..

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/0001/_0001.yaml

@@ -1,14 +1,17 @@
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
-- condition_files:
-  - _conditions.tsv
+- model_files:
+    _model:
+      location: _model.xml
+      language: sbml
   measurement_files:
   - _measurements.tsv
+  condition_files:
+  - _conditions.tsv
+  experiment_files: []
   observable_files:
   - _observables.tsv
-  model_files:
-    _model:
-      language: sbml
-      location: _model.xml
+  visualization_files: []
+  mapping_files: []
 extensions: []

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

@@ -1,14 +1,18 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
+  mapping_files: []
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv
+  visualization_files: []

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

@@ -1,14 +1,17 @@
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
-- condition_files:
-  - _conditions.tsv
+- model_files:
+    _model:
+      location: _model.xml
+      language: sbml
   measurement_files:
   - _measurements.tsv
+  condition_files:
+  - _conditions.tsv
+  experiment_files: []
   observable_files:
   - _observables.tsv
-  model_files:
-    _model:
-      language: sbml
-      location: _model.xml
+  visualization_files: []
+  mapping_files: []
 extensions: []

petabtests/cases/v2.0.0/sbml/0004/_0004.yaml

@@ -1,14 +1,17 @@
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
-- condition_files:
-  - _conditions.tsv
+- model_files:
+    _model:
+      location: _model.xml
+      language: sbml
   measurement_files:
   - _measurements.tsv
+  condition_files:
+  - _conditions.tsv
+  experiment_files: []
   observable_files:
   - _observables.tsv
-  model_files:
-    _model:
-      language: sbml
-      location: _model.xml
+  visualization_files: []
+  mapping_files: []
 extensions: []

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

@@ -1,14 +1,18 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
+  mapping_files: []
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv
+  visualization_files: []

petabtests/cases/v2.0.0/sbml/0006/_0006.yaml

@@ -1,14 +1,17 @@
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
-- condition_files:
-  - _conditions.tsv
+- model_files:
+    _model:
+      location: _model.xml
+      language: sbml
   measurement_files:
   - _measurements.tsv
+  condition_files:
+  - _conditions.tsv
+  experiment_files: []
   observable_files:
   - _observables.tsv
-  model_files:
-    _model:
-      language: sbml
-      location: _model.xml
+  visualization_files: []
+  mapping_files: []
 extensions: []

petabtests/cases/v2.0.0/sbml/0007/_0007.yaml

@@ -1,14 +1,17 @@
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
-- condition_files:
-  - _conditions.tsv
+- model_files:
+    _model:
+      location: _model.xml
+      language: sbml
   measurement_files:
   - _measurements.tsv
+  condition_files:
+  - _conditions.tsv
+  experiment_files: []
   observable_files:
   - _observables.tsv
-  model_files:
-    _model:
-      language: sbml
-      location: _model.xml
+  visualization_files: []
+  mapping_files: []
 extensions: []

petabtests/cases/v2.0.0/sbml/0008/_0008.yaml

@@ -1,14 +1,17 @@
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
-- condition_files:
-  - _conditions.tsv
+- model_files:
+    _model:
+      location: _model.xml
+      language: sbml
   measurement_files:
   - _measurements.tsv
+  condition_files:
+  - _conditions.tsv
+  experiment_files: []
   observable_files:
   - _observables.tsv
-  model_files:
-    _model:
-      language: sbml
-      location: _model.xml
+  visualization_files: []
+  mapping_files: []
 extensions: []

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

@@ -1,14 +1,18 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
+  mapping_files: []
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv
+  visualization_files: []

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

@@ -1,14 +1,18 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
+  mapping_files: []
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv
+  visualization_files: []

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

@@ -1,14 +1,18 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
+  mapping_files: []
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv
+  visualization_files: []

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

@@ -1,14 +1,18 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
+  mapping_files: []
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv
+  visualization_files: []

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

@@ -1,14 +1,18 @@
+extensions: []
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
+  experiment_files:
+  - _experiments.tsv
+  mapping_files: []
   measurement_files:
   - _measurements.tsv
-  observable_files:
-  - _observables.tsv
   model_files:
     _model:
       language: sbml
       location: _model.xml
-extensions: []
+  observable_files:
+  - _observables.tsv
+  visualization_files: []

petabtests/cases/v2.0.0/sbml/0014/_0014.yaml

@@ -1,14 +1,17 @@
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
-- condition_files:
-  - _conditions.tsv
+- model_files:
+    _model:
+      location: _model.xml
+      language: sbml
   measurement_files:
   - _measurements.tsv
+  condition_files:
+  - _conditions.tsv
+  experiment_files: []
   observable_files:
   - _observables.tsv
-  model_files:
-    _model:
-      language: sbml
-      location: _model.xml
+  visualization_files: []
+  mapping_files: []
 extensions: []