WIP

docs/requirements.txt

@@ -1 +1 @@
-ipython==7.31.1
+ipython>=7.31.1

requirements.txt

@@ -5,5 +5,5 @@ pyyaml>=5.1
 pandas>=0.23
 SALib>=1.3
 Jinja2
-Mesa>=0.8
+Mesa>=0.8.9
-tsih>=0.1.5
+tsih>=0.1.6

setup.py

@@ -49,6 +49,7 @@ setup(
     extras_require=extras_require,
     tests_require=test_reqs,
     setup_requires=['pytest-runner', ],
+    pytest_plugins = ['pytest_profiling'],
     include_package_data=True,
     entry_points={
         'console_scripts':

soil/environment.py

@@ -13,7 +13,7 @@ from networkx.readwrite import json_graph
 
 import networkx as nx
 
-from tsih import History, Record, Key, NoHistory
+from tsih import History, NoHistory, Record, Key
 
 from mesa import Model
 
@@ -33,7 +33,7 @@ class Environment(Model):
     params, which are used as shared state between agents.
 
     The environment parameters and the state of every agent can be accessed
-    both by using the environment as a dictionary or with the environment's 
+    both by using the environment as a dictionary or with the environment's
     :meth:`soil.environment.Environment.get` method.
     """
 
@@ -49,7 +49,7 @@ class Environment(Model):
                  schedule=None,
                  initial_time=0,
                  environment_params=None,
-                 history=True,
+                 history=False,
                  dir_path=None,
                  **kwargs):
 
@@ -82,10 +82,12 @@ class Environment(Model):
 
         self._env_agents = {}
         self.interval = interval
+
         if history:
             history = History
         else:
             history = NoHistory
+
         self._history = history(name=self.name,
                                 backup=True)
         self['SEED'] = seed
@@ -298,6 +300,9 @@ class Environment(Model):
             else:
                 raise ValueError('Unknown format: {}'.format(f))
 
+    def df(self):
+        return self._history[None, None, None].df()
+        
     def dump_sqlite(self, f):
         return self._history.dump(f)
 
@@ -316,8 +321,14 @@ class Environment(Model):
                              key=k,
                              value=v)
 
-    def history_to_tuples(self):
+    def history_to_tuples(self, agent_id=None):
-        return self._history.to_tuples()
+        if isinstance(self._history, NoHistory):
+            tuples = self.state_to_tuples()
+        else:
+            tuples = self._history.to_tuples()
+        if agent_id is None:
+            return tuples
+        return filter(lambda x: str(x[0]) == str(agent_id), tuples)
 
     def history_to_graph(self):
         G = nx.Graph(self.G)
@@ -329,10 +340,10 @@ class Environment(Model):
             spells = []
             lastvisible = False
             laststep = None
-            history = self[agent.id, None, None]
+            history = sorted(list(self.history_to_tuples(agent_id=agent.id)))
             if not history:
                 continue
-            for t_step, attribute, value in sorted(list(history)):
+            for _, t_step, attribute, value in history:
                 if attribute == 'visible':
                     nowvisible = value
                     if nowvisible and not lastvisible:

soil/exporters.py

@@ -1,6 +1,6 @@
 import os
 import csv as csvlib
-import time
+from time import time as current_time
 from io import BytesIO
 
 import matplotlib.pyplot as plt
@@ -133,7 +133,7 @@ class dummy(Exporter):
 
     def start(self):
         with self.output('dummy', 'w') as f:
-            f.write('simulation started @ {}\n'.format(time.time()))
+            f.write('simulation started @ {}\n'.format(current_time()))
 
     def trial(self, env, stats):
         with self.output('dummy', 'w') as f:
@@ -143,7 +143,7 @@ class dummy(Exporter):
 
     def sim(self, stats):
         with self.output('dummy', 'a') as f:
-            f.write('simulation ended @ {}\n'.format(time.time()))
+            f.write('simulation ended @ {}\n'.format(current_time()))
 
