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https://github.com/gsi-upm/soil
synced 2025-08-23 19:52:19 +00:00
Added history class
Now the environment does not deal with history directly, it delegates it to a specific class. The analysis also uses history instances instead of either using the database directly or creating a proxy environment. This should make it easier to change the implementation in the future. In fact, the change was motivated by the large size of the csv files in previous versions. This new implementation only stores results in deltas, and it fills any necessary values when needed.
This commit is contained in:
J. Fernando Sánchez
16
tests/test.csv
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16
tests/test.csv
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agent_id,t_step,key,value,value_type
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a0,0,hello,w,str
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a0,1,hello,o,str
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a0,2,hello,r,str
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a0,3,hello,l,str
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a0,4,hello,d,str
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a0,5,hello,!,str
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env,1,started,,bool
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env,2,started,True,bool
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env,7,started,,bool
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a0,0,hello,w,str
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a0,1,hello,o,str
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a0,2,hello,r,str
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a0,3,hello,l,str
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a0,4,hello,d,str
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a0,5,hello,!,str
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90
tests/test_analysis.py
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90
tests/test_analysis.py
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@@ -0,0 +1,90 @@
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from unittest import TestCase
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import os
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import pandas as pd
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import yaml
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from functools import partial
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from os.path import join
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from soil import simulation, analysis, agents
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ROOT = os.path.abspath(os.path.dirname(__file__))
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class Ping(agents.FSM):
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defaults = {
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'count': 0,
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}
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@agents.default_state
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@agents.state
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def even(self):
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self['count'] += 1
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return self.odd
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@agents.state
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def odd(self):
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self['count'] += 1
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return self.even
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class TestAnalysis(TestCase):
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# Code to generate a simple sqlite history
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def setUp(self):
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"""
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The initial states should be applied to the agent and the
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agent should be able to update its state."""
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config = {
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'name': 'analysis',
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'dry_run': True,
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'seed': 'seed',
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'network_params': {
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'generator': 'complete_graph',
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'n': 2
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},
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'agent_type': Ping,
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'states': [{'interval': 1}, {'interval': 2}],
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'max_time': 30,
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'num_trials': 1,
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'environment_params': {
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}
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}
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s = simulation.from_config(config)
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self.env = s.run_simulation()[0]
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def test_saved(self):
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env = self.env
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assert env.get_agent(0)['count', 0] == 1
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assert env.get_agent(0)['count', 29] == 30
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assert env.get_agent(1)['count', 0] == 1
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assert env.get_agent(1)['count', 29] == 15
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assert env['env', 29, None]['SEED'] == env['env', 29, 'SEED']
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def test_count(self):
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env = self.env
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df = analysis.read_sql(env._history._db)
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res = analysis.get_count(df, 'SEED', 'id')
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assert res['SEED']['seedanalysis_trial_0'].iloc[0] == 1
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assert res['SEED']['seedanalysis_trial_0'].iloc[-1] == 1
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assert res['id']['odd'].iloc[0] == 2
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assert res['id']['even'].iloc[0] == 0
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assert res['id']['odd'].iloc[-1] == 1
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assert res['id']['even'].iloc[-1] == 1
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def test_value(self):
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env = self.env
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df = analysis.read_sql(env._history._db)
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res_sum = analysis.get_value(df, 'count')
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assert res_sum['count'].iloc[0] == 2
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import numpy as np
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res_mean = analysis.get_value(df, 'count', aggfunc=np.mean)
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assert res_mean['count'].iloc[0] == 1
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res_total = analysis.get_value(df)
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res_total['SEED'].iloc[0] == 'seedanalysis_trial_0'
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90
tests/test_history.py
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90
tests/test_history.py
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@@ -0,0 +1,90 @@
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from unittest import TestCase
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import os
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import pandas as pd
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from soil import history, analysis
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ROOT = os.path.abspath(os.path.dirname(__file__))
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class TestHistory(TestCase):
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def test_history(self):
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"""
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"""
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tuples = (
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('a_0', 0, 'id', 'h', ),
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('a_0', 1, 'id', 'e', ),
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('a_0', 2, 'id', 'l', ),
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('a_0', 3, 'id', 'l', ),
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('a_0', 4, 'id', 'o', ),
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('a_1', 0, 'id', 'v', ),
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('a_1', 1, 'id', 'a', ),
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('a_1', 2, 'id', 'l', ),
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('a_1', 3, 'id', 'u', ),
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('a_1', 4, 'id', 'e', ),
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('env', 1, 'prob', 1),
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('env', 3, 'prob', 2),
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('env', 5, 'prob', 3),
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('a_2', 7, 'finished', True),
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)
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h = history.History()
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h.save_tuples(tuples)
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# assert h['env', 0, 'prob'] == 0
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for i in range(1, 7):
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assert h['env', i, 'prob'] == ((i-1)//2)+1
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for i, k in zip(range(5), 'hello'):
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assert h['a_0', i, 'id'] == k
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for record, value in zip(h['a_0', None, 'id'], 'hello'):
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t_step, val = record
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assert val == value
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for i, k in zip(range(5), 'value'):
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assert h['a_1', i, 'id'] == k
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for i in range(5, 8):
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assert h['a_1', i, 'id'] == 'e'
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for i in range(7):
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assert h['a_2', i, 'finished'] == False
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assert h['a_2', 7, 'finished']
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def test_history_gen(self):
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"""
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"""
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tuples = (
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('a_1', 0, 'id', 'v', ),
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('a_1', 1, 'id', 'a', ),
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('a_1', 2, 'id', 'l', ),
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('a_1', 3, 'id', 'u', ),
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('a_1', 4, 'id', 'e', ),
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('env', 1, 'prob', 1),
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('env', 2, 'prob', 2),
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('env', 3, 'prob', 3),
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('a_2', 7, 'finished', True),
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)
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h = history.History()
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h.save_tuples(tuples)
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for t_step, key, value in h['env', None, None]:
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assert t_step == value
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assert key == 'prob'
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records = list(h[None, 7, None])
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assert len(records) == 3
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for i in records:
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agent_id, key, value = i
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if agent_id == 'a_1':
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assert key == 'id'
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assert value == 'e'
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elif agent_id == 'a_2':
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assert key == 'finished'
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assert value == True
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else:
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assert key == 'prob'
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assert value == 3
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records = h['a_1', 7, None]
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assert records['id'] == 'e'
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@@ -22,6 +22,7 @@ class TestMain(TestCase):
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Raise an exception otherwise.
