Fix bug agent df with multiple steps per timestamp

* Add option to set scheduler and environment start times
* Add `Agent.env` method to ease migration of earlier code

.gitignore

@@ -9,4 +9,5 @@ docs/_build*
 build/*
 dist/*
 prof
-backup
+backup
+*.egg-info

benchmarks/noop/_config.py

@@ -11,6 +11,7 @@ def run_sim(model, **kwargs):
                 dump=False,
                 num_processes=1,
                 parameters={'num_agents': NUM_AGENTS},
+                seed="",
                 max_steps=MAX_STEPS,
                 iterations=NUM_ITERS)
     opts.update(kwargs)

benchmarks/noop/mesa_batchrunner.py

@@ -8,7 +8,6 @@ class NoopAgent(Agent):
         self.num_calls = 0
 
     def step(self):
-        # import pdb;pdb.set_trace()
         self.num_calls += 1 
 
 

benchmarks/noop/mesa_simulation.py

@@ -10,7 +10,6 @@ class NoopAgent(Agent):
         self.num_calls = 0
 
     def step(self):
-        # import pdb;pdb.set_trace()
         self.num_calls += 1 
 
 

benchmarks/noop/soil_state.py

@@ -0,0 +1,21 @@
+from soil import Agent, Environment, Simulation, state
+
+
+class NoopAgent(Agent):
+    num_calls = 0
+
+    @state(default=True)
+    def unique(self):
+        self.num_calls += 1
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+from _config import *
+
+run_sim(model=NoopEnvironment)

benchmarks/noop/soil_step.py

@@ -1,7 +1,7 @@
-from soil import BaseAgent, Environment, Simulation
+from soil import Agent, Environment, Simulation
 
 
-class NoopAgent(BaseAgent):
+class NoopAgent(Agent):
     num_calls = 0
 
     def step(self):
@@ -15,7 +15,6 @@ class NoopEnvironment(Environment):
         self.add_agent_reporter("num_calls")
 
 
-if __name__ == "__main__":
+from _config import *
-    from _config import *
 
-    run_sim(model=NoopEnvironment)
+run_sim(model=NoopEnvironment)

benchmarks/noop/soilent_async.py

@@ -1,5 +1,5 @@
 from soil import Agent, Environment, Simulation
-from soilent import Scheduler
+from soil.time import SoilentActivation
 
 
 class NoopAgent(Agent):
@@ -14,7 +14,7 @@ class NoopAgent(Agent):
 
 class NoopEnvironment(Environment):
     num_agents = 100
-    schedule_class = Scheduler
+    schedule_class = SoilentActivation
 
     def init(self):
         self.add_agents(NoopAgent, k=self.num_agents)
@@ -26,4 +26,4 @@ if __name__ == "__main__":
 
     res = run_sim(model=NoopEnvironment)
     for r in res:
-        assert isinstance(r.schedule, Scheduler)
+        assert isinstance(r.schedule, SoilentActivation)

benchmarks/noop/soilent_async_pqueue.py

@@ -1,5 +1,5 @@
 from soil import Agent, Environment
-from soilent import PQueueScheduler
+from soil.time import SoilentPQueueActivation
 
 
 class NoopAgent(Agent):
@@ -12,7 +12,7 @@ class NoopAgent(Agent):
 
 class NoopEnvironment(Environment):
     num_agents = 100
-    schedule_class = PQueueScheduler
+    schedule_class = SoilentPQueueActivation
 
     def init(self):
         self.add_agents(NoopAgent, k=self.num_agents)
@@ -24,4 +24,4 @@ if __name__ == "__main__":
 
     res = run_sim(model=NoopEnvironment)
     for r in res:
-        assert isinstance(r.schedule, PQueueScheduler)
+        assert isinstance(r.schedule, SoilentPQueueActivation)

benchmarks/noop/soilent_gens.py

@@ -1,5 +1,5 @@
 from soil import Agent, Environment, Simulation
-from soilent import Scheduler
+from soil.time import SoilentActivation
 
 
 class NoopAgent(Agent):
@@ -13,7 +13,7 @@ class NoopAgent(Agent):
 
 class NoopEnvironment(Environment):
     num_agents = 100
-    schedule_class = Scheduler
+    schedule_class = SoilentActivation
 
     def init(self):
         self.add_agents(NoopAgent, k=self.num_agents)
@@ -25,4 +25,4 @@ if __name__ == "__main__":
 
     res = run_sim(model=NoopEnvironment)
     for r in res:
-        assert isinstance(r.schedule, Scheduler)
+        assert isinstance(r.schedule, SoilentActivation)

benchmarks/noop/soilent_gens_pqueue.py

@@ -1,5 +1,5 @@
 from soil import Agent, Environment
-from soilent import PQueueScheduler
+from soil.time import SoilentPQueueActivation
 
 
 class NoopAgent(Agent):
@@ -13,7 +13,7 @@ class NoopAgent(Agent):
 
 class NoopEnvironment(Environment):
     num_agents = 100
-    schedule_class = PQueueScheduler
+    schedule_class = SoilentPQueueActivation
 
     def init(self):
         self.add_agents(NoopAgent, k=self.num_agents)
@@ -25,4 +25,4 @@ if __name__ == "__main__":
 
     res = run_sim(model=NoopEnvironment)
     for r in res:
-        assert isinstance(r.schedule, PQueueScheduler)
+        assert isinstance(r.schedule, SoilentPQueueActivation)

benchmarks/noop/soilent_state.py

@@ -0,0 +1,30 @@
+from soil import Agent, Environment, Simulation, state
+from soil.time import SoilentActivation
+
+
+class NoopAgent(Agent):
+    num_calls = 0
+
+    @state(default=True)
+    async def unique(self):
+        while True:
+            self.num_calls += 1
+            # yield self.delay(1)
+            await self.delay()
+
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+    schedule_class = SoilentActivation
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    res = run_sim(model=NoopEnvironment)
+    for r in res:
+        assert isinstance(r.schedule, SoilentActivation)

benchmarks/noop/soilent_step.py

@@ -1,5 +1,5 @@
 from soil import BaseAgent, Environment, Simulation
-from soilent import Scheduler
+from soil.time import SoilentActivation
 
 
 class NoopAgent(BaseAgent):
@@ -10,7 +10,7 @@ class NoopAgent(BaseAgent):
 
 class NoopEnvironment(Environment):
     num_agents = 100
-    schedule_class = Scheduler
+    schedule_class = SoilentActivation
 
     def init(self):
         self.add_agents(NoopAgent, k=self.num_agents)
@@ -21,4 +21,4 @@ if __name__ == "__main__":
     from _config import *
     res = run_sim(model=NoopEnvironment)
     for r in res:
-        assert isinstance(r.schedule, Scheduler)
+        assert isinstance(r.schedule, SoilentActivation)

benchmarks/noop/soilent_step_pqueue.py

@@ -1,5 +1,5 @@
 from soil import BaseAgent, Environment, Simulation
-from soilent import PQueueScheduler
+from soil.time import SoilentPQueueActivation
 
 
 class NoopAgent(BaseAgent):
@@ -10,7 +10,7 @@ class NoopAgent(BaseAgent):
 
 class NoopEnvironment(Environment):
     num_agents = 100
-    schedule_class = PQueueScheduler
+    schedule_class = SoilentPQueueActivation
 
     def init(self):
         self.add_agents(NoopAgent, k=self.num_agents)
@@ -21,4 +21,4 @@ if __name__ == "__main__":
     from _config import *
     res = run_sim(model=NoopEnvironment)
     for r in res:
-        assert isinstance(r.schedule, PQueueScheduler)
+        assert isinstance(r.schedule, SoilentPqueueActivation)

benchmarks/virusonnetwork/_config.py

@@ -1,8 +1,9 @@
 import os
+from soil import simulation
 
 NUM_AGENTS = int(os.environ.get('NUM_AGENTS', 100))
 NUM_ITERS = int(os.environ.get('NUM_ITERS', 10))
-MAX_STEPS = int(os.environ.get('MAX_STEPS', 1000))
+MAX_STEPS = int(os.environ.get('MAX_STEPS', 500))
 
 
 def run_sim(model, **kwargs):
@@ -22,11 +23,16 @@ def run_sim(model, **kwargs):
                 iterations=NUM_ITERS)
     opts.update(kwargs)
     its = Simulation(**opts).run()
+    assert len(its) == NUM_ITERS
 
-    assert all(it.schedule.steps == MAX_STEPS for it in its)
+    if not simulation._AVOID_RUNNING:
-    ratios = list(it.resistant_susceptible_ratio() for it in its)
+        ratios = list(it.resistant_susceptible_ratio for it in its)
-    print("Max - Avg - Min ratio:", max(ratios), sum(ratios)/len(ratios), min(ratios))
+        print("Max - Avg - Min ratio:", max(ratios), sum(ratios)/len(ratios), min(ratios))
-    assert all(sum([it.number_susceptible,
+        infected = list(it.number_infected for it in its)
-                    it.number_infected,
+        print("Max - Avg - Min infected:", max(infected), sum(infected)/len(infected), min(infected))
-                    it.number_resistant]) == NUM_AGENTS for it in its)
+
-    return its
+        assert all((it.schedule.steps == MAX_STEPS or it.number_infected == 0) for it in its)
+        assert all(sum([it.number_susceptible,
+                        it.number_infected,
+                        it.number_resistant]) == NUM_AGENTS for it in its)
+    return its

benchmarks/virusonnetwork/mesa_basic.py

@@ -100,6 +100,7 @@ class VirusOnNetwork(mesa.Model):
     def number_infected(self):
         return number_infected(self)
 
+    @property
     def resistant_susceptible_ratio(self):
         try:
             return number_state(self, State.RESISTANT) / number_state(
@@ -176,5 +177,4 @@ class VirusAgent(mesa.Agent):
 
 
 from _config import run_sim
-
 run_sim(model=VirusOnNetwork)

benchmarks/virusonnetwork/soil_states.py

@@ -30,8 +30,12 @@ class VirusOnNetwork(Environment):
         for a in self.agents(node_id=infected_nodes):
             a.set_state(VirusAgent.infected)
         assert self.number_infected == self.initial_outbreak_size
+    
+    def step(self):
+        super().step()
 
     @report
+    @property
     def resistant_susceptible_ratio(self):
         try:
             return self.number_resistant / self.number_susceptible
@@ -59,34 +63,29 @@ class VirusAgent(Agent):
     virus_check_frequency = None # Inherit from model
     recovery_chance = None # Inherit from model
     gain_resistance_chance = None # Inherit from model
-    just_been_infected = False
 
     @state(default=True)
-    def susceptible(self):
+    async def susceptible(self):
-        if self.just_been_infected:
+        await self.received()
-            self.just_been_infected = False
+        return self.infected
-            return self.infected
 
     @state
     def infected(self):
         susceptible_neighbors = self.get_neighbors(state_id=self.susceptible.id)
         for a in susceptible_neighbors:
             if self.prob(self.virus_spread_chance):
-                a.just_been_infected = True
+                a.tell(True, sender=self)
         if self.prob(self.virus_check_frequency):
             if self.prob(self.recovery_chance):
                 if self.prob(self.gain_resistance_chance):
                     return self.resistant
                 else:
                     return self.susceptible
-            else:
-                return self.infected
 
     @state
     def resistant(self):
         return self.at(INFINITY)
 
 
-if __name__ == "__main__":
+from _config import run_sim
-    from _config import run_sim
+run_sim(model=VirusOnNetwork)
-    run_sim(model=VirusOnNetwork)

benchmarks/virusonnetwork/soil_step.py

@@ -38,6 +38,7 @@ class VirusOnNetwork(Environment):
         assert self.number_infected == self.initial_outbreak_size
 
     @report
+    @property
     def resistant_susceptible_ratio(self):
         try:
             return self.number_resistant / self.number_susceptible
@@ -99,6 +100,5 @@ class VirusAgent(Agent):
 
 
 
-if __name__ == "__main__":
+from _config import run_sim
-    from _config import run_sim
+run_sim(model=VirusOnNetwork)
-    run_sim(model=VirusOnNetwork)

examples/cars/cars_sim.py

@@ -43,7 +43,7 @@ class Journey:
     driver: Optional[Driver] = None
 
 
-class City(EventedEnvironment):
+class City(Environment):
     """
     An environment with a grid where drivers and passengers will be placed.
 
