WIP: removed stats

examples/mesa/mesa.yml

@@ -14,7 +14,6 @@ network_agents:
     weight: 1
 environment_class: social_wealth.MoneyEnv
 environment_params:
-  num_mesa_agents: 5
   mesa_agent_type: social_wealth.MoneyAgent
   N: 10
   width: 50

examples/mesa/social_wealth.py

@@ -71,10 +71,9 @@ class SocialMoneyAgent(NetworkAgent, MoneyAgent):
 
 class MoneyEnv(Environment):
     """A model with some number of agents."""
-    def __init__(self, N, width, height, *args, network_params, **kwargs):
+    def __init__(self, width, height, *args, topologies, **kwargs):
 
-        network_params['n'] = N
+        super().__init__(*args, topologies=topologies, **kwargs)
-        super().__init__(*args, network_params=network_params, **kwargs)
         self.grid = MultiGrid(width, height, False)
 
         # Create agents

examples/newsspread/newsspread.py

@@ -1,8 +1,8 @@
-from soil.agents import FSM, state, default_state, prob
+from soil.agents import FSM, NetworkAgent, state, default_state, prob
 import logging
 
 
-class DumbViewer(FSM):
+class DumbViewer(FSM, NetworkAgent):
     '''
     A viewer that gets infected via TV (if it has one) and tries to infect
     its neighbors once it's infected.

examples/pubcrawl/pubcrawl.py

@@ -1,4 +1,4 @@
-from soil.agents import FSM, state, default_state
+from soil.agents import FSM, NetworkAgent, state, default_state
 from soil import Environment
 from random import random, shuffle
 from itertools import islice
@@ -53,7 +53,7 @@ class CityPubs(Environment):
                 pub['occupancy'] -= 1
 
 
-class Patron(FSM):
+class Patron(FSM, NetworkAgent):
     '''Agent that looks for friends to drink with. It will do three things:
         1) Look for other patrons to drink with
         2) Look for a bar where the agent and other agents in the same group can get in.
@@ -151,7 +151,7 @@ class Patron(FSM):
         return befriended
 
 
-class Police(FSM):
+class Police(FSM, NetworkAgent):
     '''Simple agent to take drunk people out of pubs.'''
     level = logging.INFO
 

examples/rabbits/rabbit_agents.py

@@ -10,7 +10,7 @@ class Genders(Enum):
     female = 'female'
 
 
-class RabbitModel(FSM):
+class RabbitModel(FSM, NetworkAgent):
 
     defaults = {
         'age': 0,
@@ -110,12 +110,12 @@ class Female(RabbitModel):
             self.info('A mother has died carrying a baby!!')
 
 
-class RandomAccident(NetworkAgent):
+class RandomAccident(BaseAgent):
 
     level = logging.DEBUG
 
     def step(self):
-        rabbits_total = self.topology.number_of_nodes()
+        rabbits_total = self.env.topology.number_of_nodes()
         if 'rabbits_alive' not in self.env:
             self.env['rabbits_alive'] = 0
         rabbits_alive = self.env.get('rabbits_alive', rabbits_total)
@@ -131,5 +131,5 @@ class RandomAccident(NetworkAgent):
                 self.log('Rabbits alive: {}'.format(self.env['rabbits_alive']))
                 i.set_state(i.dead)
         self.log('Rabbits alive: {}/{}'.format(rabbits_alive, rabbits_total))
-        if self.count_agents(state_id=RabbitModel.dead.id) == self.topology.number_of_nodes():
+        if self.env.count_agents(state_id=RabbitModel.dead.id) == self.env.topology.number_of_nodes():
             self.die()

soil/agents/__init__.py

@@ -55,6 +55,7 @@ class BaseAgent(MesaAgent, MutableMapping):
             raise Exception()
         assert isinstance(unique_id, int)
         super().__init__(unique_id=unique_id, model=model)
+
         self.name = str(name) if name else'{}[{}]'.format(type(self).__name__, self.unique_id)
 
 
@@ -78,6 +79,9 @@ class BaseAgent(MesaAgent, MutableMapping):
             if not hasattr(self, k) or getattr(self, k) is None:
                 setattr(self, k, v)
 
+    def __hash__(self):
+        return hash(self.unique_id)
+
     # TODO: refactor to clean up mesa compatibility
     @property
     def id(self):
@@ -185,16 +189,14 @@ class BaseAgent(MesaAgent, MutableMapping):
 # Agent = BaseAgent
 
 class NetworkAgent(BaseAgent):
-    def __init__(self,
+
-                 *args,
+    @property
-                 graph_name: str,
+    def topology(self):
-                 node_id: int = None,
+        return self.env.topology_for(self.unique_id)
-                 **kwargs,
+
-    ):
+    @property
-        super().__init__(*args, **kwargs)
+    def node_id(self):
-        self.graph_name = graph_name
+        return self.env.node_id_for(self.unique_id)
-        self.topology = self.env.topologies[self.graph_name]
-        self.node_id = node_id
 
     @property
     def G(self):
@@ -215,15 +217,19 @@ class NetworkAgent(BaseAgent):
             it = islice(it, limit)
         return list(it)
 
-    def iter_agents(self, agents=None, limit_neighbors=False, **kwargs):
+    def iter_agents(self, unique_id=None, limit_neighbors=False, **kwargs):
         if limit_neighbors:
-            agents = self.topology.neighbors(self.unique_id)
+            unique_id = [self.topology.nodes[node]['agent_id'] for node in self.topology.neighbors(self.node_id)]
+            if not unique_id:
+                return
+
+        yield from self.model.agents(unique_id=unique_id, **kwargs)
 
