def test__get_header_string():
f = PyposmatBadParametersFile()
parameter_names = ['a', 'b', 'c']
filename = 'test.out'
f = PyposmatBadParametersFile()
s = f.get_header_string(parameter_names=parameter_names)
assert type(s) is str
header_line_1 = ['sim_id'] + parameter_names + ['reason']
header_line_2 = ['sim_id'] + len(parameter_names) * ['param'] + ['reason']
s_test = "{}\n".format(",".join(header_line_1))
s_test += "{}\n".format(",".join(header_line_2))
assert s_test == s
def configure_pyposmat_badparameters_file(self, filename=None):
if filename is not None:
assert type(filename) is str
self.pyposmat_badparameters_filename = filename
self.pyposmat_badparameters = PyposmatBadParametersFile(
filename=self.pyposmat_badparameters_filename,
o_config=self.configuration)
def dev__get_header_string():
testing_set = get_testing_set()
print(os.path.isfile(testing_set['config_fn']), testing_set['config_fn'])
o = PyposmatBadParametersFile(filename=testing_set['badparameters_out_fn'],
config_fn=testing_set['config_fn'])
print(o.get_header_string())
def test____init____w_filename():
test_badparameters_fn = 'test_filename.out'
if os.path.isfile(test_badparameters_fn):
os.remove(test_badparameters_fn)
o = PyposmatBadParametersFile(filename=test_badparameters_fn)
assert o.filename == test_badparameters_fn
assert not os.path.isfile(test_badparameters_fn)
assert o.configuration is None
def test__write_header_string__no_args():
testing_set = get_testing_set()
o = PyposmatBadParametersFile(filename=testing_set['badparameters_out_fn'],
config_fn=testing_set['config_fn'])
o.write_header_section()
assert os.path.isfile(testing_set['badparameters_out_fn'])
if os.path.isfile(testing_set['badparameters_out_fn']):
os.remove(testing_set['badparameters_out_fn'])
def test__write_header_string__w_filename():
testing_set = get_testing_set()
badparameters_out_fn = 'pyposmat.badparameters.test'
o = PyposmatBadParametersFile(filename=testing_set['badparameters_out_fn'],
config_fn=testing_set['config_fn'])
o.write_header_section(filename=badparameters_out_fn)
assert os.path.isfile(badparameters_out_fn)
if os.path.isfile(badparameters_out_fn):
os.remove(badparameters_out_fn)
def test__write_header_section():
parameter_names = ['a,b,c']
filename = 'test.out'
if os.path.isfile(filename):
os.remove(filename)
f = PyposmatBadParametersFile()
f.write_header_section(parameter_names=parameter_names, filename=filename)
assert os.path.isfile(filename)
if os.path.isfile(filename):
os.remove(filename)
def dev__get_header_string():
parameter_names = ['a', 'b', 'c']
filename = 'test.out'
f = PyposmatBadParametersFile()
s = f.get_header_string(parameter_names=parameter_names)
header_line_1 = ['sim_id'] + parameter_names + ['reason']
header_line_2 = ['sim_id'] + len(parameter_names) * ['param'] + ['reason']
s_test = "{}\n".format(",".join(header_line_1))
s_test += "{}\n".format(",".join(header_line_2))
print(s_test)
print(s)
print(s_test == s)
def dev__write_header_section():
print(80 * '-')
print('{:^80}'.format('write_header_section'))
print(80 * '-')
testing_set = get_testing_set()
if os.path.isfile(testing_set['filename']):
os.remove(testing_set['filename'])
f = PyposmatBadParametersFile()
f.write_header_section(parameter_names=testing_set['parameter_names'],
filename=testing_set['filename'])
with open(testing_set['filename'], 'r') as f:
print(f.read())
def test__read():
testing_set = get_testing_set()
assert os.path.isfile(testing_set['badparameters_in_fn'])
assert os.path.isfile(testing_set['config_fn'])
if os.path.isfile(testing_set['badparameters_out_fn']):
m = "removing the badparameter_out_file:{}".format(
testing_set['badparameters_out_fn'])
print(m)
os.remove(testing_set['badparameters_out_fn'])
o = PyposmatBadParametersFile(
filename=testing_set['badparameters_out_fn'],
config_fn=testing_set['config_fn'])
o.read(filename=testing_set['badparameters_in_fn'])
assert isinstance(o.df,pd.DataFrame)
def dev__write_simulation_exception():
import importlib
testing_set = get_testing_set()
o = PyposmatBadParametersFile()
o.write_header_section(parameter_names=testing_set['parameter_names'],
filename=testing_set['filename'])
module_name = 'pypospack.exceptions'
module = importlib.import_module(module_name)
class_names = ['LammpsSimulationError']
for class_name in class_names:
sim_id = class_name
m = "message"
exception = getattr(module,
class_name)(m,
parameters=testing_set['parameters'])
o.write_simulation_exception(sim_id=sim_id, exception=exception)
def test____init____w_filename_config_fn():
testing_set = get_testing_set()
assert os.path.isfile(testing_set['badparameters_in_fn'])
assert os.path.isfile(testing_set['config_fn'])
if os.path.isfile(testing_set['badparameters_out_fn']):
m = "removing the badparameter_out_file:{}".format(
testing_set['badparameters_out_fn'])
print(m)
os.remove(testing_set['badparameters_out_fn'])
o = PyposmatBadParametersFile(filename=testing_set['badparameters_out_fn'],
config_fn=testing_set['config_fn'])
assert o.filename == testing_set['badparameters_out_fn']
from pypospack.pyposmat.data import PyposmatConfigurationFile
o_config = PyposmatConfigurationFile()
o_config.read(filename=testing_set['config_fn'])
assert isinstance(o.configuration, PyposmatConfigurationFile)
assert isinstance(o.parameter_names, list)
assert set(o.parameter_names) == set(o_config.parameter_names)
def test__get_header_string():
testing_set = get_testing_set()
o_config = PyposmatConfigurationFile()
o_config.read(filename=testing_set['config_fn'])
assert os.path.isfile(testing_set['config_fn'])
f = PyposmatBadParametersFile(filename=testing_set['badparameters_out_fn'],
config_fn=testing_set['config_fn'])
s = f.get_header_string()
assert type(s) is str
header_line_1 = ['sim_id'] \
+ o_config.parameter_names \
+ ['reason']
header_line_2 = ['sim_id'] \
+ len(o_config.parameter_names)*['param'] \
+ ['reason']
s_test = "{}\n".format(",".join(header_line_1))
s_test += "{}\n".format(",".join(header_line_2))
assert s_test == s
def test____init____wo_filename():
o = PyposmatBadParametersFile()
assert o.filename == 'pyposmat.badparameters.out'
assert o.configuration is None
def merge_error_files(self, i_iteration):
""" merge the pyposmat data files
Args:
i_iteration(int): the current iteration which just finished
last_datafile_fn(str,optional): the filename of the last dataset in the data directory.
new_datafile_fn(str,optional): where to output the file results
"""
badparameters_fn = os.path.join(self.data_directory,
'pyposmat.badparameters.out')
data_dir = self.data_directory
rank_dirs = [
v for v in os.listdir(self.root_directory) if v.startswith('rank_')
]
filenames = [
os.path.join(self.root_directory, v, 'pyposmat.badparameters.out')
for v in rank_dirs
]
# consolidate rank directories
badparameters_new = None
badparameters_next = None
for i, v in enumerate(filenames):
if badparameters_new is None:
try:
badparameters_new = PyposmatBadParametersFile(
o_config=self.configuration)
badparameters_new.read(filename=v)
except FileNotFoundError as e:
self.log("no bad parameters file at {}".format(v))
else:
try:
badparameters_next = PyposmatBadParametersFile(
o_config=self.configuration)
badparameters_next.read(filename=v)
badparameters_new.df = pd.concat(
[badparameters_new.df, badparameters_next.df])
except FileNotFoundError as e:
self.log("no bad parameters file as {}".format(v))
# determine the sim_id for bad parameters of the sim_id
if badparameters_new.df is None:
# no previous bad paramters found
# TODO: need to implement something here to deal with bad parameters
pass
else:
nrows = len(badparameters_new.df)
sim_id_fmt = '{:0>2}_{:0>6}'
sim_id_str = [
sim_id_fmt.format(i_iteration, i) for i in range(nrows)
]
badparameters_new.df['sim_id'] = sim_id_str
if self.configuration.sampling_type[i_iteration][
'type'] == "from_file":
badparameters_new.write(filename=badparameters_fn)
else:
self.log(
"merging with bad candidates from previous simulations")
self.log("\tfilename:{}".format(badparameters_fn))
badparameters = PyposmatBadParametersFile(
o_config=self.configuration)
try:
badparameters.read(filename=badparameters_fn)
badparameters.df = pd.concat(
[badparameters.df, badparameters_new.df])
badparameters.write(filename=badparameters_fn)
except FileNotFoundError as e:
if i_iteration == 0:
badparameters_new.write(filename=badparameters_fn)
else:
raise