@@ -85,11 +85,12 @@ class Driver(Evented, FSM):
     journey = None
     earnings = 0
 
-    def on_receive(self, msg, sender):
+    # TODO: remove
-        """This is not a state. It will run (and block) every time process_messages is invoked"""
+    # def on_receive(self, msg, sender):
-        if self.journey is None and isinstance(msg, Journey) and msg.driver is None:
+    #     """This is not a state. It will run (and block) every time process_messages is invoked"""
-            msg.driver = self
+    #     if self.journey is None and isinstance(msg, Journey) and msg.driver is None:
-            self.journey = msg
+    #         msg.driver = self
+    #         self.journey = msg
 
     def check_passengers(self):
         """If there are no more passengers, stop forever"""
@@ -104,7 +105,7 @@ class Driver(Evented, FSM):
         if not self.check_passengers():
             return self.die("No passengers left")
         self.journey = None
-        while self.journey is None:  # No potential journeys detected (see on_receive)
+        while self.journey is None:  # No potential journeys detected
             if target is None or not self.move_towards(target):
                 target = self.random.choice(
                     self.model.grid.get_neighborhood(self.pos, moore=False)
@@ -113,7 +114,7 @@ class Driver(Evented, FSM):
             if not self.check_passengers():
                 return self.die("No passengers left")
             # This will call on_receive behind the scenes, and the agent's status will be updated
-            self.process_messages()
+
             await self.delay(30)  # Wait at least 30 seconds before checking again
 
         try:
@@ -167,12 +168,13 @@ class Driver(Evented, FSM):
 class Passenger(Evented, FSM):
     pos = None
 
-    def on_receive(self, msg, sender):
+    # TODO: Remove
-        """This is not a state. It will be run synchronously every time `process_messages` is run"""
+    # def on_receive(self, msg, sender):
+    #     """This is not a state. It will be run synchronously every time `process_messages` is run"""
 
-        if isinstance(msg, Journey):
+    #     if isinstance(msg, Journey):
-            self.journey = msg
+    #         self.journey = msg
-            return msg
+    #         return msg
 
     @default_state
     @state
@@ -192,17 +194,34 @@ class Passenger(Evented, FSM):
         timeout = 60
         expiration = self.now + timeout
         self.info(f"Asking for journey at: { self.pos }")
-        self.model.broadcast(journey, ttl=timeout, sender=self, agent_class=Driver)
+        self.broadcast(journey, ttl=timeout, agent_class=Driver)
         while not self.journey:
             self.debug(f"Waiting for responses at: { self.pos }")
             try:
-                # This will call process_messages behind the scenes, and the agent's status will be updated
+                offers = await self.received(expiration=expiration, delay=10)
-                # If you want to avoid that, you can call it with: check=False
+                accepted = None
-                await self.received(expiration=expiration, delay=10)
+                for event in offers:
+                    offer = event.payload
+                    if isinstance(offer, Journey):
+                        self.journey = offer
+                    assert isinstance(event.sender, Driver)
+                    try:
+                        answer = await event.sender.ask(True, sender=self, timeout=60, delay=5)
+                        if answer:
+                            accepted = offer
+                            self.journey = offer
+                            break
+                    except events.TimedOut:
+                        pass
+                if accepted:
+                    for event in offers:
+                        if event.payload != accepted:
+                            event.sender.tell(False, timeout=60, delay=5)
+
             except events.TimedOut:
                 self.info(f"Still no response. Waiting at: { self.pos }")
-                self.model.broadcast(
+                self.broadcast(
-                    journey, ttl=timeout, sender=self, agent_class=Driver
+                    journey, ttl=timeout, agent_class=Driver
                 )
                 expiration = self.now + timeout
         self.info(f"Got a response! Waiting for driver")

examples/newsspread/newsspread_sim.py

@@ -1,4 +1,4 @@
-from soil.agents import FSM, NetworkAgent, state, default_state, prob
+from soil.agents import FSM, NetworkAgent, state, default_state
 from soil.parameters import *
 import logging
 

examples/rabbits/README.md

@@ -1,7 +1,7 @@
 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.
+- `improved`. Using more advanced features such as the delays to avoid unnecessary computations (i.e., skip steps).
 
 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`:

examples/rabbits/rabbit_improved_sim.py

@@ -1,22 +1,33 @@
-from soil import FSM, state, default_state, BaseAgent, NetworkAgent, Environment, Simulation
+from soil import Evented, FSM, state, default_state, BaseAgent, NetworkAgent, Environment, parameters, report, TimedOut
-from enum import Enum
-from collections import Counter
-import logging
 import math
 
-from rabbits_basic_sim import RabbitEnv
 
+class RabbitsImprovedEnv(Environment):
+    prob_death: parameters.probability = 1e-3
 
-class RabbitsImprovedEnv(RabbitEnv):
     def init(self):
-        """Initialize the environment with the new versions of the agents"""
         a1 = self.add_node(Male)
         a2 = self.add_node(Female)
         a1.add_edge(a2)
         self.add_agent(RandomAccident)
 
+    @report
+    @property
+    def num_rabbits(self):
+        return self.count_agents(agent_class=Rabbit)
 
-class Rabbit(FSM, NetworkAgent):
+    @report
+    @property
+    def num_males(self):
+        return self.count_agents(agent_class=Male)
+
+    @report
+    @property
+    def num_females(self):
+        return self.count_agents(agent_class=Female)
+
+
+class Rabbit(Evented, FSM, NetworkAgent):
 
     sexual_maturity = 30
     life_expectancy = 300
@@ -31,42 +42,40 @@ class Rabbit(FSM, NetworkAgent):
     @default_state
     @state
     def newborn(self):
-        self.info("I am a newborn.")
+        self.debug("I am a newborn.")
         self.birth = self.now
         self.offspring = 0
-        return self.youngling.delay(self.sexual_maturity - self.age)
+        return self.youngling
 
     @state
-    def youngling(self):
+    async def youngling(self):
-        if self.age >= self.sexual_maturity:
+        self.debug("I am a youngling.")
-            self.info(f"I am fertile! My age is {self.age}")
+        await self.delay(self.sexual_maturity - self.age)
-            return self.fertile
+        assert self.age >= self.sexual_maturity
+        self.debug(f"I am fertile! My age is {self.age}")
+        return self.fertile
 
     @state
     def fertile(self):
         raise Exception("Each subclass should define its fertile state")
 
-    @state
-    def dead(self):
-        self.die()
-
 
 class Male(Rabbit):
     max_females = 5
-    mating_prob = 0.001
+    mating_prob = 0.005
 
     @state
     def fertile(self):
         if self.age > self.life_expectancy:
-            return self.dead
+            return self.die()
 
         # 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)
+            self.debug(f"FOUND A FEMALE: {repr(f)}. Mating with prob {self.mating_prob}")
             if self.prob(self["mating_prob"]):
-                f.impregnate(self)
+                f.tell(self.unique_id, sender=self, timeout=1)
                 break  # Do not try to impregnate other females
 
 
@@ -75,78 +84,91 @@ class Female(Rabbit):
     conception = None
 
     @state
-    def fertile(self):
+    async def fertile(self):
         # Just wait for a Male
-        if self.age > self.life_expectancy:
+        try:
-            return self.dead
+            timeout = self.life_expectancy - self.age
-        if self.conception is not None:
+            while timeout > 0:
-            return self.pregnant
+                mates = await self.received(timeout=timeout)
-
+                # assert self.age <= self.life_expectancy
-    @property
+                for mate in mates:
-    def pregnancy(self):
+                    try:
-        if self.conception is None:
+                        male = self.model.agents[mate.payload]
-            return None
+                    except ValueError:
-        return self.now - self.conception
+                        continue
-
+                    self.debug(f"impregnated by {repr(male)}")
-    def impregnate(self, male):
+                    self.mate = male
-        self.info(f"impregnated by {repr(male)}")
+                    self.number_of_babies = int(8 + 4 * self.random.random())
-        self.mate = male
+                    self.conception = self.now
-        self.conception = self.now
+                    return self.pregnant
-        self.number_of_babies = int(8 + 4 * self.random.random())
+        except TimedOut:
+            pass
+        return self.die()
 
     @state
-    def pregnant(self):
+    async def pregnant(self):
         self.debug("I am pregnant")
+        # assert self.mate is not None
+
+        when = min(self.gestation, self.life_expectancy - self.age)
+        if when < 0:
+            return self.die()
+        await self.delay(when)
 
         if self.age > self.life_expectancy:
-            self.info("Dying before giving birth")
+            self.debug("Dying before giving birth")
             return self.die()
 
-        if self.pregnancy >= self.gestation:
+        # assert self.now - self.conception >= self.gestation
-            self.info("Having {} babies".format(self.number_of_babies))
+        if not self.alive:
-            for i in range(self.number_of_babies):
+            return self.die()
-                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.debug("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")
+
+            self.offspring += 1
+        self.mate = None
+        self.conception = None
+        return self.fertile
 
     def die(self):
-        if self.pregnancy is not None:
+        if self.conception is not None:
-            self.info("A mother has died carrying a baby!!")
+            self.debug("A mother has died carrying a baby!!")
         return super().die()
 
 
 class RandomAccident(BaseAgent):
+    # Default value, but the value from the environment takes precedence
+    prob_death = 1e-3
+
     def step(self):
-        rabbits_alive = self.model.G.number_of_nodes()
 
-        if not rabbits_alive:
+        alive = self.get_agents(agent_class=Rabbit, alive=True)
-            return self.die()
 
-        prob_death = self.model.get("prob_death", 1e-100) * math.floor(
+        if not alive:
-            math.log10(max(1, rabbits_alive))
+            return self.die("No more rabbits to kill")
-        )
+
+        num_alive = len(alive)
+        prob_death = min(1, self.prob_death * num_alive/10)
         self.debug("Killing some rabbits with prob={}!".format(prob_death))
-        for i in self.iter_agents(agent_class=Rabbit):
+        
+        for i in alive:
             if i.state_id == i.dead.id:
                 continue
             if self.prob(prob_death):
-                self.info("I killed a rabbit: {}".format(i.id))
+                self.debug("I killed a rabbit: {}".format(i.unique_id))
-                rabbits_alive -= 1
+                num_alive -= 1
-                i.die()
+                self.model.remove_agent(i)
-        self.debug("Rabbits alive: {}".format(rabbits_alive))
+        self.debug("Rabbits alive: {}".format(num_alive))
 
 
-sim = Simulation(model=RabbitsImprovedEnv, max_time=100, seed="MySeed", iterations=1)
+RabbitsImprovedEnv.run(max_time=1000, seed="MySeed", iterations=1)
-
-if __name__ == "__main__":
-    sim.run()

examples/rabbits/rabbits_basic_sim.py

@@ -1,11 +1,9 @@
-from soil import FSM, state, default_state, BaseAgent, NetworkAgent, Environment, Simulation, report, parameters as params
+from soil import FSM, state, default_state, BaseAgent, NetworkAgent, Environment, report, parameters as params
-from collections import Counter
-import logging
 import math
 
 
 class RabbitEnv(Environment):
-    prob_death: params.probability = 1e-100
+    prob_death: params.probability = 1e-3
 
     def init(self):
         a1 = self.add_node(Male)
@@ -37,7 +35,7 @@ class Rabbit(NetworkAgent, FSM):
     @default_state
     @state
     def newborn(self):
-        self.info("I am a newborn.")
+        self.debug("I am a newborn.")
         self.age = 0
         self.offspring = 0
         return self.youngling
@@ -46,7 +44,7 @@ class Rabbit(NetworkAgent, FSM):
     def youngling(self):
         self.age += 1
         if self.age >= self.sexual_maturity:
-            self.info(f"I am fertile! My age is {self.age}")
+            self.debug(f"I am fertile! My age is {self.age}")
             return self.fertile
 
     @state
@@ -60,7 +58,7 @@ class Rabbit(NetworkAgent, FSM):
 
 class Male(Rabbit):
     max_females = 5
-    mating_prob = 0.001
+    mating_prob = 0.005
 
     @state
     def fertile(self):
@@ -70,9 +68,8 @@ class Male(Rabbit):
             return self.dead
 
         # Males try to mate
-        for f in self.model.agents(
+        for f in self.model.agents.filter(
-            agent_class=Female, state_id=Female.fertile.id, limit=self.max_females
+            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)
@@ -93,14 +90,14 @@ class Female(Rabbit):
             return self.pregnant
 
     def impregnate(self, male):
-        self.info(f"impregnated by {repr(male)}")
+        self.debug(f"impregnated by {repr(male)}")
         self.mate = male
         self.pregnancy = 0
         self.number_of_babies = int(8 + 4 * self.random.random())
 
     @state
     def pregnant(self):
-        self.info("I am pregnant")
+        self.debug("I am pregnant")
         self.age += 1
 
         if self.age >= self.life_expectancy:
@@ -110,7 +107,7 @@ class Female(Rabbit):
             self.pregnancy += 1
             return
 
-        self.info("Having {} babies".format(self.number_of_babies))
+        self.debug("Having {} babies".format(self.number_of_babies))
         for i in range(self.number_of_babies):
             state = {}
             agent_class = self.random.choice([Male, Female])
@@ -129,33 +126,32 @@ class Female(Rabbit):
 
     def die(self):
         if "pregnancy" in self and self["pregnancy"] > -1:
-            self.info("A mother has died carrying a baby!!")
+            self.debug("A mother has died carrying a baby!!")
         return super().die()
 
 
 class RandomAccident(BaseAgent):
+    prob_death = None
     def step(self):
-        rabbits_alive = self.model.G.number_of_nodes()
+        alive = self.get_agents(agent_class=Rabbit, alive=True)
 
-        if not rabbits_alive:
+        if not alive:
-            return self.die()
+            return self.die("No more rabbits to kill")
 
-        prob_death = self.model.prob_death * math.floor(
+        num_alive = len(alive)
-            math.log10(max(1, rabbits_alive))
+        prob_death = min(1, self.prob_death * num_alive/10)
-        )
         self.debug("Killing some rabbits with prob={}!".format(prob_death))
-        for i in self.get_agents(agent_class=Rabbit):
+
+        for i in alive:
             if i.state_id == i.dead.id:
                 continue
             if self.prob(prob_death):
-                self.info("I killed a rabbit: {}".format(i.id))
+                self.debug("I killed a rabbit: {}".format(i.unique_id))
-                rabbits_alive -= 1
+                num_alive -= 1
-                i.die()
+                self.model.remove_agent(i)
-        self.debug("Rabbits alive: {}".format(rabbits_alive))
+                i.alive = False
+                i.killed = True
+        self.debug("Rabbits alive: {}".format(num_alive))
 
