two version of R2R are here HEAD master

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diff --git a/.venv/lib/python3.12/site-packages/networkx/classes/tests/test_multigraph.py b/.venv/lib/python3.12/site-packages/networkx/classes/tests/test_multigraph.py
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+from collections import UserDict
+
+import pytest
+
+import networkx as nx
+from networkx.utils import edges_equal
+
+from .test_graph import BaseAttrGraphTester
+from .test_graph import TestGraph as _TestGraph
+
+
+class BaseMultiGraphTester(BaseAttrGraphTester):
+    def test_has_edge(self):
+        G = self.K3
+        assert G.has_edge(0, 1)
+        assert not G.has_edge(0, -1)
+        assert G.has_edge(0, 1, 0)
+        assert not G.has_edge(0, 1, 1)
+
+    def test_get_edge_data(self):
+        G = self.K3
+        assert G.get_edge_data(0, 1) == {0: {}}
+        assert G[0][1] == {0: {}}
+        assert G[0][1][0] == {}
+        assert G.get_edge_data(10, 20) is None
+        assert G.get_edge_data(0, 1, 0) == {}
+
+    def test_adjacency(self):
+        G = self.K3
+        assert dict(G.adjacency()) == {
+            0: {1: {0: {}}, 2: {0: {}}},
+            1: {0: {0: {}}, 2: {0: {}}},
+            2: {0: {0: {}}, 1: {0: {}}},
+        }
+
+    def deepcopy_edge_attr(self, H, G):
+        assert G[1][2][0]["foo"] == H[1][2][0]["foo"]
+        G[1][2][0]["foo"].append(1)
+        assert G[1][2][0]["foo"] != H[1][2][0]["foo"]
+
+    def shallow_copy_edge_attr(self, H, G):
+        assert G[1][2][0]["foo"] == H[1][2][0]["foo"]
+        G[1][2][0]["foo"].append(1)
+        assert G[1][2][0]["foo"] == H[1][2][0]["foo"]
+
+    def graphs_equal(self, H, G):
+        assert G._adj == H._adj
+        assert G._node == H._node
+        assert G.graph == H.graph
+        assert G.name == H.name
+        if not G.is_directed() and not H.is_directed():
+            assert H._adj[1][2][0] is H._adj[2][1][0]
+            assert G._adj[1][2][0] is G._adj[2][1][0]
+        else:  # at least one is directed
+            if not G.is_directed():
+                G._pred = G._adj
+                G._succ = G._adj
+            if not H.is_directed():
+                H._pred = H._adj
+                H._succ = H._adj
+            assert G._pred == H._pred
+            assert G._succ == H._succ
+            assert H._succ[1][2][0] is H._pred[2][1][0]
+            assert G._succ[1][2][0] is G._pred[2][1][0]
+
+    def same_attrdict(self, H, G):
+        # same attrdict in the edgedata
+        old_foo = H[1][2][0]["foo"]
+        H.adj[1][2][0]["foo"] = "baz"
+        assert G._adj == H._adj
+        H.adj[1][2][0]["foo"] = old_foo
+        assert G._adj == H._adj
+
+        old_foo = H.nodes[0]["foo"]
+        H.nodes[0]["foo"] = "baz"
+        assert G._node == H._node
+        H.nodes[0]["foo"] = old_foo
+        assert G._node == H._node
+
+    def different_attrdict(self, H, G):
+        # used by graph_equal_but_different
+        old_foo = H[1][2][0]["foo"]
+        H.adj[1][2][0]["foo"] = "baz"
+        assert G._adj != H._adj
+        H.adj[1][2][0]["foo"] = old_foo
+        assert G._adj == H._adj
+
+        old_foo = H.nodes[0]["foo"]
+        H.nodes[0]["foo"] = "baz"
