pysb 6+7

PEtab-dev · Dec 18, 2024 · 2f3a873 · 2f3a873
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commit 2f3a873
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diff --git a/.ci_pip_reqs.txt b/.ci_pip_reqs.txt
@@ -1,4 +1,4 @@
 pytest
 ruff
-git+https://github.com/PEtab-dev/libpetab-python@long_conditions
+git+https://github.com/PEtab-dev/libpetab-python@develop
 sympy>=1.12.1
diff --git a/petabtests/cases/v2.0.0/pysb/0006/0006.py b/petabtests/cases/v2.0.0/pysb/0006/0006.py
@@ -1,9 +1,10 @@
 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
@@ -21,45 +22,34 @@
 """)
 
 # 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: [10, 15],
-    }
+problem.add_observable(
+    "obs_a", "observableParameter1_obs_a * A", noise_formula=1
 )
 
-observable_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a"],
-        OBSERVABLE_FORMULA: ["observableParameter1_obs_a * A"],
-        NOISE_FORMULA: [1],
-    }
-).set_index([OBSERVABLE_ID])
-
-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_measurement(
+    "obs_a", "c0", time=0, measurement=0.7, observable_parameters=(10,)
+)
+problem.add_measurement(
+    "obs_a", "c0", time=10, measurement=0.1, observable_parameters=(15,)
+)
 
+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
+)
 # 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 +63,9 @@
     "overrides.",
     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/0006/_0006.yaml b/petabtests/cases/v2.0.0/pysb/0006/_0006.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/0006/_measurements.tsv b/petabtests/cases/v2.0.0/pysb/0006/_measurements.tsv
@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	measurement	observableParameters
+observableId	experimentId	time	measurement	observableParameters
 obs_a	c0	0	0.7	10
 obs_a	c0	10	0.1	15
diff --git a/petabtests/cases/v2.0.0/pysb/0006/_parameters.tsv b/petabtests/cases/v2.0.0/pysb/0006/_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
diff --git a/petabtests/cases/v2.0.0/pysb/0006/_simulations.tsv b/petabtests/cases/v2.0.0/pysb/0006/_simulations.tsv
@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	simulation	observableParameters
+observableId	experimentId	time	simulation	observableParameters
 obs_a	c0	0	10.0	10
 obs_a	c0	10	6.42857855596045	15
diff --git a/petabtests/cases/v2.0.0/pysb/0007/0007.py b/petabtests/cases/v2.0.0/pysb/0007/0007.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,
@@ -26,45 +26,31 @@
 """)
 
 # problem --------------------------------------------------------------------
+problem = Problem()
 
-condition_df = pd.DataFrame(
-    data={
-        CONDITION_ID: ["c0"],
-    }
-).set_index([CONDITION_ID])
+problem.add_observable("obs_a", "A", noise_formula=0.5)
+problem.add_observable("obs_b", "B", noise_formula=0.6)
 
-measurement_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a", "obs_b"],
-        SIMULATION_CONDITION_ID: ["c0", "c0"],
-        TIME: [10, 10],
-        MEASUREMENT: [0.2, 0.8],
-    }
-)
+problem.add_measurement("obs_a", "", time=10, measurement=0.2)
+problem.add_measurement("obs_b", "", time=10, measurement=0.8)
 
-observable_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a", "obs_b"],
-        OBSERVABLE_FORMULA: ["A", "B"],
-        OBSERVABLE_TRANSFORMATION: [LIN, LOG10],
-        NOISE_FORMULA: [0.5, 0.6],
-    }
-).set_index([OBSERVABLE_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
+)
 
-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)
 
 # 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 +63,9 @@
     brief="Simulation. Observable transformation log10.",
     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/0007/_0007.yaml b/petabtests/cases/v2.0.0/pysb/0007/_0007.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/0007/_0007_solution.yaml b/petabtests/cases/v2.0.0/pysb/0007/_0007_solution.yaml
@@ -1,5 +1,5 @@
-chi2: 0.2682957616817
-llh: -1.378941036858
+chi2: 0.35410578063106
+llh: -0.81095715239894
 simulation_files:
 - _simulations.tsv
 tol_chi2: 0.001

diff --git a/petabtests/cases/v2.0.0/pysb/0007/_measurements.tsv b/petabtests/cases/v2.0.0/pysb/0007/_measurements.tsv
@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	measurement
-obs_a	c0	10	0.2
-obs_b	c0	10	0.8
+observableId	experimentId	time	measurement
+obs_a		10	0.2
+obs_b		10	0.8
diff --git a/petabtests/cases/v2.0.0/pysb/0007/_observables.tsv b/petabtests/cases/v2.0.0/pysb/0007/_observables.tsv
@@ -1,3 +1,3 @@
-observableId	observableFormula	observableTransformation	noiseFormula
-obs_a	A	lin	0.5
-obs_b	B	log10	0.6
+observableId	observableFormula	noiseFormula
+obs_a	A	0.5
+obs_b	B	0.6
diff --git a/petabtests/cases/v2.0.0/pysb/0007/_parameters.tsv b/petabtests/cases/v2.0.0/pysb/0007/_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
diff --git a/petabtests/cases/v2.0.0/pysb/0007/_simulations.tsv b/petabtests/cases/v2.0.0/pysb/0007/_simulations.tsv
@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	simulation
-obs_a	c0	10	0.42857190373069665
-obs_b	c0	10	0.5714280962693035
+observableId	experimentId	time	simulation
+obs_a		10	0.42857190373069665
+obs_b		10	0.5714280962693035