Version 0.30.0rc2

* Fix CLI arguments not being used when easy is passed a simulation instance
* Docs for `examples/events_and_messages/cars.py`

CHANGELOG.md

@@ -3,7 +3,7 @@ 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).
 
-## [0.3 UNRELEASED]
+## [0.30 UNRELEASED]
 ### Added
 * Simple debugging capabilities in `soil.debugging`, with a custom `pdb.Debugger` subclass that exposes commands to list agents and their status and set breakpoints on states (for FSM agents). Try it with `soil --debug <simulation file>`
 * Ability to run 

examples/custom_generator/mymodule.py

@@ -2,16 +2,17 @@ from networkx import Graph
 import random
 import networkx as nx
 
+
 def mygenerator(n=5, n_edges=5):
-    '''
+    """
     Just a simple generator that creates a network with n nodes and
     n_edges edges. Edges are assigned randomly, only avoiding self loops.
-    '''
+    """
     G = nx.Graph()
 
     for i in range(n):
         G.add_node(i)
-    
+
     for i in range(n_edges):
         nodes = list(G.nodes)
         n_in = random.choice(nodes)
@@ -19,9 +20,3 @@ def mygenerator(n=5, n_edges=5):
         n_out = random.choice(nodes)
         G.add_edge(n_in, n_out)
     return G
-    
-
-
-
-
-    

examples/custom_timeouts/custom_timeouts.py

@@ -2,34 +2,37 @@ from soil.agents import FSM, state, default_state
 
 
 class Fibonacci(FSM):
-    '''Agent that only executes in t_steps that are Fibonacci numbers'''
+    """Agent that only executes in t_steps that are Fibonacci numbers"""
 
-    defaults = {
+    defaults = {"prev": 1}
-        'prev': 1
-    }
 
     @default_state
     @state
     def counting(self):
-        self.log('Stopping at {}'.format(self.now))
+        self.log("Stopping at {}".format(self.now))
-        prev, self['prev'] = self['prev'], max([self.now, self['prev']])
+        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'''
+    """Agent that only executes in odd t_steps"""
+
     @default_state
     @state
     def odds(self):
-        self.log('Stopping at {}'.format(self.now))
+        self.log("Stopping at {}".format(self.now))
-        return None, self.env.timeout(1+self.now%2)
+        return None, self.env.timeout(1 + self.now % 2)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     from soil import Simulation
-    s = Simulation(network_agents=[{'ids': [0], 'agent_class': Fibonacci},
+
-                                   {'ids': [1], 'agent_class': Odds}],
+    s = Simulation(
-                   network_params={"generator": "complete_graph", "n": 2},
+        network_agents=[
-                   max_time=100,
+            {"ids": [0], "agent_class": Fibonacci},
-                   )
+            {"ids": [1], "agent_class": Odds},
+        ],
+        network_params={"generator": "complete_graph", "n": 2},
+        max_time=100,
+    )
     s.run(dry_run=True)

examples/events_and_messages/README.md

@@ -0,0 +1,7 @@
+This example can be run like with command-line options, like this:
+
+```bash
+python cars.py --level DEBUG  -e summary --csv
+```
+
+This will set the `CSV` (save the agent and model data to a CSV) and `summary` (print the a summary of the data to stdout) exporters, and set the log level to DEBUG.

examples/events_and_messages/cars.py

@@ -0,0 +1,205 @@
+"""
+This is an example of a simplified city, where there are Passengers and Drivers that can take those passengers
+from their location to their desired location.
+
+An example scenario could play like the following:
+
+- Drivers start in the `wandering` state, where they wander around the city until they have been assigned a journey
+- Passenger(1) tells every driver that it wants to request a Journey.
+- Each driver receives the request.
+  If Driver(2) is interested in providing the Journey, it asks Passenger(1) to confirm that it accepts Driver(2)'s request
+- When Passenger(1) accepts the request, two things happen:
+    - Passenger(1) changes its state to `driving_home`
+    - Driver(2) starts moving towards the origin of the Journey
+- Once Driver(2) reaches the origin, it starts moving itself and Passenger(1) to the destination of the Journey
+- When Driver(2) reaches the destination (carrying Passenger(1) along):
+    - Driver(2) starts wondering again
+    - Passenger(1) dies, and is removed from the simulation
+- If there are no more passengers available in the simulation, Drivers die
+"""
+from __future__ import annotations
+from soil import *
+from soil import events
+from mesa.space import MultiGrid
+
+
+# More complex scenarios may use more than one type of message  between objects.
+# A common pattern is to use `enum.Enum` to represent state changes in a request.
+@dataclass
+class Journey:
+    """
+    This represents a request for a journey. Passengers and drivers exchange this object. 
+
+    A journey may have a driver assigned or not. If the driver has not been assigned, this
+    object is considered a "request for a journey".
+    """
+    origin: (int, int)
+    destination: (int, int)
+    tip: float
+
+    passenger: Passenger
+    driver: Driver = None
+
+
+class City(EventedEnvironment):
+    """
+    An environment with a grid where drivers and passengers will be placed.
+
+    The number of drivers and riders is configurable through its parameters:
+
+    :param str n_cars: The total number of drivers to add
+    :param str n_passengers: The number of passengers in the simulation
+    :param list agents: Specific agents to use in the simulation. It overrides the `n_passengers`
+    and `n_cars` params.
+    :param int height: Height of the internal grid
+    :param int width: Width of the internal grid
+    """
+    def __init__(self, *args, n_cars=1, n_passengers=10,
+                 height=100, width=100, agents=None,
+                 model_reporters=None,
+                 **kwargs):
+        self.grid = MultiGrid(width=width, height=height, torus=False)
+        if agents is None:
+            agents = []
+            for i in range(n_cars):
+                agents.append({'agent_class': Driver})
+            for i in range(n_passengers):
+                agents.append({'agent_class': Passenger})
+        model_reporters = model_reporters or {'earnings': 'total_earnings', 'n_passengers': 'number_passengers'}
+        print('REPORTERS', model_reporters)
+        super().__init__(*args, agents=agents, model_reporters=model_reporters, **kwargs)
+        for agent in self.agents:
+            self.grid.place_agent(agent, (0, 0))
+            self.grid.move_to_empty(agent)
+
+    @property
+    def total_earnings(self):
+        return sum(d.earnings for d in self.agents(agent_class=Driver))
+
+    @property
+    def number_passengers(self):
+        return self.count_agents(agent_class=Passenger)
+
+
+class Driver(Evented, FSM):
+    pos = None
+    journey = None
+    earnings = 0
+
+    def on_receive(self, msg, sender):
+        '''This is not a state. It will run (and block) every time check_messages is invoked'''
+        if self.journey is None and isinstance(msg, Journey) and msg.driver is None:
+            msg.driver = self
+            self.journey = msg
+
+    def check_passengers(self):
+        '''If there are no more passengers, stop forever'''
+        c = self.count_agents(agent_class=Passenger)
+        self.info(f"Passengers left {c}")
+        if not c:
+            self.die()
+
+    @default_state
+    @state
+    def wandering(self):
+        '''Move around the city until a journey is accepted'''
+        target = None
+        self.check_passengers()
+        self.journey = None
+        while self.journey is None:  # No potential journeys detected (see on_receive)
+            if target is None or not self.move_towards(target):
+                target = self.random.choice(self.model.grid.get_neighborhood(self.pos, moore=False))
+
+            self.check_passengers()
+            self.check_messages() # This will call on_receive behind the scenes, and the agent's status will be updated
+            yield Delta(30) # Wait at least 30 seconds before checking again
+
+        try:
+            # Re-send the journey to the passenger, to confirm that we have been selected
+            self.journey = yield self.journey.passenger.ask(self.journey, timeout=60)
+        except events.TimedOut:
+            # No journey has been accepted. Try again
+            self.journey = None
+            return
+
+        return self.driving
+
+    @state
+    def driving(self):
+        '''The journey has been accepted. Pick them up and take them to their destination'''
+        while self.move_towards(self.journey.origin):
+            yield
+        while self.move_towards(self.journey.destination, with_passenger=True):
+            yield
+        self.earnings += self.journey.tip
+        self.check_passengers()
+        return self.wandering
+
+    def move_towards(self, target, with_passenger=False):
+        '''Move one cell at a time towards a target'''
+        self.info(f"Moving { self.pos } -> { target }")
+        if target[0] == self.pos[0] and target[1] == self.pos[1]:
+            return False
+
+        next_pos = [self.pos[0], self.pos[1]]
+        for idx in [0, 1]:
+            if self.pos[idx] < target[idx]:
+                next_pos[idx] += 1
+                break
+            if self.pos[idx] > target[idx]:
+                next_pos[idx] -= 1
+                break
+        self.model.grid.move_agent(self, tuple(next_pos))
+        if with_passenger:
+            self.journey.passenger.pos = self.pos  # This could be communicated through messages
+        return True
+            
+
+class Passenger(Evented, FSM):
+    pos = None
+
+    def on_receive(self, msg, sender):
+        '''This is not a state. It will be run synchronously every time `check_messages` is run'''
+
+        if isinstance(msg, Journey):
+            self.journey = msg
+            return msg
+
+
+    @default_state
+    @state
+    def asking(self):
+        destination = (self.random.randint(0, self.model.grid.height), self.random.randint(0, self.model.grid.width))
+        self.journey = None
+        journey = Journey(origin=self.pos,
+                          destination=destination,
+                          tip=self.random.randint(10, 100),
+                          passenger=self)
+
+        timeout = 60
+        expiration = self.now + timeout
+        self.model.broadcast(journey, ttl=timeout, sender=self, agent_class=Driver)
+        while not self.journey:
+            self.info(f"Passenger at: { self.pos }. Checking for responses.")
+            try:
+                yield self.received(expiration=expiration)
+            except events.TimedOut:
+                self.info(f"Passenger at: { self.pos }. Asking for journey.")
+                self.model.broadcast(journey, ttl=timeout, sender=self, agent_class=Driver)
+                expiration = self.now + timeout
+            self.check_messages()
+        return self.driving_home
+
+    @state
+    def driving_home(self):
+        while self.pos[0] != self.journey.destination[0] or self.pos[1] != self.journey.destination[1]:
+            yield self.received(timeout=60)
+        self.info("Got home safe!")
+        self.die()
+
+
+simulation = Simulation(name='RideHailing', model_class=City, model_params={'n_passengers': 2})
+
+if __name__ == "__main__":
+    with easy(simulation) as s:
+        s.run()

examples/mesa/server.py

@@ -14,16 +14,18 @@ def network_portrayal(env):
     # The model ensures there is 0 or 1 agent per node
 
     portrayal = dict()
-    wealths = {node_id: data['agent'].wealth for (node_id, data) in env.G.nodes(data=True)}
+    wealths = {
+        node_id: data["agent"].wealth for (node_id, data) in env.G.nodes(data=True)
+    }
     portrayal["nodes"] = [
         {
             "id": node_id,
-            "size": 2*(wealth+1),
+            "size": 2 * (wealth + 1),
             "color": "#CC0000" if wealth == 0 else "#007959",
             # "color": "#CC0000",
             "label": f"{node_id}: {wealth}",
-        } for (node_id, wealth) in wealths.items()
+        }
-
+        for (node_id, wealth) in wealths.items()
     ]
 
     portrayal["edges"] = [
@@ -41,7 +43,7 @@ def gridPortrayal(agent):
     :param agent:  the agent in the simulation
     :return: the portrayal dictionary
     """
-    color = max(10, min(agent.wealth*10, 100))
+    color = max(10, min(agent.wealth * 10, 100))
     return {
         "Shape": "rect",
         "w": 1,
@@ -52,7 +54,7 @@ def gridPortrayal(agent):
         "Text": agent.unique_id,
         "x": agent.pos[0],
         "y": agent.pos[1],
-        "Color": f"rgba(31, 10, 255, 0.{color})"
+        "Color": f"rgba(31, 10, 255, 0.{color})",
     }
 
 
@@ -79,7 +81,7 @@ model_params = {
         10,
         1,
         description="Grid height",
-        ),
+    ),
     "width": UserSettableParameter(
         "slider",
         "width",
@@ -88,16 +90,20 @@ model_params = {
         10,
         1,
         description="Grid width",
-        ),
+    ),
-    "agent_class": UserSettableParameter('choice', 'Agent class', value='MoneyAgent',
+    "agent_class": UserSettableParameter(
-                                         choices=['MoneyAgent', 'SocialMoneyAgent']),
+        "choice",
+        "Agent class",
+        value="MoneyAgent",
+        choices=["MoneyAgent", "SocialMoneyAgent"],
+    ),
     "generator": graph_generator,
 }
 
 
-canvas_element = CanvasGrid(gridPortrayal,
+canvas_element = CanvasGrid(
-                            model_params["width"].value,
+    gridPortrayal, model_params["width"].value, model_params["height"].value, 500, 500
-                            model_params["height"].value, 500, 500)
+)
 
 
 server = ModularServer(

examples/mesa/social_wealth.py

@@ -1,9 +1,10 @@
-'''
+"""
 This is an example that adds soil agents and environment in a normal
 mesa workflow.
-'''
+"""
 from mesa import Agent as MesaAgent
 from mesa.space import MultiGrid
+
 # from mesa.time import RandomActivation
 from mesa.datacollection import DataCollector
 from mesa.batchrunner import BatchRunner
@@ -12,12 +13,13 @@ import networkx as nx
 
 from soil import NetworkAgent, Environment, serialization
 
+
 def compute_gini(model):
     agent_wealths = [agent.wealth for agent in model.agents]
     x = sorted(agent_wealths)
     N = len(list(model.agents))
-    B = sum( xi * (N-i) for i,xi in enumerate(x) ) / (N*sum(x))
+    B = sum(xi * (N - i) for i, xi in enumerate(x)) / (N * sum(x))
-    return (1 + (1/N) - 2*B)
+    return 1 + (1 / N) - 2 * B
 
 
 class MoneyAgent(MesaAgent):
@@ -32,9 +34,8 @@ class MoneyAgent(MesaAgent):
 
     def move(self):
         possible_steps = self.model.grid.get_neighborhood(
-            self.pos,
+            self.pos, moore=True, include_center=False
-            moore=True,
+        )
-            include_center=False)
         new_position = self.random.choice(possible_steps)
         self.model.grid.move_agent(self, new_position)
 
@@ -57,7 +58,7 @@ class SocialMoneyAgent(NetworkAgent, MoneyAgent):
 
     def give_money(self):
         cellmates = set(self.model.grid.get_cell_list_contents([self.pos]))
-        friends = set(self.get_neighboring_agents())
+        friends = set(self.get_neighbors())
         self.info("Trying to give money")
         self.info("Cellmates: ", cellmates)
         self.info("Friends: ", friends)
@@ -69,6 +70,7 @@ class SocialMoneyAgent(NetworkAgent, MoneyAgent):
             other.wealth += 1
             self.wealth -= 1
 
