Fix state and networkx dynamic attributes

soil/VERSION

@@ -1 +1 @@
-0.11.1
+0.11.3

soil/agents/__init__.py

@@ -53,7 +53,7 @@ class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
         self.alive = True
         real_state = deepcopy(self.defaults)
         real_state.update(state or {})
-        self._state = real_state
+        self.state = real_state
         self.interval = interval
 
         if not hasattr(self, 'level'):
@@ -67,10 +67,17 @@ class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
 
     @property
     def state(self):
-        return self._state
+        '''
+        Return the agent itself, which behaves as a dictionary.
+        Changes made to `agent.state` will be reflected in the history.
+
+        This method shouldn't be used, but is kept here for backwards compatibility.
+        '''
+        return self
 
     @state.setter
     def state(self, value):
+        self._state = {}
         for k, v in value.items():
             self[k] = v
 
@@ -79,21 +86,24 @@ class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
             key, t_step = key
             k = history.Key(key=key, t_step=t_step, agent_id=self.id)
             return self.env[k]
-        return self.state.get(key, None)
+        return self._state.get(key, None)
 
     def __delitem__(self, key):
-        self.state[key] = None
+        self._state[key] = None
 
     def __contains__(self, key):
-        return key in self.state
+        return key in self._state
 
     def __setitem__(self, key, value):
-        self.state[key] = value
+        self._state[key] = value
         k = history.Key(t_step=self.now,
                         agent_id=self.id,
                         key=key)
         self.env[k] = value
 
+    def items(self):
+        return self._state.items()
+
     def get(self, key, default=None):
         return self[key] if key in self else default
 

soil/environment.py

@@ -263,31 +263,30 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
             history = self[agent.id, None, None]
             if not history:
                 continue
-            for t_step, state in reversed(sorted(list(history.items()))):
+            for t_step, attribute, value in sorted(list(history)):
-                for attribute, value in state.items():
+                if attribute == 'visible':
-                    if attribute == 'visible':
+                    nowvisible = value
-                        nowvisible = state[attribute]
+                    if nowvisible and not lastvisible:
-                        if nowvisible and not lastvisible:
+                        laststep = t_step
-                            laststep = t_step
+                    if not nowvisible and lastvisible:
-                        if not nowvisible and lastvisible:
+                        spells.append((laststep, t_step))
-                            spells.append((laststep, t_step))
 
-                        lastvisible = nowvisible
+                    lastvisible = nowvisible
-                    else:
+                    continue
-                        key = 'attr_' + attribute
+                key = 'attr_' + attribute
-                        if key not in attributes:
+                if key not in attributes:
-                            attributes[key] = list()
+                    attributes[key] = list()
-                        if key not in lastattributes:
+                if key not in lastattributes:
-                            lastattributes[key] = (state[attribute], t_step)
+                    lastattributes[key] = (value, t_step)
-                        elif lastattributes[key][0] != value:
+                elif lastattributes[key][0] != value:
-                            last_value, laststep = lastattributes[key]
+                    last_value, laststep = lastattributes[key]
-                            value = (last_value, t_step, laststep)
+                    commit_value = (last_value, laststep, t_step)
-                            if key not in attributes:
+                    if key not in attributes:
-                                attributes[key] = list()
+                        attributes[key] = list()
-                            attributes[key].append(value)
+                    attributes[key].append(commit_value)
-                            lastattributes[key] = (state[attribute], t_step)
+                    lastattributes[key] = (value, t_step)
             for k, v in lastattributes.items():
-                attributes[k].append((v[0], 0, v[1]))
+                attributes[k].append((v[0], v[1], None))
             if lastvisible:
                 spells.append((laststep, None))
             if spells:

soil/history.py

@@ -102,7 +102,9 @@ class History:
                            t_steps=t_steps,
                            keys=keys)
         r = Records(df, filter=key, dtypes=self._dtypes)
-        return r.value()
+        if r.resolved:
+            return r.value()
+        return r
 
 
 
@@ -216,16 +218,23 @@ class Records():
                 return i.iloc[ix]
             except KeyError:
                 return self.dtypes[f.key][2]()
-        return self
+        return list(self)
 
     def __getitem__(self, k):
         n = copy.copy(self)
         n.filter(k)
-        return n.value()
+        if n.resolved:
+            return n.value()
+        return n
 
     def __len__(self):
         return len(self._df)
 
+    def __str__(self):
+        if self.resolved:
+            return str(self.value())
+        return '<Records for [{}]>'.format(self._filter)
+
 
 Key = namedtuple('Key', ['agent_id', 't_step', 'key'])
 Record = namedtuple('Record', 'agent_id t_step key value')

tests/test_main.py

@@ -233,10 +233,26 @@ class TestMain(TestCase):
         There is a bug in networkx that prevents it from creating a GEXF file 
         from geometric models. We should work around it.
         """
-        G = nx.random_geometric_graph(20,0.1)
+        G = nx.random_geometric_graph(20, 0.1)
         env = environment.SoilEnvironment(topology=G, dry_run=True)
         env.dump_gexf('/tmp/dump-gexf')
 
+    def test_save_graph(self):
+        '''
+        The history_to_graph method should return a valid networkx graph.
+
+        The state of the agent should be encoded as intervals in the nx graph.
+        '''
+        G = nx.cycle_graph(5)
+        distribution = agents.calculate_distribution(None, agents.BaseAgent)
+        env = environment.SoilEnvironment(topology=G, network_agents=distribution, dry_run=True)
+        env[0, 0, 'testvalue'] = 'start'
+        env[0, 10, 'testvalue'] = 'finish'
+        nG = env.history_to_graph()
+        values = nG.node[0]['attr_testvalue']
+        assert ('start', 0, 10) in values
+        assert ('finish', 10, None) in values
+
 
 def make_example_test(path, config):
     def wrapped(self):