core.py 37 KB
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#! /usr/bin/env python
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# graph_tool -- a general graph manipulation python module
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#
# Copyright (C) 2007 Tiago de Paula Peixoto <tiago@forked.de>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

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from dl_import import *
dl_import("import libgraph_tool_core as libcore")
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__version__ = libcore.mod_info().version
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import io # sets up libcore io routines
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import sys, os, os.path, re, struct, fcntl, termios, gzip, bz2, string,\
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       textwrap, time, signal, traceback, shutil, time, math, inspect, \
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       functools, types, weakref, copy
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from StringIO import StringIO
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from decorators import _wraps, _require, _attrs, _limit_args
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################################################################################
# Utility functions
################################################################################

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def _prop(t, g, prop):
    """Returns either a property map, or an internal vertex property map with a
    given name"""
    if type(prop) == str:
        try:
            pmap = g.properties[(t,prop)]
        except KeyError:
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            raise KeyError("no internal %s property named: %s" %\
                           ("vertex" if t == "v" else \
                            ("edge" if t == "e" else "graph"), prop))
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    else:
        pmap = prop
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    if pmap == None:
        return libcore.any()
    else:
        return pmap._PropertyMap__map.get_map()

def _degree(g, name):
    """Retrieve the degree type from string, or returns the corresponding
    property map"""
    deg = name
    if name == "in-degree" or name == "in":
        deg = libcore.Degree.In
    elif name == "out-degree" or name == "out":
        deg = libcore.Degree.Out
    elif name == "total-degree" or name == "total":
        deg = libcore.Degree.Total
    else:
        deg = _prop("v", g, deg)
    return deg
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def _parse_range(range):
    """Parse a range in the form 'lower[*] upper[*]' (where an '*' indicates
    a closed boundary) or 'comp val', where 'comp' is [==|=|!=|>=|<=|>|<].
    """
    try:
        rcomp = re.compile(r"(>|<|>=|<=|==|=|!=)\s*([^=<>!]+)")
        rrange = re.compile(r"([^\*]+)(\*?)\s+([^\*]+)(\*?)")
        inverted = False
        if rcomp.match(range):
            comp = rcomp.match(range).group(1)
            thres = rcomp.match(range).group(2)
            thres = float(thres)
            if "<" in comp:
                ran = (float('-Inf'), thres)
                if "=" in comp:
                    inc = (False, True)
                else:
                    inc = (False, False)
            elif ">" in comp:
                ran = (thres, float('Inf'))
                if "=" in comp:
                    inc = (True, False)
                else:
                    inc = (False, False)
            elif comp == "==" or comp == "=" or comp == "!=":
                ran = (thres, thres)
                inc = (True, True)
                if comp == "!=":
                    inverted = True
        elif rrange.match(range):
            m = rrange.match(range)
            r1 = float(m.group(1))
            i1 = "*" in m.group(2)
            r2 = float(m.group(3))
            i2 = "*" in m.group(4)
            ran = (r1, r2)
            inc = (i1, i2)
        else:
            raise ValueError("invalid value for range: " + range)
    except (ValueError, TypeError), e:
        raise ValueError("invalid value for range: %s: %s " % (range, str(e)))
    return (ran, inc, inverted)

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def _type_alias(type_name):
    alias = {"int8_t":"bool",
             "boolean":"bool",
             "int":"int32_t",
             "long":"int32_t",
             "long long":"int64_t",
             "object":"python::object"}
    if type_name in value_types():
        return type_name
    if alias.has_key(type_name):
        return alias[type_name]
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    ma = re.compile(r"vector<(.*)>").match(type_name)
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    if ma:
        t = ma.group(1)
        if alias.has_key(t):
            return "vector<%s>" % alias[t]
    raise ValueError("invalid property value type: " + type_name)

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def show_config():
    info = libcore.mod_info()
    print "version:", info.version
    print "gcc version:", info.gcc_version
    print "compilation flags:", info.cxxflags
    print "install prefix:", info.install_prefix
    print "python dir:", info.python_dir
    print "graph filtering:", libcore.graph_filtering_enabled()
    print "openmp:", libcore.openmp_enabled()
    print "uname:", " ".join(os.uname())
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################################################################################
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# Property Maps
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################################################################################

