From 11e1613aac4f51c6a4410fe778c82ae920e1d5a4 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 14:10:41 +0000
Subject: [PATCH 1/6] Initial plan


From 909e7747da4687464ba5bd9de6c5493546a276d2 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 14:23:14 +0000
Subject: [PATCH 2/6] Fix invalid mapping table entries in PySB test cases
 0010, 0011, 0013, 0017; add lint regression test

---
 petabtests/cases/v2.0.0/pysb/0010/0010.py     |  8 ++--
 .../cases/v2.0.0/pysb/0010/_conditions.tsv    |  4 +-
 .../cases/v2.0.0/pysb/0010/_mapping.tsv       |  4 +-
 petabtests/cases/v2.0.0/pysb/0011/0011.py     |  6 +--
 .../cases/v2.0.0/pysb/0011/_conditions.tsv    |  2 +-
 .../cases/v2.0.0/pysb/0011/_mapping.tsv       |  4 +-
 petabtests/cases/v2.0.0/pysb/0013/0013.py     |  6 +--
 .../cases/v2.0.0/pysb/0013/_conditions.tsv    |  2 +-
 .../cases/v2.0.0/pysb/0013/_mapping.tsv       |  4 +-
 petabtests/cases/v2.0.0/pysb/0017/0017.py     |  8 ++--
 .../cases/v2.0.0/pysb/0017/_conditions.tsv    |  6 +--
 .../cases/v2.0.0/pysb/0017/_mapping.tsv       |  4 +-
 test/test_general.py                          | 39 +++++++++++++++++++
 13 files changed, 68 insertions(+), 29 deletions(-)

diff --git a/petabtests/cases/v2.0.0/pysb/0010/0010.py b/petabtests/cases/v2.0.0/pysb/0010/0010.py
index a0c475f..96d7276 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/0010.py
+++ b/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_o=0)
+problem.add_condition("c0", k1=0.8, B_o=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_o", "A_() ** compartment")
+problem.add_mapping("B_o", "B_() ** compartment")
 
 
 # solutions ------------------------------------------------------------------
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv
index 01d5b3d..2e21373 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv
+++ b/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_o	0.0
 c0	k1	0.8
-c0	B	1.0
+c0	B_o	1.0
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
index 2fee7f7..54ec18f 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_o	A_() ** compartment	
+B_o	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0011/0011.py b/petabtests/cases/v2.0.0/pysb/0011/0011.py
index c904997..b7bb9b3 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/0011.py
+++ b/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_o=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_o", "A_() ** compartment")
+problem.add_mapping("B_o", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
index 5d968f9..334c5ff 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
@@ -1,2 +1,2 @@
 conditionId	targetId	targetValue
-c0	B	2.0
+c0	B_o	2.0
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
index 2fee7f7..54ec18f 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_o	A_() ** compartment	
+B_o	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0013/0013.py b/petabtests/cases/v2.0.0/pysb/0013/0013.py
index 0a16c1a..c0c05fb 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/0013.py
+++ b/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_o="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_o", "A_() ** compartment")
+problem.add_mapping("B_o", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
index d2e474f..04c824b 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
@@ -1,2 +1,2 @@
 conditionId	targetId	targetValue
-c0	B	par
+c0	B_o	par
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
index 2fee7f7..54ec18f 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_o	A_() ** compartment	
+B_o	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0017/0017.py b/petabtests/cases/v2.0.0/pysb/0017/0017.py
index d2af56e..fb8ba30 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/0017.py
+++ b/petabtests/cases/v2.0.0/pysb/0017/0017.py
@@ -32,8 +32,8 @@
 
 # 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_o=2.0, A_o=0)
+problem.add_condition("c0", k1=0.8, A_o=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)
@@ -41,8 +41,8 @@
 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_o", "A_() ** compartment")
+problem.add_mapping("B_o", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv
index 934e234..34068e1 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv
+++ b/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_o	2.0
+preeq_c0	A_o	0.0
 c0	k1	0.8
-c0	A	1.0
+c0	A_o	1.0
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
index 2fee7f7..54ec18f 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_o	A_() ** compartment	
+B_o	B_() ** compartment	
diff --git a/test/test_general.py b/test/test_general.py
index e1178b2..2c7aa9b 100644
--- a/test/test_general.py
+++ b/test/test_general.py
@@ -1,5 +1,7 @@
 import petabtests
 import os
+import pytest
+from pathlib import Path
 
 
 def test_cases_dir_exists():
@@ -14,3 +16,40 @@ 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())
+        )
+    )

From a63bad7344ec0e9cfde4d0b12c39eb233ee006d9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 14:29:10 +0000
Subject: [PATCH 3/6] Fix PySB mapping table conflicts: rename observables A/B
 to A_o/B_o

