.immediate_dominators(G, 0) == {0: 0}
+
+    def test_path(self):
+        n = 5
+        G = nx.path_graph(n, create_using=nx.DiGraph())
+        assert nx.immediate_dominators(G, 0) == {i: max(i - 1, 0) for i in range(n)}
+
+    def test_cycle(self):
+        n = 5
+        G = nx.cycle_graph(n, create_using=nx.DiGraph())
+        assert nx.immediate_dominators(G, 0) == {i: max(i - 1, 0) for i in range(n)}
+
+    def test_unreachable(self):
+        n = 5
+        assert n > 1
+        G = nx.path_graph(n, create_using=nx.DiGraph())
+        assert nx.immediate_dominators(G, n // 2) == {
+            i: max(i - 1, n // 2) for i in range(n // 2, n)
+        }
+
+    def test_irreducible1(self):
+        # Graph taken from Figure 2 of
+        # K. D. Cooper, T. J. Harvey, and K. Kennedy.
+        # A simple, fast dominance algorithm.
+        # Software Practice & Experience, 4:110, 2001.
+        edges = [(1, 2), (2, 1), (3, 2), (4, 1), (5, 3), (5, 4)]
+        G = nx.DiGraph(edges)
+        assert nx.immediate_dominators(G, 5) == {i: 5 for i in range(1, 6)}
+
+    def test_irreducible2(self):
+        # Graph taken from Figure 4 of
+        # K. D. Cooper, T. J. Harvey, and K. Kennedy.
+        # A simple, fast dominance algorithm.
+        # Software Practice & Experience, 4:110, 2001.
+        edges = [(1, 2), (2, 1), (2, 3), (3, 2), (4, 2), (4, 3), (5, 1), (6, 4), (6, 5)]
+        G = nx.DiGraph(edges)
+        result = nx.immediate_dominators(G, 6)
+        assert result == {i: 6 for i in range(1, 7)}
+
+    def test_domrel_png(self):
+        # Graph taken from https://commons.wikipedia.org/wiki/File:Domrel.png
+        edges = [(1, 2), (2, 3), (2, 4), (2, 6), (3, 5), (4, 5), (5, 2)]
+        G = nx.DiGraph(edges)
+        result = nx.immediate_dominators(G, 1)
+        assert result == {1: 1, 2: 1, 3: 2, 4: 2, 5: 2, 6: 2}
+        # Test postdominance.
+        result = nx.immediate_dominators(G.reverse(copy=False), 6)
+        assert result == {1: 2, 2: 6, 3: 5, 4: 5, 5: 2, 6: 6}
+
+    def test_boost_example(self):
+        # Graph taken from Figure 1 of
+        # http://www.boost.org/doc/libs/1_56_0/libs/graph/doc/lengauer_tarjan_dominator.htm
+        edges = [(0, 1), (1, 2), (1, 3), (2, 7), (3, 4), (4, 5), (4, 6), (5, 7), (6, 4)]
+        G = nx.DiGraph(edges)
+        result = nx.immediate_dominators(G, 0)
+        assert result == {0: 0, 1: 0, 2: 1, 3: 1, 4: 3, 5: 4, 6: 4, 7: 1}
+        # Test postdominance.
+        result = nx.immediate_dominators(G.reverse(copy=False), 7)
+        assert result == {0: 1, 1: 7, 2: 7, 3: 4, 4: 5, 5: 7, 6: 4, 7: 7}
+
+
+class TestDominanceFrontiers:
+    def test_exceptions(self):
+        G = nx.Graph()
+        G.add_node(0)
+        pytest.raises(nx.NetworkXNotImplemented, nx.dominance_frontiers, G, 0)
+        G = nx.MultiGraph(G)
+        pytest.raises(nx.NetworkXNotImplemented, nx.dominance_frontiers, G, 0)
+        G = nx.DiGraph([[0, 0]])
+        pytest.raises(nx.NetworkXError, nx.dominance_frontiers, G, 1)
+
+    def test_singleton(self):
+        G = nx.DiGraph()
+        G.add_node(0)
+        assert nx.dominance_frontiers(G, 0) == {0: set()}
+        G.add_edge(0, 0)
+        assert nx.dominance_frontiers(G, 0) == {0: set()}
+
+    def test_path(self):
+        n = 5
+        G = nx.path_graph(n, create_using=nx.DiGraph())
+        assert nx.dominance_frontiers(G, 0) == {i: set() for i in range(n)}
+
+    def test_cycle(self):
+        n = 5
+        G = nx.cycle_graph(n, create_using=nx.DiGraph())
+        assert nx.dominance_frontiers(G, 0) == {i: set() for i in range(n)}
+
+    def test_unreachable(self):
+        n = 5
+        assert n > 1
+        G = nx.path_graph(n, create_using=nx.DiGraph())
+        assert nx.dominance_frontiers(G, n // 2) == {i: set() for i in range(n // 2, n)}
+
+    def test_irreducible1(self):
+        # Graph taken from Figure 2 of
+        # K. D. Cooper, T. J. Harvey, and K. Kennedy.
+        # A simple, fast dominance algorithm.
+        # Software Practice & Experience, 4:110, 2001.
+        edges = [(1, 2), (2, 1), (3, 2), (4, 1), (5, 3), (5, 4)]
+        G = nx.DiGraph(edges)
+        assert dict(nx.dominance_frontiers(G, 5).items()) == {
+            1: {2},
+            2: {1},
+            3: {2},
+            4: {1},
+            5: set(),
+        }
+
+    def test_irreducible2(self):
+        # Graph taken from Figure 4 of
+        # K. D. Cooper, T. J. Harvey, and K. Kennedy.
+        # A simple, fast dominance algorithm.
+        # Software Practice & Experience, 4:110, 2001.
+        edges = [(1, 2), (2, 1), (2, 3), (3, 2), (4, 2), (4, 3), (5, 1), (6, 4), (6, 5)]
+        G = nx.DiGraph(edges)
+        assert nx.dominance_frontiers(G, 6) == {
+            1: {2},
+            2: {1, 3},
+            3: {2},
+            4: {2, 3},
+            5: {1},
+            6: set(),
+        }
+
+    def test_domrel_png(self):
+        # Graph taken from https://commons.wikipedia.org/wiki/File:Domrel.png
+        edges = [(1, 2), (2, 3), (2, 4), (2, 6), (3, 5), (4, 5), (5, 2)]
+        G = nx.DiGraph(edges)
+        assert nx.dominance_frontiers(G, 1) == {
+            1: set(),
+            2: {2},
+            3: {5},
+            4: {5},
+            5: {2},
+            6: set(),
+        }
+        # Test postdominance.
+        result = nx.dominance_frontiers(G.reverse(copy=False), 6)
+        assert result == {1: set(), 2: {2}, 3: {2}, 4: {2}, 5: {2}, 6: set()}
+
+    def test_boost_example(self):
+        # Graph taken from Figure 1 of
+        # http://www.boost.org/doc/libs/1_56_0/libs/graph/doc/lengauer_tarjan_dominator.htm
+        edges = [(0, 1), (1, 2), (1, 3), (2, 7), (3, 4), (4, 5), (4, 6), (5, 7), (6, 4)]
+        G = nx.DiGraph(edges)
+        assert nx.dominance_frontiers(G, 0) == {
+            0: set(),
+            1: set(),
+            2: {7},
+            3: {7},
+            4: {4, 7},
+            5: {7},
+            6: {4},
+            7: set(),
+        }
+        # Test postdominance.
+        result = nx.dominance_frontiers(G.reverse(copy=False), 7)
+        expected = {
+            0: set(),
+            1: set(),
+            2: {1},
+            3: {1},
+            4: {1, 4},
+            5: {1},
+            6: {4},
+            7: set(),
+        }
+        assert result == expected
+
+    def test_discard_issue(self):
+        # https://github.com/networkx/networkx/issues/2071
+        g = nx.DiGraph()
+        g.add_edges_from(
+            [
+                ("b0", "b1"),
+                ("b1", "b2"),
+                ("b2", "b3"),
+                ("b3", "b1"),
+                ("b1", "b5"),
+                ("b5", "b6"),
+                ("b5", "b8"),
+                ("b6", "b7"),
+                ("b8", "b7"),
+                ("b7", "b3"),
+                ("b3", "b4"),
+            ]
+        )
+        df = nx.dominance_frontiers(g, "b0")
+        assert df == {
+            "b4": set(),
+            "b5": {"b3"},
+            "b6": {"b7"},
+            "b7": {"b3"},
+            "b0": set(),
+            "b1": {"b1"},
+            "b2": {"b3"},
+            "b3": {"b1"},
+            "b8": {"b7"},
+        }
+
+    def test_loop(self):
+        g = nx.DiGraph()
+        g.add_edges_from([("a", "b"), ("b", "c"), ("b", "a")])
+        df = nx.dominance_frontiers(g, "a")
+        assert df == {"a": set(), "b": set(), "c": set()}
+
+    def test_missing_immediate_doms(self):
+        # see https://github.com/networkx/networkx/issues/2070
+        g = nx.DiGraph()
+        edges = [
+            ("entry_1", "b1"),
+            ("b1", "b2"),
+            ("b2", "b3"),
+            ("b3", "exit"),
+            ("entry_2", "b3"),
+        ]
+
+        # entry_1
+        #   |
+        #   b1
+        #   |
+        #   b2  entry_2
+        #    |  /
+        #    b3
+        #    |
+        #   exit
+
+        g.add_edges_from(edges)
+        # formerly raised KeyError on entry_2 when parsing b3
+        # because entry_2 does not have immediate doms (no path)
+        nx.dominance_frontiers(g, "entry_1")
+
+    def test_loops_larger(self):
+        # from
+        # http://ecee.colorado.edu/~waite/Darmstadt/motion.html
+        g = nx.DiGraph()
+        edges = [
+            ("entry", "exit"),
+            ("entry", "1"),
+            ("1", "2"),
+            ("2", "3"),
+            ("3", "4"),
+            ("4", "5"),
+            ("5", "6"),
+            ("6", "exit"),
+            ("6", "2"),
+            ("5", "3"),
+            ("4", "4"),
+        ]
+
+        g.add_edges_from(edges)
+        df = nx.dominance_frontiers(g, "entry")
+        answer = {
+            "entry": set(),
+            "1": {"exit"},
+            "2": {"exit", "2"},
+            "3": {"exit", "3", "2"},
+            "4": {"exit", "4", "3", "2"},
+            "5": {"exit", "3", "2"},
+            "6": {"exit", "2"},
+            "exit": set(),
+        }
+        for n in df:
+            assert set(df[n]) == set(answer[n])

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_dominating.py

@@ -0,0 +1,46 @@
+import pytest
+
+import networkx as nx
+
+
+def test_dominating_set():
+    G = nx.gnp_random_graph(100, 0.1)
+    D = nx.dominating_set(G)
+    assert nx.is_dominating_set(G, D)
+    D = nx.dominating_set(G, start_with=0)
+    assert nx.is_dominating_set(G, D)
+
+
+def test_complete():
+    """In complete graphs each node is a dominating set.
+    Thus the dominating set has to be of cardinality 1.
+    """
+    K4 = nx.complete_graph(4)
+    assert len(nx.dominating_set(K4)) == 1
+    K5 = nx.complete_graph(5)
+    assert len(nx.dominating_set(K5)) == 1
+
+
+def test_raise_dominating_set():
+    with pytest.raises(nx.NetworkXError):
+        G = nx.path_graph(4)
+        D = nx.dominating_set(G, start_with=10)
+
+
+def test_is_dominating_set():
+    G = nx.path_graph(4)
+    d = {1, 3}
+    assert nx.is_dominating_set(G, d)
+    d = {0, 2}
+    assert nx.is_dominating_set(G, d)
+    d = {1}
+    assert not nx.is_dominating_set(G, d)
+
+
+def test_wikipedia_is_dominating_set():
+    """Example from https://en.wikipedia.org/wiki/Dominating_set"""
+    G = nx.cycle_graph(4)
+    G.add_edges_from([(0, 4), (1, 4), (2, 5)])
+    assert nx.is_dominating_set(G, {4, 3, 5})
+    assert nx.is_dominating_set(G, {0, 2})
+    assert nx.is_dominating_set(G, {1, 2})

