pysb 4+5

PEtab-dev · Dec 18, 2024 · ab57318 · ab57318
1 parent 573dc63
commit ab57318
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Showing 13 changed files with 191 additions and 108 deletions.
diff --git a/petabtests/cases/v2.0.0/pysb/0002/_parameters.tsv b/petabtests/cases/v2.0.0/pysb/0002/_parameters.tsv
@@ -1,3 +1,3 @@
 parameterId	estimate	nominalValue	parameterScale	lowerBound	upperBound
-k1	True	0.8	lin	0	10
-k2	True	0.6	lin	0	10
+k1	1	0.8	lin	0	10
+k2	1	0.6	lin	0	10
diff --git a/petabtests/cases/v2.0.0/pysb/0004/0004.py b/petabtests/cases/v2.0.0/pysb/0004/0004.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
 
@@ -24,44 +24,80 @@
 """)
 
 # problem --------------------------------------------------------------------
+problem = Problem()
 
-condition_df = pd.DataFrame(
-    data={
-        CONDITION_ID: ["c0"],
-    }
-).set_index([CONDITION_ID])
+problem.add_observable(
+    "obs_a",
+    "scaling_A * A + offset_A",
+    noise_formula=1,
+)
 
-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_measurement(
+    "obs_a",
+    "",
+    time=0,
+    measurement=0.7,
+)
+problem.add_measurement(
+    "obs_a",
+    "",
+    time=10,
+    measurement=0.1,
 )
 
-observable_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a"],
-        OBSERVABLE_FORMULA: ["scaling_A * A + offset_A"],
-        NOISE_FORMULA: [1],
-    }
-).set_index([OBSERVABLE_ID])
+problem.add_parameter(
+    "scaling_A",
+    lb=0,
+    ub=10,
+    nominal_value=0.5,
+    scale=LIN,
+    estimate=False,
+)
+problem.add_parameter(
+    "offset_A",
+    lb=0,
+    ub=10,
+    nominal_value=2,
+    scale=LIN,
+    estimate=False,
+)
+problem.add_parameter(
+    "a0",
+    lb=0,
+    ub=10,
+    nominal_value=1,
+    scale=LIN,
+    estimate=True,
+)
+problem.add_parameter(
+    "b0",
+    lb=0,
+    ub=10,
+    nominal_value=0,
+    scale=LIN,
+    estimate=True,
+)
+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,
+)
 
-parameter_df = pd.DataFrame(
-    data={
-        PARAMETER_ID: ["a0", "b0", "k1", "k2", "scaling_A", "offset_A"],
-        PARAMETER_SCALE: [LIN] * 6,
-        LOWER_BOUND: [0] * 6,
-        UPPER_BOUND: [10] * 6,
-        NOMINAL_VALUE: [1, 0, 0.8, 0.6, 0.5, 2],
-        ESTIMATE: [1] * 6,
-    }
-).set_index(PARAMETER_ID)
 
 # solutions ------------------------------------------------------------------
 
-simulation_df = measurement_df.copy(deep=True).rename(
+simulation_df = problem.measurement_df.copy(deep=True).rename(
     columns={MEASUREMENT: SIMULATION}
 )
 simulation_df[SIMULATION] = [
@@ -73,9 +109,9 @@
     brief="Simulation. Observable parameters only defined in parameter 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,
 )
diff --git a/petabtests/cases/v2.0.0/pysb/0004/_0004.yaml b/petabtests/cases/v2.0.0/pysb/0004/_0004.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:

diff --git a/petabtests/cases/v2.0.0/pysb/0004/_measurements.tsv b/petabtests/cases/v2.0.0/pysb/0004/_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
diff --git a/petabtests/cases/v2.0.0/pysb/0004/_parameters.tsv b/petabtests/cases/v2.0.0/pysb/0004/_parameters.tsv
@@ -1,7 +1,7 @@
-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
-scaling_A	lin	0	10	0.5	1
-offset_A	lin	0	10	2.0	1
+parameterId	estimate	nominalValue	parameterScale	lowerBound	upperBound
+scaling_A	0	0.5	lin	0	10
+offset_A	0	2.0	lin	0	10
+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
diff --git a/petabtests/cases/v2.0.0/pysb/0004/_simulations.tsv b/petabtests/cases/v2.0.0/pysb/0004/_simulations.tsv
@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	simulation
-obs_a	c0	0	2.5
-obs_a	c0	10	2.214285951865348
+observableId	experimentId	time	simulation
+obs_a		0	2.5
+obs_a		10	2.214285951865348
diff --git a/petabtests/cases/v2.0.0/pysb/0005/0005.py b/petabtests/cases/v2.0.0/pysb/0005/0005.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 PetabTestCase, analytical_a
 
