two version of R2R are here HEAD master

1 files changed, 330 insertions, 0 deletions

diff --git a/.venv/lib/python3.12/site-packages/networkx/readwrite/json_graph/node_link.py b/.venv/lib/python3.12/site-packages/networkx/readwrite/json_graph/node_link.py
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+++ b/.venv/lib/python3.12/site-packages/networkx/readwrite/json_graph/node_link.py
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+import warnings
+from itertools import count
+
+import networkx as nx
+
+__all__ = ["node_link_data", "node_link_graph"]
+
+
+def _to_tuple(x):
+    """Converts lists to tuples, including nested lists.
+
+    All other non-list inputs are passed through unmodified. This function is
+    intended to be used to convert potentially nested lists from json files
+    into valid nodes.
+
+    Examples
+    --------
+    >>> _to_tuple([1, 2, [3, 4]])
+    (1, 2, (3, 4))
+    """
+    if not isinstance(x, tuple | list):
+        return x
+    return tuple(map(_to_tuple, x))
+
+
+def node_link_data(
+    G,
+    *,
+    source="source",
+    target="target",
+    name="id",
+    key="key",
+    edges=None,
+    nodes="nodes",
+    link=None,
+):
+    """Returns data in node-link format that is suitable for JSON serialization
+    and use in JavaScript documents.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+    source : string
+        A string that provides the 'source' attribute name for storing NetworkX-internal graph data.
+    target : string
+        A string that provides the 'target' attribute name for storing NetworkX-internal graph data.
+    name : string
+        A string that provides the 'name' attribute name for storing NetworkX-internal graph data.
+    key : string
+        A string that provides the 'key' attribute name for storing NetworkX-internal graph data.
+    edges : string
+        A string that provides the 'edges' attribute name for storing NetworkX-internal graph data.
+    nodes : string
+        A string that provides the 'nodes' attribute name for storing NetworkX-internal graph data.
+    link : string
+        .. deprecated:: 3.4
+
+           The `link` argument is deprecated and will be removed in version `3.6`.
+           Use the `edges` keyword instead.
+
+        A string that provides the 'edges' attribute name for storing NetworkX-internal graph data.
+
+    Returns
+    -------
+    data : dict
+       A dictionary with node-link formatted data.
+
+    Raises
+    ------
+    NetworkXError
+        If the values of 'source', 'target' and 'key' are not unique.
+
+    Examples
+    --------
+    >>> from pprint import pprint
+    >>> G = nx.Graph([("A", "B")])
+    >>> data1 = nx.node_link_data(G, edges="edges")
+    >>> pprint(data1)
+    {'directed': False,
+     'edges': [{'source': 'A', 'target': 'B'}],
+     'graph': {},
+     'multigraph': False,
+     'nodes': [{'id': 'A'}, {'id': 'B'}]}
+
+    To serialize with JSON
+
+    >>> import json
+    >>> s1 = json.dumps(data1)
+    >>> s1
+    '{"directed": false, "multigraph": false, "graph": {}, "nodes": [{"id": "A"}, {"id": "B"}], "edges": [{"source": "A", "target": "B"}]}'
+
+    A graph can also be serialized by passing `node_link_data` as an encoder function.
+
+    >>> s1 = json.dumps(G, default=nx.node_link_data)
+    >>> s1
+    '{"directed": false, "multigraph": false, "graph": {}, "nodes": [{"id": "A"}, {"id": "B"}], "links": [{"source": "A", "target": "B"}]}'
+
+    The attribute names for storing NetworkX-internal graph data can
+    be specified as keyword options.
+
+    >>> H = nx.gn_graph(2)
+    >>> data2 = nx.node_link_data(
+    ...     H, edges="links", source="from", target="to", nodes="vertices"
+    ... )
+    >>> pprint(data2)
+    {'directed': True,
+     'graph': {},
+     'links': [{'from': 1, 'to': 0}],
+     'multigraph': False,
+     'vertices': [{'id': 0}, {'id': 1}]}
+
+    Notes
+    -----
+    Graph, node, and link attributes are stored in this format.  Note that
+    attribute keys will be converted to strings in order to comply with JSON.
+
+    Attribute 'key' is only used for multigraphs.
+
+    To use `node_link_data` in conjunction with `node_link_graph`,
+    the keyword names for the attributes must match.
+
+    See Also
+    --------
+    node_link_graph, adjacency_data, tree_data
+    """
+    # TODO: Remove between the lines when `link` deprecation expires
+    # -------------------------------------------------------------
+    if link is not None:
+        warnings.warn(
+            "Keyword argument 'link' is deprecated; use 'edges' instead",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        if edges is not None:
+            raise ValueError(
+                "Both 'edges' and 'link' are specified. Use 'edges', 'link' will be remove in a future release"
+            )
+        else:
+            edges = link
+    else:
+        if edges is None:
+            warnings.warn(
+                (
+                    '\nThe default value will be `edges="edges" in NetworkX 3.6.\n\n'
+                    "To make this warning go away, explicitly set the edges kwarg, e.g.:\n\n"
+                    '  nx.node_link_data(G, edges="links") to preserve current behavior, or\n'
+                    '  nx.node_link_data(G, edges="edges") for forward compatibility.'
+                ),
+                FutureWarning,
+            )
+            edges = "links"
+    # ------------------------------------------------------------
+
+    multigraph = G.is_multigraph()
+
+    # Allow 'key' to be omitted from attrs if the graph is not a multigraph.
+    key = None if not multigraph else key
+    if len({source, target, key}) < 3:
+        raise nx.NetworkXError("Attribute names are not unique.")
