Add rescheduling for received

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/rabbits/rabbit_improved_sim.py

@@ -167,7 +167,7 @@ class RandomAccident(BaseAgent):
             if self.prob(prob_death):
                 self.debug("I killed a rabbit: {}".format(i.unique_id))
                 num_alive -= 1
-                i.die()
+                self.model.remove_agent(i)
         self.debug("Rabbits alive: {}".format(num_alive))
 
 

examples/rabbits/rabbits_basic_sim.py

@@ -142,13 +142,15 @@ class RandomAccident(BaseAgent):
         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.debug("I killed a rabbit: {}".format(i.unique_id))
                 num_alive -= 1
-                i.die()
+                self.model.remove_agent(i)
+                i.alive = False
+                i.killed = True
         self.debug("Rabbits alive: {}".format(num_alive))
 
 

soil/__init__.py

@@ -259,7 +259,6 @@ def main(
     except Exception as ex:
         if args.pdb:
             from .debugging import post_mortem
-
             print(traceback.format_exc())
             post_mortem()
         else:

soil/agents/__init__.py

@@ -30,8 +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 = (
@@ -191,25 +194,25 @@ 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)
 
 
-class Noop(BaseAgent):
-    def step(self):
-        return
-
-
 from .network_agents import *
 from .fsm import *
 from .evented import *
 from .view import *
 
 
+class Noop(EventedAgent, BaseAgent):
+    def step(self):
+        return
+
+
 class Agent(FSM, EventedAgent, NetworkAgent):
     """Default agent class, has network, FSM and event capabilities"""
 

soil/agents/evented.py

@@ -16,7 +16,7 @@ class EventedAgent(BaseAgent):
         self.model.register(self)
 
     def received(self, **kwargs):
-        return self.model.received(self, **kwargs)
+        return self.model.received(agent=self, **kwargs)
 
     def tell(self, msg, **kwargs):
         return self.model.tell(msg, recipient=self, **kwargs)

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()
@@ -139,6 +158,7 @@ class FSM(BaseAgent, metaclass=MetaFSM):
             raise ValueError("Cannot change state after init")
         self._set_state(value)
 
+    @coroutine
     def step(self):
         if self._state is None:
             if len(self._states) == 1:
@@ -146,8 +166,7 @@ class FSM(BaseAgent, metaclass=MetaFSM):
             else:
                 raise Exception("Invalid state (None) for agent {}".format(self))
 
-        self._check_alive()
+        next_state = yield from self._state()
-        next_state = yield from self._state.step(self)
 
         try:
             next_state, when = next_state
@@ -167,7 +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
 
@@ -177,4 +198,4 @@ class FSM(BaseAgent, metaclass=MetaFSM):
 
     @state
     def dead(self):
-        return time.INFINITY
+        return time.INFINITY

soil/agents/meta.py

@@ -2,44 +2,14 @@ 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
 
-def decorate_generator_step(func, name):
-    @wraps(func)
-    def decorated(self):
-        if not self.alive:
-            return time.INFINITY
 
-        if self._coroutine is None:
+class MetaAnnotations(ABCMeta):
-            self._coroutine = func(self)
+    """This metaclass sets default values for agents based on class attributes"""
-        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_step(func, name):
-    @wraps(func)
-    def decorated(self):
-        # if not self.alive:
-        #     return time.INFINITY
-        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 = {}
 
@@ -53,22 +23,7 @@ class MetaAgent(ABCMeta):
         }
 
         for attr, func in namespace.items():
-            if attr == "step":
+            if (
-                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_step(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)
@@ -82,6 +37,28 @@ class MetaAgent(ABCMeta):
             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, new_nmspc)
+        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/view.py

@@ -1,5 +1,6 @@
 from collections.abc import Mapping, Set
 from itertools import islice
+from mesa import Agent
 
 
 class AgentView(Mapping, Set):
@@ -55,6 +56,8 @@ class AgentView(Mapping, Set):
         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):

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(),
@@ -48,9 +49,5 @@ def read_sql(fpath=None, name=None, include_agents=False):
         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=["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

