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Modified the parameters used to call the Gaussian and exponential HMC…
… walks in bindings. Added tests to check they work as expected
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# dingo : a python library for metabolic networks sampling and analysis | ||
# dingo is part of GeomScale project | ||
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# Copyright (c) 2022 Apostolos Chalkis | ||
# Copyright (c) 2022 Vissarion Fisikopoulos | ||
# Copyright (c) 2022 Haris Zafeiropoulos | ||
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# Licensed under GNU LGPL.3, see LICENCE file | ||
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import unittest | ||
import os | ||
from dingo import MetabolicNetwork, PolytopeSampler | ||
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class TestSampling(unittest.TestCase): | ||
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def test_sample_json(self): | ||
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input_file_json = os.getcwd() + "/ext_data/e_coli_core.json" | ||
model = MetabolicNetwork.from_json( input_file_json ) | ||
sampler = PolytopeSampler(model) | ||
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#gaussian hmc sampling | ||
steady_states = sampler.generate_steady_states_no_multiphase(method = 'gaussian_hmc_walk') | ||
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self.assertTrue( steady_states.shape[0] == 95 ) | ||
self.assertTrue( abs( steady_states[12].mean() - 2.504 ) < 1e-03 ) | ||
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#exponential hmc sampling | ||
steady_states = sampler.generate_steady_states_no_multiphase(method = 'exponential_hmc_walk') | ||
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self.assertTrue( steady_states.shape[0] == 95 ) | ||
self.assertTrue( abs( steady_states[12].mean() - 2.504 ) < 1e-03 ) | ||
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def test_sample_mat(self): | ||
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input_file_mat = os.getcwd() + "/ext_data/e_coli_core.mat" | ||
model = MetabolicNetwork.from_mat(input_file_mat) | ||
sampler = PolytopeSampler(model) | ||
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#gaussian hmc sampling | ||
steady_states = sampler.generate_steady_states_no_multiphase(method = 'gaussian_hmc_walk') | ||
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self.assertTrue( steady_states.shape[0] == 95 ) | ||
self.assertTrue( abs( steady_states[12].mean() - 2.504 ) < 1e-03 ) | ||
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#exponential hmc sampling | ||
steady_states = sampler.generate_steady_states_no_multiphase(method = 'exponential_hmc_walk') | ||
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self.assertTrue( steady_states.shape[0] == 95 ) | ||
self.assertTrue( abs( steady_states[12].mean() - 2.504 ) < 1e-03 ) | ||
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def test_sample_sbml(self): | ||
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input_file_sbml = os.getcwd() + "/ext_data/e_coli_core.xml" | ||
model = MetabolicNetwork.from_sbml( input_file_sbml ) | ||
sampler = PolytopeSampler(model) | ||
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#gaussian hmc sampling | ||
steady_states = sampler.generate_steady_states_no_multiphase(method = 'gaussian_hmc_walk') | ||
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self.assertTrue( steady_states.shape[0] == 95 ) | ||
self.assertTrue( abs( steady_states[12].mean() - 2.504 ) < 1e-03 ) | ||
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#exponential hmc sampling | ||
steady_states = sampler.generate_steady_states_no_multiphase(method = 'exponential_hmc_walk') | ||
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self.assertTrue( steady_states.shape[0] == 95 ) | ||
self.assertTrue( abs( steady_states[12].mean() - 2.504 ) < 1e-03 ) | ||
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if __name__ == "__main__": | ||
unittest.main() |