 
-
+RabbitEnv.run(max_time=1000, seed="MySeed", iterations=1)
-sim = Simulation(model=RabbitEnv, max_time=100, seed="MySeed", iterations=1)
-
-if __name__ == "__main__":
-    sim.run()

examples/terrorism/TerroristNetworkModel_sim.py

@@ -1,5 +1,5 @@
 import networkx as nx
-from soil.agents import NetworkAgent, FSM, custom, state, default_state
+from soil.agents import FSM, state, default_state
 from soil.agents.geo import Geo
 from soil import Environment, Simulation
 from soil.parameters import *

requirements.txt

@@ -6,7 +6,6 @@ pandas>=1
 SALib>=1.3
 Jinja2
 Mesa>=1.2
-pydantic>=1.9
 sqlalchemy>=1.4
 typing-extensions>=4.4
 annotated-types>=0.4

soil/VERSION

@@ -1 +1 @@
-1.0.0rc3
+1.0.0rc10

soil/__init__.py

@@ -19,7 +19,7 @@ from pathlib import Path
 from .agents import *
 from . import agents
 from .simulation import *
-from .environment import Environment, EventedEnvironment
+from .environment import Environment
 from .datacollection import SoilCollector
 from . import serialization
 from .utils import logger
@@ -117,13 +117,13 @@ def main(
     )
     parser.add_argument(
         "--max_time",
-        default="-1",
+        default="",
         help="Set maximum time for the simulation to run. ",
     )
 
     parser.add_argument(
         "--max_steps",
-        default="-1",
+        default="",
         help="Set maximum number of steps for the simulation to run.",
     )
 
@@ -249,14 +249,16 @@ def main(
             if args.only_convert:
                 print(sim.to_yaml())
                 continue
-            max_time = float(args.max_time) if args.max_time != "-1" else None
+            d = {}
-            max_steps = float(args.max_steps) if args.max_steps != "-1" else None
+            if args.max_time:
-            res.append(sim.run(max_time=max_time, max_steps=max_steps))
+                d["max_time"] = float(args.max_time) 
+            if args.max_steps:
+                d["max_steps"] = int(args.max_steps)
+            res.append(sim.run(**d))
 
     except Exception as ex:
         if args.pdb:
             from .debugging import post_mortem
-
             print(traceback.format_exc())
             post_mortem()
         else:

soil/agents/__init__.py

@@ -1,107 +1,23 @@
 from __future__ import annotations
 
 import logging
-from collections import OrderedDict, defaultdict
+from collections.abc import MutableMapping
-from collections.abc import MutableMapping, Mapping, Set
+from copy import deepcopy
-from abc import ABCMeta
-from copy import deepcopy, copy
-from functools import partial, wraps
-from itertools import islice, chain
 import inspect
-import types
 import textwrap
-import networkx as nx
 import warnings
 import sys
 
-from typing import Any
+from mesa import Agent as MesaAgent
 
-from mesa import Agent as MesaAgent, Model
+from .. import utils, time
-from typing import Dict, List
 
-from .. import serialization, network, utils, time, config
+from .meta import MetaAgent
 
 
 IGNORED_FIELDS = ("model", "logger")
 
 
-def decorate_generator_step(func, name):
-    @wraps(func)
-    def decorated(self):
-        while True:
-            if self._coroutine is None:
-                self._coroutine = func(self)
-            try:
-                if self._last_except:
-                    val = self._coroutine.throw(self._last_except)
-                else:
-                    val = self._coroutine.send(self._last_return)
-            except StopIteration as ex:
-                self._coroutine = None
-                val = ex.value
-            finally:
-                self._last_return = None
-                self._last_except = None
-            return float(val) if val is not None else val
-    return decorated
-
-
-def decorate_normal_func(func, name):
-    @wraps(func)
-    def decorated(self):
-        val = func(self)
-        return float(val) if val is not None else val
-    return decorated
-
-
-class MetaAgent(ABCMeta):
-    def __new__(mcls, name, bases, namespace):
-        defaults = {}
-
-        # Re-use defaults from inherited classes
-        for i in bases:
-            if isinstance(i, MetaAgent):
-                defaults.update(i._defaults)
-
-        new_nmspc = {
-            "_defaults": defaults,
-        }
-
-        for attr, func in namespace.items():
-            if attr == "step":
-                if inspect.isgeneratorfunction(func) or inspect.iscoroutinefunction(func):
-                    func = decorate_generator_step(func, attr)
-                    new_nmspc.update({
-                        "_last_return": None,
-                        "_last_except": None,
-                        "_coroutine": None,
-                    })
-                elif inspect.isasyncgenfunction(func):
-                    raise ValueError("Illegal step function: {}. It probably mixes both async/await and yield".format(func))
-                elif inspect.isfunction(func):
-                    func = decorate_normal_func(func, attr)
-                else:
-                    raise ValueError("Illegal step function: {}".format(func))
-                new_nmspc[attr] = func
-            elif (
-                isinstance(func, types.FunctionType)
-                or isinstance(func, property)
-                or isinstance(func, classmethod)
-                or attr[0] == "_"
-            ):
-                new_nmspc[attr] = func
-            elif attr == "defaults":
-                defaults.update(func)
-            elif inspect.isfunction(func):
-                new_nmspc[attr] = func
-            else:
-                defaults[attr] = copy(func)
-
-
-        # Add attributes for their use in the decorated functions
-        return super().__new__(mcls, name, bases, new_nmspc)
-
-
 class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
     """
     A special type of Mesa Agent that:
@@ -114,8 +30,11 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
     Any attribute that is not preceded by an underscore (`_`) will also be added to its state.
     """
 
-    def __init__(self, unique_id, model, name=None, init=True, **kwargs):
+    def __init__(self, unique_id=None, model=None, name=None, init=True, **kwargs):
-        assert isinstance(unique_id, int)
+        # Ideally, model should be the first argument, but Mesa's Agent class has unique_id first
+        assert not (model is None), "Must provide a model"
+        if unique_id is None:
+            unique_id = model.next_id()
         super().__init__(unique_id=unique_id, model=model)
 
         self.name = (
@@ -154,11 +73,11 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
         return hash(self.unique_id)
 
     def prob(self, probability):
-        return prob(probability, self.model.random)
+        return utils.prob(probability, self.model.random)
 
     @classmethod
     def w(cls, **kwargs):
-        return custom(cls, **kwargs)
+        return utils.custom(cls, **kwargs)
 
     # TODO: refactor to clean up mesa compatibility
     @property
@@ -168,20 +87,12 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
         print(msg, file=sys.stderr)
         return self.unique_id
 
-    @classmethod
+    @property
-    def from_dict(cls, model, attrs, warn_extra=True):
+    def env(self):
-        ignored = {}
+        msg = "This attribute is deprecated. Use `model` instead"
-        args = {}
+        warnings.warn(msg, DeprecationWarning)
-        for k, v in attrs.items():
+        print(msg, file=sys.stderr)
-            if k in inspect.signature(cls).parameters:
+        return self.model
-                args[k] = v
-            else:
-                ignored[k] = v
-        if ignored and warn_extra:
-            utils.logger.info(
-                f"Ignoring the following arguments for agent class { agent_class.__name__ }: { ignored }"
-            )
-        return cls(model=model, **args)
 
     def __getitem__(self, key):
         try:
@@ -237,10 +148,6 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
         else:
             self.debug(f"agent dying")
         self.alive = False
-        try:
-            self.model.schedule.remove(self)
-        except KeyError:
-            pass
         return time.Delay(time.INFINITY)
 
     def step(self):
@@ -294,407 +201,31 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
 
     def __repr__(self):
         return f"{self.__class__.__name__}({self.unique_id})"
-    
+
     def at(self, at):
         return time.Delay(float(at) - self.now)
-    
+
     def delay(self, delay=1):
         return time.Delay(delay)
 
 
-def prob(prob, random):
-    """
-    A true/False uniform distribution with a given probability.
-    To be used like this:
-
-    .. code-block:: python
-
-          if prob(0.3):
-              do_something()
-
-    """
-    r = random.random()
-    return r < prob
-
-
-def calculate_distribution(network_agents=None, agent_class=None):
-    """
-    Calculate the threshold values (thresholds for a uniform distribution)
-    of an agent distribution given the weights of each agent type.
-
-    The input has this form: ::
-
-            [
-            {'agent_class': 'agent_class_1',
-                'weight': 0.2,
-                'state': {
-                    'id': 0
-                }
-            },
-            {'agent_class': 'agent_class_2',
-                'weight': 0.8,
-                'state': {
-                    'id': 1
-                }
-            }
-            ]
-
-    In this example, 20% of the nodes will be marked as type
-    'agent_class_1'.
-    """
-    if network_agents:
-        network_agents = [
-            deepcopy(agent) for agent in network_agents if not hasattr(agent, "id")
-        ]
-    elif agent_class:
-        network_agents = [{"agent_class": agent_class}]
-    else:
-        raise ValueError("Specify a distribution or a default agent type")
-
-    # Fix missing weights and incompatible types
-    for x in network_agents:
-        x["weight"] = float(x.get("weight", 1))
-
-    # Calculate the thresholds
-    total = sum(x["weight"] for x in network_agents)
-    acc = 0
-    for v in network_agents:
-        if "ids" in v:
-            continue
-        upper = acc + (v["weight"] / total)
-        v["threshold"] = [acc, upper]
-        acc = upper
-    return network_agents
-
-
-def _serialize_type(agent_class, known_modules=[], **kwargs):
-    if isinstance(agent_class, str):
-        return agent_class
-    known_modules += ["soil.agents"]
-    return serialization.serialize(agent_class, known_modules=known_modules, **kwargs)[
-        1
-    ]  # Get the name of the class
-
-
-def _deserialize_type(agent_class, known_modules=[]):
-    if not isinstance(agent_class, str):
-        return agent_class
-    known = known_modules + ["soil.agents", "soil.agents.custom"]
-    agent_class = serialization.deserializer(agent_class, known_modules=known)
-    return agent_class
-
-
-class AgentView(Mapping, Set):
-    """A lazy-loaded list of agents."""
-
-    __slots__ = ("_agents",)
-
-    def __init__(self, agents):
-        self._agents = agents
-
-    def __getstate__(self):
-        return {"_agents": self._agents}
-
-    def __setstate__(self, state):
-        self._agents = state["_agents"]
-
-    # Mapping methods
-    def __len__(self):
-        return len(self._agents)
-
-    def __iter__(self):
-        yield from self._agents.values()
-
-    def __getitem__(self, agent_id):
-        if isinstance(agent_id, slice):
-            raise ValueError(f"Slicing is not supported")
-        if agent_id in self._agents:
-            return self._agents[agent_id]
-        raise ValueError(f"Agent {agent_id} not found")
-
-    def filter(self, *args, **kwargs):
-        yield from filter_agents(self._agents, *args, **kwargs)
-
-    def one(self, *args, **kwargs):
-        return next(filter_agents(self._agents, *args, **kwargs))
-
-    def __call__(self, *args, **kwargs):
-        return list(self.filter(*args, **kwargs))
-
-    def __contains__(self, agent_id):
-        return agent_id in self._agents
-
-    def __str__(self):
-        return str(list(unique_id for unique_id in self.keys()))
-
-    def __repr__(self):
-        return f"{self.__class__.__name__}({self})"
-
-
-def filter_agents(
-    agents: dict,
-    *id_args,
-    unique_id=None,
-    state_id=None,
-    agent_class=None,
-    ignore=None,
-    state=None,
-    limit=None,
-    **kwargs,
-):
-    """
-    Filter agents given as a dict, by the criteria given as arguments (e.g., certain type or state id).
-    """
-    assert isinstance(agents, dict)
-
-    ids = []
-
-    if unique_id is not None:
-        if isinstance(unique_id, list):
-            ids += unique_id
-        else:
-            ids.append(unique_id)
-
-    if id_args:
-        ids += id_args
-
-    if ids:
-        f = (agents[aid] for aid in ids if aid in agents)
-    else:
-        f = agents.values()
-
-    if state_id is not None and not isinstance(state_id, (tuple, list)):
-        state_id = tuple([state_id])
-
-    if agent_class is not None:
-        agent_class = _deserialize_type(agent_class)
-        try:
-            agent_class = tuple(agent_class)
-        except TypeError:
-            agent_class = tuple([agent_class])
-
-    if ignore:
-        f = filter(lambda x: x not in ignore, f)
-
-    if state_id is not None:
-        f = filter(lambda agent: agent.get("state_id", None) in state_id, f)
-
-    if agent_class is not None:
-        f = filter(lambda agent: isinstance(agent, agent_class), f)
-
-    state = state or dict()
-    state.update(kwargs)
-
-    for k, vs in state.items():
-        if not isinstance(vs, list):
-            vs = [vs]
-        f = filter(lambda agent: any(getattr(agent, k, None) == v for v in vs), f)
-
-    if limit is not None:
-        f = islice(f, limit)
-
-    yield from f
-
-
-def from_config(
-    cfg: config.AgentConfig, random, topology: nx.Graph = None
-) -> List[Dict[str, Any]]:
-    """
-    This function turns an agentconfig into a list of individual "agent specifications", which are just a dictionary
-    with the parameters that the environment will use to construct each agent.
-
-    This function does NOT return a list of agents, mostly because some attributes to the agent are not known at the
-    time of calling this function, such as `unique_id`.
-    """
-    default = cfg or config.AgentConfig()
-    if not isinstance(cfg, config.AgentConfig):
-        cfg = config.AgentConfig(**cfg)
-
-    agents = []
-
-    assigned_total = 0
-    assigned_network = 0
-
-    if cfg.fixed is not None:
-        agents, assigned_total, assigned_network = _from_fixed(
-            cfg.fixed, topology=cfg.topology, default=cfg
-        )
-
-    n = cfg.n
-
-    if cfg.distribution:
-        topo_size = len(topology) if topology else 0
-
-        networked = []
-        total = []
-
-        for d in cfg.distribution:
-            if d.strategy == config.Strategy.topology:
-                topo = d.topology if ("topology" in d.__fields_set__) else cfg.topology
-                if not topo:
-                    raise ValueError(
-                        'The "topology" strategy only works if the topology parameter is set to True'
-                    )
-                if not topo_size:
-                    raise ValueError(
-                        f"Topology does not have enough free nodes to assign one to the agent"
-                    )
-
-                networked.append(d)
-
-            if d.strategy == config.Strategy.total:
-                if not cfg.n:
-                    raise ValueError(
-                        'Cannot use the "total" strategy without providing the total number of agents'
-                    )
-                total.append(d)
-
-        if networked:
-            new_agents = _from_distro(
-                networked,
-                n=topo_size - assigned_network,
-                topology=topo,
-                default=cfg,
-                random=random,
-            )
-            assigned_total += len(new_agents)
-            assigned_network += len(new_agents)
-            agents += new_agents
-
-        if total:
-            remaining = n - assigned_total
-            agents += _from_distro(total, n=remaining, default=cfg, random=random)
-
-        if assigned_network < topo_size:
-            utils.logger.warn(
-                f"The total number of agents does not match the total number of nodes in "
-                "every topology. This may be due to a definition error: assigned: "
-                f"{ assigned } total size: { topo_size }"
-            )
-
-    return agents
-
-
-def _from_fixed(
-    lst: List[config.FixedAgentConfig],
-    topology: bool,
-    default: config.SingleAgentConfig,
-) -> List[Dict[str, Any]]:
-    agents = []
-
-    counts_total = 0
-    counts_network = 0
-
-    for fixed in lst:
-        agent = {}
-        if default:
-            agent = default.state.copy()
-        agent.update(fixed.state)
-        cls = serialization.deserialize(
-            fixed.agent_class or (default and default.agent_class)
-        )
-        agent["agent_class"] = cls
-        topo = (
-            fixed.topology
-            if ("topology" in fixed.__fields_set__)
-            else topology or default.topology
-        )
-
-        if topo:
-            agent["topology"] = True
-            counts_network += 1
-        if not fixed.hidden:
-            counts_total += 1
-        agents.append(agent)
-
-    return agents, counts_total, counts_network
-
-
-def _from_distro(
-    distro: List[config.AgentDistro],
-    n: int,
-    default: config.SingleAgentConfig,
-    random,
-    topology: str = None
-) -> List[Dict[str, Any]]:
-
-    agents = []
-
-    if n is None:
-        if any(lambda dist: dist.n is None, distro):
-            raise ValueError(
-                "You must provide a total number of agents, or the number of each type"
-            )
-        n = sum(dist.n for dist in distro)
-
-    weights = list(dist.weight if dist.weight is not None else 1 for dist in distro)
-    minw = min(weights)
-    norm = list(weight / minw for weight in weights)
-    total = sum(norm)
-    chunk = n // total
-
-    # random.choices would be enough to get a weighted distribution. But it can vary a lot for smaller k
-    # So instead we calculate our own distribution to make sure the actual ratios are close to what we would expect
-
-    # Calculate how many times each has to appear
-    indices = list(
-        chain.from_iterable([idx] * int(n * chunk) for (idx, n) in enumerate(norm))
-    )
-
-    # Complete with random agents following the original weight distribution
-    if len(indices) < n:
-        indices += random.choices(
-            list(range(len(distro))),
-            weights=[d.weight for d in distro],
-            k=n - len(indices),
-        )
-
-    # Deserialize classes for efficiency
-    classes = list(
-        serialization.deserialize(i.agent_class or default.agent_class) for i in distro
-    )
-
-    # Add them in random order
-    random.shuffle(indices)
-
-    for idx in indices:
-        d = distro[idx]
-        agent = d.state.copy()
-        cls = classes[idx]
-        agent["agent_class"] = cls
-        if default:
-            agent.update(default.state)
-        topology = (
-            d.topology
-            if ("topology" in d.__fields_set__)
-            else topology or default.topology
-        )
-        if topology:
-            agent["topology"] = topology
-        agents.append(agent)
-
-    return agents
-
-
 from .network_agents import *
 from .fsm import *
 from .evented import *
-from typing import Optional
+from .view import *
 
