Make py3 compatibility explicit

soil/__init__.py

@@ -2,7 +2,7 @@ import importlib
 import sys
 import os
 
-__version__ = "0.9.4"
+__version__ = "0.9.6"
 
 try:
     basestring

soil/__main__.py

@@ -0,0 +1,32 @@
+import importlib
+import sys
+import argparse
+from . import simulation
+
+
+def main():
+
+    parser = argparse.ArgumentParser(description='Run a SOIL simulation')
+    parser.add_argument('file', type=str,
+                        nargs="?",
+                        default='simulation.yml',
+                        help='python module containing the simulation configuration.')
+    parser.add_argument('--module', '-m', type=str,
+                        help='file containing the code of any custom agents.')
+    parser.add_argument('--dry-run', '--dry', action='store_true',
+                        help='Do not store the results of the simulation.')
+    parser.add_argument('--output', '-o', type=str,
+                        help='folder to write results to. It defaults to the current directory.')
+
+    args = parser.parse_args()
+
+    if args.module:
+        sys.path.append(os.getcwd())
+        importlib.import_module(args.module)
+
+    print('Loading config file: {}'.format(args.file, args.output))
+    simulation.run_from_config(args.file, dump=not args.dry_run, results_dir=args.output)
+
+
+if __name__ == '__main__':
+    main()

soil/agents/BaseBehaviour.py

@@ -1,123 +0,0 @@
-import nxsim
-from collections import OrderedDict
-from copy import deepcopy
-import json
-
-from functools import wraps
-
-
-class BaseAgent(nxsim.BaseAgent):
-    """
-    A special simpy BaseAgent that keeps track of its state history.
-    """
-
-    def __init__(self, *args, **kwargs):
-        self._history = OrderedDict()
-        self._neighbors = None
-        super().__init__(*args, **kwargs)
-        self._history[None] = deepcopy(self.state)
-
-    @property
-    def now(self):
-        try:
-            return self.env.now
-        except AttributeError:
-            # No environment
-            return None
-
-    def run(self):
-        while True:
-            res = self.step()
-            self._history[self.env.now] = deepcopy(self.state)
-            yield res or self.env.timeout(self.env.interval)
-
-    def step(self):
-        pass
-
-    def to_json(self):
-        return json.dumps(self._history)
-
-class NetworkAgent(BaseAgent, nxsim.BaseNetworkAgent):
-
-    def count_agents(self, state_id=None, limit_neighbors=False):
-        if limit_neighbors:
-            agents = self.global_topology.neighbors(self.id)
-        else:
-            agents = self.global_topology.nodes()
-        count = 0
-        for agent in agents:
-            if state_id and state_id != self.global_topology.node[agent]['agent'].state['id']:
-                continue
-            count += 1
-        return count
-
-    def count_neighboring_agents(self, state_id=None):
-        return self.count_agents(state_id, limit_neighbors=True)
-
-
-def state(func):
-
-    @wraps(func)
-    def func_wrapper(self):
-        when = None
-        next_state = func(self)
-        try:
-            next_state, when = next_state
-        except TypeError:
-            pass
-        if next_state:
-            try:
-                self.state['id'] = next_state.id
-            except AttributeError:
-                raise NotImplemented('State id %s is not valid.' % next_state)
-        return when
-
-    func_wrapper.id = func.__name__
-    func_wrapper.is_default = False
-    return func_wrapper
-
-
-def default_state(func):
-    func.is_default = True
-    return func
-
-
-class MetaFSM(type):
-    def __init__(cls, name, bases, nmspc):
-        super(MetaFSM, cls).__init__(name, bases, nmspc)
-        states = {}
-        # Re-use states from inherited classes
-        default_state = None
-        for i in bases:
-            if isinstance(i, MetaFSM):
-                for state_id, state in i.states.items():
-                    if state.is_default:
-                        default_state = state
-                    states[state_id] = state
-
-        # Add new states
-        for name, func in nmspc.items():
-            if hasattr(func, 'id'):
-                if func.is_default:
-                    default_state = func
-                states[func.id] = func
-        cls.default_state = default_state
-        cls.states = states
-
-
-class FSM(BaseAgent, metaclass=MetaFSM):
-    def __init__(self, *args, **kwargs):
-        super(FSM, self).__init__(*args, **kwargs)
-        if 'id' not in self.state:
-            self.state['id'] = self.default_state.id
-
-    def step(self):
-        if 'id' in self.state:
-            next_state = self.state['id']
-        elif self.default_state:
-            next_state = self.default_state.id
-        else:
-            raise Exception('{} has no valid state id or default state'.format(self))
-        if next_state not in self.states:
-            raise Exception('{} is not a valid id for {}'.format(next_state, self))
-        self.states[next_state](self)

soil/agents/SISaModel.py

@@ -1,9 +1,9 @@
 import random
 import numpy as np
-from . import FSM, state
+from . import FSM, NetworkAgent, state
 
 
-class SISaModel(FSM):
+class SISaModel(FSM, NetworkAgent):
     """
     Settings:
         neutral_discontent_spon_prob