Source code for gcmpy.utils

# Utilities for gcmpy
#
# Copyright (C) 2021 Peter Mann
#
# This file is part of gcmpy, generalised configuration model networks in Python.
#
# gcmpy 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 2 of the License, or
# (at your option) any later version.
#
# gcmpy 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 gcmpy. If not, see <http://www.gnu.org/licenses/gpl.html>.

import io
import pickle
from typing import List

import networkx as nx

from .types import _EDGES, _EDGE

[docs]class edge_list(object): '''Network represented as an edge list. The GCM class uses this structure to generate networks which can then be converted to other network libraries.''' def __init__(self): self._edge_list : _EDGES = []
[docs] def add_edge(self, e : _EDGE): '''Adds an edge to the networkx''' self._edge_list.append(e)
[docs] def add_edges_from(self, edges : _EDGES)->None: '''Adds edges from list of tuples (int,int) to the edge list. :param edges: list of tuples of ints.''' for e in edges: self.add_edge(e)
[docs] def find_cliques(self): '''Returns all maximal cliques in an undirected graph by converting the edge list to a nx graph object first.''' G = nx.Graph() G.add_edges_from(self._edge_list) return list(nx.find_cliques(G))
[docs] def remove_edge(self, i : int, j : int)->None: '''Removes edge (i,j) from G. Assumes i<j and no duplicates.''' try: self._edge_list.remove((i,j)) except ValueError: pass
[docs] def has_edges(self)->bool: '''True if graph has edges remaining''' return len(self._edge_list) > 0
[docs]class output_data(object): '''An object to store output data from the process. :param i: integer for experiment index''' def __init__(self, i : int): self._experiment : int = i # experiment index self._name : str = '' # tags for network self._network : edge_list = None # network
[docs]class results(object): '''A collection of output_data objects that can be serialised and converted to other graph formats.''' def __init__(self): self.res : List[output_data] = []
[docs] def add_result(self, r : output_data)->None: self.res.append(r)
[docs] def serialise_results_to_file(self, filename : str)->None: '''Dump the results structure to a binary file. :param filename: name of file to create.''' binary_file = open(filename, mode='wb') pickle.dump(self.res, binary_file) binary_file.close()
[docs] def read_results_from_binary_file(self, filename : str)->None: '''read the results structure from a binary file. :param filename: name of the file to read.''' f : io.BufferedReader = open(filename,mode='rb') bin_data : bytes = f.read() sio : io.StringIO = io.StringIO(bin_data) self.res : List[output_data] = pickle.load(sio)