---
 petabtests/cases/v2.0.0/pysb/0010/0010.py     | 15 +++++-----
 .../cases/v2.0.0/pysb/0010/_conditions.tsv    |  4 +--
 .../cases/v2.0.0/pysb/0010/_mapping.tsv       |  4 +--
 petabtests/cases/v2.0.0/pysb/0010/_model.py   |  4 +--
 .../cases/v2.0.0/pysb/0010/_observables.tsv   |  2 +-
 .../cases/v2.0.0/pysb/0010/conversion_pysb.py | 29 +++++++++++++++++++
 petabtests/cases/v2.0.0/pysb/0011/0011.py     |  8 ++---
 .../cases/v2.0.0/pysb/0011/_conditions.tsv    |  2 +-
 .../cases/v2.0.0/pysb/0011/_mapping.tsv       |  4 +--
 petabtests/cases/v2.0.0/pysb/0011/_model.py   |  4 +--
 .../cases/v2.0.0/pysb/0011/_observables.tsv   |  2 +-
 .../pysb/0011/conversion_modified_pysb.py     |  4 +--
 petabtests/cases/v2.0.0/pysb/0013/0013.py     |  8 ++---
 .../cases/v2.0.0/pysb/0013/_conditions.tsv    |  2 +-
 .../cases/v2.0.0/pysb/0013/_mapping.tsv       |  4 +--
 petabtests/cases/v2.0.0/pysb/0013/_model.py   |  4 +--
 .../cases/v2.0.0/pysb/0013/_observables.tsv   |  2 +-
 .../pysb/0013/conversion_modified_pysb.py     |  4 +--
 petabtests/cases/v2.0.0/pysb/0017/0017.py     | 14 ++++-----
 .../cases/v2.0.0/pysb/0017/_conditions.tsv    |  6 ++--
 .../cases/v2.0.0/pysb/0017/_mapping.tsv       |  4 +--
 petabtests/cases/v2.0.0/pysb/0017/_model.py   |  4 +--
 .../cases/v2.0.0/pysb/0017/_observables.tsv   |  2 +-
 .../cases/v2.0.0/pysb/0017/conversion_pysb.py | 29 +++++++++++++++++++
 pyproject.toml                                |  1 +
 25 files changed, 113 insertions(+), 53 deletions(-)
 create mode 100644 petabtests/cases/v2.0.0/pysb/0010/conversion_pysb.py
 create mode 100644 petabtests/cases/v2.0.0/pysb/0017/conversion_pysb.py

diff --git a/petabtests/cases/v2.0.0/pysb/0010/0010.py b/petabtests/cases/v2.0.0/pysb/0010/0010.py
index 96d7276..4d3a140 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/0010.py
+++ b/petabtests/cases/v2.0.0/pysb/0010/0010.py
@@ -1,9 +1,10 @@
 from inspect import cleandoc
+from pathlib import Path
 
 from petab.v2 import Problem
 from petab.v2.C import *
 
-from petabtests import DEFAULT_PYSB_FILE, PetabV2TestCase, analytical_a
+from petabtests import PetabV2TestCase, analytical_a
 
 DESCRIPTION = cleandoc("""
 ## Objective
@@ -24,19 +25,19 @@
 # problem --------------------------------------------------------------------
 problem = Problem()
 
-problem.add_condition("preeq_c0", k1=0.3, B_o=0)
-problem.add_condition("c0", k1=0.8, B_o=1)
+problem.add_condition("preeq_c0", k1=0.3, B=0)
+problem.add_condition("c0", k1=0.8, B=1)
 
 problem.add_experiment("e0", TIME_PREEQUILIBRATION, "preeq_c0", 0, "c0")
 
-problem.add_observable("obs_a", "A", noise_formula=0.5)
+problem.add_observable("obs_a", "A_o", 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, estimate=True)
-problem.add_mapping("A_o", "A_() ** compartment")
-problem.add_mapping("B_o", "B_() ** compartment")
+problem.add_mapping("A", "A_() ** compartment")
+problem.add_mapping("B", "B_() ** compartment")
 
 
 # solutions ------------------------------------------------------------------
@@ -56,7 +57,7 @@
     brief="Simulation. Preequilibration. One species reinitialized, one not. "
     "InitialAssignment to species overridden.",
     description=DESCRIPTION,
-    model=DEFAULT_PYSB_FILE,
+    model=Path("conversion_pysb.py"),
     condition_dfs=[problem.condition_df],
     observable_dfs=[problem.observable_df],
     measurement_dfs=[problem.measurement_df],
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv
index 2e21373..01d5b3d 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv
@@ -1,5 +1,5 @@
 conditionId	targetId	targetValue
 preeq_c0	k1	0.3
-preeq_c0	B_o	0.0
+preeq_c0	B	0.0
 c0	k1	0.8
-c0	B_o	1.0
+c0	B	1.0
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
index 54ec18f..2fee7f7 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A_o	A_() ** compartment	
-B_o	B_() ** compartment	
+A	A_() ** compartment	
+B	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_model.py b/petabtests/cases/v2.0.0/pysb/0010/_model.py
index 71263df..d7e8f35 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_model.py
+++ b/petabtests/cases/v2.0.0/pysb/0010/_model.py
@@ -25,5 +25,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A", A_())
-Observable("B", B_())
+Observable("A_o", A_())
+Observable("B_o", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_observables.tsv b/petabtests/cases/v2.0.0/pysb/0010/_observables.tsv
index 251acc7..d73fd30 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_observables.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0010/_observables.tsv
@@ -1,2 +1,2 @@
 observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
-obs_a		A	0.500000000000000	normal		
+obs_a		A_o	0.500000000000000	normal		
diff --git a/petabtests/cases/v2.0.0/pysb/0010/conversion_pysb.py b/petabtests/cases/v2.0.0/pysb/0010/conversion_pysb.py
new file mode 100644
index 0000000..d7e8f35
--- /dev/null
+++ b/petabtests/cases/v2.0.0/pysb/0010/conversion_pysb.py
@@ -0,0 +1,29 @@
+from pysb import (
+    Model,
+    Monomer,
+    Parameter,
+    Compartment,
+    Rule,
+    Initial,
+    Observable,
+)
+
+Model()
+
+Compartment("compartment")
+
+Monomer("A_")
+Monomer("B_")
+
+Parameter("a0", 1.0)
+Parameter("b0", 1.0)
+Parameter("k1", 0.0)
+Parameter("k2", 0.0)
+
+Rule("conversion", A_() ** compartment | B_() ** compartment, k1, k2)
+
+Initial(A_() ** compartment, a0)
+Initial(B_() ** compartment, b0)
+
+Observable("A_o", A_())
+Observable("B_o", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0011/0011.py b/petabtests/cases/v2.0.0/pysb/0011/0011.py
index b7bb9b3..858501c 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/0011.py
+++ b/petabtests/cases/v2.0.0/pysb/0011/0011.py
@@ -21,11 +21,11 @@
 # problem --------------------------------------------------------------------
 problem = Problem()
 
