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Code Issues Releases Wiki Activity

WIP: exporters

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This commit is contained in:
J. Fernando Sánchez 2019-04-29 18:47:15 +02:00
parent 9bc036d185
commit d1006bd55c
16 changed files with 288 additions and 195 deletions
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11
CHANGELOG.md
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@ -9,12 +9,21 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
The definition of the variables and their possible values (i.e., a problem in SALib terms), as well as a sampler function, can be provided.
Soil uses this definition and the template to generate a set of configurations.
* Simulation group names, to link related simulations. For now, they are only used to group all simulations in the same group under the same folder.
* Exporters unify exporting/dumping results and other files to disk. If `dry_run` is set to `True`, exporters will write to stdout instead of a file (useful for testing/debugging).
* Distribution exporter, to write statistics about values and value_counts in every simulation. The results are dumped to two CSV files.
### Changed
* `dir_path` is now the directory for resources (modules, files), and the output dir has been renamed to `outdir`
* `dir_path` is now the directory for resources (modules, files)
* Environments and simulations do not export or write anything by default. That task is delegated to Exporters
### Removed
* The output dir for environments and simulations (see Exporters)
* DrawingAgent, because it wrote to disk and was not being used. We provide a partial alternative in the form of the GraphDrawing exporter. A complete alternative will be provided once the network at each state can be accessed by exporters.
## Fixed
* Modules with custom agents/environments failed to load when they were run from outside the directory of the definition file. Modules are now loaded from the directory of the simulation file in addition to the working directory
* Memory databases (in history) can now be shared between threads.
* Testing all examples, not just subdirectories
## [0.13.8]
### Changed

2
examples/complete.yml
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@ -3,11 +3,9 @@ name: simple
group: tests
dir_path: "/tmp/"
num_trials: 3
dry_run: True
max_time: 100
interval: 1
seed: "CompleteSeed!"
dump: false
network_params:
generator: complete_graph
n: 10

3
examples/custom_generator/custom_generator.yml
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@ -2,7 +2,6 @@
name: custom-generator
description: Using a custom generator for the network
num_trials: 3
dry_run: True
max_time: 100
interval: 1
network_params:
@ -14,4 +13,4 @@ network_agents:
- agent_type: CounterModel
weight: 1
state:
id: 0
id: 0

3
examples/custom_timeouts/custom_timeouts.py
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@ -29,8 +29,7 @@ if __name__ == '__main__':
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()
s.run(dry_run=True)

20
soil/__init__.py
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@ -57,18 +57,20 @@ def main():
logging.info('Loading config file: {}'.format(args.file))
try:
dump = []
if not args.dry_run:
if args.csv:
dump.append('csv')
if args.graph:
dump.append('gexf')
exporters = list(args.exporter or [])
if args.csv:
exporters.append('CSV')
if args.graph:
exporters.append('Gexf')
exp_params = {}
if args.dry_run:
exp_params['copy_to'] = sys.stdout
simulation.run_from_config(args.file,
dry_run=args.dry_run,
dump=dump,
exporters=args.exporter,
exporters=exporters,
parallel=(not args.synchronous),
outdir=args.output)
outdir=args.output,
exporter_params=exp_params)
except Exception:
if args.pdb:
pdb.post_mortem()

18
soil/agents/DrawingAgent.py
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@ -1,18 +0,0 @@
from . import BaseAgent
import os.path
import matplotlib
import matplotlib.pyplot as plt
import networkx as nx
class DrawingAgent(BaseAgent):
"""
Agent that draws the state of the network.
"""
def step(self):
# Outside effects
f = plt.figure()
nx.draw(self.env.G, node_size=10, width=0.2, pos=nx.spring_layout(self.env.G, scale=100), ax=f.add_subplot(111))
f.savefig(os.path.join(self.env.get_path(), "graph-"+str(self.env.now)+".png"))

1
soil/agents/__init__.py
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@ -515,4 +515,3 @@ from .ModelM2 import *
from .SentimentCorrelationModel import *
from .SISaModel import *
from .CounterModel import *
from .DrawingAgent import *

