Refactoring v0.15.1

See CHANGELOG.md for a full list of changes

* Removed nxsim
* Refactored `agents.NetworkAgent` and `agents.BaseAgent`
* Refactored exporters
* Added stats to history

tests/test_analysis.py

@@ -66,8 +66,8 @@ class TestAnalysis(TestCase):
         env = self.env
         df = analysis.read_sql(env._history.db_path)
         res = analysis.get_count(df, 'SEED', 'id')
-        assert res['SEED']['seedanalysis_trial_0'].iloc[0] == 1
-        assert res['SEED']['seedanalysis_trial_0'].iloc[-1] == 1
+        assert res['SEED'][self.env['SEED']].iloc[0] == 1
+        assert res['SEED'][self.env['SEED']].iloc[-1] == 1
         assert res['id']['odd'].iloc[0] == 2
         assert res['id']['even'].iloc[0] == 0
         assert res['id']['odd'].iloc[-1] == 1
@@ -75,7 +75,7 @@ class TestAnalysis(TestCase):
 
     def test_value(self):
         env = self.env
-        df = analysis.read_sql(env._history._db)
+        df = analysis.read_sql(env._history.db_path)
         res_sum = analysis.get_value(df, 'count')
 
         assert res_sum['count'].iloc[0] == 2
@@ -86,4 +86,4 @@ class TestAnalysis(TestCase):
 
         res_total = analysis.get_value(df)
 
-        res_total['SEED'].iloc[0] == 'seedanalysis_trial_0'
+        res_total['SEED'].iloc[0] == self.env['SEED']

tests/test_examples.py

@@ -31,7 +31,7 @@ def make_example_test(path, config):
                 try:
                     n = config['network_params']['n']
                     assert len(list(env.network_agents)) == n
-                    assert env.now > 2  # It has run
+                    assert env.now > 0  # It has run
                     assert env.now <= config['max_time']  # But not further than allowed
                 except KeyError:
                     pass

tests/test_exporters.py

@@ -6,26 +6,32 @@ from time import time
 
 from unittest import TestCase
 from soil import exporters
-from soil.utils import safe_open
 from soil import simulation
 
+from soil.stats import distribution
 
 class Dummy(exporters.Exporter):
     started = False
     trials = 0
     ended = False
     total_time = 0
+    called_start = 0
+    called_trial = 0
+    called_end = 0
 
     def start(self):
+        self.__class__.called_start += 1
         self.__class__.started = True
 
-    def trial_end(self, env):
+    def trial(self, env, stats):
         assert env
         self.__class__.trials += 1
         self.__class__.total_time += env.now
+        self.__class__.called_trial += 1
 
-    def end(self):
+    def end(self, stats):
         self.__class__.ended = True
+        self.__class__.called_end += 1
 
 
 class Exporters(TestCase):
@@ -39,32 +45,17 @@ class Exporters(TestCase):
             'environment_params': {}
         }
         s = simulation.from_config(config)
-        s.run_simulation(exporters=[Dummy], dry_run=True)
+        for env in s.run_simulation(exporters=[Dummy], dry_run=True):
+            assert env.now <= 2
+
         assert Dummy.started
         assert Dummy.ended
+        assert Dummy.called_start == 1
+        assert Dummy.called_end == 1
+        assert Dummy.called_trial == 5
         assert Dummy.trials == 5
         assert Dummy.total_time == 2*5
 
-    def test_distribution(self):
-        '''The distribution exporter should write the number of agents in each state'''
-        config = {
-            'name': 'exporter_sim',
-            'network_params': {
-                'generator': 'complete_graph',
-                'n': 4
-            },
-            'agent_type': 'CounterModel',
-            'max_time': 2,
-            'num_trials': 5,
-            'environment_params': {}
-        }
-        output = io.StringIO()
-        s = simulation.from_config(config)
-        s.run_simulation(exporters=[exporters.distribution], dry_run=True, exporter_params={'copy_to': output})
-        result = output.getvalue()
-        assert 'count' in result
-        assert 'SEED,Noneexporter_sim_trial_3,1,,1,1,1,1' in result
-
     def test_writing(self):
         '''Try to write CSV, GEXF, sqlite and YAML (without dry_run)'''
         n_trials = 5
@@ -86,8 +77,8 @@ class Exporters(TestCase):
             exporters.default,
             exporters.csv,
             exporters.gexf,
-            exporters.distribution,
         ],
+                                stats=[distribution,],
                                 outdir=tmpdir,
                                 exporter_params={'copy_to': output})
         result = output.getvalue()

