Partial MESA compatibility and several fixes

Documentation for the new APIs is still a work in progress :)

.gitignore

@@ -8,3 +8,4 @@ soil_output
 docs/_build*
 build/*
 dist/*
+prof

CHANGELOG.md

@@ -5,23 +5,20 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 ### Added
-* [WIP] Integration with MESA
+* Integration with MESA
 * `not_agent_ids` paramter to get sql in history
 ### Changed
 * `soil.Environment` now also inherits from `mesa.Model`
 * `soil.Agent` now also inherits from `mesa.Agent`
 * `soil.time` to replace `simpy` events, delays, duration, etc.
+* `agent.id` is not `agent.unique_id` to be compatible with `mesa`. A property `BaseAgent.id` has been added for compatibility.
+* `agent.environment` is now `agent.model`, for the same reason as above. The parameter name in `BaseAgent.__init__` has also been renamed.
 ### Removed
 * `simpy` dependency and compatibility. Each agent used to be a simpy generator, but that made debugging and error handling more complex. That has been replaced by a scheduler within the `soil.Environment` class, similar to how `mesa` does it.
+* `soil.history` is now a separate package named `tsih`. The keys namedtuple uses `dict_id` instead of `agent_id`.
 
-### TODO:
+### Added
-* agent_id -> unique_id?
+* An option to choose whether a database should be used for history 
-* mesa has Agent.model and soil has Agent.env
-* Environments.agents and mesa.Agent.agents are not the same. env is a property, and it only takes into account network and environment agents. Might rename environment_agents to other_agents or sth like that
-* soil.History should mimic a mesa.datacollector :/
-* soil.Simulation *could* mimic a mesa.batchrunner
-* DONE include scheduler in environment
-* DONE environment inherits from `mesa.Model`
 
 
 ## [0.15.2]

README.md

@@ -5,6 +5,9 @@ Learn how to run your own simulations with our [documentation](http://soilsim.re
 
 Follow our [tutorial](examples/tutorial/soil_tutorial.ipynb) to develop your own agent models.
 
+## Citation 
+
+
 If you use Soil in your research, don't forget to cite this paper:
 
 ```bibtex
@@ -28,7 +31,24 @@ If you use Soil in your research, don't forget to cite this paper:
 
 ```
 
-@Copyright GSI - Universidad Politécnica de Madrid 2017
+## Mesa compatibility
+
+Soil is in the process of becoming fully compatible with MESA.
+As of this writing, 
+
+This is a non-exhaustive list of tasks to achieve compatibility:
+
+* Environments.agents and mesa.Agent.agents are not the same. env is a property, and it only takes into account network and environment agents. Might rename environment_agents to other_agents or sth like that
+- [ ] Integrate `soil.Simulation` with mesa's runners:
+  - [ ] `soil.Simulation` could mimic/become a `mesa.batchrunner`
+- [ ] Integrate `soil.Environment` with `mesa.Model`:
+  - [x] `Soil.Environment` inherits from `mesa.Model`
+  - [x] `Soil.Environment` includes a Mesa-like Scheduler (see the `soil.time` module.
+- [ ] Integrate `soil.Agent` with `mesa.Agent`:
+  - [x] Rename agent.id to unique_id?
+  - [x] mesa agents can be used in soil simulations (see `examples/mesa`)
+- [ ] Document the new APIs and usage
+
+@Copyright GSI - Universidad Politécnica de Madrid 2017-2021
 
 [![SOIL](logo_gsi.png)](https://www.gsi.upm.es)
-

examples/complete.yml

@@ -13,7 +13,7 @@ network_agents:
   - agent_type: CounterModel
     weight: 1
     state:
-      id: 0
+      state_id: 0
   - agent_type: AggregatedCounter
     weight: 0.2
 environment_agents: []

examples/custom_generator/custom_generator.yml

@@ -13,4 +13,4 @@ network_agents:
   - agent_type: CounterModel
     weight: 1
     state:
-      id: 0
+      state_id: 0

examples/mesa/server.py

@@ -23,7 +23,6 @@ def network_portrayal(env):
         }
         for (agent_id) in env.G.nodes
     ]
-    # import pdb;pdb.set_trace()
 
     portrayal["edges"] = [
         {"id": edge_id, "source": source, "target": target, "color": "#000000"}
@@ -65,7 +64,7 @@ model_params = {
     "N": UserSettableParameter(
         "slider",
         "N",
-        1,
+        5,
         1,
         10,
         1,