@@ -23,44 +23,85 @@
 
 # problem --------------------------------------------------------------------
 
-condition_df = pd.DataFrame(
-    data={
-        CONDITION_ID: ["c0", "c1"],
-        "offset_A": ["offset_A_c0", "offset_A_c1"],
-    }
-).set_index([CONDITION_ID])
-
-measurement_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a", "obs_a"],
-        SIMULATION_CONDITION_ID: ["c0", "c1"],
-        TIME: [10, 10],
-        MEASUREMENT: [2.1, 3.2],
-    }
+problem = Problem()
+
+problem.add_condition("c0", offset_A=(VT_CONSTANT, "offset_A_c0"))
+problem.add_condition("c1", offset_A=(VT_CONSTANT, "offset_A_c1"))
+
+problem.add_experiment("e0", 0, "c0")
+problem.add_experiment("e1", 0, "c1")
+
+problem.add_observable(
+    "obs_a",
+    "A + offset_A",
+    noise_formula=1,
+)
+
+problem.add_measurement(
+    "obs_a",
+    "e0",
+    time=10,
+    measurement=2.1,
+)
+problem.add_measurement(
+    "obs_a",
+    "e1",
+    time=10,
+    measurement=3.2,
 )
 
-observable_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a"],
-        OBSERVABLE_FORMULA: ["A + offset_A"],
-        NOISE_FORMULA: [1],
-    }
-).set_index([OBSERVABLE_ID])
-
-parameter_df = pd.DataFrame(
-    data={
-        PARAMETER_ID: ["a0", "b0", "k1", "k2", "offset_A_c0", "offset_A_c1"],
-        PARAMETER_SCALE: [LIN] * 6,
-        LOWER_BOUND: [0] * 6,
-        UPPER_BOUND: [10] * 6,
-        NOMINAL_VALUE: [1, 0, 0.8, 0.6, 2, 3],
-        ESTIMATE: [1] * 6,
-    }
-).set_index(PARAMETER_ID)
+problem.add_parameter(
+    "a0",
+    lb=0,
+    ub=10,
+    nominal_value=1,
+    scale=LIN,
+    estimate=True,
+)
+problem.add_parameter(
+    "b0",
+    lb=0,
+    ub=10,
+    nominal_value=0,
+    scale=LIN,
+    estimate=True,
+)
+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,
+)
+problem.add_parameter(
+    "offset_A_c0",
+    lb=0,
+    ub=10,
+    nominal_value=2,
+    scale=LIN,
+    estimate=False,
+)
+problem.add_parameter(
+    "offset_A_c1",
+    lb=0,
+    ub=10,
+    nominal_value=3,
+    scale=LIN,
+    estimate=False,
+)
 
 # solutions ------------------------------------------------------------------
 
-simulation_df = measurement_df.copy(deep=True).rename(
+simulation_df = problem.measurement_df.copy(deep=True).rename(
     columns={MEASUREMENT: SIMULATION}
 )
 simulation_df[SIMULATION] = [
@@ -73,9 +114,10 @@
     "parameter table.",
     description=DESCRIPTION,
     model="conversion_modified_pysb.py",
-    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,
+    experiment_dfs=[problem.experiment_df],
 )
diff --git a/petabtests/cases/v2.0.0/pysb/0005/_0005.yaml b/petabtests/cases/v2.0.0/pysb/0005/_0005.yaml
@@ -3,6 +3,8 @@ parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
   model_files:

diff --git a/petabtests/cases/v2.0.0/pysb/0005/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0005/_conditions.tsv
@@ -1,3 +1,3 @@
-conditionId	offset_A
-c0	offset_A_c0
-c1	offset_A_c1
+conditionId	targetId	valueType	targetValue
+c0	offset_A	constant	offset_A_c0
+c1	offset_A	constant	offset_A_c1
diff --git a/petabtests/cases/v2.0.0/pysb/0005/_experiments.tsv b/petabtests/cases/v2.0.0/pysb/0005/_experiments.tsv
@@ -0,0 +1,3 @@
+experimentId	time	conditionId
+e0	0	c0
+e1	0	c1
diff --git a/petabtests/cases/v2.0.0/pysb/0005/_measurements.tsv b/petabtests/cases/v2.0.0/pysb/0005/_measurements.tsv
@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	measurement
-obs_a	c0	10	2.1
-obs_a	c1	10	3.2
+observableId	experimentId	time	measurement
+obs_a	e0	10	2.1
+obs_a	e1	10	3.2
diff --git a/petabtests/cases/v2.0.0/pysb/0005/_parameters.tsv b/petabtests/cases/v2.0.0/pysb/0005/_parameters.tsv
@@ -1,7 +1,7 @@
-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
-offset_A_c0	lin	0	10	2.0	1
-offset_A_c1	lin	0	10	3.0	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
+offset_A_c0	0	2.0	lin	0	10
+offset_A_c1	0	3.0	lin	0	10
diff --git a/petabtests/cases/v2.0.0/pysb/0005/_simulations.tsv b/petabtests/cases/v2.0.0/pysb/0005/_simulations.tsv
@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	simulation
-obs_a	c0	10	2.4285719037306968
-obs_a	c1	10	3.4285719037306968
+observableId	experimentId	time	simulation
+obs_a	e0	10	2.4285719037306968
+obs_a	e1	10	3.4285719037306968