WIP

soil/__init__.py

@@ -36,13 +36,13 @@ def main():
     parser.add_argument('--module', '-m', type=str,
                         help='file containing the code of any custom agents.')
     parser.add_argument('--dry-run', '--dry', action='store_true',
-                        help='Do not store the results of the simulation.')
+                        help='Do not store the results of the simulation to disk, show in terminal instead.')
     parser.add_argument('--pdb', action='store_true',
                         help='Use a pdb console in case of exception.')
     parser.add_argument('--graph', '-g', action='store_true',
-                        help='Dump GEXF graph. Defaults to false.')
+                        help='Dump each trial\'s network topology as a GEXF graph. Defaults to false.')
     parser.add_argument('--csv', action='store_true',
-                        help='Dump history in CSV format. Defaults to false.')
+                        help='Dump all data collected in CSV format. Defaults to false.')
     parser.add_argument('--level', type=str,
                         help='Logging level')
     parser.add_argument('--output', '-o', type=str, default="soil_output",

soil/agents/__init__.py

@@ -26,7 +26,14 @@ class DeadAgent(Exception):
 
 class BaseAgent(Agent):
     """
-    A special Agent that keeps track of its state history.
+    A special type of Mesa Agent that:
+
+    * Can be used as a dictionary to access its state.
+    * Has logging built-in
+    * Can be given default arguments through a defaults class attribute,
+    which will be used on construction to initialize each agent's state
+
+    Any attribute that is not preceded by an underscore (`_`) will also be added to its state.
     """
 
     defaults = {}
@@ -61,6 +68,9 @@ class BaseAgent(Agent):
         for (k, v) in kwargs.items():
             setattr(self, k, v)
 
+        for (k, v) in getattr(self, 'defaults', {}).items():
+            if not hasattr(self, k) or getattr(self, k) is None:
+                setattr(self, k, v)
 
     # TODO: refactor to clean up mesa compatibility
     @property
@@ -79,7 +89,6 @@ class BaseAgent(Agent):
     def state(self):
         '''
         Return the agent itself, which behaves as a dictionary.
-        Changes made to `agent.state` will be reflected in the history.
 
         This method shouldn't be used, but is kept here for backwards compatibility.
         '''

soil/config.py

@@ -0,0 +1,251 @@
+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', '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'
+
+    def __init__(self, name=None,
+                 group=None,
+                 agent_type='BaseAgent',
+                 network_agents=None,
+                 environment_agents=None,
+                 states=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):
+
+        self.network_params = network_params
+        self.name = name or 'Unnamed'
+        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._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 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 self.__getstate__()
+
+    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/datacollection.py

@@ -8,19 +8,17 @@ class SoilDataCollector(MDC):
         # Populate model and env reporters so they have a key per 
         # So they can be shown in the web interface
         self.environment = environment
-
+        raise NotImplementedError()
 
     @property
     def model_vars(self):
-        pass
+        raise NotImplementedError()
 
     @model_vars.setter
     def model_vars(self, value):
-        pass
+        raise NotImplementedError()
 
     @property
     def agent_reporters(self):
-        self.model._history._
-
-        pass
+        raise NotImplementedError()
 

soil/environment.py

@@ -1,23 +1,20 @@
+from __future__ import annotations
 import os
 import sqlite3
-import csv
 import math
 import random
-import yaml
-import tempfile
-import logging
-import pandas as pd
 from time import time as current_time
 from copy import deepcopy
 from networkx.readwrite import json_graph
 
-import networkx as nx
 
-from tsih import History, NoHistory, Record, Key
+import networkx as nx
 
 from mesa import Model
 
-from . import serialization, agents, analysis, utils, time
+from tsih import Record
+
+from . import serialization, agents, analysis, utils, time, config
 
 # These properties will be copied when pickling/unpickling the environment
 _CONFIG_PROPS = [ 'name',
@@ -49,7 +46,6 @@ class Environment(Model):
                  schedule=None,
                  initial_time=0,
                  environment_params=None,
-                 history=False,
                  dir_path=None,
                  **kwargs):
 
