def test_setup_simu_use_json_file(self, mock_json_object):
mcstat = gf.setup_mcmc_case_cp(initialize=False)
mcstat.simulation_options.json_restart_file = 1
mcstat._MCMC__setup_simulator(use_previous_results=False)
self.assertTrue(np.array_equal(
mcstat.simulation_options.qcov,
np.array([[0.2, 0.1, 0.05], [0.1, 0.4, 0.02], [0.05, 0.02, 0.6]])),
msg='Expect arrays to match')
self.assertEqual(mcstat.parameters.parameters[0]['theta0'],
0.2,
msg='Expect theta0 = 0.2')
self.assertEqual(mcstat.parameters.parameters[1]['theta0'],
-5.0,
msg='Expect theta0 = -5.0 because sample = 0')
self.assertEqual(mcstat.parameters.parameters[2]['theta0'],
0.7,
msg='Expect theta0 = 0.7')
self.assertEqual(mcstat._MCMC__chain_index,
0,
msg='Chain index should be 0')
self.assertEqual(mcstat._MCMC__chain.shape,
(mcstat.simulation_options.nsimu, 2),
msg=str('Shape should be (nsimu,2) -> {}'.format(
mcstat._MCMC__chain.shape)))
self.assertEqual(mcstat._MCMC__sschain.shape,
(mcstat.simulation_options.nsimu, 1),
msg=str('Shape should be (nsimu,1) -> {}'.format(
mcstat._MCMC__sschain.shape)))
self.assertEqual(mcstat._MCMC__s2chain.shape,
(mcstat.simulation_options.nsimu, 1),
msg=str('Shape should be (nsimu,1) -> {}'.format(
mcstat._MCMC__s2chain.shape)))
def test_standard_print(self):
mcstat = gf.setup_mcmc_case_cp()
capturedOutput = io.StringIO() # Create StringIO object
sys.stdout = capturedOutput # and redirect stdout.
mcstat.display_current_mcmc_settings()
sys.stdout = sys.__stdout__ # Reset redirect.
self.assertTrue(isinstance(capturedOutput.getvalue(), str),
msg='Caputured string')
def common_setup(cls):
mcstat = gf.setup_mcmc_case_cp()
rejectedin = {
'total': 10,
'in_adaptation_interval': 4,
'outside_bounds': 1
}
mcstat._MCMC__rejected = rejectedin.copy()
return mcstat, rejectedin
def setup_pseudo_results(initialize=True):
mcstat = gf.setup_mcmc_case_cp(initialize=initialize)
rejectedin = {
'total': 10,
'in_adaptation_interval': 4,
'outside_bounds': 1
}
mcstat._MCMC__rejected = rejectedin.copy()
mcstat._MCMC__simulation_time = 0.1
return mcstat
def test_cpwe_creation_with_txt(self):
mcstat = gf.setup_mcmc_case_cp()
mcstat.simulation_options.savedir = 'test'
chainfile, s2chainfile, sschainfile, covchainfile = CP._create_path_with_extension_for_all_logs(
options=mcstat.simulation_options, extension='txt')
self.assertEqual(chainfile,
'test/chainfile.txt',
msg='Expect matching string')
self.assertEqual(s2chainfile,
'test/s2chainfile.txt',
msg='Expect matching string')
self.assertEqual(sschainfile,
'test/sschainfile.txt',
msg='Expect matching string')
self.assertEqual(covchainfile,
'test/covchainfile.txt',
msg='Expect matching string')
def test_setup_simu_use_prev_false(self):
mcstat = gf.setup_mcmc_case_cp(initialize=False)
mcstat._MCMC__setup_simulator(use_previous_results=False)
self.assertEqual(mcstat._MCMC__chain_index,
0,
msg='Chain index should be 0')
self.assertEqual(mcstat._MCMC__chain.shape,
(mcstat.simulation_options.nsimu, 2),
msg=str('Shape should be (nsimu,2) -> {}'.format(
mcstat._MCMC__chain.shape)))
self.assertEqual(mcstat._MCMC__sschain.shape,
(mcstat.simulation_options.nsimu, 1),
msg=str('Shape should be (nsimu,1) -> {}'.format(
mcstat._MCMC__sschain.shape)))
self.assertEqual(mcstat._MCMC__s2chain.shape,
(mcstat.simulation_options.nsimu, 1),
msg=str('Shape should be (nsimu,1) -> {}'.format(
mcstat._MCMC__s2chain.shape)))
def test_setup_simu_use_prev_true_causes_error(self):
mcstat = gf.setup_mcmc_case_cp(initialize=False)
with self.assertRaises(SystemExit, msg='No previous results exist'):
mcstat._MCMC__setup_simulator(use_previous_results=True)