0.13.8

CHANGELOG.md

@@ -0,0 +1,27 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.13.8]
+### Changed
+* Moved TerroristNetworkModel to examples
+### Added
+* `get_agents` and `count_agents` methods now accept lists as inputs. They can be used to retrieve agents from node ids
+* `subgraph` in BaseAgent
+* `agents.select` method, to filter out agents
+* `skip_test` property in yaml definitions, to force skipping some examples
+* `agents.Geo`, with a search function based on postition
+* `BaseAgent.ego_search` to get nodes from the ego network of a node
+* `BaseAgent.degree` and `BaseAgent.betweenness`
+### Fixed
+
+## [0.13.7]
+### Changed
+* History now defaults to not backing up! This makes it more intuitive to load the history for examination, at the expense of rewriting something. That should not happen because History is only created in the Environment, and that has `backup=True`.
+### Added
+* Agent names are assigned based on their agent types
+* Agent logging uses the agent name.
+* FSM agents can now return a timeout in addition to a new state. e.g. `return self.idle, self.env.timeout(2)` will execute the *different_state* in 2 *units of time* (`t_step=now+2`).
+* Example of using timeouts in FSM (custom_timeouts)
+* `network_agents` entries may include an `ids` entry. If set, it should be a list of node ids that should be assigned that agent type. This complements the previous behavior of setting agent type with `weights`.

MANIFEST.in

@@ -1,4 +1,7 @@
 include requirements.txt
 include test-requirements.txt
 include README.rst
-graft soil
+graft soil
+global-exclude __pycache__
+global-exclude soil_output
+global-exclude *.py[co]

examples/custom_timeouts/custom_timeouts.py

@@ -0,0 +1,36 @@
+from soil.agents import FSM, state, default_state
+
+
+class Fibonacci(FSM):
+    '''Agent that only executes in t_steps that are Fibonacci numbers'''
+
+    defaults = {
+        'prev': 1
+    }
+
+    @default_state
+    @state
+    def counting(self):
+        self.log('Stopping at {}'.format(self.now))
+        prev, self['prev'] = self['prev'], max([self.now, self['prev']])
+        return None, self.env.timeout(prev)
+
+class Odds(FSM):
+    '''Agent that only executes in odd t_steps'''
+    @default_state
+    @state
+    def odds(self):
+        self.log('Stopping at {}'.format(self.now))
+        return None, self.env.timeout(1+self.now%2)
+
+if __name__ == '__main__':
+    import logging
+    logging.basicConfig(level=logging.INFO)
+    from soil import Simulation
+    s = Simulation(network_agents=[{'ids': [0], 'agent_type': Fibonacci},
+                                   {'ids': [1], 'agent_type': Odds}],
+                   dry_run=True,
+                   network_params={"generator": "complete_graph", "n": 2},
+                   max_time=100,
+                   )
+    s.run()

examples/newsspread/NewsSpread.yml

@@ -6,7 +6,7 @@ environment_params:
   prob_neighbor_spread: 0.0
   prob_tv_spread: 0.01
 interval: 1
-max_time: 30
+max_time: 300
 name: Sim_all_dumb
 network_agents:
 - agent_type: DumbViewer
@@ -30,7 +30,7 @@ environment_params:
   prob_neighbor_spread: 0.0
   prob_tv_spread: 0.01
 interval: 1
-max_time: 30
+max_time: 300
 name: Sim_half_herd
 network_agents:
 - agent_type: DumbViewer
@@ -62,7 +62,7 @@ environment_params:
   prob_neighbor_spread: 0.0
   prob_tv_spread: 0.01
 interval: 1
-max_time: 30
+max_time: 300
 name: Sim_all_herd
 network_agents:
 - agent_type: HerdViewer
@@ -89,7 +89,7 @@ environment_params:
   prob_tv_spread: 0.01
   prob_neighbor_cure: 0.1
 interval: 1
-max_time: 30
+max_time: 300
 name: Sim_wise_herd
 network_agents:
 - agent_type: HerdViewer
@@ -115,7 +115,7 @@ environment_params:
   prob_tv_spread: 0.01
   prob_neighbor_cure: 0.1
 interval: 1
-max_time: 30
+max_time: 300
 name: Sim_all_wise
 network_agents:
 - agent_type: WiseViewer