 
 

soil/simulation.py

@@ -1,4 +1,5 @@
 import os
+from time import time as current_time, strftime 
 import importlib
 import sys
 import yaml
@@ -6,7 +7,6 @@ import traceback
 import logging
 import networkx as nx
 
-from time import strftime
 from networkx.readwrite import json_graph
 from multiprocessing import Pool
 from functools import partial
@@ -83,8 +83,9 @@ class Simulation:
         Class for the environment. It defailts to soil.environment.Environment
     load_module : str, module name, deprecated
         If specified, soil will load the content of this module under 'soil.agents.custom'
-
+    history: tsih.History subclass, optional
-
+        Class to use to store the history of the simulation (and environments). It defailts to tsih.History
+        If set to True, tsih.History will be used. If set to False or None, tsih.NoHistory will be used.
     """
 
     def __init__(self, name=None, group=None, topology=None, network_params=None,
@@ -93,7 +94,7 @@ class Simulation:
                  max_time=100, load_module=None, seed=None,
                  dir_path=None, environment_agents=None,
                  environment_params=None, environment_class=None,
-                 **kwargs):
+                 history=History, **kwargs):
 
         self.load_module = load_module
         self.network_params = network_params
@@ -133,7 +134,12 @@ class Simulation:
         self.states = agents._validate_states(states,
                                               self.topology)
 
-        self._history = History(name=self.name,
+        if history == True:
+            history = History
+        elif not history:
+            history = NoHistory
+
+        self._history = history(name=self.name,
                                 backup=False)
 
     def run_simulation(self, *args, **kwargs):
@@ -233,6 +239,7 @@ class Simulation:
             'states': self.states,
             'dir_path': self.dir_path,
             'default_state': self.default_state,
+            'history': bool(self._history),
             'environment_agents': self.environment_agents,
         })
         opts.update(kwargs)

soil/stats.py

@@ -35,7 +35,7 @@ class distribution(Stats):
         self.counts = []
 
     def trial(self, env):
-        df = env[None, None, None].df()
+        df = env.df()
         df = df.drop('SEED', axis=1)
         ix = df.index[-1]
         attrs = df.columns.get_level_values(0)

soil/utils.py

@@ -1,5 +1,5 @@
 import logging
-import time
+from time import time as current_time, strftime, gmtime, localtime
 import os
 
 from shutil import copyfile
@@ -13,13 +13,13 @@ logger = logging.getLogger('soil')
 
 @contextmanager
 def timer(name='task', pre="", function=logger.info, to_object=None):
-    start = time.time()
+    start = current_time()
     function('{}Starting {} at {}.'.format(pre, name,
-                                           time.strftime("%X", time.gmtime(start))))
+                                           strftime("%X", gmtime(start))))
     yield start
-    end = time.time()
+    end = current_time()
     function('{}Finished {} at {} in {} seconds'.format(pre, name,
-                                                        time.strftime("%X", time.gmtime(end)),
+                                                        strftime("%X", gmtime(end)),
                                                         str(end-start)))
     if to_object:
         to_object.start = start
@@ -34,7 +34,7 @@ def safe_open(path, mode='r', backup=True, **kwargs):
         os.makedirs(outdir)
     if backup and 'w' in mode and os.path.exists(path):
         creation = os.path.getctime(path)
-        stamp = time.strftime('%Y-%m-%d_%H.%M.%S', time.localtime(creation))
+        stamp = strftime('%Y-%m-%d_%H.%M.%S', localtime(creation))
 
         backup_dir = os.path.join(outdir, 'backup')
         if not os.path.exists(backup_dir):
@@ -45,11 +45,13 @@ def safe_open(path, mode='r', backup=True, **kwargs):
     return open(path, mode=mode, **kwargs)
 
