WIP: mesa compat

All tests pass but some features are still missing/unclear:

- Mesa agents do not have a `state`, so their "metrics" don't get stored. I will
probably refactor this to remove some magic in this regard. This should get rid
of the `_state` dictionary and the setitem/getitem magic.
- Simulation is still different from a runner. So far only Agent and
Environment/Model have been updated.

examples/rabbits/rabbit_agents.py

@@ -1,7 +1,6 @@
 from soil.agents import FSM, state, default_state, BaseAgent, NetworkAgent
 from enum import Enum
 from random import random, choice
-from itertools import islice
 import logging
 import math
 
@@ -22,7 +21,7 @@ class RabbitModel(FSM):
         'offspring': 0,
     }
 
-    sexual_maturity = 4*30
+    sexual_maturity = 3 #4*30
     life_expectancy = 365 * 3
     gestation = 33
     pregnancy = -1
@@ -31,9 +30,11 @@ class RabbitModel(FSM):
     @default_state
     @state
     def newborn(self):
+        self.debug(f'I am a newborn at age {self["age"]}')
         self['age'] += 1
 
         if self['age'] >= self.sexual_maturity:
+            self.debug('I am fertile!')
             return self.fertile
 
     @state
@@ -46,8 +47,7 @@ class RabbitModel(FSM):
             return
 
         # Males try to mate
-        females = self.get_agents(state_id=self.fertile.id, gender=Genders.female.value, limit_neighbors=False)
+        for f in self.get_agents(state_id=self.fertile.id, gender=Genders.female.value, limit_neighbors=False, limit=self.max_females):
-        for f in islice(females, self.max_females):
             r = random()
             if r < self['mating_prob']:
                 self.impregnate(f)

examples/rabbits/rabbits.yml

@@ -1,7 +1,7 @@
 ---
 load_module: rabbit_agents
 name: rabbits_example
-max_time: 500
+max_time: 200
 interval: 1
 seed: MySeed
 agent_type: RabbitModel

soil/agents/Geo.py

@@ -1,5 +1,6 @@
 from scipy.spatial import cKDTree as KDTree
-from . import NetworkAgent
+import networkx as nx
+from . import NetworkAgent, as_node
 
 class Geo(NetworkAgent):
     '''In this type of network, nodes have a "pos" attribute.'''

soil/agents/__init__.py

@@ -1,12 +1,11 @@
 import logging
 from collections import OrderedDict, defaultdict
 from copy import deepcopy
-from functools import partial
+from functools import partial, wraps
+from itertools import islice
 import json
 import networkx as nx
 
-from functools import wraps
-
 from .. import serialization, history, utils, time
 
 from mesa import Agent
@@ -91,7 +90,7 @@ class BaseAgent(Agent):
     def __getitem__(self, key):
         if isinstance(key, tuple):
             key, t_step = key
-            k = history.Key(key=key, t_step=t_step, agent_id=self.id)
+            k = history.Key(key=key, t_step=t_step, agent_id=self.unique_id)
             return self.model[k]
         return self._state.get(key, None)
 
@@ -151,25 +150,25 @@ class BaseAgent(Agent):
     def info(self, *args, **kwargs):
         return self.log(*args, level=logging.INFO, **kwargs)
 
-    def __getstate__(self):
+    # def __getstate__(self):
-        '''
+    #     '''
-        Serializing an agent will lose all its running information (you cannot
+    #     Serializing an agent will lose all its running information (you cannot
-        serialize an iterator), but it keeps the state and link to the environment,
+    #     serialize an iterator), but it keeps the state and link to the environment,
-        so it can be used for inspection and dumping to a file
+    #     so it can be used for inspection and dumping to a file
-        '''
+    #     '''
-        state = {}
+    #     state = {}
-        state['id'] = self.id
+    #     state['id'] = self.id
-        state['environment'] = self.model
+    #     state['environment'] = self.model
-        state['_state'] = self._state
+    #     state['_state'] = self._state
-        return state
+    #     return state
 
-    def __setstate__(self, state):
+    # def __setstate__(self, state):
-        '''
+    #     '''
-        Get back a serialized agent and try to re-compose it
+    #     Get back a serialized agent and try to re-compose it
-        '''
+    #     '''
-        self.state_id = state['id']
+    #     self.state_id = state['id']
-        self._state = state['_state']
+    #     self._state = state['_state']
-        self.model = state['environment']
+    #     self.model = state['environment']
 
 class NetworkAgent(BaseAgent):
 
@@ -190,7 +189,13 @@ class NetworkAgent(BaseAgent):
     def get_neighboring_agents(self, state_id=None, **kwargs):
         return self.get_agents(limit_neighbors=True, state_id=state_id, **kwargs)
 
-    def get_agents(self, agents=None, limit_neighbors=False, **kwargs):
+    def get_agents(self, *args, limit=None, **kwargs):
+        it = self.iter_agents(*args, **kwargs)
+        if limit is not None:
+            it = islice(it, limit)
+        return list(it)
+
+    def iter_agents(self, agents=None, limit_neighbors=False, **kwargs):
         if limit_neighbors:
             agents = self.topology.neighbors(self.unique_id)
 
