two version of R2R are hereHEADmaster

1 files changed, 1066 insertions, 0 deletions

diff --git a/.venv/lib/python3.12/site-packages/networkx/readwrite/gexf.py b/.venv/lib/python3.12/site-packages/networkx/readwrite/gexf.py
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+"""Read and write graphs in GEXF format.
+
+.. warning::
+    This parser uses the standard xml library present in Python, which is
+    insecure - see :external+python:mod:`xml` for additional information.
+    Only parse GEFX files you trust.
+
+GEXF (Graph Exchange XML Format) is a language for describing complex
+network structures, their associated data and dynamics.
+
+This implementation does not support mixed graphs (directed and
+undirected edges together).
+
+Format
+------
+GEXF is an XML format.  See http://gexf.net/schema.html for the
+specification and http://gexf.net/basic.html for examples.
+"""
+
+import itertools
+import time
+from xml.etree.ElementTree import (
+    Element,
+    ElementTree,
+    SubElement,
+    register_namespace,
+    tostring,
+)
+
+import networkx as nx
+from networkx.utils import open_file
+
+__all__ = ["write_gexf", "read_gexf", "relabel_gexf_graph", "generate_gexf"]
+
+
+@open_file(1, mode="wb")
+def write_gexf(G, path, encoding="utf-8", prettyprint=True, version="1.2draft"):
+    """Write G in GEXF format to path.
+
+    "GEXF (Graph Exchange XML Format) is a language for describing
+    complex networks structures, their associated data and dynamics" [1]_.
+
+    Node attributes are checked according to the version of the GEXF
+    schemas used for parameters which are not user defined,
+    e.g. visualization 'viz' [2]_. See example for usage.
+
+    Parameters
+    ----------
+    G : graph
+       A NetworkX graph
+    path : file or string
+       File or file name to write.
+       File names ending in .gz or .bz2 will be compressed.
+    encoding : string (optional, default: 'utf-8')
+       Encoding for text data.
+    prettyprint : bool (optional, default: True)
+       If True use line breaks and indenting in output XML.
+    version: string (optional, default: '1.2draft')
+       The version of GEXF to be used for nodes attributes checking
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_gexf(G, "test.gexf")
+
+    # visualization data
+    >>> G.nodes[0]["viz"] = {"size": 54}
+    >>> G.nodes[0]["viz"]["position"] = {"x": 0, "y": 1}
+    >>> G.nodes[0]["viz"]["color"] = {"r": 0, "g": 0, "b": 256}
+
+
+    Notes
+    -----
+    This implementation does not support mixed graphs (directed and undirected
+    edges together).
+
+    The node id attribute is set to be the string of the node label.
+    If you want to specify an id use set it as node data, e.g.
+    node['a']['id']=1 to set the id of node 'a' to 1.
+
+    References
+    ----------
+    .. [1] GEXF File Format, http://gexf.net/
+    .. [2] GEXF schema, http://gexf.net/schema.html
+    """
+    writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint, version=version)
+    writer.add_graph(G)
+    writer.write(path)
+
+
+def generate_gexf(G, encoding="utf-8", prettyprint=True, version="1.2draft"):
+    """Generate lines of GEXF format representation of G.
+
+    "GEXF (Graph Exchange XML Format) is a language for describing
+    complex networks structures, their associated data and dynamics" [1]_.
+
+    Parameters
+    ----------
+    G : graph
+    A NetworkX graph
+    encoding : string (optional, default: 'utf-8')
+    Encoding for text data.
+    prettyprint : bool (optional, default: True)
+    If True use line breaks and indenting in output XML.
+    version : string (default: 1.2draft)
+    Version of GEFX File Format (see http://gexf.net/schema.html)
+    Supported values: "1.1draft", "1.2draft"
+
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> linefeed = chr(10)  # linefeed=\n
+    >>> s = linefeed.join(nx.generate_gexf(G))
+    >>> for line in nx.generate_gexf(G):  # doctest: +SKIP
+    ...     print(line)
+
+    Notes
+    -----
+    This implementation does not support mixed graphs (directed and undirected
+    edges together).
+
+    The node id attribute is set to be the string of the node label.
+    If you want to specify an id use set it as node data, e.g.
+    node['a']['id']=1 to set the id of node 'a' to 1.
+
+    References
+    ----------
+    .. [1] GEXF File Format, https://gephi.org/gexf/format/
+    """
+    writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint, version=version)
+    writer.add_graph(G)
+    yield from str(writer).splitlines()
+
+
+@open_file(0, mode="rb")
+@nx._dispatchable(graphs=None, returns_graph=True)
+def read_gexf(path, node_type=None, relabel=False, version="1.2draft"):
+    """Read graph in GEXF format from path.
