__init__.py 55.4 KB
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#! /usr/bin/env python
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# -*- coding: utf-8 -*-
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#
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# graph_tool -- a general graph manipulation python module
#
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# Copyright (C) 2007-2010 Tiago de Paula Peixoto <tiago@skewed.de>
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#
# 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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"""
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graph_tool - efficient graph analysis and manipulation
======================================================

Summary
-------

.. autosummary::
   :nosignatures:

   Graph
   GraphView
   Vertex
   Edge
   PropertyMap
   PropertyArray
   load_graph
   group_vector_property
   ungroup_vector_property
   value_types
   show_config

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This module provides:
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   1. A Graph object for graph representation and manipulation
   2. Property maps for Vertex, Edge or Graph.
   3. Fast algorithms implemented in C++.
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How to use the documentation
----------------------------
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Documentation is available in two forms: docstrings provided
with the code, and the full documentation available in
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`the graph-tool homepage <http://graph-tool.skewed.de>`_.
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We recommend exploring the docstrings using `IPython
<http://ipython.scipy.org>`_, an advanced Python shell with TAB-completion and
introspection capabilities.

The docstring examples assume that ``graph_tool.all`` has been imported as
``gt``::

   >>> import graph_tool.all as gt

Code snippets are indicated by three greater-than signs::

   >>> x = x + 1

Use the built-in ``help`` function to view a function's docstring::

   >>> help(gt.Graph)

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Contents
--------
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"""
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__author__ = "Tiago de Paula Peixoto <tiago@skewed.de>"
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__copyright__ = "Copyright 2007-2010 Tiago de Paula Peixoto"
__license__ = "GPL version 3 or above"
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__URL__ = "http://graph-tool.skewed.de"
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# import numpy and scipy before everything to avoid weird segmentation faults
# depending on the order things are imported.

import numpy
import scipy
import scipy.stats

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from dl_import import *
dl_import("import libgraph_tool_core as libcore")
import libgraph_tool_core as libcore   # for pylint
__version__ = libcore.mod_info().version

import io  # sets up libcore io routines

import sys
import os
import re
import gzip
import bz2
import weakref
import copy

from StringIO import StringIO
from decorators import _wraps, _require, _attrs, _limit_args
from inspect import ismethod
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__all__ = ["Graph", "GraphView", "Vertex", "Edge", "Vector_bool",
           "Vector_int32_t", "Vector_int64_t", "Vector_double",
           "Vector_long_double", "Vector_string", "value_types", "load_graph",
           "PropertyMap", "group_vector_property", "ungroup_vector_property",
           "show_config", "PropertyArray", "__author__", "__copyright__",
           "__URL__", "__version__"]
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################################################################################
# Utility functions
################################################################################


def _prop(t, g, prop):
    """Return either a property map, or an internal property map with a given
    name."""
    if type(prop) == str:
        try:
            pmap = g.properties[(t, prop)]
        except KeyError:
            raise KeyError("no internal %s property named: %s" %\
                           ("vertex" if t == "v" else \
                            ("edge" if t == "e" else "graph"), prop))
    else:
        pmap = prop
    if pmap == None:
        return libcore.any()
    else:
        if t != prop.key_type():
            names = {'e': 'edge', 'v': 'vertex', 'g': 'graph'}
            raise ValueError("Expected '%s' property map, got '%s'" %
                             (names[t], names[prop.key_type()]))
        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


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


def _python_type(type_name):
    type_name = _type_alias(type_name)
    if "vector" in type_name:
        ma = re.compile(r"vector<(.*)>").match(type_name)
        t = ma.group(1)
        return list, _python_type(t)
    if "int" in type_name:
        return int
    if type_name == "bool":
        return bool
    if "double" in type_name:
        return float
    if "string" in type_name:
        return str
    return object


def show_config():
    """Show ``graph_tool`` build configuration."""
    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())

################################################################################
# Property Maps
################################################################################


class PropertyArray(numpy.ndarray):
    """This is a :class:`~numpy.ndarray` subclass which keeps a reference of its :class:`~graph_tool.PropertyMap` owner, and detects if the underlying data has been invalidated."""