-        return self.model.agents(ids=agents, **kwargs)
 
     def subgraph(self, center=True, **kwargs):
         include = [self] if center else []
-        return self.topology.subgraph(n.unique_id for n in list(self.get_agents(**kwargs))+include)
+        G = self.topology.subgraph(n.node_id for n in list(self.get_agents(**kwargs)+include))
+        return G
 
     def remove_node(self, unique_id):
         self.topology.remove_node(unique_id)
@@ -366,7 +372,7 @@ def prob(prob=1):
 
 
 def calculate_distribution(network_agents=None,
-                           agent_type=None):
+                           agent_class=None):
     '''
     Calculate the threshold values (thresholds for a uniform distribution)
     of an agent distribution given the weights of each agent type.
@@ -374,13 +380,13 @@ def calculate_distribution(network_agents=None,
     The input has this form: ::
 
             [
-            {'agent_type': 'agent_type_1',
+            {'agent_class': 'agent_class_1',
                 'weight': 0.2,
                 'state': {
                     'id': 0
                 }
             },
-            {'agent_type': 'agent_type_2',
+            {'agent_class': 'agent_class_2',
                 'weight': 0.8,
                 'state': {
                     'id': 1
@@ -389,12 +395,12 @@ def calculate_distribution(network_agents=None,
             ]
 
     In this example, 20% of the nodes will be marked as type
-    'agent_type_1'.
+    'agent_class_1'.
     '''
     if network_agents:
         network_agents = [deepcopy(agent) for agent in network_agents if not hasattr(agent, 'id')]
-    elif agent_type:
+    elif agent_class:
-        network_agents = [{'agent_type': agent_type}]
+        network_agents = [{'agent_class': agent_class}]
     else:
         raise ValueError('Specify a distribution or a default agent type')
 
@@ -414,11 +420,11 @@ def calculate_distribution(network_agents=None,
     return network_agents
 
 
-def serialize_type(agent_type, known_modules=[], **kwargs):
+def serialize_type(agent_class, known_modules=[], **kwargs):
-    if isinstance(agent_type, str):
+    if isinstance(agent_class, str):
-        return agent_type
+        return agent_class
     known_modules += ['soil.agents']
-    return serialization.serialize(agent_type, known_modules=known_modules, **kwargs)[1] # Get the name of the class
+    return serialization.serialize(agent_class, known_modules=known_modules, **kwargs)[1] # Get the name of the class
 
 
 def serialize_definition(network_agents, known_modules=[]):
@@ -430,23 +436,23 @@ def serialize_definition(network_agents, known_modules=[]):
     for v in d:
         if 'threshold' in v:
             del v['threshold']
-        v['agent_type'] = serialize_type(v['agent_type'],
+        v['agent_class'] = serialize_type(v['agent_class'],
                                          known_modules=known_modules)
     return d
 
 
-def deserialize_type(agent_type, known_modules=[]):
+def deserialize_type(agent_class, known_modules=[]):
-    if not isinstance(agent_type, str):
+    if not isinstance(agent_class, str):
-        return agent_type
+        return agent_class
     known = known_modules + ['soil.agents', 'soil.agents.custom' ]
-    agent_type = serialization.deserializer(agent_type, known_modules=known)
+    agent_class = serialization.deserializer(agent_class, known_modules=known)
-    return agent_type
+    return agent_class
 
 
 def deserialize_definition(ind, **kwargs):
     d = deepcopy(ind)
     for v in d:
-        v['agent_type'] = deserialize_type(v['agent_type'], **kwargs)
+        v['agent_class'] = deserialize_type(v['agent_class'], **kwargs)
     return d
 
 
@@ -461,7 +467,7 @@ def _validate_states(states, topology):
     return states
 
 
-def _convert_agent_types(ind, to_string=False, **kwargs):
+def _convert_agent_classs(ind, to_string=False, **kwargs):
     '''Convenience method to allow specifying agents by class or class name.'''
     if to_string:
         return serialize_definition(ind, **kwargs)
@@ -480,7 +486,7 @@ def _agent_from_definition(definition, value=-1, unique_id=None):
             state = {}
             if 'state' in d:
                 state = deepcopy(d['state'])
-            return d['agent_type'], state
+            return d['agent_class'], state
 
     raise Exception('Definition for value {} not found in: {}'.format(value, definition))
 
@@ -576,8 +582,11 @@ class AgentView(Mapping, Set):
                 return group[agent_id]
         raise ValueError(f"Agent {agent_id} not found")
 
-    def filter(self, *group_ids, **kwargs):
+    def filter(self, *args, **kwargs):
-        yield from filter_groups(self._agents, group_ids=group_ids, **kwargs)
+        yield from filter_groups(self._agents, *args, **kwargs)
+
+    def one(self, *args, **kwargs):
+        return next(filter_groups(self._agents, *args, **kwargs))
 
     def __call__(self, *args, **kwargs):
         return list(self.filter(*args, **kwargs))
@@ -586,16 +595,20 @@ class AgentView(Mapping, Set):
         return any(agent_id in g for g in self._agents)
 
     def __str__(self):
-        return str(list(a.id for a in self))
+        return str(list(a.unique_id for a in self))
 
     def __repr__(self):
         return f"{self.__class__.__name__}({self})"
 
 
-def filter_groups(groups, group_ids=None, **kwargs):
+def filter_groups(groups, *, group=None, **kwargs):
     assert isinstance(groups, dict)
-    if group_ids:
+
-        groups = list(groups[g] for g in group_ids if g in groups)
+    if group is not None and not isinstance(group, list):
+        group = [group]
+
+    if group:
+        groups = list(groups[g] for g in group if g in groups)
     else:
         groups = list(groups.values())
 
@@ -604,23 +617,35 @@ def filter_groups(groups, group_ids=None, **kwargs):
     yield from agents
 
 
-def filter_group(group, ids=None, state_id=None, agent_type=None, ignore=None, state=None, **kwargs):
+def filter_group(group, *id_args, unique_id=None, state_id=None, agent_class=None, ignore=None, state=None, **kwargs):
     '''
     Filter agents given as a dict, by the criteria given as arguments (e.g., certain type or state id).
     '''
     assert isinstance(group, dict)
 