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_efficiency.py

@@ -0,0 +1,58 @@
+"""Unit tests for the :mod:`networkx.algorithms.efficiency` module."""
+
+import networkx as nx
+
+
+class TestEfficiency:
+    def setup_method(self):
+        # G1 is a disconnected graph
+        self.G1 = nx.Graph()
+        self.G1.add_nodes_from([1, 2, 3])
+        # G2 is a cycle graph
+        self.G2 = nx.cycle_graph(4)
+        # G3 is the triangle graph with one additional edge
+        self.G3 = nx.lollipop_graph(3, 1)
+
+    def test_efficiency_disconnected_nodes(self):
+        """
+        When nodes are disconnected, efficiency is 0
+        """
+        assert nx.efficiency(self.G1, 1, 2) == 0
+
+    def test_local_efficiency_disconnected_graph(self):
+        """
+        In a disconnected graph the efficiency is 0
+        """
+        assert nx.local_efficiency(self.G1) == 0
+
+    def test_efficiency(self):
+        assert nx.efficiency(self.G2, 0, 1) == 1
+        assert nx.efficiency(self.G2, 0, 2) == 1 / 2
+
+    def test_global_efficiency(self):
+        assert nx.global_efficiency(self.G2) == 5 / 6
+
+    def test_global_efficiency_complete_graph(self):
+        """
+        Tests that the average global efficiency of the complete graph is one.
+        """
+        for n in range(2, 10):
+            G = nx.complete_graph(n)
+            assert nx.global_efficiency(G) == 1
+
+    def test_local_efficiency_complete_graph(self):
+        """
+        Test that the local efficiency for a complete graph with at least 3
+        nodes should be one. For a graph with only 2 nodes, the induced
+        subgraph has no edges.
+        """
+        for n in range(3, 10):
+            G = nx.complete_graph(n)
+            assert nx.local_efficiency(G) == 1
+
+    def test_using_ego_graph(self):
+        """
+        Test that the ego graph is used when computing local efficiency.
+        For more information, see GitHub issue #2710.
+        """
+        assert nx.local_efficiency(self.G3) == 7 / 12

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_euler.py

@@ -0,0 +1,314 @@
+import collections
+
+import pytest
+
+import networkx as nx
+
+
+@pytest.mark.parametrize("f", (nx.is_eulerian, nx.is_semieulerian))
+def test_empty_graph_raises(f):
+    G = nx.Graph()
+    with pytest.raises(nx.NetworkXPointlessConcept, match="Connectivity is undefined"):
+        f(G)
+
+
+class TestIsEulerian:
+    def test_is_eulerian(self):
+        assert nx.is_eulerian(nx.complete_graph(5))
+        assert nx.is_eulerian(nx.complete_graph(7))
+        assert nx.is_eulerian(nx.hypercube_graph(4))
+        assert nx.is_eulerian(nx.hypercube_graph(6))
+
+        assert not nx.is_eulerian(nx.complete_graph(4))
+        assert not nx.is_eulerian(nx.complete_graph(6))
+        assert not nx.is_eulerian(nx.hypercube_graph(3))
+        assert not nx.is_eulerian(nx.hypercube_graph(5))
+
+        assert not nx.is_eulerian(nx.petersen_graph())
+        assert not nx.is_eulerian(nx.path_graph(4))
+
+    def test_is_eulerian2(self):
+        # not connected
+        G = nx.Graph()
+        G.add_nodes_from([1, 2, 3])
+        assert not nx.is_eulerian(G)
+        # not strongly connected
+        G = nx.DiGraph()
+        G.add_nodes_from([1, 2, 3])
+        assert not nx.is_eulerian(G)
+        G = nx.MultiDiGraph()
+        G.add_edge(1, 2)
+        G.add_edge(2, 3)
+        G.add_edge(2, 3)
+        G.add_edge(3, 1)
+        assert not nx.is_eulerian(G)
+
+
+class TestEulerianCircuit:
+    def test_eulerian_circuit_cycle(self):
+        G = nx.cycle_graph(4)
+
+        edges = list(nx.eulerian_circuit(G, source=0))
+        nodes = [u for u, v in edges]
+        assert nodes == [0, 3, 2, 1]
+        assert edges == [(0, 3), (3, 2), (2, 1), (1, 0)]
+
+        edges = list(nx.eulerian_circuit(G, source=1))
+        nodes = [u for u, v in edges]
+        assert nodes == [1, 2, 3, 0]
+        assert edges == [(1, 2), (2, 3), (3, 0), (0, 1)]
+
+        G = nx.complete_graph(3)
+
+        edges = list(nx.eulerian_circuit(G, source=0))
+        nodes = [u for u, v in edges]
+        assert nodes == [0, 2, 1]
+        assert edges == [(0, 2), (2, 1), (1, 0)]
+
+        edges = list(nx.eulerian_circuit(G, source=1))
+        nodes = [u for u, v in edges]
+        assert nodes == [1, 2, 0]
+        assert edges == [(1, 2), (2, 0), (0, 1)]
+
+    def test_eulerian_circuit_digraph(self):
+        G = nx.DiGraph()
+        nx.add_cycle(G, [0, 1, 2, 3])
+
+        edges = list(nx.eulerian_circuit(G, source=0))
+        nodes = [u for u, v in edges]
+        assert nodes == [0, 1, 2, 3]
+        assert edges == [(0, 1), (1, 2), (2, 3), (3, 0)]
+
+        edges = list(nx.eulerian_circuit(G, source=1))
+        nodes = [u for u, v in edges]
+        assert nodes == [1, 2, 3, 0]
+        assert edges == [(1, 2), (2, 3), (3, 0), (0, 1)]
+
+    def test_multigraph(self):
+        G = nx.MultiGraph()
+        nx.add_cycle(G, [0, 1, 2, 3])
+        G.add_edge(1, 2)
+        G.add_edge(1, 2)
+        edges = list(nx.eulerian_circuit(G, source=0))
+        nodes = [u for u, v in edges]
+        assert nodes == [0, 3, 2, 1, 2, 1]
+        assert edges == [(0, 3), (3, 2), (2, 1), (1, 2), (2, 1), (1, 0)]
+
+    def test_multigraph_with_keys(self):
+        G = nx.MultiGraph()
+        nx.add_cycle(G, [0, 1, 2, 3])
+        G.add_edge(1, 2)
+        G.add_edge(1, 2)
+        edges = list(nx.eulerian_circuit(G, source=0, keys=True))
+        nodes = [u for u, v, k in edges]
+        assert nodes == [0, 3, 2, 1, 2, 1]
+        assert edges[:2] == [(0, 3, 0), (3, 2, 0)]
+        assert collections.Counter(edges[2:5]) == collections.Counter(
+            [(2, 1, 0), (1, 2, 1), (2, 1, 2)]
+        )
+        assert edges[5:] == [(1, 0, 0)]
+
+    def test_not_eulerian(self):
+        with pytest.raises(nx.NetworkXError):
+            f = list(nx.eulerian_circuit(nx.complete_graph(4)))
+
+
+class TestIsSemiEulerian:
+    def test_is_semieulerian(self):
+        # Test graphs with Eulerian paths but no cycles return True.
+        assert nx.is_semieulerian(nx.path_graph(4))
+        G = nx.path_graph(6, create_using=nx.DiGraph)
+        assert nx.is_semieulerian(G)
+
+        # Test graphs with Eulerian cycles return False.
+        assert not nx.is_semieulerian(nx.complete_graph(5))
+        assert not nx.is_semieulerian(nx.complete_graph(7))
+        assert not nx.is_semieulerian(nx.hypercube_graph(4))
+        assert not nx.is_semieulerian(nx.hypercube_graph(6))
+
+
+class TestHasEulerianPath:
+    def test_has_eulerian_path_cyclic(self):
+        # Test graphs with Eulerian cycles return True.
+        assert nx.has_eulerian_path(nx.complete_graph(5))
+        assert nx.has_eulerian_path(nx.complete_graph(7))
+        assert nx.has_eulerian_path(nx.hypercube_graph(4))
+        assert nx.has_eulerian_path(nx.hypercube_graph(6))
+
+    def test_has_eulerian_path_non_cyclic(self):
+        # Test graphs with Eulerian paths but no cycles return True.
+        assert nx.has_eulerian_path(nx.path_graph(4))
+        G = nx.path_graph(6, create_using=nx.DiGraph)
+        assert nx.has_eulerian_path(G)
+
+    def test_has_eulerian_path_directed_graph(self):
+        # Test directed graphs and returns False
+        G = nx.DiGraph()
+        G.add_edges_from([(0, 1), (1, 2), (0, 2)])
+        assert not nx.has_eulerian_path(G)
+
+        # Test directed graphs without isolated node returns True
+        G = nx.DiGraph()
+        G.add_edges_from([(0, 1), (1, 2), (2, 0)])
+        assert nx.has_eulerian_path(G)
+
+        # Test directed graphs with isolated node returns False
+        G.add_node(3)
+        assert not nx.has_eulerian_path(G)
+
+    @pytest.mark.parametrize("G", (nx.Graph(), nx.DiGraph()))
+    def test_has_eulerian_path_not_weakly_connected(self, G):
+        G.add_edges_from([(0, 1), (2, 3), (3, 2)])
+        assert not nx.has_eulerian_path(G)
+
+    @pytest.mark.parametrize("G", (nx.Graph(), nx.DiGraph()))
+    def test_has_eulerian_path_unbalancedins_more_than_one(self, G):
+        G.add_edges_from([(0, 1), (2, 3)])
+        assert not nx.has_eulerian_path(G)
+
+
+class TestFindPathStart:
+    def testfind_path_start(self):
+        find_path_start = nx.algorithms.euler._find_path_start
+        # Test digraphs return correct starting node.
+        G = nx.path_graph(6, create_using=nx.DiGraph)
+        assert find_path_start(G) == 0
+        edges = [(0, 1), (1, 2), (2, 0), (4, 0)]
+        assert find_path_start(nx.DiGraph(edges)) == 4
+
+        # Test graph with no Eulerian path return None.
+        edges = [(0, 1), (1, 2), (2, 3), (2, 4)]
+        assert find_path_start(nx.DiGraph(edges)) is None
+
+
+class TestEulerianPath:
+    def test_eulerian_path(self):
+        x = [(4, 0), (0, 1), (1, 2), (2, 0)]
+        for e1, e2 in zip(x, nx.eulerian_path(nx.DiGraph(x))):
+            assert e1 == e2
+
+    def test_eulerian_path_straight_link(self):
+        G = nx.DiGraph()
+        result = [(1, 2), (2, 3), (3, 4), (4, 5)]
+        G.add_edges_from(result)
+        assert result == list(nx.eulerian_path(G))
+        assert result == list(nx.eulerian_path(G, source=1))
+        with pytest.raises(nx.NetworkXError):
+            list(nx.eulerian_path(G, source=3))
+        with pytest.raises(nx.NetworkXError):
+            list(nx.eulerian_path(G, source=4))
+        with pytest.raises(nx.NetworkXError):
+            list(nx.eulerian_path(G, source=5))
+
+    def test_eulerian_path_multigraph(self):
+        G = nx.MultiDiGraph()
+        result = [(2, 1), (1, 2), (2, 1), (1, 2), (2, 3), (3, 4), (4, 3)]
+        G.add_edges_from(result)
+        assert result == list(nx.eulerian_path(G))
+        assert result == list(nx.eulerian_path(G, source=2))
+        with pytest.raises(nx.NetworkXError):
+            list(nx.eulerian_path(G, source=3))
+        with pytest.raises(nx.NetworkXError):
+            list(nx.eulerian_path(G, source=4))
+
+    def test_eulerian_path_eulerian_circuit(self):
+        G = nx.DiGraph()
+        result = [(1, 2), (2, 3), (3, 4), (4, 1)]
+        result2 = [(2, 3), (3, 4), (4, 1), (1, 2)]
+        result3 = [(3, 4), (4, 1), (1, 2), (2, 3)]
+        G.add_edges_from(result)
+        assert result == list(nx.eulerian_path(G))
+        assert result == list(nx.eulerian_path(G, source=1))
+        assert result2 == list(nx.eulerian_path(G, source=2))
+        assert result3 == list(nx.eulerian_path(G, source=3))
+
+    def test_eulerian_path_undirected(self):
+        G = nx.Graph()
+        result = [(1, 2), (2, 3), (3, 4), (4, 5)]
+        result2 = [(5, 4), (4, 3), (3, 2), (2, 1)]
+        G.add_edges_from(result)
+        assert list(nx.eulerian_path(G)) in (result, result2)
+        assert result == list(nx.eulerian_path(G, source=1))
+        assert result2 == list(nx.eulerian_path(G, source=5))
+        with pytest.raises(nx.NetworkXError):
+            list(nx.eulerian_path(G, source=3))
+        with pytest.raises(nx.NetworkXError):
+            list(nx.eulerian_path(G, source=2))
+
+    def test_eulerian_path_multigraph_undirected(self):
+        G = nx.MultiGraph()
+        result = [(2, 1), (1, 2), (2, 1), (1, 2), (2, 3), (3, 4)]
+        G.add_edges_from(result)
+        assert result == list(nx.eulerian_path(G))
+        assert result == list(nx.eulerian_path(G, source=2))
+        with pytest.raises(nx.NetworkXError):
+            list(nx.eulerian_path(G, source=3))
+        with pytest.raises(nx.NetworkXError):
+            list(nx.eulerian_path(G, source=1))
+
+    @pytest.mark.parametrize(
+        ("graph_type", "result"),
+        (
+            (nx.MultiGraph, [(0, 1, 0), (1, 0, 1)]),
+            (nx.MultiDiGraph, [(0, 1, 0), (1, 0, 0)]),
+        ),
+    )
+    def test_eulerian_with_keys(self, graph_type, result):
+        G = graph_type([(0, 1), (1, 0)])
+        answer = nx.eulerian_path(G, keys=True)
+        assert list(answer) == result
+
+
+class TestEulerize:
+    def test_disconnected(self):
+        with pytest.raises(nx.NetworkXError):
+            G = nx.from_edgelist([(0, 1), (2, 3)])
+            nx.eulerize(G)
+
+    def test_null_graph(self):
+        with pytest.raises(nx.NetworkXPointlessConcept):
+            nx.eulerize(nx.Graph())
+
+    def test_null_multigraph(self):
+        with pytest.raises(nx.NetworkXPointlessConcept):
+            nx.eulerize(nx.MultiGraph())
+
+    def test_on_empty_graph(self):
+        with pytest.raises(nx.NetworkXError):
+            nx.eulerize(nx.empty_graph(3))
+
+    def test_on_eulerian(self):
+        G = nx.cycle_graph(3)
+        H = nx.eulerize(G)
+        assert nx.is_isomorphic(G, H)
+
+    def test_on_eulerian_multigraph(self):
+        G = nx.MultiGraph(nx.cycle_graph(3))
+        G.add_edge(0, 1)
+        H = nx.eulerize(G)
+        assert nx.is_eulerian(H)
+
+    def test_on_complete_graph(self):
+        G = nx.complete_graph(4)
+        assert nx.is_eulerian(nx.eulerize(G))
+        assert nx.is_eulerian(nx.eulerize(nx.MultiGraph(G)))
+
+    def test_on_non_eulerian_graph(self):
+        G = nx.cycle_graph(18)
+        G.add_edge(0, 18)
+        G.add_edge(18, 19)
+        G.add_edge(17, 19)
+        G.add_edge(4, 20)
+        G.add_edge(20, 21)
+        G.add_edge(21, 22)
+        G.add_edge(22, 23)
+        G.add_edge(23, 24)
+        G.add_edge(24, 25)
+        G.add_edge(25, 26)
+        G.add_edge(26, 27)
+        G.add_edge(27, 28)
+        G.add_edge(28, 13)
+        assert not nx.is_eulerian(G)
+        G = nx.eulerize(G)
+        assert nx.is_eulerian(G)
+        assert nx.number_of_edges(G) == 39