@@ -76,20 +72,11 @@ class Environment(Model):
             topology = nx.Graph()
         self.G = nx.Graph(topology) 
 
-
         self.environment_params = environment_params or {}
         self.environment_params.update(kwargs)
 
         self._env_agents = {}
         self.interval = interval
-
-        if history:
-            history = History
-        else:
-            history = NoHistory
-
-        self._history = history(name=self.name,
-                                backup=True)
         self['SEED'] = seed
 
         if network_agents:
@@ -106,6 +93,19 @@ class Environment(Model):
 
         self.logger = utils.logger.getChild(self.name)
 
+    @staticmethod
+    def from_config(conf: config.Config, trial_id, **kwargs) -> Environment:
+        '''Create an environment for a trial of the simulation'''
+
+        conf = config.Config(conf, **kwargs)
+        conf.seed = '{}_{}'.format(conf.seed, trial_id)
+        conf.name = '{}_trial_{}'.format(conf.name, trial_id).replace('.', '-')
+        opts = conf.environment_params.copy()
+        opts.update(conf)
+        opts.update(kwargs)
+        env = serialization.deserialize(conf.environment_class)(**opts)
+        return env
+
     @property
     def now(self):
         if self.schedule:
@@ -212,11 +212,14 @@ class Environment(Model):
         return self.logger.log(level, message, extra=extra)
 
     def step(self):
+        '''
+        Advance one step in the simulation, and update the data collection and scheduler appropriately
+        '''
         super().step()
         self.schedule.step()
 
     def run(self, until, *args, **kwargs):
-        self._save_state()
+        until = until or float('inf')
 
         while self.schedule.next_time < until:
             self.step()
@@ -252,14 +255,16 @@ class Environment(Model):
 
     def get(self, key, default=None):
         '''
-        Get the value of an environment attribute in a
-        given point in the simulation (history).
-        If key is an attribute name, this method returns
-        the current value.
-        To get values at other times, use a
-        :meth: `soil.history.Key` tuple.
+        Get the value of an environment attribute.
+        Return `default` if the value is not set.
         '''
-        return self[key] if key in self else default
+        return self.environment_params.get(key, default)
+
+    def __getitem__(self, key):
+        return self.environment_params.get(key)
+
+    def __setitem__(self, key, value):
+        return self.environment_params.__setitem__(key, value)
 
     def get_agent(self, agent_id):
         return self.G.nodes[agent_id]['agent']
@@ -269,112 +274,31 @@ class Environment(Model):
             return self.agents
         return (self.G.nodes[i]['agent'] for i in nodes)
 
