__init__.py 75.3 KB
Newer Older
1
#! /usr/bin/env python
2
# -*- coding: utf-8 -*-
3
#
4
5
# graph_tool -- a general graph manipulation python module
#
Tiago Peixoto's avatar
Tiago Peixoto committed
6
# Copyright (C) 2006-2013 Tiago de Paula Peixoto <tiago@skewed.de>
7
8
9
10
11
12
13
14
15
16
17
18
19
20
#
# 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/>.

21
"""
Tiago Peixoto's avatar
Tiago Peixoto committed
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
graph_tool - efficient graph analysis and manipulation
======================================================

Summary
-------

.. autosummary::
   :nosignatures:

   Graph
   GraphView
   Vertex
   Edge
   PropertyMap
   PropertyArray
   load_graph
   group_vector_property
   ungroup_vector_property
40
41
   infect_vertex_property
   edge_difference
Tiago Peixoto's avatar
Tiago Peixoto committed
42
43
44
   value_types
   show_config

Tiago Peixoto's avatar
Tiago Peixoto committed
45
46

This module provides:
47

48
   1. A :class:`~graph_tool.Graph` class for graph representation and manipulation
49
50
   2. Property maps for Vertex, Edge or Graph.
   3. Fast algorithms implemented in C++.
51

52
53
How to use the documentation
----------------------------
54

55
56
Documentation is available in two forms: docstrings provided
with the code, and the full documentation available in
Tiago Peixoto's avatar
Tiago Peixoto committed
57
`the graph-tool homepage <http://graph-tool.skewed.de>`_.
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75

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)

Tiago Peixoto's avatar
Tiago Peixoto committed
76
77
Contents
--------
78
"""
79

80
from __future__ import division, absolute_import, print_function
81
82
83
import sys
if sys.version_info < (3,):
    range = xrange
84

Tiago Peixoto's avatar
Tiago Peixoto committed
85
__author__ = "Tiago de Paula Peixoto <tiago@skewed.de>"
Tiago Peixoto's avatar
Tiago Peixoto committed
86
__copyright__ = "Copyright 2006-2013 Tiago de Paula Peixoto"
Tiago Peixoto's avatar
Tiago Peixoto committed
87
__license__ = "GPL version 3 or above"
Tiago Peixoto's avatar
Tiago Peixoto committed
88
__URL__ = "http://graph-tool.skewed.de"
89

90
91
92
93
# import numpy and scipy before everything to avoid weird segmentation faults
# depending on the order things are imported.

import numpy
94
import numpy.ma
95
96
97
import scipy
import scipy.stats

98
99
100

from .dl_import import *
dl_import("from . import libgraph_tool_core as libcore")
Tiago Peixoto's avatar
Tiago Peixoto committed
101
102
__version__ = libcore.mod_info().version

103
from . import io  # sets up libcore io routines
Tiago Peixoto's avatar
Tiago Peixoto committed
104
105
106
107
108
109
110
111

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

Tiago Peixoto's avatar
Tiago Peixoto committed
112
from io import BytesIO
113
from .decorators import _wraps, _require, _attrs, _limit_args
Tiago Peixoto's avatar
Tiago Peixoto committed
114
from inspect import ismethod
Tiago Peixoto's avatar
Tiago Peixoto committed
115
116

__all__ = ["Graph", "GraphView", "Vertex", "Edge", "Vector_bool",
117
           "Vector_int16_t", "Vector_int32_t", "Vector_int64_t", "Vector_double",
Tiago Peixoto's avatar
Tiago Peixoto committed
118
119
           "Vector_long_double", "Vector_string", "value_types", "load_graph",
           "PropertyMap", "group_vector_property", "ungroup_vector_property",
120
           "infect_vertex_property", "edge_difference", "seed_rng", "show_config",
Tiago Peixoto's avatar
Tiago Peixoto committed
121
122
           "PropertyArray", "__author__", "__copyright__", "__URL__",
           "__version__"]
Tiago Peixoto's avatar
Tiago Peixoto committed
123

Tiago Peixoto's avatar
Tiago Peixoto committed
124
125
# this is rather pointless, but it works around a sphinx bug
graph_tool = sys.modules[__name__]
Tiago Peixoto's avatar
Tiago Peixoto committed
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171

################################################################################
# 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",
172
             "short": "int16_t",
Tiago Peixoto's avatar
Tiago Peixoto committed
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
             "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


207
208
209
210
def _gt_type(obj):
    t = type(obj)
    if t is numpy.longlong or t is numpy.uint64:
        return "long long"
211
212
    if issubclass(t, numpy.int16):
        return "short"
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
    if t is int or issubclass(t, numpy.int):
        return "int"
    if t is numpy.float128:
        return "long double"
    if t is float or issubclass(t, numpy.float):
        return "double"
    if t is str:
        return "string"
    if t is bool:
        return "bool"
    if issubclass(t, list) or issubclass(t, numpy.ndarray):
        return "vector<%s>" % _gt_type(obj[0])
    return "object"


228
229
230
231
232
233
234
235
236
def _convert(prop, val):
    # attempt to convert to a compatible python type. This is useful,
    # for instance, when dealing with numpy types.
    vtype = _python_type(prop.value_type())
    if type(vtype) is tuple:
        return [vtype[1](x) for x in val]
    return vtype(val)


Tiago Peixoto's avatar
Tiago Peixoto committed
237
238
239
def show_config():
    """Show ``graph_tool`` build configuration."""
    info = libcore.mod_info()
240
241
242
243
244
245
246
247
    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()))
Tiago Peixoto's avatar
Tiago Peixoto committed
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275

################################################################################
# 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
276
            # do a copy
Tiago Peixoto's avatar
Tiago Peixoto committed
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
            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.

