Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/networkx/readwrite/tests/test_gexf.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/networkx/readwrite/tests/test_gexf.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,658 @@ +import io +import sys +import time +import pytest + +import networkx as nx + + +class TestGEXF: + @classmethod + def setup_class(cls): + _ = pytest.importorskip("xml.etree.ElementTree") + + cls.simple_directed_data = """<?xml version="1.0" encoding="UTF-8"?> +<gexf xmlns="http://www.gexf.net/1.2draft" version="1.2"> + <graph mode="static" defaultedgetype="directed"> + <nodes> + <node id="0" label="Hello" /> + <node id="1" label="Word" /> + </nodes> + <edges> + <edge id="0" source="0" target="1" /> + </edges> + </graph> +</gexf> +""" + cls.simple_directed_graph = nx.DiGraph() + cls.simple_directed_graph.add_node("0", label="Hello") + cls.simple_directed_graph.add_node("1", label="World") + cls.simple_directed_graph.add_edge("0", "1", id="0") + + cls.simple_directed_fh = io.BytesIO(cls.simple_directed_data.encode("UTF-8")) + + cls.attribute_data = """<?xml version="1.0" encoding="UTF-8"?>\ +<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi="http://www.w3.\ +org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.gexf.net/\ +1.2draft http://www.gexf.net/1.2draft/gexf.xsd" version="1.2"> + <meta lastmodifieddate="2009-03-20"> + <creator>Gephi.org</creator> + <description>A Web network</description> + </meta> + <graph defaultedgetype="directed"> + <attributes class="node"> + <attribute id="0" title="url" type="string"/> + <attribute id="1" title="indegree" type="integer"/> + <attribute id="2" title="frog" type="boolean"> + <default>true</default> + </attribute> + </attributes> + <nodes> + <node id="0" label="Gephi"> + <attvalues> + <attvalue for="0" value="https://gephi.org"/> + <attvalue for="1" value="1"/> + <attvalue for="2" value="false"/> + </attvalues> + </node> + <node id="1" label="Webatlas"> + <attvalues> + <attvalue for="0" value="http://webatlas.fr"/> + <attvalue for="1" value="2"/> + <attvalue for="2" value="false"/> + </attvalues> + </node> + <node id="2" label="RTGI"> + <attvalues> + <attvalue for="0" value="http://rtgi.fr"/> + <attvalue for="1" value="1"/> + <attvalue for="2" value="true"/> + </attvalues> + </node> + <node id="3" label="BarabasiLab"> + <attvalues> + <attvalue for="0" value="http://barabasilab.com"/> + <attvalue for="1" value="1"/> + <attvalue for="2" value="true"/> + </attvalues> + </node> + </nodes> + <edges> + <edge id="0" source="0" target="1" label="foo"/> + <edge id="1" source="0" target="2"/> + <edge id="2" source="1" target="0"/> + <edge id="3" source="2" target="1"/> + <edge id="4" source="0" target="3"/> + </edges> + </graph> +</gexf> +""" + cls.attribute_graph = nx.DiGraph() + cls.attribute_graph.graph["node_default"] = {"frog": True} + cls.attribute_graph.add_node( + "0", label="Gephi", url="https://gephi.org", indegree=1, frog=False + ) + cls.attribute_graph.add_node( + "1", label="Webatlas", url="http://webatlas.fr", indegree=2, frog=False + ) + cls.attribute_graph.add_node( + "2", label="RTGI", url="http://rtgi.fr", indegree=1, frog=True + ) + cls.attribute_graph.add_node( + "3", + label="BarabasiLab", + url="http://barabasilab.com", + indegree=1, + frog=True, + ) + cls.attribute_graph.add_edge("0", "1", id="0", label="foo") + cls.attribute_graph.add_edge("0", "2", id="1") + cls.attribute_graph.add_edge("1", "0", id="2") + cls.attribute_graph.add_edge("2", "1", id="3") + cls.attribute_graph.add_edge("0", "3", id="4") + cls.attribute_fh = io.BytesIO(cls.attribute_data.encode("UTF-8")) + + cls.simple_undirected_data = """<?xml version="1.0" encoding="UTF-8"?