+
+    "GEXF (Graph Exchange XML Format) is a language for describing
+    complex networks structures, their associated data and dynamics" [1]_.
+
+    Parameters
+    ----------
+    path : file or string
+       File or file name to read.
+       File names ending in .gz or .bz2 will be decompressed.
+    node_type: Python type (default: None)
+       Convert node ids to this type if not None.
+    relabel : bool (default: False)
+       If True relabel the nodes to use the GEXF node "label" attribute
+       instead of the node "id" attribute as the NetworkX node label.
+    version : string (default: 1.2draft)
+    Version of GEFX File Format (see http://gexf.net/schema.html)
+       Supported values: "1.1draft", "1.2draft"
+
+    Returns
+    -------
+    graph: NetworkX graph
+        If no parallel edges are found a Graph or DiGraph is returned.
+        Otherwise a MultiGraph or MultiDiGraph is returned.
+
+    Notes
+    -----
+    This implementation does not support mixed graphs (directed and undirected
+    edges together).
+
+    References
+    ----------
+    .. [1] GEXF File Format, http://gexf.net/
+    """
+    reader = GEXFReader(node_type=node_type, version=version)
+    if relabel:
+        G = relabel_gexf_graph(reader(path))
+    else:
+        G = reader(path)
+    return G
+
+
+class GEXF:
+    versions = {
+        "1.1draft": {
+            "NS_GEXF": "http://www.gexf.net/1.1draft",
+            "NS_VIZ": "http://www.gexf.net/1.1draft/viz",
+            "NS_XSI": "http://www.w3.org/2001/XMLSchema-instance",
+            "SCHEMALOCATION": " ".join(
+                [
+                    "http://www.gexf.net/1.1draft",
+                    "http://www.gexf.net/1.1draft/gexf.xsd",
+                ]
+            ),
+            "VERSION": "1.1",
+        },
+        "1.2draft": {
+            "NS_GEXF": "http://www.gexf.net/1.2draft",
+            "NS_VIZ": "http://www.gexf.net/1.2draft/viz",
+            "NS_XSI": "http://www.w3.org/2001/XMLSchema-instance",
+            "SCHEMALOCATION": " ".join(
+                [
+                    "http://www.gexf.net/1.2draft",
+                    "http://www.gexf.net/1.2draft/gexf.xsd",
+                ]
+            ),
+            "VERSION": "1.2",
+        },
+    }
+
+    def construct_types(self):
+        types = [
+            (int, "integer"),
+            (float, "float"),
+            (float, "double"),
+            (bool, "boolean"),
+            (list, "string"),
+            (dict, "string"),
+            (int, "long"),
+            (str, "liststring"),
+            (str, "anyURI"),
+            (str, "string"),
+        ]
+
+        # These additions to types allow writing numpy types
+        try:
+            import numpy as np
+        except ImportError:
+            pass
+        else:
+            # prepend so that python types are created upon read (last entry wins)
+            types = [
+                (np.float64, "float"),
+                (np.float32, "float"),
+                (np.float16, "float"),
+                (np.int_, "int"),
+                (np.int8, "int"),
+                (np.int16, "int"),
+                (np.int32, "int"),
+                (np.int64, "int"),
+                (np.uint8, "int"),
+                (np.uint16, "int"),
+                (np.uint32, "int"),
+                (np.uint64, "int"),
+                (np.int_, "int"),
+                (np.intc, "int"),
+                (np.intp, "int"),
+            ] + types
+
+        self.xml_type = dict(types)
+        self.python_type = dict(reversed(a) for a in types)
+
+    # http://www.w3.org/TR/xmlschema-2/#boolean
+    convert_bool = {
+        "true": True,
+        "false": False,
+        "True": True,
+        "False": False,
+        "0": False,
+        0: False,
+        "1": True,
+        1: True,
+    }
+
+    def set_version(self, version):
+        d = self.versions.get(version)
+        if d is None:
+            raise nx.NetworkXError(f"Unknown GEXF version {version}.")