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class PropertyMap(object):
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    """Property map class"""
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    def __init__(self, pmap, g, key_type, key_trans = None):
        self.__map = pmap
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        self.__g = weakref.ref(g)
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        self.__key_type = key_type
        self.__key_trans = key_trans if key_trans != None else lambda k: k
        self.__register_map()

    def __register_map(self):
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        if self.__g() == None:
            return
        self.__g()._Graph__known_properties.append((self.key_type(),
                                                    weakref.ref(self.__map)))
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    def __unregister_map(self):
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        if self.__g() == None:
            return
        i = self.__g()._Graph__known_properties.index((self.key_type(),
                                                       weakref.ref(self.__map)))
        del self.__g()._Graph__known_properties[i]
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    def __del__(self):
        self.__unregister_map()

    def __getitem__(self, k):
        return self.__map[self.__key_trans(k)]

    def __setitem__(self, k, v):
        self.__map[self.__key_trans(k)] = v

    def get_graph(self):
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        """Get the graph class to which the map refers"""
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        return self.__g()
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    def key_type(self):
        """The key type of the map. Either 'g', 'v' or 'e'"""
        return self.__key_type

    def value_type(self):
        """The value type of the map"""
        return self.__map.value_type()

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    def get_array(self):
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        """Get an array with property values.
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        .. WARNING::

           The returned array does not own the data, which belongs to the
           property map. Therefore, the returned array cannot have a longer
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           lifespan than the property map itself! Furthermore, if the graph
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           changes, it may leave the pointer to the data in the array dangling!
           Do *not* store the array if the graph is to be modified, or the
           original property map deleted; *store a copy instead*!
        """
        if self.__key_type == 'v':
            n = self.__g().num_vertices()
        elif self.__key_type == 'e':
            n = self.__g().num_edges()
        else:
            n = 1
        return self.__map.get_array(n)

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    def __get_array(self):
        return self.get_array()[:]

    def __set_array(self, v):
        self.get_array()[:] = v

    a = property(__get_array, __set_array,
                 doc=r"""Shortcut to the :meth:`~PropertyMap.get_array` method
                 as a property. A view to the array is returned, instead of the
                 array, for convenience.""")

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    def is_writable(self):
        """Return True if the property is writable."""
        return self.__map.is_writable()

def _check_prop_writable(prop, name=None):
    if not prop.is_writable():
        raise ValueError("property map%s is not writable." %\
                         ((" '%s'" % name) if name != None else ""))

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def _check_prop_scalar(prop, name=None, floating=False):
    scalars = ["bool", "int32_t", "int64_t", "unsigned long",
               "double", "long double"]
    if floating:
        scalars = ["double", "long double"]

    if prop.value_type() not in scalars:
        raise ValueError("property map%s is not of scalar%s type." %\
                         (((" '%s'" % name) if name != None else ""),
                          (" floating" if floating else "")))

def _check_prop_vector(prop, name=None, floating=False):
    scalars = ["bool", "int32_t", "int64_t", "unsigned long",
               "double", "long double"]
    if floating:
        scalars = ["double", "long double"]
    vals = ["vector<%s>" % v for v in scalars]
    if prop.value_type() not in vals:
        raise ValueError("property map%s is not of vector%s type." %\
                         (((" '%s'" % name) if name != None else ""),
                          (" floating" if floating else "")))

def group_vector_property(g, props, value_type=None, vprop=None, pos=None):
    types = set()
    keys = set()
    for i,p in enumerate(props):
        if "vector" in p.value_type():
            raise ValueError("property map 'props[%d]' is a vector property." %
                             i)
        types.add(p.value_type())
        keys.add(p.key_type())
    if len(keys) > 1:
        raise ValueError("'props' must be of the same key type." )
    k = keys.pop()

    if vprop == None:
        if value_type == None and len(types) == 1:
             value_type = types.pop()

