def test_no_chains(self):
# we don't have chains for optimize
exe = os.path.join(datafiles_path, 'bernoulli')
sampler_args = FixedParamArgs()
jinits = os.path.join(datafiles_path, 'bernoulli.init.json')
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=None,
inits=jinits,
method_args=sampler_args,
)
self.assertIn('init=', cmdstan_args.compose_command(None, 'out.csv'))
with self.assertRaises(ValueError):
CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=None,
seed=[1, 2, 3],
inits=jinits,
method_args=sampler_args,
)
with self.assertRaises(ValueError):
CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=None,
inits=[jinits],
method_args=sampler_args,
)
def test_no_chains(self):
exe = os.path.join(datafiles_path, 'bernoulli')
jdata = os.path.join(datafiles_path, 'bernoulli.data.json')
jinits = os.path.join(datafiles_path, 'bernoulli.init.json')
sampler_args = SamplerArgs()
with self.assertRaises(ValueError):
CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=None,
seed=[1, 2, 3],
data=jdata,
inits=jinits,
method_args=sampler_args
)
with self.assertRaises(ValueError):
CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=None,
data=jdata,
inits=[jinits],
method_args=sampler_args
)
def test_save_latent_dynamics(self):
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)
self.assertIn(_TMPDIR, 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)
self.assertIn(os.path.abspath('.'), runset.diagnostic_files[0])
def test_validate_big_run(self):
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
sampler_args = SamplerArgs(iter_warmup=1500, iter_sampling=1000)
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[1, 2],
seed=12345,
output_dir=DATAFILES_PATH,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=2)
runset._csv_files = [
os.path.join(DATAFILES_PATH, 'runset-big',
'output_icar_nyc-1.csv'),
os.path.join(DATAFILES_PATH, 'runset-big',
'output_icar_nyc-1.csv'),
]
fit = CmdStanMCMC(runset)
phis = ['phi[{}]'.format(str(x + 1)) for x in range(2095)]
column_names = SAMPLER_STATE + phis
self.assertEqual(fit.num_draws_sampling, 1000)
self.assertEqual(fit.column_names, tuple(column_names))
self.assertEqual(fit.metric_type, 'diag_e')
self.assertEqual(fit.step_size.shape, (2, ))
self.assertEqual(fit.metric.shape, (2, 2095))
self.assertEqual((1000, 2, 2102), fit.draws().shape)
phis = fit.draws_pd(params=['phi'])
self.assertEqual((2000, 2095), phis.shape)
with self.assertRaisesRegex(ValueError, r'unknown parameter: gamma'):
fit.draws_pd(params=['gamma'])
def test_instantiate(self):
stan = os.path.join(DATAFILES_PATH, 'variational',
'eta_should_be_big.stan')
model = CmdStanModel(stan_file=stan)
no_data = {}
args = VariationalArgs(algorithm='meanfield')
cmdstan_args = CmdStanArgs(
model_name=model.name,
model_exe=model.exe_file,
chain_ids=None,
data=no_data,
method_args=args,
)
runset = RunSet(args=cmdstan_args, chains=1)
runset._csv_files = [
os.path.join(DATAFILES_PATH, 'variational', 'eta_big_output.csv')
]
variational = CmdStanVB(runset)
self.assertIn('CmdStanVB: model=eta_should_be_big',
variational.__repr__())
self.assertIn('method=variational', variational.__repr__())
self.assertEqual(
variational.column_names,
('lp__', 'log_p__', 'log_g__', 'mu[1]', 'mu[2]'),
)
self.assertAlmostEqual(variational.variational_params_dict['mu[1]'],
31.0299,
places=2)
self.assertAlmostEqual(variational.variational_params_dict['mu[2]'],
28.8141,
places=2)
self.assertEqual(variational.variational_sample.shape, (1000, 5))
def __init__(self,
args: CmdStanArgs,
chains: int = 4,
logger: logging.Logger = None) -> None:
"""Initialize object."""