examples/terrorism/TerroristNetworkModel.py

@@ -0,0 +1,208 @@
+import random
+import networkx as nx
+from soil.agents import Geo, NetworkAgent, FSM, state, default_state
+from soil import Environment
+
+
+class TerroristSpreadModel(FSM, Geo):
+    """
+    Settings:
+        information_spread_intensity
+
+        terrorist_additional_influence
+
+        min_vulnerability (optional else zero)
+
+        max_vulnerability
+
+        prob_interaction
+    """
+
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+
+        self.information_spread_intensity = environment.environment_params['information_spread_intensity']
+        self.terrorist_additional_influence = environment.environment_params['terrorist_additional_influence']
+        self.prob_interaction = environment.environment_params['prob_interaction']
+
+        if self['id'] == self.civilian.id:       # Civilian
+            self.mean_belief = random.uniform(0.00, 0.5)
+        elif self['id'] == self.terrorist.id:     # Terrorist
+            self.mean_belief = random.uniform(0.8, 1.00)
+        elif self['id'] == self.leader.id:     # Leader
+            self.mean_belief = 1.00
+        else:
+            raise Exception('Invalid state id: {}'.format(self['id']))
+
+        if 'min_vulnerability' in environment.environment_params:
+            self.vulnerability = random.uniform( environment.environment_params['min_vulnerability'], environment.environment_params['max_vulnerability'] )
+        else :
+            self.vulnerability = random.uniform( 0, environment.environment_params['max_vulnerability'] )
+
+
+    @state
+    def civilian(self):
+        neighbours = list(self.get_neighboring_agents(agent_type=TerroristSpreadModel))
+        if len(neighbours) > 0:
+            # Only interact with some of the neighbors
+            interactions = list(n for n in neighbours if random.random() <= self.prob_interaction)
+            influence = sum( self.degree(i) for i in interactions )
+            mean_belief = sum( i.mean_belief * self.degree(i) / influence for i in interactions )
+            mean_belief = mean_belief * self.information_spread_intensity + self.mean_belief * ( 1 - self.information_spread_intensity )
+            self.mean_belief = mean_belief * self.vulnerability + self.mean_belief * ( 1 - self.vulnerability )
+        
+        if self.mean_belief >= 0.8:
+            return self.terrorist
+
+    @state
+    def leader(self):
+        self.mean_belief = self.mean_belief ** ( 1 - self.terrorist_additional_influence )
+        for neighbour in self.get_neighboring_agents(state_id=[self.terrorist.id, self.leader.id]):
+            if self.betweenness(neighbour) > self.betweenness(self):
+                return self.terrorist
+
+    @state
+    def terrorist(self):
+        neighbours = self.get_agents(state_id=[self.terrorist.id, self.leader.id],
+                                     agent_type=TerroristSpreadModel,
+                                     limit_neighbors=True)
+        if len(neighbours) > 0:
+            influence = sum( self.degree(n) for n in neighbours )
+            mean_belief = sum( n.mean_belief * self.degree(n) / influence for n in neighbours )
+            mean_belief = mean_belief * self.vulnerability + self.mean_belief * ( 1 - self.vulnerability )
+            self.mean_belief = self.mean_belief ** ( 1 - self.terrorist_additional_influence )
+
+        # Check if there are any leaders in the group
+        leaders = list(filter(lambda x: x.state.id == self.leader.id, neighbours))
+        if not leaders:
+            # Check if this is the potential leader
+            # Stop once it's found. Otherwise, set self as leader
+            for neighbour in neighbours:
+                if self.betweenness(self) < self.betweenness(neighbour):
+                    return
+            return self.leader
+
+
+class TrainingAreaModel(FSM, Geo):
+    """
+    Settings:
+        training_influence
+
+        min_vulnerability
+
+    Requires TerroristSpreadModel.
+    """
+
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        self.training_influence = environment.environment_params['training_influence']
+        if 'min_vulnerability' in environment.environment_params:
+            self.min_vulnerability = environment.environment_params['min_vulnerability']
+        else: self.min_vulnerability = 0
+
+    @default_state
+    @state
+    def terrorist(self):
+        for neighbour in self.get_neighboring_agents(agent_type=TerroristSpreadModel):
+            if neighbour.vulnerability > self.min_vulnerability:
+                neighbour.vulnerability = neighbour.vulnerability ** ( 1 - self.training_influence )        
+
+
+class HavenModel(FSM, Geo):
+    """
+    Settings:
+        haven_influence
+
+        min_vulnerability
+
+        max_vulnerability
+
+    Requires TerroristSpreadModel.
+    """
+
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        self.haven_influence = environment.environment_params['haven_influence']
+        if 'min_vulnerability' in environment.environment_params:
+            self.min_vulnerability = environment.environment_params['min_vulnerability']
+        else: self.min_vulnerability = 0
+        self.max_vulnerability = environment.environment_params['max_vulnerability']
+
+    def get_occupants(self, **kwargs):
+        return self.get_neighboring_agents(agent_type=TerroristSpreadModel, **kwargs)
+
+    @state
+    def civilian(self):
+        civilians = self.get_occupants(state_id=self.civilian.id)
+        if not civilians:
+            return self.terrorist
+
+        for neighbour in self.get_occupants():
+            if neighbour.vulnerability > self.min_vulnerability:
+                neighbour.vulnerability = neighbour.vulnerability * ( 1 - self.haven_influence )
+        return self.civilian
+
+    @state
+    def terrorist(self):
+        for neighbour in self.get_occupants():
+            if neighbour.vulnerability < self.max_vulnerability:
+                neighbour.vulnerability = neighbour.vulnerability ** ( 1 - self.haven_influence )
+        return self.terrorist
+
+
+class TerroristNetworkModel(TerroristSpreadModel):
+    """
+    Settings:
+        sphere_influence
+
+        vision_range
+
+        weight_social_distance
+
+        weight_link_distance
+    """
+
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+
+        self.vision_range = environment.environment_params['vision_range']
+        self.sphere_influence = environment.environment_params['sphere_influence']
+        self.weight_social_distance = environment.environment_params['weight_social_distance']
+        self.weight_link_distance = environment.environment_params['weight_link_distance']
+
+    @state
+    def terrorist(self):
+        self.update_relationships()
+        return super().terrorist()
+
+    @state
+    def leader(self):
+        self.update_relationships()
+        return super().leader()
+
+    def update_relationships(self):
+        if self.count_neighboring_agents(state_id=self.civilian.id) == 0:
+            close_ups = set(self.geo_search(radius=self.vision_range, agent_type=TerroristNetworkModel))
+            step_neighbours = set(self.ego_search(self.sphere_influence, agent_type=TerroristNetworkModel, center=False))
+            neighbours = set(agent.id for agent in self.get_neighboring_agents(agent_type=TerroristNetworkModel))
+            search = (close_ups | step_neighbours) - neighbours
+            for agent in self.get_agents(search):
+                social_distance = 1 / self.shortest_path_length(agent.id)
+                spatial_proximity = ( 1 - self.get_distance(agent.id) )
+                prob_new_interaction = self.weight_social_distance * social_distance + self.weight_link_distance * spatial_proximity
+                if agent['id'] == agent.civilian.id and random.random() < prob_new_interaction:
+                    self.add_edge(agent)
+                    break
+
+    def get_distance(self, target):
+        source_x, source_y = nx.get_node_attributes(self.global_topology, 'pos')[self.id]
+        target_x, target_y = nx.get_node_attributes(self.global_topology, 'pos')[target]
+        dx = abs( source_x - target_x )
+        dy = abs( source_y - target_y )
+        return ( dx ** 2 + dy ** 2 ) ** ( 1 / 2 )
+
+    def shortest_path_length(self, target):
+        try:
+            return nx.shortest_path_length(self.global_topology, self.id, target)
+        except nx.NetworkXNoPath:
+            return float('inf')