        if value_type != None:
            value_type = "vector<%s>" % value_type
            if k == 'v':
                vprop = g.new_vertex_property(value_type)
            elif k == 'e':
                vprop = g.new_edge_property(value_type)
            else:
                vprop = g.new_graph_property(value_type)
        else:
            ValueError("Can't automatically determine property map value" +
                       " type. Please provide the 'value_type' parameter.")
    _check_prop_vector(vprop, name="vprop")

    for i,p in enumerate(props):
        if k != "g":
            g.stash_filter(directed=True, reversed=True)
            g.set_directed(True)
            g.set_reversed(False)
            libcore.group_vector_property(g._Graph__graph,
                                          _prop(k, g, vprop),
                                          _prop(k, g, p),
                                          i if pos == None else pos[i],
                                          k == 'e')
            g.pop_filter(directed=True, reversed=True)
        else:
            vprop[g][i if pos == None else pos[i]] = p[g]
    return vprop

def ungroup_vector_property(g, vprop, pos, props=None):
    _check_prop_vector(vprop, name="vprop")
    k = vprop.key_type()
    value_type = vprop.value_type().split("<")[1].split(">")[0]
    if props == None:
        if k == 'v':
            props = [g.new_vertex_property(value_type) for i in pos]
        elif k == 'e':
            props = [g.new_edge_property(value_type) for i in pos]
        else:
            props = [g.new_graph_property(value_type) for i in pos]

    for i,p in enumerate(pos):
        if props[i].key_type() != k:
            raise ValueError("'props' must be of the same key type as 'vprop'.")

        if k != 'g':
            g.stash_filter(directed=True, reversed=True)
            g.set_directed(True)
            g.set_reversed(False)
            libcore.ungroup_vector_property(g._Graph__graph,
                                            _prop(k, g, vprop),
                                            _prop(k, g, props[i]),
                                            pos[i], k == 'e')
            g.pop_filter(directed=True, reversed=True)
        else:
            if len(vprop[g]) <= pos[i]:
                vprop[g].resize(pos[i]+1)
            props[i][g] = vprop[g][pos[i]]
    return props
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class PropertyDict(dict):
    """Wrapper for the dict of vertex, graph or edge properties, which sets the
    value on the property map when changed in the dict."""
    def __init__(self, g, old, get_func, set_func, del_func):
        dict.__init__(self)
        dict.update(self, old)
        self.g = g
        self.get_func = get_func
        self.set_func = set_func
        self.del_func = del_func

    def __setitem__(self, key, val):
        if self.set_func != None:
            self.set_func(self.g, key, val)
        else:
            raise KeyError("Property dict cannot be set")
        dict.__setitem__(self, key, val)

    def __delitem__(self, key):
        self.del_func(self.g, key)
        dict.__delitem__(self, key)
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################################################################################
# Graph class
# The main graph interface
################################################################################

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from libgraph_tool_core import Vertex, Edge, Vector_bool, Vector_int32_t, \
     Vector_int64_t, Vector_double, Vector_long_double, Vector_string, \
     new_vertex_property, new_edge_property, new_graph_property
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class Graph(object):
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    """This class encapsulates either a directed multigraph (default or if
    ``directed=True``) or an undirected multigraph (if ``directed=False``), with
    optional internal edge, vertex or graph properties.
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    It is implemented as an adjacency list, where both vertex and edge lists are
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    C++ STL vectors.
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    """
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    def __init__(self, g = None, directed=True):
        """Construct a graph. If 'g' is specified, the graph (and its internal
        properties) will be copied. The 'directed' parameter specified whether
        the graph should be directed or undirected."""
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        self.__properties = {}
        self.__known_properties = []
        self.__filter_state = {"reversed": False,
                               "edge_filter": (None,False),
                               "vertex_filter": (None,False),
                               "directed": True,
                               "reversed": False}
        self.__stashed_filter_state = []

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        if g == None:
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            self.__graph = libcore.GraphInterface()
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            self.set_directed(directed)
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        else:
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            self.__graph = libcore.GraphInterface(g.__graph)
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            for k,v in g.__properties.iteritems():
                new_p = self.new_property(v.key_type(), v.value_type())
                self.copy_property(v, new_p, g)
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                self.properties[k] = new_p
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            self.__stashed_filter_state = [self.get_filter_state()]