+
 def graph_generator(n=5):
     G = nx.Graph()
     for ix in range(n):
@@ -78,16 +80,22 @@ def graph_generator(n=5):
 
 class MoneyEnv(Environment):
     """A model with some number of agents."""
-    def __init__(self, width, height, N, generator=graph_generator,
+
-                 agent_class=SocialMoneyAgent,
+    def __init__(
-                 topology=None, **kwargs):
+        self,
+        width,
+        height,
+        N,
+        generator=graph_generator,
+        agent_class=SocialMoneyAgent,
+        topology=None,
+        **kwargs
+    ):
 
         generator = serialization.deserialize(generator)
         agent_class = serialization.deserialize(agent_class, globs=globals())
         topology = generator(n=N)
-        super().__init__(topology=topology,
+        super().__init__(topology=topology, N=N, **kwargs)
-                         N=N,
-                         **kwargs)
         self.grid = MultiGrid(width, height, False)
 
         self.populate_network(agent_class=agent_class)
@@ -99,26 +107,29 @@ class MoneyEnv(Environment):
             self.grid.place_agent(agent, (x, y))
 
         self.datacollector = DataCollector(
-            model_reporters={"Gini": compute_gini},
+            model_reporters={"Gini": compute_gini}, agent_reporters={"Wealth": "wealth"}
-            agent_reporters={"Wealth": "wealth"})
+        )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
 
-    fixed_params = {"generator": nx.complete_graph,
+    fixed_params = {
-                    "width": 10,
+        "generator": nx.complete_graph,
-                    "network_agents": [{"agent_class": SocialMoneyAgent,
+        "width": 10,
-                                       'weight': 1}],
+        "network_agents": [{"agent_class": SocialMoneyAgent, "weight": 1}],
-                    "height": 10}
+        "height": 10,
+    }
 
     variable_params = {"N": range(10, 100, 10)}
 
-    batch_run = BatchRunner(MoneyEnv,
+    batch_run = BatchRunner(
-                            variable_parameters=variable_params,
+        MoneyEnv,
-                            fixed_parameters=fixed_params,
+        variable_parameters=variable_params,
-                            iterations=5,
+        fixed_parameters=fixed_params,
-                            max_steps=100,
+        iterations=5,
-                            model_reporters={"Gini": compute_gini})
+        max_steps=100,
+        model_reporters={"Gini": compute_gini},
+    )
     batch_run.run_all()
 
     run_data = batch_run.get_model_vars_dataframe()

examples/mesa/wealth.py

@@ -4,24 +4,26 @@ from mesa.time import RandomActivation
 from mesa.datacollection import DataCollector
 from mesa.batchrunner import BatchRunner
 
+
 def compute_gini(model):
     agent_wealths = [agent.wealth for agent in model.schedule.agents]
     x = sorted(agent_wealths)
     N = model.num_agents
-    B = sum( xi * (N-i) for i,xi in enumerate(x) ) / (N*sum(x))
+    B = sum(xi * (N - i) for i, xi in enumerate(x)) / (N * sum(x))
-    return (1 + (1/N) - 2*B)
+    return 1 + (1 / N) - 2 * B
+
 
 class MoneyAgent(Agent):
-    """ An agent with fixed initial wealth."""
+    """An agent with fixed initial wealth."""
+
     def __init__(self, unique_id, model):
         super().__init__(unique_id, model)
         self.wealth = 1
 
     def move(self):
         possible_steps = self.model.grid.get_neighborhood(
-            self.pos,
+            self.pos, moore=True, include_center=False
-            moore=True,
+        )
-            include_center=False)
         new_position = self.random.choice(possible_steps)
         self.model.grid.move_agent(self, new_position)
 
@@ -37,8 +39,10 @@ class MoneyAgent(Agent):
         if self.wealth > 0:
             self.give_money()
 
+
 class MoneyModel(Model):
     """A model with some number of agents."""
+
     def __init__(self, N, width, height):
         self.num_agents = N
         self.grid = MultiGrid(width, height, True)
@@ -55,29 +59,29 @@ class MoneyModel(Model):
             self.grid.place_agent(a, (x, y))
 
         self.datacollector = DataCollector(
-            model_reporters={"Gini": compute_gini},
+            model_reporters={"Gini": compute_gini}, agent_reporters={"Wealth": "wealth"}
-            agent_reporters={"Wealth": "wealth"})
+        )
 
     def step(self):
         self.datacollector.collect(self)
         self.schedule.step()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
 
-    fixed_params = {"width": 10,
+    fixed_params = {"width": 10, "height": 10}
-                    "height": 10}
     variable_params = {"N": range(10, 500, 10)}
 
-    batch_run = BatchRunner(MoneyModel,
+    batch_run = BatchRunner(
-                            variable_params,
+        MoneyModel,
-                            fixed_params,
+        variable_params,
-                            iterations=5,
+        fixed_params,
-                            max_steps=100,
+        iterations=5,
-                            model_reporters={"Gini": compute_gini})
+        max_steps=100,
+        model_reporters={"Gini": compute_gini},
+    )
     batch_run.run_all()
 
     run_data = batch_run.get_model_vars_dataframe()
     run_data.head()
     print(run_data.Gini)
-

examples/newsspread/newsspread.py

@@ -3,84 +3,85 @@ import logging
 
 
 class DumbViewer(FSM, NetworkAgent):
-    '''
+    """
     A viewer that gets infected via TV (if it has one) and tries to infect
     its neighbors once it's infected.
-    '''
+    """
-    defaults = {
+
-        'prob_neighbor_spread': 0.5,
+    prob_neighbor_spread = 0.5
-        'prob_tv_spread': 0.1,
+    prob_tv_spread = 0.1
-    }
+    has_been_infected = False
 
     @default_state
     @state
     def neutral(self):
-        if self['has_tv']:
+        if self["has_tv"]:
-            if self.prob(self.model['prob_tv_spread']):
+            if self.prob(self.model["prob_tv_spread"]):
                 return self.infected
+        if self.has_been_infected:
+            return self.infected
 
     @state
     def infected(self):
-        for neighbor in self.get_neighboring_agents(state_id=self.neutral.id):
+        for neighbor in self.get_neighbors(state_id=self.neutral.id):
-            if self.prob(self.model['prob_neighbor_spread']):
+            if self.prob(self.model["prob_neighbor_spread"]):
                 neighbor.infect()
 
     def infect(self):
-        '''
+        """
         This is not a state. It is a function that other agents can use to try to
         infect this agent. DumbViewer always gets infected, but other agents like
         HerdViewer might not become infected right away
-        '''
+        """
 
-        self.set_state(self.infected)
+        self.has_been_infected = True
 
 
 class HerdViewer(DumbViewer):
-    '''
+    """
     A viewer whose probability of infection depends on the state of its neighbors.
-    '''
+    """
 
     def infect(self):
-        '''Notice again that this is NOT a state. See DumbViewer.infect for reference'''
+        """Notice again that this is NOT a state. See DumbViewer.infect for reference"""
-        infected = self.count_neighboring_agents(state_id=self.infected.id)
+        infected = self.count_neighbors(state_id=self.infected.id)
-        total = self.count_neighboring_agents()
+        total = self.count_neighbors()
-        prob_infect = self.model['prob_neighbor_spread'] * infected/total
+        prob_infect = self.model["prob_neighbor_spread"] * infected / total
-        self.debug('prob_infect', prob_infect)
+        self.debug("prob_infect", prob_infect)
         if self.prob(prob_infect):
-            self.set_state(self.infected)
+            self.has_been_infected = True
 
 
 class WiseViewer(HerdViewer):
-    '''
+    """
     A viewer that can change its mind.
-    '''
+    """
 
     defaults = {
-        'prob_neighbor_spread': 0.5,
+        "prob_neighbor_spread": 0.5,
-        'prob_neighbor_cure': 0.25,
+        "prob_neighbor_cure": 0.25,
-        'prob_tv_spread': 0.1,
+        "prob_tv_spread": 0.1,
     }
 
     @state
     def cured(self):
-        prob_cure = self.model['prob_neighbor_cure']
+        prob_cure = self.model["prob_neighbor_cure"]
-        for neighbor in self.get_neighboring_agents(state_id=self.infected.id):
+        for neighbor in self.get_neighbors(state_id=self.infected.id):
             if self.prob(prob_cure):
                 try:
                     neighbor.cure()
                 except AttributeError:
-                    self.debug('Viewer {} cannot be cured'.format(neighbor.id))
+                    self.debug("Viewer {} cannot be cured".format(neighbor.id))
 
     def cure(self):
-        self.set_state(self.cured.id)
+        self.has_been_cured = True
 
     @state
     def infected(self):
-        cured = max(self.count_neighboring_agents(self.cured.id),
+        if self.has_been_cured:
-                    1.0)
+            return self.cured
-        infected = max(self.count_neighboring_agents(self.infected.id),
+        cured = max(self.count_neighbors(self.cured.id), 1.0)
-                       1.0)
+        infected = max(self.count_neighbors(self.infected.id), 1.0)
-        prob_cure = self.model['prob_neighbor_cure'] * (cured/infected)
+        prob_cure = self.model["prob_neighbor_cure"] * (cured / infected)
         if self.prob(prob_cure):
             return self.cured
-        return self.set_state(super().infected)

examples/programmatic/programmatic.py

@@ -1,6 +1,6 @@
-'''
+"""
 Example of a fully programmatic simulation, without definition files.
-'''
+"""
 from soil import Simulation, agents
 from networkx import Graph
 import logging
@@ -14,21 +14,22 @@ def mygenerator():
 
 
 class MyAgent(agents.FSM):
-
     @agents.default_state
     @agents.state
     def neutral(self):
-        self.debug('I am running')
+        self.debug("I am running")
         if agents.prob(0.2):
-            self.info('This runs 2/10 times on average')
+            self.info("This runs 2/10 times on average")
 
 
-s = Simulation(name='Programmatic',
+s = Simulation(
-               network_params={'generator': mygenerator},
+    name="Programmatic",
-               num_trials=1,
+    network_params={"generator": mygenerator},
-               max_time=100,
+    num_trials=1,
-               agent_class=MyAgent,
+    max_time=100,
-               dry_run=True)
+    agent_class=MyAgent,
+    dry_run=True,
+)
 
 
 # By default, logging will only print WARNING logs (and above).

examples/pubcrawl/pubcrawl.py

@@ -5,7 +5,8 @@ import logging
 
 
 class CityPubs(Environment):
-    '''Environment with Pubs'''
+    """Environment with Pubs"""
+
     level = logging.INFO
 
     def __init__(self, *args, number_of_pubs=3, pub_capacity=10, **kwargs):
@@ -13,68 +14,70 @@ class CityPubs(Environment):
         pubs = {}
         for i in range(number_of_pubs):
             newpub = {
-                'name': 'The awesome pub #{}'.format(i),
+                "name": "The awesome pub #{}".format(i),
-                'open': True,
+                "open": True,
-                'capacity': pub_capacity,
+                "capacity": pub_capacity,
-                'occupancy': 0,
+                "occupancy": 0,
             }
-            pubs[newpub['name']] = newpub
+            pubs[newpub["name"]] = newpub
-        self['pubs'] = pubs
+        self["pubs"] = pubs
 
     def enter(self, pub_id, *nodes):
-        '''Agents will try to enter. The pub checks if it is possible'''
+        """Agents will try to enter. The pub checks if it is possible"""
         try:
-            pub = self['pubs'][pub_id]
+            pub = self["pubs"][pub_id]
         except KeyError:
-            raise ValueError('Pub {} is not available'.format(pub_id))
+            raise ValueError("Pub {} is not available".format(pub_id))
-        if not pub['open'] or (pub['capacity'] < (len(nodes) + pub['occupancy'])):
+        if not pub["open"] or (pub["capacity"] < (len(nodes) + pub["occupancy"])):
             return False
-        pub['occupancy'] += len(nodes)
+        pub["occupancy"] += len(nodes)
         for node in nodes:
-            node['pub'] = pub_id
+            node["pub"] = pub_id
         return True
 
     def available_pubs(self):
-        for pub in self['pubs'].values():
+        for pub in self["pubs"].values():
-            if pub['open'] and (pub['occupancy'] < pub['capacity']):
+            if pub["open"] and (pub["occupancy"] < pub["capacity"]):
-                yield pub['name']
+                yield pub["name"]
 
     def exit(self, pub_id, *node_ids):
-        '''Agents will notify the pub they want to leave'''
+        """Agents will notify the pub they want to leave"""
         try:
-            pub = self['pubs'][pub_id]
+            pub = self["pubs"][pub_id]
         except KeyError:
-            raise ValueError('Pub {} is not available'.format(pub_id))
+            raise ValueError("Pub {} is not available".format(pub_id))
         for node_id in node_ids:
             node = self.get_agent(node_id)
-            if pub_id == node['pub']:
+            if pub_id == node["pub"]:
-                del node['pub']
+                del node["pub"]
-                pub['occupancy'] -= 1
+                pub["occupancy"] -= 1
 
 
 class Patron(FSM, NetworkAgent):
-    '''Agent that looks for friends to drink with. It will do three things:
+    """Agent that looks for friends to drink with. It will do three things:
-        1) Look for other patrons to drink with
+    1) Look for other patrons to drink with
-        2) Look for a bar where the agent and other agents in the same group can get in.
+    2) Look for a bar where the agent and other agents in the same group can get in.
-        3) While in the bar, patrons only drink, until they get drunk and taken home.
+    3) While in the bar, patrons only drink, until they get drunk and taken home.
-    '''
+    """
+
     level = logging.DEBUG
 
     pub = None
     drunk = False
     pints = 0
     max_pints = 3
+    kicked_out = False
 
     @default_state
     @state
     def looking_for_friends(self):
-        '''Look for friends to drink with'''
+        """Look for friends to drink with"""
-        self.info('I am looking for friends')
+        self.info("I am looking for friends")
-        available_friends = list(self.get_agents(drunk=False,
+        available_friends = list(
-                                                 pub=None,
+            self.get_agents(drunk=False, pub=None, state_id=self.looking_for_friends.id)
-                                                 state_id=self.looking_for_friends.id))
+        )
         if not available_friends:
-            self.info('Life sucks and I\'m alone!')
+            self.info("Life sucks and I'm alone!")
             return self.at_home
         befriended = self.try_friends(available_friends)
         if befriended:
@@ -82,91 +85,91 @@ class Patron(FSM, NetworkAgent):
 
     @state
     def looking_for_pub(self):
-        '''Look for a pub that accepts me and my friends'''
+        """Look for a pub that accepts me and my friends"""
-        if self['pub'] != None:
+        if self["pub"] != None:
             return self.sober_in_pub
-        self.debug('I am looking for a pub')
+        self.debug("I am looking for a pub")
-        group = list(self.get_neighboring_agents())
+        group = list(self.get_neighbors())
         for pub in self.model.available_pubs():
-            self.debug('We\'re trying to get into {}: total: {}'.format(pub, len(group)))
+            self.debug("We're trying to get into {}: total: {}".format(pub, len(group)))
             if self.model.enter(pub, self, *group):
-                self.info('We\'re all {} getting in {}!'.format(len(group), pub))
+                self.info("We're all {} getting in {}!".format(len(group), pub))
                 return self.sober_in_pub
 