+        self.NS_GEXF = d["NS_GEXF"]
+        self.NS_VIZ = d["NS_VIZ"]
+        self.NS_XSI = d["NS_XSI"]
+        self.SCHEMALOCATION = d["SCHEMALOCATION"]
+        self.VERSION = d["VERSION"]
+        self.version = version
+
+
+class GEXFWriter(GEXF):
+    # class for writing GEXF format files
+    # use write_gexf() function
+    def __init__(
+        self, graph=None, encoding="utf-8", prettyprint=True, version="1.2draft"
+    ):
+        self.construct_types()
+        self.prettyprint = prettyprint
+        self.encoding = encoding
+        self.set_version(version)
+        self.xml = Element(
+            "gexf",
+            {
+                "xmlns": self.NS_GEXF,
+                "xmlns:xsi": self.NS_XSI,
+                "xsi:schemaLocation": self.SCHEMALOCATION,
+                "version": self.VERSION,
+            },
+        )
+
+        # Make meta element a non-graph element
+        # Also add lastmodifieddate as attribute, not tag
+        meta_element = Element("meta")
+        subelement_text = f"NetworkX {nx.__version__}"
+        SubElement(meta_element, "creator").text = subelement_text
+        meta_element.set("lastmodifieddate", time.strftime("%Y-%m-%d"))
+        self.xml.append(meta_element)
+
+        register_namespace("viz", self.NS_VIZ)
+
+        # counters for edge and attribute identifiers
+        self.edge_id = itertools.count()
+        self.attr_id = itertools.count()
+        self.all_edge_ids = set()
+        # default attributes are stored in dictionaries
+        self.attr = {}
+        self.attr["node"] = {}
+        self.attr["edge"] = {}
+        self.attr["node"]["dynamic"] = {}
+        self.attr["node"]["static"] = {}
+        self.attr["edge"]["dynamic"] = {}
+        self.attr["edge"]["static"] = {}
+
+        if graph is not None:
+            self.add_graph(graph)
+
+    def __str__(self):
+        if self.prettyprint:
+            self.indent(self.xml)
+        s = tostring(self.xml).decode(self.encoding)
+        return s
+
+    def add_graph(self, G):
+        # first pass through G collecting edge ids
+        for u, v, dd in G.edges(data=True):
+            eid = dd.get("id")
+            if eid is not None:
+                self.all_edge_ids.add(str(eid))
+        # set graph attributes
+        if G.graph.get("mode") == "dynamic":
+            mode = "dynamic"
+        else:
+            mode = "static"
+        # Add a graph element to the XML
+        if G.is_directed():
+            default = "directed"
+        else:
+            default = "undirected"
+        name = G.graph.get("name", "")
+        graph_element = Element("graph", defaultedgetype=default, mode=mode, name=name)
+        self.graph_element = graph_element
+        self.add_nodes(G, graph_element)
+        self.add_edges(G, graph_element)
+        self.xml.append(graph_element)
+
+    def add_nodes(self, G, graph_element):
+        nodes_element = Element("nodes")
+        for node, data in G.nodes(data=True):
+            node_data = data.copy()
+            node_id = str(node_data.pop("id", node))
+            kw = {"id": node_id}
+            label = str(node_data.pop("label", node))
+            kw["label"] = label
+            try:
+                pid = node_data.pop("pid")
+                kw["pid"] = str(pid)
+            except KeyError:
+                pass
+            try:
+                start = node_data.pop("start")
+                kw["start"] = str(start)
+                self.alter_graph_mode_timeformat(start)
+            except KeyError:
+                pass
+            try:
+                end = node_data.pop("end")
+                kw["end"] = str(end)
+                self.alter_graph_mode_timeformat(end)
+            except KeyError:
+                pass
+            # add node element with attributes
+            node_element = Element("node", **kw)
+            # add node element and attr subelements
+            default = G.graph.get("node_default", {})
+            node_data = self.add_parents(node_element, node_data)
+            if self.VERSION == "1.1":
+                node_data = self.add_slices(node_element, node_data)
+            else:
+                node_data = self.add_spells(node_element, node_data)
+            node_data = self.add_viz(node_element, node_data)
+            node_data = self.add_attributes("node", node_element, node_data, default)
+            nodes_element.append(node_element)
+        graph_element.append(nodes_element)
+
+    def add_edges(self, G, graph_element):
+        def edge_key_data(G):
+            # helper function to unify multigraph and graph edge iterator
+            if G.is_multigraph():
+                for u, v, key, data in G.edges(data=True, keys=True):
+                    edge_data = data.copy()
+                    edge_data.update(key=key)
+                    edge_id = edge_data.pop("id", None)
+                    if edge_id is None:
+                        edge_id = next(self.edge_id)
+                        while str(edge_id) in self.all_edge_ids:
+                            edge_id = next(self.edge_id)
+                        self.all_edge_ids.add(str(edge_id))
+                    yield u, v, edge_id, edge_data
+            else:
+                for u, v, data in G.edges(data=True):
+                    edge_data = data.copy()
+                    edge_id = edge_data.pop("id", None)
+                    if edge_id is None:
+                        edge_id = next(self.edge_id)
+                        while str(edge_id) in self.all_edge_ids:
+                            edge_id = next(self.edge_id)
+                        self.all_edge_ids.add(str(edge_id))
+                    yield u, v, edge_id, edge_data
+
+        edges_element = Element("edges")
+        for u, v, key, edge_data in edge_key_data(G):
+            kw = {"id": str(key)}
+            try:
+                edge_label = edge_data.pop("label")
+                kw["label"] = str(edge_label)
+            except KeyError:
+                pass
+            try:
+                edge_weight = edge_data.pop("weight")
+                kw["weight"] = str(edge_weight)
+            except KeyError:
+                pass
+            try:
+                edge_type = edge_data.pop("type")
+                kw["type"] = str(edge_type)
+            except KeyError:
+                pass
+            try:
+                start = edge_data.pop("start")
+                kw["start"] = str(start)
+                self.alter_graph_mode_timeformat(start)
+            except KeyError:
+                pass
+            try:
+                end = edge_data.pop("end")
+                kw["end"] = str(end)
+                self.alter_graph_mode_timeformat(end)
+            except KeyError:
+                pass
+            source_id = str(G.nodes[u].get("id", u))
+            target_id = str(G.nodes[v].get("id", v))
+            edge_element = Element("edge", source=source_id, target=target_id, **kw)
+            default = G.graph.get("edge_default", {})
+            if self.VERSION == "1.1":
+                edge_data = self.add_slices(edge_element, edge_data)
+            else:
+                edge_data = self.add_spells(edge_element, edge_data)
+            edge_data = self.add_viz(edge_element, edge_data)
+            edge_data = self.add_attributes("edge", edge_element, edge_data, default)
+            edges_element.append(edge_element)
+        graph_element.append(edges_element)
+
+    def add_attributes(self, node_or_edge, xml_obj, data, default):
+        # Add attrvalues to node or edge
+        attvalues = Element("attvalues")
+        if len(data) == 0:
+            return data
+        mode = "static"
+        for k, v in data.items():
+            # rename generic multigraph key to avoid any name conflict
+            if k == "key":
+                k = "networkx_key"
+            val_type = type(v)
+            if val_type not in self.xml_type:
+                raise TypeError(f"attribute value type is not allowed: {val_type}")
+            if isinstance(v, list):
+                # dynamic data
+                for val, start, end in v:
+                    val_type = type(val)
+                    if start is not None or end is not None:
+                        mode = "dynamic"
+                        self.alter_graph_mode_timeformat(start)
+                        self.alter_graph_mode_timeformat(end)
+                        break
+                attr_id = self.get_attr_id(
+                    str(k), self.xml_type[val_type], node_or_edge, default, mode
+                )
+                for val, start, end in v:
+                    e = Element("attvalue")
+                    e.attrib["for"] = attr_id
+                    e.attrib["value"] = str(val)
+                    # Handle nan, inf, -inf differently
+                    if val_type == float:
+                        if e.attrib["value"] == "inf":
+                            e.attrib["value"] = "INF"
+                        elif e.attrib["value"] == "nan":
+                            e.attrib["value"] = "NaN"
+                        elif e.attrib["value"] == "-inf":
+                            e.attrib["value"] = "-INF"
+                    if start is not None:
+                        e.attrib["start"] = str(start)
+                    if end is not None:
+                        e.attrib["end"] = str(end)
+                    attvalues.append(e)
+            else:
+                # static data
+                mode = "static"
+                attr_id = self.get_attr_id(
+                    str(k), self.xml_type[val_type], node_or_edge, default, mode
+                )
+                e = Element("attvalue")
+                e.attrib["for"] = attr_id
+                if isinstance(v, bool):
+                    e.attrib["value"] = str(v).lower()
+                else:
+                    e.attrib["value"] = str(v)
+                    # Handle float nan, inf, -inf differently
+                    if val_type == float:
+                        if e.attrib["value"] == "inf":
+                            e.attrib["value"] = "INF"
+                        elif e.attrib["value"] == "nan":
+                            e.attrib["value"] = "NaN"
+                        elif e.attrib["value"] == "-inf":
+                            e.attrib["value"] = "-INF"
+                attvalues.append(e)
+        xml_obj.append(attvalues)
+        return data
+
+    def get_attr_id(self, title, attr_type, edge_or_node, default, mode):
+        # find the id of the attribute or generate a new id
+        try:
+            return self.attr[edge_or_node][mode][title]
+        except KeyError:
+            # generate new id
+            new_id = str(next(self.attr_id))
+            self.attr[edge_or_node][mode][title] = new_id
+            attr_kwargs = {"id": new_id, "title": title, "type": attr_type}
+            attribute = Element("attribute", **attr_kwargs)
+            # add subelement for data default value if present
+            default_title = default.get(title)
+            if default_title is not None:
+                default_element = Element("default")
+                default_element.text = str(default_title)
+                attribute.append(default_element)
+            # new insert it into the XML
+            attributes_element = None
+            for a in self.graph_element.findall("attributes"):
+                # find existing attributes element by class and mode
+                a_class = a.get("class")
+                a_mode = a.get("mode", "static")
+                if a_class == edge_or_node and a_mode == mode:
+                    attributes_element = a
+            if attributes_element is None:
+                # create new attributes element
+                attr_kwargs = {"mode": mode, "class": edge_or_node}
+                attributes_element = Element("attributes", **attr_kwargs)
+                self.graph_element.insert(0, attributes_element)
+            attributes_element.append(attribute)
+        return new_id
+
+    def add_viz(self, element, node_data):