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_graph_hashing.py

@@ -0,0 +1,686 @@
+import pytest
+
+import networkx as nx
+from networkx.generators import directed
+
+# Unit tests for the :func:`~networkx.weisfeiler_lehman_graph_hash` function
+
+
+def test_empty_graph_hash():
+    """
+    empty graphs should give hashes regardless of other params
+    """
+    G1 = nx.empty_graph()
+    G2 = nx.empty_graph()
+
+    h1 = nx.weisfeiler_lehman_graph_hash(G1)
+    h2 = nx.weisfeiler_lehman_graph_hash(G2)
+    h3 = nx.weisfeiler_lehman_graph_hash(G2, edge_attr="edge_attr1")
+    h4 = nx.weisfeiler_lehman_graph_hash(G2, node_attr="node_attr1")
+    h5 = nx.weisfeiler_lehman_graph_hash(
+        G2, edge_attr="edge_attr1", node_attr="node_attr1"
+    )
+    h6 = nx.weisfeiler_lehman_graph_hash(G2, iterations=10)
+
+    assert h1 == h2
+    assert h1 == h3
+    assert h1 == h4
+    assert h1 == h5
+    assert h1 == h6
+
+
+def test_directed():
+    """
+    A directed graph with no bi-directional edges should yield different a graph hash
+    to the same graph taken as undirected if there are no hash collisions.
+    """
+    r = 10
+    for i in range(r):
+        G_directed = nx.gn_graph(10 + r, seed=100 + i)
+        G_undirected = nx.to_undirected(G_directed)
+
+        h_directed = nx.weisfeiler_lehman_graph_hash(G_directed)
+        h_undirected = nx.weisfeiler_lehman_graph_hash(G_undirected)
+
+        assert h_directed != h_undirected
+
+
+def test_reversed():
+    """
+    A directed graph with no bi-directional edges should yield different a graph hash
+    to the same graph taken with edge directions reversed if there are no hash collisions.
+    Here we test a cycle graph which is the minimal counterexample
+    """
+    G = nx.cycle_graph(5, create_using=nx.DiGraph)
+    nx.set_node_attributes(G, {n: str(n) for n in G.nodes()}, name="label")
+
+    G_reversed = G.reverse()
+
+    h = nx.weisfeiler_lehman_graph_hash(G, node_attr="label")
+    h_reversed = nx.weisfeiler_lehman_graph_hash(G_reversed, node_attr="label")
+
+    assert h != h_reversed
+
+
+def test_isomorphic():
+    """
+    graph hashes should be invariant to node-relabeling (when the output is reindexed
+    by the same mapping)
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G1 = nx.erdos_renyi_graph(n, p * i, seed=200 + i)
+        G2 = nx.relabel_nodes(G1, {u: -1 * u for u in G1.nodes()})
+
+        g1_hash = nx.weisfeiler_lehman_graph_hash(G1)
+        g2_hash = nx.weisfeiler_lehman_graph_hash(G2)
+
+        assert g1_hash == g2_hash
+
+
+def test_isomorphic_edge_attr():
+    """
+    Isomorphic graphs with differing edge attributes should yield different graph
+    hashes if the 'edge_attr' argument is supplied and populated in the graph,
+    and there are no hash collisions.
+    The output should still be invariant to node-relabeling
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G1 = nx.erdos_renyi_graph(n, p * i, seed=300 + i)
+
+        for a, b in G1.edges:
+            G1[a][b]["edge_attr1"] = f"{a}-{b}-1"
+            G1[a][b]["edge_attr2"] = f"{a}-{b}-2"
+
+        g1_hash_with_edge_attr1 = nx.weisfeiler_lehman_graph_hash(
+            G1, edge_attr="edge_attr1"
+        )
+        g1_hash_with_edge_attr2 = nx.weisfeiler_lehman_graph_hash(
+            G1, edge_attr="edge_attr2"
+        )
+        g1_hash_no_edge_attr = nx.weisfeiler_lehman_graph_hash(G1, edge_attr=None)
+
+        assert g1_hash_with_edge_attr1 != g1_hash_no_edge_attr
+        assert g1_hash_with_edge_attr2 != g1_hash_no_edge_attr
+        assert g1_hash_with_edge_attr1 != g1_hash_with_edge_attr2
+
+        G2 = nx.relabel_nodes(G1, {u: -1 * u for u in G1.nodes()})
+
+        g2_hash_with_edge_attr1 = nx.weisfeiler_lehman_graph_hash(
+            G2, edge_attr="edge_attr1"
+        )
+        g2_hash_with_edge_attr2 = nx.weisfeiler_lehman_graph_hash(
+            G2, edge_attr="edge_attr2"
+        )
+
+        assert g1_hash_with_edge_attr1 == g2_hash_with_edge_attr1
+        assert g1_hash_with_edge_attr2 == g2_hash_with_edge_attr2
+
+
+def test_missing_edge_attr():
+    """
+    If the 'edge_attr' argument is supplied but is missing from an edge in the graph,
+    we should raise a KeyError
+    """
+    G = nx.Graph()
+    G.add_edges_from([(1, 2, {"edge_attr1": "a"}), (1, 3, {})])
+    pytest.raises(KeyError, nx.weisfeiler_lehman_graph_hash, G, edge_attr="edge_attr1")
+
+
+def test_isomorphic_node_attr():
+    """
+    Isomorphic graphs with differing node attributes should yield different graph
+    hashes if the 'node_attr' argument is supplied and populated in the graph, and
+    there are no hash collisions.
+    The output should still be invariant to node-relabeling
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G1 = nx.erdos_renyi_graph(n, p * i, seed=400 + i)
+
+        for u in G1.nodes():
+            G1.nodes[u]["node_attr1"] = f"{u}-1"
+            G1.nodes[u]["node_attr2"] = f"{u}-2"
+
+        g1_hash_with_node_attr1 = nx.weisfeiler_lehman_graph_hash(
+            G1, node_attr="node_attr1"
+        )
+        g1_hash_with_node_attr2 = nx.weisfeiler_lehman_graph_hash(
+            G1, node_attr="node_attr2"
+        )
+        g1_hash_no_node_attr = nx.weisfeiler_lehman_graph_hash(G1, node_attr=None)
+
+        assert g1_hash_with_node_attr1 != g1_hash_no_node_attr
+        assert g1_hash_with_node_attr2 != g1_hash_no_node_attr
+        assert g1_hash_with_node_attr1 != g1_hash_with_node_attr2
+
+        G2 = nx.relabel_nodes(G1, {u: -1 * u for u in G1.nodes()})
+
+        g2_hash_with_node_attr1 = nx.weisfeiler_lehman_graph_hash(
+            G2, node_attr="node_attr1"
+        )
+        g2_hash_with_node_attr2 = nx.weisfeiler_lehman_graph_hash(
+            G2, node_attr="node_attr2"
+        )
+
+        assert g1_hash_with_node_attr1 == g2_hash_with_node_attr1
+        assert g1_hash_with_node_attr2 == g2_hash_with_node_attr2
+
+
+def test_missing_node_attr():
+    """
+    If the 'node_attr' argument is supplied but is missing from a node in the graph,
+    we should raise a KeyError
+    """
+    G = nx.Graph()
+    G.add_nodes_from([(1, {"node_attr1": "a"}), (2, {})])
+    G.add_edges_from([(1, 2), (2, 3), (3, 1), (1, 4)])
+    pytest.raises(KeyError, nx.weisfeiler_lehman_graph_hash, G, node_attr="node_attr1")
+
+
+def test_isomorphic_edge_attr_and_node_attr():
+    """
+    Isomorphic graphs with differing node attributes should yield different graph
+    hashes if the 'node_attr' and 'edge_attr' argument is supplied and populated in
+    the graph, and there are no hash collisions.
+    The output should still be invariant to node-relabeling
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G1 = nx.erdos_renyi_graph(n, p * i, seed=500 + i)
+
+        for u in G1.nodes():
+            G1.nodes[u]["node_attr1"] = f"{u}-1"
+            G1.nodes[u]["node_attr2"] = f"{u}-2"
+
+        for a, b in G1.edges:
+            G1[a][b]["edge_attr1"] = f"{a}-{b}-1"
+            G1[a][b]["edge_attr2"] = f"{a}-{b}-2"
+
+        g1_hash_edge1_node1 = nx.weisfeiler_lehman_graph_hash(
+            G1, edge_attr="edge_attr1", node_attr="node_attr1"
+        )
+        g1_hash_edge2_node2 = nx.weisfeiler_lehman_graph_hash(
+            G1, edge_attr="edge_attr2", node_attr="node_attr2"
+        )
+        g1_hash_edge1_node2 = nx.weisfeiler_lehman_graph_hash(
+            G1, edge_attr="edge_attr1", node_attr="node_attr2"
+        )
+        g1_hash_no_attr = nx.weisfeiler_lehman_graph_hash(G1)
+
+        assert g1_hash_edge1_node1 != g1_hash_no_attr
+        assert g1_hash_edge2_node2 != g1_hash_no_attr
+        assert g1_hash_edge1_node1 != g1_hash_edge2_node2
+        assert g1_hash_edge1_node2 != g1_hash_edge2_node2
+        assert g1_hash_edge1_node2 != g1_hash_edge1_node1
+
+        G2 = nx.relabel_nodes(G1, {u: -1 * u for u in G1.nodes()})
+
+        g2_hash_edge1_node1 = nx.weisfeiler_lehman_graph_hash(
+            G2, edge_attr="edge_attr1", node_attr="node_attr1"
+        )
+        g2_hash_edge2_node2 = nx.weisfeiler_lehman_graph_hash(
+            G2, edge_attr="edge_attr2", node_attr="node_attr2"
+        )
+
+        assert g1_hash_edge1_node1 == g2_hash_edge1_node1
+        assert g1_hash_edge2_node2 == g2_hash_edge2_node2
+
+
+def test_digest_size():
+    """
+    The hash string lengths should be as expected for a variety of graphs and
+    digest sizes
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G = nx.erdos_renyi_graph(n, p * i, seed=1000 + i)
+
+        h16 = nx.weisfeiler_lehman_graph_hash(G)
+        h32 = nx.weisfeiler_lehman_graph_hash(G, digest_size=32)
+
+        assert h16 != h32
+        assert len(h16) == 16 * 2
+        assert len(h32) == 32 * 2
+
+
+# Unit tests for the :func:`~networkx.weisfeiler_lehman_hash_subgraphs` function
+
+
+def is_subiteration(a, b):
+    """
+    returns True if that each hash sequence in 'a' is a prefix for
+    the corresponding sequence indexed by the same node in 'b'.
+    """
+    return all(b[node][: len(hashes)] == hashes for node, hashes in a.items())
+
+
+def hexdigest_sizes_correct(a, digest_size):
+    """
+    returns True if all hex digest sizes are the expected length in a node:subgraph-hashes
+    dictionary. Hex digest string length == 2 * bytes digest length since each pair of hex
+    digits encodes 1 byte (https://docs.python.org/3/library/hashlib.html)
+    """
+    hexdigest_size = digest_size * 2
+    list_digest_sizes_correct = lambda l: all(len(x) == hexdigest_size for x in l)
+    return all(list_digest_sizes_correct(hashes) for hashes in a.values())
+
+
+def test_empty_graph_subgraph_hash():
+    """ "
+    empty graphs should give empty dict subgraph hashes regardless of other params
+    """
+    G = nx.empty_graph()
+
+    subgraph_hashes1 = nx.weisfeiler_lehman_subgraph_hashes(G)
+    subgraph_hashes2 = nx.weisfeiler_lehman_subgraph_hashes(G, edge_attr="edge_attr")
+    subgraph_hashes3 = nx.weisfeiler_lehman_subgraph_hashes(G, node_attr="edge_attr")
+    subgraph_hashes4 = nx.weisfeiler_lehman_subgraph_hashes(G, iterations=2)
+    subgraph_hashes5 = nx.weisfeiler_lehman_subgraph_hashes(G, digest_size=64)
+
+    assert subgraph_hashes1 == {}
+    assert subgraph_hashes2 == {}
+    assert subgraph_hashes3 == {}
+    assert subgraph_hashes4 == {}
+    assert subgraph_hashes5 == {}
+
+
+def test_directed_subgraph_hash():
+    """
+    A directed graph with no bi-directional edges should yield different subgraph hashes
+    to the same graph taken as undirected, if all hashes don't collide.
+    """
+    r = 10
+    for i in range(r):
+        G_directed = nx.gn_graph(10 + r, seed=100 + i)
+        G_undirected = nx.to_undirected(G_directed)
+
+        directed_subgraph_hashes = nx.weisfeiler_lehman_subgraph_hashes(G_directed)
+        undirected_subgraph_hashes = nx.weisfeiler_lehman_subgraph_hashes(G_undirected)
+
+        assert directed_subgraph_hashes != undirected_subgraph_hashes
+
+
+def test_reversed_subgraph_hash():
+    """
+    A directed graph with no bi-directional edges should yield different subgraph hashes
+    to the same graph taken with edge directions reversed if there are no hash collisions.
+    Here we test a cycle graph which is the minimal counterexample
+    """
+    G = nx.cycle_graph(5, create_using=nx.DiGraph)
+    nx.set_node_attributes(G, {n: str(n) for n in G.nodes()}, name="label")
+
+    G_reversed = G.reverse()
+
+    h = nx.weisfeiler_lehman_subgraph_hashes(G, node_attr="label")
+    h_reversed = nx.weisfeiler_lehman_subgraph_hashes(G_reversed, node_attr="label")
+
+    assert h != h_reversed
+
+
+def test_isomorphic_subgraph_hash():
+    """
+    the subgraph hashes should be invariant to node-relabeling when the output is reindexed
+    by the same mapping and all hashes don't collide.
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G1 = nx.erdos_renyi_graph(n, p * i, seed=200 + i)
+        G2 = nx.relabel_nodes(G1, {u: -1 * u for u in G1.nodes()})
+
+        g1_subgraph_hashes = nx.weisfeiler_lehman_subgraph_hashes(G1)
+        g2_subgraph_hashes = nx.weisfeiler_lehman_subgraph_hashes(G2)
+
+        assert g1_subgraph_hashes == {-1 * k: v for k, v in g2_subgraph_hashes.items()}
+
+
+def test_isomorphic_edge_attr_subgraph_hash():
+    """
+    Isomorphic graphs with differing edge attributes should yield different subgraph
+    hashes if the 'edge_attr' argument is supplied and populated in the graph, and
