Update petab v2 tests

petabtests/cases/v1.0.0/sbml/0005/_model.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
+<!-- Created by libAntimony version v2.15.0 with libSBML version 5.20.2. -->
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
   <model metaid="petab_test_0011" id="petab_test_0011">
     <listOfCompartments>

petabtests/cases/v1.0.0/sbml/0011/_model.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
+<!-- Created by libAntimony version v2.15.0 with libSBML version 5.20.2. -->
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
   <model metaid="petab_test_0011" id="petab_test_0011">
     <listOfCompartments>

petabtests/cases/v1.0.0/sbml/0018/_model.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
+<!-- Created by libAntimony version v2.15.0 with libSBML version 5.20.2. -->
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
   <model metaid="petab_test_0018" id="petab_test_0018">
     <listOfCompartments>

petabtests/cases/v1.0.0/sbml/0018/model.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
+<!-- Created by libAntimony version v2.15.0 with libSBML version 5.20.2. -->
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
   <model metaid="petab_test_0018" id="petab_test_0018">
     <listOfCompartments>

petabtests/cases/v1.0.0/sbml/0019/_model.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
+<!-- Created by libAntimony version v2.15.0 with libSBML version 5.20.2. -->
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
   <model metaid="petab_test_0011" id="petab_test_0011">
     <listOfCompartments>

petabtests/cases/v2.0.0/pysb/0001/0001.py

@@ -1,9 +1,8 @@
 from inspect import cleandoc
 
-import pandas as pd
-from petab.v1.C import *
-
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
+from petab.v2 import Problem
+from petab.v2.C import *
 
 DESCRIPTION = cleandoc("""
 ## Objective
@@ -19,43 +18,21 @@
 
 # problem --------------------------------------------------------------------
 
-condition_df = pd.DataFrame(
-    data={
-        CONDITION_ID: ["c0"],
-    }
-).set_index([CONDITION_ID])
+problem = Problem()
 
-measurement_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a", "obs_a"],
-        SIMULATION_CONDITION_ID: ["c0", "c0"],
-        TIME: [0, 10],
-        MEASUREMENT: [0.7, 0.1],
-    }
-)
+problem.add_observable("obs_a", "A", noise_formula=0.5)
 
-observable_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a"],
-        OBSERVABLE_FORMULA: ["A"],
-        NOISE_FORMULA: [0.5],
-    }
-).set_index([OBSERVABLE_ID])
+problem.add_measurement("obs_a", "", time=0, measurement=0.7)
+problem.add_measurement("obs_a", "", time=10, measurement=0.1)
 
-parameter_df = pd.DataFrame(
-    data={
-        PARAMETER_ID: ["a0", "b0", "k1", "k2"],
-        PARAMETER_SCALE: [LIN] * 4,
-        LOWER_BOUND: [0] * 4,
-        UPPER_BOUND: [10] * 4,
-        NOMINAL_VALUE: [1, 0, 0.8, 0.6],
-        ESTIMATE: [1] * 4,
-    }
-).set_index(PARAMETER_ID)
+problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, scale=LIN)
+problem.add_parameter("b0", lb=0, ub=10, nominal_value=0, scale=LIN)
+problem.add_parameter("k1", lb=0, ub=10, nominal_value=0.8, scale=LIN)
+problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, scale=LIN)
 
 # solutions ------------------------------------------------------------------
 
-simulation_df = measurement_df.copy(deep=True).rename(
+simulation_df = problem.measurement_df.copy(deep=True).rename(
     columns={MEASUREMENT: SIMULATION}
 )
 simulation_df[SIMULATION] = [
@@ -68,9 +45,9 @@
     brief="Simulation. Nothing special.",
     description=DESCRIPTION,
     model=DEFAULT_PYSB_FILE,
-    condition_dfs=[condition_df],
-    observable_dfs=[observable_df],
-    measurement_dfs=[measurement_df],
+    condition_dfs=[problem.condition_df],
+    observable_dfs=[problem.observable_df],
+    measurement_dfs=[problem.measurement_df],
     simulation_dfs=[simulation_df],
-    parameter_df=parameter_df,
+    parameter_df=problem.parameter_df,
 )

petabtests/cases/v2.0.0/pysb/0001/_0001.yaml

@@ -1,8 +1,8 @@
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
-- condition_files:
-  - _conditions.tsv
+- condition_files: []
+  experiment_files: []
   measurement_files:
   - _measurements.tsv
   model_files:

petabtests/cases/v2.0.0/pysb/0001/_measurements.tsv

@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	measurement
-obs_a	c0	0	0.7
-obs_a	c0	10	0.1
+observableId	experimentId	time	measurement
+obs_a		0	0.7
+obs_a		10	0.1

