WIP: all tests pass

Documentation needs some improvement

The API has been simplified to only allow for ONE topology per
NetworkEnvironment.
This covers the main use case, and simplifies the code.

examples/rabbits/basic/rabbit_agents.py

@@ -57,7 +57,7 @@ class Male(RabbitModel):
 
 
 class Female(RabbitModel):
-    gestation = 100
+    gestation = 30
 
     @state
     def fertile(self):
@@ -72,10 +72,10 @@ class Female(RabbitModel):
         self.pregnancy = -1
         self.set_state(self.pregnant, when=self.now)
         self.number_of_babies = int(8+4*self.random.random())
-        self.debug('I am pregnant')
 
     @state
     def pregnant(self):
+        self.debug('I am pregnant')
         self.age += 1
         self.pregnancy += 1
 
@@ -88,7 +88,6 @@ class Female(RabbitModel):
                 state = {}
                 agent_class = self.random.choice([Male, Female])
                 child = self.model.add_node(agent_class=agent_class,
-                                            topology=self.topology,
                                             **state)
                 child.add_edge(self)
                 try:
@@ -113,7 +112,7 @@ class RandomAccident(BaseAgent):
     level = logging.INFO
 
     def step(self):
-        rabbits_alive = self.model.topology.number_of_nodes()
+        rabbits_alive = self.model.G.number_of_nodes()
 
         if not rabbits_alive:
             return self.die()
@@ -121,10 +120,15 @@ class RandomAccident(BaseAgent):
         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.iter_agents(agent_class=RabbitModel):
-            if i.state.id == i.dead.id:
+            if i.state_id == i.dead.id:
                 continue
             if self.prob(prob_death):
                 self.info('I killed a rabbit: {}'.format(i.id))
                 rabbits_alive -= 1
                 i.set_state(i.dead)
         self.debug('Rabbits alive: {}'.format(rabbits_alive))
+
+if __name__ == '__main__':
+    from soil import easy
+    sim = easy('rabbits.yml')
+    sim.run()

examples/rabbits/basic/rabbits.yml

@@ -10,18 +10,16 @@ max_time: 100
 model_class: soil.environment.Environment
 model_params:
   agents:
-    topology: default
+    topology: true
     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
+      topology: false
       hidden: true
       state:
         group: environment
@@ -29,13 +27,12 @@ model_params:
       group: network
       mating_prob: 0.1
   prob_death: 0.001
-  topologies:
-    default:
-      topology:
-        directed: true
-        links: []
-        nodes:
-        - id: 1
-        - id: 0
+  topology:
+    fixed:
+      directed: true
+      links: []
+      nodes:
+      - id: 1
+      - id: 0
 extra:
   visualization_params: {}

examples/rabbits/improved/rabbits.yml

@@ -10,18 +10,16 @@ max_time: 100
 model_class: soil.environment.Environment
 model_params:
   agents:
-    topology: default
+    topology: true
     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
+      topology: false
       hidden: true
       state:
         group: environment
@@ -29,13 +27,12 @@ model_params:
       group: network
       mating_prob: 0.1
   prob_death: 0.001
-  topologies:
-    default:
-      topology:
-        directed: true
-        links: []
-        nodes:
-        - id: 1
-        - id: 0
+  topology:
+    fixed:
+      directed: true
+      links: []
+      nodes:
+      - id: 1
+      - id: 0
 extra:
   visualization_params: {}