-    def dump_csv(self, f):
-        with utils.open_or_reuse(f, 'w') as f:
-            cr = csv.writer(f)
-            cr.writerow(('agent_id', 't_step', 'key', 'value'))
-            for i in self.history_to_tuples():
-                cr.writerow(i)
-
-    def dump_gexf(self, f):
-        G = self.history_to_graph()
-        # Workaround for geometric models
-        # See soil/soil#4
-        for node in G.nodes():
-            if 'pos' in G.nodes[node]:
-                G.nodes[node]['viz'] = {"position": {"x": G.nodes[node]['pos'][0], "y": G.nodes[node]['pos'][1], "z": 0.0}}
-                del (G.nodes[node]['pos'])
-
-        nx.write_gexf(G, f, version="1.2draft")
-
-    def dump(self, *args, formats=None, **kwargs):
-        if not formats:
-            return
-        functions = {
-            'csv': self.dump_csv,
-            'gexf': self.dump_gexf
-        }
-        for f in formats:
-            if f in functions:
-                functions[f](*args, **kwargs)
-            else:
-                raise ValueError('Unknown format: {}'.format(f))
-
-    def df(self):
-        return self._history[None, None, None].df()
-        
-    def dump_sqlite(self, f):
-        return self._history.dump(f)
-
-    def state_to_tuples(self, now=None):
+    def _agent_to_tuples(self, agent, now=None):
         if now is None:
             now = self.now
+        for k, v in agent.state.items():
+            yield Record(dict_id=agent.id,
+                          t_step=now,
+                          key=k,
+                          value=v)
+
+    def state_to_tuples(self, agent_id=None, now=None):
+        if now is None:
+            now = self.now
+
+        if agent_id:
+            agent = self.get_agent(agent_id)
+            yield from self._agent_to_tuples(agent, now)
+            return
+
         for k, v in self.environment_params.items():
             yield Record(dict_id='env',
                          t_step=now,
                          key=k,
                          value=v)
         for agent in self.agents:
-            for k, v in agent.state.items():
-                yield Record(dict_id=agent.id,
-                             t_step=now,
-                             key=k,
-                             value=v)
-
-    def history_to_tuples(self, agent_id=None):
-        if isinstance(self._history, NoHistory):
-            tuples = self.state_to_tuples()
-        else:
-            tuples = self._history.to_tuples()
-        if agent_id is None:
-            return tuples
-        return filter(lambda x: str(x[0]) == str(agent_id), tuples)
-
-    def history_to_graph(self):
-        G = nx.Graph(self.G)
-
-        for agent in self.network_agents:
-
-            attributes = {'agent': str(agent.__class__)}
-            lastattributes = {}
-            spells = []
-            lastvisible = False
-            laststep = None
-            history = sorted(list(self.history_to_tuples(agent_id=agent.id)))
-            if not history:
-                continue
-            for _, t_step, attribute, value in history:
-                if attribute == 'visible':
-                    nowvisible = value
-                    if nowvisible and not lastvisible:
-                        laststep = t_step
-                    if not nowvisible and lastvisible:
-                        spells.append((laststep, t_step))
-
-                    lastvisible = nowvisible
-                    continue
-                key = 'attr_' + attribute
-                if key not in attributes:
-                    attributes[key] = list()
-                if key not in lastattributes:
-                    lastattributes[key] = (value, t_step)
-                elif lastattributes[key][0] != value:
-                    last_value, laststep = lastattributes[key]
-                    commit_value = (last_value, laststep, t_step)
-                    if key not in attributes:
-                        attributes[key] = list()
-                    attributes[key].append(commit_value)
-                    lastattributes[key] = (value, t_step)
-            for k, v in lastattributes.items():
-                attributes[k].append((v[0], v[1], None))
-            if lastvisible:
-                spells.append((laststep, None))
-            if spells:
-                G.add_node(agent.id, spells=spells, **attributes)
-            else:
-                G.add_node(agent.id, **attributes)
-
-        return G
+            yield from self._agent_to_tuples(agent, now)
 
     def __getstate__(self):
         state = {}
@@ -382,7 +306,6 @@ class Environment(Model):
             state[prop] = self.__dict__[prop]
         state['G'] = json_graph.node_link_data(self.G)
         state['environment_agents'] = self._env_agents
-        state['history'] = self._history
         state['schedule'] = self.schedule
         return state
 
@@ -391,7 +314,6 @@ class Environment(Model):
             self.__dict__[prop] = state[prop]
         self._env_agents = state['environment_agents']
         self.G = json_graph.node_link_graph(state['G'])
-        self._history = state['history']
         # self._env = None
         self.schedule = state['schedule']
         self._queue = []

soil/exporters.py

@@ -48,20 +48,24 @@ class Exporter:
         self.simulation = simulation
         outdir = outdir or os.path.join(os.getcwd(), 'soil_output')
         self.outdir = os.path.join(outdir,
-                                   simulation.group or '',
-                                   simulation.name)
+                                   simulation.config.group or '',
+                                   simulation.config.name)
         self.dry_run = dry_run
         self.copy_to = copy_to
 
-    def start(self):
+    def sim_start(self):
         '''Method to call when the simulation starts'''
         pass
 
-    def end(self, stats):
+    def sim_end(self, stats):
         '''Method to call when the simulation ends'''
         pass
 
-    def trial(self, env, stats):
+    def trial_start(self, env):
+        '''Method to call when a trial start'''
+        pass
+
+    def trial_end(self, env, stats):
         '''Method to call when a trial ends'''
         pass
 
