Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/networkx/utils/misc.py @ 4:79f47841a781 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
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date | Thu, 14 May 2020 16:47:39 -0400 |
parents | 26e78fe6e8c4 |
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""" Miscellaneous Helpers for NetworkX. These are not imported into the base networkx namespace but can be accessed, for example, as >>> import networkx >>> networkx.utils.is_string_like('spam') True """ # Authors: Aric Hagberg (hagberg@lanl.gov), # Dan Schult(dschult@colgate.edu), # Ben Edwards(bedwards@cs.unm.edu) # Copyright (C) 2004-2019 by # Aric Hagberg <hagberg@lanl.gov> # Dan Schult <dschult@colgate.edu> # Pieter Swart <swart@lanl.gov> # All rights reserved. # BSD license. from collections import defaultdict from collections import deque import warnings import sys import uuid from itertools import tee, chain import networkx as nx # itertools.accumulate is only available on Python 3.2 or later. # # Once support for Python versions less than 3.2 is dropped, this code should # be removed. try: from itertools import accumulate except ImportError: import operator # The code for this function is from the Python 3.5 documentation, # distributed under the PSF license: # <https://docs.python.org/3.5/library/itertools.html#itertools.accumulate> def accumulate(iterable, func=operator.add): it = iter(iterable) try: total = next(it) except StopIteration: return yield total for element in it: total = func(total, element) yield total # 2.x/3.x compatibility try: basestring except NameError: basestring = str unicode = str # some cookbook stuff # used in deciding whether something is a bunch of nodes, edges, etc. # see G.add_nodes and others in Graph Class in networkx/base.py def is_string_like(obj): # from John Hunter, types-free version """Check if obj is string.""" return isinstance(obj, basestring) def iterable(obj): """ Return True if obj is iterable with a well-defined len().""" if hasattr(obj, "__iter__"): return True try: len(obj) except: return False return True def flatten(obj, result=None): """ Return flattened version of (possibly nested) iterable object. """ if not iterable(obj) or is_string_like(obj): return obj if result is None: result = [] for item in obj: if not iterable(item) or is_string_like(item): result.append(item) else: flatten(item, result) return obj.__class__(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 """ msg = 'sequence is not all integers: %s' if not isinstance(sequence, list): result = [] for i in sequence: try: ii = int(i) except ValueError: raise nx.NetworkXError(msg % i) from None if ii != i: raise nx.NetworkXError(msg % i) result.append(ii) return result # original sequence is a list... in-place conversion to ints for indx, i in enumerate(sequence): if isinstance(i, int): continue try: ii = int(i) except ValueError: raise nx.NetworkXError(msg % i) from None if ii != i: raise nx.NetworkXError(msg % i) sequence[indx] = ii return sequence def is_list_of_ints(intlist): """ Return True if list is a list of ints. """ if not isinstance(intlist, list): return False for i in intlist: if not isinstance(i, int): return False return True PY2 = sys.version_info[0] == 2 if PY2: def make_str(x): """Returns the string representation of t.""" if isinstance(x, unicode): return x else: # Note, this will not work unless x is ascii-encoded. # That is good, since we should be working with unicode anyway. # Essentially, unless we are reading a file, we demand that users # convert any encoded strings to unicode before using the library. # # Also, the str() is necessary to convert integers, etc. # unicode(3) works, but unicode(3, 'unicode-escape') wants a buffer # return unicode(str(x), 'unicode-escape') else: def make_str(x): """Returns the string representation of t.""" return str(x) def generate_unique_node(): """ Generate a unique node label.""" return str(uuid.uuid1()) def default_opener(filename): """Opens `filename` using system's default program. Parameters ---------- filename : str The path of the file to be opened. """ from subprocess import call cmds = {'darwin': ['open'], 'linux': ['xdg-open'], 'linux2': ['xdg-open'], 'win32': ['cmd.exe', '/C', 'start', '']} cmd = cmds[sys.platform] + [filename] call(cmd) 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): # AttributeError is when no mapping was provided and v.keys() fails. # TypeError is when a mapping was provided and d[k1][k2] fails. 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 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 = numpy.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 if mapping is None: s = set(d.keys()) mapping = dict(zip(s, range(len(s)))) n = len(mapping) a = numpy.zeros(n) for k1, i in mapping.items(): i = mapping[k1] a[i] = d[k1] return a def is_iterator(obj): """Returns True if and only if the given object is an iterator object. """ has_next_attr = hasattr(obj, '__next__') or hasattr(obj, 'next') return iter(obj) is obj and has_next_attr 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:: >>> arbitrary_element({3, 2, 1}) 1 >>> arbitrary_element('hello') 'h' This function raises a :exc:`ValueError` if `iterable` is an iterator (because the current implementation of this function would consume an element from the iterator):: >>> iterator = iter([1, 2, 3]) >>> arbitrary_element(iterator) Traceback (most recent call last): ... ValueError: cannot return an arbitrary item from an iterator """ if is_iterator(iterable): raise ValueError('cannot return an arbitrary item from an iterator') # Another possible implementation is ``for x in iterable: return x``. return next(iter(iterable)) # Recipe from the itertools documentation. def consume(iterator): "Consume the iterator entirely." # Feed the entire iterator into a zero-length deque. deque(iterator, maxlen=0) # Recipe from the itertools documentation. 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. For example:: >>> 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: {'d', 'e'}} """ 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 to_tuple(x): """Converts lists to tuples. For example:: >>> from networkx.utils import to_tuple >>> a_list = [1, 2, [1, 4]] >>> to_tuple(a_list) (1, 2, (1, 4)) """ if not isinstance(x, (tuple, list)): return x return tuple(map(to_tuple, x)) def create_random_state(random_state=None): """Returns a numpy.random.RandomState instance depending on input. Parameters ---------- random_state : int or RandomState instance or None optional (default=None) If int, return a numpy.random.RandomState instance set with seed=int. if numpy.random.RandomState 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) msg = '%r cannot be used to generate a numpy.random.RandomState instance' raise ValueError(msg % random_state) class PythonRandomInterface(object): try: def __init__(self, rng=None): import numpy if rng is None: self._rng = numpy.random.mtrand._rand self._rng = rng except ImportError: msg = 'numpy not found, only random.random available.' warnings.warn(msg, ImportWarning) def random(self): return self._rng.random_sample() def uniform(self, a, b): return a + (b - a) * self._rng.random_sample() def randrange(self, a, b=None): return self._rng.randint(a, b) def choice(self, seq): return seq[self._rng.randint(0, len(seq))] def gauss(self, mu, sigma): return self._rng.normal(mu, sigma) def shuffle(self, seq): return self._rng.shuffle(seq) # Some methods don't match API for numpy RandomState. # Commented out versions are not used by NetworkX def sample(self, seq, k): return self._rng.choice(list(seq), size=(k,), replace=False) def randint(self, a, b): return self._rng.randint(a, b + 1) # exponential as expovariate with 1/argument, def expovariate(self, scale): return self._rng.exponential(1/scale) # pareto as paretovariate with 1/argument, def paretovariate(self, shape): return self._rng.pareto(shape) # weibull as weibullvariate multiplied by beta, # def weibullvariate(self, alpha, beta): # return self._rng.weibull(alpha) * beta # # def triangular(self, low, high, mode): # return self._rng.triangular(low, mode, high) # # def choices(self, seq, weights=None, cum_weights=None, k=1): # return self._rng.choice(seq 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 `random` package, return the global random number generator used by `random`. if np.random package, return the global numpy random number generator wrapped in a PythonRandomInterface class. if np.random.RandomState instance, return it wrapped in PythonRandomInterface if a PythonRandomInterface instance, return it """ import random try: import numpy as np if random_state is np.random: return PythonRandomInterface(np.random.mtrand._rand) if isinstance(random_state, np.random.RandomState): return PythonRandomInterface(random_state) if isinstance(random_state, PythonRandomInterface): return random_state has_numpy = True except ImportError: has_numpy = False 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) msg = '%r cannot be used to generate a random.Random instance' raise ValueError(msg % random_state) # fixture for pytest def setup_module(module): import pytest numpy = pytest.importorskip('numpy')