2
soil/analysis.py
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@ -34,7 +34,7 @@ def _read_data(pattern, *args, from_csv=False, process_args=None, **kwargs):
def read_sql(db, *args, **kwargs):
h = history.History(db, backup=False)
h = history.History(db_path=db, backup=False)
df = h.read_sql(*args, **kwargs)
return df

46
soil/environment.py
View File

@ -14,15 +14,13 @@ from networkx.readwrite import json_graph
import networkx as nx
import nxsim
from . import serialization, agents, analysis, history
from . import serialization, agents, analysis, history, utils
# These properties will be copied when pickling/unpickling the environment
_CONFIG_PROPS = [ 'name',
'states',
'default_state',
'interval',
'dry_run',
'outdir',
]
class Environment(nxsim.NetworkEnvironment):
@ -43,8 +41,6 @@ class Environment(nxsim.NetworkEnvironment):
default_state=None,
interval=1,
seed=None,
dry_run=False,
outdir=None,
topology=None,
*args, **kwargs):
self.name = name or 'UnnamedEnvironment'
@ -56,13 +52,8 @@ class Environment(nxsim.NetworkEnvironment):
topology = nx.Graph()
super().__init__(*args, topology=topology, **kwargs)
self._env_agents = {}
self.dry_run = dry_run
self.interval = interval
self.outdir = outdir or tempfile.mkdtemp('soil-env')
if not dry_run:
self.get_path()
self._history = history.History(name=self.name if not dry_run else None,
outdir=self.outdir,
self._history = history.History(name=self.name,
backup=True)
# Add environment agents first, so their events get
# executed before network agents
@ -167,8 +158,6 @@ class Environment(nxsim.NetworkEnvironment):
self.log_stats()
def _save_state(self, now=None):
# for agent in self.agents:
# agent.save_state()
serialization.logger.debug('Saving state @{}'.format(self.now))
self._history.save_records(self.state_to_tuples(now=now))
@ -222,15 +211,6 @@ class Environment(nxsim.NetworkEnvironment):
'''
return self[key] if key in self else default
def get_path(self, outdir=None):
outdir = outdir or self.outdir
if not os.path.exists(outdir):
try:
os.makedirs(outdir)
except FileExistsError:
pass
return outdir
def get_agent(self, agent_id):
return self.G.node[agent_id]['agent']
@ -239,20 +219,15 @@ class Environment(nxsim.NetworkEnvironment):
return list(self.agents)
return [self.G.node[i]['agent'] for i in nodes]
def dump_csv(self, outdir=None):
csv_name = os.path.join(self.get_path(outdir),
'{}.environment.csv'.format(self.name))
with open(csv_name, 'w') as f:
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, outdir=None):
def dump_gexf(self, f):
G = self.history_to_graph()
graph_path = os.path.join(self.get_path(outdir),
self.name+".gexf")
# Workaround for geometric models
# See soil/soil#4
for node in G.nodes():
@ -260,9 +235,9 @@ class Environment(nxsim.NetworkEnvironment):
G.node[node]['viz'] = {"position": {"x": G.node[node]['pos'][0], "y": G.node[node]['pos'][1], "z": 0.0}}
del (G.node[node]['pos'])
nx.write_gexf(G, graph_path, version="1.2draft")
nx.write_gexf(G, f, version="1.2draft")
def dump(self, outdir=None, formats=None):
def dump(self, *args, formats=None, **kwargs):
if not formats:
return
functions = {
@ -271,10 +246,13 @@ class Environment(nxsim.NetworkEnvironment):
}
for f in formats:
if f in functions:
functions[f](outdir)
functions[f](*args, **kwargs)
else:
raise ValueError('Unknown format: {}'.format(f))
def dump_sqlite(self, f):
return self._history.dump(f)
def state_to_tuples(self, now=None):
if now is None:
now = self.now
@ -338,7 +316,7 @@ class Environment(nxsim.NetworkEnvironment):
G.add_node(agent.id, **attributes)
return G
def stats(self):
stats = {}
stats['network'] = {}

