Don't fail petablint for PEtab v2 problems with only warnings

CHANGELOG.md

@@ -59,6 +59,9 @@
   that PEtab condition changes are applied before its assignments.
   Previously, their order was undefined
   (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/562)
+* `petablint` no longer fails for PEtab v2 problems with only warnings,
+  consistent with PEtab v1. Warnings are still reported
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/569)
 
 **Features**
 * `petab1to2` and `petab_files_1to2` can skip validation via `validate=False`

petab/petablint.py

@@ -198,9 +198,9 @@ def main():
 
                 try:
                     validation_issues = lint_problem(args.yaml_file_name)
-                    if validation_issues:
-                        # Handle petab.v2.lint.ValidationTask issues
-                        validation_issues.log(logger=logger)
+                    # Handle petab.v2.lint.ValidationTask issues
+                    validation_issues.log(logger=logger)
+                    if validation_issues.has_errors():
                         sys.exit(1)
                     logger.info("PEtab format check completed successfully.")
                     sys.exit(0)

tests/v2/test_core.py

@@ -1044,6 +1044,35 @@ def test_petablint_v2(tmpdir):
         check=True,
     )
 
+    # warnings are reported, but don't make petablint fail
+    problem.add_condition("unused_condition", B=1)
+    problem.condition_tables[0].rel_path = "conditions.tsv"
+    problem.config.condition_files = ["conditions.tsv"]
+    issues = problem.validate()
+    assert issues
+    assert not issues.has_errors()
+    problem.to_files(Path(tmpdir))
+    result = subprocess.run(  # noqa S607
+        ["petablint", str(Path(tmpdir, "problem.yaml"))],  # noqa S607
+        capture_output=True,
+        text=True,
+    )
+    assert result.returncode == 0
+    assert "CheckUnusedConditions" in result.stdout + result.stderr
+
+    # errors make petablint fail
+    problem.add_measurement(
+        "obs_undefined", time=10, measurement=2.5, experiment_id=""
+    )
+    assert problem.validate().has_errors()
+    problem.to_files(Path(tmpdir))
+    result = subprocess.run(  # noqa S607
+        ["petablint", str(Path(tmpdir, "problem.yaml"))],  # noqa S607
+        capture_output=True,
+        text=True,
+    )
+    assert result.returncode == 1
+
 
 def test_problem_id(tmpdir):
     """Test that the problem ID works as expected."""