WIP

soil/agents/CounterModel.py

@@ -7,9 +7,15 @@ class CounterModel(NetworkAgent):
     in each step and adds it to its state.
     """
 
+    defaults = {
+        'times': 0,
+        'neighbors': 0,
+        'total': 0
+    }
+
     def step(self):
         # Outside effects
-        total = len(list(self.get_agents()))
+        total = len(list(self.env.agents))
         neighbors = len(list(self.get_neighboring_agents()))
         self['times'] = self.get('times', 0) + 1
         self['neighbors'] = neighbors
@@ -33,6 +39,6 @@ class AggregatedCounter(NetworkAgent):
         self['times'] += 1
         neighbors = len(list(self.get_neighboring_agents()))
         self['neighbors'] += neighbors
-        total = len(list(self.get_agents()))
+        total = len(list(self.env.agents))
         self['total'] += total
         self.debug('Running for step: {}. Total: {}'.format(self.now, total))

soil/agents/__init__.py

@@ -1,16 +1,17 @@
 import logging
 from collections import OrderedDict, defaultdict
+from collections.abc import Mapping, Set
 from copy import deepcopy
 from functools import partial, wraps
-from itertools import islice
+from itertools import islice, chain
 import json
 import networkx as nx
 
-from .. import serialization, utils, time
+from mesa import Agent as MesaAgent
+from typing import Dict, List
 
-from tsih import Key
+from .. import serialization, utils, time, config
 
-from mesa import Agent
 
 
 def as_node(agent):
@@ -24,7 +25,7 @@ IGNORED_FIELDS = ('model', 'logger')
 class DeadAgent(Exception):
     pass
 
-class BaseAgent(Agent):
+class BaseAgent(MesaAgent):
     """
     A special type of Mesa Agent that:
 
@@ -47,9 +48,8 @@ class BaseAgent(Agent):
     ):
         # Check for REQUIRED arguments
         # Initialize agent parameters
-        if isinstance(unique_id, Agent):
+        if isinstance(unique_id, MesaAgent):
             raise Exception()
-        self._saved = set()
         super().__init__(unique_id=unique_id, model=model)
         self.name = name or '{}[{}]'.format(type(self).__name__, self.unique_id)
 
@@ -57,7 +57,7 @@ class BaseAgent(Agent):
         self.alive = True
 
         self.interval = interval or self.get('interval', 1)
-        self.logger = logging.getLogger(self.model.name).getChild(self.name)
+        self.logger = logging.getLogger(self.model.id).getChild(self.name)
 
         if hasattr(self, 'level'):
             self.logger.setLevel(self.level)
@@ -66,6 +66,7 @@ class BaseAgent(Agent):
                 setattr(self, k, deepcopy(v))
 
         for (k, v) in kwargs.items():
+
             setattr(self, k, v)
 
         for (k, v) in getattr(self, 'defaults', {}).items():
@@ -107,23 +108,7 @@ class BaseAgent(Agent):
     def environment_params(self, value):
         self.model.environment_params = value
 
-    def __setattr__(self, key, value):
-        if not key.startswith('_') and key not in IGNORED_FIELDS:
-            try:
-                k = Key(t_step=self.now,
-                        dict_id=self.unique_id,
-                        key=key)
-                self._saved.add(key)
-                self.model[k] = value
-            except AttributeError:
-                pass
-        super().__setattr__(key, value)
-
     def __getitem__(self, key):
-        if isinstance(key, tuple):
-            key, t_step = key
-            k = Key(key=key, t_step=t_step, dict_id=self.unique_id)
-            return self.model[k]
         return getattr(self, key)
 
     def __delitem__(self, key):
@@ -135,8 +120,11 @@ class BaseAgent(Agent):
     def __setitem__(self, key, value):
         setattr(self, key, value)
 
+    def keys(self):
+        return (k for k in self.__dict__ if k[0] != '_')
+
     def items(self):
-        return ((k, getattr(self, k)) for k in self._saved)
+        return ((k, v) for (k, v) in self.__dict__.items() if k[0] != '_')
 
     def get(self, key, default=None):
         return self[key] if key in self else default
@@ -174,22 +162,32 @@ class BaseAgent(Agent):
         extra['agent_name'] = self.name
         return self.logger.log(level, message, extra=extra)
 