357
358
359
    See :ref:`sec_property_maps` for more details.

    The possible property value types are listed below.
Tiago Peixoto's avatar
Tiago Peixoto committed
360
361
362
363
364
365
366

    .. table::

        =======================     ======================
         Type name                  Alias
        =======================     ======================
        ``bool``                    ``uint8_t``
367
        ``int16_t``                 ``short``
Tiago Peixoto's avatar
Tiago Peixoto committed
368
369
370
371
372
373
        ``int32_t``                 ``int``
        ``int64_t``                 ``long``, ``long long``
        ``double``                  ``float``
        ``long double``
        ``string``
        ``vector<bool>``            ``vector<uint8_t>``
374
        ``vector<int16_t>``         ``short``
Tiago Peixoto's avatar
Tiago Peixoto committed
375
376
377
378
379
380
381
382
        ``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``
        =======================     ======================
    """
383
    def __init__(self, pmap, g, key_type):
Tiago Peixoto's avatar
Tiago Peixoto committed
384
385
        self.__map = pmap
        self.__g = weakref.ref(g)
386
387
388
389
390
391
392
393
        self.__base_g = lambda: None
        try:
            if isinstance(g, GraphView):
                self.__base_g = weakref.ref(g.base)  # keep reference to the
                                                     # base graph, in case the
                                                     # graph view is deleted.
        except NameError:
            pass  # ignore if GraphView is yet undefined
Tiago Peixoto's avatar
Tiago Peixoto committed
394
395
396
        self.__key_type = key_type
        self.__register_map()

397
398
399
400
401
402
403
    def __key_trans(self, key):
        if self.key_type() == "g":
            return key._Graph__graph
        else:
            return key


Tiago Peixoto's avatar
Tiago Peixoto committed
404
    def __register_map(self):
405
406
        for g in [self.__g(), self.__base_g()]:
            if g is not None:
407
                g._Graph__known_properties[id(self)] = weakref.ref(self)
Tiago Peixoto's avatar
Tiago Peixoto committed
408
409

    def __unregister_map(self):
410
411
        for g in [self.__g(), self.__base_g()]:
            if g is not None:
412
                del g._Graph__known_properties[id(self)]
Tiago Peixoto's avatar
Tiago Peixoto committed
413
414
415
416
417
418
419
420
421
422
423
424

    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:
425
            self.__map[key] = _convert(self, v)
Tiago Peixoto's avatar
Tiago Peixoto committed
426
427
428
429
430
431
432
433
434

    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"
435
        g = self.get_graph()
Tiago Peixoto's avatar
Tiago Peixoto committed
436
437
438
439
440
441
442
        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))

443
444
445
446
    def copy(self, value_type=None):
        """Return a copy of the property map. If ``value_type`` is specified,
        the value type is converted to the chosen type."""
        return self.get_graph().copy_property(self, value_type=value_type)
447

Tiago Peixoto's avatar
Tiago Peixoto committed
448
449
    def get_graph(self):
        """Get the graph class to which the map refers."""
450
451
452
453
        g = self.__g()
        if g is None:
            g = self.__base_g()
        return g
Tiago Peixoto's avatar
Tiago Peixoto committed
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469

    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.

470
471
472
473
474
475
476
        .. note::

           An array is returned *only if* the value type of the property map is
           a scalar. For vector, string or object types, ``None`` is returned
           instead.

        .. warning::
Tiago Peixoto's avatar
Tiago Peixoto committed
477
478
479
480
481
482
483
484
485
486
487
488
489

           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):
490
491
        g = self.get_graph()
        if g is None:
Tiago Peixoto's avatar
Tiago Peixoto committed
492
            return None
493
        g.stash_filter(edge=True, vertex=True)
Tiago Peixoto's avatar
Tiago Peixoto committed
494
        if self.__key_type == 'v':
495
            n = g.num_vertices()
Tiago Peixoto's avatar
Tiago Peixoto committed
496
        elif self.__key_type == 'e':
497
            n = max(g.max_edge_index, 1)
Tiago Peixoto's avatar
Tiago Peixoto committed
498
499
        else:
            n = 1
500
        g.pop_filter(edge=True, vertex=True)
Tiago Peixoto's avatar
Tiago Peixoto committed
501
502
503
504
        a = self.__map.get_array(n)
        return a

    def __set_array(self, v):
505
506
507
508
        a = self.get_array()
        if a is None:
            return
        a[:] = v
Tiago Peixoto's avatar
Tiago Peixoto committed
509

510
    a = property(get_array, __set_array,
Tiago Peixoto's avatar
Tiago Peixoto committed
511
                 doc=r"""Shortcut to the :meth:`~PropertyMap.get_array` method
512
513
514
515
                 as an attribute. This makes assignments more convenient, e.g.:

                 >>> g = gt.Graph()
                 >>> g.add_vertex(10)
Tiago Peixoto's avatar
Tiago Peixoto committed
516
                 <...>
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
                 >>> prop = g.new_vertex_property("double")
                 >>> prop.a = np.random.random(10)           # Assignment from array
                 """)

    def __get_set_f_array(self, v=None, get=True):
        g = self.get_graph()
        if g is None:
            return None
        a = self.get_array()
        filt = [None]
        if self.__key_type == 'v':
            filt = g.get_vertex_filter()
        elif self.__key_type == 'e':
            filt = g.get_edge_filter()
        if get:
532
533
534
535
            if a is None:
                return a
            if filt[0] is None:
                return a
536
537
            return a[filt[0].a == (not filt[1])]
        else:
538
539
540
            if a is None:
                return
            if filt[0] is None:
541
542
543
544
                try:
                    a[:] = v
                except ValueError:
                    a[:] = v[:len(a)]
545
            else:
546
547
548
549
550
                m = filt[0].a == (not filt[1])
                try:
                    a[m] = v
                except ValueError:
                    a[m] = v[:len(m)][m]
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593

    fa = property(__get_set_f_array,
                  lambda self, v: self.__get_set_f_array(v, False),
                  doc=r"""The same as the :attr:`~PropertyMap.a` attribute, but
                  instead an *indexed* array is returned, which contains only
                  entries for vertices/edges which are not filtered out. If
                  there are no filters in place, the array is not indexed, and
                  is identical to the :attr:`~PropertyMap.a` attribute.