167
soil/exporters.py
View File

@ -1,43 +1,174 @@
from .serialization import deserialize
import os
import time
from io import BytesIO
import matplotlib.pyplot as plt
import networkx as nx
import pandas as pd
from .serialization import deserialize
from .utils import open_or_reuse, logger, timer
def for_sim(simulation, names, dir_path=None):
from . import utils
def for_sim(simulation, names, *args, **kwargs):
'''Return the set of exporters for a simulation, given the exporter names'''
exporters = []
for name in names:
mod = deserialize(name, known_modules=['soil.exporters'])
exporters.append(mod(simulation))
exporters.append(mod(simulation, *args, **kwargs))
return exporters
class DryRunner(BytesIO):
def __init__(self, fname, *args, copy_to=None, **kwargs):
super().__init__(*args, **kwargs)
self.__fname = fname
self.__copy_to = copy_to
class Base:
def write(self, txt):
if self.__copy_to:
self.__copy_to.write('{}:::{}'.format(self.__fname, txt))
try:
super().write(txt)
except TypeError:
super().write(bytes(txt, 'utf-8'))
def __init__(self, simulation):
def close(self):
logger.info('**Not** written to {} (dry run mode):\n\n{}\n\n'.format(self.__fname,
self.getvalue().decode()))
super().close()
class Exporter:
'''
Interface for all exporters. It is not necessary, but it is useful
if you don't plan to implement all the methods.
'''
def __init__(self, simulation, outdir=None, dry_run=None, copy_to=None):
self.sim = simulation
outdir = outdir or os.getcwd()
self.outdir = os.path.join(outdir,
simulation.group or '',
simulation.name)
self.dry_run = dry_run
self.copy_to = copy_to
def start(self):
pass
'''Method to call when the simulation starts'''
def end(self):
pass
'''Method to call when the simulation ends'''
def env(self):
pass
def trial_end(self, env):
'''Method to call when a trial ends'''
def output(self, f, mode='w', **kwargs):
if self.dry_run:
f = DryRunner(f, copy_to=self.copy_to)
else:
try:
if not os.path.isabs(f):
f = os.path.join(self.outdir, f)
except TypeError:
pass
return open_or_reuse(f, mode=mode, **kwargs)
class Dummy(Base):
class Default(Exporter):
'''Default exporter. Writes CSV and sqlite results, as well as the simulation YAML'''
def start(self):
with open(os.path.join(self.sim.outdir, 'dummy')) as f:
f.write('simulation started @ {}'.format(time.time()))
if not self.dry_run:
logger.info('Dumping results to %s', self.outdir)
self.sim.dump_yaml(outdir=self.outdir)
else:
logger.info('NOT dumping results')
def env(self, env):
with open(os.path.join(self.sim.outdir, 'dummy-trial-{}'.format(env.name))) as f:
def trial_end(self, env):
if not self.dry_run:
with timer('Dumping simulation {} trial {}'.format(self.sim.name,
env.name)):
with self.output('{}.sqlite'.format(env.name), mode='wb') as f:
env.dump_sqlite(f)
class CSV(Exporter):
def trial_end(self, env):
if not self.dry_run:
with timer('[CSV] Dumping simulation {} trial {}'.format(self.sim.name,
env.name)):
with self.output('{}.csv'.format(env.name)) as f:
env.dump_csv(f)
class Gexf(Exporter):
def trial_end(self, env):
if not self.dry_run:
with timer('[CSV] Dumping simulation {} trial {}'.format(self.sim.name,
env.name)):
with self.output('{}.gexf'.format(env.name), mode='wb') as f:
env.dump_gexf(f)
class Dummy(Exporter):
def start(self):
with self.output('dummy', 'w') as f:
f.write('simulation started @ {}\n'.format(time.time()))
def trial_end(self, env):
with self.output('dummy', 'w') as f:
for i in env.history_to_tuples():
f.write(','.join(i))
f.write(','.join(map(str, i)))
f.write('\n')
def end(self):
with open(os.path.join(self.sim.outdir, 'dummy')) as f:
f.write('simulation ended @ {}'.format(time.time()))
with self.output('dummy', 'a') as f:
f.write('simulation ended @ {}\n'.format(time.time()))
class Distribution(Exporter):
'''
Write the distribution of agent states at the end of each trial,
the mean value, and its deviation.
'''
def start(self):
self.means = []
self.counts = []
def trial_end(self, env):
df = env[None, None, None].df()
ix = df.index[-1]
attrs = df.columns.levels[0]
vc = {}
stats = {}
for a in attrs:
t = df.loc[(ix, a)]
try:
self.means.append(('mean', a, t.mean()))
except TypeError:
for name, count in t.value_counts().iteritems():
self.counts.append(('count', a, name, count))
def end(self):
dfm = pd.DataFrame(self.means, columns=['metric', 'key', 'value'])
dfc = pd.DataFrame(self.counts, columns=['metric', 'key', 'value', 'count'])
dfm = dfm.groupby(by=['key']).agg(['mean', 'std', 'count', 'median', 'max', 'min'])
dfc = dfc.groupby(by=['key', 'value']).agg(['mean', 'std', 'count', 'median', 'max', 'min'])
with self.output('counts.csv') as f:
dfc.to_csv(f)
with self.output('metrics.csv') as f:
dfm.to_csv(f)
class GraphDrawing(Exporter):
def trial_end(self, env):
# Outside effects
f = plt.figure()
nx.draw(env.G, node_size=10, width=0.2, pos=nx.spring_layout(env.G, scale=100), ax=f.add_subplot(111))
with open('graph-{}.png'.format(env.name)) as f:
f.savefig(f)

