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soil
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Add workaround for geometric models

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Closes soil/soil#4
history 0.11
J. Fernando Sánchez 6 years ago
parent 7d1c800490
commit 497c8a55db
3 changed files with 64 additions and 31 deletions
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17
soil/environment.py
Unescape Escape View File

@ -4,6 +4,7 @@ import time
import csv
import random
import simpy
import tempfile
from copy import deepcopy
from networkx.readwrite import json_graph
@ -24,13 +25,16 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
seed=None,
dry_run=False,
dir_path=None,
topology=None,
*args, **kwargs):
self.name = name or 'UnnamedEnvironment'
if isinstance(states, list):
states = dict(enumerate(states))
self.states = deepcopy(states) if states else {}
self.default_state = deepcopy(default_state) or {}
super().__init__(*args, **kwargs)
if not topology:
topology = nx.Graph()
super().__init__(*args, topology=topology, **kwargs)
self._env_agents = {}
self.dry_run = dry_run
self.interval = interval
@ -41,7 +45,7 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
self.process(self.save_state())
self.environment_agents = environment_agents or []
self.network_agents = network_agents or []
self.dir_path = dir_path
self.dir_path = dir_path or tempfile.mkdtemp('soil-env')
if self.dry_run:
self._db_path = ":memory:"
else:
@ -88,6 +92,8 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
@network_agents.setter
def network_agents(self, network_agents):
if not network_agents:
return
for ix in self.G.nodes():
i = ix
node = self.G.node[i]
@ -223,6 +229,13 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
G = self.history_to_graph()
graph_path = os.path.join(self.get_path(dir_path),
self.name+".gexf")
# Workaround for geometric models
# See soil/soil#4
for node in G.nodes():
if 'pos' in G.node[node]:
G.node[node]['viz'] = {"position": {"x": G.node[node]['pos'][0], "y": G.node[node]['pos'][1], "z": 0.0}}
del (G.node[node]['pos'])
nx.write_gexf(G, graph_path, version="1.2draft")
def dump(self, dir_path=None, formats=None):

46
soil/simulation.py
Unescape Escape View File

@ -92,40 +92,46 @@ class SoilSimulation(NetworkSimulation):
def run(self, *args, **kwargs):
return list(self.run_simulation_gen(*args, **kwargs))
def run_simulation_gen(self, *args, parallel=False, **kwargs):
def run_simulation_gen(self, *args, parallel=False, dry_run=False,
**kwargs):
p = Pool()
with utils.timer('simulation'):
if parallel:
func = partial(self.run_trial, return_env=not parallel)
func = partial(self.run_trial, dry_run=dry_run,
return_env=not parallel, **kwargs)
for i in p.imap_unordered(func, range(self.num_trials)):
yield i
else:
for i in range(self.num_trials):
yield self.run_trial(i)
if not self.dry_run:
yield self.run_trial(i, dry_run=dry_run, **kwargs)
if not dry_run or self.dry_run:
logger.info('Dumping results to {}'.format(self.dir_path))
self.dump_pickle(self.dir_path)
self.dump_yaml(self.dir_path)
else:
logger.info('NOT dumping results')
def get_env(self, trial_id=0, dump=False, dir_path=None):
def get_env(self, trial_id=0, **kwargs):
opts = self.environment_params.copy()
env_name = '{}_trial_{}'.format(self.name, trial_id)
env = environment.SoilEnvironment(name=env_name,
topology=self.topology.copy(),
seed=self.seed+env_name,
initial_time=0,
dry_run=self.dry_run,
interval=self.interval,
network_agents=self.network_agents,
states=self.states,
default_state=self.default_state,
environment_agents=self.environment_agents,
dir_path=dir_path or self.dir_path,
**self.environment_params)
opts.update({
'name': env_name,
'topology': self.topology.copy(),
'seed': self.seed+env_name,
'initial_time': 0,
'dry_run': self.dry_run,
'interval': self.interval,
'network_agents': self.network_agents,
'states': self.states,
'default_state': self.default_state,
'environment_agents': self.environment_agents,
'dir_path': self.dir_path,
})
opts.update(kwargs)
env = environment.SoilEnvironment(**opts)
return env
def run_trial(self, trial_id=0, dump=False, dir_path=None, until=None, return_env=False):
def run_trial(self, trial_id=0, until=None, return_env=True, **opts):
"""Run a single trial of the simulation
Parameters
@ -134,13 +140,13 @@ class SoilSimulation(NetworkSimulation):
"""
# Set-up trial environment and graph
until = until or self.max_time
env = self.get_env(trial_id=trial_id, dump=dump, dir_path=dir_path)
env = self.get_env(trial_id=trial_id, **opts)
# Set up agents on nodes
with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)):
env.run(until)
if self.dump and not self.dry_run:
with utils.timer('Dumping simulation {} trial {}'.format(self.name, trial_id)):
env.dump(dir_path, formats=self.dump)
env.dump(formats=self.dump)
if return_env:
return env