+    ids = []
+
+    if unique_id is not None:
+        if isinstance(unique_id, list):
+            ids += unique_id
+        else:
+            ids.append(unique_id)
+
+    if id_args:
+        ids += id_args
+
     if state_id is not None and not isinstance(state_id, (tuple, list)):
         state_id = tuple([state_id])
 
-    if agent_type is not None:
+    if agent_class is not None:
+        agent_class = deserialize_type(agent_class)
         try:
-            agent_type = tuple(agent_type)
+            agent_class = tuple(agent_class)
         except TypeError:
-            agent_type = tuple([agent_type])
+            agent_class = tuple([agent_class])
 
     if ids:
-        agents = (v[aid] for aid in ids if aid in group)
+        agents = (group[aid] for aid in ids if aid in group)
     else:
         agents = (a for a in group.values())
 
@@ -631,8 +656,8 @@ def filter_group(group, ids=None, state_id=None, agent_type=None, ignore=None, s
     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:
+    if agent_class is not None:
-        f = filter(lambda agent: isinstance(agent, agent_type), f)
+        f = filter(lambda agent: isinstance(agent, agent_class), f)
 
     state = state or dict()
     state.update(kwargs)
@@ -660,7 +685,7 @@ def _group_from_config(cfg: config.AgentConfig, default: config.SingleAgentConfi
     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])
+        n = cfg.n or len(env.topologies[cfg.topology or default.topology])
         target = n - len(agents)
         agents.update(_from_distro(cfg.distribution, target,
                                    topology=cfg.topology or default.topology,
@@ -674,6 +699,8 @@ def _group_from_config(cfg: config.AgentConfig, default: config.SingleAgentConfi
             else:
                 filtered = list(agents)
 
+            if attrs.n > len(filtered):
+                raise ValueError(f'Not enough agents to sample. Got {len(filtered)}, expected >= {attrs.n}')
             for agent in random.sample(filtered, attrs.n):
                 agent.state.update(attrs.state)
 
@@ -693,8 +720,10 @@ def _from_fixed(lst: List[config.FixedAgentConfig], topology: str, default: conf
         state.update(default.state)
         agent = cls(unique_id=agent_id,
                     model=env,
-                  graph_name=fixed.topology or topology or default.topology,
                     **state)
+        topology = fixed.topology if (fixed.topology is not None) else (topology or default.topology)
+        if topology:
+            env.agent_to_node(agent_id, topology, fixed.node_id)
         agents[agent.unique_id] = agent
 
     return agents
@@ -741,8 +770,12 @@ def _from_distro(distro: List[config.AgentDistro],
         cls = classes[idx]
         agent_id = env.next_id()
         state = d.state.copy()
+        if default:
             state.update(default.state)
-        agent = cls(unique_id=agent_id, model=env, graph_name=d.topology or topology or default.topology, **state)
+        agent = cls(unique_id=agent_id, model=env, **state)
+        topology = d.topology if (d.topology is not None) else topology or default.topology
+        if topology:
+            env.agent_to_node(agent.unique_id, topology)
         assert agent.name is not None
         assert agent.name != 'None'
         assert agent.name

soil/config.py

@@ -7,6 +7,7 @@ import sys
 
 from typing import Any, Callable, Dict, List, Optional, Union, Type
 from pydantic import BaseModel, Extra
+import networkx as nx
 
 class General(BaseModel):
     id: str = 'Unnamed Simulation'
@@ -50,9 +51,12 @@ class NetParams(BaseModel, extra=Extra.allow):
 class NetConfig(BaseModel):
     group: str = 'network'
     params: Optional[NetParams]
-    topology: Optional[Topology]
+    topology: Optional[Union[Topology, nx.Graph]]
     path: Optional[str]
 
+    class Config:
+        arbitrary_types_allowed = True
+
     @staticmethod
     def default():
         return NetConfig(topology=None, params=None)
@@ -77,7 +81,8 @@ class EnvConfig(BaseModel):
 class SingleAgentConfig(BaseModel):
     agent_class: Optional[Union[Type, str]] = None
     agent_id: Optional[int] = None
-    topology: Optional[str] = 'default'
+    topology: Optional[str] = None
+    node_id: Optional[Union[int, str]] = None
     name: Optional[str] = None
     state: Optional[Dict[str, Any]] = {}
 
@@ -187,8 +192,6 @@ def convert_old(old, strict=True):
             agent['name'] = agent['agent_id']
             del agent['agent_id']
         agents['environment']['fixed'].append(updated_agent(agent))
-        else:
-            agents['environment']['distribution'].append(updated_agent(agent))
 
     by_weight = []
     fixed = []
@@ -206,10 +209,10 @@ def convert_old(old, strict=True):
 
     if 'agent_type' in old and (not fixed and not by_weight):
         agents['network']['topology'] = 'default'
-        by_weight = [{'agent_type': old['agent_type']}]
+        by_weight = [{'agent_class': old['agent_type']}]
 