-problem.add_condition("c0", B_o=2)
+problem.add_condition("c0", B=2)
 
 problem.add_experiment("e0", 0, "c0")
 
-problem.add_observable("obs_a", "A", noise_formula=0.5)
+problem.add_observable("obs_a", "A_o", noise_formula=0.5)
 
 problem.add_measurement("obs_a", experiment_id="e0", time=0, measurement=0.7)
 problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)
@@ -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_o", "A_() ** compartment")
-problem.add_mapping("B_o", "B_() ** compartment")
+problem.add_mapping("A", "A_() ** compartment")
+problem.add_mapping("B", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
index 334c5ff..5d968f9 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
@@ -1,2 +1,2 @@
 conditionId	targetId	targetValue
-c0	B_o	2.0
+c0	B	2.0
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
index 54ec18f..2fee7f7 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A_o	A_() ** compartment	
-B_o	B_() ** compartment	
+A	A_() ** compartment	
+B	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_model.py b/petabtests/cases/v2.0.0/pysb/0011/_model.py
index 57ec588..60ba1e6 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_model.py
+++ b/petabtests/cases/v2.0.0/pysb/0011/_model.py
@@ -17,5 +17,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A", A_())
-Observable("B", B_())
+Observable("A_o", A_())
+Observable("B_o", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_observables.tsv b/petabtests/cases/v2.0.0/pysb/0011/_observables.tsv
index 251acc7..d73fd30 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_observables.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0011/_observables.tsv
@@ -1,2 +1,2 @@
 observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
-obs_a		A	0.500000000000000	normal		
+obs_a		A_o	0.500000000000000	normal		
diff --git a/petabtests/cases/v2.0.0/pysb/0011/conversion_modified_pysb.py b/petabtests/cases/v2.0.0/pysb/0011/conversion_modified_pysb.py
index 57ec588..60ba1e6 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/conversion_modified_pysb.py
+++ b/petabtests/cases/v2.0.0/pysb/0011/conversion_modified_pysb.py
@@ -17,5 +17,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A", A_())
-Observable("B", B_())
+Observable("A_o", A_())
+Observable("B_o", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0013/0013.py b/petabtests/cases/v2.0.0/pysb/0013/0013.py
index c0c05fb..4be1bd3 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/0013.py
+++ b/petabtests/cases/v2.0.0/pysb/0013/0013.py
@@ -19,9 +19,9 @@
 # problem --------------------------------------------------------------------
 problem = Problem()
 
-problem.add_condition("c0", B_o="par")
+problem.add_condition("c0", B="par")
 problem.add_experiment("e0", 0, "c0")
-problem.add_observable("obs_a", "A", noise_formula=0.5)
+problem.add_observable("obs_a", "A_o", noise_formula=0.5)
 
 problem.add_measurement("obs_a", experiment_id="e0", time=0, measurement=0.7)
 problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)
@@ -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_o", "A_() ** compartment")
-problem.add_mapping("B_o", "B_() ** compartment")
+problem.add_mapping("A", "A_() ** compartment")
+problem.add_mapping("B", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
index 04c824b..d2e474f 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
@@ -1,2 +1,2 @@
 conditionId	targetId	targetValue
-c0	B_o	par
+c0	B	par
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
index 54ec18f..2fee7f7 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A_o	A_() ** compartment	
-B_o	B_() ** compartment	
+A	A_() ** compartment	
+B	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_model.py b/petabtests/cases/v2.0.0/pysb/0013/_model.py
index 57ec588..60ba1e6 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_model.py
+++ b/petabtests/cases/v2.0.0/pysb/0013/_model.py
@@ -17,5 +17,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A", A_())
-Observable("B", B_())
+Observable("A_o", A_())
+Observable("B_o", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_observables.tsv b/petabtests/cases/v2.0.0/pysb/0013/_observables.tsv
index 251acc7..d73fd30 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_observables.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0013/_observables.tsv
@@ -1,2 +1,2 @@
 observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
-obs_a		A	0.500000000000000	normal		
+obs_a		A_o	0.500000000000000	normal		
diff --git a/petabtests/cases/v2.0.0/pysb/0013/conversion_modified_pysb.py b/petabtests/cases/v2.0.0/pysb/0013/conversion_modified_pysb.py
index 57ec588..60ba1e6 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/conversion_modified_pysb.py
+++ b/petabtests/cases/v2.0.0/pysb/0013/conversion_modified_pysb.py
@@ -17,5 +17,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A", A_())
-Observable("B", B_())
+Observable("A_o", A_())
+Observable("B_o", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0017/0017.py b/petabtests/cases/v2.0.0/pysb/0017/0017.py
index fb8ba30..0cfad62 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/0017.py
+++ b/petabtests/cases/v2.0.0/pysb/0017/0017.py
@@ -1,10 +1,10 @@
 from inspect import cleandoc
+from pathlib import Path
 
