..

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

@@ -29,10 +29,10 @@
 )
 
 problem.add_measurement(
-    "obs_a", "c0", time=0, measurement=0.7, observable_parameters=(10,)
+    "obs_a", "", time=0, measurement=0.7, observable_parameters=(10,)
 )
 problem.add_measurement(
-    "obs_a", "c0", time=10, measurement=0.1, observable_parameters=(15,)
+    "obs_a", "", time=10, measurement=0.1, observable_parameters=(15,)
 )
 
 problem.add_parameter(

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

@@ -1,3 +1,3 @@
 observableId	experimentId	time	measurement	observableParameters
-obs_a	c0	0	0.7	10
-obs_a	c0	10	0.1	15
+obs_a		0	0.7	10
+obs_a		10	0.1	15

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

@@ -1,3 +1,3 @@
 observableId	experimentId	time	simulation	observableParameters
-obs_a	c0	0	10.0	10
-obs_a	c0	10	6.42857855596045	15
+obs_a		0	10.0	10
+obs_a		10	6.42857855596045	15

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

@@ -72,4 +72,5 @@
     measurement_dfs=[problem.measurement_df],
     simulation_dfs=[simulation_df],
     parameter_df=problem.parameter_df,
+    experiment_dfs=[problem.experiment_df],
 )

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

@@ -3,7 +3,8 @@ parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
-  experiment_files: []
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
   model_files:

petabtests/cases/v2.0.0/pysb/0009/_experiments.tsv

@@ -0,0 +1,3 @@
+experimentId	time	conditionId
+e0	-inf	preeq_c0
+e0	0.0	c0

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

@@ -1,14 +1,16 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv

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

@@ -1,5 +1,3 @@
 conditionId	targetId	targetValue	valueType
 c0	a0	0.8	constant
 c1	a0	0.9	constant
-c0	b0		constant
-c1	b0		constant

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

@@ -1,14 +1,16 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv

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

@@ -1,14 +1,16 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv

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

@@ -1,14 +1,16 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv

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

@@ -1,14 +1,16 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv

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

@@ -1,14 +1,16 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv

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

@@ -1,14 +1,16 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv

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

@@ -1,14 +1,16 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv

petabtests/cases/v2.0.0/sbml/0017/_conditions.tsv

@@ -2,6 +2,5 @@ conditionId	targetId	targetValue	valueType
 preeq_c0	k1	0.3	constant
 c0	k1	0.8	constant
 preeq_c0	B	2.0	initial
-c0	B		initial
 preeq_c0	A	0.0	initial
 c0	A	1.0	initial

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

@@ -1,14 +1,16 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv

petabtests/cases/v2.0.0/sbml/0018/_conditions.tsv

@@ -2,6 +2,5 @@ conditionId	targetId	targetValue	valueType
 preeq_c0	k1	0.3	constant
 c0	k1	0.8	constant
 preeq_c0	B	2.0	initial
-c0	B		initial
 preeq_c0	A	0.0	initial
 c0	A	1.0	initial

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

@@ -18,9 +18,8 @@
 # problem --------------------------------------------------------------------
 problem = Problem()
 # TODO use mapping here
-problem.add_condition("c0")
-problem.add_measurement("obs_a", "c0", 0, 0.7)
-problem.add_measurement("obs_a", "c0", 10, 0.1)
+problem.add_measurement("obs_a", "", 0, 0.7)
+problem.add_measurement("obs_a", "", 10, 0.1)
 problem.add_observable("obs_a", "maps_to_A", 0.5)
 problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, scale=LIN)
 problem.add_parameter("maps_to_b0", lb=0, ub=10, nominal_value=0, scale=LIN)

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

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

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

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

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

@@ -1,14 +1,16 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv

petabtests/file.py

@@ -258,6 +258,12 @@ def write_problem(
         tmp_exp_file = Path(dir_, "experiments.tsv")
         if tmp_exp_file.exists():
             tmp_exp_file.rename(exp_file)
+            # update in yaml
+            with open(yaml_path) as f:
+                config = yaml.safe_load(f)
+            config[PROBLEMS][0][EXPERIMENT_FILES] = ["_experiments.tsv"]
+            with open(yaml_path, "w") as f:
+                yaml.dump(config, f, default_flow_style=False)
         format_version = 2
 
     # FIXME Until a first libpetab with petab.v1 subpackage is released

test/test_generate.py

@@ -22,7 +22,7 @@ def test_create_case():
 
     Mostly for debugging purposes.
     """
-    format_ = "pysb"
+    format_ = "sbml"
     version = "v2.0.0"
-    id_ = "0002"
+    id_ = "0019"
     create_case(format_=format_, version=version, id_=id_)