examples/terrorism/TerroristNetworkModel.yml

@@ -60,3 +60,4 @@ visualization_params:
   background_image: 'map_4800x2860.jpg'
   background_opacity: '0.9'
   background_filter_color: 'blue'
+skip_test: true  # This simulation takes too long for automated tests.

requirements.txt

@@ -5,3 +5,4 @@ numpy
 matplotlib
 pyyaml
 pandas
+scipy

soil/VERSION

@@ -1 +1 @@
-0.13.6
+0.13.8

soil/__init__.py

@@ -14,6 +14,7 @@ except NameError:
 from . import agents
 from .simulation import *
 from .environment import Environment
+from .history import History
 from . import utils
 from . import analysis
 

soil/agents/CounterModel.py

@@ -22,11 +22,17 @@ class AggregatedCounter(BaseAgent):
     in each step and adds it to its state.
     """
 
+    defaults = {
+        'times': 0,
+        'neighbors': 0,
+        'total': 0
+    }
+
     def step(self):
         # Outside effects
-        total = len(list(self.get_all_agents()))
+        self['times'] += 1
         neighbors = len(list(self.get_neighboring_agents()))
-        self['times'] = self.get('times', 0) + 1
-        self['neighbors'] = self.get('neighbors', 0) + neighbors
-        self['total'] = total = self.get('total', 0) + total
+        self['neighbors'] += neighbors
+        total = len(list(self.get_all_agents()))
+        self['total'] += total
         self.debug('Running for step: {}. Total: {}'.format(self.now, total))

soil/agents/__init__.py

@@ -10,6 +10,7 @@ import logging
 from collections import OrderedDict
 from copy import deepcopy
 from functools import partial
+from scipy.spatial import cKDTree as KDTree
 import json
 
 from functools import wraps
@@ -17,6 +18,12 @@ from functools import wraps
 from .. import utils, history
 
 
+def as_node(agent):
+    if isinstance(agent, BaseAgent):
+        return agent.id
+    return agent
+
+
 class BaseAgent(nxsim.BaseAgent):
     """
     A special simpy BaseAgent that keeps track of its state history.
@@ -25,13 +32,13 @@ class BaseAgent(nxsim.BaseAgent):
     defaults = {}
 
     def __init__(self, environment, agent_id, state=None,
-                 name='network_process', interval=None, **state_params):
+                 name=None, interval=None, **state_params):
         # Check for REQUIRED arguments
         assert environment is not None, TypeError('__init__ missing 1 required keyword argument: \'environment\'. '
                                                   'Cannot be NoneType.')
         # Initialize agent parameters
         self.id = agent_id
-        self.name = name
+        self.name = name or '{}[{}]'.format(type(self).__name__, self.id)
         self.state_params = state_params
 
         # Register agent to environment
@@ -46,8 +53,7 @@ class BaseAgent(nxsim.BaseAgent):
 
         if not hasattr(self, 'level'):
             self.level = logging.DEBUG
-        self.logger = logging.getLogger('{}-Agent-{}'.format(self.env.name,
-                                                             self.id))
+        self.logger = logging.getLogger(self.env.name)
         self.logger.setLevel(self.level)
 
         # initialize every time an instance of the agent is created
@@ -134,47 +140,25 @@ class BaseAgent(nxsim.BaseAgent):
     def step(self):
         pass
 
-    def count_agents(self, state_id=None, limit_neighbors=False):
+    def count_agents(self, **kwargs):
+        return len(list(self.get_agents(**kwargs)))
+
+    def count_neighboring_agents(self, state_id=None, **kwargs):
+        return len(super().get_neighboring_agents(state_id=state_id, **kwargs))
+
+    def get_neighboring_agents(self, state_id=None, **kwargs):
+        return self.get_agents(limit_neighbors=True, state_id=state_id, **kwargs)
+
+    def get_agents(self, agents=None, limit_neighbors=False, **kwargs):
         if limit_neighbors:
-            agents = self.global_topology.neighbors(self.id)
+            agents = super().get_agents(limit_neighbors=limit_neighbors)
         else:
-            agents = self.global_topology.nodes()
-        count = 0
-        for agent in agents:
-            if state_id and state_id != self.global_topology.node[agent]['agent']['id']:
-                continue
-            count += 1
-        return count
-
-    def count_neighboring_agents(self, state_id=None):
-        return len(super().get_agents(state_id, limit_neighbors=True))
-
-    def get_agents(self, state_id=None, agent_type=None, limit_neighbors=False, iterator=False, **kwargs):
-        agents = self.env.agents
-        if limit_neighbors:
-            agents = super().get_agents(state_id, limit_neighbors)
-
-        def matches_all(agent):
-            if state_id is not None:
-                if agent.state.get('id', None) != state_id:
-                    return False
-            if agent_type is not None:
-                if type(agent) != agent_type:
-                    return False
-            state = agent.state
-            for k, v in kwargs.items():
-                if state.get(k, None) != v:
-                    return False
-            return True
-
-        f = filter(matches_all, agents)
-        if iterator:
-            return f
-        return list(f)
+            agents = self.env.get_agents(agents)
+        return select(agents, **kwargs)
 
     def log(self, message, *args, level=logging.INFO, **kwargs):
         message = message + " ".join(str(i) for i in args)
-        message = "\t@{:>5}:\t{}".format(self.now, message)
+        message = "\t{:10}@{:>5}:\t{}".format(self.name, self.now, message)
         for k, v in kwargs:
             message += " {k}={v} ".format(k, v)
         extra = {}
@@ -208,31 +192,76 @@ class BaseAgent(nxsim.BaseAgent):
         self._state = state['_state']
         self.env = state['environment']
 