+        viz = node_data.pop("viz", False)
+        if viz:
+            color = viz.get("color")
+            if color is not None:
+                if self.VERSION == "1.1":
+                    e = Element(
+                        f"{{{self.NS_VIZ}}}color",
+                        r=str(color.get("r")),
+                        g=str(color.get("g")),
+                        b=str(color.get("b")),
+                    )
+                else:
+                    e = Element(
+                        f"{{{self.NS_VIZ}}}color",
+                        r=str(color.get("r")),
+                        g=str(color.get("g")),
+                        b=str(color.get("b")),
+                        a=str(color.get("a", 1.0)),
+                    )
+                element.append(e)
+
+            size = viz.get("size")
+            if size is not None:
+                e = Element(f"{{{self.NS_VIZ}}}size", value=str(size))
+                element.append(e)
+
+            thickness = viz.get("thickness")
+            if thickness is not None:
+                e = Element(f"{{{self.NS_VIZ}}}thickness", value=str(thickness))
+                element.append(e)
+
+            shape = viz.get("shape")
+            if shape is not None:
+                if shape.startswith("http"):
+                    e = Element(
+                        f"{{{self.NS_VIZ}}}shape", value="image", uri=str(shape)
+                    )
+                else:
+                    e = Element(f"{{{self.NS_VIZ}}}shape", value=str(shape))
+                element.append(e)
+
+            position = viz.get("position")
+            if position is not None:
+                e = Element(
+                    f"{{{self.NS_VIZ}}}position",
+                    x=str(position.get("x")),
+                    y=str(position.get("y")),
+                    z=str(position.get("z")),
+                )
+                element.append(e)
+        return node_data
+
+    def add_parents(self, node_element, node_data):
+        parents = node_data.pop("parents", False)
+        if parents:
+            parents_element = Element("parents")
+            for p in parents:
+                e = Element("parent")
+                e.attrib["for"] = str(p)
+                parents_element.append(e)
+            node_element.append(parents_element)
+        return node_data
+
+    def add_slices(self, node_or_edge_element, node_or_edge_data):
+        slices = node_or_edge_data.pop("slices", False)
+        if slices:
+            slices_element = Element("slices")
+            for start, end in slices:
+                e = Element("slice", start=str(start), end=str(end))
+                slices_element.append(e)
+            node_or_edge_element.append(slices_element)
+        return node_or_edge_data
+
+    def add_spells(self, node_or_edge_element, node_or_edge_data):
+        spells = node_or_edge_data.pop("spells", False)
+        if spells:
+            spells_element = Element("spells")
+            for start, end in spells:
+                e = Element("spell")
+                if start is not None:
+                    e.attrib["start"] = str(start)
+                    self.alter_graph_mode_timeformat(start)
+                if end is not None:
+                    e.attrib["end"] = str(end)
+                    self.alter_graph_mode_timeformat(end)
+                spells_element.append(e)
+            node_or_edge_element.append(spells_element)
+        return node_or_edge_data
+
+    def alter_graph_mode_timeformat(self, start_or_end):
+        # If 'start' or 'end' appears, alter Graph mode to dynamic and
+        # set timeformat
+        if self.graph_element.get("mode") == "static":
+            if start_or_end is not None:
+                if isinstance(start_or_end, str):
+                    timeformat = "date"
+                elif isinstance(start_or_end, float):
+                    timeformat = "double"
+                elif isinstance(start_or_end, int):
+                    timeformat = "long"
+                else:
+                    raise nx.NetworkXError(
+                        "timeformat should be of the type int, float or str"
+                    )
+                self.graph_element.set("timeformat", timeformat)
+                self.graph_element.set("mode", "dynamic")
+
+    def write(self, fh):
+        # Serialize graph G in GEXF to the open fh
+        if self.prettyprint:
+            self.indent(self.xml)
+        document = ElementTree(self.xml)
+        document.write(fh, encoding=self.encoding, xml_declaration=True)
+
+    def indent(self, elem, level=0):
+        # in-place prettyprint formatter
+        i = "\n" + "  " * level
+        if len(elem):
+            if not elem.text or not elem.text.strip():
+                elem.text = i + "  "
+            if not elem.tail or not elem.tail.strip():
+                elem.tail = i
+            for elem in elem:
+                self.indent(elem, level + 1)
+            if not elem.tail or not elem.tail.strip():
+                elem.tail = i
+        else:
+            if level and (not elem.tail or not elem.tail.strip()):
+                elem.tail = i
+
+
+class GEXFReader(GEXF):
+    # Class to read GEXF format files
+    # use read_gexf() function
+    def __init__(self, node_type=None, version="1.2draft"):
+        self.construct_types()
+        self.node_type = node_type
+        # assume simple graph and test for multigraph on read
+        self.simple_graph = True
+        self.set_version(version)
+
+    def __call__(self, stream):
+        self.xml = ElementTree(file=stream)
+        g = self.xml.find(f"{{{self.NS_GEXF}}}graph")
+        if g is not None:
+            return self.make_graph(g)
+        # try all the versions
+        for version in self.versions:
+            self.set_version(version)
+            g = self.xml.find(f"{{{self.NS_GEXF}}}graph")
+            if g is not None:
+                return self.make_graph(g)
+        raise nx.NetworkXError("No <graph> element in GEXF file.")
