black formatting

examples/terrorism/TerroristNetworkModel.py

@@ -258,9 +258,7 @@ class TerroristNetworkModel(TerroristSpreadModel):
             )
             neighbours = set(
                 agent.id
-                for agent in self.get_neighbors(
+                for agent in self.get_neighbors(agent_class=TerroristNetworkModel)
-                    agent_class=TerroristNetworkModel
-                )
             )
             search = (close_ups | step_neighbours) - neighbours
             for agent in self.get_agents(search):

soil/__init__.py

@@ -47,7 +47,7 @@ def main(
         "file",
         type=str,
         nargs="?",
-        default=cfg if sim is None else '',
+        default=cfg if sim is None else "",
         help="Configuration file for the simulation (e.g., YAML or JSON)",
     )
     parser.add_argument(
@@ -169,22 +169,26 @@ def main(
             sim.exporters = exporters
             sim.parallel = parallel
             sim.outdir = output
-            sims = [sim, ]
+            sims = [
+                sim,
+            ]
         else:
             logger.info("Loading config file: {}".format(args.file))
             if not os.path.exists(args.file):
                 logger.error("Please, input a valid file")
                 return
 
-            sims = list(simulation.iter_from_config(
+            sims = list(
-                args.file,
+                simulation.iter_from_config(
-                dry_run=args.dry_run,
+                    args.file,
-                exporters=exporters,
+                    dry_run=args.dry_run,
-                parallel=parallel,
+                    exporters=exporters,
-                outdir=output,
+                    parallel=parallel,
-                exporter_params=exp_params,
+                    outdir=output,
-                **kwargs,
+                    exporter_params=exp_params,
-            ))
+                    **kwargs,
+                )
+            )
 
         for sim in sims:
 

soil/agents/__init__.py

@@ -261,7 +261,6 @@ def prob(prob, random):
     return r < prob
 
 
-
 def calculate_distribution(network_agents=None, agent_class=None):
     """
     Calculate the threshold values (thresholds for a uniform distribution)
@@ -632,7 +631,8 @@ from .CounterModel import *
 
 
 class Agent(NetworkAgent, EventedAgent):
-    '''Default agent class, has both network and event capabilities'''
+    """Default agent class, has both network and event capabilities"""
+
 
 try:
     import scipy

soil/agents/evented.py

@@ -6,7 +6,9 @@ from collections import deque
 
 
 class ReceivedOrTimeout(BaseCond):
-    def __init__(self, agent, expiration=None, timeout=None, check=True, ignore=False, **kwargs):
+    def __init__(
+        self, agent, expiration=None, timeout=None, check=True, ignore=False, **kwargs
+    ):
         if expiration is None:
             if timeout is not None:
                 expiration = agent.now + timeout
@@ -23,7 +25,7 @@ class ReceivedOrTimeout(BaseCond):
 
     def return_value(self, agent):
         if not self.ignore and self.expired(agent.now):
-            raise TimedOut('No messages received')
+            raise TimedOut("No messages received")
         if self.check:
             agent.check_messages()
         return None
@@ -34,7 +36,7 @@ class ReceivedOrTimeout(BaseCond):
         return (time + delta, self)
 
     def __repr__(self):
-        return f'ReceivedOrTimeout(expires={self.expiration})'
+        return f"ReceivedOrTimeout(expires={self.expiration})"
 
 
 class EventedAgent(BaseAgent):
@@ -55,7 +57,7 @@ class EventedAgent(BaseAgent):
     def ask(self, msg, timeout=None, **kwargs):
         ask = Ask(timestamp=self.now, payload=msg, sender=self)
         self._inbox.append(ask)
-        expiration = float('inf') if timeout is None else self.now + timeout
+        expiration = float("inf") if timeout is None else self.now + timeout
         return ask.replied(expiration=expiration, **kwargs)
 
     def check_messages(self):
@@ -71,4 +73,5 @@ class EventedAgent(BaseAgent):
                 msg.reply = reply
         return changed
 
+
 Evented = EventedAgent

soil/agents/fsm.py

@@ -38,8 +38,6 @@ def state(name=None):
                         self._last_return = None
                         self._last_except = None
 
-
-
         func.id = name or func.__name__
         func.is_default = False
         return func

soil/agents/network_agents.py

@@ -81,4 +81,5 @@ class NetworkAgent(BaseAgent):
             self.remove_node()
         return super().die()
 