petabtests/cases/v2.0.0/pysb/0001/_parameters.tsv

@@ -1,5 +1,5 @@
-parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-a0	lin	0	10	1.0	1
-b0	lin	0	10	0.0	1
-k1	lin	0	10	0.8	1
-k2	lin	0	10	0.6	1
+parameterId	estimate	nominalValue	parameterScale	lowerBound	upperBound
+a0	1	1.0	lin	0	10
+b0	1	0.0	lin	0	10
+k1	1	0.8	lin	0	10
+k2	1	0.6	lin	0	10

petabtests/cases/v2.0.0/pysb/0001/_simulations.tsv

@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	simulation
-obs_a	c0	0	1.0
-obs_a	c0	10	0.42857190373069665
+observableId	experimentId	time	simulation
+obs_a		0	1.0
+obs_a		10	0.42857190373069665

petabtests/cases/v2.0.0/pysb/0002/0002.py

@@ -1,8 +1,7 @@
 from inspect import cleandoc
-from math import nan
 
-import pandas as pd
-from petab.v1.C import *
+from petab.v2 import Problem
+from petab.v2.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 
@@ -24,61 +23,46 @@
 """)
 
 # problem --------------------------------------------------------------------
+problem = Problem()
 
-condition_df = pd.DataFrame(
-    data={
-        CONDITION_ID: ["c0", "c1"],
-        "a0": [0.8, 0.9],
-        "b0": [nan, nan],
-    }
-).set_index([CONDITION_ID])
-
-measurement_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a"] * 4,
-        SIMULATION_CONDITION_ID: ["c0", "c0", "c1", "c1"],
-        TIME: [0, 10, 0, 10],
-        MEASUREMENT: [0.7, 0.1, 0.8, 0.2],
-    }
-)
+problem.add_condition("c0", a0=(VT_INITIAL, 0.8))
+problem.add_condition("c1", a0=(VT_INITIAL, 0.9))
+
+problem.add_experiment("e0", 0, "c0")
+problem.add_experiment("e1", 0, "c1")
 
-observable_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a"],
-        OBSERVABLE_FORMULA: ["A"],
-        NOISE_FORMULA: [1],
-    }
-).set_index([OBSERVABLE_ID])
-
-parameter_df = pd.DataFrame(
-    data={
-        PARAMETER_ID: ["k1", "k2"],
-        PARAMETER_SCALE: [LIN] * 2,
-        LOWER_BOUND: [0] * 2,
-        UPPER_BOUND: [10] * 2,
-        NOMINAL_VALUE: [0.8, 0.6],
-        ESTIMATE: [1] * 2,
-    }
-).set_index(PARAMETER_ID)
+problem.add_observable("obs_a", "A", noise_formula=1)
+
+problem.add_measurement("obs_a", "e0", time=0, measurement=0.7)
+problem.add_measurement("obs_a", "e0", time=10, measurement=0.1)
+problem.add_measurement("obs_a", "e1", time=0, measurement=0.8)
+problem.add_measurement("obs_a", "e1", time=10, measurement=0.2)
+
+problem.add_parameter(
+    "k1", lb=0, ub=10, nominal_value=0.8, scale=LIN, estimate=True
+)
+problem.add_parameter(
+    "k2", lb=0, ub=10, nominal_value=0.6, scale=LIN, estimate=True
+)
 
 # solutions ------------------------------------------------------------------
 
-simulation_df = measurement_df.copy(deep=True).rename(
+simulation_df = problem.measurement_df.copy(deep=True).rename(
     columns={MEASUREMENT: SIMULATION}
 )
 simulation_df[SIMULATION] = [
     *[analytical_a(t, 0.8, 1, 0.8, 0.6) for t in [0, 10]],
     *[analytical_a(t, 0.9, 1, 0.8, 0.6) for t in [0, 10]],
 ]
-
 case = PetabTestCase(
     id=2,
     brief="Simulation. Two conditions. Numeric parameter override.",
     description=DESCRIPTION,
     model=DEFAULT_PYSB_FILE,
-    condition_dfs=[condition_df],
-    observable_dfs=[observable_df],
-    measurement_dfs=[measurement_df],
+    condition_dfs=[problem.condition_df],
+    observable_dfs=[problem.observable_df],
+    measurement_dfs=[problem.measurement_df],
     simulation_dfs=[simulation_df],
-    parameter_df=parameter_df,
+    experiment_dfs=[problem.experiment_df],
+    parameter_df=problem.parameter_df,
 )