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            v_filt, v_rev = g.__filter_state["vertex_filter"]
            if v_filt != None:
                if v_filt not in g.vertex_properties.values():
                    new_filt = self.new_vertex_property("bool")
                    self.copy_property(v_filt, new_filt)

                else:
                    for k,v in g.vertex_properties.iteritems():
                        if v == v_filt:
                            new_filt = self.vertex_properties[k]
                self.__stashed_filter_state[0]["vertex_filter"] = (new_filt,
                                                                   v_rev)
            e_filt, e_rev = g.__filter_state["edge_filter"]
            if e_filt != None:
                if e_filt not in g.edge_properties.values():
                    new_filt = self.new_edge_property("bool")
                    self.copy_property(e_filt, new_filt)

                else:
                    for k,v in g.edge_properties.iteritems():
                        if v == e_filt:
                            new_filt = self.edge_properties[k]
                self.__stashed_filter_state[0]["edge_filter"] = (new_filt,
                                                                 e_rev)
            self.pop_filter()
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        # internal index maps
        self.__vertex_index = \
                 PropertyMap(libcore.get_vertex_index(self.__graph), self, "v")
        self.__edge_index = \
                 PropertyMap(libcore.get_edge_index(self.__graph), self, "e")
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    def copy(self):
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        """Returns a deep copy of self. All internal property maps are also
        copied."""
        return Graph(self)
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    # Graph access
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    # ============
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    def vertices(self):
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        """Return an iterator over the vertices

        Examples
        --------

        >>> g = gt.Graph()
        >>> vlist = g.add_vertex(5)
        >>> vlist2 = []
        >>> for v in g.vertices():
        ...     vlist2.append(v)
        ...
        >>> assert(vlist == vlist2)

        """
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        return self.__graph.Vertices()

    def vertex(self, i):
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        """Return the i-th vertex from the graph."""
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        return self.__graph.Vertex(int(i))
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    def edges(self):
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        """Return iterator over the edges."""
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        return self.__graph.Edges()

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    def add_vertex(self, n=1):
        """Add a vertices to the graph, and return it. If n > 1, n vertices are
        inserted and a list is returned."""
        if n == 1:
            return self.__graph.AddVertex()
        else:
            return [self.__graph.AddVertex() for i in xrange(0,n)]
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    def remove_vertex(self, vertex):
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        """Remove a vertex from the graph."""
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        k = vertex.in_degree() + vertex.out_degree()
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        index = self.vertex_index[vertex]
        for pmap in self.__known_properties:
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            if pmap[0] == "v" and pmap[1]() != None and \
                   pmap[1]() != self.__vertex_index._PropertyMap__map:
                self.__graph.ShiftVertexProperty(pmap[1]().get_map(), index)
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        self.clear_vertex(vertex)
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        self.__graph.RemoveVertex(vertex)

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    def remove_vertex_if(self, predicate):
        """Remove all the vertices from the graph for which predicate(v)
        evaluates to True."""
        N = self.num_vertices()
        for i in xrange(0, N):
            v = self.vertex(N - i - 1)
            if predicate(v):
                self.remove_vertex(v)

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    def clear_vertex(self, vertex):
        """Removes all in and out-edges from the given vertex."""
        del_es = []
        for e in vertex.all_edges():
            del_es.append(e)
        for e in del_es:
            self.remove_edge(e)

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    def add_edge(self, source, target):
        """Add a new edge from 'source' to 'target' to the graph, and return
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        it."""
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        return self.__graph.AddEdge(source, target)

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    def remove_edge(self, edge):
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        """Remove an edge from the graph."""
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        self.__graph.RemoveEdge(edge)

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    def remove_edge_if(self, predicate):
        """Remove all the edges from the graph for which predicate(e) evaluates
        to True."""
        for v in self.vertices():
            del_es = []
            for e in v.out_edges():
                if predicate(e):
                    del_es.append(e)
            for e in del_es:
                self.remove_edge(e)

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    def clear(self):
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        """Remove all vertices and edges from the graph."""
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        self.__graph.Clear()

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    def clear_edges(self):
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        """Remove all edges from the graph."""
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        self.__graph.ClearEdges()

