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Merge pull request #567 from stan-dev/fix/566-overzealous-string-search
Emit warnings rather than errors when sampling has exceptions
2 parents 62ab5db + 34be12f commit ebd02ee

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4 files changed

+241
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‎cmdstanpy/model.py‎

Lines changed: 8 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1176,14 +1176,21 @@ def sample(
11761176
)
11771177

11781178
errors = runset.get_err_msgs()
1179-
if errors or not runset._check_retcodes():
1179+
if not runset._check_retcodes():
11801180
msg = (
11811181
f'Error during sampling:\n{errors}\n'
11821182
+ f'Command and output files:\n{repr(runset)}\n'
11831183
+ 'Consider re-running with show_console=True if the above'
11841184
+ ' output is unclear!'
11851185
)
11861186
raise RuntimeError(msg)
1187+
if errors:
1188+
msg = (
1189+
f'Non-fatal error during sampling:\n{errors}\n'
1190+
+ 'Consider re-running with show_console=True if the above'
1191+
+ ' output is unclear!'
1192+
)
1193+
get_logger().warning(msg)
11871194

11881195
mcmc = CmdStanMCMC(runset)
11891196
return mcmc

‎test/data/linear_regression.data.json‎

Lines changed: 207 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,207 @@
1+
{
2+
"x": [
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"y": [
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1.0027971008115968
205+
],
206+
"N": 100
207+
}

‎test/data/linear_regression.stan‎

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
1+
data {
2+
int<lower=0> N;
3+
vector[N] x;
4+
vector[N] y;
5+
}
6+
parameters {
7+
real alpha;
8+
real beta;
9+
real<lower=0> sigma;
10+
}
11+
model {
12+
y ~ normal(alpha + beta * x, sigma);
13+
}

‎test/test_sample.py‎

Lines changed: 13 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@
1414
from time import time
1515

1616
import numpy as np
17-
from testfixtures import LogCapture
17+
from testfixtures import LogCapture, StringComparison
1818

1919
try:
2020
import ujson as json
@@ -1238,6 +1238,18 @@ def test_validate_bad_run(self):
12381238
):
12391239
CmdStanMCMC(runset)
12401240

1241+
def test_sample_sporadic_exception(self):
1242+
stan = os.path.join(DATAFILES_PATH, 'linear_regression.stan')
1243+
jdata = os.path.join(DATAFILES_PATH, 'linear_regression.data.json')
1244+
linear_model = CmdStanModel(stan_file=stan)
1245+
# will produce a failure due to calling normal_lpdf with 0 for scale
1246+
# but then continue sampling normally
1247+
with LogCapture() as log:
1248+
linear_model.sample(data=jdata, inits=0)
1249+
log.check_present(
1250+
('cmdstanpy', 'WARNING', StringComparison(r"Non-fatal error.*"))
1251+
)
1252+
12411253
def test_save_warmup(self):
12421254
stan = os.path.join(DATAFILES_PATH, 'bernoulli.stan')
12431255
jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')

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