    __array_priority__ = -10

    def _get_pmap(self):
        return self._prop_map

    def _set_pmap(self, value):
        self._prop_map = value

    prop_map = property(_get_pmap, _set_pmap,
                        doc=":class:`~graph_tool.PropertyMap` owner instance.")

    def __new__(cls, input_array, prop_map):
        obj = numpy.asarray(input_array).view(cls)
        obj.prop_map = prop_map

        # check if data really belongs to property map
        if (prop_map._get_data().__array_interface__['data'][0] !=
            obj._get_base_data()):
            obj.prop_map = None
            obj = numpy.asarray(obj)

        return obj

    def _get_base(self):
        base = self
        while base.base is not None:
            base = base.base
        return base

    def _get_base_data(self):
        return self._get_base().__array_interface__['data'][0]

    def _check_data(self):
        if self.prop_map is None:
            return

        data = self.prop_map._get_data()

        if (data is None or
            data.__array_interface__['data'][0] != self._get_base_data()):
            raise ValueError(("The graph correspondig to the underlying" +
                              " property map %s has changed. The" +
                              " PropertyArray at 0x%x is no longer valid!") %
                             (repr(self.prop_map), id(self)))

    def __array_finalize__(self, obj):
        if type(obj) is PropertyArray:
            obj._check_data()

        if obj is not None:
            # inherit prop_map only if the data is the same
            if (type(obj) is PropertyArray and
                self._get_base_data() == obj._get_base_data()):
                self.prop_map = getattr(obj, 'prop_map', None)
            else:
                self.prop_map = None
        self._check_data()

    def __array_prepare__(self, out_arr, context=None):
        self._check_data()
        return numpy.ndarray.__array_prepare__(self, out_arr, context)

    def __array_wrap__(self, out_arr, context=None):
        #demote to ndarray
        obj = numpy.ndarray.__array_wrap__(self, out_arr, context)
        return numpy.asarray(obj)

    # Overload members and operators to add data checking

    def _wrap_method(method):
        method = getattr(numpy.ndarray, method)

        def checked_method(self, *args, **kwargs):
            self._check_data()
            return method(self, *args, **kwargs)

        if ismethod(method):
            checked_method = _wraps(method)(checked_method)
        checked_method.__doc__ = getattr(method, "__doc__", None)
        return checked_method

    for method in ['all', 'any', 'argmax', 'argmin', 'argsort', 'astype',
                   'byteswap', 'choose', 'clip', 'compress', 'conj',
                   'conjugate', 'copy', 'cumprod', 'cumsum', 'diagonal', 'dot',
                   'dump', 'dumps', 'fill', 'flat', 'flatten', 'getfield',
                   'imag', 'item', 'itemset', 'itemsize', 'max', 'mean', 'min',
                   'newbyteorder', 'nonzero', 'prod', 'ptp', 'put', 'ravel',
                   'real', 'repeat', 'reshape', 'resize', 'round',
                   'searchsorted', 'setfield', 'setflags', 'sort', 'squeeze',
                   'std', 'sum', 'swapaxes', 'take', 'tofile', 'tolist',
                   'tostring', 'trace', 'transpose', 'var', 'view',
                   '__getitem__']:
        if hasattr(numpy.ndarray, method):
            locals()[method] = _wrap_method(method)


class PropertyMap(object):
    """This class provides a mapping from vertices, edges or whole graphs to arbitrary properties.

    The possible property types are listed below.

