Bug fixes and minor improvements

CHANGELOG.md

@@ -3,6 +3,19 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.20.3]
+### Fixed
+* Default state values are now deepcopied again.
+* Seeds for environments only concatenate the trial id (i.e., a number), to provide repeatable results.
+* `Environment.run` now calls `Environment.step`, to allow for easy overloading of the environment step
+### Removed
+* Datacollectors are not being used for now.
+* `time.TimedActivation.step` does not use an `until` parameter anymore.
+### Changed
+* Simulations now run right up to `until` (open interval)
+* Time instants (`time.When`) don't need to be floats anymore. Now we can avoid precision issues with big numbers by using ints.
+* Rabbits simulation is more idiomatic (using subclasses)
+
 ## [0.20.2]
 ### Fixed
 * CI/CD testing issues

examples/rabbits/rabbit_agents.py

@@ -34,6 +34,17 @@ class RabbitModel(FSM):
         if self['age'] >= self.sexual_maturity:
             self.debug('I am fertile!')
             return self.fertile
+    @state
+    def fertile(self):
+        raise Exception("Each subclass should define its fertile state")
+
+    @state
+    def dead(self):
+        self.info('Agent {} is dying'.format(self.id))
+        self.die()
+
+
+class Male(RabbitModel):
 
     @state
     def fertile(self):
@@ -45,20 +56,26 @@ class RabbitModel(FSM):
             return
 
         # Males try to mate
-        for f in self.get_agents(state_id=self.fertile.id, gender=Genders.female.value, limit_neighbors=False, limit=self.max_females):
+        for f in self.get_agents(state_id=Female.fertile.id,
+                                 agent_type=Female,
+                                 limit_neighbors=False,
+                                 limit=self.max_females):
             r = random()
             if r < self['mating_prob']:
                 self.impregnate(f)
                 break # Take a break
-
     def impregnate(self, whom):
-        if self['gender'] == Genders.female.value:
-            raise NotImplementedError('Females cannot impregnate')
         whom['pregnancy'] = 0
         whom['mate'] = self.id
         whom.set_state(whom.pregnant)
         self.debug('{} impregnating: {}. {}'.format(self.id, whom.id, whom.state))
 
+class Female(RabbitModel):
+    @state
+    def fertile(self):
+        # Just wait for a Male
+        pass
+
     @state
     def pregnant(self):
         self['age'] += 1
@@ -88,11 +105,9 @@ class RabbitModel(FSM):
 
     @state
     def dead(self):
-        self.info('Agent {} is dying'.format(self.id))
+        super().dead()
         if 'pregnancy' in self and self['pregnancy'] > -1:
             self.info('A mother has died carrying a baby!!')
-        self.die()
-        return
 
 
 class RandomAccident(NetworkAgent):

examples/rabbits/rabbits.yml

@@ -4,9 +4,9 @@ name: rabbits_example
 max_time: 100
 interval: 1
 seed: MySeed
-agent_type: RabbitModel
+agent_type: rabbit_agents.RabbitModel
 environment_agents:
-    - agent_type: RandomAccident
+    - agent_type: rabbit_agents.RandomAccident
 environment_params:
   prob_death: 0.001
 default_state:
@@ -14,10 +14,8 @@ default_state:
 topology:
   nodes:
     - id: 1
-      state:
+      agent_type: rabbit_agents.Male
-        gender: female
     - id: 0
-      state:
+      agent_type: rabbit_agents.Female
-        gender: male
   directed: true
   links: []

soil/VERSION

@@ -1 +1 @@
-0.20.1
+0.20.3

soil/__init__.py

@@ -65,6 +65,10 @@ def main():
 
     logger.info('Loading config file: {}'.format(args.file))
 
+    if args.pdb:
+        args.synchronous = True
+
+
     try:
         exporters = list(args.exporter or ['default', ])
         if args.csv:

soil/environment.py

@@ -169,11 +169,12 @@ class Environment(Model):
         if agent_type:
             state = defstate
             a = agent_type(model=self,
-                           unique_id=agent_id)
+                           unique_id=agent_id
+            )
 
         for (k, v) in getattr(a, 'defaults', {}).items():
             if not hasattr(a, k) or getattr(a, k) is None:
-                setattr(a, k, v)
+                setattr(a, k, deepcopy(v))
 
         for (k, v) in state.items():
             setattr(a, k, v)
@@ -199,15 +200,15 @@ class Environment(Model):
 
     def step(self):
         super().step()
-        self.datacollector.collect(self)
         self.schedule.step()
 
     def run(self, until, *args, **kwargs):
         self._save_state()
 
