Fix gephi representation. Add sqlite

examples/complete.yml

@@ -4,6 +4,8 @@ dir_path: "/tmp/"
 num_trials: 3
 max_time: 100
 interval: 1
+seed: "CompleteSeed!"
+dump: false
 network_params:
   generator: complete_graph
   n: 10
@@ -21,4 +23,4 @@ default_state:
   incidents: 0
 states:
   - name: 'The first node'
-  - name: 'The second node'
+  - name: 'The second node'

examples/rabbits/rabbit_agents.py

@@ -1,10 +1,10 @@
-import logging
 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
 
-logger = logging.getLogger(__name__)
 
 class Genders(Enum):
     male = 'male'
@@ -13,6 +13,8 @@ class Genders(Enum):
 
 class RabbitModel(NetworkAgent, FSM):
 
+    level = logging.INFO
+
     defaults = {
         'age': 0,
         'gender': Genders.male.value,
@@ -24,7 +26,7 @@ class RabbitModel(NetworkAgent, FSM):
     life_expectancy = 365 * 3
     gestation = 33
     pregnancy = -1
-    max_females = 10
+    max_females = 2
 
     @default_state
     @state
@@ -57,7 +59,7 @@ class RabbitModel(NetworkAgent, FSM):
         whom['pregnancy'] = 0
         whom['mate'] = self.id
         whom.set_state(whom.pregnant)
-        logger.debug('{} impregnating: {}. {}'.format(self.id, whom.id, whom.state))
+        self.debug('{} impregnating: {}. {}'.format(self.id, whom.id, whom.state))
 
     @state
     def pregnant(self):
@@ -66,38 +68,52 @@ class RabbitModel(NetworkAgent, FSM):
             return self.dead
 
         self['pregnancy'] += 1
-        logger.debug('Pregnancy: {}'.format(self['pregnancy']))
+        self.debug('Pregnancy: {}'.format(self['pregnancy']))
         if self['pregnancy'] >= self.gestation:
-
-            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()
-            logger.info("A rabbit has been born: {}. Total: {}".format(child.id, len(self.global_topology.nodes)))
-            self['offspring'] += 1
-            self.env.get_agent(self['mate'])['offspring'] += 1
-            del self['mate']
-            self['pregnancy'] = -1
-            return self.fertile
+            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):
-        logger.info('Agent {} is dying'.format(self.id))
+        self.info('Agent {} is dying'.format(self.id))
         if 'pregnancy' in self and self['pregnancy'] > -1:
-            logger.info('A mother has died carrying a baby!: {}!'.format(self.state))
+            self.info('A mother has died carrying a baby!!')
         self.die()
         return
 
 
 class RandomAccident(BaseAgent):
 
+    level = logging.INFO
+
     def step(self):
-        logger.debug('Killing some rabbits!')
-        prob_death = self.env.get('prob_death', -1)
+        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:
-                logger.info('I killed a rabbit: {}'.format(i.id))
+                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

@@ -1,14 +1,16 @@
 ---
-load_module: custom_agents
-name: custom_agent_example
-max_time: 2500
+load_module: rabbit_agents
+name: rabbits_example
+max_time: 1500
 interval: 1
-seed: MySimulationSeed
+seed: MySeed
 agent_type: RabbitModel
 environment_agents:
     - agent_type: RandomAccident
+environment_params:
+  prob_death: 0.0001
 default_state:
-  mating_prob: 1
+  mating_prob: 0.01
 topology:
   nodes:
     - id: 1