+
+
     def debug(self, *args, **kwargs):
         return self.log(*args, level=logging.DEBUG, **kwargs)
 
     def info(self, *args, **kwargs):
         return self.log(*args, level=logging.INFO, **kwargs)
 
+# Alias
+# Agent = BaseAgent
 
 class NetworkAgent(BaseAgent):
-
-    @property
-    def topology(self):
-        return self.model.G
+    def __init__(self,
+                 *args,
+                 graph_name: str,
+                 node_id: int = None,
+                 **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.graph_name = graph_name
+        self.topology = self.env.topologies[self.graph_name]
+        self.node_id = node_id
 
     @property
     def G(self):
-        return self.model.G
+        return self.model.topologies[self._topology]
 
     def count_agents(self, **kwargs):
         return len(list(self.get_agents(**kwargs)))
@@ -210,8 +208,7 @@ class NetworkAgent(BaseAgent):
         if limit_neighbors:
             agents = self.topology.neighbors(self.unique_id)
 
-        agents = self.model.get_agents(agents)
-        return select(agents, **kwargs)
+        return self.model.agents(ids=agents, **kwargs)
 
     def subgraph(self, center=True, **kwargs):
         include = [self] if center else []
@@ -229,7 +226,6 @@ class NetworkAgent(BaseAgent):
 
         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):
         '''Get a list of nodes in the ego network of *node* of radius *steps*'''
         node = as_node(node if node is not None else self)
@@ -311,7 +307,7 @@ class MetaFSM(type):
         cls.states = states
 
 
-class FSM(NetworkAgent, metaclass=MetaFSM):
+class FSM(BaseAgent, metaclass=MetaFSM):
     def __init__(self, *args, **kwargs):
         super(FSM, self).__init__(*args, **kwargs)
         if not hasattr(self, 'state_id'):
@@ -537,32 +533,171 @@ def _definition_to_dict(definition, size=None, default_state=None):
     return agents
 
 
-def select(agents, state_id=None, agent_type=None, ignore=None, iterator=False, **kwargs):
+class AgentView(Mapping, Set):
+    """A lazy-loaded list of agents.
+    """
 
-    if state_id is not None and not isinstance(state_id, (tuple, list)):
-        state_id = tuple([state_id])
-    if agent_type is not None:
-        try:
-            agent_type = tuple(agent_type)
-        except TypeError:
-            agent_type = tuple([agent_type])
+    __slots__ = ("_agents",)
 
-    f = agents
 
-    if ignore:
-        f = filter(lambda x: x not in ignore, f)
+    def __init__(self, agents):
+        self._agents = agents
 
-    if state_id is not None:
-        f = filter(lambda agent: agent.get('state_id', None) in state_id, f)
+    def __getstate__(self):
+        return {"_agents": self._agents}
 
-    if agent_type is not None:
-        f = filter(lambda agent: isinstance(agent, agent_type), f)
-    for k, v in kwargs.items():
-        f = filter(lambda agent: agent.state.get(k, None) == v, f)
+    def __setstate__(self, state):
+        self._agents = state["_agents"]
 