+    all hashes don't collide.
+    The output should still be invariant to node-relabeling
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G1 = nx.erdos_renyi_graph(n, p * i, seed=300 + i)
+
+        for a, b in G1.edges:
+            G1[a][b]["edge_attr1"] = f"{a}-{b}-1"
+            G1[a][b]["edge_attr2"] = f"{a}-{b}-2"
+
+        g1_hash_with_edge_attr1 = nx.weisfeiler_lehman_subgraph_hashes(
+            G1, edge_attr="edge_attr1"
+        )
+        g1_hash_with_edge_attr2 = nx.weisfeiler_lehman_subgraph_hashes(
+            G1, edge_attr="edge_attr2"
+        )
+        g1_hash_no_edge_attr = nx.weisfeiler_lehman_subgraph_hashes(G1, edge_attr=None)
+
+        assert g1_hash_with_edge_attr1 != g1_hash_no_edge_attr
+        assert g1_hash_with_edge_attr2 != g1_hash_no_edge_attr
+        assert g1_hash_with_edge_attr1 != g1_hash_with_edge_attr2
+
+        G2 = nx.relabel_nodes(G1, {u: -1 * u for u in G1.nodes()})
+
+        g2_hash_with_edge_attr1 = nx.weisfeiler_lehman_subgraph_hashes(
+            G2, edge_attr="edge_attr1"
+        )
+        g2_hash_with_edge_attr2 = nx.weisfeiler_lehman_subgraph_hashes(
+            G2, edge_attr="edge_attr2"
+        )
+
+        assert g1_hash_with_edge_attr1 == {
+            -1 * k: v for k, v in g2_hash_with_edge_attr1.items()
+        }
+        assert g1_hash_with_edge_attr2 == {
+            -1 * k: v for k, v in g2_hash_with_edge_attr2.items()
+        }
+
+
+def test_missing_edge_attr_subgraph_hash():
+    """
+    If the 'edge_attr' argument is supplied but is missing from an edge in the graph,
+    we should raise a KeyError
+    """
+    G = nx.Graph()
+    G.add_edges_from([(1, 2, {"edge_attr1": "a"}), (1, 3, {})])
+    pytest.raises(
+        KeyError, nx.weisfeiler_lehman_subgraph_hashes, G, edge_attr="edge_attr1"
+    )
+
+
+def test_isomorphic_node_attr_subgraph_hash():
+    """
+    Isomorphic graphs with differing node attributes should yield different subgraph
+    hashes if the 'node_attr' argument is supplied and populated in the graph, and
+    all hashes don't collide.
+    The output should still be invariant to node-relabeling
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G1 = nx.erdos_renyi_graph(n, p * i, seed=400 + i)
+
+        for u in G1.nodes():
+            G1.nodes[u]["node_attr1"] = f"{u}-1"
+            G1.nodes[u]["node_attr2"] = f"{u}-2"
+
+        g1_hash_with_node_attr1 = nx.weisfeiler_lehman_subgraph_hashes(
+            G1, node_attr="node_attr1"
+        )
+        g1_hash_with_node_attr2 = nx.weisfeiler_lehman_subgraph_hashes(
+            G1, node_attr="node_attr2"
+        )
+        g1_hash_no_node_attr = nx.weisfeiler_lehman_subgraph_hashes(G1, node_attr=None)
+
+        assert g1_hash_with_node_attr1 != g1_hash_no_node_attr
+        assert g1_hash_with_node_attr2 != g1_hash_no_node_attr
+        assert g1_hash_with_node_attr1 != g1_hash_with_node_attr2
+
+        G2 = nx.relabel_nodes(G1, {u: -1 * u for u in G1.nodes()})
+
+        g2_hash_with_node_attr1 = nx.weisfeiler_lehman_subgraph_hashes(
+            G2, node_attr="node_attr1"
+        )
+        g2_hash_with_node_attr2 = nx.weisfeiler_lehman_subgraph_hashes(
+            G2, node_attr="node_attr2"
+        )
+
+        assert g1_hash_with_node_attr1 == {
+            -1 * k: v for k, v in g2_hash_with_node_attr1.items()
+        }
+        assert g1_hash_with_node_attr2 == {
+            -1 * k: v for k, v in g2_hash_with_node_attr2.items()
+        }
+
+
+def test_missing_node_attr_subgraph_hash():
+    """
+    If the 'node_attr' argument is supplied but is missing from a node in the graph,
+    we should raise a KeyError
+    """
+    G = nx.Graph()
+    G.add_nodes_from([(1, {"node_attr1": "a"}), (2, {})])
+    G.add_edges_from([(1, 2), (2, 3), (3, 1), (1, 4)])
+    pytest.raises(
+        KeyError, nx.weisfeiler_lehman_subgraph_hashes, G, node_attr="node_attr1"
+    )
+
+
+def test_isomorphic_edge_attr_and_node_attr_subgraph_hash():
+    """
+    Isomorphic graphs with differing node attributes should yield different subgraph
+    hashes if the 'node_attr' and 'edge_attr' argument is supplied and populated in
+    the graph, and all hashes don't collide
+    The output should still be invariant to node-relabeling
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G1 = nx.erdos_renyi_graph(n, p * i, seed=500 + i)
+
+        for u in G1.nodes():
+            G1.nodes[u]["node_attr1"] = f"{u}-1"
+            G1.nodes[u]["node_attr2"] = f"{u}-2"
+
+        for a, b in G1.edges:
+            G1[a][b]["edge_attr1"] = f"{a}-{b}-1"
+            G1[a][b]["edge_attr2"] = f"{a}-{b}-2"
+
+        g1_hash_edge1_node1 = nx.weisfeiler_lehman_subgraph_hashes(
+            G1, edge_attr="edge_attr1", node_attr="node_attr1"
+        )
+        g1_hash_edge2_node2 = nx.weisfeiler_lehman_subgraph_hashes(
+            G1, edge_attr="edge_attr2", node_attr="node_attr2"
+        )
+        g1_hash_edge1_node2 = nx.weisfeiler_lehman_subgraph_hashes(
+            G1, edge_attr="edge_attr1", node_attr="node_attr2"
+        )
+        g1_hash_no_attr = nx.weisfeiler_lehman_subgraph_hashes(G1)
+
+        assert g1_hash_edge1_node1 != g1_hash_no_attr
+        assert g1_hash_edge2_node2 != g1_hash_no_attr
+        assert g1_hash_edge1_node1 != g1_hash_edge2_node2
+        assert g1_hash_edge1_node2 != g1_hash_edge2_node2
+        assert g1_hash_edge1_node2 != g1_hash_edge1_node1
+
+        G2 = nx.relabel_nodes(G1, {u: -1 * u for u in G1.nodes()})
+
+        g2_hash_edge1_node1 = nx.weisfeiler_lehman_subgraph_hashes(
+            G2, edge_attr="edge_attr1", node_attr="node_attr1"
+        )
+        g2_hash_edge2_node2 = nx.weisfeiler_lehman_subgraph_hashes(
+            G2, edge_attr="edge_attr2", node_attr="node_attr2"
+        )
+
+        assert g1_hash_edge1_node1 == {
+            -1 * k: v for k, v in g2_hash_edge1_node1.items()
+        }
+        assert g1_hash_edge2_node2 == {
+            -1 * k: v for k, v in g2_hash_edge2_node2.items()
+        }
+
+
+def test_iteration_depth():
+    """
+    All nodes should have the correct number of subgraph hashes in the output when
+    using degree as initial node labels
+    Subsequent iteration depths for the same graph should be additive for each node
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G = nx.erdos_renyi_graph(n, p * i, seed=600 + i)
+
+        depth3 = nx.weisfeiler_lehman_subgraph_hashes(G, iterations=3)
+        depth4 = nx.weisfeiler_lehman_subgraph_hashes(G, iterations=4)
+        depth5 = nx.weisfeiler_lehman_subgraph_hashes(G, iterations=5)
+
+        assert all(len(hashes) == 3 for hashes in depth3.values())
+        assert all(len(hashes) == 4 for hashes in depth4.values())
+        assert all(len(hashes) == 5 for hashes in depth5.values())
+
+        assert is_subiteration(depth3, depth4)
+        assert is_subiteration(depth4, depth5)
+        assert is_subiteration(depth3, depth5)
+
+
+def test_iteration_depth_edge_attr():
+    """
+    All nodes should have the correct number of subgraph hashes in the output when
+    setting initial node labels empty and using an edge attribute when aggregating
+    neighborhoods.
+    Subsequent iteration depths for the same graph should be additive for each node
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G = nx.erdos_renyi_graph(n, p * i, seed=700 + i)
+
+        for a, b in G.edges:
+            G[a][b]["edge_attr1"] = f"{a}-{b}-1"
+
+        depth3 = nx.weisfeiler_lehman_subgraph_hashes(
+            G, edge_attr="edge_attr1", iterations=3
+        )
+        depth4 = nx.weisfeiler_lehman_subgraph_hashes(
+            G, edge_attr="edge_attr1", iterations=4
+        )
+        depth5 = nx.weisfeiler_lehman_subgraph_hashes(
+            G, edge_attr="edge_attr1", iterations=5
+        )
+
+        assert all(len(hashes) == 3 for hashes in depth3.values())
+        assert all(len(hashes) == 4 for hashes in depth4.values())
+        assert all(len(hashes) == 5 for hashes in depth5.values())
+
+        assert is_subiteration(depth3, depth4)
+        assert is_subiteration(depth4, depth5)
+        assert is_subiteration(depth3, depth5)
+
+
+def test_iteration_depth_node_attr():
+    """
+    All nodes should have the correct number of subgraph hashes in the output when
+    setting initial node labels to an attribute.
+    Subsequent iteration depths for the same graph should be additive for each node
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G = nx.erdos_renyi_graph(n, p * i, seed=800 + i)
+
+        for u in G.nodes():
+            G.nodes[u]["node_attr1"] = f"{u}-1"
+
+        depth3 = nx.weisfeiler_lehman_subgraph_hashes(
+            G, node_attr="node_attr1", iterations=3
+        )
+        depth4 = nx.weisfeiler_lehman_subgraph_hashes(
+            G, node_attr="node_attr1", iterations=4
+        )
+        depth5 = nx.weisfeiler_lehman_subgraph_hashes(
+            G, node_attr="node_attr1", iterations=5
+        )
+
+        assert all(len(hashes) == 3 for hashes in depth3.values())
+        assert all(len(hashes) == 4 for hashes in depth4.values())
+        assert all(len(hashes) == 5 for hashes in depth5.values())
+
+        assert is_subiteration(depth3, depth4)
+        assert is_subiteration(depth4, depth5)
+        assert is_subiteration(depth3, depth5)
+
+
+def test_iteration_depth_node_edge_attr():
+    """
+    All nodes should have the correct number of subgraph hashes in the output when
+    setting initial node labels to an attribute and also using an edge attribute when
+    aggregating neighborhoods.
+    Subsequent iteration depths for the same graph should be additive for each node
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G = nx.erdos_renyi_graph(n, p * i, seed=900 + i)
+
+        for u in G.nodes():
+            G.nodes[u]["node_attr1"] = f"{u}-1"
+
+        for a, b in G.edges:
+            G[a][b]["edge_attr1"] = f"{a}-{b}-1"
+
+        depth3 = nx.weisfeiler_lehman_subgraph_hashes(
+            G, edge_attr="edge_attr1", node_attr="node_attr1", iterations=3
+        )
+        depth4 = nx.weisfeiler_lehman_subgraph_hashes(
+            G, edge_attr="edge_attr1", node_attr="node_attr1", iterations=4
+        )
+        depth5 = nx.weisfeiler_lehman_subgraph_hashes(
+            G, edge_attr="edge_attr1", node_attr="node_attr1", iterations=5
+        )
+
+        assert all(len(hashes) == 3 for hashes in depth3.values())
+        assert all(len(hashes) == 4 for hashes in depth4.values())
+        assert all(len(hashes) == 5 for hashes in depth5.values())
+
+        assert is_subiteration(depth3, depth4)
+        assert is_subiteration(depth4, depth5)
+        assert is_subiteration(depth3, depth5)
+
+
+def test_digest_size_subgraph_hash():
+    """
+    The hash string lengths should be as expected for a variety of graphs and
+    digest sizes
+    """
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(1, r + 1):
+        G = nx.erdos_renyi_graph(n, p * i, seed=1000 + i)
+
+        digest_size16_hashes = nx.weisfeiler_lehman_subgraph_hashes(G)
+        digest_size32_hashes = nx.weisfeiler_lehman_subgraph_hashes(G, digest_size=32)
+
+        assert digest_size16_hashes != digest_size32_hashes
+
+        assert hexdigest_sizes_correct(digest_size16_hashes, 16)
+        assert hexdigest_sizes_correct(digest_size32_hashes, 32)
+
+
+def test_initial_node_labels_subgraph_hash():
+    """
+    Including the hashed initial label prepends an extra hash to the lists
+    """
+    G = nx.path_graph(5)
+    nx.set_node_attributes(G, {i: int(0 < i < 4) for i in G}, "label")
+    # initial node labels:
+    # 0--1--1--1--0
+
+    without_initial_label = nx.weisfeiler_lehman_subgraph_hashes(G, node_attr="label")
+    assert all(len(v) == 3 for v in without_initial_label.values())
+    # 3 different 1 hop nhds
+    assert len({v[0] for v in without_initial_label.values()}) == 3
+
+    with_initial_label = nx.weisfeiler_lehman_subgraph_hashes(
+        G, node_attr="label", include_initial_labels=True
+    )
+    assert all(len(v) == 4 for v in with_initial_label.values())
+    # 2 different initial labels
+    assert len({v[0] for v in with_initial_label.values()}) == 2
+
+    # check hashes match otherwise
+    for u in G:
+        for a, b in zip(
+            with_initial_label[u][1:], without_initial_label[u], strict=True
+        ):
+            assert a == b