50
soil/history.py
View File

@ -4,6 +4,7 @@ import pandas as pd
import sqlite3
import copy
import logging
import tempfile
logger = logging.getLogger(__name__)
@ -17,16 +18,18 @@ class History:
Store and retrieve values from a sqlite database.
"""
def __init__(self, db_path=None, name=None, outdir=None, backup=False):
if db_path is None and name:
db_path = os.path.join(outdir or os.getcwd(),
'{}.db.sqlite'.format(name))
if db_path:
if backup and os.path.exists(db_path):
newname = db_path + '.backup{}.sqlite'.format(time.time())
os.rename(db_path, newname)
else:
db_path = ":memory:"
def __init__(self, name=None, db_path=None, backup=False):
self._db = None
if db_path is None:
if not name:
name = time.time()
_, db_path = tempfile.mkstemp(suffix='{}.sqlite'.format(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
@ -49,6 +52,7 @@ class History:
@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))
@ -56,6 +60,13 @@ class History:
else:
self._db = db_path
def _close(self):
if self._db is None:
return
self.flush_cache()
self._db.close()
self._db = None
@property
def dtypes(self):
self.read_types()
@ -110,7 +121,6 @@ class History:
raise ValueError("Unknown datatype for {} and {}".format(key, value))
return self._dtypes[key][2](value)
def flush_cache(self):
'''
Use a cache to save state changes to avoid opening a session for every change.
@ -154,8 +164,6 @@ class History:
return r.value()
return r
def read_sql(self, keys=None, agent_ids=None, t_steps=None, convert_types=False, limit=-1):
self.read_types()
@ -214,16 +222,22 @@ class History:
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(self.db_path, 'rb'):
f.write(line)
class Records():
@ -274,10 +288,13 @@ class Records():
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:
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)
@ -293,6 +310,5 @@ class Records():
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')

12
soil/serialization.py
View File

@ -2,16 +2,15 @@ import os
import logging
import ast
import sys
import yaml
import importlib
from glob import glob
from random import random
from copy import deepcopy
from itertools import product, chain
import yaml
import networkx as nx
from jinja2 import Template
import networkx as nx
logger = logging.getLogger('soil')
logger.setLevel(logging.INFO)
@ -36,6 +35,9 @@ def load_network(network_params, dir_path=None):
return method(path, **kwargs)
net_args = network_params.copy()
if 'generator' not in net_args:
return nx.Graph()
net_gen = net_args.pop('generator')
if dir_path not in sys.path:
@ -51,6 +53,7 @@ def load_file(infile):
with open(infile, 'r') as f:
return list(chain.from_iterable(map(expand_template, load_string(f))))
def load_string(string):
yield from yaml.load_all(string)
@ -91,7 +94,6 @@ def expand_template(config):
blank = list(load_string(blank_str))
if len(blank) > 1:
raise ValueError('Templates must not return more than one configuration')
if 'name' in blank[0]:
raise ValueError('Templates cannot be named, use group instead')

