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test_runset.py
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"""RunSet tests"""
import os
from cmdstanpy import _TMPDIR
from cmdstanpy.cmdstan_args import CmdStanArgs, SamplerArgs
from cmdstanpy.stanfit import RunSet
from cmdstanpy.utils import EXTENSION
HERE = os.path.dirname(os.path.abspath(__file__))
DATAFILES_PATH = os.path.join(HERE, 'data')
def test_check_repr() -> None:
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
sampler_args = SamplerArgs()
chain_ids = [1, 2, 3, 4] # default
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=chain_ids,
data=jdata,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=4)
assert 'RunSet: chains=4' in repr(runset)
assert 'method=sample' in repr(runset)
assert 'retcodes=[-1, -1, -1, -1]' in repr(runset)
assert 'csv_file' in repr(runset)
assert 'console_msgs' in repr(runset)
assert 'diagnostics_file' not in repr(runset)
def test_check_retcodes() -> None:
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
sampler_args = SamplerArgs()
chain_ids = [1, 2, 3, 4] # default
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=chain_ids,
data=jdata,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=4)
retcodes = runset._retcodes
assert 4 == len(retcodes)
for i in range(len(retcodes)):
assert -1 == runset._retcode(i)
runset._set_retcode(0, 0)
assert 0 == runset._retcode(0)
for i in range(1, len(retcodes)):
assert -1 == runset._retcode(i)
assert not runset._check_retcodes()
for i in range(1, len(retcodes)):
runset._set_retcode(i, 0)
assert runset._check_retcodes()
def test_get_err_msgs() -> None:
exe = os.path.join(DATAFILES_PATH, 'logistic' + EXTENSION)
rdata = os.path.join(DATAFILES_PATH, 'logistic.missing_data.R')
sampler_args = SamplerArgs()
chain_ids = [1, 2, 3]
cmdstan_args = CmdStanArgs(
model_name='logistic',
model_exe=exe,
chain_ids=chain_ids,
data=rdata,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=3, chain_ids=chain_ids)
for i in range(3):
runset._set_retcode(i, 70)
stdout_file = 'chain-' + str(i + 1) + '-missing-data-stdout.txt'
path = os.path.join(DATAFILES_PATH, stdout_file)
runset._stdout_files[i] = path
errs = runset.get_err_msgs()
assert 'Exception: variable does not exist' in errs
def test_output_filenames() -> None:
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
sampler_args = SamplerArgs()
chain_ids = [1, 2, 3, 4]
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=chain_ids,
data=jdata,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=4)
assert 'bernoulli-' in runset._csv_files[0]
assert '_1.csv' in runset._csv_files[0]
assert '_4.csv' in runset._csv_files[3]
def test_commands() -> None:
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
sampler_args = SamplerArgs()
chain_ids = [1, 2, 3, 4]
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=chain_ids,
data=jdata,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=4)
assert 'id=1' in runset.cmd(0)
assert 'id=4' in runset.cmd(3)
def test_save_latent_dynamics() -> None:
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
sampler_args = SamplerArgs()
chain_ids = [1, 2, 3, 4]
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=chain_ids,
data=jdata,
method_args=sampler_args,
save_latent_dynamics=True,
)
runset = RunSet(args=cmdstan_args, chains=4)
assert _TMPDIR in runset.diagnostic_files[0]
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=chain_ids,
data=jdata,
method_args=sampler_args,
save_latent_dynamics=True,
output_dir=os.path.abspath('.'),
)
runset = RunSet(args=cmdstan_args, chains=4)
assert os.path.abspath('.') in runset.diagnostic_files[0]
def test_chain_ids() -> None:
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
sampler_args = SamplerArgs()
chain_ids = [11, 12, 13, 14]
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=chain_ids,
data=jdata,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=4, chain_ids=chain_ids)
assert 'id=11' in runset.cmd(0)
assert '_11.csv' in runset._csv_files[0]
assert 'id=14' in runset.cmd(3)
assert '_14.csv' in runset._csv_files[3]