+
+    def make_graph(self, graph_xml):
+        # start with empty DiGraph or MultiDiGraph
+        edgedefault = graph_xml.get("defaultedgetype", None)
+        if edgedefault == "directed":
+            G = nx.MultiDiGraph()
+        else:
+            G = nx.MultiGraph()
+
+        # graph attributes
+        graph_name = graph_xml.get("name", "")
+        if graph_name != "":
+            G.graph["name"] = graph_name
+        graph_start = graph_xml.get("start")
+        if graph_start is not None:
+            G.graph["start"] = graph_start
+        graph_end = graph_xml.get("end")
+        if graph_end is not None:
+            G.graph["end"] = graph_end
+        graph_mode = graph_xml.get("mode", "")
+        if graph_mode == "dynamic":
+            G.graph["mode"] = "dynamic"
+        else:
+            G.graph["mode"] = "static"
+
+        # timeformat
+        self.timeformat = graph_xml.get("timeformat")
+        if self.timeformat == "date":
+            self.timeformat = "string"
+
+        # node and edge attributes
+        attributes_elements = graph_xml.findall(f"{{{self.NS_GEXF}}}attributes")
+        # dictionaries to hold attributes and attribute defaults
+        node_attr = {}
+        node_default = {}
+        edge_attr = {}
+        edge_default = {}
+        for a in attributes_elements:
+            attr_class = a.get("class")
+            if attr_class == "node":
+                na, nd = self.find_gexf_attributes(a)
+                node_attr.update(na)
+                node_default.update(nd)
+                G.graph["node_default"] = node_default
+            elif attr_class == "edge":
+                ea, ed = self.find_gexf_attributes(a)
+                edge_attr.update(ea)
+                edge_default.update(ed)
+                G.graph["edge_default"] = edge_default
+            else:
+                raise  # unknown attribute class
+
+        # Hack to handle Gephi0.7beta bug
+        # add weight attribute
+        ea = {"weight": {"type": "double", "mode": "static", "title": "weight"}}
+        ed = {}
+        edge_attr.update(ea)
+        edge_default.update(ed)
+        G.graph["edge_default"] = edge_default
+
+        # add nodes
+        nodes_element = graph_xml.find(f"{{{self.NS_GEXF}}}nodes")
+        if nodes_element is not None:
+            for node_xml in nodes_element.findall(f"{{{self.NS_GEXF}}}node"):
+                self.add_node(G, node_xml, node_attr)
+
+        # add edges
+        edges_element = graph_xml.find(f"{{{self.NS_GEXF}}}edges")
+        if edges_element is not None:
+            for edge_xml in edges_element.findall(f"{{{self.NS_GEXF}}}edge"):
+                self.add_edge(G, edge_xml, edge_attr)
+
+        # switch to Graph or DiGraph if no parallel edges were found.
