diff env/lib/python3.9/site-packages/networkx/readwrite/adjlist.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/adjlist.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,296 @@
+"""
+**************
+Adjacency List
+**************
+Read and write NetworkX graphs as adjacency lists.
+
+Adjacency list format is useful for graphs without data associated
+with nodes or edges and for nodes that can be meaningfully represented
+as strings.
+
+Format
+------
+The adjacency list format consists of lines with node labels.  The
+first label in a line is the source node.  Further labels in the line
+are considered target nodes and are added to the graph along with an edge
+between the source node and target node.
+
+The graph with edges a-b, a-c, d-e can be represented as the following
+adjacency list (anything following the # in a line is a comment)::
+
+     a b c # source target target
+     d e
+"""
+
+__all__ = ["generate_adjlist", "write_adjlist", "parse_adjlist", "read_adjlist"]
+
+from networkx.utils import open_file
+import networkx as nx
+
+
+def generate_adjlist(G, delimiter=" "):
+    """Generate a single line of the graph G in adjacency list format.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    delimiter : string, optional
+       Separator for node labels
+
+    Returns
+    -------
+    lines : string
+        Lines of data in adjlist format.
+
+    Examples
+    --------
+    >>> G = nx.lollipop_graph(4, 3)
+    >>> for line in nx.generate_adjlist(G):
+    ...     print(line)
+    0 1 2 3
+    1 2 3
+    2 3
+    3 4
+    4 5
+    5 6
+    6
+
+    See Also
+    --------
+    write_adjlist, read_adjlist
+
+    """
+    directed = G.is_directed()
+    seen = set()
+    for s, nbrs in G.adjacency():
+        line = str(s) + delimiter
+        for t, data in nbrs.items():
+            if not directed and t in seen:
+                continue
+            if G.is_multigraph():
+                for d in data.values():
+                    line += str(t) + delimiter
+            else:
+                line += str(t) + delimiter
+        if not directed:
+            seen.add(s)
+        yield line[: -len(delimiter)]
+
+
+@open_file(1, mode="wb")
+def write_adjlist(G, path, comments="#", delimiter=" ", encoding="utf-8"):
+    """Write graph G in single-line adjacency-list format to path.
+
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    path : string or file
+       Filename or file handle for data output.
+       Filenames ending in .gz or .bz2 will be compressed.
+
+    comments : string, optional
+       Marker for comment lines
+
+    delimiter : string, optional
+       Separator for node labels
+
+    encoding : string, optional
+       Text encoding.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_adjlist(G, "test.adjlist")
+
+    The path can be a filehandle or a string with the name of the file. If a
+    filehandle is provided, it has to be opened in 'wb' mode.
+
+    >>> fh = open("test.adjlist", "wb")
+    >>> nx.write_adjlist(G, fh)
+
+    Notes
+    -----
+    This format does not store graph, node, or edge data.
+
+    See Also
+    --------
+    read_adjlist, generate_adjlist
+    """
+    import sys
+    import time
+
+    pargs = comments + " ".join(sys.argv) + "\n"
+    header = (
+        pargs
+        + comments
+        + f" GMT {time.asctime(time.gmtime())}\n"
+        + comments
+        + f" {G.name}\n"
+    )
+    path.write(header.encode(encoding))
+
+    for line in generate_adjlist(G, delimiter):
+        line += "\n"
+        path.write(line.encode(encoding))
+
+
+def parse_adjlist(
+    lines, comments="#", delimiter=None, create_using=None, nodetype=None
+):
+    """Parse lines of a graph adjacency list representation.
+
+    Parameters
+    ----------
+    lines : list or iterator of strings
+        Input data in adjlist format
+
+    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.
+
+    comments : string, optional
+       Marker for comment lines
+
+    delimiter : string, optional
+       Separator for node labels.  The default is whitespace.
+
+    Returns
+    -------
+    G: NetworkX graph
+        The graph corresponding to the lines in adjacency list format.
+
+    Examples
+    --------
+    >>> lines = ["1 2 5", "2 3 4", "3 5", "4", "5"]
+    >>> G = nx.parse_adjlist(lines, nodetype=int)
+    >>> nodes = [1, 2, 3, 4, 5]
+    >>> all(node in G for node in nodes)
+    True
+    >>> edges = [(1, 2), (1, 5), (2, 3), (2, 4), (3, 5)]
+    >>> all((u, v) in G.edges() or (v, u) in G.edges() for (u, v) in edges)
+    True
+
+    See Also
+    --------
+    read_adjlist
+
+    """
+    G = nx.empty_graph(0, create_using)
+    for line in lines:
+        p = line.find(comments)
+        if p >= 0:
+            line = line[:p]
+        if not len(line):
+            continue
+        vlist = line.strip().split(delimiter)
+        u = vlist.pop(0)
+        # convert types
+        if nodetype is not None:
+            try:
+                u = nodetype(u)
+            except BaseException as e:
+                raise TypeError(
+                    f"Failed to convert node ({u}) to type " f"{nodetype}"
+                ) from e
+        G.add_node(u)
+        if nodetype is not None:
+            try:
+                vlist = list(map(nodetype, vlist))
+            except BaseException as e:
+                raise TypeError(
+                    f"Failed to convert nodes ({','.join(vlist)}) "
+                    f"to type {nodetype}"
+                ) from e
+        G.add_edges_from([(u, v) for v in vlist])
+    return G
+
+
+@open_file(0, mode="rb")
+def read_adjlist(
+    path,
+    comments="#",
+    delimiter=None,
+    create_using=None,
+    nodetype=None,
+    encoding="utf-8",
+):
+    """Read graph in adjacency list format from path.
+
+    Parameters
+    ----------
+    path : string or file
+       Filename or file handle to read.
+       Filenames ending in .gz or .bz2 will be uncompressed.
+
+    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.
+
+    comments : string, optional
+       Marker for comment lines
+
+    delimiter : string, optional
+       Separator for node labels.  The default is whitespace.
+
+    Returns
+    -------
+    G: NetworkX graph
+        The graph corresponding to the lines in adjacency list format.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_adjlist(G, "test.adjlist")
+    >>> G = nx.read_adjlist("test.adjlist")
+
+    The path can be a filehandle or a string with the name of the file. If a
+    filehandle is provided, it has to be opened in 'rb' mode.
+
+    >>> fh = open("test.adjlist", "rb")
+    >>> G = nx.read_adjlist(fh)
+
+    Filenames ending in .gz or .bz2 will be compressed.
+
+    >>> nx.write_adjlist(G, "test.adjlist.gz")
+    >>> G = nx.read_adjlist("test.adjlist.gz")
+
+    The optional nodetype is a function to convert node strings to nodetype.
+
+    For example
+
+    >>> G = nx.read_adjlist("test.adjlist", nodetype=int)
+
+    will attempt to convert all nodes to integer type.
+
+    Since nodes must be hashable, the function nodetype must return hashable
+    types (e.g. int, float, str, frozenset - or tuples of those, etc.)
+
+    The optional create_using parameter indicates the type of NetworkX graph
+    created.  The default is `nx.Graph`, an undirected graph.
+    To read the data as a directed graph use
+
+    >>> G = nx.read_adjlist("test.adjlist", create_using=nx.DiGraph)
+
+    Notes
+    -----
+    This format does not store graph or node data.
+
+    See Also
+    --------
+    write_adjlist
+    """
+    lines = (line.decode(encoding) for line in path)
+    return parse_adjlist(
+        lines,
+        comments=comments,
+        delimiter=delimiter,
+        create_using=create_using,
+        nodetype=nodetype,
+    )