 
-class Agent(NetworkAgent, FSM, EventedAgent):
+class Noop(EventedAgent, BaseAgent):
-    """Default agent class, has both network and event capabilities"""
+    def step(self):
+        return
 
 
-from ..environment import NetworkEnvironment
+class Agent(FSM, EventedAgent, NetworkAgent):
+    """Default agent class, has network, FSM and event capabilities"""
 
 
+# Additional types of agents
 from .BassModel import *
 from .IndependentCascadeModel import *
 from .SISaModel import *
 from .CounterModel import *
-
-
-def custom(cls, **kwargs):
-    """Create a new class from a template class and keyword arguments"""
-    return type(cls.__name__, (cls,), kwargs)

soil/agents/evented.py

@@ -1,58 +1,34 @@
 from . import BaseAgent
 from ..events import Message, Tell, Ask, TimedOut
+from .. import environment, events
 from functools import partial
 from collections import deque
 from types import coroutine
 
+# from soilent import Scheduler
+
 
 class EventedAgent(BaseAgent):
+    # scheduler_class = Scheduler
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self._inbox = deque()
+        assert isinstance(self.model, environment.EventedEnvironment), "EventedAgent requires an EventedEnvironment"
-        self._processed = 0
+        self.model.register(self)
 
-    def on_receive(self, *args, **kwargs):
+    def received(self, **kwargs):
-        pass
+        return self.model.received(agent=self, **kwargs)
 
-    @coroutine
+    def tell(self, msg, **kwargs):
-    def received(self, expiration=None, timeout=60, delay=1, process=True):
+        return self.model.tell(msg, recipient=self, **kwargs)
-        if not expiration:
-            expiration = self.now + timeout
-        while self.now < expiration:
-            if self._inbox:
-                msgs = self._inbox
-                if process:
-                    self.process_messages()
-                return msgs
-            yield self.delay(delay)
-        raise TimedOut("No message received")
 
-    def tell(self, msg, sender=None):
+    def broadcast(self, msg, **kwargs):
-        self._inbox.append(Tell(timestamp=self.now, payload=msg, sender=sender))
+        return self.model.broadcast(msg, sender=self, **kwargs)
 
-    @coroutine
+    def ask(self, msg, **kwargs):
-    def ask(self, msg, expiration=None, timeout=None, delay=1):
+        return self.model.ask(msg, recipient=self, **kwargs)
-        ask = Ask(timestamp=self.now, payload=msg, sender=self)
-        self._inbox.append(ask)
-        expiration = float("inf") if timeout is None else self.now + timeout
-        while self.now < expiration:
-            if ask.reply:
-                return ask.reply
-            yield self.delay(delay)
-        raise TimedOut("No reply received")
 
     def process_messages(self):
-        valid = list()
+        return self.model.process_messages(self.model.inbox_for(self))
-        for msg in self._inbox:
-            self._processed += 1
-            if msg.expired(self.now):
-                continue
-            valid.append(msg)
-            reply = self.on_receive(msg.payload, sender=msg.sender)
-            if isinstance(msg, Ask):
-                msg.reply = reply
-        self._inbox.clear()
-        return valid
 
 
 Evented = EventedAgent

soil/agents/fsm.py

@@ -6,39 +6,38 @@ import inspect
 
 
 class State:
-    __slots__ = ("awaitable", "f", "generator", "name", "default")
+    __slots__ = ("awaitable", "f", "attribute", "generator", "name", "default")
 
     def __init__(self, f, name, default, generator, awaitable):
         self.f = f
         self.name = name
+        self.attribute = "_{}".format(name)
         self.generator = generator
         self.awaitable = awaitable
         self.default = default
 
-    @coroutine
-    def step(self, obj):
-        if self.generator or self.awaitable:
-            f = self.f
-            next_state = yield from f(obj)
-            return next_state
-
-        else:
-            return self.f(obj)
-
     @property
     def id(self):
         return self.name
-
+    
-    def __call__(self, *args, **kwargs):
+    def __get__(self, obj, owner=None):
-        raise Exception("States should not be called directly")
+        if obj is None:
-
+            return self
-class UnboundState(State):
+        try:
+            return getattr(obj, self.attribute)
+        except AttributeError:
+            b = self.bind(obj)
+            setattr(obj, self.attribute, b)
+            return b
 
     def bind(self, obj):
         bs = BoundState(self.f, self.name, self.default, self.generator, self.awaitable, obj=obj)
         setattr(obj, self.name, bs)
         return bs
 
+    def __call__(self, *args, **kwargs):
+        raise Exception("States should not be called directly")
+
 
 class BoundState(State):
     __slots__ = ("obj", )
@@ -46,10 +45,21 @@ class BoundState(State):
     def __init__(self, *args, obj):
         super().__init__(*args)
         self.obj = obj
-    
+
+    @coroutine
+    def __call__(self):
+        if self.generator or self.awaitable:
+            f = self.f
+            next_state = yield from f(self.obj)
+            return next_state
+
+        else:
+            return self.f(self.obj)
+
+
     def delay(self, delta=0):
         return self, self.obj.delay(delta)
-    
+
     def at(self, when):
         return self, self.obj.at(when)
 
@@ -63,7 +73,7 @@ def state(name=None, default=False):
         name = name or func.__name__
         generator = inspect.isgeneratorfunction(func)
         awaitable = inspect.iscoroutinefunction(func) or inspect.isasyncgen(func)
-        return UnboundState(func, name, default, generator, awaitable)
+        return State(func, name, default, generator, awaitable)
 
     if callable(name):
         return decorator(name)
@@ -113,15 +123,24 @@ class MetaFSM(MetaAgent):
 class FSM(BaseAgent, metaclass=MetaFSM):
     def __init__(self, init=True, state_id=None, **kwargs):
         super().__init__(**kwargs, init=False)
+        bound_states = {}
+        for (k, v) in list(self._states.items()):
+            if isinstance(v, State):
+                v = v.bind(self)
+            bound_states[k] = v
+            setattr(self, k, v)
+
+        self._states = bound_states
+
         if state_id is not None:
             self._set_state(state_id)
+        else:
+            self._set_state(self._state)
         # If more than "dead" state is defined, but no default state
         if len(self._states) > 1 and not self._state:
             raise ValueError(
                 f"No default state specified for {type(self)}({self.unique_id})"
             )
-        for (k, v) in self._states.items():
-            setattr(self, k, v.bind(self))
 
         if init:
             self.init()
@@ -139,12 +158,20 @@ class FSM(BaseAgent, metaclass=MetaFSM):
             raise ValueError("Cannot change state after init")
         self._set_state(value)
 
+    @coroutine
     def step(self):
-        self._check_alive()
+        if self._state is None:
-        next_state = yield from self._state.step(self)
+            if len(self._states) == 1:
+                raise Exception("Agent class has no valid states: {}. Make sure to define states or define a custom step function".format(self.__class__.__name__))
+            else:
+                raise Exception("Invalid state (None) for agent {}".format(self))
+
+        next_state = yield from self._state()
 
         try:
             next_state, when = next_state
+            self._set_state(next_state)
+            return when
         except (TypeError, ValueError) as ex:
             try:
                 self._set_state(next_state)
@@ -152,9 +179,6 @@ class FSM(BaseAgent, metaclass=MetaFSM):
             except ValueError:
                 return next_state
 
-        self._set_state(next_state)
-        return when
-
     def _set_state(self, state):
         if state is None:
             return
@@ -162,7 +186,9 @@ class FSM(BaseAgent, metaclass=MetaFSM):
             if state not in self._states:
                 raise ValueError("{} is not a valid state".format(state))
             state = self._states[state]
-        if not isinstance(state, State):
+        if isinstance(state, State):
+            state = state.bind(self)
+        elif not isinstance(state, BoundState):
             raise ValueError("{} is not a valid state".format(state))
         self._state = state
 
@@ -172,4 +198,4 @@ class FSM(BaseAgent, metaclass=MetaFSM):
 