+    def add_edge(self, node1, node2, **attrs):
+        node1 = as_node(node1)
+        node2 = as_node(node2)
 
-def state(func):
-    '''
-    A state function should return either a state id, or a tuple (state_id, when)
-    The default value for state_id is the current state id.
-    The default value for when is the interval defined in the nevironment.
-    '''
+        for n in [node1, node2]:
+            if n not in self.global_topology.nodes(data=False):
+                raise ValueError('"{}" not in the graph'.format(n))
+        return self.global_topology.add_edge(node1, node2, **attrs)
 
-    @wraps(func)
-    def func_wrapper(self):
-        next_state = func(self)
-        when = None
-        if next_state is None:
+    def subgraph(self, center=True, **kwargs):
+        include = [self] if center else []
+        return self.global_topology.subgraph(n.id for n in self.get_agents(**kwargs)+include)
+
+
+class NetworkAgent(BaseAgent):
+
+    def add_edge(self, other, **kwargs):
+        return super(NetworkAgent, self).add_edge(node1=self.id, node2=other, **kwargs)
+
+    def ego_search(self, steps=1, center=False, node=None, **kwargs):
+        '''Get a list of nodes in the ego network of *node* of radius *steps*'''
+        node = as_node(node if node is not None else self)
+        G = self.subgraph(**kwargs)
+        return nx.ego_graph(G, node, center=center, radius=steps).nodes()
+
+    def degree(self, node, force=False):
+        node = as_node(node)
+        if force or (not hasattr(self.env, '_degree')) or getattr(self.env, '_last_step', 0) < self.now:
+            self.env._degree = nx.degree_centrality(self.global_topology)
+            self.env._last_step = self.now
+        return self.env._degree[node]
+
+    def betweenness(self, node, force=False):
+        node = as_node(node)
+        if force or (not hasattr(self.env, '_betweenness')) or getattr(self.env, '_last_step', 0) < self.now:
+            self.env._betweenness = nx.betweenness_centrality(self.global_topology)
+            self.env._last_step = self.now
+        return self.env._betweenness[node]
+
+
+def state(name=None):
+    def decorator(func, name=None):
+        '''
+        A state function should return either a state id, or a tuple (state_id, when)
+        The default value for state_id is the current state id.
+        The default value for when is the interval defined in the environment.
+        '''
+
+        @wraps(func)
+        def func_wrapper(self):
+            next_state = func(self)
+            when = None
+            if next_state is None:
+                return when
+            try:
+                next_state, when = next_state
+            except (ValueError, TypeError):
+                pass
+            if next_state:
+                self.set_state(next_state)
             return when
-        try:
-            next_state, when = next_state
-        except (ValueError, TypeError):
-            pass
-        if next_state:
-            self.set_state(next_state)
-        return when
 
-    func_wrapper.id = func.__name__
-    func_wrapper.is_default = False
-    return func_wrapper
+        func_wrapper.id = name or func.__name__
+        func_wrapper.is_default = False
+        return func_wrapper
+
+    if callable(name):
+        return decorator(name)
+    else:
+        return partial(decorator, name=name)
 
 
 def default_state(func):
@@ -280,7 +309,7 @@ class FSM(BaseAgent, metaclass=MetaFSM):
             raise Exception('{} has no valid state id or default state'.format(self))
         if next_state not in self.states:
             raise Exception('{} is not a valid id for {}'.format(next_state, self))
-        self.states[next_state](self)
+        return self.states[next_state](self)
 
     def set_state(self, state):
         if hasattr(state, 'id'):
@@ -306,6 +335,9 @@ def prob(prob=1):
     return r < prob
 
 
+STATIC_THRESHOLD = (-1, -1)
+
+
 def calculate_distribution(network_agents=None,
                            agent_type=None):
     '''
@@ -337,12 +369,15 @@ def calculate_distribution(network_agents=None,
     elif agent_type:
         network_agents = [{'agent_type': agent_type}]
     else:
-        return []
+        raise ValueError('Specify a distribution or a default agent type')
 
     # Calculate the thresholds
     total = sum(x.get('weight', 1) for x in network_agents)
     acc = 0
     for v in network_agents:
+        if 'ids' in v:
+            v['threshold'] = STATIC_THRESHOLD
+            continue
         upper = acc + (v.get('weight', 1)/total)
         v['threshold'] = [acc, upper]
         acc = upper
@@ -403,21 +438,76 @@ def _convert_agent_types(ind, to_string=False, **kwargs):
     return deserialize_distribution(ind, **kwargs)
 
 
-def _agent_from_distribution(distribution, value=-1):
+def _agent_from_distribution(distribution, value=-1, agent_id=None):
     """Used in the initialization of agents given an agent distribution."""
     if value < 0:
         value = random.random()
-    for d in distribution:
+    for d in sorted(distribution, key=lambda x: x['threshold']):
         threshold = d['threshold']
-        if value >= threshold[0] and value < threshold[1]:
-            state = {}
-            if 'state' in d:
-                state = deepcopy(d['state'])
-            return d['agent_type'], state
+        # Check if the definition matches by id (first) or by threshold
+        if not ((agent_id is not None and threshold == STATIC_THRESHOLD and agent_id in d['ids']) or \
+                (value >= threshold[0] and value < threshold[1])):
+            continue
+        state = {}
+        if 'state' in d:
+            state = deepcopy(d['state'])
+        return d['agent_type'], state
 
     raise Exception('Distribution for value {} not found in: {}'.format(value, distribution))
 