     @state
     def sober_in_pub(self):
-        '''Drink up.'''
+        """Drink up."""
         self.drink()
-        if self['pints'] > self['max_pints']:
+        if self["pints"] > self["max_pints"]:
             return self.drunk_in_pub
 
     @state
     def drunk_in_pub(self):
-        '''I'm out. Take me home!'''
+        """I'm out. Take me home!"""
-        self.info('I\'m so drunk. Take me home!')
+        self.info("I'm so drunk. Take me home!")
-        self['drunk'] = True
+        self["drunk"] = True
-        pass  # out drunk
+        if self.kicked_out:
+            return self.at_home
+        pass  # out drun
 
     @state
     def at_home(self):
-        '''The end'''
+        """The end"""
         others = self.get_agents(state_id=Patron.at_home.id, limit_neighbors=True)
-        self.debug('I\'m home. Just like {} of my friends'.format(len(others)))
+        self.debug("I'm home. Just like {} of my friends".format(len(others)))
-    
+
     def drink(self):
-        self['pints'] += 1
+        self["pints"] += 1
-        self.debug('Cheers to that')
+        self.debug("Cheers to that")
-    
+
     def kick_out(self):
-        self.set_state(self.at_home)
+        self.kicked_out = True
 
     def befriend(self, other_agent, force=False):
-        '''
+        """
         Try to become friends with another agent. The chances of
         success depend on both agents' openness.
-        '''
+        """
-        if force or self['openness'] > self.random.random():
+        if force or self["openness"] > self.random.random():
             self.add_edge(self, other_agent)
-            self.info('Made some friend {}'.format(other_agent))
+            self.info("Made some friend {}".format(other_agent))
             return True
         return False
 
     def try_friends(self, others):
-        ''' Look for random agents around me and try to befriend them'''
+        """Look for random agents around me and try to befriend them"""
         befriended = False
-        k = int(10*self['openness'])
+        k = int(10 * self["openness"])
         self.random.shuffle(others)
         for friend in islice(others, k):  # random.choice >= 3.7
             if friend == self:
                 continue
             if friend.befriend(self):
                 self.befriend(friend, force=True)
-                self.debug('Hooray! new friend: {}'.format(friend.id))
+                self.debug("Hooray! new friend: {}".format(friend.id))
                 befriended = True
             else:
-                self.debug('{} does not want to be friends'.format(friend.id))
+                self.debug("{} does not want to be friends".format(friend.id))
         return befriended
 
 
 class Police(FSM):
-    '''Simple agent to take drunk people out of pubs.'''
+    """Simple agent to take drunk people out of pubs."""
+
     level = logging.INFO
 
     @default_state
     @state
     def patrol(self):
-        drunksters = list(self.get_agents(drunk=True,
+        drunksters = list(self.get_agents(drunk=True, state_id=Patron.drunk_in_pub.id))
-                                          state_id=Patron.drunk_in_pub.id))
         for drunk in drunksters:
-            self.info('Kicking out the trash: {}'.format(drunk.id))
+            self.info("Kicking out the trash: {}".format(drunk.id))
             drunk.kick_out()
         else:
-            self.info('No trash to take out. Too bad.')
+            self.info("No trash to take out. Too bad.")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     from soil import simulation
-    simulation.run_from_config('pubcrawl.yml',
+
-                               dry_run=True,
+    simulation.run_from_config("pubcrawl.yml", dry_run=True, dump=None, parallel=False)
-                               dump=None,
-                               parallel=False)

examples/rabbits/README.md

@@ -2,3 +2,13 @@ There are two similar implementations of this simulation.
 
 - `basic`. Using simple primites
 - `improved`. Using more advanced features such as the `time` module to avoid unnecessary computations (i.e., skip steps), and generator functions.
+
+The examples can be run directly in the terminal, and they accept command like arguments.
+For example, to enable the CSV exporter and the Summary exporter, while setting `max_time` to `100` and `seed` to `CustomSeed`:
+
+```
+python rabbit_agents.py  --set max_time=100 --csv -e summary  --set 'seed="CustomSeed"'
+```
+
+To learn more about how this functionality works, check out the `soil.easy` function.
+

examples/rabbits/basic/rabbit_agents.py

@@ -1,13 +1,10 @@
 from soil import FSM, state, default_state, BaseAgent, NetworkAgent, Environment
-from soil.time import Delta
-from enum import Enum
 from collections import Counter
 import logging
 import math
 
 
 class RabbitEnv(Environment):
-
     @property
     def num_rabbits(self):
         return self.count_agents(agent_class=Rabbit)
@@ -21,8 +18,7 @@ class RabbitEnv(Environment):
         return self.count_agents(agent_class=Female)
 
 
-
+class Rabbit(NetworkAgent, FSM):
-class Rabbit(FSM, NetworkAgent):
 
     sexual_maturity = 30
     life_expectancy = 300
@@ -30,7 +26,7 @@ class Rabbit(FSM, NetworkAgent):
     @default_state
     @state
     def newborn(self):
-        self.info('I am a newborn.')
+        self.info("I am a newborn.")
         self.age = 0
         self.offspring = 0
         return self.youngling
@@ -39,7 +35,7 @@ class Rabbit(FSM, NetworkAgent):
     def youngling(self):
         self.age += 1
         if self.age >= self.sexual_maturity:
-            self.info(f'I am fertile! My age is {self.age}')
+            self.info(f"I am fertile! My age is {self.age}")
             return self.fertile
 
     @state
@@ -63,17 +59,18 @@ class Male(Rabbit):
             return self.dead
 
         # Males try to mate
-        for f in self.model.agents(agent_class=Female,
+        for f in self.model.agents(
-                                   state_id=Female.fertile.id,
+            agent_class=Female, state_id=Female.fertile.id, limit=self.max_females
-                                   limit=self.max_females):
+        ):
-            self.debug('FOUND A FEMALE: ', repr(f), self.mating_prob)
+            self.debug("FOUND A FEMALE: ", repr(f), self.mating_prob)
-            if self.prob(self['mating_prob']):
+            if self.prob(self["mating_prob"]):
                 f.impregnate(self)
                 break  # Take a break
 
 
 class Female(Rabbit):
-    gestation = 30
+    gestation = 10
+    pregnancy = -1
 
     @state
     def fertile(self):
@@ -81,70 +78,73 @@ class Female(Rabbit):
         self.age += 1
         if self.age > self.life_expectancy:
             return self.dead
+        if self.pregnancy >= 0:
+            return self.pregnant
 
     def impregnate(self, male):
-        self.info(f'{repr(male)} impregnating female {repr(self)}')
+        self.info(f"impregnated by {repr(male)}")
         self.mate = male
-        self.pregnancy = -1
+        self.pregnancy = 0
-        self.set_state(self.pregnant, when=self.now)
+        self.number_of_babies = int(8 + 4 * self.random.random())
-        self.number_of_babies = int(8+4*self.random.random())
 
     @state
     def pregnant(self):
-        self.debug('I am pregnant')
+        self.info("I am pregnant")
         self.age += 1
-        self.pregnancy += 1
 
-        if self.prob(self.age / self.life_expectancy):
+        if self.age >= self.life_expectancy:
             return self.die()
 
-        if self.pregnancy >= self.gestation:
+        if self.pregnancy < self.gestation:
-            self.info('Having {} babies'.format(self.number_of_babies))
+            self.pregnancy += 1
-            for i in range(self.number_of_babies):
+            return
-                state = {}
-                agent_class = self.random.choice([Male, Female])
-                child = self.model.add_node(agent_class=agent_class,
-                                            **state)
-                child.add_edge(self)
-                try:
-                    child.add_edge(self.mate)
-                    self.model.agents[self.mate].offspring += 1
-                except ValueError:
-                    self.debug('The father has passed away')
 
-                self.offspring += 1
+        self.info("Having {} babies".format(self.number_of_babies))
-            self.mate = None
+        for i in range(self.number_of_babies):
-            return self.fertile
+            state = {}
+            agent_class = self.random.choice([Male, Female])
+            child = self.model.add_node(agent_class=agent_class, **state)
+            child.add_edge(self)
+            try:
+                child.add_edge(self.mate)
+                self.model.agents[self.mate].offspring += 1
+            except ValueError:
+                self.debug("The father has passed away")
 
-    @state
+            self.offspring += 1
-    def dead(self):
+        self.mate = None
-        super().dead()
+        self.pregnancy = -1
-        if 'pregnancy' in self and self['pregnancy'] > -1:
+        return self.fertile
-            self.info('A mother has died carrying a baby!!')
+
+    def die(self):
+        if "pregnancy" in self and self["pregnancy"] > -1:
+            self.info("A mother has died carrying a baby!!")
+        return super().die()
 
 
 class RandomAccident(BaseAgent):
-
-    level = logging.INFO
-
     def step(self):
         rabbits_alive = self.model.G.number_of_nodes()
 
         if not rabbits_alive:
             return self.die()
 
-        prob_death = self.model.get('prob_death', 1e-100)*math.floor(math.log10(max(1, rabbits_alive)))
+        prob_death = self.model.get("prob_death", 1e-100) * math.floor(
-        self.debug('Killing some rabbits with prob={}!'.format(prob_death))
+            math.log10(max(1, rabbits_alive))
+        )
+        self.debug("Killing some rabbits with prob={}!".format(prob_death))
         for i in self.iter_agents(agent_class=Rabbit):
             if i.state_id == i.dead.id:
                 continue
             if self.prob(prob_death):
-                self.info('I killed a rabbit: {}'.format(i.id))
+                self.info("I killed a rabbit: {}".format(i.id))
                 rabbits_alive -= 1
-                i.set_state(i.dead)
+                i.die()
-        self.debug('Rabbits alive: {}'.format(rabbits_alive))
+        self.debug("Rabbits alive: {}".format(rabbits_alive))
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     from soil import easy
-    sim = easy('rabbits.yml')
+
-    sim.run()
+    with easy("rabbits.yml") as sim:
+        sim.run()

examples/rabbits/improved/rabbit_agents.py

@@ -1,130 +1,157 @@
-from soil.agents import FSM, state, default_state, BaseAgent, NetworkAgent
+from soil import FSM, state, default_state, BaseAgent, NetworkAgent, Environment
-from soil.time import Delta, When, NEVER
+from soil.time import Delta
 from enum import Enum
+from collections import Counter
 import logging
 import math
 
 
-class RabbitModel(FSM, NetworkAgent):
+class RabbitEnv(Environment):
+    @property
+    def num_rabbits(self):
+        return self.count_agents(agent_class=Rabbit)
 
-    mating_prob = 0.005
+    @property
-    offspring = 0
+    def num_males(self):
+        return self.count_agents(agent_class=Male)
+
+    @property
+    def num_females(self):
+        return self.count_agents(agent_class=Female)
+
+
+class Rabbit(FSM, NetworkAgent):
+
+    sexual_maturity = 30
+    life_expectancy = 300
     birth = None
 
-    sexual_maturity = 3
+    @property
-    life_expectancy = 30
+    def age(self):
+        if self.birth is None:
+            return None
+        return self.now - self.birth
 
     @default_state
     @state
     def newborn(self):
+        self.info("I am a newborn.")
         self.birth = self.now
-        self.info(f'I am a newborn.')
+        self.offspring = 0
-        self.model['rabbits_alive'] = self.model.get('rabbits_alive', 0) + 1
+        return self.youngling, Delta(self.sexual_maturity - self.age)
 
-        # Here we can skip the `youngling` state by using a coroutine/generator. 
+    @state
-        while self.age < self.sexual_maturity:
+    def youngling(self):
-            interval = self.sexual_maturity - self.age
+        if self.age >= self.sexual_maturity:
-            yield Delta(interval)
+            self.info(f"I am fertile! My age is {self.age}")
-
+            return self.fertile
-        self.info(f'I am fertile! My age is {self.age}')
-        return self.fertile
-
-    @property
-    def age(self):
-        return self.now - self.birth
 
     @state
     def fertile(self):
         raise Exception("Each subclass should define its fertile state")
 
-    def step(self):
+    @state
-        super().step()
+    def dead(self):
-        if self.prob(self.age / self.life_expectancy):
+        self.die()
-            return self.die()
 
 
-class Male(RabbitModel):
+class Male(Rabbit):
-
     max_females = 5
+    mating_prob = 0.001
 
     @state
     def fertile(self):
-        # Males try to mate
-        for f in self.model.agents(agent_class=Female,
-                                   state_id=Female.fertile.id,
-                                   limit=self.max_females):
-            self.debug('Found a female:', repr(f))
-            if self.prob(self['mating_prob']):
-                f.impregnate(self)
-                break  # Take a break, don't try to impregnate the rest
-
-            
-class Female(RabbitModel):
-    due_date = None
-    age_of_pregnancy = None
-    gestation = 10
-    mate = None
-
-    @state
-    def fertile(self):
-        return self.fertile, NEVER
-
-    @state
-    def pregnant(self):
-        self.info('I am pregnant')
         if self.age > self.life_expectancy:
             return self.dead
 
-        self.due_date = self.now + self.gestation
+        # Males try to mate
+        for f in self.model.agents(
+            agent_class=Female, state_id=Female.fertile.id, limit=self.max_females
+        ):
+            self.debug("FOUND A FEMALE: ", repr(f), self.mating_prob)
+            if self.prob(self["mating_prob"]):
+                f.impregnate(self)
+                break  # Do not try to impregnate other females
 
-        number_of_babies = int(8+4*self.random.random())
 
-        while self.now < self.due_date:
+class Female(Rabbit):
-            yield When(self.due_date)
+    gestation = 10
-
+    conception = None
-        self.info('Having {} babies'.format(number_of_babies))
-        for i in range(number_of_babies):
-            agent_class = self.random.choice([Male, Female])
-            child = self.model.add_node(agent_class=agent_class,
-                                        topology=self.topology)
-            self.model.add_edge(self, child)
-            self.model.add_edge(self.mate, child)
-            self.offspring += 1
-            self.model.agents[self.mate].offspring += 1
-        self.mate = None
-        self.due_date = None
-        return self.fertile
 