-    if iterator:
-        return f
-    return f
+    # Mapping methods
+    def __len__(self):
+        return sum(len(x) for x in self._agents.values())
+
+    def __iter__(self):
+        return iter(chain.from_iterable(g.values() for g in self._agents.values()))
+
+    def __getitem__(self, agent_id):
+        if isinstance(agent_id, slice):
+            raise ValueError(f"Slicing is not supported")
+        for group in self._agents.values():
+            if agent_id in group:
+                return group[agent_id]
+        raise ValueError(f"Agent {agent_id} not found")
+
+    def filter(self, ids=None, groups=None, state_id=None, agent_type=None, ignore=None, iterator=False, **kwargs):
+
+        if state_id is not None and not isinstance(state_id, (tuple, list)):
+            state_id = tuple([state_id])
+
+        agents = self._agents
+
+        if groups:
+            agents = {(k,v) for (k, v) in agents.items() if k in groups}
+
+        if agent_type is not None:
+            try:
+                agent_type = tuple(agent_type)
+            except TypeError:
+                agent_type = tuple([agent_type])
+
+        if ids:
+            agents = (v[aid] for v in agents.values() for aid in ids if aid in v)
+        else:
+            agents = (a for v in agents.values() for a in v.values())
+
+        f = agents
+        if ignore:
+            f = filter(lambda x: x not in ignore, f)
+
+        if state_id is not None:
+            f = filter(lambda agent: agent.get('state_id', None) in state_id, f)
+
+        if agent_type is not None:
+            f = filter(lambda agent: isinstance(agent, agent_type), f)
+        for k, v in kwargs.items():
+            f = filter(lambda agent: agent.state.get(k, None) == v, f)
+
+        if iterator:
+            return f
+        return list(f)
+
+    def __call__(self, *args, **kwargs):
+        return self.filter(*args, **kwargs)
+
+    def __contains__(self, agent_id):
+        return any(agent_id in g for g in self._agents)
+
+    def __str__(self):
+        return str(list(a.id for a in self))
+
+    def __repr__(self):
+        return f"{self.__class__.__name__}({self})"
+
+
+def from_config(cfg: Dict[str, config.AgentConfig], env):
+    '''
+    Agents are specified in groups.
+    Each group can be specified in two ways, either through a fixed list in which each item has
+    has the agent type, number of agents to create, and the other parameters, or through what we call
+    an `agent distribution`, which is similar but instead of number of agents, it specifies the weight
+    of each agent type.
+    '''
+    default = cfg.get('default', None)
+    return {k: _group_from_config(c, default=default, env=env) for (k, c)  in cfg.items() if k is not 'default'}
+
+
+def _group_from_config(cfg: config.AgentConfig, default: config.SingleAgentConfig, env):
+    agents = {}
+    if cfg.fixed is not None:
+        agents = _from_fixed(cfg.fixed, topology=cfg.topology, default=default, env=env)
+    if cfg.distribution:
+        n = cfg.n or len(env.topologies[cfg.topology])
+        agents.update(_from_distro(cfg.distribution, n - len(agents),
+                                   topology=cfg.topology or default.topology,
+                                   default=default,
+                                   env=env))
+    return agents
+
+
+def _from_fixed(lst: List[config.FixedAgentConfig], topology: str, default: config.SingleAgentConfig, env):
+    agents = {}
+
+    for fixed in lst:
+      agent_id = fixed.agent_id
+      if agent_id is None:
+          agent_id = env.next_id()
+
+      cls = serialization.deserialize(fixed.agent_class or default.agent_class)
+      state = fixed.state.copy()
+      state.update(default.state)
+      agents[agent_id] = cls(unique_id=agent_id,
+                             model=env,
+                             graph_name=fixed.topology or topology or default.topology,
+                             **state)
+
+    return agents
+
+
+def _from_distro(distro: List[config.AgentDistro],
+                 n: int,
+                 topology: str,
+                 default: config.SingleAgentConfig,
+                 env):
+
+    agents = {}
+
+    if n is None:
+        if any(lambda dist: dist.n is None, distro):
+            raise ValueError('You must provide a total number of agents, or the number of each type')
+        n = sum(dist.n for dist in distro)
+
+
+    total = sum((dist.weight if dist.weight is not None else 1) for dist in distro)
+    thres = {}
+    last = 0
+    for i in sorted(distro, key=lambda x: x.weight):
+
+        cls = serialization.deserialize(i.agent_class or default.agent_class)
+        thres[(last, last + i.weight/total)] = (cls, i)
+
+    acc = 0
+
+    # using np.choice would be more efficient, but this allows us to use soil without
+    # numpy
+    for i in range(n):
+        r = random.random()
+        for (t, (cls, d)) in thres.items():
+            if r >= t[0] and r <= t[1]:
+                agent_id = d.agent_id
+                if agent_id is None:
+                    agent_id = env.next_id()
+
+                state = d.state.copy()
+                state.update(default.state)
+                agents[agent_id] = cls(unique_id=agent_id, model=env, graph_name=d.topology or topology or default.topology, **state)
+                break
+
+    return agents
 
 
 from .BassModel import *

soil/config.py

@@ -11,7 +11,7 @@ from pydantic import BaseModel, Extra
 class General(BaseModel):
     id: str = 'Unnamed Simulation'
     group: str = None
-    dir_path: str = None
+    dir_path: Optional[str] = None
     num_trials: int = 1
     max_time: float = 100
     interval: float = 1
@@ -27,13 +27,13 @@ nodeId = int
 