@@ -80,21 +84,21 @@ class Exporter:
 class default(Exporter):
     '''Default exporter. Writes sqlite results, as well as the simulation YAML'''
 
-    def start(self):
+    def sim_start(self):
         if not self.dry_run:
             logger.info('Dumping results to %s', self.outdir)
             self.simulation.dump_yaml(outdir=self.outdir)
         else:
             logger.info('NOT dumping results')
 
-    def trial(self, env, stats):
+    def trial_start(self, env, stats):
         if not self.dry_run:
             with timer('Dumping simulation {} trial {}'.format(self.simulation.name,
                                                                env.name)):
                 with self.output('{}.sqlite'.format(env.name), mode='wb') as f:
                     env.dump_sqlite(f)
 
-    def end(self, stats):
+    def sim_end(self, stats):
           with timer('Dumping simulation {}\'s stats'.format(self.simulation.name)):
               with self.output('{}.sqlite'.format(self.simulation.name), mode='wb') as f:
                   self.simulation.dump_sqlite(f)
@@ -102,15 +106,14 @@ class default(Exporter):
 
 
 class csv(Exporter):
+
     '''Export the state of each environment (and its agents) in a separate CSV file'''
-    def trial(self, env, stats):
+    def trial_end(self, env, stats):
         with timer('[CSV] Dumping simulation {} trial {} @ dir {}'.format(self.simulation.name,
                                                                           env.name,
                                                                           self.outdir)):
-            with self.output('{}.csv'.format(env.name)) as f:
-                env.dump_csv(f)
 
-            with self.output('{}.stats.csv'.format(env.name)) as f:
+            with self.output('{}.stats.{}.csv'.format(env.name, stats.name)) as f:
                 statwriter = csvlib.writer(f, delimiter='\t', quotechar='"', quoting=csvlib.QUOTE_ALL)
 
                 for stat in stats:
@@ -118,7 +121,7 @@ class csv(Exporter):
 
 
 class gexf(Exporter):
-    def trial(self, env, stats):
+    def trial_end(self, env, stats):
         if self.dry_run:
             logger.info('Not dumping GEXF in dry_run mode')
             return
@@ -126,22 +129,32 @@ class gexf(Exporter):
         with timer('[GEXF] Dumping simulation {} trial {}'.format(self.simulation.name,
                                                                   env.name)):
             with self.output('{}.gexf'.format(env.name), mode='wb') as f:
-                env.dump_gexf(f)
+                self.dump_gexf(env, f)
 
+    def dump_gexf(self, env, f):
+        G = env.history_to_graph()
+        # Workaround for geometric models
+        # See soil/soil#4
+        for node in G.nodes():
+            if 'pos' in G.nodes[node]:
+                G.nodes[node]['viz'] = {"position": {"x": G.nodes[node]['pos'][0], "y": G.nodes[node]['pos'][1], "z": 0.0}}
+                del (G.nodes[node]['pos'])
+
+        nx.write_gexf(G, f, version="1.2draft")
 
 class dummy(Exporter):
 
-    def start(self):
+    def sim_start(self):
         with self.output('dummy', 'w') as f:
             f.write('simulation started @ {}\n'.format(current_time()))
 
-    def trial(self, env, stats):
+    def trial_end(self, env, stats):
         with self.output('dummy', 'w') as f:
-            for i in env.history_to_tuples():
+            for i in stats:
                 f.write(','.join(map(str, i)))
                 f.write('\n')
 
-    def sim(self, stats):
+    def sim_end(self, stats):
         with self.output('dummy', 'a') as f:
             f.write('simulation ended @ {}\n'.format(current_time()))
 
@@ -149,10 +162,57 @@ class dummy(Exporter):
 
 class graphdrawing(Exporter):
 
-    def trial(self, env, stats):
+    def trial_end(self, env, stats):
         # 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:
             f.savefig(f)
 
