Improved docs

Fixed several bugs
Added convenience methods in soil.analysis

soil/agents/BassModel.py

@@ -1,8 +1,8 @@
 import random
-from . import NetworkAgent
+from . import BaseAgent
 
 
-class BassModel(NetworkAgent):
+class BassModel(BaseAgent):
     """
     Settings:
         innovation_prob

soil/agents/BigMarketModel.py

@@ -1,8 +1,8 @@
 import random
-from . import NetworkAgent
+from . import BaseAgent
 
 
-class BigMarketModel(NetworkAgent):
+class BigMarketModel(BaseAgent):
     """
     Settings:
         Names:

soil/agents/CounterModel.py

@@ -1,7 +1,7 @@
-from . import NetworkAgent
+from . import BaseAgent
 
 
-class CounterModel(NetworkAgent):
+class CounterModel(BaseAgent):
     """
     Dummy behaviour. It counts the number of nodes in the network and neighbors
     in each step and adds it to its state.
@@ -16,7 +16,7 @@ class CounterModel(NetworkAgent):
         self.state['total'] = total
 
 
-class AggregatedCounter(NetworkAgent):
+class AggregatedCounter(BaseAgent):
     """
     Dummy behaviour. It counts the number of nodes in the network and neighbors
     in each step and adds it to its state.
@@ -28,4 +28,5 @@ class AggregatedCounter(NetworkAgent):
         neighbors = len(list(self.get_neighboring_agents()))
         self.state['times'] = self.state.get('times', 0) + 1
         self.state['neighbors'] = self.state.get('neighbors', 0) + neighbors
-        self.state['total'] = self.state.get('total', 0) + total
+        self.state['total'] = total = self.state.get('total', 0) + total
+        self.debug('Running for step: {}. Total: {}'.format(self.now, total))

soil/agents/ModelM2.py

@@ -1,9 +1,9 @@
 import random
 import numpy as np
-from . import NetworkAgent
+from . import BaseAgent
 
 
-class SpreadModelM2(NetworkAgent):
+class SpreadModelM2(BaseAgent):
     """
     Settings:
         prob_neutral_making_denier
@@ -104,7 +104,7 @@ class SpreadModelM2(NetworkAgent):
                 neighbor.state['id'] = 2  # Cured
 
 
-class ControlModelM2(NetworkAgent):
+class ControlModelM2(BaseAgent):
     """
     Settings:
         prob_neutral_making_denier

soil/agents/SISaModel.py

@@ -1,9 +1,9 @@
 import random
 import numpy as np
-from . import FSM, NetworkAgent, state
+from . import FSM, state
 
 
-class SISaModel(FSM, NetworkAgent):
+class SISaModel(FSM):
     """
     Settings:
         neutral_discontent_spon_prob

soil/agents/SentimentCorrelationModel.py

@@ -1,8 +1,8 @@
 import random
-from . import NetworkAgent
+from . import BaseAgent
 
 
-class SentimentCorrelationModel(NetworkAgent):
+class SentimentCorrelationModel(BaseAgent):
     """
     Settings:
         outside_effects_prob

soil/agents/__init__.py

@@ -72,9 +72,10 @@ class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
             return None
 
     def run(self):
+        interval = self.env.interval
         while self.alive:
             res = self.step()
-            yield res or self.env.timeout(self.env.interval)
+            yield res or self.env.timeout(interval)
 
     def die(self, remove=False):
         self.alive = False
@@ -99,7 +100,10 @@ class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
             count += 1
         return count
 
-    def get_agents(self, state_id=None, limit_neighbors=False, **kwargs):
+    def count_neighboring_agents(self, state_id=None):
+        return len(super().get_agents(state_id, limit_neighbors=True))
+
+    def get_agents(self, state_id=None, limit_neighbors=False, iterator=False, **kwargs):
         if limit_neighbors:
             agents = super().get_agents(state_id, limit_neighbors)
         else:
@@ -113,9 +117,13 @@ class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
                     return False
             return True
 
-        return filter(matches_all, agents)
+        f = filter(matches_all, agents)
+        if iterator:
+            return f
+        return list(f)
 
-    def log(self, message, level=logging.INFO, **kwargs):
+    def log(self, message, *args, level=logging.INFO, **kwargs):
+        message = message + " ".join(str(i) for i in args)
         message = "\t@{:>5}:\t{}".format(self.now, message)
         for k, v in kwargs:
             message += " {k}={v} ".format(k, v)
@@ -130,11 +138,6 @@ class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
     def info(self, *args, **kwargs):
         return self.log(*args, level=logging.INFO, **kwargs)
 
-class NetworkAgent(BaseAgent, nxsim.BaseNetworkAgent):
-
-    def count_neighboring_agents(self, state_id=None):
-        return self.count_agents(state_id, limit_neighbors=True)
-
 
 def state(func):
 
@@ -150,7 +153,7 @@ def state(func):
             try:
                 self.state['id'] = next_state.id
             except AttributeError:
-                raise NotImplemented('State id %s is not valid.' % next_state)
+                raise ValueError('State id %s is not valid.' % next_state)
         return when
 
     func_wrapper.id = func.__name__