     
-    # TODO: translate states
+    # TODO: translate states properly
     if 'states' in old:
         states = old['states']
         if isinstance(states, dict):
@@ -217,7 +220,7 @@ def convert_old(old, strict=True):
         else:
             states = enumerate(states)
         for (k, v) in states:
-            override.append({'filter': {'id': k},
+            override.append({'filter': {'node_id': k},
                              'state': v
             })
 

soil/config_old.py

@@ -1,264 +0,0 @@
-from pydantic import BaseModel, ValidationError, validator
-
-import yaml
-import os
-import sys
-import networkx as nx
-import collections.abc
-
-from . import serialization, utils, basestring, agents
-
-class Config(collections.abc.Mapping):
-    """
-
-        1) agent type can be specified by name or by class.
-        2) instead of just one type, a network agents distribution can be used.
-           The distribution specifies the weight (or probability) of each
-           agent type in the topology. This is an example distribution: ::
-
-                  [
-                    {'agent_type': 'agent_type_1',
-                     'weight': 0.2,
-                     'state': {
-                         'id': 0
-                      }
-                    },
-                    {'agent_type': 'agent_type_2',
-                     'weight': 0.8,
-                     'state': {
-                         'id': 1
-                      }
-                    }
-                  ]
-
-          In this example, 20% of the nodes will be marked as type
-          'agent_type_1'.
-        3) if no initial state is given, each node's state will be set
-           to `{'id': 0}`.
-
-    Parameters
-    ---------
-    name : str, optional
-        name of the Simulation
-    group : str, optional
-        a group name can be used to link simulations
-    topology (optional): networkx.Graph instance or Node-Link topology as a dict or string (will be loaded with `json_graph.node_link_graph(topology`).
-    network_params : dict
-        parameters used to create a topology with networkx, if no topology is given
-    network_agents : dict
-        definition of agents to populate the topology with
-    agent_type : NetworkAgent subclass, optional
-        Default type of NetworkAgent to use for nodes not specified in network_agents
-    states : list, optional
-        List of initial states corresponding to the nodes in the topology. Basic form is a list of integers
-        whose value indicates the state
-    dir_path: str, optional
-        Directory path to load simulation assets (files, modules...)
-    seed : str, optional
-        Seed to use for the random generator
-    num_trials : int, optional
-        Number of independent simulation runs
-    max_time : int, optional
-        Maximum step/time for each simulation
-    environment_params : dict, optional
-        Dictionary of globally-shared environmental parameters
-    environment_agents: dict, optional
-        Similar to network_agents. Distribution of Agents that control the environment
-    environment_class: soil.environment.Environment subclass, optional
-        Class for the environment. It defailts to soil.environment.Environment
-    """
-    __slots__ = 'name', 'agent_type', 'group', 'description', 'network_agents', 'environment_agents', 'states', 'default_state', 'interval', 'network_params', 'seed', 'num_trials', 'max_time', 'topology', 'schedule', 'initial_time', 'environment_params', 'environment_class', 'dir_path', '_added_to_path', 'visualization_params'
-
-    def __init__(self, name=None,
-                 group=None,
-                 agent_type='BaseAgent',
-                 network_agents=None,
-                 environment_agents=None,
-                 states=None,
-                 description=None,
-                 default_state=None,
-                 interval=1,
-                 network_params=None,
-                 seed=None,
-                 num_trials=1,
-                 max_time=None,
-                 topology=None,
-                 schedule=None,
-                 initial_time=0,
-                 environment_params={},
-                 environment_class='soil.Environment',
-                 dir_path=None,
-                 visualization_params=None,
-    ):
-
-        self.network_params = network_params
-        self.name = name or 'Unnamed'
-        self.description = description or 'No simulation description available'
-        self.seed = str(seed or name)
-        self.group = group or ''
-        self.num_trials = num_trials
-        self.max_time = max_time
-        self.default_state = default_state or {}
-        self.dir_path = dir_path or os.getcwd()
-        self.interval = interval
-        self.visualization_params = visualization_params or {}
-
-        self._added_to_path = list(x for x in [os.getcwd(), self.dir_path] if x not in sys.path)
-        sys.path += self._added_to_path
-
-        self.topology = topology
-
-        self.schedule = schedule
-        self.initial_time = initial_time
-
-
-        self.environment_class = environment_class
-        self.environment_params = dict(environment_params)
-
-        #TODO: Check agent distro vs fixed agents
-        self.environment_agents = environment_agents or []
-        
-        self.agent_type = agent_type
-
-        self.network_agents = network_agents or {}
-
-        self.states = states or {}
-
-
-    def validate(self):
-        agents._validate_states(self.states,
-                                self._topology)
-
-    def calculate(self):
-        return CalculatedConfig(self)
-
-    def restore_path(self):
-        for added in self._added_to_path:
-            sys.path.remove(added)
-
-    def to_yaml(self):
-        return yaml.dump(self.to_dict())
-
-    def dump_yaml(self, f=None, outdir=None):
-        if not f and not outdir:
-            raise ValueError('specify a file or an output directory')
-
-        if not f:
-            f = os.path.join(outdir, '{}.dumped.yml'.format(self.name))
-
-        with utils.open_or_reuse(f, 'w') as f:
-            f.write(self.to_yaml())
-
-    def to_yaml(self):
-        return yaml.dump(self.to_dict())
-
-    # TODO: See note on getstate
-    def to_dict(self):
-        return dict(self)
-
-    def __repr__(self):
-        return self.to_yaml()
-
-    def dump_yaml(self, f=None, outdir=None):
-        if not f and not outdir:
-            raise ValueError('specify a file or an output directory')
-
-        if not f:
-            f = os.path.join(outdir, '{}.dumped.yml'.format(self.name))
-
-        with utils.open_or_reuse(f, 'w') as f:
-            f.write(self.to_yaml())
-
-    def __getitem__(self, key):
-        return getattr(self, key)
-
-    def __iter__(self):
-        return (k for k in self.__slots__ if k[0] != '_')
-
-    def __len__(self):
-        return len(self.__slots__)
-
-    def dump_pickle(self, f=None, outdir=None):
-        if not outdir and not f:
-            raise ValueError('specify a file or an output directory')
-
-        if not f:
-            f = os.path.join(outdir,
-                             '{}.simulation.pickle'.format(self.name))
-        with utils.open_or_reuse(f, 'wb') as f:
-            pickle.dump(self, f)
-
-    # TODO: remove this. A config should be sendable regardless. Non-pickable objects could be computed via properties and the like
-    # def __getstate__(self):
-    #     state={}
-    #     for k, v in self.__dict__.items():
-    #         if k[0] != '_':
-    #             state[k] = v
-    #             state['topology'] = json_graph.node_link_data(self.topology)
-    #             state['network_agents'] = agents.serialize_definition(self.network_agents,
-    #                                                                   known_modules = [])
-    #             state['environment_agents'] = agents.serialize_definition(self.environment_agents,
-    #                                                                       known_modules = [])
-    #             state['environment_class'] = serialization.serialize(self.environment_class,
-    #                                                                  known_modules=['soil.environment'])[1]  # func, name
-    #     if state['load_module'] is None:
-    #         del state['load_module']
-    #     return state
-
-    # # TODO: remove, same as __getstate__
-    # def __setstate__(self, state):
-    #     self.__dict__ = state
-    #     self.load_module = getattr(self, 'load_module', None)
-    #     if self.dir_path not in sys.path:
-    #         sys.path += [self.dir_path, os.getcwd()]
-    #     self.topology = json_graph.node_link_graph(state['topology'])
-    #     self.network_agents = agents.calculate_distribution(agents._convert_agent_types(self.network_agents))
-    #     self.environment_agents = agents._convert_agent_types(self.environment_agents,
-    #                                                           known_modules=[self.load_module])
-    #     self.environment_class = serialization.deserialize(self.environment_class,
-                                                           # known_modules=[self.load_module,
-                                                           #                'soil.environment', ])  # func, name
-
-class CalculatedConfig(Config):
-    def __init__(self, config):
-        """
-        Returns a configuration object that replaces some "plain" attributes (e.g., `environment_class` string) into
-        a Python object (`soil.environment.Environment` class).
-        """
-        self._config = config
-        values = dict(config)
-        values['environment_class'] = self._environment_class()
-        values['environment_agents'] = self._environment_agents()
-        values['topology'] = self._topology()
-        values['network_agents'] = self._network_agents()
-        values['agent_type'] = serialization.deserialize(self.agent_type, known_modules=['soil.agents'])
-
-        return values
-
-    def _topology(self):
-        topology = self._config.topology
-        if topology is None:
-            topology = serialization.load_network(self._config.network_params,
-                                                  dir_path=self._config.dir_path)
-
-        elif isinstance(topology, basestring) or isinstance(topology, dict):
-            topology = json_graph.node_link_graph(topology)
-
-        return nx.Graph(topology)
-
-    def _environment_class(self):
-        return serialization.deserialize(self._config.environment_class,
-                                         known_modules=['soil.environment', ]) or Environment
-
-    def _environment_agents(self):
-        return agents._convert_agent_types(self._config.environment_agents)
-
-    def _network_agents(self):
-        distro = agents.calculate_distribution(self._config.network_agents,
-                                               self._config.agent_type)
-        return agents._convert_agent_types(distro)
-
-    def _environment_class(self):
-        return serialization.deserialize(self._config.environment_class,
-                                         known_modules=['soil.environment', ])  # func, name
-

