|
""" |
|
Miscellaneous Helpers for NetworkX. |
|
|
|
These are not imported into the base networkx namespace but |
|
can be accessed, for example, as |
|
|
|
>>> import networkx |
|
>>> networkx.utils.make_list_of_ints({1, 2, 3}) |
|
[1, 2, 3] |
|
>>> networkx.utils.arbitrary_element({5, 1, 7}) # doctest: +SKIP |
|
1 |
|
""" |
|
|
|
import random |
|
import sys |
|
import uuid |
|
import warnings |
|
from collections import defaultdict, deque |
|
from collections.abc import Iterable, Iterator, Sized |
|
from itertools import chain, tee |
|
|
|
import networkx as nx |
|
|
|
__all__ = [ |
|
"flatten", |
|
"make_list_of_ints", |
|
"dict_to_numpy_array", |
|
"arbitrary_element", |
|
"pairwise", |
|
"groups", |
|
"create_random_state", |
|
"create_py_random_state", |
|
"PythonRandomInterface", |
|
"PythonRandomViaNumpyBits", |
|
"nodes_equal", |
|
"edges_equal", |
|
"graphs_equal", |
|
"_clear_cache", |
|
] |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
def flatten(obj, result=None): |
|
"""Return flattened version of (possibly nested) iterable object.""" |
|
if not isinstance(obj, Iterable | Sized) or isinstance(obj, str): |
|
return obj |
|
if result is None: |
|
result = [] |
|
for item in obj: |
|
if not isinstance(item, Iterable | Sized) or isinstance(item, str): |
|
result.append(item) |
|
else: |
|
flatten(item, result) |
|
return tuple(result) |
|
|
|
|
|
def make_list_of_ints(sequence): |
|
"""Return list of ints from sequence of integral numbers. |
|
|
|
All elements of the sequence must satisfy int(element) == element |
|
or a ValueError is raised. Sequence is iterated through once. |
|
|
|
If sequence is a list, the non-int values are replaced with ints. |
|
So, no new list is created |
|
""" |
|
if not isinstance(sequence, list): |
|
result = [] |
|
for i in sequence: |
|
errmsg = f"sequence is not all integers: {i}" |
|
try: |
|
ii = int(i) |
|
except ValueError: |
|
raise nx.NetworkXError(errmsg) from None |
|
if ii != i: |
|
raise nx.NetworkXError(errmsg) |
|
result.append(ii) |
|
return result |
|
|
|
for indx, i in enumerate(sequence): |
|
errmsg = f"sequence is not all integers: {i}" |
|
if isinstance(i, int): |
|
continue |
|
try: |
|
ii = int(i) |
|
except ValueError: |
|
raise nx.NetworkXError(errmsg) from None |
|
if ii != i: |
|
raise nx.NetworkXError(errmsg) |
|
sequence[indx] = ii |
|
return sequence |
|
|
|
|
|
def dict_to_numpy_array(d, mapping=None): |
|
"""Convert a dictionary of dictionaries to a numpy array |
|
with optional mapping.""" |
|
try: |
|
return _dict_to_numpy_array2(d, mapping) |
|
except (AttributeError, TypeError): |
|
|
|
|
|
return _dict_to_numpy_array1(d, mapping) |
|
|
|
|
|
def _dict_to_numpy_array2(d, mapping=None): |
|
"""Convert a dictionary of dictionaries to a 2d numpy array |
|
with optional mapping. |
|
|
|
""" |
|
import numpy as np |
|
|
|
if mapping is None: |
|
s = set(d.keys()) |
|
for k, v in d.items(): |
|
s.update(v.keys()) |
|
mapping = dict(zip(s, range(len(s)))) |
|
n = len(mapping) |
|
a = np.zeros((n, n)) |
|
for k1, i in mapping.items(): |
|
for k2, j in mapping.items(): |
|
try: |
|
a[i, j] = d[k1][k2] |
|
except KeyError: |
|
pass |
|
return a |
|
|
|
|
|
def _dict_to_numpy_array1(d, mapping=None): |
|
"""Convert a dictionary of numbers to a 1d numpy array with optional mapping.""" |
|
import numpy as np |
|
|
|
if mapping is None: |
|
s = set(d.keys()) |
|
mapping = dict(zip(s, range(len(s)))) |
|