 from petab.v2 import Problem
 from petab.v2.C import *
 
 from petabtests import (
-    DEFAULT_PYSB_FILE,
     PetabV2TestCase,
     analytical_a,
     analytical_b,
@@ -32,17 +32,17 @@
 
 # problem --------------------------------------------------------------------
 problem = Problem()
-problem.add_condition("preeq_c0", k1=0.3, B_o=2.0, A_o=0)
-problem.add_condition("c0", k1=0.8, A_o=1)
+problem.add_condition("preeq_c0", k1=0.3, B=2.0, A=0)
+problem.add_condition("c0", k1=0.8, A=1)
 problem.add_experiment("e0", TIME_PREEQUILIBRATION, "preeq_c0", 0, "c0")
-problem.add_observable("obs_a", "A", noise_formula=0.5)
+problem.add_observable("obs_a", "A_o", 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_o", "A_() ** compartment")
-problem.add_mapping("B_o", "B_() ** compartment")
+problem.add_mapping("A", "A_() ** compartment")
+problem.add_mapping("B", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
@@ -61,7 +61,7 @@
     brief="Simulation. Preequilibration. One species reinitialized, one not "
     "(NaN in condition table). InitialAssignment to species overridden.",
     description=DESCRIPTION,
-    model=DEFAULT_PYSB_FILE,
+    model=Path("conversion_pysb.py"),
     condition_dfs=[problem.condition_df],
     observable_dfs=[problem.observable_df],
     measurement_dfs=[problem.measurement_df],
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv
index 34068e1..934e234 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv
@@ -1,6 +1,6 @@
 conditionId	targetId	targetValue
 preeq_c0	k1	0.3
-preeq_c0	B_o	2.0
-preeq_c0	A_o	0.0
+preeq_c0	B	2.0
+preeq_c0	A	0.0
 c0	k1	0.8
-c0	A_o	1.0
+c0	A	1.0
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
index 54ec18f..2fee7f7 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A_o	A_() ** compartment	
-B_o	B_() ** compartment	
+A	A_() ** compartment	
+B	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_model.py b/petabtests/cases/v2.0.0/pysb/0017/_model.py
index 71263df..d7e8f35 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_model.py
+++ b/petabtests/cases/v2.0.0/pysb/0017/_model.py
@@ -25,5 +25,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A", A_())
-Observable("B", B_())
+Observable("A_o", A_())
+Observable("B_o", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_observables.tsv b/petabtests/cases/v2.0.0/pysb/0017/_observables.tsv
index 251acc7..d73fd30 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_observables.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0017/_observables.tsv
@@ -1,2 +1,2 @@
 observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
-obs_a		A	0.500000000000000	normal		
+obs_a		A_o	0.500000000000000	normal		
diff --git a/petabtests/cases/v2.0.0/pysb/0017/conversion_pysb.py b/petabtests/cases/v2.0.0/pysb/0017/conversion_pysb.py
new file mode 100644
index 0000000..d7e8f35
--- /dev/null
+++ b/petabtests/cases/v2.0.0/pysb/0017/conversion_pysb.py
@@ -0,0 +1,29 @@
+from pysb import (
+    Model,
+    Monomer,
+    Parameter,
+    Compartment,
+    Rule,
+    Initial,
+    Observable,
+)
+
+Model()
+
+Compartment("compartment")
+
+Monomer("A_")
+Monomer("B_")
+
+Parameter("a0", 1.0)
+Parameter("b0", 1.0)
+Parameter("k1", 0.0)
+Parameter("k2", 0.0)
+
+Rule("conversion", A_() ** compartment | B_() ** compartment, k1, k2)
+
+Initial(A_() ** compartment, a0)
+Initial(B_() ** compartment, b0)
+
+Observable("A_o", A_())
+Observable("B_o", B_())
diff --git a/pyproject.toml b/pyproject.toml
index ec12816..38da3de 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -56,6 +56,7 @@ exclude = ["petabtests/cases/**/*.md", "cases/**"]
 [tool.ruff.lint.per-file-ignores]
 "petabtests/cases/v2.0.0/pysb/*/_model.py" = ["F821"]
 "petabtests/cases/v2.0.0/pysb/*/conversion_modified_pysb.py" = ["F821"]
+"petabtests/cases/v2.0.0/pysb/*/conversion_pysb.py" = ["F821"]
 "petabtests/conversion_*pysb.py" = ["F821"]
 
 # add UP rules for ruff via extend-select

From 14003f92d8a3d74d0760c163b41658c0e0774f68 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 14:41:46 +0000
Subject: [PATCH 4/6] Revert unnecessary DEFAULT_PYSB_FILE changes and remove
 newly generated model files