soil/environment.py

@@ -15,6 +15,7 @@ from networkx.readwrite import json_graph
 import networkx as nx
 
 from mesa import Model
+from mesa.datacollection import DataCollector
 
 from . import serialization, agents, analysis, utils, time, config, network
 
@@ -41,6 +42,9 @@ class Environment(Model):
                  interval=1,
                  agents: Dict[str, config.AgentConfig] = {},
                  topologies: Dict[str, config.NetConfig] = {},
+                 agent_reporters: Optional[Any] = None,
+                 model_reporters: Optional[Any] = None,
+                 tables: Optional[Any] = None,
                  **env_params):
 
         super().__init__()
@@ -61,6 +65,7 @@ class Environment(Model):
 
 
         self.topologies = {}
+        self._node_ids = {}
         for (name, cfg) in topologies.items():
             self.set_topology(cfg=cfg,
                               graph=name)
@@ -72,6 +77,7 @@ class Environment(Model):
         self['SEED'] = seed
 
         self.logger = utils.logger.getChild(self.id)
+        self.datacollector = DataCollector(model_reporters, agent_reporters, tables)
 
     @property
     def topology(self):
@@ -79,8 +85,7 @@ class Environment(Model):
 
     @property
     def network_agents(self):
-        yield from self.agents(agent_type=agents.NetworkAgent, iterator=False)
+        yield from self.agents(agent_class=agents.NetworkAgent)
-
 
     @staticmethod
     def from_config(conf: config.Config, trial_id, **kwargs) -> Environment:
@@ -91,9 +96,10 @@ class Environment(Model):
         seed = '{}_{}'.format(conf.general.seed, trial_id)
         id = '{}_trial_{}'.format(conf.general.id, trial_id).replace('.', '-')
         opts = conf.environment.params.copy()
+        dir_path = conf.general.dir_path
         opts.update(conf)
         opts.update(kwargs)
-        env = serialization.deserialize(conf.environment.environment_class)(env_id=id, seed=seed, **opts)
+        env = serialization.deserialize(conf.environment.environment_class)(env_id=id, seed=seed, dir_path=dir_path, **opts)
         return env
 
     @property
@@ -103,13 +109,32 @@ class Environment(Model):
         raise Exception('The environment has not been scheduled, so it has no sense of time')
 
 
+    def topology_for(self, agent_id):
+        return self.topologies[self._node_ids[agent_id][0]]
+
+    def node_id_for(self, agent_id):
+        return self._node_ids[agent_id][1]
+
     def set_topology(self, cfg=None, dir_path=None, graph='default'):
-        self.topologies[graph] = network.from_config(cfg, dir_path=dir_path)
+        topology = cfg
+        if not isinstance(cfg, nx.Graph):
+            topology = network.from_config(cfg, dir_path=dir_path or self.dir_path)
+
+        self.topologies[graph] = topology
 
     @property
     def agents(self):
         return agents.AgentView(self._agents)
     