@@ -11,6 +11,7 @@ import networkx as nx
 
 
 from mesa import Model
+from time import time as current_time
 
 from . import agents as agentmod, datacollection, utils, time, network, events
 
@@ -43,6 +44,7 @@ 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
@@ -136,7 +138,7 @@ 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"
@@ -160,6 +162,10 @@ 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]
@@ -188,12 +194,15 @@ 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):
@@ -297,6 +306,11 @@ 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")
@@ -344,6 +358,7 @@ class NetworkEnvironment(BaseEnvironment):
                 )
             if node_id is None:
                 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)
@@ -417,7 +432,10 @@ class EventedEnvironment(BaseEnvironment):
     def __init__(self, *args, **kwargs):
         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] = []
 
@@ -429,24 +447,47 @@ class EventedEnvironment(BaseEnvironment):
                             "Make sure your agent is of type EventedAgent and it is registered with the environment.")
 
     @coroutine
-    def received(self, agent, expiration=None, timeout=60, delay=1):
+    def _polling_callback(self, agent, expiration, delay):
-        if not expiration:
+        # this wakes the agent up at every step. It is better to wait until timeout (or inf)
-            expiration = self.now + timeout
+        # and if a message is received before that, reschedule the agent
+        # (That is implemented in the `received` method)
         inbox = self.inbox_for(agent)
-        if inbox:
-            return self.process_messages(inbox)
         while self.now < expiration:
-            # TODO: this wakes the agent up at every step. It would be better to wait until timeout (or inf)
-            # and if a message is received before that, reschedule the agent when
             if inbox:
                 return self.process_messages(inbox)
             yield time.Delay(delay)
         raise events.TimedOut("No message received")
 
-    def tell(self, msg, sender, recipient, expiration=None, timeout=None, **kwargs):
+    @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.inbox_for(recipient).append(
+        self._add_to_inbox(recipient.unique_id,
             events.Tell(timestamp=self.now,
                         payload=msg,
                         sender=sender,
@@ -463,18 +504,23 @@ class EventedEnvironment(BaseEnvironment):
             if agent_class and not isinstance(self.agents(unique_id=agent_id), agent_class):
                 continue
             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,
                 )
             )
+    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.inbox_for(recipient).append(ask)
+        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:
@@ -493,4 +539,4 @@ class EventedEnvironment(BaseEnvironment):
 
 
 class Environment(EventedEnvironment, NetworkEnvironment):
-    pass
+    pass

soil/exporters.py

@@ -75,6 +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:
@@ -90,7 +97,7 @@ class Exporter:
     def get_dfs(self, env, params_id, **kwargs):
         yield from get_dc_dfs(env.datacollector,
                               params_id,
-                              iteration_id=env.id,
+                              iteration_id=self.env_id(env),
                               **kwargs)
 
 
@@ -157,11 +164,11 @@ 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,
                            "params_id": params_id,
-                           "iteration_id": env.id,
+                           "iteration_id": self.env_id(env),
             }
             for (k,v) in params.items():
                 d[k] = serialize(v)[0]
@@ -173,7 +180,7 @@ class SQLite(Exporter):
             pd.DataFrame([{
                 "simulation_id": self.simulation.id,
                 "params_id": params_id,
-                "iteration_id": env.id,
+                "iteration_id": self.env_id(env),
             }]).reset_index().to_sql("iterations",
                                      con=self.engine,
                                      if_exists="append",
@@ -191,11 +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)
 
 
@@ -206,9 +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)
 
 
@@ -242,7 +249,7 @@ 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)
 
 

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

@@ -24,7 +24,10 @@ class Delay:
 
     def __float__(self):
         return self.delta
-    
+
+    def __eq__(self, other):
+        return float(self) == float(other)
+
     def __await__(self):
         return (yield self.delta)
 
@@ -87,6 +90,9 @@ class PQueueSchedule:
                 del self._queue[i]
                 break
 