 class Node(BaseModel):
     id: nodeId
-    state: Dict[str, Any]
+    state: Optional[Dict[str, Any]] = {}
 
 
 class Edge(BaseModel):
     source: nodeId
     target: nodeId
-    value: float = 1
+    value: Optional[float] = 1
 
 
 class Topology(BaseModel):
@@ -75,46 +75,62 @@ class EnvConfig(BaseModel):
 
 
 class SingleAgentConfig(BaseModel):
-    agent_class: Union[Type, str] = 'soil.Agent'
+    agent_class: Optional[Union[Type, str]] = None
     agent_id: Optional[Union[str, int]] = None
-    params: Dict[str, Any] = {}
-    state: Dict[str, Any] = {}
+    topology: Optional[str] = None
+    state: Optional[Dict[str, Any]] = {}
 
-
-class AgentDistro(SingleAgentConfig):
-    weight: Optional[float] = None
-    n: Optional[int] = None
+class FixedAgentConfig(SingleAgentConfig):
+    n: Optional[int] = 1
 
     @root_validator
     def validate_all(cls,  values):
-        if 'weight' in values and 'count' in values:
-            raise ValueError("You may either specify a weight in the distribution or an agent count")
+        if 'agent_id' in values and values.get('n', 1) > 1:
+            raise ValueError("An agent_id can only be provided when there is only one agent")
         return values
 
 
+class AgentDistro(SingleAgentConfig):
+    weight: Optional[float] = 1
+
+
 class AgentConfig(SingleAgentConfig):
     n: Optional[int] = None
+    topology: Optional[str] = None
     distribution: Optional[List[AgentDistro]] = None
-    fixed: Optional[List[SingleAgentConfig]] = None
+    fixed: Optional[List[FixedAgentConfig]] = None
 
     @staticmethod
     def default():
         return AgentConfig()
 
+    @root_validator
+    def validate_all(cls,  values):
+        if 'distribution' in values and ('n' not in values and 'topology' not in values):
+            raise ValueError("You need to provide the number of agents or a topology to extract the value from.")
+        return values
+
 
 class Config(BaseModel, extra=Extra.forbid):
+    version: Optional[str] = '1'
     general: General = General.default()
-    network: Optional[NetConfig] = None
+    topologies: Optional[Dict[str, NetConfig]] = {}
     environment: EnvConfig = EnvConfig.default()
-    agents: Dict[str, AgentConfig] = {}
+    agents: Optional[Dict[str, AgentConfig]] = {}
 
 
-def convert_old(old):
+def convert_old(old, strict=True):
     '''
     Try to convert old style configs into the new format.
 
     This is still a work in progress and might not work in many cases.
     '''
+
+    # TODO: translate states
+
+    if strict and old.get('states', {}):
+        raise ValueError('Custom (i.e., manual) agent states cannot be translated to v2 configuration files. Please, convert your configuration file to the new format.')
+
     new = {}
 
 
@@ -129,7 +145,10 @@ def convert_old(old):
         if k in old:
             general[k] = old[k]
 
-    network = {'group': 'network'}
+    if 'name' in old:
+        general['id'] = old['name']
+
+    network = {}
 
 
     if 'network_params' in old and old['network_params']:
@@ -143,9 +162,6 @@ def convert_old(old):
         network['topology'] = old['topology']
 
     agents = {
-        'environment': {
-            'fixed': []
-        },
         'network': {},
         'default': {},
     }
@@ -164,10 +180,31 @@ def convert_old(old):
         return newagent
 
     for agent in old.get('environment_agents', []):
-        agents['environment']['fixed'].append(updated_agent(agent))
+        agents['environment'] = {'distribution': [], 'fixed': []}
+        if 'agent_id' not in agent:
+            agents['environment']['distribution'].append(updated_agent(agent))
+        else:
+            agents['environment']['fixed'].append(updated_agent(agent))
 