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_graphical.py

@@ -0,0 +1,163 @@
+import pytest
+
+import networkx as nx
+
+
+def test_valid_degree_sequence1():
+    n = 100
+    p = 0.3
+    for i in range(10):
+        G = nx.erdos_renyi_graph(n, p)
+        deg = (d for n, d in G.degree())
+        assert nx.is_graphical(deg, method="eg")
+        assert nx.is_graphical(deg, method="hh")
+
+
+def test_valid_degree_sequence2():
+    n = 100
+    for i in range(10):
+        G = nx.barabasi_albert_graph(n, 1)
+        deg = (d for n, d in G.degree())
+        assert nx.is_graphical(deg, method="eg")
+        assert nx.is_graphical(deg, method="hh")
+
+
+def test_string_input():
+    pytest.raises(nx.NetworkXException, nx.is_graphical, [], "foo")
+    pytest.raises(nx.NetworkXException, nx.is_graphical, ["red"], "hh")
+    pytest.raises(nx.NetworkXException, nx.is_graphical, ["red"], "eg")
+
+
+def test_non_integer_input():
+    pytest.raises(nx.NetworkXException, nx.is_graphical, [72.5], "eg")
+    pytest.raises(nx.NetworkXException, nx.is_graphical, [72.5], "hh")
+
+
+def test_negative_input():
+    assert not nx.is_graphical([-1], "hh")
+    assert not nx.is_graphical([-1], "eg")
+
+
+class TestAtlas:
+    @classmethod
+    def setup_class(cls):
+        global atlas
+        from networkx.generators import atlas
+
+        cls.GAG = atlas.graph_atlas_g()
+
+    def test_atlas(self):
+        for graph in self.GAG:
+            deg = (d for n, d in graph.degree())
+            assert nx.is_graphical(deg, method="eg")
+            assert nx.is_graphical(deg, method="hh")
+
+
+def test_small_graph_true():
+    z = [5, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1]
+    assert nx.is_graphical(z, method="hh")
+    assert nx.is_graphical(z, method="eg")
+    z = [10, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2]
+    assert nx.is_graphical(z, method="hh")
+    assert nx.is_graphical(z, method="eg")
+    z = [1, 1, 1, 1, 1, 2, 2, 2, 3, 4]
+    assert nx.is_graphical(z, method="hh")
+    assert nx.is_graphical(z, method="eg")
+
+
+def test_small_graph_false():
+    z = [1000, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1]
+    assert not nx.is_graphical(z, method="hh")
+    assert not nx.is_graphical(z, method="eg")
+    z = [6, 5, 4, 4, 2, 1, 1, 1]
+    assert not nx.is_graphical(z, method="hh")
+    assert not nx.is_graphical(z, method="eg")
+    z = [1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 4]
+    assert not nx.is_graphical(z, method="hh")
+    assert not nx.is_graphical(z, method="eg")
+
+
+def test_directed_degree_sequence():
+    # Test a range of valid directed degree sequences
+    n, r = 100, 10
+    p = 1.0 / r
+    for i in range(r):
+        G = nx.erdos_renyi_graph(n, p * (i + 1), None, True)
+        din = (d for n, d in G.in_degree())
+        dout = (d for n, d in G.out_degree())
+        assert nx.is_digraphical(din, dout)
+
+
+def test_small_directed_sequences():
+    dout = [5, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1]
+    din = [3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 1]
+    assert nx.is_digraphical(din, dout)
+    # Test nongraphical directed sequence
+    dout = [1000, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1]
+    din = [103, 102, 102, 102, 102, 102, 102, 102, 102, 102]
+    assert not nx.is_digraphical(din, dout)
+    # Test digraphical small sequence
+    dout = [1, 1, 1, 1, 1, 2, 2, 2, 3, 4]
+    din = [2, 2, 2, 2, 2, 2, 2, 2, 1, 1]
+    assert nx.is_digraphical(din, dout)
+    # Test nonmatching sum
+    din = [2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1]
+    assert not nx.is_digraphical(din, dout)
+    # Test for negative integer in sequence
+    din = [2, 2, 2, -2, 2, 2, 2, 2, 1, 1, 4]
+    assert not nx.is_digraphical(din, dout)
+    # Test for noninteger
+    din = dout = [1, 1, 1.1, 1]
+    assert not nx.is_digraphical(din, dout)
+    din = dout = [1, 1, "rer", 1]
+    assert not nx.is_digraphical(din, dout)
+
+
+def test_multi_sequence():
+    # Test nongraphical multi sequence
+    seq = [1000, 3, 3, 3, 3, 2, 2, 2, 1, 1]
+    assert not nx.is_multigraphical(seq)
+    # Test small graphical multi sequence
+    seq = [6, 5, 4, 4, 2, 1, 1, 1]
+    assert nx.is_multigraphical(seq)
+    # Test for negative integer in sequence
+    seq = [6, 5, 4, -4, 2, 1, 1, 1]
+    assert not nx.is_multigraphical(seq)
+    # Test for sequence with odd sum
+    seq = [1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 4]
+    assert not nx.is_multigraphical(seq)
+    # Test for noninteger
+    seq = [1, 1, 1.1, 1]
+    assert not nx.is_multigraphical(seq)
+    seq = [1, 1, "rer", 1]
+    assert not nx.is_multigraphical(seq)
+
+
+def test_pseudo_sequence():
+    # Test small valid pseudo sequence
+    seq = [1000, 3, 3, 3, 3, 2, 2, 2, 1, 1]
+    assert nx.is_pseudographical(seq)
+    # Test for sequence with odd sum
+    seq = [1000, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1]
+    assert not nx.is_pseudographical(seq)
+    # Test for negative integer in sequence
+    seq = [1000, 3, 3, 3, 3, 2, 2, -2, 1, 1]
+    assert not nx.is_pseudographical(seq)
+    # Test for noninteger
+    seq = [1, 1, 1.1, 1]
+    assert not nx.is_pseudographical(seq)
+    seq = [1, 1, "rer", 1]
+    assert not nx.is_pseudographical(seq)
+
+
+def test_numpy_degree_sequence():
+    np = pytest.importorskip("numpy")
+    ds = np.array([1, 2, 2, 2, 1], dtype=np.int64)
+    assert nx.is_graphical(ds, "eg")
+    assert nx.is_graphical(ds, "hh")
+    ds = np.array([1, 2, 2, 2, 1], dtype=np.float64)
+    assert nx.is_graphical(ds, "eg")
+    assert nx.is_graphical(ds, "hh")
+    ds = np.array([1.1, 2, 2, 2, 1], dtype=np.float64)
+    pytest.raises(nx.NetworkXException, nx.is_graphical, ds, "eg")
+    pytest.raises(nx.NetworkXException, nx.is_graphical, ds, "hh")