 
+class Geo(NetworkAgent):
+    '''In this type of network, nodes have a "pos" attribute.'''
+
+    def geo_search(self, radius, node=None, center=False, **kwargs):
+        '''Get a list of nodes whose coordinates are closer than *radius* to *node*.'''
+        node = as_node(node if node is not None else self)
+
+        G = self.subgraph(**kwargs)
+
+        pos = nx.get_node_attributes(G, 'pos')
+        if not pos:
+            return []
+        nodes, coords = list(zip(*pos.items()))
+        kdtree = KDTree(coords)  # Cannot provide generator.
+        indices = kdtree.query_ball_point(pos[node], radius)
+        return [nodes[i] for i in indices if center or (nodes[i] != node)]
+
+
+def select(agents, state_id=None, agent_type=None, ignore=None, iterator=False, **kwargs):
+
+    if state_id is not None:
+        try:
+            state_id = tuple(state_id)
+        except TypeError:
+            state_id = tuple([state_id])
+    if agent_type is not None:
+        try:
+            agent_type = tuple(agent_type)
+        except TypeError:
+            agent_type = tuple([agent_type])
+
+    def matches_all(agent):
+        if state_id is not None:
+            if agent.state.get('id', None) not in state_id:
+                return False
+        if agent_type is not None:
+            if not isinstance(agent, agent_type):
+                return False
+        state = agent.state
+        for k, v in kwargs.items():
+            if state.get(k, None) != v:
+                return False
+        return True
+
+    f = filter(matches_all, agents)
+    if ignore:
+        f = filter(lambda x: x not in ignore, f)
+    if iterator:
+        return f
+    return list(f)
+
+
 from .BassModel import *
 from .BigMarketModel import *
 from .IndependentCascadeModel import *

soil/environment.py

@@ -4,9 +4,11 @@ import time
 import csv
 import random
 import simpy
+import yaml
 import tempfile
 import pandas as pd
 from copy import deepcopy
+from collections import Counter
 from networkx.readwrite import json_graph
 
 import networkx as nx
@@ -60,7 +62,8 @@ class Environment(nxsim.NetworkEnvironment):
         if not dry_run:
             self.get_path()
         self._history = history.History(name=self.name if not dry_run else None,
-                                        dir_path=self.dir_path)
+                                        dir_path=self.dir_path,
+                                        backup=True)
         # Add environment agents first, so their events get
         # executed before network agents
         self.environment_agents = environment_agents or []
@@ -99,8 +102,7 @@ class Environment(nxsim.NetworkEnvironment):
 
     @network_agents.setter
     def network_agents(self, network_agents):
-        if not network_agents:
-            return
+        self._network_agents = network_agents
         for ix in self.G.nodes():
             self.init_agent(ix, agent_distribution=network_agents)
 
@@ -111,7 +113,7 @@ class Environment(nxsim.NetworkEnvironment):
 
         agent_type = None
         if 'agent_type' in self.states.get(agent_id, {}):
-            agent_type = self.states[agent_id]
+            agent_type = self.states[agent_id]['agent_type']
         elif 'agent_type' in node:
             agent_type = node['agent_type']
         elif 'agent_type' in self.default_state:
@@ -119,8 +121,11 @@ class Environment(nxsim.NetworkEnvironment):
 
         if agent_type:
             agent_type = agents.deserialize_type(agent_type)
+        elif agent_distribution:
+            agent_type, state = agents._agent_from_distribution(agent_distribution, agent_id=agent_id)
         else:
-            agent_type, state = agents._agent_from_distribution(agent_distribution)
+            utils.logger.debug('Skipping node {}'.format(agent_id))
+            return
         return self.set_agent(agent_id, agent_type, state)
 
     def set_agent(self, agent_id, agent_type, state=None):
@@ -130,10 +135,12 @@ class Environment(nxsim.NetworkEnvironment):
         defstate.update(node.get('state', {}))
         if state:
             defstate.update(state)
-        state = defstate
-        a = agent_type(environment=self,
-                       agent_id=agent_id,
-                       state=state)
+        a = None
+        if agent_type:
+            state = defstate
+            a = agent_type(environment=self,
+                           agent_id=agent_id,
+                           state=state)
         node['agent'] = a
         return a
 
@@ -144,17 +151,20 @@ class Environment(nxsim.NetworkEnvironment):
         a['visible'] = True
         return a
 
-    def add_edge(self, agent1, agent2, attrs=None):
+    def add_edge(self, agent1, agent2, start=None, **attrs):
         if hasattr(agent1, 'id'):
             agent1 = agent1.id
         if hasattr(agent2, 'id'):
             agent2 = agent2.id
-        return self.G.add_edge(agent1, agent2)
+        start = start or self.now
+        return self.G.add_edge(agent1, agent2, **attrs)
 
     def run(self, *args, **kwargs):
         self._save_state()
+        self.log_stats()
         super().run(*args, **kwargs)
         self._history.flush_cache()
+        self.log_stats()
 
     def _save_state(self, now=None):
         # for agent in self.agents:
@@ -224,8 +234,10 @@ class Environment(nxsim.NetworkEnvironment):
     def get_agent(self, agent_id):
         return self.G.node[agent_id]['agent']
 