self._args = args
self._chains = chains
self._logger = logger or get_logger()
if chains < 1:
raise ValueError('chains must be positive integer value, '
'found {i]}'.format(chains))
self._csv_files = []
if args.output_basename is None:
csv_basename = 'stan-{}-{}'.format(args.model_name, args.method)
for i in range(chains):
fd_name = create_named_text_file(
dir=TMPDIR,
prefix='{}-{}-'.format(csv_basename, i + 1),
suffix='.csv',
)
self._csv_files.append(fd_name)
else:
for i in range(chains):
self._csv_files.append('{}-{}.csv'.format(
args.output_basename, i + 1))
self._console_files = []
for i in range(chains):
txt_file = ''.join(
[os.path.splitext(self._csv_files[i])[0], '.txt'])
self._console_files.append(txt_file)
self._cmds = [
args.compose_command(i, self._csv_files[i]) for i in range(chains)
]
self._retcodes = [-1 for _ in range(chains)]
def test_variables(self):
# construct fit using existing sampler output
exe = os.path.join(DATAFILES_PATH, 'lotka-volterra' + EXTENSION)
jdata = os.path.join(DATAFILES_PATH, 'lotka-volterra.data.json')
sampler_args = SamplerArgs(iter_sampling=20)
cmdstan_args = CmdStanArgs(
model_name='lotka-volterra',
model_exe=exe,
chain_ids=[1],
seed=12345,
data=jdata,
output_dir=DATAFILES_PATH,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=1)
runset._csv_files = [
os.path.join(DATAFILES_PATH, 'lotka-volterra.csv')
]
runset._set_retcode(0, 0)
fit = CmdStanMCMC(runset)
self.assertEqual(20, fit.num_draws)
self.assertEqual(8, len(fit._stan_variable_dims))
self.assertTrue('z' in fit._stan_variable_dims)
self.assertEqual(fit._stan_variable_dims['z'], (20, 2))
vars = fit.stan_variables()
self.assertEqual(len(vars), len(fit._stan_variable_dims))
self.assertTrue('z' in vars)
self.assertEqual(vars['z'].shape, (20, 20, 2))
self.assertTrue('theta' in vars)
self.assertEqual(vars['theta'].shape, (20, 4))
def test_diagnose_divergences(self):
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
sampler_args = SamplerArgs()
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[1],
output_dir=DATAFILES_PATH,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=1)
runset._csv_files = [
os.path.join(DATAFILES_PATH, 'diagnose-good',
'corr_gauss_depth8-1.csv')
]
fit = CmdStanMCMC(runset)
# TODO - use cmdstan test files instead
expected = '\n'.join([
'Checking sampler transitions treedepth.',
'424 of 1000 (42%) transitions hit the maximum '
'treedepth limit of 8, or 2^8 leapfrog steps.',
'Trajectories that are prematurely terminated '
'due to this limit will result in slow exploration.',
'For optimal performance, increase this limit.',
])
self.assertIn(expected, fit.diagnose().replace('\r\n', '\n'))
def test_set_mle_attrs(self):
stan = os.path.join(datafiles_path, 'optimize', 'rosenbrock.stan')
model = CmdStanModel(stan_file=stan)
no_data = {}
args = OptimizeArgs(algorithm='Newton')
cmdstan_args = CmdStanArgs(
model_name=model.name,
model_exe=model.exe_file,
chain_ids=None,
data=no_data,
method_args=args,
)
runset = RunSet(args=cmdstan_args, chains=1)
mle = CmdStanMLE(runset)
self.assertIn('CmdStanMLE: model=rosenbrock', mle.__repr__())
self.assertIn('method=optimize', mle.__repr__())
self.assertEqual(mle._column_names, ())
self.assertEqual(mle._mle, {})
output = os.path.join(datafiles_path, 'optimize', 'rosenbrock_mle.csv')