n = len(mapping) |
|
a = np.zeros(n) |
|
for k1, i in mapping.items(): |
|
i = mapping[k1] |
|
a[i] = d[k1] |
|
return a |
|
|
|
|
|
def arbitrary_element(iterable): |
|
"""Returns an arbitrary element of `iterable` without removing it. |
|
|
|
This is most useful for "peeking" at an arbitrary element of a set, |
|
but can be used for any list, dictionary, etc., as well. |
|
|
|
Parameters |
|
---------- |
|
iterable : `abc.collections.Iterable` instance |
|
Any object that implements ``__iter__``, e.g. set, dict, list, tuple, |
|
etc. |
|
|
|
Returns |
|
------- |
|
The object that results from ``next(iter(iterable))`` |
|
|
|
Raises |
|
------ |
|
ValueError |
|
If `iterable` is an iterator (because the current implementation of |
|
this function would consume an element from the iterator). |
|
|
|
Examples |
|
-------- |
|
Arbitrary elements from common Iterable objects: |
|
|
|
>>> nx.utils.arbitrary_element([1, 2, 3]) # list |
|
1 |
|
>>> nx.utils.arbitrary_element((1, 2, 3)) # tuple |
|
1 |
|
>>> nx.utils.arbitrary_element({1, 2, 3}) # set |
|
1 |
|
>>> d = {k: v for k, v in zip([1, 2, 3], [3, 2, 1])} |
|
>>> nx.utils.arbitrary_element(d) # dict_keys |
|
1 |
|
>>> nx.utils.arbitrary_element(d.values()) # dict values |
|
3 |
|
|
|
`str` is also an Iterable: |
|
|
|
>>> nx.utils.arbitrary_element("hello") |
|
'h' |
|
|
|
:exc:`ValueError` is raised if `iterable` is an iterator: |
|
|
|
>>> iterator = iter([1, 2, 3]) # Iterator, *not* Iterable |
|
>>> nx.utils.arbitrary_element(iterator) |
|
Traceback (most recent call last): |
|
... |
|
ValueError: cannot return an arbitrary item from an iterator |
|
|
|
Notes |
|
----- |
|
This function does not return a *random* element. If `iterable` is |
|
ordered, sequential calls will return the same value:: |
|
|
|
>>> l = [1, 2, 3] |
|
>>> nx.utils.arbitrary_element(l) |
|
1 |
|
>>> nx.utils.arbitrary_element(l) |
|
1 |
|
|
|
""" |
|
if isinstance(iterable, Iterator): |
|
raise ValueError("cannot return an arbitrary item from an iterator") |
|
|
|
return next(iter(iterable)) |
|
|
|
|
|
|
|
def pairwise(iterable, cyclic=False): |
|
"s -> (s0, s1), (s1, s2), (s2, s3), ..." |
|
a, b = tee(iterable) |
|
first = next(b, None) |
|
if cyclic is True: |
|
return zip(a, chain(b, (first,))) |
|
return zip(a, b) |
|
|
|
|
|
def groups(many_to_one): |
|
"""Converts a many-to-one mapping into a one-to-many mapping. |
|
|
|
`many_to_one` must be a dictionary whose keys and values are all |
|
:term:`hashable`. |
|
|
|
The return value is a dictionary mapping values from `many_to_one` |
|
to sets of keys from `many_to_one` that have that value. |
|
|
|
Examples |
|
-------- |
|
>>> from networkx.utils import groups |
|
>>> many_to_one = {"a": 1, "b": 1, "c": 2, "d": 3, "e": 3} |
|
>>> groups(many_to_one) # doctest: +SKIP |
|
{1: {'a', 'b'}, 2: {'c'}, 3: {'e', 'd'}} |
|
""" |
|
one_to_many = defaultdict(set) |
|
for v, k in many_to_one.items(): |
|
one_to_many[k].add(v) |
|
return dict(one_to_many) |
|
|
|
|
|
def create_random_state(random_state=None): |
|
"""Returns a numpy.random.RandomState or numpy.random.Generator instance |
|
depending on input. |
|
|
|
Parameters |
|
---------- |
|
random_state : int or NumPy RandomState or Generator instance, optional (default=None) |
|
If int, return a numpy.random.RandomState instance set with seed=int. |
|
if `numpy.random.RandomState` instance, return it. |
|
if `numpy.random.Generator` instance, return it. |
