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‎petabtests/cases/v2.0.0/pysb/0006/0006.py

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)
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problem.add_measurement(
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"obs_a", "c0", time=0, measurement=0.7, observable_parameters=(10,)
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"obs_a", "", time=0, measurement=0.7, observable_parameters=(10,)
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)
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problem.add_measurement(
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"obs_a", "c0", time=10, measurement=0.1, observable_parameters=(15,)
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"obs_a", "", time=10, measurement=0.1, observable_parameters=(15,)
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)
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problem.add_parameter(

‎petabtests/cases/v2.0.0/pysb/0006/_measurements.tsv

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observableId experimentId time measurement observableParameters
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obs_a c0 0 0.7 10
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obs_a c0 10 0.1 15
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obs_a 0 0.7 10
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obs_a 10 0.1 15

‎petabtests/cases/v2.0.0/pysb/0006/_simulations.tsv

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observableId experimentId time simulation observableParameters
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obs_a c0 0 10.0 10
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obs_a c0 10 6.42857855596045 15
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obs_a 0 10.0 10
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obs_a 10 6.42857855596045 15

‎petabtests/cases/v2.0.0/pysb/0009/0009.py

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measurement_dfs=[problem.measurement_df],
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simulation_dfs=[simulation_df],
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parameter_df=problem.parameter_df,
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experiment_dfs=[problem.experiment_df],
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)

‎petabtests/cases/v2.0.0/pysb/0009/_0009.yaml

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problems:
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- condition_files:
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- _conditions.tsv
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experiment_files: []
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experiment_files:
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- _experiments.tsv
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measurement_files:
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- _measurements.tsv
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model_files:

‎petabtests/cases/v2.0.0/sbml/0001/_experiments.tsv

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‎petabtests/cases/v2.0.0/sbml/0002/_0002.yaml

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extensions: []
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format_version: 2.0.0
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parameter_file: _parameters.tsv
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problems:
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- condition_files:
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- _conditions.tsv
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experiment_files:
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- _experiments.tsv
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measurement_files:
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- _measurements.tsv
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observable_files:
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- _observables.tsv
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model_files:
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_model:
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language: sbml
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location: _model.xml
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extensions: []
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observable_files:
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- _observables.tsv

‎petabtests/cases/v2.0.0/sbml/0003/_experiments.tsv

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‎petabtests/cases/v2.0.0/sbml/0004/_experiments.tsv

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‎petabtests/cases/v2.0.0/sbml/0005/_0005.yaml

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extensions: []
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format_version: 2.0.0
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parameter_file: _parameters.tsv
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problems:
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- condition_files:
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- _conditions.tsv
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experiment_files:
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- _experiments.tsv
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measurement_files:
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- _measurements.tsv
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observable_files:
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- _observables.tsv
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model_files:
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_model:
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language: sbml
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location: _model.xml
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extensions: []
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observable_files:
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- _observables.tsv

‎petabtests/cases/v2.0.0/sbml/0006/_experiments.tsv

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‎petabtests/cases/v2.0.0/sbml/0007/_experiments.tsv

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‎petabtests/cases/v2.0.0/sbml/0008/_experiments.tsv

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‎petabtests/cases/v2.0.0/sbml/0009/_0009.yaml

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extensions: []
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format_version: 2.0.0
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parameter_file: _parameters.tsv
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problems:
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- condition_files:
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- _conditions.tsv
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experiment_files:
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- _experiments.tsv
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measurement_files:
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- _measurements.tsv
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observable_files:
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- _observables.tsv
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model_files:
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_model:
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language: sbml
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location: _model.xml
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extensions: []
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observable_files:
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- _observables.tsv

‎petabtests/cases/v2.0.0/sbml/0010/_0010.yaml

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extensions: []
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format_version: 2.0.0
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parameter_file: _parameters.tsv
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problems:
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- condition_files:
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- _conditions.tsv
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experiment_files:
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- _experiments.tsv
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measurement_files:
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- _measurements.tsv
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observable_files:
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- _observables.tsv
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model_files:
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_model:
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language: sbml
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location: _model.xml
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extensions: []
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observable_files:
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- _observables.tsv

‎petabtests/cases/v2.0.0/sbml/0011/_0011.yaml

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extensions: []
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format_version: 2.0.0
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parameter_file: _parameters.tsv
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problems:
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- _conditions.tsv
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experiment_files:
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- _experiments.tsv
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measurement_files:
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observable_files:
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model_files:
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location: _model.xml
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extensions: []
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- _observables.tsv