> +<gexf xmlns="http://www.gexf.net/1.2draft" version="1.2"> + <graph mode="static" defaultedgetype="undirected"> + <nodes> + <node id="0" label="Hello" /> + <node id="1" label="Word" /> + </nodes> + <edges> + <edge id="0" source="0" target="1" /> + </edges> + </graph> +</gexf> +""" + cls.simple_undirected_graph = nx.Graph() + cls.simple_undirected_graph.add_node("0", label="Hello") + cls.simple_undirected_graph.add_node("1", label="World") + cls.simple_undirected_graph.add_edge("0", "1", id="0") + + cls.simple_undirected_fh = io.BytesIO( + cls.simple_undirected_data.encode("UTF-8") + ) + + def test_read_simple_directed_graphml(self): + G = self.simple_directed_graph + H = nx.read_gexf(self.simple_directed_fh) + assert sorted(G.nodes()) == sorted(H.nodes()) + assert sorted(G.edges()) == sorted(H.edges()) + assert sorted(G.edges(data=True)) == sorted(H.edges(data=True)) + self.simple_directed_fh.seek(0) + + def test_write_read_simple_directed_graphml(self): + G = self.simple_directed_graph + fh = io.BytesIO() + nx.write_gexf(G, fh) + fh.seek(0) + H = nx.read_gexf(fh) + assert sorted(G.nodes()) == sorted(H.nodes()) + assert sorted(G.edges()) == sorted(H.edges()) + assert sorted(G.edges(data=True)) == sorted(H.edges(data=True)) + self.simple_directed_fh.seek(0) + + def test_read_simple_undirected_graphml(self): + G = self.simple_undirected_graph + H = nx.read_gexf(self.simple_undirected_fh) + assert sorted(G.nodes()) == sorted(H.nodes()) + assert sorted(sorted(e) for e in G.edges()) == sorted( + sorted(e) for e in H.edges() + ) + self.simple_undirected_fh.seek(0) + + def test_read_attribute_graphml(self): + G = self.attribute_graph + H = nx.read_gexf(self.attribute_fh) + assert sorted(G.nodes(True)) == sorted(H.nodes(data=True)) + ge = sorted(G.edges(data=True)) + he = sorted(H.edges(data=True)) + for a, b in zip(ge, he): + assert a == b + self.attribute_fh.seek(0) + + def test_directed_edge_in_undirected(self): + s = """<?xml version="1.0" encoding="UTF-8"?> +<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'> + <graph mode="static" defaultedgetype="undirected" name=""> + <nodes> + <node id="0" label="Hello" /> + <node id="1" label="Word" /> + </nodes> + <edges> + <edge id="0" source="0" target="1" type="directed"/> + </edges> + </graph> +</gexf> +""" + fh = io.BytesIO(s.encode("UTF-8")) + pytest.raises(nx.NetworkXError, nx.read_gexf, fh) + + def test_undirected_edge_in_directed(self): + s = """<?xml version="1.0" encoding="UTF-8"?> +<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'> + <graph mode="static" defaultedgetype="directed" name=""> + <nodes> + <node id="0" label="Hello" /> + <node id="1" label="Word" /> + </nodes> + <edges> + <edge id="0" source="0" target="1" type="undirected"/> + </edges> + </graph> +</gexf> +""" + fh = io.BytesIO(s.encode("UTF-8")) + pytest.raises(nx.NetworkXError, nx.read_gexf, fh) + + def test_key_raises(self): + s = """<?xml version="1.0" encoding="UTF-8"?> +<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'> + <graph mode="static" defaultedgetype="directed" name=""> + <nodes> + <node id="0" label="Hello"> + <attvalues> + <attvalue for='0' value='1'/> + </attvalues> + </node> + <node id="1" label="Word" /> + </nodes> + <edges> + <edge id="0" source="0" target="1" type="undirected"/> + </edges> + </graph> +</gexf> +""" + fh = io.BytesIO(s.encode("UTF-8")) + pytest.raises(nx.NetworkXError, nx.read_gexf, fh) + + def test_relabel(self): + s = """<?xml version="1.0" encoding="UTF-8"?> +<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'> + <graph mode="static" defaultedgetype="directed" name=""> + <nodes> + <node id="0" label="Hello" /> + <node id="1" label="Word" /> + </nodes> + <edges> + <edge id="0" source="0" target="1"/> + </edges> + </graph> +</gexf> +""" + fh = io.BytesIO(s.encode("UTF-8")) + G = nx.read_gexf(fh, relabel=True) + assert sorted(G.nodes()) == ["Hello", "Word"] + + def test_default_attribute(self): + G = nx.Graph() + G.add_node(1, label="1", color="green") + nx.add_path(G, [0, 1, 2, 3]) + G.add_edge(1, 2, foo=3) + G.graph["node_default"] = {"color": "yellow"} + G.graph["edge_default"] = {"foo": 7} + fh = io.BytesIO() + nx.write_gexf(G, fh) + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + assert sorted(G.nodes()) == sorted(H.nodes()) + assert sorted(sorted(e) for e in G.edges()) == sorted( + sorted(e) for e in H.edges() + ) + # Reading