mle._set_mle_attrs(output)
self.assertEqual(mle.column_names, ('lp__', 'x', 'y'))
self.assertAlmostEqual(mle.optimized_params_dict['x'], 1, places=3)
self.assertAlmostEqual(mle.optimized_params_dict['y'], 1, places=3)
def test_check_retcodes(self):
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
self.assertEqual(4, len(retcodes))
for i in range(len(retcodes)):
self.assertEqual(-1, runset._retcode(i))
runset._set_retcode(0, 0)
self.assertEqual(0, runset._retcode(0))
for i in range(1, len(retcodes)):
self.assertEqual(-1, runset._retcode(i))
self.assertFalse(runset._check_retcodes())
for i in range(1, len(retcodes)):
runset._set_retcode(i, 0)
self.assertTrue(runset._check_retcodes())
def test_set_variational_attrs(self):
stan = os.path.join(datafiles_path, 'variational',
'eta_should_be_big.stan')
model = CmdStanModel(stan_file=stan)
no_data = {}
args = VariationalArgs(algorithm='meanfield')
cmdstan_args = CmdStanArgs(model_name=model.name,
model_exe=model.exe_file,
chain_ids=None,
data=no_data,
method_args=args)
runset = RunSet(args=cmdstan_args, chains=1)
vi = CmdStanVB(runset)
self.assertIn('CmdStanVB: model=eta_should_be_big', vi.__repr__())
self.assertIn('method=variational', vi.__repr__())
# check CmdStanVB.__init__ state
self.assertEqual(vi._column_names, ())
self.assertEqual(vi._variational_mean, {})
self.assertEqual(vi._variational_sample, None)
# process csv file, check attrs
output = os.path.join(datafiles_path, 'variational',
'eta_big_output.csv')
vi._set_variational_attrs(output)
self.assertEqual(vi.column_names,
('lp__', 'log_p__', 'log_g__', 'mu.1', 'mu.2'))
self.assertAlmostEqual(vi.variational_params_dict['mu.1'],
31.0299,
places=2)
self.assertAlmostEqual(vi.variational_params_dict['mu.2'],
28.8141,
places=2)
self.assertEqual(vi.variational_sample.shape, (1000, 5))
def test_good(self):
# construct fit using existing sampler output
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
sampler_args = SamplerArgs(iter_sampling=100,
max_treedepth=11,
adapt_delta=0.95)
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[1, 2, 3, 4],
seed=12345,
data=jdata,
output_dir=DATAFILES_PATH,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args)
runset._csv_files = [
os.path.join(DATAFILES_PATH, 'runset-good', 'bern-1.csv'),
os.path.join(DATAFILES_PATH, 'runset-good', 'bern-2.csv'),
os.path.join(DATAFILES_PATH, 'runset-good', 'bern-3.csv'),
os.path.join(DATAFILES_PATH, 'runset-good', 'bern-4.csv'),
]
retcodes = runset._retcodes
for i in range(len(retcodes)):
runset._set_retcode(i, 0)
config = check_sampler_csv(
path=runset.csv_files[i],
is_fixed_param=False,
iter_sampling=100,
iter_warmup=1000,
save_warmup=False,
thin=1,
)
expected = 'Metadata:\n{}\n'.format(config)
metadata = InferenceMetadata(config)
actual = '{}'.format(metadata)
self.assertEqual(expected, actual)
self.assertEqual(config, metadata.cmdstan_config)
hmc_vars = {
'lp__',
'accept_stat__',
'stepsize__',
'treedepth__',
'n_leapfrog__',
'divergent__',
'energy__',
}
sampler_vars_cols = metadata.sampler_vars_cols
self.assertEqual(hmc_vars, sampler_vars_cols.keys())
bern_model_vars = {'theta'}
self.assertEqual(bern_model_vars, metadata.stan_vars_dims.keys())
self.assertEqual((), metadata.stan_vars_dims['theta'])