+        if self.simple_graph:
+            if G.is_directed():
+                G = nx.DiGraph(G)
+            else:
+                G = nx.Graph(G)
+        return G
+
+    def add_node(self, G, node_xml, node_attr, node_pid=None):
+        # add a single node with attributes to the graph
+
+        # get attributes and subattributues for node
+        data = self.decode_attr_elements(node_attr, node_xml)
+        data = self.add_parents(data, node_xml)  # add any parents
+        if self.VERSION == "1.1":
+            data = self.add_slices(data, node_xml)  # add slices
+        else:
+            data = self.add_spells(data, node_xml)  # add spells
+        data = self.add_viz(data, node_xml)  # add viz
+        data = self.add_start_end(data, node_xml)  # add start/end
+
+        # find the node id and cast it to the appropriate type
+        node_id = node_xml.get("id")
+        if self.node_type is not None:
+            node_id = self.node_type(node_id)
+
+        # every node should have a label
+        node_label = node_xml.get("label")
+        data["label"] = node_label
+
+        # parent node id
+        node_pid = node_xml.get("pid", node_pid)
+        if node_pid is not None:
+            data["pid"] = node_pid
+
+        # check for subnodes, recursive
+        subnodes = node_xml.find(f"{{{self.NS_GEXF}}}nodes")
+        if subnodes is not None:
+            for node_xml in subnodes.findall(f"{{{self.NS_GEXF}}}node"):
+                self.add_node(G, node_xml, node_attr, node_pid=node_id)
+
+        G.add_node(node_id, **data)
+
+    def add_start_end(self, data, xml):
+        # start and end times
+        ttype = self.timeformat
+        node_start = xml.get("start")
+        if node_start is not None:
+            data["start"] = self.python_type[ttype](node_start)
+        node_end = xml.get("end")
+        if node_end is not None:
+            data["end"] = self.python_type[ttype](node_end)
+        return data
+
+    def add_viz(self, data, node_xml):
+        # add viz element for node
+        viz = {}
+        color = node_xml.find(f"{{{self.NS_VIZ}}}color")
+        if color is not None:
+            if self.VERSION == "1.1":
+                viz["color"] = {
+                    "r": int(color.get("r")),
+                    "g": int(color.get("g")),
+                    "b": int(color.get("b")),
+                }
+            else:
+                viz["color"] = {
+                    "r": int(color.get("r")),
+                    "g": int(color.get("g")),
+                    "b": int(color.get("b")),
+                    "a": float(color.get("a", 1)),
+                }
+
+        size = node_xml.find(f"{{{self.NS_VIZ}}}size")
+        if size is not None:
+            viz["size"] = float(size.get("value"))
+
+        thickness = node_xml.find(f"{{{self.NS_VIZ}}}thickness")
+        if thickness is not None:
+            viz["thickness"] = float(thickness.get("value"))
+
+        shape = node_xml.find(f"{{{self.NS_VIZ}}}shape")
+        if shape is not None:
+            viz["shape"] = shape.get("shape")
+            if viz["shape"] == "image":
+                viz["shape"] = shape.get("uri")
+
+        position = node_xml.find(f"{{{self.NS_VIZ}}}position")
+        if position is not None:
+            viz["position"] = {
+                "x": float(position.get("x", 0)),
+                "y": float(position.get("y", 0)),
+                "z": float(position.get("z", 0)),
+            }
+
+        if len(viz) > 0:
+            data["viz"] = viz
+        return data
+
+    def add_parents(self, data, node_xml):
+        parents_element = node_xml.find(f"{{{self.NS_GEXF}}}parents")
+        if parents_element is not None:
+            data["parents"] = []
+            for p in parents_element.findall(f"{{{self.NS_GEXF}}}parent"):
+                parent = p.get("for")
+                data["parents"].append(parent)
+        return data
+
+    def add_slices(self, data, node_or_edge_xml):
+        slices_element = node_or_edge_xml.find(f"{{{self.NS_GEXF}}}slices")
+        if slices_element is not None:
+            data["slices"] = []
+            for s in slices_element.findall(f"{{{self.NS_GEXF}}}slice"):
+                start = s.get("start")
+                end = s.get("end")
+                data["slices"].append((start, end))
+        return data
+
+    def add_spells(self, data, node_or_edge_xml):
+        spells_element = node_or_edge_xml.find(f"{{{self.NS_GEXF}}}spells")
+        if spells_element is not None:
+            data["spells"] = []
+            ttype = self.timeformat
+            for s in spells_element.findall(f"{{{self.NS_GEXF}}}spell"):
+                start = self.python_type[ttype](s.get("start"))
+                end = self.python_type[ttype](s.get("end"))
+                data["spells"].append((start, end))
+        return data
+
+    def add_edge(self, G, edge_element, edge_attr):
+        # add an edge to the graph
+
+        # raise error if we find mixed directed and undirected edges
+        edge_direction = edge_element.get("type")
+        if G.is_directed() and edge_direction == "undirected":
+            raise nx.NetworkXError("Undirected edge found in directed graph.")
+        if (not G.is_directed()) and edge_direction == "directed":
+            raise nx.NetworkXError("Directed edge found in undirected graph.")