---
 petabtests/cases/v2.0.0/pysb/0010/0010.py     | 15 +++++-----
 .../cases/v2.0.0/pysb/0010/_conditions.tsv    |  4 +--
 .../cases/v2.0.0/pysb/0010/_mapping.tsv       |  4 +--
 petabtests/cases/v2.0.0/pysb/0010/_model.py   |  4 +--
 .../cases/v2.0.0/pysb/0010/_observables.tsv   |  2 +-
 .../cases/v2.0.0/pysb/0010/conversion_pysb.py | 29 -------------------
 petabtests/cases/v2.0.0/pysb/0011/0011.py     |  8 ++---
 .../cases/v2.0.0/pysb/0011/_conditions.tsv    |  2 +-
 .../cases/v2.0.0/pysb/0011/_mapping.tsv       |  4 +--
 petabtests/cases/v2.0.0/pysb/0011/_model.py   |  4 +--
 .../cases/v2.0.0/pysb/0011/_observables.tsv   |  2 +-
 .../pysb/0011/conversion_modified_pysb.py     |  4 +--
 petabtests/cases/v2.0.0/pysb/0013/0013.py     |  8 ++---
 .../cases/v2.0.0/pysb/0013/_conditions.tsv    |  2 +-
 .../cases/v2.0.0/pysb/0013/_mapping.tsv       |  4 +--
 petabtests/cases/v2.0.0/pysb/0013/_model.py   |  4 +--
 .../cases/v2.0.0/pysb/0013/_observables.tsv   |  2 +-
 .../pysb/0013/conversion_modified_pysb.py     |  4 +--
 petabtests/cases/v2.0.0/pysb/0017/0017.py     | 14 ++++-----
 .../cases/v2.0.0/pysb/0017/_conditions.tsv    |  6 ++--
 .../cases/v2.0.0/pysb/0017/_mapping.tsv       |  4 +--
 petabtests/cases/v2.0.0/pysb/0017/_model.py   |  4 +--
 .../cases/v2.0.0/pysb/0017/_observables.tsv   |  2 +-
 .../cases/v2.0.0/pysb/0017/conversion_pysb.py | 29 -------------------
 pyproject.toml                                |  1 -
 25 files changed, 53 insertions(+), 113 deletions(-)
 delete mode 100644 petabtests/cases/v2.0.0/pysb/0010/conversion_pysb.py
 delete mode 100644 petabtests/cases/v2.0.0/pysb/0017/conversion_pysb.py

diff --git a/petabtests/cases/v2.0.0/pysb/0010/0010.py b/petabtests/cases/v2.0.0/pysb/0010/0010.py
index 4d3a140..96d7276 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/0010.py
+++ b/petabtests/cases/v2.0.0/pysb/0010/0010.py
@@ -1,10 +1,9 @@
 from inspect import cleandoc
-from pathlib import Path
 
 from petab.v2 import Problem
 from petab.v2.C import *
 
-from petabtests import PetabV2TestCase, analytical_a
+from petabtests import DEFAULT_PYSB_FILE, PetabV2TestCase, analytical_a
 
 DESCRIPTION = cleandoc("""
 ## Objective
@@ -25,19 +24,19 @@
 # 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_o=0)
+problem.add_condition("c0", k1=0.8, B_o=1)
 
 problem.add_experiment("e0", TIME_PREEQUILIBRATION, "preeq_c0", 0, "c0")
 
-problem.add_observable("obs_a", "A_o", noise_formula=0.5)
+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, estimate=True)
-problem.add_mapping("A", "A_() ** compartment")
-problem.add_mapping("B", "B_() ** compartment")
+problem.add_mapping("A_o", "A_() ** compartment")
+problem.add_mapping("B_o", "B_() ** compartment")
 
 
 # solutions ------------------------------------------------------------------
@@ -57,7 +56,7 @@
     brief="Simulation. Preequilibration. One species reinitialized, one not. "
     "InitialAssignment to species overridden.",
     description=DESCRIPTION,
-    model=Path("conversion_pysb.py"),
+    model=DEFAULT_PYSB_FILE,
     condition_dfs=[problem.condition_df],
     observable_dfs=[problem.observable_df],
     measurement_dfs=[problem.measurement_df],
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv
index 01d5b3d..2e21373 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv
+++ b/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_o	0.0
 c0	k1	0.8
-c0	B	1.0
+c0	B_o	1.0
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
index 2fee7f7..54ec18f 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_o	A_() ** compartment	
+B_o	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_model.py b/petabtests/cases/v2.0.0/pysb/0010/_model.py
index d7e8f35..71263df 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_model.py
+++ b/petabtests/cases/v2.0.0/pysb/0010/_model.py
@@ -25,5 +25,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A_o", A_())
-Observable("B_o", B_())
+Observable("A", A_())
+Observable("B", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_observables.tsv b/petabtests/cases/v2.0.0/pysb/0010/_observables.tsv
index d73fd30..251acc7 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_observables.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0010/_observables.tsv
@@ -1,2 +1,2 @@
 observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
-obs_a		A_o	0.500000000000000	normal		
+obs_a		A	0.500000000000000	normal		
diff --git a/petabtests/cases/v2.0.0/pysb/0010/conversion_pysb.py b/petabtests/cases/v2.0.0/pysb/0010/conversion_pysb.py
deleted file mode 100644
index d7e8f35..0000000
--- a/petabtests/cases/v2.0.0/pysb/0010/conversion_pysb.py
+++ /dev/null
@@ -1,29 +0,0 @@
-from pysb import (
-    Model,
-    Monomer,
-    Parameter,
-    Compartment,
-    Rule,
-    Initial,
-    Observable,
-)
-
-Model()
-
-Compartment("compartment")
-
-Monomer("A_")
-Monomer("B_")
-
-Parameter("a0", 1.0)
-Parameter("b0", 1.0)
-Parameter("k1", 0.0)
-Parameter("k2", 0.0)
-
-Rule("conversion", A_() ** compartment | B_() ** compartment, k1, k2)
-
-Initial(A_() ** compartment, a0)
-Initial(B_() ** compartment, b0)
-
-Observable("A_o", A_())
-Observable("B_o", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0011/0011.py b/petabtests/cases/v2.0.0/pysb/0011/0011.py
index 858501c..b7bb9b3 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/0011.py
+++ b/petabtests/cases/v2.0.0/pysb/0011/0011.py
@@ -21,11 +21,11 @@
 # problem --------------------------------------------------------------------
 problem = Problem()
 
