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v2: Don't merge tables when creating Problem #405

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Jul 21, 2025
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v2: Don't merge tables when creating Problem #405

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v2: Don't merge tables when creating `Problem`
dweindl Jul 21, 2025
7bc254d
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dweindl Jul 21, 2025
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56 changes: 29 additions & 27 deletions petab/v2/converters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,13 @@
import libsbml
from sbmlmath import sbml_math_to_sympy, set_math

from .core import Change, Condition, Experiment, ExperimentPeriod
from .core import (
Change,
Condition,
ConditionTable,
Experiment,
ExperimentPeriod,
)
from .models._sbml_utils import add_sbml_parameter, check
from .models.sbml_model import SbmlModel
from .problem import Problem
Expand Down Expand Up @@ -176,7 +182,7 @@ def convert(self) -> Problem:

self._add_preequilibration_indicator()

for experiment in self._new_problem.experiment_table.experiments:
for experiment in self._new_problem.experiments:
self._convert_experiment(experiment)

self._add_indicators_to_conditions()
Expand Down Expand Up @@ -226,7 +232,7 @@ def _convert_experiment(self, experiment: Experiment) -> None:
self._create_event_assignments_for_period(
ev,
[
self._new_problem.condition_table[condition_id]
self._new_problem[condition_id]
for condition_id in period.condition_ids
],
)
Expand Down Expand Up @@ -365,24 +371,18 @@ def _add_indicators_to_conditions(self) -> None:
problem = self._new_problem

# create conditions for indicator parameters
problem.condition_table.conditions.append(
Condition(
id=self.CONDITION_ID_PREEQ_ON,
changes=[
Change(target_id=self._preeq_indicator, target_value=1)
],
)
problem += Condition(
id=self.CONDITION_ID_PREEQ_ON,
changes=[Change(target_id=self._preeq_indicator, target_value=1)],
)
problem.condition_table.conditions.append(
Condition(
id=self.CONDITION_ID_PREEQ_OFF,
changes=[
Change(target_id=self._preeq_indicator, target_value=0)
],
)

problem += Condition(
id=self.CONDITION_ID_PREEQ_OFF,
changes=[Change(target_id=self._preeq_indicator, target_value=0)],
)

# add conditions for the experiment indicators
for experiment in problem.experiment_table.experiments:
for experiment in problem.experiments:
cond_id = self._get_experiment_indicator_condition_id(
experiment.id
)
Expand All @@ -392,17 +392,19 @@ def _add_indicators_to_conditions(self) -> None:
target_value=1,
)
]
problem.condition_table.conditions.append(
Condition(
id=cond_id,
changes=changes,
)
problem += Condition(
id=cond_id,
changes=changes,
)

# All changes have been encoded in event assignments and can be
# removed. Only keep the conditions setting our indicators.
problem.condition_table.conditions = [
condition
for condition in problem.condition_table.conditions
if condition.id.startswith("_petab")
problem.condition_tables = [
ConditionTable(
conditions=[
condition
for condition in problem.conditions
if condition.id.startswith("_petab")
]
)
]
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