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Merged
dweindl merged 2 commits into from
Mar 27, 2025
Merged

lint: Don't fail on missing noiseFormula #367

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c57a713
lint: Don't fail on missing noiseFormula
dweindl Mar 25, 2025
4e248ba
Check measurements after observables
dweindl Mar 25, 2025
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30 changes: 15 additions & 15 deletions petab/v1/lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -906,21 +906,6 @@ def lint_problem(problem: "petab.Problem") -> bool:
else:
logger.warning("Model not available. Skipping.")

if problem.measurement_df is not None:
logger.info("Checking measurement table...")
try:
check_measurement_df(problem.measurement_df, problem.observable_df)

if problem.condition_df is not None:
assert_measurement_conditions_present_in_condition_table(
problem.measurement_df, problem.condition_df
)
except AssertionError as e:
logger.error(e)
errors_occurred = True
else:
logger.warning("Measurement table not available. Skipping.")

if problem.condition_df is not None:
logger.info("Checking condition table...")
try:
Expand Down Expand Up @@ -953,6 +938,21 @@ def lint_problem(problem: "petab.Problem") -> bool:
else:
logger.warning("Observable table not available. Skipping.")

if problem.measurement_df is not None:
logger.info("Checking measurement table...")
try:
check_measurement_df(problem.measurement_df, problem.observable_df)

if problem.condition_df is not None:
assert_measurement_conditions_present_in_condition_table(
problem.measurement_df, problem.condition_df
)
except AssertionError as e:
logger.error(e)
errors_occurred = True
else:
logger.warning("Measurement table not available. Skipping.")

if problem.parameter_df is not None:
logger.info("Checking parameter table...")
try:
Expand Down
24 changes: 14 additions & 10 deletions petab/v1/measurements.py
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Original file line number Diff line number Diff line change
Expand Up @@ -277,16 +277,20 @@ def assert_overrides_match_parameter_count(
strict=True,
)
}
noise_parameters_count = {
obs_id: len(
observables.get_formula_placeholders(formula, obs_id, "noise")
)
for obs_id, formula in zip(
observable_df.index.values,
observable_df[NOISE_FORMULA],
strict=True,
)
}
noise_parameters_count = (
{
obs_id: len(
observables.get_formula_placeholders(formula, obs_id, "noise")
)
for obs_id, formula in zip(
observable_df.index.values,
observable_df[NOISE_FORMULA],
strict=True,
)
}
if NOISE_FORMULA in observable_df.columns
else {obs_id: 0 for obs_id in observable_df.index.values}
)

for _, row in measurement_df.iterrows():
# check observable parameters
Expand Down