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J. Fernando Sánchez 2022-10-16 17:58:19 +02:00
parent d9947c2c52
commit 78833a9e08
26 changed files with 1254 additions and 899 deletions
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177
soil/__init__.py
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@ -22,58 +22,107 @@ from .utils import logger
from .time import * from .time import *
def main(cfg='simulation.yml', exporters=None, parallel=None, output="soil_output", *, do_run=False, debug=False, **kwargs): def main(
cfg="simulation.yml",
exporters=None,
parallel=None,
output="soil_output",
*,
do_run=False,
debug=False,
**kwargs,
):
import argparse import argparse
from . import simulation from . import simulation
logger.info('Running SOIL version: {}'.format(__version__)) logger.info("Running SOIL version: {}".format(__version__))
parser = argparse.ArgumentParser(description='Run a SOIL simulation') parser = argparse.ArgumentParser(description="Run a SOIL simulation")
parser.add_argument('file', type=str, parser.add_argument(
nargs="?", "file",
default=cfg, type=str,
help='Configuration file for the simulation (e.g., YAML or JSON)') nargs="?",
parser.add_argument('--version', action='store_true', default=cfg,
help='Show version info and exit') help="Configuration file for the simulation (e.g., YAML or JSON)",
parser.add_argument('--module', '-m', type=str, )
help='file containing the code of any custom agents.') parser.add_argument(
parser.add_argument('--dry-run', '--dry', action='store_true', "--version", action="store_true", help="Show version info and exit"
help='Do not store the results of the simulation to disk, show in terminal instead.') )
parser.add_argument('--pdb', action='store_true', parser.add_argument(
help='Use a pdb console in case of exception.') "--module",
parser.add_argument('--debug', action='store_true', "-m",
help='Run a customized version of a pdb console to debug a simulation.') type=str,
parser.add_argument('--graph', '-g', action='store_true', help="file containing the code of any custom agents.",
help='Dump each trial\'s network topology as a GEXF graph. Defaults to false.') )
parser.add_argument('--csv', action='store_true', parser.add_argument(
help='Dump all data collected in CSV format. Defaults to false.') "--dry-run",
parser.add_argument('--level', type=str, "--dry",
help='Logging level') action="store_true",
parser.add_argument('--output', '-o', type=str, default=output or "soil_output", help="Do not store the results of the simulation to disk, show in terminal instead.",
help='folder to write results to. It defaults to the current directory.') )
parser.add_argument(
"--pdb", action="store_true", help="Use a pdb console in case of exception."
)
parser.add_argument(
"--debug",
action="store_true",
help="Run a customized version of a pdb console to debug a simulation.",
)
parser.add_argument(
"--graph",
"-g",
action="store_true",
help="Dump each trial's network topology as a GEXF graph. Defaults to false.",
)
parser.add_argument(
"--csv",
action="store_true",
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=output or "soil_output",
help="folder to write results to. It defaults to the current directory.",
)
if parallel is None: if parallel is None:
parser.add_argument('--synchronous', action='store_true', parser.add_argument(
help='Run trials serially and synchronously instead of in parallel. Defaults to false.') "--synchronous",
action="store_true",
help="Run trials serially and synchronously instead of in parallel. Defaults to false.",
)
parser.add_argument('-e', '--exporter', action='append', parser.add_argument(
default=[], "-e",
help='Export environment and/or simulations using this exporter') "--exporter",
action="append",
default=[],
help="Export environment and/or simulations using this exporter",
)
parser.add_argument('--only-convert', '--convert', action='store_true', parser.add_argument(
help='Do not run the simulation, only convert the configuration file(s) and output them.') "--only-convert",
"--convert",
action="store_true",
help="Do not run the simulation, only convert the configuration file(s) and output them.",
)
parser.add_argument("--set", parser.add_argument(
metavar="KEY=VALUE", "--set",
action='append', metavar="KEY=VALUE",
help="Set a number of parameters that will be passed to the simulation." action="append",
"(do not put spaces before or after the = sign). " help="Set a number of parameters that will be passed to the simulation."
"If a value contains spaces, you should define " "(do not put spaces before or after the = sign). "
"it with double quotes: " "If a value contains spaces, you should define "
'foo="this is a sentence". Note that ' "it with double quotes: "
"values are always treated as strings.") 'foo="this is a sentence". Note that '
"values are always treated as strings.",
)
args = parser.parse_args() args = parser.parse_args()
logger.setLevel(getattr(logging, (args.level or 'INFO').upper())) logger.setLevel(getattr(logging, (args.level or "INFO").upper()))
if args.version: if args.version:
return return
@ -81,14 +130,16 @@ def main(cfg='simulation.yml', exporters=None, parallel=None, output="soil_outpu
if parallel is None: if parallel is None:
parallel = not args.synchronous parallel = not args.synchronous
exporters = exporters or ['default', ] exporters = exporters or [
"default",
]
for exp in args.exporter: for exp in args.exporter:
if exp not in exporters: if exp not in exporters:
exporters.append(exp) exporters.append(exp)
if args.csv: if args.csv:
exporters.append('csv') exporters.append("csv")
if args.graph: if args.graph:
exporters.append('gexf') exporters.append("gexf")
if os.getcwd() not in sys.path: if os.getcwd() not in sys.path:
sys.path.append(os.getcwd()) sys.path.append(os.getcwd())
@ -97,38 +148,38 @@ def main(cfg='simulation.yml', exporters=None, parallel=None, output="soil_outpu
if output is None: if output is None:
output = args.output output = args.output
logger.info("Loading config file: {}".format(args.file))
logger.info('Loading config file: {}'.format(args.file))
debug = debug or args.debug debug = debug or args.debug
if args.pdb or debug: if args.pdb or debug:
args.synchronous = True args.synchronous = True
res = [] res = []
try: try:
exp_params = {} exp_params = {}
if not os.path.exists(args.file): if not os.path.exists(args.file):
logger.error('Please, input a valid file') logger.error("Please, input a valid file")
return return
for sim in simulation.iter_from_config(args.file, for sim in simulation.iter_from_config(
dry_run=args.dry_run, args.file,
exporters=exporters, dry_run=args.dry_run,
parallel=parallel, exporters=exporters,
outdir=output, parallel=parallel,
exporter_params=exp_params, outdir=output,
**kwargs): exporter_params=exp_params,
**kwargs,
):
if args.set: if args.set:
for s in args.set: for s in args.set:
k, v = s.split('=', 1)[:2] k, v = s.split("=", 1)[:2]
v = eval(v) v = eval(v)
tail, *head = k.rsplit('.', 1)[::-1] tail, *head = k.rsplit(".", 1)[::-1]
target = sim target = sim
if head: if head:
for part in head[0].split('.'): for part in head[0].split("."):
try: try:
target = getattr(target, part) target = getattr(target, part)
except AttributeError: except AttributeError:
@ -144,19 +195,21 @@ def main(cfg='simulation.yml', exporters=None, parallel=None, output="soil_outpu
if do_run: if do_run:
res.append(sim.run()) res.append(sim.run())
else: else:
print('not running') print("not running")
res.append(sim) res.append(sim)
except Exception as ex: except Exception as ex:
if args.pdb: if args.pdb:
from .debugging import post_mortem from .debugging import post_mortem
print(traceback.format_exc()) print(traceback.format_exc())
post_mortem() post_mortem()
else: else:
raise raise
if debug: if debug:
from .debugging import set_trace from .debugging import set_trace
os.environ['SOIL_DEBUG'] = 'true'
os.environ["SOIL_DEBUG"] = "true"
set_trace() set_trace()
return res return res
@ -165,5 +218,5 @@ def easy(cfg, debug=False, **kwargs):
return main(cfg, **kwargs)[0] return main(cfg, **kwargs)[0]
if __name__ == '__main__': if __name__ == "__main__":
main(do_run=True) main(do_run=True)

4
soil/__main__.py
View File

@ -1,7 +1,9 @@
from . import main as init_main from . import main as init_main
def main(): def main():
init_main(do_run=True) init_main(do_run=True)
if __name__ == '__main__':
if __name__ == "__main__":
init_main(do_run=True) init_main(do_run=True)

3
soil/agents/BassModel.py
View File

@ -7,6 +7,7 @@ class BassModel(FSM):
innovation_prob innovation_prob
imitation_prob imitation_prob
""" """
sentimentCorrelation = 0 sentimentCorrelation = 0
def step(self): def step(self):
@ -21,7 +22,7 @@ class BassModel(FSM):
else: else:
aware_neighbors = self.get_neighboring_agents(state_id=self.aware.id) aware_neighbors = self.get_neighboring_agents(state_id=self.aware.id)
num_neighbors_aware = len(aware_neighbors) num_neighbors_aware = len(aware_neighbors)
if self.prob((self['imitation_prob']*num_neighbors_aware)): if self.prob((self["imitation_prob"] * num_neighbors_aware)):
self.sentimentCorrelation = 1 self.sentimentCorrelation = 1
return self.aware return self.aware

72
soil/agents/BigMarketModel.py
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@ -6,42 +6,54 @@ class BigMarketModel(FSM):
Settings: Settings:
Names: Names:
enterprises [Array] enterprises [Array]
tweet_probability_enterprises [Array] tweet_probability_enterprises [Array]
Users: Users:
tweet_probability_users tweet_probability_users
tweet_relevant_probability tweet_relevant_probability
tweet_probability_about [Array] tweet_probability_about [Array]
sentiment_about [Array] sentiment_about [Array]
""" """
def __init__(self, *args, **kwargs): def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs) super().__init__(*args, **kwargs)
self.enterprises = self.env.environment_params['enterprises'] self.enterprises = self.env.environment_params["enterprises"]
self.type = "" self.type = ""
if self.id < len(self.enterprises): # Enterprises if self.id < len(self.enterprises): # Enterprises
self.set_state(self.enterprise.id) self.set_state(self.enterprise.id)
self.type = "Enterprise" self.type = "Enterprise"
self.tweet_probability = environment.environment_params['tweet_probability_enterprises'][self.id] self.tweet_probability = environment.environment_params[
"tweet_probability_enterprises"
][self.id]
else: # normal users else: # normal users
self.type = "User" self.type = "User"
self.set_state(self.user.id) self.set_state(self.user.id)
self.tweet_probability = environment.environment_params['tweet_probability_users'] self.tweet_probability = environment.environment_params[
self.tweet_relevant_probability = environment.environment_params['tweet_relevant_probability'] "tweet_probability_users"
self.tweet_probability_about = environment.environment_params['tweet_probability_about'] # List ]
self.sentiment_about = environment.environment_params['sentiment_about'] # List self.tweet_relevant_probability = environment.environment_params[
"tweet_relevant_probability"
]
self.tweet_probability_about = environment.environment_params[
"tweet_probability_about"
] # List
self.sentiment_about = environment.environment_params[
"sentiment_about"
] # List
@state @state
def enterprise(self): def enterprise(self):
if self.random.random() < self.tweet_probability: # Tweets if self.random.random() < self.tweet_probability: # Tweets
aware_neighbors = self.get_neighboring_agents(state_id=self.number_of_enterprises) # Nodes neighbour users aware_neighbors = self.get_neighboring_agents(
state_id=self.number_of_enterprises
) # Nodes neighbour users
for x in aware_neighbors: for x in aware_neighbors:
if self.random.uniform(0,10) < 5: if self.random.uniform(0, 10) < 5:
x.sentiment_about[self.id] += 0.1 # Increments for enterprise x.sentiment_about[self.id] += 0.1 # Increments for enterprise
else: else:
x.sentiment_about[self.id] -= 0.1 # Decrements for enterprise x.sentiment_about[self.id] -= 0.1 # Decrements for enterprise
@ -49,15 +61,19 @@ class BigMarketModel(FSM):
# Establecemos limites # Establecemos limites
if x.sentiment_about[self.id] > 1: if x.sentiment_about[self.id] > 1:
x.sentiment_about[self.id] = 1 x.sentiment_about[self.id] = 1
if x.sentiment_about[self.id]< -1: if x.sentiment_about[self.id] < -1:
x.sentiment_about[self.id] = -1 x.sentiment_about[self.id] = -1
x.attrs['sentiment_enterprise_%s'% self.enterprises[self.id]] = x.sentiment_about[self.id] x.attrs[
"sentiment_enterprise_%s" % self.enterprises[self.id]
] = x.sentiment_about[self.id]
@state @state
def user(self): def user(self):
if self.random.random() < self.tweet_probability: # Tweets if self.random.random() < self.tweet_probability: # Tweets
if self.random.random() < self.tweet_relevant_probability: # Tweets something relevant if (
self.random.random() < self.tweet_relevant_probability
): # Tweets something relevant
# Tweet probability per enterprise # Tweet probability per enterprise
for i in range(len(self.enterprises)): for i in range(len(self.enterprises)):
random_num = self.random.random() random_num = self.random.random()
@ -65,23 +81,29 @@ class BigMarketModel(FSM):
# The condition is fulfilled, sentiments are evaluated towards that enterprise # The condition is fulfilled, sentiments are evaluated towards that enterprise
if self.sentiment_about[i] < 0: if self.sentiment_about[i] < 0:
# NEGATIVO # NEGATIVO
self.userTweets("negative",i) self.userTweets("negative", i)
elif self.sentiment_about[i] == 0: elif self.sentiment_about[i] == 0:
# NEUTRO # NEUTRO
pass pass
else: else:
# POSITIVO # POSITIVO
self.userTweets("positive",i) self.userTweets("positive", i)
for i in range(len(self.enterprises)): # So that it never is set to 0 if there are not changes (logs) for i in range(
self.attrs['sentiment_enterprise_%s'% self.enterprises[i]] = self.sentiment_about[i] len(self.enterprises)
): # So that it never is set to 0 if there are not changes (logs)
self.attrs[
"sentiment_enterprise_%s" % self.enterprises[i]
] = self.sentiment_about[i]
def userTweets(self, sentiment,enterprise): def userTweets(self, sentiment, enterprise):
aware_neighbors = self.get_neighboring_agents(state_id=self.number_of_enterprises) # Nodes neighbours users aware_neighbors = self.get_neighboring_agents(
state_id=self.number_of_enterprises
) # Nodes neighbours users
for x in aware_neighbors: for x in aware_neighbors:
if sentiment == "positive": if sentiment == "positive":
x.sentiment_about[enterprise] +=0.003 x.sentiment_about[enterprise] += 0.003
elif sentiment == "negative": elif sentiment == "negative":
x.sentiment_about[enterprise] -=0.003 x.sentiment_about[enterprise] -= 0.003
else: else:
pass pass
@ -91,4 +113,6 @@ class BigMarketModel(FSM):
if x.sentiment_about[enterprise] < -1: if x.sentiment_about[enterprise] < -1:
x.sentiment_about[enterprise] = -1 x.sentiment_about[enterprise] = -1
x.attrs['sentiment_enterprise_%s'% self.enterprises[enterprise]] = x.sentiment_about[enterprise] x.attrs[
"sentiment_enterprise_%s" % self.enterprises[enterprise]
] = x.sentiment_about[enterprise]

14
soil/agents/CounterModel.py
View File

@ -15,9 +15,9 @@ class CounterModel(NetworkAgent):
# Outside effects # Outside effects
total = len(list(self.model.schedule._agents)) total = len(list(self.model.schedule._agents))
neighbors = len(list(self.get_neighboring_agents())) neighbors = len(list(self.get_neighboring_agents()))
self['times'] = self.get('times', 0) + 1 self["times"] = self.get("times", 0) + 1
self['neighbors'] = neighbors self["neighbors"] = neighbors
self['total'] = total self["total"] = total
class AggregatedCounter(NetworkAgent): class AggregatedCounter(NetworkAgent):
@ -32,9 +32,9 @@ class AggregatedCounter(NetworkAgent):
def step(self): def step(self):
# Outside effects # Outside effects
self['times'] += 1 self["times"] += 1
neighbors = len(list(self.get_neighboring_agents())) neighbors = len(list(self.get_neighboring_agents()))
self['neighbors'] += neighbors self["neighbors"] += neighbors
total = len(list(self.model.schedule.agents)) total = len(list(self.model.schedule.agents))
self['total'] += total self["total"] += total
self.debug('Running for step: {}. Total: {}'.format(self.now, total)) self.debug("Running for step: {}. Total: {}".format(self.now, total))

8
soil/agents/Geo.py
View File

@ -2,20 +2,20 @@ from scipy.spatial import cKDTree as KDTree
import networkx as nx import networkx as nx
from . import NetworkAgent, as_node from . import NetworkAgent, as_node
class Geo(NetworkAgent): class Geo(NetworkAgent):
'''In this type of network, nodes have a "pos" attribute.''' """In this type of network, nodes have a "pos" attribute."""
def geo_search(self, radius, node=None, center=False, **kwargs): def geo_search(self, radius, node=None, center=False, **kwargs):
'''Get a list of nodes whose coordinates are closer than *radius* to *node*.''' """Get a list of nodes whose coordinates are closer than *radius* to *node*."""
node = as_node(node if node is not None else self) node = as_node(node if node is not None else self)
G = self.subgraph(**kwargs) G = self.subgraph(**kwargs)
pos = nx.get_node_attributes(G, 'pos') pos = nx.get_node_attributes(G, "pos")
if not pos: if not pos:
return [] return []
nodes, coords = list(zip(*pos.items())) nodes, coords = list(zip(*pos.items()))
kdtree = KDTree(coords) # Cannot provide generator. kdtree = KDTree(coords) # Cannot provide generator.
indices = kdtree.query_ball_point(pos[node], radius) indices = kdtree.query_ball_point(pos[node], radius)
return [nodes[i] for i in indices if center or (nodes[i] != node)] return [nodes[i] for i in indices if center or (nodes[i] != node)]

28
soil/agents/IndependentCascadeModel.py
View File

@ -11,10 +11,10 @@ class IndependentCascadeModel(BaseAgent):
def __init__(self, *args, **kwargs): def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs) super().__init__(*args, **kwargs)
self.innovation_prob = self.env.environment_params['innovation_prob'] self.innovation_prob = self.env.environment_params["innovation_prob"]
self.imitation_prob = self.env.environment_params['imitation_prob'] self.imitation_prob = self.env.environment_params["imitation_prob"]
self.state['time_awareness'] = 0 self.state["time_awareness"] = 0
self.state['sentimentCorrelation'] = 0 self.state["sentimentCorrelation"] = 0
def step(self): def step(self):
self.behaviour() self.behaviour()
@ -23,25 +23,27 @@ class IndependentCascadeModel(BaseAgent):
aware_neighbors_1_time_step = [] aware_neighbors_1_time_step = []
# Outside effects # Outside effects
if self.prob(self.innovation_prob): if self.prob(self.innovation_prob):
if self.state['id'] == 0: if self.state["id"] == 0:
self.state['id'] = 1 self.state["id"] = 1
self.state['sentimentCorrelation'] = 1 self.state["sentimentCorrelation"] = 1
self.state['time_awareness'] = self.env.now # To know when they have been infected self.state[
"time_awareness"
] = self.env.now # To know when they have been infected
else: else:
pass pass
return return
# Imitation effects # Imitation effects
if self.state['id'] == 0: if self.state["id"] == 0:
aware_neighbors = self.get_neighboring_agents(state_id=1) aware_neighbors = self.get_neighboring_agents(state_id=1)
for x in aware_neighbors: for x in aware_neighbors:
if x.state['time_awareness'] == (self.env.now-1): if x.state["time_awareness"] == (self.env.now - 1):
aware_neighbors_1_time_step.append(x) aware_neighbors_1_time_step.append(x)
num_neighbors_aware = len(aware_neighbors_1_time_step) num_neighbors_aware = len(aware_neighbors_1_time_step)
if self.prob(self.imitation_prob*num_neighbors_aware): if self.prob(self.imitation_prob * num_neighbors_aware):
self.state['id'] = 1 self.state["id"] = 1
self.state['sentimentCorrelation'] = 1 self.state["sentimentCorrelation"] = 1
else: else:
pass pass

