PEtab-dev · dweindl · Dec 9, 2024
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@develop
+git+https://github.com/PEtab-dev/libpetab-python@long_conditions
 sympy>=1.12.1
diff --git a/petabtests/cases/v2.0.0/sbml/0001/_0001.yaml b/petabtests/cases/v2.0.0/sbml/0001/_0001.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0001/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0001/_conditions.tsv
@@ -1,2 +1 @@
-conditionId
-c0
+conditionId	targetId	valueType	targetValue
diff --git a/petabtests/cases/v2.0.0/sbml/0001/_measurements.tsv b/petabtests/cases/v2.0.0/sbml/0001/_measurements.tsv
@@ -1,3 +1,3 @@
 observableId	simulationConditionId	time	measurement
-obs_a	c0	0	0.7
-obs_a	c0	10	0.1
+obs_a		0	0.7
+obs_a		10	0.1
diff --git a/petabtests/cases/v2.0.0/sbml/0002/_0002.yaml b/petabtests/cases/v2.0.0/sbml/0002/_0002.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0002/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0002/_conditions.tsv
@@ -1,3 +1,5 @@
-conditionId	a0	b0
-c0	0.8	
-c1	0.9	
+conditionId	targetId	targetValue	valueType
+c0	a0	0.8	constant
+c1	a0	0.9	constant
+c0	b0		constant
+c1	b0		constant
diff --git a/petabtests/cases/v2.0.0/sbml/0003/_0003.yaml b/petabtests/cases/v2.0.0/sbml/0003/_0003.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0003/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0003/_conditions.tsv
@@ -1,2 +1 @@
-conditionId
-c0
+conditionId	targetId	valueType	targetValue
diff --git a/petabtests/cases/v2.0.0/sbml/0003/_measurements.tsv b/petabtests/cases/v2.0.0/sbml/0003/_measurements.tsv
@@ -1,3 +1,3 @@
 observableId	simulationConditionId	time	measurement	observableParameters
-obs_a	c0	0	0.7	0.5;2
-obs_a	c0	10	0.1	0.5;2
+obs_a		0	0.7	0.5;2
+obs_a		10	0.1	0.5;2
diff --git a/petabtests/cases/v2.0.0/sbml/0004/_0004.yaml b/petabtests/cases/v2.0.0/sbml/0004/_0004.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0004/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0004/_conditions.tsv
@@ -1,2 +1 @@
-conditionId
-c0
+conditionId	targetId	valueType	targetValue
diff --git a/petabtests/cases/v2.0.0/sbml/0004/_measurements.tsv b/petabtests/cases/v2.0.0/sbml/0004/_measurements.tsv
@@ -1,3 +1,3 @@
 observableId	simulationConditionId	time	measurement
-obs_a	c0	0	0.7
-obs_a	c0	10	0.1
+obs_a		0	0.7
+obs_a		10	0.1
diff --git a/petabtests/cases/v2.0.0/sbml/0005/_0005.yaml b/petabtests/cases/v2.0.0/sbml/0005/_0005.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0005/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0005/_conditions.tsv
@@ -1,3 +1,3 @@
-conditionId	offset_A
-c0	offset_A_c0
-c1	offset_A_c1
+conditionId	targetId	targetValue	valueType
+c0	offset_A	offset_A_c0	constant
+c1	offset_A	offset_A_c1	constant
diff --git a/petabtests/cases/v2.0.0/sbml/0006/_0006.yaml b/petabtests/cases/v2.0.0/sbml/0006/_0006.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0006/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0006/_conditions.tsv
@@ -1,2 +1 @@
-conditionId
-c0
+conditionId	targetId	valueType	targetValue
diff --git a/petabtests/cases/v2.0.0/sbml/0006/_measurements.tsv b/petabtests/cases/v2.0.0/sbml/0006/_measurements.tsv
@@ -1,3 +1,3 @@
 observableId	simulationConditionId	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
diff --git a/petabtests/cases/v2.0.0/sbml/0007/_0007.yaml b/petabtests/cases/v2.0.0/sbml/0007/_0007.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0007/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0007/_conditions.tsv
@@ -1,2 +1 @@
-conditionId
-c0
+conditionId	targetId	valueType	targetValue
diff --git a/petabtests/cases/v2.0.0/sbml/0007/_measurements.tsv b/petabtests/cases/v2.0.0/sbml/0007/_measurements.tsv
@@ -1,3 +1,3 @@
 observableId	simulationConditionId	time	measurement
-obs_a	c0	10	0.2
-obs_b	c0	10	0.8
+obs_a		10	0.2
+obs_b		10	0.8
diff --git a/petabtests/cases/v2.0.0/sbml/0008/_0008.yaml b/petabtests/cases/v2.0.0/sbml/0008/_0008.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0008/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0008/_conditions.tsv
@@ -1,2 +1 @@
-conditionId
-c0
+conditionId	targetId	valueType	targetValue
diff --git a/petabtests/cases/v2.0.0/sbml/0008/_measurements.tsv b/petabtests/cases/v2.0.0/sbml/0008/_measurements.tsv
@@ -1,4 +1,4 @@
 observableId	simulationConditionId	time	measurement
