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https://github.com/gsi-upm/soil
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Bug fixes and minor improvements
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13
CHANGELOG.md
13
CHANGELOG.md
@ -3,6 +3,19 @@ All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [0.20.3]
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### Fixed
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* Default state values are now deepcopied again.
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* Seeds for environments only concatenate the trial id (i.e., a number), to provide repeatable results.
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* `Environment.run` now calls `Environment.step`, to allow for easy overloading of the environment step
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### Removed
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* Datacollectors are not being used for now.
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* `time.TimedActivation.step` does not use an `until` parameter anymore.
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### Changed
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* Simulations now run right up to `until` (open interval)
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* Time instants (`time.When`) don't need to be floats anymore. Now we can avoid precision issues with big numbers by using ints.
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* Rabbits simulation is more idiomatic (using subclasses)
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## [0.20.2]
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### Fixed
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* CI/CD testing issues
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@ -34,6 +34,17 @@ class RabbitModel(FSM):
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if self['age'] >= self.sexual_maturity:
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self.debug('I am fertile!')
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return self.fertile
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@state
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def fertile(self):
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raise Exception("Each subclass should define its fertile state")
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@state
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def dead(self):
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self.info('Agent {} is dying'.format(self.id))
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self.die()
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class Male(RabbitModel):
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@state
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def fertile(self):
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@ -45,20 +56,26 @@ class RabbitModel(FSM):
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return
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# Males try to mate
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for f in self.get_agents(state_id=self.fertile.id, gender=Genders.female.value, limit_neighbors=False, limit=self.max_females):
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for f in self.get_agents(state_id=Female.fertile.id,
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agent_type=Female,
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limit_neighbors=False,
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limit=self.max_females):
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r = random()
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if r < self['mating_prob']:
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self.impregnate(f)
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break # Take a break
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def impregnate(self, whom):
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if self['gender'] == Genders.female.value:
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raise NotImplementedError('Females cannot impregnate')
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whom['pregnancy'] = 0
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whom['mate'] = self.id
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whom.set_state(whom.pregnant)
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self.debug('{} impregnating: {}. {}'.format(self.id, whom.id, whom.state))
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class Female(RabbitModel):
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@state
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def fertile(self):
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# Just wait for a Male
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pass
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@state
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def pregnant(self):
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self['age'] += 1
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@ -88,11 +105,9 @@ class RabbitModel(FSM):
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@state
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def dead(self):
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self.info('Agent {} is dying'.format(self.id))
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super().dead()
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if 'pregnancy' in self and self['pregnancy'] > -1:
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self.info('A mother has died carrying a baby!!')
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self.die()
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return
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class RandomAccident(NetworkAgent):
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@ -4,9 +4,9 @@ name: rabbits_example
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max_time: 100
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interval: 1
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seed: MySeed
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agent_type: RabbitModel
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agent_type: rabbit_agents.RabbitModel
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environment_agents:
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- agent_type: RandomAccident
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- agent_type: rabbit_agents.RandomAccident
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environment_params:
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prob_death: 0.001
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default_state:
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@ -14,10 +14,8 @@ default_state:
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topology:
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nodes:
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- id: 1
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state:
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gender: female
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agent_type: rabbit_agents.Male
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- id: 0
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state:
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gender: male
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agent_type: rabbit_agents.Female
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directed: true
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links: []
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@ -1 +1 @@
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0.20.1
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0.20.3
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@ -65,6 +65,10 @@ def main():
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logger.info('Loading config file: {}'.format(args.file))
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if args.pdb:
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args.synchronous = True
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try:
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exporters = list(args.exporter or ['default', ])
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if args.csv:
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@ -169,11 +169,12 @@ class Environment(Model):
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if agent_type:
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state = defstate
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a = agent_type(model=self,
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unique_id=agent_id)
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unique_id=agent_id
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)
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for (k, v) in getattr(a, 'defaults', {}).items():
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if not hasattr(a, k) or getattr(a, k) is None:
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setattr(a, k, v)
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setattr(a, k, deepcopy(v))
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for (k, v) in state.items():
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setattr(a, k, v)
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@ -199,15 +200,15 @@ class Environment(Model):
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def step(self):
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super().step()
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self.datacollector.collect(self)
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self.schedule.step()
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def run(self, until, *args, **kwargs):
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self._save_state()
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while self.schedule.next_time <= until and not math.isinf(self.schedule.next_time):
