WIP: all tests pass

examples/rabbits/improved/rabbit_agents.py

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+from soil.agents import FSM, state, default_state, BaseAgent, NetworkAgent
+from soil.time import Delta, When, NEVER
+from enum import Enum
+import logging
+import math
+
+
+class RabbitModel(FSM, NetworkAgent):
+
+    mating_prob = 0.005
+    offspring = 0
+    birth = None
+
+    sexual_maturity = 3
+    life_expectancy = 30
+
+    @default_state
+    @state
+    def newborn(self):
+        self.birth = self.now
+        self.info(f'I am a newborn.')
+        self.model['rabbits_alive'] = self.model.get('rabbits_alive', 0) + 1
+
+        # Here we can skip the `youngling` state by using a coroutine/generator. 
+        while self.age < self.sexual_maturity:
+            interval = self.sexual_maturity - self.age
+            yield Delta(interval)
+
+        self.info(f'I am fertile! My age is {self.age}')
+        return self.fertile
+
+    @property
+    def age(self):
+        return self.now - self.birth
+
+    @state
+    def fertile(self):
+        raise Exception("Each subclass should define its fertile state")
+
+    def step(self):
+        super().step()
+        if self.prob(self.age / self.life_expectancy):
+            return self.die()
+
+
+class Male(RabbitModel):
+
+    max_females = 5
+
+    @state
+    def fertile(self):
+        # Males try to mate
+        for f in self.model.agents(agent_class=Female,
+                                   state_id=Female.fertile.id,
+                                   limit=self.max_females):
+            self.debug('Found a female:', repr(f))
+            if self.prob(self['mating_prob']):
+                f.impregnate(self)
+                break  # Take a break, don't try to impregnate the rest
+
+            
+class Female(RabbitModel):
+    due_date = None
+    age_of_pregnancy = None
+    gestation = 10
+    mate = None
+
+    @state
+    def fertile(self):
+        return self.fertile, NEVER
+
+    @state
+    def pregnant(self):
+        self.info('I am pregnant')
+        if self.age > self.life_expectancy:
+            return self.dead
+
+        self.due_date = self.now + self.gestation
+
+        number_of_babies = int(8+4*self.random.random())
+
+        while self.now < self.due_date:
+            yield When(self.due_date)
+
+        self.info('Having {} babies'.format(number_of_babies))
+        for i in range(number_of_babies):
+            agent_class = self.random.choice([Male, Female])
+            child = self.model.add_node(agent_class=agent_class,
+                                        topology=self.topology)
+            self.model.add_edge(self, child)
+            self.model.add_edge(self.mate, child)
+            self.offspring += 1
+            self.model.agents[self.mate].offspring += 1
+        self.mate = None
+        self.due_date = None
+        return self.fertile
+
+    @state
+    def dead(self):
+        super().dead()
+        if self.due_date is not None:
+            self.info('A mother has died carrying a baby!!')
+
+    def impregnate(self, male):
+        self.info(f'{repr(male)} impregnating female {repr(self)}')
+        self.mate = male
+        self.set_state(self.pregnant, when=self.now)
+
+
+class RandomAccident(BaseAgent):
+
+    level = logging.INFO
+
+    def step(self):
+        rabbits_total = self.model.topology.number_of_nodes()
+        if 'rabbits_alive' not in self.model:
+            self.model['rabbits_alive'] = 0
+        rabbits_alive = self.model.get('rabbits_alive', rabbits_total)
+        prob_death = self.model.get('prob_death', 1e-100)*math.floor(math.log10(max(1, rabbits_alive)))
+        self.debug('Killing some rabbits with prob={}!'.format(prob_death))
+        for i in self.model.network_agents:
+            if i.state.id == i.dead.id:
+                continue
+            if self.prob(prob_death):
+                self.info('I killed a rabbit: {}'.format(i.id))
+                rabbits_alive = self.model['rabbits_alive'] = rabbits_alive -1
+                i.set_state(i.dead)
+        self.debug('Rabbits alive: {}/{}'.format(rabbits_alive, rabbits_total))
+        if self.model.count_agents(state_id=RabbitModel.dead.id) == self.model.topology.number_of_nodes():
+            self.die()

examples/rabbits/improved/rabbits.yml

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+---
+version: '2'
+name: rabbits_improved
+num_trials: 1
+seed: MySeed
+description: null
+group: null
+interval: 1.0
+max_time: 100
+model_class: soil.environment.Environment
+model_params:
+  agents:
+    topology: default
+    agent_class: rabbit_agents.RabbitModel
+    distribution:
+    - agent_class: rabbit_agents.Male
+      topology: default
+      weight: 1
+    - agent_class: rabbit_agents.Female
+      topology: default
+      weight: 1
+    fixed:
+    - agent_class: rabbit_agents.RandomAccident
+      topology: null
+      hidden: true
+      state:
+        group: environment
+    state:
+      group: network
+      mating_prob: 0.1
+  prob_death: 0.001
+  topologies:
+    default:
+      topology:
+        directed: true
+        links: []
+        nodes:
+        - id: 1
+        - id: 0
+extra:
+  visualization_params: {}