     @state
     def dead(self):
-        return time.INFINITY
+        return time.INFINITY

soil/agents/meta.py

@@ -0,0 +1,64 @@
+from abc import ABCMeta
+from copy import copy
+from functools import wraps
+from .. import time
+from ..decorators import syncify, while_alive
+
+import types
+import inspect
+
+
+class MetaAnnotations(ABCMeta):
+    """This metaclass sets default values for agents based on class attributes"""
+    def __new__(mcls, name, bases, namespace):
+        defaults = {}
+
+        # Re-use defaults from inherited classes
+        for i in bases:
+            if isinstance(i, MetaAgent):
+                defaults.update(i._defaults)
+
+        new_nmspc = {
+            "_defaults": defaults,
+        }
+
+        for attr, func in namespace.items():
+            if (
+                isinstance(func, types.FunctionType)
+                or isinstance(func, property)
+                or isinstance(func, classmethod)
+                or attr[0] == "_"
+            ):
+                new_nmspc[attr] = func
+            elif attr == "defaults":
+                defaults.update(func)
+            elif inspect.isfunction(func):
+                new_nmspc[attr] = func
+            else:
+                defaults[attr] = copy(func)
+
+        return super().__new__(mcls, name, bases, new_nmspc)
+
+
+class AutoAgent(ABCMeta):
+    def __new__(mcls, name, bases, namespace):
+        if "step" in namespace:
+            func = namespace["step"]
+            namespace["_orig_step"] = func
+            if inspect.isfunction(func):
+                if inspect.isgeneratorfunction(func) or inspect.iscoroutinefunction(func):
+                    func = syncify(func, method=True)
+                namespace["step"] = while_alive(func)
+            elif inspect.isasyncgenfunction(func):
+                raise ValueError("Illegal step function: {}. It probably mixes both async/await and yield".format(func))
+            else:
+                raise ValueError("Illegal step function: {}".format(func))
+
+        # Add attributes for their use in the decorated functions
+        return super().__new__(mcls, name, bases, namespace)
+
+
+class MetaAgent(AutoAgent, MetaAnnotations):
+    """This metaclass sets default values for agents based on class attributes"""
+    pass
+

soil/agents/network_agents.py

@@ -1,9 +1,11 @@
 from . import BaseAgent
+from .. import environment
 
 
 class NetworkAgent(BaseAgent):
     def __init__(self, *args, topology=None, init=True, node_id=None, **kwargs):
         super().__init__(*args, init=False, **kwargs)
+        assert isinstance(self.model, environment.NetworkEnvironment), "NetworkAgent requires a NetworkEnvironment"
 
         self.G = topology or self.model.G
         assert self.G is not None, "Network agents should have a network"
@@ -16,7 +18,7 @@ class NetworkAgent(BaseAgent):
             else:
                 node_id = len(self.G)
                 self.info(f"All nodes ({len(self.G)}) have an agent assigned, adding a new node to the graph for agent {self.unique_id}")
-                self.G.add_node(node_id)
+                self.G.add_node(node_id, find_unassigned=True)
         assert node_id is not None
         self.G.nodes[node_id]["agent"] = self
         self.node_id = node_id

soil/agents/view.py

@@ -0,0 +1,139 @@
+from collections.abc import Mapping, Set
+from itertools import islice
+from mesa import Agent
+
+
+class AgentView(Mapping, Set):
+    """A lazy-loaded list of agents."""
+
+    __slots__ = ("_agents", "agents_by_type")
+
+    def __init__(self, agents, agents_by_type):
+        self._agents = agents
+        self.agents_by_type = agents_by_type
+
+    def __getstate__(self):
+        return {"_agents": self._agents}
+
+    def __setstate__(self, state):
+        self._agents = state["_agents"]
+
+    # Mapping methods
+    def __len__(self):
+        return len(self._agents)
+
+    def __iter__(self):
+        yield from self._agents.values()
+
+    def __getitem__(self, agent_id):
+        if isinstance(agent_id, slice):
+            raise ValueError(f"Slicing is not supported")
+        if agent_id in self._agents:
+            return self._agents[agent_id]
+        raise ValueError(f"Agent {agent_id} not found")
+
+    def filter(self, agent_class=None, include_subclasses=True, **kwargs):
+        if agent_class and self.agents_by_type:
+            if not include_subclasses:
+                return filter_agents(self.agents_by_type[agent_class],
+                                    **kwargs)
+            else:
+                d = {}
+                for k, v in self.agents_by_type.items():
+                    if (k == agent_class) or issubclass(k, agent_class):
+                        d.update(v)
+                return filter_agents(d, **kwargs)
+        return filter_agents(self._agents, agent_class=agent_class, **kwargs)
+
+
+    def one(self, *args, **kwargs):
+        try:
+            return next(self.filter(*args, **kwargs))
+        except StopIteration:
+            return None
+
+    def __call__(self, *args, **kwargs):
+        return list(self.filter(*args, **kwargs))
+
+    def __contains__(self, agent_id):
+        if isinstance(agent_id, Agent):
+            agent_id = agent_id.unique_id
+        return agent_id in self._agents
+
+    def __str__(self):
+        return str(list(unique_id for unique_id in self.keys()))
+
+    def __repr__(self):
+        return f"{self.__class__.__name__}({self})"
+
+
+def filter_agents(
+    agents: dict,
+    *id_args,
+    unique_id=None,
+    state_id=None,
+    agent_class=None,
+    ignore=None,
+    state=None,
+    limit=None,
+    **kwargs,
+):
+    """
+    Filter agents given as a dict, by the criteria given as arguments (e.g., certain type or state id).
+    """
+    assert isinstance(agents, dict)
+
+    ids = []
+
+    if unique_id is not None:
+        if isinstance(unique_id, list):
+            ids += unique_id
+        else:
+            ids.append(unique_id)
+
+    if id_args:
+        ids += id_args
+
+    if ids:
+        f = list(agents[aid] for aid in ids if aid in agents)
+    else:
+        f = agents.values()
+
+    if state_id is not None and not isinstance(state_id, (tuple, list)):
+        state_id = tuple([state_id])
+
+    if ignore:
+        f = filter(lambda x: x not in ignore, f)
+
+    if state_id is not None:
+        f = filter(lambda agent: agent.get("state_id", None) in state_id, f)
+
+    if agent_class is not None:
+        f = filter(lambda agent: isinstance(agent, agent_class), f)
+
+    state = state or dict()
+    state.update(kwargs)
+
+    for k, vs in state.items():
+        if not isinstance(vs, list):
+            vs = [vs]
+        f = filter(lambda agent: any(getattr(agent, k, None) == v for v in vs), f)
+
+    if limit is not None:
+        f = islice(f, limit)
+
+    return AgentResult(f)
+
+class AgentResult:
+    def __init__(self, iterator):
+        self.iterator = iterator
+    
+    def limit(self, limit):
+        self.iterator = islice(self.iterator, limit)
+        return self
+
+    def __iter__(self):
+        return iter(self.iterator)
+
+    def __next__(self):
+        return next(self.iterator)

soil/analysis.py

@@ -19,7 +19,8 @@ def plot(env, agent_df=None, model_df=None, steps=False, ignore=["agent_count",
         try:
             agent_df = env.agent_df()
         except UserWarning:
-            print("No agent dataframe provided and no agent reporters found. Skipping agent plot.", file=sys.stderr)
+            print("No agent dataframe provided and no agent reporters found. "
+                  "Skipping agent plot.", file=sys.stderr)
             return
     if not agent_df.empty:
         agent_df.unstack().apply(lambda x: x.value_counts(),
@@ -43,15 +44,10 @@ def read_sql(fpath=None, name=None, include_agents=False):
     with engine.connect() as conn:
         env = pd.read_sql_table("env", con=conn,
                                 index_col="step").reset_index().set_index([
-                                    "simulation_id", "params_id",
+                                    "params_id", "iteration_id", "step"
-                                    "iteration_id", "step"
                                 ])
-        agents = pd.read_sql_table("agents", con=conn, index_col=["simulation_id", "params_id", "iteration_id", "step", "agent_id"])
+        agents = pd.read_sql_table("agents", con=conn, index_col=["params_id", "iteration_id", "step", "agent_id"])
         config = pd.read_sql_table("configuration", con=conn, index_col="simulation_id")
-        parameters = pd.read_sql_table("parameters", con=conn, index_col=["iteration_id", "params_id", "simulation_id"])
+        parameters = pd.read_sql_table("parameters", con=conn, index_col=["simulation_id", "params_id", "iteration_id"])
-        try:
-            parameters = parameters.pivot(columns="key", values="value")
-        except Exception as e:
-            print(f"warning: coult not pivot parameters: {e}")
 
         return Results(config, parameters, env, agents)

soil/decorators.py

@@ -1,6 +1,42 @@
+from functools import wraps
+from .time import INFINITY
+
 def report(f: property):
     if isinstance(f, property):
         setattr(f.fget, "add_to_report", True)
     else:
         setattr(f, "add_to_report", True)
-    return f
+    return f
+
+
+def syncify(func, method=True):
+    _coroutine = None
+
+    @wraps(func)
+    def wrapped(*args, **kwargs):
+        if not method:
+            nonlocal _coroutine
+        else:
+            _coroutine = getattr(args[0], "_coroutine", None)
+        _coroutine = _coroutine or func(*args, **kwargs)
+        try:
+            val = _coroutine.send(None)
+        except StopIteration as ex:
+            _coroutine = None
+            val = ex.value
+        finally:
+            if method:
+                args[0]._coroutine = _coroutine
+        return val
+
+    return wrapped
+
+
+def while_alive(func):
+    @wraps(func)
+    def wrapped(self, *args, **kwargs):
+        if self.alive:
+            return func(self, *args, **kwargs)
+        return INFINITY
+
+    return wrapped

soil/environment.py

@@ -1,20 +1,18 @@
 from __future__ import annotations
 
 import os
-import sqlite3
+import sys
-import math
 import logging
-import inspect
+from datetime import datetime
 
 from typing import Any, Callable, Dict, Optional, Union, List, Type
-from collections import namedtuple
+from types import coroutine
-from time import time as current_time
-from copy import deepcopy
-
 
 import networkx as nx
 
-from mesa import Model, Agent
+
+from mesa import Model
+from time import time as current_time
 
 from . import agents as agentmod, datacollection, utils, time, network, events
 
@@ -36,6 +34,8 @@ class BaseEnvironment(Model):
 
     collector_class = datacollection.SoilCollector
     schedule_class = time.TimedActivation
+    start_time = 0
+    time_format = "%Y-%m-%d %H:%M:%S"
 
     def __new__(cls,
                 *args: Any,
@@ -47,6 +47,7 @@ class BaseEnvironment(Model):
                 tables: Optional[Any] = None,
                 **kwargs: Any) -> Any:
         """Create a new model with a default seed value"""
+        seed = seed or str(current_time())
         self = super().__new__(cls, *args, seed=seed, **kwargs)
         self.dir_path = dir_path or os.getcwd()
         collector_class = collector_class or cls.collector_class
@@ -77,6 +78,8 @@ class BaseEnvironment(Model):
         collector_class: type = datacollection.SoilCollector,
         agent_reporters: Optional[Any] = None,
         model_reporters: Optional[Any] = None,
+        start_time=None,
+        time_format=None,
         tables: Optional[Any] = None,
         init: bool = True,
         **env_params,
@@ -93,12 +96,21 @@ class BaseEnvironment(Model):
             self.logger = logger
         else:
             self.logger = utils.logger.getChild(self.id)
+        if start_time is not None:
+            self.start_time = start_time
+        if time_format is not None:
+            self.time_format = time_format
+
+        if isinstance(self.start_time, str):
+            self.start_time = datetime.strptime(self.start_time, self.time_format)
+        if isinstance(self.start_time, datetime):
+            self.start_time = self.start_time.timestamp()
 
         self.schedule = schedule
         if schedule is None:
             if schedule_class is None:
                 schedule_class = self.schedule_class
-            self.schedule = schedule_class(self)
+            self.schedule = schedule_class(self, time=self.start_time)
 
         for (k, v) in env_params.items():
             self[k] = v
@@ -114,22 +126,23 @@ class BaseEnvironment(Model):
 
     @property
     def agents(self):
-        return agentmod.AgentView(self.schedule._agents)
+        return agentmod.AgentView(self.schedule._agents, getattr(self.schedule, "agents_by_type", None))
 
     def agent(self, *args, **kwargs):
-        return agentmod.AgentView(self.schedule._agents).one(*args, **kwargs)
+        return agentmod.AgentView(self.schedule._agents, self.schedule.agents_by_type).one(*args, **kwargs)
 
     def count_agents(self, *args, **kwargs):
         return sum(1 for i in self.agents(*args, **kwargs))
-    
+
     def agent_df(self, steps=False):
         df = self.datacollector.get_agent_vars_dataframe()
+        df.index.rename(["step", "agent_id"], inplace=True)
         if steps:
-            df.index.rename(["step", "agent_id"], inplace=True)
             return df
+        df = df.reset_index()
         model_df = self.datacollector.get_model_vars_dataframe()
-        df.index = df.index.set_levels(model_df.time, level=0).rename(["time", "agent_id"])
+        df['time'] = df.apply(lambda row: model_df.loc[row.step].time, axis=1)
-        return df
+        return df.groupby(["time", "agent_id"]).last()
 
     def model_df(self, steps=False):
         df = self.datacollector.get_model_vars_dataframe()
@@ -140,7 +153,7 @@ class BaseEnvironment(Model):
 
     @property
     def now(self):
-        if self.schedule:
+        if self.schedule is not None:
             return self.schedule.time
         raise Exception(
             "The environment has not been scheduled, so it has no sense of time"
@@ -164,6 +177,10 @@ class BaseEnvironment(Model):
         self.schedule.add(a)
         return a
 
+    def remove_agent(self, agent):
+        agent.alive = False
+        self.schedule.remove(agent)
+
     def add_agents(self, agent_classes: List[type], k, weights: Optional[List[float]] = None, **kwargs):
         if isinstance(agent_classes, type):
             agent_classes = [agent_classes]
@@ -192,12 +209,15 @@ class BaseEnvironment(Model):
         super().step()
         self.schedule.step()
         self.datacollector.collect(self)
+        if self.now == time.INFINITY:
+            self.running = False
 
         if self.logger.isEnabledFor(logging.DEBUG):
             msg = "Model data:\n"
             max_width = max(len(k) for k in self.datacollector.model_vars.keys())
             for (k, v) in self.datacollector.model_vars.items():
-                msg += f"\t{k:<{max_width}}: {v[-1]:>6}\n"
+                # msg += f"\t{k:<{max_width}}"
+                msg += f"\t{k:<{max_width}}: {v[-1]}\n"
             self.logger.debug(f"--- Steps: {self.schedule.steps:^5} - Time: {self.now:^5} --- " + msg)
 
     def add_model_reporter(self, name, func=None):
@@ -205,11 +225,18 @@ class BaseEnvironment(Model):
             func = name
         self.datacollector._new_model_reporter(name, func)
 