+
 NetAgent = NetworkAgent

soil/environment.py

@@ -313,19 +313,27 @@ class NetworkEnvironment(BaseEnvironment):
 
 
 class EventedEnvironment(BaseEnvironment):
-    def broadcast(self, msg,  sender=None, expiration=None, ttl=None, **kwargs):
+    def broadcast(self, msg, sender=None, expiration=None, ttl=None, **kwargs):
         for agent in self.agents(**kwargs):
             if agent == sender:
                 continue
-            self.logger.info(f'Telling {repr(agent)}: {msg} ttl={ttl}')
+            self.logger.info(f"Telling {repr(agent)}: {msg} ttl={ttl}")
             try:
                 inbox = agent._inbox
             except AttributeError:
-                self.logger.info(f'Agent {agent.unique_id} cannot receive events because it does not have an inbox')
+                self.logger.info(
+                    f"Agent {agent.unique_id} cannot receive events because it does not have an inbox"
+                )
                 continue
             # Allow for AttributeError exceptions in this part of the code
-            inbox.append(events.Tell(payload=msg, sender=sender, expiration=expiration if ttl is None else self.now+ttl))
+            inbox.append(
+                events.Tell(
+                    payload=msg,
+                    sender=sender,
+                    expiration=expiration if ttl is None else self.now + ttl,
+                )
+            )
 
 
 class Environment(NetworkEnvironment, EventedEnvironment):
-    '''Default environment class, has both network and event capabilities'''
+    """Default environment class, has both network and event capabilities"""

soil/events.py

@@ -3,9 +3,11 @@ from dataclasses import dataclass, field
 from typing import Any
 from uuid import uuid4
 
+
 class Event:
     pass
 
+
 @dataclass
 class Message:
     payload: Any
@@ -17,6 +19,7 @@ class Message:
     def expired(self, when):
         return self.expiration is not None and self.expiration < when
 
+
 class Reply(Message):
     source: Message
 

soil/time.py

@@ -112,8 +112,9 @@ class TimedActivation(BaseScheduler):
     def _schedule(self, agent, condition=None, when=None):
         if condition:
             if not when:
-                when, condition = condition.schedule_next(when or self.time,
+                when, condition = condition.schedule_next(
-                                                          self.step_interval)
+                    when or self.time, self.step_interval
+                )
         else:
             if when is None:
                 when = self.time + self.step_interval
@@ -125,7 +126,6 @@ class TimedActivation(BaseScheduler):
         self._next[agent.unique_id] = key
         heappush(self._queue, (key, agent))
 
-
     def step(self) -> None:
         """
         Executes agents in order, one at a time. After each step,
@@ -170,7 +170,9 @@ class TimedActivation(BaseScheduler):
                 continue
 
             if returned:
-                next_check = returned.schedule_next(self.time, self.step_interval, first=True)
+                next_check = returned.schedule_next(
+                    self.time, self.step_interval, first=True
+                )
                 self._schedule(agent, when=next_check[0], condition=next_check[1])
             else:
                 next_check = (self.time + self.step_interval, None)

tests/test_agents.py

@@ -14,31 +14,32 @@ class Dead(agents.FSM):
 
 class TestAgents(TestCase):
     def test_die_returns_infinity(self):
-        '''The last step of a dead agent should return time.INFINITY'''
+        """The last step of a dead agent should return time.INFINITY"""
         d = Dead(unique_id=0, model=environment.Environment())
         ret = d.step()
         assert ret == stime.NEVER
 
     def test_die_raises_exception(self):
-        '''A dead agent should raise an exception if it is stepped after death'''
+        """A dead agent should raise an exception if it is stepped after death"""
         d = Dead(unique_id=0, model=environment.Environment())
         d.step()
         with pytest.raises(stime.DeadAgent):
             d.step()
 
-
     def test_agent_generator(self):
-        '''
+        """
         The step function of an agent could be a generator. In that case, the state of the
         agent will be resumed after every call to step.
-        '''
+        """
         a = 0
+
         class Gen(agents.BaseAgent):
             def step(self):
                 nonlocal a
                 for i in range(5):
                     yield
                     a += 1
+
         e = environment.Environment()
         g = Gen(model=e, unique_id=e.next_id())
         e.schedule.add(g)
@@ -50,8 +51,9 @@ class TestAgents(TestCase):
     def test_state_decorator(self):
         class MyAgent(agents.FSM):
             run = 0
+
             @agents.default_state
-            @agents.state('original')
+            @agents.state("original")
             def root(self):
                 self.run += 1
                 return self.other
@@ -66,19 +68,19 @@ class TestAgents(TestCase):
         assert a.run == 1
         a.step()
 
