Rename compartment-backed PySB mapping IDs to _c, fixes #113

petabtests/cases/v2.0.0/pysb/0010/0010.py

@@ -24,8 +24,8 @@
 # problem --------------------------------------------------------------------
 problem = Problem()
 
-problem.add_condition("preeq_c0", k1=0.3, B=0)
-problem.add_condition("c0", k1=0.8, B=1)
+problem.add_condition("preeq_c0", k1=0.3, B_c=0)
+problem.add_condition("c0", k1=0.8, B_c=1)
 
 problem.add_experiment("e0", TIME_PREEQUILIBRATION, "preeq_c0", 0, "c0")
 
@@ -35,8 +35,8 @@
 problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)
 
 problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, estimate=True)
-problem.add_mapping("A", "A_() ** compartment")
-problem.add_mapping("B", "B_() ** compartment")
+problem.add_mapping("A_c", "A_() ** compartment")
+problem.add_mapping("B_c", "B_() ** compartment")
 
 
 # solutions ------------------------------------------------------------------

petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv

@@ -1,5 +1,5 @@
 conditionId	targetId	targetValue
 preeq_c0	k1	0.3
-preeq_c0	B	0.0
+preeq_c0	B_c	0.0
 c0	k1	0.8
-c0	B	1.0
+c0	B_c	1.0

petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv

@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_c	A_() ** compartment	
+B_c	B_() ** compartment	

petabtests/cases/v2.0.0/pysb/0011/0011.py

@@ -21,7 +21,7 @@
 # problem --------------------------------------------------------------------
 problem = Problem()
 
-problem.add_condition("c0", B=2)
+problem.add_condition("c0", B_c=2)
 
 problem.add_experiment("e0", 0, "c0")
 
@@ -33,8 +33,8 @@
 problem.add_parameter("k1", lb=0, ub=10, nominal_value=0.8, estimate=True)
 problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, estimate=True)
 
-problem.add_mapping("A", "A_() ** compartment")
-problem.add_mapping("B", "B_() ** compartment")
+problem.add_mapping("A_c", "A_() ** compartment")
+problem.add_mapping("B_c", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 

petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv

@@ -1,2 +1,2 @@
 conditionId	targetId	targetValue
-c0	B	2.0
+c0	B_c	2.0

petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv

@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_c	A_() ** compartment	
+B_c	B_() ** compartment	

petabtests/cases/v2.0.0/pysb/0013/0013.py

@@ -19,7 +19,7 @@
 # problem --------------------------------------------------------------------
 problem = Problem()
 
-problem.add_condition("c0", B="par")
+problem.add_condition("c0", B_c="par")
 problem.add_experiment("e0", 0, "c0")
 problem.add_observable("obs_a", "A", noise_formula=0.5)
 
@@ -30,8 +30,8 @@
 problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, estimate=True)
 problem.add_parameter("par", lb=0, ub=10, nominal_value=7, estimate=True)
 
-problem.add_mapping("A", "A_() ** compartment")
-problem.add_mapping("B", "B_() ** compartment")
+problem.add_mapping("A_c", "A_() ** compartment")
+problem.add_mapping("B_c", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 

petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv

@@ -1,2 +1,2 @@
 conditionId	targetId	targetValue
-c0	B	par
+c0	B_c	par

petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv

@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_c	A_() ** compartment	
+B_c	B_() ** compartment	

petabtests/cases/v2.0.0/pysb/0017/0017.py

@@ -32,17 +32,17 @@
 
 # problem --------------------------------------------------------------------
 problem = Problem()
-problem.add_condition("preeq_c0", k1=0.3, B=2.0, A=0)
-problem.add_condition("c0", k1=0.8, A=1)
+problem.add_condition("preeq_c0", k1=0.3, B_c=2.0, A_c=0)
+problem.add_condition("c0", k1=0.8, A_c=1)
 problem.add_experiment("e0", TIME_PREEQUILIBRATION, "preeq_c0", 0, "c0")
 problem.add_observable("obs_a", "A", noise_formula=0.5)
 problem.add_measurement("obs_a", experiment_id="e0", time=1, measurement=0.7)
 problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)
 problem.add_parameter(
     "k2", lb=0, ub=10, nominal_value=0.6, scale=LIN, estimate=True
 )
-problem.add_mapping("A", "A_() ** compartment")
-problem.add_mapping("B", "B_() ** compartment")
+problem.add_mapping("A_c", "A_() ** compartment")
+problem.add_mapping("B_c", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 

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

@@ -1,6 +1,6 @@
 conditionId	targetId	targetValue
 preeq_c0	k1	0.3
-preeq_c0	B	2.0
-preeq_c0	A	0.0
+preeq_c0	B_c	2.0
+preeq_c0	A_c	0.0
 c0	k1	0.8
-c0	A	1.0
+c0	A_c	1.0

petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv

@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_c	A_() ** compartment	
+B_c	B_() ** compartment	

test/test_general.py

@@ -1,5 +1,6 @@
 import petabtests
 import os
+import pytest
 
 
 def test_cases_dir_exists():
@@ -14,3 +15,40 @@ def test_cases_dir_exists():
     assert os.path.isdir(
         petabtests.get_cases_dir(format_="pysb", version="v2.0.0")
     )
+
+
+@pytest.mark.parametrize(
+    "format_,version",
+    [
+        ("sbml", "v2.0.0"),
+        ("pysb", "v2.0.0"),
+    ],
+)
+def test_lint_all_v2_cases(format_, version):
+    """Regression test: all v2 test cases must pass PEtab linting."""
+    from petab.v2.lint import lint_problem
+
+    cases_dir = petabtests.get_cases_dir(format_=format_, version=version)
+    cases = sorted(
+        f.name
+        for f in os.scandir(cases_dir)
+        if f.is_dir() and f.name.isdigit()
+    )
+    assert cases, f"No cases found in {cases_dir}"
+
+    failures = {}
+    for case_id in cases:
+        yaml_path = cases_dir / case_id / f"_{case_id}.yaml"
+        if not yaml_path.exists():
+            continue
+        results = lint_problem(yaml_path)
+        if results:
+            failures[case_id] = [str(r) for r in results]
+
+    assert not failures, (
+        "Linting failed for the following test cases:\n"
+        + "\n".join(
+            f"  {case_id}: {'; '.join(errs)}"
+            for case_id, errs in sorted(failures.items())
+        )
+    )