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_hierarchy.py

@@ -0,0 +1,39 @@
+import pytest
+
+import networkx as nx
+
+
+def test_hierarchy_exception():
+    G = nx.cycle_graph(5)
+    pytest.raises(nx.NetworkXError, nx.flow_hierarchy, G)
+
+
+def test_hierarchy_cycle():
+    G = nx.cycle_graph(5, create_using=nx.DiGraph())
+    assert nx.flow_hierarchy(G) == 0.0
+
+
+def test_hierarchy_tree():
+    G = nx.full_rary_tree(2, 16, create_using=nx.DiGraph())
+    assert nx.flow_hierarchy(G) == 1.0
+
+
+def test_hierarchy_1():
+    G = nx.DiGraph()
+    G.add_edges_from([(0, 1), (1, 2), (2, 3), (3, 1), (3, 4), (0, 4)])
+    assert nx.flow_hierarchy(G) == 0.5
+
+
+def test_hierarchy_weight():
+    G = nx.DiGraph()
+    G.add_edges_from(
+        [
+            (0, 1, {"weight": 0.3}),
+            (1, 2, {"weight": 0.1}),
+            (2, 3, {"weight": 0.1}),
+            (3, 1, {"weight": 0.1}),
+            (3, 4, {"weight": 0.3}),
+            (0, 4, {"weight": 0.3}),
+        ]
+    )
+    assert nx.flow_hierarchy(G, weight="weight") == 0.75

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_isolate.py

@@ -0,0 +1,26 @@
+"""Unit tests for the :mod:`networkx.algorithms.isolates` module."""
+
+import networkx as nx
+
+
+def test_is_isolate():
+    G = nx.Graph()
+    G.add_edge(0, 1)
+    G.add_node(2)
+    assert not nx.is_isolate(G, 0)
+    assert not nx.is_isolate(G, 1)
+    assert nx.is_isolate(G, 2)
+
+
+def test_isolates():
+    G = nx.Graph()
+    G.add_edge(0, 1)
+    G.add_nodes_from([2, 3])
+    assert sorted(nx.isolates(G)) == [2, 3]
+
+
+def test_number_of_isolates():
+    G = nx.Graph()
+    G.add_edge(0, 1)
+    G.add_nodes_from([2, 3])
+    assert nx.number_of_isolates(G) == 2

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_link_prediction.py

@@ -0,0 +1,586 @@
+import math
+from functools import partial
+
+import pytest
+
+import networkx as nx
+
+
+def _test_func(G, ebunch, expected, predict_func, **kwargs):
+    result = predict_func(G, ebunch, **kwargs)
+    exp_dict = {tuple(sorted([u, v])): score for u, v, score in expected}
+    res_dict = {tuple(sorted([u, v])): score for u, v, score in result}
+
+    assert len(exp_dict) == len(res_dict)
+    for p in exp_dict:
+        assert exp_dict[p] == pytest.approx(res_dict[p], abs=1e-7)
+
+
+class TestResourceAllocationIndex:
+    @classmethod
+    def setup_class(cls):
+        cls.func = staticmethod(nx.resource_allocation_index)
+        cls.test = partial(_test_func, predict_func=cls.func)
+
+    def test_K5(self):
+        G = nx.complete_graph(5)
+        self.test(G, [(0, 1)], [(0, 1, 0.75)])
+
+    def test_P3(self):
+        G = nx.path_graph(3)
+        self.test(G, [(0, 2)], [(0, 2, 0.5)])
+
+    def test_S4(self):
+        G = nx.star_graph(4)
+        self.test(G, [(1, 2)], [(1, 2, 0.25)])
+
+    @pytest.mark.parametrize("graph_type", (nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph))
+    def test_notimplemented(self, graph_type):
+        assert pytest.raises(
+            nx.NetworkXNotImplemented, self.func, graph_type([(0, 1), (1, 2)]), [(0, 2)]
+        )
+
+    def test_node_not_found(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        assert pytest.raises(nx.NodeNotFound, self.func, G, [(0, 4)])
+
+    def test_no_common_neighbor(self):
+        G = nx.Graph()
+        G.add_nodes_from([0, 1])
+        self.test(G, [(0, 1)], [(0, 1, 0)])
+
+    def test_equal_nodes(self):
+        G = nx.complete_graph(4)
+        self.test(G, [(0, 0)], [(0, 0, 1)])
+
+    def test_all_nonexistent_edges(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        self.test(G, None, [(0, 3, 0.5), (1, 2, 0.5), (1, 3, 0)])
+
+
+class TestJaccardCoefficient:
+    @classmethod
+    def setup_class(cls):
+        cls.func = staticmethod(nx.jaccard_coefficient)
+        cls.test = partial(_test_func, predict_func=cls.func)
+
+    def test_K5(self):
+        G = nx.complete_graph(5)
+        self.test(G, [(0, 1)], [(0, 1, 0.6)])
+
+    def test_P4(self):
+        G = nx.path_graph(4)
+        self.test(G, [(0, 2)], [(0, 2, 0.5)])
+
+    @pytest.mark.parametrize("graph_type", (nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph))
+    def test_notimplemented(self, graph_type):
+        assert pytest.raises(
+            nx.NetworkXNotImplemented, self.func, graph_type([(0, 1), (1, 2)]), [(0, 2)]
+        )
+
+    def test_node_not_found(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        assert pytest.raises(nx.NodeNotFound, self.func, G, [(0, 4)])
+
+    def test_no_common_neighbor(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (2, 3)])
+        self.test(G, [(0, 2)], [(0, 2, 0)])
+
+    def test_isolated_nodes(self):
+        G = nx.Graph()
+        G.add_nodes_from([0, 1])
+        self.test(G, [(0, 1)], [(0, 1, 0)])
+
+    def test_all_nonexistent_edges(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        self.test(G, None, [(0, 3, 0.5), (1, 2, 0.5), (1, 3, 0)])
+
+
+class TestAdamicAdarIndex:
+    @classmethod
+    def setup_class(cls):
+        cls.func = staticmethod(nx.adamic_adar_index)
+        cls.test = partial(_test_func, predict_func=cls.func)
+
+    def test_K5(self):
+        G = nx.complete_graph(5)
+        self.test(G, [(0, 1)], [(0, 1, 3 / math.log(4))])
+
+    def test_P3(self):
+        G = nx.path_graph(3)
+        self.test(G, [(0, 2)], [(0, 2, 1 / math.log(2))])
+
+    def test_S4(self):
+        G = nx.star_graph(4)
+        self.test(G, [(1, 2)], [(1, 2, 1 / math.log(4))])
+
+    @pytest.mark.parametrize("graph_type", (nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph))
+    def test_notimplemented(self, graph_type):
+        assert pytest.raises(
+            nx.NetworkXNotImplemented, self.func, graph_type([(0, 1), (1, 2)]), [(0, 2)]
+        )
+
+    def test_node_not_found(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        assert pytest.raises(nx.NodeNotFound, self.func, G, [(0, 4)])
+
+    def test_no_common_neighbor(self):
+        G = nx.Graph()
+        G.add_nodes_from([0, 1])
+        self.test(G, [(0, 1)], [(0, 1, 0)])
+
+    def test_equal_nodes(self):
+        G = nx.complete_graph(4)
+        self.test(G, [(0, 0)], [(0, 0, 3 / math.log(3))])
+
+    def test_all_nonexistent_edges(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        self.test(
+            G, None, [(0, 3, 1 / math.log(2)), (1, 2, 1 / math.log(2)), (1, 3, 0)]
+        )
+
+
+class TestCommonNeighborCentrality:
+    @classmethod
+    def setup_class(cls):
+        cls.func = staticmethod(nx.common_neighbor_centrality)
+        cls.test = partial(_test_func, predict_func=cls.func)
+
+    def test_K5(self):
+        G = nx.complete_graph(5)
+        self.test(G, [(0, 1)], [(0, 1, 3.0)], alpha=1)
+        self.test(G, [(0, 1)], [(0, 1, 5.0)], alpha=0)
+
+    def test_P3(self):
+        G = nx.path_graph(3)
+        self.test(G, [(0, 2)], [(0, 2, 1.25)], alpha=0.5)
+
+    def test_S4(self):
+        G = nx.star_graph(4)
+        self.test(G, [(1, 2)], [(1, 2, 1.75)], alpha=0.5)
+
+    @pytest.mark.parametrize("graph_type", (nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph))
+    def test_notimplemented(self, graph_type):
+        assert pytest.raises(
+            nx.NetworkXNotImplemented, self.func, graph_type([(0, 1), (1, 2)]), [(0, 2)]
+        )
+
+    def test_node_u_not_found(self):
+        G = nx.Graph()
+        G.add_edges_from([(1, 3), (2, 3)])
+        assert pytest.raises(nx.NodeNotFound, self.func, G, [(0, 1)])
+
+    def test_node_v_not_found(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        assert pytest.raises(nx.NodeNotFound, self.func, G, [(0, 4)])
+
+    def test_no_common_neighbor(self):
+        G = nx.Graph()
+        G.add_nodes_from([0, 1])
+        self.test(G, [(0, 1)], [(0, 1, 0)])
+
+    def test_equal_nodes(self):
+        G = nx.complete_graph(4)
+        assert pytest.raises(nx.NetworkXAlgorithmError, self.test, G, [(0, 0)], [])
+
+    def test_equal_nodes_with_alpha_one_raises_error(self):
+        G = nx.complete_graph(4)
+        assert pytest.raises(
+            nx.NetworkXAlgorithmError, self.test, G, [(0, 0)], [], alpha=1.0
+        )
+
+    def test_all_nonexistent_edges(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        self.test(G, None, [(0, 3, 1.5), (1, 2, 1.5), (1, 3, 2 / 3)], alpha=0.5)
+
+
+class TestPreferentialAttachment:
+    @classmethod
+    def setup_class(cls):
+        cls.func = staticmethod(nx.preferential_attachment)
+        cls.test = partial(_test_func, predict_func=cls.func)
+
+    def test_K5(self):
+        G = nx.complete_graph(5)
+        self.test(G, [(0, 1)], [(0, 1, 16)])
+
+    def test_P3(self):
+        G = nx.path_graph(3)
+        self.test(G, [(0, 1)], [(0, 1, 2)])
+
+    def test_S4(self):
+        G = nx.star_graph(4)
+        self.test(G, [(0, 2)], [(0, 2, 4)])
+
+    @pytest.mark.parametrize("graph_type", (nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph))
+    def test_notimplemented(self, graph_type):
+        assert pytest.raises(
+            nx.NetworkXNotImplemented, self.func, graph_type([(0, 1), (1, 2)]), [(0, 2)]
+        )
+
+    def test_node_not_found(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        assert pytest.raises(nx.NodeNotFound, self.func, G, [(0, 4)])
+
+    def test_zero_degrees(self):
+        G = nx.Graph()
+        G.add_nodes_from([0, 1])
+        self.test(G, [(0, 1)], [(0, 1, 0)])
+
+    def test_all_nonexistent_edges(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        self.test(G, None, [(0, 3, 2), (1, 2, 2), (1, 3, 1)])
+
+
+class TestCNSoundarajanHopcroft:
+    @classmethod
+    def setup_class(cls):
+        cls.func = staticmethod(nx.cn_soundarajan_hopcroft)
+        cls.test = partial(_test_func, predict_func=cls.func, community="community")