166
soil/agents/ModelM2.py
View File

@ -23,36 +23,49 @@ class SpreadModelM2(BaseAgent):
def __init__(self, model=None, unique_id=0, state=()): def __init__(self, model=None, unique_id=0, state=()):
super().__init__(model=environment, unique_id=unique_id, state=state) super().__init__(model=environment, unique_id=unique_id, state=state)
# Use a single generator with the same seed as `self.random` # Use a single generator with the same seed as `self.random`
random = np.random.default_rng(seed=self._seed) random = np.random.default_rng(seed=self._seed)
self.prob_neutral_making_denier = random.normal(environment.environment_params['prob_neutral_making_denier'], self.prob_neutral_making_denier = random.normal(
environment.environment_params['standard_variance']) environment.environment_params["prob_neutral_making_denier"],
environment.environment_params["standard_variance"],
)
self.prob_infect = random.normal(environment.environment_params['prob_infect'], self.prob_infect = random.normal(
environment.environment_params['standard_variance']) environment.environment_params["prob_infect"],
environment.environment_params["standard_variance"],
)
self.prob_cured_healing_infected = random.normal(environment.environment_params['prob_cured_healing_infected'], self.prob_cured_healing_infected = random.normal(
environment.environment_params['standard_variance']) environment.environment_params["prob_cured_healing_infected"],
self.prob_cured_vaccinate_neutral = random.normal(environment.environment_params['prob_cured_vaccinate_neutral'], environment.environment_params["standard_variance"],
environment.environment_params['standard_variance']) )
self.prob_cured_vaccinate_neutral = random.normal(
environment.environment_params["prob_cured_vaccinate_neutral"],
environment.environment_params["standard_variance"],
)
self.prob_vaccinated_healing_infected = random.normal(environment.environment_params['prob_vaccinated_healing_infected'], self.prob_vaccinated_healing_infected = random.normal(
environment.environment_params['standard_variance']) environment.environment_params["prob_vaccinated_healing_infected"],
self.prob_vaccinated_vaccinate_neutral = random.normal(environment.environment_params['prob_vaccinated_vaccinate_neutral'], environment.environment_params["standard_variance"],
environment.environment_params['standard_variance']) )
self.prob_generate_anti_rumor = random.normal(environment.environment_params['prob_generate_anti_rumor'], self.prob_vaccinated_vaccinate_neutral = random.normal(
environment.environment_params['standard_variance']) environment.environment_params["prob_vaccinated_vaccinate_neutral"],
environment.environment_params["standard_variance"],
)
self.prob_generate_anti_rumor = random.normal(
environment.environment_params["prob_generate_anti_rumor"],
environment.environment_params["standard_variance"],
)
def step(self): def step(self):
if self.state['id'] == 0: # Neutral if self.state["id"] == 0: # Neutral
self.neutral_behaviour() self.neutral_behaviour()
elif self.state['id'] == 1: # Infected elif self.state["id"] == 1: # Infected
self.infected_behaviour() self.infected_behaviour()
elif self.state['id'] == 2: # Cured elif self.state["id"] == 2: # Cured
self.cured_behaviour() self.cured_behaviour()
elif self.state['id'] == 3: # Vaccinated elif self.state["id"] == 3: # Vaccinated
self.vaccinated_behaviour() self.vaccinated_behaviour()
def neutral_behaviour(self): def neutral_behaviour(self):
@ -61,7 +74,7 @@ class SpreadModelM2(BaseAgent):
infected_neighbors = self.get_neighboring_agents(state_id=1) infected_neighbors = self.get_neighboring_agents(state_id=1)
if len(infected_neighbors) > 0: if len(infected_neighbors) > 0:
if self.prob(self.prob_neutral_making_denier): if self.prob(self.prob_neutral_making_denier):
self.state['id'] = 3 # Vaccinated making denier self.state["id"] = 3 # Vaccinated making denier
def infected_behaviour(self): def infected_behaviour(self):
@ -69,7 +82,7 @@ class SpreadModelM2(BaseAgent):
neutral_neighbors = self.get_neighboring_agents(state_id=0) neutral_neighbors = self.get_neighboring_agents(state_id=0)
for neighbor in neutral_neighbors: for neighbor in neutral_neighbors:
if self.prob(self.prob_infect): if self.prob(self.prob_infect):
neighbor.state['id'] = 1 # Infected neighbor.state["id"] = 1 # Infected
def cured_behaviour(self): def cured_behaviour(self):
@ -77,13 +90,13 @@ class SpreadModelM2(BaseAgent):
neutral_neighbors = self.get_neighboring_agents(state_id=0) neutral_neighbors = self.get_neighboring_agents(state_id=0)
for neighbor in neutral_neighbors: for neighbor in neutral_neighbors:
if self.prob(self.prob_cured_vaccinate_neutral): if self.prob(self.prob_cured_vaccinate_neutral):
neighbor.state['id'] = 3 # Vaccinated neighbor.state["id"] = 3 # Vaccinated
# Cure # Cure
infected_neighbors = self.get_neighboring_agents(state_id=1) infected_neighbors = self.get_neighboring_agents(state_id=1)
for neighbor in infected_neighbors: for neighbor in infected_neighbors:
if self.prob(self.prob_cured_healing_infected): if self.prob(self.prob_cured_healing_infected):
neighbor.state['id'] = 2 # Cured neighbor.state["id"] = 2 # Cured
def vaccinated_behaviour(self): def vaccinated_behaviour(self):
@ -91,19 +104,19 @@ class SpreadModelM2(BaseAgent):
infected_neighbors = self.get_neighboring_agents(state_id=1) infected_neighbors = self.get_neighboring_agents(state_id=1)
for neighbor in infected_neighbors: for neighbor in infected_neighbors:
if self.prob(self.prob_cured_healing_infected): if self.prob(self.prob_cured_healing_infected):
neighbor.state['id'] = 2 # Cured neighbor.state["id"] = 2 # Cured
# Vaccinate # Vaccinate
neutral_neighbors = self.get_neighboring_agents(state_id=0) neutral_neighbors = self.get_neighboring_agents(state_id=0)
for neighbor in neutral_neighbors: for neighbor in neutral_neighbors:
if self.prob(self.prob_cured_vaccinate_neutral): if self.prob(self.prob_cured_vaccinate_neutral):
neighbor.state['id'] = 3 # Vaccinated neighbor.state["id"] = 3 # Vaccinated
# Generate anti-rumor # Generate anti-rumor
infected_neighbors_2 = self.get_neighboring_agents(state_id=1) infected_neighbors_2 = self.get_neighboring_agents(state_id=1)
for neighbor in infected_neighbors_2: for neighbor in infected_neighbors_2:
if self.prob(self.prob_generate_anti_rumor): if self.prob(self.prob_generate_anti_rumor):
neighbor.state['id'] = 2 # Cured neighbor.state["id"] = 2 # Cured
class ControlModelM2(BaseAgent): class ControlModelM2(BaseAgent):
@ -112,63 +125,76 @@ class ControlModelM2(BaseAgent):
prob_neutral_making_denier prob_neutral_making_denier
prob_infect prob_infect
prob_cured_healing_infected prob_cured_healing_infected
prob_cured_vaccinate_neutral prob_cured_vaccinate_neutral
prob_vaccinated_healing_infected prob_vaccinated_healing_infected
prob_vaccinated_vaccinate_neutral prob_vaccinated_vaccinate_neutral
prob_generate_anti_rumor prob_generate_anti_rumor
""" """
def __init__(self, model=None, unique_id=0, state=()): def __init__(self, model=None, unique_id=0, state=()):
super().__init__(model=environment, unique_id=unique_id, state=state) super().__init__(model=environment, unique_id=unique_id, state=state)
self.prob_neutral_making_denier = np.random.normal(environment.environment_params['prob_neutral_making_denier'], self.prob_neutral_making_denier = np.random.normal(
environment.environment_params['standard_variance']) environment.environment_params["prob_neutral_making_denier"],
environment.environment_params["standard_variance"],
)
self.prob_infect = np.random.normal(environment.environment_params['prob_infect'], self.prob_infect = np.random.normal(
environment.environment_params['standard_variance']) environment.environment_params["prob_infect"],
environment.environment_params["standard_variance"],
)
self.prob_cured_healing_infected = np.random.normal(environment.environment_params['prob_cured_healing_infected'], self.prob_cured_healing_infected = np.random.normal(
environment.environment_params['standard_variance']) environment.environment_params["prob_cured_healing_infected"],
self.prob_cured_vaccinate_neutral = np.random.normal(environment.environment_params['prob_cured_vaccinate_neutral'], environment.environment_params["standard_variance"],
environment.environment_params['standard_variance']) )
self.prob_cured_vaccinate_neutral = np.random.normal(
environment.environment_params["prob_cured_vaccinate_neutral"],
environment.environment_params["standard_variance"],
)
self.prob_vaccinated_healing_infected = np.random.normal(environment.environment_params['prob_vaccinated_healing_infected'], self.prob_vaccinated_healing_infected = np.random.normal(
environment.environment_params['standard_variance']) environment.environment_params["prob_vaccinated_healing_infected"],
self.prob_vaccinated_vaccinate_neutral = np.random.normal(environment.environment_params['prob_vaccinated_vaccinate_neutral'], environment.environment_params["standard_variance"],
environment.environment_params['standard_variance']) )
self.prob_generate_anti_rumor = np.random.normal(environment.environment_params['prob_generate_anti_rumor'], self.prob_vaccinated_vaccinate_neutral = np.random.normal(
environment.environment_params['standard_variance']) environment.environment_params["prob_vaccinated_vaccinate_neutral"],
environment.environment_params["standard_variance"],
)
self.prob_generate_anti_rumor = np.random.normal(
environment.environment_params["prob_generate_anti_rumor"],
environment.environment_params["standard_variance"],
)
def step(self): def step(self):
if self.state['id'] == 0: # Neutral if self.state["id"] == 0: # Neutral
self.neutral_behaviour() self.neutral_behaviour()
elif self.state['id'] == 1: # Infected elif self.state["id"] == 1: # Infected
self.infected_behaviour() self.infected_behaviour()
elif self.state['id'] == 2: # Cured elif self.state["id"] == 2: # Cured
self.cured_behaviour() self.cured_behaviour()
elif self.state['id'] == 3: # Vaccinated elif self.state["id"] == 3: # Vaccinated
self.vaccinated_behaviour() self.vaccinated_behaviour()
elif self.state['id'] == 4: # Beacon-off elif self.state["id"] == 4: # Beacon-off
self.beacon_off_behaviour() self.beacon_off_behaviour()
elif self.state['id'] == 5: # Beacon-on elif self.state["id"] == 5: # Beacon-on
self.beacon_on_behaviour() self.beacon_on_behaviour()
def neutral_behaviour(self): def neutral_behaviour(self):
self.state['visible'] = False self.state["visible"] = False
# Infected # Infected
infected_neighbors = self.get_neighboring_agents(state_id=1) infected_neighbors = self.get_neighboring_agents(state_id=1)
if len(infected_neighbors) > 0: if len(infected_neighbors) > 0:
if self.random(self.prob_neutral_making_denier): if self.random(self.prob_neutral_making_denier):
self.state['id'] = 3 # Vaccinated making denier self.state["id"] = 3 # Vaccinated making denier
def infected_behaviour(self): def infected_behaviour(self):
@ -176,69 +202,69 @@ class ControlModelM2(BaseAgent):
neutral_neighbors = self.get_neighboring_agents(state_id=0) neutral_neighbors = self.get_neighboring_agents(state_id=0)
for neighbor in neutral_neighbors: for neighbor in neutral_neighbors:
if self.prob(self.prob_infect): if self.prob(self.prob_infect):
neighbor.state['id'] = 1 # Infected neighbor.state["id"] = 1 # Infected
self.state['visible'] = False self.state["visible"] = False
def cured_behaviour(self): def cured_behaviour(self):
self.state['visible'] = True self.state["visible"] = True
# Vaccinate # Vaccinate
neutral_neighbors = self.get_neighboring_agents(state_id=0) neutral_neighbors = self.get_neighboring_agents(state_id=0)
for neighbor in neutral_neighbors: for neighbor in neutral_neighbors:
if self.prob(self.prob_cured_vaccinate_neutral): if self.prob(self.prob_cured_vaccinate_neutral):
neighbor.state['id'] = 3 # Vaccinated neighbor.state["id"] = 3 # Vaccinated
# Cure # Cure
infected_neighbors = self.get_neighboring_agents(state_id=1) infected_neighbors = self.get_neighboring_agents(state_id=1)
for neighbor in infected_neighbors: for neighbor in infected_neighbors:
if self.prob(self.prob_cured_healing_infected): if self.prob(self.prob_cured_healing_infected):
neighbor.state['id'] = 2 # Cured neighbor.state["id"] = 2 # Cured
def vaccinated_behaviour(self): def vaccinated_behaviour(self):
self.state['visible'] = True self.state["visible"] = True
# Cure # Cure
infected_neighbors = self.get_neighboring_agents(state_id=1) infected_neighbors = self.get_neighboring_agents(state_id=1)
for neighbor in infected_neighbors: for neighbor in infected_neighbors:
if self.prob(self.prob_cured_healing_infected): if self.prob(self.prob_cured_healing_infected):
neighbor.state['id'] = 2 # Cured neighbor.state["id"] = 2 # Cured
# Vaccinate # Vaccinate
neutral_neighbors = self.get_neighboring_agents(state_id=0) neutral_neighbors = self.get_neighboring_agents(state_id=0)
for neighbor in neutral_neighbors: for neighbor in neutral_neighbors:
if self.prob(self.prob_cured_vaccinate_neutral): if self.prob(self.prob_cured_vaccinate_neutral):
neighbor.state['id'] = 3 # Vaccinated neighbor.state["id"] = 3 # Vaccinated
# Generate anti-rumor # Generate anti-rumor
infected_neighbors_2 = self.get_neighboring_agents(state_id=1) infected_neighbors_2 = self.get_neighboring_agents(state_id=1)
for neighbor in infected_neighbors_2: for neighbor in infected_neighbors_2:
if self.prob(self.prob_generate_anti_rumor): if self.prob(self.prob_generate_anti_rumor):
neighbor.state['id'] = 2 # Cured neighbor.state["id"] = 2 # Cured
def beacon_off_behaviour(self): def beacon_off_behaviour(self):
self.state['visible'] = False self.state["visible"] = False
infected_neighbors = self.get_neighboring_agents(state_id=1) infected_neighbors = self.get_neighboring_agents(state_id=1)
if len(infected_neighbors) > 0: if len(infected_neighbors) > 0:
self.state['id'] == 5 # Beacon on self.state["id"] == 5 # Beacon on
def beacon_on_behaviour(self): def beacon_on_behaviour(self):
self.state['visible'] = False self.state["visible"] = False
# Cure (M2 feature added) # Cure (M2 feature added)
infected_neighbors = self.get_neighboring_agents(state_id=1) infected_neighbors = self.get_neighboring_agents(state_id=1)
for neighbor in infected_neighbors: for neighbor in infected_neighbors:
if self.prob(self.prob_generate_anti_rumor): if self.prob(self.prob_generate_anti_rumor):
neighbor.state['id'] = 2 # Cured neighbor.state["id"] = 2 # Cured
neutral_neighbors_infected = neighbor.get_neighboring_agents(state_id=0) neutral_neighbors_infected = neighbor.get_neighboring_agents(state_id=0)
for neighbor in neutral_neighbors_infected: for neighbor in neutral_neighbors_infected:
if self.prob(self.prob_generate_anti_rumor): if self.prob(self.prob_generate_anti_rumor):
neighbor.state['id'] = 3 # Vaccinated neighbor.state["id"] = 3 # Vaccinated
infected_neighbors_infected = neighbor.get_neighboring_agents(state_id=1) infected_neighbors_infected = neighbor.get_neighboring_agents(state_id=1)
for neighbor in infected_neighbors_infected: for neighbor in infected_neighbors_infected:
if self.prob(self.prob_generate_anti_rumor): if self.prob(self.prob_generate_anti_rumor):
neighbor.state['id'] = 2 # Cured neighbor.state["id"] = 2 # Cured
# Vaccinate # Vaccinate
neutral_neighbors = self.get_neighboring_agents(state_id=0) neutral_neighbors = self.get_neighboring_agents(state_id=0)
for neighbor in neutral_neighbors: for neighbor in neutral_neighbors:
if self.prob(self.prob_cured_vaccinate_neutral): if self.prob(self.prob_cured_vaccinate_neutral):
neighbor.state['id'] = 3 # Vaccinated neighbor.state["id"] = 3 # Vaccinated

64
soil/agents/SISaModel.py
View File

@ -6,25 +6,25 @@ class SISaModel(FSM):
""" """
Settings: Settings:
neutral_discontent_spon_prob neutral_discontent_spon_prob
neutral_discontent_infected_prob neutral_discontent_infected_prob
neutral_content_spon_prob neutral_content_spon_prob
neutral_content_infected_prob neutral_content_infected_prob
discontent_neutral discontent_neutral
discontent_content discontent_content
variance_d_c variance_d_c
content_discontent content_discontent
variance_c_d variance_c_d
content_neutral content_neutral
standard_variance standard_variance
""" """
@ -33,24 +33,32 @@ class SISaModel(FSM):
random = np.random.default_rng(seed=self._seed) random = np.random.default_rng(seed=self._seed)
self.neutral_discontent_spon_prob = random.normal(self.env['neutral_discontent_spon_prob'], self.neutral_discontent_spon_prob = random.normal(
self.env['standard_variance']) self.env["neutral_discontent_spon_prob"], self.env["standard_variance"]
self.neutral_discontent_infected_prob = random.normal(self.env['neutral_discontent_infected_prob'], )
self.env['standard_variance']) self.neutral_discontent_infected_prob = random.normal(
self.neutral_content_spon_prob = random.normal(self.env['neutral_content_spon_prob'], self.env["neutral_discontent_infected_prob"], self.env["standard_variance"]
self.env['standard_variance']) )
self.neutral_content_infected_prob = random.normal(self.env['neutral_content_infected_prob'], self.neutral_content_spon_prob = random.normal(
self.env['standard_variance']) self.env["neutral_content_spon_prob"], self.env["standard_variance"]
)
self.neutral_content_infected_prob = random.normal(
self.env["neutral_content_infected_prob"], self.env["standard_variance"]
)
self.discontent_neutral = random.normal(self.env['discontent_neutral'], self.discontent_neutral = random.normal(
self.env['standard_variance']) self.env["discontent_neutral"], self.env["standard_variance"]
self.discontent_content = random.normal(self.env['discontent_content'], )
self.env['variance_d_c']) self.discontent_content = random.normal(
self.env["discontent_content"], self.env["variance_d_c"]
)
self.content_discontent = random.normal(self.env['content_discontent'], self.content_discontent = random.normal(
self.env['variance_c_d']) self.env["content_discontent"], self.env["variance_c_d"]
self.content_neutral = random.normal(self.env['content_neutral'], )
self.env['standard_variance']) self.content_neutral = random.normal(
self.env["content_neutral"], self.env["standard_variance"]
)
@state @state
def neutral(self): def neutral(self):
@ -88,7 +96,9 @@ class SISaModel(FSM):
return self.neutral return self.neutral
# Superinfected # Superinfected
discontent_neighbors = self.count_neighboring_agents(state_id=self.discontent.id) discontent_neighbors = self.count_neighboring_agents(
state_id=self.discontent.id
)
if self.prob(scontent_neighbors * self.content_discontent): if self.prob(scontent_neighbors * self.content_discontent):
self.discontent self.discontent
return self.content return self.content