|
if None or numpy.random, return the global random number generator used |
|
by numpy.random. |
|
""" |
|
import numpy as np |
|
|
|
if random_state is None or random_state is np.random: |
|
return np.random.mtrand._rand |
|
if isinstance(random_state, np.random.RandomState): |
|
return random_state |
|
if isinstance(random_state, int): |
|
return np.random.RandomState(random_state) |
|
if isinstance(random_state, np.random.Generator): |
|
return random_state |
|
msg = ( |
|
f"{random_state} cannot be used to create a numpy.random.RandomState or\n" |
|
"numpy.random.Generator instance" |
|
) |
|
raise ValueError(msg) |
|
|
|
|
|
class PythonRandomViaNumpyBits(random.Random): |
|
"""Provide the random.random algorithms using a numpy.random bit generator |
|
|
|
The intent is to allow people to contribute code that uses Python's random |
|
library, but still allow users to provide a single easily controlled random |
|
bit-stream for all work with NetworkX. This implementation is based on helpful |
|
comments and code from Robert Kern on NumPy's GitHub Issue #24458. |
|
|
|
This implementation supercedes that of `PythonRandomInterface` which rewrote |
|
methods to account for subtle differences in API between `random` and |
|
`numpy.random`. Instead this subclasses `random.Random` and overwrites |
|
the methods `random`, `getrandbits`, `getstate`, `setstate` and `seed`. |
|
It makes them use the rng values from an input numpy `RandomState` or `Generator`. |
|
Those few methods allow the rest of the `random.Random` methods to provide |
|
the API interface of `random.random` while using randomness generated by |
|
a numpy generator. |
|
""" |
|
|
|
def __init__(self, rng=None): |
|
try: |
|
import numpy as np |
|
except ImportError: |
|
msg = "numpy not found, only random.random available." |
|
warnings.warn(msg, ImportWarning) |
|
|
|
if rng is None: |
|
self._rng = np.random.mtrand._rand |
|
else: |
|
self._rng = rng |
|
|
|
|
|
|
|
self.gauss_next = None |
|
|
|
def random(self): |
|
"""Get the next random number in the range 0.0 <= X < 1.0.""" |
|
return self._rng.random() |
|
|
|
def getrandbits(self, k): |
|
"""getrandbits(k) -> x. Generates an int with k random bits.""" |
|
if k < 0: |
|
raise ValueError("number of bits must be non-negative") |
|
numbytes = (k + 7) // 8 |
|
x = int.from_bytes(self._rng.bytes(numbytes), "big") |
|
return x >> (numbytes * 8 - k) |
|
|
|
def getstate(self): |
|
return self._rng.__getstate__() |
|
|
|
def setstate(self, state): |
|
self._rng.__setstate__(state) |
|
|
|
def seed(self, *args, **kwds): |
|
"Do nothing override method." |
|
raise NotImplementedError("seed() not implemented in PythonRandomViaNumpyBits") |
|
|
|
|
|
|
|
class PythonRandomInterface: |
|
"""PythonRandomInterface is included for backward compatibility |
|
New code should use PythonRandomViaNumpyBits instead. |
|
""" |
|
|
|
def __init__(self, rng=None): |
|
try: |
|
import numpy as np |
|
except ImportError: |
|
msg = "numpy not found, only random.random available." |
|
warnings.warn(msg, ImportWarning) |
|
|
|
if rng is None: |
|
self._rng = np.random.mtrand._rand |
|
else: |
|
self._rng = rng |
|
|
|
def random(self): |
|
return self._rng.random() |
|
|
|
def uniform(self, a, b): |
|
return a + (b - a) * self._rng.random() |
|
|
|
def randrange(self, a, b=None): |
|
import numpy as np |
|
|
|
if b is None: |
|
a, b = 0, a |
|
if b > 9223372036854775807: |
|