-    for agent in old.get('network_agents', []):
-        agents['network'].setdefault('distribution', []).append(updated_agent(agent))
+    by_weight = []
+    fixed = []
+
+    if 'network_agents' in old:
+        agents['network']['topology'] = 'default'
+
+        for agent in old['network_agents']:
+            agent = updated_agent(agent)
+            if 'agent_id' in agent:
+                fixed.append(agent)
+            else:
+                by_weight.append(agent)
+
+    if 'agent_type' in old and (not fixed and not by_weight):
+        agents['network']['topology'] = 'default'
+        by_weight = [{'agent_type': old['agent_type']}]
+
+    agents['network']['fixed'] = fixed
+    agents['network']['distribution'] = by_weight
 
     environment = {'params': {}}
     if 'environment_class' in old:
@@ -176,8 +213,8 @@ def convert_old(old):
     for (k, v) in old.get('environment_params', {}).items():
         environment['params'][k] = v
 
-
-    return Config(general=general,
-                  network=network,
+    return Config(version='2',
+                  general=general,
+                  topologies={'default': network},
                   environment=environment,
                   agents=agents)

soil/environment.py

@@ -3,6 +3,10 @@ import os
 import sqlite3
 import math
 import random
+import logging
+
+from typing import Dict
+from collections import namedtuple
 from time import time as current_time
 from copy import deepcopy
 from networkx.readwrite import json_graph
@@ -12,9 +16,11 @@ import networkx as nx
 
 from mesa import Model
 
-from tsih import Record
+from . import serialization, agents, analysis, utils, time, config, network
+
+
+Record = namedtuple('Record', 'dict_id t_step key value')
 
-from . import serialization, agents, analysis, utils, time, config
 
 class Environment(Model):
     """
@@ -28,15 +34,17 @@ class Environment(Model):
     """
 
     def __init__(self,
-                 env_id,
+                 env_id='unnamed_env',
                  seed='default',
                  schedule=None,
-                 env_params=None,
                  dir_path=None,
-                 **kwargs):
+                 interval=1,
+                 agents: Dict[str, config.AgentConfig] = {},
+                 topologies: Dict[str, config.NetConfig] = {},
+                 **env_params):
 
         super().__init__()
-
+        self.current_id = -1
 
         self.seed = '{}_{}'.format(seed, env_id)
         self.id = env_id
@@ -51,25 +59,28 @@ class Environment(Model):
 
         random.seed(seed)
 
-        if isinstance(states, list):
-            states = dict(enumerate(states))
-        self.states = deepcopy(states) if states else {}
-        self.default_state = deepcopy(default_state) or {}
-
-
-        self.set_topology(topology=topology,
-                          network_params=network_params)
 
+        self.topologies = {}
+        for (name, cfg) in topologies.items():
+            self.set_topology(cfg=cfg,
+                              graph=name)
         self.agents = agents or {}
 
         self.env_params = env_params or {}
-        self.env_params.update(kwargs)
 
         self.interval = interval
         self['SEED'] = seed
 
+        self.logger = utils.logger.getChild(self.id)
+
+    @property
+    def topology(self):
+        return self.topologies['default']
+
+    @property
+    def network_agents(self):
+        yield from self.agents(agent_type=agents.NetworkAgent, iterator=True)
 
-        self.logger = utils.logger.getChild(self.name)
 
     @staticmethod
     def from_config(conf: config.Config, trial_id, **kwargs) -> Environment:
@@ -92,39 +103,30 @@ class Environment(Model):
         raise Exception('The environment has not been scheduled, so it has no sense of time')
 
 
-    def set_topology(self, topology, network_params=None, dir_path=None):
-        if topology is None:
-            network_params = network_params or {}
-            topology = serialization.load_network(network_params,
-                                                  dir_path=dir_path or self.dir_path)
-        if not topology:
-            topology = nx.Graph()
-        self.G = nx.Graph(topology)
+    def set_topology(self, cfg=None, dir_path=None, graph='default'):
+        self.topologies[graph] = network.from_config(cfg, dir_path=dir_path)
 
     @property
     def agents(self):
-        for agents in self.agents.values():
-            yield from agents
+        return agents.AgentView(self._agents)
 
     @agents.setter
-    def agents(self, agents):
-        self.agents = {}
+    def agents(self, agents_def: Dict[str, config.AgentConfig]):
+        self._agents = agents.from_config(agents_def, env=self)
+        for d in self._agents.values():
+            for a in d.values():
+                self.schedule.add(a)
 