100
soil/agents/SentimentCorrelationModel.py
View File

@ -5,27 +5,31 @@ class SentimentCorrelationModel(BaseAgent):
""" """
Settings: Settings:
outside_effects_prob outside_effects_prob
anger_prob anger_prob
joy_prob joy_prob
sadness_prob sadness_prob
disgust_prob disgust_prob
""" """
def __init__(self, environment, unique_id=0, state=()): def __init__(self, environment, unique_id=0, state=()):
super().__init__(model=environment, unique_id=unique_id, state=state) super().__init__(model=environment, unique_id=unique_id, state=state)
self.outside_effects_prob = environment.environment_params['outside_effects_prob'] self.outside_effects_prob = environment.environment_params[
self.anger_prob = environment.environment_params['anger_prob'] "outside_effects_prob"
self.joy_prob = environment.environment_params['joy_prob'] ]
self.sadness_prob = environment.environment_params['sadness_prob'] self.anger_prob = environment.environment_params["anger_prob"]
self.disgust_prob = environment.environment_params['disgust_prob'] self.joy_prob = environment.environment_params["joy_prob"]
self.state['time_awareness'] = [] self.sadness_prob = environment.environment_params["sadness_prob"]
self.disgust_prob = environment.environment_params["disgust_prob"]
self.state["time_awareness"] = []
for i in range(4): # In this model we have 4 sentiments for i in range(4): # In this model we have 4 sentiments
self.state['time_awareness'].append(0) # 0-> Anger, 1-> joy, 2->sadness, 3 -> disgust self.state["time_awareness"].append(
self.state['sentimentCorrelation'] = 0 0
) # 0-> Anger, 1-> joy, 2->sadness, 3 -> disgust
self.state["sentimentCorrelation"] = 0
def step(self): def step(self):
self.behaviour() self.behaviour()
@ -39,63 +43,73 @@ class SentimentCorrelationModel(BaseAgent):
angry_neighbors = self.get_neighboring_agents(state_id=1) angry_neighbors = self.get_neighboring_agents(state_id=1)
for x in angry_neighbors: for x in angry_neighbors:
if x.state['time_awareness'][0] > (self.env.now-500): if x.state["time_awareness"][0] > (self.env.now - 500):
angry_neighbors_1_time_step.append(x) angry_neighbors_1_time_step.append(x)
num_neighbors_angry = len(angry_neighbors_1_time_step) num_neighbors_angry = len(angry_neighbors_1_time_step)
joyful_neighbors = self.get_neighboring_agents(state_id=2) joyful_neighbors = self.get_neighboring_agents(state_id=2)
for x in joyful_neighbors: for x in joyful_neighbors:
if x.state['time_awareness'][1] > (self.env.now-500): if x.state["time_awareness"][1] > (self.env.now - 500):
joyful_neighbors_1_time_step.append(x) joyful_neighbors_1_time_step.append(x)
num_neighbors_joyful = len(joyful_neighbors_1_time_step) num_neighbors_joyful = len(joyful_neighbors_1_time_step)
sad_neighbors = self.get_neighboring_agents(state_id=3) sad_neighbors = self.get_neighboring_agents(state_id=3)
for x in sad_neighbors: for x in sad_neighbors:
if x.state['time_awareness'][2] > (self.env.now-500): if x.state["time_awareness"][2] > (self.env.now - 500):
sad_neighbors_1_time_step.append(x) sad_neighbors_1_time_step.append(x)
num_neighbors_sad = len(sad_neighbors_1_time_step) num_neighbors_sad = len(sad_neighbors_1_time_step)
disgusted_neighbors = self.get_neighboring_agents(state_id=4) disgusted_neighbors = self.get_neighboring_agents(state_id=4)
for x in disgusted_neighbors: for x in disgusted_neighbors:
if x.state['time_awareness'][3] > (self.env.now-500): if x.state["time_awareness"][3] > (self.env.now - 500):
disgusted_neighbors_1_time_step.append(x) disgusted_neighbors_1_time_step.append(x)
num_neighbors_disgusted = len(disgusted_neighbors_1_time_step) num_neighbors_disgusted = len(disgusted_neighbors_1_time_step)
anger_prob = self.anger_prob+(len(angry_neighbors_1_time_step)*self.anger_prob) anger_prob = self.anger_prob + (
joy_prob = self.joy_prob+(len(joyful_neighbors_1_time_step)*self.joy_prob) len(angry_neighbors_1_time_step) * self.anger_prob
sadness_prob = self.sadness_prob+(len(sad_neighbors_1_time_step)*self.sadness_prob) )
disgust_prob = self.disgust_prob+(len(disgusted_neighbors_1_time_step)*self.disgust_prob) joy_prob = self.joy_prob + (len(joyful_neighbors_1_time_step) * self.joy_prob)
sadness_prob = self.sadness_prob + (
len(sad_neighbors_1_time_step) * self.sadness_prob
)
disgust_prob = self.disgust_prob + (
len(disgusted_neighbors_1_time_step) * self.disgust_prob
)
outside_effects_prob = self.outside_effects_prob outside_effects_prob = self.outside_effects_prob
num = self.random.random() num = self.random.random()
if num<outside_effects_prob: if num < outside_effects_prob:
self.state['id'] = self.random.randint(1, 4) self.state["id"] = self.random.randint(1, 4)
self.state['sentimentCorrelation'] = self.state['id'] # It is stored when it has been infected for the dynamic network self.state["sentimentCorrelation"] = self.state[
self.state['time_awareness'][self.state['id']-1] = self.env.now "id"
self.state['sentiment'] = self.state['id'] ] # It is stored when it has been infected for the dynamic network
self.state["time_awareness"][self.state["id"] - 1] = self.env.now
self.state["sentiment"] = self.state["id"]
if num < anger_prob:
if(num<anger_prob): self.state["id"] = 1
self.state["sentimentCorrelation"] = 1
self.state["time_awareness"][self.state["id"] - 1] = self.env.now
elif num < joy_prob + anger_prob and num > anger_prob:
self.state['id'] = 1 self.state["id"] = 2
self.state['sentimentCorrelation'] = 1 self.state["sentimentCorrelation"] = 2
self.state['time_awareness'][self.state['id']-1] = self.env.now self.state["time_awareness"][self.state["id"] - 1] = self.env.now
elif (num<joy_prob+anger_prob and num>anger_prob): elif num < sadness_prob + anger_prob + joy_prob and num > joy_prob + anger_prob:
self.state['id'] = 2 self.state["id"] = 3
self.state['sentimentCorrelation'] = 2 self.state["sentimentCorrelation"] = 3
self.state['time_awareness'][self.state['id']-1] = self.env.now self.state["time_awareness"][self.state["id"] - 1] = self.env.now
elif (num<sadness_prob+anger_prob+joy_prob and num>joy_prob+anger_prob): elif (
num < disgust_prob + sadness_prob + anger_prob + joy_prob
and num > sadness_prob + anger_prob + joy_prob
):
self.state['id'] = 3 self.state["id"] = 4
self.state['sentimentCorrelation'] = 3 self.state["sentimentCorrelation"] = 4
self.state['time_awareness'][self.state['id']-1] = self.env.now self.state["time_awareness"][self.state["id"] - 1] = self.env.now
elif (num<disgust_prob+sadness_prob+anger_prob+joy_prob and num>sadness_prob+anger_prob+joy_prob):
self.state['id'] = 4 self.state["sentiment"] = self.state["id"]
self.state['sentimentCorrelation'] = 4
self.state['time_awareness'][self.state['id']-1] = self.env.now
self.state['sentiment'] = self.state['id']