+        assert G._node != H._node
+        H.nodes[0]["foo"] = old_foo
+        assert G._node == H._node
+
+    def test_to_undirected(self):
+        G = self.K3
+        self.add_attributes(G)
+        H = nx.MultiGraph(G)
+        self.is_shallow_copy(H, G)
+        H = G.to_undirected()
+        self.is_deepcopy(H, G)
+
+    def test_to_directed(self):
+        G = self.K3
+        self.add_attributes(G)
+        H = nx.MultiDiGraph(G)
+        self.is_shallow_copy(H, G)
+        H = G.to_directed()
+        self.is_deepcopy(H, G)
+
+    def test_number_of_edges_selfloops(self):
+        G = self.K3
+        G.add_edge(0, 0)
+        G.add_edge(0, 0)
+        G.add_edge(0, 0, key="parallel edge")
+        G.remove_edge(0, 0, key="parallel edge")
+        assert G.number_of_edges(0, 0) == 2
+        G.remove_edge(0, 0)
+        assert G.number_of_edges(0, 0) == 1
+
+    def test_edge_lookup(self):
+        G = self.Graph()
+        G.add_edge(1, 2, foo="bar")
+        G.add_edge(1, 2, "key", foo="biz")
+        assert edges_equal(G.edges[1, 2, 0], {"foo": "bar"})
+        assert edges_equal(G.edges[1, 2, "key"], {"foo": "biz"})
+
+    def test_edge_attr(self):
+        G = self.Graph()
+        G.add_edge(1, 2, key="k1", foo="bar")
+        G.add_edge(1, 2, key="k2", foo="baz")
+        assert isinstance(G.get_edge_data(1, 2), G.edge_key_dict_factory)
+        assert all(
+            isinstance(d, G.edge_attr_dict_factory) for u, v, d in G.edges(data=True)
+        )
+        assert edges_equal(
+            G.edges(keys=True, data=True),
+            [(1, 2, "k1", {"foo": "bar"}), (1, 2, "k2", {"foo": "baz"})],
+        )
+        assert edges_equal(
+            G.edges(keys=True, data="foo"), [(1, 2, "k1", "bar"), (1, 2, "k2", "baz")]
+        )
+
+    def test_edge_attr4(self):
+        G = self.Graph()
+        G.add_edge(1, 2, key=0, data=7, spam="bar", bar="foo")
+        assert edges_equal(
+            G.edges(data=True), [(1, 2, {"data": 7, "spam": "bar", "bar": "foo"})]
+        )
+        G[1][2][0]["data"] = 10  # OK to set data like this
+        assert edges_equal(
+            G.edges(data=True), [(1, 2, {"data": 10, "spam": "bar", "bar": "foo"})]
+        )
+
+        G.adj[1][2][0]["data"] = 20
+        assert edges_equal(
+            G.edges(data=True), [(1, 2, {"data": 20, "spam": "bar", "bar": "foo"})]
+        )
+        G.edges[1, 2, 0]["data"] = 21  # another spelling, "edge"
+        assert edges_equal(
+            G.edges(data=True), [(1, 2, {"data": 21, "spam": "bar", "bar": "foo"})]
+        )
+        G.adj[1][2][0]["listdata"] = [20, 200]
+        G.adj[1][2][0]["weight"] = 20
+        assert edges_equal(
+            G.edges(data=True),
+            [
+                (
+                    1,
+                    2,
+                    {
+                        "data": 21,
+                        "spam": "bar",
+                        "bar": "foo",
+                        "listdata": [20, 200],
+                        "weight": 20,
+                    },
+                )
+            ],
+        )
+
+
+class TestMultiGraph(BaseMultiGraphTester, _TestGraph):
+    def setup_method(self):
+        self.Graph = nx.MultiGraph
+        # build K3