103
soil/simulation.py
View File

@ -15,7 +15,7 @@ from nxsim import NetworkSimulation
from . import serialization, utils, basestring, agents
from .environment import Environment
from .serialization import logger
from .utils import logger
from .exporters import for_sim as exporters_for_sim
@ -65,8 +65,6 @@ class Simulation(NetworkSimulation):
whose value indicates the state
dir_path: str, optional
Directory path to load simulation assets (files, modules...)
outdir : str, optional
Directory path to save simulation results
seed : str, optional
Seed to use for the random generator
num_trials : int, optional
@ -87,11 +85,11 @@ class Simulation(NetworkSimulation):
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, dump=None, dry_run=False,
outdir=None, num_trials=1, max_time=100,
load_module=None, seed=None, dir_path=None,
environment_agents=None, environment_params=None,
environment_class=None, **kwargs):
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,
**kwargs):
self.seed = str(seed) or str(time.time())
self.load_module = load_module
@ -101,18 +99,10 @@ class Simulation(NetworkSimulation):
self.num_trials = num_trials
self.max_time = max_time
self.default_state = default_state or {}
if not outdir:
outdir = os.path.join(os.getcwd(),
'soil_output')
self.outdir = os.path.join(outdir,
self.group or '',
self.name)
self.dir_path = dir_path or os.getcwd()
self.interval = interval
self.dump = dump
self.dry_run = dry_run
sys.path += list(x for x in [self.outdir, os.getcwd(), self.dir_path] if x not in sys.path)
sys.path += list(x for x in [os.getcwd(), self.dir_path] if x not in sys.path)
if topology is None:
topology = serialization.load_network(network_params,
@ -142,6 +132,7 @@ class Simulation(NetworkSimulation):
return self.run(*args, **kwargs)
def run(self, *args, **kwargs):
'''Run the simulation and return the list of resulting environments'''
return list(self._run_simulation_gen(*args, **kwargs))
def _run_sync_or_async(self, parallel=False, *args, **kwargs):
@ -152,7 +143,7 @@ class Simulation(NetworkSimulation):
**kwargs)
for i in p.imap_unordered(func, range(self.num_trials)):
if isinstance(i, Exception):
logger.error('Trial failed:\n\t{}'.format(i.message))
logger.error('Trial failed:\n\t%s', i.message)
continue
yield i
else:
@ -162,29 +153,30 @@ class Simulation(NetworkSimulation):
**kwargs)
def _run_simulation_gen(self, *args, parallel=False, dry_run=False,
exporters=None, **kwargs):
exporters=None, outdir=None, exporter_params={}, **kwargs):
logger.info('Using exporters: %s', exporters or [])
logger.info('Output directory: %s', outdir)
exporters = exporters_for_sim(self,
exporters or [])
exporters or [],
dry_run=dry_run,
outdir=outdir,
**exporter_params)
with utils.timer('simulation {}'.format(self.name)):
if not (dry_run or self.dry_run):
logger.info('Dumping results to {}'.format(self.outdir))
self.dump_pickle(self.outdir)
self.dump_yaml(self.outdir)
else:
logger.info('NOT dumping results')
for exporter in exporters:
exporter.start()
for env in self._run_sync_or_async(*args, parallel=parallel,
dry_run=dry_run, **kwargs):
**kwargs):
for exporter in exporters:
exporter.env(env)
exporter.trial_end(env)
yield env
for exporter in exporters:
exporter.end()
def get_env(self, trial_id = 0, **kwargs):
'''Create an environment for a trial of the simulation'''
opts = self.environment_params.copy()
env_name = '{}_trial_{}'.format(self.name, trial_id)
opts.update({
@ -192,19 +184,17 @@ class Simulation(NetworkSimulation):
'topology': self.topology.copy(),
'seed': self.seed+env_name,
'initial_time': 0,
'dry_run': self.dry_run,
'interval': self.interval,
'network_agents': self.network_agents,
'states': self.states,
'default_state': self.default_state,
'environment_agents': self.environment_agents,
'outdir': self.outdir,
})
opts.update(kwargs)
env = self.environment_class(**opts)
return env
def run_trial(self, trial_id=0, until=None, dry_run=False, **opts):
def run_trial(self, trial_id=0, until=None, **opts):
"""Run a single trial of the simulation
Parameters
@ -214,13 +204,9 @@ class Simulation(NetworkSimulation):
# Set-up trial environment and graph
until = until or self.max_time
env = self.get_env(trial_id = trial_id, **opts)
dry_run = self.dry_run or dry_run
# Set up agents on nodes
with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)):
env.run(until)
if self.dump and not dry_run:
with utils.timer('Dumping simulation {} trial {}'.format(self.name, trial_id)):
env.dump(formats = self.dump)
return env
def run_trial_exceptions(self, *args, **kwargs):
'''
@ -240,24 +226,25 @@ class Simulation(NetworkSimulation):
def to_yaml(self):
return yaml.dump(self.to_dict())
def dump_yaml(self, outdir = None, file_name = None):
outdir = outdir or self.outdir
if not os.path.exists(outdir):
os.makedirs(outdir)
if not file_name:
file_name=os.path.join(outdir,
'{}.dumped.yml'.format(self.name))
with open(file_name, 'w') as f:
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, outdir = None, pickle_name = None):
outdir = outdir or self.outdir
if not os.path.exists(outdir):
os.makedirs(outdir)
if not pickle_name:
pickle_name=os.path.join(outdir,
'{}.simulation.pickle'.format(self.name))
with open(pickle_name, 'wb') as f:
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 __getstate__(self):
@ -279,8 +266,6 @@ class Simulation(NetworkSimulation):
def __setstate__(self, state):
self.__dict__ = state
self.load_module = getattr(self, 'load_module', None)
if self.outdir not in sys.path:
sys.path += [self.outdir, os.getcwd()]
if self.dir_path not in sys.path:
sys.path += [self.dir_path, os.getcwd()]
self.topology = json_graph.node_link_graph(state['topology'])
@ -308,24 +293,14 @@ def from_config(conf_or_path):
return sim
def run_from_config(*configs, outdir=None, dump=None, timestamp=False, **kwargs):
def run_from_config(*configs, **kwargs):
for config_def in configs:
# logger.info("Found {} config(s)".format(len(ls)))
for config, path in serialization.load_config(config_def):
name = config.get('name', 'unnamed')
logger.info("Using config(s): {name}".format(name=name))
if timestamp:
sim_folder = '{}_{}'.format(name,
time.strftime("%Y-%m-%d_%H:%M:%S"))
else:
sim_folder = name
if dump is not None:
config['dump'] = dump
dir_path = config.pop('dir_path', os.path.dirname(path))
outdir = config.pop('outdir', outdir)
sim = Simulation(dir_path=dir_path,
outdir=outdir,
**config)
logger.info('Dumping results to {} : {}'.format(sim.outdir, sim.dump))
sim.run_simulation(**kwargs)