-    def get_agents(self):
-        return list(self.agents)
+    def get_agents(self, nodes=None):
+        if nodes is None:
+            return list(self.agents)
+        return [self.G.node[i]['agent'] for i in nodes]
 
     def dump_csv(self, dir_path=None):
         csv_name = os.path.join(self.get_path(dir_path),
@@ -327,6 +339,25 @@ class Environment(nxsim.NetworkEnvironment):
 
         return G
     
+    def stats(self):
+        stats = {}
+        stats['network'] = {}
+        stats['network']['n_nodes'] = self.G.number_of_nodes()
+        stats['network']['n_edges'] = self.G.number_of_edges()
+        c = Counter()
+        c.update(a.__class__.__name__ for a in self.network_agents)
+        stats['agents'] = {}
+        stats['agents']['model_count'] = dict(c)
+        c2 = Counter()
+        c2.update(a['id'] for a in self.network_agents)
+        stats['agents']['state_count'] = dict(c2)
+        stats['params'] = self.environment_params
+        return stats
+
+    def log_stats(self):
+        stats = self.stats()
+        utils.logger.info('Environment stats: \n{}'.format(yaml.dump(stats, default_flow_style=False)))
+    
     def __getstate__(self):
         state = {}
         for prop in _CONFIG_PROPS:

soil/history.py

@@ -3,6 +3,10 @@ import os
 import pandas as pd
 import sqlite3
 import copy
+import logging
+
+logger = logging.getLogger(__name__)
+
 from collections import UserDict, namedtuple
 
 from . import utils
@@ -13,7 +17,7 @@ class History:
     Store and retrieve values from a sqlite database.
     """
 
-    def __init__(self, db_path=None, name=None, dir_path=None, backup=True):
+    def __init__(self, db_path=None, name=None, dir_path=None, backup=False):
         if db_path is None and name:
             db_path = os.path.join(dir_path or os.getcwd(),
                                    '{}.db.sqlite'.format(name))
@@ -28,6 +32,7 @@ class History:
         self.db = db_path
 
         with self.db:
+            logger.debug('Creating database {}'.format(self.db_path))
             self.db.execute('''CREATE TABLE IF NOT EXISTS history (agent_id text, t_step int, key text, value text text)''')
             self.db.execute('''CREATE TABLE IF NOT EXISTS value_types (key text, value_type text)''')
             self.db.execute('''CREATE UNIQUE INDEX IF NOT EXISTS idx_history ON history (agent_id, t_step, key);''')
@@ -46,6 +51,7 @@ class History:
     def db(self, db_path=None):
         db_path = db_path or self.db_path
         if isinstance(db_path, str):
+            logger.debug('Connecting to database {}'.format(db_path))
             self._db = sqlite3.connect(db_path)
         else:
             self._db = db_path
@@ -110,6 +116,7 @@ class History:
         Use a cache to save state changes to avoid opening a session for every change.
         The cache will be flushed at the end of the simulation, and when history is accessed.
         '''
+        logger.debug('Flushing cache {}'.format(self.db_path))
         with self.db:
             for rec in self._tups:
                 self.db.execute("replace into history(agent_id, t_step, key, value) values (?, ?, ?, ?)", (rec.agent_id, rec.t_step, rec.key, rec.value))

soil/utils.py

@@ -147,7 +147,7 @@ def deserializer(type_, known_modules=[]):
             module = importlib.import_module(modname)
             cls = getattr(module, tname)
             return getattr(cls, 'deserialize', cls)
-        except (ImportError, AttributeError) as ex:
+        except (ModuleNotFoundError, AttributeError) as ex:
             errors.append((modname, tname, ex))
     raise Exception('Could not find type {}. Tried: {}'.format(type_, errors))
 