-obs_a	c0	0	0.7
-obs_a	c0	10	0.1
-obs_a	c0	10	0.2
+obs_a		0	0.7
+obs_a		10	0.1
+obs_a		10	0.2
diff --git a/petabtests/cases/v2.0.0/sbml/0009/_0009.yaml b/petabtests/cases/v2.0.0/sbml/0009/_0009.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0009/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0009/_conditions.tsv
@@ -1,3 +1,3 @@
-conditionId	k1
-preeq_c0	0.3
-c0	0.8
+conditionId	targetId	targetValue	valueType
+preeq_c0	k1	0.3	constant
+c0	k1	0.8	constant
diff --git a/petabtests/cases/v2.0.0/sbml/0010/_0010.yaml b/petabtests/cases/v2.0.0/sbml/0010/_0010.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0010/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0010/_conditions.tsv
@@ -1,3 +1,5 @@
-conditionId	k1	B
-preeq_c0	0.3	0
-c0	0.8	1
+conditionId	targetId	targetValue	valueType
+preeq_c0	k1	0.3	constant
+c0	k1	0.8	constant
+preeq_c0	B	0.0	initial
+c0	B	1.0	initial
diff --git a/petabtests/cases/v2.0.0/sbml/0011/_0011.yaml b/petabtests/cases/v2.0.0/sbml/0011/_0011.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0011/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0011/_conditions.tsv
@@ -1,2 +1,2 @@
-conditionId	B
-c0	2
+conditionId	targetId	targetValue	valueType
+c0	B	2	initial
diff --git a/petabtests/cases/v2.0.0/sbml/0012/_0012.yaml b/petabtests/cases/v2.0.0/sbml/0012/_0012.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0012/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0012/_conditions.tsv
@@ -1,2 +1,2 @@
-conditionId	compartment
-c0	3
+conditionId	targetId	targetValue	valueType
+c0	compartment	3	initial
diff --git a/petabtests/cases/v2.0.0/sbml/0013/_0013.yaml b/petabtests/cases/v2.0.0/sbml/0013/_0013.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0013/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0013/_conditions.tsv
@@ -1,2 +1,2 @@
-conditionId	B
-c0	par
+conditionId	targetId	targetValue	valueType
+c0	B	par	initial
diff --git a/petabtests/cases/v2.0.0/sbml/0014/_0014.yaml b/petabtests/cases/v2.0.0/sbml/0014/_0014.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0014/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0014/_conditions.tsv
@@ -1,2 +1 @@
-conditionId
-c0
+conditionId	targetId	valueType	targetValue
diff --git a/petabtests/cases/v2.0.0/sbml/0014/_measurements.tsv b/petabtests/cases/v2.0.0/sbml/0014/_measurements.tsv
@@ -1,3 +1,3 @@
 observableId	simulationConditionId	time	measurement	noiseParameters
-obs_a	c0	0	0.7	0.5;2
-obs_a	c0	10	0.1	0.5;2
+obs_a		0	0.7	0.5;2
+obs_a		10	0.1	0.5;2
diff --git a/petabtests/cases/v2.0.0/sbml/0015/_0015.yaml b/petabtests/cases/v2.0.0/sbml/0015/_0015.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0015/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0015/_conditions.tsv
@@ -1,2 +1 @@
-conditionId
-c0
+conditionId	targetId	valueType	targetValue
diff --git a/petabtests/cases/v2.0.0/sbml/0015/_measurements.tsv b/petabtests/cases/v2.0.0/sbml/0015/_measurements.tsv
@@ -1,3 +1,3 @@
 observableId	simulationConditionId	time	measurement	noiseParameters
-obs_a	c0	0	0.7	noise
-obs_a	c0	10	0.1	noise
+obs_a		0	0.7	noise
+obs_a		10	0.1	noise
diff --git a/petabtests/cases/v2.0.0/sbml/0016/_0016.yaml b/petabtests/cases/v2.0.0/sbml/0016/_0016.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0016/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0016/_conditions.tsv
@@ -1,2 +1 @@
-conditionId
-c0
+conditionId	targetId	valueType	targetValue
diff --git a/petabtests/cases/v2.0.0/sbml/0016/_measurements.tsv b/petabtests/cases/v2.0.0/sbml/0016/_measurements.tsv
@@ -1,3 +1,3 @@
 observableId	simulationConditionId	time	measurement
-obs_a	c0	10	0.2
-obs_b	c0	10	0.8
+obs_a		10	0.2
+obs_b		10	0.8
diff --git a/petabtests/cases/v2.0.0/sbml/0017/_0017.yaml b/petabtests/cases/v2.0.0/sbml/0017/_0017.yaml
@@ -5,9 +5,10 @@ problems:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  observable_files:
+  - _observables.tsv
   model_files:
-    model_0:
+    _model:
       language: sbml
       location: _model.xml
-  observable_files:
-  - _observables.tsv
+extensions: []
diff --git a/petabtests/cases/v2.0.0/sbml/0017/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0017/_conditions.tsv
@@ -1,3 +1,7 @@
-conditionId	k1	B	A
-preeq_c0	0.3	2.0	0
-c0	0.8	NaN	1
+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