examples/mesa/social_wealth.py

@@ -34,9 +34,7 @@ class MoneyAgent(MesaAgent):
             self.pos,
             moore=True,
             include_center=False)
-        print(self.pos, possible_steps)
         new_position = self.random.choice(possible_steps)
-        print(self.pos, new_position)
         self.model.grid.move_agent(self, new_position)
 
     def give_money(self):
@@ -74,21 +72,13 @@ class SocialMoneyAgent(NetworkAgent, MoneyAgent):
 class MoneyEnv(Environment):
     """A model with some number of agents."""
     def __init__(self, N, width, height, *args, network_params, **kwargs):
-        self.initialized = True
-        # import pdb;pdb.set_trace()
 
         network_params['n'] = N
         super().__init__(*args, network_params=network_params, **kwargs)
         self.grid = MultiGrid(width, height, False)
-        # self.schedule = RandomActivation(self)
-        self.running = True
 
         # Create agents
         for agent in self.agents:
-            self.schedule.add(agent)
-            # a = MoneyAgent(i, self)
-            # self.schedule.add(a)
-            # Add the agent to a random grid cell
             x = self.random.randrange(self.grid.width)
             y = self.random.randrange(self.grid.height)
             self.grid.place_agent(agent, (x, y))
@@ -97,10 +87,6 @@ class MoneyEnv(Environment):
             model_reporters={"Gini": compute_gini},
             agent_reporters={"Wealth": "wealth"})
 
-    def step(self):
-        super().step()
-        self.datacollector.collect(self)
-        self.schedule.step()
 
 def graph_generator(n=5):
     G = nx.Graph()

examples/newsspread/NewsSpread.yml

@@ -68,12 +68,12 @@ network_agents:
 - agent_type: HerdViewer
   state:
     has_tv: true
-    id: neutral
+    state_id: neutral
   weight: 1
 - agent_type: HerdViewer
   state:
     has_tv: true
-    id: neutral
+    state_id: neutral
   weight: 1
 network_params:
   generator: barabasi_albert_graph
@@ -95,7 +95,7 @@ network_agents:
 - agent_type: HerdViewer
   state:
     has_tv: true
-    id: neutral
+    state_id: neutral
   weight: 1
 - agent_type: WiseViewer
   state:
@@ -121,7 +121,7 @@ network_agents:
 - agent_type: WiseViewer
   state:
     has_tv: true
-    id: neutral
+    state_id: neutral
   weight: 1
 - agent_type: WiseViewer
   state:

examples/newsspread/newsspread.py

@@ -34,8 +34,6 @@ class HerdViewer(DumbViewer):
     A viewer whose probability of infection depends on the state of its neighbors.
     '''
 
-    level = logging.DEBUG
-
     def infect(self):
         infected = self.count_neighboring_agents(state_id=self.infected.id)
         total = self.count_neighboring_agents()

examples/rabbits/rabbits.yml

@@ -1,7 +1,7 @@
 ---
 load_module: rabbit_agents
 name: rabbits_example
-max_time: 200
+max_time: 150
 interval: 1
 seed: MySeed
 agent_type: RabbitModel

examples/template.yml

@@ -16,7 +16,7 @@ template:
     - agent_type: CounterModel
       weight: "{{ x1 }}"
       state:
-        id: 0
+        state_id: 0
     - agent_type: AggregatedCounter
       weight: "{{ 1 - x1 }}"
   environment_params:

requirements.txt

@@ -6,3 +6,4 @@ pandas>=0.23
 SALib>=1.3
 Jinja2
 Mesa>=0.8
+tsih>=0.1.5

soil/VERSION

@@ -1 +1 @@
-0.15.2
+0.20.0

soil/__init__.py

@@ -15,7 +15,6 @@ from .agents import *
 from . import agents
 from .simulation import *
 from .environment import Environment
-from .history import History
 from . import serialization
 from . import analysis
 from .utils import logger

soil/agents/__init__.py

@@ -6,7 +6,9 @@ from itertools import islice
 import json
 import networkx as nx
 
-from .. import serialization, history, utils, time
+from .. import serialization, utils, time
+
+from tsih import Key
 
 from mesa import Agent
 
@@ -16,6 +18,7 @@ def as_node(agent):
         return agent.id
     return agent
 
+IGNORED_FIELDS = ('model', 'logger')
 
 class BaseAgent(Agent):
     """
@@ -27,23 +30,20 @@ class BaseAgent(Agent):
     def __init__(self,
                  unique_id,
                  model,
-                 state=None,
                  name=None,
                  interval=None):
         # Check for REQUIRED arguments
         # Initialize agent parameters
         if isinstance(unique_id, Agent):
             raise Exception()
+        self._saved = set()
         super().__init__(unique_id=unique_id, model=model)
         self.name = name or '{}[{}]'.format(type(self).__name__, self.unique_id)
 
         self._neighbors = None
         self.alive = True
-        real_state = deepcopy(self.defaults)
-        real_state.update(state or {})
-        self.state = real_state
 