     @state
-    def dead(self):
+    def fertile(self):
-        super().dead()
+        # Just wait for a Male
-        if self.due_date is not None:
+        if self.age > self.life_expectancy:
-            self.info('A mother has died carrying a baby!!')
+            return self.dead
+        if self.conception is not None:
+            return self.pregnant
+
+    @property
+    def pregnancy(self):
+        if self.conception is None:
+            return None
+        return self.now - self.conception
 
     def impregnate(self, male):
-        self.info(f'{repr(male)} impregnating female {repr(self)}')
+        self.info(f"impregnated by {repr(male)}")
         self.mate = male
-        self.set_state(self.pregnant, when=self.now)
+        self.conception = self.now
+        self.number_of_babies = int(8 + 4 * self.random.random())
+
+    @state
+    def pregnant(self):
+        self.debug("I am pregnant")
+
+        if self.age > self.life_expectancy:
+            self.info("Dying before giving birth")
+            return self.die()
+
+        if self.pregnancy >= self.gestation:
+            self.info("Having {} babies".format(self.number_of_babies))
+            for i in range(self.number_of_babies):
+                state = {}
+                agent_class = self.random.choice([Male, Female])
+                child = self.model.add_node(agent_class=agent_class, **state)
+                child.add_edge(self)
+                if self.mate:
+                    child.add_edge(self.mate)
+                    self.mate.offspring += 1
+                else:
+                    self.debug("The father has passed away")
+
+                self.offspring += 1
+            self.mate = None
+            return self.fertile
+
+    def die(self):
+        if self.pregnancy is not None:
+            self.info("A mother has died carrying a baby!!")
+        return super().die()
 
 
 class RandomAccident(BaseAgent):
-
-    level = logging.INFO
-
     def step(self):
-        rabbits_total = self.model.topology.number_of_nodes()
+        rabbits_alive = self.model.G.number_of_nodes()
-        if 'rabbits_alive' not in self.model:
+
-            self.model['rabbits_alive'] = 0
+        if not rabbits_alive:
-        rabbits_alive = self.model.get('rabbits_alive', rabbits_total)
+            return self.die()
-        prob_death = self.model.get('prob_death', 1e-100)*math.floor(math.log10(max(1, rabbits_alive)))
+
-        self.debug('Killing some rabbits with prob={}!'.format(prob_death))
+        prob_death = self.model.get("prob_death", 1e-100) * math.floor(
-        for i in self.model.network_agents:
+            math.log10(max(1, rabbits_alive))
-            if i.state.id == i.dead.id:
+        )
+        self.debug("Killing some rabbits with prob={}!".format(prob_death))
+        for i in self.iter_agents(agent_class=Rabbit):
+            if i.state_id == i.dead.id:
                 continue
             if self.prob(prob_death):
-                self.info('I killed a rabbit: {}'.format(i.id))
+                self.info("I killed a rabbit: {}".format(i.id))
-                rabbits_alive = self.model['rabbits_alive'] = rabbits_alive -1
+                rabbits_alive -= 1
-                i.set_state(i.dead)
+                i.die()
-        self.debug('Rabbits alive: {}/{}'.format(rabbits_alive, rabbits_total))
+        self.debug("Rabbits alive: {}".format(rabbits_alive))
-        if self.model.count_agents(state_id=RabbitModel.dead.id) == self.model.topology.number_of_nodes():
+
-            self.die()
+
+if __name__ == "__main__":
+    from soil import easy
+
+    with easy("rabbits.yml") as sim:
+        sim.run()

examples/rabbits/improved/rabbits.yml

@@ -7,11 +7,10 @@ description: null
 group: null
 interval: 1.0
 max_time: 100
-model_class: soil.environment.Environment
+model_class: rabbit_agents.RabbitEnv
 model_params:
   agents:
     topology: true
-    agent_class: rabbit_agents.RabbitModel
     distribution:
     - agent_class: rabbit_agents.Male
       weight: 1
@@ -34,5 +33,10 @@ model_params:
       nodes:
       - id: 1
       - id: 0
+  model_reporters:
+    num_males: 'num_males'
+    num_females: 'num_females'
+    num_rabbits: |
+      py:lambda env: env.num_males + env.num_females
 extra:
   visualization_params: {}

examples/random_delays/random_delays.py

@@ -1,42 +1,43 @@
-'''
+"""
 Example of setting a 
 Example of a fully programmatic simulation, without definition files.
-'''
+"""
 from soil import Simulation, agents
 from soil.time import Delta
 
 
-
 class MyAgent(agents.FSM):
-    '''
+    """
     An agent that first does a ping
-    '''
+    """
 
-    defaults = {'pong_counts': 2}
+    defaults = {"pong_counts": 2}
 
     @agents.default_state
     @agents.state
     def ping(self):
-        self.info('Ping')
+        self.info("Ping")
-        return self.pong, Delta(self.random.expovariate(1/16))
+        return self.pong, Delta(self.random.expovariate(1 / 16))
 
     @agents.state
     def pong(self):
-        self.info('Pong')
+        self.info("Pong")
         self.pong_counts -= 1
         self.info(str(self.pong_counts))
         if self.pong_counts < 1:
             return self.die()
-        return None, Delta(self.random.expovariate(1/16))
+        return None, Delta(self.random.expovariate(1 / 16))
 
 
-s = Simulation(name='Programmatic',
+s = Simulation(
-               network_agents=[{'agent_class': MyAgent, 'id': 0}],
+    name="Programmatic",
-               topology={'nodes': [{'id': 0}], 'links': []},
+    network_agents=[{"agent_class": MyAgent, "id": 0}],
-               num_trials=1,
+    topology={"nodes": [{"id": 0}], "links": []},
-               max_time=100,
+    num_trials=1,
-               agent_class=MyAgent,
+    max_time=100,
-               dry_run=True)
+    agent_class=MyAgent,
+    dry_run=True,
+)
 
 
 envs = s.run()

examples/terrorism/TerroristNetworkModel.py

@@ -20,56 +20,83 @@ class TerroristSpreadModel(FSM, Geo):
     def __init__(self, model=None, unique_id=0, state=()):
         super().__init__(model=model, unique_id=unique_id, state=state)
 
-        self.information_spread_intensity = model.environment_params['information_spread_intensity']
+        self.information_spread_intensity = model.environment_params[
-        self.terrorist_additional_influence = model.environment_params['terrorist_additional_influence']
+            "information_spread_intensity"
-        self.prob_interaction = model.environment_params['prob_interaction']
+        ]
+        self.terrorist_additional_influence = model.environment_params[
+            "terrorist_additional_influence"
+        ]
+        self.prob_interaction = model.environment_params["prob_interaction"]
 
-        if self['id'] == self.civilian.id:       # Civilian
+        if self["id"] == self.civilian.id:  # Civilian
             self.mean_belief = self.random.uniform(0.00, 0.5)
-        elif self['id'] == self.terrorist.id:     # Terrorist
+        elif self["id"] == self.terrorist.id:  # Terrorist
             self.mean_belief = self.random.uniform(0.8, 1.00)
-        elif self['id'] == self.leader.id:     # Leader
+        elif self["id"] == self.leader.id:  # Leader
             self.mean_belief = 1.00
         else:
-            raise Exception('Invalid state id: {}'.format(self['id']))
+            raise Exception("Invalid state id: {}".format(self["id"]))
-
-        if 'min_vulnerability' in model.environment_params:
-            self.vulnerability = self.random.uniform( model.environment_params['min_vulnerability'], model.environment_params['max_vulnerability'] )
-        else :
-            self.vulnerability = self.random.uniform( 0, model.environment_params['max_vulnerability'] )
 
+        if "min_vulnerability" in model.environment_params:
+            self.vulnerability = self.random.uniform(
+                model.environment_params["min_vulnerability"],
+                model.environment_params["max_vulnerability"],
+            )
+        else:
+            self.vulnerability = self.random.uniform(
+                0, model.environment_params["max_vulnerability"]
+            )
 
     @state
     def civilian(self):
-        neighbours = list(self.get_neighboring_agents(agent_class=TerroristSpreadModel))
+        neighbours = list(self.get_neighbors(agent_class=TerroristSpreadModel))
         if len(neighbours) > 0:
             # Only interact with some of the neighbors
-            interactions = list(n for n in neighbours if self.random.random() <= self.prob_interaction)
+            interactions = list(
-            influence = sum( self.degree(i) for i in interactions )
+                n for n in neighbours if self.random.random() <= self.prob_interaction
-            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 )
+            influence = sum(self.degree(i) for i in interactions)
-            self.mean_belief = mean_belief * self.vulnerability + self.mean_belief * ( 1 - self.vulnerability )
+            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 )
+        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]):
+        for neighbour in self.get_neighbors(
+            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],
+        neighbours = self.get_agents(
-                                     agent_class=TerroristSpreadModel,
+            state_id=[self.terrorist.id, self.leader.id],
-                                     limit_neighbors=True)
+            agent_class=TerroristSpreadModel,
+            limit_neighbors=True,
+        )
         if len(neighbours) > 0:
-            influence = sum( self.degree(n) for n in neighbours )
+            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 = sum(
-            mean_belief = mean_belief * self.vulnerability + self.mean_belief * ( 1 - self.vulnerability )
+                n.mean_belief * self.degree(n) / influence for n in neighbours
-            self.mean_belief = self.mean_belief ** ( 1 - self.terrorist_additional_influence )
+            )
+            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))
@@ -82,21 +109,29 @@ class TerroristSpreadModel(FSM, Geo):
             return self.leader
 
     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*'''
+        """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.model, '_degree')) or getattr(self.model, '_last_step', 0) < self.now:
+        if (
+            force
+            or (not hasattr(self.model, "_degree"))
+            or getattr(self.model, "_last_step", 0) < self.now
+        ):
             self.model._degree = nx.degree_centrality(self.G)
             self.model._last_step = self.now
         return self.model._degree[node]
 
     def betweenness(self, node, force=False):
         node = as_node(node)
-        if force or (not hasattr(self.model, '_betweenness')) or getattr(self.model, '_last_step', 0) < self.now:
+        if (
+            force
+            or (not hasattr(self.model, "_betweenness"))
+            or getattr(self.model, "_last_step", 0) < self.now
+        ):
             self.model._betweenness = nx.betweenness_centrality(self.G)
             self.model._last_step = self.now
         return self.model._betweenness[node]
@@ -114,17 +149,20 @@ class TrainingAreaModel(FSM, Geo):
 
     def __init__(self, model=None, unique_id=0, state=()):
         super().__init__(model=model, unique_id=unique_id, state=state)
-        self.training_influence = model.environment_params['training_influence']
+        self.training_influence = model.environment_params["training_influence"]
-        if 'min_vulnerability' in model.environment_params:
+        if "min_vulnerability" in model.environment_params:
-            self.min_vulnerability = model.environment_params['min_vulnerability']
+            self.min_vulnerability = model.environment_params["min_vulnerability"]
-        else: self.min_vulnerability = 0
+        else:
+            self.min_vulnerability = 0
 
     @default_state
     @state
     def terrorist(self):
-        for neighbour in self.get_neighboring_agents(agent_class=TerroristSpreadModel):
+        for neighbour in self.get_neighbors(agent_class=TerroristSpreadModel):
             if neighbour.vulnerability > self.min_vulnerability:
-                neighbour.vulnerability = neighbour.vulnerability ** ( 1 - self.training_influence )        
+                neighbour.vulnerability = neighbour.vulnerability ** (
+                    1 - self.training_influence
+                )
 
 
 class HavenModel(FSM, Geo):
@@ -141,14 +179,15 @@ class HavenModel(FSM, Geo):
 
     def __init__(self, model=None, unique_id=0, state=()):
         super().__init__(model=model, unique_id=unique_id, state=state)
-        self.haven_influence = model.environment_params['haven_influence']
+        self.haven_influence = model.environment_params["haven_influence"]
-        if 'min_vulnerability' in model.environment_params:
+        if "min_vulnerability" in model.environment_params:
-            self.min_vulnerability = model.environment_params['min_vulnerability']
+            self.min_vulnerability = model.environment_params["min_vulnerability"]
-        else: self.min_vulnerability = 0
+        else:
-        self.max_vulnerability = model.environment_params['max_vulnerability']
+            self.min_vulnerability = 0
+        self.max_vulnerability = model.environment_params["max_vulnerability"]
 
     def get_occupants(self, **kwargs):
-        return self.get_neighboring_agents(agent_class=TerroristSpreadModel, **kwargs)
+        return self.get_neighbors(agent_class=TerroristSpreadModel, **kwargs)
 
     @state
     def civilian(self):
@@ -158,14 +197,18 @@ class HavenModel(FSM, Geo):
 
         for neighbour in self.get_occupants():
             if neighbour.vulnerability > self.min_vulnerability:
-                neighbour.vulnerability = neighbour.vulnerability * ( 1 - self.haven_influence )
+                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 )
+                neighbour.vulnerability = neighbour.vulnerability ** (
+                    1 - self.haven_influence
+                )
         return self.terrorist
 
 
@@ -184,10 +227,10 @@ class TerroristNetworkModel(TerroristSpreadModel):
     def __init__(self, model=None, unique_id=0, state=()):
         super().__init__(model=model, unique_id=unique_id, state=state)
 
-        self.vision_range = model.environment_params['vision_range']
+        self.vision_range = model.environment_params["vision_range"]
-        self.sphere_influence = model.environment_params['sphere_influence']
+        self.sphere_influence = model.environment_params["sphere_influence"]
-        self.weight_social_distance = model.environment_params['weight_social_distance']
+        self.weight_social_distance = model.environment_params["weight_social_distance"]
-        self.weight_link_distance = model.environment_params['weight_link_distance']
+        self.weight_link_distance = model.environment_params["weight_link_distance"]
 
     @state
     def terrorist(self):
@@ -200,28 +243,49 @@ class TerroristNetworkModel(TerroristSpreadModel):
         return super().leader()
 
     def update_relationships(self):
-        if self.count_neighboring_agents(state_id=self.civilian.id) == 0:
+        if self.count_neighbors(state_id=self.civilian.id) == 0:
-            close_ups = set(self.geo_search(radius=self.vision_range, agent_class=TerroristNetworkModel))
+            close_ups = set(
-            step_neighbours = set(self.ego_search(self.sphere_influence, agent_class=TerroristNetworkModel, center=False))
+                self.geo_search(
-            neighbours = set(agent.id for agent in self.get_neighboring_agents(agent_class=TerroristNetworkModel))
+                    radius=self.vision_range, agent_class=TerroristNetworkModel
+                )
+            )
+            step_neighbours = set(
+                self.ego_search(
+                    self.sphere_influence,
+                    agent_class=TerroristNetworkModel,
+                    center=False,
+                )
+            )
+            neighbours = set(
+                agent.id
+                for agent in self.get_neighbors(
+                    agent_class=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) )
+                spatial_proximity = 1 - self.get_distance(agent.id)
-                prob_new_interaction = self.weight_social_distance * social_distance + self.weight_link_distance * spatial_proximity
+                prob_new_interaction = (
-                if agent['id'] == agent.civilian.id and self.random.random() < prob_new_interaction:
+                    self.weight_social_distance * social_distance
+                    + self.weight_link_distance * spatial_proximity
+                )
+                if (
+                    agent["id"] == agent.civilian.id
+                    and self.random.random() < prob_new_interaction
+                ):
                     self.add_edge(agent)
                     break
 
     def get_distance(self, target):
-        source_x, source_y = nx.get_node_attributes(self.G, 'pos')[self.id]
+        source_x, source_y = nx.get_node_attributes(self.G, "pos")[self.id]
-        target_x, target_y = nx.get_node_attributes(self.G, 'pos')[target]
+        target_x, target_y = nx.get_node_attributes(self.G, "pos")[target]
-        dx = abs( source_x - target_x )
+        dx = abs(source_x - target_x)
-        dy = abs( source_y - target_y )
+        dy = abs(source_y - target_y)
-        return ( dx ** 2 + dy ** 2 ) ** ( 1 / 2 )
+        return (dx**2 + dy**2) ** (1 / 2)
 
     def shortest_path_length(self, target):
         try:
             return nx.shortest_path_length(self.G, self.id, target)
         except nx.NetworkXNoPath:
-            return float('inf')
+            return float("inf")

soil/VERSION

@@ -1 +1 @@
-0.20.7
+0.30.0rc2

soil/__init__.py

@@ -5,6 +5,7 @@ import sys
 import os
 import logging
 import traceback
+from contextlib import contextmanager
 
 from .version import __version__
 
@@ -16,7 +17,7 @@ except NameError:
 from .agents import *
 from . import agents
 from .simulation import *
-from .environment import Environment
+from .environment import Environment, EventedEnvironment
 from . import serialization
 from .utils import logger
 from .time import *
@@ -30,8 +31,12 @@ def main(
     *,
     do_run=False,
     debug=False,
+    pdb=False,
     **kwargs,
 ):
+
+    if isinstance(cfg, Simulation):
+        sim = cfg
     import argparse
     from . import simulation
 