tmp_rng = PythonRandomViaNumpyBits(self._rng) |
|
return tmp_rng.randrange(a, b) |
|
|
|
if isinstance(self._rng, np.random.Generator): |
|
return self._rng.integers(a, b) |
|
return self._rng.randint(a, b) |
|
|
|
|
|
|
|
def choice(self, seq): |
|
import numpy as np |
|
|
|
if isinstance(self._rng, np.random.Generator): |
|
idx = self._rng.integers(0, len(seq)) |
|
else: |
|
idx = self._rng.randint(0, len(seq)) |
|
return seq[idx] |
|
|
|
def gauss(self, mu, sigma): |
|
return self._rng.normal(mu, sigma) |
|
|
|
def shuffle(self, seq): |
|
return self._rng.shuffle(seq) |
|
|
|
|
|
|
|
|
|
def sample(self, seq, k): |
|
return self._rng.choice(list(seq), size=(k,), replace=False) |
|
|
|
def randint(self, a, b): |
|
import numpy as np |
|
|
|
if b > 9223372036854775807: |
|
tmp_rng = PythonRandomViaNumpyBits(self._rng) |
|
return tmp_rng.randint(a, b) |
|
|
|
if isinstance(self._rng, np.random.Generator): |
|
return self._rng.integers(a, b + 1) |
|
return self._rng.randint(a, b + 1) |
|
|
|
|
|
def expovariate(self, scale): |
|
return self._rng.exponential(1 / scale) |
|
|
|
|
|
def paretovariate(self, shape): |
|
return self._rng.pareto(shape) |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
def create_py_random_state(random_state=None): |
|
"""Returns a random.Random instance depending on input. |
|
|
|
Parameters |
|
---------- |
|
random_state : int or random number generator or None (default=None) |
|
- If int, return a `random.Random` instance set with seed=int. |
|
- If `random.Random` instance, return it. |
|
- If None or the `np.random` package, return the global random number |
|
generator used by `np.random`. |
|
- If an `np.random.Generator` instance, or the `np.random` package, or |
|
the global numpy random number generator, then return it. |
|
wrapped in a `PythonRandomViaNumpyBits` class. |
|
- If a `PythonRandomViaNumpyBits` instance, return it. |
|
- If a `PythonRandomInterface` instance, return it. |
|
- If a `np.random.RandomState` instance and not the global numpy default, |
|
return it wrapped in `PythonRandomInterface` for backward bit-stream |
|
matching with legacy code. |
|
|
|
Notes |
|
----- |
|
- A diagram intending to illustrate the relationships behind our support |
|
for numpy random numbers is called |
|
`NetworkX Numpy Random Numbers <https://excalidraw.com/#room=b5303f2b03d3af7ccc6a,e5ZDIWdWWCTTsg8OqoRvPA>`_. |
|
- More discussion about this support also appears in |
|
`gh-6869#comment <https://github.com/networkx/networkx/pull/6869#issuecomment-1944799534>`_. |
|
- Wrappers of numpy.random number generators allow them to mimic the Python random |
|
number generation algorithms. For example, Python can create arbitrarily large |
|
random ints, and the wrappers use Numpy bit-streams with CPython's random module |
|
to choose arbitrarily large random integers too. |
|
- We provide two wrapper classes: |
|
`PythonRandomViaNumpyBits` is usually what you want and is always used for |
|
`np.Generator` instances. But for users who need to recreate random numbers |
|
produced in NetworkX 3.2 or earlier, we maintain the `PythonRandomInterface` |
|
wrapper as well. We use it only used if passed a (non-default) `np.RandomState` |
|
instance pre-initialized from a seed. Otherwise the newer wrapper is used. |
|
""" |
|
if random_state is None or random_state is random: |
|
return random._inst |
|
if isinstance(random_state, random.Random): |
|
return random_state |
|