-        self.interval = interval or self.get('interval', getattr(self.model, 'interval', 1))
+        self.interval = interval or self.get('interval', 1)
         self.logger = logging.getLogger(self.model.name).getChild(self.name)
 
         if hasattr(self, 'level'):
@@ -75,7 +75,6 @@ class BaseAgent(Agent):
 
     @state.setter
     def state(self, value):
-        self._state = {}
         for k, v in value.items():
             self[k] = v
 
@@ -87,28 +86,36 @@ class BaseAgent(Agent):
     def environment_params(self, value):
         self.model.environment_params = value
 
+    def __setattr__(self, key, value):
+        if not key.startswith('_') and key not in IGNORED_FIELDS:
+            try:
+                k = Key(t_step=self.now,
+                        dict_id=self.unique_id,
+                        key=key)
+                self._saved.add(key)
+                self.model[k] = value
+            except AttributeError:
+                pass
+        super().__setattr__(key, value)
+
     def __getitem__(self, key):
         if isinstance(key, tuple):
             key, t_step = key
-            k = history.Key(key=key, t_step=t_step, agent_id=self.unique_id)
+            k = Key(key=key, t_step=t_step, dict_id=self.unique_id)
             return self.model[k]
-        return self._state.get(key, None)
+        return getattr(self, key)
 
     def __delitem__(self, key):
-        self._state[key] = None
+        return delattr(self, key)
 
     def __contains__(self, key):
-        return key in self._state
+        return hasattr(self, key)
 
     def __setitem__(self, key, value):
-        self._state[key] = value
+        setattr(self, key, value)
-        k = history.Key(t_step=self.now,
-                        agent_id=self.id,
-                        key=key)
-        self.model[k] = value
 
     def items(self):
-        return self._state.items()
+        return ((k, getattr(self, k)) for k in self._saved)
 
     def get(self, key, default=None):
         return self[key] if key in self else default
@@ -150,25 +157,6 @@ class BaseAgent(Agent):
     def info(self, *args, **kwargs):
         return self.log(*args, level=logging.INFO, **kwargs)
 
-    # def __getstate__(self):
-    #     '''
-    #     Serializing an agent will lose all its running information (you cannot
-    #     serialize an iterator), but it keeps the state and link to the environment,
-    #     so it can be used for inspection and dumping to a file
-    #     '''
-    #     state = {}
-    #     state['id'] = self.id
-    #     state['environment'] = self.model
-    #     state['_state'] = self._state
-    #     return state
-
-    # def __setstate__(self, state):
-    #     '''
-    #     Get back a serialized agent and try to re-compose it
-    #     '''
-    #     self.state_id = state['id']
-    #     self._state = state['_state']
-    #     self.model = state['environment']
 
 class NetworkAgent(BaseAgent):
 
@@ -303,15 +291,15 @@ class MetaFSM(type):
 class FSM(NetworkAgent, metaclass=MetaFSM):
     def __init__(self, *args, **kwargs):
         super(FSM, self).__init__(*args, **kwargs)
-        if 'id' not in self.state:
+        if not hasattr(self, 'state_id'):
             if not self.default_state:
                 raise ValueError('No default state specified for {}'.format(self.unique_id))
-            self['id'] = self.default_state.id
+            self.state_id = self.default_state.id
 
-        self.set_state(self.state['id'])
+        self.set_state(self.state_id)
 
     def step(self):
-        self.debug(f'Agent {self.unique_id} @ state {self["id"]}')
+        self.debug(f'Agent {self.unique_id} @ state {self.state_id}')
         interval = super().step()
         if 'id' not in self.state:
             # if 'id' in self.state:
@@ -320,14 +308,14 @@ class FSM(NetworkAgent, metaclass=MetaFSM):
                 self.set_state(self.default_state.id)
             else:
                 raise Exception('{} has no valid state id or default state'.format(self))
-        return self.states[self.state['id']](self) or interval
+        return self.states[self.state_id](self) or interval
 
     def set_state(self, state):
         if hasattr(state, 'id'):
             state = state.id
         if state not in self.states:
             raise ValueError('{} is not a valid state'.format(state))
-        self.state['id'] = state
+        self.state_id = state
         return state
 