@@ -42,7 +47,7 @@ def main(
         "file",
         type=str,
         nargs="?",
-        default=cfg,
+        default=cfg if sim is None else '',
         help="Configuration file for the simulation (e.g., YAML or JSON)",
     )
     parser.add_argument(
@@ -148,30 +153,41 @@ def main(
     if output is None:
         output = args.output
 
-    logger.info("Loading config file: {}".format(args.file))
-
     debug = debug or args.debug
 
     if args.pdb or debug:
         args.synchronous = True
+        os.environ["SOIL_POSTMORTEM"] = "true"
 
     res = []
     try:
         exp_params = {}
 
-        if not os.path.exists(args.file):
+        if sim:
-            logger.error("Please, input a valid file")
+            logger.info("Loading simulation instance")
-            return
+            sim.dry_run = args.dry_run
+            sim.exporters = exporters
+            sim.parallel = parallel
+            sim.outdir = output
+            sims = [sim, ]
+        else:
+            logger.info("Loading config file: {}".format(args.file))
+            if not os.path.exists(args.file):
+                logger.error("Please, input a valid file")
+                return
+
+            sims = list(simulation.iter_from_config(
+                args.file,
+                dry_run=args.dry_run,
+                exporters=exporters,
+                parallel=parallel,
+                outdir=output,
+                exporter_params=exp_params,
+                **kwargs,
+            ))
+
+        for sim in sims:
 
-        for sim in simulation.iter_from_config(
-            args.file,
-            dry_run=args.dry_run,
-            exporters=exporters,
-            parallel=parallel,
-            outdir=output,
-            exporter_params=exp_params,
-            **kwargs,
-        ):
             if args.set:
                 for s in args.set:
                     k, v = s.split("=", 1)[:2]
@@ -214,8 +230,17 @@ def main(
     return res
 
 
-def easy(cfg, debug=False, **kwargs):
+@contextmanager
-    return main(cfg, **kwargs)[0]
+def easy(cfg, pdb=False, debug=False, **kwargs):
+    try:
+        yield main(cfg, debug=debug, pdb=pdb, **kwargs)[0]
+    except Exception as e:
+        if os.environ.get("SOIL_POSTMORTEM"):
+            from .debugging import post_mortem
+
+            print(traceback.format_exc())
+            post_mortem()
+        raise
 
 
 if __name__ == "__main__":

soil/agents/BassModel.py

@@ -20,7 +20,7 @@ class BassModel(FSM):
             self.sentimentCorrelation = 1
             return self.aware
         else:
-            aware_neighbors = self.get_neighboring_agents(state_id=self.aware.id)
+            aware_neighbors = self.get_neighbors(state_id=self.aware.id)
             num_neighbors_aware = len(aware_neighbors)
             if self.prob((self["imitation_prob"] * num_neighbors_aware)):
                 self.sentimentCorrelation = 1

soil/agents/BigMarketModel.py

@@ -24,14 +24,14 @@ class BigMarketModel(FSM):
         self.type = ""
 
         if self.id < len(self.enterprises):  # Enterprises
-            self.set_state(self.enterprise.id)
+            self._set_state(self.enterprise.id)
             self.type = "Enterprise"
             self.tweet_probability = environment.environment_params[
                 "tweet_probability_enterprises"
             ][self.id]
         else:  # normal users
             self.type = "User"
-            self.set_state(self.user.id)
+            self._set_state(self.user.id)
             self.tweet_probability = environment.environment_params[
                 "tweet_probability_users"
             ]
@@ -49,7 +49,7 @@ class BigMarketModel(FSM):
     def enterprise(self):
 
         if self.random.random() < self.tweet_probability:  # Tweets
-            aware_neighbors = self.get_neighboring_agents(
+            aware_neighbors = self.get_neighbors(
                 state_id=self.number_of_enterprises
             )  # Nodes neighbour users
             for x in aware_neighbors:
@@ -96,7 +96,7 @@ class BigMarketModel(FSM):
             ] = self.sentiment_about[i]
 
     def userTweets(self, sentiment, enterprise):
-        aware_neighbors = self.get_neighboring_agents(
+        aware_neighbors = self.get_neighbors(
             state_id=self.number_of_enterprises
         )  # Nodes neighbours users
         for x in aware_neighbors:

soil/agents/CounterModel.py

@@ -14,7 +14,7 @@ class CounterModel(NetworkAgent):
     def step(self):
         # Outside effects
         total = len(list(self.model.schedule._agents))
-        neighbors = len(list(self.get_neighboring_agents()))
+        neighbors = len(list(self.get_neighbors()))
         self["times"] = self.get("times", 0) + 1
         self["neighbors"] = neighbors
         self["total"] = total
@@ -33,7 +33,7 @@ class AggregatedCounter(NetworkAgent):
     def step(self):
         # Outside effects
         self["times"] += 1
-        neighbors = len(list(self.get_neighboring_agents()))
+        neighbors = len(list(self.get_neighbors()))
         self["neighbors"] += neighbors
         total = len(list(self.model.schedule.agents))
         self["total"] += total

soil/agents/IndependentCascadeModel.py

@@ -36,7 +36,7 @@ class IndependentCascadeModel(BaseAgent):
 
         # Imitation effects
         if self.state["id"] == 0:
-            aware_neighbors = self.get_neighboring_agents(state_id=1)
+            aware_neighbors = self.get_neighbors(state_id=1)
             for x in aware_neighbors:
                 if x.state["time_awareness"] == (self.env.now - 1):
                     aware_neighbors_1_time_step.append(x)

soil/agents/ModelM2.py

@@ -71,7 +71,7 @@ class SpreadModelM2(BaseAgent):
     def neutral_behaviour(self):
 
         # Infected
-        infected_neighbors = self.get_neighboring_agents(state_id=1)
+        infected_neighbors = self.get_neighbors(state_id=1)
         if len(infected_neighbors) > 0:
             if self.prob(self.prob_neutral_making_denier):
                 self.state["id"] = 3  # Vaccinated making denier
@@ -79,7 +79,7 @@ class SpreadModelM2(BaseAgent):
     def infected_behaviour(self):
 
         # Neutral
-        neutral_neighbors = self.get_neighboring_agents(state_id=0)
+        neutral_neighbors = self.get_neighbors(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_infect):
                 neighbor.state["id"] = 1  # Infected
@@ -87,13 +87,13 @@ class SpreadModelM2(BaseAgent):
     def cured_behaviour(self):
 
         # Vaccinate
-        neutral_neighbors = self.get_neighboring_agents(state_id=0)
+        neutral_neighbors = self.get_neighbors(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_cured_vaccinate_neutral):
                 neighbor.state["id"] = 3  # Vaccinated
 
         # Cure
-        infected_neighbors = self.get_neighboring_agents(state_id=1)
+        infected_neighbors = self.get_neighbors(state_id=1)
         for neighbor in infected_neighbors:
             if self.prob(self.prob_cured_healing_infected):
                 neighbor.state["id"] = 2  # Cured
@@ -101,19 +101,19 @@ class SpreadModelM2(BaseAgent):
     def vaccinated_behaviour(self):
 
         # Cure
-        infected_neighbors = self.get_neighboring_agents(state_id=1)
+        infected_neighbors = self.get_neighbors(state_id=1)
         for neighbor in infected_neighbors:
             if self.prob(self.prob_cured_healing_infected):
                 neighbor.state["id"] = 2  # Cured
 
         # Vaccinate
-        neutral_neighbors = self.get_neighboring_agents(state_id=0)
+        neutral_neighbors = self.get_neighbors(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_cured_vaccinate_neutral):
                 neighbor.state["id"] = 3  # Vaccinated
 
         # Generate anti-rumor
-        infected_neighbors_2 = self.get_neighboring_agents(state_id=1)
+        infected_neighbors_2 = self.get_neighbors(state_id=1)
         for neighbor in infected_neighbors_2:
             if self.prob(self.prob_generate_anti_rumor):
                 neighbor.state["id"] = 2  # Cured
@@ -191,7 +191,7 @@ class ControlModelM2(BaseAgent):
         self.state["visible"] = False
 
         # Infected
-        infected_neighbors = self.get_neighboring_agents(state_id=1)
+        infected_neighbors = self.get_neighbors(state_id=1)
         if len(infected_neighbors) > 0:
             if self.random(self.prob_neutral_making_denier):
                 self.state["id"] = 3  # Vaccinated making denier
@@ -199,7 +199,7 @@ class ControlModelM2(BaseAgent):
     def infected_behaviour(self):
 
         # Neutral
-        neutral_neighbors = self.get_neighboring_agents(state_id=0)
+        neutral_neighbors = self.get_neighbors(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_infect):
                 neighbor.state["id"] = 1  # Infected
@@ -209,13 +209,13 @@ class ControlModelM2(BaseAgent):
 
         self.state["visible"] = True
         # Vaccinate
-        neutral_neighbors = self.get_neighboring_agents(state_id=0)
+        neutral_neighbors = self.get_neighbors(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_cured_vaccinate_neutral):
                 neighbor.state["id"] = 3  # Vaccinated
 
         # Cure
-        infected_neighbors = self.get_neighboring_agents(state_id=1)
+        infected_neighbors = self.get_neighbors(state_id=1)
         for neighbor in infected_neighbors:
             if self.prob(self.prob_cured_healing_infected):
                 neighbor.state["id"] = 2  # Cured
@@ -224,47 +224,47 @@ class ControlModelM2(BaseAgent):
         self.state["visible"] = True
 
         # Cure
-        infected_neighbors = self.get_neighboring_agents(state_id=1)
+        infected_neighbors = self.get_neighbors(state_id=1)
         for neighbor in infected_neighbors:
             if self.prob(self.prob_cured_healing_infected):
                 neighbor.state["id"] = 2  # Cured
 
         # Vaccinate
-        neutral_neighbors = self.get_neighboring_agents(state_id=0)
+        neutral_neighbors = self.get_neighbors(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_cured_vaccinate_neutral):
                 neighbor.state["id"] = 3  # Vaccinated
 
         # Generate anti-rumor
-        infected_neighbors_2 = self.get_neighboring_agents(state_id=1)
+        infected_neighbors_2 = self.get_neighbors(state_id=1)
         for neighbor in infected_neighbors_2:
             if self.prob(self.prob_generate_anti_rumor):
                 neighbor.state["id"] = 2  # Cured
 
     def beacon_off_behaviour(self):
         self.state["visible"] = False
-        infected_neighbors = self.get_neighboring_agents(state_id=1)
+        infected_neighbors = self.get_neighbors(state_id=1)
         if len(infected_neighbors) > 0:
             self.state["id"] == 5  # Beacon on
 
     def beacon_on_behaviour(self):
         self.state["visible"] = False
         # Cure (M2 feature added)
-        infected_neighbors = self.get_neighboring_agents(state_id=1)
+        infected_neighbors = self.get_neighbors(state_id=1)
         for neighbor in infected_neighbors:
             if self.prob(self.prob_generate_anti_rumor):
                 neighbor.state["id"] = 2  # Cured
-            neutral_neighbors_infected = neighbor.get_neighboring_agents(state_id=0)
+            neutral_neighbors_infected = neighbor.get_neighbors(state_id=0)
             for neighbor in neutral_neighbors_infected:
                 if self.prob(self.prob_generate_anti_rumor):
                     neighbor.state["id"] = 3  # Vaccinated
-            infected_neighbors_infected = neighbor.get_neighboring_agents(state_id=1)
+            infected_neighbors_infected = neighbor.get_neighbors(state_id=1)
             for neighbor in infected_neighbors_infected:
                 if self.prob(self.prob_generate_anti_rumor):
                     neighbor.state["id"] = 2  # Cured
 
         # Vaccinate
-        neutral_neighbors = self.get_neighboring_agents(state_id=0)
+        neutral_neighbors = self.get_neighbors(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_cured_vaccinate_neutral):
                 neighbor.state["id"] = 3  # Vaccinated

soil/agents/SISaModel.py

@@ -69,10 +69,10 @@ class SISaModel(FSM):
             return self.content
 
         # Infected
-        discontent_neighbors = self.count_neighboring_agents(state_id=self.discontent)
+        discontent_neighbors = self.count_neighbors(state_id=self.discontent)
         if self.prob(scontent_neighbors * self.neutral_discontent_infected_prob):
             return self.discontent
-        content_neighbors = self.count_neighboring_agents(state_id=self.content.id)
+        content_neighbors = self.count_neighbors(state_id=self.content.id)
         if self.prob(s * self.neutral_content_infected_prob):
             return self.content
         return self.neutral
@@ -84,7 +84,7 @@ class SISaModel(FSM):
             return self.neutral
 
         # Superinfected
-        content_neighbors = self.count_neighboring_agents(state_id=self.content.id)
+        content_neighbors = self.count_neighbors(state_id=self.content.id)
         if self.prob(s * self.discontent_content):
             return self.content
         return self.discontent
@@ -96,9 +96,7 @@ class SISaModel(FSM):
             return self.neutral
 
         # Superinfected
-        discontent_neighbors = self.count_neighboring_agents(
+        discontent_neighbors = self.count_neighbors(state_id=self.discontent.id)
-            state_id=self.discontent.id
-        )
         if self.prob(scontent_neighbors * self.content_discontent):
             self.discontent
         return self.content

soil/agents/SentimentCorrelationModel.py

@@ -41,25 +41,25 @@ class SentimentCorrelationModel(BaseAgent):
         sad_neighbors_1_time_step = []
         disgusted_neighbors_1_time_step = []
 
-        angry_neighbors = self.get_neighboring_agents(state_id=1)
+        angry_neighbors = self.get_neighbors(state_id=1)
         for x in angry_neighbors:
             if x.state["time_awareness"][0] > (self.env.now - 500):
                 angry_neighbors_1_time_step.append(x)
         num_neighbors_angry = len(angry_neighbors_1_time_step)
 
-        joyful_neighbors = self.get_neighboring_agents(state_id=2)
+        joyful_neighbors = self.get_neighbors(state_id=2)
         for x in joyful_neighbors:
             if x.state["time_awareness"][1] > (self.env.now - 500):
                 joyful_neighbors_1_time_step.append(x)
         num_neighbors_joyful = len(joyful_neighbors_1_time_step)
 