‎petabtests/cases/v2.0.0/sbml/0012/_0012.yaml

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extensions: []
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format_version: 2.0.0
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parameter_file: _parameters.tsv
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problems:
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experiment_files:
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measurement_files:
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observable_files:
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model_files:
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extensions: []
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- _observables.tsv

‎petabtests/cases/v2.0.0/sbml/0013/_0013.yaml

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extensions: []
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format_version: 2.0.0
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parameter_file: _parameters.tsv
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problems:
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- _conditions.tsv
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experiment_files:
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measurement_files:
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observable_files:
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model_files:
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extensions: []
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observable_files:
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- _observables.tsv

‎petabtests/cases/v2.0.0/sbml/0014/_experiments.tsv

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‎petabtests/cases/v2.0.0/sbml/0015/_experiments.tsv

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‎petabtests/cases/v2.0.0/sbml/0016/_experiments.tsv

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‎petabtests/cases/v2.0.0/sbml/0017/_0017.yaml

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extensions: []
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format_version: 2.0.0
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parameter_file: _parameters.tsv
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problems:
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- condition_files:
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- _conditions.tsv
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experiment_files:
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- _experiments.tsv
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measurement_files:
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- _measurements.tsv
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observable_files:
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- _observables.tsv
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model_files:
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extensions: []
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- _observables.tsv

‎petabtests/cases/v2.0.0/sbml/0018/_0018.yaml

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extensions: []
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format_version: 2.0.0
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parameter_file: _parameters.tsv
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problems:
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- condition_files:
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- _conditions.tsv
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experiment_files:
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- _experiments.tsv
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measurement_files:
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- _measurements.tsv
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observable_files:
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- _observables.tsv
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model_files:
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location: _model.xml
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extensions: []
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- _observables.tsv

‎petabtests/cases/v2.0.0/sbml/0019/0019.py

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# problem --------------------------------------------------------------------
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problem = Problem()
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# TODO use mapping here
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problem.add_condition("c0")
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problem.add_measurement("obs_a", "c0", 0, 0.7)
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problem.add_measurement("obs_a", "c0", 10, 0.1)
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problem.add_measurement("obs_a", "", 0, 0.7)
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problem.add_measurement("obs_a", "", 10, 0.1)
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problem.add_observable("obs_a", "maps_to_A", 0.5)
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problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, scale=LIN)
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problem.add_parameter("maps_to_b0", lb=0, ub=10, nominal_value=0, scale=LIN)

‎petabtests/cases/v2.0.0/sbml/0019/_measurements.tsv

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observableId experimentId time measurement
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obs_a c0 0 0.7
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obs_a c0 10 0.1
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obs_a 0 0.7
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obs_a 10 0.1

‎petabtests/cases/v2.0.0/sbml/0019/_simulations.tsv

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observableId experimentId time simulation
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obs_a c0 0 1.0
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obs_a c0 10 0.42857190373069665
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obs_a 0 1.0
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obs_a 10 0.42857190373069665

‎petabtests/cases/v2.0.0/sbml/0020/_0020.yaml

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extensions: []
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format_version: 2.0.0
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parameter_file: _parameters.tsv
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problems:
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- condition_files:
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- _conditions.tsv
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experiment_files:
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- _experiments.tsv
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measurement_files:
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- _measurements.tsv
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observable_files:
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- _observables.tsv
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model_files:
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_model:
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language: sbml
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location: _model.xml
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extensions: []
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observable_files:
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- _observables.tsv

‎petabtests/file.py

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tmp_exp_file = Path(dir_, "experiments.tsv")
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if tmp_exp_file.exists():
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tmp_exp_file.rename(exp_file)
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# update in yaml
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with open(yaml_path) as f:
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config = yaml.safe_load(f)
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config[PROBLEMS][0][EXPERIMENT_FILES] = ["_experiments.tsv"]
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with open(yaml_path, "w") as f:
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yaml.dump(config, f, default_flow_style=False)
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format_version = 2
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# FIXME Until a first libpetab with petab.v1 subpackage is released

‎test/test_generate.py

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Mostly for debugging purposes.
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"""
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format_ = "pysb"
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format_ = "sbml"
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version = "v2.0.0"
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id_ = "0002"
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id_ = "0019"
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create_case(format_=format_, version=version, id_=id_)

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