-        for (k, v) in agents.items():
-            self.agents[k] = agents.from_config(v)
-        for agent in self.agents.get('network', []):
-            node = self.G.nodes[agent.unique_id]
-            node['agent'] = agent
 
-    @property
-    def network_agents(self):
-        for i in self.G.nodes():
-            node = self.G.nodes[i]
-            if 'agent' in node:
-                yield node['agent']
+    # @property
+    # def network_agents(self):
+    #     for i in self.G.nodes():
+    #         node = self.G.nodes[i]
+    #         if 'agent' in node:
+    #             yield node['agent']
 
-    def init_agent(self, agent_id, agent_definitions):
-        node = self.G.nodes[agent_id]
+    def init_agent(self, agent_id, agent_definitions, graph='default'):
+        node = self.topologies[graph].nodes[agent_id]
         init = False
         state = dict(node)
 
@@ -145,8 +147,8 @@ class Environment(Model):
             return
         return self.set_agent(agent_id, agent_type, state)
 
-    def set_agent(self, agent_id, agent_type, state=None):
-        node = self.G.nodes[agent_id]
+    def set_agent(self, agent_id, agent_type, state=None, graph='default'):
+        node = self.topologies[graph].nodes[agent_id]
         defstate = deepcopy(self.default_state) or {}
         defstate.update(self.states.get(agent_id, {}))
         defstate.update(node.get('state', {}))
@@ -166,20 +168,20 @@ class Environment(Model):
         self.schedule.add(a)
         return a
 
-    def add_node(self, agent_type, state=None):
-        agent_id = int(len(self.G.nodes()))
-        self.G.add_node(agent_id)
-        a = self.set_agent(agent_id, agent_type, state)
+    def add_node(self, agent_type, state=None, graph='default'):
+        agent_id = int(len(self.topologies[graph].nodes()))
+        self.topologies[graph].add_node(agent_id)
+        a = self.set_agent(agent_id, agent_type, state, graph=graph)
         a['visible'] = True
         return a
 
-    def add_edge(self, agent1, agent2, start=None, **attrs):
+    def add_edge(self, agent1, agent2, start=None, graph='default', **attrs):
         if hasattr(agent1, 'id'):
             agent1 = agent1.id
         if hasattr(agent2, 'id'):
             agent2 = agent2.id
         start = start or self.now
-        return self.G.add_edge(agent1, agent2, **attrs)
+        return self.topologies[graph].add_edge(agent1, agent2, **attrs)
 
     def log(self, message, *args, level=logging.INFO, **kwargs):
         if not self.logger.isEnabledFor(level):
@@ -190,7 +192,7 @@ class Environment(Model):
             message += " {k}={v} ".format(k, v)
         extra = {}
         extra['now'] = self.now
-        extra['unique_id'] = self.name
+        extra['unique_id'] = self.id
         return self.logger.log(level, message, extra=extra)
 
     def step(self):
@@ -207,30 +209,6 @@ class Environment(Model):
             self.step()
             utils.logger.debug(f'Simulation step {self.schedule.time}/{until}. Next: {self.schedule.next_time}')
         self.schedule.time = until
-        self._history.flush_cache()
-
-    def _save_state(self, now=None):
-        serialization.logger.debug('Saving state @{}'.format(self.now))
-        self._history.save_records(self.state_to_tuples(now=now))
-
-    def __getitem__(self, key):
-        if isinstance(key, tuple):
-            self._history.flush_cache()
-            return self._history[key]
-
-        return self.environment_params[key]
-
-    def __setitem__(self, key, value):
-        if isinstance(key, tuple):
-            k = Key(*key)
-            self._history.save_record(*k,
-                                      value=value)
-            return
-        self.environment_params[key] = value
-        self._history.save_record(dict_id='env',
-                                  t_step=self.now,
-                                  key=key,
-                                  value=value)
 
     def __contains__(self, key):
         return key in self.env_params
@@ -248,14 +226,6 @@ class Environment(Model):
     def __setitem__(self, key, value):
         return self.env_params.__setitem__(key, value)
 