    # Internal property maps
    # ======================

    # all properties
    def __get_properties(self):
        return PropertyDict(self, self.__properties,
                            lambda g,k: g.__properties[k],
                            lambda g,k,v: g.__set_property(k[0],k[1],v),
                            lambda g,k: g.__del_property(k[0],k[1]))

    @_limit_args({"t":["v", "e", "g"]})
    @_require("k", str)
    @_require("v", PropertyMap)
    def __set_property(self, t, k, v):
        if t != v.key_type():
            raise ValueError("wrong key type for property map")
        self.__properties[(t,k)] = v

    @_limit_args({"t":["v", "e", "g"]})
    @_require("k", str)
    def __del_property(self, t, k):
        del self.__properties[(t,k)]

    properties = property(__get_properties,
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                          doc=
    """Dictionary of internal properties. Keys must always be a tuple, where the
    first element if a string from the set {'v', 'e', 'g'}, representing a
    vertex, edge or graph property, and the second element is the name of the
    property map.

    Examples
    --------
    >>> g = gt.Graph()
    >>> g.properties[("e", "foo")] = g.new_edge_property("vector<double>")
    >>> del g.properties[("e", "foo")]
    """)
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    def __get_specific_properties(self, t):
        props = dict([(k[1],v) for k,v in self.__properties.iteritems() \
                      if k[0] == t ])
        return props

    # vertex properties
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    def __get_vertex_properties(self):
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        return PropertyDict(self, self.__get_specific_properties("v"),
                            lambda g,k: g.__properties[("v",k)],
                            lambda g,k,v: g.__set_property("v",k,v),
                            lambda g,k: g.__del_property("v",k))
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    vertex_properties = property(__get_vertex_properties,
                                 doc="Dictionary of vertex properties")
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    # edge properties
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    def __get_edge_properties(self):
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        return PropertyDict(self, self.__get_specific_properties("e"),
                            lambda g,k: g.__properties[("e",k)],
                            lambda g,k,v: g.__set_property("e",k,v),
                            lambda g,k: g.__del_property("e",k))
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    edge_properties = property(__get_edge_properties,
                                 doc="Dictionary of edge properties")

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    # graph properties
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    def __get_graph_properties(self):
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        return PropertyDict(self, self.__get_specific_properties("g"),
                            lambda g,k: g.__properties[("g",k)],
                            lambda g,k,v: g.__set_property("g",k,v),
                            lambda g,k: g.__del_property("g",k))
    graph_properties = property(__get_graph_properties,
                                 doc="Dictionary of graph properties")

    def list_properties(self):
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        """List all internal properties for convenience.

        Examples
        --------
        >>> g = gt.Graph()
        >>> g.properties[("e", "foo")] = g.new_edge_property("vector<double>")
        >>> g.vertex_properties["foo"] = g.new_vertex_property("double")
        >>> g.vertex_properties["bar"] = g.new_vertex_property("python::object")
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        >>> g.graph_properties["gnat"] = g.new_graph_property("string",\
                                                              "hi there!")
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        >>> g.list_properties()
        gnat           (graph)   (type: string, val: hi there!)
        bar            (vertex)  (type: python::object)
        foo            (vertex)  (type: double)
        foo            (edge)    (type: vector<double>)
        """

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        if len(self.__properties) == 0:
            return
        w = max([len(x[0]) for x in self.__properties.keys()]) + 4
        w = w if w > 14 else 14
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        for k,v in self.__properties.iteritems():
            if k[0] == "g":
                print "%%-%ds (graph)   (type: %%s, val: %%s)" % w % \
                      (k[1], v.value_type(), str(v[self]))
        for k,v in self.__properties.iteritems():
            if k[0] == "v":
                print "%%-%ds (vertex)  (type: %%s)" % w % (k[1],
                                                            v.value_type())
        for k,v in self.__properties.iteritems():
            if k[0] == "e":
                print "%%-%ds (edge)    (type: %%s)" % w % (k[1],
                                                            v.value_type())