                  Note that because advanced indexing is triggered, a **copy**
                  of the array is returned, not a view, as for the
                  :attr:`~PropertyMap.a` attribute. Nevertheless, the assignment
                  of values to the *whole* array at once works as expected.""")

    def __get_set_m_array(self, v=None, get=True):
        g = self.get_graph()
        if g is None:
            return None
        a = self.get_array()
        filt = [None]
        if self.__key_type == 'v':
            filt = g.get_vertex_filter()
        elif self.__key_type == 'e':
            filt = g.get_edge_filter()
        if filt[0] is None or a is None:
            if get:
                return a
            else:
                return
        ma = numpy.ma.array(a, mask=(filt[0].a == False) if not filt[1] else (filt[0].a == True))
        if get:
            return ma
        else:
            ma[:] = v

    ma = property(__get_set_m_array,
                  lambda self, v: self.__get_set_m_array(v, False),
                  doc=r"""The same as the :attr:`~PropertyMap.a` attribute, but
                  instead a :class:`~numpy.ma.MaskedArray` object is returned,
                  which contains only entries for vertices/edges which are not
                  filtered out. If there are no filters in place, a regular
                  :class:`~graph_tool.PropertyArray` is returned, which is
                  identical to the :attr:`~PropertyMap.a` attribute.""")
Tiago Peixoto's avatar
Tiago Peixoto committed
594
595
596
597
598

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

599
600
601
602
603
    def __call__(self, a):
        p = self.copy()
        p.fa = a
        return p

Tiago Peixoto's avatar
Tiago Peixoto committed
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656

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``.
657
658
659
660
661
662

    Examples
    --------
    >>> from numpy.random import seed, randint
    >>> from numpy import array
    >>> seed(42)
Tiago Peixoto's avatar
Tiago Peixoto committed
663
    >>> gt.seed_rng(42)
664
    >>> g = gt.random_graph(100, lambda: (3, 3))
665
666
    >>> props = [g.new_vertex_property("int") for i in range(3)]
    >>> for i in range(3):
667
668
    ...    props[i].a = randint(0, 100, g.num_vertices())
    >>> gprop = gt.group_vector_property(props)
669
    >>> print(gprop[g.vertex(0)].a)
Tiago Peixoto's avatar
Tiago Peixoto committed
670
    [51 25  8]
671
    >>> print(array([p[g.vertex(0)] for p in props]))
Tiago Peixoto's avatar
Tiago Peixoto committed
672
    [51 25  8]
Tiago Peixoto's avatar
Tiago Peixoto committed
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
    """
    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)
709
            libcore.group_vector_property(g._Graph__graph, _prop(k, g, vprop),
Tiago Peixoto's avatar
Tiago Peixoto committed
710
711
712
713
714
                                          _prop(k, g, p),
                                          i if pos == None else pos[i],
                                          k == 'e')
            g.pop_filter(directed=True, reversed=True)
        else:
715
            vprop[g][i if pos is None else pos[i]] = p[g]
Tiago Peixoto's avatar
Tiago Peixoto committed
716
717
718
719
720
721
    return vprop


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

722
    Parameters
Tiago Peixoto's avatar
Tiago Peixoto committed
723
724
725
    ----------
    vprop : :class:`~graph_tool.PropertyMap`
        Vector property map to be ungrouped.
726
727
728
    pos : list of ints
        A list of indexes corresponding to where each element of ``vprop``
        should be inserted into the ungrouped list.
Tiago Peixoto's avatar
Tiago Peixoto committed
729
730
731
732
733
734
735
736
    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``.
737
738
739
740
741
742

    Examples
    --------
    >>> from numpy.random import seed, randint
    >>> from numpy import array
    >>> seed(42)
Tiago Peixoto's avatar
Tiago Peixoto committed
743
    >>> gt.seed_rng(42)
744
745
746
747
748
    >>> g = gt.random_graph(100, lambda: (3, 3))
    >>> prop = g.new_vertex_property("vector<int>")
    >>> for v in g.vertices():
    ...    prop[v] = randint(0, 100, 3)
    >>> uprops = gt.ungroup_vector_property(prop, [0, 1, 2])
749
    >>> print(prop[g.vertex(0)].a)
Tiago Peixoto's avatar
Tiago Peixoto committed
750
    [51 92 14]
751
    >>> print(array([p[g.vertex(0)] for p in uprops]))
Tiago Peixoto's avatar
Tiago Peixoto committed
752
    [51 92 14]
Tiago Peixoto's avatar
Tiago Peixoto committed
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
    """

    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


787
788
789
790
791
792
793
794
795
796
797
798
799
800
def infect_vertex_property(g, prop, vals=None):
    """Propagate the `prop` values of vertices with value `val` to all their
    out-neighbours.