+        ed1, ed2, ed3 = ({0: {}}, {0: {}}, {0: {}})
+        self.k3adj = {0: {1: ed1, 2: ed2}, 1: {0: ed1, 2: ed3}, 2: {0: ed2, 1: ed3}}
+        self.k3edges = [(0, 1), (0, 2), (1, 2)]
+        self.k3nodes = [0, 1, 2]
+        self.K3 = self.Graph()
+        self.K3._adj = self.k3adj
+        self.K3._node = {}
+        self.K3._node[0] = {}
+        self.K3._node[1] = {}
+        self.K3._node[2] = {}
+
+    def test_data_input(self):
+        G = self.Graph({1: [2], 2: [1]}, name="test")
+        assert G.name == "test"
+        expected = [(1, {2: {0: {}}}), (2, {1: {0: {}}})]
+        assert sorted(G.adj.items()) == expected
+
+    def test_data_multigraph_input(self):
+        # standard case with edge keys and edge data
+        edata0 = {"w": 200, "s": "foo"}
+        edata1 = {"w": 201, "s": "bar"}
+        keydict = {0: edata0, 1: edata1}
+        dododod = {"a": {"b": keydict}}
+
+        multiple_edge = [("a", "b", 0, edata0), ("a", "b", 1, edata1)]
+        single_edge = [("a", "b", 0, keydict)]
+
+        G = self.Graph(dododod, multigraph_input=True)
+        assert list(G.edges(keys=True, data=True)) == multiple_edge
+        G = self.Graph(dododod, multigraph_input=None)
+        assert list(G.edges(keys=True, data=True)) == multiple_edge
+        G = self.Graph(dododod, multigraph_input=False)
+        assert list(G.edges(keys=True, data=True)) == single_edge
+
+        # test round-trip to_dict_of_dict and MultiGraph constructor
+        G = self.Graph(dododod, multigraph_input=True)
+        H = self.Graph(nx.to_dict_of_dicts(G))
+        assert nx.is_isomorphic(G, H) is True  # test that default is True
+        for mgi in [True, False]:
+            H = self.Graph(nx.to_dict_of_dicts(G), multigraph_input=mgi)
+            assert nx.is_isomorphic(G, H) == mgi
+
+    # Set up cases for when incoming_graph_data is not multigraph_input
+    etraits = {"w": 200, "s": "foo"}
+    egraphics = {"color": "blue", "shape": "box"}
+    edata = {"traits": etraits, "graphics": egraphics}
+    dodod1 = {"a": {"b": edata}}
+    dodod2 = {"a": {"b": etraits}}
+    dodod3 = {"a": {"b": {"traits": etraits, "s": "foo"}}}
+    dol = {"a": ["b"]}
+
+    multiple_edge = [("a", "b", "traits", etraits), ("a", "b", "graphics", egraphics)]
+    single_edge = [("a", "b", 0, {})]  # type: ignore[var-annotated]
+    single_edge1 = [("a", "b", 0, edata)]
+    single_edge2 = [("a", "b", 0, etraits)]
+    single_edge3 = [("a", "b", 0, {"traits": etraits, "s": "foo"})]
+
+    cases = [  # (dod, mgi, edges)
+        (dodod1, True, multiple_edge),
+        (dodod1, False, single_edge1),
+        (dodod2, False, single_edge2),
+        (dodod3, False, single_edge3),
+        (dol, False, single_edge),
+    ]
+
+    @pytest.mark.parametrize("dod, mgi, edges", cases)
+    def test_non_multigraph_input(self, dod, mgi, edges):
+        G = self.Graph(dod, multigraph_input=mgi)
+        assert list(G.edges(keys=True, data=True)) == edges
+        G = nx.to_networkx_graph(dod, create_using=self.Graph, multigraph_input=mgi)
+        assert list(G.edges(keys=True, data=True)) == edges
+
+    mgi_none_cases = [
+        (dodod1, multiple_edge),
+        (dodod2, single_edge2),
+        (dodod3, single_edge3),
+    ]
+
