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Code Issues Releases Wiki Activity

fix timeout in FSM. Improve logs

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J. Fernando Sánchez 2019-02-01 19:05:07 +01:00
parent 09e14c6e84
commit 65f6aa72f3
8 changed files with 124 additions and 26 deletions
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19
CHANGELOG.md Normal file
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@ -0,0 +1,19 @@
# Changelog
All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased]
### Changed
### Added
### Fixed
## [0.13.7]
### Changed
* History now defaults to not backing up! This makes it more intuitive to load the history for examination, at the expense of rewriting something. That should not happen because History is only created in the Environment, and that has `backup=True`.
### Added
* Agent names are assigned based on their agent types
* Agent logging uses the agent name.
* FSM agents can now return a timeout in addition to a new state. e.g. `return self.idle, self.env.timeout(2)` will execute the *different_state* in 2 *units of time* (`t_step=now+2`).
* Example of using timeouts in FSM (custom_timeouts)
* `network_agents` entries may include an `ids` entry. If set, it should be a list of node ids that should be assigned that agent type. This complements the previous behavior of setting agent type with `weights`.

36
examples/custom_timeouts/custom_timeouts.py Normal file
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@ -0,0 +1,36 @@
from soil.agents import FSM, state, default_state
class Fibonacci(FSM):
'''Agent that only executes in t_steps that are Fibonacci numbers'''
defaults = {
'prev': 1
}
@default_state
@state
def counting(self):
self.log('Stopping at {}'.format(self.now))
prev, self['prev'] = self['prev'], max([self.now, self['prev']])
return None, self.env.timeout(prev)
class Odds(FSM):
'''Agent that only executes in odd t_steps'''
@default_state
@state
def odds(self):
self.log('Stopping at {}'.format(self.now))
return None, self.env.timeout(1+self.now%2)
if __name__ == '__main__':
import logging
logging.basicConfig(level=logging.INFO)
from soil import Simulation
s = Simulation(network_agents=[{'ids': [0], 'agent_type': Fibonacci},
{'ids': [1], 'agent_type': Odds}],
dry_run=True,
network_params={"generator": "complete_graph", "n": 2},
max_time=100,
)
s.run()

2
soil/VERSION
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@ -1 +1 @@
0.13.6
0.13.7

1
soil/__init__.py
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@ -14,6 +14,7 @@ except NameError:
from . import agents
from .simulation import *
from .environment import Environment
from .history import History
from . import utils
from . import analysis

35
soil/agents/__init__.py
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@ -25,13 +25,13 @@ class BaseAgent(nxsim.BaseAgent):
defaults = {}
def __init__(self, environment, agent_id, state=None,
name='network_process', interval=None, **state_params):
name=None, interval=None, **state_params):
# Check for REQUIRED arguments
assert environment is not None, TypeError('__init__ missing 1 required keyword argument: \'environment\'. '
'Cannot be NoneType.')
# Initialize agent parameters
self.id = agent_id
self.name = name
self.name = name or '{}[{}]'.format(type(self).__name__, self.id)
self.state_params = state_params
# Register agent to environment
@ -46,8 +46,8 @@ class BaseAgent(nxsim.BaseAgent):
if not hasattr(self, 'level'):
self.level = logging.DEBUG
self.logger = logging.getLogger('{}-Agent-{}'.format(self.env.name,
self.id))
self.logger = logging.getLogger('{}.{}'.format(self.env.name,
self.id))
self.logger.setLevel(self.level)
# initialize every time an instance of the agent is created
@ -174,7 +174,7 @@ class BaseAgent(nxsim.BaseAgent):
def log(self, message, *args, level=logging.INFO, **kwargs):
message = message + " ".join(str(i) for i in args)
message = "\t@{:>5}:\t{}".format(self.now, message)
message = "\t{:10}@{:>5}:\t{}".format(self.name, self.now, message)
for k, v in kwargs:
message += " {k}={v} ".format(k, v)
extra = {}
@ -280,7 +280,7 @@ class FSM(BaseAgent, metaclass=MetaFSM):
raise Exception('{} has no valid state id or default state'.format(self))
if next_state not in self.states:
raise Exception('{} is not a valid id for {}'.format(next_state, self))
self.states[next_state](self)
return self.states[next_state](self)
def set_state(self, state):
if hasattr(state, 'id'):
@ -306,6 +306,9 @@ def prob(prob=1):
return r < prob
STATIC_THRESHOLD = (-1, -1)
def calculate_distribution(network_agents=None,
agent_type=None):
'''
@ -343,6 +346,9 @@ def calculate_distribution(network_agents=None,
total = sum(x.get('weight', 1) for x in network_agents)
acc = 0
for v in network_agents:
if 'ids' in v:
v['threshold'] = STATIC_THRESHOLD
continue
upper = acc + (v.get('weight', 1)/total)
v['threshold'] = [acc, upper]
acc = upper
@ -403,17 +409,20 @@ def _convert_agent_types(ind, to_string=False, **kwargs):
return deserialize_distribution(ind, **kwargs)
def _agent_from_distribution(distribution, value=-1):
def _agent_from_distribution(distribution, value=-1, agent_id=None):
"""Used in the initialization of agents given an agent distribution."""
if value < 0:
value = random.random()
for d in distribution:
for d in sorted(distribution, key=lambda x: x['threshold']):
threshold = d['threshold']
if value >= threshold[0] and value < threshold[1]:
state = {}
if 'state' in d:
state = deepcopy(d['state'])
return d['agent_type'], state
# Check if the definition matches by id (first) or by threshold
if not ((agent_id is not None and threshold == STATIC_THRESHOLD and agent_id in d['ids']) or \
(value >= threshold[0] and value < threshold[1])):
continue
state = {}
if 'state' in d:
state = deepcopy(d['state'])
return d['agent_type'], state
raise Exception('Distribution for value {} not found in: {}'.format(value, distribution))