    Parameters
    ----------
    prop : :class:`~graph_tool.PropertyMap`
        Property map to be modified.
    vals : list (optional, default: `None`)
        List of values to be propagated. If not provided, all values
        will be propagated.

    Returns
    -------
801
    None : ``None``
802
803
804
805
806

    Examples
    --------
    >>> from numpy.random import seed
    >>> seed(42)
Tiago Peixoto's avatar
Tiago Peixoto committed
807
    >>> gt.seed_rng(42)
808
    >>> g = gt.random_graph(100, lambda: (3, 3))
Tiago Peixoto's avatar
Tiago Peixoto committed
809
    >>> prop = g.vertex_index.copy("int32_t")
810
    >>> gt.infect_vertex_property(g, prop, [10])
811
    >>> print(sum(prop.a == 10))
Tiago Peixoto's avatar
Tiago Peixoto committed
812
    4
813
814
815
816
    """
    libcore.infect_vertex_property(g._Graph__graph, _prop("v", g, prop),
                                   vals)

Tiago Peixoto's avatar
Tiago Peixoto committed
817
818
819
820
821
822
823
824
825
826

def edge_difference(g, prop, ediff=None):
    """Return an edge property map corresponding to the difference between the
    values of `prop` of target and source vertices of each edge.

    Parameters
    ----------
    prop : :class:`~graph_tool.PropertyMap`
        Vertex property map to be used to compute the difference..
    ediff : :class:`~graph_tool.PropertyMap` (optional, default: `None`)
827
        If provided, the difference values will be stored in this property map.
Tiago Peixoto's avatar
Tiago Peixoto committed
828
829
830
831
832
833
834
835

    Returns
    -------
    ediff : :class:`~graph_tool.PropertyMap`
        Edge differences.

    Examples
    --------
Tiago Peixoto's avatar
Tiago Peixoto committed
836
    >>> gt.seed_rng(42)
Tiago Peixoto's avatar
Tiago Peixoto committed
837
838
    >>> g = gt.random_graph(100, lambda: (3, 3))
    >>> ediff = gt.edge_difference(g, g.vertex_index)
839
    >>> print(ediff.a)
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
    [ 22   7  90   1 -48 -21 -26 -39 -60 -84 -18 -12   3 -67 -48 -53 -79 -29
      13 -46 -16 -43  -4 -23  26 -64 -52  25 -64 -34  33 -15  31  29 -19 -51
      13   5  47   3   4  34  20 -32  55  19 -23  58 -22 -12  50 -21  37  63
      20 -23  -3   7  32 -18  52   1  -3  58  80  21  38  67  85  85  59  54
      24  14  66 -37 -10 -55  95  17  24  58  65  40  37   8  93  67  -1  68
      10  37   6  23  28  39  16  22  11   9  56  48  65 -11  12  61 -17  35
      36 -14 -10 -17  65  52 -29  26  -4 -23 -36 -17  26  -5  17 -38 -22 -29
     -10  -3  11  32 -24  24 -61  17 -25  17  -4  10  14 -40 -62 -74 -82 -44
     -87 -50 -46 -23 -56 -72  -4  22  24 -61 -36 -27 -30 -18 -51 -21 -27 -17
     -43 -11 -46 -42   1 -76  -2 -70   8  -7  -9 -77 -76 -67 -72 -12 -77 -43
      -5 -12 -59 -79 -68  -7 -20 -24 -10 -45   4  10 -19   1 -11 -30 -41 -46
      17 -16 -62   2  15 -28 -38  14 -29  11   3 -30 -46   7  16  44  37  19
     -21  44  23  64  14  71  31  66  30  15 -50 -20  33  65 -13  24  60  30
      49  -8  71  70  73  56  65  12  21 -20  32  17  56 -19   9  64   7  52
       3  27  22  -1  -8  10 -10 -22 -18  15 -31 -15  15  -8  10  -2  -8   9
       6 -24  18  50  12  36  -5  45  14   7 -50 -39   4  36  37 -11   7 -31
      14  22  27 -63 -53 -42 -39 -37  15 -37 -58  32]
Tiago Peixoto's avatar
Tiago Peixoto committed
857
858
859
860
861
862
863
864
865
866
867
868
869
870
    """
    val_t = prop.value_type()
    if val_t == "unsigned long":
        val_t = "int32_t"
    if ediff is None:
        ediff = g.new_edge_property(val_t)
    if ediff.value_type() != val_t:
        raise ValueError("'ediff' must be of the same value type as 'prop': " +
                         val_t)
    libcore.edge_difference(g._Graph__graph, _prop("v", g, prop),
                            _prop("e", g, ediff))
    return ediff


Tiago Peixoto's avatar
Tiago Peixoto committed
871
872
class PropertyDict(dict):
    """Wrapper for the dict of vertex, graph or edge properties, which sets the
873
874
875
876
877
878
879
880
881
    value on the property map when changed in the dict.