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self.schedule.step(until=until)
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while self.schedule.next_time < until:
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self.step()
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utils.logger.debug(f'Simulation step {self.schedule.time}/{until}. Next: {self.schedule.next_time}')
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self.schedule.time = until
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self._history.flush_cache()
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def _save_state(self, now=None):
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@ -145,9 +145,7 @@ class Simulation:
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def _run_sync_or_async(self, parallel=False, *args, **kwargs):
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if parallel and not os.environ.get('SENPY_DEBUG', None):
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p = Pool()
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func = partial(self.run_trial_exceptions,
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*args,
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**kwargs)
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func = lambda x: self.run_trial_exceptions(trial_id=x, *args, **kwargs)
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for i in p.imap_unordered(func, range(self.num_trials)):
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if isinstance(i, Exception):
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logger.error('Trial failed:\n\t%s', i.message)
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@ -155,7 +153,8 @@ class Simulation:
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yield i
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else:
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for i in range(self.num_trials):
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yield self.run_trial(*args,
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yield self.run_trial(trial_id=i,
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*args,
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**kwargs)
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def run_gen(self, *args, parallel=False, dry_run=False,
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@ -224,7 +223,7 @@ class Simulation:
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'''Create an environment for a trial of the simulation'''
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opts = self.environment_params.copy()
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opts.update({
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'name': trial_id,
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'name': '{}_trial_{}'.format(self.name, trial_id),
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'topology': self.topology.copy(),
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'network_params': self.network_params,
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'seed': '{}_trial_{}'.format(self.seed, trial_id),
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@ -241,12 +240,11 @@ class Simulation:
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env = self.environment_class(**opts)
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return env
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def run_trial(self, until=None, log_level=logging.INFO, **opts):
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def run_trial(self, trial_id=0, until=None, log_level=logging.INFO, **opts):
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"""
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Run a single trial of the simulation
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"""
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trial_id = '{}_trial_{}'.format(self.name, time.time()).replace('.', '-')
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if log_level:
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logger.setLevel(log_level)
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# Set-up trial environment and graph
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60
soil/time.py
60
soil/time.py
@ -6,9 +6,11 @@ from .utils import logger
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from mesa import Agent
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INFINITY = float('inf')
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class When:
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def __init__(self, time):
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self._time = float(time)
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self._time = time
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def abs(self, time):
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return self._time
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@ -40,48 +42,34 @@ class TimedActivation(BaseScheduler):
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heappush(self._queue, (self.time, agent.unique_id))
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super().add(agent)
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def step(self, until: float =float('inf')) -> None:
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def step(self) -> None:
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"""
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Executes agents in order, one at a time. After each step,
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an agent will signal when it wants to be scheduled next.
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"""
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when = None
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agent_id = None
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unsched = []
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until = until or float('inf')
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if self.next_time == INFINITY:
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return
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self.time = self.next_time
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when = self.time
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while self._queue and self._queue[0][0] == self.time:
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(when, agent_id) = heappop(self._queue)
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logger.debug(f'Stepping agent {agent_id}')
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when = (self._agents[agent_id].step() or Delta(1)).abs(self.time)
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if when < self.time:
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raise Exception("Cannot schedule an agent for a time in the past ({} < {})".format(when, self.time))
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heappush(self._queue, (when, agent_id))
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self.steps += 1
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if not self._queue:
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self.time = until
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self.next_time = float('inf')
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self.time = INFINITY
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self.next_time = INFINITY
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return
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(when, agent_id) = self._queue[0]
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self.next_time = self._queue[0][0]
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if until and when > until:
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self.time = until
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self.next_time = when
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return
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self.time = when
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next_time = float("inf")
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while when == self.time:
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heappop(self._queue)
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logger.debug(f'Stepping agent {agent_id}')
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when = (self._agents[agent_id].step() or Delta(1)).abs(self.time)
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heappush(self._queue, (when, agent_id))
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if when < next_time:
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next_time = when
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if not self._queue or self._queue[0][0] > self.time:
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agent_id = None
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break
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else:
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(when, agent_id) = self._queue[0]
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if when and when < self.time:
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raise Exception("Invalid scheduling time")
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self.next_time = next_time
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self.steps += 1
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env = s.run_simulation(dry_run=True)[0]
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for agent in env.network_agents:
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last = 0
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assert len(agent[None, None]) == 11
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assert len(agent[None, None]) == 10
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for step, total in sorted(agent['total', None]):
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assert total == last + 2
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last = total
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