+
+    def test_K5(self):
+        G = nx.complete_graph(5)
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        G.nodes[4]["community"] = 1
+        self.test(G, [(0, 1)], [(0, 1, 5)])
+
+    def test_P3(self):
+        G = nx.path_graph(3)
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 0
+        self.test(G, [(0, 2)], [(0, 2, 1)])
+
+    def test_S4(self):
+        G = nx.star_graph(4)
+        G.nodes[0]["community"] = 1
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 1
+        G.nodes[3]["community"] = 0
+        G.nodes[4]["community"] = 0
+        self.test(G, [(1, 2)], [(1, 2, 2)])
+
+    @pytest.mark.parametrize("graph_type", (nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph))
+    def test_notimplemented(self, graph_type):
+        G = graph_type([(0, 1), (1, 2)])
+        G.add_nodes_from([0, 1, 2], community=0)
+        assert pytest.raises(nx.NetworkXNotImplemented, self.func, G, [(0, 2)])
+
+    def test_node_not_found(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        assert pytest.raises(nx.NodeNotFound, self.func, G, [(0, 4)])
+
+    def test_no_common_neighbor(self):
+        G = nx.Graph()
+        G.add_nodes_from([0, 1])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        self.test(G, [(0, 1)], [(0, 1, 0)])
+
+    def test_equal_nodes(self):
+        G = nx.complete_graph(3)
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        self.test(G, [(0, 0)], [(0, 0, 4)])
+
+    def test_different_community(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (1, 3), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 1
+        self.test(G, [(0, 3)], [(0, 3, 2)])
+
+    def test_no_community_information(self):
+        G = nx.complete_graph(5)
+        assert pytest.raises(nx.NetworkXAlgorithmError, list, self.func(G, [(0, 1)]))
+
+    def test_insufficient_community_information(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (1, 3), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[3]["community"] = 0
+        assert pytest.raises(nx.NetworkXAlgorithmError, list, self.func(G, [(0, 3)]))
+
+    def test_sufficient_community_information(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (1, 2), (1, 3), (2, 4), (3, 4), (4, 5)])
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        G.nodes[4]["community"] = 0
+        self.test(G, [(1, 4)], [(1, 4, 4)])
+
+    def test_custom_community_attribute_name(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (1, 3), (2, 3)])
+        G.nodes[0]["cmty"] = 0
+        G.nodes[1]["cmty"] = 0
+        G.nodes[2]["cmty"] = 0
+        G.nodes[3]["cmty"] = 1
+        self.test(G, [(0, 3)], [(0, 3, 2)], community="cmty")
+
+    def test_all_nonexistent_edges(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        self.test(G, None, [(0, 3, 2), (1, 2, 1), (1, 3, 0)])
+
+
+class TestRAIndexSoundarajanHopcroft:
+    @classmethod
+    def setup_class(cls):
+        cls.func = staticmethod(nx.ra_index_soundarajan_hopcroft)
+        cls.test = partial(_test_func, predict_func=cls.func, community="community")
+
+    def test_K5(self):
+        G = nx.complete_graph(5)
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        G.nodes[4]["community"] = 1
+        self.test(G, [(0, 1)], [(0, 1, 0.5)])
+
+    def test_P3(self):
+        G = nx.path_graph(3)
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 0
+        self.test(G, [(0, 2)], [(0, 2, 0)])
+
+    def test_S4(self):
+        G = nx.star_graph(4)
+        G.nodes[0]["community"] = 1
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 1
+        G.nodes[3]["community"] = 0
+        G.nodes[4]["community"] = 0
+        self.test(G, [(1, 2)], [(1, 2, 0.25)])
+
+    @pytest.mark.parametrize("graph_type", (nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph))
+    def test_notimplemented(self, graph_type):
+        G = graph_type([(0, 1), (1, 2)])
+        G.add_nodes_from([0, 1, 2], community=0)
+        assert pytest.raises(nx.NetworkXNotImplemented, self.func, G, [(0, 2)])
+
+    def test_node_not_found(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        assert pytest.raises(nx.NodeNotFound, self.func, G, [(0, 4)])
+
+    def test_no_common_neighbor(self):
+        G = nx.Graph()
+        G.add_nodes_from([0, 1])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        self.test(G, [(0, 1)], [(0, 1, 0)])
+
+    def test_equal_nodes(self):
+        G = nx.complete_graph(3)
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        self.test(G, [(0, 0)], [(0, 0, 1)])
+
+    def test_different_community(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (1, 3), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 1
+        self.test(G, [(0, 3)], [(0, 3, 0)])
+
+    def test_no_community_information(self):
+        G = nx.complete_graph(5)
+        assert pytest.raises(nx.NetworkXAlgorithmError, list, self.func(G, [(0, 1)]))
+
+    def test_insufficient_community_information(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (1, 3), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[3]["community"] = 0
+        assert pytest.raises(nx.NetworkXAlgorithmError, list, self.func(G, [(0, 3)]))
+
+    def test_sufficient_community_information(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (1, 2), (1, 3), (2, 4), (3, 4), (4, 5)])
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        G.nodes[4]["community"] = 0
+        self.test(G, [(1, 4)], [(1, 4, 1)])
+
+    def test_custom_community_attribute_name(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (1, 3), (2, 3)])
+        G.nodes[0]["cmty"] = 0
+        G.nodes[1]["cmty"] = 0
+        G.nodes[2]["cmty"] = 0
+        G.nodes[3]["cmty"] = 1
+        self.test(G, [(0, 3)], [(0, 3, 0)], community="cmty")
+
+    def test_all_nonexistent_edges(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        self.test(G, None, [(0, 3, 0.5), (1, 2, 0), (1, 3, 0)])
+
+
+class TestWithinInterCluster:
+    @classmethod
+    def setup_class(cls):
+        cls.delta = 0.001
+        cls.func = staticmethod(nx.within_inter_cluster)
+        cls.test = partial(
+            _test_func, predict_func=cls.func, delta=cls.delta, community="community"
+        )
+
+    def test_K5(self):
+        G = nx.complete_graph(5)
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        G.nodes[4]["community"] = 1
+        self.test(G, [(0, 1)], [(0, 1, 2 / (1 + self.delta))])
+
+    def test_P3(self):
+        G = nx.path_graph(3)
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 0
+        self.test(G, [(0, 2)], [(0, 2, 0)])
+
+    def test_S4(self):
+        G = nx.star_graph(4)
+        G.nodes[0]["community"] = 1
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 1
+        G.nodes[3]["community"] = 0
+        G.nodes[4]["community"] = 0
+        self.test(G, [(1, 2)], [(1, 2, 1 / self.delta)])
+
+    @pytest.mark.parametrize("graph_type", (nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph))
+    def test_notimplemented(self, graph_type):
+        G = graph_type([(0, 1), (1, 2)])
+        G.add_nodes_from([0, 1, 2], community=0)
+        assert pytest.raises(nx.NetworkXNotImplemented, self.func, G, [(0, 2)])
+
+    def test_node_not_found(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        assert pytest.raises(nx.NodeNotFound, self.func, G, [(0, 4)])
+
+    def test_no_common_neighbor(self):
+        G = nx.Graph()
+        G.add_nodes_from([0, 1])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        self.test(G, [(0, 1)], [(0, 1, 0)])
+
+    def test_equal_nodes(self):
+        G = nx.complete_graph(3)
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        self.test(G, [(0, 0)], [(0, 0, 2 / self.delta)])
+
+    def test_different_community(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (1, 3), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 1
+        self.test(G, [(0, 3)], [(0, 3, 0)])
+
+    def test_no_inter_cluster_common_neighbor(self):
+        G = nx.complete_graph(4)
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        self.test(G, [(0, 3)], [(0, 3, 2 / self.delta)])
+
+    def test_no_community_information(self):
+        G = nx.complete_graph(5)
+        assert pytest.raises(nx.NetworkXAlgorithmError, list, self.func(G, [(0, 1)]))
+
+    def test_insufficient_community_information(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (1, 3), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 0
+        G.nodes[3]["community"] = 0
+        assert pytest.raises(nx.NetworkXAlgorithmError, list, self.func(G, [(0, 3)]))
+
+    def test_sufficient_community_information(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (1, 2), (1, 3), (2, 4), (3, 4), (4, 5)])
+        G.nodes[1]["community"] = 0
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        G.nodes[4]["community"] = 0
+        self.test(G, [(1, 4)], [(1, 4, 2 / self.delta)])
+
+    def test_invalid_delta(self):
+        G = nx.complete_graph(3)
+        G.add_nodes_from([0, 1, 2], community=0)
+        assert pytest.raises(nx.NetworkXAlgorithmError, self.func, G, [(0, 1)], 0)
+        assert pytest.raises(nx.NetworkXAlgorithmError, self.func, G, [(0, 1)], -0.5)
+
+    def test_custom_community_attribute_name(self):
+        G = nx.complete_graph(4)
+        G.nodes[0]["cmty"] = 0
+        G.nodes[1]["cmty"] = 0
+        G.nodes[2]["cmty"] = 0
+        G.nodes[3]["cmty"] = 0
+        self.test(G, [(0, 3)], [(0, 3, 2 / self.delta)], community="cmty")
+
+    def test_all_nonexistent_edges(self):
+        G = nx.Graph()
+        G.add_edges_from([(0, 1), (0, 2), (2, 3)])
+        G.nodes[0]["community"] = 0
+        G.nodes[1]["community"] = 1
+        G.nodes[2]["community"] = 0
+        G.nodes[3]["community"] = 0
+        self.test(G, None, [(0, 3, 1 / self.delta), (1, 2, 0), (1, 3, 0)])