-    def get_agent(self, agent_id):
-        return self.G.nodes[agent_id]['agent']
-
-    def get_agents(self, nodes=None):
-        if nodes is None:
-            return self.agents
-        return (self.G.nodes[i]['agent'] for i in nodes)
-
     def _agent_to_tuples(self, agent, now=None):
         if now is None:
             now = self.now
@@ -270,7 +240,7 @@ class Environment(Model):
             now = self.now
 
         if agent_id:
-            agent = self.get_agent(agent_id)
+            agent = self.agents[agent_id]
             yield from self._agent_to_tuples(agent, now)
             return
 
@@ -283,4 +253,5 @@ class Environment(Model):
             yield from self._agent_to_tuples(agent, now)
 
 
+
 SoilEnvironment = Environment

soil/serialization.py

@@ -16,39 +16,39 @@ from jinja2 import Template
 logger = logging.getLogger('soil')
 
 
-def load_network(network_params, dir_path=None):
-    G = nx.Graph()
+# def load_network(network_params, dir_path=None):
+#     G = nx.Graph()
 
-    if not network_params:
-        return G
+#     if not network_params:
+#         return G
 
-    if 'path' in network_params:
-        path = network_params['path']
-        if dir_path and not os.path.isabs(path):
-            path = os.path.join(dir_path, path)
-        extension = os.path.splitext(path)[1][1:]
-        kwargs = {}
-        if extension == 'gexf':
-            kwargs['version'] = '1.2draft'
-            kwargs['node_type'] = int
-        try:
-            method = getattr(nx.readwrite, 'read_' + extension)
-        except AttributeError:
-            raise AttributeError('Unknown format')
-        G = method(path, **kwargs)
+#     if 'path' in network_params:
+#         path = network_params['path']
+#         if dir_path and not os.path.isabs(path):
+#             path = os.path.join(dir_path, path)
+#         extension = os.path.splitext(path)[1][1:]
+#         kwargs = {}
+#         if extension == 'gexf':
+#             kwargs['version'] = '1.2draft'
+#             kwargs['node_type'] = int
+#         try:
+#             method = getattr(nx.readwrite, 'read_' + extension)
+#         except AttributeError:
+#             raise AttributeError('Unknown format')
+#         G = method(path, **kwargs)
 
-    elif 'generator' in network_params:
-        net_args = network_params.copy()
-        net_gen = net_args.pop('generator')
+#     elif 'generator' in network_params:
+#         net_args = network_params.copy()
+#         net_gen = net_args.pop('generator')
 
-        if dir_path not in sys.path:
-            sys.path.append(dir_path)
+#         if dir_path not in sys.path:
+#             sys.path.append(dir_path)
 
-        method = deserializer(net_gen,
-                              known_modules=['networkx.generators',])
-        G = method(**net_args)
+#         method = deserializer(net_gen,
+#                               known_modules=['networkx.generators',])
+#         G = method(**net_args)
 
-    return G
+#     return G
 
 
 def load_file(infile):
@@ -122,8 +122,8 @@ def load_files(*patterns, **kwargs):
         for i in glob(pattern, **kwargs):
             for config in load_file(i):
                 path = os.path.abspath(i)
-                if 'dir_path' not in config:
-                    config['dir_path'] = os.path.dirname(path)
+                if 'general' in config and 'dir_path' not in config['general']:
+                    config['general']['dir_path'] = os.path.dirname(path)
                 yield config, path
 
 

soil/simulation.py

@@ -96,7 +96,7 @@ class Simulation:
                 stat.sim_start()
 
             for exporter in exporters:
-                exporter.start()
+                exporter.sim_start()
 
             for env in self._run_sync_or_async(parallel=parallel,
                                                log_level=log_level,
@@ -107,7 +107,7 @@ class Simulation:
 
                 collected = list(stat.trial_end(env) for stat in stats)
 
-                saved = self._update_stats(collected, t_step=env.now, trial_id=env.name)
+                saved = self._update_stats(collected, t_step=env.now, trial_id=env.id)
 
                 for exporter in exporters:
                     exporter.trial_end(env, saved)
@@ -117,6 +117,9 @@ class Simulation:
             collected = list(stat.end() for stat in stats)
             saved = self._update_stats(collected)
 
+            for stat in stats:
+                stat.sim_end()
+
             for exporter in exporters:
                 exporter.sim_end(saved)
 