-problem.add_condition("c0", B=2)
+problem.add_condition("c0", B_o=2)
 
 problem.add_experiment("e0", 0, "c0")
 
-problem.add_observable("obs_a", "A_o", noise_formula=0.5)
+problem.add_observable("obs_a", "A", noise_formula=0.5)
 
 problem.add_measurement("obs_a", experiment_id="e0", time=0, measurement=0.7)
 problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)
@@ -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_o", "A_() ** compartment")
+problem.add_mapping("B_o", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
index 5d968f9..334c5ff 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
@@ -1,2 +1,2 @@
 conditionId	targetId	targetValue
-c0	B	2.0
+c0	B_o	2.0
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
index 2fee7f7..54ec18f 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_o	A_() ** compartment	
+B_o	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_model.py b/petabtests/cases/v2.0.0/pysb/0011/_model.py
index 60ba1e6..57ec588 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_model.py
+++ b/petabtests/cases/v2.0.0/pysb/0011/_model.py
@@ -17,5 +17,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A_o", A_())
-Observable("B_o", B_())
+Observable("A", A_())
+Observable("B", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_observables.tsv b/petabtests/cases/v2.0.0/pysb/0011/_observables.tsv
index d73fd30..251acc7 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_observables.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0011/_observables.tsv
@@ -1,2 +1,2 @@
 observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
-obs_a		A_o	0.500000000000000	normal		
+obs_a		A	0.500000000000000	normal		
diff --git a/petabtests/cases/v2.0.0/pysb/0011/conversion_modified_pysb.py b/petabtests/cases/v2.0.0/pysb/0011/conversion_modified_pysb.py
index 60ba1e6..57ec588 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/conversion_modified_pysb.py
+++ b/petabtests/cases/v2.0.0/pysb/0011/conversion_modified_pysb.py
@@ -17,5 +17,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A_o", A_())
-Observable("B_o", B_())
+Observable("A", A_())
+Observable("B", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0013/0013.py b/petabtests/cases/v2.0.0/pysb/0013/0013.py
index 4be1bd3..c0c05fb 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/0013.py
+++ b/petabtests/cases/v2.0.0/pysb/0013/0013.py
@@ -19,9 +19,9 @@
 # problem --------------------------------------------------------------------
 problem = Problem()
 
-problem.add_condition("c0", B="par")
+problem.add_condition("c0", B_o="par")
 problem.add_experiment("e0", 0, "c0")
-problem.add_observable("obs_a", "A_o", noise_formula=0.5)
+problem.add_observable("obs_a", "A", noise_formula=0.5)
 
 problem.add_measurement("obs_a", experiment_id="e0", time=0, measurement=0.7)
 problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)
@@ -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_o", "A_() ** compartment")
+problem.add_mapping("B_o", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
index d2e474f..04c824b 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
@@ -1,2 +1,2 @@
 conditionId	targetId	targetValue
-c0	B	par
+c0	B_o	par
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
index 2fee7f7..54ec18f 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_o	A_() ** compartment	
+B_o	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_model.py b/petabtests/cases/v2.0.0/pysb/0013/_model.py
index 60ba1e6..57ec588 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_model.py
+++ b/petabtests/cases/v2.0.0/pysb/0013/_model.py
@@ -17,5 +17,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A_o", A_())
-Observable("B_o", B_())
+Observable("A", A_())
+Observable("B", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_observables.tsv b/petabtests/cases/v2.0.0/pysb/0013/_observables.tsv
index d73fd30..251acc7 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_observables.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0013/_observables.tsv
@@ -1,2 +1,2 @@
 observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
-obs_a		A_o	0.500000000000000	normal		
+obs_a		A	0.500000000000000	normal		
diff --git a/petabtests/cases/v2.0.0/pysb/0013/conversion_modified_pysb.py b/petabtests/cases/v2.0.0/pysb/0013/conversion_modified_pysb.py
index 60ba1e6..57ec588 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/conversion_modified_pysb.py
+++ b/petabtests/cases/v2.0.0/pysb/0013/conversion_modified_pysb.py
@@ -17,5 +17,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A_o", A_())
-Observable("B_o", B_())
+Observable("A", A_())
+Observable("B", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0017/0017.py b/petabtests/cases/v2.0.0/pysb/0017/0017.py
index 0cfad62..fb8ba30 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/0017.py
+++ b/petabtests/cases/v2.0.0/pysb/0017/0017.py
@@ -1,10 +1,10 @@
 from inspect import cleandoc
-from pathlib import Path
 