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

@@ -3,6 +3,8 @@ parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
   model_files:

petabtests/cases/v2.0.0/pysb/0002/_conditions.tsv

@@ -1,3 +1,3 @@
-conditionId	a0	b0
-c0	0.8	
-c1	0.9	
+conditionId	targetId	valueType	targetValue
+c0	a0	initial	0.8
+c1	a0	initial	0.9

petabtests/cases/v2.0.0/pysb/0002/_experiments.tsv

@@ -0,0 +1,3 @@
+experimentId	time	conditionId
+e0	0	c0
+e1	0	c1

petabtests/cases/v2.0.0/pysb/0002/_measurements.tsv

@@ -1,5 +1,5 @@
-observableId	simulationConditionId	time	measurement
-obs_a	c0	0	0.7
-obs_a	c0	10	0.1
-obs_a	c1	0	0.8
-obs_a	c1	10	0.2
+observableId	experimentId	time	measurement
+obs_a	e0	0	0.7
+obs_a	e0	10	0.1
+obs_a	e1	0	0.8
+obs_a	e1	10	0.2

petabtests/cases/v2.0.0/pysb/0002/_parameters.tsv

@@ -1,3 +1,3 @@
-parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-k1	lin	0	10	0.8	1
-k2	lin	0	10	0.6	1
+parameterId	estimate	nominalValue	parameterScale	lowerBound	upperBound
+k1	1	0.8	lin	0	10
+k2	1	0.6	lin	0	10

petabtests/cases/v2.0.0/pysb/0002/_simulations.tsv

@@ -1,5 +1,5 @@
-observableId	simulationConditionId	time	simulation
-obs_a	c0	0	0.8
-obs_a	c0	10	0.771428595186535
-obs_a	c1	0	0.9
-obs_a	c1	10	0.8142857855596045
+observableId	experimentId	time	simulation
+obs_a	e0	0	0.8
+obs_a	e0	10	0.771428595186535
+obs_a	e1	0	0.9
+obs_a	e1	10	0.8142857855596045

petabtests/cases/v2.0.0/pysb/0003/0003.py

@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
-import pandas as pd
-from petab.v1.C import *
+from petab.v2 import Problem
+from petab.v2.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 
@@ -24,47 +24,29 @@
 """)
 
 # problem --------------------------------------------------------------------
+problem = Problem()
 
-condition_df = pd.DataFrame(
-    data={
-        CONDITION_ID: ["c0"],
-    }
-).set_index([CONDITION_ID])
-
-measurement_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a", "obs_a"],
-        SIMULATION_CONDITION_ID: ["c0", "c0"],
-        TIME: [0, 10],
-        MEASUREMENT: [0.7, 0.1],
-        OBSERVABLE_PARAMETERS: ["0.5;2", "0.5;2"],
-    }
+problem.add_observable(
+    "obs_a",
+    "observableParameter1_obs_a * A + observableParameter2_obs_a",
+    noise_formula=0.5,
 )
 
-observable_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a"],
-        OBSERVABLE_FORMULA: [
-            "observableParameter1_obs_a * A + " "observableParameter2_obs_a"
-        ],
-        NOISE_FORMULA: [0.5],
-    }
-).set_index([OBSERVABLE_ID])
+problem.add_measurement(
+    "obs_a", "", time=0, measurement=0.7, observable_parameters=(0.5, 2)
+)
+problem.add_measurement(
+    "obs_a", "", time=10, measurement=0.1, observable_parameters=(0.5, 2)
+)
 
-parameter_df = pd.DataFrame(
-    data={
-        PARAMETER_ID: ["a0", "b0", "k1", "k2"],
-        PARAMETER_SCALE: [LIN] * 4,
-        LOWER_BOUND: [0] * 4,
-        UPPER_BOUND: [10] * 4,
-        NOMINAL_VALUE: [1, 0, 0.8, 0.6],
-        ESTIMATE: [1] * 4,
-    }
-).set_index(PARAMETER_ID)
+problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, scale=LIN)
+problem.add_parameter("b0", lb=0, ub=10, nominal_value=0, scale=LIN)
+problem.add_parameter("k1", lb=0, ub=10, nominal_value=0.8, scale=LIN)
+problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, scale=LIN)
 
 # solutions ------------------------------------------------------------------
 
-simulation_df = measurement_df.copy(deep=True).rename(
+simulation_df = problem.measurement_df.copy(deep=True).rename(
     columns={MEASUREMENT: SIMULATION}
 )
 simulation_df[SIMULATION] = [
@@ -77,9 +59,9 @@
     "table.",
     description=DESCRIPTION,
     model=DEFAULT_PYSB_FILE,
-    condition_dfs=[condition_df],
-    observable_dfs=[observable_df],
-    measurement_dfs=[measurement_df],
+    condition_dfs=[problem.condition_df],
+    observable_dfs=[problem.observable_df],
+    measurement_dfs=[problem.measurement_df],
     simulation_dfs=[simulation_df],
-    parameter_df=parameter_df,
+    parameter_df=problem.parameter_df,
 )

petabtests/cases/v2.0.0/pysb/0003/_0003.yaml

@@ -1,8 +1,8 @@
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
-- condition_files:
-  - _conditions.tsv
+- condition_files: []
+  experiment_files: []
   measurement_files:
   - _measurements.tsv
   model_files: