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Removed random decorators #227

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Nov 17, 2022
Merged

Removed random decorators #227

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7e46035
Removed all decorators and replaced with setting the seed
nwlandry Nov 16, 2022
4459acf
corrected some documentation
nwlandry Nov 16, 2022
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7 changes: 4 additions & 3 deletions xgi/drawing/layout.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@

from .. import convert
from ..classes import SimplicialComplex, max_edge_order
from ..utils import np_random_state

__all__ = [
"random_layout",
Expand All @@ -14,7 +13,6 @@
]


@np_random_state("seed")
def random_layout(H, center=None, dim=2, seed=None):
"""Position nodes uniformly at random in the unit square. Exactly as networkx does.
For every node, a position is generated by choosing each of dim
Expand Down Expand Up @@ -52,8 +50,11 @@ def random_layout(H, center=None, dim=2, seed=None):
"""
import numpy as np

if seed is not None:
np.random.seed(seed)

H, center = nx.drawing.layout._process_params(H, center, dim)
pos = seed.rand(len(H), dim) + center
pos = np.random.rand(len(H), dim) + center
pos = pos.astype(np.float32)
pos = dict(zip(H, pos))

Expand Down
10 changes: 7 additions & 3 deletions xgi/generators/classic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@

"""

import random
from collections import defaultdict
from itertools import combinations
from warnings import warn
Expand All @@ -13,7 +14,6 @@

from ..classes.function import subfaces
from ..exception import XGIError
from ..utils import py_random_state

__all__ = [
"empty_hypergraph",
Expand Down Expand Up @@ -177,7 +177,6 @@ def star_clique(n_star, n_clique, d_max):
return H


@py_random_state("seed")
def flag_complex(G, max_order=2, ps=None, seed=None):
"""Generate a flag (or clique) complex from a
NetworkX graph by filling all cliques up to dimension max_order.
Expand All @@ -193,6 +192,8 @@ def flag_complex(G, max_order=2, ps=None, seed=None):
hyperedge from a clique, at each order d. For example,
ps[0] is the probability of promoting any 3-node clique (triangle) to
a 3-hyperedge.
seed: int or None (default)
The seed for the random number generator

Returns
-------
Expand All @@ -207,6 +208,9 @@ def flag_complex(G, max_order=2, ps=None, seed=None):
# defined. Otherwise, a circular import error would happen.
from ..classes import SimplicialComplex

if seed is not None:
random.seed(seed)

nodes = G.nodes()
edges = G.edges()

Expand All @@ -233,7 +237,7 @@ def flag_complex(G, max_order=2, ps=None, seed=None):
# promote cliques with a given probability
for i, p in enumerate(ps[: max_order - 1]):
d = i + 2 # simplex order
cliques_d_to_add = [el for el in cliques_d[d + 1] if seed.random() <= p]
cliques_d_to_add = [el for el in cliques_d[d + 1] if random.random() <= p]
S.add_simplices_from(cliques_d_to_add, max_order=max_order)

return S
Expand Down
59 changes: 35 additions & 24 deletions xgi/generators/nonuniform.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
"""Generate random (non-uniform) hypergraphs."""
import math
import random
import warnings
from collections import defaultdict
from itertools import combinations
Expand All @@ -8,7 +9,6 @@
import numpy as np

from ..classes import SimplicialComplex
from ..utils import np_random_state, py_random_state
from .classic import empty_hypergraph, ring_lattice

__all__ = [
Expand All @@ -22,7 +22,6 @@
]


@py_random_state("seed")
def chung_lu_hypergraph(k1, k2, seed=None):
"""A function to generate a Chung-Lu hypergraph

Expand All @@ -34,8 +33,8 @@ def chung_lu_hypergraph(k1, k2, seed=None):
k2 : dictionary
Dictionary where the keys are edge ids
and the values are edge sizes.
seed : integer, random_state, or None (default)
Indicator of random number generation state.
seed : integer or None (default)
The seed for the random number generator.

Returns
-------
Expand Down Expand Up @@ -68,6 +67,9 @@ def chung_lu_hypergraph(k1, k2, seed=None):
>>> H = xgi.chung_lu_hypergraph(k1, k2)

"""
if seed is not None:
random.seed(seed)

# sort dictionary by degree in decreasing order
node_labels = [n for n, _ in sorted(k1.items(), key=lambda d: d[1], reverse=True)]
edge_labels = [m for m, _ in sorted(k2.items(), key=lambda d: d[1], reverse=True)]
Expand All @@ -91,7 +93,7 @@ def chung_lu_hypergraph(k1, k2, seed=None):

while j < m:
if p != 1:
r = seed.random()
r = random.random()
try:
j = j + math.floor(math.log(r) / math.log(1 - p))
except ZeroDivisionError:
Expand All @@ -100,7 +102,7 @@ def chung_lu_hypergraph(k1, k2, seed=None):
if j < m:
v = edge_labels[j]
q = min((k1[u] * k2[v]) / S, 1)
r = seed.random()
r = random.random()
if r < q / p:
# no duplicates
H.add_node_to_edge(v, u)
Expand All @@ -110,7 +112,6 @@ def chung_lu_hypergraph(k1, k2, seed=None):
return H


@py_random_state("seed")
def dcsbm_hypergraph(k1, k2, g1, g2, omega, seed=None):
"""A function to generate a DCSBM hypergraph.

Expand All @@ -136,8 +137,8 @@ def dcsbm_hypergraph(k1, k2, g1, g2, omega, seed=None):
The number of rows must match the number of node communities
and the number of columns must match the number of edge
communities.
seed : int, random_state, or None (default)
Indicator of random number generation state.
seed : int or None (default)
Seed for the random number generator.

Returns
-------
Expand Down Expand Up @@ -175,6 +176,8 @@ def dcsbm_hypergraph(k1, k2, g1, g2, omega, seed=None):
>>> # H = xgi.dcsbm_hypergraph(k1, k2, g1, g2, omega)

"""
if seed is not None:
random.seed(seed)

# sort dictionary by degree in decreasing order
node_labels = [n for n, _ in sorted(k1.items(), key=lambda d: d[1], reverse=True)]
Expand Down Expand Up @@ -230,15 +233,15 @@ def dcsbm_hypergraph(k1, k2, g1, g2, omega, seed=None):
p = min(k1[u] * k2[v] * group_constant, 1)
while j < len(community2_nodes[group2]):
if p != 1:
r = seed.random()
r = random.random()
try:
j = j + math.floor(math.log(r) / math.log(1 - p))
except ZeroDivisionError:
j = np.inf
if j < len(community2_nodes[group2]):
v = community2_nodes[group2][j]
q = min((k1[u] * k2[v]) * group_constant, 1)
r = seed.random()
r = random.random()
if r < q / p:
# no duplicates
H.add_node_to_edge(v, u)
Expand All @@ -247,7 +250,6 @@ def dcsbm_hypergraph(k1, k2, g1, g2, omega, seed=None):
return H


@py_random_state("seed")
def random_hypergraph(N, ps, seed=None):
"""Generates a random hypergraph

Expand All @@ -263,8 +265,8 @@ def random_hypergraph(N, ps, seed=None):
hyperedge at each order d between any d+1 nodes. For example,
ps[0] is the wiring probability of any edge (2 nodes), ps[1]
of any triangles (3 nodes).
seed : integer, random_state, or None (default)
Indicator of random number generation state.
seed : integer or None (default)
Seed for the random number generator.

Returns
-------
Expand All @@ -281,6 +283,8 @@ def random_hypergraph(N, ps, seed=None):
>>> H = xgi.random_hypergraph(50, [0.1, 0.01])

"""
if seed is not None:
random.seed(seed)

if (np.any(np.array(ps) < 0)) or (np.any(np.array(ps) > 1)):
raise ValueError("All elements of ps must be between 0 and 1 included.")
Expand All @@ -292,7 +296,7 @@ def random_hypergraph(N, ps, seed=None):
d = i + 1 # order, ps[0] is prob of edges (d=1)

for hyperedge in combinations(nodes, d + 1):
if seed.random() <= p:
if random.random() <= p:
hyperedges.append(hyperedge)

hyperedges += [[i] for i in nodes] # add singleton edges
Expand All @@ -304,7 +308,6 @@ def random_hypergraph(N, ps, seed=None):
return H


@py_random_state("seed")
def random_simplicial_complex(N, ps, seed=None):
"""Generates a random hypergraph

Expand All @@ -321,6 +324,8 @@ def random_simplicial_complex(N, ps, seed=None):
hyperedge at each order d between any d+1 nodes. For example,
ps[0] is the wiring probability of any edge (2 nodes), ps[1]
of any triangles (3 nodes).
seed : int or None (default)
The seed for the random number generator

Returns
-------
Expand All @@ -340,6 +345,8 @@ def random_simplicial_complex(N, ps, seed=None):
>>> H = xgi.random_simplicial_complex(20, [0.1, 0.01])

"""
if seed is not None:
random.seed(seed)

if (np.any(np.array(ps) < 0)) or (np.any(np.array(ps) > 1)):
raise ValueError("All elements of ps must be between 0 and 1 included.")
Expand All @@ -351,7 +358,7 @@ def random_simplicial_complex(N, ps, seed=None):
d = i + 1 # order, ps[0] is prob of edges (d=1)

for simplex in combinations(nodes, d + 1):
if seed.random() <= p:
if random.random() <= p:
simplices.append(simplex)