    # index properties

    def _get_vertex_index(self):
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        return self.__vertex_index
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    vertex_index = property(_get_vertex_index,
                            doc="Vertex index map. This map is immutable.")
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    def _get_edge_index(self):
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        return self.__edge_index
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    edge_index = property(_get_edge_index, doc="Edge index map.")
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    # Property map creation

    def new_property(self, key_type, type):
        """Create a new (uninitialized) vertex property map of key type
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        `key_type` (``v``, ``e`` or ``g``), value type ``type``, and return it.
        """
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        if key_type == "v" or key_type == "vertex":
            return self.new_vertex_property(type)
        if key_type == "e" or key_type == "edge":
            return self.new_edge_property(type)
        if key_type == "g" or key_type == "graph":
            return self.new_graph_property(type)
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        raise ValueError("unknown key type: " + key_type)
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    def new_vertex_property(self, type):
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        """Create a new (uninitialized) vertex property map of type `type`, and
        return it."""
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        return PropertyMap(new_vertex_property(_type_alias(type),
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                                               self.__graph.GetVertexIndex()),
                           self, "v")
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    def new_edge_property(self, type):
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        """Create a new (uninitialized) edge property map of type `type`, and
        return it."""
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        return PropertyMap(new_edge_property(_type_alias(type),
                                             self.__graph.GetEdgeIndex()),
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                           self, "e")

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    def new_graph_property(self, type, val=None):
        """Create a new graph property map of type `type`, and return it. If
        `val` is not None, the property is initialized to its value."""
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        prop = PropertyMap(new_graph_property(_type_alias(type),
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                                              self.__graph.GetGraphIndex()),
                           self, "g", lambda k: k.__graph)
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        if val != None:
            prop[self] = val
        return prop
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    # property map copying
    @_require("src", PropertyMap)
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    @_require("tgt", (PropertyMap, type(None)))
    def copy_property(self, src, tgt=None, g=None):
        """Copy contents of `src` property to `tgt` property. If `tgt` is None,
        then a new property map of the same type is created, and returned. The
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        optional parameter g specifies the (identical) source graph to copy
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        properties from (defaults to self).
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        """
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        if tgt == None:
            tgt = self.new_property(src.key_type(), src.value_type())
            ret = tgt
        else:
            ret = None

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        if src.key_type() != tgt.key_type():
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            raise ValueError("source and target properties must have the same" +
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                             " key type")
        if g == None:
            g = self
        if g != self:
            g.stash_filter()
        self.stash_filter()
        if src.key_type() == "v":
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            self.__graph.CopyVertexProperty(g.__graph, _prop("v", g, src),
                                            _prop("v", g, tgt))
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        elif src.key_type() == "e":
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            self.__graph.CopyEdgeProperty(g.__graph, _prop("e", g, src),
                                            _prop("e", g, tgt))
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        else:
            tgt[self] = src[g]
        self.pop_filter()
        if g != self:
            g.pop_filter()
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        return ret
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    # degree property map
    @_limit_args({"deg":["in","out","total"]})
    def degree_property_map(self, deg):
        """Create and return a vertex property map containing the degree type
        given by `deg`"""
        return PropertyMap(self.__graph.DegreeMap(deg), self, "v")