+    def count_agents(self, *args, **kwargs):
+        return sum(1 for i in self.find_all(*args, **kwargs))
+
+    def find_all(self, *args, **kwargs):
+        return agents.AgentView(self._agents).filter(*args, **kwargs)
+
+    def find_one(self, *args, **kwargs):
+        return agents.AgentView(self._agents).one(*args, **kwargs)
+
     @agents.setter
     def agents(self, agents_def: Dict[str, config.AgentConfig]):
         self._agents = agents.from_config(agents_def, env=self)
@@ -117,37 +142,47 @@ class Environment(Model):
             for a in d.values():
                 self.schedule.add(a)
 
-
-    # @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, graph='default'):
         node = self.topologies[graph].nodes[agent_id]
         init = False
         state = dict(node)
 
-        agent_type = None
+        agent_class = None
-        if 'agent_type' in self.states.get(agent_id, {}):
+        if 'agent_class' in self.states.get(agent_id, {}):
-            agent_type = self.states[agent_id]['agent_type']
+            agent_class = self.states[agent_id]['agent_class']
-        elif 'agent_type' in node:
+        elif 'agent_class' in node:
-            agent_type = node['agent_type']
+            agent_class = node['agent_class']
-        elif 'agent_type' in self.default_state:
+        elif 'agent_class' in self.default_state:
-            agent_type = self.default_state['agent_type']
+            agent_class = self.default_state['agent_class']
 
-        if agent_type:
+        if agent_class:
-            agent_type = agents.deserialize_type(agent_type)
+            agent_class = agents.deserialize_type(agent_class)
         elif agent_definitions:
-            agent_type, state = agents._agent_from_definition(agent_definitions, unique_id=agent_id)
+            agent_class, state = agents._agent_from_definition(agent_definitions, unique_id=agent_id)
         else:
             serialization.logger.debug('Skipping node {}'.format(agent_id))
             return
-        return self.set_agent(agent_id, agent_type, state)
+        return self.set_agent(agent_id, agent_class, state)
 
-    def set_agent(self, agent_id, agent_type, state=None, graph='default'):
+    def agent_to_node(self, agent_id, graph_name='default', node_id=None, shuffle=False):
+        #TODO: test
+        if node_id is None:
+            G = self.topologies[graph_name]
+            candidates = list(G.nodes(data=True))
+            if shuffle:
+                random.shuffle(candidates)
+            for next_id, data in candidates:
+                if data.get('agent_id', None) is None:
+                    node_id = next_id
+                    data['agent_id'] = agent_id
+                    break
+                    
+
+        self._node_ids[agent_id] = (graph_name, node_id)
+        print(self._node_ids)
+
+
+    def set_agent(self, agent_id, agent_class, state=None, graph='default'):
         node = self.topologies[graph].nodes[agent_id]
         defstate = deepcopy(self.default_state) or {}
         defstate.update(self.states.get(agent_id, {}))
@@ -155,9 +190,9 @@ class Environment(Model):
         if state:
             defstate.update(state)
         a = None
-        if agent_type:
+        if agent_class:
             state = defstate
-            a = agent_type(model=self,
+            a = agent_class(model=self,
                            unique_id=agent_id
             )
 
@@ -168,10 +203,10 @@ class Environment(Model):
         self.schedule.add(a)
         return a
 
-    def add_node(self, agent_type, state=None, graph='default'):
+    def add_node(self, agent_class, 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 = self.set_agent(agent_id, agent_class, state, graph=graph)
         a['visible'] = True
         return a
 
@@ -201,6 +236,7 @@ class Environment(Model):
         '''
         super().step()
         self.schedule.step()
+        self.datacollector.collect(self)
 
     def run(self, until, *args, **kwargs):
         until = until or float('inf')

soil/exporters.py

@@ -1,5 +1,4 @@
 import os
-import csv as csvlib
 from time import time as current_time
 from io import BytesIO
 from sqlalchemy import create_engine
@@ -59,7 +58,7 @@ class Exporter:
         '''Method to call when the simulation starts'''
         pass
 
-    def sim_end(self, stats):
+    def sim_end(self):
         '''Method to call when the simulation ends'''
         pass
 
@@ -67,7 +66,7 @@ class Exporter:
         '''Method to call when a trial start'''
         pass
 
-    def trial_end(self, env, stats):
+    def trial_end(self, env):
         '''Method to call when a trial ends'''
         pass
 
@@ -115,31 +114,35 @@ class default(Exporter):
     #               self.simulation.dump_sqlite(f)
 
 
+def get_dc_dfs(dc):
+    dfs = {'env': dc.get_model_vars_dataframe(),
+        'agents': dc.get_agent_vars_dataframe }
+    for table_name in dc.tables:
+        dfs[table_name] = dc.get_table_dataframe(table_name)
+    yield from dfs.items() 
+
 
 class csv(Exporter):
 
     '''Export the state of each environment (and its agents) in a separate CSV file'''
-    def trial_end(self, env, stats):
+    def trial_end(self, env):
         with timer('[CSV] Dumping simulation {} trial {} @ dir {}'.format(self.simulation.name,
-                                                                          env.name,
+                                                                          env.id,
                                                                           self.outdir)):
-
+            for (df_name, df) in get_dc_dfs(env.datacollector):
-            with self.output('{}.stats.{}.csv'.format(env.name, stats.name)) as f:
+                with self.output('{}.stats.{}.csv'.format(env.id, df_name)) as f:
-                statwriter = csvlib.writer(f, delimiter='\t', quotechar='"', quoting=csvlib.QUOTE_ALL)
+                    df.to_csv(f)
-
-                for stat in stats:
-                    statwriter.writerow(stat)
 
 
 class gexf(Exporter):
-    def trial_end(self, env, stats):
+    def trial_end(self, env):
         if self.dry_run:
             logger.info('Not dumping GEXF in dry_run mode')
             return
 
         with timer('[GEXF] Dumping simulation {} trial {}'.format(self.simulation.name,
-                                                                  env.name)):
+                                                                  env.id)):
-            with self.output('{}.gexf'.format(env.name), mode='wb') as f:
+            with self.output('{}.gexf'.format(env.id), mode='wb') as f:
                 self.dump_gexf(env, f)
 
     def dump_gexf(self, env, f):
@@ -159,25 +162,25 @@ class dummy(Exporter):
         with self.output('dummy', 'w') as f:
             f.write('simulation started @ {}\n'.format(current_time()))
 