+    data = {
+        "directed": G.is_directed(),
+        "multigraph": multigraph,
+        "graph": G.graph,
+        nodes: [{**G.nodes[n], name: n} for n in G],
+    }
+    if multigraph:
+        data[edges] = [
+            {**d, source: u, target: v, key: k}
+            for u, v, k, d in G.edges(keys=True, data=True)
+        ]
+    else:
+        data[edges] = [{**d, source: u, target: v} for u, v, d in G.edges(data=True)]
+    return data
+
+
+@nx._dispatchable(graphs=None, returns_graph=True)
+def node_link_graph(
+    data,
+    directed=False,
+    multigraph=True,
+    *,
+    source="source",
+    target="target",
+    name="id",
+    key="key",
+    edges=None,
+    nodes="nodes",
+    link=None,
+):
+    """Returns graph from node-link data format.
+
+    Useful for de-serialization from JSON.
+
+    Parameters
+    ----------
+    data : dict
+        node-link formatted graph data
+
+    directed : bool
+        If True, and direction not specified in data, return a directed graph.
+
+    multigraph : bool
+        If True, and multigraph not specified in data, return a multigraph.
+
+    source : string
+        A string that provides the 'source' attribute name for storing NetworkX-internal graph data.
+    target : string
+        A string that provides the 'target' attribute name for storing NetworkX-internal graph data.
+    name : string
+        A string that provides the 'name' attribute name for storing NetworkX-internal graph data.
+    key : string
+        A string that provides the 'key' attribute name for storing NetworkX-internal graph data.
+    edges : string
+        A string that provides the 'edges' attribute name for storing NetworkX-internal graph data.
+    nodes : string
+        A string that provides the 'nodes' attribute name for storing NetworkX-internal graph data.
+    link : string
+        .. deprecated:: 3.4
+
+           The `link` argument is deprecated and will be removed in version `3.6`.
+           Use the `edges` keyword instead.
+
+        A string that provides the 'edges' attribute name for storing NetworkX-internal graph data.
+
+    Returns
+    -------
+    G : NetworkX graph
+        A NetworkX graph object
+
+    Examples
+    --------
+
+    Create data in node-link format by converting a graph.
+
+    >>> from pprint import pprint
+    >>> G = nx.Graph([("A", "B")])
+    >>> data = nx.node_link_data(G, edges="edges")
+    >>> pprint(data)
+    {'directed': False,
+     'edges': [{'source': 'A', 'target': 'B'}],
+     'graph': {},
+     'multigraph': False,
+     'nodes': [{'id': 'A'}, {'id': 'B'}]}
+
+    Revert data in node-link format to a graph.
+
+    >>> H = nx.node_link_graph(data, edges="edges")
+    >>> print(H.edges)
+    [('A', 'B')]
+
+    To serialize and deserialize a graph with JSON,
+
+    >>> import json
+    >>> d = json.dumps(nx.node_link_data(G, edges="edges"))
+    >>> H = nx.node_link_graph(json.loads(d), edges="edges")
+    >>> print(G.edges, H.edges)
+    [('A', 'B')] [('A', 'B')]
+
+
+    Notes
+    -----
+    Attribute 'key' is only used for multigraphs.
+
+    To use `node_link_data` in conjunction with `node_link_graph`,
+    the keyword names for the attributes must match.
+
+    See Also
+    --------
+    node_link_data, adjacency_data, tree_data
+    """
+    # TODO: Remove between the lines when `link` deprecation expires
+    # -------------------------------------------------------------
+    if link is not None:
+        warnings.warn(
+            "Keyword argument 'link' is deprecated; use 'edges' instead",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        if edges is not None:
+            raise ValueError(
+                "Both 'edges' and 'link' are specified. Use 'edges', 'link' will be remove in a future release"
+            )
+        else:
+            edges = link
+    else:
+        if edges is None:
+            warnings.warn(
+                (
+                    '\nThe default value will be changed to `edges="edges" in NetworkX 3.6.\n\n'
+                    "To make this warning go away, explicitly set the edges kwarg, e.g.:\n\n"
+                    '  nx.node_link_graph(data, edges="links") to preserve current behavior, or\n'
+                    '  nx.node_link_graph(data, edges="edges") for forward compatibility.'
+                ),
+                FutureWarning,
+            )
+            edges = "links"
+    # -------------------------------------------------------------
+
+    multigraph = data.get("multigraph", multigraph)
+    directed = data.get("directed", directed)
+    if multigraph:
+        graph = nx.MultiGraph()
+    else:
+        graph = nx.Graph()
+    if directed:
+        graph = graph.to_directed()
+
+    # Allow 'key' to be omitted from attrs if the graph is not a multigraph.
+    key = None if not multigraph else key
+    graph.graph = data.get("graph", {})
+    c = count()
+    for d in data[nodes]:
+        node = _to_tuple(d.get(name, next(c)))
+        nodedata = {str(k): v for k, v in d.items() if k != name}
+        graph.add_node(node, **nodedata)
+    for d in data[edges]:
+        src = tuple(d[source]) if isinstance(d[source], list) else d[source]
+        tgt = tuple(d[target]) if isinstance(d[target], list) else d[target]
+        if not multigraph:
+            edgedata = {str(k): v for k, v in d.items() if k != source and k != target}
+            graph.add_edge(src, tgt, **edgedata)
+        else:
+            ky = d.get(key, None)
+            edgedata = {
+                str(k): v
+                for k, v in d.items()
+                if k != source and k != target and k != key
+            }
+            graph.add_edge(src, tgt, ky, **edgedata)
+    return graph