self.assertEqual(bern_model_vars, metadata.stan_vars_cols.keys())
self.assertEqual((7, ), metadata.stan_vars_cols['theta'])
def test_validate_good_run(self):
# construct fit using existing sampler output
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
sampler_args = SamplerArgs(iter_sampling=100,
max_treedepth=11,
adapt_delta=0.95)
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[1, 2, 3, 4],
seed=12345,
data=jdata,
output_dir=DATAFILES_PATH,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=4)
runset._csv_files = [
os.path.join(DATAFILES_PATH, 'runset-good', 'bern-1.csv'),
os.path.join(DATAFILES_PATH, 'runset-good', 'bern-2.csv'),
os.path.join(DATAFILES_PATH, 'runset-good', 'bern-3.csv'),
os.path.join(DATAFILES_PATH, 'runset-good', 'bern-4.csv'),
]
self.assertEqual(4, runset.chains)
retcodes = runset._retcodes
for i in range(len(retcodes)):
runset._set_retcode(i, 0)
self.assertTrue(runset._check_retcodes())
fit = CmdStanMCMC(runset)
self.assertEqual(100, fit.num_draws)
self.assertEqual(len(BERNOULLI_COLS), len(fit.column_names))
self.assertEqual('lp__', fit.column_names[0])
drawset = fit.get_drawset()
self.assertEqual(
drawset.shape,
(fit.runset.chains * fit.num_draws, len(fit.column_names)),
)
_ = fit.summary()
self.assertTrue(True)
# TODO - use cmdstan test files instead
expected = '\n'.join([
'Checking sampler transitions treedepth.',
'Treedepth satisfactory for all transitions.',
'\nChecking sampler transitions for divergences.',
'No divergent transitions found.',
'\nChecking E-BFMI - sampler transitions HMC potential energy.',
'E-BFMI satisfactory for all transitions.',
'\nEffective sample size satisfactory.',
])
self.assertIn(expected, fit.diagnose().replace('\r\n', '\n'))
def test_args_good(self):
exe = os.path.join(datafiles_path, 'bernoulli')
jdata = os.path.join(datafiles_path, 'bernoulli.data.json')
sampler_args = SamplerArgs()
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[1, 2, 3, 4],
data=jdata,
method_args=sampler_args,
)
self.assertEqual(cmdstan_args.method, Method.SAMPLE)
cmd = cmdstan_args.compose_command(idx=0, csv_file='bern-output-1.csv')
self.assertIn('id=1 random seed=', ' '.join(cmd))
self.assertIn('data file=', ' '.join(cmd))
self.assertIn('output file=', ' '.join(cmd))
self.assertIn('method=sample algorithm=hmc', ' '.join(cmd))
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[7, 11, 18, 29],
data=jdata,
method_args=sampler_args,
)
cmd = cmdstan_args.compose_command(idx=0, csv_file='bern-output-1.csv')
self.assertIn('id=7 random seed=', ' '.join(cmd))
def test_gen_quantities_good(self):
stan = os.path.join(datafiles_path, 'bernoulli_ppc.stan')
model = Model(stan_file=stan)
model.compile()
jdata = os.path.join(datafiles_path, 'bernoulli.data.json')
# synthesize stanfit object -
# see test_stanfit.py, method 'test_validate_good_run'
goodfiles_path = os.path.join(datafiles_path, 'runset-good')
output = os.path.join(goodfiles_path, 'bern')
sampler_args = SamplerArgs(
sampling_iters=100, max_treedepth=11, adapt_delta=0.95
)
cmdstan_args = CmdStanArgs(
model_name=model.name,
model_exe=model.exe_file,
chain_ids=[1, 2, 3, 4],
seed=12345,
data=jdata,
output_basename=output,
method_args=sampler_args,
)
sampler_fit = StanFit(args=cmdstan_args, chains=4)
for i in range(4):
