Fix gephi representation. Add sqlite

examples/rabbits/rabbit_agents.py

@@ -0,0 +1,119 @@
+from soil.agents import NetworkAgent, FSM, state, default_state, BaseAgent
+from enum import Enum
+from random import random, choice
+from itertools import islice
+import logging
+import math
+
+
+class Genders(Enum):
+    male = 'male'
+    female = 'female'
+
+
+class RabbitModel(NetworkAgent, FSM):
+
+    level = logging.INFO
+
+    defaults = {
+        'age': 0,
+        'gender': Genders.male.value,
+        'mating_prob': 0.001,
+        'offspring': 0,
+    }
+
+    sexual_maturity = 4*30
+    life_expectancy = 365 * 3
+    gestation = 33
+    pregnancy = -1
+    max_females = 2
+
+    @default_state
+    @state
+    def newborn(self):
+        self['age'] += 1
+
+        if self['age'] >= self.sexual_maturity:
+            return self.fertile
+
+    @state
+    def fertile(self):
+        self['age'] += 1
+        if self['age'] > self.life_expectancy:
+            return self.dead
+
+        if self['gender'] == Genders.female.value:
+            return
+
+        # Males try to mate
+        females = self.get_agents(state_id=self.fertile.id, gender=Genders.female.value, limit_neighbors=False)
+        for f in islice(females, 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))
+
+    @state
+    def pregnant(self):
+        self['age'] += 1
+        if self['age'] > self.life_expectancy:
+            return self.dead
+
+        self['pregnancy'] += 1
+        self.debug('Pregnancy: {}'.format(self['pregnancy']))
+        if self['pregnancy'] >= self.gestation:
+            number_of_babies = int(8+4*random())
+            for i in range(number_of_babies):
+                state = {}
+                state['gender'] = choice(list(Genders)).value
+                child = self.env.add_node(self.__class__, state)
+                self.env.add_edge(self.id, child.id)
+                self.env.add_edge(self['mate'], child.id)
+                # self.add_edge()
+                self.debug('A BABY IS COMING TO LIFE')
+                self.env['rabbits_alive'] = self.env.get('rabbits_alive', 0)+1
+                self.debug('Rabbits alive: {}'.format(self.env['rabbits_alive']))
+                self['offspring'] += 1
+                self.env.get_agent(self['mate'])['offspring'] += 1
+                del self['mate']
+                self['pregnancy'] = -1
+                return self.fertile
+
+    @state
+    def dead(self):
+        self.info('Agent {} is dying'.format(self.id))
+        if 'pregnancy' in self and self['pregnancy'] > -1:
+            self.info('A mother has died carrying a baby!!')
+        self.die()
+        return
+
+
+class RandomAccident(BaseAgent):
+
+    level = logging.INFO
+
+    def step(self):
+        rabbits_total = self.global_topology.number_of_nodes()
+        rabbits_alive = self.env.get('rabbits_alive', rabbits_total)
+        prob_death = self.env.get('prob_death', 1e-100)*math.log(max(1, rabbits_alive))
+        self.debug('Killing some rabbits with prob={}!'.format(prob_death))
+        for i in self.env.network_agents:
+            if i.state['id'] == i.dead.id:
+                continue
+            r = random()
+            if r < prob_death:
+                self.debug('I killed a rabbit: {}'.format(i.id))
+                rabbits_alive = self.env['rabbits_alive'] = rabbits_alive -1
+                self.log('Rabbits alive: {}'.format(self.env['rabbits_alive']))
+                i.set_state(i.dead)
+        self.log('Rabbits alive: {}/{}'.format(rabbits_alive, rabbits_total))
+        if self.count_agents(state_id=RabbitModel.dead.id) == self.global_topology.number_of_nodes():
+            self.die()

examples/rabbits/rabbits.yml

@@ -0,0 +1,23 @@
+---
+load_module: rabbit_agents
+name: rabbits_example
+max_time: 1500
+interval: 1
+seed: MySeed
+agent_type: RabbitModel
+environment_agents:
+    - agent_type: RandomAccident
+environment_params:
+  prob_death: 0.0001
+default_state:
+  mating_prob: 0.01
+topology:
+  nodes:
+    - id: 1
+      state:
+        gender: female
+    - id: 0
+      state:
+        gender: male
+  directed: true
+  links: []