-        while self.schedule.next_time <= until and not math.isinf(self.schedule.next_time):
+        while self.schedule.next_time < until:
-            self.schedule.step(until=until)
+            self.step()
             utils.logger.debug(f'Simulation step {self.schedule.time}/{until}. Next: {self.schedule.next_time}')
+        self.schedule.time = until
         self._history.flush_cache()
 
     def _save_state(self, now=None):

soil/simulation.py

@@ -145,9 +145,7 @@ class Simulation:
     def _run_sync_or_async(self, parallel=False, *args, **kwargs):
         if parallel and not os.environ.get('SENPY_DEBUG', None):
             p = Pool()
-            func = partial(self.run_trial_exceptions,
+            func = lambda x: self.run_trial_exceptions(trial_id=x, *args, **kwargs)
-                           *args,
-                           **kwargs)
             for i in p.imap_unordered(func, range(self.num_trials)):
                 if isinstance(i, Exception):
                     logger.error('Trial failed:\n\t%s', i.message)
@@ -155,7 +153,8 @@ class Simulation:
                 yield i
         else:
             for i in range(self.num_trials):
-                yield self.run_trial(*args,
+                yield self.run_trial(trial_id=i,
+                                     *args,
                                      **kwargs)
 
     def run_gen(self, *args, parallel=False, dry_run=False,
@@ -224,7 +223,7 @@ class Simulation:
         '''Create an environment for a trial of the simulation'''
         opts = self.environment_params.copy()
         opts.update({
-            'name': trial_id,
+            'name': '{}_trial_{}'.format(self.name, trial_id),
             'topology': self.topology.copy(),
             'network_params': self.network_params,
             'seed': '{}_trial_{}'.format(self.seed, trial_id),
@@ -241,12 +240,11 @@ class Simulation:
         env = self.environment_class(**opts)
         return env
 
-    def run_trial(self, until=None, log_level=logging.INFO, **opts):
+    def run_trial(self, trial_id=0, until=None, log_level=logging.INFO, **opts):
         """
         Run a single trial of the simulation
 
         """
-        trial_id = '{}_trial_{}'.format(self.name, time.time()).replace('.', '-')
         if log_level:
             logger.setLevel(log_level)
         # Set-up trial environment and graph

soil/time.py

@@ -6,9 +6,11 @@ from .utils import logger
 from mesa import Agent
 
 
+INFINITY = float('inf')
+
 class When:
     def __init__(self, time):
-        self._time = float(time)
+        self._time = time
 
     def abs(self, time):
         return self._time
@@ -40,48 +42,34 @@ class TimedActivation(BaseScheduler):
             heappush(self._queue, (self.time, agent.unique_id))
             super().add(agent)
 
-    def step(self, until: float =float('inf')) -> None:
+    def step(self) -> None:
         """
         Executes agents in order, one at a time. After each step,
         an agent will signal when it wants to be scheduled next.
         """
 
-        when = None
+        if self.next_time == INFINITY:
-        agent_id = None
+            return
-        unsched = []
+
-        until = until or float('inf')
+        self.time = self.next_time
+        when = self.time
+
+        while self._queue and self._queue[0][0] == self.time:
+            (when, agent_id) = heappop(self._queue)
+            logger.debug(f'Stepping agent {agent_id}')
+
+            when = (self._agents[agent_id].step() or Delta(1)).abs(self.time)
+            if when < self.time:
+                raise Exception("Cannot schedule an agent for a time in the past ({} < {})".format(when, self.time))
+
+            heappush(self._queue, (when, agent_id))
+
+        self.steps += 1
 
         if not self._queue:
-            self.time = until
+            self.time = INFINITY
-            self.next_time = float('inf')
+            self.next_time = INFINITY
             return
 
-        (when, agent_id) = self._queue[0]
+        self.next_time = self._queue[0][0]
 
-        if until and when > until:
-            self.time = until
-            self.next_time = when
-            return
-
-        self.time = when
-        next_time = float("inf")
-
-        while when == self.time:
-            heappop(self._queue)
-            logger.debug(f'Stepping agent {agent_id}')
-            when = (self._agents[agent_id].step() or Delta(1)).abs(self.time)
-            heappush(self._queue, (when, agent_id))
-            if when < next_time:
-                next_time = when
-
-            if not self._queue or self._queue[0][0] > self.time:
-                agent_id = None
-                break
-            else:
-                (when, agent_id) = self._queue[0]
-
-        if when and when < self.time:
-            raise Exception("Invalid scheduling time")
-
-        self.next_time = next_time
-        self.steps += 1

tests/test_main.py

@@ -127,7 +127,7 @@ class TestMain(TestCase):
         env = s.run_simulation(dry_run=True)[0]
         for agent in env.network_agents:
             last = 0
-            assert len(agent[None, None]) == 11
+            assert len(agent[None, None]) == 10
             for step, total in sorted(agent['total', None]):
                 assert total == last + 2
                 last = total