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"""
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config = {
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'dry_run': True,
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'network_params': {
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'path': join(ROOT, 'test.gexf')
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}
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@@ -31,6 +32,7 @@ class TestMain(TestCase):
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assert len(G) == 2
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with self.assertRaises(AttributeError):
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config = {
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'dry_run': True,
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'network_params': {
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'path': join(ROOT, 'unknown.extension')
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}
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@@ -44,6 +46,7 @@ class TestMain(TestCase):
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should be used to generate a network
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"""
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config = {
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'dry_run': True,
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'network_params': {
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'generator': 'barabasi_albert_graph'
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}
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@@ -58,6 +61,7 @@ class TestMain(TestCase):
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def test_empty_simulation(self):
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"""A simulation with a base behaviour should do nothing"""
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config = {
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'dry_run': True,
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'network_params': {
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'path': join(ROOT, 'test.gexf')
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},
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@@ -74,11 +78,12 @@ class TestMain(TestCase):
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agent should be able to update its state."""
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config = {
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'name': 'CounterAgent',
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'dry_run': True,
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'network_params': {
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'path': join(ROOT, 'test.gexf')
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},
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'agent_type': 'CounterModel',
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'states': [{'neighbors': 10}, {'total': 12}],
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'states': [{'times': 10}, {'times': 20}],
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'max_time': 2,
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'num_trials': 1,
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'environment_params': {
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@@ -86,10 +91,10 @@ class TestMain(TestCase):
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}
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s = simulation.from_config(config)
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env = s.run_simulation(dry_run=True)[0]
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assert env.get_agent(0)['neighbors', 0] == 10
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assert env.get_agent(0)['neighbors', 1] == 1
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assert env.get_agent(1)['total', 0] == 12
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assert env.get_agent(1)['neighbors', 1] == 1
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assert env.get_agent(0)['times', 0] == 11
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assert env.get_agent(0)['times', 1] == 12
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assert env.get_agent(1)['times', 0] == 21
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assert env.get_agent(1)['times', 1] == 22
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def test_counter_agent_history(self):
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"""
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@@ -97,6 +102,7 @@ class TestMain(TestCase):
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"""
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config = {
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'name': 'CounterAgent',
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'dry_run': True,
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'network_params': {
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'path': join(ROOT, 'test.gexf')
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},
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@@ -114,11 +120,10 @@ class TestMain(TestCase):
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env = s.run_simulation(dry_run=True)[0]
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for agent in env.network_agents:
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last = 0
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assert len(agent[None, None]) == 11
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for step, total in agent['total', None].items():
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if step > 0:
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assert total == last + 2
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last = total
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assert len(agent[None, None]) == 10
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for step, total in sorted(agent['total', None]):
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assert total == last + 2
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last = total
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def test_custom_agent(self):
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"""Allow for search of neighbors with a certain state_id"""
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@@ -127,6 +132,7 @@ class TestMain(TestCase):
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self.state['neighbors'] = self.count_agents(state_id=0,
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limit_neighbors=True)
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config = {
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'dry_run': True,
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'network_params': {
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'path': join(ROOT, 'test.gexf')
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},
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@@ -150,7 +156,8 @@ class TestMain(TestCase):
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config['network_params']['path'] = join(EXAMPLES,
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config['network_params']['path'])
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s = simulation.from_config(config)
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env = s.run_simulation(dry_run=True)[0]
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s.dry_run = True
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env = s.run_simulation()[0]
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for a in env.network_agents:
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skill_level = a.state['skill_level']
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if a.id == 'Torvalds':
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@@ -174,14 +181,15 @@ class TestMain(TestCase):
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with utils.timer('loading'):
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config = utils.load_file(join(EXAMPLES, 'complete.yml'))[0]
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s = simulation.from_config(config)
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s.dry_run = True
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with utils.timer('serializing'):
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serial = s.to_yaml()
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with utils.timer('recovering'):
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recovered = yaml.load(serial)
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with utils.timer('deleting'):
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del recovered['topology']
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del recovered['dry_run']
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del recovered['load_module']
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del recovered['dry_run']
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assert config == recovered
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def test_configuration_changes(self):
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@@ -191,6 +199,7 @@ class TestMain(TestCase):
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"""
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config = utils.load_file('examples/complete.yml')[0]
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s = simulation.from_config(config)
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s.dry_run = True
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for i in range(5):
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s.run_simulation(dry_run=True)
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nconfig = s.to_dict()
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@@ -206,17 +215,14 @@ class TestMain(TestCase):
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pass
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def test_row_conversion(self):
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sim = simulation.SoilSimulation()
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env = environment.SoilEnvironment(dry_run=True)
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env['test'] = 'test_value'
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env._save_state(now=0)
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res = list(env.history_to_tuples())
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assert len(res) == len(env.environment_params)
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assert ('env', 0, 'test', 'test_value', 'str') in res
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env._now = 1
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env['test'] = 'second_value'
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env._save_state(now=1)
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res = list(env.history_to_tuples())
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assert env['env', 0, 'test' ] == 'test_value'
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