    .. note::

        The class is only an one-way proxy to the internally-kept properties. If
        you modify this object, the change will be propagated to the internal
        dictionary, but not vice-versa. Keep this in mind if you intend to keep
        a copy of the class instance.
    """
Tiago Peixoto's avatar
Tiago Peixoto committed
882
883
884
885
886
887
888
889
    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

890
891
892
893
    def __getitem__(self, key):
        if self.get_func != None:
            val = self.get_func(self.g, key)
            dict.__setitem__(self, key, val)
894
            return val
895
896
897
        else:
            raise KeyError("Property dict cannot be gotten")

Tiago Peixoto's avatar
Tiago Peixoto committed
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
    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
################################################################################

914
915
916
from .libgraph_tool_core import Vertex, EdgeBase, Vector_bool, Vector_int16_t, \
    Vector_int32_t, Vector_int64_t, Vector_double, Vector_long_double, \
    Vector_string, new_vertex_property, new_edge_property, new_graph_property
Tiago Peixoto's avatar
Tiago Peixoto committed
917
918
919
920
921


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

922
923
    This class encapsulates either a directed multigraph (default or if
    ``directed=True``) or an undirected multigraph (if ``directed=False``),
924
    with optional internal edge, vertex or graph properties.
Tiago Peixoto's avatar
Tiago Peixoto committed
925
926
927
928

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

929
930
931
932
933
    If ``prune`` is set to ``True``, and ``g`` is specified, only the filtered
    graph will be copied, and the new graph object will not be
    filtered. Optionally, a tuple of three booleans can be passed as value to
    ``prune``, to specify a different behavior to vertex, edge, and reversal
    filters, respectively.
934

Tiago Peixoto's avatar
Tiago Peixoto committed
935
936
937
938
939
940
941
    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

    """

942
    def __init__(self, g=None, directed=True, prune=False):
Tiago Peixoto's avatar
Tiago Peixoto committed
943
        self.__properties = {}
944
        self.__known_properties = {}
Tiago Peixoto's avatar
Tiago Peixoto committed
945
946
947
948
949
950
        self.__filter_state = {"reversed": False,
                               "edge_filter": (None, False),
                               "vertex_filter": (None, False),
                               "directed": True}
        self.__stashed_filter_state = []

951
        if g is None:
Tiago Peixoto's avatar
Tiago Peixoto committed
952
953
954
            self.__graph = libcore.GraphInterface()
            self.set_directed(directed)
        else:
955
956
957
958
959
960
            if isinstance(prune, bool):
                vprune = eprune = rprune = prune
            else:
                vprune, eprune, rprune = prune
            if not (vprune or eprune or rprune):
                g.stash_filter(vertex=vprune, edge=vprune, reversed=rprune)
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992

            # Copy all internal properties from original graph.
            vprops = []
            eprops = []
            for k, v in g.vertex_properties.items():
                vprops.append([_prop("v", g, v), libcore.any()])
            for k, v in g.edge_properties.items():
                eprops.append([_prop("e", g, v), libcore.any()])

            # The actual copying of the graph and property maps
            self.__graph = libcore.GraphInterface(g.__graph, False, vprops, eprops)

            # Put the copied properties in the internal dictionary
            for k, v in g.vertex_properties.items():
                pmap = new_vertex_property(v.value_type(),
                                           self.__graph.GetVertexIndex(),
                                           vprops[0][1])
                self.vertex_properties[k] = PropertyMap(pmap, self, "v")
                del vprops[0]

            for k, v in g.edge_properties.items():
                pmap = new_edge_property(v.value_type(),
                                         self.__graph.GetEdgeIndex(),
                                         eprops[0][1])
                self.edge_properties[k] = PropertyMap(pmap, self, "e")
                del eprops[0]

            for k, v in g.graph_properties.items():
                new_p = self.new_graph_property(v.value_type())
                new_p[self] = v[g]
                self.graph_properties[k] = new_p

993
994
995
            if not (vprune or eprune or rprune):
                g.pop_filter(vertex=vprune, edge=vprune, reversed=rprune)

Tiago Peixoto's avatar
Tiago Peixoto committed
996
997
            self.__stashed_filter_state = [self.get_filter_state()]

998
999
1000
            if not vprune:
                v_filt, v_rev = g.__filter_state["vertex_filter"]
                if v_filt != None:
1001
                    if v_filt not in list(g.vertex_properties.values()):
1002
1003
1004
1005
                        new_filt = self.new_vertex_property("bool")
                        self.copy_property(v_filt, new_filt)

                    else:
1006
                        for k, v in g.vertex_properties.items():
1007
1008
1009
1010
1011
1012
1013
                            if v == v_filt:
                                new_filt = self.vertex_properties[k]
                    self.__stashed_filter_state[0]["vertex_filter"] = (new_filt,
                                                                       v_rev)
            if not eprune:
                e_filt, e_rev = g.__filter_state["edge_filter"]
                if e_filt != None:
1014
                    if e_filt not in list(g.edge_properties.values()):
1015
1016
1017
1018
                        new_filt = self.new_edge_property("bool")
                        self.copy_property(e_filt, new_filt)

                    else:
1019
                        for k, v in g.edge_properties.items():
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
                            if v == e_filt:
                                new_filt = self.edge_properties[k]
                    self.__stashed_filter_state[0]["edge_filter"] = (new_filt,
                                                                     e_rev)
            if not rprune:
                self.__stashed_filter_state[0]["reversed"] = g.is_reversed()

            # directedness is always a filter
            self.__stashed_filter_state[0]["directed"] = g.is_directed()

Tiago Peixoto's avatar
Tiago Peixoto committed
1030
            self.pop_filter()
1031

Tiago Peixoto's avatar
Tiago Peixoto committed
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
        # 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):
1043
1044
        """Return a deep copy of self. All :ref:`internal property maps <sec_internal_props>`
        are also copied."""
Tiago Peixoto's avatar
Tiago Peixoto committed
1045
1046
1047
        return Graph(self)

    def __repr__(self):
1048
        # provide more useful information
Tiago Peixoto's avatar
Tiago Peixoto committed
1049
1050
1051
        d = "directed" if self.is_directed() else "undirected"
        fr = ", reversed" if self.is_reversed() and self.is_directed() else ""
        f = ""
1052
        if self.get_edge_filter()[0] is not None:
Tiago Peixoto's avatar
Tiago Peixoto committed
1053
            f += ", edges filtered by %s" % (str(self.get_edge_filter()))
1054
        if self.get_vertex_filter()[0] is not None:
Tiago Peixoto's avatar
Tiago Peixoto committed
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
            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):
1071
1072
1073
1074
1075
1076
1077
        """Return an :meth:`iterator <iterator.__iter__>` over the vertices.

