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Diffstat (limited to 'lib/python2.7/site-packages/setoolsgui/networkx/readwrite/adjlist.py')
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diff --git a/lib/python2.7/site-packages/setoolsgui/networkx/readwrite/adjlist.py b/lib/python2.7/site-packages/setoolsgui/networkx/readwrite/adjlist.py new file mode 100644 index 0000000..57f1e24 --- /dev/null +++ b/lib/python2.7/site-packages/setoolsgui/networkx/readwrite/adjlist.py @@ -0,0 +1,314 @@ +# -*- coding: utf-8 -*- +""" +************** +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 +""" +__author__ = '\n'.join(['Aric Hagberg <hagberg@lanl.gov>', + 'Dan Schult <dschult@colgate.edu>', + 'Loïc Séguin-C. <loicseguin@gmail.com>']) +# Copyright (C) 2004-2013 by +# Aric Hagberg <hagberg@lanl.gov> +# Dan Schult <dschult@colgate.edu> +# Pieter Swart <swart@lanl.gov> +# All rights reserved. +# BSD license. + +__all__ = ['generate_adjlist', + 'write_adjlist', + 'parse_adjlist', + 'read_adjlist'] + +from networkx.utils import make_str, 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_iter(): + line = make_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 += make_str(t) + delimiter + else: + line += make_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 + " GMT %s\n" % (time.asctime(time.gmtime())) + + comments + " %s\n" % (G.name)) + 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 container + Use given NetworkX graph for holding nodes or edges. + + 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. + + create_using: NetworkX graph container + Use given NetworkX graph for holding nodes or edges. + + + 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) + >>> G.nodes() + [1, 2, 3, 4, 5] + >>> G.edges() + [(1, 2), (1, 5), (2, 3), (2, 4), (3, 5)] + + See Also + -------- + read_adjlist + + """ + if create_using is None: + G=nx.Graph() + else: + try: + G=create_using + G.clear() + except: + raise TypeError("Input graph is not a NetworkX graph type") + + 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: + raise TypeError("Failed to convert node (%s) to type %s"\ + %(u,nodetype)) + G.add_node(u) + if nodetype is not None: + try: + vlist=map(nodetype,vlist) + except: + raise TypeError("Failed to convert nodes (%s) to type %s"\ + %(','.join(vlist),nodetype)) + 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 container + Use given NetworkX graph for holding nodes or edges. + + 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. + + create_using: NetworkX graph container + Use given NetworkX graph for holding nodes or edges. + + + 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 is a NetworkX graph container. + The default is 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) + +# fixture for nose tests +def teardown_module(module): + import os + os.unlink('test.adjlist') + os.unlink('test.adjlist.gz') |