+
+        # Get source and target and recast type if required
+        source = edge_element.get("source")
+        target = edge_element.get("target")
+        if self.node_type is not None:
+            source = self.node_type(source)
+            target = self.node_type(target)
+
+        data = self.decode_attr_elements(edge_attr, edge_element)
+        data = self.add_start_end(data, edge_element)
+
+        if self.VERSION == "1.1":
+            data = self.add_slices(data, edge_element)  # add slices
+        else:
+            data = self.add_spells(data, edge_element)  # add spells
+
+        # GEXF stores edge ids as an attribute
+        # NetworkX uses them as keys in multigraphs
+        # if networkx_key is not specified as an attribute
+        edge_id = edge_element.get("id")
+        if edge_id is not None:
+            data["id"] = edge_id
+
+        # check if there is a 'multigraph_key' and use that as edge_id
+        multigraph_key = data.pop("networkx_key", None)
+        if multigraph_key is not None:
+            edge_id = multigraph_key
+
+        weight = edge_element.get("weight")
+        if weight is not None:
+            data["weight"] = float(weight)
+
+        edge_label = edge_element.get("label")
+        if edge_label is not None:
+            data["label"] = edge_label
+
+        if G.has_edge(source, target):
+            # seen this edge before - this is a multigraph
+            self.simple_graph = False
+        G.add_edge(source, target, key=edge_id, **data)
+        if edge_direction == "mutual":
+            G.add_edge(target, source, key=edge_id, **data)
+
+    def decode_attr_elements(self, gexf_keys, obj_xml):
+        # Use the key information to decode the attr XML
+        attr = {}
+        # look for outer '<attvalues>' element
+        attr_element = obj_xml.find(f"{{{self.NS_GEXF}}}attvalues")
+        if attr_element is not None:
+            # loop over <attvalue> elements
+            for a in attr_element.findall(f"{{{self.NS_GEXF}}}attvalue"):
+                key = a.get("for")  # for is required
+                try:  # should be in our gexf_keys dictionary
+                    title = gexf_keys[key]["title"]
+                except KeyError as err:
+                    raise nx.NetworkXError(f"No attribute defined for={key}.") from err
+                atype = gexf_keys[key]["type"]
+                value = a.get("value")
+                if atype == "boolean":
+                    value = self.convert_bool[value]
+                else:
+                    value = self.python_type[atype](value)
+                if gexf_keys[key]["mode"] == "dynamic":
+                    # for dynamic graphs use list of three-tuples
+                    # [(value1,start1,end1), (value2,start2,end2), etc]
+                    ttype = self.timeformat
+                    start = self.python_type[ttype](a.get("start"))
+                    end = self.python_type[ttype](a.get("end"))
+                    if title in attr:
+                        attr[title].append((value, start, end))
+                    else:
+                        attr[title] = [(value, start, end)]
+                else:
+                    # for static graphs just assign the value
+                    attr[title] = value
+        return attr
+
+    def find_gexf_attributes(self, attributes_element):
+        # Extract all the attributes and defaults
+        attrs = {}
+        defaults = {}
+        mode = attributes_element.get("mode")
+        for k in attributes_element.findall(f"{{{self.NS_GEXF}}}attribute"):
+            attr_id = k.get("id")
+            title = k.get("title")
+            atype = k.get("type")
+            attrs[attr_id] = {"title": title, "type": atype, "mode": mode}
+            # check for the 'default' subelement of key element and add
+            default = k.find(f"{{{self.NS_GEXF}}}default")
+            if default is not None:
+                if atype == "boolean":
+                    value = self.convert_bool[default.text]
+                else:
+                    value = self.python_type[atype](default.text)
+                defaults[title] = value
+        return attrs, defaults
+
+
+def relabel_gexf_graph(G):
+    """Relabel graph using "label" node keyword for node label.
+
+    Parameters
+    ----------
+    G : graph
+       A NetworkX graph read from GEXF data
+
+    Returns
+    -------
+    H : graph
+      A NetworkX graph with relabeled nodes
+
+    Raises
+    ------
+    NetworkXError
+        If node labels are missing or not unique while relabel=True.
+
+    Notes
+    -----
+    This function relabels the nodes in a NetworkX graph with the
+    "label" attribute.  It also handles relabeling the specific GEXF
+    node attributes "parents", and "pid".
+    """
+    # build mapping of node labels, do some error checking
+    try:
+        mapping = [(u, G.nodes[u]["label"]) for u in G]
+    except KeyError as err:
+        raise nx.NetworkXError(
+            "Failed to relabel nodes: missing node labels found. Use relabel=False."
+        ) from err
+    x, y = zip(*mapping)
+    if len(set(y)) != len(G):
+        raise nx.NetworkXError(
+            "Failed to relabel nodes: "
+            "duplicate node labels found. "
+            "Use relabel=False."
+        )
+    mapping = dict(mapping)
+    H = nx.relabel_nodes(G, mapping)
+    # relabel attributes
+    for n in G:
+        m = mapping[n]
+        H.nodes[m]["id"] = n
+        H.nodes[m].pop("label")
+        if "pid" in H.nodes[m]:
+            H.nodes[m]["pid"] = mapping[G.nodes[n]["pid"]]
+        if "parents" in H.nodes[m]:
+            H.nodes[m]["parents"] = [mapping[p] for p in G.nodes[n]["parents"]]
+    return H