env-llmeval/lib/python3.10/site-packages/networkx/algorithms/tests/test_lowest_common_ancestors.py

@@ -0,0 +1,427 @@
+from itertools import chain, combinations, product
+
+import pytest
+
+import networkx as nx
+
+tree_all_pairs_lca = nx.tree_all_pairs_lowest_common_ancestor
+all_pairs_lca = nx.all_pairs_lowest_common_ancestor
+
+
+def get_pair(dictionary, n1, n2):
+    if (n1, n2) in dictionary:
+        return dictionary[n1, n2]
+    else:
+        return dictionary[n2, n1]
+
+
+class TestTreeLCA:
+    @classmethod
+    def setup_class(cls):
+        cls.DG = nx.DiGraph()
+        edges = [(0, 1), (0, 2), (1, 3), (1, 4), (2, 5), (2, 6)]
+        cls.DG.add_edges_from(edges)
+        cls.ans = dict(tree_all_pairs_lca(cls.DG, 0))
+        gold = {(n, n): n for n in cls.DG}
+        gold.update({(0, i): 0 for i in range(1, 7)})
+        gold.update(
+            {
+                (1, 2): 0,
+                (1, 3): 1,
+                (1, 4): 1,
+                (1, 5): 0,
+                (1, 6): 0,
+                (2, 3): 0,
+                (2, 4): 0,
+                (2, 5): 2,
+                (2, 6): 2,
+                (3, 4): 1,
+                (3, 5): 0,
+                (3, 6): 0,
+                (4, 5): 0,
+                (4, 6): 0,
+                (5, 6): 2,
+            }
+        )
+
+        cls.gold = gold
+
+    @staticmethod
+    def assert_has_same_pairs(d1, d2):
+        for a, b in ((min(pair), max(pair)) for pair in chain(d1, d2)):
+            assert get_pair(d1, a, b) == get_pair(d2, a, b)
+
+    def test_tree_all_pairs_lca_default_root(self):
+        assert dict(tree_all_pairs_lca(self.DG)) == self.ans
+
+    def test_tree_all_pairs_lca_return_subset(self):
+        test_pairs = [(0, 1), (0, 1), (1, 0)]
+        ans = dict(tree_all_pairs_lca(self.DG, 0, test_pairs))
+        assert (0, 1) in ans and (1, 0) in ans
+        assert len(ans) == 2
+
+    def test_tree_all_pairs_lca(self):
+        all_pairs = chain(combinations(self.DG, 2), ((node, node) for node in self.DG))
+
+        ans = dict(tree_all_pairs_lca(self.DG, 0, all_pairs))
+        self.assert_has_same_pairs(ans, self.ans)
+
+    def test_tree_all_pairs_gold_example(self):
+        ans = dict(tree_all_pairs_lca(self.DG))
+        self.assert_has_same_pairs(self.gold, ans)
+
+    def test_tree_all_pairs_lca_invalid_input(self):
+        empty_digraph = tree_all_pairs_lca(nx.DiGraph())
+        pytest.raises(nx.NetworkXPointlessConcept, list, empty_digraph)
+
+        bad_pairs_digraph = tree_all_pairs_lca(self.DG, pairs=[(-1, -2)])
+        pytest.raises(nx.NodeNotFound, list, bad_pairs_digraph)
+
+    def test_tree_all_pairs_lca_subtrees(self):
+        ans = dict(tree_all_pairs_lca(self.DG, 1))
+        gold = {
+            pair: lca
+            for (pair, lca) in self.gold.items()
+            if all(n in (1, 3, 4) for n in pair)
+        }
+        self.assert_has_same_pairs(gold, ans)
+
+    def test_tree_all_pairs_lca_disconnected_nodes(self):
+        G = nx.DiGraph()
+        G.add_node(1)
+        assert {(1, 1): 1} == dict(tree_all_pairs_lca(G))
+
+        G.add_node(0)
+        assert {(1, 1): 1} == dict(tree_all_pairs_lca(G, 1))
+        assert {(0, 0): 0} == dict(tree_all_pairs_lca(G, 0))
+
+        pytest.raises(nx.NetworkXError, list, tree_all_pairs_lca(G))
+
+    def test_tree_all_pairs_lca_error_if_input_not_tree(self):
+        # Cycle
+        G = nx.DiGraph([(1, 2), (2, 1)])
+        pytest.raises(nx.NetworkXError, list, tree_all_pairs_lca(G))
+        # DAG
+        G = nx.DiGraph([(0, 2), (1, 2)])
+        pytest.raises(nx.NetworkXError, list, tree_all_pairs_lca(G))
+
+    def test_tree_all_pairs_lca_generator(self):
+        pairs = iter([(0, 1), (0, 1), (1, 0)])
+        some_pairs = dict(tree_all_pairs_lca(self.DG, 0, pairs))
+        assert (0, 1) in some_pairs and (1, 0) in some_pairs
+        assert len(some_pairs) == 2
+
+    def test_tree_all_pairs_lca_nonexisting_pairs_exception(self):
+        lca = tree_all_pairs_lca(self.DG, 0, [(-1, -1)])
+        pytest.raises(nx.NodeNotFound, list, lca)
+        # check if node is None
+        lca = tree_all_pairs_lca(self.DG, None, [(-1, -1)])
+        pytest.raises(nx.NodeNotFound, list, lca)
+
+    def test_tree_all_pairs_lca_routine_bails_on_DAGs(self):
+        G = nx.DiGraph([(3, 4), (5, 4)])
+        pytest.raises(nx.NetworkXError, list, tree_all_pairs_lca(G))
+
+    def test_tree_all_pairs_lca_not_implemented(self):
+        NNI = nx.NetworkXNotImplemented
+        G = nx.Graph([(0, 1)])
+        with pytest.raises(NNI):
+            next(tree_all_pairs_lca(G))
+        with pytest.raises(NNI):
+            next(all_pairs_lca(G))
+        pytest.raises(NNI, nx.lowest_common_ancestor, G, 0, 1)
+        G = nx.MultiGraph([(0, 1)])
+        with pytest.raises(NNI):
+            next(tree_all_pairs_lca(G))
+        with pytest.raises(NNI):
+            next(all_pairs_lca(G))
+        pytest.raises(NNI, nx.lowest_common_ancestor, G, 0, 1)
+
+    def test_tree_all_pairs_lca_trees_without_LCAs(self):
+        G = nx.DiGraph()
+        G.add_node(3)
+        ans = list(tree_all_pairs_lca(G))
+        assert ans == [((3, 3), 3)]
+
+
+class TestMultiTreeLCA(TestTreeLCA):
+    @classmethod
+    def setup_class(cls):
+        cls.DG = nx.MultiDiGraph()
+        edges = [(0, 1), (0, 2), (1, 3), (1, 4), (2, 5), (2, 6)]
+        cls.DG.add_edges_from(edges)
+        cls.ans = dict(tree_all_pairs_lca(cls.DG, 0))
+        # add multiedges
+        cls.DG.add_edges_from(edges)
+
+        gold = {(n, n): n for n in cls.DG}
+        gold.update({(0, i): 0 for i in range(1, 7)})
+        gold.update(
+            {
+                (1, 2): 0,
+                (1, 3): 1,
+                (1, 4): 1,
+                (1, 5): 0,
+                (1, 6): 0,
+                (2, 3): 0,
+                (2, 4): 0,
+                (2, 5): 2,
+                (2, 6): 2,
+                (3, 4): 1,
+                (3, 5): 0,
+                (3, 6): 0,
+                (4, 5): 0,
+                (4, 6): 0,
+                (5, 6): 2,
+            }
+        )
+
+        cls.gold = gold
+
+
+class TestDAGLCA:
+    @classmethod
+    def setup_class(cls):
+        cls.DG = nx.DiGraph()
+        nx.add_path(cls.DG, (0, 1, 2, 3))
+        nx.add_path(cls.DG, (0, 4, 3))
+        nx.add_path(cls.DG, (0, 5, 6, 8, 3))
+        nx.add_path(cls.DG, (5, 7, 8))
+        cls.DG.add_edge(6, 2)
+        cls.DG.add_edge(7, 2)
+
+        cls.root_distance = nx.shortest_path_length(cls.DG, source=0)
+
+        cls.gold = {
+            (1, 1): 1,
+            (1, 2): 1,
+            (1, 3): 1,
+            (1, 4): 0,
+            (1, 5): 0,
+            (1, 6): 0,
+            (1, 7): 0,
+            (1, 8): 0,
+            (2, 2): 2,
+            (2, 3): 2,
+            (2, 4): 0,
+            (2, 5): 5,
+            (2, 6): 6,
+            (2, 7): 7,
+            (2, 8): 7,
+            (3, 3): 3,
+            (3, 4): 4,
+            (3, 5): 5,
+            (3, 6): 6,
+            (3, 7): 7,
+            (3, 8): 8,
+            (4, 4): 4,
+            (4, 5): 0,
+            (4, 6): 0,
+            (4, 7): 0,
+            (4, 8): 0,
+            (5, 5): 5,
+            (5, 6): 5,
+            (5, 7): 5,
+            (5, 8): 5,
+            (6, 6): 6,
+            (6, 7): 5,
+            (6, 8): 6,
+            (7, 7): 7,
+            (7, 8): 7,
+            (8, 8): 8,
+        }
+        cls.gold.update(((0, n), 0) for n in cls.DG)
+
+    def assert_lca_dicts_same(self, d1, d2, G=None):
+        """Checks if d1 and d2 contain the same pairs and
+        have a node at the same distance from root for each.
+        If G is None use self.DG."""
+        if G is None:
+            G = self.DG
+            root_distance = self.root_distance
+        else:
+            roots = [n for n, deg in G.in_degree if deg == 0]
+            assert len(roots) == 1
+            root_distance = nx.shortest_path_length(G, source=roots[0])
+
+        for a, b in ((min(pair), max(pair)) for pair in chain(d1, d2)):
+            assert (
+                root_distance[get_pair(d1, a, b)] == root_distance[get_pair(d2, a, b)]
+            )
+
+    def test_all_pairs_lca_gold_example(self):
+        self.assert_lca_dicts_same(dict(all_pairs_lca(self.DG)), self.gold)
+
+    def test_all_pairs_lca_all_pairs_given(self):
+        all_pairs = list(product(self.DG.nodes(), self.DG.nodes()))
+        ans = all_pairs_lca(self.DG, pairs=all_pairs)
+        self.assert_lca_dicts_same(dict(ans), self.gold)
+
+    def test_all_pairs_lca_generator(self):
+        all_pairs = product(self.DG.nodes(), self.DG.nodes())
+        ans = all_pairs_lca(self.DG, pairs=all_pairs)
+        self.assert_lca_dicts_same(dict(ans), self.gold)
+
+    def test_all_pairs_lca_input_graph_with_two_roots(self):
+        G = self.DG.copy()
+        G.add_edge(9, 10)
+        G.add_edge(9, 4)
+        gold = self.gold.copy()
+        gold[9, 9] = 9
+        gold[9, 10] = 9
+        gold[9, 4] = 9
+        gold[9, 3] = 9
+        gold[10, 4] = 9
+        gold[10, 3] = 9
+        gold[10, 10] = 10
+
+        testing = dict(all_pairs_lca(G))
+
+        G.add_edge(-1, 9)
+        G.add_edge(-1, 0)
+        self.assert_lca_dicts_same(testing, gold, G)
+
+    def test_all_pairs_lca_nonexisting_pairs_exception(self):
+        pytest.raises(nx.NodeNotFound, all_pairs_lca, self.DG, [(-1, -1)])
+
+    def test_all_pairs_lca_pairs_without_lca(self):
+        G = self.DG.copy()
+        G.add_node(-1)
+        gen = all_pairs_lca(G, [(-1, -1), (-1, 0)])
+        assert dict(gen) == {(-1, -1): -1}
+
+    def test_all_pairs_lca_null_graph(self):
+        pytest.raises(nx.NetworkXPointlessConcept, all_pairs_lca, nx.DiGraph())
+
+    def test_all_pairs_lca_non_dags(self):
+        pytest.raises(nx.NetworkXError, all_pairs_lca, nx.DiGraph([(3, 4), (4, 3)]))
+
+    def test_all_pairs_lca_nonempty_graph_without_lca(self):
+        G = nx.DiGraph()
+        G.add_node(3)
+        ans = list(all_pairs_lca(G))
+        assert ans == [((3, 3), 3)]
+
+    def test_all_pairs_lca_bug_gh4942(self):
+        G = nx.DiGraph([(0, 2), (1, 2), (2, 3)])
+        ans = list(all_pairs_lca(G))
+        assert len(ans) == 9
+
+    def test_all_pairs_lca_default_kwarg(self):
+        G = nx.DiGraph([(0, 1), (2, 1)])
+        sentinel = object()
+        assert nx.lowest_common_ancestor(G, 0, 2, default=sentinel) is sentinel
+
+    def test_all_pairs_lca_identity(self):
+        G = nx.DiGraph()
+        G.add_node(3)
+        assert nx.lowest_common_ancestor(G, 3, 3) == 3
+
+    def test_all_pairs_lca_issue_4574(self):
+        G = nx.DiGraph()
+        G.add_nodes_from(range(17))
+        G.add_edges_from(
+            [
+                (2, 0),
+                (1, 2),
+                (3, 2),
+                (5, 2),
+                (8, 2),
+                (11, 2),
+                (4, 5),
+                (6, 5),
+                (7, 8),
+                (10, 8),
+                (13, 11),
+                (14, 11),
+                (15, 11),
+                (9, 10),
+                (12, 13),
+                (16, 15),
+            ]
+        )
+
+        assert nx.lowest_common_ancestor(G, 7, 9) == None
+
+    def test_all_pairs_lca_one_pair_gh4942(self):
+        G = nx.DiGraph()
+        # Note: order edge addition is critical to the test
+        G.add_edge(0, 1)
+        G.add_edge(2, 0)
+        G.add_edge(2, 3)
+        G.add_edge(4, 0)
+        G.add_edge(5, 2)
+
+        assert nx.lowest_common_ancestor(G, 1, 3) == 2
+
+
+class TestMultiDiGraph_DAGLCA(TestDAGLCA):
+    @classmethod
+    def setup_class(cls):
+        cls.DG = nx.MultiDiGraph()
+        nx.add_path(cls.DG, (0, 1, 2, 3))
+        # add multiedges
+        nx.add_path(cls.DG, (0, 1, 2, 3))
+        nx.add_path(cls.DG, (0, 4, 3))
+        nx.add_path(cls.DG, (0, 5, 6, 8, 3))
+        nx.add_path(cls.DG, (5, 7, 8))
+        cls.DG.add_edge(6, 2)
+        cls.DG.add_edge(7, 2)
+
+        cls.root_distance = nx.shortest_path_length(cls.DG, source=0)
+
+        cls.gold = {
+            (1, 1): 1,
+            (1, 2): 1,
+            (1, 3): 1,
+            (1, 4): 0,
+            (1, 5): 0,
+            (1, 6): 0,
+            (1, 7): 0,
+            (1, 8): 0,
+            (2, 2): 2,
+            (2, 3): 2,
+            (2, 4): 0,
+            (2, 5): 5,
+            (2, 6): 6,
+            (2, 7): 7,
+            (2, 8): 7,
+            (3, 3): 3,
+            (3, 4): 4,
+            (3, 5): 5,
+            (3, 6): 6,
+            (3, 7): 7,
+            (3, 8): 8,
+            (4, 4): 4,
+            (4, 5): 0,
+            (4, 6): 0,
+            (4, 7): 0,
+            (4, 8): 0,
+            (5, 5): 5,
+            (5, 6): 5,
+            (5, 7): 5,
+            (5, 8): 5,
+            (6, 6): 6,
+            (6, 7): 5,
+            (6, 8): 6,
+            (7, 7): 7,
+            (7, 8): 7,
+            (8, 8): 8,
+        }
+        cls.gold.update(((0, n), 0) for n in cls.DG)
+
+
+def test_all_pairs_lca_self_ancestors():
+    """Self-ancestors should always be the node itself, i.e. lca of (0, 0) is 0.
+    See gh-4458."""
+    # DAG for test - note order of node/edge addition is relevant
+    G = nx.DiGraph()
+    G.add_nodes_from(range(5))
+    G.add_edges_from([(1, 0), (2, 0), (3, 2), (4, 1), (4, 3)])
+
+    ap_lca = nx.all_pairs_lowest_common_ancestor
+    assert all(u == v == a for (u, v), a in ap_lca(G) if u == v)
+    MG = nx.MultiDiGraph(G)
+    assert all(u == v == a for (u, v), a in ap_lca(MG) if u == v)
+    MG.add_edges_from([(1, 0), (2, 0)])
+    assert all(u == v == a for (u, v), a in ap_lca(MG) if u == v)