15
soil/utils.py
View File

@ -1,5 +1,6 @@
import logging
import time
import os
from contextlib import contextmanager
@ -20,3 +21,17 @@ def timer(name='task', pre="", function=logger.info, to_object=None):
if to_object:
to_object.start = start
to_object.end = end
def safe_open(path, *args, **kwargs):
outdir = os.path.dirname(path)
if outdir and not os.path.exists(outdir):
os.makedirs(outdir)
return open(path, *args, **kwargs)
def open_or_reuse(f, *args, **kwargs):
try:
return safe_open(f, *args, **kwargs)
except TypeError:
return f

5
tests/test_analysis.py
View File

@ -39,7 +39,6 @@ class TestAnalysis(TestCase):
agent should be able to update its state."""
config = {
'name': 'analysis',
'dry_run': True,
'seed': 'seed',
'network_params': {
'generator': 'complete_graph',
@ -53,7 +52,7 @@ class TestAnalysis(TestCase):
}
}
s = simulation.from_config(config)
self.env = s.run_simulation()[0]
self.env = s.run_simulation(dry_run=True)[0]
def test_saved(self):
env = self.env
@ -65,7 +64,7 @@ class TestAnalysis(TestCase):
def test_count(self):
env = self.env
df = analysis.read_sql(env._history._db)
df = analysis.read_sql(env._history.db_path)
res = analysis.get_count(df, 'SEED', 'id')
assert res['SEED']['seedanalysis_trial_0'].iloc[0] == 1
assert res['SEED']['seedanalysis_trial_0'].iloc[-1] == 1