-    def add_agent_reporter(self, name, reporter=None, agent_type=None):
+    def add_agent_reporter(self, name, reporter=None, agent_class=None, *, agent_type=None):
-        if not agent_type and not reporter:
+        if agent_type:
+            print("agent_type is deprecated, use agent_class instead", file=sys.stderr)
+        agent_class = agent_type or agent_class
+        if not reporter and not agent_class:
             reporter = name
-        elif agent_type:
+        if agent_class:
-            reporter = lambda a: reporter(a) if isinstance(a, agent_type) else None
+            if reporter:
+                _orig = reporter
+            else:
+                _orig = lambda a: getattr(a, name)
+            reporter = lambda a: (_orig(a) if isinstance(a, agent_class) else None)
         self.datacollector._new_agent_reporter(name, reporter)
 
     @classmethod
@@ -294,6 +321,11 @@ class NetworkEnvironment(BaseEnvironment):
         self.G.nodes[node_id]["agent"] = a
         return a
 
+    def remove_agent(self, agent, remove_node=True):
+        super().remove_agent(agent)
+        if remove_node and hasattr(agent, "remove_node"):
+            agent.remove_node()
+
     def add_agents(self, *args, k=None, **kwargs):
         if not k and not self.G:
             raise ValueError("Cannot add agents to an empty network")
@@ -331,15 +363,17 @@ class NetworkEnvironment(BaseEnvironment):
                 if getattr(agent, "alive", True):
                     yield agent
 
-    def add_node(self, agent_class, unique_id=None, node_id=None, **kwargs):
+    def add_node(self, agent_class, unique_id=None, node_id=None, find_unassigned=False, **kwargs):
         if unique_id is None:
             unique_id = self.next_id()
         if node_id is None:
-            node_id = network.find_unassigned(
+            if find_unassigned:
-                G=self.G, shuffle=True, random=self.random
+                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}"
+                node_id = f"Node_for_agent_{unique_id}"
+            assert node_id not in self.G.nodes
 
         if node_id not in self.G.nodes:
             self.G.add_node(node_id)
@@ -409,27 +443,115 @@ class NetworkEnvironment(BaseEnvironment):
 
 
 class EventedEnvironment(BaseEnvironment):
-    def broadcast(self, msg, sender=None, expiration=None, ttl=None, **kwargs):
+
-        for agent in self.agents(**kwargs):
+    def __init__(self, *args, **kwargs):
-            if agent == sender:
+        self._inbox = dict()
+        super().__init__(*args, **kwargs)
+        self._can_reschedule = hasattr(self.schedule, "add_callback") and hasattr(self.schedule, "remove_callback")
+        self._can_reschedule = True
+        self._callbacks = {}
+
+    def register(self, agent):
+        self._inbox[agent.unique_id] = []
+
+    def inbox_for(self, agent):
+        try:
+            return self._inbox[agent.unique_id]
+        except KeyError:
+            raise ValueError(f"Trying to access inbox for unregistered agent: {agent} (class: {type(agent)}). "
+                            "Make sure your agent is of type EventedAgent and it is registered with the environment.")
+
+    @coroutine
+    def _polling_callback(self, agent, expiration, delay):
+        # this wakes the agent up at every step. It is better to wait until timeout (or inf)
+        # and if a message is received before that, reschedule the agent
+        # (That is implemented in the `received` method)
+        inbox = self.inbox_for(agent)
+        while self.now < expiration:
+            if inbox:
+                return self.process_messages(inbox)
+            yield time.Delay(delay)
+        raise events.TimedOut("No message received")
+
+    @coroutine
+    def received(self, agent, expiration=None, timeout=None, delay=1):
+        if not expiration:
+            if timeout:
+                expiration = self.now + timeout
+            else:
+                expiration = float("inf")
+        inbox = self.inbox_for(agent)
+        if inbox:
+            return self.process_messages(inbox)
+
+        if self._can_reschedule:
+            checked = False
+            def cb():
+                nonlocal checked
+                if checked:
+                    return time.INFINITY
+                checked = True
+                self.schedule.add_callback(self.now, agent.step)
+            self.schedule.add_callback(expiration, cb)
+            self._callbacks[agent.unique_id] = cb
+            yield time.INFINITY
+        res = yield from self._polling_callback(agent, expiration, delay)
+        return res
+
+
+    def tell(self, msg, recipient, sender=None, expiration=None, timeout=None, **kwargs):
+        if expiration is None:
+            expiration = float("inf") if timeout is None else self.now + timeout
+        self._add_to_inbox(recipient.unique_id,
+            events.Tell(timestamp=self.now,
+                        payload=msg,
+                        sender=sender,
+                        expiration=expiration,
+                        **kwargs))
+
+    def broadcast(self, msg, sender, ttl=None, expiration=None, agent_class=None):
+        expiration = expiration if ttl is None else self.now + ttl
+        # This only works for Soil environments. Mesa agents do not have an `agents` method
+        sender_id = sender.unique_id
+        for (agent_id, inbox) in self._inbox.items():
+            if agent_id == sender_id:
                 continue
-            self.logger.debug(f"Telling {repr(agent)}: {msg} ttl={ttl}")
+            if agent_class and not isinstance(self.agents(unique_id=agent_id), agent_class):
-            try:
-                inbox = agent._inbox
-            except AttributeError:
-                self.logger.info(
-                    f"Agent {agent.unique_id} cannot receive events because it does not have an inbox"
-                )
                 continue
-            # Allow for AttributeError exceptions in this part of the code
+            self.logger.debug(f"Telling {agent_id}: {msg} ttl={ttl}")
-            inbox.append(
+            self._add_to_inbox(agent_id,
                 events.Tell(
                     payload=msg,
                     sender=sender,
-                    expiration=expiration if ttl is None else self.now + ttl,
+                    expiration=expiration,
                 )
             )
+    def _add_to_inbox(self, inbox_id, msg):
+        self._inbox[inbox_id].append(msg)
+        if inbox_id in self._callbacks:
+            cb = self._callbacks.pop(inbox_id)
+            cb()
+
+    @coroutine
+    def ask(self, msg, recipient, sender=None, expiration=None, timeout=None, delay=1):
+        ask = events.Ask(timestamp=self.now, payload=msg, sender=sender)
+        self._add_to_inbox(recipient.unique_id, ask)
+        expiration = float("inf") if timeout is None else self.now + timeout
+        while self.now < expiration:
+            if ask.reply:
+                return ask.reply
+            yield time.Delay(delay)
+        raise events.TimedOut("No reply received")
+
+    def process_messages(self, inbox):
+        valid = list()
+        for msg in inbox:
+            if msg.expired(self.now):
+                continue
+            valid.append(msg)
+        inbox.clear()
+        return valid
 
 
-class Environment(NetworkEnvironment, EventedEnvironment):
+class Environment(EventedEnvironment, NetworkEnvironment):
-    """Default environment class, has both network and event capabilities"""
+    pass

soil/events.py

@@ -18,7 +18,6 @@ class Message:
     def expired(self, when):
         return self.expiration is not None and self.expiration < when
 
-
 class Reply(Message):
     source: Message
 
@@ -28,7 +27,9 @@ class Ask(Message):
 
 
 class Tell(Message):
-    pass
+    def __post_init__(self):
+        assert self.sender is not None, "Tell requires a sender"
+
 
 
 class TimedOut(Exception):

soil/exporters.py

@@ -1,6 +1,7 @@
 import os
 import sys
 from time import time as current_time
+from datetime import datetime
 from io import BytesIO
 from textwrap import dedent, indent
 
@@ -74,6 +75,13 @@ class Exporter:
     def iteration_end(self, env, params, params_id):
         """Method to call when a iteration ends"""
         pass
+    
+    def env_id(self, env):
+        try:
+            return env.id
+        except AttributeError:
+            return f"{env.__class__.__name__}_{current_time()}"
+
 
     def output(self, f, mode="w", **kwargs):
         if not self.dump:
@@ -86,20 +94,21 @@ class Exporter:
                 pass
         return open_or_reuse(f, mode=mode, backup=self.simulation.backup, **kwargs)
 
-    def get_dfs(self, env, **kwargs):
+    def get_dfs(self, env, params_id, **kwargs):
         yield from get_dc_dfs(env.datacollector,
-                              simulation_id=self.simulation.id,
+                              params_id,
-                              iteration_id=env.id,
+                              iteration_id=self.env_id(env),
                               **kwargs)
 
 
-def get_dc_dfs(dc, **kwargs):
+def get_dc_dfs(dc, params_id, **kwargs):
     dfs = {}
     dfe = dc.get_model_vars_dataframe()
     dfe.index.rename("step", inplace=True)
     dfs["env"] = dfe
+    kwargs["params_id"] = params_id
     try:
-        dfa = dc.get_agent_vars_dataframe() 
+        dfa = dc.get_agent_vars_dataframe()
         dfa.index.rename(["step", "agent_id"], inplace=True)
         dfs["agents"] = dfa
     except UserWarning:
@@ -108,9 +117,13 @@ def get_dc_dfs(dc, **kwargs):
         dfs[table_name] = dc.get_table_dataframe(table_name)
     for (name, df) in dfs.items():
         for (k, v) in kwargs.items():
-            df[k] = v
+            if v:
-        df.set_index(["simulation_id", "iteration_id"], append=True, inplace=True)
+                df[k] = v
-    
+            else:
+                df[k] = pd.Series(dtype="object")
+        df.reset_index(inplace=True)
+        df.set_index(["params_id", "iteration_id"], inplace=True)
+
     yield from dfs.items()
 
 
@@ -129,17 +142,21 @@ class SQLite(Exporter):
         logger.info("Dumping results to %s", self.dbpath)
         if self.simulation.backup:
             try_backup(self.dbpath, remove=True)
-        
+
         if self.simulation.overwrite:
             if os.path.exists(self.dbpath):
                 os.remove(self.dbpath)
-        
+
+        outdir = os.path.dirname(self.dbpath)
+        if outdir and not os.path.exists(outdir):
+            os.makedirs(outdir)
+
         self.engine = create_engine(f"sqlite:///{self.dbpath}", echo=False)
 
         sim_dict = {k: serialize(v)[0] for (k,v) in self.simulation.to_dict().items()}
         sim_dict["simulation_id"] = self.simulation.id
         df = pd.DataFrame([sim_dict])
-        df.to_sql("configuration", con=self.engine, if_exists="append")
+        df.reset_index().to_sql("configuration", con=self.engine, if_exists="append", index=False)
 
     def iteration_end(self, env, params, params_id, *args, **kwargs):
         if not self.dump:
@@ -147,17 +164,30 @@ class SQLite(Exporter):
             return
 
         with timer(
-            "Dumping simulation {} iteration {}".format(self.simulation.name, env.id)
+            "Dumping simulation {} iteration {}".format(self.simulation.name, self.env_id(env))
         ):
-
+            d = {"simulation_id": self.simulation.id,
-            pd.DataFrame([{"simulation_id": self.simulation.id,
                            "params_id": params_id,
-                           "iteration_id": env.id,
+                           "iteration_id": self.env_id(env),
-                           "key": k,
+            }
-                           "value": serialize(v)[0]} for (k,v) in params.items()]).to_sql("parameters", con=self.engine, if_exists="append")
+            for (k,v) in params.items():
+                d[k] = serialize(v)[0]
+
+            pd.DataFrame([d]).reset_index().to_sql("parameters",
+                                                   con=self.engine,
+                                                   if_exists="append",
+                                                   index=False)
+            pd.DataFrame([{
+                "simulation_id": self.simulation.id,
+                "params_id": params_id,
+                "iteration_id": self.env_id(env),
+            }]).reset_index().to_sql("iterations",
+                                     con=self.engine,
+                                     if_exists="append",
+                                     index=False)
 
             for (t, df) in self.get_dfs(env, params_id=params_id):
-                df.to_sql(t, con=self.engine, if_exists="append")
+                df.reset_index().to_sql(t, con=self.engine, if_exists="append", index=False)
 
 class csv(Exporter):
     """Export the state of each environment (and its agents) a CSV file for the simulation"""
@@ -168,11 +198,11 @@ class csv(Exporter):
     def iteration_end(self, env, params, params_id, *args, **kwargs):
         with timer(
             "[CSV] Dumping simulation {} iteration {} @ dir {}".format(
-                self.simulation.name, env.id, self.outdir
+                self.simulation.name, self.env_id(env), self.outdir
             )
         ):
             for (df_name, df) in self.get_dfs(env, params_id=params_id):
-                with self.output("{}.{}.csv".format(env.id, df_name), mode="a") as f:
+                with self.output("{}.{}.csv".format(self.env_id(env), df_name), mode="a") as f:
                     df.to_csv(f)
 
 
@@ -183,9 +213,9 @@ class gexf(Exporter):
             return
 
         with timer(
-            "[GEXF] Dumping simulation {} iteration {}".format(self.simulation.name, env.id)
+            "[GEXF] Dumping simulation {} iteration {}".format(self.simulation.name, self.env_id(env))
         ):
-            with self.output("{}.gexf".format(env.id), mode="wb") as f:
+            with self.output("{}.gexf".format(self.env_id(env)), mode="wb") as f:
                 nx.write_gexf(env.G, f)
 