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    # I/O operations
    # ==============
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    def load(self, filename, format="auto"):
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        """Load graph from 'filename' (which can also be a file-like
        object). The format is guessed from the file name, or can be specified
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        by 'format', which can be either 'xml' or 'dot'. Alternatively, filename
        can be file-like object."""
        if type(filename) == str:
            filename = os.path.expanduser(filename)
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        if format == 'auto' and isinstance(filename, str):
            if filename.endswith(".xml") or filename.endswith(".xml.gz") or \
                   filename.endswith(".xml.bz2"):
                format = "xml"
            elif filename.endswith(".dot") or filename.endswith(".dot.gz") or \
                     filename.endswith(".dot.bz2"):
                format = "dot"
            else:
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                raise ValueError("cannot determine file format of: " + filename)
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        elif format == "auto":
            format = "xml"
        if isinstance(filename, str):
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            props = self.__graph.ReadFromFile(filename, None, format)
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        else:
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            props = self.__graph.ReadFromFile("", filename, format)
        for name, prop in props[0].iteritems():
            self.vertex_properties[name] = PropertyMap(prop, self, "v")
        for name, prop in props[1].iteritems():
            self.edge_properties[name] = PropertyMap(prop, self, "e")
        for name, prop in props[2].iteritems():
            self.graph_properties[name] = PropertyMap(prop, self, "g",
                                                      lambda k: k.__graph)
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    def save(self, filename, format="auto"):
        """Save graph to file. The format is guessed from the 'file' name, or
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        can be specified by 'format', which can be either 'xml' or
        'dot'. Alternatively, filename can be file-like object."""
        if type(filename) == str:
            filename = os.path.expanduser(filename)
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        if format == 'auto' and isinstance(filename, str):
            if filename.endswith(".xml") or filename.endswith(".xml.gz") or \
                   filename.endswith(".xml.bz2"):
                format = "xml"
            elif filename.endswith(".dot") or filename.endswith(".dot.gz") or \
                     filename.endswith(".dot.bz2"):
                format = "dot"
            else:
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                raise ValueError("cannot determine file format of: " + filename)
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        elif format == "auto":
            format = "xml"
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        props = [(name[1], prop._PropertyMap__map) for name,prop in \
                 self.__properties.iteritems()]
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        if isinstance(filename, str):
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            self.__graph.WriteToFile(filename, None, format, props)
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        else:
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            self.__graph.WriteToFile("", filename, format, props)
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    # Directedness
    # ============
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    def set_directed(self, is_directed):
        """Set the directedness of the graph"""
        self.__graph.SetDirected(is_directed)

    def is_directed(self):
        """Get the directedness of the graph"""
        return self.__graph.GetDirected()

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    # Reversedness
    # ============

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    def set_reversed(self, is_reversed):
        """Reverse the direction of the edges, if 'reversed' is True, or
        maintain the original direction otherwise."""
        self.__graph.SetReversed(is_reversed)

    def is_reversed(self):
        """Return 'True' if the edges are reversed, and 'False' otherwise."""
        return self.__graph.GetReversed()

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    # Filtering
    # =========

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    def set_vertex_filter(self, property, inverted=False):
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        """Choose vertex boolean filter property. Only the vertices with value
        different than zero are kept in the filtered graph. If the 'inverted'
        option is supplied with value 'True', only the vertices with value zero
        are kept. If the supplied property is 'None', any previous filtering is
        removed."""
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        self.__graph.SetVertexFilterProperty(_prop("v", self, property), inverted)
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        self.__filter_state["vertex_filter"] = (property, inverted)
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    def get_vertex_filter(self):
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        """Get the vertex filter property and whether or not it is inverted"""
        return self.__filter_state["vertex_filter"]
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    def set_edge_filter(self, property, inverted=False):
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        """Choose edge boolean filter property. Only the edges with value
        different than zero are kept in the filtered graph. If the 'inverted'
        option is supplied with value 'True', only the edges with value zero are
        kept. If the supplied property is 'None', any previous filtering is
        removed."""
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        self.__graph.SetEdgeFilterProperty(_prop("e", self, property), inverted)
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        self.__filter_state["edge_filter"] = (property, inverted)
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    def get_edge_filter(self):
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        """Get the edge filter property and whether or not it is inverted"""
        return self.__filter_state["edge_filter"]
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    def purge_vertices(self):
        """Remove all vertices of the graph which are currently being filtered
        out, and return to the unfiltered state"""
        self.__graph.PurgeVertices()
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        self.__graph.SetVertexFilterProperty(None)
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    def purge_edges(self):
        """Remove all edges of the graph which are currently being filtered out,
        and return to the unfiltered state"""
        self.__graph.PurgeEdges()
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        self.__graph.SetEdgeFilterProperty(None)
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    def stash_filter(self, edge=False, vertex=False,
                     directed=False, reversed=False, all=True):
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        """Stash current filter state and recover unfiltered graph. The optional
        keyword arguments specify which type of filter should be stashed."""
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        if edge or vertex or directed or reversed:
            all = False
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        self.__stashed_filter_state.append(self.get_filter_state())
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        if libcore.graph_filtering_enabled():
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            if vertex or all:
                self.set_vertex_filter(None)
            if edge or all:
                self.set_edge_filter(None)
        if directed or all:
            self.set_directed(True)
        if reversed or all:
            self.set_reversed(False)

