Fix multithreading

Multithreading needs pickling to work.
Pickling/unpickling didn't work in some situations, like when the
environment_agents parameter was left blank.
This was due to two reasons:

1) agents and history didn't have a setstate method, and some of their
attributes cannot be pickled (generators, sqlite connection)
2) the environment was adding generators (agents) to its state.

This fixes the situation by restricting the keys that the environment exports
when it pickles, and by adding the set/getstate methods in agents.

The resulting pickles should contain enough information to inspect
them (history, state values, etc), but very limited.

soil/agents/__init__.py

@@ -24,7 +24,7 @@ class BaseAgent(nxsim.BaseAgent):
 
     defaults = {}
 
-    def __init__(self, environment, agent_id=None, state=None,
+    def __init__(self, environment, agent_id, state=None,
                  name='network_process', interval=None, **state_params):
         # Check for REQUIRED arguments
         assert environment is not None, TypeError('__init__ missing 1 required keyword argument: \'environment\'. '
@@ -34,10 +34,6 @@ class BaseAgent(nxsim.BaseAgent):
         self.name = name
         self.state_params = state_params
 
-        # Global parameters
-        self.global_topology = environment.G
-        self.environment_params = environment.environment_params
-
         # Register agent to environment
         self.env = environment
 
@@ -73,6 +69,18 @@ class BaseAgent(nxsim.BaseAgent):
         for k, v in value.items():
             self[k] = v
 
+    @property
+    def global_topology(self):
+        return self.env.G
+    
+    @property
+    def environment_params(self):
+        return self.env.environment_params
+    
+    @environment_params.setter
+    def environment_params(self, value):
+        self.env.environment_params = value
+
     def __getitem__(self, key):
         if isinstance(key, tuple):
             key, t_step = key
@@ -126,9 +134,6 @@ class BaseAgent(nxsim.BaseAgent):
     def step(self):
         pass
 
-    def to_json(self):
-        return json.dumps(self.state)
-
     def count_agents(self, state_id=None, limit_neighbors=False):
         if limit_neighbors:
             agents = self.global_topology.neighbors(self.id)
@@ -182,6 +187,26 @@ class BaseAgent(nxsim.BaseAgent):
 
     def info(self, *args, **kwargs):
         return self.log(*args, level=logging.INFO, **kwargs)
+    
+    def __getstate__(self):
+        '''
+        Serializing an agent will lose all its running information (you cannot
+        serialize an iterator), but it keeps the state and link to the environment,
+        so it can be used for inspection and dumping to a file
+        '''
+        state = {}
+        state['id'] = self.id
+        state['environment'] = self.env
+        state['_state'] = self._state
+        return state
+
+    def __setstate__(self, state):
+        '''
+        Get back a serialized agent and try to re-compose it
+        '''
+        self.id = state['id']
+        self._state = state['_state']
+        self.env = state['environment']
 
 
 def state(func):
@@ -336,7 +361,7 @@ def serialize_distribution(network_agents, known_modules=[]):
     When serializing an agent distribution, remove the thresholds, in order
     to avoid cluttering the YAML definition file.
     '''
-    d = deepcopy(network_agents)
+    d = deepcopy(list(network_agents))
     for v in d:
         if 'threshold' in v:
             del v['threshold']