 
+@contextmanager
 def open_or_reuse(f, *args, **kwargs):
     try:
-        return safe_open(f, *args, **kwargs)
+        with safe_open(f, *args, **kwargs) as f:
+            yield f
     except (AttributeError, TypeError):
-        return f
+        yield f
 
 def flatten_dict(d):
     if not isinstance(d, dict):

test-requirements.txt

@@ -1,4 +1,4 @@
 pytest
-mesa>=0.8.9
+pytest-profiling
 scipy>=1.3
 tornado

tests/test_analysis.py

@@ -50,6 +50,7 @@ class TestAnalysis(TestCase):
             'states': [{'interval': 1}, {'interval': 2}],
             'max_time': 30,
             'num_trials': 1,
+            'history': True,
             'environment_params': {
             }
         }

tests/test_exporters.py

@@ -2,7 +2,6 @@ import os
 import io
 import tempfile
 import shutil
-from time import time
 
 from unittest import TestCase
 from soil import exporters
@@ -68,6 +67,7 @@ class Exporters(TestCase):
             'agent_type': 'CounterModel',
             'max_time': 2,
             'num_trials': n_trials,
+            'dry_run': False,
             'environment_params': {}
         }
         output = io.StringIO()
@@ -79,6 +79,7 @@ class Exporters(TestCase):
                                     exporters.gexf,
                                 ],
                                 stats=[distribution,],
+                                dry_run=False,
                                 outdir=tmpdir,
                                 exporter_params={'copy_to': output})
         result = output.getvalue()

tests/test_main.py

@@ -11,6 +11,7 @@ from os.path import join
 from soil import (simulation, Environment, agents, serialization,
                   utils)
 from soil.time import Delta
+from tsih import NoHistory, History
 
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
@@ -205,7 +206,7 @@ class TestMain(TestCase):
         assert config == nconfig
 
     def test_row_conversion(self):
-        env = Environment()
+        env = Environment(history=True)
         env['test'] = 'test_value'
 
         res = list(env.history_to_tuples())
@@ -228,7 +229,14 @@ class TestMain(TestCase):
         f = io.BytesIO()
         env.dump_gexf(f)
 
-    def test_save_graph(self):
+    def test_nohistory(self):
+        '''
+        Make sure that no history(/sqlite) is used by default
+        '''
+        env = Environment(topology=nx.Graph(), network_agents=[])
+        assert isinstance(env._history, NoHistory)
+
+    def test_save_graph_history(self):
         '''
         The history_to_graph method should return a valid networkx graph.
 
@@ -236,7 +244,7 @@ class TestMain(TestCase):
         '''
         G = nx.cycle_graph(5)
         distribution = agents.calculate_distribution(None, agents.BaseAgent)
-        env = Environment(topology=G, network_agents=distribution)
+        env = Environment(topology=G, network_agents=distribution, history=True)
         env[0, 0, 'testvalue'] = 'start'
         env[0, 10, 'testvalue'] = 'finish'
         nG = env.history_to_graph()
@@ -244,6 +252,23 @@ class TestMain(TestCase):
         assert ('start', 0, 10) in values
         assert ('finish', 10, None) in values
 
+    def test_save_graph_nohistory(self):
+        '''
+        The history_to_graph method should return a valid networkx graph.
+
+        When NoHistory is used, only the last known value is known
+        '''
+        G = nx.cycle_graph(5)
+        distribution = agents.calculate_distribution(None, agents.BaseAgent)
+        env = Environment(topology=G, network_agents=distribution, history=False)
+        env.get_agent(0)['testvalue'] = 'start'
+        env.schedule.time = 10
+        env.get_agent(0)['testvalue'] = 'finish'
+        nG = env.history_to_graph()
+        values = nG.nodes[0]['attr_testvalue']
+        assert ('start', 0, None) not in values
+        assert ('finish', 10, None) in values
+
     def test_serialize_class(self):
         ser, name = serialization.serialize(agents.BaseAgent)
         assert name == 'soil.agents.BaseAgent'
@@ -303,7 +328,7 @@ class TestMain(TestCase):
         pickle.dumps(converted)
 
     def test_pickle_agent_environment(self):
-        env = Environment(name='Test')
+        env = Environment(name='Test', history=True)
         a = agents.BaseAgent(model=env, unique_id=25)
 
         a['key'] = 'test'