sampler_fit._set_retcode(i, 0)
bern_fit = model.run_generated_quantities(
csv_files=sampler_fit.csv_files,
data=jdata)
# check results - ouput files, quantities of interest, draws
self.assertEqual(bern_fit.chains, 4)
for i in range(4):
self.assertEqual(bern_fit._retcodes[i], 0)
csv_file = bern_fit.csv_files[i]
self.assertTrue(os.path.exists(csv_file))
column_names = [
'y_rep.1',
'y_rep.2',
'y_rep.3',
'y_rep.4',
'y_rep.5',
'y_rep.6',
'y_rep.7',
'y_rep.8',
'y_rep.9',
'y_rep.10'
]
self.assertEqual(bern_fit.column_names, tuple(column_names))
self.assertEqual(bern_fit.draws, 100)
def test_commands(self):
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
sampler_args = SamplerArgs()
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[1, 2, 3, 4],
data=jdata,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=4)
self.assertIn('id=1', runset._cmds[0])
self.assertIn('id=4', runset._cmds[3])
def test_validate_big_run(self):
exe = os.path.join(DATAFILES_PATH, 'bernoulli' + EXTENSION)
sampler_args = SamplerArgs()
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[1, 2],
seed=12345,
output_dir=DATAFILES_PATH,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=2)
runset._csv_files = [
os.path.join(DATAFILES_PATH, 'runset-big',
'output_icar_nyc-1.csv'),
os.path.join(DATAFILES_PATH, 'runset-big',
'output_icar_nyc-1.csv'),
]
fit = CmdStanMCMC(runset)
fit._validate_csv_files()
sampler_state = [
'lp__',
'accept_stat__',
'stepsize__',
'treedepth__',
'n_leapfrog__',
'divergent__',
'energy__',
]
phis = ['phi.{}'.format(str(x + 1)) for x in range(2095)]
column_names = sampler_state + phis
self.assertEqual(fit.columns, len(column_names))
self.assertEqual(fit.column_names, tuple(column_names))
self.assertEqual(fit.metric_type, 'diag_e')
self.assertEqual(fit.stepsize.shape, (2, ))
self.assertEqual(fit.metric.shape, (2, 2095))
self.assertEqual((1000, 2, 2102), fit.sample.shape)
phis = fit.get_drawset(params=['phi'])
self.assertEqual((2000, 2095), phis.shape)
phi1 = fit.get_drawset(params=['phi.1'])
self.assertEqual((2000, 1), phi1.shape)
mo_phis = fit.get_drawset(params=['phi.1', 'phi.10', 'phi.100'])
self.assertEqual((2000, 3), mo_phis.shape)
phi2095 = fit.get_drawset(params=['phi.2095'])
self.assertEqual((2000, 1), phi2095.shape)
with self.assertRaises(Exception):
fit.get_drawset(params=['phi.2096'])
with self.assertRaises(Exception):
fit.get_drawset(params=['ph'])
def __init__(self,
args: CmdStanArgs,
chains: int = 4,
logger: logging.Logger = None) -> None:
"""Initialize object."""
self._args = args
self._is_optimizing = isinstance(self._args.method_args, OptimizeArgs)
self._chains = chains
self._logger = logger or get_logger()
if chains < 1:
raise ValueError('chains must be positive integer value, '
'found {i]}'.format(chains))
self.csv_files = []
"""per-chain sample csv files."""
if args.output_basename is None:
csv_basename = 'stan-{}-draws'.format(args.model_name)
for i in range(chains):
fd = tempfile.NamedTemporaryFile(
mode='w+',
prefix='{}-{}-'.format(csv_basename, i + 1),
suffix='.csv',
dir=TMPDIR,
delete=False,
)
self.csv_files.append(fd.name)
else:
for i in range(chains):
self.csv_files.append('{}-{}.csv'.format(
args.output_basename, i + 1))
self.console_files = []
"""per-chain sample console output files."""