        .. note::

           The order of the vertices traversed by the iterator **always**
           corresponds to the vertex index ordering, as given by the
           :attr:`~graph_tool.Graph.vertex_index` property map.
Tiago Peixoto's avatar
Tiago Peixoto committed
1078
1079
1080
1081

        Examples
        --------
        >>> g = gt.Graph()
Tiago Peixoto's avatar
Tiago Peixoto committed
1082
        >>> vlist = list(g.add_vertex(5))
Tiago Peixoto's avatar
Tiago Peixoto committed
1083
1084
1085
1086
1087
1088
1089
        >>> vlist2 = []
        >>> for v in g.vertices():
        ...     vlist2.append(v)
        ...
        >>> assert(vlist == vlist2)

        """
1090
        return libcore.get_vertices(weakref.ref(self))
Tiago Peixoto's avatar
Tiago Peixoto committed
1091
1092
1093
1094
1095
1096
1097
1098

    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:
1099
            v = libcore.get_vertex(weakref.ref(self), int(i))
Tiago Peixoto's avatar
Tiago Peixoto committed
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
        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):
1126
1127
1128
1129
1130
        """Return an :meth:`iterator <iterator.__iter__>` over the edges.

        .. note::

           The order of the edges traversed by the iterator **does not**
Tiago Peixoto's avatar
Tiago Peixoto committed
1131
           necessarily correspond to the edge index ordering, as given by the
1132
1133
1134
1135
1136
1137
1138
           :attr:`~graph_tool.Graph.edge_index` property map. This will only
           happen after :meth:`~graph_tool.Graph.reindex_edges` is called, or in
           certain situations such as just after a graph is loaded from a
           file. However, further manipulation of the graph may destroy the
           ordering.

        """
1139
        return libcore.get_edges(weakref.ref(self))
Tiago Peixoto's avatar
Tiago Peixoto committed
1140
1141
1142

    def add_vertex(self, n=1):
        """Add a vertex to the graph, and return it. If ``n > 1``, ``n``
1143
        vertices are inserted and an iterator over the new vertices is returned."""
Tiago Peixoto's avatar
Tiago Peixoto committed
1144
        self.__check_perms("add_vertex")
1145
1146
1147
1148
1149
1150
        v = libcore.add_vertex(weakref.ref(self), n)

        if n <= 1:
            return v
        else:
            pos = self.num_vertices() - n
1151
            return (self.vertex(i) for i in range(pos, pos + n))
Tiago Peixoto's avatar
Tiago Peixoto committed
1152
1153
1154
1155

    def remove_vertex(self, vertex):
        """Remove a vertex from the graph."""
        self.__check_perms("del_vertex")
1156
        vertex = self.vertex(int(vertex))
Tiago Peixoto's avatar
Tiago Peixoto committed
1157
        index = self.vertex_index[vertex]
1158
1159
1160
        for pmap in self.__known_properties.values():
            if pmap() is not None and pmap().key_type() == "v" and pmap().is_writable():
                self.__graph.ShiftVertexProperty(pmap()._PropertyMap__map.get_map(), index)
Tiago Peixoto's avatar
Tiago Peixoto committed
1161
1162
1163
1164
1165
1166
1167
        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()
1168
        for i in range(0, N):
Tiago Peixoto's avatar
Tiago Peixoto committed
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
            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")
1185
1186
        e = libcore.add_edge(weakref.ref(self), self.vertex(int(source)),
                             self.vertex(int(target)))
1187
1188
1189
1190
        efilt = self.get_edge_filter()
        if efilt[0] is not None:
            efilt[0][e] = not efilt[1]
        return e
Tiago Peixoto's avatar
Tiago Peixoto committed
1191
1192
1193
1194

    def remove_edge(self, edge):
        """Remove an edge from the graph."""
        self.__check_perms("del_edge")
Tiago Peixoto's avatar
Tiago Peixoto committed
1195
        return libcore.remove_edge(self.__graph, edge)
Tiago Peixoto's avatar
Tiago Peixoto committed
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231

    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)
    def __set_property(self, t, k, v):
1232
1233
1234
1235
1236
1237
        if t == "g" and not isinstance(v, PropertyMap):
            self.__properties[(t, k)][self] = v
        else:
            if t != v.key_type():
                raise ValueError("wrong key type for property map")
            self.__properties[(t, k)] = v
Tiago Peixoto's avatar
Tiago Peixoto committed
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247

    @_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
1248
1249
    vertex, edge or graph property, respectively, and the second element is the
    name of the property map.
Tiago Peixoto's avatar
Tiago Peixoto committed
1250
1251
1252
1253
1254
1255
1256
1257
1258

    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):
1259
        props = dict([(k[1], v) for k, v in self.__properties.items() \
1260
                      if k[0] == t])
Tiago Peixoto's avatar
Tiago Peixoto committed
1261
1262
1263
1264
1265
1266
1267
1268
1269
        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,
1270
                                 doc="Dictionary of internal vertex properties. The keys are the property names.")
1271
1272
    vp = property(__get_vertex_properties,
                  doc="Alias to :attr:`~Graph.vertex_properties`.")
Tiago Peixoto's avatar
Tiago Peixoto committed
1273
1274
1275
1276
1277
1278
1279
1280

    # 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,
1281
                                 doc="Dictionary of internal edge properties. The keys are the property names.")
Tiago Peixoto's avatar
Tiago Peixoto committed
1282
    ep = property(__get_edge_properties,
1283
                  doc="Alias to :attr:`~Graph.edge_properties`.")
Tiago Peixoto's avatar
Tiago Peixoto committed
1284
1285
1286
1287

    # graph properties
    def __get_graph_properties(self):
        return PropertyDict(self, self.__get_specific_properties("g"),
1288
                            lambda g, k: g.__properties[("g", k)][g],
Tiago Peixoto's avatar
Tiago Peixoto committed
1289
1290
1291
                            lambda g, k, v: g.__set_property("g", k, v),
                            lambda g, k: g.__del_property("g", k))
    graph_properties = property(__get_graph_properties,
1292
                                 doc="Dictionary of internal graph properties. The keys are the property names.")
1293
1294
    gp = property(__get_graph_properties,
                  doc="Alias to :attr:`~Graph.graph_properties`.")
Tiago Peixoto's avatar
Tiago Peixoto committed
1295

1296
1297
1298
1299
    def own_property(self, prop):
        """'Own' property map 'prop', which may belong to another graph."""
        return PropertyMap(prop._PropertyMap__map, self, prop.key_type())

Tiago Peixoto's avatar
Tiago Peixoto committed
1300
    def list_properties(self):
1301
        """Print a list of all internal properties.
Tiago Peixoto's avatar
Tiago Peixoto committed
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318

        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
1319
        w = max([len(x[0]) for x in list(self.__properties.keys())]) + 4
Tiago Peixoto's avatar
Tiago Peixoto committed
1320
1321
        w = w if w > 14 else 14

1322
        for k, v in self.__properties.items():
Tiago Peixoto's avatar
Tiago Peixoto committed
1323
            if k[0] == "g":
1324
1325
1326
                print("%%-%ds (graph)   (type: %%s, val: %%s)" % w % \
                      (k[1], v.value_type(), str(v[self])))
        for k, v in self.__properties.items():
Tiago Peixoto's avatar
Tiago Peixoto committed
1327
            if k[0] == "v":
1328
1329
1330
                print("%%-%ds (vertex)  (type: %%s)" % w % (k[1],
                                                            v.value_type()))
        for k, v in self.__properties.items():
Tiago Peixoto's avatar
Tiago Peixoto committed
1331
            if k[0] == "e":
1332
1333
                print("%%-%ds (edge)    (type: %%s)" % w % (k[1],
                                                            v.value_type()))
Tiago Peixoto's avatar
Tiago Peixoto committed
1334
1335
1336
1337
1338
1339

    # index properties

    def _get_vertex_index(self):
        return self.__vertex_index
    vertex_index = property(_get_vertex_index,
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
                            doc="""Vertex index map.

                            It maps for each vertex in the graph an unique
                            integer in the range [0, :meth:`~graph_tool.Graph.num_vertices` - 1].

                            .. note::

                                This is a special instance of a :class:`~graph_tool.PropertyMap`
                                class, which is **immutable**, and cannot be
                                accessed as an array.""")
Tiago Peixoto's avatar
Tiago Peixoto committed
1350
1351
1352

    def _get_edge_index(self):
        return self.__edge_index
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
    edge_index = property(_get_edge_index, doc="""Edge index map.

                            It maps for each edge in the graph an unique
                            integer.

                            .. warning::

                                Differently from :attr:`~graph_tool.Graph.vertex_index`,
                                this is a **regular** instance of a :class:`~graph_tool.PropertyMap`
                                class, and is therefore **mutable**!

                                Additionally, the indexes may not necessarily
                                lie in the range [0, :meth:`~graph_tool.Graph.num_edges` - 1].
                                However this will always happen whenever no
                                edges are deleted from the graph.

                                The internal consistency expected by most
                                algorithms and the proper functioning of
                                property maps assume that the indexes are unique
                                and constant, which is guaranteed by the
                                library.  Therefore it is recommended **never**
                                to modify these values, unless you know what you
                                are doing.""")
Tiago Peixoto's avatar
Tiago Peixoto committed
1376
1377
1378

    def _get_max_edge_index(self):
        return self.__graph.GetMaxEdgeIndex()
1379

Tiago Peixoto's avatar
Tiago Peixoto committed
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
    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
1393
1394
           be usable, but their contents will still be tied to the old indexes,
           and thus may become scrambled.
Tiago Peixoto's avatar
Tiago Peixoto committed
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
        """
        self.__graph.ReIndexEdges()

    # Property map creation

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

    def new_vertex_property(self, value_type):
        """Create a new (uninitialized) vertex property map of type
        ``value_type``, and return it."""
        return PropertyMap(new_vertex_property(_type_alias(value_type),
1417
1418
                                               self.__graph.GetVertexIndex(),
                                               libcore.any()),
Tiago Peixoto's avatar
Tiago Peixoto committed
1419
1420
1421
1422
1423
1424
                           self, "v")

    def new_edge_property(self, value_type):
        """Create a new (uninitialized) edge property map of type
        ``value_type``, and return it."""
        return PropertyMap(new_edge_property(_type_alias(value_type),
1425
1426
                                             self.__graph.GetEdgeIndex(),
                                             libcore.any()),
Tiago Peixoto's avatar
Tiago Peixoto committed
1427
1428
1429
1430
1431
1432
                           self, "e")

    def new_graph_property(self, value_type, val=None):
        """Create a new graph property map of type ``value_type``, and return
        it. If ``val`` is not None, the property is initialized to its value."""
        prop = PropertyMap(new_graph_property(_type_alias(value_type),
1433
1434
1435
1436
                                              self.__graph.GetGraphIndex(),
                                              libcore.any()),
                           self, "g")
        if val is not None:
Tiago Peixoto's avatar
Tiago Peixoto committed
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
            prop[self] = val
        return prop

