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Support valid AMICI noise distributions that are invalid in PEtab #1157

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merged 7 commits into from
Nov 3, 2023
Merged

Support valid AMICI noise distributions that are invalid in PEtab #1157

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a6889d7
pass petab validation flag to amici
dilpath Oct 25, 2023
91187bd
only if sbml
dilpath Oct 25, 2023
38dcbc9
Merge branch 'develop' into fix_petab_importer_amici_validation
dilpath Oct 25, 2023
114d207
Merge branch 'develop' into fix_petab_importer_amici_validation
dilpath Oct 26, 2023
819ca46
Merge branch 'develop' into fix_petab_importer_amici_validation
dilpath Oct 30, 2023
eccd02b
Merge branch 'develop' into fix_petab_importer_amici_validation
dweindl Oct 31, 2023
9a0101d
Merge branch 'develop' into fix_petab_importer_amici_validation
dilpath Oct 31, 2023
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12 changes: 10 additions & 2 deletions pypesto/petab/importer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@
import amici.petab_objective
import petab
from petab.C import PREEQUILIBRATION_CONDITION_ID, SIMULATION_CONDITION_ID
from petab.models import MODEL_TYPE_SBML
except ImportError:
pass

Expand Down Expand Up @@ -128,7 +129,8 @@ def __init__(

self.validate_inner_options()

if validate_petab:
self.validate_petab = validate_petab
if self.validate_petab:
if petab.lint_problem(petab_problem):
raise ValueError("Invalid PEtab problem.")
if self._hierarchical and validate_petab_hierarchical:
Expand Down Expand Up @@ -280,7 +282,13 @@ def create_model(
logger.info(
f"Compiling amici model to folder " f"{self.output_folder}."
)
self.compile_model(**kwargs)
if self.petab_problem.model.type_id == MODEL_TYPE_SBML:
self.compile_model(
validate=self.validate_petab,
**kwargs,
)
else:
self.compile_model(**kwargs)
else:
logger.debug(
f"Using existing amici model in folder "
Expand Down