+    @pytest.mark.parametrize("dod, edges", mgi_none_cases)
+    def test_non_multigraph_input_mgi_none(self, dod, edges):
+        # test constructor without to_networkx_graph for mgi=None
+        G = self.Graph(dod)
+        assert list(G.edges(keys=True, data=True)) == edges
+
+    raise_cases = [dodod2, dodod3, dol]
+
+    @pytest.mark.parametrize("dod", raise_cases)
+    def test_non_multigraph_input_raise(self, dod):
+        # cases where NetworkXError is raised
+        pytest.raises(nx.NetworkXError, self.Graph, dod, multigraph_input=True)
+        pytest.raises(
+            nx.NetworkXError,
+            nx.to_networkx_graph,
+            dod,
+            create_using=self.Graph,
+            multigraph_input=True,
+        )
+
+    def test_getitem(self):
+        G = self.K3
+        assert G[0] == {1: {0: {}}, 2: {0: {}}}
+        with pytest.raises(KeyError):
+            G.__getitem__("j")
+        with pytest.raises(TypeError):
+            G.__getitem__(["A"])
+
+    def test_remove_node(self):
+        G = self.K3
+        G.remove_node(0)
+        assert G.adj == {1: {2: {0: {}}}, 2: {1: {0: {}}}}
+        with pytest.raises(nx.NetworkXError):
+            G.remove_node(-1)
+
+    def test_add_edge(self):
+        G = self.Graph()
+        G.add_edge(0, 1)
+        assert G.adj == {0: {1: {0: {}}}, 1: {0: {0: {}}}}
+        G = self.Graph()
+        G.add_edge(*(0, 1))
+        assert G.adj == {0: {1: {0: {}}}, 1: {0: {0: {}}}}
+        G = self.Graph()
+        with pytest.raises(ValueError):
+            G.add_edge(None, "anything")
+
+    def test_add_edge_conflicting_key(self):
+        G = self.Graph()
+        G.add_edge(0, 1, key=1)
+        G.add_edge(0, 1)
+        assert G.number_of_edges() == 2
+        G = self.Graph()
+        G.add_edges_from([(0, 1, 1, {})])
+        G.add_edges_from([(0, 1)])
+        assert G.number_of_edges() == 2
+
+    def test_add_edges_from(self):
+        G = self.Graph()
+        G.add_edges_from([(0, 1), (0, 1, {"weight": 3})])
+        assert G.adj == {
+            0: {1: {0: {}, 1: {"weight": 3}}},
+            1: {0: {0: {}, 1: {"weight": 3}}},
+        }
+        G.add_edges_from([(0, 1), (0, 1, {"weight": 3})], weight=2)
+        assert G.adj == {
+            0: {1: {0: {}, 1: {"weight": 3}, 2: {"weight": 2}, 3: {"weight": 3}}},
+            1: {0: {0: {}, 1: {"weight": 3}, 2: {"weight": 2}, 3: {"weight": 3}}},
+        }
+        G = self.Graph()
+        edges = [
+            (0, 1, {"weight": 3}),
+            (0, 1, (("weight", 2),)),
+            (0, 1, 5),
+            (0, 1, "s"),
+        ]
+        G.add_edges_from(edges)
+        keydict = {0: {"weight": 3}, 1: {"weight": 2}, 5: {}, "s": {}}
+        assert G._adj == {0: {1: keydict}, 1: {0: keydict}}
+
+        # too few in tuple
+        with pytest.raises(nx.NetworkXError):
+            G.add_edges_from([(0,)])
+        # too many in tuple
+        with pytest.raises(nx.NetworkXError):
+            G.add_edges_from([(0, 1, 2, 3, 4)])
+        # not a tuple
+        with pytest.raises(TypeError):
+            G.add_edges_from([0])
+
+    def test_multigraph_add_edges_from_four_tuple_misordered(self):
+        """add_edges_from expects 4-tuples of the format (u, v, key, data_dict).