 
@@ -219,16 +249,16 @@ class graphdrawing(Exporter):
             pos=nx.spring_layout(env.G, scale=100),
             ax=f.add_subplot(111),
         )
-        with open("graph-{}.png".format(env.id)) as f:
+        with open("graph-{}.png".format(self.env_id(env))) as f:
             f.savefig(f)
 
 
 class summary(Exporter):
     """Print a summary of each iteration to sys.stdout"""
 
-    def iteration_end(self, env, *args, **kwargs):
+    def iteration_end(self, env, params_id, *args, **kwargs):
         msg = ""
-        for (t, df) in self.get_dfs(env):
+        for (t, df) in self.get_dfs(env, params_id):
             if not len(df):
                 continue
             tabs = "\t" * 2
@@ -262,21 +292,5 @@ class YAML(Exporter):
             logger.info(f"Dumping simulation configuration to {self.outdir}")
             f.write(self.simulation.to_yaml())
 
-class default(Exporter):
-    """Default exporter. Writes sqlite results, as well as the simulation YAML"""
 
-    def __init__(self, *args, exporter_cls=[], **kwargs):
+default = SQLite
-        exporter_cls = exporter_cls or [YAML, SQLite]
-        self.inner = [cls(*args, **kwargs) for cls in exporter_cls]
-
-    def sim_start(self, *args, **kwargs):
-        for exporter in self.inner:
-            exporter.sim_start(*args, **kwargs)
-
-    def sim_end(self, *args, **kwargs):
-        for exporter in self.inner:
-            exporter.sim_end(*args, **kwargs)
-
-    def iteration_end(self, *args, **kwargs):
-        for exporter in self.inner:
-            exporter.iteration_end(*args, **kwargs)

soil/simulation.py

@@ -44,8 +44,8 @@ def do_not_run():
 
 def _iter_queued():
     while _QUEUED:
-        (cls, params) = _QUEUED.pop(0)
+        slf = _QUEUED.pop(0)
-        yield replace(cls, parameters=params)
+        yield slf
 
 
 # TODO: change documentation for simulation
@@ -130,11 +130,11 @@ class Simulation:
     def run(self, **kwargs):
         """Run the simulation and return the list of resulting environments"""
         if kwargs:
-            return replace(self, **kwargs).run()
+            res = replace(self, **kwargs)
+            return res.run()
 
-        param_combinations = self._collect_params(**kwargs)
         if _AVOID_RUNNING:
-            _QUEUED.extend((self, param) for param in param_combinations)
+            _QUEUED.append(self)
             return []
 
         self.logger.debug("Using exporters: %s", self.exporters or [])
@@ -154,6 +154,8 @@ class Simulation:
         for exporter in exporters:
             exporter.sim_start()
 
+        param_combinations = self._collect_params(**kwargs)
+
         for params in tqdm(param_combinations, desc=self.name, unit="configuration"):
             for (k, v) in params.items():
                 tqdm.write(f"{k} = {v}")
@@ -204,6 +206,7 @@ class Simulation:
                 for env in tqdm(utils.run_parallel(
                     func=func,
                     iterable=range(self.iterations),
+                    num_processes=self.num_processes,
                     **params,
                 ), total=self.iterations, leave=False):
                     if env is None and self.dry_run:
@@ -338,12 +341,13 @@ def iter_from_py(pyfile, module_name='imported_file', **kwargs):
             sims.append(sim)
         for sim in _iter_queued():
             sims.append(sim)
+        # Try to find environments to run, because we did not import a script that ran simulations
         if not sims:
             for (_name, env) in inspect.getmembers(module,
-                                                   lambda x: inspect.isclass(x) and
+                                                lambda x: inspect.isclass(x) and
-                                                   issubclass(x, environment.Environment) and
+                                                issubclass(x, environment.Environment) and
-                                                   (getattr(x, "__module__", None) != environment.__name__)):
+                                                (getattr(x, "__module__", None) != environment.__name__)):
-                sims.append(Simulation(model=env, **kwargs))
+                    sims.append(Simulation(model=env, **kwargs))
         del sys.modules[module_name]
     assert not _AVOID_RUNNING
     if not sims:

soil/time.py

@@ -1,13 +1,14 @@
 from mesa.time import BaseScheduler
 from queue import Empty
 from heapq import heappush, heappop, heapreplace
-from collections import deque
+from collections import deque, defaultdict
 import math
 import logging
 
 from inspect import getsource
 from numbers import Number
 from textwrap import dedent
+import random as random_std
 
 from .utils import logger
 from mesa import Agent as MesaAgent
@@ -23,55 +24,79 @@ class Delay:
 
     def __float__(self):
         return self.delta
-    
+
+    def __eq__(self, other):
+        return float(self) == float(other)
+
     def __await__(self):
         return (yield self.delta)
 
+class When:
+    def __init__(self, when):
+        raise Exception("The use of When is deprecated. Use the `Agent.at` and `Agent.delay` methods instead")
+
+class Delta:
+    def __init__(self, delta):
+        raise Exception("The use of Delay is deprecated. Use the `Agent.at` and `Agent.delay` methods instead")
 
 class DeadAgent(Exception):
     pass
 
 
-class PQueueActivation(BaseScheduler):
+class Event(object):
+    def __init__(self, when: float, func, order=1):
+        self.when = when
+        self.func = func
+        self.order = order
+
+    def __repr__(self):
+        return f'Event @ {self.when} - Func: {self.func}'
+
+    def __lt__(self, other):
+        return (self.when < other.when) or (self.when == other.when and self.order < other.order)
+
+
+class PQueueSchedule:
     """
-    A scheduler which activates each agent with a delay returned by the agent's step method.
+    A scheduler which activates each function with a delay returned by the function at each step.
     If no delay is returned, a default of 1 is used.
-    
-    In each activation, each agent will update its 'next_time'.
     """
 
-    def __init__(self, *args, shuffle=True, **kwargs):
+    def __init__(self, shuffle=True, seed=None, time=0, **kwargs):
-        super().__init__(*args, **kwargs)
         self._queue = []
         self._shuffle = shuffle
-        self.logger = getattr(self.model, "logger", logger).getChild(f"time_{ self.model }")
+        self.time = time
+        self.steps = 0
+        self.random = random_std.Random(seed)
         self.next_time = self.time
 
-    def add(self, agent: MesaAgent, when=None):
+    def insert(self, when, callback, replace=False):
         if when is None:
             when = self.time
         else:
             when = float(when)
-
+        order = 1
-        self._schedule(agent, None, when)
-        super().add(agent)
-
-    def _schedule(self, agent, when=None, replace=False):
-        if when is None:
-            when = self.time
         if self._shuffle:
-            key = (when, self.model.random.random())
+            order = self.random.random()
-        else:
+        event = Event(when, callback, order=order)
-            key = (when, agent.unique_id)
         if replace:
-            heapreplace(self._queue, (key, agent))
+            heapreplace(self._queue, event)
         else:
-            heappush(self._queue, (key, agent))
+            heappush(self._queue, event)
+
+    def remove(self, callback):
+        for i, event in enumerate(self._queue):
+            if callback == event.func:
+                del self._queue[i]
+                break
+
+    def __len__(self):
+        return len(self._queue)
 
     def step(self) -> None:
         """
-        Executes agents in order, one at a time. After each step,
+        Executes events in order, one at a time. After each step,
-        an agent will signal when it wants to be scheduled next.
+        an event will signal when it wants to be scheduled next.
         """
 
         if self.time == INFINITY:
@@ -82,66 +107,86 @@ class PQueueActivation(BaseScheduler):
         now = self.time
 
         while self._queue:
-            ((when, _id), agent) = self._queue[0]
+            event = self._queue[0]
+            when = event.when
             if when > now:
                 next_time = when
                 break
 
-            try:
+            when = event.func() 
-                when = agent.step() or 1
+            when = float(when) if when is not None else 1.0
-                when += now
-            except DeadAgent:
-                heappop(self._queue)
-                continue
 
             if when == INFINITY:
                 heappop(self._queue)
                 continue
 
-            self._schedule(agent, when, replace=True)
+            when += now
+
+            self.insert(when, event.func, replace=True)
 
         self.steps += 1
 
         self.time = next_time
 
         if next_time == INFINITY:
-            self.model.running = False
             self.time = INFINITY
             return
 
 
-class TimedActivation(BaseScheduler):
+class Schedule:
-    def __init__(self, *args, shuffle=True, **kwargs):
+    def __init__(self, shuffle=True, seed=None, time=0, **kwargs):
-        super().__init__(*args, **kwargs)
         self._queue = deque()
         self._shuffle = shuffle
-        self.logger = getattr(self.model, "logger", logger).getChild(f"time_{ self.model }")
+        self.time = time
+        self.steps = 0
+        self.random = random_std.Random(seed)
         self.next_time = self.time
 
-    def add(self, agent: MesaAgent, when=None):
+    def _find_loc(self, when=None):
         if when is None:
             when = self.time
         else:
             when = float(when)
-        self._schedule(agent, None, when)
-        super().add(agent)
-
-    def _schedule(self, agent, when=None, replace=False):
         when = when or self.time
         pos = len(self._queue)
         for (ix, l) in enumerate(self._queue):
             if l[0] == when:
-                l[1].append(agent)
+                return l[1]
-                return
             if l[0] > when:
                 pos = ix
                 break
-        self._queue.insert(pos, (when, [agent]))
+        lst = []
+        self._queue.insert(pos, (when, lst))
+        return lst
+
+    def insert(self, when, func, replace=False):
+        if when == INFINITY:
+            return
+        lst = self._find_loc(when)
+        lst.append(func)
+    
+    def add_bulk(self, funcs, when=None):
+        lst = self._find_loc(when)
+        n = len(funcs)
+        #TODO: remove for performance
+        before = len(self)
+        lst.extend(funcs)
+        assert len(self) == before + n
+
+    def remove(self, func):
+        for bucket in self._queue:
+            for (ix, e) in enumerate(bucket):
+                if e == func:
+                    bucket.remove(ix)
+                    return
+
+    def __len__(self):
+        return sum(len(bucket[1]) for bucket in self._queue)
 
     def step(self) -> None:
         """
-        Executes agents in order, one at a time. After each step,
+        Executes events in order, one at a time. After each step,
-        an agent will signal when it wants to be scheduled next.
+        an event will signal when it wants to be scheduled next.
         """
         if not self._queue:
             return
@@ -156,16 +201,20 @@ class TimedActivation(BaseScheduler):
 
         bucket = self._queue.popleft()[1]
         if self._shuffle:
-            self.model.random.shuffle(bucket)
+            self.random.shuffle(bucket)
-        for agent in bucket:
+        next_batch = defaultdict(list)
-            try:
+        for func in bucket:
-                when = agent.step() or 1
+            when = func()
-                when += now
+            when = float(when) if when is not None else 1
-            except DeadAgent:
+
+            if when == INFINITY:
                 continue
 
-            if when != INFINITY:
+            when += now
-                self._schedule(agent, when, replace=True)
+            next_batch[when].append(func) 
+        
+        for (when, bucket) in next_batch.items():
+            self.add_bulk(bucket, when)
 
         self.steps += 1
         if self._queue:
@@ -174,6 +223,77 @@ class TimedActivation(BaseScheduler):
             self.time = INFINITY
 
 
+class InnerActivation(BaseScheduler):
+    inner_class = Schedule
+
+    def __init__(self, model, shuffle=True, time=0, **kwargs):
+        self.model = model
+        self.logger = getattr(self.model, "logger", logger).getChild(f"time_{ self.model }")
+        self._agents = {}
+        self.agents_by_type = defaultdict(dict)
+        self.inner = self.inner_class(shuffle=shuffle, seed=self.model._seed, time=time)
+
+    @property
+    def steps(self):
+        return self.inner.steps
+
+    @property
+    def time(self):
+        return self.inner.time
+
+    def add(self, agent: MesaAgent, when=None):
+        when = when or self.inner.time
+        self.inner.insert(when, agent.step)
+        agent_class = type(agent)
+        self.agents_by_type[agent_class][agent.unique_id] = agent
+        super().add(agent)
+    
+    def add_callback(self, when, cb):
+        self.inner.insert(when, cb)
+
+    def remove_callback(self, when, cb):
+        self.inner.remove(cb)
+    
+    def remove(self, agent):
+        del self._agents[agent.unique_id]
+        del self.agents_by_type[type(agent)][agent.unique_id]
+        self.inner.remove(agent.step)
+
+    def step(self) -> None:
+        """
+        Executes agents in order, one at a time. After each step,
+        an agent will signal when it wants to be scheduled next.
+        """
+        self.inner.step()
+
+    def __len__(self):
+        return len(self.inner)
+
+
+class BucketTimedActivation(InnerActivation):
+    inner_class = Schedule
+
+
+class PQueueActivation(InnerActivation):
+    inner_class = PQueueSchedule
+
+
+#Set the bucket implementation as default
+TimedActivation = BucketTimedActivation
+
+try:
+    from soilent.soilent import BucketScheduler, PQueueScheduler
+
+    class SoilentActivation(InnerActivation):
+        inner_class = BucketScheduler
+    class SoilentPQueueActivation(InnerActivation):
+        inner_class = PQueueScheduler
+
+    # TimedActivation = SoilentBucketActivation
+except ImportError:
+    pass
+
+
 class ShuffledTimedActivation(TimedActivation):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, shuffle=True, **kwargs)
@@ -182,5 +302,3 @@ class ShuffledTimedActivation(TimedActivation):
 class OrderedTimedActivation(TimedActivation):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, shuffle=False, **kwargs)
-
-

soil/utils.py

@@ -93,15 +93,12 @@ def flatten_dict(d):
 
 def _flatten_dict(d, prefix=""):
     if not isinstance(d, dict):
-        # print('END:', prefix, d)
         yield prefix, d
         return
     if prefix:
         prefix = prefix + "."
     for k, v in d.items():
-        # print(k, v)
         res = list(_flatten_dict(v, prefix="{}{}".format(prefix, k)))
-        # print('RES:', res)
         yield from res
 