for i in range(chains):
txt_file = ''.join(
[os.path.splitext(self.csv_files[i])[0], '.txt'])
self.console_files.append(txt_file)
self.cmds = [
args.compose_command(i, self.csv_files[i]) for i in range(chains)
]
"""per-chain sampler command."""
self._retcodes = [-1 for _ in range(chains)]
self._draws = None
self._column_names = None
self._num_params = None # metric dim(s)
self._metric_type = None
self._metric = None
self._stepsize = None
self._sample = None
self._first_draw = None
def test_output_filenames(self):
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)
self.assertIn('bernoulli-', runset._csv_files[0])
self.assertIn('_1.csv', runset._csv_files[0])
self.assertIn('_4.csv', runset._csv_files[3])
def test_ctor_checks(self):
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,
)
with self.assertRaises(ValueError):
RunSet(args=cmdstan_args, chains=0)
with self.assertRaises(ValueError):
RunSet(args=cmdstan_args, chains=4, chain_ids=[1, 2, 3])
def test_chain_ids(self):
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)
self.assertIn('id=11', runset.cmd(0))
self.assertIn('_11.csv', runset._csv_files[0])
self.assertIn('id=14', runset.cmd(3))
self.assertIn('_14.csv', runset._csv_files[3])
def test_validate_good_run(self):
# construct fit using existing sampler output
exe = os.path.join(datafiles_path, 'bernoulli' + EXTENSION)
jdata = os.path.join(datafiles_path, 'bernoulli.data.json')
output = os.path.join(goodfiles_path, 'bern')
sampler_args = SamplerArgs(sampling_iters=100,
max_treedepth=11,
adapt_delta=0.95)
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[1, 2, 3, 4],
seed=12345,
data=jdata,
output_basename=output,
method_args=sampler_args,
)
fit = StanFit(args=cmdstan_args, chains=4)
retcodes = fit._retcodes
for i in range(len(retcodes)):
fit._set_retcode(i, 0)
self.assertTrue(fit._check_retcodes())
fit._check_console_msgs()
fit._validate_csv_files()
self.assertEqual(4, fit.chains)
self.assertEqual(100, fit.draws)
self.assertEqual(8, len(fit.column_names))
self.assertEqual('lp__', fit.column_names[0])
df = fit.get_drawset()
self.assertEqual(df.shape,
(fit.chains * fit.draws, len(fit.column_names)))
_ = fit.summary()
# TODO - use cmdstan test files instead
expected = '\n'.join([
'Checking sampler transitions treedepth.',
'Treedepth satisfactory for all transitions.',
'\nChecking sampler transitions for divergences.',
'No divergent transitions found.',
'\nChecking E-BFMI - sampler transitions HMC potential energy.',
'E-BFMI satisfactory for all transitions.',
'\nEffective sample size satisfactory.',
])
self.assertIn(expected, fit.diagnose().replace("\r\n", "\n"))
def test_validate_summary_sig_figs(self):
# construct CmdStanMCMC from logistic model output, config
exe = os.path.join(DATAFILES_PATH, 'logistic' + EXTENSION)
rdata = os.path.join(DATAFILES_PATH, 'logistic.data.R')
sampler_args = SamplerArgs(iter_sampling=100)
cmdstan_args = CmdStanArgs(
model_name='logistic',
model_exe=exe,
chain_ids=[1, 2, 3, 4],
seed=12345,
data=rdata,
output_dir=DATAFILES_PATH,
sig_figs=17,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args)
runset._csv_files = [
os.path.join(DATAFILES_PATH, 'logistic_output_1.csv'),
os.path.join(DATAFILES_PATH, 'logistic_output_2.csv'),