25
tests/test_main.py
View File

@ -28,7 +28,6 @@ class TestMain(TestCase):
Raise an exception otherwise.
"""
config = {
'dry_run': True,
'network_params': {
'path': join(ROOT, 'test.gexf')
}
@ -38,7 +37,6 @@ class TestMain(TestCase):
assert len(G) == 2
with self.assertRaises(AttributeError):
config = {
'dry_run': True,
'network_params': {
'path': join(ROOT, 'unknown.extension')
}
@ -52,7 +50,6 @@ class TestMain(TestCase):
should be used to generate a network
"""
config = {
'dry_run': True,
'network_params': {
'generator': 'barabasi_albert_graph'
}
@ -67,7 +64,6 @@ class TestMain(TestCase):
def test_empty_simulation(self):
"""A simulation with a base behaviour should do nothing"""
config = {
'dry_run': True,
'network_params': {
'path': join(ROOT, 'test.gexf')
},
@ -84,7 +80,6 @@ class TestMain(TestCase):
agent should be able to update its state."""
config = {
'name': 'CounterAgent',
'dry_run': True,
'network_params': {
'path': join(ROOT, 'test.gexf')
},
@ -108,7 +103,6 @@ class TestMain(TestCase):
"""
config = {
'name': 'CounterAgent',
'dry_run': True,
'network_params': {
'path': join(ROOT, 'test.gexf')
},
@ -134,7 +128,6 @@ class TestMain(TestCase):
def test_custom_agent(self):
"""Allow for search of neighbors with a certain state_id"""
config = {
'dry_run': True,
'network_params': {
'path': join(ROOT, 'test.gexf')
},
@ -158,8 +151,7 @@ class TestMain(TestCase):
config['network_params']['path'] = join(EXAMPLES,
config['network_params']['path'])
s = simulation.from_config(config)
s.dry_run = True
env = s.run_simulation()[0]
env = s.run_simulation(dry_run=True)[0]
for a in env.network_agents:
skill_level = a.state['skill_level']
if a.id == 'Torvalds':
@ -183,14 +175,12 @@ class TestMain(TestCase):
with utils.timer('loading'):
config = serialization.load_file(join(EXAMPLES, 'complete.yml'))[0]
s = simulation.from_config(config)
s.dry_run = True
with utils.timer('serializing'):
serial = s.to_yaml()
with utils.timer('recovering'):
recovered = yaml.load(serial)
with utils.timer('deleting'):
del recovered['topology']
del recovered['outdir']
assert config == recovered
def test_configuration_changes(self):
@ -200,16 +190,14 @@ class TestMain(TestCase):
"""
config = serialization.load_file(join(EXAMPLES, 'complete.yml'))[0]
s = simulation.from_config(config)
s.dry_run = True
for i in range(5):
s.run_simulation(dry_run=True)
nconfig = s.to_dict()
del nconfig['topology']
del nconfig['outdir']
assert config == nconfig
def test_row_conversion(self):
env = Environment(dry_run=True)
env = Environment()
env['test'] = 'test_value'
res = list(env.history_to_tuples())
@ -228,8 +216,8 @@ class TestMain(TestCase):
from geometric models. We should work around it.
"""
G = nx.random_geometric_graph(20, 0.1)
env = Environment(topology=G, dry_run=True)
env.dump_gexf('/tmp/dump-gexf')
env = Environment(topology=G)
env.dump_gexf('/tmp/dump-gexf/prueba.gexf')
def test_save_graph(self):
'''
@ -239,7 +227,7 @@ class TestMain(TestCase):
'''
G = nx.cycle_graph(5)
distribution = agents.calculate_distribution(None, agents.BaseAgent)
env = Environment(topology=G, network_agents=distribution, dry_run=True)
env = Environment(topology=G, network_agents=distribution)
env[0, 0, 'testvalue'] = 'start'
env[0, 10, 'testvalue'] = 'finish'
nG = env.history_to_graph()
@ -315,8 +303,9 @@ class TestMain(TestCase):
recovered = pickle.loads(pickled)
assert recovered.env.name == 'Test'
assert recovered['key'] == 'test'
assert list(recovered.env._history.to_tuples())
assert recovered['key', 0] == 'test'
assert recovered['key'] == 'test'
def test_history(self):
'''Test storing in and retrieving from history (sqlite)'''