 
@@ -541,7 +529,7 @@ def select(agents, state_id=None, agent_type=None, ignore=None, iterator=False,
         f = filter(lambda x: x not in ignore, f)
 
     if state_id is not None:
-        f = filter(lambda agent: agent.state.get('id', None) in state_id, f)
+        f = filter(lambda agent: agent.get('state_id', None) in state_id, f)
 
     if agent_type is not None:
         f = filter(lambda agent: isinstance(agent, agent_type), f)

soil/analysis.py

@@ -4,7 +4,8 @@ import glob
 import yaml
 from os.path import join
 
-from . import serialization, history
+from . import serialization
+from tsih import History
 
 
 def read_data(*args, group=False, **kwargs):
@@ -34,7 +35,7 @@ def _read_data(pattern, *args, from_csv=False, process_args=None, **kwargs):
 
 
 def read_sql(db, *args, **kwargs):
-    h = history.History(db_path=db, backup=False, readonly=True)
+    h = History(db_path=db, backup=False, readonly=True)
     df = h.read_sql(*args, **kwargs)
     return df
 

soil/environment.py

@@ -12,9 +12,11 @@ from networkx.readwrite import json_graph
 
 import networkx as nx
 
+from tsih import History, Record, Key, NoHistory
+
 from mesa import Model
 
-from . import serialization, agents, analysis, history, utils, time
+from . import serialization, agents, analysis, utils, time
 
 # These properties will be copied when pickling/unpickling the environment
 _CONFIG_PROPS = [ 'name',
@@ -46,6 +48,7 @@ class Environment(Model):
                  schedule=None,
                  initial_time=0,
                  environment_params=None,
+                 history=True,
                  dir_path=None,
                  **kwargs):
 
@@ -78,7 +81,11 @@ class Environment(Model):
 
         self._env_agents = {}
         self.interval = interval
-        self._history = history.History(name=self.name,
+        if history:
+            history = History
+        else:
+            history = NoHistory
+        self._history = history(name=self.name,
                                 backup=True)
         self['SEED'] = seed
 
@@ -162,8 +169,15 @@ class Environment(Model):
         if agent_type:
             state = defstate
             a = agent_type(model=self,
-                           unique_id=agent_id,
+                           unique_id=agent_id)
-                           state=state)
+
+        for (k, v) in getattr(a, 'defaults', {}).items():
+            if not hasattr(a, k) or getattr(a, k) is None:
+                setattr(a, k, v)
+
+        for (k, v) in state.items():
+            setattr(a, k, v)
+
         node['agent'] = a
         self.schedule.add(a)
         return a
@@ -183,6 +197,11 @@ class Environment(Model):
         start = start or self.now
         return self.G.add_edge(agent1, agent2, **attrs)
 
+    def step(self):
+        super().step()
+        self.datacollector.collect(self)
+        self.schedule.step()
+
     def run(self, until, *args, **kwargs):
         self._save_state()
 
@@ -204,12 +223,12 @@ class Environment(Model):
 
     def __setitem__(self, key, value):
         if isinstance(key, tuple):
-            k = history.Key(*key)
+            k = Key(*key)
             self._history.save_record(*k,
                                       value=value)
             return
         self.environment_params[key] = value
-        self._history.save_record(agent_id='env',
+        self._history.save_record(dict_id='env',
                                   t_step=self.now,
                                   key=key,
                                   value=value)
@@ -274,13 +293,13 @@ class Environment(Model):
         if now is None:
             now = self.now
         for k, v in self.environment_params.items():
-            yield history.Record(agent_id='env',
+            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 history.Record(agent_id=agent.id,
+                yield Record(dict_id=agent.id,
                              t_step=now,
                              key=k,
                              value=v)

