def test_save_to_binary_file(self):
tmpfile = gf.generate_temp_file(extension='h5')
CP._save_to_bin_file(filename=tmpfile,
datasetname='d1',
mtx=np.array([0.1, 0.2]))
self.assertTrue(os.path.isfile(tmpfile), msg='File exists')
os.remove(tmpfile)
def test_add_to_log(self):
tmpfile = gf.generate_temp_file(extension='txt')
CP._add_to_log(filename=tmpfile, logstr='hello world')
self.assertTrue(os.path.isfile(tmpfile), msg='File exists')
with open(tmpfile, 'r') as file:
loadstr = file.read()
self.assertEqual(loadstr, 'hello world', msg='Message should match')
os.remove(tmpfile)
def test_save_to_text_file(self):
tmpfile = gf.generate_temp_file(extension='txt')
CP._save_to_txt_file(filename=tmpfile, mtx=np.array([0.1, 0.2]))
self.assertTrue(os.path.isfile(tmpfile), msg='File exists')
loadmtx = np.loadtxt(tmpfile)
self.assertTrue(np.array_equal(loadmtx, np.array([0.1, 0.2])),
msg=str('Arrays should match: {}'.format(loadmtx)))
os.remove(tmpfile)
def test_readingbinaryfile_array(self):
tmpfile = gf.generate_temp_file(extension='h5')
CP._save_to_bin_file(filename=tmpfile,
datasetname='d1',
mtx=np.array([[0.1, 0.2]]))
self.assertTrue(os.path.isfile(tmpfile), msg='File exists')
out = CP.read_in_bin_file(filename=tmpfile)
self.assertTrue(np.array_equal(out, np.array([[0.1, 0.2]])),
msg=str('Expected array match: {}'.format(out)))
os.remove(tmpfile)
def test_dump_to_json_file(self):
RS = ResultsStructure()
tmpfile = gf.generate_temp_file(extension='json')
results = {'model': 4, 'data': np.random.random_sample(size=(1000, 2))}
RS.save_json_object(results=results, filename=tmpfile)
retres = RS.load_json_object(filename=tmpfile)
self.assertEqual(retres['model'],
results['model'],
msg='Model set to 4')
self.assertTrue(np.array_equal(retres['data'], results['data']),
msg='Arrays should be equal')
os.remove(tmpfile)
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)