a gexf graph always sets mode attribute to either + # 'static' or 'dynamic'. Remove the mode attribute from the + # read graph for the sake of comparing remaining attributes. + del H.graph["mode"] + assert G.graph == H.graph + + def test_serialize_ints_to_strings(self): + G = nx.Graph() + G.add_node(1, id=7, label=77) + fh = io.BytesIO() + nx.write_gexf(G, fh) + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + assert list(H) == [7] + assert H.nodes[7]["label"] == "77" + + # FIXME: We should test xml without caring about their order This is causing a + # problem b/c of a change in Python 3.8 + # + # "Prior to Python 3.8, the serialisation order of the XML attributes of + # elements was artificially made predictable by sorting the attributes by their + # name. Based on the now guaranteed ordering of dicts, this arbitrary + # reordering was removed in Python 3.8 to preserve the order in which + # attributes were originally parsed or created by user code." + # + # https://docs.python.org/3.8/library/xml.etree.elementtree.html + # https://bugs.python.org/issue34160 + + def test_write_with_node_attributes(self): + # Addresses #673. + G = nx.OrderedGraph() + G.add_edges_from([(0, 1), (1, 2), (2, 3)]) + for i in range(4): + G.nodes[i]["id"] = i + G.nodes[i]["label"] = i + G.nodes[i]["pid"] = i + G.nodes[i]["start"] = i + G.nodes[i]["end"] = i + 1 + + if sys.version_info < (3, 8): + expected = f"""<gexf version="1.2" xmlns="http://www.gexf.net/1.2\ +draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:\ +schemaLocation="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/\ +gexf.xsd"> + <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}"> + <creator>NetworkX {nx.__version__}</creator> + </meta> + <graph defaultedgetype="undirected" mode="dynamic" name="" timeformat="long"> + <nodes> + <node end="1" id="0" label="0" pid="0" start="0" /> + <node end="2" id="1" label="1" pid="1" start="1" /> + <node end="3" id="2" label="2" pid="2" start="2" /> + <node end="4" id="3" label="3" pid="3" start="3" /> + </nodes> + <edges> + <edge id="0" source="0" target="1" /> + <edge id="1" source="1" target="2" /> + <edge id="2" source="2" target="3" /> + </edges> + </graph> +</gexf>""" + else: + expected = f"""<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi\ +="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation=\ +"http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/\ +gexf.xsd" version="1.2"> + <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}"> + <creator>NetworkX {nx.__version__}</creator> + </meta> + <graph defaultedgetype="undirected" mode="dynamic" name="" timeformat="long"> + <nodes> + <node id="0" label="0" pid="0" start="0" end="1" /> + <node id="1" label="1" pid="1" start="1" end="2" /> + <node id="2" label="2" pid="2" start="2" end="3" /> + <node id="3" label="3" pid="3" start="3" end="4" /> + </nodes> + <edges> + <edge source="0" target="1" id="0" /> + <edge source="1" target="2" id="1" /> + <edge source="2" target="3" id="2" /> + </edges> + </graph> +</gexf>""" + obtained = "\n".join(nx.generate_gexf(G)) + assert expected == obtained + + def test_edge_id_construct(self): + G = nx.Graph() + G.add_edges_from([(0, 1, {"id": 0}), (1, 2, {"id": 2}), (2, 3)]) + + if sys.version_info < (3, 8): + expected = f"""<gexf version="1.2" xmlns="http://www.gexf.net/\ +1.2draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:\ +schemaLocation="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/\ +gexf.xsd"> + <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}"> + <creator>NetworkX {nx.__version__}</creator> + </meta> + <graph defaultedgetype="undirected" mode="static" name=""> + <nodes> + <node id="0" label="0" /> + <node id="1" label="1" /> + <node id="2" label="2" /> + <node id="3" label="3" /> + </nodes> + <edges> + <edge id="0" source="0" target="1" /> + <edge id="2" source="1" target="2" /> + <edge id="1" source="2" target="3" /> + </edges> + </graph> +</gexf>""" + else: + expected = f"""<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi\ +="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.