Added history class

Now the environment does not deal with history directly, it delegates it to a
specific class. The analysis also uses history instances instead of either
using the database directly or creating a proxy environment.

This should make it easier to change the implementation in the future.

In fact, the change was motivated by the large size of the csv files in previous
versions. This new implementation only stores results in deltas, and it fills
any necessary values when needed.

tests/test_main.py

@@ -22,6 +22,7 @@ class TestMain(TestCase):
         Raise an exception otherwise.
         """
         config = {
+            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             }
@@ -31,6 +32,7 @@ class TestMain(TestCase):
         assert len(G) == 2
         with self.assertRaises(AttributeError):
             config = {
+            'dry_run': True,
                 'network_params': {
                     'path': join(ROOT, 'unknown.extension')
                 }
@@ -44,6 +46,7 @@ class TestMain(TestCase):
         should be used to generate a network
         """
         config = {
+            'dry_run': True,
             'network_params': {
                 'generator': 'barabasi_albert_graph'
             }
@@ -58,6 +61,7 @@ class TestMain(TestCase):
     def test_empty_simulation(self):
         """A simulation with a base behaviour should do nothing"""
         config = {
+            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             },
@@ -74,11 +78,12 @@ class TestMain(TestCase):
         agent should be able to update its state."""
         config = {
             'name': 'CounterAgent',
+            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             },
             'agent_type': 'CounterModel',
-            'states': [{'neighbors': 10}, {'total': 12}],
+            'states': [{'times': 10}, {'times': 20}],
             'max_time': 2,
             'num_trials': 1,
             'environment_params': {
@@ -86,10 +91,10 @@ class TestMain(TestCase):
         }
         s = simulation.from_config(config)
         env = s.run_simulation(dry_run=True)[0]
-        assert env.get_agent(0)['neighbors', 0] == 10
-        assert env.get_agent(0)['neighbors', 1] == 1
-        assert env.get_agent(1)['total', 0] == 12
-        assert env.get_agent(1)['neighbors', 1] == 1
+        assert env.get_agent(0)['times', 0] == 11
+        assert env.get_agent(0)['times', 1] == 12
+        assert env.get_agent(1)['times', 0] == 21
+        assert env.get_agent(1)['times', 1] == 22
 
     def test_counter_agent_history(self):
         """
@@ -97,6 +102,7 @@ class TestMain(TestCase):
         """
         config = {
             'name': 'CounterAgent',
+            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             },
@@ -114,11 +120,10 @@ class TestMain(TestCase):
         env = s.run_simulation(dry_run=True)[0]
         for agent in env.network_agents:
             last = 0
-            assert len(agent[None, None]) == 11
-            for step, total in agent['total', None].items():
-                if step > 0:
-                    assert total == last + 2
-                    last = total
+            assert len(agent[None, None]) == 10
+            for step, total in sorted(agent['total', None]):
+                assert total == last + 2
+                last = total
 
     def test_custom_agent(self):
         """Allow for search of neighbors with a certain state_id"""
@@ -127,6 +132,7 @@ class TestMain(TestCase):
                 self.state['neighbors'] = self.count_agents(state_id=0,
                                                             limit_neighbors=True)
         config = {
+            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             },
@@ -150,7 +156,8 @@ class TestMain(TestCase):
         config['network_params']['path'] = join(EXAMPLES,
                                                 config['network_params']['path'])
         s = simulation.from_config(config)
-        env = s.run_simulation(dry_run=True)[0]
+        s.dry_run = True
+        env = s.run_simulation()[0]
         for a in env.network_agents:
             skill_level = a.state['skill_level']
             if a.id == 'Torvalds':
@@ -174,14 +181,15 @@ class TestMain(TestCase):
         with utils.timer('loading'):
             config = utils.load_file(join(EXAMPLES, 'complete.yml'))[0]
             s = simulation.from_config(config)
+            s.dry_run = True
         with utils.timer('serializing'):
             serial = s.to_yaml()
         with utils.timer('recovering'):
             recovered = yaml.load(serial)
         with utils.timer('deleting'):
             del recovered['topology']
-            del recovered['dry_run']
             del recovered['load_module']
+            del recovered['dry_run']
         assert config == recovered
 
     def test_configuration_changes(self):
@@ -191,6 +199,7 @@ class TestMain(TestCase):
         """
         config = utils.load_file('examples/complete.yml')[0]
         s = simulation.from_config(config)
+        s.dry_run = True
         for i in range(5):
             s.run_simulation(dry_run=True)
             nconfig = s.to_dict()
@@ -206,17 +215,14 @@ class TestMain(TestCase):
         pass
 
     def test_row_conversion(self):
-        sim = simulation.SoilSimulation()
         env = environment.SoilEnvironment(dry_run=True)
         env['test'] = 'test_value'
-        env._save_state(now=0)
 
         res = list(env.history_to_tuples())
         assert len(res) == len(env.environment_params)
-        assert ('env', 0, 'test', 'test_value', 'str') in res
 
+        env._now = 1
         env['test'] = 'second_value'
-        env._save_state(now=1)
         res = list(env.history_to_tuples())
 
         assert env['env', 0, 'test' ] == 'test_value'