    .. table::

        =======================     ======================
         Type name                  Alias
        =======================     ======================
        ``bool``                    ``uint8_t``
        ``int32_t``                 ``int``
        ``int64_t``                 ``long``, ``long long``
        ``double``                  ``float``
        ``long double``
        ``string``
        ``vector<bool>``            ``vector<uint8_t>``
        ``vector<int32_t>``         ``vector<int>``
        ``vector<int64_t>``         ``vector<long>``, ``vector<long long>``
        ``vector<double>``          ``vector<float>``
        ``vector<long double>``
        ``vector<string>``
        ``python::object``          ``object``
        =======================     ======================
    """
    def __init__(self, pmap, g, key_type, key_trans=None):
        self.__map = pmap
        self.__g = weakref.ref(g)
        self.__key_type = key_type
        self.__key_trans = key_trans if key_trans is not None else lambda k: k
        self.__register_map()

    def __register_map(self):
        if self.__g() == None:
            return
        self.__g()._Graph__known_properties.append((self.key_type(),
                                                    weakref.ref(self.__map)))

    def __unregister_map(self):
        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]

    def __del__(self):
        self.__unregister_map()

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

    def __setitem__(self, k, v):
        key = self.__key_trans(k)
        try:
            self.__map[key] = v
        except TypeError:
            # attempt to convert to a compatible python type. This is useful,
            # for instance, when dealing with numpy scalar types.
            valtype = self.python_value_type()
            if isinstance(valtype, tuple):
                val = [valtype[1](x) for x in v]
            else:
                val = valtype(v)
            self.__map[key] = val

    def __repr__(self):
        # provide some more useful information
        if self.key_type() == "e":
            k = "Edge"
        elif self.key_type() == "v":
            k = "Vertex"
        else:
            k = "Graph"
        g = self.__g()
        if g == None:
            g = "a non-existent graph"
        else:
            g = "Graph 0x%x" % id(g)
        return ("<PropertyMap object with key type '%s' and value type '%s',"
                + " for %s, at 0x%x>") % (k, self.value_type(), g, id(self))

    def get_graph(self):
        """Get the graph class to which the map refers."""
        return self.__g()

    def key_type(self):
        """Return the key type of the map. Either 'g', 'v' or 'e'."""
        return self.__key_type

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

    def python_value_type(self):
        """Return the python-compatible value type of the map."""
        return _python_type(self.__map.value_type())

    def get_array(self):
        """Get a :class:`~graph_tool.PropertyArray` with the property values.

        .. WARNING::

           The returned array does not own the data, which belongs to the
           property map. Therefore, if the graph changes, the array may become
           *invalid* and any operation on it will fail with a
           :class:`ValueError` exception. Do **not** store the array if
           the graph is to be modified; store a **copy** instead.
        """
        a = self._get_data()
        if a is None:
            return None
        return PropertyArray(a, prop_map=self)

    def _get_data(self):
        if self.__g() is None:
            return None
        self.__g().stash_filter(edge=True, vertex=True)
        if self.__key_type == 'v':
            n = self.__g().num_vertices()
        elif self.__key_type == 'e':
            n = self.__g()._Graph__graph.GetMaxEdgeIndex() + 1
        else:
            n = 1
        self.__g().pop_filter(edge=True, vertex=True)
        a = self.__map.get_array(n)
        return a

    def __get_array(self):
        if self.get_array() is not None:
            return self.get_array()[:]
        else:
            return None

    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 itself, for convenience.""")

    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 ""))


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, scalar=True, floating=False):
    scalars = ["bool", "int32_t", "int64_t", "unsigned long",
               "double", "long double"]
    if not scalar:
        scalars += ["string"]
    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(props, value_type=None, vprop=None, pos=None):
    """Group list of properties ``props`` into a vector property map of the same type.

    Parameters
    ----------
    props : list of :class:`~graph_tool.PropertyMap`
        Properties to be grouped.
    value_type : string (optional, default: None)
        If supplied, defines the value type of the grouped property.
    vprop : :class:`~graph_tool.PropertyMap` (optional, default: None)
        If supplied, the properties are grouped into this property map.
    pos : list of ints (optional, default: None)
        If supplied, should contain a list of indexes where each corresponding
        element of ``props`` should be inserted.

