`Benchmark Collection` workflow fails for Lang_PLOSComputBiol2024
Closed this issue · 2 comments
dweindl commented
Benchmark Collection
workflow fails with:
FAILED test_petab_benchmark.py::test_benchmark_gradient[Lang_PLOSComputBiol2024-True] - RuntimeWarning: divide by zero encountered in log
FAILED test_petab_benchmark.py::test_benchmark_gradient[Lang_PLOSComputBiol2024-False] - RuntimeWarning: divide by zero encountered in log
Check why we try to compute log(0)
there.
dweindl commented
Check why we try to compute
log(0)
there.
Some log-scale parameters have a nominal value of 0 (parameter table discussion).
dweindl commented
Needs to be checked whether this is an issue in amici or petab:
/home/runner/.local/lib/python3.11/site-packages/amici/petab/simulations.py:204: in simulate_petab
fill_in_parameters(
/home/runner/.local/lib/python3.11/site-packages/amici/petab/conditions.py:76: in fill_in_parameters
fill_in_parameters_for_condition(
/home/runner/.local/lib/python3.11/site-packages/amici/petab/conditions.py:148: in fill_in_parameters_for_condition
map_sim_fix = {
/home/runner/.local/lib/python3.11/site-packages/amici/petab/conditions.py:149: in <dictcomp>
key: _get_par(key, val, map_sim_fix)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
model_par = 'initial__Cyt__CCND_sim', value = 'ic_wt_Cyt__CCND'
mapping = {'_InitialConc1': 60220000000.0, '_InitialConc10': 50629691000.0, '_InitialConc11': 4648479700.0, '_InitialConc12': 242609110000.0, ...}
def _get_par(model_par, value, mapping):
"""Replace parameter IDs in mapping dicts by values from
problem_parameters where necessary"""
if isinstance(value, str):
try:
# estimated parameter
return problem_parameters[value]
except KeyError:
# condition table overrides must have been handled already,
# e.g. by the PEtab parameter mapping, but parameters from
# InitialAssignments may still be present.
> if mapping[value] == model_par:
E KeyError: 'ic_wt_Cyt__CCND'
/home/runner/.local/lib/python3.11/site-packages/amici/petab/conditions.py:131: KeyError