330
soil/agents/__init__.py
View File

@ -20,13 +20,13 @@ from typing import Dict, List
from .. import serialization, utils, time, config from .. import serialization, utils, time, config
def as_node(agent): def as_node(agent):
if isinstance(agent, BaseAgent): if isinstance(agent, BaseAgent):
return agent.id return agent.id
return agent return agent
IGNORED_FIELDS = ('model', 'logger')
IGNORED_FIELDS = ("model", "logger")
class DeadAgent(Exception): class DeadAgent(Exception):
@ -43,13 +43,18 @@ class MetaAgent(ABCMeta):
defaults.update(i._defaults) defaults.update(i._defaults)
new_nmspc = { new_nmspc = {
'_defaults': defaults, "_defaults": defaults,
} }
for attr, func in namespace.items(): for attr, func in namespace.items():
if isinstance(func, types.FunctionType) or isinstance(func, property) or isinstance(func, classmethod) or attr[0] == '_': if (
isinstance(func, types.FunctionType)
or isinstance(func, property)
or isinstance(func, classmethod)
or attr[0] == "_"
):
new_nmspc[attr] = func new_nmspc[attr] = func
elif attr == 'defaults': elif attr == "defaults":
defaults.update(func) defaults.update(func)
else: else:
defaults[attr] = copy(func) defaults[attr] = copy(func)
@ -69,12 +74,7 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
Any attribute that is not preceded by an underscore (`_`) will also be added to its state. Any attribute that is not preceded by an underscore (`_`) will also be added to its state.
""" """
def __init__(self, def __init__(self, unique_id, model, name=None, interval=None, **kwargs):
unique_id,
model,
name=None,
interval=None,
**kwargs):
# Check for REQUIRED arguments # Check for REQUIRED arguments
# Initialize agent parameters # Initialize agent parameters
if isinstance(unique_id, MesaAgent): if isinstance(unique_id, MesaAgent):
@ -82,16 +82,19 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
assert isinstance(unique_id, int) assert isinstance(unique_id, int)
super().__init__(unique_id=unique_id, model=model) super().__init__(unique_id=unique_id, model=model)
self.name = str(name) if name else'{}[{}]'.format(type(self).__name__, self.unique_id) self.name = (
str(name) if name else "{}[{}]".format(type(self).__name__, self.unique_id)
)
self.alive = True self.alive = True
self.interval = interval or self.get('interval', 1) self.interval = interval or self.get("interval", 1)
logger = utils.logger.getChild(getattr(self.model, 'id', self.model)).getChild(self.name) logger = utils.logger.getChild(getattr(self.model, "id", self.model)).getChild(
self.logger = logging.LoggerAdapter(logger, {'agent_name': self.name}) self.name
)
self.logger = logging.LoggerAdapter(logger, {"agent_name": self.name})
if hasattr(self, 'level'): if hasattr(self, "level"):
self.logger.setLevel(self.level) self.logger.setLevel(self.level)
for (k, v) in self._defaults.items(): for (k, v) in self._defaults.items():
@ -117,20 +120,22 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
def from_dict(cls, model, attrs, warn_extra=True): def from_dict(cls, model, attrs, warn_extra=True):
ignored = {} ignored = {}
args = {} args = {}
for k, v in attrs.items(): for k, v in attrs.items():
if k in inspect.signature(cls).parameters: if k in inspect.signature(cls).parameters:
args[k] = v args[k] = v
else: else:
ignored[k] = v ignored[k] = v
if ignored and warn_extra: if ignored and warn_extra:
utils.logger.info(f'Ignoring the following arguments for agent class { agent_class.__name__ }: { ignored }') utils.logger.info(
f"Ignoring the following arguments for agent class { agent_class.__name__ }: { ignored }"
)
return cls(model=model, **args) return cls(model=model, **args)
def __getitem__(self, key): def __getitem__(self, key):
try: try:
return getattr(self, key) return getattr(self, key)
except AttributeError: except AttributeError:
raise KeyError(f'key {key} not found in agent') raise KeyError(f"key {key} not found in agent")
def __delitem__(self, key): def __delitem__(self, key):
return delattr(self, key) return delattr(self, key)
@ -148,7 +153,7 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
return self.items() return self.items()
def keys(self): def keys(self):
return (k for k in self.__dict__ if k[0] != '_' and k not in IGNORED_FIELDS) return (k for k in self.__dict__ if k[0] != "_" and k not in IGNORED_FIELDS)
def items(self, keys=None, skip=None): def items(self, keys=None, skip=None):
keys = keys if keys is not None else self.keys() keys = keys if keys is not None else self.keys()
@ -156,7 +161,7 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
if skip: if skip:
return filter(lambda x: x[0] not in skip, it) return filter(lambda x: x[0] not in skip, it)
return it return it
def get(self, key, default=None): def get(self, key, default=None):
return self[key] if key in self else default return self[key] if key in self else default
@ -169,7 +174,7 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
return None return None
def die(self): def die(self):
self.info(f'agent dying') self.info(f"agent dying")
self.alive = False self.alive = False
return time.NEVER return time.NEVER
@ -186,9 +191,9 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
for k, v in kwargs: for k, v in kwargs:
message += " {k}={v} ".format(k, v) message += " {k}={v} ".format(k, v)
extra = {} extra = {}
extra['now'] = self.now extra["now"] = self.now
extra['unique_id'] = self.unique_id extra["unique_id"] = self.unique_id
extra['agent_name'] = self.name extra["agent_name"] = self.name
return self.logger.log(level, message, extra=extra) return self.logger.log(level, message, extra=extra)
def debug(self, *args, **kwargs): def debug(self, *args, **kwargs):
@ -214,10 +219,10 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
content = dict(self.items(keys=keys)) content = dict(self.items(keys=keys))
if pretty and content: if pretty and content:
d = content d = content
content = '\n' content = "\n"
for k, v in d.items(): for k, v in d.items():
content += f'- {k}: {v}\n' content += f"- {k}: {v}\n"
content = textwrap.indent(content, ' ') content = textwrap.indent(content, " ")
return f"{repr(self)}{content}" return f"{repr(self)}{content}"
def __repr__(self): def __repr__(self):
@ -225,7 +230,6 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
class NetworkAgent(BaseAgent): class NetworkAgent(BaseAgent):
def __init__(self, *args, topology, node_id, **kwargs): def __init__(self, *args, topology, node_id, **kwargs):
super().__init__(*args, **kwargs) super().__init__(*args, **kwargs)
@ -248,18 +252,21 @@ class NetworkAgent(BaseAgent):
def node(self): def node(self):
return self.topology.nodes[self.node_id] return self.topology.nodes[self.node_id]
def iter_agents(self, unique_id=None, *, limit_neighbors=False, **kwargs): def iter_agents(self, unique_id=None, *, limit_neighbors=False, **kwargs):
unique_ids = None unique_ids = None
if isinstance(unique_id, list): if isinstance(unique_id, list):
unique_ids = set(unique_id) unique_ids = set(unique_id)
elif unique_id is not None: elif unique_id is not None:
unique_ids = set([unique_id,]) unique_ids = set(
[
unique_id,
]
)
if limit_neighbors: if limit_neighbors:
neighbor_ids = set() neighbor_ids = set()
for node_id in self.G.neighbors(self.node_id): for node_id in self.G.neighbors(self.node_id):
if self.G.nodes[node_id].get('agent') is not None: if self.G.nodes[node_id].get("agent") is not None:
neighbor_ids.add(node_id) neighbor_ids.add(node_id)
if unique_ids: if unique_ids:
unique_ids = unique_ids & neighbor_ids unique_ids = unique_ids & neighbor_ids
@ -272,7 +279,9 @@ class NetworkAgent(BaseAgent):
def subgraph(self, center=True, **kwargs): def subgraph(self, center=True, **kwargs):
include = [self] if center else [] include = [self] if center else []
G = self.G.subgraph(n.node_id for n in list(self.get_agents(**kwargs)+include)) G = self.G.subgraph(
n.node_id for n in list(self.get_agents(**kwargs) + include)
)
return G return G
def remove_node(self): def remove_node(self):
@ -280,11 +289,19 @@ class NetworkAgent(BaseAgent):
def add_edge(self, other, edge_attr_dict=None, *edge_attrs): def add_edge(self, other, edge_attr_dict=None, *edge_attrs):
if self.node_id not in self.G.nodes(data=False): if self.node_id not in self.G.nodes(data=False):
raise ValueError('{} not in list of existing agents in the network'.format(self.unique_id)) raise ValueError(
"{} not in list of existing agents in the network".format(
self.unique_id
)
)
if other.node_id not in self.G.nodes(data=False): if other.node_id not in self.G.nodes(data=False):
raise ValueError('{} not in list of existing agents in the network'.format(other)) raise ValueError(
"{} not in list of existing agents in the network".format(other)
)
self.G.add_edge(self.node_id, other.node_id, edge_attr_dict=edge_attr_dict, *edge_attrs) self.G.add_edge(
self.node_id, other.node_id, edge_attr_dict=edge_attr_dict, *edge_attrs
)
def die(self, remove=True): def die(self, remove=True):
if remove: if remove:
@ -294,11 +311,11 @@ class NetworkAgent(BaseAgent):
def state(name=None): def state(name=None):
def decorator(func, name=None): def decorator(func, name=None):
''' """
A state function should return either a state id, or a tuple (state_id, when) A state function should return either a state id, or a tuple (state_id, when)
The default value for state_id is the current state id. The default value for state_id is the current state id.
The default value for when is the interval defined in the environment. The default value for when is the interval defined in the environment.
''' """
if inspect.isgeneratorfunction(func): if inspect.isgeneratorfunction(func):
orig_func = func orig_func = func
@ -348,32 +365,38 @@ class MetaFSM(MetaAgent):
# Add new states # Add new states
for attr, func in namespace.items(): for attr, func in namespace.items():
if hasattr(func, 'id'): if hasattr(func, "id"):
if func.is_default: if func.is_default:
default_state = func default_state = func
states[func.id] = func states[func.id] = func
namespace.update({ namespace.update(
'_default_state': default_state, {
'_states': states, "_default_state": default_state,
}) "_states": states,
}
)
return super(MetaFSM, mcls).__new__(mcls=mcls, name=name, bases=bases, namespace=namespace) return super(MetaFSM, mcls).__new__(
mcls=mcls, name=name, bases=bases, namespace=namespace
)
class FSM(BaseAgent, metaclass=MetaFSM): class FSM(BaseAgent, metaclass=MetaFSM):
def __init__(self, *args, **kwargs): def __init__(self, *args, **kwargs):
super(FSM, self).__init__(*args, **kwargs) super(FSM, self).__init__(*args, **kwargs)
if not hasattr(self, 'state_id'): if not hasattr(self, "state_id"):
if not self._default_state: if not self._default_state:
raise ValueError('No default state specified for {}'.format(self.unique_id)) raise ValueError(
"No default state specified for {}".format(self.unique_id)
)
self.state_id = self._default_state.id self.state_id = self._default_state.id
self._coroutine = None self._coroutine = None
self.set_state(self.state_id) self.set_state(self.state_id)
def step(self): def step(self):
self.debug(f'Agent {self.unique_id} @ state {self.state_id}') self.debug(f"Agent {self.unique_id} @ state {self.state_id}")
default_interval = super().step() default_interval = super().step()
next_state = self._states[self.state_id](self) next_state = self._states[self.state_id](self)
@ -386,7 +409,9 @@ class FSM(BaseAgent, metaclass=MetaFSM):
elif len(when) == 1: elif len(when) == 1:
when = when[0] when = when[0]
else: else:
raise ValueError('Too many values returned. Only state (and time) allowed') raise ValueError(
"Too many values returned. Only state (and time) allowed"
)
except TypeError: except TypeError:
pass pass
@ -396,10 +421,10 @@ class FSM(BaseAgent, metaclass=MetaFSM):
return when or default_interval return when or default_interval
def set_state(self, state, when=None): def set_state(self, state, when=None):
if hasattr(state, 'id'): if hasattr(state, "id"):
state = state.id state = state.id
if state not in self._states: if state not in self._states:
raise ValueError('{} is not a valid state'.format(state)) raise ValueError("{} is not a valid state".format(state))
self.state_id = state self.state_id = state
if when is not None: if when is not None:
self.model.schedule.add(self, when=when) self.model.schedule.add(self, when=when)
@ -414,23 +439,22 @@ class FSM(BaseAgent, metaclass=MetaFSM):
def prob(prob, random): def prob(prob, random):
''' """
A true/False uniform distribution with a given probability. A true/False uniform distribution with a given probability.
To be used like this: To be used like this:
.. code-block:: python .. code-block:: python
if prob(0.3): if prob(0.3):
do_something() do_something()
''' """
r = random.random() r = random.random()
return r < prob return r < prob
def calculate_distribution(network_agents=None, def calculate_distribution(network_agents=None, agent_class=None):
agent_class=None): """
'''
Calculate the threshold values (thresholds for a uniform distribution) Calculate the threshold values (thresholds for a uniform distribution)
of an agent distribution given the weights of each agent type. of an agent distribution given the weights of each agent type.
@ -453,26 +477,28 @@ def calculate_distribution(network_agents=None,
In this example, 20% of the nodes will be marked as type In this example, 20% of the nodes will be marked as type
'agent_class_1'. 'agent_class_1'.
''' """
if network_agents: if network_agents:
network_agents = [deepcopy(agent) for agent in network_agents if not hasattr(agent, 'id')] network_agents = [
deepcopy(agent) for agent in network_agents if not hasattr(agent, "id")
]
elif agent_class: elif agent_class:
network_agents = [{'agent_class': agent_class}] network_agents = [{"agent_class": agent_class}]
else: else:
raise ValueError('Specify a distribution or a default agent type') raise ValueError("Specify a distribution or a default agent type")
# Fix missing weights and incompatible types # Fix missing weights and incompatible types
for x in network_agents: for x in network_agents:
x['weight'] = float(x.get('weight', 1)) x["weight"] = float(x.get("weight", 1))
# Calculate the thresholds # Calculate the thresholds
total = sum(x['weight'] for x in network_agents) total = sum(x["weight"] for x in network_agents)
acc = 0 acc = 0
for v in network_agents: for v in network_agents:
if 'ids' in v: if "ids" in v:
continue continue
upper = acc + (v['weight']/total) upper = acc + (v["weight"] / total)
v['threshold'] = [acc, upper] v["threshold"] = [acc, upper]
acc = upper acc = upper
return network_agents return network_agents
@ -480,28 +506,29 @@ def calculate_distribution(network_agents=None,
def serialize_type(agent_class, known_modules=[], **kwargs): def serialize_type(agent_class, known_modules=[], **kwargs):
if isinstance(agent_class, str): if isinstance(agent_class, str):
return agent_class return agent_class
known_modules += ['soil.agents'] known_modules += ["soil.agents"]
return serialization.serialize(agent_class, known_modules=known_modules, **kwargs)[1] # Get the name of the class return serialization.serialize(agent_class, known_modules=known_modules, **kwargs)[
1
] # Get the name of the class
def serialize_definition(network_agents, known_modules=[]): def serialize_definition(network_agents, known_modules=[]):
''' """
When serializing an agent distribution, remove the thresholds, in order When serializing an agent distribution, remove the thresholds, in order
to avoid cluttering the YAML definition file. to avoid cluttering the YAML definition file.
''' """
d = deepcopy(list(network_agents)) d = deepcopy(list(network_agents))
for v in d: for v in d:
if 'threshold' in v: if "threshold" in v:
del v['threshold'] del v["threshold"]
v['agent_class'] = serialize_type(v['agent_class'], v["agent_class"] = serialize_type(v["agent_class"], known_modules=known_modules)
known_modules=known_modules)
return d return d
def deserialize_type(agent_class, known_modules=[]): def deserialize_type(agent_class, known_modules=[]):
if not isinstance(agent_class, str): if not isinstance(agent_class, str):
return agent_class return agent_class
known = known_modules + ['soil.agents', 'soil.agents.custom' ] known = known_modules + ["soil.agents", "soil.agents.custom"]
agent_class = serialization.deserializer(agent_class, known_modules=known) agent_class = serialization.deserializer(agent_class, known_modules=known)
return agent_class return agent_class
@ -509,12 +536,12 @@ def deserialize_type(agent_class, known_modules=[]):
def deserialize_definition(ind, **kwargs): def deserialize_definition(ind, **kwargs):
d = deepcopy(ind) d = deepcopy(ind)
for v in d: for v in d:
v['agent_class'] = deserialize_type(v['agent_class'], **kwargs) v["agent_class"] = deserialize_type(v["agent_class"], **kwargs)
return d return d
def _validate_states(states, topology): def _validate_states(states, topology):
'''Validate states to avoid ignoring states during initialization''' """Validate states to avoid ignoring states during initialization"""
states = states or [] states = states or []
if isinstance(states, dict): if isinstance(states, dict):
for x in states: for x in states:
@ -525,7 +552,7 @@ def _validate_states(states, topology):
def _convert_agent_classs(ind, to_string=False, **kwargs): def _convert_agent_classs(ind, to_string=False, **kwargs):
'''Convenience method to allow specifying agents by class or class name.''' """Convenience method to allow specifying agents by class or class name."""
if to_string: if to_string:
return serialize_definition(ind, **kwargs) return serialize_definition(ind, **kwargs)
return deserialize_definition(ind, **kwargs) return deserialize_definition(ind, **kwargs)
@ -609,12 +636,10 @@ def _convert_agent_classs(ind, to_string=False, **kwargs):
class AgentView(Mapping, Set): class AgentView(Mapping, Set):
"""A lazy-loaded list of agents. """A lazy-loaded list of agents."""
"""
__slots__ = ("_agents",) __slots__ = ("_agents",)
def __init__(self, agents): def __init__(self, agents):
self._agents = agents self._agents = agents
@ -657,11 +682,20 @@ class AgentView(Mapping, Set):
return f"{self.__class__.__name__}({self})" return f"{self.__class__.__name__}({self})"
def filter_agents(agents, *id_args, unique_id=None, state_id=None, agent_class=None, ignore=None, state=None, def filter_agents(
limit=None, **kwargs): agents,
''' *id_args,
unique_id=None,
state_id=None,
agent_class=None,
ignore=None,
state=None,
limit=None,
**kwargs,
):
"""
Filter agents given as a dict, by the criteria given as arguments (e.g., certain type or state id). Filter agents given as a dict, by the criteria given as arguments (e.g., certain type or state id).
''' """
assert isinstance(agents, dict) assert isinstance(agents, dict)
ids = [] ids = []
@ -694,7 +728,7 @@ def filter_agents(agents, *id_args, unique_id=None, state_id=None, agent_class=N
f = filter(lambda x: x not in ignore, f) f = filter(lambda x: x not in ignore, f)
if state_id is not None: if state_id is not None:
f = filter(lambda agent: agent.get('state_id', None) in state_id, f) f = filter(lambda agent: agent.get("state_id", None) in state_id, f)
if agent_class is not None: if agent_class is not None:
f = filter(lambda agent: isinstance(agent, agent_class), f) f = filter(lambda agent: isinstance(agent, agent_class), f)
@ -711,23 +745,25 @@ def filter_agents(agents, *id_args, unique_id=None, state_id=None, agent_class=N
yield from f yield from f
def from_config(cfg: config.AgentConfig, random, topology: nx.Graph = None) -> List[Dict[str, Any]]: def from_config(
''' cfg: config.AgentConfig, random, topology: nx.Graph = None
) -> List[Dict[str, Any]]:
"""
This function turns an agentconfig into a list of individual "agent specifications", which are just a dictionary This function turns an agentconfig into a list of individual "agent specifications", which are just a dictionary
with the parameters that the environment will use to construct each agent. with the parameters that the environment will use to construct each agent.
This function does NOT return a list of agents, mostly because some attributes to the agent are not known at the This function does NOT return a list of agents, mostly because some attributes to the agent are not known at the
time of calling this function, such as `unique_id`. time of calling this function, such as `unique_id`.
''' """
default = cfg or config.AgentConfig() default = cfg or config.AgentConfig()
if not isinstance(cfg, config.AgentConfig): if not isinstance(cfg, config.AgentConfig):
cfg = config.AgentConfig(**cfg) cfg = config.AgentConfig(**cfg)
return _agents_from_config(cfg, topology=topology, random=random) return _agents_from_config(cfg, topology=topology, random=random)
def _agents_from_config(cfg: config.AgentConfig, def _agents_from_config(
topology: nx.Graph, cfg: config.AgentConfig, topology: nx.Graph, random
random) -> List[Dict[str, Any]]: ) -> List[Dict[str, Any]]:
if cfg and not isinstance(cfg, config.AgentConfig): if cfg and not isinstance(cfg, config.AgentConfig):
cfg = config.AgentConfig(**cfg) cfg = config.AgentConfig(**cfg)
@ -737,7 +773,9 @@ def _agents_from_config(cfg: config.AgentConfig,
assigned_network = 0 assigned_network = 0
if cfg.fixed is not None: if cfg.fixed is not None:
agents, assigned_total, assigned_network = _from_fixed(cfg.fixed, topology=cfg.topology, default=cfg) agents, assigned_total, assigned_network = _from_fixed(
cfg.fixed, topology=cfg.topology, default=cfg
)
n = cfg.n n = cfg.n
@ -749,46 +787,56 @@ def _agents_from_config(cfg: config.AgentConfig,
for d in cfg.distribution: for d in cfg.distribution:
if d.strategy == config.Strategy.topology: if d.strategy == config.Strategy.topology:
topo = d.topology if ('topology' in d.__fields_set__) else cfg.topology topo = d.topology if ("topology" in d.__fields_set__) else cfg.topology
if not topo: if not topo:
raise ValueError('The "topology" strategy only works if the topology parameter is set to True') raise ValueError(
'The "topology" strategy only works if the topology parameter is set to True'
)
if not topo_size: if not topo_size:
raise ValueError(f'Topology does not have enough free nodes to assign one to the agent') raise ValueError(
f"Topology does not have enough free nodes to assign one to the agent"
)
networked.append(d) networked.append(d)
if d.strategy == config.Strategy.total: if d.strategy == config.Strategy.total:
if not cfg.n: if not cfg.n:
raise ValueError('Cannot use the "total" strategy without providing the total number of agents') raise ValueError(
'Cannot use the "total" strategy without providing the total number of agents'
)
total.append(d) total.append(d)
if networked: if networked:
new_agents = _from_distro(networked, new_agents = _from_distro(
n= topo_size - assigned_network, networked,
topology=topo, n=topo_size - assigned_network,
default=cfg, topology=topo,
random=random) default=cfg,
random=random,
)
assigned_total += len(new_agents) assigned_total += len(new_agents)
assigned_network += len(new_agents) assigned_network += len(new_agents)
agents += new_agents agents += new_agents
if total: if total:
remaining = n - assigned_total remaining = n - assigned_total
agents += _from_distro(total, n=remaining, agents += _from_distro(total, n=remaining, default=cfg, random=random)
default=cfg,
random=random)
if assigned_network < topo_size: if assigned_network < topo_size:
utils.logger.warn(f'The total number of agents does not match the total number of nodes in ' utils.logger.warn(
'every topology. This may be due to a definition error: assigned: ' f"The total number of agents does not match the total number of nodes in "
f'{ assigned } total size: { topo_size }') "every topology. This may be due to a definition error: assigned: "
f"{ assigned } total size: { topo_size }"
)
return agents return agents
def _from_fixed(lst: List[config.FixedAgentConfig], topology: bool, default: config.SingleAgentConfig) -> List[Dict[str, Any]]: def _from_fixed(
lst: List[config.FixedAgentConfig],
topology: bool,
default: config.SingleAgentConfig,
) -> List[Dict[str, Any]]:
agents = [] agents = []
counts_total = 0 counts_total = 0
@ -799,12 +847,18 @@ def _from_fixed(lst: List[config.FixedAgentConfig], topology: bool, default: con
if default: if default:
agent = default.state.copy() agent = default.state.copy()
agent.update(fixed.state) agent.update(fixed.state)
cls = serialization.deserialize(fixed.agent_class or (default and default.agent_class)) cls = serialization.deserialize(
agent['agent_class'] = cls fixed.agent_class or (default and default.agent_class)
topo = fixed.topology if ('topology' in fixed.__fields_set__) else topology or default.topology )
agent["agent_class"] = cls
topo = (
fixed.topology
if ("topology" in fixed.__fields_set__)
else topology or default.topology
)
if topo: if topo:
agent['topology'] = True agent["topology"] = True
counts_network += 1 counts_network += 1
if not fixed.hidden: if not fixed.hidden:
counts_total += 1 counts_total += 1
@ -813,17 +867,21 @@ def _from_fixed(lst: List[config.FixedAgentConfig], topology: bool, default: con
return agents, counts_total, counts_network return agents, counts_total, counts_network
def _from_distro(distro: List[config.AgentDistro], def _from_distro(
n: int, distro: List[config.AgentDistro],
topology: str, n: int,
default: config.SingleAgentConfig, topology: str,
random) -> List[Dict[str, Any]]: default: config.SingleAgentConfig,
random,
) -> List[Dict[str, Any]]:
agents = [] agents = []
if n is None: if n is None:
if any(lambda dist: dist.n is None, distro): if any(lambda dist: dist.n is None, distro):
raise ValueError('You must provide a total number of agents, or the number of each type') raise ValueError(
"You must provide a total number of agents, or the number of each type"
)
n = sum(dist.n for dist in distro) n = sum(dist.n for dist in distro)
weights = list(dist.weight if dist.weight is not None else 1 for dist in distro) weights = list(dist.weight if dist.weight is not None else 1 for dist in distro)
@ -836,29 +894,40 @@ def _from_distro(distro: List[config.AgentDistro],
# So instead we calculate our own distribution to make sure the actual ratios are close to what we would expect # So instead we calculate our own distribution to make sure the actual ratios are close to what we would expect
# Calculate how many times each has to appear # Calculate how many times each has to appear
indices = list(chain.from_iterable([idx] * int(n*chunk) for (idx, n) in enumerate(norm))) indices = list(
chain.from_iterable([idx] * int(n * chunk) for (idx, n) in enumerate(norm))
)
# Complete with random agents following the original weight distribution # Complete with random agents following the original weight distribution
if len(indices) < n: if len(indices) < n:
indices += random.choices(list(range(len(distro))), weights=[d.weight for d in distro], k=n-len(indices)) indices += random.choices(
list(range(len(distro))),
weights=[d.weight for d in distro],
k=n - len(indices),
)
# Deserialize classes for efficiency # Deserialize classes for efficiency
classes = list(serialization.deserialize(i.agent_class or default.agent_class) for i in distro) classes = list(
serialization.deserialize(i.agent_class or default.agent_class) for i in distro
)
# Add them in random order # Add them in random order
random.shuffle(indices) random.shuffle(indices)
for idx in indices: for idx in indices:
d = distro[idx] d = distro[idx]
agent = d.state.copy() agent = d.state.copy()
cls = classes[idx] cls = classes[idx]
agent['agent_class'] = cls agent["agent_class"] = cls
if default: if default:
agent.update(default.state) agent.update(default.state)
topology = d.topology if ('topology' in d.__fields_set__) else topology or default.topology topology = (
d.topology
if ("topology" in d.__fields_set__)
else topology or default.topology
)
if topology: if topology:
agent['topology'] = topology agent["topology"] = topology
agents.append(agent) agents.append(agent)
return agents return agents
@ -877,4 +946,5 @@ try:
from .Geo import Geo from .Geo import Geo
except ImportError: except ImportError:
import sys import sys
print('Could not load the Geo Agent, scipy is not installed', file=sys.stderr)
print("Could not load the Geo Agent, scipy is not installed", file=sys.stderr)

169
soil/config.py
View File

@ -19,6 +19,7 @@ import networkx as nx
# Could use TypeAlias in python >= 3.10 # Could use TypeAlias in python >= 3.10
nodeId = int nodeId = int
class Node(BaseModel): class Node(BaseModel):
id: nodeId id: nodeId
state: Optional[Dict[str, Any]] = {} state: Optional[Dict[str, Any]] = {}
@ -38,7 +39,7 @@ class Topology(BaseModel):
class NetParams(BaseModel, extra=Extra.allow): class NetParams(BaseModel, extra=Extra.allow):
generator: Union[Callable, str] generator: Union[Callable, str]
n: int n: int
class NetConfig(BaseModel): class NetConfig(BaseModel):
@ -54,14 +55,15 @@ class NetConfig(BaseModel):
return NetConfig(topology=None, params=None) return NetConfig(topology=None, params=None)
@root_validator @root_validator
def validate_all(cls, values): def validate_all(cls, values):
if 'params' not in values and 'topology' not in values: if "params" not in values and "topology" not in values:
raise ValueError('You must specify either a topology or the parameters to generate a graph') raise ValueError(
"You must specify either a topology or the parameters to generate a graph"
)
return values return values
class EnvConfig(BaseModel): class EnvConfig(BaseModel):
@staticmethod @staticmethod
def default(): def default():
return EnvConfig() return EnvConfig()
@ -80,9 +82,11 @@ class FixedAgentConfig(SingleAgentConfig):
hidden: Optional[bool] = False # Do not count this agent towards total agent count hidden: Optional[bool] = False # Do not count this agent towards total agent count
@root_validator @root_validator
def validate_all(cls, values): def validate_all(cls, values):
if values.get('unique_id', None) is not None and values.get('n', 1) > 1: if values.get("unique_id", None) is not None and values.get("n", 1) > 1:
raise ValueError(f"An unique_id can only be provided when there is only one agent ({values.get('n')} given)") raise ValueError(
f"An unique_id can only be provided when there is only one agent ({values.get('n')} given)"
)
return values return values
@ -91,8 +95,8 @@ class OverrideAgentConfig(FixedAgentConfig):
class Strategy(Enum): class Strategy(Enum):
topology = 'topology' topology = "topology"
total = 'total' total = "total"
class AgentDistro(SingleAgentConfig): class AgentDistro(SingleAgentConfig):
@ -111,16 +115,20 @@ class AgentConfig(SingleAgentConfig):
return AgentConfig() return AgentConfig()
@root_validator @root_validator
def validate_all(cls, values): def validate_all(cls, values):
if 'distribution' in values and ('n' not in values and 'topology' not in values): if "distribution" in values and (
raise ValueError("You need to provide the number of agents or a topology to extract the value from.") "n" not in values and "topology" not in values
):
raise ValueError(
"You need to provide the number of agents or a topology to extract the value from."
)
return values return values
class Config(BaseModel, extra=Extra.allow): class Config(BaseModel, extra=Extra.allow):
version: Optional[str] = '1' version: Optional[str] = "1"
name: str = 'Unnamed Simulation' name: str = "Unnamed Simulation"
description: Optional[str] = None description: Optional[str] = None
group: str = None group: str = None
dir_path: Optional[str] = None dir_path: Optional[str] = None
@ -140,45 +148,48 @@ class Config(BaseModel, extra=Extra.allow):
def from_raw(cls, cfg): def from_raw(cls, cfg):
if isinstance(cfg, Config): if isinstance(cfg, Config):
return cfg return cfg
if cfg.get('version', '1') == '1' and any(k in cfg for k in ['agents', 'agent_class', 'topology', 'environment_class']): if cfg.get("version", "1") == "1" and any(
k in cfg for k in ["agents", "agent_class", "topology", "environment_class"]
):
return convert_old(cfg) return convert_old(cfg)
return Config(**cfg) return Config(**cfg)
def convert_old(old, strict=True): def convert_old(old, strict=True):
''' """
Try to convert old style configs into the new format. Try to convert old style configs into the new format.
This is still a work in progress and might not work in many cases. This is still a work in progress and might not work in many cases.
''' """
utils.logger.warning('The old configuration format is deprecated. The converted file MAY NOT yield the right results') utils.logger.warning(
"The old configuration format is deprecated. The converted file MAY NOT yield the right results"
)
new = old.copy() new = old.copy()
network = {} network = {}
if 'topology' in old: if "topology" in old:
del new['topology'] del new["topology"]
network['topology'] = old['topology'] network["topology"] = old["topology"]
if 'network_params' in old and old['network_params']: if "network_params" in old and old["network_params"]:
del new['network_params'] del new["network_params"]
for (k, v) in old['network_params'].items(): for (k, v) in old["network_params"].items():
if k == 'path': if k == "path":
network['path'] = v network["path"] = v
else: else:
network.setdefault('params', {})[k] = v network.setdefault("params", {})[k] = v
topology = None topology = None
if network: if network:
topology = network topology = network
agents = {"fixed": [], "distribution": []}
agents = {'fixed': [], 'distribution': []}
def updated_agent(agent): def updated_agent(agent):
'''Convert an agent definition''' """Convert an agent definition"""
newagent = dict(agent) newagent = dict(agent)
return newagent return newagent
@ -186,80 +197,74 @@ def convert_old(old, strict=True):
fixed = [] fixed = []
override = [] override = []
if 'environment_agents' in new: if "environment_agents" in new:
for agent in new['environment_agents']: for agent in new["environment_agents"]:
agent.setdefault('state', {})['group'] = 'environment' agent.setdefault("state", {})["group"] = "environment"
if 'agent_id' in agent: if "agent_id" in agent:
agent['state']['name'] = agent['agent_id'] agent["state"]["name"] = agent["agent_id"]
del agent['agent_id'] del agent["agent_id"]
agent['hidden'] = True agent["hidden"] = True
agent['topology'] = False agent["topology"] = False
fixed.append(updated_agent(agent)) fixed.append(updated_agent(agent))
del new['environment_agents'] del new["environment_agents"]
if "agent_class" in old:
del new["agent_class"]
agents["agent_class"] = old["agent_class"]
if 'agent_class' in old: if "default_state" in old:
del new['agent_class'] del new["default_state"]
agents['agent_class'] = old['agent_class'] agents["state"] = old["default_state"]
if 'default_state' in old: if "network_agents" in old:
del new['default_state'] agents["topology"] = True
agents['state'] = old['default_state']
if 'network_agents' in old: agents.setdefault("state", {})["group"] = "network"
agents['topology'] = True
agents.setdefault('state', {})['group'] = 'network' for agent in new["network_agents"]:
for agent in new['network_agents']:
agent = updated_agent(agent) agent = updated_agent(agent)
if 'agent_id' in agent: if "agent_id" in agent:
agent['state']['name'] = agent['agent_id'] agent["state"]["name"] = agent["agent_id"]
del agent['agent_id'] del agent["agent_id"]
fixed.append(agent) fixed.append(agent)
else: else:
by_weight.append(agent) by_weight.append(agent)
del new['network_agents'] del new["network_agents"]
if 'agent_class' in old and (not fixed and not by_weight): if "agent_class" in old and (not fixed and not by_weight):
agents['topology'] = True agents["topology"] = True
by_weight = [{'agent_class': old['agent_class'], 'weight': 1}] by_weight = [{"agent_class": old["agent_class"], "weight": 1}]
# TODO: translate states properly # TODO: translate states properly
if 'states' in old: if "states" in old:
del new['states'] del new["states"]
states = old['states'] states = old["states"]
if isinstance(states, dict): if isinstance(states, dict):
states = states.items() states = states.items()
else: else:
states = enumerate(states) states = enumerate(states)
for (k, v) in states: for (k, v) in states:
override.append({'filter': {'node_id': k}, override.append({"filter": {"node_id": k}, "state": v})
'state': v})
agents['override'] = override
agents['fixed'] = fixed
agents['distribution'] = by_weight
agents["override"] = override
agents["fixed"] = fixed
agents["distribution"] = by_weight
model_params = {} model_params = {}
if 'environment_params' in new: if "environment_params" in new:
del new['environment_params'] del new["environment_params"]
model_params = dict(old['environment_params']) model_params = dict(old["environment_params"])
if 'environment_class' in old: if "environment_class" in old:
del new['environment_class'] del new["environment_class"]
new['model_class'] = old['environment_class'] new["model_class"] = old["environment_class"]
if 'dump' in old: if "dump" in old:
del new['dump'] del new["dump"]
new['dry_run'] = not old['dump'] new["dry_run"] = not old["dump"]
model_params['topology'] = topology model_params["topology"] = topology
model_params['agents'] = agents model_params["agents"] = agents
return Config(version='2', return Config(version="2", model_params=model_params, **new)
model_params=model_params,
**new)

