def test_load_ser_sim_res_no_json(self):
tmpfolder = gf.generate_temp_folder()
os.makedirs(tmpfolder)
pres = CP.load_serial_simulation_results(tmpfolder)
shutil.rmtree(tmpfolder)
self.assertTrue(isinstance(pres['chain'], list))
self.assertTrue(isinstance(pres['s2chain'], list))
self.assertEqual(pres['chain'], [])
def test_read_in_parallel_txt(self):
parallel_dir = gf.generate_temp_folder()
mcstat = setup_problem(parallel_dir, case='text')
out = CP.read_in_parallel_savedir_files(parallel_dir=parallel_dir,
extension='txt')
StandardCheck(out[0], mcstat)
StandardCheck(out[1], mcstat)
StandardCheck(out[2], mcstat)
shutil.rmtree(parallel_dir)
def test_read_in_parallel_unknown(self):
parallel_dir = gf.generate_temp_folder()
setup_problem(parallel_dir, case='binary')
out = CP.read_in_parallel_savedir_files(parallel_dir=parallel_dir,
extension='unknown')
self.assertEqual(out[0], None)
self.assertEqual(out[1], None)
self.assertEqual(out[2], None)
shutil.rmtree(parallel_dir)
def test_run_simulation(self):
mcstat = gf.basic_mcmc()
mcstat.simulation_options.nsimu = 100
mcstat.simulation_options.save_to_bin = False
mcstat.simulation_options.save_to_txt = False
mcstat.custom_samplers.append(gf.CustomSampler(nsimu=100))
tmpfolder = gf.generate_temp_folder()
mcstat.simulation_options.savedir = tmpfolder
mcstat.run_simulation()
self.assertTrue(mcstat._mcmc_status,
msg='Expect True if successfully run')
def test_id_chain_no(self):
parallel_dir = gf.generate_temp_folder()
setup_problem(parallel_dir, case='binary')
chainfolders = os.listdir(parallel_dir)
chainfolders2 = CP.check_parallel_directory_contents(
parallel_dir, chainfolders)
self.assertEqual(
chainfolders2, ['chain_0', 'chain_1', 'chain_2'],
msg='List of strings do not match ({}): {} neq {}'.format(
parallel_dir, chainfolders2,
['chain_0', 'chain_1', 'chain_2']))
shutil.rmtree(parallel_dir)
def test_run_simulation(self):
mcstat = gf.basic_mcmc()
mcstat.simulation_options.nsimu = 100
mcstat.simulation_options.save_to_bin = False
mcstat.simulation_options.save_to_txt = False
tmpfolder = gf.generate_temp_folder()
mcstat.simulation_options.savedir = tmpfolder
mcstat.run_simulation()
self.assertTrue(mcstat._mcmc_status,
msg='Expect True if successfully run')
check_these = ['mcmcplot', 'PI', 'chainstats']
for ci in check_these:
self.assertTrue(hasattr(mcstat, ci),
msg=str('object has attribute: {}'.format(ci)))
def test_load_ser_sim_res(self):
tmpfolder = gf.generate_temp_folder()
tmpfolder0 = os.path.join(tmpfolder, 'chain_0')
os.makedirs(tmpfolder0)
tmpfile0 = 'chain_0.json'
tmpfile0 = os.path.join(tmpfolder0, tmpfile0)
results = dict(a=[0, 1], b='hello')
RS = ResultsStructure()
RS.save_json_object(results, tmpfile0)
pres = CP.load_serial_simulation_results(tmpfolder0)
shutil.rmtree(tmpfolder)
self.assertTrue(isinstance(pres['a'], np.ndarray))
self.assertTrue(isinstance(pres['b'], str))
self.assertEqual(pres['b'], 'hello')
def test_save_to_log_file_txt(self):
mcstat = gf.basic_mcmc()
mcstat.simulation_options.save_to_bin = False
mcstat.simulation_options.save_to_txt = True
tmpfolder = gf.generate_temp_folder()
mcstat.simulation_options.savedir = tmpfolder
chains = []
chains.append(
dict(file='chain', mtx=np.random.random_sample((1000, 3))))