soil/web/TerroristNetworkModel.py

@@ -1,255 +0,0 @@
-import random
-import networkx as nx
-from soil.agents import BaseAgent, FSM, state, default_state
-from scipy.spatial import cKDTree as KDTree
-
-global betweenness_centrality_global
-global degree_centrality_global
-
-betweenness_centrality_global = None
-degree_centrality_global = None
-
-class TerroristSpreadModel(FSM):
-    """
-    Settings:
-        information_spread_intensity
-
-        terrorist_additional_influence
-
-        min_vulnerability (optional else zero)
-
-        max_vulnerability
-
-        prob_interaction
-    """
-
-    def __init__(self, environment=None, agent_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
-
-        global betweenness_centrality_global
-        global degree_centrality_global
-        
-        if betweenness_centrality_global == None:
-            betweenness_centrality_global = nx.betweenness_centrality(self.global_topology)
-        if degree_centrality_global == None:
-            degree_centrality_global = nx.degree_centrality(self.global_topology)
-
-        self.information_spread_intensity = environment.environment_params['information_spread_intensity']
-        self.terrorist_additional_influence = environment.environment_params['terrorist_additional_influence']
-        self.prob_interaction = environment.environment_params['prob_interaction']
-
-        if self['id'] == self.civilian.id:       # Civilian
-            self.initial_belief = random.uniform(0.00, 0.5)
-        elif self['id'] == self.terrorist.id:     # Terrorist
-            self.initial_belief = random.uniform(0.8, 1.00)
-        elif self['id'] == self.leader.id:     # Leader
-            self.initial_belief = 1.00
-        else:
-            raise Exception('Invalid state id: {}'.format(self['id']))
-
-        if 'min_vulnerability' in environment.environment_params:
-            self.vulnerability = random.uniform( environment.environment_params['min_vulnerability'], environment.environment_params['max_vulnerability'] )
-        else :
-            self.vulnerability = random.uniform( 0, environment.environment_params['max_vulnerability'] )
-
-        self.mean_belief = self.initial_belief
-        self.betweenness_centrality = betweenness_centrality_global[self.id]
-        self.degree_centrality = degree_centrality_global[self.id]
-
-        # self.state['radicalism'] = self.mean_belief
-
-    def count_neighboring_agents(self, state_id=None):
-        if isinstance(state_id, list):
-            return len(self.get_neighboring_agents(state_id))
-        else:
-            return len(super().get_agents(state_id, limit_neighbors=True))
-
-    def get_neighboring_agents(self, state_id=None):
-        if isinstance(state_id, list):
-            _list = []
-            for i in state_id:
-                _list += super().get_agents(i, limit_neighbors=True)
-            return [ neighbour for neighbour in _list if isinstance(neighbour, TerroristSpreadModel) ]
-        else:
-            _list = super().get_agents(state_id, limit_neighbors=True) 
-            return [ neighbour for neighbour in _list if isinstance(neighbour, TerroristSpreadModel) ]
-
-    @state
-    def civilian(self):
-        if self.count_neighboring_agents() > 0:
-            neighbours = []
-            for neighbour in self.get_neighboring_agents():
-                if random.random() < self.prob_interaction:
-                    neighbours.append(neighbour)
-            influence = sum( neighbour.degree_centrality for neighbour in neighbours )
-            mean_belief = sum( neighbour.mean_belief * neighbour.degree_centrality / influence for neighbour in neighbours )
-            self.initial_belief = self.mean_belief
-            mean_belief = mean_belief * self.information_spread_intensity + self.initial_belief * ( 1 - self.information_spread_intensity )
-            self.mean_belief = mean_belief * self.vulnerability + self.initial_belief * ( 1 - self.vulnerability )
-        
-        if self.mean_belief >= 0.8:
-            return self.terrorist
-
-    @state
-    def leader(self):
-        self.mean_belief = self.mean_belief ** ( 1 - self.terrorist_additional_influence )
-        if self.count_neighboring_agents(state_id=[self.terrorist.id, self.leader.id]) > 0:
-            for neighbour in self.get_neighboring_agents(state_id=[self.terrorist.id, self.leader.id]):
-                if neighbour.betweenness_centrality > self.betweenness_centrality:
-                    return self.terrorist
-
-    @state
-    def terrorist(self):
-        if self.count_neighboring_agents(state_id=[self.terrorist.id, self.leader.id]) > 0:
-            neighbours = self.get_neighboring_agents(state_id=[self.terrorist.id, self.leader.id])
-            influence = sum( neighbour.degree_centrality for neighbour in neighbours )
-            mean_belief = sum( neighbour.mean_belief * neighbour.degree_centrality / influence for neighbour in neighbours )
-            self.initial_belief = self.mean_belief
-            self.mean_belief = mean_belief * self.vulnerability + self.initial_belief * ( 1 - self.vulnerability )
-            self.mean_belief = self.mean_belief ** ( 1 - self.terrorist_additional_influence )
-
-        if self.count_neighboring_agents(state_id=self.leader.id) == 0 and self.count_neighboring_agents(state_id=self.terrorist.id) > 0:
-            max_betweenness_centrality = self
-            for neighbour in self.get_neighboring_agents(state_id=self.terrorist.id):
-                if neighbour.betweenness_centrality > max_betweenness_centrality.betweenness_centrality:
-                    max_betweenness_centrality = neighbour
-            if max_betweenness_centrality == self:
-                return self.leader
-
-    def add_edge(self, G, source, target):
-        G.add_edge(source.id, target.id, start=self.env._now)
-
-    def link_search(self, G, node, radius):
-        pos = nx.get_node_attributes(G, 'pos')
-        nodes, coords = list(zip(*pos.items()))
-        kdtree = KDTree(coords)  # Cannot provide generator.
-        edge_indexes = kdtree.query_pairs(radius, 2)
-        _list = [ edge[int(not edge.index(node))] for edge in edge_indexes if node in edge ]
-        return [ G.nodes()[index]['agent'] for index in _list ]
-
-    def social_search(self, G, node, steps):
-        nodes = list(nx.ego_graph(G, node, radius=steps).nodes())
-        nodes.remove(node)
-        return [ G.nodes()[index]['agent'] for index in nodes ]
-
-
-class TrainingAreaModel(FSM):
-    """
-    Settings:
-        training_influence
-
-        min_vulnerability
-
-    Requires TerroristSpreadModel.
-    """
-
-    def __init__(self, environment=None, agent_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
-        self.training_influence = environment.environment_params['training_influence']
-        if 'min_vulnerability' in environment.environment_params:
-            self.min_vulnerability = environment.environment_params['min_vulnerability']
-        else: self.min_vulnerability = 0
-
-    @default_state
-    @state
-    def terrorist(self):
-        for neighbour in self.get_neighboring_agents():
-            if isinstance(neighbour, TerroristSpreadModel) and neighbour.vulnerability > self.min_vulnerability:
-                neighbour.vulnerability = neighbour.vulnerability ** ( 1 - self.training_influence )        
-
-
-class HavenModel(FSM):
-    """
-    Settings:
-        haven_influence
-
-        min_vulnerability
-
-        max_vulnerability
-
-    Requires TerroristSpreadModel.
-    """
-
-    def __init__(self, environment=None, agent_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
-        self.haven_influence = environment.environment_params['haven_influence']
-        if 'min_vulnerability' in environment.environment_params:
-            self.min_vulnerability = environment.environment_params['min_vulnerability']
-        else: self.min_vulnerability = 0
-        self.max_vulnerability = environment.environment_params['max_vulnerability']
-
-    @state
-    def civilian(self):
-        for neighbour_agent in self.get_neighboring_agents():
-            if isinstance(neighbour_agent, TerroristSpreadModel) and neighbour_agent['id'] == neighbour_agent.civilian.id:
-                for neighbour in self.get_neighboring_agents():
-                    if isinstance(neighbour, TerroristSpreadModel) and neighbour.vulnerability > self.min_vulnerability:
-                        neighbour.vulnerability = neighbour.vulnerability * ( 1 - self.haven_influence )
-                return self.civilian
-        return self.terrorist
-
-    @state
-    def terrorist(self):
-        for neighbour in self.get_neighboring_agents():
-            if isinstance(neighbour, TerroristSpreadModel) and neighbour.vulnerability < self.max_vulnerability:
-                neighbour.vulnerability = neighbour.vulnerability ** ( 1 - self.haven_influence )
-        return self.terrorist
-
-        
-class TerroristNetworkModel(TerroristSpreadModel):
-    """
-    Settings:
-        sphere_influence
-
-        vision_range
-
-        weight_social_distance
-
-        weight_link_distance
-    """
-
-    def __init__(self, environment=None, agent_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
-
-        self.vision_range = environment.environment_params['vision_range']
-        self.sphere_influence = environment.environment_params['sphere_influence']
-        self.weight_social_distance = environment.environment_params['weight_social_distance']
-        self.weight_link_distance = environment.environment_params['weight_link_distance']
-
-    @state
-    def terrorist(self):
-        self.update_relationships()
-        return super().terrorist()
-
-    @state
-    def leader(self):
-        self.update_relationships()
-        return super().leader()
-
-    def update_relationships(self):
-        if self.count_neighboring_agents(state_id=self.civilian.id) == 0:
-            close_ups = self.link_search(self.global_topology, self.id, self.vision_range)
-            step_neighbours = self.social_search(self.global_topology, self.id, self.sphere_influence)
-            search = list(set(close_ups).union(step_neighbours))
-            neighbours = self.get_neighboring_agents()
-            search = [item for item in search if not item in neighbours and isinstance(item, TerroristNetworkModel)]
-            for agent in search:
-                social_distance = 1 / self.shortest_path_length(self.global_topology, self.id, agent.id)
-                spatial_proximity = ( 1 - self.get_distance(self.global_topology, self.id, agent.id) )
-                prob_new_interaction = self.weight_social_distance * social_distance + self.weight_link_distance * spatial_proximity
-                if agent['id'] == agent.civilian.id and random.random() < prob_new_interaction:
-                    self.add_edge(self.global_topology, self, agent)
-                    break
-
-    def get_distance(self, G, source, target):
-        source_x, source_y = nx.get_node_attributes(G, 'pos')[source]
-        target_x, target_y = nx.get_node_attributes(G, 'pos')[target]
-        dx = abs( source_x - target_x )
-        dy = abs( source_y - target_y )
-        return ( dx ** 2 + dy ** 2 ) ** ( 1 / 2 )
-
-    def shortest_path_length(self, G, source, target):
-        try:
-            return nx.shortest_path_length(G, source, target)
-        except nx.NetworkXNoPath:
-            return float('inf')