+
+        Ensure 4-tuples of form (u, v, data_dict, key) raise exception.
+        """
+        G = nx.MultiGraph()
+        with pytest.raises(TypeError):
+            # key/data values flipped in 4-tuple
+            G.add_edges_from([(0, 1, {"color": "red"}, 0)])
+
+    def test_remove_edge(self):
+        G = self.K3
+        G.remove_edge(0, 1)
+        assert G.adj == {0: {2: {0: {}}}, 1: {2: {0: {}}}, 2: {0: {0: {}}, 1: {0: {}}}}
+
+        with pytest.raises(nx.NetworkXError):
+            G.remove_edge(-1, 0)
+        with pytest.raises(nx.NetworkXError):
+            G.remove_edge(0, 2, key=1)
+
+    def test_remove_edges_from(self):
+        G = self.K3.copy()
+        G.remove_edges_from([(0, 1)])
+        kd = {0: {}}
+        assert G.adj == {0: {2: kd}, 1: {2: kd}, 2: {0: kd, 1: kd}}
+        G.remove_edges_from([(0, 0)])  # silent fail
+        self.K3.add_edge(0, 1)
+        G = self.K3.copy()
+        G.remove_edges_from(list(G.edges(data=True, keys=True)))
+        assert G.adj == {0: {}, 1: {}, 2: {}}
+        G = self.K3.copy()
+        G.remove_edges_from(list(G.edges(data=False, keys=True)))
+        assert G.adj == {0: {}, 1: {}, 2: {}}
+        G = self.K3.copy()
+        G.remove_edges_from(list(G.edges(data=False, keys=False)))
+        assert G.adj == {0: {}, 1: {}, 2: {}}
+        G = self.K3.copy()
+        G.remove_edges_from([(0, 1, 0), (0, 2, 0, {}), (1, 2)])
+        assert G.adj == {0: {1: {1: {}}}, 1: {0: {1: {}}}, 2: {}}
+
+    def test_remove_multiedge(self):
+        G = self.K3
+        G.add_edge(0, 1, key="parallel edge")
+        G.remove_edge(0, 1, key="parallel edge")
+        assert G.adj == {
+            0: {1: {0: {}}, 2: {0: {}}},
+            1: {0: {0: {}}, 2: {0: {}}},
+            2: {0: {0: {}}, 1: {0: {}}},
+        }
+        G.remove_edge(0, 1)
+        kd = {0: {}}
+        assert G.adj == {0: {2: kd}, 1: {2: kd}, 2: {0: kd, 1: kd}}
+        with pytest.raises(nx.NetworkXError):
+            G.remove_edge(-1, 0)
+
+
+class TestEdgeSubgraph:
+    """Unit tests for the :meth:`MultiGraph.edge_subgraph` method."""
+
+    def setup_method(self):
+        # Create a doubly-linked path graph on five nodes.
+        G = nx.MultiGraph()
+        nx.add_path(G, range(5))
+        nx.add_path(G, range(5))
+        # Add some node, edge, and graph attributes.
+        for i in range(5):
+            G.nodes[i]["name"] = f"node{i}"
+        G.adj[0][1][0]["name"] = "edge010"
+        G.adj[0][1][1]["name"] = "edge011"
+        G.adj[3][4][0]["name"] = "edge340"
+        G.adj[3][4][1]["name"] = "edge341"
+        G.graph["name"] = "graph"
+        # Get the subgraph induced by one of the first edges and one of
+        # the last edges.
+        self.G = G
+        self.H = G.edge_subgraph([(0, 1, 0), (3, 4, 1)])
+
+    def test_correct_nodes(self):
+        """Tests that the subgraph has the correct nodes."""
+        assert [0, 1, 3, 4] == sorted(self.H.nodes())
+
+    def test_correct_edges(self):
+        """Tests that the subgraph has the correct edges."""