savecount, lastbin = mcstat._MCMC__save_to_log_file(chains=chains,
start=0,
end=100)
self.assertEqual(savecount, 0, msg='Expect 0')
self.assertEqual(lastbin, 100, msg='Expect lastbin = end = 100')
shutil.rmtree(tmpfolder)
def test_save_to_log_file_txt_no_append(self):
mcstat = gf.basic_mcmc()
mcstat.simulation_options.save_to_bin = False
mcstat.simulation_options.save_to_txt = True
tmpfolder = gf.generate_temp_folder()
mcstat.simulation_options.savedir = tmpfolder
tmpfile = tmpfolder + os.sep + 'txtlogfile.txt'
chains = []
chains.append(
dict(file='chain', mtx=np.random.random_sample((1000, 3))))
savecount, lastbin = mcstat._MCMC__save_to_log_file(
chains=chains, start=0, end=100, append_to_log=False)
self.assertFalse(os.path.isfile(tmpfile),
msg=str('File exists: {}'.format(tmpfile)))
shutil.rmtree(tmpfolder)
def test_no_save_to_log_file(self):
mcstat = gf.basic_mcmc()
mcstat.simulation_options.save_to_bin = False
mcstat.simulation_options.save_to_txt = False
tmpfolder = gf.generate_temp_folder()
mcstat.simulation_options.savedir = tmpfolder
chains = []
chains.append(
dict(file='chain', mtx=np.random.random_sample((1000, 3))))
savecount, lastbin = mcstat._MCMC__save_to_log_file(chains=chains,
start=0,
end=100)
self.assertEqual(savecount, 0, msg='Expect 0')
self.assertEqual(lastbin, 100, msg='Expect lastbin = end = 100')
self.assertFalse(os.path.isdir(tmpfolder),
msg=str('Folder exists: {}'.format(tmpfolder)))
def test_id_chain_no_with_bad_items(self):
parallel_dir = gf.generate_temp_folder()
setup_problem(parallel_dir, case='binary')
tmpfile = gf.generate_temp_file()
os.mkdir(parallel_dir + os.sep + 'chain')
if not os.path.exists(parallel_dir + os.sep + tmpfile):
with open(parallel_dir + os.sep + tmpfile, 'w'):
pass
chainfolders = os.listdir(parallel_dir)
chainfolders2 = CP.check_parallel_directory_contents(
parallel_dir, chainfolders)
self.assertEqual(
chainfolders2, ['chain_0', 'chain_1', 'chain_2'],
msg='List of strings do not match ({}): {} neq {}'.format(
parallel_dir, chainfolders2,
['chain_0', 'chain_1', 'chain_2']))
shutil.rmtree(parallel_dir)
def test_run_simulation_with_json(self):
mcstat = gf.basic_mcmc()
mcstat.simulation_options.nsimu = 100
mcstat.simulation_options.save_to_bin = False
mcstat.simulation_options.save_to_txt = False
tmpfile = gf.generate_temp_file(extension='json')
tmpfolder = gf.generate_temp_folder()
os.mkdir(tmpfolder)
mcstat.simulation_options.savedir = tmpfolder
mcstat.simulation_options.results_filename = tmpfile
mcstat.simulation_options.save_to_json = True
mcstat.run_simulation()
self.assertTrue(mcstat._mcmc_status,
msg='Expect True if successfully run')
check_these = ['mcmcplot', 'PI', 'chainstats']
for ci in check_these:
self.assertTrue(hasattr(mcstat, ci),
msg=str('object has attribute: {}'.format(ci)))
shutil.rmtree(tmpfolder)
def test_read_in_savedir_files_unknown(self):
mcstat = gf.setup_case()
savedir = gf.generate_temp_folder()
mcstat.simulation_options.savedir = savedir
mcstat.simulation_options.save_to_txt = True
mcstat._MCMC__save_to_log_file(chains=mcstat._MCMC__chains,
start=0,
end=100)
mcstat._MCMC__save_to_log_file(chains=[
dict(mtx=np.dot(mcstat._covariance._R.transpose(),
mcstat._covariance._R))
],
start=0,
end=100,
covmtx=True)
out = CP.read_in_savedir_files(savedir, extension='unknown')