-
     def test_broadcast(self):
-        '''
+        """
         An agent should be able to broadcast messages to every other agent, AND each receiver should be able
         to process it
-        '''
+        """
+
         class BCast(agents.Evented):
             pings_received = 0
 
             def step(self):
                 print(self.model.broadcast)
                 try:
-                    self.model.broadcast('PING')
+                    self.model.broadcast("PING")
                 except Exception as ex:
                     print(ex)
                 while True:
@@ -96,12 +98,12 @@ class TestAgents(TestCase):
         pings_received = lambda: [a.pings_received for a in e.agents]
         assert sorted(pings_received()) == list(range(1, 11))
         e.step()
-        assert all(x==10 for x in pings_received())
+        assert all(x == 10 for x in pings_received())
 
     def test_ask_messages(self):
-        '''
+        """
         An agent should be able to ask another agent, and wait for a response.
-        '''
+        """
 
         # There are two agents, they try to send pings
         # This is arguably a very contrived example. In practice, the or
@@ -124,24 +126,24 @@ class TestAgents(TestCase):
             def step(self):
                 target_id = (self.unique_id + 1) % self.count_agents()
                 target = self.model.agents[target_id]
-                print('starting')
+                print("starting")
                 while True:
-                    if pongs or not pings:  #First agent, or anyone after that
+                    if pongs or not pings:  # First agent, or anyone after that
                         pings.append(self.now)
-                        response = yield target.ask('PING')
+                        response = yield target.ask("PING")
                         responses.append(response)
                     else:
-                        print('NOT sending ping')
+                        print("NOT sending ping")
-                    print('Checking msgs')
+                    print("Checking msgs")
                     # Do not block if we have already received a PING
                     if not self.check_messages():
-                      yield self.received()
+                        yield self.received()
-                print('done')
+                print("done")
 
             def on_receive(self, msg, sender=None):
-                if msg == 'PING':
+                if msg == "PING":
                     pongs.append(self.now)
-                    return 'PONG'
+                    return "PONG"
                 raise Exception("This should never happen")
 
         e = environment.EventedEnvironment(schedule_class=stime.OrderedTimedActivation)
@@ -149,7 +151,6 @@ class TestAgents(TestCase):
             e.add_agent(agent_class=Ping)
         assert e.now == 0
 
-
         for i in range(5):
             e.step()
             time = i + 1

tests/test_examples.py

@@ -44,7 +44,7 @@ def add_example_tests():
     for cfg, path in serialization.load_files(
         join(EXAMPLES, "**", "*.yml"),
     ):
-        if 'soil_output' in path:
+        if "soil_output" in path:
             continue
         p = make_example_test(path=path, cfg=config.Config.from_raw(cfg))
         fname = os.path.basename(path)

tests/test_main.py

@@ -182,8 +182,11 @@ class TestMain(TestCase):
 
         n_trials = 50
         max_time = 2
-        s = simulation.Simulation(model_params={'agents': [{'agent_class': CheckRun}]},
+        s = simulation.Simulation(
-                                  num_trials=n_trials, max_time=max_time)
+            model_params={"agents": [{"agent_class": CheckRun}]},
+            num_trials=n_trials,
+            max_time=max_time,
+        )
         runs = list(s.run_simulation(dry_run=True))
         over = list(x.now for x in runs if x.now > 2)
         assert len(runs) == n_trials

tests/test_time.py

@@ -2,11 +2,12 @@ from unittest import TestCase
 
 from soil import time, agents, environment
 
+
 class TestMain(TestCase):
     def test_cond(self):
-        '''
+        """
         A condition should match a When if the concition is True
-        '''
+        """
 
         t = time.Cond(lambda t: True)
         f = time.Cond(lambda t: False)
@@ -16,17 +17,16 @@ class TestMain(TestCase):
             assert w is not f
 
     def test_cond(self):
-        '''
+        """
         Comparing a Cond to a Delta should always return False
-        '''
+        """
 
         c = time.Cond(lambda t: False)
         d = time.Delta(1)
         assert c is not d
 
     def test_cond_env(self):
-        '''
+        """ """
-        '''
 
         times_started = []
         times_awakened = []
@@ -35,21 +35,18 @@ class TestMain(TestCase):
         done = []
 
         class CondAgent(agents.BaseAgent):
-
             def step(self):
                 nonlocal done
                 times_started.append(self.now)
                 while True:
                     times_asleep.append(self.now)
-                    yield time.Cond(lambda agent: agent.now >= 10,
+                    yield time.Cond(lambda agent: agent.now >= 10, delta=2)
-                                    delta=2)
                     times_awakened.append(self.now)
                     if self.now >= 10:
                         break
                 done.append(self.now)
 
-        env = environment.Environment(agents=[{'agent_class': CondAgent}])
+        env = environment.Environment(agents=[{"agent_class": CondAgent}])
-
 
         while env.schedule.time < 11:
             times.append(env.now)