+'''
+Convert an environment into a NetworkX graph
+'''
+def env_to_graph(env, history=None):
+    G = nx.Graph(env.G)
+
+    for agent in env.network_agents:
+
+        attributes = {'agent': str(agent.__class__)}
+        lastattributes = {}
+        spells = []
+        lastvisible = False
+        laststep = None
+        if not history:
+            history = sorted(list(env.state_to_tuples()))
+        for _, t_step, attribute, value in history:
+            if attribute == 'visible':
+                nowvisible = value
+                if nowvisible and not lastvisible:
+                    laststep = t_step
+                if not nowvisible and lastvisible:
+                    spells.append((laststep, t_step))
+
+                lastvisible = nowvisible
+                continue
+            key = 'attr_' + attribute
+            if key not in attributes:
+                attributes[key] = list()
+            if key not in lastattributes:
+                lastattributes[key] = (value, t_step)
+            elif lastattributes[key][0] != value:
+                last_value, laststep = lastattributes[key]
+                commit_value = (last_value, laststep, t_step)
+                if key not in attributes:
+                    attributes[key] = list()
+                attributes[key].append(commit_value)
+                lastattributes[key] = (value, t_step)
+        for k, v in lastattributes.items():
+            attributes[k].append((v[0], v[1], None))
+        if lastvisible:
+            spells.append((laststep, None))
+        if spells:
+            G.add_node(agent.id, spells=spells, **attributes)
+        else:
+            G.add_node(agent.id, **attributes)
+
+    return G

soil/serialization.py

@@ -2,6 +2,7 @@ import os
 import logging
 import ast
 import sys
+import re
 import importlib
 from glob import glob
 from itertools import product, chain
@@ -18,6 +19,9 @@ logger = logging.getLogger('soil')
 def load_network(network_params, dir_path=None):
     G = nx.Graph()
 
+    if not network_params:
+        return G
+
     if 'path' in network_params:
         path = network_params['path']
         if dir_path and not os.path.isabs(path):
@@ -169,6 +173,9 @@ def serialize(v, known_modules=[]):
     func = serializer(tname)
     return func(v), tname
 
+
+IS_CLASS = re.compile(r"<class '(.*)'>")
+
 def deserializer(type_, known_modules=[]):
     if type(type_) != str:  # Already deserialized
         return type_
@@ -179,6 +186,13 @@ def deserializer(type_, known_modules=[]):
     if hasattr(builtins, type_):  # Check if it's a builtin type
         cls = getattr(builtins, type_)
         return lambda x=None: ast.literal_eval(x) if x is not None else cls()
+    match = IS_CLASS.match(type_)
+    if match:
+        modname, tname = match.group(1).rsplit(".", 1)
+        module = importlib.import_module(modname)
+        cls = getattr(module, tname)
+        return getattr(cls, 'deserialize', cls)
+        
     # Otherwise, see if we can find the module and the class
     modules = known_modules or []
     options = []
@@ -189,7 +203,7 @@ def deserializer(type_, known_modules=[]):
 
     if '.' in type_:  # Fully qualified module
         module, type_ = type_.rsplit(".", 1)
-        options.append ((module, type_))
+        options.append((module, type_))
 
     errors = []
     for modname, tname in options:
@@ -213,10 +227,10 @@ def deserialize(type_, value=None, **kwargs):
 
 
 def deserialize_all(names, *args, known_modules=['soil'], **kwargs):
-    '''Return the set of exporters for a simulation, given the exporter names'''
-    exporters = []
+    '''Return the list of deserialized objects'''
+    objects = []
     for name in names:
         mod = deserialize(name, known_modules=known_modules)
-        exporters.append(mod(*args, **kwargs))
-    return exporters
+        objects.append(mod(*args, **kwargs))
+    return objects
 

soil/simulation.py

@@ -10,8 +10,6 @@ import networkx as nx
 from networkx.readwrite import json_graph
 from multiprocessing import Pool
 from functools import partial
-from tsih import History
-
 import pickle
 
 from . import serialization, utils, basestring, agents
@@ -20,127 +18,34 @@ from .utils import logger
 from .exporters import default
 from .stats import defaultStats
 