42
soil/environment.py
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@ -4,9 +4,11 @@ import time
import csv
import random
import simpy
import yaml
import tempfile
import pandas as pd
from copy import deepcopy
from collections import Counter
from networkx.readwrite import json_graph
import networkx as nx
@ -60,7 +62,8 @@ class Environment(nxsim.NetworkEnvironment):
if not dry_run:
self.get_path()
self._history = history.History(name=self.name if not dry_run else None,
dir_path=self.dir_path)
dir_path=self.dir_path,
backup=True)
# Add environment agents first, so their events get
# executed before network agents
self.environment_agents = environment_agents or []
@ -111,7 +114,7 @@ class Environment(nxsim.NetworkEnvironment):
agent_type = None
if 'agent_type' in self.states.get(agent_id, {}):
agent_type = self.states[agent_id]
agent_type = self.states[agent_id]['agent_type']
elif 'agent_type' in node:
agent_type = node['agent_type']
elif 'agent_type' in self.default_state:
@ -119,8 +122,8 @@ class Environment(nxsim.NetworkEnvironment):
if agent_type:
agent_type = agents.deserialize_type(agent_type)
else:
agent_type, state = agents._agent_from_distribution(agent_distribution)
elif agent_distribution:
agent_type, state = agents._agent_from_distribution(agent_distribution, agent_id=agent_id)
return self.set_agent(agent_id, agent_type, state)
def set_agent(self, agent_id, agent_type, state=None):
@ -130,10 +133,12 @@ class Environment(nxsim.NetworkEnvironment):
defstate.update(node.get('state', {}))
if state:
defstate.update(state)
state = defstate
a = agent_type(environment=self,
agent_id=agent_id,
state=state)
a = None
if agent_type:
state = defstate
a = agent_type(environment=self,
agent_id=agent_id,
state=state)
node['agent'] = a
return a
@ -153,8 +158,10 @@ class Environment(nxsim.NetworkEnvironment):
def run(self, *args, **kwargs):
self._save_state()
self.log_stats()
super().run(*args, **kwargs)
self._history.flush_cache()
self.log_stats()
def _save_state(self, now=None):
# for agent in self.agents:
@ -327,6 +334,25 @@ class Environment(nxsim.NetworkEnvironment):
return G
def stats(self):
stats = {}
stats['network'] = {}
stats['network']['n_nodes'] = self.G.number_of_nodes()
stats['network']['n_edges'] = self.G.number_of_edges()
c = Counter()
c.update(a.__class__.__name__ for a in self.network_agents)
stats['agents'] = {}
stats['agents']['model_count'] = dict(c)
c2 = Counter()
c2.update(a['id'] for a in self.network_agents)
stats['agents']['state_count'] = dict(c2)
stats['params'] = self.environment_params
return stats
def log_stats(self):
stats = self.stats()
utils.logger.info('Environment stats: \n{}'.format(yaml.dump(stats, default_flow_style=False)))
def __getstate__(self):
state = {}
for prop in _CONFIG_PROPS:

9
soil/history.py
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@ -3,6 +3,10 @@ import os
import pandas as pd
import sqlite3
import copy
import logging
logger = logging.getLogger(__name__)
from collections import UserDict, namedtuple
from . import utils
@ -13,7 +17,7 @@ class History:
Store and retrieve values from a sqlite database.
"""
def __init__(self, db_path=None, name=None, dir_path=None, backup=True):
def __init__(self, db_path=None, name=None, dir_path=None, backup=False):
if db_path is None and name:
db_path = os.path.join(dir_path or os.getcwd(),
'{}.db.sqlite'.format(name))
@ -28,6 +32,7 @@ class History:
self.db = db_path
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 int, key text, value text text)''')
self.db.execute('''CREATE TABLE IF NOT EXISTS value_types (key text, value_type text)''')
self.db.execute('''CREATE UNIQUE INDEX IF NOT EXISTS idx_history ON history (agent_id, t_step, key);''')
@ -46,6 +51,7 @@ class History:
def db(self, db_path=None):
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)
else:
self._db = db_path
@ -110,6 +116,7 @@ class History:
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.
'''
logger.debug('Flushing cache {}'.format(self.db_path))
with self.db:
for rec in self._tups:
self.db.execute("replace into history(agent_id, t_step, key, value) values (?, ?, ?, ?)", (rec.agent_id, rec.t_step, rec.key, rec.value))

6
tests/test_history.py
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@ -120,18 +120,18 @@ class TestHistory(TestCase):
assert os.path.exists(db_path)
# Recover the data
recovered = history.History(db_path=db_path, backup=False)
recovered = history.History(db_path=db_path)
assert recovered['a_1', 0, 'id'] == 'v'
assert recovered['a_1', 4, 'id'] == 'e'
# Using the same name should create a backup copy
# Using backup=True should create a backup copy, and initialize an empty history
newhistory = history.History(db_path=db_path, backup=True)
backuppaths = glob(db_path + '.backup*.sqlite')
assert len(backuppaths) == 1
backuppath = backuppaths[0]
assert newhistory.db_path == h.db_path
assert os.path.exists(backuppath)
assert not len(newhistory[None, None, None])
assert len(newhistory[None, None, None]) == 0
def test_history_tuples(self):
"""