two version of R2R are hereHEADmaster

1 files changed, 557 insertions, 0 deletions

diff --git a/.venv/lib/python3.12/site-packages/networkx/readwrite/tests/test_gexf.py b/.venv/lib/python3.12/site-packages/networkx/readwrite/tests/test_gexf.py
new file mode 100644
index 00000000..6ff14c99
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/networkx/readwrite/tests/test_gexf.py
@@ -0,0 +1,557 @@
+import io
+import time
+
+import pytest
+
+import networkx as nx
+
+
+class TestGEXF:
+    @classmethod
+    def setup_class(cls):
+        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"
+
+    def test_write_with_node_attributes(self):
+        # Addresses #673.
+        G = nx.Graph()
+        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
+
+        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)])
+
+        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):
+        np = pytest.importorskip("numpy")
+        G = nx.path_graph(4)
+        nx.set_node_attributes(G, {n: n for n in np.arange(4)}, "number")
+        G[0][1]["edge-number"] = np.float64(1.1)
+
+        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", weight=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()
+        )
+
+        # Test missing alpha value for version >draft1.1 - set default alpha value
+        # to 1.0 instead of `None` when writing for better general compatibility
+        fh = io.BytesIO()
+        # G.nodes[0]["viz"]["color"] does not have an alpha value explicitly defined
+        # so the default is used instead
+        nx.write_gexf(G, fh, version="1.2draft")
+        fh.seek(0)
+        H = nx.read_gexf(fh, node_type=int)
+        assert H.nodes[0]["viz"]["color"]["a"] == 1.0
+
+        # 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()
+        )