+    def __len__(self):
+        return len(self._queue)
+
     def step(self) -> None:
         """
         Executes events in order, one at a time. After each step,
@@ -107,7 +113,8 @@ class PQueueSchedule:
                 next_time = when
                 break
 
-            when = event.func() or 1
+            when = event.func() 
+            when = float(when) if when is not None else 1.0
 
             if when == INFINITY:
                 heappop(self._queue)
@@ -153,12 +160,18 @@ class Schedule:
         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:
@@ -167,6 +180,9 @@ class Schedule:
                     bucket.remove(ix)
                     return
 
+    def __len__(self):
+        return sum(len(bucket[1]) for bucket in self._queue)
+
     def step(self) -> None:
         """
         Executes events in order, one at a time. After each step,
@@ -188,11 +204,14 @@ class Schedule:
             self.random.shuffle(bucket)
         next_batch = defaultdict(list)
         for func in bucket:
-            when = func() or 1
+            when = func()
+            when = float(when) if when is not None else 1
+
+            if when == INFINITY:
+                continue
 
-            if when != INFINITY:
+            when += now
-                when += now
+            next_batch[when].append(func) 
-                next_batch[when].append(func) 
         
         for (when, bucket) in next_batch.items():
             self.add_bulk(bucket, when)
@@ -229,6 +248,12 @@ class InnerActivation(BaseScheduler):
         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]
@@ -241,6 +266,9 @@ class InnerActivation(BaseScheduler):
         """
         self.inner.step()
 
+    def __len__(self):
+        return len(self.inner)
+
 
 class BucketTimedActivation(InnerActivation):
     inner_class = Schedule
@@ -250,16 +278,19 @@ class PQueueActivation(InnerActivation):
     inner_class = PQueueSchedule
 
 
-# Set the bucket implementation as default
+#Set the bucket implementation as default
+TimedActivation = BucketTimedActivation
+
 try:
-    from soilent.soilent import BucketScheduler
+    from soilent.soilent import BucketScheduler, PQueueScheduler
 
-    class SoilBucketActivation(InnerActivation):
+    class SoilentActivation(InnerActivation):
         inner_class = BucketScheduler
+    class SoilentPQueueActivation(InnerActivation):
+        inner_class = PQueueScheduler
 
-    TimedActivation = SoilBucketActivation
+    # TimedActivation = SoilentBucketActivation
 except ImportError:
-    TimedActivation = BucketTimedActivation
     pass
 
 

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)

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
 
 
@@ -25,7 +25,7 @@ class TestAgents(TestCase):
         assert d.alive
         d.step()
         assert not d.alive
-        when = d.step()
+        when = float(d.step())
         assert not d.alive
         assert when == stime.INFINITY
 
@@ -63,6 +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()
@@ -73,6 +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
@@ -372,22 +420,105 @@ class TestAgents(TestCase):
         assert a.now == 17
         assert a.my_state == 5
     
-    def test_send_nonevent(self):
+    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):
         '''
-        Sending a non-event should raise an error.
+        A timeout should be raised if no messages are received after an expiration time
         '''
         model = environment.Environment()
-        a = model.add_agent(agents.Noop)
+        timedout = False
         class TestAgent(agents.Agent):
             @agents.state(default=True)
             def one(self):
                 try:
-                    a.tell(b, 1)
+                    yield from self.received(timeout=10)
                     raise AssertionError('Should have raised an error.')
-                except AttributeError:
+                except events.TimedOut:
-                    self.model.tell(1, sender=self, recipient=a)
+                    nonlocal timedout
+                    timedout = True
 
-        model.add_agent(TestAgent)
+        a = model.add_agent(TestAgent)
 
-        with pytest.raises(ValueError):
+        model.step()
-            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_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__))
@@ -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
@@ -252,4 +252,34 @@ class TestMain(TestCase):
         assert df["base"][(0,0)] == "base"
         assert df["base"][(0,1)] == "base"
         assert df["subclass"][(0,0)] is None
-        assert df["subclass"][(0,1)] == "subclass"
+        assert df["subclass"][(0,1)] == "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