soil/history.py

@@ -1,388 +0,0 @@
-import time
-import os
-import pandas as pd
-import sqlite3
-import copy
-import logging
-import tempfile
-
-logger = logging.getLogger(__name__)
-
-from collections import UserDict, namedtuple
-
-from . import serialization
-from .utils import open_or_reuse, unflatten_dict
-
-
-class History:
-    """
-    Store and retrieve values from a sqlite database.
-    """
-
-    def __init__(self, name=None, db_path=None, backup=False, readonly=False):
-        if readonly and (not os.path.exists(db_path)):
-            raise Exception('The DB file does not exist. Cannot open in read-only mode')
-
-        self._db = None
-        self._temp = db_path is None
-        self._stats_columns = None
-        self.readonly = readonly
-
-        if self._temp:
-            if not name:
-                name = time.time()
-            # The file will be deleted as soon as it's closed
-            # Normally, that will be on destruction
-            db_path = tempfile.NamedTemporaryFile(suffix='{}.sqlite'.format(name)).name
-
-
-        if backup and os.path.exists(db_path):
-                newname = db_path + '.backup{}.sqlite'.format(time.time())
-                os.rename(db_path, newname)
-
-        self.db_path = db_path
-
-        self.db = db_path
-        self._dtypes = {}
-        self._tups = []
-
-
-        if self.readonly:
-            return
-
-        with self.db:
-            logger.debug('Creating database {}'.format(self.db_path))
-            self.db.execute('''CREATE TABLE IF NOT EXISTS history (agent_id text, t_step real, key text, value text)''')
-            self.db.execute('''CREATE TABLE IF NOT EXISTS value_types (key text, value_type text)''')
-            self.db.execute('''CREATE TABLE IF NOT EXISTS stats (trial_id text)''')
-            self.db.execute('''CREATE UNIQUE INDEX IF NOT EXISTS idx_history ON history (agent_id, t_step, key);''')
-
-    @property
-    def db(self):
-        try:
-            self._db.cursor()
-        except (sqlite3.ProgrammingError, AttributeError):
-            self.db = None  # Reset the database
-        return self._db
-
-    @db.setter
-    def db(self, db_path=None):
-        self._close()
-        db_path = db_path or self.db_path
-        if isinstance(db_path, str):
-            logger.debug('Connecting to database {}'.format(db_path))
-            self._db = sqlite3.connect(db_path)
-            self._db.row_factory = sqlite3.Row
-        else:
-            self._db = db_path
-
-    def _close(self):
-        if self._db is None:
-            return
-        self.flush_cache()
-        self._db.close()
-        self._db = None
-
-    def save_stats(self, stat):
-        if self.readonly:
-            print('DB in readonly mode')
-            return
-        if not stat:
-            return
-        with self.db:
-            if not self._stats_columns:
-                self._stats_columns = list(c['name'] for c in self.db.execute('PRAGMA table_info(stats)'))
-
-            for column, value in stat.items():
-                if column in self._stats_columns:
-                    continue
-                dtype = 'text'
-                if not isinstance(value, str):
-                    try:
-                        float(value)
-                        dtype = 'real'
-                        int(value)
-                        dtype = 'int'
-                    except (ValueError, OverflowError):
-                        pass
-                self.db.execute('ALTER TABLE stats ADD "{}" "{}"'.format(column, dtype))
-                self._stats_columns.append(column)
-
-            columns = ", ".join(map(lambda x: '"{}"'.format(x), stat.keys()))
-            values = ", ".join(['"{0}"'.format(col) for col in stat.values()])
-            query = "INSERT INTO stats ({columns}) VALUES ({values})".format(
-                columns=columns,
-                values=values
-            )
-            self.db.execute(query)
-
-    def get_stats(self, unflatten=True):
-        rows = self.db.execute("select * from stats").fetchall()
-        res = []
-        for row in rows:
-            d = {}
-            for k in row.keys():
-                if row[k] is None:
-                    continue
-                d[k] = row[k]
-            if unflatten:
-                d = unflatten_dict(d)
-            res.append(d)
-        return res
-
-    @property
-    def dtypes(self):
-        self._read_types()
-        return {k:v[0] for k, v in self._dtypes.items()}
