diff env/lib/python3.9/site-packages/networkx/readwrite/edgelist.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/readwrite/edgelist.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,483 @@
+"""
+**********
+Edge Lists
+**********
+Read and write NetworkX graphs as edge lists.
+
+The multi-line adjacency list format is useful for graphs with nodes
+that can be meaningfully represented as strings.  With the edgelist
+format simple edge data can be stored but node or graph data is not.
+There is no way of representing isolated nodes unless the node has a
+self-loop edge.
+
+Format
+------
+You can read or write three formats of edge lists with these functions.
+
+Node pairs with no data::
+
+ 1 2
+
+Python dictionary as data::
+
+ 1 2 {'weight':7, 'color':'green'}
+
+Arbitrary data::
+
+ 1 2 7 green
+"""
+
+__all__ = [
+    "generate_edgelist",
+    "write_edgelist",
+    "parse_edgelist",
+    "read_edgelist",
+    "read_weighted_edgelist",
+    "write_weighted_edgelist",
+]
+
+from networkx.utils import open_file
+import networkx as nx
+
+
+def generate_edgelist(G, delimiter=" ", data=True):
+    """Generate a single line of the graph G in edge list format.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    delimiter : string, optional
+       Separator for node labels
+
+    data : bool or list of keys
+       If False generate no edge data.  If True use a dictionary
+       representation of edge data.  If a list of keys use a list of data
+       values corresponding to the keys.
+
+    Returns
+    -------
+    lines : string
+        Lines of data in adjlist format.
+
+    Examples
+    --------
+    >>> G = nx.lollipop_graph(4, 3)
+    >>> G[1][2]["weight"] = 3
+    >>> G[3][4]["capacity"] = 12
+    >>> for line in nx.generate_edgelist(G, data=False):
+    ...     print(line)
+    0 1
+    0 2
+    0 3
+    1 2
+    1 3
+    2 3
+    3 4
+    4 5
+    5 6
+
+    >>> for line in nx.generate_edgelist(G):
+    ...     print(line)
+    0 1 {}
+    0 2 {}
+    0 3 {}
+    1 2 {'weight': 3}
+    1 3 {}
+    2 3 {}
+    3 4 {'capacity': 12}
+    4 5 {}
+    5 6 {}
+
+    >>> for line in nx.generate_edgelist(G, data=["weight"]):
+    ...     print(line)
+    0 1
+    0 2
+    0 3
+    1 2 3
+    1 3
+    2 3
+    3 4
+    4 5
+    5 6
+
+    See Also
+    --------
+    write_adjlist, read_adjlist
+    """
+    if data is True:
+        for u, v, d in G.edges(data=True):
+            e = u, v, dict(d)
+            yield delimiter.join(map(str, e))
+    elif data is False:
+        for u, v in G.edges(data=False):
+            e = u, v
+            yield delimiter.join(map(str, e))
+    else:
+        for u, v, d in G.edges(data=True):
+            e = [u, v]
+            try:
+                e.extend(d[k] for k in data)
+            except KeyError:
+                pass  # missing data for this edge, should warn?
+            yield delimiter.join(map(str, e))
+
+
+@open_file(1, mode="wb")
+def write_edgelist(G, path, comments="#", delimiter=" ", data=True, encoding="utf-8"):
+    """Write graph as a list of edges.
+
+    Parameters
+    ----------
+    G : graph
+       A NetworkX graph
+    path : file or string
+       File or filename to write. If a file is provided, it must be
+       opened in 'wb' mode. Filenames ending in .gz or .bz2 will be compressed.
+    comments : string, optional
+       The character used to indicate the start of a comment
+    delimiter : string, optional
+       The string used to separate values.  The default is whitespace.
+    data : bool or list, optional
+       If False write no edge data.
+       If True write a string representation of the edge data dictionary..
+       If a list (or other iterable) is provided, write the  keys specified
+       in the list.
+    encoding: string, optional
+       Specify which encoding to use when writing file.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_edgelist(G, "test.edgelist")
+    >>> G = nx.path_graph(4)
+    >>> fh = open("test.edgelist", "wb")
+    >>> nx.write_edgelist(G, fh)
+    >>> nx.write_edgelist(G, "test.edgelist.gz")
+    >>> nx.write_edgelist(G, "test.edgelist.gz", data=False)
+
+    >>> G = nx.Graph()
+    >>> G.add_edge(1, 2, weight=7, color="red")
+    >>> nx.write_edgelist(G, "test.edgelist", data=False)
+    >>> nx.write_edgelist(G, "test.edgelist", data=["color"])
+    >>> nx.write_edgelist(G, "test.edgelist", data=["color", "weight"])
+
+    See Also
+    --------
+    read_edgelist
+    write_weighted_edgelist
+    """
+
+    for line in generate_edgelist(G, delimiter, data):
+        line += "\n"
+        path.write(line.encode(encoding))
+
+
+def parse_edgelist(
+    lines, comments="#", delimiter=None, create_using=None, nodetype=None, data=True
+):
+    """Parse lines of an edge list representation of a graph.