 
@@ -142,6 +139,7 @@ def run_and_return_exceptions(func, *args, **kwargs):
 
 def run_parallel(func, iterable, num_processes=1, **kwargs):
     if num_processes > 1 and not os.environ.get("SOIL_DEBUG", None):
+        logger.info("Running simulations in {} processes".format(num_processes))
         if num_processes < 1:
             num_processes = cpu_count() - num_processes
         p = Pool(processes=num_processes)
@@ -157,4 +155,24 @@ def run_parallel(func, iterable, num_processes=1, **kwargs):
 
 
 def int_seed(seed: str):
-    return int.from_bytes(seed.encode(), "little")
+    return int.from_bytes(seed.encode(), "little")
+
+
+def prob(prob, random):
+    """
+    A true/False uniform distribution with a given probability.
+    To be used like this:
+
+    .. code-block:: python
+
+          if prob(0.3):
+              do_something()
+
+    """
+    r = random.random()
+    return r < prob
+
+
+def custom(cls, **kwargs):
+    """Create a new class from a template class and keyword arguments"""
+    return type(cls.__name__, (cls,), kwargs)

tests/test_agents.py

@@ -1,7 +1,7 @@
 from unittest import TestCase
 import pytest
 
-from soil import agents, environment
+from soil import agents, events, environment
 from soil import time as stime
 
 
@@ -20,13 +20,14 @@ class TestAgents(TestCase):
         assert ret == stime.INFINITY
 
     def test_die_raises_exception(self):
-        """A dead agent should raise an exception if it is stepped after death"""
+        """A dead agent should continue returning INFINITY after death"""
         d = Dead(unique_id=0, model=environment.Environment())
         assert d.alive
         d.step()
         assert not d.alive
-        with pytest.raises(stime.DeadAgent):
+        when = float(d.step())
-            d.step()
+        assert not d.alive
+        assert when == stime.INFINITY
 
     def test_agent_generator(self):
         """
@@ -62,6 +63,7 @@ class TestAgents(TestCase):
             def other(self):
                 self.times_run += 1
 
+        assert MyAgent.other.id == "other"
         e = environment.Environment()
         a = e.add_agent(MyAgent)
         e.step()
@@ -72,6 +74,53 @@ class TestAgents(TestCase):
         a.step()
         assert a.times_run == 2
 
+    def test_state_decorator_multiple(self):
+        class MyAgent(agents.FSM):
+            times_run = 0
+
+            @agents.state(default=True)
+            def one(self):
+                return self.two
+
+            @agents.state
+            def two(self):
+                return self.one
+
+        e = environment.Environment()
+        first = e.add_agent(MyAgent, state_id=MyAgent.one)
+        second = e.add_agent(MyAgent, state_id=MyAgent.two)
+        assert first.state_id == MyAgent.one.id
+        assert second.state_id == MyAgent.two.id
+        e.step()
+        assert first.state_id == MyAgent.two.id
+        assert second.state_id == MyAgent.one.id
+
+    def test_state_decorator_multiple_async(self):
+        class MyAgent(agents.FSM):
+            times_run = 0
+
+            @agents.state(default=True)
+            def one(self):
+                yield self.delay(1)
+                return self.two
+
+            @agents.state
+            def two(self):
+                yield self.delay(1)
+                return self.one
+
+        e = environment.Environment()
+        first = e.add_agent(MyAgent, state_id=MyAgent.one)
+        second = e.add_agent(MyAgent, state_id=MyAgent.two)
+        for i in range(2):
+            assert first.state_id == MyAgent.one.id
+            assert second.state_id == MyAgent.two.id
+            e.step()
+        for i in range(2):
+            assert first.state_id == MyAgent.two.id
+            assert second.state_id == MyAgent.one.id
+            e.step()
+
     def test_broadcast(self):
         """
         An agent should be able to broadcast messages to every other agent, AND each receiver should be able
@@ -79,30 +128,28 @@ class TestAgents(TestCase):
         """
 
         class BCast(agents.Evented):
-            pings_received = 0
+            pings_received = []
 
-            def step(self):
+            async def step(self):
-                print(self.model.broadcast)
+                self.broadcast("PING")
-                try:
+                print("PING sent")
-                    self.model.broadcast("PING")
-                except Exception as ex:
-                    print(ex)
                 while True:
-                    self.process_messages()
+                    msgs = await self.received()
-                    yield
+                    self.pings_received += msgs
 
-            def on_receive(self, msg, sender=None):
+        e = environment.Environment()
-                self.pings_received += 1
 
-        e = environment.EventedEnvironment()
+        num_agents = 10
-
+        for i in range(num_agents):
-        for i in range(10):
             e.add_agent(agent_class=BCast)
         e.step()
-        pings_received = lambda: [a.pings_received for a in e.agents]
+        # Agents are executed in order, so the first agent should have not received any messages
-        assert sorted(pings_received()) == list(range(1, 11))
+        pings_received = lambda: [len(a.pings_received) for a in e.agents]
+        assert sorted(pings_received()) == list(range(0, num_agents))
         e.step()
-        assert all(x == 10 for x in pings_received())
+        # After the second step, every agent should have received a broadcast from every other agent
+        received = pings_received()
+        assert all(x == (num_agents - 1) for x in received)
 
     def test_ask_messages(self):
         """
@@ -140,17 +187,16 @@ class TestAgents(TestCase):
                         print("NOT sending ping")
                     print("Checking msgs")
                     # Do not block if we have already received a PING
-                    if not self.process_messages():
+                    msgs = yield from self.received()
-                        yield from self.received()
+                    for ping in msgs:
-                print("done")
+                        if ping.payload == "PING":
+                            ping.reply = "PONG"
+                            pongs.append(self.now)
+                        else:
+                            raise Exception("This should never happen")
 
-            def on_receive(self, msg, sender=None):
-                if msg == "PING":
-                    pongs.append(self.now)
-                    return "PONG"
-                raise Exception("This should never happen")
 
-        e = environment.EventedEnvironment(schedule_class=stime.OrderedTimedActivation)
+        e = environment.Environment(schedule_class=stime.OrderedTimedActivation)
         for i in range(2):
             e.add_agent(agent_class=Ping)
         assert e.now == 0
@@ -372,4 +418,107 @@ class TestAgents(TestCase):
         assert a.my_state == 5
         model.step()
         assert a.now == 17
-        assert a.my_state == 5
+        assert a.my_state == 5
+    
+    def test_receive(self):
+        '''
+        An agent should be able to receive a message after waiting
+        '''
+        model = environment.Environment()
+        class TestAgent(agents.Agent):
+            sent = False
+            woken = 0
+            def step(self):
+                self.woken += 1
+                return super().step()
+
+            @agents.state(default=True)
+            async def one(self):
+                try:
+                    self.sent = await self.received(timeout=15)
+                    return self.two.at(20)
+                except events.TimedOut:
+                    pass
+            @agents.state
+            def two(self):
+                return self.die()
+
+        a = model.add_agent(TestAgent)
+
+        class Sender(agents.Agent):
+            async def step(self):
+                await self.delay(10)
+                a.tell(1)
+                return stime.INFINITY
+
+        b = model.add_agent(Sender)
+
+        # Start and wait
+        model.step()
+        assert model.now == 10
+        assert a.woken == 1
+        assert not a.sent
+
+        # Sending the message
+        model.step()
+        assert model.now == 10
+        assert a.woken == 1
+        assert not a.sent
+
+        # The receiver callback
+        model.step()
+        assert model.now == 15
+        assert a.woken == 2
+        assert a.sent[0].payload == 1
+
+        # The timeout
+        model.step()
+        assert model.now == 20
+        assert a.woken == 2
+
+        # The last state of the agent
+        model.step()
+        assert a.woken == 3
+        assert model.now == float('inf')
+
+    def test_receive_timeout(self):
+        '''
+        A timeout should be raised if no messages are received after an expiration time
+        '''
+        model = environment.Environment()
+        timedout = False
+        class TestAgent(agents.Agent):
+            @agents.state(default=True)
+            def one(self):
+                try:
+                    yield from self.received(timeout=10)
+                    raise AssertionError('Should have raised an error.')
+                except events.TimedOut:
+                    nonlocal timedout
+                    timedout = True
+
+        a = model.add_agent(TestAgent)
+
+        model.step()
+        assert model.now == 10
+        model.step()
+        # Wake up the callback
+        assert model.now == 10
+        assert not timedout
+        # The actual timeout
+        model.step()
+        assert model.now == 11
+        assert timedout
+
+    def test_attributes(self):
+        """Attributes should be individual per agent"""
+
+        class MyAgent(agents.Agent):
+            my_attribute = 0
+        
+        model = environment.Environment()
+        a = MyAgent(model=model)
+        assert a.my_attribute == 0
+        b = MyAgent(model=model, my_attribute=1)
+        assert b.my_attribute == 1
+        assert a.my_attribute == 0

tests/test_exporters.py

@@ -81,7 +81,8 @@ class Exporters(TestCase):
             model=ConstantEnv,
             name="exporter_sim",
             exporters=[
-                exporters.default,
+                exporters.YAML,
+                exporters.SQLite,
                 exporters.csv,
             ],
             exporter_params={"copy_to": output},

tests/test_main.py

@@ -6,7 +6,7 @@ import networkx as nx
 from functools import partial
 
 from os.path import join
-from soil import simulation, Environment, agents, network, serialization, utils, config, from_file
+from soil import simulation, Environment, agents, serialization, from_file, time
 from mesa import Agent as MesaAgent
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
@@ -135,9 +135,9 @@ 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 = serialization.serialize(CustomAgent, known_modules=["soil.agents"])[1]
         assert ser == "test_main.CustomAgent"
-        ser = agents._serialize_type(agents.BaseAgent)
+        ser = serialization.serialize(agents.BaseAgent, known_modules=["soil.agents"])[1]
         assert ser == "BaseAgent"
         pickle.dumps(ser)
 
@@ -194,7 +194,7 @@ class TestMain(TestCase):
                 return self.ping
 
         a = ToggleAgent(unique_id=1, model=Environment())
-        when = a.step()
+        when = float(a.step())
         assert when == 2
         when = a.step()
         assert when == None
@@ -227,3 +227,86 @@ class TestMain(TestCase):
         for i in a:
             for j in b:
                 assert {"a": i, "b": j} in configs
+
+    def test_agent_reporters(self):
+        """An environment should be able to set its own reporters"""
+        class Noop2(agents.Noop):
+            pass
+
+        e = Environment()
+        e.add_agent(agents.Noop)
+        e.add_agent(Noop2)
+        e.add_agent_reporter("now")
+        e.add_agent_reporter("base", lambda a: "base", agent_class=agents.Noop)
+        e.add_agent_reporter("subclass", lambda a:"subclass", agent_class=Noop2)
+        e.step()
+
+        # Step 0 is not present because we added the reporters
+        # after initialization.
+        df = e.agent_df()
+        assert "now" in df.columns
+        assert "base" in df.columns
+        assert "subclass" in df.columns
+        assert df["now"][(1,0)] == 1
+        assert df["now"][(1,1)] == 1
+        assert df["base"][(1,0)] == "base"
+        assert df["base"][(1,1)] == "base"
+        assert df["subclass"][(1,0)] is None
+        assert df["subclass"][(1,1)] == "subclass"
+
+    def test_remove_agent(self):
+        """An agent that is scheduled should be removed from the schedule"""
+        model = Environment()
+        model.add_agent(agents.Noop)
+        model.step()
+        model.remove_agent(model.agents[0])
+        assert not model.agents
+        when = model.step()
+        assert when == None
+        assert not model.running
+
+    def test_remove_agent(self):
+        """An agent that is scheduled should be removed from the schedule"""
+
+        allagents = []
+        class Removed(agents.BaseAgent):
+            def step(self):
+                nonlocal allagents
+                assert self.alive
+                assert self in self.model.agents
+                for agent in allagents:
+                    self.model.remove_agent(agent)
+
+        model = Environment()
+        a1 = model.add_agent(Removed)
+        a2 = model.add_agent(Removed)
+        allagents = [a1, a2]
+        model.step()
+        assert not model.agents
+
+    def test_agent_df(self):
+        '''The agent dataframe should have the right columns'''
+
+        class PeterPan(agents.BaseAgent):
+            steps = 0
+
+            def step(self):
+                self.steps += 1
+                return self.delay(0)
+
+        class AgentDF(Environment):
+            def init(self):
+                self.add_agent(PeterPan)
+                self.add_agent_reporter("steps")
+
+        e = AgentDF()
+        df = e.agent_df()
+        assert df["steps"][(0,0)] == 0
+        e.step()
+        df = e.agent_df()
+        assert len(df) == 1
+        assert df["steps"][(0,0)] == 1
+        e.step()
+        df = e.agent_df()
+        assert len(df) == 1
+        assert df["steps"][(0,0)] == 2