-
-    def save_tuples(self, tuples):
-        '''
-        Save a series of tuples, converting them to records if necessary
-        '''
-        self.save_records(Record(*tup) for tup in tuples)
-
-    def save_records(self, records):
-        '''
-        Save a collection of records
-        '''
-        for record in records:
-            if not isinstance(record, Record):
-                record = Record(*record)
-            self.save_record(*record)
-
-    def save_record(self, agent_id, t_step, key, value):
-        '''
-        Save a collection of records to the database.
-        Database writes are cached.
-        '''
-        if self.readonly:
-            raise Exception('DB in readonly mode')
-        if key not in self._dtypes:
-            self._read_types()
-            if key not in self._dtypes:
-                name = serialization.name(value)
-                serializer = serialization.serializer(name)
-                deserializer = serialization.deserializer(name)
-                self._dtypes[key] = (name, serializer, deserializer)
-                with self.db:
-                    self.db.execute("replace into value_types (key, value_type) values (?, ?)", (key, name))
-        value = self._dtypes[key][1](value)
-
-        self._tups.append(Record(agent_id=agent_id,
-                                 t_step=t_step,
-                                 key=key,
-                                 value=value))
-        if len(self._tups) > 100:
-            self.flush_cache()
-
-    def flush_cache(self):
-        '''
-        Use a cache to save state changes to avoid opening a session for every change.
-        The cache will be flushed at the end of the simulation, and when history is accessed.
-        '''
-        if self.readonly:
-            raise Exception('DB in readonly mode')
-        logger.debug('Flushing cache {}'.format(self.db_path))
-        with self.db:
-            self.db.executemany("replace into history(agent_id, t_step, key, value) values (?, ?, ?, ?)", self._tups)
-            # (rec.agent_id, rec.t_step, rec.key, rec.value))
-        self._tups.clear()
-
-    def to_tuples(self):
-        self.flush_cache()
-        with self.db:
-            res = self.db.execute("select agent_id, t_step, key, value from history ").fetchall()
-        for r in res:
-            agent_id, t_step, key, value = r
-            if key not in self._dtypes:
-                self._read_types()
-            if key not in self._dtypes:
-                raise ValueError("Unknown datatype for {} and {}".format(key, value))
-            value = self._dtypes[key][2](value)
-            yield agent_id, t_step, key, value
-
-    def _read_types(self):
-        with self.db:
-            res = self.db.execute("select key, value_type from value_types ").fetchall()
-        for k, v in res:
-            serializer = serialization.serializer(v)
-            deserializer = serialization.deserializer(v)
-            self._dtypes[k] = (v, serializer, deserializer)
-
-    def __getitem__(self, key):
-        # raise NotImplementedError()
-        self.flush_cache()
-        key = Key(*key)
-        agent_ids = [key.agent_id] if key.agent_id is not None else []
-        t_steps = [key.t_step] if key.t_step is not None else []
-        keys = [key.key] if key.key is not None else []
-
-        df = self.read_sql(agent_ids=agent_ids,
-                           t_steps=t_steps,
-                           keys=keys)
-        r = Records(df, filter=key, dtypes=self._dtypes)
-        if r.resolved:
-            return r.value()
-        return r
-
-    def read_sql(self, keys=None, agent_ids=None, not_agent_ids=None, t_steps=None, convert_types=False, limit=-1):
-
-        self._read_types()
-
-        def escape_and_join(v):
-            if v is None:
-                return
-            return ",".join(map(lambda x: "\'{}\'".format(x), v))
-
-        filters = [("key in ({})".format(escape_and_join(keys)), keys),
-                   ("agent_id in ({})".format(escape_and_join(agent_ids)), agent_ids),
-                   ("agent_id not in ({})".format(escape_and_join(not_agent_ids)), not_agent_ids)
-        ]
-        filters = list(k[0] for k in filters if k[1])
-
-        last_df = None
-        if t_steps:
-            # Convert negative indices into positive
-            if any(x<0 for x in t_steps):
-                max_t = int(self.db.execute("select max(t_step) from history").fetchone()[0])