2
soil/datacollection.py
View File

@ -1,6 +1,6 @@
from mesa import DataCollector as MDC from mesa import DataCollector as MDC
class SoilDataCollector(MDC):
class SoilDataCollector(MDC):
def __init__(self, *args, **kwargs): def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs) super().__init__(*args, **kwargs)

79
soil/debugging.py
View File

@ -18,9 +18,9 @@ def wrapcmd(func):
known = globals() known = globals()
known.update(self.curframe.f_globals) known.update(self.curframe.f_globals)
known.update(self.curframe.f_locals) known.update(self.curframe.f_locals)
known['agent'] = known.get('self', None) known["agent"] = known.get("self", None)
known['model'] = known.get('self', {}).get('model') known["model"] = known.get("self", {}).get("model")
known['attrs'] = arg.strip().split() known["attrs"] = arg.strip().split()
exec(func.__code__, known, known) exec(func.__code__, known, known)
@ -29,12 +29,12 @@ def wrapcmd(func):
class Debug(pdb.Pdb): class Debug(pdb.Pdb):
def __init__(self, *args, skip_soil=False, **kwargs): def __init__(self, *args, skip_soil=False, **kwargs):
skip = kwargs.get('skip', []) skip = kwargs.get("skip", [])
skip.append('soil') skip.append("soil")
if skip_soil: if skip_soil:
skip.append('soil') skip.append("soil")
skip.append('soil.*') skip.append("soil.*")
skip.append('mesa.*') skip.append("mesa.*")
super(Debug, self).__init__(*args, skip=skip, **kwargs) super(Debug, self).__init__(*args, skip=skip, **kwargs)
self.prompt = "[soil-pdb] " self.prompt = "[soil-pdb] "
@ -42,7 +42,7 @@ class Debug(pdb.Pdb):
def _soil_agents(model, attrs=None, pretty=True, **kwargs): def _soil_agents(model, attrs=None, pretty=True, **kwargs):
for agent in model.agents(**kwargs): for agent in model.agents(**kwargs):
d = agent d = agent
print(' - ' + indent(agent.to_str(keys=attrs, pretty=pretty), ' ')) print(" - " + indent(agent.to_str(keys=attrs, pretty=pretty), " "))
@wrapcmd @wrapcmd
def do_soil_agents(): def do_soil_agents():
@ -52,20 +52,20 @@ class Debug(pdb.Pdb):
@wrapcmd @wrapcmd
def do_soil_list(): def do_soil_list():
return Debug._soil_agents(model, attrs=['state_id'], pretty=False) return Debug._soil_agents(model, attrs=["state_id"], pretty=False)
do_sl = do_soil_list do_sl = do_soil_list
def do_continue_state(self, arg): def do_continue_state(self, arg):
self.do_break_state(arg, temporary=True) self.do_break_state(arg, temporary=True)
return self.do_continue('') return self.do_continue("")
do_cs = do_continue_state do_cs = do_continue_state
@wrapcmd @wrapcmd
def do_soil_agent(): def do_soil_agent():
if not agent: if not agent:
print('No agent available') print("No agent available")
return return
keys = None keys = None
@ -81,9 +81,9 @@ class Debug(pdb.Pdb):
do_aa = do_soil_agent do_aa = do_soil_agent
def do_break_state(self, arg: str, instances=None, temporary=False): def do_break_state(self, arg: str, instances=None, temporary=False):
''' """
Break before a specified state is stepped into. Break before a specified state is stepped into.
''' """
klass = None klass = None
state = arg state = arg
@ -95,39 +95,39 @@ class Debug(pdb.Pdb):
if tokens: if tokens:
instances = list(eval(token) for token in tokens) instances = list(eval(token) for token in tokens)
colon = state.find(':') colon = state.find(":")
if colon > 0: if colon > 0:
klass = state[:colon].rstrip() klass = state[:colon].rstrip()
state = state[colon+1:].strip() state = state[colon + 1 :].strip()
print(klass, state, tokens) print(klass, state, tokens)
klass = eval(klass, klass = eval(klass, self.curframe.f_globals, self.curframe_locals)
self.curframe.f_globals,
self.curframe_locals)
if klass: if klass:
klasses = [klass] klasses = [klass]
else: else:
klasses = [k for k in self.curframe.f_globals.values() if isinstance(k, type) and issubclass(k, FSM)] klasses = [
k
for k in self.curframe.f_globals.values()
if isinstance(k, type) and issubclass(k, FSM)
]
if not klasses: if not klasses:
self.error('No agent classes found') self.error("No agent classes found")
for klass in klasses: for klass in klasses:
try: try:
func = getattr(klass, state) func = getattr(klass, state)
except AttributeError: except AttributeError:
self.error(f'State {state} not found in class {klass}') self.error(f"State {state} not found in class {klass}")
continue continue
if hasattr(func, '__func__'): if hasattr(func, "__func__"):
func = func.__func__ func = func.__func__
code = func.__code__ code = func.__code__
#use co_name to identify the bkpt (function names # use co_name to identify the bkpt (function names
#could be aliased, but co_name is invariant) # could be aliased, but co_name is invariant)
funcname = code.co_name funcname = code.co_name
lineno = code.co_firstlineno lineno = code.co_firstlineno
filename = code.co_filename filename = code.co_filename
@ -135,38 +135,36 @@ class Debug(pdb.Pdb):
# Check for reasonable breakpoint # Check for reasonable breakpoint
line = self.checkline(filename, lineno) line = self.checkline(filename, lineno)
if not line: if not line:
raise ValueError('no line found') raise ValueError("no line found")
# now set the break point # now set the break point
cond = None cond = None
if instances: if instances:
cond = f'self.unique_id in { repr(instances) }' cond = f"self.unique_id in { repr(instances) }"
existing = self.get_breaks(filename, line) existing = self.get_breaks(filename, line)
if existing: if existing:
self.message("Breakpoint already exists at %s:%d" % self.message("Breakpoint already exists at %s:%d" % (filename, line))
(filename, line))
continue continue
err = self.set_break(filename, line, temporary, cond, funcname) err = self.set_break(filename, line, temporary, cond, funcname)
if err: if err:
self.error(err) self.error(err)
else: else:
bp = self.get_breaks(filename, line)[-1] bp = self.get_breaks(filename, line)[-1]
self.message("Breakpoint %d at %s:%d" % self.message("Breakpoint %d at %s:%d" % (bp.number, bp.file, bp.line))
(bp.number, bp.file, bp.line))
do_bs = do_break_state do_bs = do_break_state
def do_break_state_self(self, arg: str, temporary=False): def do_break_state_self(self, arg: str, temporary=False):
''' """
Break before a specified state is stepped into, for the current agent Break before a specified state is stepped into, for the current agent
''' """
agent = self.curframe.f_locals.get('self') agent = self.curframe.f_locals.get("self")
if not agent: if not agent:
self.error('No current agent.') self.error("No current agent.")
self.error('Try this again when the debugger is stopped inside an agent') self.error("Try this again when the debugger is stopped inside an agent")
return return
arg = f'{agent.__class__.__name__}:{ arg } {agent.unique_id}' arg = f"{agent.__class__.__name__}:{ arg } {agent.unique_id}"
return self.do_break_state(arg) return self.do_break_state(arg)
do_bss = do_break_state_self do_bss = do_break_state_self
@ -174,6 +172,7 @@ class Debug(pdb.Pdb):
debugger = None debugger = None
def set_trace(frame=None, **kwargs): def set_trace(frame=None, **kwargs):
global debugger global debugger
if debugger is None: if debugger is None:

132
soil/environment.py
View File

@ -35,18 +35,20 @@ class BaseEnvironment(Model):
:meth:`soil.environment.Environment.get` method. :meth:`soil.environment.Environment.get` method.
""" """
def __init__(self, def __init__(
id='unnamed_env', self,
seed='default', id="unnamed_env",
schedule=None, seed="default",
dir_path=None, schedule=None,
interval=1, dir_path=None,
agent_class=None, interval=1,
agents: [tuple[type, Dict[str, Any]]] = {}, agent_class=None,
agent_reporters: Optional[Any] = None, agents: [tuple[type, Dict[str, Any]]] = {},
model_reporters: Optional[Any] = None, agent_reporters: Optional[Any] = None,
tables: Optional[Any] = None, model_reporters: Optional[Any] = None,
**env_params): tables: Optional[Any] = None,
**env_params,
):
super().__init__(seed=seed) super().__init__(seed=seed)
self.env_params = env_params or {} self.env_params = env_params or {}
@ -75,27 +77,26 @@ class BaseEnvironment(Model):
) )
def _agent_from_dict(self, agent): def _agent_from_dict(self, agent):
''' """
Translate an agent dictionary into an agent Translate an agent dictionary into an agent
''' """
agent = dict(**agent) agent = dict(**agent)
cls = agent.pop('agent_class', None) or self.agent_class cls = agent.pop("agent_class", None) or self.agent_class
unique_id = agent.pop('unique_id', None) unique_id = agent.pop("unique_id", None)
if unique_id is None: if unique_id is None:
unique_id = self.next_id() unique_id = self.next_id()
return serialization.deserialize(cls)(unique_id=unique_id, return serialization.deserialize(cls)(unique_id=unique_id, model=self, **agent)
model=self, **agent)
def init_agents(self, agents: Union[config.AgentConfig, [Dict[str, Any]]] = {}): def init_agents(self, agents: Union[config.AgentConfig, [Dict[str, Any]]] = {}):
''' """
Initialize the agents in the model from either a `soil.config.AgentConfig` or a list of Initialize the agents in the model from either a `soil.config.AgentConfig` or a list of
dictionaries that each describes an agent. dictionaries that each describes an agent.
If given a list of dictionaries, an agent will be created for each dictionary. The agent If given a list of dictionaries, an agent will be created for each dictionary. The agent
class can be specified through the `agent_class` key. The rest of the items will be used class can be specified through the `agent_class` key. The rest of the items will be used
as parameters to the agent. as parameters to the agent.
''' """
if not agents: if not agents:
return return
@ -108,11 +109,10 @@ class BaseEnvironment(Model):
override = lst.override override = lst.override
lst = self._agent_dict_from_config(lst) lst = self._agent_dict_from_config(lst)
#TODO: check override is working again. It cannot (easily) be part of agents.from_config anymore, # TODO: check override is working again. It cannot (easily) be part of agents.from_config anymore,
# because it needs attribute such as unique_id, which are only present after init # because it needs attribute such as unique_id, which are only present after init
new_agents = [self._agent_from_dict(agent) for agent in lst] new_agents = [self._agent_from_dict(agent) for agent in lst]
for a in new_agents: for a in new_agents:
self.schedule.add(a) self.schedule.add(a)
@ -122,8 +122,7 @@ class BaseEnvironment(Model):
setattr(agent, attr, value) setattr(agent, attr, value)
def _agent_dict_from_config(self, cfg): def _agent_dict_from_config(self, cfg):
return agentmod.from_config(cfg, return agentmod.from_config(cfg, random=self.random)
random=self.random)
@property @property
def agents(self): def agents(self):
@ -131,7 +130,7 @@ class BaseEnvironment(Model):
def find_one(self, *args, **kwargs): def find_one(self, *args, **kwargs):
return agentmod.AgentView(self.schedule._agents).one(*args, **kwargs) return agentmod.AgentView(self.schedule._agents).one(*args, **kwargs)
def count_agents(self, *args, **kwargs): def count_agents(self, *args, **kwargs):
return sum(1 for i in self.agents(*args, **kwargs)) return sum(1 for i in self.agents(*args, **kwargs))
@ -139,18 +138,16 @@ class BaseEnvironment(Model):
def now(self): def now(self):
if self.schedule: if self.schedule:
return self.schedule.time return self.schedule.time
raise Exception('The environment has not been scheduled, so it has no sense of time') raise Exception(
"The environment has not been scheduled, so it has no sense of time"
)
def add_agent(self, agent_class, unique_id=None, **kwargs): def add_agent(self, agent_class, unique_id=None, **kwargs):
a = None a = None
if unique_id is None: if unique_id is None:
unique_id = self.next_id() unique_id = self.next_id()
a = agent_class(model=self, unique_id=unique_id, **args)
a = agent_class(model=self,
unique_id=unique_id,
**args)
self.schedule.add(a) self.schedule.add(a)
return a return a
@ -163,16 +160,16 @@ class BaseEnvironment(Model):
for k, v in kwargs: for k, v in kwargs:
message += " {k}={v} ".format(k, v) message += " {k}={v} ".format(k, v)
extra = {} extra = {}
extra['now'] = self.now extra["now"] = self.now
extra['id'] = self.id extra["id"] = self.id
return self.logger.log(level, message, extra=extra) return self.logger.log(level, message, extra=extra)
def step(self): def step(self):
''' """
Advance one step in the simulation, and update the data collection and scheduler appropriately Advance one step in the simulation, and update the data collection and scheduler appropriately
''' """
super().step() super().step()
self.logger.info(f'--- Step {self.now:^5} ---') self.logger.info(f"--- Step {self.now:^5} ---")
self.schedule.step() self.schedule.step()
self.datacollector.collect(self) self.datacollector.collect(self)
@ -180,10 +177,10 @@ class BaseEnvironment(Model):
return key in self.env_params return key in self.env_params
def get(self, key, default=None): def get(self, key, default=None):
''' """
Get the value of an environment attribute. Get the value of an environment attribute.
Return `default` if the value is not set. Return `default` if the value is not set.
''' """
return self.env_params.get(key, default) return self.env_params.get(key, default)
def __getitem__(self, key): def __getitem__(self, key):
@ -197,13 +194,15 @@ class BaseEnvironment(Model):
class NetworkEnvironment(BaseEnvironment): class NetworkEnvironment(BaseEnvironment):
''' """
The NetworkEnvironment is an environment that includes one or more networkx.Graph intances The NetworkEnvironment is an environment that includes one or more networkx.Graph intances
and methods to associate agents to nodes and vice versa. and methods to associate agents to nodes and vice versa.
''' """
def __init__(self, *args, topology: Union[config.NetConfig, nx.Graph] = None, **kwargs): def __init__(
agents = kwargs.pop('agents', None) self, *args, topology: Union[config.NetConfig, nx.Graph] = None, **kwargs
):
agents = kwargs.pop("agents", None)
super().__init__(*args, agents=None, **kwargs) super().__init__(*args, agents=None, **kwargs)
self._set_topology(topology) self._set_topology(topology)
@ -211,37 +210,35 @@ class NetworkEnvironment(BaseEnvironment):
self.init_agents(agents) self.init_agents(agents)
def init_agents(self, *args, **kwargs): def init_agents(self, *args, **kwargs):
'''Initialize the agents from a ''' """Initialize the agents from a"""
super().init_agents(*args, **kwargs) super().init_agents(*args, **kwargs)
for agent in self.schedule._agents.values(): for agent in self.schedule._agents.values():
if hasattr(agent, 'node_id'): if hasattr(agent, "node_id"):
self._init_node(agent) self._init_node(agent)
def _init_node(self, agent): def _init_node(self, agent):
''' """
Make sure the node for a given agent has the proper attributes. Make sure the node for a given agent has the proper attributes.
''' """
self.G.nodes[agent.node_id]['agent'] = agent self.G.nodes[agent.node_id]["agent"] = agent
def _agent_dict_from_config(self, cfg): def _agent_dict_from_config(self, cfg):
return agentmod.from_config(cfg, return agentmod.from_config(cfg, topology=self.G, random=self.random)
topology=self.G,
random=self.random)
def _agent_from_dict(self, agent, unique_id=None): def _agent_from_dict(self, agent, unique_id=None):
agent = dict(agent) agent = dict(agent)
if not agent.get('topology', False): if not agent.get("topology", False):
return super()._agent_from_dict(agent) return super()._agent_from_dict(agent)
if unique_id is None: if unique_id is None:
unique_id = self.next_id() unique_id = self.next_id()
node_id = agent.get('node_id', None) node_id = agent.get("node_id", None)
if node_id is None: if node_id is None:
node_id = network.find_unassigned(self.G, random=self.random) node_id = network.find_unassigned(self.G, random=self.random)
agent['node_id'] = node_id agent["node_id"] = node_id
agent['unique_id'] = unique_id agent["unique_id"] = unique_id
agent['topology'] = self.G agent["topology"] = self.G
node_attrs = self.G.nodes[node_id] node_attrs = self.G.nodes[node_id]
node_attrs.update(agent) node_attrs.update(agent)
agent = node_attrs agent = node_attrs
@ -269,32 +266,33 @@ class NetworkEnvironment(BaseEnvironment):
if unique_id is None: if unique_id is None:
unique_id = self.next_id() unique_id = self.next_id()
if node_id is None: if node_id is None:
node_id = network.find_unassigned(G=self.G, node_id = network.find_unassigned(
shuffle=True, G=self.G, shuffle=True, random=self.random
random=self.random) )
if node_id in G.nodes: if node_id in G.nodes:
self.G.nodes[node_id]['agent'] = None # Reserve self.G.nodes[node_id]["agent"] = None # Reserve
else: else:
self.G.add_node(node_id) self.G.add_node(node_id)
a = self.add_agent(unique_id=unique_id, agent_class=agent_class, node_id=node_id, **kwargs) a = self.add_agent(
a['visible'] = True unique_id=unique_id, agent_class=agent_class, node_id=node_id, **kwargs
)
a["visible"] = True
return a return a
def agent_for_node_id(self, node_id): def agent_for_node_id(self, node_id):
return self.G.nodes[node_id].get('agent') return self.G.nodes[node_id].get("agent")
def populate_network(self, agent_class, weights=None, **agent_params): def populate_network(self, agent_class, weights=None, **agent_params):
if not hasattr(agent_class, 'len'): if not hasattr(agent_class, "len"):
agent_class = [agent_class] agent_class = [agent_class]
weights = None weights = None
for (node_id, node) in self.G.nodes(data=True): for (node_id, node) in self.G.nodes(data=True):
if 'agent' in node: if "agent" in node:
continue continue
a_class = self.random.choices(agent_class, weights)[0] a_class = self.random.choices(agent_class, weights)[0]
self.add_agent(node_id=node_id, self.add_agent(node_id=node_id, agent_class=a_class, **agent_params)
agent_class=a_class, **agent_params)
Environment = NetworkEnvironment Environment = NetworkEnvironment