os.path.join(DATAFILES_PATH, 'logistic_output_3.csv'),
os.path.join(DATAFILES_PATH, 'logistic_output_4.csv'),
]
retcodes = runset._retcodes
for i in range(len(retcodes)):
runset._set_retcode(i, 0)
fit = CmdStanMCMC(runset)
sum_default = fit.summary()
beta1_default = format(sum_default.iloc[1, 0], '.18g')
self.assertTrue(beta1_default.startswith('1.3'))
if cmdstan_version_at(2, 25):
sum_17 = fit.summary(sig_figs=17)
beta1_17 = format(sum_17.iloc[1, 0], '.18g')
self.assertTrue(beta1_17.startswith('1.345767078273'))
sum_10 = fit.summary(sig_figs=10)
beta1_10 = format(sum_10.iloc[1, 0], '.18g')
self.assertTrue(beta1_10.startswith('1.34576707'))
with self.assertRaises(ValueError):
fit.summary(sig_figs=20)
with self.assertRaises(ValueError):
fit.summary(sig_figs=-1)
def test_compose(self):
exe = os.path.join(datafiles_path, 'bernoulli')
sampler_args = SamplerArgs()
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[1, 2, 3, 4],
method_args=sampler_args,
)
with self.assertRaises(ValueError):
cmdstan_args.compose_command(idx=4, csv_file='foo')
with self.assertRaises(ValueError):
cmdstan_args.compose_command(idx=-1, csv_file='foo')
def test_get_err_msgs(self):
exe = os.path.join(DATAFILES_PATH, 'logistic' + EXTENSION)
rdata = os.path.join(DATAFILES_PATH, 'logistic.data.R')
sampler_args = SamplerArgs()
cmdstan_args = CmdStanArgs(
model_name='logistic',
model_exe=exe,
chain_ids=[1, 2, 3],
data=rdata,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=3)
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 = '\n\t'.join(runset._get_err_msgs())
self.assertIn('Exception', errs)
def test_check_repr(self):
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)
self.assertIn('RunSet: chains=4', runset.__repr__())
self.assertIn('method=sample', runset.__repr__())
self.assertIn('retcodes=[-1, -1, -1, -1]', runset.__repr__())
self.assertIn('csv_file', runset.__repr__())
self.assertIn('console_msgs', runset.__repr__())
self.assertNotIn('diagnostics_file', runset.__repr__())
def test_args_good(self):
exe = os.path.join(DATAFILES_PATH, 'bernoulli')
jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
sampler_args = SamplerArgs()
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[1, 2, 3, 4],
data=jdata,
method_args=sampler_args,
refresh=10,
)
self.assertEqual(cmdstan_args.method, Method.SAMPLE)
cmd = cmdstan_args.compose_command(idx=0, csv_file='bern-output-1.csv')
self.assertIn('id=1 random seed=', ' '.join(cmd))
self.assertIn('data file=', ' '.join(cmd))
self.assertIn('output file=', ' '.join(cmd))
self.assertIn('method=sample algorithm=hmc', ' '.join(cmd))
self.assertIn('refresh=10', ' '.join(cmd))
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[7, 11, 18, 29],
data=jdata,
method_args=sampler_args,
)
cmd = cmdstan_args.compose_command(idx=0, csv_file='bern-output-1.csv')
self.assertIn('id=7 random seed=', ' '.join(cmd))
dirname = 'tmp' + str(time())
if os.path.exists(dirname):
os.rmdir(dirname)
CmdStanArgs(
model_name='bernoulli',
model_exe='bernoulli.exe',
chain_ids=[1, 2, 3, 4],
output_dir=dirname,
method_args=sampler_args,
)
self.assertTrue(os.path.exists(dirname))
os.rmdir(dirname)
def test_args_sig_figs(self):
sampler_args = SamplerArgs()
cmdstan_path() # sets os.environ['CMDSTAN']