tests/test_examples.py

@@ -7,6 +7,8 @@ from soil import utils, simulation
 ROOT = os.path.abspath(os.path.dirname(__file__))
 EXAMPLES = join(ROOT, '..', 'examples')
 
+FORCE_TESTS = os.environ.get('FORCE_TESTS', '')
+
 
 class TestExamples(TestCase):
     pass
@@ -19,7 +21,10 @@ def make_example_test(path, config):
         s = simulation.from_config(config)
         iterations = s.max_time * s.num_trials
         if iterations > 1000:
-            self.skipTest('This example would probably take too long')
+            s.max_time = 100
+            s.num_trials = 1
+        if config.get('skip_test', False) and not FORCE_TESTS:
+            self.skipTest('Example ignored.')
         envs = s.run_simulation(dry_run=True)
         assert envs
         for env in envs:

tests/test_history.py

@@ -120,18 +120,18 @@ class TestHistory(TestCase):
         assert os.path.exists(db_path)
 
         # Recover the data
-        recovered = history.History(db_path=db_path, backup=False)
+        recovered = history.History(db_path=db_path)
         assert recovered['a_1', 0, 'id'] == 'v'
         assert recovered['a_1', 4, 'id'] == 'e'
 
-        # Using the same name should create a backup copy
+        # Using backup=True should create a backup copy, and initialize an empty history
         newhistory = history.History(db_path=db_path, backup=True)
         backuppaths = glob(db_path + '.backup*.sqlite')
         assert len(backuppaths) == 1
         backuppath = backuppaths[0]
         assert newhistory.db_path == h.db_path
         assert os.path.exists(backuppath)
-        assert not len(newhistory[None, None, None])
+        assert len(newhistory[None, None, None]) == 0
 
     def test_history_tuples(self):
         """

tests/test_main.py

@@ -320,3 +320,19 @@ class TestMain(TestCase):
         h = history.History()
         h.save_record(agent_id=0, t_step=0, key="test", value="hello")
         assert h[0, 0, "test"] == "hello"
+
+    def test_subgraph(self):
+        '''An agent should be able to subgraph the global topology'''
+        G = nx.Graph()
+        G.add_node(3)
+        G.add_edge(1, 2)
+        distro = agents.calculate_distribution(agent_type=agents.NetworkAgent)
+        env = Environment(name='Test', topology=G, network_agents=distro)
+        lst = list(env.network_agents)
+
+        a2 = env.get_agent(2)
+        a3 = env.get_agent(3)
+        assert len(a2.subgraph(limit_neighbors=True)) == 2
+        assert len(a3.subgraph(limit_neighbors=True)) == 1
+        assert len(a3.subgraph(limit_neighbors=True, center=False)) == 0
+        assert len(a3.subgraph(agent_type=agents.NetworkAgent)) == 3