Merge pull request #799 from Axelrod-Python/graph_moran

Implemented the Moran process on graphs

Author: meatballs

axelrod/__init__.py

@@ -5,6 +5,7 @@
 
 # The order of imports matters!
 from .version import __version__
+from . import graph
 from .actions import Actions, flip_action
 from .random_ import random_choice, seed
 from .plot import Plot
@@ -13,7 +14,7 @@
     obey_axelrod, update_history, update_state_distribution, Player
 from .mock_player import MockPlayer, simulate_play
 from .match import Match
-from .moran import MoranProcess
+from .moran import MoranProcess, MoranProcessGraph
 from .strategies import *
 from .deterministic_cache import DeterministicCache
 from .match_generator import *

axelrod/graph.py

@@ -0,0 +1,128 @@
+"""
+Weighted undirected sparse graphs.
+
+Original source:
+https://github.com/marcharper/stationary/blob/master/stationary/utils/graph.py
+"""
+
+from collections import defaultdict
+
+
+class Graph(object):
+    """Weighted and directed graph object intended for the graph associated to a
+    Markov process. Gives easy access to the neighbors of a particular state
+    needed for various calculations.
+
+    Vertices can be any hashable / immutable python object. Initialize with a
+    list of edges:
+        [[node1, node2, weights], ...]
+    Weights can be omitted for an undirected graph.
+
+    For efficiency, neighbors are cached in dictionaries. Undirected graphs
+    are implemented as directed graphs in which every edge (s, t) has the
+    opposite edge (t, s).
+    """
+
+    def __init__(self, edges=None, directed=False):
+        self.directed = directed
+        self.original_edges = edges
+        self.out_mapping = defaultdict(lambda: defaultdict(float))
+        self.in_mapping = defaultdict(lambda: defaultdict(float))
+        self._edges = []
+        if edges:
+            self.add_edges(edges)
+
+    def add_edge(self, source, target, weight=None):
+        if (source, target) not in self._edges:
+            self._edges.append((source, target))
+            self.out_mapping[source][target] = weight
+            self.in_mapping[target][source] = weight
+        if not self.directed and (source != target) and \
+                (target, source) not in self._edges:
+            self._edges.append((target, source))
+            self.out_mapping[target][source] = weight
+            self.in_mapping[source][target] = weight
+
+    def add_edges(self, edges):
+        for edge in edges:
+            self.add_edge(*edge)
+
+    def edges(self):
+        return self._edges
+
+    def vertices(self):
+        """Returns the set of vertices of the graph."""
+        return list(self.out_mapping.keys())
+
+    def out_dict(self, source):
+        """Returns a dictionary of the outgoing edges of source with weights."""
+        return self.out_mapping[source]
+
+    def out_vertices(self, source):
+        """Returns a list of the outgoing vertices."""
+        return list(self.out_mapping[source].keys())
+
+    def in_dict(self, target):
+        """Returns a dictionary of the incoming edges of source with weights."""
+        return self.in_mapping[target]
+
+    def in_vertices(self, source):
+        """Returns a list of the outgoing vertices."""
+        return list(self.in_mapping[source].keys())
+
+    def __repr__(self):
+        s = "<Graph: {}>".format(repr(self.original_edges))
+        return s
+
+
+## Example Graphs
+
+
+def cycle(length, directed=False):
+    """
+    Produces a cycle of length `length`.
+    Parameters
+    ----------
+    length: int
+        Number of vertices in the cycle
+    directed: bool, False
+        Is the cycle directed?
+    Returns
+    -------
+    a Graph object
+    """
+
+    graph = Graph(directed=directed)
+    edges = []
+    for i in range(length - 1):
+        edges.append((i, i+1))
+    edges.append((length - 1, 0))
+    graph.add_edges(edges)
+    return graph
+
+
+def complete_graph(length, loops=True):
+    """
+    Produces a complete graph of size `length`, with loops.
+    https://en.wikipedia.org/wiki/Complete_graph
+
+    Parameters
+    ----------
+    length: int
+        Number of vertices in the cycle
+    directed: bool, False
+        Is the graph directed?
+    Returns
+    -------
+    a Graph object
+    """
+    offset = 1
+    if loops:
+        offset = 0
+    graph = Graph(directed=False)
+    edges = []
+    for i in range(length):
+        for j in range(i + offset, length):
+            edges.append((i, j))
+    graph.add_edges(edges)
+    return graph