-    def trial_end(self, env, stats):
+    def trial_start(self, env):
         with self.output('dummy', 'w') as f:
-            for i in stats:
+            f.write('trial started@ {}\n'.format(current_time()))
-                f.write(','.join(map(str, i)))
-                f.write('\n')
 
-    def sim_end(self, stats):
+    def trial_end(self, env):
+        with self.output('dummy', 'w') as f:
+            f.write('trial ended@ {}\n'.format(current_time()))
+
+    def sim_end(self):
         with self.output('dummy', 'a') as f:
             f.write('simulation ended @ {}\n'.format(current_time()))
 
-
-
 class graphdrawing(Exporter):
 
-    def trial_end(self, env, stats):
+    def trial_end(self, env):
         # Outside effects
         f = plt.figure()
         nx.draw(env.G, node_size=10, width=0.2, pos=nx.spring_layout(env.G, scale=100), ax=f.add_subplot(111))
-        with open('graph-{}.png'.format(env.name)) as f:
+        with open('graph-{}.png'.format(env.id)) as f:
             f.savefig(f)
 
 '''

soil/simulation.py

@@ -16,7 +16,6 @@ from . import serialization, utils, basestring, agents
 from .environment import Environment
 from .utils import logger
 from .exporters import default
-from .stats import defaultStats
 
 from .config import Config, convert_old
 
@@ -71,8 +70,8 @@ class Simulation:
                                      **kwargs)
 
     def run_gen(self, parallel=False, dry_run=False,
-                exporters=[default, ], stats=[], outdir=None, exporter_params={},
+                exporters=[default, ], outdir=None, exporter_params={},
-                stats_params={}, log_level=None,
+                log_level=None,
                 **kwargs):
         '''Run the simulation and yield the resulting environments.'''
         if log_level:
@@ -85,15 +84,8 @@ class Simulation:
                                                   dry_run=dry_run,
                                                   outdir=outdir,
                                                   **exporter_params)
-        stats = serialization.deserialize_all(simulation=self,
-                                             names=stats,
-                                             known_modules=['soil.stats',],
-                                             **stats_params)
 
         with utils.timer('simulation {}'.format(self.config.general.id)):
-            for stat in stats:
-                stat.sim_start()
-
             for exporter in exporters:
                 exporter.sim_start()
 
@@ -104,32 +96,13 @@ class Simulation:
                 for exporter in exporters:
                     exporter.trial_start(env)
 
-                collected = list(stat.trial_end(env) for stat in stats)
-
-                saved = self._update_stats(collected, t_step=env.now, trial_id=env.id)
-
                 for exporter in exporters:
-                    exporter.trial_end(env, saved)
+                    exporter.trial_end(env)
 
                 yield env
 
-            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)
+                exporter.sim_end()
-
-    def _update_stats(self, collection, **kwargs):
-        stats = dict(kwargs)
-        for stat in collection:
-            stats.update(stat)
-        return stats
-
-    def log_stats(self, stats):
-        logger.info('Stats: \n{}'.format(yaml.dump(stats, default_flow_style=False)))
 
     def get_env(self, trial_id=0, **kwargs):
         '''Create an environment for a trial of the simulation'''

soil/stats.py

@@ -1,111 +0,0 @@
-import pandas as pd
-
-from collections import Counter
-
-class Stats:
-    '''
-    Interface for all stats. It is not necessary, but it is useful
-    if you don't plan to implement all the methods.
-    '''
-
-    def __init__(self, simulation, name=None):
-        self.name = name or type(self).__name__
-        self.simulation = simulation
-
-    def sim_start(self):
-        '''Method to call when the simulation starts'''
-        pass
-
-    def sim_end(self):
-        '''Method to call when the simulation ends'''
-        return {}
-
-    def trial_start(self, env):
-        '''Method to call when a trial starts'''
-        return {}
-
-    def trial_end(self, env):
-        '''Method to call when a trial ends'''
-        return {}
-
-
-class distribution(Stats):
-    '''
-    Calculate the distribution of agent states at the end of each trial,
-    the mean value, and its deviation.
-    '''
-
-    def sim_start(self):
-        self.means = []
-        self.counts = []
-
-    def trial_end(self, env):
-        df = pd.DataFrame(env.state_to_tuples())
-        df = df.drop('SEED', axis=1)
-        ix = df.index[-1]
-        attrs = df.columns.get_level_values(0)
-        vc = {}
-        stats = {
-            'mean': {},
-            'count': {},
-        }
-        for a in attrs:
-            t = df.loc[(ix, a)]
-            try:
-                stats['mean'][a] = t.mean()
-                self.means.append(('mean', a, t.mean()))
-            except TypeError:
-                pass
-
-            for name, count in t.value_counts().iteritems():
-                if a not in stats['count']:
-                    stats['count'][a] = {}
-                stats['count'][a][name] = count
-                self.counts.append(('count', a, name, count))
-
-        return stats
-
-    def sim_end(self):
-        dfm = pd.DataFrame(self.means, columns=['metric', 'key', 'value'])
-        dfc = pd.DataFrame(self.counts, columns=['metric', 'key', 'value', 'count'])
-
-        count = {}
-        mean = {}
-
-        if self.means:
-            res = dfm.groupby(by=['key']).agg(['mean', 'std', 'count', 'median', 'max', 'min'])
-            mean = res['value'].to_dict()
-        if self.counts:
-            res = dfc.groupby(by=['key', 'value']).agg(['mean', 'std', 'count', 'median', 'max', 'min'])
-            for k,v in res['count'].to_dict().items():
-                if k not in count:
-                    count[k] = {}
-                for tup, times in v.items():
-                    subkey, subcount = tup
-                    if subkey not in count[k]:
-                        count[k][subkey] = {}
-                    count[k][subkey][subcount] = times
-
-
-        return {'count': count, 'mean': mean}
-
-
-class defaultStats(Stats):
-
-    def trial_end(self, env):
-        c = Counter()
-        c.update(a.__class__.__name__ for a in env.network_agents)
-
-        c2 = Counter()
-        c2.update(a['id'] for a in env.network_agents)
-
-        return {
-            'network ': {
-                'n_nodes': env.G.number_of_nodes(),
-                'n_edges': env.G.number_of_edges(),
-            },
-            'agents': {
-                'model_count': dict(c),
-                'state_count': dict(c2),
-            }
-        }