-        sad_neighbors = self.get_neighboring_agents(state_id=3)
+        sad_neighbors = self.get_neighbors(state_id=3)
         for x in sad_neighbors:
             if x.state["time_awareness"][2] > (self.env.now - 500):
                 sad_neighbors_1_time_step.append(x)
         num_neighbors_sad = len(sad_neighbors_1_time_step)
 
-        disgusted_neighbors = self.get_neighboring_agents(state_id=4)
+        disgusted_neighbors = self.get_neighbors(state_id=4)
         for x in disgusted_neighbors:
             if x.state["time_awareness"][3] > (self.env.now - 500):
                 disgusted_neighbors_1_time_step.append(x)

soil/agents/__init__.py

@@ -29,10 +29,6 @@ def as_node(agent):
 IGNORED_FIELDS = ("model", "logger")
 
 
-class DeadAgent(Exception):
-    pass
-
-
 class MetaAgent(ABCMeta):
     def __new__(mcls, name, bases, namespace):
         defaults = {}
@@ -44,10 +40,36 @@ class MetaAgent(ABCMeta):
 
         new_nmspc = {
             "_defaults": defaults,
+            "_last_return": None,
+            "_last_except": None,
         }
 
         for attr, func in namespace.items():
-            if (
+            if attr == "step" and inspect.isgeneratorfunction(func):
+                orig_func = func
+                new_nmspc["_coroutine"] = None
+
+                @wraps(func)
+                def func(self):
+                    while True:
+                        if not self._coroutine:
+                            self._coroutine = orig_func(self)
+                        try:
+                            if self._last_except:
+                                return self._coroutine.throw(self._last_except)
+                            else:
+                                return self._coroutine.send(self._last_return)
+                        except StopIteration as ex:
+                            self._coroutine = None
+                            return ex.value
+                        finally:
+                            self._last_return = None
+                            self._last_except = None
+
+                func.id = name or func.__name__
+                func.is_default = False
+                new_nmspc[attr] = func
+            elif (
                 isinstance(func, types.FunctionType)
                 or isinstance(func, property)
                 or isinstance(func, classmethod)
@@ -176,11 +198,15 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
     def die(self):
         self.info(f"agent dying")
         self.alive = False
+        try:
+            self.model.schedule.remove(self)
+        except KeyError:
+            pass
         return time.NEVER
 
     def step(self):
         if not self.alive:
-            raise DeadAgent(self.unique_id)
+            raise time.DeadAgent(self.unique_id)
         return super().step() or time.Delta(self.interval)
 
     def log(self, message, *args, level=logging.INFO, **kwargs):
@@ -229,215 +255,6 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
         return f"{self.__class__.__name__}({self.unique_id})"
 
 
-class NetworkAgent(BaseAgent):
-    def __init__(self, *args, topology, node_id, **kwargs):
-        super().__init__(*args, **kwargs)
-
-        assert topology is not None
-        assert node_id is not None
-        self.G = topology
-        assert self.G
-        self.node_id = node_id
-
-    def count_neighboring_agents(self, state_id=None, **kwargs):
-        return len(self.get_neighboring_agents(state_id=state_id, **kwargs))
-
-    def get_neighboring_agents(self, **kwargs):
-        return list(self.iter_agents(limit_neighbors=True, **kwargs))
-
-    def add_edge(self, other):
-        self.topology.add_edge(self.node_id, other.node_id)
-
-    @property
-    def node(self):
-        return self.topology.nodes[self.node_id]
-
-    def iter_agents(self, unique_id=None, *, limit_neighbors=False, **kwargs):
-        unique_ids = None
-        if isinstance(unique_id, list):
-            unique_ids = set(unique_id)
-        elif unique_id is not None:
-            unique_ids = set(
-                [
-                    unique_id,
-                ]
-            )
-
-        if limit_neighbors:
-            neighbor_ids = set()
-            for node_id in self.G.neighbors(self.node_id):
-                if self.G.nodes[node_id].get("agent") is not None:
-                    neighbor_ids.add(node_id)
-            if unique_ids:
-                unique_ids = unique_ids & neighbor_ids
-            else:
-                unique_ids = neighbor_ids
-            if not unique_ids:
-                return
-            unique_ids = list(unique_ids)
-        yield from super().iter_agents(unique_id=unique_ids, **kwargs)
-
-    def subgraph(self, center=True, **kwargs):
-        include = [self] if center else []
-        G = self.G.subgraph(
-            n.node_id for n in list(self.get_agents(**kwargs) + include)
-        )
-        return G
-
-    def remove_node(self):
-        self.G.remove_node(self.node_id)
-
-    def add_edge(self, other, edge_attr_dict=None, *edge_attrs):
-        if self.node_id not in self.G.nodes(data=False):
-            raise ValueError(
-                "{} not in list of existing agents in the network".format(
-                    self.unique_id
-                )
-            )
-        if other.node_id not in self.G.nodes(data=False):
-            raise ValueError(
-                "{} not in list of existing agents in the network".format(other)
-            )
-
-        self.G.add_edge(
-            self.node_id, other.node_id, edge_attr_dict=edge_attr_dict, *edge_attrs
-        )
-
-    def die(self, remove=True):
-        if remove:
-            self.remove_node()
-        return super().die()
-
-
-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.
-        """
-        if inspect.isgeneratorfunction(func):
-            orig_func = func
-
-            @wraps(func)
-            def func(self):
-                while True:
-                    if not self._coroutine:
-                        self._coroutine = orig_func(self)
-                    try:
-                        n = next(self._coroutine)
-                        if n:
-                            return None, n
-                        return
-                    except StopIteration as ex:
-                        self._coroutine = None
-                        next_state = ex.value
-                        if next_state is not None:
-                            self.set_state(next_state)
-                        return next_state
-
-        func.id = name or func.__name__
-        func.is_default = False
-        return func
-
-    if callable(name):
-        return decorator(name)
-    else:
-        return partial(decorator, name=name)
-
-
-def default_state(func):
-    func.is_default = True
-    return func
-
-
-class MetaFSM(MetaAgent):
-    def __new__(mcls, name, bases, namespace):
-        states = {}
-        # Re-use states from inherited classes
-        default_state = None
-        for i in bases:
-            if isinstance(i, MetaFSM):
-                for state_id, state in i._states.items():
-                    if state.is_default:
-                        default_state = state
-                    states[state_id] = state
-
-        # Add new states
-        for attr, func in namespace.items():
-            if hasattr(func, "id"):
-                if func.is_default:
-                    default_state = func
-                states[func.id] = func
-
-        namespace.update(
-            {
-                "_default_state": default_state,
-                "_states": states,
-            }
-        )
-
-        return super(MetaFSM, mcls).__new__(
-            mcls=mcls, name=name, bases=bases, namespace=namespace
-        )
-
-
-class FSM(BaseAgent, metaclass=MetaFSM):
-    def __init__(self, *args, **kwargs):
-        super(FSM, self).__init__(*args, **kwargs)
-        if not hasattr(self, "state_id"):
-            if not self._default_state:
-                raise ValueError(
-                    "No default state specified for {}".format(self.unique_id)
-                )
-            self.state_id = self._default_state.id
-
-        self._coroutine = None
-        self.set_state(self.state_id)
-
-    def step(self):
-        self.debug(f"Agent {self.unique_id} @ state {self.state_id}")
-        default_interval = super().step()
-
-        next_state = self._states[self.state_id](self)
-
-        when = None
-        try:
-            next_state, *when = next_state
-            if not when:
-                when = None
-            elif len(when) == 1:
-                when = when[0]
-            else:
-                raise ValueError(
-                    "Too many values returned. Only state (and time) allowed"
-                )
-        except TypeError:
-            pass
-
-        if next_state is not None:
-            self.set_state(next_state)
-
-        return when or default_interval
-
-    def set_state(self, state, when=None):
-        if hasattr(state, "id"):
-            state = state.id
-        if state not in self._states:
-            raise ValueError("{} is not a valid state".format(state))
-        self.state_id = state
-        if when is not None:
-            self.model.schedule.add(self, when=when)
-        return state
-
-    def die(self):
-        return self.dead, super().die()
-
-    @state
-    def dead(self):
-        return self.die()
-
-
 def prob(prob, random):
     """
     A true/False uniform distribution with a given probability.
@@ -503,7 +320,7 @@ def calculate_distribution(network_agents=None, agent_class=None):
     return network_agents
 
 
-def serialize_type(agent_class, known_modules=[], **kwargs):
+def _serialize_type(agent_class, known_modules=[], **kwargs):
     if isinstance(agent_class, str):
         return agent_class
     known_modules += ["soil.agents"]
@@ -512,20 +329,7 @@ def serialize_type(agent_class, known_modules=[], **kwargs):
     ]  # Get the name of the class
 
 
-def serialize_definition(network_agents, known_modules=[]):
+def _deserialize_type(agent_class, known_modules=[]):
-    """
-    When serializing an agent distribution, remove the thresholds, in order
-    to avoid cluttering the YAML definition file.
-    """
-    d = deepcopy(list(network_agents))
-    for v in d:
-        if "threshold" in v:
-            del v["threshold"]
-        v["agent_class"] = serialize_type(v["agent_class"], known_modules=known_modules)
-    return d
-
-
-def deserialize_type(agent_class, known_modules=[]):
     if not isinstance(agent_class, str):
         return agent_class
     known = known_modules + ["soil.agents", "soil.agents.custom"]
@@ -533,108 +337,6 @@ def deserialize_type(agent_class, known_modules=[]):
     return agent_class
 
 
-def deserialize_definition(ind, **kwargs):
-    d = deepcopy(ind)
-    for v in d:
-        v["agent_class"] = deserialize_type(v["agent_class"], **kwargs)
-    return d
-
-
-def _validate_states(states, topology):
-    """Validate states to avoid ignoring states during initialization"""
-    states = states or []
-    if isinstance(states, dict):
-        for x in states:
-            assert x in topology.nodes
-    else:
-        assert len(states) <= len(topology)
-    return states
-
-
-def _convert_agent_classs(ind, to_string=False, **kwargs):
-    """Convenience method to allow specifying agents by class or class name."""
-    if to_string:
-        return serialize_definition(ind, **kwargs)
-    return deserialize_definition(ind, **kwargs)
-
-
-# def _agent_from_definition(definition, random, value=-1, unique_id=None):
-#     """Used in the initialization of agents given an agent distribution."""
-#     if value < 0:
-#         value = random.random()
-#     for d in sorted(definition, key=lambda x: x.get('threshold')):
-#         threshold = d.get('threshold', (-1, -1))
-#         # Check if the definition matches by id (first) or by threshold
-#         if (unique_id is not None and unique_id in d.get('ids', [])) or \
-#            (value >= threshold[0] and value < threshold[1]):
-#             state = {}
-#             if 'state' in d:
-#                 state = deepcopy(d['state'])
-#             return d['agent_class'], state
-
-#     raise Exception('Definition for value {} not found in: {}'.format(value, definition))
-
-
-# def _definition_to_dict(definition, random, size=None, default_state=None):
-#     state = default_state or {}
-#     agents = {}
-#     remaining = {}
-#     if size:
-#         for ix in range(size):
-#             remaining[ix] = copy(state)
-#     else:
-#         remaining = defaultdict(lambda x: copy(state))
-
-#     distro = sorted([item for item in definition if 'weight' in item])
-
-#     id = 0
-
-#     def init_agent(item, id=ix):
-#         while id in agents:
-#             id += 1
-
-#         agent = remaining[id]
-#         agent['state'].update(copy(item.get('state', {})))
-#         agents[agent.unique_id] = agent
-#         del remaining[id]
-#         return agent
-
-#     for item in definition:
-#         if 'ids' in item:
-#             ids = item['ids']
-#             del item['ids']
-#             for id in ids:
-#                 agent = init_agent(item, id)
-
-#     for item in definition:
-#         if 'number' in item:
-#             times = item['number']
-#             del item['number']
-#             for times in range(times):
-#                 if size:
-#                     ix = random.choice(remaining.keys())
-#                     agent = init_agent(item, id)
-#                 else:
-#                     agent = init_agent(item)
-#     if not size:
-#         return agents
-
-#     if len(remaining) < 0:
-#         raise Exception('Invalid definition. Too many agents to add')
-
-
-#     total_weight = float(sum(s['weight'] for s in distro))
-#     unit = size / total_weight
-
-#     for item in distro:
-#         times = unit * item['weight']
-#         del item['weight']
-#         for times in range(times):
-#             ix = random.choice(remaining.keys())
-#             agent = init_agent(item, id)
-#     return agents
-
-
 class AgentView(Mapping, Set):
     """A lazy-loaded list of agents."""
 
@@ -718,7 +420,7 @@ def filter_agents(
         state_id = tuple([state_id])
 
     if agent_class is not None:
-        agent_class = deserialize_type(agent_class)
+        agent_class = _deserialize_type(agent_class)
         try:
             agent_class = tuple(agent_class)
         except TypeError:
@@ -758,14 +460,6 @@ def from_config(
     default = cfg or config.AgentConfig()
     if not isinstance(cfg, config.AgentConfig):
         cfg = config.AgentConfig(**cfg)
-    return _agents_from_config(cfg, topology=topology, random=random)
-
-
-def _agents_from_config(
-    cfg: config.AgentConfig, topology: nx.Graph, random
-) -> List[Dict[str, Any]]:
-    if cfg and not isinstance(cfg, config.AgentConfig):
-        cfg = config.AgentConfig(**cfg)
 
     agents = []
 