+from .config import Config
+
 
 #TODO: change documentation for simulation
-
 class Simulation:
     """
-    Similar to nsim.NetworkSimulation with three main differences:
-        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
+    config (optional): :class:`config.Config`
         name of the Simulation
-    group : str, optional
-        a group name can be used to link simulations
-    topology : networkx.Graph instance, optional
-    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
-        Time how long the simulation should run
-    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
-    load_module : str, module name, deprecated
-        If specified, soil will load the content of this module under 'soil.agents.custom'
-    history: tsih.History subclass, optional
-        Class to use to store the history of the simulation (and environments). It defailts to tsih.History
-        If set to True, tsih.History will be used. If set to False or None, tsih.NoHistory will be used.
+
+    kwargs: parameters to use to initialize a new configuration, if one has not been provided.
     """
 
-    def __init__(self, name=None, group=None, topology=None, network_params=None,
-                 network_agents=None, agent_type=None, states=None,
-                 default_state=None, interval=1, num_trials=1,
-                 max_time=100, load_module=None, seed=None,
-                 dir_path=None, environment_agents=None,
-                 environment_params=None, environment_class=None,
-                 history=History, **kwargs):
+    def __init__(self, config=None,
+                 **kwargs):
 
-        self.load_module = load_module
-        self.network_params = network_params
-        self.name = name or 'Unnamed'
-        self.seed = str(seed or name)
-        self._id = '{}_{}'.format(self.name, strftime("%Y-%m-%d_%H.%M.%S"))
-        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
+        if bool(config) == bool(kwargs):
+            raise ValueError("Specify either a configuration or the parameters to initialize a configuration")
 
-        sys.path += list(x for x in [os.getcwd(), self.dir_path] if x not in sys.path)
+        if kwargs:
+            config = Config(**kwargs)
 
-        if topology is None:
-            topology = serialization.load_network(network_params,
-                                                  dir_path=self.dir_path)
-        elif isinstance(topology, basestring) or isinstance(topology, dict):
-            topology = json_graph.node_link_graph(topology)
-        self.topology = nx.Graph(topology)
+        self.config = config
 
-
-        self.environment_params = environment_params or {}
-        self.environment_class = serialization.deserialize(environment_class,
-                                                   known_modules=['soil.environment', ]) or Environment
-
-        environment_agents = environment_agents or []
-        self.environment_agents = agents._convert_agent_types(environment_agents,
-                                                              known_modules=[self.load_module])
-
-        distro = agents.calculate_distribution(network_agents,
-                                               agent_type)
-        self.network_agents = agents._convert_agent_types(distro,
-                                                          known_modules=[self.load_module])
-
-        self.states = agents._validate_states(states,
-                                              self.topology)
-
-        if history == True:
-            history = History
-        elif not history:
-            history = NoHistory
-
-        self._history = history(name=self.name,
-                                backup=False)
+    @property
+    def name(self) -> str:
+        return self.config.name
 
     def run_simulation(self, *args, **kwargs):
         return self.run(*args, **kwargs)
@@ -153,13 +58,13 @@ class Simulation:
         if parallel and not os.environ.get('SENPY_DEBUG', None):
             p = Pool()
             func = partial(self.run_trial_exceptions, **kwargs)
-            for i in p.imap_unordered(func, range(self.num_trials)):
+            for i in p.imap_unordered(func, range(self.config.num_trials)):
                 if isinstance(i, Exception):
                     logger.error('Trial failed:\n\t%s', i.message)
                     continue
                 yield i
         else:
-            for i in range(self.num_trials):
+            for i in range(self.config.num_trials):
                 yield self.run_trial(trial_id=i,
                                      **kwargs)
 
@@ -179,51 +84,48 @@ class Simulation:
                                                   outdir=outdir,
                                                   **exporter_params)
         stats = serialization.deserialize_all(simulation=self,
-                                              names=stats,
-                                              known_modules=['soil.stats',],
-                                              **stats_params)
+                                             names=stats,
+                                             known_modules=['soil.stats',],
+                                             **stats_params)
 
-        with utils.timer('simulation {}'.format(self.name)):
+        with utils.timer('simulation {}'.format(self.config.name)):
             for stat in stats:
-                stat.start()
+                stat.sim_start()
 
             for exporter in exporters:
                 exporter.start()
+
             for env in self._run_sync_or_async(parallel=parallel,
                                                log_level=log_level,
                                                **kwargs):
 