self.assertEqual(out, None, msg='Expect None')
shutil.rmtree(savedir)
def test_read_in_savedir_files_txt(self):
mcstat = gf.setup_case()
savedir = gf.generate_temp_folder()
mcstat.simulation_options.savedir = savedir
mcstat.simulation_options.save_to_txt = True
mcstat._MCMC__save_to_log_file(chains=mcstat._MCMC__chains,
start=0,
end=100)
mcstat._MCMC__save_to_log_file(chains=[
dict(mtx=np.dot(mcstat._covariance._R.transpose(),
mcstat._covariance._R))
],
start=0,
end=100,
covmtx=True)
out = CP.read_in_savedir_files(savedir, extension='txt')
StandardCheck(out, mcstat)
shutil.rmtree(savedir)
def test_print_log_files(self):
mcstat = gf.setup_case()
savedir = gf.generate_temp_folder()
mcstat.simulation_options.savedir = savedir
mcstat.simulation_options.save_to_bin = True
chains = mcstat._MCMC__chains
mcstat._MCMC__save_to_log_file(chains=chains, start=0, end=100)
capturedOutput = io.StringIO()
sys.stdout = capturedOutput
CP.print_log_files(savedir)
sys.stdout = sys.__stdout__
self.assertTrue(isinstance(capturedOutput.getvalue(), str),
msg='Should contain a string')
self.assertTrue('Display log file:' in capturedOutput.getvalue(),
msg='Expect string to contain these words')
shutil.rmtree(savedir)
def test_covmtx_save_to_log_file(self):
mcstat = gf.setup_case()
mcstat.simulation_options.save_to_bin = False
mcstat.simulation_options.save_to_txt = True
tmpfolder = gf.generate_temp_folder()
mcstat.simulation_options.savedir = tmpfolder
tmpfile = tmpfolder + os.sep + 'txtlogfile.txt'
tmptxtfile = tmpfolder + os.sep + 'covchainfile.txt'
savecount, lastbin = mcstat._MCMC__save_to_log_file(chains=[
dict(mtx=np.dot(mcstat._covariance._R.transpose(),
mcstat._covariance._R))
],
start=0,
end=100,
covmtx=True)
self.assertEqual(savecount, 0, msg='Expect 0')
self.assertEqual(lastbin, 100, msg='Expect lastbin = end = 100')
self.assertTrue(os.path.isfile(tmpfile),
msg=str('File exists: {}'.format(tmpfile)))
self.assertTrue(os.path.isfile(tmptxtfile),
msg=str('File exists: {}'.format(tmptxtfile)))
mcstat.simulation_options.save_to_bin = True
mcstat.simulation_options.save_to_txt = False
tmpfile = tmpfolder + os.sep + 'binlogfile.txt'
tmpbinfile = tmpfolder + os.sep + 'covchainfile.h5'
savecount, lastbin = mcstat._MCMC__save_to_log_file(chains=[
dict(mtx=np.dot(mcstat._covariance._R.transpose(),
mcstat._covariance._R))
],
start=0,
end=100,
covmtx=True)
self.assertEqual(savecount, 0, msg='Expect 0')
self.assertEqual(lastbin, 100, msg='Expect lastbin = end = 100')
self.assertTrue(os.path.isfile(tmpfile),
msg=str('File exists: {}'.format(tmpfile)))
self.assertTrue(os.path.isfile(tmpbinfile),
msg=str('File exists: {}'.format(tmpbinfile)))
shutil.rmtree(tmpfolder)
def test_check_directory(self):
tmpfolder = gf.generate_temp_folder()
CP._check_directory(tmpfolder)
self.assertTrue(os.path.isdir(tmpfolder), msg='Directory exists')
os.removedirs(tmpfolder)
def setup_par_mcmc_basic():
mcstat = gf.basic_mcmc()
tmpfolder = gf.generate_temp_folder()
mcstat.simulation_options.savedir = tmpfolder
return mcstat, tmpfolder
def test_check_directory(self):
tmpfolder = gf.generate_temp_folder()
check_directory(tmpfolder)
self.assertTrue(os.path.exists(tmpfolder),
msg='Directory should exist')
shutil.rmtree(tmpfolder)