\ +gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd" version="1.2"> + <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}"> + <creator>NetworkX {nx.__version__}</creator> + </meta> + <graph defaultedgetype="undirected" mode="static" name=""> + <nodes> + <node id="0" label="0" /> + <node id="1" label="1" /> + <node id="2" label="2" /> + <node id="3" label="3" /> + </nodes> + <edges> + <edge source="0" target="1" id="0" /> + <edge source="1" target="2" id="2" /> + <edge source="2" target="3" id="1" /> + </edges> + </graph> +</gexf>""" + + obtained = "\n".join(nx.generate_gexf(G)) + assert expected == obtained + + def test_numpy_type(self): + G = nx.path_graph(4) + try: + import numpy + except ImportError: + return + nx.set_node_attributes(G, {n: n for n in numpy.arange(4)}, "number") + G[0][1]["edge-number"] = numpy.float64(1.1) + + if sys.version_info < (3, 8): + expected = f"""<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft"\ + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation\ +="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd"> + <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}"> + <creator>NetworkX {nx.__version__}</creator> + </meta> + <graph defaultedgetype="undirected" mode="static" name=""> + <attributes class="edge" mode="static"> + <attribute id="1" title="edge-number" type="float" /> + </attributes> + <attributes class="node" mode="static"> + <attribute id="0" title="number" type="int" /> + </attributes> + <nodes> + <node id="0" label="0"> + <attvalues> + <attvalue for="0" value="0" /> + </attvalues> + </node> + <node id="1" label="1"> + <attvalues> + <attvalue for="0" value="1" /> + </attvalues> + </node> + <node id="2" label="2"> + <attvalues> + <attvalue for="0" value="2" /> + </attvalues> + </node> + <node id="3" label="3"> + <attvalues> + <attvalue for="0" value="3" /> + </attvalues> + </node> + </nodes> + <edges> + <edge id="0" source="0" target="1"> + <attvalues> + <attvalue for="1" value="1.1" /> + </attvalues> + </edge> + <edge id="1" source="1" target="2" /> + <edge id="2" source="2" target="3" /> + </edges> + </graph> +</gexf>""" + else: + expected = f"""<gexf xmlns="http://www.gexf.net/1.2draft"\ + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation\ +="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd"\ + version="1.2"> + <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}"> + <creator>NetworkX {nx.__version__}</creator> + </meta> + <graph defaultedgetype="undirected" mode="static" name=""> + <attributes mode="static" class="edge"> + <attribute id="1" title="edge-number" type="float" /> + </attributes> + <attributes mode="static" class="node"> + <attribute id="0" title="number" type="int" /> + </attributes> + <nodes> + <node id="0" label="0"> + <attvalues> + <attvalue for="0" value="0" /> + </attvalues> + </node> + <node id="1" label="1"> + <attvalues> + <attvalue for="0" value="1" /> + </attvalues> + </node> + <node id="2" label="2"> + <attvalues> + <attvalue for="0" value="2" /> + </attvalues> + </node> + <node id="3" label="3"> + <attvalues> + <attvalue for="0" value="3" /> + </attvalues> + </node> + </nodes> + <edges> + <edge source="0" target="1" id="0"> + <attvalues> + <attvalue for="1" value="1.1" /> + </attvalues> + </edge> + <edge source="1" target="2" id="1" /> + <edge source="2" target="3" id="2" /> + </edges> + </graph> +</gexf>""" + obtained = "\n".join(nx.generate_gexf(G)) + assert expected == obtained + + def test_bool(self): + G = nx.Graph() + G.add_node(1, testattr=True) + fh = io.BytesIO() + nx.write_gexf(G, fh) + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + assert H.nodes[1]["testattr"] + + # Test for NaN, INF and -INF + def test_specials(self): + from math import isnan + + inf, nan = float("inf"), float("nan") + G = nx.Graph() + G.add_node(1, testattr=inf, strdata="inf", key="a") + G.add_node(2, testattr=nan, strdata="nan", key="b") + G.add_node(3, testattr=-inf, strdata="-inf", key="c") + + fh = io.BytesIO() + nx.write_gexf(G, fh) + fh.seek(0) + filetext = fh.read() + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + + assert b"INF" in filetext + assert b"NaN" in filetext + assert b"-INF" in filetext + + assert H.nodes[1]["testattr"] == inf + assert isnan(H.nodes[2]["testattr"]) + assert H.nodes[3]["testattr"] == -inf + + assert H.nodes[1]["strdata"] == "inf" + assert H.nodes[2]["strdata"] == "nan" + assert H.nodes[3]["strdata"] == "-inf" + + assert H.nodes[1]["networkx_key"] == "a" + assert H.nodes[2]["networkx_key"] == "b" + assert H.nodes[3]["networkx_key"] == "c" + + def test_simple_list(self): + G = nx.Graph() + list_value = [(1, 2, 3), (9, 1, 2)] + G.add_node(1, key=list_value) + fh = io.BytesIO() + nx.write_gexf(G, fh) + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + assert H.nodes[1]["networkx_key"] == list_value + + def test_dynamic_mode(self): + G = nx.Graph() + G.add_node(1, label="1", color="green") + G.graph["mode"] = "dynamic" + fh = io.BytesIO() + nx.write_gexf(G, fh) + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + assert sorted(G.nodes()) == sorted(H.nodes()) + assert sorted(sorted(e) for e in G.edges()) == sorted( + sorted(e) for e in H.edges() + ) + + def test_multigraph_with_missing_attributes(self): + G = nx.MultiGraph() + G.add_node(0, label="1", color="green") + G.add_node(1, label="2", color="green") + G.add_edge(0, 1, id="0", wight=3, type="undirected", start=0, end=1) + G.add_edge(0, 1, id="1", label="foo", start=0, end=1) + G.add_edge(0, 1) + fh = io.BytesIO() + nx.write_gexf(G, fh) + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + assert sorted(G.nodes()) == sorted(H.nodes()) + assert sorted(sorted(e) for e in G.edges()) == sorted( + sorted(e) for e in H.edges() + ) + + def test_missing_viz_attributes(self): + G = nx.Graph() + G.add_node(0, label="1", color="green") + G.nodes[0]["viz"] = {"size": 54} + G.nodes[0]["viz"]["position"] = {"x": 0, "y": 1, "z": 0} + G.nodes[0]["viz"]["color"] = {"r": 0, "g": 0, "b": 256} + G.nodes[0]["viz"]["shape"] = "http://random.url" + G.nodes[0]["viz"]["thickness"] = 2 + fh = io.BytesIO() + nx.write_gexf(G, fh, version="1.1draft") + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + assert sorted(G.nodes()) == sorted(H.nodes()) + assert sorted(sorted(e) for e in G.edges()) == sorted( + sorted(e) for e in H.edges() + ) + + # Second graph for the other branch + G = nx.Graph() + G.add_node(0, label="1", color="green") + G.nodes[0]["viz"] = {"size": 54} + G.nodes[0]["viz"]["position"] = {"x": 0, "y": 1, "z": 0} + G.nodes[0]["viz"]["color"] = {"r": 0, "g": 0, "b": 256, "a": 0.5} + G.nodes[0]["viz"]["shape"] = "ftp://random.url" + G.nodes[0]["viz"]["thickness"] = 2 + fh = io.BytesIO() + nx.write_gexf(G, fh) + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + assert sorted(G.nodes()) == sorted(H.nodes()) + assert sorted(sorted(e) for e in G.edges()) == sorted( + sorted(e) for e in H.edges() + ) + + def test_slice_and_spell(self): + # Test spell first, so version = 1.2 + G = nx.Graph() + G.add_node(0, label="1", color="green") + G.nodes[0]["spells"] = [(1, 2)] + fh = io.BytesIO() + nx.write_gexf(G, fh) + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + assert sorted(G.nodes()) == sorted(H.nodes()) + assert sorted(sorted(e) for e in G.edges()) == sorted( + sorted(e) for e in H.edges() + ) + + G = nx.Graph() + G.add_node(0, label="1", color="green") + G.nodes[0]["slices"] = [(1, 2)] + fh = io.BytesIO() + nx.write_gexf(G, fh, version="1.1draft") + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + assert sorted(G.nodes()) == sorted(H.nodes()) + assert sorted(sorted(e) for e in G.edges()) == sorted( + sorted(e) for e in H.edges() + ) + + def test_add_parent(self): + G = nx.Graph() + G.add_node(0, label="1", color="green", parents=[1, 2]) + fh = io.BytesIO() + nx.write_gexf(G, fh) + fh.seek(0) + H = nx.read_gexf(fh, node_type=int) + assert sorted(G.nodes()) == sorted(H.nodes()) + assert sorted(sorted(e) for e in G.edges()) == sorted( + sorted(e) for e in H.edges() + )