@@ -131,24 +134,24 @@ class Simulation:
 
     def get_env(self, trial_id=0, **kwargs):
         '''Create an environment for a trial of the simulation'''
-        opts = self.environment_params.copy()
-        opts.update({
-            'name': '{}_trial_{}'.format(self.name, trial_id),
-            'topology': self.topology.copy(),
-            'network_params': self.network_params,
-            'seed': '{}_trial_{}'.format(self.seed, trial_id),
-            'initial_time': 0,
-            'interval': self.interval,
-            'network_agents': self.network_agents,
-            'initial_time': 0,
-            '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)
-        env = self.environment_class(**opts)
+        # opts = self.environment_params.copy()
+        # opts.update({
+        #     'name': '{}_trial_{}'.format(self.name, trial_id),
+        #     'topology': self.topology.copy(),
+        #     'network_params': self.network_params,
+        #     'seed': '{}_trial_{}'.format(self.seed, trial_id),
+        #     'initial_time': 0,
+        #     'interval': self.interval,
+        #     'network_agents': self.network_agents,
+        #     'initial_time': 0,
+        #     '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)
+        env = Environment.from_config(self.config, trial_id=trial_id, **kwargs)
         return env
 
     def run_trial(self, trial_id=None, until=None, log_level=logging.INFO, **opts):
@@ -162,7 +165,7 @@ class Simulation:
         # Set-up trial environment and graph
         until = until or self.config.general.max_time
 
-        env = Environment.from_config(self.config, trial_id=trial_id)
+        env = self.get_env(trial_id, **opts)
         # Set up agents on nodes
         with utils.timer('Simulation {} trial {}'.format(self.config.general.id, trial_id)):
             env.run(until)
@@ -181,21 +184,31 @@ class Simulation:
             ex.message = ''.join(traceback.format_exception(type(ex), ex, ex.__traceback__)[:])
             return ex
 
+    def to_dict(self):
+        return self.config.dict()
+
+    def to_yaml(self):
+        return yaml.dump(self.config.dict())
+
 
 def all_from_config(config):
     configs = list(serialization.load_config(config))
-    for config, _ in configs:
-        sim = Simulation(**config)
+    for config, path in configs:
+        if config.get('version', '1') == '1':
+            config = convert_old(config)
+        if not isinstance(config, Config):
+            config = Config(**config)
+        if not config.general.dir_path:
+            config.general.dir_path = os.path.dirname(path)
+        sim = Simulation(config=config)
         yield sim
 
 
 def from_config(conf_or_path):
-    config = list(serialization.load_config(conf_or_path))
-    if len(config) > 1:
+    lst = list(all_from_config(conf_or_path))
+    if len(lst) > 1:
         raise AttributeError('Provide only one configuration')
-    config = config[0][0]
-    sim = Simulation(**config)
-    return sim
+    return lst[0]
 
 def from_old_config(conf_or_path):
     config = list(serialization.load_config(conf_or_path))
@@ -206,13 +219,7 @@ def from_old_config(conf_or_path):
 
 
 def run_from_config(*configs, **kwargs):
-    for config_def in configs:
-        # logger.info("Found {} config(s)".format(len(ls)))
-        for config, path in serialization.load_config(config_def):
-            name = config.general.id
-            logger.info("Using config(s): {name}".format(name=name))
-
-            dir_path = config.general.dir_path or os.path.dirname(path)
-            sim = Simulation(dir_path=dir_path,
-                             **config)
-            sim.run_simulation(**kwargs)
+    for sim in all_from_config(configs):
+        name = config.general.id
+        logger.info("Using config(s): {name}".format(name=name))
+        sim.run_simulation(**kwargs)

soil/time.py

@@ -3,7 +3,7 @@ from queue import Empty
 from heapq import heappush, heappop
 import math
 from .utils import logger
-from mesa import Agent
+from mesa import Agent as MesaAgent
 
 
 INFINITY = float('inf')
@@ -41,7 +41,7 @@ class TimedActivation(BaseScheduler):
         self._queue = []
         self.next_time = 0
 
-    def add(self, agent: Agent):
+    def add(self, agent: MesaAgent):
         if agent.unique_id not in self._agents:
             heappush(self._queue, (self.time, agent.unique_id))
             super().add(agent)