diff env/lib/python3.9/site-packages/networkx/drawing/nx_pydot.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/networkx/drawing/nx_pydot.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,338 @@
+"""
+*****
+Pydot
+*****
+
+Import and export NetworkX graphs in Graphviz dot format using pydot.
+
+Either this module or nx_agraph can be used to interface with graphviz.
+
+See Also
+--------
+pydot:         https://github.com/erocarrera/pydot
+Graphviz:      https://www.graphviz.org
+DOT Language:  http://www.graphviz.org/doc/info/lang.html
+"""
+from locale import getpreferredencoding
+from networkx.utils import open_file
+import networkx as nx
+
+__all__ = [
+    "write_dot",
+    "read_dot",
+    "graphviz_layout",
+    "pydot_layout",
+    "to_pydot",
+    "from_pydot",
+]
+
+
+@open_file(1, mode="w")
+def write_dot(G, path):
+    """Write NetworkX graph G to Graphviz dot format on path.
+
+    Path can be a string or a file handle.
+    """
+    P = to_pydot(G)
+    path.write(P.to_string())
+    return
+
+
+@open_file(0, mode="r")
+def read_dot(path):
+    """Returns a NetworkX :class:`MultiGraph` or :class:`MultiDiGraph` from the
+    dot file with the passed path.
+
+    If this file contains multiple graphs, only the first such graph is
+    returned. All graphs _except_ the first are silently ignored.
+
+    Parameters
+    ----------
+    path : str or file
+        Filename or file handle.
+
+    Returns
+    -------
+    G : MultiGraph or MultiDiGraph
+        A :class:`MultiGraph` or :class:`MultiDiGraph`.
+
+    Notes
+    -----
+    Use `G = nx.Graph(read_dot(path))` to return a :class:`Graph` instead of a
+    :class:`MultiGraph`.
+    """
+    import pydot
+
+    data = path.read()
+
+    # List of one or more "pydot.Dot" instances deserialized from this file.
+    P_list = pydot.graph_from_dot_data(data)
+
+    # Convert only the first such instance into a NetworkX graph.
+    return from_pydot(P_list[0])
+
+
+def from_pydot(P):
+    """Returns a NetworkX graph from a Pydot graph.
+
+    Parameters
+    ----------
+    P : Pydot graph
+      A graph created with Pydot
+
+    Returns
+    -------
+    G : NetworkX multigraph
+        A MultiGraph or MultiDiGraph.
+
+    Examples
+    --------
+    >>> K5 = nx.complete_graph(5)
+    >>> A = nx.nx_pydot.to_pydot(K5)
+    >>> G = nx.nx_pydot.from_pydot(A)  # return MultiGraph
+
+    # make a Graph instead of MultiGraph
+    >>> G = nx.Graph(nx.nx_pydot.from_pydot(A))
+
+    """
+    if P.get_strict(None):  # pydot bug: get_strict() shouldn't take argument
+        multiedges = False
+    else:
+        multiedges = True
+
+    if P.get_type() == "graph":  # undirected
+        if multiedges:
+            N = nx.MultiGraph()
+        else:
+            N = nx.Graph()
+    else:
+        if multiedges:
+            N = nx.MultiDiGraph()
+        else:
+            N = nx.DiGraph()
+
+    # assign defaults
+    name = P.get_name().strip('"')
+    if name != "":
+        N.name = name
+
+    # add nodes, attributes to N.node_attr
+    for p in P.get_node_list():
+        n = p.get_name().strip('"')
+        if n in ("node", "graph", "edge"):
+            continue
+        N.add_node(n, **p.get_attributes())
+
+    # add edges
+    for e in P.get_edge_list():
+        u = e.get_source()
+        v = e.get_destination()
+        attr = e.get_attributes()
+        s = []
+        d = []
+
+        if isinstance(u, str):
+            s.append(u.strip('"'))
+        else:
+            for unodes in u["nodes"]:
+                s.append(unodes.strip('"'))
+
+        if isinstance(v, str):
+            d.append(v.strip('"'))
+        else:
+            for vnodes in v["nodes"]:
+                d.append(vnodes.strip('"'))
+
+        for source_node in s:
+            for destination_node in d:
+                N.add_edge(source_node, destination_node, **attr)
+
+    # add default attributes for graph, nodes, edges
+    pattr = P.get_attributes()
+    if pattr:
+        N.graph["graph"] = pattr
+    try:
+        N.graph["node"] = P.get_node_defaults()[0]
+    except (IndexError, TypeError):
+        pass  # N.graph['node']={}
+    try:
+        N.graph["edge"] = P.get_edge_defaults()[0]
+    except (IndexError, TypeError):
+        pass  # N.graph['edge']={}
+    return N
+
+
+def to_pydot(N):
+    """Returns a pydot graph from a NetworkX graph N.