 from petab.v2 import Problem
 from petab.v2.C import *
 
 from petabtests import (
+    DEFAULT_PYSB_FILE,
     PetabV2TestCase,
     analytical_a,
     analytical_b,
@@ -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_o=2.0, A_o=0)
+problem.add_condition("c0", k1=0.8, A_o=1)
 problem.add_experiment("e0", TIME_PREEQUILIBRATION, "preeq_c0", 0, "c0")
-problem.add_observable("obs_a", "A_o", noise_formula=0.5)
+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_o", "A_() ** compartment")
+problem.add_mapping("B_o", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
@@ -61,7 +61,7 @@
     brief="Simulation. Preequilibration. One species reinitialized, one not "
     "(NaN in condition table). InitialAssignment to species overridden.",
     description=DESCRIPTION,
-    model=Path("conversion_pysb.py"),
+    model=DEFAULT_PYSB_FILE,
     condition_dfs=[problem.condition_df],
     observable_dfs=[problem.observable_df],
     measurement_dfs=[problem.measurement_df],
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv
index 934e234..34068e1 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv
+++ b/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_o	2.0
+preeq_c0	A_o	0.0
 c0	k1	0.8
-c0	A	1.0
+c0	A_o	1.0
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
index 2fee7f7..54ec18f 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A	A_() ** compartment	
-B	B_() ** compartment	
+A_o	A_() ** compartment	
+B_o	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_model.py b/petabtests/cases/v2.0.0/pysb/0017/_model.py
index d7e8f35..71263df 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_model.py
+++ b/petabtests/cases/v2.0.0/pysb/0017/_model.py
@@ -25,5 +25,5 @@
 Initial(A_() ** compartment, a0)
 Initial(B_() ** compartment, b0)
 
-Observable("A_o", A_())
-Observable("B_o", B_())
+Observable("A", A_())
+Observable("B", B_())
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_observables.tsv b/petabtests/cases/v2.0.0/pysb/0017/_observables.tsv
index d73fd30..251acc7 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_observables.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0017/_observables.tsv
@@ -1,2 +1,2 @@
 observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
-obs_a		A_o	0.500000000000000	normal		
+obs_a		A	0.500000000000000	normal		
diff --git a/petabtests/cases/v2.0.0/pysb/0017/conversion_pysb.py b/petabtests/cases/v2.0.0/pysb/0017/conversion_pysb.py
deleted file mode 100644
index d7e8f35..0000000
--- a/petabtests/cases/v2.0.0/pysb/0017/conversion_pysb.py
+++ /dev/null
@@ -1,29 +0,0 @@
-from pysb import (
-    Model,
-    Monomer,
-    Parameter,
-    Compartment,
-    Rule,
-    Initial,
-    Observable,
-)
-
-Model()
-
-Compartment("compartment")
-
-Monomer("A_")
-Monomer("B_")
-
-Parameter("a0", 1.0)
-Parameter("b0", 1.0)
-Parameter("k1", 0.0)
-Parameter("k2", 0.0)
-
-Rule("conversion", A_() ** compartment | B_() ** compartment, k1, k2)
-
-Initial(A_() ** compartment, a0)
-Initial(B_() ** compartment, b0)
-
-Observable("A_o", A_())
-Observable("B_o", B_())
diff --git a/pyproject.toml b/pyproject.toml
index 38da3de..ec12816 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -56,7 +56,6 @@ exclude = ["petabtests/cases/**/*.md", "cases/**"]
 [tool.ruff.lint.per-file-ignores]
 "petabtests/cases/v2.0.0/pysb/*/_model.py" = ["F821"]
 "petabtests/cases/v2.0.0/pysb/*/conversion_modified_pysb.py" = ["F821"]
-"petabtests/cases/v2.0.0/pysb/*/conversion_pysb.py" = ["F821"]
 "petabtests/conversion_*pysb.py" = ["F821"]
 
 # add UP rules for ruff via extend-select

From e3c52378b8a1dffc34eaf5e0b7c00afafe0636d0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 15:00:01 +0000
Subject: [PATCH 5/6] Update progress after renaming PySB mapping IDs

---
 petabtests/cases/v2.0.0/pysb/0010/0010.py         | 8 ++++----
 petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv | 4 ++--
 petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv    | 4 ++--
 petabtests/cases/v2.0.0/pysb/0011/0011.py         | 6 +++---
 petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv | 2 +-
 petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv    | 4 ++--
 petabtests/cases/v2.0.0/pysb/0013/0013.py         | 6 +++---
 petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv | 2 +-
 petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv    | 4 ++--
 petabtests/cases/v2.0.0/pysb/0017/0017.py         | 8 ++++----
 petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv | 6 +++---
 petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv    | 4 ++--
 12 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/petabtests/cases/v2.0.0/pysb/0010/0010.py b/petabtests/cases/v2.0.0/pysb/0010/0010.py
index 96d7276..ee25c5e 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/0010.py
+++ b/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_o=0)
-problem.add_condition("c0", k1=0.8, B_o=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_o", "A_() ** compartment")
-problem.add_mapping("B_o", "B_() ** compartment")
+problem.add_mapping("A_c", "A_() ** compartment")
+problem.add_mapping("B_c", "B_() ** compartment")
 