+        assert [(0, 1, 0, "edge010"), (3, 4, 1, "edge341")] == sorted(
+            self.H.edges(keys=True, data="name")
+        )
+
+    def test_add_node(self):
+        """Tests that adding a node to the original graph does not
+        affect the nodes of the subgraph.
+
+        """
+        self.G.add_node(5)
+        assert [0, 1, 3, 4] == sorted(self.H.nodes())
+
+    def test_remove_node(self):
+        """Tests that removing a node in the original graph does
+        affect the nodes of the subgraph.
+
+        """
+        self.G.remove_node(0)
+        assert [1, 3, 4] == sorted(self.H.nodes())
+
+    def test_node_attr_dict(self):
+        """Tests that the node attribute dictionary of the two graphs is
+        the same object.
+
+        """
+        for v in self.H:
+            assert self.G.nodes[v] == self.H.nodes[v]
+        # Making a change to G should make a change in H and vice versa.
+        self.G.nodes[0]["name"] = "foo"
+        assert self.G.nodes[0] == self.H.nodes[0]
+        self.H.nodes[1]["name"] = "bar"
+        assert self.G.nodes[1] == self.H.nodes[1]
+
+    def test_edge_attr_dict(self):
+        """Tests that the edge attribute dictionary of the two graphs is
+        the same object.
+
+        """
+        for u, v, k in self.H.edges(keys=True):
+            assert self.G._adj[u][v][k] == self.H._adj[u][v][k]
+        # Making a change to G should make a change in H and vice versa.
+        self.G._adj[0][1][0]["name"] = "foo"
+        assert self.G._adj[0][1][0]["name"] == self.H._adj[0][1][0]["name"]
+        self.H._adj[3][4][1]["name"] = "bar"
+        assert self.G._adj[3][4][1]["name"] == self.H._adj[3][4][1]["name"]
+
+    def test_graph_attr_dict(self):
+        """Tests that the graph attribute dictionary of the two graphs
+        is the same object.
+
+        """
+        assert self.G.graph is self.H.graph
+
+
+class CustomDictClass(UserDict):
+    pass
+
+
+class MultiGraphSubClass(nx.MultiGraph):
+    node_dict_factory = CustomDictClass  # type: ignore[assignment]
+    node_attr_dict_factory = CustomDictClass  # type: ignore[assignment]
+    adjlist_outer_dict_factory = CustomDictClass  # type: ignore[assignment]
+    adjlist_inner_dict_factory = CustomDictClass  # type: ignore[assignment]
+    edge_key_dict_factory = CustomDictClass  # type: ignore[assignment]
+    edge_attr_dict_factory = CustomDictClass  # type: ignore[assignment]
+    graph_attr_dict_factory = CustomDictClass  # type: ignore[assignment]
+
+
+class TestMultiGraphSubclass(TestMultiGraph):
+    def setup_method(self):
+        self.Graph = MultiGraphSubClass
+        # build K3
+        self.k3edges = [(0, 1), (0, 2), (1, 2)]
+        self.k3nodes = [0, 1, 2]
+        self.K3 = self.Graph()
+        self.K3._adj = self.K3.adjlist_outer_dict_factory(
+            {
+                0: self.K3.adjlist_inner_dict_factory(),
+                1: self.K3.adjlist_inner_dict_factory(),
+                2: self.K3.adjlist_inner_dict_factory(),
+            }
+        )
+        self.K3._pred = {0: {}, 1: {}, 2: {}}
+        for u in self.k3nodes:
+            for v in self.k3nodes:
+                if u != v:
+                    d = {0: {}}
+                    self.K3._adj[u][v] = d
+                    self.K3._adj[v][u] = d
+        self.K3._node = self.K3.node_dict_factory()
+        self.K3._node[0] = self.K3.node_attr_dict_factory()
+        self.K3._node[1] = self.K3.node_attr_dict_factory()
+        self.K3._node[2] = self.K3.node_attr_dict_factory()