+
+    Parameters
+    ----------
+    lines : list or iterator of strings
+        Input data in edgelist format
+    comments : string, optional
+       Marker for comment lines. Default is `'#'`
+    delimiter : string, optional
+       Separator for node labels. Default is `None`, meaning any whitespace.
+    create_using : NetworkX graph constructor, optional (default=nx.Graph)
+       Graph type to create. If graph instance, then cleared before populated.
+    nodetype : Python type, optional
+       Convert nodes to this type. Default is `None`, meaning no conversion is
+       performed.
+    data : bool or list of (label,type) tuples
+       If `False` generate no edge data or if `True` use a dictionary
+       representation of edge data or a list tuples specifying dictionary
+       key names and types for edge data.
+
+    Returns
+    -------
+    G: NetworkX Graph
+        The graph corresponding to lines
+
+    Examples
+    --------
+    Edgelist with no data:
+
+    >>> lines = ["1 2", "2 3", "3 4"]
+    >>> G = nx.parse_edgelist(lines, nodetype=int)
+    >>> list(G)
+    [1, 2, 3, 4]
+    >>> list(G.edges())
+    [(1, 2), (2, 3), (3, 4)]
+
+    Edgelist with data in Python dictionary representation:
+
+    >>> lines = ["1 2 {'weight': 3}", "2 3 {'weight': 27}", "3 4 {'weight': 3.0}"]
+    >>> G = nx.parse_edgelist(lines, nodetype=int)
+    >>> list(G)
+    [1, 2, 3, 4]
+    >>> list(G.edges(data=True))
+    [(1, 2, {'weight': 3}), (2, 3, {'weight': 27}), (3, 4, {'weight': 3.0})]
+
+    Edgelist with data in a list:
+
+    >>> lines = ["1 2 3", "2 3 27", "3 4 3.0"]
+    >>> G = nx.parse_edgelist(lines, nodetype=int, data=(("weight", float),))
+    >>> list(G)
+    [1, 2, 3, 4]
+    >>> list(G.edges(data=True))
+    [(1, 2, {'weight': 3.0}), (2, 3, {'weight': 27.0}), (3, 4, {'weight': 3.0})]
+
+    See Also
+    --------
+    read_weighted_edgelist
+    """
+    from ast import literal_eval
+
+    G = nx.empty_graph(0, create_using)
+    for line in lines:
+        p = line.find(comments)
+        if p >= 0:
+            line = line[:p]
+        if not line:
+            continue
+        # split line, should have 2 or more
+        s = line.strip().split(delimiter)
+        if len(s) < 2:
+            continue
+        u = s.pop(0)
+        v = s.pop(0)
+        d = s
+        if nodetype is not None:
+            try:
+                u = nodetype(u)
+                v = nodetype(v)
+            except Exception as e:
+                raise TypeError(
+                    f"Failed to convert nodes {u},{v} to type {nodetype}."
+                ) from e
+
+        if len(d) == 0 or data is False:
+            # no data or data type specified
+            edgedata = {}
+        elif data is True:
+            # no edge types specified
+            try:  # try to evaluate as dictionary
+                if delimiter == ",":
+                    edgedata_str = ",".join(d)
+                else:
+                    edgedata_str = " ".join(d)
+                edgedata = dict(literal_eval(edgedata_str.strip()))
+            except Exception as e:
+                raise TypeError(
+                    f"Failed to convert edge data ({d}) to dictionary."
+                ) from e
+        else:
+            # convert edge data to dictionary with specified keys and type
+            if len(d) != len(data):
+                raise IndexError(
+                    f"Edge data {d} and data_keys {data} are not the same length"
+                )
+            edgedata = {}
+            for (edge_key, edge_type), edge_value in zip(data, d):
+                try:
+                    edge_value = edge_type(edge_value)
+                except Exception as e:
+                    raise TypeError(
+                        f"Failed to convert {edge_key} data {edge_value} "
+                        f"to type {edge_type}."
+                    ) from e
+                edgedata.update({edge_key: edge_value})
+        G.add_edge(u, v, **edgedata)
+    return G
+
+
+@open_file(0, mode="rb")
+def read_edgelist(
+    path,
+    comments="#",
+    delimiter=None,
+    create_using=None,
+    nodetype=None,
+    data=True,
+    edgetype=None,
+    encoding="utf-8",
+):
+    """Read a graph from a list of edges.
+
+    Parameters
+    ----------
+    path : file or string
+       File or filename to read. If a file is provided, it must be
+       opened in 'rb' mode.
+       Filenames ending in .gz or .bz2 will be uncompressed.
+    comments : string, optional
+       The character used to indicate the start of a comment.
+    delimiter : string, optional
+       The string used to separate values.  The default is whitespace.
+    create_using : NetworkX graph constructor, optional (default=nx.Graph)
+       Graph type to create. If graph instance, then cleared before populated.