@@ -933,6 +627,9 @@ def _from_distro(
     return agents
 
 
+from .network_agents import *
+from .fsm import *
+from .evented import *
 from .BassModel import *
 from .BigMarketModel import *
 from .IndependentCascadeModel import *

soil/agents/evented.py

@@ -0,0 +1,57 @@
+from . import BaseAgent
+from ..events import Message, Tell, Ask, Reply, TimedOut
+from ..time import Cond
+from functools import partial
+from collections import deque
+
+
+class Evented(BaseAgent):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._inbox = deque()
+        self._received = 0
+        self._processed = 0
+
+
+    def on_receive(self, *args, **kwargs):
+        pass
+
+    def received(self, expiration=None, timeout=None):
+        current = self._received
+        if expiration is None:
+            expiration = float('inf') if timeout is None else self.now + timeout
+
+        if expiration < self.now:
+            raise ValueError("Invalid expiration time")
+
+        def ready(agent):
+            return agent._received > current or agent.now >= expiration
+
+        def value(agent):
+            if agent.now > expiration:
+                raise TimedOut("No message received")
+
+        c = Cond(func=ready, return_func=value)
+        c._checked = True
+        return c
+
+    def tell(self, msg, sender):
+        self._received += 1
+        self._inbox.append(Tell(payload=msg, sender=sender))
+
+    def ask(self, msg, timeout=None):
+        self._received += 1
+        ask = Ask(payload=msg)
+        self._inbox.append(ask)
+        expiration = float('inf') if timeout is None else self.now + timeout
+        return ask.replied(expiration=expiration)
+
+    def check_messages(self):
+        while self._inbox:
+            msg = self._inbox.popleft()
+            self._processed += 1
+            if msg.expired(self.now):
+                continue
+            reply = self.on_receive(msg.payload, sender=msg.sender)
+            if isinstance(msg, Ask):
+                msg.reply = reply

soil/agents/fsm.py

@@ -0,0 +1,142 @@
+from . import MetaAgent, BaseAgent
+
+from functools import partial, wraps
+import inspect
+
+
+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.
+        """
+        if inspect.isgeneratorfunction(func):
+            orig_func = func
+
+            @wraps(func)
+            def func(self):
+                while True:
+                    if not self._coroutine:
+                        self._coroutine = orig_func(self)
+
+                    try:
+                        if self._last_except:
+                            n = self._coroutine.throw(self._last_except)
+                        else:
+                            n = self._coroutine.send(self._last_return)
+                        if n:
+                            return None, n
+                        return n
+                    except StopIteration as ex:
+                        self._coroutine = None
+                        next_state = ex.value
+                        if next_state is not None:
+                            self._set_state(next_state)
+                        return next_state
+                    finally:
+                        self._last_return = None
+                        self._last_except = None
+
+
+
+        func.id = name or func.__name__
+        func.is_default = False
+        return func
+
+    if callable(name):
+        return decorator(name)
+    else:
+        return partial(decorator, name=name)
+
+
+def default_state(func):
+    func.is_default = True
+    return func
+
+
+class MetaFSM(MetaAgent):
+    def __new__(mcls, name, bases, namespace):
+        states = {}
+        # Re-use states from inherited classes
+        default_state = None
+        for i in bases:
+            if isinstance(i, MetaFSM):
+                for state_id, state in i._states.items():
+                    if state.is_default:
+                        default_state = state
+                    states[state_id] = state
+
+        # Add new states
+        for attr, func in namespace.items():
+            if hasattr(func, "id"):
+                if func.is_default:
+                    default_state = func
+                states[func.id] = func
+
+        namespace.update(
+            {
+                "_default_state": default_state,
+                "_states": states,
+            }
+        )
+
+        return super(MetaFSM, mcls).__new__(
+            mcls=mcls, name=name, bases=bases, namespace=namespace
+        )
+
+
+class FSM(BaseAgent, metaclass=MetaFSM):
+    def __init__(self, **kwargs):
+        super(FSM, self).__init__(**kwargs)
+        if not hasattr(self, "state_id"):
+            if not self._default_state:
+                raise ValueError(
+                    "No default state specified for {}".format(self.unique_id)
+                )
+            self.state_id = self._default_state.id
+
+        self._coroutine = None
+        self._set_state(self.state_id)
+
+    def step(self):
+        self.debug(f"Agent {self.unique_id} @ state {self.state_id}")
+        default_interval = super().step()
+
+        next_state = self._states[self.state_id](self)
+
+        when = None
+        try:
+            next_state, *when = next_state
+            if not when:
+                when = None
+            elif len(when) == 1:
+                when = when[0]
+            else:
+                raise ValueError(
+                    "Too many values returned. Only state (and time) allowed"
+                )
+        except TypeError:
+            pass
+
+        if next_state is not None:
+            self._set_state(next_state)
+
+        return when or default_interval
+
+    def _set_state(self, state, when=None):
+        if hasattr(state, "id"):
+            state = state.id
+        if state not in self._states:
+            raise ValueError("{} is not a valid state".format(state))
+        self.state_id = state
+        if when is not None:
+            self.model.schedule.add(self, when=when)
+        return state
+
+    def die(self):
+        return self.dead, super().die()
+
+    @state
+    def dead(self):
+        return self.die()

soil/agents/network_agents.py

@@ -0,0 +1,82 @@
+from . import BaseAgent
+
+
+class NetworkAgent(BaseAgent):
+    def __init__(self, *args, topology, node_id, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        assert topology is not None
+        assert node_id is not None
+        self.G = topology
+        assert self.G
+        self.node_id = node_id
+
+    def count_neighbors(self, state_id=None, **kwargs):
+        return len(self.get_neighbors(state_id=state_id, **kwargs))
+
+    def get_neighbors(self, **kwargs):
+        return list(self.iter_agents(limit_neighbors=True, **kwargs))
+
+    @property
+    def node(self):
+        return self.G.nodes[self.node_id]
+
+    def iter_agents(self, unique_id=None, *, limit_neighbors=False, **kwargs):
+        unique_ids = None
+        if isinstance(unique_id, list):
+            unique_ids = set(unique_id)
+        elif unique_id is not None:
+            unique_ids = set(
+                [
+                    unique_id,
+                ]
+            )
+
+        if limit_neighbors:
+            neighbor_ids = set()
+            for node_id in self.G.neighbors(self.node_id):
+                if self.G.nodes[node_id].get("agent") is not None:
+                    neighbor_ids.add(node_id)
+            if unique_ids:
+                unique_ids = unique_ids & neighbor_ids
+            else:
+                unique_ids = neighbor_ids
+            if not unique_ids:
+                return
+            unique_ids = list(unique_ids)
+        yield from super().iter_agents(unique_id=unique_ids, **kwargs)
+
+    def subgraph(self, center=True, **kwargs):
+        include = [self] if center else []
+        G = self.G.subgraph(
+            n.node_id for n in list(self.get_agents(**kwargs) + include)
+        )
+        return G
+
+    def remove_node(self):
+        print(f"Removing node for {self.unique_id}: {self.node_id}")
+        self.G.remove_node(self.node_id)
+        self.node_id = None
+
+    def add_edge(self, other, edge_attr_dict=None, *edge_attrs):
+        if self.node_id not in self.G.nodes(data=False):
+            raise ValueError(
+                "{} not in list of existing agents in the network".format(
+                    self.unique_id
+                )
+            )
+        if other.node_id not in self.G.nodes(data=False):
+            raise ValueError(
+                "{} not in list of existing agents in the network".format(other)
+            )
+
+        self.G.add_edge(
+            self.node_id, other.node_id, edge_attr_dict=edge_attr_dict, *edge_attrs
+        )
+
+    def die(self, remove=True):
+        if not self.alive:
+            return None
+        if remove:
+            self.remove_node()
+        return super().die()

soil/debugging.py

@@ -30,9 +30,9 @@ def wrapcmd(func):
 class Debug(pdb.Pdb):
     def __init__(self, *args, skip_soil=False, **kwargs):
         skip = kwargs.get("skip", [])
-        skip.append("soil")
         if skip_soil:
             skip.append("soil")
+            skip.append("contextlib")
             skip.append("soil.*")
             skip.append("mesa.*")
         super(Debug, self).__init__(*args, skip=skip, **kwargs)
@@ -181,7 +181,7 @@ def set_trace(frame=None, **kwargs):
     debugger.set_trace(frame)
 
 
-def post_mortem(traceback=None):
+def post_mortem(traceback=None, **kwargs):
     global debugger
     if debugger is None:
         debugger = Debug(**kwargs)

soil/environment.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 import os
 import sqlite3
 import math
-import random
 import logging
 import inspect
 
@@ -19,7 +18,7 @@ import networkx as nx
 from mesa import Model
 from mesa.datacollection import DataCollector
 
-from . import agents as agentmod, config, serialization, utils, time, network
+from . import agents as agentmod, config, serialization, utils, time, network, events
 
 
 class BaseEnvironment(Model):
@@ -142,12 +141,12 @@ class BaseEnvironment(Model):
             "The environment has not been scheduled, so it has no sense of time"
         )
 
-    def add_agent(self, agent_class, unique_id=None, **kwargs):
+    def add_agent(self, unique_id=None, **kwargs):
-        a = None
         if unique_id is None:
             unique_id = self.next_id()
 
-        a = agent_class(model=self, unique_id=unique_id, **args)
+        kwargs["unique_id"] = unique_id
+        a = self._agent_from_dict(kwargs)
 
         self.schedule.add(a)
         return a
@@ -169,7 +168,9 @@ class BaseEnvironment(Model):
         Advance one step in the simulation, and update the data collection and scheduler appropriately
         """
         super().step()
-        self.logger.info(f"--- Step {self.now:^5} ---")
+        self.logger.info(
+            f"--- Step: {self.schedule.steps:^5} - Time: {self.now:^5} ---"
+        )
         self.schedule.step()
         self.datacollector.collect(self)
 
@@ -236,6 +237,7 @@ class NetworkEnvironment(BaseEnvironment):
         node_id = agent.get("node_id", None)
         if node_id is None:
             node_id = network.find_unassigned(self.G, random=self.random)
+        self.G.nodes[node_id]["agent"] = None
         agent["node_id"] = node_id
         agent["unique_id"] = unique_id
         agent["topology"] = self.G
@@ -269,18 +271,31 @@ class NetworkEnvironment(BaseEnvironment):
             node_id = network.find_unassigned(
                 G=self.G, shuffle=True, random=self.random
             )
+            if node_id is None:
+                node_id = f"node_for_{unique_id}"
 
-        if node_id in G.nodes:
+        if node_id not in self.G.nodes:
-            self.G.nodes[node_id]["agent"] = None  # Reserve
-        else:
             self.G.add_node(node_id)
 
+        assert "agent" not in self.G.nodes[node_id]
+        self.G.nodes[node_id]["agent"] = None  # Reserve
+
         a = self.add_agent(
-            unique_id=unique_id, agent_class=agent_class, node_id=node_id, **kwargs
+            unique_id=unique_id,
+            agent_class=agent_class,
+            topology=self.G,
+            node_id=node_id,
+            **kwargs,
         )
         a["visible"] = True
         return a
 
+    def add_agent(self, *args, **kwargs):
+        a = super().add_agent(*args, **kwargs)
+        if "node_id" in a:
+            assert self.G.nodes[a.node_id]["agent"] == a
+        return a
+
     def agent_for_node_id(self, node_id):
         return self.G.nodes[node_id].get("agent")
 
@@ -296,3 +311,14 @@ class NetworkEnvironment(BaseEnvironment):
 
 
 Environment = NetworkEnvironment
+
+
+class EventedEnvironment(Environment):
+    def broadcast(self, msg,  sender, expiration=None, ttl=None, **kwargs):
+        for agent in self.agents(**kwargs):
+            self.logger.info(f'Telling {repr(agent)}: {msg} ttl={ttl}')
+            try:
+                agent._inbox.append(events.Tell(payload=msg, sender=sender, expiration=expiration if ttl is None else self.now+ttl))
+            except AttributeError:
+                self.info(f'Agent {agent.unique_id} cannot receive events')
+

soil/events.py

@@ -0,0 +1,43 @@
+from .time import Cond
+from dataclasses import dataclass, field
+from typing import Any
+from uuid import uuid4
+
+class Event:
+    pass
+
+@dataclass
+class Message:
+    payload: Any
+    sender: Any = None
+    expiration: float = None
+    id: int = field(default_factory=uuid4)
+
+    def expired(self, when):
+        return self.expiration is not None and self.expiration < when
+
+class Reply(Message):
+    source: Message
+
+
+class Ask(Message):
+    reply: Message = None
+
+    def replied(self, expiration=None):
+        def ready(agent):
+            return self.reply is not None or agent.now > expiration
+
+        def value(agent):
+            if agent.now > expiration:
+                raise TimedOut(f'No answer received for {self}')
+            return self.reply
+
+        return Cond(func=ready, return_func=value)
+
+
+class Tell(Message):
+    pass
+
+
+class TimedOut(Exception):
+    pass

soil/exporters.py

@@ -3,6 +3,7 @@ import sys
 from time import time as current_time
 from io import BytesIO
 from sqlalchemy import create_engine
+from textwrap import dedent, indent
 
 
 import matplotlib.pyplot as plt
@@ -86,6 +87,22 @@ class Exporter:
                 pass
         return open_or_reuse(f, mode=mode, **kwargs)
 
+    def get_dfs(self, env):
+        yield from get_dc_dfs(env.datacollector, trial_id=env.id)
+
+
+def get_dc_dfs(dc, trial_id=None):
+    dfs = {
+        "env": dc.get_model_vars_dataframe(),
+        "agents": dc.get_agent_vars_dataframe(),
+    }
+    for table_name in dc.tables:
+        dfs[table_name] = dc.get_table_dataframe(table_name)
+    if trial_id:
+        for (name, df) in dfs.items():
+            df["trial_id"] = trial_id
+    yield from dfs.items()
+
 
 class default(Exporter):
     """Default exporter. Writes sqlite results, as well as the simulation YAML"""
@@ -98,7 +115,7 @@ class default(Exporter):
         with self.output(self.simulation.name + ".dumped.yml") as f:
             f.write(self.simulation.to_yaml())
         self.dbpath = os.path.join(self.outdir, f"{self.simulation.name}.sqlite")
-        try_backup(self.dbpath, move=True)
+        try_backup(self.dbpath, remove=True)
 
     def trial_end(self, env):
         if self.dry_run:
@@ -111,24 +128,10 @@ class default(Exporter):
 
             engine = create_engine(f"sqlite:///{self.dbpath}", echo=False)
 
-            dc = env.datacollector
+            for (t, df) in self.get_dfs(env):
-            for (t, df) in get_dc_dfs(dc, trial_id=env.id):
                 df.to_sql(t, con=engine, if_exists="append")
 
 
-def get_dc_dfs(dc, trial_id=None):
-    dfs = {
-        "env": dc.get_model_vars_dataframe(),
-        "agents": dc.get_agent_vars_dataframe(),
-    }
-    for table_name in dc.tables:
-        dfs[table_name] = dc.get_table_dataframe(table_name)
-    if trial_id:
-        for (name, df) in dfs.items():
-            df['trial_id'] = trial_id
-    yield from dfs.items()
-
-
 class csv(Exporter):
 
     """Export the state of each environment (and its agents) in a separate CSV file"""
@@ -139,7 +142,7 @@ class csv(Exporter):
                 self.simulation.name, env.id, self.outdir
             )
         ):
-            for (df_name, df) in get_dc_dfs(env.datacollector, trial_id=env.id):
+            for (df_name, df) in self.get_dfs(env):
                 with self.output("{}.{}.csv".format(env.id, df_name)) as f:
                     df.to_csv(f)
 
@@ -192,52 +195,19 @@ class graphdrawing(Exporter):
             f.savefig(f)
 
 
-"""
+class summary(Exporter):
-Convert an environment into a NetworkX graph
+    """Print a summary of each trial to sys.stdout"""
-"""
 