    # property map copying
    @_require("src", PropertyMap)
    @_require("tgt", (PropertyMap, type(None)))
    def copy_property(self, src, tgt=None, value_type=None, g=None):
        """Copy contents of ``src`` property to ``tgt`` property. If ``tgt`` is
        None, then a new property map of the same type (or with the type given
        by the optional ``value_type`` parameter) is created, and returned. The
        optional parameter g specifies the (identical) source graph to copy
        properties from (defaults to self).
        """
1450
        if tgt is None:
Tiago Peixoto's avatar
Tiago Peixoto committed
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
            tgt = self.new_property(src.key_type(),
                                    (src.value_type()
                                     if value_type == None else value_type))
            ret = tgt
        else:
            ret = None

        if src.key_type() != tgt.key_type():
            raise ValueError("source and target properties must have the same" +
                             " key type")
1461
        if g is None:
Tiago Peixoto's avatar
Tiago Peixoto committed
1462
            g = self
1463
1464
1465
        if g is not self:
            g.stash_filter(directed=True, reversed=True)
        self.stash_filter(directed=True, reversed=True)
Tiago Peixoto's avatar
Tiago Peixoto committed
1466
1467
        if src.key_type() == "v":
            self.__graph.CopyVertexProperty(g.__graph, _prop("v", g, src),
1468
                                            _prop("v", self, tgt))
Tiago Peixoto's avatar
Tiago Peixoto committed
1469
1470
        elif src.key_type() == "e":
            self.__graph.CopyEdgeProperty(g.__graph, _prop("e", g, src),
1471
                                            _prop("e", self, tgt))
Tiago Peixoto's avatar
Tiago Peixoto committed
1472
1473
        else:
            tgt[self] = src[g]
1474
1475
1476
        self.pop_filter(directed=True, reversed=True)
        if g is not self:
            g.pop_filter(directed=True, reversed=True)
Tiago Peixoto's avatar
Tiago Peixoto committed
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
        return ret

    # 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")

    # I/O operations
    # ==============
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
    def __get_file_format(self, file_name):
        fmt = None
        for f in ["xml", "dot", "gml"]:
            names = ["." + f, ".%s.gz" % f, ".%s.bz2" % f]
            for name in names:
                if file_name.endswith(name):
                    fmt = f
                    break
        if fmt is None:
            raise ValueError("cannot determine file format of: " + file_name)
        return fmt

    def load(self, file_name, fmt="auto"):
Tiago Peixoto's avatar
Tiago Peixoto committed
1501
1502
        """Load graph from ``file_name`` (which can be either a string or a
        file-like object). The format is guessed from ``file_name``, or can be
1503
        specified by ``fmt``, which can be either "xml", "dot" or "gml". """
Tiago Peixoto's avatar
Tiago Peixoto committed
1504
1505
1506

        if type(file_name) == str:
            file_name = os.path.expanduser(file_name)
1507
1508
1509
1510
        if fmt == 'auto' and isinstance(file_name, str):
            fmt = self.__get_file_format(file_name)
        elif fmt == "auto":
            fmt = "xml"
Tiago Peixoto's avatar
Tiago Peixoto committed
1511
        if isinstance(file_name, str):
1512
            props = self.__graph.ReadFromFile(file_name, None, fmt)
Tiago Peixoto's avatar
Tiago Peixoto committed
1513
        else:
1514
            props = self.__graph.ReadFromFile("", file_name, fmt)
1515
        for name, prop in props[0].items():
Tiago Peixoto's avatar
Tiago Peixoto committed
1516
            self.vertex_properties[name] = PropertyMap(prop, self, "v")
1517
        for name, prop in props[1].items():
Tiago Peixoto's avatar
Tiago Peixoto committed
1518
            self.edge_properties[name] = PropertyMap(prop, self, "e")
1519
        for name, prop in props[2].items():
1520
            self.graph_properties[name] = PropertyMap(prop, self, "g")
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
        if "_Graph__save__vfilter" in self.graph_properties:
            self.set_vertex_filter(self.vertex_properties["_Graph__save__vfilter"],
                                   self.graph_properties["_Graph__save__vfilter"])
            del self.vertex_properties["_Graph__save__vfilter"]
            del self.graph_properties["_Graph__save__vfilter"]
        if "_Graph__save__efilter" in self.graph_properties:
            self.set_edge_filter(self.edge_properties["_Graph__save__efilter"],
                                 self.graph_properties["_Graph__save__efilter"])
            del self.edge_properties["_Graph__save__efilter"]
            del self.graph_properties["_Graph__save__efilter"]
        if "_Graph__reversed" in self.graph_properties:
            self.set_reversed(True)
            del self.graph_properties["_Graph__reversed"]


Tiago Peixoto's avatar
Tiago Peixoto committed
1536

1537
    def save(self, file_name, fmt="auto"):
Tiago Peixoto's avatar
Tiago Peixoto committed
1538
1539
        """Save graph to ``file_name`` (which can be either a string or a
        file-like object). The format is guessed from the ``file_name``, or can
1540
        be specified by ``fmt``, which can be either "xml", "dot" or "gml". """
Tiago Peixoto's avatar
Tiago Peixoto committed
1541

1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
        if self.g