+    nodetype : int, float, str, Python type, optional
+       Convert node data from strings to specified type
+    data : bool or list of (label,type) tuples
+       Tuples specifying dictionary key names and types for edge data
+    edgetype : int, float, str, Python type, optional OBSOLETE
+       Convert edge data from strings to specified type and use as 'weight'
+    encoding: string, optional
+       Specify which encoding to use when reading file.
+
+    Returns
+    -------
+    G : graph
+       A networkx Graph or other type specified with create_using
+
+    Examples
+    --------
+    >>> nx.write_edgelist(nx.path_graph(4), "test.edgelist")
+    >>> G = nx.read_edgelist("test.edgelist")
+
+    >>> fh = open("test.edgelist", "rb")
+    >>> G = nx.read_edgelist(fh)
+    >>> fh.close()
+
+    >>> G = nx.read_edgelist("test.edgelist", nodetype=int)
+    >>> G = nx.read_edgelist("test.edgelist", create_using=nx.DiGraph)
+
+    Edgelist with data in a list:
+
+    >>> textline = "1 2 3"
+    >>> fh = open("test.edgelist", "w")
+    >>> d = fh.write(textline)
+    >>> fh.close()
+    >>> G = nx.read_edgelist("test.edgelist", nodetype=int, data=(("weight", float),))
+    >>> list(G)
+    [1, 2]
+    >>> list(G.edges(data=True))
+    [(1, 2, {'weight': 3.0})]
+
+    See parse_edgelist() for more examples of formatting.
+
+    See Also
+    --------
+    parse_edgelist
+    write_edgelist
+
+    Notes
+    -----
+    Since nodes must be hashable, the function nodetype must return hashable
+    types (e.g. int, float, str, frozenset - or tuples of those, etc.)
+    """
+    lines = (line if isinstance(line, str) else line.decode(encoding) for line in path)
+    return parse_edgelist(
+        lines,
+        comments=comments,
+        delimiter=delimiter,
+        create_using=create_using,
+        nodetype=nodetype,
+        data=data,
+    )
+
+
+def write_weighted_edgelist(G, path, comments="#", delimiter=" ", encoding="utf-8"):
+    """Write graph G as a list of edges with numeric weights.
+
+    Parameters
+    ----------
+    G : graph
+       A NetworkX graph
+    path : file or string
+       File or filename to write. If a file is provided, it must be
+       opened in 'wb' mode.
+       Filenames ending in .gz or .bz2 will be compressed.
+    comments : string, optional
+       The character used to indicate the start of a comment
+    delimiter : string, optional
+       The string used to separate values.  The default is whitespace.
+    encoding: string, optional
+       Specify which encoding to use when writing file.
+
+    Examples
+    --------
+    >>> G = nx.Graph()
+    >>> G.add_edge(1, 2, weight=7)
+    >>> nx.write_weighted_edgelist(G, "test.weighted.edgelist")
+
+    See Also
+    --------
+    read_edgelist
+    write_edgelist
+    read_weighted_edgelist
+    """
+    write_edgelist(
+        G,
+        path,
+        comments=comments,
+        delimiter=delimiter,
+        data=("weight",),
+        encoding=encoding,
+    )
+
+
+def read_weighted_edgelist(
+    path,
+    comments="#",
+    delimiter=None,
+    create_using=None,
+    nodetype=None,
+    encoding="utf-8",
+):
+    """Read a graph as list of edges with numeric weights.
+
+    Parameters
+    ----------
+    path : file or string
+       File or filename to read. If a file is provided, it must be
+       opened in 'rb' mode.
+       Filenames ending in .gz or .bz2 will be uncompressed.
+    comments : string, optional
+       The character used to indicate the start of a comment.
+    delimiter : string, optional
+       The string used to separate values.  The default is whitespace.
+    create_using : NetworkX graph constructor, optional (default=nx.Graph)
+       Graph type to create. If graph instance, then cleared before populated.
+    nodetype : int, float, str, Python type, optional
+       Convert node data from strings to specified type
+    encoding: string, optional
+       Specify which encoding to use when reading file.
+
+    Returns
+    -------
+    G : graph
+       A networkx Graph or other type specified with create_using
+
+    Notes
+    -----
+    Since nodes must be hashable, the function nodetype must return hashable
+    types (e.g. int, float, str, frozenset - or tuples of those, etc.)
+
+    Example edgelist file format.
+
+    With numeric edge data::
+
+     # read with
+     # >>> G=nx.read_weighted_edgelist(fh)
+     # source target data
+     a b 1
+     a c 3.14159
+     d e 42
+
+    See Also
+    --------
+    write_weighted_edgelist
+    """
+    return read_edgelist(
+        path,
+        comments=comments,
+        delimiter=delimiter,
+        create_using=create_using,
+        nodetype=nodetype,
+        data=(("weight", float),),
+        encoding=encoding,
+    )