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Code Issues Releases Wiki Activity

Add rescheduling for received

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This commit is contained in:
J. Fernando Sánchez 2023-05-19 16:19:50 +02:00
parent ee0c4517cb
commit 189836408f
34 changed files with 674 additions and 260 deletions
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1
benchmarks/noop/_config.py
View File

@ -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)

1
benchmarks/noop/mesa_batchrunner.py
View File

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

1
benchmarks/noop/mesa_simulation.py
View File

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

21
benchmarks/noop/soil_state.py Normal file
View File

@ -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)

9
benchmarks/noop/soil_step.py
View File

@ -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)

6
benchmarks/noop/soilent_async.py
View File

@ -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)

6
benchmarks/noop/soilent_async_pqueue.py
View File

@ -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)

6
benchmarks/noop/soilent_gens.py
View File

@ -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)

6
benchmarks/noop/soilent_gens_pqueue.py
View File

@ -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)

30
benchmarks/noop/soilent_state.py Normal file
View File

@ -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)

6
benchmarks/noop/soilent_step.py
View File

@ -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)

6
benchmarks/noop/soilent_step_pqueue.py
View File

@ -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)

22
benchmarks/virusonnetwork/_config.py
View File

@ -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)
ratios = list(it.resistant_susceptible_ratio() for it in its)
print("Max - Avg - Min ratio:", max(ratios), sum(ratios)/len(ratios), min(ratios))
assert all(sum([it.number_susceptible,
it.number_infected,
it.number_resistant]) == NUM_AGENTS for it in its)
return its
if not simulation._AVOID_RUNNING:
ratios = list(it.resistant_susceptible_ratio for it in its)
print("Max - Avg - Min ratio:", max(ratios), sum(ratios)/len(ratios), min(ratios))
infected = list(it.number_infected for it in its)
print("Max - Avg - Min infected:", max(infected), sum(infected)/len(infected), min(infected))
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

2
benchmarks/virusonnetwork/mesa_basic.py
View File

@ -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)

21
benchmarks/virusonnetwork/soil_states.py
View File

@ -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):
if self.just_been_infected:
self.just_been_infected = False
return self.infected
async def susceptible(self):
await self.received()
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
run_sim(model=VirusOnNetwork)
from _config import run_sim
run_sim(model=VirusOnNetwork)

6
benchmarks/virusonnetwork/soil_step.py
View File

@ -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
run_sim(model=VirusOnNetwork)
from _config import run_sim
run_sim(model=VirusOnNetwork)

187
docs/tutorial/soil_tutorial.ipynb
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File diff suppressed because one or more lines are too long

2
examples/rabbits/rabbit_improved_sim.py
View File

@ -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))

6
examples/rabbits/rabbits_basic_sim.py
View File

@ -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))

1
soil/__init__.py
View File

@ -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:

21
soil/agents/__init__.py
View File

@ -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):
assert isinstance(unique_id, int)
def __init__(self, unique_id=None, model=None, name=None, init=True, **kwargs):
# 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"""

2
soil/agents/evented.py
View File

@ -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)

71
soil/agents/fsm.py
View File

@ -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):
raise Exception("States should not be called directly")
class UnboundState(State):
def __get__(self, obj, owner=None):
if obj is None:
return self
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.step(self)
next_state = yield from self._state()
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

77
soil/agents/meta.py
View File

@ -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:
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_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):
class MetaAnnotations(ABCMeta):
"""This metaclass sets default values for agents based on class attributes"""
def __new__(mcls, name, bases, namespace):
defaults = {}
@ -53,22 +23,7 @@ class MetaAgent(ABCMeta):
}
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_step(func, attr)
else:
raise ValueError("Illegal step function: {}".format(func))
new_nmspc[attr] = func
elif (
if (
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

3
soil/agents/view.py
View File

@ -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):

7
soil/analysis.py
View File

@ -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)

38
soil/decorators.py
View File

@ -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

76
soil/environment.py
View File

@ -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):
if not expiration:
expiration = self.now + timeout
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)
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

25
soil/exporters.py
View File

@ -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)

22
soil/simulation.py
View File

@ -44,8 +44,8 @@ def do_not_run():
def _iter_queued():
while _QUEUED:
(cls, params) = _QUEUED.pop(0)
yield replace(cls, parameters=params)
slf = _QUEUED.pop(0)
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
issubclass(x, environment.Environment) and
(getattr(x, "__module__", None) != environment.__name__)):
sims.append(Simulation(model=env, **kwargs))
lambda x: inspect.isclass(x) and
issubclass(x, environment.Environment) and
(getattr(x, "__module__", None) != environment.__name__)):
sims.append(Simulation(model=env, **kwargs))
del sys.modules[module_name]
assert not _AVOID_RUNNING
if not sims:

53
soil/time.py
View File

@ -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:
when += now
next_batch[when].append(func)
if when == INFINITY:
continue
when += now
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

4
soil/utils.py
View File

@ -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)

153
tests/test_agents.py
View File

@ -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):
'''
Sending a non-event should raise an error.
An agent should be able to receive a message after waiting
'''
model = environment.Environment()
a = model.add_agent(agents.Noop)
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:
a.tell(b, 1)
yield from self.received(timeout=10)
raise AssertionError('Should have raised an error.')
except AttributeError:
self.model.tell(1, sender=self, recipient=a)
except events.TimedOut:
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

36
tests/test_main.py
View File

@ -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