if cmdstan_version_before(2, 25):
with LogCapture() as log:
logging.getLogger()
CmdStanArgs(
model_name='bernoulli',
model_exe='bernoulli.exe',
chain_ids=[1, 2, 3, 4],
sig_figs=12,
method_args=sampler_args,
)
expect = (
'Argument "sig_figs" invalid for CmdStan versions < 2.25, '
'using version {} in directory {}').format(
os.path.basename(cmdstan_path()),
os.path.dirname(cmdstan_path()),
)
log.check_present(('cmdstanpy', 'WARNING', expect))
else:
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe='bernoulli.exe',
chain_ids=[1, 2, 3, 4],
sig_figs=12,
method_args=sampler_args,
)
cmd = cmdstan_args.compose_command(idx=0,
csv_file='bern-output-1.csv')
self.assertIn('sig_figs=', ' '.join(cmd))
with self.assertRaises(ValueError):
CmdStanArgs(
model_name='bernoulli',
model_exe='bernoulli.exe',
chain_ids=[1, 2, 3, 4],
sig_figs=-1,
method_args=sampler_args,
)
with self.assertRaises(ValueError):
CmdStanArgs(
model_name='bernoulli',
model_exe='bernoulli.exe',
chain_ids=[1, 2, 3, 4],
sig_figs=20,
method_args=sampler_args,
)
def test_variables_3d(self):
# construct fit using existing sampler output
exe = os.path.join(DATAFILES_PATH, 'multidim_vars' + EXTENSION)
jdata = os.path.join(DATAFILES_PATH, 'logistic.data.R')
sampler_args = SamplerArgs(iter_sampling=20)
cmdstan_args = CmdStanArgs(
model_name='multidim_vars',
model_exe=exe,
chain_ids=[1],
seed=12345,
data=jdata,
output_dir=DATAFILES_PATH,
method_args=sampler_args,
)
runset = RunSet(args=cmdstan_args, chains=1)
runset._csv_files = [os.path.join(DATAFILES_PATH, 'multidim_vars.csv')]
runset._set_retcode(0, 0)
fit = CmdStanMCMC(runset)
self.assertEqual(20, fit.num_draws_sampling)
self.assertEqual(3, len(fit.stan_vars_dims))
self.assertTrue('y_rep' in fit.stan_vars_dims)
self.assertEqual(fit.stan_vars_dims['y_rep'], (5, 4, 3))
var_y_rep = fit.stan_variable(name='y_rep')
self.assertEqual(var_y_rep.shape, (20, 5, 4, 3))
var_beta = fit.stan_variable(name='beta')
self.assertEqual(var_beta.shape, (20, 2))
var_frac_60 = fit.stan_variable(name='frac_60')
self.assertEqual(var_frac_60.shape, (20, ))
vars = fit.stan_variables()
self.assertEqual(len(vars), len(fit.stan_vars_dims))
self.assertTrue('y_rep' in vars)
self.assertEqual(vars['y_rep'].shape, (20, 5, 4, 3))
self.assertTrue('beta' in vars)
self.assertEqual(vars['beta'].shape, (20, 2))
self.assertTrue('frac_60' in vars)
self.assertEqual(vars['frac_60'].shape, (20, ))
def test_diagnose_divergences(self):
exe = os.path.join(datafiles_path,
'bernoulli' + EXTENSION) # fake out validation
output = os.path.join(datafiles_path, 'diagnose-good',
'corr_gauss_depth8')
sampler_args = SamplerArgs()
cmdstan_args = CmdStanArgs(
model_name='bernoulli',
model_exe=exe,
chain_ids=[1],
output_basename=output,
method_args=sampler_args,
)
fit = StanFit(args=cmdstan_args, chains=1)
# TODO - use cmdstan test files instead
expected = '\n'.join([
'Checking sampler transitions treedepth.',
'424 of 1000 (42%) transitions hit the maximum '
'treedepth limit of 8, or 2^8 leapfrog steps.',
'Trajectories that are prematurely terminated '
'due to this limit will result in slow exploration.',
'For optimal performance, increase this limit.',
])
self.assertIn(expected, fit.diagnose().replace("\r\n", "\n"))