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    def pop_filter(self, edge=False, vertex=False,
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                   directed=False, reversed=False, all=True):
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        """Pop last stashed filter state. The optional keyword arguments specify
        which type of filter should be recovered."""
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        if edge or vertex or directed or reversed:
            all = False
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        state = self.__stashed_filter_state.pop()
        if libcore.graph_filtering_enabled():
            if vertex or all:
                self.set_vertex_filter(state["vertex_filter"][0],
                                       state["vertex_filter"][1])
            if edge or all:
                self.set_edge_filter(state["edge_filter"][0],
                                     state["edge_filter"][1])
        if directed or all:
            self.set_directed(state["directed"])
        if reversed or all:
            self.set_reversed(state["reversed"])
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    def get_filter_state(self):
        """Return a copy of the filter state of the graph."""
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        self.__filter_state["directed"] = self.is_directed()
        self.__filter_state["reversed"] = self.is_reversed()
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        return copy.copy(self.__filter_state)

    def set_filter_state(self, state):
        """Set the filter state of the graph."""
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        if libcore.graph_filtering_enabled():
            self.set_vertex_filter(state["vertex_filter"][0],
                                   state["vertex_filter"][1])
            self.set_edge_filter(state["edge_filter"][0],
                                 state["edge_filter"][1])
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        self.set_directed(state["directed"])
        self.set_reversed(state["reversed"])

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    # Basic graph statistics
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    # ======================
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    def num_vertices(self):
        """Get the number of vertices."""
        return self.__graph.GetNumberOfVertices()

    def num_edges(self):
        """Get the number of edges"""
        return self.__graph.GetNumberOfEdges()

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    # Pickling support
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    # ================

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    def __getstate__(self):
        state = dict()
        sio = StringIO()
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        if libcore.graph_filtering_enabled():
            if self.get_vertex_filter()[0] != None:
                self.vertex_properties["_Graph__pickle__vfilter"] = \
                    self.get_vertex_filter()[0]
                state["vfilter"] = self.get_vertex_filter()[1]
            if self.get_edge_filter()[0] != None:
                self.edge_properties["_Graph__pickle__efilter"] = \
                    self.get_edge_filter()[0]
                state["efilter"] = self.get_edge_filter()[1]
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        self.save(sio, "xml")
        state["blob"] = sio.getvalue()
        return state
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    def __setstate__(self, state):
        self.__init__()
        blob = state["blob"]
        if blob != "":
            sio = StringIO(blob)
            self.load(sio, "xml")
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        if state.has_key("vfilt"):
            vprop = self.vertex_properties["_Graph__pickle__vfilter"]
            self.set_vertex_filter(vprop, state["vfilt"])
        if state.has_key("efilt"):
            eprop = self.edge_properties["_Graph__pickle__efilter"]
            self.set_edge_filter(vprop, state["efilt"])
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def load_graph(filename, format="auto"):
    """Load a graph from file"""
    g = Graph()
    g.load(filename, format=format)
    return g

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def value_types():
    """Return a list of possible properties value types"""
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    return libcore.get_property_types()
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# Vertex and Edge Types
# =====================
from libgraph_tool_core import Vertex, Edge

def _out_neighbours(self):
    """Return an iterator over the out-neighbours"""
    for e in self.out_edges():
        yield e.target()
Vertex.out_neighbours = _out_neighbours

def _in_neighbours(self):
    """Return an iterator over the in-neighbours"""
    for e in self.in_edges():
        yield e.source()
Vertex.in_neighbours = _in_neighbours

def _all_edges(self):
    """Return an iterator over all edges (both in or out)"""
    for e in self.out_edges():
        yield e
    for e in self.in_edges():
        yield e
Vertex.all_edges = _all_edges

def _all_neighbours(self):
    """Return an iterator over all neighbours (both in or out)"""
    for v in self.out_neighbours():
        yield v
    for v in self.in_neighbours():
        yield v
Vertex.all_neighbours = _all_neighbours

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def _iter(self):
    """Iterate over the source and target"""
    for v in [self.source(), self.target()]:
        yield v
Edge.__iter__ = _iter