    Returns
    -------
    vprop : :class:`~graph_tool.PropertyMap`
       A vector property map with the grouped values of each property map in
       ``props``.
    """
    g = props[0].get_graph()
    vtypes = 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)
        vtypes.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(vtypes) == 1:
            value_type = vtypes.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", scalar=False)

    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(vprop, pos, props=None):
    """Ungroup vector property map ``vprop`` into a list of individual property maps.

    Parameters
    ----------
    vprop : :class:`~graph_tool.PropertyMap`
        Vector property map to be ungrouped.
    pos : list of ints (optional, default: None)
        If supplied, should contain a list of indexes where each corresponding
        element of ``vprop`` should be inserted into the ``props`` list.
    props : list of :class:`~graph_tool.PropertyMap`  (optional, default: None)
        If supplied, should contain a list of property maps to which ``vprop``
        should be ungroupped.

    Returns
    -------
    props : list of :class:`~graph_tool.PropertyMap`
       A list of property maps with the ungrouped values of ``vprop``.
    """

    g = vprop.get_graph()
    _check_prop_vector(vprop, name="vprop", scalar=False)
    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]),
                                            p, 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


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)

################################################################################
# Graph class
# The main graph interface
################################################################################

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


class Graph(object):
    """Generic multigraph class.

    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.

    If ``g`` is specified, the graph (and its internal properties) will be
    copied.

    The graph is implemented as an `adjacency list`_, where both vertex and edge
    lists are C++ STL vectors.

    .. _adjacency list: http://en.wikipedia.org/wiki/Adjacency_list

    """

    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 specifies whether
        the graph should be directed or undirected."""
        self.__properties = {}
        self.__known_properties = []
        self.__filter_state = {"reversed": False,
                               "edge_filter": (None, False),
                               "vertex_filter": (None, False),
                               "directed": True}
        self.__stashed_filter_state = []

        if g == None:
            self.__graph = libcore.GraphInterface()
            self.set_directed(directed)
        else:
            self.__graph = libcore.GraphInterface(g.__graph, False)
            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)
                self.properties[k] = new_p

            self.__stashed_filter_state = [self.get_filter_state()]

            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()
        # 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")

        # modification permissions
        self.__perms = {"add_edge": True, "del_edge": True,
                        "add_vertex": True, "del_vertex": True}

    def copy(self):
        """Return a deep copy of self. All internal property maps are also
        copied."""
        return Graph(self)

    def __repr__(self):
        # provide some more useful information
        d = "directed" if self.is_directed() else "undirected"
        fr = ", reversed" if self.is_reversed() and self.is_directed() else ""
        f = ""
        if self.get_edge_filter()[0] != None:
            f += ", edges filtered by %s" % (str(self.get_edge_filter()))
        if self.get_vertex_filter()[0] != None:
            f += ", vertices filtered by %s" % (str(self.get_vertex_filter()))
        n = self.num_vertices()
        e = self.num_edges()
        return "<%s object, %s%s, with %d %s and %d edge%s%s at 0x%x>"\
               % (type(self).__name__, d, fr, n,
                  "vertex" if n == 1 else "vertices", e, "" if e == 1 else "s",
                  f, id(self))

    # Graph access
    # ============

    def __check_perms(self, ptype):
        if not self.__perms[ptype]:
            raise RuntimeError("the graph cannot be modified at this point!")

    def vertices(self):
        """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)

        """
        return libcore.get_vertices(weakref.ref(self.__graph))

    def vertex(self, i, use_index=True):
        """Return the vertex with index ``i``. If ``use_index=False``, the
        ``i``-th vertex is returned (which can differ from the vertex with index
        ``i`` in case of filtered graphs). """
        if use_index:
            self.stash_filter(vertex=True)
        try:
            v = libcore.get_vertex(weakref.ref(self.__graph), int(i))
        finally:
            if use_index:
                self.pop_filter(vertex=True)
        return v

    def edge(self, s, t, all_edges=False):
        """Return the edge from vertex ``s`` to ``t``, if it exists. If
        ``all_edges=True`` then a list is returned with all the parallel edges
        from ``s`` to ``t``, otherwise only one edge is returned.