S = SimplicialComplex()
Expand All @@ -361,7 +368,6 @@ def random_simplicial_complex(N, ps, seed=None):
return S


@py_random_state("seed")
def random_flag_complex_d2(N, p, seed=None):
"""Generate a maximal simplicial complex (up to order 2) from a
:math:`G_{N,p}` Erdős-Rényi random graph by filling all empty triangles with 2-simplices.
Expand All @@ -373,6 +379,8 @@ def random_flag_complex_d2(N, p, seed=None):
p : float
Probabilities (between 0 and 1) to create an edge
between any 2 nodes
seed : int or None (default)
The seed for the random number generator

Returns
-------
Expand All @@ -382,6 +390,8 @@ def random_flag_complex_d2(N, p, seed=None):
-----
Computing all cliques quickly becomes heavy for large networks.
"""
if seed is not None:
random.seed(seed)

if (p < 0) or (p > 1):
raise ValueError("p must be between 0 and 1 included.")
Expand All @@ -404,7 +414,6 @@ def random_flag_complex_d2(N, p, seed=None):
return S


@py_random_state(3)
def random_flag_complex(N, p, max_order=2, seed=None):
"""Generate a flag (or clique) complex from a
:math:`G_{N,p}` Erdős-Rényi random graph by filling all cliques up to dimension max_order.
Expand All @@ -416,9 +425,10 @@ def random_flag_complex(N, p, max_order=2, seed=None):
p : float
Probabilities (between 0 and 1) to create an edge
between any 2 nodes

max_order : int
maximal dimension of simplices to add to the output simplicial complex
seed : int or None (default)
The seed for the random number generator

Returns
-------
Expand Down Expand Up @@ -447,16 +457,17 @@ def random_flag_complex(N, p, max_order=2, seed=None):
return S


@np_random_state("seed")
def watts_strogatz_hypergraph(n, d, k, l, p, seed=None):
if seed is not None:
np.random.seed(seed)
H = ring_lattice(n, d, k, l)
to_remove = []
to_add = []
for e in H.edges:
if seed.random() < p:
if np.random.random() < p:
to_remove.append(e)
node = H.edges.members(e)[0]
neighbors = seed.choice(H.nodes, size=d - 1)
node = min(H.edges.members(e))
neighbors = np.random.choice(H.nodes, size=d - 1)
to_add.append(np.append(neighbors, node))
H.remove_edges_from(to_remove)
H.add_edges_from(to_add)
Expand Down
14 changes: 8 additions & 6 deletions xgi/generators/uniform.py
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Original file line number Diff line number Diff line change
@@ -1,13 +1,12 @@
"""Generate random uniform hypergraphs."""
import random
import warnings

from ..utils import py_random_state
from .classic import empty_hypergraph

__all__ = ["uniform_hypergraph_configuration_model"]


@py_random_state(2)
def uniform_hypergraph_configuration_model(k, m, seed=None):
"""
A function to generate an m-uniform configuration model
Expand All @@ -19,8 +18,8 @@ def uniform_hypergraph_configuration_model(k, m, seed=None):
and the values are node degrees.
m : int
specifies the hyperedge size
seed : integer, random_state, or None (default)
Indicator of random number generation state.
seed : integer or None (default)
The seed for the random number generator

Returns
-------
Expand Down Expand Up @@ -57,13 +56,16 @@ def uniform_hypergraph_configuration_model(k, m, seed=None):
>>> H = xgi.uniform_hypergraph_configuration_model(k, m)

"""
if seed is not None:
random.seed(seed)

# Making sure we have the right number of stubs
remainder = sum(k.values()) % m
if remainder != 0:
warnings.warn(
"This degree sequence is not realizable. Increasing the degree of random nodes so that it is."
)
random_ids = seed.sample(list(k.keys()), int(round(m - remainder)))
random_ids = random.sample(list(k.keys()), int(round(m - remainder)))
for id in random_ids:
k[id] = k[id] + 1

Expand All @@ -76,7 +78,7 @@ def uniform_hypergraph_configuration_model(k, m, seed=None):
H.add_nodes_from(k.keys())

while len(stubs) != 0:
u = seed.sample(range(len(stubs)), m)
u = random.sample(range(len(stubs)), m)
edge = set()
for index in u:
edge.add(stubs[index])
Expand Down
2 changes: 1 addition & 1 deletion xgi/stats/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -490,7 +490,7 @@ def nodestat_func(func):
AttributeError:...

Use the `nodestat_func` decorator to turn `my_degree` into a valid stat.

>>> original_my_degree = my_degree
>>> my_degree = xgi.nodestat_func(my_degree)
>>> H.my_degree()
Expand Down
3 changes: 1 addition & 2 deletions xgi/utils/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,2 @@
from . import decorators, utilities
from .decorators import *
from . import utilities
from .utilities import *
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