@@ -199,7 +204,7 @@ class NetworkAgent(BaseAgent):
 
     def subgraph(self, center=True, **kwargs):
         include = [self] if center else []
-        return self.topology.subgraph(n.unique_id for n in self.get_agents(**kwargs)+include)
+        return self.topology.subgraph(n.unique_id for n in list(self.get_agents(**kwargs))+include)
 
     def remove_node(self, unique_id):
         self.topology.remove_node(unique_id)
@@ -208,10 +213,10 @@ class NetworkAgent(BaseAgent):
         # return super(NetworkAgent, self).add_edge(node1=self.id, node2=other, **kwargs)
         if self.unique_id not in self.topology.nodes(data=False):
             raise ValueError('{} not in list of existing agents in the network'.format(self.unique_id))
-        if other not in self.topology.nodes(data=False):
+        if other.unique_id not in self.topology.nodes(data=False):
             raise ValueError('{} not in list of existing agents in the network'.format(other))
 
-        self.topology.add_edge(self.unique_id, other, edge_attr_dict=edge_attr_dict, *edge_attrs)
+        self.topology.add_edge(self.unique_id, other.unique_id, edge_attr_dict=edge_attr_dict, *edge_attrs)
 
 
     def ego_search(self, steps=1, center=False, node=None, **kwargs):
@@ -308,21 +313,21 @@ class FSM(NetworkAgent, metaclass=MetaFSM):
     def step(self):
         self.debug(f'Agent {self.unique_id} @ state {self["id"]}')
         interval = super().step()
-        if 'id' not in self:
+        if 'id' not in self.state:
-            if 'id' in self.state:
+            # if 'id' in self.state:
-                self.set_state(self['state_id'])
+            #     self.set_state(self.state['id'])
-            elif self.default_state:
+            if self.default_state:
                 self.set_state(self.default_state.id)
             else:
                 raise Exception('{} has no valid state id or default state'.format(self))
-        return self.states[self['id']](self) or interval
+        return self.states[self.state['id']](self) or interval
 
     def set_state(self, state):
         if hasattr(state, 'id'):
             state = state.id
         if state not in self.states:
             raise ValueError('{} is not a valid state'.format(state))
-        self['state_id'] = state
+        self.state['id'] = state
         return state
 
 
@@ -530,8 +535,6 @@ def select(agents, state_id=None, agent_type=None, ignore=None, iterator=False,
         except TypeError:
             agent_type = tuple([agent_type])
 
-    checks = []
-
     f = agents
 
     if ignore:
@@ -547,7 +550,7 @@ def select(agents, state_id=None, agent_type=None, ignore=None, iterator=False,
 
     if iterator:
         return f
-    return list(f)
+    return f
 
 
 from .BassModel import *

soil/environment.py

@@ -81,9 +81,6 @@ class Environment(Model):
         self._history = history.History(name=self.name,
                                         backup=True)
         self['SEED'] = seed
-        # Add environment agents first, so their events get
-        # executed before network agents
-
 
         if network_agents:
             distro = agents.calculate_distribution(network_agents)
@@ -97,7 +94,6 @@ class Environment(Model):
             environment_agents = agents._convert_agent_types(distro)
         self.environment_agents = environment_agents
 
-
     @property
     def now(self):
         if self.schedule:
@@ -169,6 +165,7 @@ class Environment(Model):
                            unique_id=agent_id,
                            state=state)
         node['agent'] = a
+        self.schedule.add(a)
         return a
 
     def add_node(self, agent_type, state=None):
@@ -188,8 +185,6 @@ class Environment(Model):
 
     def run(self, until, *args, **kwargs):
         self._save_state()
-        for agent in self.agents:
-            self.schedule.add(agent)
 
         while self.schedule.next_time <= until and not math.isinf(self.schedule.next_time):
             self.schedule.step(until=until)
@@ -238,8 +233,8 @@ class Environment(Model):
 
     def get_agents(self, nodes=None):
         if nodes is None:
-            return list(self.agents)
+            return self.agents
-        return [self.G.nodes[i]['agent'] for i in nodes]
+        return (self.G.nodes[i]['agent'] for i in nodes)
 
     def dump_csv(self, f):
         with utils.open_or_reuse(f, 'w') as f:

soil/time.py

@@ -18,6 +18,9 @@ class Delta:
     def __init__(self, delta):
         self._delta = delta
 
+    def __eq__(self, other):
+        return self._delta == other._delta
+
     def abs(self, time):
         return time + self._delta
 

tests/test_main.py

@@ -10,6 +10,7 @@ from functools import partial
 from os.path import join
 from soil import (simulation, Environment, agents, serialization,
                   history, utils)
+from soil.time import Delta
 
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
@@ -356,3 +357,41 @@ class TestMain(TestCase):
         runs = list(s.run_simulation(dry_run=True))
         over = list(x.now for x in runs if x.now>2)
         assert len(over) == 0
+
+
+    def test_fsm(self):
+        '''Basic state change'''
+        class ToggleAgent(agents.FSM):
+            @agents.default_state
+            @agents.state
+            def ping(self):
+                return self.pong
+
+            @agents.state
+            def pong(self):
+                return self.ping
+
+        a = ToggleAgent(unique_id=1, model=Environment())
+        assert a.state["id"] == a.ping.id
+        a.step()
+        assert a.state["id"] == a.pong.id
+        a.step()
+        assert a.state["id"] == a.ping.id
+
+    def test_fsm_when(self):
+        '''Basic state change'''
+        class ToggleAgent(agents.FSM):
+            @agents.default_state
+            @agents.state
+            def ping(self):
+                return self.pong, 2
+
+            @agents.state
+            def pong(self):
+                return self.ping
+
+        a = ToggleAgent(unique_id=1, model=Environment())
+        when = a.step()
+        assert when == 2
+        when = a.step()
+        assert when == Delta(a.interval)