tests/complete_converted.yml

@@ -29,11 +29,11 @@ agents:
         weight: 0.6
     override:
       - filter:
-          id: 0
+          node_id: 0
         state:
           name: 'The first node'
       - filter:
-          id: 1
+          node_id: 1
         state:
           name: 'The second node'
 

tests/test_config.py

@@ -71,11 +71,11 @@ class TestConfig(TestCase):
         s = simulation.from_config(cfg)
         env = s.get_env()
         assert len(env.topologies['default'].nodes) == 10
-        assert len(env.agents('network')) == 10
+        assert len(env.agents(group='network')) == 10
-        assert len(env.agents('environment')) == 1
+        assert len(env.agents(group='environment')) == 1
         
-        assert sum(1 for a in env.agents('network') if isinstance(a, agents.CounterModel)) == 4
+        assert sum(1 for a in env.agents(group='network', agent_type=agents.CounterModel)) == 4
-        assert sum(1 for a in env.agents('network') if isinstance(a, agents.AggregatedCounter)) == 6
+        assert sum(1 for a in env.agents(group='network', agent_type=agents.AggregatedCounter)) == 6
 
 def make_example_test(path, cfg):
     def wrapped(self):

tests/test_exporters.py

@@ -7,8 +7,6 @@ from unittest import TestCase
 from soil import exporters
 from soil import simulation
 
-from soil.stats import distribution
-
 class Dummy(exporters.Exporter):
     started = False
     trials = 0
@@ -22,13 +20,13 @@ class Dummy(exporters.Exporter):
         self.__class__.called_start += 1
         self.__class__.started = True
 
-    def trial_end(self, env, stats):
+    def trial_end(self, env):
         assert env
         self.__class__.trials += 1
         self.__class__.total_time += env.now
         self.__class__.called_trial += 1
 
-    def sim_end(self, stats):
+    def sim_end(self):
         self.__class__.ended = True
         self.__class__.called_end += 1
 
@@ -78,7 +76,6 @@ class Exporters(TestCase):
                                     exporters.csv,
                                     exporters.gexf,
                                 ],
-                                stats=[distribution,],
                                 dry_run=False,
                                 outdir=tmpdir,
                                 exporter_params={'copy_to': output})

tests/test_main.py

@@ -10,7 +10,7 @@ from functools import partial
 
 from os.path import join
 from soil import (simulation, Environment, agents, network, serialization,
-                  utils)
+                  utils, config)
 from soil.time import Delta
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
@@ -200,7 +200,6 @@ class TestMain(TestCase):
             recovered = yaml.load(serial, Loader=yaml.SafeLoader)
         for (k, v) in config.items():
             assert recovered[k] == v
-        # assert config == recovered
 
     def test_configuration_changes(self):
         """
@@ -294,11 +293,13 @@ class TestMain(TestCase):
         G.add_node(3)
         G.add_edge(1, 2)
         distro = agents.calculate_distribution(agent_type=agents.NetworkAgent)
-        env = Environment(name='Test', topology=G, network_agents=distro)
+        distro[0]['topology'] = 'default'
+        aconfig = config.AgentConfig(distribution=distro, topology='default')
+        env = Environment(name='Test', topologies={'default': G}, agents={'network': aconfig})
         lst = list(env.network_agents)
 
-        a2 = env.get_agent(2)
+        a2 = env.find_one(node_id=2)
-        a3 = env.get_agent(3)
+        a3 = env.find_one(node_id=3)
         assert len(a2.subgraph(limit_neighbors=True)) == 2
         assert len(a3.subgraph(limit_neighbors=True)) == 1
         assert len(a3.subgraph(limit_neighbors=True, center=False)) == 0

tests/test_stats.py

@@ -1,34 +0,0 @@
-from unittest import TestCase
-
-from soil import simulation, stats
-from soil.utils import unflatten_dict
-
-class Stats(TestCase):
-
-    def test_distribution(self):
-        '''The distribution exporter should write the number of agents in each state'''
-        config = {
-            'name': 'exporter_sim',
-            'network_params': {
-                'generator': 'complete_graph',
-                'n': 4
-            },
-            'agent_type': 'CounterModel',
-            'max_time': 2,
-            'num_trials': 5,
-            'environment_params': {}
-        }
-        s = simulation.from_config(config)
-        for env in s.run_simulation(stats=[stats.distribution]):
-            pass
-            # stats_res = unflatten_dict(dict(env._history['stats', -1, None]))
-        allstats = s.get_stats()
-        for stat in allstats:
-            assert 'count' in stat
-            assert 'mean' in stat
-            if 'trial_id' in stat:
-                assert stat['mean']['neighbors'] == 3
-                assert stat['count']['total']['4'] == 4
-            else:
-                assert stat['count']['count']['neighbors']['3'] == 20
-                assert stat['mean']['min']['neighbors'] == stat['mean']['max']['neighbors']