if isinstance(random_state, int): |
|
return random.Random(random_state) |
|
|
|
try: |
|
import numpy as np |
|
except ImportError: |
|
pass |
|
else: |
|
if isinstance(random_state, PythonRandomInterface | PythonRandomViaNumpyBits): |
|
return random_state |
|
if isinstance(random_state, np.random.Generator): |
|
return PythonRandomViaNumpyBits(random_state) |
|
if random_state is np.random: |
|
return PythonRandomViaNumpyBits(np.random.mtrand._rand) |
|
|
|
if isinstance(random_state, np.random.RandomState): |
|
if random_state is np.random.mtrand._rand: |
|
return PythonRandomViaNumpyBits(random_state) |
|
|
|
return PythonRandomInterface(random_state) |
|
|
|
msg = f"{random_state} cannot be used to generate a random.Random instance" |
|
raise ValueError(msg) |
|
|
|
|
|
def nodes_equal(nodes1, nodes2): |
|
"""Check if nodes are equal. |
|
|
|
Equality here means equal as Python objects. |
|
Node data must match if included. |
|
The order of nodes is not relevant. |
|
|
|
Parameters |
|
---------- |
|
nodes1, nodes2 : iterables of nodes, or (node, datadict) tuples |
|
|
|
Returns |
|
------- |
|
bool |
|
True if nodes are equal, False otherwise. |
|
""" |
|
nlist1 = list(nodes1) |
|
nlist2 = list(nodes2) |
|
try: |
|
d1 = dict(nlist1) |
|
d2 = dict(nlist2) |
|
except (ValueError, TypeError): |
|
d1 = dict.fromkeys(nlist1) |
|
d2 = dict.fromkeys(nlist2) |
|
return d1 == d2 |
|
|
|
|
|
def edges_equal(edges1, edges2): |
|
"""Check if edges are equal. |
|
|
|
Equality here means equal as Python objects. |
|
Edge data must match if included. |
|
The order of the edges is not relevant. |
|
|
|
Parameters |
|
---------- |
|
edges1, edges2 : iterables of with u, v nodes as |
|
edge tuples (u, v), or |
|
edge tuples with data dicts (u, v, d), or |
|
edge tuples with keys and data dicts (u, v, k, d) |
|
|
|
Returns |
|
------- |
|
bool |
|
True if edges are equal, False otherwise. |
|
""" |
|
from collections import defaultdict |
|
|
|
d1 = defaultdict(dict) |
|
d2 = defaultdict(dict) |
|
c1 = 0 |
|
for c1, e in enumerate(edges1): |
|
u, v = e[0], e[1] |
|
data = [e[2:]] |
|
if v in d1[u]: |
|
data = d1[u][v] + data |
|
d1[u][v] = data |
|
d1[v][u] = data |
|
c2 = 0 |
|
for c2, e in enumerate(edges2): |
|
u, v = e[0], e[1] |
|
data = [e[2:]] |
|
if v in d2[u]: |
|
data = d2[u][v] + data |
|
d2[u][v] = data |
|
d2[v][u] = data |
|
if c1 != c2: |
|
return False |
|
|
|
for n, nbrdict in d1.items(): |
|
for nbr, datalist in nbrdict.items(): |
|
if n not in d2: |
|
return False |
|
if nbr not in d2[n]: |
|
return False |
|
d2datalist = d2[n][nbr] |
|
for data in datalist: |
|
if datalist.count(data) != d2datalist.count(data): |
|
return False |
|
return True |
|
|
|
|
|
def graphs_equal(graph1, graph2): |
|
"""Check if graphs are equal. |
|
|
|
Equality here means equal as Python objects (not isomorphism). |
|
Node, edge and graph data must match. |
|
|
|
Parameters |
|
---------- |
|
graph1, graph2 : graph |
|
|
|
Returns |
|
------- |
|
bool |
|
True if graphs are equal, False otherwise. |
|
""" |
|
return ( |
|
graph1.adj == graph2.adj |
|
and graph1.nodes == graph2.nodes |
|
and graph1.graph == graph2.graph |
|
) |
|
|
|
|
|
def _clear_cache(G): |
|
"""Clear the cache of a graph (currently stores converted graphs). |
|
|
|
Caching is controlled via ``nx.config.cache_converted_graphs`` configuration. |
|
""" |
|
if cache := getattr(G, "__networkx_cache__", None): |
|
cache.clear() |
|
|