127
soil/exporters.py
View File

@ -24,56 +24,58 @@ class DryRunner(BytesIO):
def write(self, txt): def write(self, txt):
if self.__copy_to: if self.__copy_to:
self.__copy_to.write('{}:::{}'.format(self.__fname, txt)) self.__copy_to.write("{}:::{}".format(self.__fname, txt))
try: try:
super().write(txt) super().write(txt)
except TypeError: except TypeError:
super().write(bytes(txt, 'utf-8')) super().write(bytes(txt, "utf-8"))
def close(self): def close(self):
content = '(binary data not shown)' content = "(binary data not shown)"
try: try:
content = self.getvalue().decode() content = self.getvalue().decode()
except UnicodeDecodeError: except UnicodeDecodeError:
pass pass
logger.info('**Not** written to {} (dry run mode):\n\n{}\n\n'.format(self.__fname, content)) logger.info(
"**Not** written to {} (dry run mode):\n\n{}\n\n".format(
self.__fname, content
)
)
super().close() super().close()
class Exporter: class Exporter:
''' """
Interface for all exporters. It is not necessary, but it is useful Interface for all exporters. It is not necessary, but it is useful
if you don't plan to implement all the methods. if you don't plan to implement all the methods.
''' """
def __init__(self, simulation, outdir=None, dry_run=None, copy_to=None): def __init__(self, simulation, outdir=None, dry_run=None, copy_to=None):
self.simulation = simulation self.simulation = simulation
outdir = outdir or os.path.join(os.getcwd(), 'soil_output') outdir = outdir or os.path.join(os.getcwd(), "soil_output")
self.outdir = os.path.join(outdir, self.outdir = os.path.join(outdir, simulation.group or "", simulation.name)
simulation.group or '',
simulation.name)
self.dry_run = dry_run self.dry_run = dry_run
if copy_to is None and dry_run: if copy_to is None and dry_run:
copy_to = sys.stdout copy_to = sys.stdout
self.copy_to = copy_to self.copy_to = copy_to
def sim_start(self): def sim_start(self):
'''Method to call when the simulation starts''' """Method to call when the simulation starts"""
pass pass
def sim_end(self): def sim_end(self):
'''Method to call when the simulation ends''' """Method to call when the simulation ends"""
pass pass
def trial_start(self, env): def trial_start(self, env):
'''Method to call when a trial start''' """Method to call when a trial start"""
pass pass
def trial_end(self, env): def trial_end(self, env):
'''Method to call when a trial ends''' """Method to call when a trial ends"""
pass pass
def output(self, f, mode='w', **kwargs): def output(self, f, mode="w", **kwargs):
if self.dry_run: if self.dry_run:
f = DryRunner(f, copy_to=self.copy_to) f = DryRunner(f, copy_to=self.copy_to)
else: else:
@ -86,102 +88,117 @@ class Exporter:
class default(Exporter): class default(Exporter):
'''Default exporter. Writes sqlite results, as well as the simulation YAML''' """Default exporter. Writes sqlite results, as well as the simulation YAML"""
def sim_start(self): def sim_start(self):
if not self.dry_run: if not self.dry_run:
logger.info('Dumping results to %s', self.outdir) logger.info("Dumping results to %s", self.outdir)
with self.output(self.simulation.name + '.dumped.yml') as f: with self.output(self.simulation.name + ".dumped.yml") as f:
f.write(self.simulation.to_yaml()) f.write(self.simulation.to_yaml())
else: else:
logger.info('NOT dumping results') logger.info("NOT dumping results")
def trial_end(self, env): def trial_end(self, env):
if self.dry_run: if self.dry_run:
logger.info('Running in DRY_RUN mode, the database will NOT be created') logger.info("Running in DRY_RUN mode, the database will NOT be created")
return return
with timer('Dumping simulation {} trial {}'.format(self.simulation.name, with timer(
env.id)): "Dumping simulation {} trial {}".format(self.simulation.name, env.id)
):
fpath = os.path.join(self.outdir, f'{env.id}.sqlite') fpath = os.path.join(self.outdir, f"{env.id}.sqlite")
engine = create_engine(f'sqlite:///{fpath}', echo=False) engine = create_engine(f"sqlite:///{fpath}", echo=False)
dc = env.datacollector dc = env.datacollector
for (t, df) in get_dc_dfs(dc): for (t, df) in get_dc_dfs(dc):
df.to_sql(t, con=engine, if_exists='append') df.to_sql(t, con=engine, if_exists="append")
def get_dc_dfs(dc): def get_dc_dfs(dc):
dfs = {'env': dc.get_model_vars_dataframe(), dfs = {
'agents': dc.get_agent_vars_dataframe() } "env": dc.get_model_vars_dataframe(),
"agents": dc.get_agent_vars_dataframe(),
}
for table_name in dc.tables: for table_name in dc.tables:
dfs[table_name] = dc.get_table_dataframe(table_name) dfs[table_name] = dc.get_table_dataframe(table_name)
yield from dfs.items() yield from dfs.items()
class csv(Exporter): class csv(Exporter):
'''Export the state of each environment (and its agents) in a separate CSV file''' """Export the state of each environment (and its agents) in a separate CSV file"""
def trial_end(self, env): def trial_end(self, env):
with timer('[CSV] Dumping simulation {} trial {} @ dir {}'.format(self.simulation.name, with timer(
env.id, "[CSV] Dumping simulation {} trial {} @ dir {}".format(
self.outdir)): self.simulation.name, env.id, self.outdir
)
):
for (df_name, df) in get_dc_dfs(env.datacollector): for (df_name, df) in get_dc_dfs(env.datacollector):
with self.output('{}.{}.csv'.format(env.id, df_name)) as f: with self.output("{}.{}.csv".format(env.id, df_name)) as f:
df.to_csv(f) df.to_csv(f)
#TODO: reimplement GEXF exporting without history # TODO: reimplement GEXF exporting without history
class gexf(Exporter): class gexf(Exporter):
def trial_end(self, env): def trial_end(self, env):
if self.dry_run: if self.dry_run:
logger.info('Not dumping GEXF in dry_run mode') logger.info("Not dumping GEXF in dry_run mode")
return return
with timer('[GEXF] Dumping simulation {} trial {}'.format(self.simulation.name, with timer(
env.id)): "[GEXF] Dumping simulation {} trial {}".format(self.simulation.name, env.id)
with self.output('{}.gexf'.format(env.id), mode='wb') as f: ):
with self.output("{}.gexf".format(env.id), mode="wb") as f:
network.dump_gexf(env.history_to_graph(), f) network.dump_gexf(env.history_to_graph(), f)
self.dump_gexf(env, f) self.dump_gexf(env, f)
class dummy(Exporter): class dummy(Exporter):
def sim_start(self): def sim_start(self):
with self.output('dummy', 'w') as f: with self.output("dummy", "w") as f:
f.write('simulation started @ {}\n'.format(current_time())) f.write("simulation started @ {}\n".format(current_time()))
def trial_start(self, env): def trial_start(self, env):
with self.output('dummy', 'w') as f: with self.output("dummy", "w") as f:
f.write('trial started@ {}\n'.format(current_time())) f.write("trial started@ {}\n".format(current_time()))
def trial_end(self, env): def trial_end(self, env):
with self.output('dummy', 'w') as f: with self.output("dummy", "w") as f:
f.write('trial ended@ {}\n'.format(current_time())) f.write("trial ended@ {}\n".format(current_time()))
def sim_end(self): def sim_end(self):
with self.output('dummy', 'a') as f: with self.output("dummy", "a") as f:
f.write('simulation ended @ {}\n'.format(current_time())) f.write("simulation ended @ {}\n".format(current_time()))
class graphdrawing(Exporter): class graphdrawing(Exporter):
def trial_end(self, env): def trial_end(self, env):
# Outside effects # Outside effects
f = plt.figure() 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)) nx.draw(
with open('graph-{}.png'.format(env.id)) as f: 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.id)) as f:
f.savefig(f) f.savefig(f)
'''
"""
Convert an environment into a NetworkX graph Convert an environment into a NetworkX graph
''' """
def env_to_graph(env, history=None): def env_to_graph(env, history=None):
G = nx.Graph(env.G) G = nx.Graph(env.G)
for agent in env.network_agents: for agent in env.network_agents:
attributes = {'agent': str(agent.__class__)} attributes = {"agent": str(agent.__class__)}
lastattributes = {} lastattributes = {}
spells = [] spells = []
lastvisible = False lastvisible = False
@ -189,7 +206,7 @@ def env_to_graph(env, history=None):
if not history: if not history:
history = sorted(list(env.state_to_tuples())) history = sorted(list(env.state_to_tuples()))
for _, t_step, attribute, value in history: for _, t_step, attribute, value in history:
if attribute == 'visible': if attribute == "visible":
nowvisible = value nowvisible = value
if nowvisible and not lastvisible: if nowvisible and not lastvisible:
laststep = t_step laststep = t_step
@ -198,7 +215,7 @@ def env_to_graph(env, history=None):
lastvisible = nowvisible lastvisible = nowvisible
continue continue
key = 'attr_' + attribute key = "attr_" + attribute
if key not in attributes: if key not in attributes:
attributes[key] = list() attributes[key] = list()
if key not in lastattributes: if key not in lastattributes:

41
soil/network.py
View File

@ -9,6 +9,7 @@ import networkx as nx
from . import config, serialization, basestring from . import config, serialization, basestring
def from_config(cfg: config.NetConfig, dir_path: str = None): def from_config(cfg: config.NetConfig, dir_path: str = None):
if not isinstance(cfg, config.NetConfig): if not isinstance(cfg, config.NetConfig):
cfg = config.NetConfig(**cfg) cfg = config.NetConfig(**cfg)
@ -19,24 +20,28 @@ def from_config(cfg: config.NetConfig, dir_path: str = None):
path = os.path.join(dir_path, path) path = os.path.join(dir_path, path)
extension = os.path.splitext(path)[1][1:] extension = os.path.splitext(path)[1][1:]
kwargs = {} kwargs = {}
if extension == 'gexf': if extension == "gexf":
kwargs['version'] = '1.2draft' kwargs["version"] = "1.2draft"
kwargs['node_type'] = int kwargs["node_type"] = int
try: try:
method = getattr(nx.readwrite, 'read_' + extension) method = getattr(nx.readwrite, "read_" + extension)
except AttributeError: except AttributeError:
raise AttributeError('Unknown format') raise AttributeError("Unknown format")
return method(path, **kwargs) return method(path, **kwargs)
if cfg.params: if cfg.params:
net_args = cfg.params.dict() net_args = cfg.params.dict()
net_gen = net_args.pop('generator') net_gen = net_args.pop("generator")
if dir_path not in sys.path: if dir_path not in sys.path:
sys.path.append(dir_path) sys.path.append(dir_path)
method = serialization.deserializer(net_gen, method = serialization.deserializer(
known_modules=['networkx.generators',]) net_gen,
known_modules=[
"networkx.generators",
],
)
return method(**net_args) return method(**net_args)
if isinstance(cfg.fixed, config.Topology): if isinstance(cfg.fixed, config.Topology):
@ -49,17 +54,17 @@ def from_config(cfg: config.NetConfig, dir_path: str = None):
def find_unassigned(G, shuffle=False, random=random): def find_unassigned(G, shuffle=False, random=random):
''' """
Link an agent to a node in a topology. Link an agent to a node in a topology.
If node_id is None, a node without an agent_id will be found. If node_id is None, a node without an agent_id will be found.
''' """
#TODO: test # TODO: test
candidates = list(G.nodes(data=True)) candidates = list(G.nodes(data=True))
if shuffle: if shuffle:
random.shuffle(candidates) random.shuffle(candidates)
for next_id, data in candidates: for next_id, data in candidates:
if 'agent' not in data: if "agent" not in data:
node_id = next_id node_id = next_id
break break
@ -68,8 +73,14 @@ def find_unassigned(G, shuffle=False, random=random):
def dump_gexf(G, f): def dump_gexf(G, f):
for node in G.nodes(): for node in G.nodes():
if 'pos' in G.nodes[node]: 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}} G.nodes[node]["viz"] = {
del (G.nodes[node]['pos']) "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") nx.write_gexf(G, f, version="1.2draft")

83
soil/serialization.py
View File

@ -15,13 +15,14 @@ import networkx as nx
from jinja2 import Template from jinja2 import Template
logger = logging.getLogger('soil') logger = logging.getLogger("soil")
def load_file(infile): def load_file(infile):
folder = os.path.dirname(infile) folder = os.path.dirname(infile)
if folder not in sys.path: if folder not in sys.path:
sys.path.append(folder) sys.path.append(folder)
with open(infile, 'r') as f: with open(infile, "r") as f:
return list(chain.from_iterable(map(expand_template, load_string(f)))) return list(chain.from_iterable(map(expand_template, load_string(f))))
@ -30,14 +31,15 @@ def load_string(string):
def expand_template(config): def expand_template(config):
if 'template' not in config: if "template" not in config:
yield config yield config
return return
if 'vars' not in config: if "vars" not in config:
raise ValueError(('You must provide a definition of variables' raise ValueError(
' for the template.')) ("You must provide a definition of variables" " for the template.")
)
template = config['template'] template = config["template"]
if not isinstance(template, str): if not isinstance(template, str):
template = yaml.dump(template) template = yaml.dump(template)
@ -49,9 +51,9 @@ def expand_template(config):
blank_str = template.render({k: 0 for k in params[0].keys()}) blank_str = template.render({k: 0 for k in params[0].keys()})
blank = list(load_string(blank_str)) blank = list(load_string(blank_str))
if len(blank) > 1: if len(blank) > 1:
raise ValueError('Templates must not return more than one configuration') raise ValueError("Templates must not return more than one configuration")
if 'name' in blank[0]: if "name" in blank[0]:
raise ValueError('Templates cannot be named, use group instead') raise ValueError("Templates cannot be named, use group instead")
for ps in params: for ps in params:
string = template.render(ps) string = template.render(ps)
@ -60,25 +62,25 @@ def expand_template(config):
def params_for_template(config): def params_for_template(config):
sampler_config = config.get('sampler', {'N': 100}) sampler_config = config.get("sampler", {"N": 100})
sampler = sampler_config.pop('method', 'SALib.sample.morris.sample') sampler = sampler_config.pop("method", "SALib.sample.morris.sample")
sampler = deserializer(sampler) sampler = deserializer(sampler)
bounds = config['vars']['bounds'] bounds = config["vars"]["bounds"]
problem = { problem = {
'num_vars': len(bounds), "num_vars": len(bounds),
'names': list(bounds.keys()), "names": list(bounds.keys()),
'bounds': list(v for v in bounds.values()) "bounds": list(v for v in bounds.values()),
} }
samples = sampler(problem, **sampler_config) samples = sampler(problem, **sampler_config)
lists = config['vars'].get('lists', {}) lists = config["vars"].get("lists", {})
names = list(lists.keys()) names = list(lists.keys())
values = list(lists.values()) values = list(lists.values())
combs = list(product(*values)) combs = list(product(*values))
allnames = names + problem['names'] allnames = names + problem["names"]
allvalues = [(list(i[0])+list(i[1])) for i in product(combs, samples)] allvalues = [(list(i[0]) + list(i[1])) for i in product(combs, samples)]
params = list(map(lambda x: dict(zip(allnames, x)), allvalues)) params = list(map(lambda x: dict(zip(allnames, x)), allvalues))
return params return params
@ -100,22 +102,24 @@ def load_config(cfg):
yield from load_files(cfg) yield from load_files(cfg)
builtins = importlib.import_module('builtins') builtins = importlib.import_module("builtins")
KNOWN_MODULES = ['soil', ] KNOWN_MODULES = [
"soil",
]
def name(value, known_modules=KNOWN_MODULES): def name(value, known_modules=KNOWN_MODULES):
'''Return a name that can be imported, to serialize/deserialize an object''' """Return a name that can be imported, to serialize/deserialize an object"""
if value is None: if value is None:
return 'None' return "None"
if not isinstance(value, type): # Get the class name first if not isinstance(value, type): # Get the class name first
value = type(value) value = type(value)
tname = value.__name__ tname = value.__name__
if hasattr(builtins, tname): if hasattr(builtins, tname):
return tname return tname
modname = value.__module__ modname = value.__module__
if modname == '__main__': if modname == "__main__":
return tname return tname
if known_modules and modname in known_modules: if known_modules and modname in known_modules:
return tname return tname
@ -125,17 +129,17 @@ def name(value, known_modules=KNOWN_MODULES):
module = importlib.import_module(kmod) module = importlib.import_module(kmod)
if hasattr(module, tname): if hasattr(module, tname):
return tname return tname
return '{}.{}'.format(modname, tname) return "{}.{}".format(modname, tname)
def serializer(type_): def serializer(type_):
if type_ != 'str' and hasattr(builtins, type_): if type_ != "str" and hasattr(builtins, type_):
return repr return repr
return lambda x: x return lambda x: x
def serialize(v, known_modules=KNOWN_MODULES): def serialize(v, known_modules=KNOWN_MODULES):
'''Get a text representation of an object.''' """Get a text representation of an object."""
tname = name(v, known_modules=known_modules) tname = name(v, known_modules=known_modules)
func = serializer(tname) func = serializer(tname)
return func(v), tname return func(v), tname
@ -160,9 +164,9 @@ IS_CLASS = re.compile(r"<class '(.*)'>")
def deserializer(type_, known_modules=KNOWN_MODULES): def deserializer(type_, known_modules=KNOWN_MODULES):
if type(type_) != str: # Already deserialized if type(type_) != str: # Already deserialized
return type_ return type_
if type_ == 'str': if type_ == "str":
return lambda x='': x return lambda x="": x
if type_ == 'None': if type_ == "None":
return lambda x=None: None return lambda x=None: None
if hasattr(builtins, type_): # Check if it's a builtin type if hasattr(builtins, type_): # Check if it's a builtin type
cls = getattr(builtins, type_) cls = getattr(builtins, type_)
@ -172,8 +176,8 @@ def deserializer(type_, known_modules=KNOWN_MODULES):
modname, tname = match.group(1).rsplit(".", 1) modname, tname = match.group(1).rsplit(".", 1)
module = importlib.import_module(modname) module = importlib.import_module(modname)
cls = getattr(module, tname) cls = getattr(module, tname)
return getattr(cls, 'deserialize', cls) return getattr(cls, "deserialize", cls)
# Otherwise, see if we can find the module and the class # Otherwise, see if we can find the module and the class
options = [] options = []
@ -181,7 +185,7 @@ def deserializer(type_, known_modules=KNOWN_MODULES):
if mod: if mod:
options.append((mod, type_)) options.append((mod, type_))
if '.' in type_: # Fully qualified module if "." in type_: # Fully qualified module
module, type_ = type_.rsplit(".", 1) module, type_ = type_.rsplit(".", 1)
options.append((module, type_)) options.append((module, type_))
@ -190,32 +194,31 @@ def deserializer(type_, known_modules=KNOWN_MODULES):
try: try:
module = importlib.import_module(modname) module = importlib.import_module(modname)
cls = getattr(module, tname) cls = getattr(module, tname)
return getattr(cls, 'deserialize', cls) return getattr(cls, "deserialize", cls)
except (ImportError, AttributeError) as ex: except (ImportError, AttributeError) as ex:
errors.append((modname, tname, ex)) errors.append((modname, tname, ex))
raise Exception('Could not find type "{}". Tried: {}'.format(type_, errors)) raise Exception('Could not find type "{}". Tried: {}'.format(type_, errors))
def deserialize(type_, value=None, globs=None, **kwargs): def deserialize(type_, value=None, globs=None, **kwargs):
'''Get an object from a text representation''' """Get an object from a text representation"""
if not isinstance(type_, str): if not isinstance(type_, str):
return type_ return type_
if globs and type_ in globs: if globs and type_ in globs:
des = globs[type_] des = globs[type_]
else: else:
des = deserializer(type_, **kwargs) des = deserializer(type_, **kwargs)
if value is None: if value is None:
return des return des
return des(value) return des(value)
def deserialize_all(names, *args, known_modules=KNOWN_MODULES, **kwargs): def deserialize_all(names, *args, known_modules=KNOWN_MODULES, **kwargs):
'''Return the list of deserialized objects''' """Return the list of deserialized objects"""
#TODO: remove # TODO: remove
print('SERIALIZATION', kwargs) print("SERIALIZATION", kwargs)
objects = [] objects = []
for name in names: for name in names:
mod = deserialize(name, known_modules=known_modules) mod = deserialize(name, known_modules=known_modules)
objects.append(mod(*args, **kwargs)) objects.append(mod(*args, **kwargs))
return objects return objects