 
 # solutions ------------------------------------------------------------------
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv
index 2e21373..b8952a9 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv
@@ -1,5 +1,5 @@
 conditionId	targetId	targetValue
 preeq_c0	k1	0.3
-preeq_c0	B_o	0.0
+preeq_c0	B_c	0.0
 c0	k1	0.8
-c0	B_o	1.0
+c0	B_c	1.0
diff --git a/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
index 54ec18f..d9834af 100644
--- a/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A_o	A_() ** compartment	
-B_o	B_() ** compartment	
+A_c	A_() ** compartment	
+B_c	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0011/0011.py b/petabtests/cases/v2.0.0/pysb/0011/0011.py
index b7bb9b3..629a483 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/0011.py
+++ b/petabtests/cases/v2.0.0/pysb/0011/0011.py
@@ -21,7 +21,7 @@
 # problem --------------------------------------------------------------------
 problem = Problem()
 
-problem.add_condition("c0", B_o=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_o", "A_() ** compartment")
-problem.add_mapping("B_o", "B_() ** compartment")
+problem.add_mapping("A_c", "A_() ** compartment")
+problem.add_mapping("B_c", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
index 334c5ff..168f21d 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv
@@ -1,2 +1,2 @@
 conditionId	targetId	targetValue
-c0	B_o	2.0
+c0	B_c	2.0
diff --git a/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
index 54ec18f..d9834af 100644
--- a/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A_o	A_() ** compartment	
-B_o	B_() ** compartment	
+A_c	A_() ** compartment	
+B_c	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0013/0013.py b/petabtests/cases/v2.0.0/pysb/0013/0013.py
index c0c05fb..69d5441 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/0013.py
+++ b/petabtests/cases/v2.0.0/pysb/0013/0013.py
@@ -19,7 +19,7 @@
 # problem --------------------------------------------------------------------
 problem = Problem()
 
-problem.add_condition("c0", B_o="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_o", "A_() ** compartment")
-problem.add_mapping("B_o", "B_() ** compartment")
+problem.add_mapping("A_c", "A_() ** compartment")
+problem.add_mapping("B_c", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
index 04c824b..646b1f2 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv
@@ -1,2 +1,2 @@
 conditionId	targetId	targetValue
-c0	B_o	par
+c0	B_c	par
diff --git a/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
index 54ec18f..d9834af 100644
--- a/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A_o	A_() ** compartment	
-B_o	B_() ** compartment	
+A_c	A_() ** compartment	
+B_c	B_() ** compartment	
diff --git a/petabtests/cases/v2.0.0/pysb/0017/0017.py b/petabtests/cases/v2.0.0/pysb/0017/0017.py
index fb8ba30..40ee328 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/0017.py
+++ b/petabtests/cases/v2.0.0/pysb/0017/0017.py
@@ -32,8 +32,8 @@
 
 # problem --------------------------------------------------------------------
 problem = Problem()
-problem.add_condition("preeq_c0", k1=0.3, B_o=2.0, A_o=0)
-problem.add_condition("c0", k1=0.8, A_o=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)
@@ -41,8 +41,8 @@
 problem.add_parameter(
     "k2", lb=0, ub=10, nominal_value=0.6, scale=LIN, estimate=True
 )
-problem.add_mapping("A_o", "A_() ** compartment")
-problem.add_mapping("B_o", "B_() ** compartment")
+problem.add_mapping("A_c", "A_() ** compartment")
+problem.add_mapping("B_c", "B_() ** compartment")
 
 # solutions ------------------------------------------------------------------
 
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv b/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv
index 34068e1..3e03b6f 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv
@@ -1,6 +1,6 @@
 conditionId	targetId	targetValue
 preeq_c0	k1	0.3
-preeq_c0	B_o	2.0
-preeq_c0	A_o	0.0
+preeq_c0	B_c	2.0
+preeq_c0	A_c	0.0
 c0	k1	0.8
-c0	A_o	1.0
+c0	A_c	1.0
diff --git a/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv b/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
index 54ec18f..d9834af 100644
--- a/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
+++ b/petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv
@@ -1,3 +1,3 @@
 petabEntityId	modelEntityId	name
-A_o	A_() ** compartment	
-B_o	B_() ** compartment	
+A_c	A_() ** compartment	
+B_c	B_() ** compartment	

From b86a10edabbd263a5941eeb242d83e7cc3d65977 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 15:00:28 +0000
Subject: [PATCH 6/6] Rename compartment mappings to _c in PySB cases and
 regenerate artifacts

---
 test/test_general.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/test_general.py b/test/test_general.py
index 2c7aa9b..ee8b1da 100644
--- a/test/test_general.py
+++ b/test/test_general.py
@@ -1,7 +1,6 @@
 import petabtests
 import os
 import pytest
-from pathlib import Path
 
 
 def test_cases_dir_exists():