-                t_steps = [t if t>0 else max_t+1+t for t in t_steps]
-
-            # We will be doing ffill interpolation, so we need to look for
-            # the last value before the minimum step in the query
-            min_step = min(t_steps)
-            last_filters = ['t_step < {}'.format(min_step),]
-            last_filters = last_filters + filters
-            condition = ' and '.join(last_filters)
-
-            last_query = '''
-            select h1.*
-            from history h1
-            inner join (
-            select agent_id, key, max(t_step) as t_step
-            from history
-            where {condition}
-            group by agent_id, key
-            ) h2
-            on h1.agent_id = h2.agent_id  and
-               h1.key      = h2.key       and
-               h1.t_step   = h2.t_step
-            '''.format(condition=condition)
-            last_df = pd.read_sql_query(last_query, self.db)
-
-            filters.append("t_step >= '{}' and t_step <= '{}'".format(min_step, max(t_steps)))
-
-        condition = ''
-        if filters:
-            condition = 'where {} '.format(' and '.join(filters))
-        query = 'select * from history {} limit {}'.format(condition, limit)
-        df = pd.read_sql_query(query, self.db)
-        if last_df is not None:
-            df = pd.concat([df, last_df])
-
-        df_p = df.pivot_table(values='value', index=['t_step'],
-                              columns=['key', 'agent_id'],
-                              aggfunc='first')
-
-        for k, v in self._dtypes.items():
-            if k in df_p:
-                dtype, _, deserial = v
-                try:
-                    df_p[k] = df_p[k].fillna(method='ffill').astype(dtype)
-                except (TypeError, ValueError):
-                    # Avoid forward-filling unknown/incompatible types
-                    continue
-        if t_steps:
-            df_p = df_p.reindex(t_steps, method='ffill')
-        return df_p.ffill()
-
-    def __getstate__(self):
-        state = dict(**self.__dict__)
-        del state['_db']
-        del state['_dtypes']
-        return state
-
-    def __setstate__(self, state):
-        self.__dict__ = state
-        self._dtypes = {}
-        self._db = None
-
-    def dump(self, f):
-        self._close()
-        for line in open_or_reuse(self.db_path, 'rb'):
-            f.write(line)
-
-
-class Records():
-
-    def __init__(self, df, filter=None, dtypes=None):
-        if not filter:
-            filter = Key(agent_id=None,
-                         t_step=None,
-                         key=None)
-        self._df = df
-        self._filter = filter
-        self.dtypes = dtypes or {}
-        super().__init__()
-
-    def mask(self, tup):
-        res = ()
-        for i, k in zip(tup[:-1], self._filter):
-            if k is None:
-                res = res + (i,)
-        res = res + (tup[-1],)
-        return res
-
-    def filter(self, newKey):
-        f = list(self._filter)
-        for ix, i in enumerate(f):
-            if i is None:
-                f[ix] = newKey
-        self._filter = Key(*f)
-
-    @property
-    def resolved(self):
-        return sum(1 for i in self._filter if i is not None) == 3
-
-    def __iter__(self):
-        for column, series in self._df.iteritems():
-            key, agent_id = column
-            for t_step, value in series.iteritems():
-                r = Record(t_step=t_step,
-                           agent_id=agent_id,
-                           key=key,
-                           value=value)
-                yield self.mask(r)
-
-    def value(self):
-        if self.resolved:
-            f = self._filter
-            try:
-                i = self._df[f.key][str(f.agent_id)]
-                ix = i.index.get_loc(f.t_step, method='ffill')
-                return i.iloc[ix]
-            except KeyError as ex:
-                return self.dtypes[f.key][2]()
-        return list(self)
-
-    def df(self):
-        return self._df
-
-    def __getitem__(self, k):
-        n = copy.copy(self)
-        n.filter(k)
-        if n.resolved:
-            return n.value()
-        return n
-
-    def __len__(self):
-        return len(self._df)
-
-    def __str__(self):
-        if self.resolved:
-            return str(self.value())
-        return '<Records for [{}]>'.format(self._filter)
-
-Key = namedtuple('Key', ['agent_id', 't_step', 'key'])
-Record = namedtuple('Record', 'agent_id t_step key value')
-
-Stat = namedtuple('Stat', 'trial_id')