32
tests/test_main.py
Unescape Escape View File

@ -2,6 +2,7 @@ from unittest import TestCase
import os
import yaml
import networkx as nx
from functools import partial
from os.path import join
@ -65,13 +66,14 @@ class TestMain(TestCase):
}
}
s = simulation.from_config(config)
s.run_simulation()
s.run_simulation(dry_run=True)
def test_counter_agent(self):
"""
The initial states should be applied to the agent and the
agent should be able to update its state."""
config = {
'name': 'CounterAgent',
'network_params': {
'path': join(ROOT, 'test.gexf')
},
@ -83,7 +85,7 @@ class TestMain(TestCase):
}
}
s = simulation.from_config(config)
env = s.run_simulation()[0]
env = s.run_simulation(dry_run=True)[0]
assert env.get_agent(0)['neighbors', 0] == 10
assert env.get_agent(0)['neighbors', 1] == 1
assert env.get_agent(1)['total', 0] == 12
@ -94,6 +96,7 @@ class TestMain(TestCase):
The evolution of the state should be recorded in the logging agent
"""
config = {
'name': 'CounterAgent',
'network_params': {
'path': join(ROOT, 'test.gexf')
},
@ -108,7 +111,7 @@ class TestMain(TestCase):
}
}
s = simulation.from_config(config)
env = s.run_simulation()[0]
env = s.run_simulation(dry_run=True)[0]
for agent in env.network_agents:
last = 0
assert len(agent[None, None]) == 11
@ -138,7 +141,7 @@ class TestMain(TestCase):
}
}
s = simulation.from_config(config)
env = s.run_simulation()[0]
env = s.run_simulation(dry_run=True)[0]
assert env.get_agent(0).state['neighbors'] == 1
def test_torvalds_example(self):
@ -147,7 +150,7 @@ class TestMain(TestCase):
config['network_params']['path'] = join(EXAMPLES,
config['network_params']['path'])
s = simulation.from_config(config)
env = s.run_simulation()[0]
env = s.run_simulation(dry_run=True)[0]
for a in env.network_agents:
skill_level = a.state['skill_level']
if a.id == 'Torvalds':
@ -177,6 +180,7 @@ class TestMain(TestCase):
recovered = yaml.load(serial)
with utils.timer('deleting'):
del recovered['topology']
del recovered['dry_run']
del recovered['load_module']
assert config == recovered
@ -188,9 +192,10 @@ class TestMain(TestCase):
config = utils.load_file('examples/complete.yml')[0]
s = simulation.from_config(config)
for i in range(5):
s.run_simulation()
s.run_simulation(dry_run=True)
nconfig = s.to_dict()
del nconfig['topology']
del nconfig['dry_run']
del nconfig['load_module']
assert config == nconfig
@ -202,7 +207,7 @@ class TestMain(TestCase):
def test_row_conversion(self):
sim = simulation.SoilSimulation()
env = environment.SoilEnvironment(simulation=sim)
env = environment.SoilEnvironment(dry_run=True)
env['test'] = 'test_value'
env._save_state(now=0)
@ -217,7 +222,14 @@ class TestMain(TestCase):
assert env['env', 0, 'test' ] == 'test_value'
assert env['env', 1, 'test' ] == 'second_value'
def test_save_geometric(self):
"""
There is a bug in networkx that prevents it from creating a GEXF file
from geometric models. We should work around it.
"""
G = nx.random_geometric_graph(20,0.1)
env = environment.SoilEnvironment(topology=G, dry_run=True)
env.dump_gexf('/tmp/dump-gexf')
def make_example_test(path, config):
@ -225,8 +237,10 @@ def make_example_test(path, config):
root = os.getcwd()
os.chdir(os.path.dirname(path))
s = simulation.from_config(config)
envs = s.run_simulation()
envs = s.run_simulation(dry_run=True)
assert envs
for env in envs:
assert env
try:
n = config['network_params']['n']
assert len(env.get_agents()) == n

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