161
soil/simulation.py
View File

@ -1,5 +1,5 @@
import os import os
from time import time as current_time, strftime from time import time as current_time, strftime
import importlib import importlib
import sys import sys
import yaml import yaml
@ -25,7 +25,7 @@ from .time import INFINITY
from .config import Config, convert_old from .config import Config, convert_old
#TODO: change documentation for simulation # TODO: change documentation for simulation
@dataclass @dataclass
class Simulation: class Simulation:
""" """
@ -36,15 +36,16 @@ class Simulation:
kwargs: parameters to use to initialize a new configuration, if one not been provided. kwargs: parameters to use to initialize a new configuration, if one not been provided.
""" """
version: str = '2'
name: str = 'Unnamed simulation' version: str = "2"
description: Optional[str] = '' name: str = "Unnamed simulation"
description: Optional[str] = ""
group: str = None group: str = None
model_class: Union[str, type] = 'soil.Environment' model_class: Union[str, type] = "soil.Environment"
model_params: dict = field(default_factory=dict) model_params: dict = field(default_factory=dict)
seed: str = field(default_factory=lambda: current_time()) seed: str = field(default_factory=lambda: current_time())
dir_path: str = field(default_factory=lambda: os.getcwd()) dir_path: str = field(default_factory=lambda: os.getcwd())
max_time: float = float('inf') max_time: float = float("inf")
max_steps: int = -1 max_steps: int = -1
interval: int = 1 interval: int = 1
num_trials: int = 3 num_trials: int = 3
@ -56,14 +57,15 @@ class Simulation:
extra: Dict[str, Any] = field(default_factory=dict) extra: Dict[str, Any] = field(default_factory=dict)
@classmethod @classmethod
def from_dict(cls, env, **kwargs): def from_dict(cls, env, **kwargs):
ignored = {k: v for k, v in env.items() ignored = {
if k not in inspect.signature(cls).parameters} k: v for k, v in env.items() if k not in inspect.signature(cls).parameters
}
d = {k:v for k, v in env.items() if k not in ignored} d = {k: v for k, v in env.items() if k not in ignored}
if ignored: if ignored:
d.setdefault('extra', {}).update(ignored) d.setdefault("extra", {}).update(ignored)
if ignored: if ignored:
print(f'Warning: Ignoring these parameters (added to "extra"): { ignored }') print(f'Warning: Ignoring these parameters (added to "extra"): { ignored }')
d.update(kwargs) d.update(kwargs)
@ -74,24 +76,34 @@ class Simulation:
return self.run(*args, **kwargs) return self.run(*args, **kwargs)
def run(self, *args, **kwargs): def run(self, *args, **kwargs):
'''Run the simulation and return the list of resulting environments''' """Run the simulation and return the list of resulting environments"""
logger.info(dedent(''' logger.info(
dedent(
"""
Simulation: Simulation:
--- ---
''') + """
self.to_yaml()) )
+ self.to_yaml()
)
return list(self.run_gen(*args, **kwargs)) return list(self.run_gen(*args, **kwargs))
def run_gen(self, parallel=False, dry_run=None, def run_gen(
exporters=None, outdir=None, exporter_params={}, self,
log_level=None, parallel=False,
**kwargs): dry_run=None,
'''Run the simulation and yield the resulting environments.''' exporters=None,
outdir=None,
exporter_params={},
log_level=None,
**kwargs,
):
"""Run the simulation and yield the resulting environments."""
if log_level: if log_level:
logger.setLevel(log_level) logger.setLevel(log_level)
outdir = outdir or self.outdir outdir = outdir or self.outdir
logger.info('Using exporters: %s', exporters or []) logger.info("Using exporters: %s", exporters or [])
logger.info('Output directory: %s', outdir) logger.info("Output directory: %s", outdir)
if dry_run is None: if dry_run is None:
dry_run = self.dry_run dry_run = self.dry_run
if exporters is None: if exporters is None:
@ -99,22 +111,28 @@ class Simulation:
if not exporter_params: if not exporter_params:
exporter_params = self.exporter_params exporter_params = self.exporter_params
exporters = serialization.deserialize_all(exporters, exporters = serialization.deserialize_all(
simulation=self, exporters,
known_modules=['soil.exporters', ], simulation=self,
dry_run=dry_run, known_modules=[
outdir=outdir, "soil.exporters",
**exporter_params) ],
dry_run=dry_run,
outdir=outdir,
**exporter_params,
)
with utils.timer('simulation {}'.format(self.name)): with utils.timer("simulation {}".format(self.name)):
for exporter in exporters: for exporter in exporters:
exporter.sim_start() exporter.sim_start()
for env in utils.run_parallel(func=self.run_trial, for env in utils.run_parallel(
iterable=range(int(self.num_trials)), func=self.run_trial,
parallel=parallel, iterable=range(int(self.num_trials)),
log_level=log_level, parallel=parallel,
**kwargs): log_level=log_level,
**kwargs,
):
for exporter in exporters: for exporter in exporters:
exporter.trial_start(env) exporter.trial_start(env)
@ -128,11 +146,12 @@ class Simulation:
exporter.sim_end() exporter.sim_end()
def get_env(self, trial_id=0, model_params=None, **kwargs): def get_env(self, trial_id=0, model_params=None, **kwargs):
'''Create an environment for a trial of the simulation''' """Create an environment for a trial of the simulation"""
def deserialize_reporters(reporters): def deserialize_reporters(reporters):
for (k, v) in reporters.items(): for (k, v) in reporters.items():
if isinstance(v, str) and v.startswith('py:'): if isinstance(v, str) and v.startswith("py:"):
reporters[k] = serialization.deserialize(value.lsplit(':', 1)[1]) reporters[k] = serialization.deserialize(value.lsplit(":", 1)[1])
return reporters return reporters
params = self.model_params.copy() params = self.model_params.copy()
@ -140,18 +159,22 @@ class Simulation:
params.update(model_params) params.update(model_params)
params.update(kwargs) params.update(kwargs)
agent_reporters = deserialize_reporters(params.pop('agent_reporters', {})) agent_reporters = deserialize_reporters(params.pop("agent_reporters", {}))
model_reporters = deserialize_reporters(params.pop('model_reporters', {})) model_reporters = deserialize_reporters(params.pop("model_reporters", {}))
env = serialization.deserialize(self.model_class) env = serialization.deserialize(self.model_class)
return env(id=f'{self.name}_trial_{trial_id}', return env(
seed=f'{self.seed}_trial_{trial_id}', id=f"{self.name}_trial_{trial_id}",
dir_path=self.dir_path, seed=f"{self.seed}_trial_{trial_id}",
agent_reporters=agent_reporters, dir_path=self.dir_path,
model_reporters=model_reporters, agent_reporters=agent_reporters,
**params) model_reporters=model_reporters,
**params,
)
def run_trial(self, trial_id=None, until=None, log_file=False, log_level=logging.INFO, **opts): def run_trial(
self, trial_id=None, until=None, log_file=False, log_level=logging.INFO, **opts
):
""" """
Run a single trial of the simulation Run a single trial of the simulation
@ -160,50 +183,58 @@ class Simulation:
logger.setLevel(log_level) logger.setLevel(log_level)
model = self.get_env(trial_id, **opts) model = self.get_env(trial_id, **opts)
trial_id = trial_id if trial_id is not None else current_time() trial_id = trial_id if trial_id is not None else current_time()
with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)): with utils.timer("Simulation {} trial {}".format(self.name, trial_id)):
return self.run_model(model=model, trial_id=trial_id, until=until, log_level=log_level) return self.run_model(
model=model, trial_id=trial_id, until=until, log_level=log_level
)
def run_model(self, model, until=None, **opts): def run_model(self, model, until=None, **opts):
# Set-up trial environment and graph # Set-up trial environment and graph
until = float(until or self.max_time or 'inf') until = float(until or self.max_time or "inf")
# Set up agents on nodes # Set up agents on nodes
def is_done(): def is_done():
return False return False
if until and hasattr(model.schedule, 'time'): if until and hasattr(model.schedule, "time"):
prev = is_done prev = is_done
def is_done(): def is_done():
return prev() or model.schedule.time >= until return prev() or model.schedule.time >= until
if self.max_steps and self.max_steps > 0 and hasattr(model.schedule, 'steps'): if self.max_steps and self.max_steps > 0 and hasattr(model.schedule, "steps"):
prev_steps = is_done prev_steps = is_done
def is_done(): def is_done():
return prev_steps() or model.schedule.steps >= self.max_steps return prev_steps() or model.schedule.steps >= self.max_steps
newline = '\n' newline = "\n"
logger.info(dedent(f''' logger.info(
dedent(
f"""
Model stats: Model stats:
Agents (total: { model.schedule.get_agent_count() }): Agents (total: { model.schedule.get_agent_count() }):
- { (newline + ' - ').join(str(a) for a in model.schedule.agents) } - { (newline + ' - ').join(str(a) for a in model.schedule.agents) }
Topology size: { len(model.G) if hasattr(model, "G") else 0 } Topology size: { len(model.G) if hasattr(model, "G") else 0 }
''')) """
)
)
while not is_done(): while not is_done():
utils.logger.debug(f'Simulation time {model.schedule.time}/{until}. Next: {getattr(model.schedule, "next_time", model.schedule.time + self.interval)}') utils.logger.debug(
f'Simulation time {model.schedule.time}/{until}. Next: {getattr(model.schedule, "next_time", model.schedule.time + self.interval)}'
)
model.step() model.step()
return model return model
def to_dict(self): def to_dict(self):
d = asdict(self) d = asdict(self)
if not isinstance(d['model_class'], str): if not isinstance(d["model_class"], str):
d['model_class'] = serialization.name(d['model_class']) d["model_class"] = serialization.name(d["model_class"])
d['model_params'] = serialization.serialize_dict(d['model_params']) d["model_params"] = serialization.serialize_dict(d["model_params"])
d['dir_path'] = str(d['dir_path']) d["dir_path"] = str(d["dir_path"])
d['version'] = '2' d["version"] = "2"
return d return d
def to_yaml(self): def to_yaml(self):
@ -215,15 +246,15 @@ def iter_from_config(*cfgs, **kwargs):
configs = list(serialization.load_config(config)) configs = list(serialization.load_config(config))
for config, path in configs: for config, path in configs:
d = dict(config) d = dict(config)
if 'dir_path' not in d: if "dir_path" not in d:
d['dir_path'] = os.path.dirname(path) d["dir_path"] = os.path.dirname(path)
yield Simulation.from_dict(d, **kwargs) yield Simulation.from_dict(d, **kwargs)
def from_config(conf_or_path): def from_config(conf_or_path):
lst = list(iter_from_config(conf_or_path)) lst = list(iter_from_config(conf_or_path))
if len(lst) > 1: if len(lst) > 1:
raise AttributeError('Provide only one configuration') raise AttributeError("Provide only one configuration")
return lst[0] return lst[0]

21
soil/time.py
View File

@ -6,7 +6,8 @@ from .utils import logger
from mesa import Agent as MesaAgent from mesa import Agent as MesaAgent
INFINITY = float('inf') INFINITY = float("inf")
class When: class When:
def __init__(self, time): def __init__(self, time):
@ -42,7 +43,7 @@ class TimedActivation(BaseScheduler):
self._next = {} self._next = {}
self._queue = [] self._queue = []
self.next_time = 0 self.next_time = 0
self.logger = logger.getChild(f'time_{ self.model }') self.logger = logger.getChild(f"time_{ self.model }")
def add(self, agent: MesaAgent, when=None): def add(self, agent: MesaAgent, when=None):
if when is None: if when is None:
@ -51,7 +52,7 @@ class TimedActivation(BaseScheduler):
self._queue.remove((self._next[agent.unique_id], agent.unique_id)) self._queue.remove((self._next[agent.unique_id], agent.unique_id))
del self._agents[agent.unique_id] del self._agents[agent.unique_id]
heapify(self._queue) heapify(self._queue)
heappush(self._queue, (when, agent.unique_id)) heappush(self._queue, (when, agent.unique_id))
self._next[agent.unique_id] = when self._next[agent.unique_id] = when
super().add(agent) super().add(agent)
@ -62,7 +63,7 @@ class TimedActivation(BaseScheduler):
an agent will signal when it wants to be scheduled next. an agent will signal when it wants to be scheduled next.
""" """
self.logger.debug(f'Simulation step {self.next_time}') self.logger.debug(f"Simulation step {self.next_time}")
if not self.model.running: if not self.model.running:
return return
@ -71,18 +72,22 @@ class TimedActivation(BaseScheduler):
while self._queue and self._queue[0][0] == self.time: while self._queue and self._queue[0][0] == self.time:
(when, agent_id) = heappop(self._queue) (when, agent_id) = heappop(self._queue)
self.logger.debug(f'Stepping agent {agent_id}') self.logger.debug(f"Stepping agent {agent_id}")
agent = self._agents[agent_id] agent = self._agents[agent_id]
returned = agent.step() returned = agent.step()
if not getattr(agent, 'alive', True): if not getattr(agent, "alive", True):
self.remove(agent) self.remove(agent)
continue continue
when = (returned or Delta(1)).abs(self.time) when = (returned or Delta(1)).abs(self.time)
if when < self.time: if when < self.time:
raise Exception("Cannot schedule an agent for a time in the past ({} < {})".format(when, self.time)) raise Exception(
"Cannot schedule an agent for a time in the past ({} < {})".format(
when, self.time
)
)
self._next[agent_id] = when self._next[agent_id] = when
heappush(self._queue, (when, agent_id)) heappush(self._queue, (when, agent_id))
@ -96,4 +101,4 @@ class TimedActivation(BaseScheduler):
return self.time return self.time
self.next_time = self._queue[0][0] self.next_time = self._queue[0][0]
self.logger.debug(f'Next step: {self.next_time}') self.logger.debug(f"Next step: {self.next_time}")

63
soil/utils.py
View File

@ -9,12 +9,12 @@ from multiprocessing import Pool
from contextlib import contextmanager from contextlib import contextmanager
logger = logging.getLogger('soil') logger = logging.getLogger("soil")
logger.setLevel(logging.INFO) logger.setLevel(logging.INFO)
timeformat = "%H:%M:%S" timeformat = "%H:%M:%S"
if os.environ.get('SOIL_VERBOSE', ''): if os.environ.get("SOIL_VERBOSE", ""):
logformat = "[%(levelname)-5.5s][%(asctime)s][%(name)s]: %(message)s" logformat = "[%(levelname)-5.5s][%(asctime)s][%(name)s]: %(message)s"
else: else:
logformat = "[%(levelname)-5.5s][%(asctime)s] %(message)s" logformat = "[%(levelname)-5.5s][%(asctime)s] %(message)s"
@ -23,38 +23,44 @@ logFormatter = logging.Formatter(logformat, timeformat)
consoleHandler = logging.StreamHandler() consoleHandler = logging.StreamHandler()
consoleHandler.setFormatter(logFormatter) consoleHandler.setFormatter(logFormatter)
logging.basicConfig(level=logging.INFO, logging.basicConfig(
handlers=[consoleHandler,]) level=logging.INFO,
handlers=[
consoleHandler,
],
)
@contextmanager @contextmanager
def timer(name='task', pre="", function=logger.info, to_object=None): def timer(name="task", pre="", function=logger.info, to_object=None):
start = current_time() start = current_time()
function('{}Starting {} at {}.'.format(pre, name, function("{}Starting {} at {}.".format(pre, name, strftime("%X", gmtime(start))))
strftime("%X", gmtime(start))))
yield start yield start
end = current_time() end = current_time()
function('{}Finished {} at {} in {} seconds'.format(pre, name, function(
strftime("%X", gmtime(end)), "{}Finished {} at {} in {} seconds".format(
str(end-start))) pre, name, strftime("%X", gmtime(end)), str(end - start)
)
)
if to_object: if to_object:
to_object.start = start to_object.start = start
to_object.end = end to_object.end = end
def safe_open(path, mode='r', backup=True, **kwargs): def safe_open(path, mode="r", backup=True, **kwargs):
outdir = os.path.dirname(path) outdir = os.path.dirname(path)
if outdir and not os.path.exists(outdir): if outdir and not os.path.exists(outdir):
os.makedirs(outdir) os.makedirs(outdir)
if backup and 'w' in mode and os.path.exists(path): if backup and "w" in mode and os.path.exists(path):
creation = os.path.getctime(path) creation = os.path.getctime(path)
stamp = strftime('%Y-%m-%d_%H.%M.%S', localtime(creation)) stamp = strftime("%Y-%m-%d_%H.%M.%S", localtime(creation))
backup_dir = os.path.join(outdir, 'backup') backup_dir = os.path.join(outdir, "backup")
if not os.path.exists(backup_dir): if not os.path.exists(backup_dir):
os.makedirs(backup_dir) os.makedirs(backup_dir)
newpath = os.path.join(backup_dir, '{}@{}'.format(os.path.basename(path), newpath = os.path.join(
stamp)) backup_dir, "{}@{}".format(os.path.basename(path), stamp)
)
copyfile(path, newpath) copyfile(path, newpath)
return open(path, mode=mode, **kwargs) return open(path, mode=mode, **kwargs)
@ -67,21 +73,23 @@ def open_or_reuse(f, *args, **kwargs):
except (AttributeError, TypeError): except (AttributeError, TypeError):
yield f yield f
def flatten_dict(d): def flatten_dict(d):
if not isinstance(d, dict): if not isinstance(d, dict):
return d return d
return dict(_flatten_dict(d)) return dict(_flatten_dict(d))
def _flatten_dict(d, prefix=''):
def _flatten_dict(d, prefix=""):
if not isinstance(d, dict): if not isinstance(d, dict):
# print('END:', prefix, d) # print('END:', prefix, d)
yield prefix, d yield prefix, d
return return
if prefix: if prefix:
prefix = prefix + '.' prefix = prefix + "."
for k, v in d.items(): for k, v in d.items():
# print(k, v) # print(k, v)
res = list(_flatten_dict(v, prefix='{}{}'.format(prefix, k))) res = list(_flatten_dict(v, prefix="{}{}".format(prefix, k)))
# print('RES:', res) # print('RES:', res)
yield from res yield from res
@ -93,7 +101,7 @@ def unflatten_dict(d):
if not isinstance(k, str): if not isinstance(k, str):
target[k] = v target[k] = v
continue continue
tokens = k.split('.') tokens = k.split(".")
if len(tokens) < 2: if len(tokens) < 2:
target[k] = v target[k] = v
continue continue
@ -106,27 +114,28 @@ def unflatten_dict(d):
def run_and_return_exceptions(func, *args, **kwargs): def run_and_return_exceptions(func, *args, **kwargs):
''' """
A wrapper for run_trial that catches exceptions and returns them. A wrapper for run_trial that catches exceptions and returns them.
It is meant for async simulations. It is meant for async simulations.
''' """
try: try:
return func(*args, **kwargs) return func(*args, **kwargs)
except Exception as ex: except Exception as ex:
if ex.__cause__ is not None: if ex.__cause__ is not None:
ex = ex.__cause__ ex = ex.__cause__
ex.message = ''.join(traceback.format_exception(type(ex), ex, ex.__traceback__)[:]) ex.message = "".join(
traceback.format_exception(type(ex), ex, ex.__traceback__)[:]
)
return ex return ex
def run_parallel(func, iterable, parallel=False, **kwargs): def run_parallel(func, iterable, parallel=False, **kwargs):
if parallel and not os.environ.get('SOIL_DEBUG', None): if parallel and not os.environ.get("SOIL_DEBUG", None):
p = Pool() p = Pool()
wrapped_func = partial(run_and_return_exceptions, wrapped_func = partial(run_and_return_exceptions, func, **kwargs)
func, **kwargs)
for i in p.imap_unordered(wrapped_func, iterable): for i in p.imap_unordered(wrapped_func, iterable):
if isinstance(i, Exception): if isinstance(i, Exception):
logger.error('Trial failed:\n\t%s', i.message) logger.error("Trial failed:\n\t%s", i.message)
continue continue
yield i yield i
else: else:

9
soil/version.py
View File

@ -4,7 +4,7 @@ import logging
logger = logging.getLogger(__name__) logger = logging.getLogger(__name__)
ROOT = os.path.dirname(__file__) ROOT = os.path.dirname(__file__)
DEFAULT_FILE = os.path.join(ROOT, 'VERSION') DEFAULT_FILE = os.path.join(ROOT, "VERSION")
def read_version(versionfile=DEFAULT_FILE): def read_version(versionfile=DEFAULT_FILE):
@ -12,9 +12,10 @@ def read_version(versionfile=DEFAULT_FILE):
with open(versionfile) as f: with open(versionfile) as f:
return f.read().strip() return f.read().strip()
except IOError: # pragma: no cover except IOError: # pragma: no cover
logger.error(('Running an unknown version of {}.' logger.error(
'Be careful!.').format(__name__)) ("Running an unknown version of {}." "Be careful!.").format(__name__)
return '0.0' )
return "0.0"
__version__ = read_version() __version__ = read_version()

1
soil/visualization.py
View File

@ -1,5 +1,6 @@
from mesa.visualization.UserParam import UserSettableParameter from mesa.visualization.UserParam import UserSettableParameter
class UserSettableParameter(UserSettableParameter): class UserSettableParameter(UserSettableParameter):
def __str__(self): def __str__(self):
return self.value return self.value

270
soil/web/__init__.py
View File

@ -20,6 +20,7 @@ from tornado.concurrent import run_on_executor
from concurrent.futures import ThreadPoolExecutor from concurrent.futures import ThreadPoolExecutor
from ..simulation import Simulation from ..simulation import Simulation
logger = logging.getLogger(__name__) logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO) logger.setLevel(logging.INFO)
@ -31,140 +32,183 @@ LOGGING_INTERVAL = 0.5
# Workaround to let Soil load the required modules # Workaround to let Soil load the required modules
sys.path.append(ROOT) sys.path.append(ROOT)
class PageHandler(tornado.web.RequestHandler): class PageHandler(tornado.web.RequestHandler):
""" Handler for the HTML template which holds the visualization. """ """Handler for the HTML template which holds the visualization."""
def get(self): def get(self):
self.render('index.html', port=self.application.port, self.render(
name=self.application.name) "index.html", port=self.application.port, name=self.application.name
)
class SocketHandler(tornado.websocket.WebSocketHandler): class SocketHandler(tornado.websocket.WebSocketHandler):
""" Handler for websocket. """ """Handler for websocket."""
executor = ThreadPoolExecutor(max_workers=MAX_WORKERS) executor = ThreadPoolExecutor(max_workers=MAX_WORKERS)
def open(self): def open(self):
if self.application.verbose: if self.application.verbose:
logger.info('Socket opened!') logger.info("Socket opened!")
def check_origin(self, origin): def check_origin(self, origin):
return True return True
def on_message(self, message): def on_message(self, message):
""" Receiving a message from the websocket, parse, and act accordingly. """ """Receiving a message from the websocket, parse, and act accordingly."""
msg = tornado.escape.json_decode(message) msg = tornado.escape.json_decode(message)
if msg['type'] == 'config_file': if msg["type"] == "config_file":
if self.application.verbose: if self.application.verbose:
print(msg['data']) print(msg["data"])
self.config = list(yaml.load_all(msg['data'])) self.config = list(yaml.load_all(msg["data"]))
if len(self.config) > 1: if len(self.config) > 1:
error = 'Please, provide only one configuration.' error = "Please, provide only one configuration."
if self.application.verbose: if self.application.verbose:
logger.error(error) logger.error(error)
self.write_message({'type': 'error', self.write_message({"type": "error", "error": error})
'error': error})
return return
self.config = self.config[0] self.config = self.config[0]
self.send_log('INFO.' + self.simulation_name, self.send_log(
'Using config: {name}'.format(name=self.config['name'])) "INFO." + self.simulation_name,
"Using config: {name}".format(name=self.config["name"]),
)
if 'visualization_params' in self.config: if "visualization_params" in self.config:
self.write_message({'type': 'visualization_params', self.write_message(
'data': self.config['visualization_params']}) {
self.name = self.config['name'] "type": "visualization_params",
"data": self.config["visualization_params"],
}
)
self.name = self.config["name"]
self.run_simulation() self.run_simulation()
settings = [] settings = []
for key in self.config['environment_params']: for key in self.config["environment_params"]:
if type(self.config['environment_params'][key]) == float or type(self.config['environment_params'][key]) == int: if (
if self.config['environment_params'][key] <= 1: type(self.config["environment_params"][key]) == float
setting_type = 'number' or type(self.config["environment_params"][key]) == int
):
if self.config["environment_params"][key] <= 1:
setting_type = "number"
else: else:
setting_type = 'great_number' setting_type = "great_number"
elif type(self.config['environment_params'][key]) == bool: elif type(self.config["environment_params"][key]) == bool:
setting_type = 'boolean' setting_type = "boolean"
else: else:
setting_type = 'undefined' setting_type = "undefined"
settings.append({ settings.append(
'label': key, {
'type': setting_type, "label": key,
'value': self.config['environment_params'][key] "type": setting_type,
}) "value": self.config["environment_params"][key],
}
)
self.write_message({'type': 'settings', self.write_message({"type": "settings", "data": settings})
'data': settings})
elif msg['type'] == 'get_trial': elif msg["type"] == "get_trial":
if self.application.verbose: if self.application.verbose:
logger.info('Trial {} requested!'.format(msg['data'])) logger.info("Trial {} requested!".format(msg["data"]))
self.send_log('INFO.' + __name__, 'Trial {} requested!'.format(msg['data'])) self.send_log("INFO." + __name__, "Trial {} requested!".format(msg["data"]))
self.write_message({'type': 'get_trial', self.write_message(
'data': self.get_trial(int(msg['data']))}) {"type": "get_trial", "data": self.get_trial(int(msg["data"]))}
)
elif msg['type'] == 'run_simulation': elif msg["type"] == "run_simulation":
if self.application.verbose: if self.application.verbose:
logger.info('Running new simulation for {name}'.format(name=self.config['name'])) logger.info(
self.send_log('INFO.' + self.simulation_name, 'Running new simulation for {name}'.format(name=self.config['name'])) "Running new simulation for {name}".format(name=self.config["name"])
self.config['environment_params'] = msg['data'] )
self.send_log(
"INFO." + self.simulation_name,
"Running new simulation for {name}".format(name=self.config["name"]),
)
self.config["environment_params"] = msg["data"]
self.run_simulation() self.run_simulation()
elif msg['type'] == 'download_gexf': elif msg["type"] == "download_gexf":
G = self.trials[ int(msg['data']) ].history_to_graph() G = self.trials[int(msg["data"])].history_to_graph()
for node in G.nodes(): for node in G.nodes():
if 'pos' in G.nodes[node]: 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}} G.nodes[node]["viz"] = {
del (G.nodes[node]['pos']) "position": {
writer = nx.readwrite.gexf.GEXFWriter(version='1.2draft') "x": G.nodes[node]["pos"][0],
"y": G.nodes[node]["pos"][1],
"z": 0.0,
}
}
del G.nodes[node]["pos"]
writer = nx.readwrite.gexf.GEXFWriter(version="1.2draft")
writer.add_graph(G) writer.add_graph(G)
self.write_message({'type': 'download_gexf', self.write_message(
'filename': self.config['name'] + '_trial_' + str(msg['data']), {
'data': tostring(writer.xml).decode(writer.encoding) }) "type": "download_gexf",
"filename": self.config["name"] + "_trial_" + str(msg["data"]),
"data": tostring(writer.xml).decode(writer.encoding),
}
)
elif msg['type'] == 'download_json': elif msg["type"] == "download_json":
G = self.trials[ int(msg['data']) ].history_to_graph() G = self.trials[int(msg["data"])].history_to_graph()
for node in G.nodes(): for node in G.nodes():
if 'pos' in G.nodes[node]: 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}} G.nodes[node]["viz"] = {
del (G.nodes[node]['pos']) "position": {
self.write_message({'type': 'download_json', "x": G.nodes[node]["pos"][0],
'filename': self.config['name'] + '_trial_' + str(msg['data']), "y": G.nodes[node]["pos"][1],
'data': nx.node_link_data(G) }) "z": 0.0,
}
}
del G.nodes[node]["pos"]
self.write_message(
{
"type": "download_json",
"filename": self.config["name"] + "_trial_" + str(msg["data"]),
"data": nx.node_link_data(G),
}
)
else: else:
if self.application.verbose: if self.application.verbose:
logger.info('Unexpected message!') logger.info("Unexpected message!")
def update_logging(self): def update_logging(self):
try: try:
if (not self.log_capture_string.closed and self.log_capture_string.getvalue()): if (
for i in range(len(self.log_capture_string.getvalue().split('\n')) - 1): not self.log_capture_string.closed
self.send_log('INFO.' + self.simulation_name, self.log_capture_string.getvalue().split('\n')[i]) and self.log_capture_string.getvalue()
):
for i in range(len(self.log_capture_string.getvalue().split("\n")) - 1):
self.send_log(
"INFO." + self.simulation_name,
self.log_capture_string.getvalue().split("\n")[i],
)
self.log_capture_string.truncate(0) self.log_capture_string.truncate(0)
self.log_capture_string.seek(0) self.log_capture_string.seek(0)
finally: finally:
if self.capture_logging: if self.capture_logging:
tornado.ioloop.IOLoop.current().call_later(LOGGING_INTERVAL, self.update_logging) tornado.ioloop.IOLoop.current().call_later(
LOGGING_INTERVAL, self.update_logging
)
def on_close(self): def on_close(self):
if self.application.verbose: if self.application.verbose:
logger.info('Socket closed!') logger.info("Socket closed!")
def send_log(self, logger, logging): def send_log(self, logger, logging):
self.write_message({'type': 'log', self.write_message({"type": "log", "logger": logger, "logging": logging})
'logger': logger,
'logging': logging})
@property @property
def simulation_name(self): def simulation_name(self):
return self.config.get('name', 'NoSimulationRunning') return self.config.get("name", "NoSimulationRunning")
@run_on_executor @run_on_executor
def nonblocking(self, config): def nonblocking(self, config):
@ -174,28 +218,31 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
@tornado.gen.coroutine @tornado.gen.coroutine
def run_simulation(self): def run_simulation(self):
# Run simulation and capture logs # Run simulation and capture logs
logger.info('Running simulation!') logger.info("Running simulation!")
if 'visualization_params' in self.config: if "visualization_params" in self.config:
del self.config['visualization_params'] del self.config["visualization_params"]
with self.logging(self.simulation_name): with self.logging(self.simulation_name):
try: try:
config = dict(**self.config) config = dict(**self.config)
config['outdir'] = os.path.join(self.application.outdir, config['name']) config["outdir"] = os.path.join(self.application.outdir, config["name"])
config['dump'] = self.application.dump config["dump"] = self.application.dump
self.trials = yield self.nonblocking(config) self.trials = yield self.nonblocking(config)
self.write_message({'type': 'trials', self.write_message(
'data': list(trial.name for trial in self.trials) }) {
"type": "trials",
"data": list(trial.name for trial in self.trials),
}
)
except Exception as ex: except Exception as ex:
error = 'Something went wrong:\n\t{}'.format(ex) error = "Something went wrong:\n\t{}".format(ex)
logging.info(error) logging.info(error)
self.write_message({'type': 'error', self.write_message({"type": "error", "error": error})
'error': error}) self.send_log("ERROR." + self.simulation_name, error)
self.send_log('ERROR.' + self.simulation_name, error)
def get_trial(self, trial): def get_trial(self, trial):
logger.info('Available trials: %s ' % len(self.trials)) logger.info("Available trials: %s " % len(self.trials))
logger.info('Ask for : %s' % trial) logger.info("Ask for : %s" % trial)
trial = self.trials[trial] trial = self.trials[trial]
G = trial.history_to_graph() G = trial.history_to_graph()
return nx.node_link_data(G) return nx.node_link_data(G)
@ -215,25 +262,28 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
self.logger_application.removeHandler(ch) self.logger_application.removeHandler(ch)
self.capture_logging = False self.capture_logging = False
return self.capture_logging return self.capture_logging
class ModularServer(tornado.web.Application): class ModularServer(tornado.web.Application):
""" Main visualization application. """ """Main visualization application."""
port = 8001 port = 8001
page_handler = (r'/', PageHandler) page_handler = (r"/", PageHandler)
socket_handler = (r'/ws', SocketHandler) socket_handler = (r"/ws", SocketHandler)
static_handler = (r'/(.*)', tornado.web.StaticFileHandler, static_handler = (
{'path': os.path.join(ROOT, 'static')}) r"/(.*)",
local_handler = (r'/local/(.*)', tornado.web.StaticFileHandler, tornado.web.StaticFileHandler,
{'path': ''}) {"path": os.path.join(ROOT, "static")},
)
local_handler = (r"/local/(.*)", tornado.web.StaticFileHandler, {"path": ""})
handlers = [page_handler, socket_handler, static_handler, local_handler] handlers = [page_handler, socket_handler, static_handler, local_handler]
settings = {'debug': True, settings = {"debug": True, "template_path": ROOT + "/templates"}
'template_path': ROOT + '/templates'}
def __init__(
self, dump=False, outdir="output", name="SOIL", verbose=True, *args, **kwargs
):
def __init__(self, dump=False, outdir='output', name='SOIL', verbose=True, *args, **kwargs):
self.verbose = verbose self.verbose = verbose
self.name = name self.name = name
self.dump = dump self.dump = dump
@ -243,12 +293,12 @@ class ModularServer(tornado.web.Application):
super().__init__(self.handlers, **self.settings) super().__init__(self.handlers, **self.settings)
def launch(self, port=None): def launch(self, port=None):
""" Run the app. """ """Run the app."""
if port is not None: if port is not None:
self.port = port self.port = port
url = 'http://127.0.0.1:{PORT}'.format(PORT=self.port) url = "http://127.0.0.1:{PORT}".format(PORT=self.port)
print('Interface starting at {url}'.format(url=url)) print("Interface starting at {url}".format(url=url))
self.listen(self.port) self.listen(self.port)
# webbrowser.open(url) # webbrowser.open(url)
tornado.ioloop.IOLoop.instance().start() tornado.ioloop.IOLoop.instance().start()
@ -263,12 +313,22 @@ def run(*args, **kwargs):
def main(): def main():
import argparse import argparse
parser = argparse.ArgumentParser(description='Visualization of a Graph Model') parser = argparse.ArgumentParser(description="Visualization of a Graph Model")
parser.add_argument('--name', '-n', nargs=1, default='SOIL', help='name of the simulation') parser.add_argument(
parser.add_argument('--dump', '-d', help='dumping results in folder output', action='store_true') "--name", "-n", nargs=1, default="SOIL", help="name of the simulation"
parser.add_argument('--port', '-p', nargs=1, default=8001, help='port for launching the server') )
parser.add_argument('--verbose', '-v', help='verbose mode', action='store_true') parser.add_argument(
"--dump", "-d", help="dumping results in folder output", action="store_true"
)
parser.add_argument(
"--port", "-p", nargs=1, default=8001, help="port for launching the server"
)
parser.add_argument("--verbose", "-v", help="verbose mode", action="store_true")
args = parser.parse_args() args = parser.parse_args()
run(name=args.name, port=(args.port[0] if isinstance(args.port, list) else args.port), verbose=args.verbose) run(
name=args.name,
port=(args.port[0] if isinstance(args.port, list) else args.port),
verbose=args.verbose,
)

2
soil/web/__main__.py
View File

@ -2,4 +2,4 @@ from . import main
if __name__ == "__main__": if __name__ == "__main__":
main() main()

27
soil/web/run.py
View File

@ -4,20 +4,33 @@ from simulator import Simulator
def run(simulator, name="SOIL", port=8001, verbose=False): def run(simulator, name="SOIL", port=8001, verbose=False):
server = ModularServer(simulator, name=(name[0] if isinstance(name, list) else name), verbose=verbose) server = ModularServer(
simulator, name=(name[0] if isinstance(name, list) else name), verbose=verbose
)
server.port = port server.port = port
server.launch() server.launch()
if __name__ == "__main__": if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Visualization of a Graph Model') parser = argparse.ArgumentParser(description="Visualization of a Graph Model")
parser.add_argument('--name', '-n', nargs=1, default='SOIL', help='name of the simulation') parser.add_argument(
parser.add_argument('--dump', '-d', help='dumping results in folder output', action='store_true') "--name", "-n", nargs=1, default="SOIL", help="name of the simulation"
parser.add_argument('--port', '-p', nargs=1, default=8001, help='port for launching the server') )
parser.add_argument('--verbose', '-v', help='verbose mode', action='store_true') parser.add_argument(
"--dump", "-d", help="dumping results in folder output", action="store_true"
)
parser.add_argument(
"--port", "-p", nargs=1, default=8001, help="port for launching the server"
)
parser.add_argument("--verbose", "-v", help="verbose mode", action="store_true")
args = parser.parse_args() args = parser.parse_args()
soil = Simulator(dump=args.dump) soil = Simulator(dump=args.dump)
run(soil, name=args.name, port=(args.port[0] if isinstance(args.port, list) else args.port), verbose=args.verbose) run(
soil,
name=args.name,
port=(args.port[0] if isinstance(args.port, list) else args.port),
verbose=args.verbose,
)