soil/simulation.py

@@ -9,6 +9,7 @@ import networkx as nx
 from networkx.readwrite import json_graph
 from multiprocessing import Pool
 from functools import partial
+from tsih import History
 
 import pickle
 
@@ -17,7 +18,6 @@ from .environment import Environment
 from .utils import logger
 from .exporters import default
 from .stats import defaultStats
-from .history import History
 
 
 #TODO: change documentation for simulation
@@ -159,7 +159,7 @@ class Simulation:
                                      **kwargs)
 
     def run_gen(self, *args, parallel=False, dry_run=False,
-                exporters=[default, ], stats=[defaultStats], outdir=None, exporter_params={},
+                exporters=[default, ], stats=[], outdir=None, exporter_params={},
                 stats_params={}, log_level=None,
                 **kwargs):
         '''Run the simulation and yield the resulting environments.'''

soil/stats.py

@@ -97,7 +97,7 @@ class defaultStats(Stats):
         return {
             'network ': {
                 'n_nodes': env.G.number_of_nodes(),
-                'n_edges': env.G.number_of_nodes(),
+                'n_edges': env.G.number_of_edges(),
             },
             'agents': {
                 'model_count': dict(c),

soil/utils.py

@@ -26,6 +26,8 @@ def timer(name='task', pre="", function=logger.info, to_object=None):
         to_object.end = end
 
 
+
+
 def safe_open(path, mode='r', backup=True, **kwargs):
     outdir = os.path.dirname(path)
     if outdir and not os.path.exists(outdir):

tests/test_analysis.py

@@ -67,13 +67,13 @@ class TestAnalysis(TestCase):
     def test_count(self):
         env = self.env
         df = analysis.read_sql(env._history.db_path)
-        res = analysis.get_count(df, 'SEED', 'id')
+        res = analysis.get_count(df, 'SEED', 'state_id')
         assert res['SEED'][self.env['SEED']].iloc[0] == 1
         assert res['SEED'][self.env['SEED']].iloc[-1] == 1
-        assert res['id']['odd'].iloc[0] == 2
+        assert res['state_id']['odd'].iloc[0] == 2
-        assert res['id']['even'].iloc[0] == 0
+        assert res['state_id']['even'].iloc[0] == 0
-        assert res['id']['odd'].iloc[-1] == 1
+        assert res['state_id']['odd'].iloc[-1] == 1
-        assert res['id']['even'].iloc[-1] == 1
+        assert res['state_id']['even'].iloc[-1] == 1
 
     def test_value(self):
         env = self.env

tests/test_main.py

@@ -9,7 +9,7 @@ from functools import partial
 
 from os.path import join
 from soil import (simulation, Environment, agents, serialization,
-                  history, utils)
+                  utils)
 from soil.time import Delta
 
 
@@ -21,7 +21,7 @@ class CustomAgent(agents.FSM):
     @agents.default_state
     @agents.state
     def normal(self):
-        self.state['neighbors'] = self.count_agents(state_id='normal',
+        self.neighbors = self.count_agents(state_id='normal',
                                            limit_neighbors=True)
     @agents.state
     def unreachable(self):
@@ -116,7 +116,7 @@ class TestMain(TestCase):
             'network_agents': [{
                 'agent_type': 'AggregatedCounter',
                 'weight': 1,
-                'state': {'id': 0}
+                'state': {'state_id': 0}
 
             }],
             'max_time': 10,
@@ -149,10 +149,9 @@ class TestMain(TestCase):
         }
         s = simulation.from_config(config)
         env = s.run_simulation(dry_run=True)[0]
-        assert env.get_agent(0).state['neighbors'] == 1
-        assert env.get_agent(0).state['neighbors'] == 1
         assert env.get_agent(1).count_agents(state_id='normal') == 2
         assert env.get_agent(1).count_agents(state_id='normal', limit_neighbors=True) == 1
+        assert env.get_agent(0).neighbors == 1
 
     def test_torvalds_example(self):
         """A complete example from a documentation should work."""
@@ -317,12 +316,6 @@ class TestMain(TestCase):
         assert recovered['key', 0] == 'test'
         assert recovered['key'] == 'test'
 
-    def test_history(self):
-        '''Test storing in and retrieving from history (sqlite)'''
-        h = history.History()
-        h.save_record(agent_id=0, t_step=0, key="test", value="hello")
-        assert h[0, 0, "test"] == "hello"
-
     def test_subgraph(self):
         '''An agent should be able to subgraph the global topology'''
         G = nx.Graph()
@@ -350,12 +343,13 @@ class TestMain(TestCase):
             'network_params': {},
             'agent_type': 'CounterModel',
             'max_time': 2,
-            'num_trials': 100,
+            'num_trials': 50,
             'environment_params': {}
         }
         s = simulation.from_config(config)
         runs = list(s.run_simulation(dry_run=True))
         over = list(x.now for x in runs if x.now>2)
+        assert len(runs) == config['num_trials']
         assert len(over) == 0
 
 
@@ -372,11 +366,11 @@ class TestMain(TestCase):
                 return self.ping
 
         a = ToggleAgent(unique_id=1, model=Environment())
-        assert a.state["id"] == a.ping.id
+        assert a.state_id == a.ping.id
         a.step()
-        assert a.state["id"] == a.pong.id
+        assert a.state_id == a.pong.id
         a.step()
-        assert a.state["id"] == a.ping.id
+        assert a.state_id == a.ping.id
 
     def test_fsm_when(self):
         '''Basic state change'''