-                collected = list(stat.trial(env) for stat in stats)
+                for exporter in exporters:
+                    exporter.trial_start(env)
 
-                saved = self.save_stats(collected, t_step=env.now, trial_id=env.name)
+                collected = list(stat.trial_end(env) for stat in stats)
+
+                saved = self._update_stats(collected, t_step=env.now, trial_id=env.name)
 
                 for exporter in exporters:
-                    exporter.trial(env, saved)
+                    exporter.trial_end(env, saved)
 
                 yield env
 
-
             collected = list(stat.end() for stat in stats)
-            saved = self.save_stats(collected)
+            saved = self._update_stats(collected)
 
             for exporter in exporters:
-                exporter.end(saved)
+                exporter.sim_end(saved)
 
-
-    def save_stats(self, collection, **kwargs):
+    def _update_stats(self, collection, **kwargs):
         stats = dict(kwargs)
         for stat in collection:
             stats.update(stat)
-        self._history.save_stats(utils.flatten_dict(stats))
         return stats
 
-    def get_stats(self, **kwargs):
-        return self._history.get_stats(**kwargs)
-
     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'''
         opts = self.environment_params.copy()
@@ -246,18 +148,20 @@ class Simulation:
         env = self.environment_class(**opts)
         return env
 
-    def run_trial(self, trial_id=0, until=None, log_level=logging.INFO, **opts):
+    def run_trial(self, trial_id=None, until=None, log_level=logging.INFO, **opts):
         """
         Run a single trial of the simulation
 
         """
+        trial_id = trial_id if trial_id is not None else current_time()
         if log_level:
             logger.setLevel(log_level)
         # Set-up trial environment and graph
-        until = until or self.max_time
-        env = self.get_env(trial_id=trial_id, **opts)
+        until = until or self.config.max_time
+
+        env = Environment.from_config(self.config, trial_id=trial_id)
         # Set up agents on nodes
-        with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)):
+        with utils.timer('Simulation {} trial {}'.format(self.config.name, trial_id)):
             env.run(until)
         return env
 
@@ -274,64 +178,6 @@ class Simulation:
             ex.message = ''.join(traceback.format_exception(type(ex), ex, ex.__traceback__)[:])
             return ex
 
-    def to_dict(self):
-        return self.__getstate__()
-
-    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 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)
-
-    def dump_sqlite(self, f):
-        return self._history.dump(f)
-
-    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
-
-    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
-
 
 def all_from_config(config):
     configs = list(serialization.load_config(config))

soil/stats.py

@@ -8,18 +8,23 @@ class Stats:
     if you don't plan to implement all the methods.
     '''
 
-    def __init__(self, simulation):
+    def __init__(self, simulation, name=None):
+        self.name = name or type(self).__name__
         self.simulation = simulation
 
-    def start(self):
+    def sim_start(self):
         '''Method to call when the simulation starts'''
         pass
 
-    def end(self):
+    def sim_end(self):
         '''Method to call when the simulation ends'''
         return {}
 
-    def trial(self, env):
+    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 {}
 
@@ -30,12 +35,12 @@ class distribution(Stats):
     the mean value, and its deviation.
     '''
 
-    def start(self):
+    def sim_start(self):
         self.means = []
         self.counts = []
 
-    def trial(self, env):
-        df = env.df()
+    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)
@@ -60,7 +65,7 @@ class distribution(Stats):
 
         return stats
 
-    def end(self):
+    def sim_end(self):
         dfm = pd.DataFrame(self.means, columns=['metric', 'key', 'value'])
         dfc = pd.DataFrame(self.counts, columns=['metric', 'key', 'value', 'count'])
 
@@ -87,7 +92,7 @@ class distribution(Stats):
 
 class defaultStats(Stats):
 
-    def trial(self, env):
+    def trial_end(self, env):
         c = Counter()
         c.update(a.__class__.__name__ for a in env.network_agents)