+
+    Parameters
+    ----------
+    N : NetworkX graph
+      A graph created with NetworkX
+
+    Examples
+    --------
+    >>> K5 = nx.complete_graph(5)
+    >>> P = nx.nx_pydot.to_pydot(K5)
+
+    Notes
+    -----
+
+    """
+    import pydot
+
+    # set Graphviz graph type
+    if N.is_directed():
+        graph_type = "digraph"
+    else:
+        graph_type = "graph"
+    strict = nx.number_of_selfloops(N) == 0 and not N.is_multigraph()
+
+    name = N.name
+    graph_defaults = N.graph.get("graph", {})
+    if name == "":
+        P = pydot.Dot("", graph_type=graph_type, strict=strict, **graph_defaults)
+    else:
+        P = pydot.Dot(
+            f'"{name}"', graph_type=graph_type, strict=strict, **graph_defaults
+        )
+    try:
+        P.set_node_defaults(**N.graph["node"])
+    except KeyError:
+        pass
+    try:
+        P.set_edge_defaults(**N.graph["edge"])
+    except KeyError:
+        pass
+
+    for n, nodedata in N.nodes(data=True):
+        str_nodedata = {k: str(v) for k, v in nodedata.items()}
+        p = pydot.Node(str(n), **str_nodedata)
+        P.add_node(p)
+
+    if N.is_multigraph():
+        for u, v, key, edgedata in N.edges(data=True, keys=True):
+            str_edgedata = {k: str(v) for k, v in edgedata.items() if k != "key"}
+            edge = pydot.Edge(str(u), str(v), key=str(key), **str_edgedata)
+            P.add_edge(edge)
+
+    else:
+        for u, v, edgedata in N.edges(data=True):
+            str_edgedata = {k: str(v) for k, v in edgedata.items()}
+            edge = pydot.Edge(str(u), str(v), **str_edgedata)
+            P.add_edge(edge)
+    return P
+
+
+def graphviz_layout(G, prog="neato", root=None):
+    """Create node positions using Pydot and Graphviz.
+
+    Returns a dictionary of positions keyed by node.
+
+    Parameters
+    ----------
+    G : NetworkX Graph
+        The graph for which the layout is computed.
+    prog : string (default: 'neato')
+        The name of the GraphViz program to use for layout.
+        Options depend on GraphViz version but may include:
+        'dot', 'twopi', 'fdp', 'sfdp', 'circo'
+    root : Node from G or None (default: None)
+        The node of G from which to start some layout algorithms.
+
+    Returns
+    -------
+      Dictionary of (x, y) positions keyed by node.
+
+    Examples
+    --------
+    >>> G = nx.complete_graph(4)
+    >>> pos = nx.nx_pydot.graphviz_layout(G)
+    >>> pos = nx.nx_pydot.graphviz_layout(G, prog="dot")
+
+    Notes
+    -----
+    This is a wrapper for pydot_layout.
+    """
+    return pydot_layout(G=G, prog=prog, root=root)
+
+
+def pydot_layout(G, prog="neato", root=None):
+    """Create node positions using :mod:`pydot` and Graphviz.
+
+    Parameters
+    --------
+    G : Graph
+        NetworkX graph to be laid out.
+    prog : string  (default: 'neato')
+        Name of the GraphViz command to use for layout.
+        Options depend on GraphViz version but may include:
+        'dot', 'twopi', 'fdp', 'sfdp', 'circo'
+    root : Node from G or None (default: None)
+        The node of G from which to start some layout algorithms.
+
+    Returns
+    --------
+    dict
+        Dictionary of positions keyed by node.
+
+    Examples
+    --------
+    >>> G = nx.complete_graph(4)
+    >>> pos = nx.nx_pydot.pydot_layout(G)
+    >>> pos = nx.nx_pydot.pydot_layout(G, prog="dot")
+
+    Notes
+    -----
+    If you use complex node objects, they may have the same string
+    representation and GraphViz could treat them as the same node.
+    The layout may assign both nodes a single location. See Issue #1568
+    If this occurs in your case, consider relabeling the nodes just
+    for the layout computation using something similar to:
+
+        H = nx.convert_node_labels_to_integers(G, label_attribute='node_label')
+        H_layout = nx.nx_pydot.pydot_layout(G, prog='dot')
+        G_layout = {H.nodes[n]['node_label']: p for n, p in H_layout.items()}
+
+    """
+    import pydot
+
+    P = to_pydot(G)
+    if root is not None:
+        P.set("root", str(root))
+
+    # List of low-level bytes comprising a string in the dot language converted
+    # from the passed graph with the passed external GraphViz command.
+    D_bytes = P.create_dot(prog=prog)
+
+    # Unique string decoded from these bytes with the preferred locale encoding
+    D = str(D_bytes, encoding=getpreferredencoding())
+
+    if D == "":  # no data returned
+        print(f"Graphviz layout with {prog} failed")
+        print()
+        print("To debug what happened try:")
+        print("P = nx.nx_pydot.to_pydot(G)")
+        print('P.write_dot("file.dot")')
+        print(f"And then run {prog} on file.dot")
+        return
+
+    # List of one or more "pydot.Dot" instances deserialized from this string.
+    Q_list = pydot.graph_from_dot_data(D)
+    assert len(Q_list) == 1
+
+    # The first and only such instance, as guaranteed by the above assertion.
+    Q = Q_list[0]
+
+    node_pos = {}
+    for n in G.nodes():
+        pydot_node = pydot.Node(str(n)).get_name()
+        node = Q.get_node(pydot_node)
+
+        if isinstance(node, list):
+            node = node[0]
+        pos = node.get_pos()[1:-1]  # strip leading and trailing double quotes
+        if pos is not None:
+            xx, yy = pos.split(",")
+            node_pos[n] = (float(xx), float(yy))
+    return node_pos