tests/test_history.py

@@ -5,6 +5,7 @@ import shutil
 from glob import glob
 
 from soil import history
+from soil import utils
 
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
@@ -154,3 +155,49 @@ class TestHistory(TestCase):
         assert recovered
         for i in recovered:
             assert i in tuples
+
+    def test_stats(self):
+        """
+        The data recovered should be equal to the one recorded.
+        """
+        tuples = (
+            ('a_1', 0, 'id', 'v'),
+            ('a_1', 1, 'id', 'a'),
+            ('a_1', 2, 'id', 'l'),
+            ('a_1', 3, 'id', 'u'),
+            ('a_1', 4, 'id', 'e'),
+            ('env', 1, 'prob', 1),
+            ('env', 2, 'prob', 2),
+            ('env', 3, 'prob', 3),
+            ('a_2', 7, 'finished', True),
+        )
+        stat_tuples = [
+            {'num_infected': 5, 'runtime': 0.2},
+            {'num_infected': 5, 'runtime': 0.2},
+            {'new': '40'},
+        ]
+        h = history.History()
+        h.save_tuples(tuples)
+        for stat in stat_tuples:
+            h.save_stats(stat)
+        recovered = h.get_stats()
+        assert recovered
+        assert recovered[0]['num_infected'] == 5
+        assert recovered[1]['runtime'] == 0.2
+        assert recovered[2]['new'] == '40'
+
+    def test_unflatten(self):
+        ex = {'count.neighbors.3': 4,
+              'count.times.2': 4,
+              'count.total.4': 4,
+              'mean.neighbors': 3,
+              'mean.times': 2,
+              'mean.total': 4,
+              't_step': 2,
+              'trial_id': 'exporter_sim_trial_1605817956-4475424'}
+        res = utils.unflatten_dict(ex)
+
+        assert 'count' in res
+        assert 'mean' in res
+        assert 't_step' in res
+        assert 'trial_id' in res

tests/test_main.py

@@ -343,4 +343,16 @@ class TestMain(TestCase):
         configs = serialization.load_file(join(EXAMPLES, 'template.yml'))
         assert len(configs) > 0
 
-
+    def test_until(self):
+        config = {
+            'name': 'exporter_sim',
+            'network_params': {},
+            'agent_type': 'CounterModel',
+            'max_time': 2,
+            'num_trials': 100,
+            'environment_params': {}
+        }
+        s = simulation.from_config(config)
+        runs = list(s.run_simulation(dry_run=True))
+        over = list(x.now for x in runs if x.now>2)
+        assert len(over) == 0

tests/test_stats.py

@@ -0,0 +1,34 @@
+from unittest import TestCase
+
+from soil import simulation, stats
+from soil.utils import unflatten_dict
+
+class Stats(TestCase):
+
+    def test_distribution(self):
+        '''The distribution exporter should write the number of agents in each state'''
+        config = {
+            'name': 'exporter_sim',
+            'network_params': {
+                'generator': 'complete_graph',
+                'n': 4
+            },
+            'agent_type': 'CounterModel',
+            'max_time': 2,
+            'num_trials': 5,
+            'environment_params': {}
+        }
+        s = simulation.from_config(config)
+        for env in s.run_simulation(stats=[stats.distribution]):
+            pass
+            # stats_res = unflatten_dict(dict(env._history['stats', -1, None]))
+        allstats = s.get_stats()
+        for stat in allstats:
+            assert 'count' in stat
+            assert 'mean' in stat
+            if 'trial_id' in stat:
+                assert stat['mean']['neighbors'] == 3
+                assert stat['count']['total']['4'] == 4
+            else:
+                assert stat['count']['count']['neighbors']['3'] == 20
+                assert stat['mean']['min']['neighbors'] == stat['mean']['max']['neighbors']