        This operation will take :math:`O(k(s))` time, where :math:`k(s)` is the
        out-degree of vertex :math:`s`.
        """
        s = self.vertex(int(s))
        t = self.vertex(int(t))
        edges = []
        for e in s.out_edges():
            if e.target() == t:
                if not all_edges:
                    return e
                edges.append(e)
        if all_edges:
            return edges
        return None

    def edges(self):
        """Return an iterator over the edges."""
        return libcore.get_edges(weakref.ref(self.__graph))

    def add_vertex(self, n=1):
        """Add a vertex to the graph, and return it. If ``n > 1``, ``n``
        vertices are inserted and a list is returned."""
        self.__check_perms("add_vertex")
        vlist = [libcore.add_vertex(weakref.ref(self.__graph)) \
                 for i in xrange(0, n)]
        if n == 1:
            return vlist[0]
        return vlist

    def remove_vertex(self, vertex):
        """Remove a vertex from the graph."""
        self.__check_perms("del_vertex")
        index = self.vertex_index[vertex]
        for pmap in self.__known_properties:
            if pmap[0] == "v" and pmap[1]() != None and \
                   pmap[1]() != self.__vertex_index._PropertyMap__map:
                self.__graph.ShiftVertexProperty(pmap[1]().get_map(), index)
        self.clear_vertex(vertex)
        libcore.remove_vertex(self.__graph, vertex)

    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)

    def clear_vertex(self, vertex):
        """Remove all in and out-edges from the given vertex."""
        del_es = set()
        for e in vertex.all_edges():
            del_es.add(e)
        for e in del_es:
            self.remove_edge(e)

    def add_edge(self, source, target):
        """Add a new edge from ``source`` to ``target`` to the graph, and return
        it."""
        self.__check_perms("add_edge")
        return libcore.add_edge(weakref.ref(self.__graph), source, target)

    def remove_edge(self, edge):
        """Remove an edge from the graph."""
        self.__check_perms("del_edge")
        return libcore.remove_edge(self.__graph, edge)

    def remove_edge_if(self, predicate):
        """Remove all 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)

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

    def clear_edges(self):
        """Remove all edges from the graph."""
        self.__check_perms("del_edge")
        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,
                          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")]
    """)

    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
    def __get_vertex_properties(self):
        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))
    vertex_properties = property(__get_vertex_properties,
                                 doc="Dictionary of vertex properties")

    # edge properties
    def __get_edge_properties(self):
        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))
    edge_properties = property(__get_edge_properties,
                                 doc="Dictionary of edge properties")

    # graph properties
    def __get_graph_properties(self):
        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):
        """List all internal properties.

        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")
        >>> g.graph_properties["gnat"] = g.new_graph_property("string", "hi there!")
        >>> g.list_properties()
        gnat           (graph)   (type: string, val: hi there!)
        bar            (vertex)  (type: python::object)
        foo            (vertex)  (type: double)
        foo            (edge)    (type: vector<double>)
        """

        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

        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):
        return self.__vertex_index
    vertex_index = property(_get_vertex_index,
                            doc="Vertex index map. This map is immutable.")

    def _get_edge_index(self):
        return self.__edge_index
    edge_index = property(_get_edge_index, doc="Edge index map.")

    def _get_max_edge_index(self):
        return self.__graph.GetMaxEdgeIndex()
    max_edge_index = property(_get_max_edge_index,
                              doc="The maximum value of the edge index map.")

    def reindex_edges(self):
        """
        Reset the edge indexes so that they lie in the [0, :meth:`~graph_tool.Graph.num_edges` - 1]
        range. The index ordering will be compatible with the sequence returned
        by the :meth:`~graph_tool.Graph.edges` function.

        .. WARNING::

           Calling this function will invalidate all existing edge property
           maps, if the index ordering is modified! The property maps will still
           be usable, but their contents will still be tied to the old indices,
           and thus may be scrambled.