-
+    def trial_end(self, env):
-def env_to_graph(env, history=None):
+        for (t, df) in self.get_dfs(env):
-    G = nx.Graph(env.G)
+            if not len(df):
-
-    for agent in env.network_agents:
-
-        attributes = {"agent": str(agent.__class__)}
-        lastattributes = {}
-        spells = []
-        lastvisible = False
-        laststep = None
-        if not history:
-            history = sorted(list(env.state_to_tuples()))
-        for _, t_step, attribute, value in history:
-            if attribute == "visible":
-                nowvisible = value
-                if nowvisible and not lastvisible:
-                    laststep = t_step
-                if not nowvisible and lastvisible:
-                    spells.append((laststep, t_step))
-
-                lastvisible = nowvisible
                 continue
-            key = "attr_" + attribute
+            msg = indent(str(df.describe()), "    ")
-            if key not in attributes:
+            logger.info(
-                attributes[key] = list()
+                dedent(
-            if key not in lastattributes:
+                    f"""
-                lastattributes[key] = (value, t_step)
+            Dataframe {t}:
-            elif lastattributes[key][0] != value:
+            """
-                last_value, laststep = lastattributes[key]
+                )
-                commit_value = (last_value, laststep, t_step)
+                + msg
-                if key not in attributes:
+            )
-                    attributes[key] = list()
-                attributes[key].append(commit_value)
-                lastattributes[key] = (value, t_step)
-        for k, v in lastattributes.items():
-            attributes[k].append((v[0], v[1], None))
-        if lastvisible:
-            spells.append((laststep, None))
-        if spells:
-            G.add_node(agent.id, spells=spells, **attributes)
-        else:
-            G.add_node(agent.id, **attributes)
-
-    return G

soil/network.py

@@ -65,10 +65,8 @@ def find_unassigned(G, shuffle=False, random=random):
         random.shuffle(candidates)
     for next_id, data in candidates:
         if "agent" not in data:
-            node_id = next_id
+            return next_id
-            break
+    return None
-
-    return node_id
 
 
 def dump_gexf(G, f):

soil/simulation.py

@@ -21,7 +21,6 @@ import pickle
 from . import serialization, exporters, utils, basestring, agents
 from .environment import Environment
 from .utils import logger, run_and_return_exceptions
-from .time import INFINITY
 from .config import Config, convert_old
 
 
@@ -48,7 +47,7 @@ class Simulation:
     max_time: float = float("inf")
     max_steps: int = -1
     interval: int = 1
-    num_trials: int = 3
+    num_trials: int = 1
     parallel: Optional[bool] = None
     exporters: Optional[List[str]] = field(default_factory=list)
     outdir: Optional[str] = None
@@ -194,7 +193,7 @@ class Simulation:
 
         # Set up agents on nodes
         def is_done():
-            return False
+            return not model.running
 
         if until and hasattr(model.schedule, "time"):
             prev = is_done
@@ -226,6 +225,11 @@ Model stats:
                 f'Simulation time {model.schedule.time}/{until}. Next: {getattr(model.schedule, "next_time", model.schedule.time + self.interval)}'
             )
             model.step()
+
+        if (
+            model.schedule.time < until
+        ):  # Simulation ended (no more steps) before the expected time
+            model.schedule.time = until
         return model
 
     def to_dict(self):

soil/time.py

@@ -2,6 +2,10 @@ from mesa.time import BaseScheduler
 from queue import Empty
 from heapq import heappush, heappop, heapify
 import math
+
+from inspect import getsource
+from numbers import Number
+
 from .utils import logger
 from mesa import Agent as MesaAgent
 
@@ -9,15 +13,76 @@ from mesa import Agent as MesaAgent
 INFINITY = float("inf")
 
 
+class DeadAgent(Exception):
+    pass
+
+
 class When:
     def __init__(self, time):
         if isinstance(time, When):
             return time
         self._time = time
 
-    def abs(self, time):
+    def next(self, time):
         return self._time
 
+    def abs(self, time):
+        return self
+
+    def __repr__(self):
+        return str(f"When({self._time})")
+
+    def __lt__(self, other):
+        if isinstance(other, Number):
+            return self._time < other
+        return self._time < other.next(self._time)
+
+    def __gt__(self, other):
+        if isinstance(other, Number):
+            return self._time > other
+        return self._time > other.next(self._time)
+
+    def ready(self, agent):
+        return self._time <= agent.model.schedule.time
+
+    def return_value(self, agent):
+        return None
+
+
+class Cond(When):
+    def __init__(self, func, delta=1, return_func=lambda agent: None):
+        self._func = func
+        self._delta = delta
+        self._checked = False
+        self._return_func = return_func
+
+    def next(self, time):
+        if self._checked:
+            return time + self._delta
+        return time
+
+    def abs(self, time):
+        return self
+
+    def ready(self, agent):
+        self._checked = True
+        return self._func(agent)
+
+    def return_value(self, agent):
+        return self._return_func(agent)
+
+    def __eq__(self, other):
+        return False
+
+    def __lt__(self, other):
+        return True
+
+    def __gt__(self, other):
+        return False
+
+    def __repr__(self):
+        return str(f'Cond("{getsource(self._func)}")')
+
 
 NEVER = When(INFINITY)
 
@@ -27,11 +92,19 @@ class Delta(When):
         self._delta = delta
 
     def __eq__(self, other):
-        return self._delta == other._delta
+        if isinstance(other, Delta):
+            return self._delta == other._delta
+        return False
 
     def abs(self, time):
+        return When(self._delta + time)
+
+    def next(self, time):
         return time + self._delta
 
+    def __repr__(self):
+        return str(f"Delta({self._delta})")
+
 
 class TimedActivation(BaseScheduler):
     """A scheduler which activates each agent when the agent requests.
@@ -47,14 +120,17 @@ class TimedActivation(BaseScheduler):
 
     def add(self, agent: MesaAgent, when=None):
         if when is None:
-            when = self.time
+            when = When(self.time)
+        elif not isinstance(when, When):
+            when = When(when)
         if agent.unique_id in self._agents:
-            self._queue.remove((self._next[agent.unique_id], agent.unique_id))
             del self._agents[agent.unique_id]
-            heapify(self._queue)
+            if agent.unique_id in self._next:
+                self._queue.remove((self._next[agent.unique_id], agent))
+                heapify(self._queue)
 
-        heappush(self._queue, (when, agent.unique_id))
         self._next[agent.unique_id] = when
+        heappush(self._queue, (when, agent))
         super().add(agent)
 
     def step(self) -> None:
@@ -63,42 +139,77 @@ class TimedActivation(BaseScheduler):
         an agent will signal when it wants to be scheduled next.
         """
 
-        self.logger.debug(f"Simulation step {self.next_time}")
+        self.logger.debug(f"Simulation step {self.time}")
         if not self.model.running:
             return
 
-        self.time = self.next_time
+        when = NEVER
-        when = self.time
 
-        while self._queue and self._queue[0][0] == self.time:
+        to_process = []
-            (when, agent_id) = heappop(self._queue)
+        skipped = []
-            self.logger.debug(f"Stepping agent {agent_id}")
+        next_time = INFINITY
 
-            agent = self._agents[agent_id]
+        ix = 0
-            returned = agent.step()
 
-            if not getattr(agent, "alive", True):
+        self.logger.debug(f"Queue length: {len(self._queue)}")
-                self.remove(agent)
+
+        while self._queue:
+            (when, agent) = self._queue[0]
+            if when > self.time:
+                break
+            heappop(self._queue)
+            if when.ready(agent):
+                try:
+                    agent._last_return = when.return_value(agent)
+                except Exception as ex:
+                    agent._last_except = ex
+
+                self._next.pop(agent.unique_id, None)
+                to_process.append(agent)
                 continue
 
-            when = (returned or Delta(1)).abs(self.time)
+            next_time = min(next_time, when.next(self.time))
-            if when < self.time:
+            self._next[agent.unique_id] = next_time
-                raise Exception(
+            skipped.append((when, agent))
-                    "Cannot schedule an agent for a time in the past ({} < {})".format(
-                        when, self.time
-                    )
-                )
 
-            self._next[agent_id] = when
+        if self._queue:
-            heappush(self._queue, (when, agent_id))
+            next_time = min(next_time, self._queue[0][0].next(self.time))
+
+        self._queue = [*skipped, *self._queue]
+
+        for agent in to_process:
+            self.logger.debug(f"Stepping agent {agent}")
+
+            try:
+                returned = ((agent.step() or Delta(1))).abs(self.time)
+            except DeadAgent:
+                if agent.unique_id in self._next:
+                    del self._next[agent.unique_id]
+                agent.alive = False
+                continue
+
+            if not getattr(agent, "alive", True):
+                continue
+
+            value = returned.next(self.time)
+            agent._last_return = value
+
+            if value < self.time:
+                raise Exception(
+                    f"Cannot schedule an agent for a time in the past ({when} < {self.time})"
+                )
+            if value < INFINITY:
+                next_time = min(value, next_time)
+
+                self._next[agent.unique_id] = returned
+                heappush(self._queue, (returned, agent))
+            else:
+                assert not self._next[agent.unique_id]
 
         self.steps += 1
+        self.logger.debug(f"Updating time step: {self.time} -> {next_time}")
+        self.time = next_time
 
-        if not self._queue:
+        if not self._queue or next_time == INFINITY:
-            self.time = INFINITY
-            self.next_time = INFINITY
             self.model.running = False
             return self.time
-
-        self.next_time = self._queue[0][0]
-        self.logger.debug(f"Next step: {self.next_time}")

soil/utils.py

@@ -47,7 +47,7 @@ def timer(name="task", pre="", function=logger.info, to_object=None):
         to_object.end = end
 
 
-def try_backup(path, move=False):
+def try_backup(path, remove=False):
     if not os.path.exists(path):
         return None
     outdir = os.path.dirname(path)
@@ -59,9 +59,7 @@ def try_backup(path, move=False):
     backup_dir = os.path.join(outdir, "backup")
     if not os.path.exists(backup_dir):
         os.makedirs(backup_dir)
-    newpath = os.path.join(
+    newpath = os.path.join(backup_dir, "{}@{}".format(os.path.basename(path), stamp))
-        backup_dir, "{}@{}".format(os.path.basename(path), stamp)
-    )
     if move:
         move(path, newpath)
     else:

tests/test_agents.py

@@ -13,14 +13,57 @@ class Dead(agents.FSM):
 
 
 class TestMain(TestCase):
-    def test_die_raises_exception(self):
-        d = Dead(unique_id=0, model=environment.Environment())
-        d.step()
-        with pytest.raises(agents.DeadAgent):
-            d.step()
-
     def test_die_returns_infinity(self):
+        '''The last step of a dead agent should return time.INFINITY'''
         d = Dead(unique_id=0, model=environment.Environment())
         ret = d.step().abs(0)
         print(ret, "next")
-        assert ret == stime.INFINITY
+        assert ret == stime.NEVER
+
+    def test_die_raises_exception(self):
+        '''A dead agent should raise an exception if it is stepped after death'''
+        d = Dead(unique_id=0, model=environment.Environment())
+        d.step()
+        with pytest.raises(stime.DeadAgent):
+            d.step()
+
+
+    def test_agent_generator(self):
+        '''
+        The step function of an agent could be a generator. In that case, the state of the
+        agent will be resumed after every call to step.
+        '''
+        a = 0
+        class Gen(agents.BaseAgent):
+            def step(self):
+                nonlocal a
+                for i in range(5):
+                    yield
+                    a += 1
+        e = environment.Environment()
+        g = Gen(model=e, unique_id=e.next_id())
+        e.schedule.add(g)
+
+        for i in range(5):
+            e.step()
+            assert a == i
+
+    def test_state_decorator(self):
+        class MyAgent(agents.FSM):
+            run = 0
+            @agents.default_state
+            @agents.state('original')
+            def root(self):
+                self.run += 1
+                return self.other
+
+            @agents.state
+            def other(self):
+                self.run += 1
+
+        e = environment.Environment()
+        a = MyAgent(model=e, unique_id=e.next_id())
+        a.step()
+        assert a.run == 1
+        a.step()
+        assert a.run == 2

tests/test_exporters.py

@@ -50,7 +50,6 @@ class Exporters(TestCase):
 
         for env in s.run_simulation(exporters=[Dummy], dry_run=True):
             assert len(env.agents) == 1
-            assert env.now == max_time
 
         assert Dummy.started
         assert Dummy.ended

tests/test_main.py

@@ -160,32 +160,12 @@ class TestMain(TestCase):
 
     def test_serialize_agent_class(self):
         """A class from soil.agents should be serialized without the module part"""
-        ser = agents.serialize_type(CustomAgent)
+        ser = agents._serialize_type(CustomAgent)
         assert ser == "test_main.CustomAgent"
-        ser = agents.serialize_type(agents.BaseAgent)
+        ser = agents._serialize_type(agents.BaseAgent)
         assert ser == "BaseAgent"
         pickle.dumps(ser)
 
-    def test_deserialize_agent_distribution(self):
-        agent_distro = [
-            {"agent_class": "CounterModel", "weight": 1},
-            {"agent_class": "test_main.CustomAgent", "weight": 2},
-        ]
-        converted = agents.deserialize_definition(agent_distro)
-        assert converted[0]["agent_class"] == agents.CounterModel
-        assert converted[1]["agent_class"] == CustomAgent
-        pickle.dumps(converted)
-
-    def test_serialize_agent_distribution(self):
-        agent_distro = [
-            {"agent_class": agents.CounterModel, "weight": 1},
-            {"agent_class": CustomAgent, "weight": 2},
-        ]
-        converted = agents.serialize_definition(agent_distro)
-        assert converted[0]["agent_class"] == "CounterModel"
-        assert converted[1]["agent_class"] == "test_main.CustomAgent"
-        pickle.dumps(converted)
-
     def test_templates(self):
         """Loading a template should result in several configs"""
         configs = serialization.load_file(join(EXAMPLES, "template.yml"))

tests/test_time.py

@@ -0,0 +1,74 @@
+from unittest import TestCase
+
+from soil import time, agents, environment
+
+class TestMain(TestCase):
+    def test_cond(self):
+        '''
+        A condition should match a When if the concition is True
+        '''
+
+        t = time.Cond(lambda t: True)
+        f = time.Cond(lambda t: False)
+        for i in range(10):
+            w = time.When(i)
+            assert w == t
+            assert w is not f
+
+    def test_cond(self):
+        '''
+        Comparing a Cond to a Delta should always return False
+        '''
+
+        c = time.Cond(lambda t: False)
+        d = time.Delta(1)
+        assert c is not d
+
+    def test_cond_env(self):
+        '''
+        '''
+
+        times_started = []
+        times_awakened = []
+        times = []
+        done = 0
+
+        class CondAgent(agents.BaseAgent):
+
+            def step(self):
+                nonlocal done
+                times_started.append(self.now)
+                while True:
+                    yield time.Cond(lambda agent: agent.model.schedule.time >= 10)
+                    times_awakened.append(self.now)
+                    if self.now >= 10:
+                        break
+                done += 1
+
+        env = environment.Environment(agents=[{'agent_class': CondAgent}])
+
+
+        while env.schedule.time < 11:
+            env.step()
+            times.append(env.now)
+        assert env.schedule.time == 11
+        assert times_started == [0]
+        assert times_awakened == [10]
+        assert done == 1
+        # The first time will produce the Cond.
+        # Since there are no other agents, time will not advance, but the number
+        # of steps will.
+        assert env.schedule.steps == 12
+        assert len(times) == 12
+
+        while env.schedule.time < 12:
+            env.step()
+            times.append(env.now)
+
+        assert env.schedule.time == 12
+        assert times_started == [0, 11]
+        assert times_awakened == [10, 11]
+        assert done == 2
+        # Once more to yield the cond, another one to continue
+        assert env.schedule.steps == 14
+        assert len(times) == 14